diff --git a/console/src/main/java/lcsb/mapviewer/run/BellExport.java b/console/src/main/java/lcsb/mapviewer/run/BellExport.java
deleted file mode 100644
index f3c63406f72f52f727ab78bb90300bd7ef08caae..0000000000000000000000000000000000000000
--- a/console/src/main/java/lcsb/mapviewer/run/BellExport.java
+++ /dev/null
@@ -1,137 +0,0 @@
-package lcsb.mapviewer.run;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-
-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.map.model.Model;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.persist.ApplicationContextLoader;
-import lcsb.mapviewer.persist.DbUtils;
-import lcsb.mapviewer.services.interfaces.IExporterService;
-import lcsb.mapviewer.services.interfaces.IExporterService.ExporterParameters;
-import lcsb.mapviewer.services.utils.data.ExportFileType;
-
-/**
- * This class prepare data for Bell format (further transformation is done by
- * Marek).
- *
- * @author Piotr Gawron
- *
- */
-public class BellExport {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(BellExport.class.getName());
-
- /**
- * Object that performs different types of export transformation.
- */
- @Autowired
- private IExporterService exporter;
-
- /**
- * Object used to annotate the model.
- */
- @Autowired
- private ModelAnnotator modelAnnotator;
-
- /**
- * Object used to annotate the model.
- */
- @Autowired
- private DbUtils dbUtils;
-
- /**
- * Static main method used to run this stand alone code.
- *
- * @param args
- * command line arguments
- */
- public static void main(String[] args) {
- ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
- BellExport main = new BellExport();
- ApplicationContextLoader.injectDependencies(main);
- main.run();
- }
-
- /**
- * Default constructor.
- */
- public BellExport() {
-
- }
-
- /**
- * Method that export pd map into file that can be exported to bell (by
- * Marek).
- *
- */
- private void run() {
- CellDesignerXmlParser p = new CellDesignerXmlParser();
- try {
- String filename = PdMapAnnotations.getLastPdFilename();
- String version = PdMapAnnotations.getLastPdVersion();
-
- // filename = "testFiles/other_full/ASTHMAP18000X8000V1_38.xml";
- // version = "1.1.38";
- dbUtils.createSessionForCurrentThread();
- Model model = p.createModel(new ConverterParams().filename(filename));
-
- modelAnnotator.performAnnotations(model, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- });
-
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).//
- fileName("out/bell/" + version + "-reactions.txt").//
- fileType(ExportFileType.TAB_SEPARATED).//
- type(Species.class).//
- moleculeEdges(false);
-
- exporter.exportReactions(params);
-
- params = new IExporterService.ExporterParameters().model(model).//
- fileName("out/bell/" + version + "-species.txt").//
- fileType(ExportFileType.TAB_SEPARATED).//
- type(Species.class).//
- // column(ExportColumn.FULL).//
- moleculeEdges(false);
- exporter.exportSpecies(params);
-
- params = new IExporterService.ExporterParameters().model(model).//
- fileName("out/bell/" + version + "-compartments.txt").//
- fileType(ExportFileType.TAB_SEPARATED).//
- type(Object.class); //
- // column(ExportColumn.FULL);
- exporter.exportCompartments(params);
-
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- } finally {
- dbUtils.closeSessionForCurrentThread();
- }
- }
-
- /**
- * @return the modelAnnotator
- * @see #modelAnnotator
- */
- public ModelAnnotator getModelAnnotator() {
- return modelAnnotator;
- }
-
- /**
- * @param modelAnnotator
- * the modelAnnotator to set
- * @see #modelAnnotator
- */
- public void setModelAnnotator(ModelAnnotator modelAnnotator) {
- this.modelAnnotator = modelAnnotator;
- }
-}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ExporterService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ExporterService.java
deleted file mode 100644
index a2a369d7114ec1686ddf67be0b749ebaced353d9..0000000000000000000000000000000000000000
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ExporterService.java
+++ /dev/null
@@ -1,1088 +0,0 @@
-package lcsb.mapviewer.services.impl;
-
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.model.celldesigner.reaction.ReactionLineData;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
-import lcsb.mapviewer.model.map.model.Model;
-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.model.map.reaction.ReactionNode;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Degraded;
-import lcsb.mapviewer.model.map.species.Drug;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.Ion;
-import lcsb.mapviewer.model.map.species.Phenotype;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.Unknown;
-import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.model.map.species.field.RnaRegion;
-import lcsb.mapviewer.services.interfaces.IExporterService;
-import lcsb.mapviewer.services.utils.data.ExportColumn;
-import lcsb.mapviewer.services.utils.data.ExportFileType;
-import lcsb.mapviewer.services.view.PubmedAnnotatedElementsView;
-import lcsb.mapviewer.services.view.PubmedAnnotatedElementsViewFactory;
-
-/**
- * Implementation of {@link IExporterService} interface that allows to export
- * {@link Model}.
- *
- * @author Piotr Gawron
- *
- */
-public class ExporterService implements IExporterService {
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ExporterService.class);
-
- /**
- * List of publications by {@link Model#getId() model id}. This is used for
- * caching, as obtaining this list on runtime is quite expensive.
- */
- private static Map<Integer, List<PubmedAnnotatedElementsView>> pubmedPublicationsForModel = new HashMap<>();
-
- /**
- * Factory used to create {@link PubmedAnnotatedElementsView publication
- * summary} elements.
- */
- @Autowired
- private PubmedAnnotatedElementsViewFactory pubmedAnnotatedElementsViewFactory;
-
- @Override
- public void exportSpecies(ExporterParameters parameters) throws IOException {
- String content = getExportSpeciesString(parameters);
- writeToFile(content, parameters.getFileName());
- }
-
- @Override
- public String getExportSpeciesString(ExporterParameters parameters) {
- Set<String> uniqeLines = new HashSet<String>();
- StringBuilder builder = new StringBuilder();
- for (ExportColumn column : parameters.getColumns()) {
- builder.append(column.getTitle() + "\t");
- }
- builder.append("\n");
- for (Model model : parameters.getModels()) {
- for (Element alias : model.getElements()) {
- if (alias instanceof Species) {
- Species speciesAlias = (Species) alias;
- boolean toBeProcessed = false;
- // check type
- for (Class<?> type : parameters.getTypes()) {
- if (type.isAssignableFrom(speciesAlias.getClass())) {
- toBeProcessed = true;
- break;
- }
- }
- if (!toBeProcessed && parameters.getTypes().size() > 0) {
- continue;
- }
-
- // check where it lays
- toBeProcessed = (parameters.getIncludedAliases().size() == 0);
- for (Compartment ca : parameters.getIncludedAliases()) {
- if (ca.cross(alias)) {
- toBeProcessed = true;
- }
- }
- for (Compartment ca : parameters.getExcludedAliases()) {
- if (ca.cross(alias)) {
- toBeProcessed = false;
- }
- }
- if (toBeProcessed) {
- List<String> elements = getExportStringForOneSpecies(speciesAlias, parameters);
- for (String string : elements) {
- uniqeLines.add(string);
- }
- }
- }
- }
- }
- List<String> sortedElements = new ArrayList<String>();
- sortedElements.addAll(uniqeLines);
- Collections.sort(sortedElements);
- for (String string : sortedElements) {
- builder.append(string);
- builder.append("\n");
- }
- return builder.toString();
- }
-
- /**
- * Returns strings with species alias exported using given parameters. Many
- * lines can be exported because one species alias can belong to many
- * pathways.
