diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
index 2c5998efc299e86a5292d50f5e8082e1ec76f1a6..1dadb9b0719c267553e8e53f9bd8d9d18b7678c0 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
@@ -28,10 +28,12 @@ import lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator;
import lcsb.mapviewer.common.EventStorageLoggerAppender;
import lcsb.mapviewer.common.IProgressUpdater;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
@@ -165,13 +167,13 @@ public class ModelAnnotator {
/**
* Performs all possible and automatic annotations on the model.
*
- * @param model
- * model to update
+ * @param project
+ * project to update
* @param progressUpdater
* callback function used for updating progress of the function
*/
- public void performAnnotations(Model model, final IProgressUpdater progressUpdater) {
- performAnnotations(model, progressUpdater, null);
+ public void performAnnotations(Project project, final IProgressUpdater progressUpdater) {
+ performAnnotations(project, progressUpdater, null);
}
/**
@@ -180,19 +182,21 @@ public class ModelAnnotator {
* @param annotators
* this map contains lists of {@link ElementAnnotator} objects that
* should be used for a given classes
- * @param model
- * model to update
+ * @param project
+ * project with models to update
* @param progressUpdater
* callback function used for updating progress of the function
*/
- public void performAnnotations(Model model, final IProgressUpdater progressUpdater, Map<Class<?>, List<ElementAnnotator>> annotators) {
+ public void performAnnotations(Project project, final IProgressUpdater progressUpdater, Map<Class<?>, List<ElementAnnotator>> annotators) {
EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
try {
Logger.getRootLogger().addAppender(appender);
progressUpdater.setProgress(0);
- List<Model> models = new ArrayList<Model>();
- models.add(model);
- models.addAll(model.getSubmodels());
+ List<Model> models = new ArrayList<>();
+ for (ModelData model: project.getModels()) {
+ models.add(model.getModel());
+ models.addAll(model.getModel().getSubmodels());
+ }
final double size = models.size();
double counter = 0;
for (Model m : models) {
@@ -215,7 +219,7 @@ public class ModelAnnotator {
counter++;
}
Logger.getRootLogger().removeAppender(appender);
- model.addLoggingInfo(appender);
+ project.addLoggingInfo(appender);
} finally {
Logger.getRootLogger().removeAppender(appender);
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
index b920636e1df0756272fad0d9ad983f95d42dd909..0402014d4290a000aee2cefaad7a8ab8b2513932 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
@@ -29,6 +29,7 @@ import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
import lcsb.mapviewer.annotation.services.annotators.ReconAnnotator;
import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
@@ -311,7 +312,9 @@ public class ModelAnnotatorTest extends AnnotationTestFunctions {
final MutableDouble maxProgress = new MutableDouble(0.0);
- modelAnnotator.performAnnotations(model, new IProgressUpdater() {
+ Project project = new Project();
+ project.addModel(model);
+ modelAnnotator.performAnnotations(project, new IProgressUpdater() {
@Override
public void setProgress(double progress) {
maxProgress.setValue(Math.max(progress, maxProgress.getValue()));
diff --git a/console/src/main/java/lcsb/mapviewer/run/BellExport.java b/console/src/main/java/lcsb/mapviewer/run/BellExport.java
index fb59ddcb953c2734f0b1e469225fb349d66df143..b70a0b9423f1d14817c996a6ca3f5d529ee0dc2e 100644
--- a/console/src/main/java/lcsb/mapviewer/run/BellExport.java
+++ b/console/src/main/java/lcsb/mapviewer/run/BellExport.java
@@ -7,6 +7,7 @@ import lcsb.mapviewer.annotation.services.ModelAnnotator;
import lcsb.mapviewer.common.IProgressUpdater;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.persist.ApplicationContextLoader;
@@ -26,25 +27,25 @@ public class BellExport {
/**
* Default class logger.
*/
- private static Logger logger = Logger.getLogger(BellExport.class.getName());
+ private static Logger logger = Logger.getLogger(BellExport.class.getName());
/**
* Object that performs different types of export transformation.
*/
@Autowired
- private IExporterService exporter;
+ private IExporterService exporter;
/**
* Object used to annotate the model.
*/
@Autowired
- private ModelAnnotator modelAnnotator;
+ private ModelAnnotator modelAnnotator;
/**
* Object used to annotate the model.
*/
@Autowired
- private DbUtils dbUtils;
+ private DbUtils dbUtils;
/**
* Static main method used to run this stand alone code.
@@ -76,23 +77,22 @@ public class BellExport {
try {
String filename = PdMapAnnotations.getLastPdFilename();
String version = PdMapAnnotations.getLastPdVersion();
-
- //filename = "testFiles/other_full/ASTHMAP18000X8000V1_38.xml";
- //version = "1.1.38";
+
+ // filename = "testFiles/other_full/ASTHMAP18000X8000V1_38.xml";
+ // version = "1.1.38";
dbUtils.createSessionForCurrentThread();
Model model = p.createModel(new ConverterParams().filename(filename));
+ Project project = new Project();
+ project.addModel(model);
- modelAnnotator.performAnnotations(model, new IProgressUpdater() {
-
+ modelAnnotator.performAnnotations(project, new IProgressUpdater() {
@Override
public void setProgress(double progress) {
- // TODO Auto-generated method stub
-
}
});
ExporterParameters params = new IExporterService.ExporterParameters().model(model).//
- fileName("out/bell/" + version + "-reactions.txt").//
+ fileName("out/bell/" + version + "-reactions.txt").//
fileType(ExportFileType.TAB_SEPARATED).//
type(Species.class).//
moleculeEdges(false);
@@ -100,15 +100,15 @@ public class BellExport {
exporter.exportReactions(params);
params = new IExporterService.ExporterParameters().model(model).//
- fileName("out/bell/" + version + "-species.txt").//
+ fileName("out/bell/" + version + "-species.txt").//
fileType(ExportFileType.TAB_SEPARATED).//
type(Species.class).//
-// column(ExportColumn.FULL).//
+ // column(ExportColumn.FULL).//
moleculeEdges(false);
exporter.exportSpecies(params);
params = new IExporterService.ExporterParameters().model(model).//
- fileName("out/bell/" + version + "-compartments.txt").//
+ fileName("out/bell/" + version + "-compartments.txt").//
fileType(ExportFileType.TAB_SEPARATED).//
type(Object.class); //
// column(ExportColumn.FULL);
diff --git a/console/src/main/java/lcsb/mapviewer/run/Statistics.java b/console/src/main/java/lcsb/mapviewer/run/Statistics.java
index bb399e4ae4f317e7aef6b5fdf75e9452d04d575a..661ba6db47c7c665ece62c7058f37c82b7cf6491 100644
--- a/console/src/main/java/lcsb/mapviewer/run/Statistics.java
+++ b/console/src/main/java/lcsb/mapviewer/run/Statistics.java
@@ -20,13 +20,14 @@ import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.IProgressUpdater;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.persist.ApplicationContextLoader;
import lcsb.mapviewer.persist.DbUtils;
@@ -112,8 +113,11 @@ public class Statistics {
try {
// String modelName = PdMapAnnotations.getLastPdFilename();
CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ Project project = new Project();
for (String name : fileNames) {
- models.add(parser.createModel(new ConverterParams().filename(name)));
+ Model model = parser.createModel(new ConverterParams().filename(name));
+ models.add(model);
+ project.addModel(model);
}
IProgressUpdater updater = new IProgressUpdater() {
@@ -122,9 +126,7 @@ public class Statistics {
logger.debug("Progress: " + progress);
}
};
- for (Model model : models) {
- modelAnnotator.performAnnotations(model, updater);
- }
+ modelAnnotator.performAnnotations(project, updater);
// modelAnnotator.removeIncorrectAnnotations(model, updater);
printStatistics(models);
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
index 45dfe52fb0bfb0aba3c7bc6fa5311a9f8b9b1762..5de0ddc5436920c2f323c701d57e0ee801001496 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
@@ -18,7 +18,6 @@ import org.w3c.dom.Document;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
-import lcsb.mapviewer.common.EventStorageLoggerAppender;
import lcsb.mapviewer.common.MimeType;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.XmlParser;
@@ -77,7 +76,6 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
/**
* Default class logger.
*/
- @SuppressWarnings("unused")
private static Logger logger = Logger.getLogger(CellDesignerXmlParser.class.getName());
/**
@@ -107,153 +105,144 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
@Override
public Model createModel(ConverterParams params) throws InvalidInputDataExecption {
- EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
- try {
- Logger.getRootLogger().addAppender(appender);
+ CellDesignerElementCollection elements = new CellDesignerElementCollection();
- CellDesignerElementCollection elements = new CellDesignerElementCollection();
+ Model model = new ModelFullIndexed(null);
+ model.setSbgnFormat(params.isSbgnFormat());
- Model model = new ModelFullIndexed(null);
- model.setSbgnFormat(params.isSbgnFormat());
+ if (params.getFilename() != null) {
+ model.setName(FilenameUtils.getBaseName(params.getFilename()));
+ }
+ speciesSbmlParser = new SpeciesCollectionXmlParser(elements);
+ aliasCollectionParser = new AliasCollectionXmlParser(elements, model);
+ compartmentCollectionXmlParser = new CompartmentCollectionXmlParser(elements);
- if (params.getFilename() != null) {
- model.setName(FilenameUtils.getBaseName(params.getFilename()));
- }
- speciesSbmlParser = new SpeciesCollectionXmlParser(elements);
- aliasCollectionParser = new AliasCollectionXmlParser(elements, model);
- compartmentCollectionXmlParser = new CompartmentCollectionXmlParser(elements);
-
- DOMParser parser = new DOMParser();
- try {
- parser.parse(params.getSource());
- } catch (IOException e) {
- throw new InvalidInputDataExecption("IO Problem with a file: " + params.getSource().getSystemId(), e);
- }
- Document doc = parser.getDocument();
- try {
+ DOMParser parser = new DOMParser();
+ try {
+ parser.parse(params.getSource());
+ } catch (IOException e) {
+ throw new InvalidInputDataExecption("IO Problem with a file: " + params.getSource().getSystemId(), e);
+ }
+ Document doc = parser.getDocument();
+ try {
- // Get the document's root XML node
- NodeList root = doc.getChildNodes();
+ // Get the document's root XML node
+ NodeList root = doc.getChildNodes();
- // Navigate down the hierarchy to get to the CEO node
- Node sbmlNode = getNode("SBML", root);
- if (sbmlNode == null) {
- throw new InvalidInputDataExecption("No SBML node");
- }
+ // Navigate down the hierarchy to get to the CEO node
+ Node sbmlNode = getNode("SBML", root);
+ if (sbmlNode == null) {
+ throw new InvalidInputDataExecption("No SBML node");
+ }
- Node modelNode = getNode("model", sbmlNode.getChildNodes());
- if (modelNode == null) {
- throw new InvalidInputDataExecption("No model node in SBML");
- }
- // we ignore metaid - it's useless and obstruct data model
- // model.setMetaId(getNodeAttr("metaId", modelNode));
- model.setIdModel(getNodeAttr("id", modelNode));
-
- Node compartmentNode = getNode("listOfCompartments", modelNode.getChildNodes());
- if (compartmentNode != null) {
- List<CellDesignerCompartment> compartments = compartmentCollectionXmlParser.parseXmlCompartmentCollection(compartmentNode);
- elements.addElements(compartments);
- }
+ Node modelNode = getNode("model", sbmlNode.getChildNodes());
+ if (modelNode == null) {
+ throw new InvalidInputDataExecption("No model node in SBML");
+ }
+ // we ignore metaid - it's useless and obstruct data model
+ // model.setMetaId(getNodeAttr("metaId", modelNode));
+ model.setIdModel(getNodeAttr("id", modelNode));
+
+ Node compartmentNode = getNode("listOfCompartments", modelNode.getChildNodes());
+ if (compartmentNode != null) {
+ List<CellDesignerCompartment> compartments = compartmentCollectionXmlParser.parseXmlCompartmentCollection(compartmentNode);
+ elements.addElements(compartments);
+ }
- InternalModelSpeciesData modelData = new InternalModelSpeciesData();
+ InternalModelSpeciesData modelData = new InternalModelSpeciesData();
- Node speciesNode = getNode("listOfSpecies", modelNode.getChildNodes());
- if (speciesNode != null) {
- List<Pair<String, ? extends CellDesignerSpecies<?>>> species = speciesSbmlParser.parseSbmlSpeciesCollection(speciesNode);
- modelData.updateSpecies(species);
- }
- Node reactionsNode = null;
-
- NodeList nodes = modelNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("annotation")) {
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("listOfSpecies")) {
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("listOfReactions")) {
- reactionsNode = node;
- } else if (node.getNodeName().equalsIgnoreCase("listOfCompartments")) {
- // we already parsed compartemnts
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("notes")) {
- String notes = rap.getNotes(node);
- if (notes != null) {
- notes = StringEscapeUtils.unescapeHtml4(notes);
- }
- model.setNotes(notes);
- } else if (node.getNodeName().equalsIgnoreCase("listOfUnitDefinitions")) {
- continue; // we can ignore unit definitions
- } else {
- throw new InvalidInputDataExecption("Unknown element of model: " + node.getNodeName());
+ Node speciesNode = getNode("listOfSpecies", modelNode.getChildNodes());
+ if (speciesNode != null) {
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> species = speciesSbmlParser.parseSbmlSpeciesCollection(speciesNode);
+ modelData.updateSpecies(species);
+ }
+ Node reactionsNode = null;
+
+ NodeList nodes = modelNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("annotation")) {
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("listOfSpecies")) {
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("listOfReactions")) {
+ reactionsNode = node;
+ } else if (node.getNodeName().equalsIgnoreCase("listOfCompartments")) {
+ // we already parsed compartemnts
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("notes")) {
+ String notes = rap.getNotes(node);
+ if (notes != null) {
+ notes = StringEscapeUtils.unescapeHtml4(notes);
}
+ model.setNotes(notes);
+ } else if (node.getNodeName().equalsIgnoreCase("listOfUnitDefinitions")) {
+ continue; // we can ignore unit definitions
+ } else {
+ throw new InvalidInputDataExecption("Unknown element of model: " + node.getNodeName());
}
}
+ }
- Node annotationNode = getNode("annotation", modelNode.getChildNodes());
- if (annotationNode == null) {
- throw new InvalidInputDataExecption("No annotation node in SBML/model");
- }
+ Node annotationNode = getNode("annotation", modelNode.getChildNodes());
+ if (annotationNode == null) {
+ throw new InvalidInputDataExecption("No annotation node in SBML/model");
+ }
- parseAnnotation(model, annotationNode, modelData, elements);
+ parseAnnotation(model, annotationNode, modelData, elements);
- if (speciesNode != null) {
- List<Pair<String, ? extends CellDesignerSpecies<?>>> species = speciesSbmlParser.parseSbmlSpeciesCollection(speciesNode);
- modelData.updateSpecies(species);
- }
+ if (speciesNode != null) {
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> species = speciesSbmlParser.parseSbmlSpeciesCollection(speciesNode);
+ modelData.updateSpecies(species);
+ }
- if (reactionsNode != null) {
- ReactionCollectionXmlParser reactionCollectionXmlParser = new ReactionCollectionXmlParser(model, elements);
- List<Reaction> reactions = reactionCollectionXmlParser.parseXmlReactionCollection(reactionsNode);
- model.addReactions(reactions);
- }
+ if (reactionsNode != null) {
+ ReactionCollectionXmlParser reactionCollectionXmlParser = new ReactionCollectionXmlParser(model, elements);
+ List<Reaction> reactions = reactionCollectionXmlParser.parseXmlReactionCollection(reactionsNode);
+ model.addReactions(reactions);
+ }
- if (params.isSizeAutoAdjust()) {
- Rectangle2D bound = getModelBound(model);
- double width = bound.getWidth() + 2 * (Math.max(0, bound.getX()));
- double height = bound.getHeight() + 2 * (Math.max(0, bound.getY()));
+ if (params.isSizeAutoAdjust()) {
+ Rectangle2D bound = getModelBound(model);
+ double width = bound.getWidth() + 2 * (Math.max(0, bound.getX()));
+ double height = bound.getHeight() + 2 * (Math.max(0, bound.getY()));
- model.setWidth(width);
- model.setHeight(height);
- }
- } catch (InvalidXmlSchemaException e) {
- throw new InvalidInputDataExecption(e);
- } catch (UnknownReactionClassException e) {
- String type = e.getReactionType();
- String reactionId = e.getReactionId();
- String newType = null;
- if ("CATALYSIS".equalsIgnoreCase(type)) {
- newType = "positive influence";
- } else if ("INHIBITION".equalsIgnoreCase(type)) {
- newType = "negative influence";
- } else if ("UNKNOWN_CATALYSIS".equalsIgnoreCase(type)) {
- newType = "unknown positive influence";
- } else if ("UNKNOWN_INHIBITION".equalsIgnoreCase(type)) {
- newType = "unknown negative influence";
- } else if ("PHYSICAL_STIMULATION".equalsIgnoreCase(type)) {
- newType = "reduced physical stimulation";
- } else if ("MODULATION".equalsIgnoreCase(type)) {
- newType = "reduced modulation";
- } else if ("TRIGGER".equalsIgnoreCase(type)) {
- newType = "reduced trigger";
- } else {
- throw new InvalidInputDataExecption(e);
- }
- throw new InvalidInputDataExecption(
- "Reaction type \"" + type + "\" is inappropriate for reaction " + reactionId + ". Suggested type: " + newType
- + " in the \"Reduced\" notation of CellDesigner.",
- e);
- } catch (CellDesignerParserException e) {
+ model.setWidth(width);
+ model.setHeight(height);
+ }
+ } catch (InvalidXmlSchemaException e) {
+ throw new InvalidInputDataExecption(e);
+ } catch (UnknownReactionClassException e) {
+ String type = e.getReactionType();
+ String reactionId = e.getReactionId();
+ String newType = null;
+ if ("CATALYSIS".equalsIgnoreCase(type)) {
+ newType = "positive influence";
+ } else if ("INHIBITION".equalsIgnoreCase(type)) {
+ newType = "negative influence";
+ } else if ("UNKNOWN_CATALYSIS".equalsIgnoreCase(type)) {
+ newType = "unknown positive influence";
+ } else if ("UNKNOWN_INHIBITION".equalsIgnoreCase(type)) {
+ newType = "unknown negative influence";
+ } else if ("PHYSICAL_STIMULATION".equalsIgnoreCase(type)) {
+ newType = "reduced physical stimulation";
+ } else if ("MODULATION".equalsIgnoreCase(type)) {
+ newType = "reduced modulation";
+ } else if ("TRIGGER".equalsIgnoreCase(type)) {
+ newType = "reduced trigger";
+ } else {
throw new InvalidInputDataExecption(e);
}
-
- Logger.getRootLogger().removeAppender(appender);
- model.addLoggingInfo(appender);
- return model;
- } finally {
- Logger.getRootLogger().removeAppender(appender);
+ throw new InvalidInputDataExecption(
+ "Reaction type \"" + type + "\" is inappropriate for reaction " + reactionId + ". Suggested type: " + newType
+ + " in the \"Reduced\" notation of CellDesigner.",
+ e);
+ } catch (CellDesignerParserException e) {
+ throw new InvalidInputDataExecption(e);
}
+
+ return model;
}
/**
@@ -451,7 +440,7 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
if (!species.getElementId().equals("")) {
elements.addElement(species);
} else {
- model.addCreationWarning(
+ logger.warn(
"Species (class: " + species.getClass().getName() + ", name: " + species.getName()
+ ") exists in CD file, but is never instantiated. It's CellDesigner file problem.");
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java
index c0d6c8925f83df9142dd484f57f26aa52b6fcf20..ac9d237edfe67225d9b64bd99c7e6ee74332b30f 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java
@@ -24,9 +24,9 @@ import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.AntisenseRna;
import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Rna;
@@ -310,8 +310,8 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
@Test
public void testWarningInParser() throws Exception {
try {
- Model model = getModelForFile("testFiles/problematic/invalid_elements_name.xml");
- assertTrue(model.getCreationWarnings().size() > 0);
+ getModelForFile("testFiles/problematic/invalid_elements_name.xml");
+ assertTrue(getWarnings().size() > 0);
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
index 95d5bd72fed6b4f9083e1d0f8e725737cf675162..adc4fbff1c1912131303412721531f3133b0e74a 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
@@ -36,8 +36,8 @@ import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.model.SubmodelType;
import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Phenotype;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Species;
@@ -59,11 +59,12 @@ public class ComplexZipConverter<T extends IConverter> {
* stream.