- *
- * @param parameters
- * {@link ExporterParameters export parameters}
- * @param species
- * export string are generated for this alias
- * @return list of strings representing exported data
- */
- protected List<String> getExportStringForOneSpecies(Species species, ExporterParameters parameters) {
- if (parameters.getFileType() != ExportFileType.TAB_SEPARATED) {
- throw new InvalidArgumentException("Unhandled file type: " + parameters.getFileType());
- }
-
- List<Compartment> aliases = getComponentList(species);
- List<String> result = new ArrayList<String>();
-
- Compartment smallestCompartment = getCompartment(species);
-
- List<ExportColumn> processedColumns = new ArrayList<ExportColumn>();
- for (ExportColumn column : parameters.getColumns()) {
- if (column.getClazz().isAssignableFrom(Species.class)) {
- processedColumns.add(column);
- }
- }
-
- for (Compartment compartment : aliases) {
- String separator = "";
- StringBuilder line = new StringBuilder();
- for (ExportColumn column : processedColumns) {
- line.append(separator);
- separator = "\t";
- if (column == ExportColumn.COMPARTMENT_NAME) {
- if (smallestCompartment == null) {
- line.append("null");
- } else {
- line.append(smallestCompartment.getName());
- }
- } else if (column == ExportColumn.POSITION_TO_COMPARTMENT) {
- line.append(species.getPositionToCompartment());
- } else if (column == ExportColumn.COMPONENT_NAME) {
- line.append(compartment.getName());
- } else if (column == ExportColumn.NAME) {
- if (species instanceof Complex) {
- if (!parameters.isComplexElementsName()) {
- line.append(species.getName());
- } else {
- line.append(getComplexNameWithElements((Complex) species, parameters));
- }
- } else {
- line.append(species.getName());
- }
- } else if (column == ExportColumn.ID) {
- line.append(getId(species));
- } else if (column == ExportColumn.TYPE) {
- line.append(species.getClass().getSimpleName());
- } else if (column == ExportColumn.SUBMODEL) {
- line.append(species.getModelData().getName());
- } else if (column == ExportColumn.COMPLEX) {
- String complex = null;
- if (species.getComplex() != null) {
- complex = species.getComplex().getName();
-
- complex += " [id=" + getId(species.getComplex()) + "]";
- }
- line.append(complex);
- } else {
- throw new InvalidArgumentException("Unhandled column type: " + column);
- }
- }
- for (MiriamType mt : parameters.getMiriamTypes()) {
- line.append(separator);
- String types = "";
- for (MiriamData md : species.getMiriamData()) {
- if (md.getDataType().equals(mt)) {
- if (!types.isEmpty()) {
- types += ",";
- }
- types += md.getResource();
- }
- }
- if (types.equals("")) {
- line.append(mt.toString() + ": N/A");
- } else {
- line.append(mt.toString() + ": " + types);
- }
- }
- result.add(line.toString().replaceAll("[\n\r]+", " "));
- }
- return result;
- }
-
- /**
- * Returns {@link Compartment} to which element belongs to.
- *
- * @param element
- * alias of the element
- * @return {@link Compartment} to which element belongs to
- */
- private Compartment getCompartment(Species element) {
- Compartment smallestAlias = null;
- List<Compartment> compartmentAliases = new ArrayList<Compartment>();
-
- for (Compartment alias : element.getModel().getCompartments()) {
- if (alias.cross(element)) {
- if (!(alias instanceof PathwayCompartment)) {
- compartmentAliases.add(alias);
- }
- }
- }
-
- if (compartmentAliases.size() > 0) {
- smallestAlias = compartmentAliases.get(0);
- }
- for (Compartment compartmentAlias : compartmentAliases) {
- if (compartmentAlias.getSize() < smallestAlias.getSize()) {
- smallestAlias = compartmentAlias;
- }
- }
- return smallestAlias;
- }
-
- /**
- * Returns a list of pathways to which element belongs to.
- *
- * @param element
- * alias of the element
- * @return list of {@link Compartment} representing pathways
- */
- private List<Compartment> getComponentList(Species element) {
- Model model = element.getModel();
-
- List<Compartment> aliases = new ArrayList<Compartment>();
- for (Compartment alias : model.getCompartments()) {
- if (alias instanceof PathwayCompartment) {
- if (alias.cross(element)) {
- aliases.add(alias);
- }
- }
- }
-
- // in case the element is outside any component then we have to crate
- // artifical null component
- if (aliases.size() == 0) {
- PathwayCompartment nullAlias = new PathwayCompartment("default");
- nullAlias.setName("null");
- aliases.add(nullAlias);
- }
-
- return aliases;
- }
-
- /**
- * Returns name of a complex with the names of all species included in this
- * complex.
- *
- * @param complex
- * complex for which name is computed
- * @param parameters
- * parameter limits the species that will be included in generated
- * name
- * @return name of a complex with the names of all species included in this
- * complex
- */
- private String getComplexNameWithElements(Complex complex, ExporterParameters parameters) {
- StringBuilder result = new StringBuilder();
- String separator = "";
- for (Element species2 : complex.getAllSimpleChildren()) {
- boolean add = false;
- if (parameters.getTypes().size() == 0) {
- add = true;
- }
- for (Class<?> class1 : parameters.getTypes()) {
- if (class1.isAssignableFrom(species2.getClass())) {
- add = true;
- }
- }
- if (add) {
- result.append(separator);
- result.append(species2.getName());
- separator = ":";
- }
-
- }
- if (result.length() == 0) {
- return complex.getName();
- } else {
- return result.toString();
- }
- }
-
- /**
- * Writes content into a file.
- *
- * @param content
- * content that should be written into the file.
- * @param fileName
- * file name
- * @throws IOException
- * thrown when there is a problem with accessing file
- */
- protected void writeToFile(String content, String fileName) throws IOException {
- logger.debug("Save file: " + fileName);
- File file = new File(fileName);
-
- // if file doesnt exists, then create it
- if (!file.exists()) {
- // first create directory structure
- file.getParentFile().mkdirs();
- file.createNewFile();
- }
-
- FileWriter fw = new FileWriter(file.getAbsoluteFile());
- BufferedWriter bw = new BufferedWriter(fw);
- bw.write(content);
- bw.close();
- }
-
- @Override
- public String getExportInteractionString(ExporterParameters parameters) {
- Set<String> uniqueLines = new HashSet<String>();
- if (parameters.getFileType() != ExportFileType.SIF && parameters.getFileType() != ExportFileType.TAB_SEPARATED) {
- throw new InvalidArgumentException("Unsupported file format: " + parameters.getFileType());
- }
-
- for (Model model : parameters.getModels()) {
- for (Reaction reaction : model.getReactions()) {
- int counter = 0;
- for (ReactionNode node : reaction.getReactionNodes()) {
- Element element = node.getElement();
- for (Class<?> type : parameters.getTypes()) {
- if (type.isAssignableFrom(element.getClass())) {
- counter++;
- break;
- }
- }
- }
- if (counter > 1) {
- uniqueLines.addAll(getExportSingleInteractionString(reaction, parameters));
- }
- }
- }
- if (parameters.isMoleculeEdges()) {
- for (Model model : parameters.getModels()) {
- for (Element element : model.getElements()) {
- if (element instanceof Species) {
- if (element instanceof SimpleMolecule) {
- boolean ok = false;
- for (Compartment alias : parameters.getIncludedAliases()) {
- if (alias.cross(element)) {
- ok = true;
- }
- }
- for (Compartment alias : parameters.getExcludedAliases()) {
- if (alias.cross(element)) {
- ok = false;
- }
- }
- if (ok) {
- String string = getExportSingleInteractionStringFromSpecies((SimpleMolecule) element, parameters);
- if (parameters.getFileType() == ExportFileType.SIF) {
- if (!uniqueLines.contains(string.replace("molecule_type", "reaction_type"))) {
- uniqueLines.add(string);
- }
- } else {
- uniqueLines.add(string);
- }
- }
- }
- }
- }
- }
- }
- List<String> sortedLines = new ArrayList<String>();
- sortedLines.addAll(uniqueLines);
- Collections.sort(sortedLines);
- StringBuilder result = new StringBuilder();
- for (String string : sortedLines) {
- if (!string.equals("")) {
- result.append(string);
- result.append("\n");
- }
- }
-
- return result.toString();
- }
-
- /**
- * Creates interaction from molecule (molecule is used as extension of
- * reaction between different types of elements).
- *
- * @param species
- * molecule which is treaded as a reaction element
- * @param parameters
- * {@link ExporterParameters export parameters}
- * @return string representing exported reaction
- */
- protected String getExportSingleInteractionStringFromSpecies(SimpleMolecule species, ExporterParameters parameters) {
- if (parameters.getFileType() != ExportFileType.SIF) {
- throw new InvalidArgumentException("Unsupported file format: " + parameters.getFileType());
- }
- StringBuilder result = new StringBuilder();
- Set<String> elements = new HashSet<String>();
- for (Model model : parameters.getModels()) {
- for (Reaction reaction : model.getReactions()) {
- boolean goodReaction = false;
- for (ReactionNode node : reaction.getReactionNodes()) {
- if (node.getElement() instanceof SimpleMolecule) {
- Element species2 = node.getElement();
- if (species.getName().equalsIgnoreCase(species2.getName())) {
- goodReaction = true;
- }
- }
- }
- if (!goodReaction) {
- continue;
- }
- for (ReactionNode node : reaction.getReactionNodes()) {
- boolean ok = false;
- if (parameters.getIncludedAliases().size() == 0) {
- ok = true;
- }
- for (Compartment alias2 : parameters.getIncludedAliases()) {
- if (alias2.cross(node.getElement())) {
- ok = true;
- break;
- }
- }
- for (Compartment alias2 : parameters.getExcludedAliases()) {
- if (alias2.cross(node.getElement())) {
- ok = false;
- break;
- }
- }
- if (ok) {
- Element element = node.getElement();
- for (Class<?> type : parameters.getTypes()) {
- if (type.isAssignableFrom(element.getClass())) {
- if (element instanceof Complex) {
- if (!parameters.isComplexElementsName()) {
- elements.add(((Species) element).getName());
- } else {
- String name = getComplexNameWithElements((Complex) element, parameters);
- elements.add(name);
- }
- } else {
- elements.add(((Species) element).getName());
- }
- break;
- }
- }
- }
- }
- }
- }
- if (elements.size() <= 1) {
- return "";
- }
- List<String> list = new ArrayList<String>();
- list.addAll(elements);
- result.append(list.get(0));
- result.append("\tmolecule_type");
- for (int i = 1; i < list.size(); i++) {
- result.append("\t");
- result.append(list.get(i));
- }
- return result.toString();
-
- }
-
- /**
- * Returns strings with reactions exported using given parameters. Many lines
- * can be exported because one species alias can belong to many pathways.
- *
- * @param parameters
- * {@link ExporterParameters export parameters}
- * @param reaction
- * export string are generated for this reaction
- * @return list of strings representing exported data
- */
- protected List<String> getExportSingleInteractionString(Reaction reaction, ExporterParameters parameters) {
- List<String> result = new ArrayList<String>();
- if (parameters.getFileType() == ExportFileType.SIF) {
- StringBuilder builder = new StringBuilder();
- Set<Element> elements = new HashSet<>();
- for (ReactionNode node : reaction.getReactionNodes()) {
- boolean ok = false;
- if (parameters.getIncludedAliases().size() == 0) {
- ok = true;
- }
- for (Compartment alias2 : parameters.getIncludedAliases()) {
- if (alias2.cross(node.getElement())) {
- ok = true;
- break;
- }
- }
- for (Compartment alias2 : parameters.getExcludedAliases()) {
- if (alias2.cross(node.getElement())) {
- ok = false;
- break;
- }
- }
- if (ok) {
- Element element = node.getElement();
- if (parameters.getTypes().size() == 0) {
- elements.add(element);
- } else {
- for (Class<?> type : parameters.getTypes()) {
- if (type.isAssignableFrom(element.getClass())) {
- elements.add(element);
- break;
- }
- }
- }
- }
- }
- Set<String> elementsNames = new HashSet<>();
- for (Element element : elements) {
- if (element instanceof Complex) {
- if (!parameters.isComplexElementsName()) {
- elementsNames.add(((Species) element).getName());
- } else {
- String name = getComplexNameWithElements((Complex) element, parameters);
- elementsNames.add(name);
- }
-
- } else {
- elementsNames.add(((Species) element).getName());
- }
- }
-
- if (elementsNames.size() <= 1) {
- return result;
- }
- List<String> list = new ArrayList<String>();
- list.addAll(elementsNames);
- builder.append(list.get(0));
- builder.append("\treaction_type");
- for (int i = 1; i < list.size(); i++) {
- builder.append("\t");
- builder.append(list.get(i));
- }
- result.add(builder.toString());
- } else if (parameters.getFileType() == ExportFileType.TAB_SEPARATED) {
- if (parameters.getColumns() == null || parameters.getColumns().size() == 0) {
- result.add(getOldFormatString(reaction, parameters));
- } else {
- result.addAll(getNewFormatString(reaction, parameters));
- }
- } else {
- throw new InvalidArgumentException("Unsupported file format: " + parameters.getFileType());
- }
- return result;
- }
-
- /**
- * Creates tab separated string for reaction in old format...
- *
- * @param reaction
- * reaction to transform
- * @param parameters
- * {@link ExporterParameters export parameters}
- * @return export string representation of the reaction
- */
- private String getOldFormatString(Reaction reaction, ExporterParameters parameters) {
- StringBuilder result = new StringBuilder();
- result.append(reaction.getIdReaction());
- result.append("\t");
- result.append(ReactionLineData.getByReactionType(reaction.getClass()));
- result.append("\t");
- result.append("reversible=" + reaction.isReversible());
- result.append("\t");
- if (reaction.getMiriamData().size() > 0) {
- result.append("REACTION_MIRIAM_DATA");
- result.append("\t");
- for (MiriamData md : reaction.getMiriamData()) {
- result.append("data_type=" + md.getDataType().getUris().get(0));
- result.append("\t");
- result.append("relation_type=" + md.getRelationType().getStringRepresentation());
- result.append("\t");
- result.append("resource=" + md.getResource());
- result.append("\t");
- }
- }
- for (Reactant reactant : reaction.getReactants()) {
- result.append("REACTANT");
- result.append("\t");
- result.append(getExportSingleSpecies((Species) reactant.getElement(), parameters));
- result.append("\t");
- }
- for (Product product : reaction.getProducts()) {
- result.append("PRODUCT");
- result.append("\t");
- result.append(getExportSingleSpecies((Species) product.getElement(), parameters));
- result.append("\t");
- }
- for (Modifier modifier : reaction.getModifiers()) {
- result.append("MODIFIER");
- result.append("\t");
- result.append("type=" + modifier.getClass().getSimpleName());
- result.append("\t");
- result.append(getExportSingleSpecies((Species) modifier.getElement(), parameters));
- result.append("\t");
- }
- return result.toString();
- }
-
- /**
- * Creates tab separated string for reaction in new format...
- *
- * @param reaction
- * reaction to transform
- * @param parameters
- * {@link ExporterParameters export parameters}
- * @return export string representation of the reaction
- */
- private List<String> getNewFormatString(Reaction reaction, ExporterParameters parameters) {
- List<String> result = new ArrayList<String>();
- StringBuilder builder = new StringBuilder();
- boolean splitReaction = false;
- for (ExportColumn column : parameters.getColumns()) {
- if (column.getClazz().isAssignableFrom(Reaction.class)) {
- if (column.equals(ExportColumn.REACTION_ID)) {
- builder.append(reaction.getIdReaction());
- } else if (column.equals(ExportColumn.REACTION_REVERSIBLE)) {
- builder.append(reaction.isReversible());
- } else if (column.equals(ExportColumn.REACTION_TYPE)) {
- builder.append(ReactionLineData.getByReactionType(reaction.getClass()));
- } else if (column.equals(ExportColumn.REACTION_TWO_ELEMENT)) {
- splitReaction = true;
- continue;
- } else {
- throw new InvalidArgumentException("Unknown column type: " + column);
- }
- }
- builder.append("\t");
- }
- for (MiriamType mt : parameters.getMiriamTypes()) {
- String types = "";
- for (MiriamData md : reaction.getMiriamData()) {
- if (md.getDataType().equals(mt)) {
- if (!types.isEmpty()) {
- types += ",";
- }
- types += md.getResource();
- }
- }
- if (types.equals("")) {
- builder.append(mt.toString() + ": N/A");
- } else {
- builder.append(mt.toString() + ": " + types);
- }
- builder.append("\t");
- }
-
- int counter = 0;
-
- if (splitReaction) {
- String base = builder.toString();
- Set<Element> inputs = new HashSet<Element>();
- Set<Element> outputs = new HashSet<Element>();
- for (Reactant reactant : reaction.getReactants()) {
- if (!isAssignable(parameters, reactant.getElement())) {
- continue;
- }
- if (reactant.getElement() instanceof Complex) {
- inputs.addAll(((Complex) (reactant.getElement())).getAllChildren());
- } else {
- inputs.add(reactant.getElement());
- }
- }
- for (Product product : reaction.getProducts()) {
- if (!isAssignable(parameters, product.getElement())) {
- continue;
- }
- if (product.getElement() instanceof Complex) {
- outputs.addAll(((Complex) (product.getElement())).getAllChildren());
- } else {
- outputs.add(product.getElement());
- }
- }
- for (Modifier modifier : reaction.getModifiers()) {
- if (!isAssignable(parameters, modifier.getElement())) {
- continue;
- }
- if (modifier.getElement() instanceof Complex) {
- inputs.addAll(((Complex) (modifier.getElement())).getAllChildren());
- } else {
- inputs.add(modifier.getElement());
- }
- }
- for (Element input : inputs) {
- if (!isAssignable(parameters, input)) {
- continue;
- }
- for (Element output : outputs) {
- if (!isAssignable(parameters, output)) {
- continue;
- }
- String line = base + "\t" + getId(input) + "\t" + getId(output);
- result.add(line);
- }
- }
- } else {
-
- for (Reactant reactant : reaction.getReactants()) {
- if (!isAssignable(parameters, reactant.getElement())) {
- continue;
- }
- counter++;
-
- builder.append("REACTANT");
- builder.append("\t");
- builder.append(getId(reactant.getElement()));
- builder.append("\t");
- }
- for (Product product : reaction.getProducts()) {
- if (!isAssignable(parameters, product.getElement())) {
- continue;
- }
- counter++;
-
- builder.append("PRODUCT");
- builder.append("\t");
- builder.append(getId(product.getElement()));
- builder.append("\t");
- }
- for (Modifier modifier : reaction.getModifiers()) {
- if (!isAssignable(parameters, modifier.getElement())) {
- continue;
- }
- counter++;
-
- builder.append("MODIFIER");
- builder.append("\t");
- builder.append(getId(modifier.getElement()));
- builder.append("\t");
- }
- if (counter > 1) {
- result.add(builder.toString());
- }
- }
- return result;
- }
-
- /**
- * Checks if element is acceptable by {@link ExporterParameters export
- * parameters}.