*/
private static final int BUFFER_SIZE = 1024;
+
/**
* Default class logger.
*/
- @SuppressWarnings("unused")
private static Logger logger = Logger.getLogger(ComplexZipConverter.class);
+
/**
* Class used to create single submap from a file.
*/
@@ -202,31 +203,27 @@ public class ComplexZipConverter<T extends IConverter> {
*/
public void processReaction(String mapping, Map<String, Model> nameModelMap, Model topModel, Reaction reaction) {
if (reaction.getReactants().size() > 1) {
- topModel.addCreationWarning(
- "[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains too many reactants. Skipped");
+ logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains too many reactants. Skipped");
} else if (reaction.getProducts().size() > 1) {
- topModel.addCreationWarning(
- "[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains too many products. Skipped");
+ logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains too many products. Skipped");
} else if (reaction.getModifiers().size() > 0) {
- topModel
- .addCreationWarning("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains modifiers. Skipped");
+ logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains modifiers. Skipped");
} else {
Element fromAlias = reaction.getReactants().get(0).getElement();
Element toAlias = reaction.getProducts().get(0).getElement();
if (!(fromAlias instanceof Species)) {
- topModel.addCreationWarning(
- "[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't start in species. Skipped");
+ logger
+ .warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't start in species. Skipped");
} else if (!(toAlias instanceof Species)) {
- topModel.addCreationWarning(
- "[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't end in species. Skipped");
+ logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't end in species. Skipped");
} else {
Complex complexFrom = ((Species) fromAlias).getComplex();
Complex complexTo = ((Species) toAlias).getComplex();
if (complexFrom == null) {
- topModel.addCreationWarning(
+ logger.warn(
"[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't start inside complex. Skipped");
} else if (complexTo == null && (!(toAlias instanceof Complex))) {
- topModel.addCreationWarning(
+ logger.warn(
"[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't end inside complex. Skipped");
} else {
if (complexTo == null) {
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java b/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
index 8060021ba71c66965135eb29bfb3d4f5af56595c..e17ac596abfc01b292edf3e731403967135a2972 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
@@ -36,13 +36,15 @@ import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Phenotype;
import lcsb.mapviewer.model.map.species.Species;
public class ComplexZipConverterTest {
+
+ @SuppressWarnings("unused")
private static Logger logger = Logger.getLogger(ComplexZipConverterTest.class);
private abstract class AbstractConverter implements IConverter {
@@ -492,10 +494,7 @@ public class ComplexZipConverterTest {
params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
try {
- Model model = converter.createModel(params);
- for (String string : model.getCreationWarnings()) {
- logger.debug(string);
- }
+ converter.createModel(params);
fail("Exception expected");
} catch (InvalidArgumentException e) {
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
index 02a8aac49a6fcdbb036f7c180c5c6c0aec8a70ef..070d2109aeb85b503b677f6baa6b8d64b4d2a450 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
@@ -36,6 +36,7 @@ public class CopyCommand extends NewModelCommand {
/**
* Defaul class logger.
*/
+ @SuppressWarnings("unused")
private static Logger logger = Logger.getLogger(CopyCommand.class);
/**
@@ -54,7 +55,7 @@ public class CopyCommand extends NewModelCommand {
* @return copy of the model
*/
public Model execute() {
- Map<Model, Model> copies = new HashMap<Model, Model>();
+ Map<Model, Model> copies = new HashMap<>();
Model model = getModel();
@@ -70,7 +71,6 @@ public class CopyCommand extends NewModelCommand {
}
}
if (parent != null) {
- logger.warn("Dirty copying of submodel");
CopyCommand copyParentCommand = new CopyCommand(parent.getParentModel().getModel());
Model copy = copyParentCommand.execute();
for (ModelSubmodelConnection submodel : copy.getSubmodelConnections()) {
@@ -258,8 +258,6 @@ public class CopyCommand extends NewModelCommand {
copy.setIdModel(original.getIdModel());
copy.setZoomLevels(original.getZoomLevels());
copy.setTileSize(original.getTileSize());
-
- copy.addCreationWarnings(original.getCreationWarnings());
}
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/Project.java b/model/src/main/java/lcsb/mapviewer/model/Project.java
index ba235988a14662705b353facc9b89fd8f99bd224..3dd760de58e3ba51f01a07ef79a4808835642d59 100644
--- a/model/src/main/java/lcsb/mapviewer/model/Project.java
+++ b/model/src/main/java/lcsb/mapviewer/model/Project.java
@@ -1,7 +1,9 @@
package lcsb.mapviewer.model;
import java.io.Serializable;
+import java.util.ArrayList;
import java.util.HashSet;
+import java.util.List;
import java.util.Set;
import javax.persistence.Basic;
@@ -15,10 +17,14 @@ import javax.persistence.OneToMany;
import javax.persistence.OneToOne;
import javax.persistence.Table;
+import org.apache.log4j.Appender;
import org.apache.log4j.Logger;
+import org.apache.log4j.spi.LoggingEvent;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
+import lcsb.mapviewer.common.EventStorageLoggerAppender;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
@@ -37,7 +43,6 @@ public class Project implements Serializable {
/**
* Default class logger.
*/
- @SuppressWarnings("unused")
private static Logger logger = Logger.getLogger(Project.class);
/**
@@ -91,12 +96,18 @@ public class Project implements Serializable {
*/
private String errors = null;
+ /**
+ * Short description of the map.
+ */
+ @Column(columnDefinition = "TEXT")
+ private String warnings;
+
/**
* Map models in the project.
*/
@Cascade({ CascadeType.ALL })
@OneToMany(mappedBy = "project", orphanRemoval = true)
- private Set<ModelData> models = new HashSet<ModelData>();
+ private Set<ModelData> models = new HashSet<>();
/**
* Here we store input file.
@@ -365,4 +376,88 @@ public class Project implements Serializable {
public MiriamData getOrganism() {
return organism;
}
+
+ /**
+ * Adds a warning to a list of warnings generated during model creation.
+ *
+ * @param warning
+ * warning to add
+ */
+ public void addWarning(String warning) {
+ if (warning.trim().contains("\n")) {
+ throw new InvalidArgumentException("Warning must be one line of text");
+ }
+ if (warning.trim().equals("")) {
+ return;
+ }
+ if (warnings == null) {
+ warnings = warning.trim();
+ } else {
+ warnings = warnings + "\n" + warning.trim();
+ }
+ }
+
+ /**
+ * Returns list of warnings set during creation of mode.
+ *
+ * @return list of warnings set during creation of mode
+ */
+ public List<String> getWarnings() {
+ List<String> result = new ArrayList<>();
+ if (warnings == null) {
+ return result;
+ }
+ String[] warningsArray = warnings.split("\n");
+ for (String string : warningsArray) {
+ result.add(string);
+ }
+ return result;
+ }
+
+ /**
+ * Adds warnings to a list of warnings generated during model creation.
+ *
+ * @param warnings
+ * list of warnings to add
+ */
+ public void addWarnings(List<String> warnings) {
+ StringBuilder sb = new StringBuilder("");
+ if (this.warnings != null) {
+ sb.append(this.warnings);
+ }
+ for (String string : warnings) {
+ if (string.trim().equals("")) {
+ continue;
+ }
+ if (string.contains("\n")) {
+ throw new InvalidArgumentException("Warning must be one line of text, but found:\n" + string);
+ }
+ if (sb.length() > 0) {
+ sb.append("\n");
+ }
+ sb.append(string.trim());
+ }
+ if (sb.length() != 0) {
+ this.warnings = sb.toString();
+ }
+ }
+
+ /**
+ * Adds warning log information to a project.
+ *
+ * @param appender
+ * {@link Appender log4j appender} that gathered logs
+ */
+ public void addLoggingInfo(EventStorageLoggerAppender appender) {
+ List<String> warnings = new ArrayList<>();
+ for (LoggingEvent event : appender.getWarnings()) {
+ if (event.getMessage() instanceof String) {
+ warnings.add(((String) event.getMessage()).replaceAll("\n", "_NEW_LINE_"));
+ } else {
+ logger.warn("Unknown message class: " + event.getClass());
+ }
+ }
+ addWarnings(warnings);
+ }
+
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
index eaaa741a2baf098789efd892457461715fb846be..198209731d452f3f01ca8da3119ca6703aabe3a5 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
@@ -5,9 +5,6 @@ import java.util.Collection;
import java.util.List;
import java.util.Set;
-import org.apache.log4j.Appender;
-
-import lcsb.mapviewer.common.EventStorageLoggerAppender;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
@@ -121,7 +118,8 @@ public interface Model {
Set<Element> getElements();
/**
- * Returns element with the given element identfier ({@link Element#elementId}).
+ * Returns element with the given element identfier ({@link Element#elementId}
+ * ).
*
* @param idElement
* element identifier
@@ -220,29 +218,6 @@ public interface Model {
*/
void addBlockDiagream(BlockDiagram blockDiagram);
- /**
- * Adds warnings to a list of warnings generated during model creation.
- *
- * @param warnings
- * list of warnings to add
- */
- void addCreationWarnings(List<String> warnings);
-
- /**
- * Returns list of warnings set during creation of mode.
- *
- * @return list of warnings set during creation of mode
- */
- List<String> getCreationWarnings();
-
- /**
- * Adds a warning to a list of warnings generated during model creation.
- *
- * @param warning
- * warning to add
- */
- void addCreationWarning(String warning);
-
/**
* @param notifyEmail
* the notifyEmail to set
@@ -666,13 +641,4 @@ public interface Model {
* @return list od all {@link AnnotatedObject} in the map
*/
List<AnnotatedObject> getAnnotatedObjects();
-
- /**
- * Adds warning log information to a model.
- *
- * @param appender
- * {@link Appender log4j appender} that gathered logs
- */
- void addLoggingInfo(EventStorageLoggerAppender appender);
-
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
index c957eea0078d25f0bfe49688313137b0f1857b82..81632a39d66299421e7f733cc3807eabb722fd72 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
@@ -82,7 +82,7 @@ public class ModelData implements Serializable {
*/
@Cascade({ CascadeType.ALL })
@OneToMany(mappedBy = "model", orphanRemoval = true)
- private Set<Layer> layers = new HashSet<Layer>();
+ private Set<Layer> layers = new HashSet<>();
/**
* Unique database identifier.
@@ -100,7 +100,7 @@ public class ModelData implements Serializable {
*/
@Cascade({ CascadeType.ALL })
@OneToMany(mappedBy = "model", orphanRemoval = true)
- private Set<Reaction> reactions = new HashSet<Reaction>();
+ private Set<Reaction> reactions = new HashSet<>();
/**
* Version of the map.
@@ -143,11 +143,6 @@ public class ModelData implements Serializable {
*/
private String notifyEmail;
- /**
- * Short description of the map.
- */
- @Column(columnDefinition = "TEXT")
- private String creationWarnings;
/**
* How many hierarchical levels are in this map.
@@ -170,7 +165,7 @@ public class ModelData implements Serializable {
@Cascade({ CascadeType.ALL })
@OneToMany(fetch = FetchType.EAGER, mappedBy = "model", orphanRemoval = true)
@OrderBy("id")
- private List<Layout> layouts = new ArrayList<Layout>();
+ private List<Layout> layouts = new ArrayList<>();
/**
* Project to which this model belong to.
@@ -192,7 +187,7 @@ public class ModelData implements Serializable {
*/
@Cascade({ CascadeType.ALL })
@OneToMany(fetch = FetchType.EAGER, mappedBy = "parentModel", orphanRemoval = true)
- private Set<ModelSubmodelConnection> submodels = new HashSet<ModelSubmodelConnection>();
+ private Set<ModelSubmodelConnection> submodels = new HashSet<>();
/**
* List of connections with parent model (by definition one map can be a
@@ -200,7 +195,7 @@ public class ModelData implements Serializable {
*/
@Cascade({ CascadeType.ALL })
@OneToMany(fetch = FetchType.LAZY, mappedBy = "submodel")
- private Set<SubmodelConnection> parentModels = new HashSet<SubmodelConnection>();
+ private Set<SubmodelConnection> parentModels = new HashSet<>();
/**
* List of overview images describing this model. This list should be set only
@@ -211,7 +206,7 @@ public class ModelData implements Serializable {
@Cascade({ CascadeType.ALL })
@OneToMany(mappedBy = "model", orphanRemoval = true)
@OrderBy("id")
- private List<OverviewImage> overviewImages = new ArrayList<OverviewImage>();
+ private List<OverviewImage> overviewImages = new ArrayList<>();
/**
* List of {@link DataMiningSet} in the model. These data mining sets are used
@@ -220,7 +215,7 @@ public class ModelData implements Serializable {
@Cascade({ CascadeType.ALL })
@OneToMany(mappedBy = "model", orphanRemoval = true)
@OrderBy("id")
- private List<DataMiningSet> dataMiningSets = new ArrayList<DataMiningSet>();
+ private List<DataMiningSet> dataMiningSets = new ArrayList<>();
/**
* Default constructor.
@@ -546,71 +541,6 @@ public class ModelData implements Serializable {
this.notifyEmail = notifyEmail;
}
- /**
- * Adds a warning to a list of warnings generated during model creation.
- *
- * @param warning
- * warning to add
- */
- public void addCreationWarning(String warning) {
- if (warning.trim().contains("\n")) {
- throw new InvalidArgumentException("Warning must be one line of text");
- }
- if (warning.trim().equals("")) {
- return;
- }
- if (creationWarnings == null) {
- creationWarnings = warning.trim();
- } else {
- creationWarnings = creationWarnings + "\n" + warning.trim();
- }
- }
-
- /**
- * Returns list of warnings set during creation of mode.
- *
- * @return list of warnings set during creation of mode
- */
- public List<String> getCreationWarnings() {
- List<String> result = new ArrayList<String>();
- if (creationWarnings == null) {
- return result;
- }
- String[] warnings = creationWarnings.split("\n");
- for (String string : warnings) {
- result.add(string);
- }
- return result;
- }
-
- /**
- * Adds warnings to a list of warnings generated during model creation.