- *
- * @param parameters
- * {@link ExporterParameters export parameters}
- * @param element
- * element to check
- * @return true if element can exist in export string, <code>false</code>
- * otherwise
- */
- private boolean isAssignable(ExporterParameters parameters, Element element) {
- boolean ok = false;
- for (Class<?> clazz : parameters.getTypes()) {
- if (clazz.isAssignableFrom(element.getClass())) {
- ok = true;
- }
- }
- return ok;
- }
-
- /**
- * Creates tab separated string for species for full mode.
- *
- * @param alias
- * alias of the element to transform
- * @param parameters
- * {@link ExporterParameters export parameters}
- * @return export string representation of the element
- */
- private String getExportSingleSpecies(Species alias, ExporterParameters parameters) {
- if (parameters.getFileType() != ExportFileType.TAB_SEPARATED) {
- throw new InvalidArgumentException("Unsupported file format: " + parameters.getFileType());
- }
- StringBuilder sb = new StringBuilder();
- sb.append(alias.getClass().getSimpleName() + "\t");
- sb.append("id=" + getId(alias) + "\t");
- sb.append("name=" + alias.getName() + "\t");
- sb.append("fullName=" + alias.getFullName() + "\t");
- sb.append("charge=" + alias.getCharge() + "\t");
- sb.append("initialAmount=" + alias.getInitialAmount() + "\t");
- sb.append("initialConcentration=" + alias.getInitialConcentration() + "\t");
- String compartment = null;
- if (alias.getCompartment() != null) {
- compartment = alias.getCompartment().getName();
- }
- sb.append("compartment=" + compartment);
- sb.append("\t");
- String complexId = null;
- if (alias.getComplex() != null) {
- complexId = getId(alias.getComplex());
- }
- sb.append("complex=" + complexId);
- sb.append("\t");
- sb.append("hasOnlySubstanceUnits=" + alias.hasOnlySubstanceUnits());
- sb.append("\t");
- sb.append("positionToCompartment=" + alias.getPositionToCompartment());
- sb.append("\t");
-
- if (alias instanceof Protein) {
- Protein protein = (Protein) alias;
- sb.append("dimer=" + protein.getHomodimer());
- sb.append("\t");
- sb.append("structuralState=" + protein.getStructuralState());
- sb.append("\t");
- sb.append("hypothetical=" + protein.isHypothetical());
- sb.append("\t");
- for (ModificationResidue mr : protein.getModificationResidues()) {
- sb.append("MODIFICATION RESIDUE");
- sb.append("\t");
- sb.append("angle=" + mr.getAngle());
- sb.append("\t");
- sb.append("name=" + mr.getName());
- if (mr.getState() != null) {
- sb.append("\t");
- sb.append("shortName=" + mr.getState().getAbbreviation());
- }
- sb.append("\t");
- sb.append("side=" + mr.getSide());
- sb.append("\t");
- sb.append("size=" + mr.getSize());
- sb.append("\t");
- if (mr.getState() != null) {
- sb.append("state=" + mr.getState().getFullName() + "\t");
- }
- }
- } else if (alias instanceof Gene) {
- Gene gene = (Gene) alias;
- for (ModificationResidue mr : gene.getModificationResidues()) {
- sb.append("MODIFICATION RESIDUE");
- sb.append("\t");
- sb.append("angle=" + mr.getAngle());
- sb.append("\t");
- sb.append("name=" + mr.getName());
- sb.append("\t");
- if (mr.getState() != null) {
- sb.append("shortName=" + mr.getState().getAbbreviation() + "\t");
- }
- sb.append("side=" + mr.getSide());
- sb.append("\t");
- sb.append("size=" + mr.getSize());
- sb.append("\t");
- if (mr.getState() != null) {
- sb.append("state=" + mr.getState().getFullName() + "\t");
- }
- }
- } else if (alias instanceof Complex) {
- Complex complex = (Complex) alias;
- sb.append("dimer=" + complex.getHomodimer());
- sb.append("\t");
- sb.append("hypothetical=" + complex.isHypothetical());
- sb.append("\t");
- } else if (alias instanceof SimpleMolecule) {
- SimpleMolecule molecule = (SimpleMolecule) alias;
- sb.append("dimer=" + molecule.getHomodimer());
- sb.append("\t");
- } else if (alias instanceof Ion) {
- sb.append("");
- } else if (alias instanceof Phenotype) {
- sb.append("");
- } else if (alias instanceof Drug) {
- sb.append("");
-
- } else if (alias instanceof Rna) {
- Rna rna = (Rna) alias;
- for (RnaRegion region : rna.getRegions()) {
- sb.append("RNA_REGION");
- sb.append("\t");
- sb.append("type=" + region.getType());
- sb.append("\t");
- if (region.getState() != null) {
- sb.append("state=" + region.getState().getFullName() + "\t");
- }
- sb.append("\t");
- sb.append("size=" + region.getSize());
- sb.append("\t");
- sb.append("pos=" + region.getPos());
- sb.append("\t");
- }
- } else if (alias instanceof AntisenseRna) {
- AntisenseRna antisenseRna = (AntisenseRna) alias;
- for (AntisenseRnaRegion region : antisenseRna.getRegions()) {
- sb.append("RNA_REGION" + "\t");
- if (region.getType() != null) {
- sb.append("type=" + region.getType().getName() + "\t");
- }
- sb.append("name=" + region.getName() + "\t");
- sb.append("size=" + region.getSize() + "\t");
- sb.append("pos=" + region.getPos() + "\t");
- }
- } else if (alias instanceof Unknown) {
- sb.append("");
- } else if (alias instanceof Degraded) {
- sb.append("");
- } else {
- throw new InvalidArgumentException("Invalid class type: " + alias.getClass());
- }
- if (alias.getMiriamData().size() > 0) {
- sb.append("MIRIAM_DATA");
- sb.append("\t");
- for (MiriamData md : alias.getMiriamData()) {
- sb.append("data_type=" + md.getDataType().getUris().get(0));
- sb.append("\t");
- sb.append("relation_type=" + md.getRelationType().getStringRepresentation());
- sb.append("\t");
- sb.append("resource=" + md.getResource());
- sb.append("\t");
- }
- }
- return sb.toString();
- }
-
- @Override
- public void exportReactions(ExporterParameters parameters) throws IOException {
- String content = getExportInteractionString(parameters);
- writeToFile(content, parameters.getFileName());
- }
-
- @Override
- public void exportCompartments(ExporterParameters parameters) throws IOException {
- String content = getExportCompartmentsString(parameters);
- writeToFile(content, parameters.getFileName());
- }
-
- @Override
- public String getExportCompartmentsString(ExporterParameters parameters) {
- Set<String> uniqeLines = new HashSet<>();
- StringBuilder builder = new StringBuilder();
- for (Model model : parameters.getModels()) {
- for (Compartment alias : model.getCompartments()) {
-
- // check where it lays
- boolean toBeProcessed = (parameters.getIncludedAliases().size() == 0);
- for (Compartment ca : parameters.getIncludedAliases()) {
- if (ca.cross(alias)) {
- toBeProcessed = true;
- }
- }
- for (Compartment ca : parameters.getExcludedAliases()) {
- if (ca.cross(alias)) {
- toBeProcessed = false;
- }
- }
- if (toBeProcessed) {
- List<String> elements = getExportStringForOneCompartment(alias, parameters);
- for (String string : elements) {
- uniqeLines.add(string);
- }
- }
- }
- }
- List<String> sortedElements = new ArrayList<>();
- sortedElements.addAll(uniqeLines);
- Collections.sort(sortedElements);
- for (String string : sortedElements) {
- builder.append(string);
- builder.append("\n");
- }
- return builder.toString();
- }
-
- /**
- * Exports compartments into set of text lines defining a compartment.