- *
- * @param warnings
- * list of warnings to add
- */
- public void addCreationWarnings(List<String> warnings) {
- StringBuilder sb = new StringBuilder("");
- if (creationWarnings != null) {
- sb.append(creationWarnings);
- }
- for (String string : warnings) {
- if (string.trim().equals("")) {
- continue;
- }
- if (string.contains("\n")) {
- throw new InvalidArgumentException("Warning must be one line of text, but found:\n" + string);
- }
- if (sb.length() > 0) {
- sb.append("\n");
- }
- sb.append(string.trim());
- }
- if (sb.length() != 0) {
- creationWarnings = sb.toString();
- }
- }
-
/**
* @return the model
* @see #model
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
index 80e382b845be31d8c23888d6ad406b4c71135519..920e5f16de1d6b69f8ced1e64b58ea072b285923 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
@@ -11,9 +11,7 @@ import java.util.Map;
import java.util.Set;
import org.apache.log4j.Logger;
-import org.apache.log4j.spi.LoggingEvent;
-import lcsb.mapviewer.common.EventStorageLoggerAppender;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.AnnotatedObject;
@@ -474,21 +472,6 @@ public class ModelFullIndexed implements Model {
modelData.setNotifyEmail(notifyEmail);
}
- @Override
- public void addCreationWarning(String warning) {
- modelData.addCreationWarning(warning);
- }
-
- @Override
- public List<String> getCreationWarnings() {
- return modelData.getCreationWarnings();
- }
-
- @Override
- public void addCreationWarnings(List<String> warnings) {
- modelData.addCreationWarnings(warnings);
- }
-
@Override
public ModelData getModelData() {
return modelData;
@@ -694,19 +677,6 @@ public class ModelFullIndexed implements Model {
return result;
}
- @Override
- public void addLoggingInfo(EventStorageLoggerAppender appender) {
- List<String> warnings = new ArrayList<>();
- for (LoggingEvent event : appender.getWarnings()) {
- if (event.getMessage() instanceof String) {
- warnings.add(((String) event.getMessage()).replaceAll("\n", "_NEW_LINE_"));
- } else {
- logger.warn("Unknown message class: " + event.getClass());
- }
- }
- addCreationWarnings(warnings);
- }
-
@Override
public List<Element> getElementsByName(String name) {
List<Element> result = new ArrayList<>();
diff --git a/model/src/test/java/lcsb/mapviewer/model/ProjectTest.java b/model/src/test/java/lcsb/mapviewer/model/ProjectTest.java
index 917ebae588b496ca276621eaf5dfa8be8574c690..ec95a2738e445d55b50cba9db379c214ccaa0ce5 100644
--- a/model/src/test/java/lcsb/mapviewer/model/ProjectTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/ProjectTest.java
@@ -2,22 +2,30 @@ package lcsb.mapviewer.model;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+import java.util.ArrayList;
import java.util.HashSet;
+import java.util.List;
import java.util.Set;
import org.apache.commons.lang3.SerializationUtils;
+import org.apache.log4j.Logger;
+import org.apache.log4j.spi.LoggingEvent;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.EventStorageLoggerAppender;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
public class ProjectTest {
+ Logger logger = Logger.getLogger(ProjectTest.class);
@Before
public void setUp() throws Exception {
@@ -127,4 +135,126 @@ public class ProjectTest {
}
}
+ @Test
+ public void testAddCreationWarning() {
+ try {
+ Project md = new Project();
+ md.addWarning("text\ntext");
+
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddCreationWarning2() {
+ try {
+ Project md = new Project();
+ md.addWarning("");
+ List<String> warnings = md.getWarnings();
+ assertEquals(0, warnings.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddCreationWarning3() {
+ try {
+ Project md = new Project();
+ md.addWarning("xqw");
+ List<String> warnings = md.getWarnings();
+ assertEquals(1, warnings.size());
+ assertEquals("xqw", warnings.get(0));
+
+ md.addWarning("WER");
+ warnings = md.getWarnings();
+ assertEquals(2, warnings.size());
+ assertEquals("WER", warnings.get(1));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddCreationWarnings() {
+ try {
+ List<String> warnings = new ArrayList<>();
+ warnings.add("xqw");
+ warnings.add("aso");
+ warnings.add("");
+ Project project = new Project();
+ project.addWarnings(warnings);
+
+ project.addWarning("WER");
+ warnings = project.getWarnings();
+ assertEquals(3, warnings.size());
+ assertEquals("aso", warnings.get(1));
+
+ project.addWarnings(warnings);
+ warnings = project.getWarnings();
+ assertEquals(6, warnings.size());
+ assertEquals("aso", warnings.get(1));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddCreationWarnings2() {
+ try {
+ List<String> warnings = new ArrayList<>();
+ warnings.add("xqw\nwer\nt");
+ Project md = new Project();
+ md.addWarnings(warnings);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddCreationWarnings3() {
+ try {
+ List<String> warnings = new ArrayList<>();
+ Project md = new Project();
+ md.addWarnings(warnings);
+ assertEquals(0, md.getWarnings().size());
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddLoggingInfo() {
+ try {
+ Project project = new Project();
+ EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
+ logger.addAppender(appender);
+ logger.warn("test");
+ logger.warn("test2");
+ LoggingEvent event = appender.getWarnings().get(0);
+ appender.getWarnings().add(new LoggingEvent("St", event.getLogger(), null, new Object(), null));
+ logger.removeAppender(appender);
+
+ project.addLoggingInfo(appender);
+ assertEquals(2, project.getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelDataTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelDataTest.java
index aad0ee4aae9aeb687f5b2603c4cb740dfea00531..000ca61d9449e91062a5ea331a5a0bf463f3d8cd 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelDataTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelDataTest.java
@@ -205,106 +205,6 @@ public class ModelDataTest {
}
}
- @Test
- public void testAddCreationWarning() {
- try {
- ModelData md = new ModelData();
- md.addCreationWarning("text\ntext");
-
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddCreationWarning2() {
- try {
- ModelData md = new ModelData();
- md.addCreationWarning("");
- List<String> warnings = md.getCreationWarnings();
- assertEquals(0, warnings.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddCreationWarning3() {
- try {
- ModelData md = new ModelData();
- md.addCreationWarning("xqw");
- List<String> warnings = md.getCreationWarnings();
- assertEquals(1, warnings.size());
- assertEquals("xqw", warnings.get(0));
-
- md.addCreationWarning("WER");
- warnings = md.getCreationWarnings();
- assertEquals(2, warnings.size());
- assertEquals("WER", warnings.get(1));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddCreationWarnings() {
- try {
- List<String> warnings = new ArrayList<>();
- warnings.add("xqw");
- warnings.add("aso");
- warnings.add("");
- ModelData md = new ModelData();
- md.addCreationWarnings(warnings);
-
- md.addCreationWarning("WER");
- warnings = md.getCreationWarnings();
- assertEquals(3, warnings.size());
- assertEquals("aso", warnings.get(1));
-
- md.addCreationWarnings(warnings);
- warnings = md.getCreationWarnings();
- assertEquals(6, warnings.size());
- assertEquals("aso", warnings.get(1));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddCreationWarnings2() {
- try {
- List<String> warnings = new ArrayList<>();
- warnings.add("xqw\nwer\nt");
- ModelData md = new ModelData();
- md.addCreationWarnings(warnings);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddCreationWarnings3() {
- try {
- List<String> warnings = new ArrayList<>();
- ModelData md = new ModelData();
- md.addCreationWarnings(warnings);
- assertEquals(0, md.getCreationWarnings().size());
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
@Test
public void testAddSubmodel() {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java
index ed871452d4c59498b942a521815d739d1d9a5862..8fdcfd03523fcabff5167c03291cbb17a760fae2 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java
@@ -14,14 +14,12 @@ import java.util.List;
import java.util.Set;
import org.apache.log4j.Logger;
-import org.apache.log4j.spi.LoggingEvent;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import org.mockito.Mockito;
import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.EventStorageLoggerAppender;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.AnnotatedObject;
@@ -118,7 +116,7 @@ public class ModelFullIndexedTest {
assertEquals(1, elements.size());
assertEquals(0, unkElements.size());
-
+
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -136,11 +134,10 @@ public class ModelFullIndexedTest {
model.addElement(protein2);
model.addElement(new Compartment("compId"));
-
List<Species> speciesList = model.getSpeciesList();
-
+
assertEquals(2, speciesList.size());
-
+
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -200,20 +197,6 @@ public class ModelFullIndexedTest {
}
}
- @Test
- public void testAddCreationWarning() {
- try {
- ModelFullIndexed model = new ModelFullIndexed(null);
- model.addCreationWarning("str");
-
- assertEquals(1, model.getCreationWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
@Test
public void testAddSpeciesWithParent() {
try {
@@ -447,7 +430,6 @@ public class ModelFullIndexedTest {
}
}
-
@Test
public void testAddInvalidElement2() {
try {
@@ -806,7 +788,6 @@ public class ModelFullIndexedTest {
String notifyEmail = "email@email.lu";
String idModel = "model_ID";
Calendar creationDate = Calendar.getInstance();
- List<String> warnings = new ArrayList<>();
boolean sbgnFormat = true;
model.setWidth(widthStr);
@@ -850,8 +831,6 @@ public class ModelFullIndexedTest {
assertEquals(creationDate, model.getCreationDate());
model.setMapVersion(mapVersion);
assertEquals(mapVersion, model.getMapVersion());
- model.addCreationWarnings(warnings);
- assertEquals(warnings, model.getCreationWarnings());
model.setSbgnFormat(sbgnFormat);
assertEquals(sbgnFormat, model.isSbgnFormat());
@@ -883,25 +862,4 @@ public class ModelFullIndexedTest {
}
}
- @Test
- public void testAddLoggingInfo() {
- try {
- ModelFullIndexed model = new ModelFullIndexed(null);
- EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
- logger.addAppender(appender);
- logger.warn("test");
- logger.warn("test2");
- LoggingEvent event = appender.getWarnings().get(0);
- appender.getWarnings().add(new LoggingEvent("St", event.getLogger(), null, new Object(), null));
- logger.removeAppender(appender);
-
- model.addLoggingInfo(appender);
- assertEquals(2, model.getCreationWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/ImportExport.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/ImportExport.java
index e4de0af6b3305917b7b8a88e952d8df19a625f4f..31511781b93c5625331b6f4c2c28211ddf07d8f7 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/ImportExport.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/ImportExport.java
@@ -151,7 +151,12 @@ public class ImportExport implements Plugin {
/**
* {@link Model} that was created using this {@link PathwayExporter}.
*/
- private Model model = null;
+ private Model model = null;
+
+ /**
+ * List of export warnings.
+ */
+ private List<String> warnings = new ArrayList<>();
@Override
public String[] getExtensions() {
@@ -165,29 +170,52 @@ public class ImportExport implements Plugin {
@Override
public List<String> getWarnings() {
- if (model == null) {
- logger.warn("Getting warnings without parsing");
- return new ArrayList<>();
- }
- return model.getCreationWarnings();
+ return warnings;
}
@Override
public void doExport(File file, Pathway pathway) throws ConverterException {
+ EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
try {
+ Logger.getRootLogger().addAppender(appender);
pathway.writeToXml(new File("tmp.gpml"), false);
model = new GPMLToModel().getModel("tmp.gpml");
- model.addCreationWarning("Please manually change extension of saved file from .cell to .xml");
+
+ Logger.getRootLogger().removeAppender(appender);
+ warnings = createWarnings(appender);
CellDesignerXmlParser parser = new CellDesignerXmlParser();
String xml = parser.toXml(model);
PrintWriter writer = new PrintWriter(file.getPath(), "UTF-8");
writer.println(xml);
writer.close();
+
+ warnings.add("Please manually change extension of saved file from .cell to .xml");
} catch (Exception e) {
logger.error(e.getMessage(), e);
throw new ConverterException(e);
+ } finally {
+ Logger.getRootLogger().removeAppender(appender);
+ }
+ }
+
+ /**
+ * Creates list of warnings from log4j appender data.
+ *
+ * @param appender
+ * appender with the logs
+ * @return list of warnings from log4j appender data
+ */
+ private List<String> createWarnings(EventStorageLoggerAppender appender) {
+ List<String> warnings = new ArrayList<>();
+ for (LoggingEvent event : appender.getWarnings()) {
+ if (event.getMessage() instanceof String) {
+ warnings.add(((String) event.getMessage()).replaceAll("\n", "_NEW_LINE_"));
+ } else {
+ logger.warn("Unknown message class: " + event.getClass());
+ }
}
+ return warnings;
}
}
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GPMLToModel.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GPMLToModel.java
index 5522e76654bb81b743de852aa000c7c13cb9690e..52e273300c88f0aa5e84c74b97b46da01d01ae89 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GPMLToModel.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GPMLToModel.java
@@ -4,9 +4,6 @@ import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.EventStorageLoggerAppender;
import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.wikipathway.model.Graph;
@@ -31,17 +28,9 @@ public class GPMLToModel {
* thrown when model couldn't be created
*/
public Model getModel(InputStream stream) throws IOException, ConverterException {
- EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
- try {
- Logger.getRootLogger().addAppender(appender);
- Graph graph = new GpmlParser().createGraph(stream);
- Logger.getRootLogger().removeAppender(appender);
- Model model = new ModelContructor().getModel(graph);
- model.addLoggingInfo(appender);
- return model;
- } finally {
- Logger.getRootLogger().removeAppender(appender);
- }
+ Graph graph = new GpmlParser().createGraph(stream);
+ Model model = new ModelContructor().getModel(graph);
+ return model;
}
/**
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
index 6ccd58e182e43cac1244390fd2a900e75ae3aa0a..4d4440f15a348c59e3318c403dd8ae5d98b3ee00 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
@@ -16,7 +16,6 @@ import org.apache.commons.lang3.StringEscapeUtils;
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.EventStorageLoggerAppender;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidStateException;
@@ -886,9 +885,7 @@ public class ModelContructor {
*
*/
public Model getModel(Graph graph) throws ConverterException {
- EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
try {
- Logger.getRootLogger().addAppender(appender);
Data data = new Data();
Model model = new ModelFullIndexed(null);
model.setWidth(graph.getBoardWidth());
@@ -940,13 +937,9 @@ public class ModelContructor {
putAliasesIntoCompartments(model);
- Logger.getRootLogger().removeAppender(appender);
- model.addLoggingInfo(appender);
return model;
} catch (UnknownChildClassException e) {
throw new ConverterException(e);
- } finally {
- Logger.getRootLogger().removeAppender(appender);
}
}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ComplexReactionToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ComplexReactionToModelTest.java
index 7b8690e29c538a6a83e900b3754e1b1e088d124f..9ddcf820eebd6a4ea86a5bf74c4c6a4e9ebed315 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ComplexReactionToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ComplexReactionToModelTest.java
@@ -21,7 +21,7 @@ import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
import org.apache.log4j.Logger;
import org.junit.Test;
-public class ComplexReactionToModelTest {
+public class ComplexReactionToModelTest extends WikipathwaysTestFunctions{
/**
* Default class logger.
*/
@@ -41,7 +41,7 @@ public class ComplexReactionToModelTest {
assertEquals(1, reaction.getReactants().size());
assertEquals(1, reaction.getProducts().size());
- assertEquals(0, model1.getCreationWarnings().size());
+ assertEquals(0, getWarnings().size());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -62,7 +62,7 @@ public class ComplexReactionToModelTest {
assertEquals(2, reaction.getReactants().size());
assertEquals(1, reaction.getProducts().size());
- assertEquals(1, model1.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -83,7 +83,7 @@ public class ComplexReactionToModelTest {
assertEquals(1, reaction.getReactants().size());
assertEquals(2, reaction.getProducts().size());
- assertEquals(0, model1.getCreationWarnings().size());
+ assertEquals(0, getWarnings().size());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -106,7 +106,7 @@ public class ComplexReactionToModelTest {
Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
assertEquals("File " + fileName + " different after transformation", 0, mc.compare(model1, model2));
- assertEquals(7, model1.getCreationWarnings().size());
+ assertEquals(7, getWarnings().size());
} catch (Exception e) {
e.printStackTrace();
@@ -130,7 +130,7 @@ public class ComplexReactionToModelTest {
Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
assertEquals("File " + fileName + " different after transformation", 0, mc.compare(model1, model2));
- assertEquals(3, model1.getCreationWarnings().size());
+ assertEquals(3, getWarnings().size());
} catch (Exception e) {
e.printStackTrace();
@@ -156,7 +156,7 @@ public class ComplexReactionToModelTest {
assertEquals("File " + fileName + " different after transformation", 0, mc.compare(model1, model2));
- assertEquals(5, model1.getCreationWarnings().size());
+ assertEquals(5, getWarnings().size());
} catch (Exception e) {
e.printStackTrace();
@@ -181,7 +181,7 @@ public class ComplexReactionToModelTest {
assertFalse(Color.BLACK.equals(redAlias.getColor()));
assertTrue(Color.WHITE.equals(blackAlias.getColor()));
- assertEquals(1, model.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -206,7 +206,7 @@ public class ComplexReactionToModelTest {
assertEquals(4, lineCount);
- assertEquals(1, model.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
index e7c8ca27736ee50f28d23e12d0412184b65e6965..00c46bbbc7fcf0c4c6cb35aa560a01d763fc45f9 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
@@ -29,7 +29,7 @@ import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
-public class GPMLToModelTest {
+public class GPMLToModelTest extends WikipathwaysTestFunctions{
/**
* Default class logger.
*/
@@ -45,7 +45,7 @@ public class GPMLToModelTest {
Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
- assertEquals(22, model1.getCreationWarnings().size());
+ assertEquals(22, getWarnings().size());
CellDesignerXmlParser parser = new CellDesignerXmlParser();
String xml = parser.toXml(model1);
InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
@@ -67,7 +67,7 @@ public class GPMLToModelTest {
Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
- assertEquals(22, model1.getCreationWarnings().size());
+ assertEquals(22, getWarnings().size());
CellDesignerXmlParser parser = new CellDesignerXmlParser();
String xml = parser.toXml(model1);
InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
@@ -90,7 +90,7 @@ public class GPMLToModelTest {
Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
- assertEquals(15, model1.getCreationWarnings().size());
+ assertEquals(15, getWarnings().size());
CellDesignerXmlParser parser = new CellDesignerXmlParser();
String xml = parser.toXml(model1);
InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
@@ -112,7 +112,7 @@ public class GPMLToModelTest {
Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
- assertEquals(16, model1.getCreationWarnings().size());
+ assertEquals(16, getWarnings().size());
CellDesignerXmlParser parser = new CellDesignerXmlParser();
String xml = parser.toXml(model1);
@@ -135,7 +135,7 @@ public class GPMLToModelTest {
Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
- assertEquals(3, model1.getCreationWarnings().size());
+ assertEquals(3, getWarnings().size());
CellDesignerXmlParser parser = new CellDesignerXmlParser();
String xml = parser.toXml(model1);
@@ -158,7 +158,7 @@ public class GPMLToModelTest {
Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
- assertEquals(38, model1.getCreationWarnings().size());
+ assertEquals(38, getWarnings().size());
CellDesignerXmlParser parser = new CellDesignerXmlParser();
String xml = parser.toXml(model1);
@@ -182,7 +182,7 @@ public class GPMLToModelTest {
Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
- assertEquals(41, model1.getCreationWarnings().size());
+ assertEquals(41, getWarnings().size());
CellDesignerXmlParser parser = new CellDesignerXmlParser();
String xml = parser.toXml(model1);
@@ -206,7 +206,7 @@ public class GPMLToModelTest {
Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
- assertEquals(20, model1.getCreationWarnings().size());
+ assertEquals(22, getWarnings().size());
CellDesignerXmlParser parser = new CellDesignerXmlParser();
String xml = parser.toXml(model1);
@@ -230,7 +230,7 @@ public class GPMLToModelTest {
Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
- assertEquals(48, model1.getCreationWarnings().size());
+ assertEquals(48, getWarnings().size());
CellDesignerXmlParser parser = new CellDesignerXmlParser();
String xml = parser.toXml(model1);
@@ -254,7 +254,7 @@ public class GPMLToModelTest {
Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
- assertEquals(0, model1.getCreationWarnings().size());
+ assertEquals(0, getWarnings().size());
CellDesignerXmlParser parser = new CellDesignerXmlParser();
String xml = parser.toXml(model1);
@@ -279,7 +279,7 @@ public class GPMLToModelTest {
Model model1 = new GPMLToModel().getModel(pathToFile);
assertEquals(2, model1.getReactions().iterator().next().getMiriamData().size());
- assertEquals(0, model1.getCreationWarnings().size());
+ assertEquals(0, getWarnings().size());
CellDesignerXmlParser parser = new CellDesignerXmlParser();
String xml = parser.toXml(model1);
@@ -304,7 +304,7 @@ public class GPMLToModelTest {
Model model1 = new GPMLToModel().getModel(pathToFile);
assertTrue(model1.getNotes().contains("Metabolic Process"));
- assertEquals(0, model1.getCreationWarnings().size());
+ assertEquals(0, getWarnings().size());
CellDesignerXmlParser parser = new CellDesignerXmlParser();
String xml = parser.toXml(model1);
@@ -328,7 +328,7 @@ public class GPMLToModelTest {
Model model1 = new GPMLToModel().getModel(pathToFile);
- assertEquals(3, model1.getCreationWarnings().size());
+ assertEquals(3, getWarnings().size());
CellDesignerXmlParser parser = new CellDesignerXmlParser();
String xml = parser.toXml(model1);
@@ -352,7 +352,7 @@ public class GPMLToModelTest {
Model model1 = new GPMLToModel().getModel(pathToFile);
- assertEquals(3, model1.getCreationWarnings().size());
+ assertEquals(3, getWarnings().size());
CellDesignerXmlParser parser = new CellDesignerXmlParser();
String xml = parser.toXml(model1);
@@ -375,7 +375,7 @@ public class GPMLToModelTest {
String fileName = "testFiles/small/model_with_line.gpml";
Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(0, model1.getCreationWarnings().size());
+ assertEquals(0, getWarnings().size());
assertEquals(1, model1.getLayers().iterator().next().getLines().size());
} catch (Exception e) {
@@ -388,9 +388,9 @@ public class GPMLToModelTest {
public void testModelShapes() throws Exception {
try {
String fileName = "testFiles/small/shapes.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
+ new GPMLToModel().getModel(fileName);
- assertEquals(11, model1.getCreationWarnings().size());
+ assertEquals(11, getWarnings().size());
} catch (Exception e) {
e.printStackTrace();
@@ -407,7 +407,7 @@ public class GPMLToModelTest {
assertTrue("Complex parsed from gpml should be hypothetical", species.isHypothetical());
}
- assertEquals(0, model.getCreationWarnings().size());
+ assertEquals(0, getWarnings().size());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -422,7 +422,7 @@ public class GPMLToModelTest {
for (Complex species : model.getComplexList()) {
assertFalse("Complex parsed from gpml should be hypothetical", species.isHypothetical());
}
- assertEquals(0, model.getCreationWarnings().size());
+ assertEquals(0, getWarnings().size());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -441,7 +441,7 @@ public class GPMLToModelTest {
}
}
assertTrue("Complex parsed from gpml should have a valid name", nameFound);
- assertEquals(1, model.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -456,7 +456,7 @@ public class GPMLToModelTest {
for (Compartment compartment : model.getCompartments()) {
assertEquals("Compartment parsed from gpml should have a valid name", "Label", compartment.getName());
}
- assertEquals(0, model.getCreationWarnings().size());
+ assertEquals(0, getWarnings().size());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -507,7 +507,7 @@ public class GPMLToModelTest {
assertEquals(0, mc.compare(model1, model2));
- assertEquals(2, model1.getCreationWarnings().size());
+ assertEquals(2, getWarnings().size());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -528,7 +528,7 @@ public class GPMLToModelTest {
assertEquals(0, mc.compare(model1, model2));
- assertEquals(54, model1.getCreationWarnings().size());
+ assertEquals(54, getWarnings().size());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -578,7 +578,7 @@ public class GPMLToModelTest {
try {
String fileName = "testFiles/small/protein_with_modification.gpml";
Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(0, model1.getCreationWarnings().size());
+ assertEquals(0, getWarnings().size());
Gene protein = (Gene)model1.getElementByElementId("be3de");
assertNotNull(protein);
@@ -603,7 +603,7 @@ public class GPMLToModelTest {
try {
String fileName = "testFiles/small/protein_with_modification_2.gpml";
Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(0, model1.getCreationWarnings().size());
+ assertEquals(0, getWarnings().size());
Gene protein = (Gene)model1.getElementByElementId("be3de");
assertNotNull(protein);
@@ -634,7 +634,7 @@ public class GPMLToModelTest {
double distance = reaction.getCenterPoint().distance(reaction.getModifiers().get(0).getLine().getEndPoint());
assertTrue("Modifier is too far from center point: " + distance, distance < ReactionCellDesignerConverter.RECT_SIZE);
- assertEquals(1, model1.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
} catch (Exception e) {
e.printStackTrace();
@@ -648,7 +648,7 @@ public class GPMLToModelTest {
String fileName = "testFiles/small/reaction_to_label.gpml";
Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, model1.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
assertEquals(1, model1.getReactions().size());
@@ -674,7 +674,7 @@ public class GPMLToModelTest {
assertEquals(1, model1.getReactions().size());
assertEquals(3, model1.getReactions().iterator().next().getNodes().size());
- assertEquals(1, model1.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
CellDesignerXmlParser parser = new CellDesignerXmlParser();
String xml = parser.toXml(model1);
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionElbowsTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionElbowsTest.java
index 5d9b66f3ee38a806a80d7741f73e77d2f509b40f..7fc254299ab01907c414605d1ba86e2a224725b2 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionElbowsTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionElbowsTest.java
@@ -1,875 +1,875 @@
-package lcsb.mapviewer.wikipathway;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.geom.Line2D;
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.reaction.AbstractNode;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
-
-import org.apache.log4j.Logger;
-import org.junit.Test;
-
-public class ReactionElbowsTest {
- private final static double EPSILON = 1e-6;
-
- /**
- * Default class logger.
- */
- static Logger logger = Logger.getLogger(ReactionElbowsTest.class);
-
- private ModelComparator mc = new ModelComparator(1.0);
-
- @Test
- public void LineReactionNorthToNorth() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_n_n.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(5, lines);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionNorthToEast() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_n_e.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(6, lines);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionNorthToEast2() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_n_e_2.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(4, lines);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionNorthToSouth() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_n_s.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(7, lines);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionNorthToWest() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_n_w.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(6, lines);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionNorthToWest2() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_n_w_2.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(4, lines);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionEastToNorth() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_e_n.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(4, lines);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionEastToNorth2() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_e_n_2.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(6, lines);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionEastToEast() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_e_e.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(5, lines);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionEastToSouth() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_e_s.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(6, lines);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionEastToSouth2() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_e_s_2.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(4, lines);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionEastToWest() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_e_w.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(5, lines);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionSouthToNorth() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_s_n.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(5, lines);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionSouthToEast() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_s_e.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(6, lines);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionSouthToEast2() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_s_e_2.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(4, lines);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionSouthToSouth() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_s_s.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(5, lines);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionSouthToWest() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_s_w.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(4, lines);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionSouthToWest2() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_s_w_2.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(6, lines);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionWestToNorth() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_w_n.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(6, lines);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionWestToNorth2() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_w_n_2.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(4, lines);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionWestToEast() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_w_e.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(7, lines);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionWestToSouth() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_w_s.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(6, lines);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionWestToSouth2() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_w_s_2.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(4, lines);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionWestToWest() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_w_w.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(5, lines);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private boolean isHvLine(Line2D line) {
- return Math.abs(line.getX1() - line.getX2()) < EPSILON || Math.abs(line.getY1() - line.getY2()) < EPSILON;
- }
-}
+package lcsb.mapviewer.wikipathway;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.geom.Line2D;
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
+
+import org.apache.log4j.Logger;
+import org.junit.Test;
+
+public class ReactionElbowsTest extends WikipathwaysTestFunctions{
+ private final static double EPSILON = 1e-6;
+
+ /**
+ * Default class logger.
+ */
+ static Logger logger = Logger.getLogger(ReactionElbowsTest.class);
+
+ private ModelComparator mc = new ModelComparator(1.0);
+
+ @Test
+ public void LineReactionNorthToNorth() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_n_n.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(5, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionNorthToEast() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_n_e.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(6, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionNorthToEast2() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_n_e_2.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(4, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionNorthToSouth() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_n_s.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(7, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionNorthToWest() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_n_w.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(6, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionNorthToWest2() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_n_w_2.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(4, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionEastToNorth() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_e_n.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(4, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionEastToNorth2() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_e_n_2.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(6, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionEastToEast() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_e_e.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(5, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionEastToSouth() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_e_s.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(6, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionEastToSouth2() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_e_s_2.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(4, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionEastToWest() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_e_w.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(5, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionSouthToNorth() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_s_n.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(5, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionSouthToEast() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_s_e.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(6, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionSouthToEast2() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_s_e_2.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(4, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionSouthToSouth() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_s_s.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(5, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionSouthToWest() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_s_w.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(4, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionSouthToWest2() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_s_w_2.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(6, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionWestToNorth() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_w_n.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(6, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionWestToNorth2() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_w_n_2.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(4, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionWestToEast() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_w_e.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(7, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionWestToSouth() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_w_s.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(6, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionWestToSouth2() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_w_s_2.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(4, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionWestToWest() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_w_w.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(5, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private boolean isHvLine(Line2D line) {
+ return Math.abs(line.getX1() - line.getX2()) < EPSILON || Math.abs(line.getY1() - line.getY2()) < EPSILON;
+ }
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlInputToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlInputToModelTest.java
index a27c5176604eb4cd6d5cb05b167023b881bb11aa..d0b7a19add525e20c5fb1b5289c8a504264bc46b 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlInputToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlInputToModelTest.java
@@ -1,1417 +1,1417 @@
-package lcsb.mapviewer.wikipathway;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.modifier.Catalysis;
-import lcsb.mapviewer.model.map.modifier.Inhibition;
-import lcsb.mapviewer.model.map.modifier.Modulation;
-import lcsb.mapviewer.model.map.modifier.PhysicalStimulation;
-import lcsb.mapviewer.model.map.modifier.UnknownCatalysis;
-import lcsb.mapviewer.model.map.modifier.UnknownInhibition;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
-
-import org.apache.log4j.Logger;
-import org.junit.Test;
-
-public class ReactionGpmlInputToModelTest {
- /**
- * Default class logger.
- */
- static Logger logger = Logger.getLogger(ReactionGpmlInputToModelTest.class);
-
- private ModelComparator mc = new ModelComparator(1.0);
-
- @Test
- public void LineInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_line_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(0, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void ArrowInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_arrow_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void DashedLineInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_line_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void DashedArrowInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_arrow_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void TBarInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_tbar_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Inhibition);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(0, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void NecessaryStimulationInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_necessary_stimulation_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof PhysicalStimulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(0, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void BindingInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_binding_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void ConversionInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_conversion_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void StimulationInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_stimulation_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof PhysicalStimulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(0, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void ModificationInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_modification_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(0, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void CatalystInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_catalyst_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Catalysis);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(0, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void InhibitionInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_inhibition_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Inhibition);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(0, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void CleavageInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_cleavage_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void CovalentBondInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_covalent_bond_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void BranchingLeftInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_branching_left_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(0, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void BranchingRightInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_branching_right_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(0, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void TranscriptionTranslationInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_transcription_translation_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void GapInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_gap_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void TBarInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_tbar_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof UnknownInhibition);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void NecessaryStimulationInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_necessary_stimulation_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(2, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void BindingInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_binding_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(2, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void ConversionInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_conversion_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(2, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void StimulationInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_stimulation_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(2, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void ModificationInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_modification_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(2, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void CatalystInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_catalyst_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof UnknownCatalysis);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void InhibitionInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_inhibition_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof UnknownInhibition);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(2, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void CleavageInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_cleavage_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(2, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void CovalentBondInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_covalent_bond_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(2, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void BranchingLeftInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_branching_left_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(2, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void BranchingRightInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_branching_right_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(2, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void TranscriptionTranslationInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_transcription_translation_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(2, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void GapInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_gap_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(2, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.wikipathway;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.modifier.Catalysis;
+import lcsb.mapviewer.model.map.modifier.Inhibition;
+import lcsb.mapviewer.model.map.modifier.Modulation;
+import lcsb.mapviewer.model.map.modifier.PhysicalStimulation;
+import lcsb.mapviewer.model.map.modifier.UnknownCatalysis;
+import lcsb.mapviewer.model.map.modifier.UnknownInhibition;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
+
+import org.apache.log4j.Logger;
+import org.junit.Test;
+
+public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
+ /**
+ * Default class logger.
+ */
+ static Logger logger = Logger.getLogger(ReactionGpmlInputToModelTest.class);
+
+ private ModelComparator mc = new ModelComparator(1.0);
+
+ @Test
+ public void LineInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_line_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void ArrowInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_arrow_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void DashedLineInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_line_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void DashedArrowInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_arrow_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void TBarInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_tbar_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Inhibition);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void NecessaryStimulationInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_necessary_stimulation_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof PhysicalStimulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void BindingInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_binding_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void ConversionInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_conversion_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void StimulationInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_stimulation_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof PhysicalStimulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void ModificationInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_modification_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void CatalystInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_catalyst_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Catalysis);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void InhibitionInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_inhibition_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Inhibition);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void CleavageInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_cleavage_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void CovalentBondInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_covalent_bond_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void BranchingLeftInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_branching_left_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void BranchingRightInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_branching_right_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void TranscriptionTranslationInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_transcription_translation_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void GapInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_gap_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void TBarInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_tbar_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof UnknownInhibition);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void NecessaryStimulationInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_necessary_stimulation_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void BindingInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_binding_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void ConversionInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_conversion_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void StimulationInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_stimulation_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void ModificationInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_modification_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void CatalystInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_catalyst_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof UnknownCatalysis);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void InhibitionInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_inhibition_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof UnknownInhibition);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void CleavageInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_cleavage_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void CovalentBondInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_covalent_bond_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void BranchingLeftInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_branching_left_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void BranchingRightInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_branching_right_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void TranscriptionTranslationInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_transcription_translation_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void GapInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_gap_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlOutputToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlOutputToModelTest.java
index 90d62631d20162c0a3b1d44bcb31a1f78a2b90b6..c6522070e1163dbac619ccfb1fb44932b0971dac 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlOutputToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlOutputToModelTest.java
@@ -1,1444 +1,1444 @@
-package lcsb.mapviewer.wikipathway;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.modifier.Catalysis;
-import lcsb.mapviewer.model.map.modifier.Inhibition;
-import lcsb.mapviewer.model.map.modifier.Modulation;
-import lcsb.mapviewer.model.map.modifier.PhysicalStimulation;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
-
-import org.apache.log4j.Logger;
-import org.junit.Test;
-
-public class ReactionGpmlOutputToModelTest {
- /**
- * Default class logger.
- */
- static Logger logger = Logger.getLogger(ReactionGpmlOutputToModelTest.class);
-
- private ModelComparator mc = new ModelComparator(1.0);
-
- @Test
- public void LineInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_line_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(0, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void ArrowInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_arrow_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(0, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void DashedLineInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_line_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void DashedArrowInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_arrow_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void TBarInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_tbar_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Inhibition);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void NecessaryStimulationInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_necessary_stimulation_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof PhysicalStimulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void BindingInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_binding_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void ConversionInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_conversion_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(0, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void StimulationInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_stimulation_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof PhysicalStimulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void ModificationInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_modification_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void CatalystInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_catalyst_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Catalysis);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void InhibitionInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_inhibition_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Inhibition);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void CleavageInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_cleavage_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(0, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void CovalentBondInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_covalent_bond_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void BranchingLeftInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_branching_left_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(0, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void BranchingRightInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_branching_right_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(0, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void TranscriptionTranslationInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_transcription_translation_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void GapInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_gap_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void TBarInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_tbar_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Inhibition);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void NecessaryStimulationInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_necessary_stimulation_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof PhysicalStimulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void BindingInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_binding_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void ConversionInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_conversion_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void StimulationInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_stimulation_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof PhysicalStimulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void ModificationInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_modification_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void CatalystInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_catalyst_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Catalysis);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void InhibitionInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_inhibition_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Inhibition);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void CleavageInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_cleavage_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void CovalentBondInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_covalent_bond_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void BranchingLeftInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_branching_left_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(2, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void BranchingRightInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_branching_right_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(2, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void TranscriptionTranslationInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_transcription_translation_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void GapInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_gap_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, model1.getCreationWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.wikipathway;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.modifier.Catalysis;
+import lcsb.mapviewer.model.map.modifier.Inhibition;
+import lcsb.mapviewer.model.map.modifier.Modulation;
+import lcsb.mapviewer.model.map.modifier.PhysicalStimulation;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
+
+import org.apache.log4j.Logger;
+import org.junit.Test;
+
+public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
+ /**
+ * Default class logger.
+ */
+ static Logger logger = Logger.getLogger(ReactionGpmlOutputToModelTest.class);
+
+ private ModelComparator mc = new ModelComparator(1.0);
+
+ @Test
+ public void LineInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_line_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void ArrowInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_arrow_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void DashedLineInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_line_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void DashedArrowInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_arrow_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void TBarInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_tbar_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Inhibition);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void NecessaryStimulationInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_necessary_stimulation_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof PhysicalStimulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BindingInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_binding_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void ConversionInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_conversion_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void StimulationInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_stimulation_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof PhysicalStimulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void ModificationInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_modification_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void CatalystInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_catalyst_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Catalysis);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void InhibitionInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_inhibition_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Inhibition);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void CleavageInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_cleavage_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void CovalentBondInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_covalent_bond_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BranchingLeftInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_branching_left_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BranchingRightInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_branching_right_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void TranscriptionTranslationInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_transcription_translation_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void GapInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_gap_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void TBarInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_tbar_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Inhibition);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void NecessaryStimulationInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_necessary_stimulation_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof PhysicalStimulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BindingInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_binding_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void ConversionInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_conversion_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void StimulationInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_stimulation_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof PhysicalStimulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void ModificationInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_modification_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void CatalystInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_catalyst_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Catalysis);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void InhibitionInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_inhibition_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Inhibition);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void CleavageInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_cleavage_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void CovalentBondInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_covalent_bond_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BranchingLeftInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_branching_left_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BranchingRightInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_branching_right_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void TranscriptionTranslationInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_transcription_translation_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void GapInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_gap_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlToModelTest.java
index b8de14bad47912a3837d61327d632f7118067e1f..bacd853e5227903437db4d8589fa4d36f4cb4161 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlToModelTest.java
@@ -26,7 +26,7 @@ import lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction;
import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
-public class ReactionGpmlToModelTest {
+public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
/**
* Default class logger.