- *
- * @param compartment
- * alias of the compartment to export
- * @param parameters
- * parameters used in export
- * @return string srepresenting compartment in export format
- */
- private List<String> getExportStringForOneCompartment(Compartment compartment, ExporterParameters parameters) {
- List<String> result = new ArrayList<String>();
- if (parameters.getFileType() != ExportFileType.TAB_SEPARATED) {
- throw new InvalidArgumentException("Unhandled file type: " + parameters.getFileType());
- }
- StringBuilder sb = new StringBuilder();
- sb.append(getId(compartment) + "\t");
- sb.append("name=" + compartment.getName() + "\t");
- sb.append("fullname=" + compartment.getFullName() + "\t");
- if (compartment.getMiriamData().size() > 0) {
- sb.append("MIRIAM_DATA");
- sb.append("\t");
- for (MiriamData md : compartment.getMiriamData()) {
- sb.append("data_type=" + md.getDataType().getUris().get(0));
- sb.append("\t");
- sb.append("relation_type=" + md.getRelationType().getStringRepresentation());
- sb.append("\t");
- sb.append("resource=" + md.getResource());
- sb.append("\t");
- }
- }
- result.add(sb.toString());
- return result;
- }
-
- /**
- * Returns identifier that should be used for a given alias.
- *
- * @param alias
- * alis for which identifier will be returned
- * @return identifier that should be used for a given alias
- */
- private String getId(Element alias) {
- return alias.getElementId();
- }
-
- @Override
- public List<PubmedAnnotatedElementsView> getPublicationModelSummary(Model model) {
- List<PubmedAnnotatedElementsView> result = pubmedPublicationsForModel.get(model.getId());
- if (result != null) {
- return result;
- } else {
- result = new ArrayList<>();
- pubmedPublicationsForModel.put(model.getId(), result);
- }
- List<Model> models = new ArrayList<>();
- models.add(model);
- models.addAll(model.getSubmodels());
- Set<MiriamData> miriamDatas = new HashSet<>();
- for (Model m : models) {
- for (Element element : m.getElements()) {
- for (MiriamData md : element.getMiriamData()) {
- if (MiriamType.PUBMED.equals(md.getDataType())) {
- miriamDatas.add(md);
- }
- }
- }
- for (Reaction reaction : m.getReactions()) {
- for (MiriamData md : reaction.getMiriamData()) {
- if (MiriamType.PUBMED.equals(md.getDataType())) {
- miriamDatas.add(md);
- }
- }
- }
- }
- for (MiriamData miriamData : miriamDatas) {
- result.add(pubmedAnnotatedElementsViewFactory.create(miriamData, model));
- }
- return result;
- }
-
-}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IExporterService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IExporterService.java
deleted file mode 100644
index 1895e4acd5a37704bd29d8fb4bedbda470430366..0000000000000000000000000000000000000000
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IExporterService.java
+++ /dev/null
@@ -1,557 +0,0 @@
-package lcsb.mapviewer.services.interfaces;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.services.utils.data.ExportColumn;
-import lcsb.mapviewer.services.utils.data.ExportFileType;
-import lcsb.mapviewer.services.view.PubmedAnnotatedElementsView;
-
-/**
- * Interface used for simple export of the {@link Model}.
- *
- * @author Piotr Gawron
- *
- */
-public interface IExporterService {
- /**
- * Class that contains parameters used for exporting data.
- *
- * @author Piotr Gawron
- *
- */
- class ExporterParameters {
- /**
- * File where the export data should be saved.
- */
- private String fileName = null;
- /**
- * List of models from which data is exported.
- */
- private List<Model> models = new ArrayList<Model>();
- /**
- * List of compartment names that should be included in export (empty list
- * means that everything should be included).
- */
- private List<String> included = new ArrayList<String>();
- /**
- * List of compartment names that should be excluded in export (empty list
- * means that anything should be excluded).
- */
- private List<String> excluded = new ArrayList<String>();
- /**
- * Type of file to which export should be performed.
- */
- private ExportFileType fileType = null;
- /**
- * Elements that should be exported.
- */
- private List<Class<?>> types = new ArrayList<Class<?>>();
- /**
- * Columns that should be included in the export data.
- */
- private List<ExportColumn> columns = new ArrayList<ExportColumn>();
- /**
- * Miriam annotations that should be included in the export data.
- */
- private List<MiriamType> miriamTypes = new ArrayList<MiriamType>();
- /**
- * List of compartment aliases that should be included in export (empty list
- * means that everything should be included).
- */
- private Set<Compartment> includedAliases = new HashSet<Compartment>();
- /**
- * List of compartment aliases that should be excluded in export (empty list
- * means that anything should be excluded).
- */
- private Set<Compartment> excludedAliases = new HashSet<Compartment>();
- /**
- * If false default complex name will be used for exporting complexes. If
- * true then the name will be a concatenated string of all complex
- * subspecies.
- */
- private boolean complexElementsName = false;
-
- /**
- * Should the molecules be considered as edges. Might be usefull for <a
- * href=
- * "http://en.wikipedia.org/wiki/Protein%E2%80%93protein_interaction">PPI
- * </a>.
- */
- private boolean moleculeEdges = false;
-
- /**
- *
- */
- public ExporterParameters() {
- }
-
- /**
- * Sets {@link #fileName}.
- *
- * @param fileName
- * new {@link #fileName}
- * @return object with all parameters set
- */
- public ExporterParameters fileName(String fileName) {
- this.fileName = fileName;
- return this;
- }
-
- /**
- * Sets {@link #model}.
- *
- * @param model
- * new {@link #model}
- * @return object with all parameters set
- */
- public ExporterParameters model(Model model) {
- this.models = new ArrayList<Model>();
- models.add(model);
- for (Model m : model.getSubmodels()) {
- models.add(m);
- }
-
- for (Model modelElement : models) {
- includedAliases.clear();
- for (String string : included) {
- for (Compartment alias : modelElement.getCompartments()) {
- if (alias.getName().equalsIgnoreCase(string)) {
- includedAliases.add(alias);
- }
- }
- }
-
- excludedAliases.clear();
- for (String string : excluded) {
- for (Compartment alias : modelElement.getCompartments()) {
- if (alias.getName().equalsIgnoreCase(string)) {
- excludedAliases.add(alias);
- }
- }
- }
- }
- return this;
- }
-
- /**
- * Adds element to {@link #included}.
- *
- * @param included
- * new element in {@link #included}
- * @return object with all parameters set
- */
- public ExporterParameters included(String included) {
- this.included.add(included);
-
- if (models.size() > 0) {
- for (Model model : models) {
- for (Compartment alias : model.getCompartments()) {
- if (alias.getName().equalsIgnoreCase(included)) {
- includedAliases.add(alias);
- }
- }
- }
- }
- return this;
- }
-
- /**
- * Adds elements to {@link #included}.
- *
- * @param included
- * list of elements to add to {@link #included}
- * @return object with all parameters set
- */
- public ExporterParameters included(List<String> included) {
- for (String string : included) {
- included(string);
- }
- return this;
- }
-
- /**
- * Adds element to {@link #excluded}.
- *
- * @param excluded
- * new element in {@link #excluded}
- * @return object with all parameters set
- */
- public ExporterParameters excluded(String excluded) {
- this.excluded.add(excluded);
-
- if (models.size() > 0) {
- for (Model model : models) {
- for (Compartment alias : model.getCompartments()) {
- if (alias.getName().equalsIgnoreCase(excluded)) {
- excludedAliases.add(alias);
- }
- }
- }
- }
- return this;
- }
-
- /**
- * Adds element to {@link #excluded}.