*/
@@ -45,7 +45,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, model1.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
assertTrue(reaction instanceof UnknownTransitionReaction);
assertTrue(reaction.isReversible());
@@ -75,7 +75,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(0, model1.getCreationWarnings().size());
+ assertEquals(0, getWarnings().size());
assertTrue(reaction instanceof StateTransitionReaction);
assertFalse(reaction.isReversible());
@@ -104,7 +104,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(0, model1.getCreationWarnings().size());
+ assertEquals(0, getWarnings().size());
assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
assertFalse(reaction.isReversible());
@@ -133,7 +133,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, model1.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
assertTrue(reaction instanceof UnknownTransitionReaction);
assertTrue(reaction.isReversible());
@@ -163,7 +163,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, model1.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
assertTrue(reaction instanceof UnknownTransitionReaction);
assertFalse(reaction.isReversible());
@@ -193,7 +193,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(model1.getCreationWarnings().toString(), 0, model1.getCreationWarnings().size());
+ assertEquals(getWarnings().toString(), 0, getWarnings().size());
assertTrue(reaction instanceof HeterodimerAssociationReaction);
assertFalse(reaction.isReversible());
assertEquals(2, reaction.getReactants().size());
@@ -223,7 +223,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, model1.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
assertTrue(reaction instanceof UnknownTransitionReaction);
assertTrue(reaction.isReversible());
@@ -252,7 +252,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, model1.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
assertTrue(reaction instanceof UnknownTransitionReaction);
assertTrue(reaction.isReversible());
@@ -281,7 +281,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, model1.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
assertTrue(reaction instanceof PositiveInfluenceReaction);
assertFalse(reaction.isReversible());
@@ -310,7 +310,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(0, model1.getCreationWarnings().size());
+ assertEquals(0, getWarnings().size());
assertTrue(reaction instanceof StateTransitionReaction);
assertFalse(reaction.isReversible());
@@ -339,7 +339,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(0, model1.getCreationWarnings().size());
+ assertEquals(0, getWarnings().size());
assertTrue(reaction instanceof StateTransitionReaction);
assertFalse(reaction.isReversible());
@@ -368,7 +368,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, model1.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
assertTrue(reaction instanceof UnknownTransitionReaction);
assertTrue(reaction.isReversible());
@@ -397,7 +397,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, model1.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
assertTrue(reaction instanceof UnknownTransitionReaction);
assertTrue(reaction.isReversible());
@@ -426,7 +426,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(0, model1.getCreationWarnings().size());
+ assertEquals(0, getWarnings().size());
assertTrue(reaction instanceof NegativeInfluenceReaction);
assertFalse(reaction.isReversible());
@@ -455,7 +455,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, model1.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
assertTrue(reaction instanceof PositiveInfluenceReaction);
assertFalse(reaction.isReversible());
@@ -484,7 +484,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(0, model1.getCreationWarnings().size());
+ assertEquals(0, getWarnings().size());
assertTrue(reaction instanceof ReducedPhysicalStimulationReaction);
assertFalse(reaction.isReversible());
@@ -513,7 +513,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, model1.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
assertTrue(reaction instanceof ReducedPhysicalStimulationReaction);
assertFalse(reaction.isReversible());
@@ -542,7 +542,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, model1.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
assertTrue(reaction instanceof PositiveInfluenceReaction);
assertFalse(reaction.isReversible());
@@ -571,7 +571,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, model1.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
assertTrue(reaction instanceof NegativeInfluenceReaction);
assertFalse(reaction.isReversible());
@@ -601,7 +601,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, model1.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
assertTrue(reaction instanceof UnknownTransitionReaction);
assertTrue(reaction.isReversible());
@@ -631,7 +631,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(0, model1.getCreationWarnings().size());
+ assertEquals(0, getWarnings().size());
assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
assertFalse(reaction.isReversible());
@@ -660,7 +660,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, model1.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
assertTrue(reaction instanceof UnknownTransitionReaction);
assertTrue(reaction.isReversible());
@@ -689,7 +689,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, model1.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
assertTrue(reaction instanceof UnknownTransitionReaction);
assertTrue(reaction.isReversible());
@@ -718,7 +718,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, model1.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
assertFalse(reaction.isReversible());
@@ -747,7 +747,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, model1.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
assertTrue(reaction instanceof UnknownTransitionReaction);
assertFalse(reaction.isReversible());
@@ -776,7 +776,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(0, model1.getCreationWarnings().size());
+ assertEquals(0, getWarnings().size());
assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
assertFalse(reaction.isReversible());
@@ -805,7 +805,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, model1.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
assertTrue(reaction instanceof UnknownTransitionReaction);
assertTrue(reaction.isReversible());
@@ -834,7 +834,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, model1.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
assertTrue(reaction instanceof UnknownTransitionReaction);
assertTrue(reaction.isReversible());
@@ -863,7 +863,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, model1.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
assertTrue(reaction instanceof UnknownNegativeInfluenceReaction);
assertFalse(reaction.isReversible());
@@ -892,7 +892,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(0, model1.getCreationWarnings().size());
+ assertEquals(0, getWarnings().size());
assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
assertFalse(reaction.isReversible());
@@ -921,7 +921,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, model1.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
assertFalse(reaction.isReversible());
@@ -950,7 +950,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, model1.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
assertFalse(reaction.isReversible());
@@ -979,7 +979,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, model1.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
assertTrue(reaction instanceof PositiveInfluenceReaction);
assertFalse(reaction.isReversible());
@@ -1008,7 +1008,7 @@ public class ReactionGpmlToModelTest {
Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, model1.getCreationWarnings().size());
+ assertEquals(1, getWarnings().size());
assertTrue(reaction instanceof UnknownNegativeInfluenceReaction);
assertFalse(reaction.isReversible());
@@ -1035,7 +1035,7 @@ public class ReactionGpmlToModelTest {
assertEquals(4, model1.getReactions().size());
- assertEquals(4, model1.getCreationWarnings().size());
+ assertEquals(4, getWarnings().size());
CellDesignerXmlParser parser = new CellDesignerXmlParser();
String xml = parser.toXml(model1);
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BugTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BugTest.java
index 80442db55bc7089b08c0e1b59f77d53997df9095..f955ec36c12f13bc7d06bb6425f0497a7bceb9f2 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BugTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BugTest.java
@@ -42,7 +42,7 @@ public class BugTest extends WikipathwaysTestFunctions {
String filename = "testFiles/bugs/error_328.gpml";
Model model1 = new GPMLToModel().getModel(filename);
- assertEquals(7, model1.getCreationWarnings().size());
+ assertEquals(7, getWarnings().size());
int complexes = 0;
for (Element alias : model1.getElements()) {
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelToGPMLTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelToGPMLTest.java
index 233155016416cd53a3e76c174738d921da7c34ba..82c58720f523ed95e0b6ddc1d6f09cbd5b6783a1 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelToGPMLTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelToGPMLTest.java
@@ -41,7 +41,6 @@ public class ModelToGPMLTest extends WikipathwaysTestFunctions {
Model model = cellDesignerXmlParser.createModel(new ConverterParams().filename("testFiles/other_full/GSTP1 subnetwork_220214.xml"));
String xml = parser.getGPML(model);
assertNotNull(xml);
- assertEquals(0, model.getCreationWarnings().size());
assertEquals(10, getWarnings().size());
Model model2 = new GPMLToModel().getModel(new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8)));
diff --git a/persist/src/db/10.0.3/fix_db_20161026.sql b/persist/src/db/10.0.3/fix_db_20161026.sql
new file mode 100644
index 0000000000000000000000000000000000000000..da2d2fd21298ac7ab430ae2193886ac06a4b8b09
--- /dev/null
+++ b/persist/src/db/10.0.3/fix_db_20161026.sql
@@ -0,0 +1,3 @@
+--merging project and model logs
+alter table project_table add column warnings text;
+update project_table set warnings = (select creationwarnings from model_table where project_iddb = project_table.iddb);
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java
index bc43440560de033d093eb732800ddd78cd7075ed..75636b31ce21634d1418faeffcad20a67b951329 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java
@@ -263,4 +263,31 @@ public class ProjectDaoTest extends PersistTestFunctions {
}
}
+ /**
+ * After adding model to db with creation warnings...
+ *
+ * @throws Exception
+ */
+ @Test
+ public void testCreationWarnings() throws Exception {
+ try {
+ Project project = new Project();
+ project.addWarning("warning A");
+ project.addWarning("warning B");
+ assertEquals(2, project.getWarnings().size());
+
+ projectDao.add(project);
+
+ projectDao.evict(project);
+ Project project2 = projectDao.getById(project.getId());
+
+ assertEquals(2, project2.getWarnings().size());
+
+ projectDao.delete(project2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java
index dd51cd7bc75fc67b2a29271b70c8bd2f23e5b2e5..315bc6abbdf11dcc840555fb1b5baff4647597d8 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java
@@ -230,37 +230,6 @@ public class ModelDaoTest extends PersistTestFunctions {
}
}
- /**
- * After adding model to db with creation warnings...
- *
- * @throws Exception
- */
- @Test
- public void testCreationWarnings() throws Exception {
- try {
- Model model = createModel();
- model.addCreationWarning("warning A");
- model.addCreationWarning("warning B");
- assertEquals(2, model.getCreationWarnings().size());
-
- Project project = new Project();
- project.addModel(model);
- projectDao.add(project);
-
- modelDao.evict(model);
- projectDao.evict(project);
- ModelData model2 = modelDao.getById(model.getId());
-
- assertEquals(2, model2.getCreationWarnings().size());
-
- project = projectDao.getById(project.getId());
- projectDao.delete(project);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
/**
* After adding model to db, miriam annotations disappear...
*
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
index 8288bfdfce3141b5d603d23824545f7fb2b43517..4c0f70bd4c0226f7b1213fe62697481be01daf3c 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -735,7 +735,7 @@ public class ProjectService implements IProjectService {
}
}
logger.debug("Updating annotations");
- modelAnnotator.performAnnotations(model, new IProgressUpdater() {
+ modelAnnotator.performAnnotations(project, new IProgressUpdater() {
@Override
public void setProgress(final double progress) {
@@ -780,51 +780,43 @@ public class ProjectService implements IProjectService {
* thrown when one of the files is invalid
*/
private void processDataMining(Model model, List<DataMiningSet> dataMiningSets, final IProgressUpdater progressUpdater) throws InvalidDataMiningInputFile {
- EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
- try {
- Logger.getRootLogger().addAppender(appender);
- Set<Element> nodes = new HashSet<>();
- nodes.addAll(model.getElements());
- for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
- nodes.addAll(connection.getSubmodel().getElements());
- }
- Set<Reaction> reactions = new HashSet<Reaction>();
- reactions.addAll(model.getReactions());
- for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
- reactions.addAll(connection.getSubmodel().getReactions());
- }
+ Set<Element> nodes = new HashSet<>();
+ nodes.addAll(model.getElements());
+ for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
+ nodes.addAll(connection.getSubmodel().getElements());
+ }
+ Set<Reaction> reactions = new HashSet<Reaction>();
+ reactions.addAll(model.getReactions());
+ for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
+ reactions.addAll(connection.getSubmodel().getReactions());
+ }
- int fileCounter = 0;
- final int filesCount = dataMiningSets.size();
- for (DataMiningSet dmSet : dataMiningSets) {
+ int fileCounter = 0;
+ final int filesCount = dataMiningSets.size();
+ for (DataMiningSet dmSet : dataMiningSets) {
- final double offset = IProgressUpdater.MAX_PROGRESS * fileCounter / filesCount;
- IProgressUpdater secondPartUpdater = new IProgressUpdater() {
+ final double offset = IProgressUpdater.MAX_PROGRESS * fileCounter / filesCount;
+ IProgressUpdater secondPartUpdater = new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- progressUpdater.setProgress((progress * CREATION_OF_DATA) / ((double) filesCount) + offset);
- }
- };
- Set<DataMining> result = dataMiningService.parseData(dmSet, nodes, reactions, secondPartUpdater);
- double size = result.size();
- double count = 0;
-
- double updateOffset = IProgressUpdater.MAX_PROGRESS * fileCounter / filesCount + CREATION_OF_DATA / ((double) filesCount);
- dbUtils.setAutoFlush(false);
- for (DataMining missingConnection : result) {
- missingConnection.setType(dmSet.getType());
- missingConnectionDao.add(missingConnection);
- count++;
- progressUpdater.setProgress(updateOffset + IProgressUpdater.MAX_PROGRESS * count / size * UPLOAD_OF_DATA);
+ @Override
+ public void setProgress(double progress) {
+ progressUpdater.setProgress((progress * CREATION_OF_DATA) / ((double) filesCount) + offset);
}
- dbUtils.setAutoFlush(true);
- missingConnectionDao.flush();
+ };
+ Set<DataMining> result = dataMiningService.parseData(dmSet, nodes, reactions, secondPartUpdater);
+ double size = result.size();
+ double count = 0;
+
+ double updateOffset = IProgressUpdater.MAX_PROGRESS * fileCounter / filesCount + CREATION_OF_DATA / ((double) filesCount);
+ dbUtils.setAutoFlush(false);
+ for (DataMining missingConnection : result) {
+ missingConnection.setType(dmSet.getType());
+ missingConnectionDao.add(missingConnection);
+ count++;
+ progressUpdater.setProgress(updateOffset + IProgressUpdater.MAX_PROGRESS * count / size * UPLOAD_OF_DATA);
}
- Logger.getRootLogger().removeAppender(appender);
- model.addLoggingInfo(appender);
- } finally {
- Logger.getRootLogger().removeAppender(appender);
+ dbUtils.setAutoFlush(true);
+ missingConnectionDao.flush();
}
}
@@ -897,7 +889,9 @@ public class ProjectService implements IProjectService {
}
waitForInitialData.countDown();
double[] outOfMemoryBuffer;
+ EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
try {
+ Logger.getRootLogger().addAppender(appender);
logger.debug("Running: " + params.getProjectId() + "; " + params.getProjectFile());
outOfMemoryBuffer = new double[OUT_OF_MEMORY_BACKUP_BUFFER_SIZE];
for (int i = 0; i < OUT_OF_MEMORY_BACKUP_BUFFER_SIZE; i++) {
@@ -931,16 +925,16 @@ public class ProjectService implements IProjectService {
if (meshParser.isValidMeshId(disease)) {
project.setDisease(disease);
} else {
- originalModel.addCreationWarning("No valid disease is provided for project:" + project.getName());
+ logger.warn("No valid disease is provided for project:" + project.getName());
}
} catch (AnnotatorException e1) {
- originalModel.addCreationWarning("Problem with accessing mesh db. More info in logs.");
+ logger.warn("Problem with accessing mesh db. More info in logs.");
}
if (taxonomyBackend.getNameForTaxonomy(organism) != null) {
project.setOrganism(organism);
} else {
- originalModel.addCreationWarning("No valid organism is provided for project:" + project.getName());
+ logger.warn("No valid organism is provided for project:" + project.getName());
}
modelDao.update(originalModel);
@@ -952,8 +946,8 @@ public class ProjectService implements IProjectService {
if (params.isAnalyzeAnnotations()) {
analyzeAnnotations(originalModel, params);
}
- modelDao.update(originalModel);
-
+ Logger.getRootLogger().removeAppender(appender);
+ project.addLoggingInfo(appender);
updateProjectStatus(project, ProjectStatus.DONE, IProgressUpdater.MAX_PROGRESS, params);
if (originalModel.getNotifyEmail() != null && !originalModel.getNotifyEmail().equals("")) {
try {
@@ -987,10 +981,9 @@ public class ProjectService implements IProjectService {
// close the transaction for this thread
dbUtils.closeSessionForCurrentThread();
}
+ Logger.getRootLogger().removeAppender(appender);
}
-
}
-
});
if (params.isAsync()) {
computations.start();
@@ -1227,7 +1220,7 @@ public class ProjectService implements IProjectService {
updateProjectStatus(originalModel.getProject(), ProjectStatus.VALIDATING_MIRIAM, progress, params);
}
}, params.getValidAnnotations());
- List<String> res = new ArrayList<String>();
+ List<String> res = new ArrayList<>();
for (ProblematicAnnotation improperAnnotation : improperAnnotations) {
res.add(improperAnnotation.toString());
}
@@ -1237,8 +1230,9 @@ public class ProjectService implements IProjectService {
for (ProblematicAnnotation improperAnnotation : missingAnnotations) {
res.add(improperAnnotation.toString());
}
- originalModel.addCreationWarnings(res);
- modelDao.update(originalModel);
+ for (String message: res) {
+ logger.warn(message);
+ }
logger.debug("Analyze finished");
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/view/ModelView.java b/service/src/main/java/lcsb/mapviewer/services/view/ModelView.java
index cb53baff24fd83df2076906192ce2df09e8f75da..2780593bd456eb2f2f407d6a645ca4158bcafe00 100644
--- a/service/src/main/java/lcsb/mapviewer/services/view/ModelView.java
+++ b/service/src/main/java/lcsb/mapviewer/services/view/ModelView.java
@@ -1,440 +1,418 @@
-package lcsb.mapviewer.services.view;
-
-import java.io.Serializable;
-import java.util.List;
-
-import lcsb.mapviewer.model.map.model.Model;
-
-import org.apache.log4j.Logger;
-import org.primefaces.model.map.LatLng;
-
-/**
- * View representatin of a model. It's a light structre that present
- * {@link Model} data to the client side.
- *
- * @author Piotr Gawron
- *
- */
-public class ModelView extends AbstractView<Model> implements Serializable {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(ModelView.class);
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Version of the model.
- */
- private String version;
-
- /**
- * Name of the model.
- */
- private String name;
-
- /**
- * {@link lcsb.mapviewer.model.Project#projectId Project identifier}.
- */
- private String projectId;
-
- /**
- * Description of the model.
- */
- private String description;
- /**
- * Size in pixels of the single square tile (small image used for graphical
- * representation).
- */
- private Integer tileSize;
- /**
- * Size of the whole map.
- */
- private Integer pictureSize;
- /**
- * Minimum zoom level that should be allowed by the Google Maps API.
- */
- private Integer minZoom;
- /**
- * Maximum zoom level that should be allowed by the Google Maps API.
- */
- private Integer maxZoom;
- /**
- * Public layouts available for the model.
- */
- private List<LayoutView> layouts;
-
- /**
- * Custom layouts available only for the current user.
- */
- private List<LayoutView> customLayouts;
-
- /**
- * List of submodels in the model.
- */
- private List<ModelView> submodels;
-
- /**
- * Where is the center of the map in latituted, longiude format.
- */
- private LatLng centerLatLng;
-
- /**
- * Top-Left corner of the map (0,0) as a latLng coordinates.
- */
- private LatLng topLeftLatLng;
-
- /**
- * Bottom-Right corner of the map (width,height) as a latLng coordinates.
- */
- private LatLng bottomRightLatLng;
-
- /**
- * Should the map be automatically fit in the browser window. Bean should
- * change this value if the map was already viewed by user and there is
- * information about zoom level and coordinates where user is browsing it.
- */
- private Boolean fitMapBounds = true;
-
- /**
- * List of warnings that appeard during model creation.
- */
- private List<String> creationWarnings;
-
- /**
- * List of overview images attached to this model.
- */
- private List<OverviewImageView> overviewImageViews;
-
- /**
- * Top level overview image.
- */
- private OverviewImageView topOverviewImage;
-
- /**
- * Default constructor which creates view representation from the orignial
- * model.
- *
- * @param model
- * source map model
- */
- protected ModelView(Model model) {
- super(model);
- }
-
- /**
- * Default constructor. Should be used only for deserialization.
- */
- protected ModelView() {
- }
-
- /**
- * @return the version
- * @see #version
- */
- public String getVersion() {
- return version;
- }
-
- /**
- * @param version
- * the version to set
- * @see #version
- */
- public void setVersion(String version) {
- this.version = version;
- }
-
- /**
- * @return the description
- * @see #description
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * @param description
- * the description to set
- * @see #description
- */
- public void setDescription(String description) {
- this.description = description;
- }
-
- /**
- * @return the tileSize
- * @see #tileSize
- */
- public Integer getTileSize() {
- return tileSize;
- }
-
- /**
- * @param tileSize
- * the tileSize to set
- * @see #tileSize
- */
- public void setTileSize(Integer tileSize) {
- this.tileSize = tileSize;
- }
-
- /**
- * @return the pictureSize
- * @see #pictureSize
- */
- public Integer getPictureSize() {
- return pictureSize;
- }
-
- /**
- * @param pictureSize
- * the pictureSize to set
- * @see #pictureSize
- */
- public void setPictureSize(Integer pictureSize) {
- this.pictureSize = pictureSize;
- }
-
- /**
- * @return the minZoom
- * @see #minZoom
- */
- public Integer getMinZoom() {
- return minZoom;
- }
-
- /**
- * @param minZoom
- * the minZoom to set
- * @see #minZoom
- */
- public void setMinZoom(Integer minZoom) {
- this.minZoom = minZoom;
- }
-
- /**
- * @return the maxZoom
- * @see #maxZoom
- */
- public Integer getMaxZoom() {
- return maxZoom;
- }
-
- /**
- * @param maxZoom
- * the maxZoom to set
- * @see #maxZoom
- */
- public void setMaxZoom(Integer maxZoom) {
- this.maxZoom = maxZoom;
- }
-
- /**
- * @return the layouts
- * @see #layouts
- */
- public List<LayoutView> getLayouts() {
- return layouts;
- }
-
- /**
- * @param layouts
- * the layouts to set
- * @see #layouts
- */
- public void setLayouts(List<LayoutView> layouts) {
- this.layouts = layouts;
- }
-
- /**
- * @return the centerLatLng
- * @see #centerLatLng
- */
- public LatLng getCenterLatLng() {
- return centerLatLng;
- }
-
- /**
- * @param centerLatLng
- * the centerLatLng to set
- * @see #centerLatLng
- */
- public void setCenterLatLng(LatLng centerLatLng) {
- this.centerLatLng = centerLatLng;
- }
-
- /**
- * @return the creationWarnings
- * @see #creationWarnings
- */
- public List<String> getCreationWarnings() {
- return creationWarnings;
- }
-
- /**
- * @param creationWarnings
- * the creationWarnings to set
- * @see #creationWarnings
- */
- public void setCreationWarnings(List<String> creationWarnings) {
- this.creationWarnings = creationWarnings;
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return the customLayouts
- * @see #customLayouts
- */
- public List<LayoutView> getCustomLayouts() {
- return customLayouts;
- }
-
- /**
- * @param customLayouts
- * the customLayouts to set
- * @see #customLayouts
- */
- public void setCustomLayouts(List<LayoutView> customLayouts) {
- this.customLayouts = customLayouts;
- }
-
- /**
- * @return the submodels
- * @see #submodels
- */
- public List<ModelView> getSubmodels() {
- return submodels;
- }
-
- /**
- * @param submodels
- * the submodels to set
- * @see #submodels
- */
- public void setSubmodels(List<ModelView> submodels) {
- this.submodels = submodels;
- }
-
- /**
- * @return the overviewImageViews
- * @see #overviewImageViews
- */
- public List<OverviewImageView> getOverviewImageViews() {
- return overviewImageViews;
- }
-
- /**
- * @param overviewImageViews
- * the overviewImageViews to set
- * @see #overviewImageViews
- */
- public void setOverviewImageViews(List<OverviewImageView> overviewImageViews) {
- this.overviewImageViews = overviewImageViews;
- }
-
- /**
- * @return the topOverviewImage
- * @see #topOverviewImage
- */
- public OverviewImageView getTopOverviewImage() {
- return topOverviewImage;
- }
-
- /**
- * @param topOverviewImage
- * the topOverviewImage to set
- * @see #topOverviewImage
- */
- public void setTopOverviewImage(OverviewImageView topOverviewImage) {
- this.topOverviewImage = topOverviewImage;
- }
-
- /**
- * @return the topLeftLatLng
- * @see #topLeftLatLng
- */
- public LatLng getTopLeftLatLng() {
- return topLeftLatLng;
- }
-
- /**
- * @param topLeftLatLng
- * the topLeftLatLng to set
- * @see #topLeftLatLng
- */
- public void setTopLeftLatLng(LatLng topLeftLatLng) {
- this.topLeftLatLng = topLeftLatLng;
- }
-
- /**
- * @return the bottomRightLatLng
- * @see #bottomRightLatLng
- */
- public LatLng getBottomRightLatLng() {
- return bottomRightLatLng;
- }
-
- /**
- * @param bottomRightLatLng
- * the bottomRightLatLng to set
- * @see #bottomRightLatLng
- */
- public void setBottomRightLatLng(LatLng bottomRightLatLng) {
- this.bottomRightLatLng = bottomRightLatLng;
- }
-
- /**
- * @return the fitMapBounds
- * @see #fitMapBounds
- */
- public Boolean getFitMapBounds() {
- return fitMapBounds;
- }
-
- /**
- * @param fitMapBounds
- * the fitMapBounds to set
- * @see #fitMapBounds
- */
- public void setFitMapBounds(Boolean fitMapBounds) {
- this.fitMapBounds = fitMapBounds;
- }
-
- /**
- * @return the projectId
- * @see #projectId
- */
- public String getProjectId() {
- return projectId;
- }
-
- /**
- * @param projectId
- * the projectName to set
- * @see #projectId
- */
- public void setProjectId(String projectId) {
- this.projectId = projectId;
- }
-
-}
+package lcsb.mapviewer.services.view;
+
+import java.io.Serializable;
+import java.util.List;
+
+import lcsb.mapviewer.model.map.model.Model;
+
+import org.apache.log4j.Logger;
+import org.primefaces.model.map.LatLng;
+
+/**
+ * View representatin of a model. It's a light structre that present
+ * {@link Model} data to the client side.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ModelView extends AbstractView<Model> implements Serializable {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(ModelView.class);
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Version of the model.
+ */
+ private String version;
+
+ /**
+ * Name of the model.
+ */
+ private String name;
+
+ /**
+ * {@link lcsb.mapviewer.model.Project#projectId Project identifier}.
+ */
+ private String projectId;
+
+ /**
+ * Description of the model.
+ */
+ private String description;
+ /**
+ * Size in pixels of the single square tile (small image used for graphical
+ * representation).
+ */
+ private Integer tileSize;
+ /**
+ * Size of the whole map.
+ */
+ private Integer pictureSize;
+ /**
+ * Minimum zoom level that should be allowed by the Google Maps API.
+ */
+ private Integer minZoom;
+ /**
+ * Maximum zoom level that should be allowed by the Google Maps API.
+ */
+ private Integer maxZoom;
+ /**
+ * Public layouts available for the model.
+ */
+ private List<LayoutView> layouts;
+
+ /**
+ * Custom layouts available only for the current user.
+ */
+ private List<LayoutView> customLayouts;
+
+ /**
+ * List of submodels in the model.
+ */
+ private List<ModelView> submodels;
+
+ /**
+ * Where is the center of the map in latituted, longiude format.
+ */
+ private LatLng centerLatLng;
+
+ /**
+ * Top-Left corner of the map (0,0) as a latLng coordinates.
+ */
+ private LatLng topLeftLatLng;
+
+ /**
+ * Bottom-Right corner of the map (width,height) as a latLng coordinates.
+ */
+ private LatLng bottomRightLatLng;
+
+ /**
+ * Should the map be automatically fit in the browser window. Bean should
+ * change this value if the map was already viewed by user and there is
+ * information about zoom level and coordinates where user is browsing it.
+ */
+ private Boolean fitMapBounds = true;
+
+ /**
+ * List of overview images attached to this model.
+ */
+ private List<OverviewImageView> overviewImageViews;
+
+ /**
+ * Top level overview image.
+ */
+ private OverviewImageView topOverviewImage;
+
+ /**
+ * Default constructor which creates view representation from the orignial
+ * model.
+ *
+ * @param model
+ * source map model
+ */
+ protected ModelView(Model model) {
+ super(model);
+ }
+
+ /**
+ * Default constructor. Should be used only for deserialization.
+ */
+ protected ModelView() {
+ }
+
+ /**
+ * @return the version
+ * @see #version
+ */
+ public String getVersion() {
+ return version;
+ }
+
+ /**
+ * @param version
+ * the version to set
+ * @see #version
+ */
+ public void setVersion(String version) {
+ this.version = version;
+ }
+
+ /**
+ * @return the description
+ * @see #description
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * @param description
+ * the description to set
+ * @see #description
+ */
+ public void setDescription(String description) {
+ this.description = description;
+ }
+
+ /**
+ * @return the tileSize
+ * @see #tileSize
+ */
+ public Integer getTileSize() {
+ return tileSize;
+ }
+
+ /**
+ * @param tileSize
+ * the tileSize to set
+ * @see #tileSize
+ */
+ public void setTileSize(Integer tileSize) {
+ this.tileSize = tileSize;
+ }
+
+ /**
+ * @return the pictureSize
+ * @see #pictureSize
+ */
+ public Integer getPictureSize() {
+ return pictureSize;
+ }
+
+ /**
+ * @param pictureSize
+ * the pictureSize to set
+ * @see #pictureSize
+ */
+ public void setPictureSize(Integer pictureSize) {
+ this.pictureSize = pictureSize;
+ }
+
+ /**
+ * @return the minZoom
+ * @see #minZoom
+ */
+ public Integer getMinZoom() {
+ return minZoom;
+ }
+
+ /**
+ * @param minZoom
+ * the minZoom to set
+ * @see #minZoom
+ */
+ public void setMinZoom(Integer minZoom) {
+ this.minZoom = minZoom;
+ }
+
+ /**
+ * @return the maxZoom
+ * @see #maxZoom
+ */
+ public Integer getMaxZoom() {
+ return maxZoom;
+ }
+
+ /**
+ * @param maxZoom
+ * the maxZoom to set
+ * @see #maxZoom
+ */
+ public void setMaxZoom(Integer maxZoom) {
+ this.maxZoom = maxZoom;
+ }
+
+ /**
+ * @return the layouts
+ * @see #layouts
+ */
+ public List<LayoutView> getLayouts() {
+ return layouts;
+ }
+
+ /**
+ * @param layouts
+ * the layouts to set
+ * @see #layouts
+ */
+ public void setLayouts(List<LayoutView> layouts) {
+ this.layouts = layouts;
+ }
+
+ /**
+ * @return the centerLatLng
+ * @see #centerLatLng
+ */
+ public LatLng getCenterLatLng() {
+ return centerLatLng;
+ }
+
+ /**
+ * @param centerLatLng
+ * the centerLatLng to set
+ * @see #centerLatLng
+ */
+ public void setCenterLatLng(LatLng centerLatLng) {
+ this.centerLatLng = centerLatLng;
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @return the customLayouts
+ * @see #customLayouts
+ */
+ public List<LayoutView> getCustomLayouts() {
+ return customLayouts;
+ }
+
+ /**
+ * @param customLayouts
+ * the customLayouts to set
+ * @see #customLayouts
+ */
+ public void setCustomLayouts(List<LayoutView> customLayouts) {
+ this.customLayouts = customLayouts;
+ }
+
+ /**
+ * @return the submodels
+ * @see #submodels
+ */
+ public List<ModelView> getSubmodels() {
+ return submodels;
+ }
+
+ /**
+ * @param submodels
+ * the submodels to set
+ * @see #submodels
+ */
+ public void setSubmodels(List<ModelView> submodels) {
+ this.submodels = submodels;
+ }
+
+ /**
+ * @return the overviewImageViews
+ * @see #overviewImageViews
+ */
+ public List<OverviewImageView> getOverviewImageViews() {
+ return overviewImageViews;
+ }
+
+ /**
+ * @param overviewImageViews
+ * the overviewImageViews to set
+ * @see #overviewImageViews
+ */
+ public void setOverviewImageViews(List<OverviewImageView> overviewImageViews) {
+ this.overviewImageViews = overviewImageViews;
+ }
+
+ /**
+ * @return the topOverviewImage
+ * @see #topOverviewImage
+ */
+ public OverviewImageView getTopOverviewImage() {
+ return topOverviewImage;
+ }
+
+ /**
+ * @param topOverviewImage
+ * the topOverviewImage to set
+ * @see #topOverviewImage
+ */
+ public void setTopOverviewImage(OverviewImageView topOverviewImage) {
+ this.topOverviewImage = topOverviewImage;
+ }
+
+ /**
+ * @return the topLeftLatLng
+ * @see #topLeftLatLng
+ */
+ public LatLng getTopLeftLatLng() {
+ return topLeftLatLng;
+ }
+
+ /**
+ * @param topLeftLatLng
+ * the topLeftLatLng to set
+ * @see #topLeftLatLng
+ */
+ public void setTopLeftLatLng(LatLng topLeftLatLng) {
+ this.topLeftLatLng = topLeftLatLng;
+ }
+
+ /**
+ * @return the bottomRightLatLng
+ * @see #bottomRightLatLng
+ */
+ public LatLng getBottomRightLatLng() {
+ return bottomRightLatLng;
+ }
+
+ /**
+ * @param bottomRightLatLng
+ * the bottomRightLatLng to set
+ * @see #bottomRightLatLng
+ */
+ public void setBottomRightLatLng(LatLng bottomRightLatLng) {
+ this.bottomRightLatLng = bottomRightLatLng;
+ }
+
+ /**
+ * @return the fitMapBounds
+ * @see #fitMapBounds
+ */
+ public Boolean getFitMapBounds() {
+ return fitMapBounds;
+ }
+
+ /**
+ * @param fitMapBounds
+ * the fitMapBounds to set
+ * @see #fitMapBounds
+ */
+ public void setFitMapBounds(Boolean fitMapBounds) {
+ this.fitMapBounds = fitMapBounds;
+ }
+
+ /**
+ * @return the projectId
+ * @see #projectId
+ */
+ public String getProjectId() {
+ return projectId;
+ }
+
+ /**
+ * @param projectId
+ * the projectName to set
+ * @see #projectId
+ */
+ public void setProjectId(String projectId) {
+ this.projectId = projectId;
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/view/ModelViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/view/ModelViewFactory.java
index 36c649437f5e94b6086b7fd72f3ad1cf74e676d7..434de14923c2cc4c2a42b0fd16db7b14523dc97a 100644
--- a/service/src/main/java/lcsb/mapviewer/services/view/ModelViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/view/ModelViewFactory.java
@@ -1,102 +1,100 @@
-package lcsb.mapviewer.services.view;
-
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.List;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.services.utils.gmap.CoordinationConverter;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-import com.google.gson.Gson;
-
-/**
- * Factory class for {@link ModelView} class.
- *
- * @author Piotr Gawron
- *
- */
-@Transactional(value = "txManager")
-public class ModelViewFactory extends AbstractViewFactory<Model, ModelView> {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ModelViewFactory.class);
-
- /**
- * Factory object used for creation of {@link LayoutView} elements.
- */
- @Autowired
- private LayoutViewFactory layoutViewFactory;
-
- /**
- * Factory object used for creation of {@link OverviewImageView} elements.
- */
- @Autowired
- private OverviewImageViewFactory overviewImageViewFactory;
-
- @Override
- public ModelView create(Model model) {
- ModelView result = new ModelView(model);
- if (model == null) {
- logger.warn("Empty model...");
- return result;
- }
- if (model.getProject() != null) {
- result.setProjectId(model.getProject().getProjectId());
- }
- result.setLayouts(new ArrayList<LayoutView>());
- result.setCustomLayouts(new ArrayList<LayoutView>());
- result.setVersion(model.getMapVersion());
- result.setName(model.getName());
-
- result.setMinZoom(Configuration.MIN_ZOOM_LEVEL);
- result.setMaxZoom(result.getMinZoom() + model.getZoomLevels());
- result.setTileSize(model.getTileSize());
- result.setPictureSize((int) Math.max(model.getWidth(), model.getHeight()));
- // we have to add copies (originals contain reference to model which
- // shouldn't be passed to simple structure)
- for (Layout layout : model.getLayouts()) {
- if (layout.isPublicLayout()) {
- result.getLayouts().add(layoutViewFactory.create(layout));
- }
- }
- CoordinationConverter cConverter = new CoordinationConverter(model);
- result.setCenterLatLng(cConverter.toLatLng(new Point2D.Double(result.getPictureSize() / 2, result.getPictureSize() / 2)));
- result.setBottomRightLatLng(cConverter.toLatLng(new Point2D.Double(model.getWidth(), model.getHeight())));
- result.setTopLeftLatLng(cConverter.toLatLng(new Point2D.Double(0, 0)));
-
- result.setDescription(model.getNotes());
-
- result.setCreationWarnings(model.getCreationWarnings());
-
- List<ModelView> submodels = new ArrayList<ModelView>();
- for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
- submodels.add(create(connection.getSubmodel().getModel()));
- }
- result.setSubmodels(submodels);
- result.setOverviewImageViews(overviewImageViewFactory.createList(model.getOverviewImages()));
- if (result.getOverviewImageViews().size() > 0) {
- result.setTopOverviewImage(overviewImageViewFactory.create(model.getTopOverviewImage()));
- }
- return result;
- }
-
- @Override
- public String createGson(ModelView object) {
- return new Gson().toJson(object);
- }
-
- @Override
- public Model viewToObject(ModelView view) {
- throw new NotImplementedException();
- }
-}
+package lcsb.mapviewer.services.view;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.List;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
+import lcsb.mapviewer.services.utils.gmap.CoordinationConverter;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+import com.google.gson.Gson;
+
+/**
+ * Factory class for {@link ModelView} class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Transactional(value = "txManager")
+public class ModelViewFactory extends AbstractViewFactory<Model, ModelView> {
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ModelViewFactory.class);
+
+ /**
+ * Factory object used for creation of {@link LayoutView} elements.
+ */
+ @Autowired
+ private LayoutViewFactory layoutViewFactory;
+
+ /**
+ * Factory object used for creation of {@link OverviewImageView} elements.