- *
- * @param excluded
- * new element in {@link #excluded}
- * @return object with all parameters set
- */
- public ExporterParameters excluded(Compartment excluded) {
- this.excluded.add(excluded.getName());
-
- excludedAliases.add(excluded);
- return this;
- }
-
- /**
- * Adds elements to {@link #excluded}.
- *
- * @param excluded
- * list of elements to add to {@link #excluded}
- * @return object with all parameters set
- */
- public ExporterParameters excluded(List<String> excluded) {
- for (String string : excluded) {
- excluded(string);
- }
- return this;
- }
-
- /**
- * Adds elements to {@link #excluded}.
- *
- * @param excluded
- * list of elements to add to {@link #excluded}
- * @return object with all parameters set
- */
- public ExporterParameters excluded(Collection<Compartment> excluded) {
- for (Compartment string : excluded) {
- excluded(string);
- }
- return this;
- }
-
- /**
- * Sets {@link #fileType}.
- *
- * @param fileType
- * new {@link #fileType}
- * @return object with all parameters set
- */
- public ExporterParameters fileType(ExportFileType fileType) {
- this.fileType = fileType;
- return this;
- }
-
- /**
- * Adds type to {@link #types}.
- *
- * @param type
- * new element in {@link #types}
- * @return object with all parameters set
- */
- public ExporterParameters type(Class<?> type) {
- this.types.add(type);
- return this;
- }
-
- /**
- * Adds types to {@link #types}.
- *
- * @param types
- * new elements in {@link #types}
- * @return object with all parameters set
- */
- public ExporterParameters type(List<Class<?>> types) {
- this.types.addAll(types);
- return this;
- }
-
- /**
- * Adds column to {@link #columns}.
- *
- * @param column
- * new element in {@link #columns}
- * @return object with all parameters set
- */
- public ExporterParameters column(ExportColumn column) {
- this.columns.add(column);
- return this;
- }
-
- /**
- * Adds columns to {@link #columns}.
- *
- * @param columns
- * new elements in {@link #columns}
- * @return object with all parameters set
- */
- public ExporterParameters column(List<ExportColumn> columns) {
- this.columns.addAll(columns);
- return this;
- }
-
- /**
- * Adds {@link MiriamType} to {@link #miriamTypes}.
- *
- * @param mt
- * new element in {@link #miriamTypes}
- * @return object with all parameters set
- */
- public ExporterParameters miriamType(MiriamType mt) {
- this.miriamTypes.add(mt);
- return this;
- }
-
- /**
- * Adds {@link MiriamType miriam types} to {@link #miriamTypes list}.
- *
- * @param mts
- * new elements in {@link #miriamTypes}
- * @return object with all parameters set
- */
- public ExporterParameters miriamTypes(List<MiriamType> mts) {
- this.miriamTypes.addAll(mts);
- return this;
- }
-
- /**
- * Adds columns to {@link #columns}.
- *
- * @param columns2
- * new elements in {@link #columns}
- * @return object with all parameters set
- */
- public ExporterParameters column(ExportColumn[] columns2) {
- for (ExportColumn exportColumn : columns2) {
- column(exportColumn);
- }
- return this;
- }
-
- /**
- * Sets {@link #moleculeEdges}.
- *
- * @param moleculeEdges
- * new {@link #moleculeEdges}
- * @return object with all parameters set
- */
- public ExporterParameters moleculeEdges(boolean moleculeEdges) {
- this.moleculeEdges = moleculeEdges;
- return this;
- }
-
- /**
- * Adds elements to {@link #included}.
- *
- * @param included
- * list of elements to add to {@link #included}
- * @return object with all parameters set
- */
- public ExporterParameters included(String[] included) {
- for (String string : included) {
- included(string);
- }
- return this;
- }
-
- /**
- * Adds elements to {@link #excluded}.
- *
- * @param excluded
- * list of elements to add to {@link #excluded}
- * @return object with all parameters set
- */
- public ExporterParameters excluded(String[] excluded) {
- for (String string : excluded) {
- excluded(string);
- }
- return this;
- }
-
- /**
- * Sets {@link #complexElementsName}.
- *
- * @param complexElementsName
- * new {@link #complexElementsName}
- * @return object with all parameters set
- */
- public ExporterParameters complexElementsName(boolean complexElementsName) {
- this.complexElementsName = complexElementsName;
- return this;
- }
-
- /**
- * @return the fileName
- * @see #fileName
- */
- public String getFileName() {
- return fileName;
- }
-
- /**
- * @return the model
- * @see #model
- */
- public List<Model> getModels() {
- return models;
- }
-
- /**
- * @return the included
- * @see #included
- */
- public List<String> getIncluded() {
- return included;
- }
-
- /**
- * @return the excluded
- * @see #excluded
- */
- public List<String> getExcluded() {
- return excluded;
- }
-
- /**
- * @return the fileType
- * @see #fileType
- */
- public ExportFileType getFileType() {
- return fileType;
- }
-
- /**
- * @return the types
- * @see #types
- */
- public List<Class<?>> getTypes() {
- return types;
- }
-
- /**
- * @return the columns
- * @see #columns
- */
- public List<ExportColumn> getColumns() {
- return columns;
- }
-
- /**
- * @return the includedAliases
- * @see #includedAliases
- */
- public Set<Compartment> getIncludedAliases() {
- return includedAliases;
- }
-
- /**
- * @return the excludedAliases
- * @see #excludedAliases
- */
- public Set<Compartment> getExcludedAliases() {
- return excludedAliases;
- }
-
- /**
- * @return the complexElementsName
- * @see #complexElementsName
- */
- public boolean isComplexElementsName() {
- return complexElementsName;
- }
-
- /**
- * @return the moleculeEdges
- * @see #moleculeEdges
- */
- public boolean isMoleculeEdges() {
- return moleculeEdges;
- }
-
- /**
- * @return the miriamTypes
- * @see #miriamTypes
- */
- public List<MiriamType> getMiriamTypes() {
- return miriamTypes;
- }
-
- }
-
- /**
- * Export species using given parameters.
- *
- * @param parameters
- * {@link ExporterParameters export parameters}
- * @throws IOException
- * thrown when there is a problem with accessing output file
- */
- void exportSpecies(ExporterParameters parameters) throws IOException;
-
- /**
- * Returns string with all species exported using given parameters.
- *
- * @param parameters
- * {@link ExporterParameters export parameters}
- * @return String representing exported data
- */
- String getExportSpeciesString(ExporterParameters parameters);
-
- /**
- * Returns string with all compartments exported using given parameters.
- *
- * @param parameters
- * {@link ExporterParameters export parameters}
- * @return String representing exported data
- */
- String getExportCompartmentsString(ExporterParameters parameters);
-
- /**
- * Export compartments using given parameters.
- *
- * @param parameters
- * {@link ExporterParameters export parameters}
- * @throws IOException
- * thrown when there is a problem with accessing output file
- */
- void exportCompartments(ExporterParameters parameters) throws IOException;
-
- /**
- * Export reactions using given parameters.
- *
- * @param parameters
- * {@link ExporterParameters export parameters}
- * @throws IOException
- * thrown when there is a problem with accessing output file
- */
- void exportReactions(ExporterParameters parameters) throws IOException;
-
- /**
- * Returns string with all reactions exported using given parameters.
- *
- * @param parameters
- * {@link ExporterParameters export parameters}
- * @return String representing exported data
- */
- String getExportInteractionString(ExporterParameters parameters);
-
- /**
- * Returns list of publciations for given model.