+ */
+ @Autowired
+ private OverviewImageViewFactory overviewImageViewFactory;
+
+ @Override
+ public ModelView create(Model model) {
+ ModelView result = new ModelView(model);
+ if (model == null) {
+ logger.warn("Empty model...");
+ return result;
+ }
+ if (model.getProject() != null) {
+ result.setProjectId(model.getProject().getProjectId());
+ }
+ result.setLayouts(new ArrayList<LayoutView>());
+ result.setCustomLayouts(new ArrayList<LayoutView>());
+ result.setVersion(model.getMapVersion());
+ result.setName(model.getName());
+
+ result.setMinZoom(Configuration.MIN_ZOOM_LEVEL);
+ result.setMaxZoom(result.getMinZoom() + model.getZoomLevels());
+ result.setTileSize(model.getTileSize());
+ result.setPictureSize((int) Math.max(model.getWidth(), model.getHeight()));
+ // we have to add copies (originals contain reference to model which
+ // shouldn't be passed to simple structure)
+ for (Layout layout : model.getLayouts()) {
+ if (layout.isPublicLayout()) {
+ result.getLayouts().add(layoutViewFactory.create(layout));
+ }
+ }
+ CoordinationConverter cConverter = new CoordinationConverter(model);
+ result.setCenterLatLng(cConverter.toLatLng(new Point2D.Double(result.getPictureSize() / 2, result.getPictureSize() / 2)));
+ result.setBottomRightLatLng(cConverter.toLatLng(new Point2D.Double(model.getWidth(), model.getHeight())));
+ result.setTopLeftLatLng(cConverter.toLatLng(new Point2D.Double(0, 0)));
+
+ result.setDescription(model.getNotes());
+
+ List<ModelView> submodels = new ArrayList<ModelView>();
+ for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
+ submodels.add(create(connection.getSubmodel().getModel()));
+ }
+ result.setSubmodels(submodels);
+ result.setOverviewImageViews(overviewImageViewFactory.createList(model.getOverviewImages()));
+ if (result.getOverviewImageViews().size() > 0) {
+ result.setTopOverviewImage(overviewImageViewFactory.create(model.getTopOverviewImage()));
+ }
+ return result;
+ }
+
+ @Override
+ public String createGson(ModelView object) {
+ return new Gson().toJson(object);
+ }
+
+ @Override
+ public Model viewToObject(ModelView view) {
+ throw new NotImplementedException();
+ }
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/view/ProjectView.java b/service/src/main/java/lcsb/mapviewer/services/view/ProjectView.java
index ae6a0f96420135d27ecf98bbe83d55c8821a341b..6e1ed975ea37398c6e56a39020d759674f3932f2 100644
--- a/service/src/main/java/lcsb/mapviewer/services/view/ProjectView.java
+++ b/service/src/main/java/lcsb/mapviewer/services/view/ProjectView.java
@@ -1,551 +1,527 @@
-package lcsb.mapviewer.services.view;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-import lcsb.mapviewer.common.comparator.IntegerComparator;
-import lcsb.mapviewer.model.Project;
-
-/**
- * This class is a client view that represents {@link Project} class. Right now
- * this class highly entangles {@link Project} and
- * {@link lcsb.mapviewer.model.map.model.db.model.map.Model Model}. In the
- * future it should separate it.
- *
- * @author Piotr Gawron
- *
- */
-public class ProjectView extends AbstractView<Project> implements Comparable<ProjectView>, Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Identifier of the model that is represented in this project view (this must
- * be refactorized in the future).
- */
- private Integer modelId;
-
- /**
- * List of layouts in the model (identified by {@link #modelId}).
- */
- private List<LayoutView> layouts = new ArrayList<LayoutView>();
-
- /**
- * {@link Project#projectId Identifier} of the project.
- */
- private String projectId;
-
- /**
- * {@link Project#name Name} of the project.
- */
- private String projectName;
-
- /**
- * {@link Project#name newDiseaseName} of the project.
- */
- private String newDiseaseName;
-
- /**
- * {@link Project#organism newOrganismName} of the project.
- */
- private String newOrganismName;
-
- /**
- * {@link Project#disease Disease} of the project.
- */
- private AnnotationView projectDiseaseLink;
-
- /**
- * {@link Project#disease Disease name} of the project.
- */
- private String diseaseName = "N/A";
-
- /**
- * {@link Project#organism Organism} of the project.
- */
- private AnnotationView organismLink;
-
- /**
- * Email used for notification obut the events connected to this project.
- */
- private String notifyEmail;
-
- /**
- * Status of the project processing.
- */
- private String status;
-
- /**
- * Errors that appeard in the project.
- */
- private String errors;
-
- /**
- * Progress of the project processng (value between 0..100).
- */
- private Integer progress;
-
- /**
- * List of warnings that appeard during model creation.
- */
- private String creationWarnings;
-
- /**
- * Short list of warnings that appeard during model creation.
- */
- private String creationWarningsPreview;
-
- /**
- * List of warnings that appeard during model creation.
- */
- private List<String> warnings;
-
- /**
- * Description of the model.
- */
- private String description;
- /**
- * Version of the model.
- */
- private String version;
-
- /**
- * "true" if input file from which project was created is available, "false"
- * otherwise.
- */
- private String inputDataAvailable;
-
- /**
- * List of data mining sets used to gernerate suggested connections.
- */
- private List<DataMiningSetView> dataMiningSets = new ArrayList<DataMiningSetView>();
-
- /**
- * Default constructor.
- *
- * @param project
- * {@link Project} for which this view is created
- */
- protected ProjectView(Project project) {
- super(project);
- }
-
- /**
- * Default constructor. Should be used only for deserialization.
- */
- protected ProjectView() {
- }
-
- /**
- * Constructor that creates copy of the {@link ProjectView}.
- *
- * @param row
- * original object
- */
- public ProjectView(ProjectView row) {
- super(null);
- setIdObject(row.getIdObject());
- modelId = row.getModelId();
- layouts.addAll(row.getLayouts());
- projectId = row.getProjectId();
- projectName = row.getProjectName();
- newDiseaseName = row.getNewDiseaseName();
- newOrganismName = row.getNewOrganismName();
- projectDiseaseLink = row.getProjectDiseaseLink();
- organismLink = row.getOrganismLink();
- notifyEmail = row.getNotifyEmail();
- status = row.getStatus();
- progress = row.getProgress();
- description = row.getDescription();
- version = row.getVersion();
- errors = row.getErrors();
- creationWarnings = row.getCreationWarnings();
- creationWarningsPreview = row.getCreationWarningsPreview();
- warnings = row.getWarnings();
- for (DataMiningSetView view : row.getDataMiningSets()) {
- dataMiningSets.add(new DataMiningSetView(view));
- }
- inputDataAvailable = row.getInputDataAvailable();
- }
-
- @Override
- public int compareTo(ProjectView o) {
- if (o == null) {
- new IntegerComparator().compare(getIdObject(), null);
- }
- return new IntegerComparator().compare(getIdObject(), o.getIdObject());
- }
-
- /**
- * @return the modelId
- * @see #modelId
- */
- public Integer getModelId() {
- return modelId;
- }
-
- /**
- * @param modelId
- * the modelId to set
- * @see #modelId
- */
- public void setModelId(Integer modelId) {
- this.modelId = modelId;
- }
-
- /**
- * @return the layouts
- * @see #layouts
- */
- public List<LayoutView> getLayouts() {
- return layouts;
- }
-
- /**
- * @param layouts
- * the layouts to set
- * @see #layouts
- */
- public void setLayouts(List<LayoutView> layouts) {
- this.layouts = layouts;
- }
-
- /**
- * @return the name
- * @see #projectId
- */
- public String getProjectId() {
- return projectId;
- }
-
- /**
- * @param projectId
- * project identifier
- * @see #projectId
- */
- public void setProjectId(String projectId) {
- this.projectId = projectId;
- }
-
- /**
- * @return the notifyEmail
- * @see #notifyEmail
- */
- public String getNotifyEmail() {
- return notifyEmail;
- }
-
- /**
- * @param notifyEmail
- * the notifyEmail to set
- * @see #notifyEmail
- */
- public void setNotifyEmail(String notifyEmail) {
- this.notifyEmail = notifyEmail;
- }
-
- /**
- * @return the status
- * @see #status
- */
- public String getStatus() {
- return status;
- }
-
- /**
- * @param status
- * the status to set
- * @see #status
- */
- public void setStatus(String status) {
- this.status = status;
- }
-
- /**
- * @return the progress
- * @see #progress
- */
- public Integer getProgress() {
- return progress;
- }
-
- /**
- * @param progress
- * the progress to set
- * @see #progress
- */
- public void setProgress(Integer progress) {
- this.progress = progress;
- }
-
- /**
- * @return the description
- * @see #description
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * @param description
- * the description to set
- * @see #description
- */
- public void setDescription(String description) {
- this.description = description;
- }
-
- /**
- * @return the version
- * @see #version
- */
- public String getVersion() {
- return version;
- }
-
- /**
- * @param version
- * the version to set
- * @see #version
- */
- public void setVersion(String version) {
- this.version = version;
- }
-
- /**
- * Adds layout to the view.
- *
- * @param row
- * layout to add
- */
- public void addLayout(LayoutView row) {
- layouts.add(row);
- }
-
- /**
- * @return the creationWarnings
- * @see #creationWarnings
- */
- public String getCreationWarnings() {
- return creationWarnings;
- }
-
- /**
- * @param creationWarnings
- * the creationWarnings to set
- * @see #creationWarnings
- */
- public void setCreationWarnings(String creationWarnings) {
- this.creationWarnings = creationWarnings;
- }
-
- /**
- * @return the warnings
- * @see #warnings
- */
- public List<String> getWarnings() {
- return warnings;
- }
-
- /**
- * @param warnings
- * the warnings to set
- * @see #warnings
- */
- public void setWarnings(List<String> warnings) {
- this.warnings = warnings;
- }
-
- /**
- * @return the errors
- * @see #errors
- */
- public String getErrors() {
- return errors;
- }
-
- /**
- * @param errors
- * the errors to set
- * @see #errors
- */
- public void setErrors(String errors) {
- this.errors = errors;
- }
-
- /**
- * @return the dataMiningSets
- * @see #dataMiningSets
- */
- public List<DataMiningSetView> getDataMiningSets() {
- return dataMiningSets;
- }
-
- /**
- * @param dataMiningSets
- * the dataMiningSets to set
- * @see #dataMiningSets
- */
- public void setDataMiningSets(List<DataMiningSetView> dataMiningSets) {
- this.dataMiningSets = dataMiningSets;
- }
-
- /**
- * Adds {@link DataMiningSetView} to {@link #dataMiningSets}.
- *
- * @param dataMiningSetView
- * object to add
- */
- public void addDataMiningSet(DataMiningSetView dataMiningSetView) {
- dataMiningSets.add(dataMiningSetView);
- }
-
- /**
- * @return the creationWarningsPreview
- * @see #creationWarningsPreview
- */
- public String getCreationWarningsPreview() {
- return creationWarningsPreview;
- }
-
- /**
- * @param creationWarningsPreview
- * the creationWarningsPreview to set
- * @see #creationWarningsPreview
- */
- public void setCreationWarningsPreview(String creationWarningsPreview) {
- this.creationWarningsPreview = creationWarningsPreview;
- }
-
- /**
- * @return the projectName
- * @see #projectName
- */
- public String getProjectName() {
- return projectName;
- }
-
- /**
- * @param projectName
- * the projectName to set
- * @see #projectName
- */
- public void setProjectName(String projectName) {
- this.projectName = projectName;
- }
-
- /**
- * @return project disease link
- */
- public AnnotationView getProjectDiseaseLink() {
- return projectDiseaseLink;
- }
-
- /**
- * @param projectDiseaseLink
- * the link for the disease.
- */
- public void setProjectDiseaseLink(AnnotationView projectDiseaseLink) {
- this.projectDiseaseLink = projectDiseaseLink;
- }
-
- /**
- * @return this is used to update or add different disease association.
- */
- public String getNewDiseaseName() {
- return newDiseaseName;
- }
-
- /**
- * @param newDiseaseName
- * this is used to update or add different disease association.
- */
- public void setNewDiseaseName(String newDiseaseName) {
- this.newDiseaseName = newDiseaseName;
- }
-
- /**
- * @return the diseaseName
- * @see #diseaseName
- */
- public String getDiseaseName() {
- return diseaseName;
- }
-
- /**
- * @param diseaseName
- * the diseaseName to set
- * @see #diseaseName
- */
- public void setDiseaseName(String diseaseName) {
- this.diseaseName = diseaseName;
- }
-
- /**
- * @return the inputDataAvailable
- * @see #inputDataAvailable
- */
- public String getInputDataAvailable() {
- return inputDataAvailable;
- }
-
- /**
- * @param inputDataAvailable
- * the inputDataAvailable to set
- * @see #inputDataAvailable
- */
- public void setInputDataAvailable(String inputDataAvailable) {
- this.inputDataAvailable = inputDataAvailable;
- }
-
- /**
- * @param value
- * the inputDataAvailable to set
- * @see #inputDataAvailable
- */
- public void setInputDataAvailable(boolean value) {
- if (value) {
- this.inputDataAvailable = "true";
- } else {
- this.inputDataAvailable = "false";
- }
-
- }
-
- /**
- * @return the organismLink
- * @see #organismLink
- */
- public AnnotationView getOrganismLink() {
- return organismLink;
- }
-
- /**
- * @param organismLink the organismLink to set
- * @see #organismLink
- */
- public void setOrganismLink(AnnotationView organismLink) {
- this.organismLink = organismLink;
- }
-
- /**
- * @return the newOrganismName
- * @see #newOrganismName
- */
- public String getNewOrganismName() {
- return newOrganismName;
- }
-
- /**
- * @param newOrganismName the newOrganismName to set
- * @see #newOrganismName
- */
- public void setNewOrganismName(String newOrganismName) {
- this.newOrganismName = newOrganismName;
- }
-
-}
+package lcsb.mapviewer.services.view;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+import lcsb.mapviewer.common.comparator.IntegerComparator;
+import lcsb.mapviewer.model.Project;
+
+/**
+ * This class is a client view that represents {@link Project} class. Right now
+ * this class highly entangles {@link Project} and
+ * {@link lcsb.mapviewer.model.map.model.db.model.map.Model Model}. In the
+ * future it should separate it.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ProjectView extends AbstractView<Project> implements Comparable<ProjectView>, Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Identifier of the model that is represented in this project view (this must
+ * be refactorized in the future).
+ */
+ private Integer modelId;
+
+ /**
+ * List of layouts in the model (identified by {@link #modelId}).
+ */
+ private List<LayoutView> layouts = new ArrayList<LayoutView>();
+
+ /**
+ * {@link Project#projectId Identifier} of the project.
+ */
+ private String projectId;
+
+ /**
+ * {@link Project#name Name} of the project.
+ */
+ private String projectName;
+
+ /**
+ * {@link Project#name newDiseaseName} of the project.
+ */
+ private String newDiseaseName;
+
+ /**
+ * {@link Project#organism newOrganismName} of the project.
+ */
+ private String newOrganismName;
+
+ /**
+ * {@link Project#disease Disease} of the project.
+ */
+ private AnnotationView projectDiseaseLink;
+
+ /**
+ * {@link Project#disease Disease name} of the project.
+ */
+ private String diseaseName = "N/A";
+
+ /**
+ * {@link Project#organism Organism} of the project.
+ */
+ private AnnotationView organismLink;
+
+ /**
+ * Email used for notification obut the events connected to this project.
+ */
+ private String notifyEmail;
+
+ /**
+ * Status of the project processing.
+ */
+ private String status;
+
+ /**
+ * Errors that appeard in the project.
+ */
+ private String errors;
+
+ /**
+ * Progress of the project processng (value between 0..100).
+ */
+ private Integer progress;
+
+ /**
+ * Short list of warnings that appeard during model creation.
+ */
+ private String warningsPreview;
+
+ /**
+ * List of warnings that appeard during model creation.
+ */
+ private List<String> warnings;
+
+ /**
+ * Description of the model.
+ */
+ private String description;
+ /**
+ * Version of the model.
+ */
+ private String version;
+
+ /**
+ * "true" if input file from which project was created is available, "false"
+ * otherwise.
+ */
+ private String inputDataAvailable;
+
+ /**
+ * List of data mining sets used to gernerate suggested connections.
+ */
+ private List<DataMiningSetView> dataMiningSets = new ArrayList<DataMiningSetView>();
+
+ /**
+ * Default constructor.
+ *
+ * @param project
+ * {@link Project} for which this view is created
+ */
+ protected ProjectView(Project project) {
+ super(project);
+ }
+
+ /**
+ * Default constructor. Should be used only for deserialization.
+ */
+ protected ProjectView() {
+ }
+
+ /**
+ * Constructor that creates copy of the {@link ProjectView}.
+ *
+ * @param row
+ * original object
+ */
+ public ProjectView(ProjectView row) {
+ super(null);
+ setIdObject(row.getIdObject());
+ modelId = row.getModelId();
+ layouts.addAll(row.getLayouts());
+ projectId = row.getProjectId();
+ projectName = row.getProjectName();
+ newDiseaseName = row.getNewDiseaseName();
+ newOrganismName = row.getNewOrganismName();
+ projectDiseaseLink = row.getProjectDiseaseLink();
+ organismLink = row.getOrganismLink();
+ notifyEmail = row.getNotifyEmail();
+ status = row.getStatus();
+ progress = row.getProgress();
+ description = row.getDescription();
+ version = row.getVersion();
+ errors = row.getErrors();
+ warningsPreview = row.getWarningsPreview();
+ warnings = row.getWarnings();
+ for (DataMiningSetView view : row.getDataMiningSets()) {
+ dataMiningSets.add(new DataMiningSetView(view));
+ }
+ inputDataAvailable = row.getInputDataAvailable();
+ }
+
+ @Override
+ public int compareTo(ProjectView o) {
+ if (o == null) {
+ new IntegerComparator().compare(getIdObject(), null);
+ }
+ return new IntegerComparator().compare(getIdObject(), o.getIdObject());
+ }
+
+ /**
+ * @return the modelId
+ * @see #modelId
+ */
+ public Integer getModelId() {
+ return modelId;
+ }
+
+ /**
+ * @param modelId
+ * the modelId to set
+ * @see #modelId
+ */
+ public void setModelId(Integer modelId) {
+ this.modelId = modelId;
+ }
+
+ /**
+ * @return the layouts
+ * @see #layouts
+ */
+ public List<LayoutView> getLayouts() {
+ return layouts;
+ }
+
+ /**
+ * @param layouts
+ * the layouts to set
+ * @see #layouts
+ */
+ public void setLayouts(List<LayoutView> layouts) {
+ this.layouts = layouts;
+ }
+
+ /**
+ * @return the name
+ * @see #projectId
+ */
+ public String getProjectId() {
+ return projectId;
+ }
+
+ /**
+ * @param projectId
+ * project identifier
+ * @see #projectId
+ */
+ public void setProjectId(String projectId) {
+ this.projectId = projectId;
+ }
+
+ /**
+ * @return the notifyEmail
+ * @see #notifyEmail
+ */
+ public String getNotifyEmail() {
+ return notifyEmail;
+ }
+
+ /**
+ * @param notifyEmail
+ * the notifyEmail to set
+ * @see #notifyEmail
+ */
+ public void setNotifyEmail(String notifyEmail) {
+ this.notifyEmail = notifyEmail;
+ }
+
+ /**
+ * @return the status
+ * @see #status
+ */
+ public String getStatus() {
+ return status;
+ }
+
+ /**
+ * @param status
+ * the status to set
+ * @see #status
+ */
+ public void setStatus(String status) {
+ this.status = status;
+ }
+
+ /**
+ * @return the progress
+ * @see #progress
+ */
+ public Integer getProgress() {
+ return progress;
+ }
+
+ /**
+ * @param progress
+ * the progress to set
+ * @see #progress
+ */
+ public void setProgress(Integer progress) {
+ this.progress = progress;
+ }
+
+ /**
+ * @return the description
+ * @see #description
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * @param description
+ * the description to set
+ * @see #description
+ */
+ public void setDescription(String description) {
+ this.description = description;
+ }
+
+ /**
+ * @return the version
+ * @see #version
+ */
+ public String getVersion() {
+ return version;
+ }
+
+ /**
+ * @param version
+ * the version to set
+ * @see #version
+ */
+ public void setVersion(String version) {
+ this.version = version;
+ }
+
+ /**
+ * Adds layout to the view.
+ *
+ * @param row
+ * layout to add
+ */
+ public void addLayout(LayoutView row) {
+ layouts.add(row);
+ }
+
+ /**
+ * @return the warnings
+ * @see #warnings
+ */
+ public List<String> getWarnings() {
+ return warnings;
+ }
+
+ /**
+ * @param warnings
+ * the warnings to set
+ * @see #warnings
+ */
+ public void setWarnings(List<String> warnings) {
+ this.warnings = warnings;
+ }
+
+ /**
+ * @return the errors
+ * @see #errors
+ */
+ public String getErrors() {
+ return errors;
+ }
+
+ /**
+ * @param errors
+ * the errors to set
+ * @see #errors
+ */
+ public void setErrors(String errors) {
+ this.errors = errors;
+ }
+
+ /**
+ * @return the dataMiningSets
+ * @see #dataMiningSets
+ */
+ public List<DataMiningSetView> getDataMiningSets() {
+ return dataMiningSets;
+ }
+
+ /**
+ * @param dataMiningSets
+ * the dataMiningSets to set
+ * @see #dataMiningSets
+ */
+ public void setDataMiningSets(List<DataMiningSetView> dataMiningSets) {
+ this.dataMiningSets = dataMiningSets;
+ }
+
+ /**
+ * Adds {@link DataMiningSetView} to {@link #dataMiningSets}.
+ *
+ * @param dataMiningSetView
+ * object to add
+ */
+ public void addDataMiningSet(DataMiningSetView dataMiningSetView) {
+ dataMiningSets.add(dataMiningSetView);
+ }
+
+ /**
+ * @return the projectName
+ * @see #projectName
+ */
+ public String getProjectName() {
+ return projectName;
+ }
+
+ /**
+ * @param projectName
+ * the projectName to set
+ * @see #projectName
+ */
+ public void setProjectName(String projectName) {
+ this.projectName = projectName;
+ }
+
+ /**
+ * @return project disease link
+ */
+ public AnnotationView getProjectDiseaseLink() {
+ return projectDiseaseLink;
+ }
+
+ /**
+ * @param projectDiseaseLink
+ * the link for the disease.
+ */
+ public void setProjectDiseaseLink(AnnotationView projectDiseaseLink) {
+ this.projectDiseaseLink = projectDiseaseLink;
+ }
+
+ /**
+ * @return this is used to update or add different disease association.
+ */
+ public String getNewDiseaseName() {
+ return newDiseaseName;
+ }
+
+ /**
+ * @param newDiseaseName
+ * this is used to update or add different disease association.
+ */
+ public void setNewDiseaseName(String newDiseaseName) {
+ this.newDiseaseName = newDiseaseName;
+ }
+
+ /**
+ * @return the diseaseName
+ * @see #diseaseName
+ */
+ public String getDiseaseName() {
+ return diseaseName;
+ }
+
+ /**
+ * @param diseaseName
+ * the diseaseName to set
+ * @see #diseaseName
+ */
+ public void setDiseaseName(String diseaseName) {
+ this.diseaseName = diseaseName;
+ }
+
+ /**
+ * @return the inputDataAvailable
+ * @see #inputDataAvailable
+ */
+ public String getInputDataAvailable() {
+ return inputDataAvailable;
+ }
+
+ /**
+ * @param inputDataAvailable
+ * the inputDataAvailable to set
+ * @see #inputDataAvailable
+ */
+ public void setInputDataAvailable(String inputDataAvailable) {
+ this.inputDataAvailable = inputDataAvailable;
+ }
+
+ /**
+ * @param value
+ * the inputDataAvailable to set
+ * @see #inputDataAvailable
+ */
+ public void setInputDataAvailable(boolean value) {
+ if (value) {
+ this.inputDataAvailable = "true";
+ } else {
+ this.inputDataAvailable = "false";
+ }
+
+ }
+
+ /**
+ * @return the organismLink
+ * @see #organismLink
+ */
+ public AnnotationView getOrganismLink() {
+ return organismLink;
+ }
+
+ /**
+ * @param organismLink the organismLink to set
+ * @see #organismLink
+ */
+ public void setOrganismLink(AnnotationView organismLink) {
+ this.organismLink = organismLink;
+ }
+
+ /**
+ * @return the newOrganismName
+ * @see #newOrganismName
+ */
+ public String getNewOrganismName() {
+ return newOrganismName;
+ }
+
+ /**
+ * @param newOrganismName the newOrganismName to set
+ * @see #newOrganismName
+ */
+ public void setNewOrganismName(String newOrganismName) {
+ this.newOrganismName = newOrganismName;
+ }
+
+ /**
+ * @return the warningsPreview
+ * @see #warningsPreview
+ */
+ public String getWarningsPreview() {
+ return warningsPreview;
+ }
+
+ /**
+ * @param warningsPreview the warningsPreview to set
+ * @see #warningsPreview
+ */
+ public void setWarningsPreview(String warningsPreview) {
+ this.warningsPreview = warningsPreview;
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/view/ProjectViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/view/ProjectViewFactory.java
index 85e7784a551a5ec2c6dc5abc9ecfb9df2d6a9215..1d98eb8894d2cb3bb1e4ef4865aab8725b965989 100644
--- a/service/src/main/java/lcsb/mapviewer/services/view/ProjectViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/view/ProjectViewFactory.java
@@ -1,122 +1,119 @@
-package lcsb.mapviewer.services.view;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import com.google.gson.Gson;
-
-import lcsb.mapviewer.annotation.data.MeSH;
-import lcsb.mapviewer.annotation.services.MeSHParser;
-import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.graph.DataMiningSet;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.model.ModelData;
-
-/**
- * Factory class for {@link ProjectView} class.
- *
- * @author Piotr Gawron
- *
- */
-public class ProjectViewFactory extends AbstractViewFactory<Project, ProjectView> {
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ProjectViewFactory.class);
-
- /**
- * Factory object for {@link LayoutView} elements.
- */
- @Autowired
- private LayoutViewFactory layoutViewFactory;
-
- /**
- * Factory object used for creation of {@link AnnotationView} elements.
- */
- @Autowired
- private AnnotationViewFactory annotationViewFactory;
-
- /**
- * Access object for information about mesh terms.
- */
- @Autowired
- private MeSHParser meSHParser;
-
- @Override
- public ProjectView create(Project project) {
- ProjectView result = new ProjectView(project);
- if (project == null) {
- return result;
- }
- result.setIdObject(project.getId());
- result.setErrors(project.getErrors());
- result.setProjectId(project.getProjectId());
- result.setProjectName(project.getName());
- if (project.getDisease() != null) {
- result.setProjectDiseaseLink(annotationViewFactory.create(project.getDisease()));
- result.setNewDiseaseName(project.getDisease().getResource());
- MeSH mesh;
- try {
- mesh = meSHParser.getMeSH(project.getDisease());
- if (mesh != null) {
- result.setDiseaseName(mesh.getName());
- }
- } catch (AnnotatorException e) {
- logger.error("Problem with getting info about mesh entry: ", e);
- }
- }
-
- if (project.getOrganism() != null) {
- result.setOrganismLink(annotationViewFactory.create(project.getOrganism()));
- result.setNewOrganismName(project.getOrganism().getResource());
- }
- result.setStatus(project.getStatus().toString());
- result.setProgress(Integer.valueOf((int) project.getProgress()));
- result.setInputDataAvailable(project.getInputFileName() != null);
- for (ModelData model : project.getModels()) {
- result.setModelId(model.getId());
- result.setDescription(model.getNotes());
- result.getLayouts().clear();
- result.setVersion(model.getMapVersion());
- result.setNotifyEmail(model.getNotifyEmail());
- for (Layout layout : model.getLayouts()) {
- LayoutView layoutRow = layoutViewFactory.create(layout);
- result.addLayout(layoutRow);
- }
- StringBuilder warningBuilder = new StringBuilder("");
-
- int warnCount = 0;
- String warnPreview = "";
- for (String w : model.getCreationWarnings()) {
- if (!"".equals(w)) {
- warningBuilder.append(w + "\n");
- if (warnCount <= 2) {
- warnPreview += w + "\n";
- }
- warnCount++;
-
- }
- }
- result.setCreationWarnings(warningBuilder.toString());
- result.setCreationWarningsPreview(warnPreview);
- result.setWarnings(model.getCreationWarnings());
- for (DataMiningSet dms : model.getDataMiningSets()) {
- result.addDataMiningSet(new DataMiningSetView(dms));
- }
- }
- return result;
- }
-
- @Override
- public String createGson(ProjectView object) {
- return new Gson().toJson(object);
- }
-
- @Override
- public Project viewToObject(ProjectView view) {
- throw new NotImplementedException();
- }
-}
+package lcsb.mapviewer.services.view;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import com.google.gson.Gson;
+
+import lcsb.mapviewer.annotation.data.MeSH;
+import lcsb.mapviewer.annotation.services.MeSHParser;
+import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.graph.DataMiningSet;
+import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.model.ModelData;
+
+/**
+ * Factory class for {@link ProjectView} class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ProjectViewFactory extends AbstractViewFactory<Project, ProjectView> {
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ProjectViewFactory.class);
+
+ /**
+ * Factory object for {@link LayoutView} elements.
+ */
+ @Autowired
+ private LayoutViewFactory layoutViewFactory;
+
+ /**
+ * Factory object used for creation of {@link AnnotationView} elements.
+ */
+ @Autowired
+ private AnnotationViewFactory annotationViewFactory;
+
+ /**
+ * Access object for information about mesh terms.
+ */
+ @Autowired
+ private MeSHParser meSHParser;
+
+ @Override
+ public ProjectView create(Project project) {
+ ProjectView result = new ProjectView(project);
+ if (project == null) {
+ return result;
+ }
+ result.setIdObject(project.getId());
+ result.setErrors(project.getErrors());
+ result.setProjectId(project.getProjectId());
+ result.setProjectName(project.getName());
+ if (project.getDisease() != null) {
+ result.setProjectDiseaseLink(annotationViewFactory.create(project.getDisease()));
+ result.setNewDiseaseName(project.getDisease().getResource());
+ MeSH mesh;
+ try {
+ mesh = meSHParser.getMeSH(project.getDisease());
+ if (mesh != null) {
+ result.setDiseaseName(mesh.getName());
+ }
+ } catch (AnnotatorException e) {
+ logger.error("Problem with getting info about mesh entry: ", e);
+ }
+ }
+
+ if (project.getOrganism() != null) {
+ result.setOrganismLink(annotationViewFactory.create(project.getOrganism()));
+ result.setNewOrganismName(project.getOrganism().getResource());
+ }
+ result.setStatus(project.getStatus().toString());
+ result.setProgress(Integer.valueOf((int) project.getProgress()));
+ result.setInputDataAvailable(project.getInputFileName() != null);
+
+ int warnCount = 0;
+ String warnPreview = "";
+ for (String w : project.getWarnings()) {
+ if (!"".equals(w)) {
+ if (warnCount <= 2) {
+ warnPreview += w + "\n";
+ }
+ warnCount++;
+ }
+ }
+ result.setWarningsPreview(warnPreview);
+ result.setWarnings(project.getWarnings());
+
+ for (ModelData model : project.getModels()) {
+ result.setModelId(model.getId());
+ result.setDescription(model.getNotes());
+ result.getLayouts().clear();
+ result.setVersion(model.getMapVersion());
+ result.setNotifyEmail(model.getNotifyEmail());
+ for (Layout layout : model.getLayouts()) {
+ LayoutView layoutRow = layoutViewFactory.create(layout);
+ result.addLayout(layoutRow);
+ }
+ for (DataMiningSet dms : model.getDataMiningSets()) {
+ result.addDataMiningSet(new DataMiningSetView(dms));
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public String createGson(ProjectView object) {
+ return new Gson().toJson(object);
+ }
+
+ @Override
+ public Project viewToObject(ProjectView view) {
+ throw new NotImplementedException();
+ }
+}
diff --git a/service/src/test/java/lcsb/mapviewer/services/view/ModelViewFactoryTest.java b/service/src/test/java/lcsb/mapviewer/services/view/ModelViewFactoryTest.java
index 7451dc126b2e6b2981d37fe4035d80e1a2d7a056..32a78c241c5fd296359e71eea7c5afe6211cb508 100644
--- a/service/src/test/java/lcsb/mapviewer/services/view/ModelViewFactoryTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/view/ModelViewFactoryTest.java
@@ -1,77 +1,76 @@
-package lcsb.mapviewer.services.view;
-
-import static org.junit.Assert.assertNotNull;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import lcsb.mapviewer.services.ServiceTestFunctions;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.primefaces.model.map.LatLng;
-import org.springframework.beans.factory.annotation.Autowired;
-
-public class ModelViewFactoryTest extends ServiceTestFunctions{
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(ModelViewFactoryTest .class);
-
- @Autowired
- ModelViewFactory modelViewFactory;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testCreateEmpty() throws Exception {
- try {
- Object object = modelViewFactory.create(null);
- assertNotNull(object);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateJson() throws Exception {
- try {
- ModelView object = modelViewFactory.create(null);
- String json = modelViewFactory.createGson(object);
- assertNotNull(json);
-
- object.setCenterLatLng(new LatLng(1, 2));
- List<String> list = new ArrayList<String>();
- list.add("ASS");
- object.setCreationWarnings(list);
- object.setDescription("ASDAS");
- object.setIdObject(2);
- List<LayoutView> views = new ArrayList<LayoutView>();
- LayoutView view = new LayoutView();
- view.setCreator("AA");
- view.setDirectory("C:\\test\\directory/");
- views.add(view);
- object.setLayouts(views);
- object.setMaxZoom(4);
- object.setMinZoom(3);
- object.setPictureSize(123);
- object.setTileSize(234);
- object.setVersion("#$#$#");
- json = modelViewFactory.createGson(object);
- assertNotNull(json);
-
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.services.view;
+
+import static org.junit.Assert.assertNotNull;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import lcsb.mapviewer.services.ServiceTestFunctions;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.primefaces.model.map.LatLng;
+import org.springframework.beans.factory.annotation.Autowired;
+
+public class ModelViewFactoryTest extends ServiceTestFunctions{
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(ModelViewFactoryTest .class);
+
+ @Autowired
+ ModelViewFactory modelViewFactory;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testCreateEmpty() throws Exception {
+ try {
+ Object object = modelViewFactory.create(null);
+ assertNotNull(object);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateJson() throws Exception {
+ try {
+ ModelView object = modelViewFactory.create(null);
+ String json = modelViewFactory.createGson(object);
+ assertNotNull(json);
+
+ object.setCenterLatLng(new LatLng(1, 2));
+ List<String> list = new ArrayList<>();
+ list.add("ASS");
+ object.setDescription("ASDAS");
+ object.setIdObject(2);
+ List<LayoutView> views = new ArrayList<LayoutView>();
+ LayoutView view = new LayoutView();
+ view.setCreator("AA");
+ view.setDirectory("C:\\test\\directory/");
+ views.add(view);
+ object.setLayouts(views);
+ object.setMaxZoom(4);
+ object.setMinZoom(3);
+ object.setPictureSize(123);
+ object.setTileSize(234);
+ object.setVersion("#$#$#");
+ json = modelViewFactory.createGson(object);
+ assertNotNull(json);
+
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/ProjectBean.java b/web/src/main/java/lcsb/mapviewer/bean/ProjectBean.java
index 1d69c76afc2d5c6d757b4a3e7b58d8bcc123962c..834e15225e1668c50aadee9ca73b8566dc113d94 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/ProjectBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/ProjectBean.java
@@ -26,6 +26,7 @@ import javax.faces.bean.ViewScoped;
import javax.faces.event.ActionEvent;
import org.apache.commons.io.FilenameUtils;
+import org.apache.commons.lang3.StringUtils;
import org.apache.log4j.Logger;
import org.primefaces.event.FileUploadEvent;
import org.primefaces.event.TransferEvent;
@@ -1092,7 +1093,7 @@ public class ProjectBean extends AbstractManagedBean implements Serializable {
*/
public void downloadWarnings() throws IOException {
// and send it as response
- sendFileAsResponse(selectedProject.getCreationWarnings(), "warnings.txt", MimeType.TEXT);
+ sendFileAsResponse(StringUtils.join(selectedProject.getWarnings(), "\n"), "warnings.txt", MimeType.TEXT);
}
/**
diff --git a/web/src/main/webapp/admin/projects.xhtml b/web/src/main/webapp/admin/projects.xhtml
index 7c743cf2c049a33e384c25e36f3fca401016ab43..a036465233728e14a31fb7ed97666ede4951fb0d 100644
--- a/web/src/main/webapp/admin/projects.xhtml
+++ b/web/src/main/webapp/admin/projects.xhtml
@@ -50,8 +50,8 @@
<p:commandLink update=":#{p:component('warningsDlg')}"
id="warningButton" oncomplete="PF('warningsDialog').show()"
- title="#{project.creationWarningsPreview}"
- rendered="#{not empty project.creationWarnings}" >
+ title="#{project.warningsPreview}"
+ rendered="#{not empty project.warnings}" >
<h:graphicImage library="images" name="icons/warning.png" width="24px" class="imgMiddle" />
<f:setPropertyActionListener value="#{project}" target="#{projectMB.selectedProject}" />
</p:commandLink >