- *
- * @param model
- * model for which list of publication will be returned
- * @return list of publciations for given model
- */
- List<PubmedAnnotatedElementsView> getPublicationModelSummary(Model model);
-}
diff --git a/service/src/main/resources/applicationContext-service.xml b/service/src/main/resources/applicationContext-service.xml
index 08cd8531e2246247b3f680f3332ab4f3cda736a6..45127552d31965209f09675d98bacc199f830e7b 100644
--- a/service/src/main/resources/applicationContext-service.xml
+++ b/service/src/main/resources/applicationContext-service.xml
@@ -19,8 +19,6 @@
<bean id="DrugService" class="lcsb.mapviewer.services.search.db.drug.DrugService"/>
- <bean id="ExporterService" class="lcsb.mapviewer.services.impl.ExporterService"/>
-
<bean id="ExternalServicesService" class="lcsb.mapviewer.services.impl.ExternalServicesService"/>
<bean id="LayoutService" class="lcsb.mapviewer.services.impl.LayoutService"/>
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/AllImplServiceTests.java b/service/src/test/java/lcsb/mapviewer/services/impl/AllImplServiceTests.java
index c190d180cf2a44b141055a62e0e74d30f093ea28..a5f016714de7a25ea45263a08df7156d9e3993eb 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/AllImplServiceTests.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/AllImplServiceTests.java
@@ -9,7 +9,6 @@ import org.junit.runners.Suite.SuiteClasses;
ConfigurationServiceTest.class, //
DataMiningServiceTest.class, //
DataMiningServiceTest2.class, //
- ExporterServiceTest.class, //
ExternalServicesServiceTest.class, //
LayoutServiceTest.class, //
Md5PasswordEncoderTest.class, //
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/ExporterServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/ExporterServiceTest.java
deleted file mode 100644
index e65556f1044b7cf57849214923809461a2670647..0000000000000000000000000000000000000000
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ExporterServiceTest.java
+++ /dev/null
@@ -1,540 +0,0 @@
-package lcsb.mapviewer.services.impl;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-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.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.commands.CreateHierarchyCommand;
-import lcsb.mapviewer.converter.model.celldesigner.reaction.ReactionLineData;
-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.reaction.ReactionNode;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.services.ServiceTestFunctions;
-import lcsb.mapviewer.services.interfaces.IExporterService;
-import lcsb.mapviewer.services.interfaces.IExporterService.ExporterParameters;
-import lcsb.mapviewer.services.utils.data.ExportColumn;
-import lcsb.mapviewer.services.utils.data.ExportFileType;
-import lcsb.mapviewer.services.view.PubmedAnnotatedElementsView;
-
-public class ExporterServiceTest extends ServiceTestFunctions {
- Logger logger = Logger.getLogger(ExporterServiceTest.class);
- @Autowired
- IExporterService exporter2;
-
- ExporterService exporter;
-
- @Before
- public void setUp() throws Exception {
- exporter = (ExporterService) exporter2;
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetExportSpeciesStringForTabSeparatedFile() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export_with_artifitial_comp.xml", false);
- ExportColumn columns[] = { ExportColumn.NAME, ExportColumn.ID, ExportColumn.COMPONENT_NAME,
- ExportColumn.COMPARTMENT_NAME, ExportColumn.TYPE };
-
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).column(columns)
- .fileType(ExportFileType.TAB_SEPARATED);
-
- // full export (all elements)
- String string = exporter.getExportSpeciesString(params);
- String lines[] = string.split("\n");
- assertTrue("Not enough elements in the result file", lines.length > 1);
-
- String response = lines[0];
- String textColumns[] = response.split("\t");
- assertEquals(5, textColumns.length);
-
- // only proteins for self-made modules
- new CreateHierarchyCommand(model, 8, 80).execute();
- string = exporter.getExportSpeciesString(params.type(GenericProtein.class));
- lines = string.split("\n");
- assertTrue(lines.length > 1);
-
- boolean differenceBetweenComponentCompartmnet = false;
- int lineCount = 0;
- for (String string2 : lines) {
- if (lineCount == 0) {
- textColumns = string2.split("\t");
- assertEquals(ExportColumn.TYPE.getTitle(), textColumns[4]);
- } else {
- textColumns = string2.split("\t");
- assertEquals(GenericProtein.class.getSimpleName(), textColumns[4]);
- if (!textColumns[2].equalsIgnoreCase(textColumns[3])) {
- differenceBetweenComponentCompartmnet = true;
- }
- }
- lineCount++;
- }
- assertTrue(differenceBetweenComponentCompartmnet);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDuplicatesInGetExportSpeciesString() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export_duplicate_elements.xml", false);
- ExportColumn columns[] = { ExportColumn.NAME, ExportColumn.COMPONENT_NAME, ExportColumn.TYPE };
-
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).column(columns)
- .fileType(ExportFileType.TAB_SEPARATED);
-
- // full export (all elements)
- String string = exporter.getExportSpeciesString(params);
-
- String lines[] = string.split("\n");
- Set<String> uniqueNames = new HashSet<String>();
- for (String string2 : lines) {
- uniqueNames.add(string2);
- }
- assertEquals(uniqueNames.size(), lines.length);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetExportStringForOneSpecies_Complex() {
- try {
- Model model = getModelForFile("testFiles/export/hsp70.xml", true);
-
- Species alias = (Species) model.getElementByElementId("csa1");
- ExportColumn columns[] = { ExportColumn.NAME };
-
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).//
- column(columns).//
- complexElementsName(false).//
- fileType(ExportFileType.TAB_SEPARATED);
-
- List<String> elements = exporter.getExportStringForOneSpecies(alias, params);
- assertTrue(elements.contains("HSP70:chaperon"));
-
- // now the results are concatenated children
- params.complexElementsName(true);
-
- elements = exporter.getExportStringForOneSpecies(alias, params);
- assertTrue(elements.size() > 0);
- String string = elements.get(0);
- assertFalse(string.equals("HSP70:chaperon"));
- assertTrue(string.contains("HSP70"));
- assertTrue(string.contains("STUB1"));
- assertTrue(string.contains("DNAJB2"));
- assertTrue(string.contains("BAG1"));
-
- // and now check complexes with mix of proteins and molecules
- alias = (Species) model.getElementByElementId("csa3");
-
- elements = exporter.getExportStringForOneSpecies(alias, params);
- assertTrue(elements.size() > 0);
- string = elements.get(0);
- assertTrue(string.contains("UBA1"));
- assertTrue(string.contains("UBA6"));
- assertTrue(string.contains("AMP"));
-
- elements = exporter.getExportStringForOneSpecies(alias, params.type(Protein.class));
- assertTrue(elements.size() > 0);
- string = elements.get(0);
- assertTrue(string.contains("UBA1"));
- assertTrue(string.contains("UBA6"));
- assertFalse(string.contains("AMP"));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Exception occured");
- }
- }
-
- @Test
- public void testGetExportStringForOneReaction() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export/reaction.xml", false);
- Set<Compartment> aliases = new HashSet<>();
- for (Compartment alias : model.getCompartments()) {
- if (alias.getName().equalsIgnoreCase("Dopamine loaded synaptic vesicle"))
- aliases.add(alias);
- }
-
- Reaction reaction = model.getReactionByReactionId("re2");
-
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).//
- fileType(ExportFileType.SIF).//
- type(Protein.class).//
- type(Complex.class).//
- fileType(ExportFileType.SIF).//
- complexElementsName(false).//
- excluded(aliases);
-
- String string = exporter.getExportSingleInteractionString(reaction, params).get(0);
- assertNotNull(string);
- assertTrue(string.contains("Calcium channel:RIMBP:RIM:MUNC13:RAB"));
- assertTrue(string.contains("CSP:Hsc70:SGT"));
- assertTrue(string.contains("SNCA"));
- assertTrue(string.contains("trans-SNARE complex"));
- assertFalse(string.contains("VAMP2"));
-
- params = new IExporterService.ExporterParameters().model(model).fileType(ExportFileType.SIF).type(Complex.class)
- .type(Protein.class);
- string = exporter.getExportSingleInteractionString(reaction, params).get(0);
- assertTrue(string.contains("VAMP2"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetExportStringForOneReactionInGeneral() {
- try {
- Model model = getModelForFile("testFiles/export/reaction.xml", true);
- Reaction reaction = model.getReactionByReactionId("re2");
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).//
- fileType(ExportFileType.SIF).//
- complexElementsName(false).//
- type(Complex.class).type(Protein.class);
- String string = exporter.getExportSingleInteractionString(reaction, params).get(0);
- assertNotNull(string);
- assertTrue(string.contains("Calcium channel:RIMBP:RIM:MUNC13:RAB"));
- assertTrue(string.contains("CSP:Hsc70:SGT"));
- assertTrue(string.contains("SNCA"));
- assertTrue(string.contains("trans-SNARE complex"));
- assertTrue(string.contains("SNAP25"));
- assertFalse(string.contains("RAB3A"));
-
- params.complexElementsName(true);
- string = exporter.getExportSingleInteractionString(reaction, params).get(0);
- assertFalse(string.contains("trans-SNARE complex"));
- assertTrue(string.contains("RAB3A"));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Exception occured");
- }
-
- }
-
- @Test
- public void testGetExportStringForOneReactionInGeneralWithOnlyOneElement() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export/reaction.xml", false);
- Reaction reaction = model.getReactionByReactionId("re11");
- model.removeReactions(model.getReactions());
- model.addReaction(reaction);
- Set<Compartment> aliases = new HashSet<>();
- aliases.add((Compartment) model.getElementByElementId("ca1"));
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).fileType(ExportFileType.SIF)
- .included("dopamine loaded synaptic vesicle");
- assertEquals(0, exporter.getExportSingleInteractionString(reaction, params).size());
-
- params = new IExporterService.ExporterParameters().model(model).fileType(ExportFileType.SIF);
- assertEquals(1, exporter.getExportSingleInteractionString(reaction, params).size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetExportSingleInteractionString_text() {
- try {
- Model model = getModelForFile("testFiles/export_with_artifitial_comp.xml", false);
- for (Reaction reaction : model.getReactions()) {
- String str = exporter
- .getExportSingleInteractionString(reaction,
- new IExporterService.ExporterParameters().fileType(ExportFileType.TAB_SEPARATED).type(Species.class))
- .get(0);
-
- List<String> strings = new ArrayList<String>();
- strings.add(ReactionLineData.getByReactionType(reaction.getClass()).getCellDesignerString());
- strings.add(reaction.getIdReaction());
- for (ReactionNode node : reaction.getReactionNodes()) {
- strings.add(node.getElement().getName());
-
- }
- for (String string : strings) {
- assertTrue(
- "Description \"" + str + "\" doesn't contain " + string + ". reactionId=" + reaction.getIdReaction(),
- str.contains(string));
- }
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Exception occured");
- }
- }
-
- @Test
- public void testGetExportComponentAndCompartments() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export/export_model.xml", false);
- new CreateHierarchyCommand(model, 7, 80).execute();
- ExporterParameters params = new IExporterService.ExporterParameters().model(model)
- .fileType(ExportFileType.TAB_SEPARATED).column(ExportColumn.NAME).column(ExportColumn.COMPONENT_NAME)
- .column(ExportColumn.COMPARTMENT_NAME);
-
- List<String> list = exporter.getExportStringForOneSpecies((Species) model.getElementByElementId("sa1"), params);
- String desc = list.get(0);
- String compartment = desc.split("\t")[2];
- assertEquals("c1", compartment);
- String component = desc.split("\t")[1];
- assertEquals("Test3", component);
-
- list = exporter.getExportStringForOneSpecies((Species) model.getElementByElementId("sa2"), params);
- desc = null;
- for (String string : list) {
- if (string.contains("Test 1")) {
- desc = string;
- }
- }
- compartment = desc.split("\t")[2];
- assertEquals("c2", compartment);
- component = desc.split("\t")[1];
- assertEquals("Test 1", component);
-
- for (String string : list) {
- if (string.contains("Test2")) {
- desc = string;
- }
- }
- compartment = desc.split("\t")[2];
- assertEquals("c2", compartment);
- component = desc.split("\t")[1];
- assertEquals("Test2", component);
-
- for (String string : list) {
- if (string.contains("Test3")) {
- desc = string;
- }
- }
- compartment = desc.split("\t")[2];
- assertEquals("c2", compartment);
- component = desc.split("\t")[1];
- assertEquals("Test3", component);
-
- list = exporter.getExportStringForOneSpecies((Species) model.getElementByElementId("sa3"), params);
- boolean ok = false;
- for (String string : list) {
- if (string.split("\t")[2].equals("null") && string.split("\t")[1].equals("Test2")) {
- ok = true;
- }
- }
- assertTrue(ok);
-
- list = exporter.getExportStringForOneSpecies((Species) model.getElementByElementId("sa4"), params);
- desc = list.get(0);
- compartment = desc.split("\t")[2];
- assertEquals("null", compartment);
- component = desc.split("\t")[1];
- assertEquals("Test3", component);
-
- list = exporter.getExportStringForOneSpecies((Species) model.getElementByElementId("sa5"), params);
- desc = list.get(0);
- compartment = desc.split("\t")[2];
- assertEquals("c3", compartment);
- component = desc.split("\t")[1];
- assertEquals("null", component);
-
- list = exporter.getExportStringForOneSpecies((Species) model.getElementByElementId("sa6"), params);
- desc = list.get(0);
- compartment = desc.split("\t")[2];
- assertEquals("null", compartment);
- component = desc.split("\t")[1];
- assertEquals("null", component);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetExportSpeciesStringForTabSeparatedFile2() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export_with_artifitial_comp.xml", false);
- ExportColumn columns[] = { ExportColumn.NAME, ExportColumn.ID, ExportColumn.COMPONENT_NAME,
- ExportColumn.COMPARTMENT_NAME, ExportColumn.TYPE };
-
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).column(columns)
- .fileType(ExportFileType.TAB_SEPARATED).type(Object.class);
-
- // full export (all elements)
- String string = exporter.getExportSpeciesString(params);
- String lines[] = string.split("\n");
- assertTrue("Not enough elements in the result file", lines.length > 1);
-
- String response = lines[0];
- String textColumns[] = response.split("\t");
- assertEquals(columns.length, textColumns.length);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetExportCompartmentsString() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export/export_compartments.xml", false);
-
- ExporterParameters params = new IExporterService.ExporterParameters().model(model)
- .fileType(ExportFileType.TAB_SEPARATED).type(Object.class);
-
- // full export (all compartments)
- String string = exporter.getExportCompartmentsString(params);
- String lines[] = string.split("\n");
- assertTrue("Not enough elements in the result file", lines.length >= 2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAllExportColumnsSpecies() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export_with_artifitial_comp.xml", false);
- List<ExportColumn> columns = new ArrayList<ExportColumn>();
- for (ExportColumn column : ExportColumn.values()) {
- if (column.getClazz().isAssignableFrom(Species.class)) {
- columns.add(column);
- }
- }
-
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).column(columns)
- .fileType(ExportFileType.TAB_SEPARATED);
-
- // full export (all elements)
- String string = exporter.getExportSpeciesString(params);
- assertNotNull(string);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAllExportColumnsReaction() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export_with_artifitial_comp.xml", false);
- List<ExportColumn> columns = new ArrayList<ExportColumn>();
- for (ExportColumn column : ExportColumn.values()) {
- if (column.getClazz().isAssignableFrom(Reaction.class)) {
- columns.add(column);
- }
- }
-
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).column(columns)
- .fileType(ExportFileType.TAB_SEPARATED);
-
- // full export (all elements)
- String string = exporter.getExportInteractionString(params);
- assertNotNull(string);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetTabSeparatedReaction() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export/reaction.xml", false);
- Set<Compartment> aliases = new HashSet<>();
- for (Compartment alias : model.getCompartments()) {
- if (alias.getName().equalsIgnoreCase("Dopamine loaded synaptic vesicle"))
- aliases.add(alias);
- }
-
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).//
- fileType(ExportFileType.TAB_SEPARATED).//
- column(ExportColumn.REACTION_ID).//
- column(ExportColumn.REACTION_TYPE).//
- type(Species.class);
-
- String string = exporter.getExportInteractionString(params);
- assertTrue(string.indexOf("STATE_TRANSITION REACTANT") >= 0);
- assertTrue(string.indexOf("sa7") >= 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void test() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export/new_line_file.xml", false);
- List<ExportColumn> columns = new ArrayList<ExportColumn>();
- for (ExportColumn column : ExportColumn.values()) {
- if (column.getClazz().isAssignableFrom(Species.class)) {
- columns.add(column);
- }
- }
-
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).column(columns)
- .fileType(ExportFileType.TAB_SEPARATED);
-
- // full export (all elements)
- String string = exporter.getExportSpeciesString(params);
- String tmp[] = string.split("\n");
- for (String string2 : tmp) {
- assertTrue(string2, columns.size() <= string2.split("\t", -1).length);
- }
- assertNotNull(string);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testPubmedSummary() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export/reaction.xml", false);
- List<PubmedAnnotatedElementsView> result = exporter.getPublicationModelSummary(model);
- assertNotNull(result);
- for (PubmedAnnotatedElementsView pubmedAnnotatedElementsView : result) {
- assertNotNull(pubmedAnnotatedElementsView.getArticle());
- assertNotNull(pubmedAnnotatedElementsView.getArticle().getTitle());
- assertTrue(pubmedAnnotatedElementsView.getElements().size() > 0);
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}