diff --git a/model/src/main/java/lcsb/mapviewer/model/LogMarker.java b/model/src/main/java/lcsb/mapviewer/model/LogMarker.java
index af9310d7d93f4851b220e2b7b07b2bdcd9f7f3d5..23ae2a0d457869bb2b59a287b09455e85aeaa2c8 100644
--- a/model/src/main/java/lcsb/mapviewer/model/LogMarker.java
+++ b/model/src/main/java/lcsb/mapviewer/model/LogMarker.java
@@ -32,6 +32,14 @@ public class LogMarker implements Marker {
entry = new ProjectLogEntry(marker.getEntry());
}
+ public LogMarker(ProjectLogEntryType type, String objectClass, String objectIdentifier, String mapName) {
+ entry = new ProjectLogEntry();
+ entry.setType(type);
+ entry.setObjectIdentifier(objectIdentifier);
+ entry.setObjectClass(objectClass);
+ entry.setMapName(mapName);
+ }
+
@Override
public Marker addParents(Marker... markers) {
throw new NotImplementedException();
diff --git a/model/src/main/java/lcsb/mapviewer/model/ProjectLogEntryType.java b/model/src/main/java/lcsb/mapviewer/model/ProjectLogEntryType.java
index 42d1186ca6c3e6b5d50d9c543797e5c11bfba02a..a04c2a007b8d6fe16d2fbf550bf3a39b0af1318e 100644
--- a/model/src/main/java/lcsb/mapviewer/model/ProjectLogEntryType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/ProjectLogEntryType.java
@@ -9,5 +9,6 @@ public enum ProjectLogEntryType {
MISSING_ANNOTATION,
MISSING_REQUIRED_ANNOTATION,
OUT_OF_MEMORY,
- OTHER,
+ OTHER,
+ PARSING_ISSUE,
}
diff --git a/pathvisio/pom.xml b/pathvisio/pom.xml
index 30ee0f01455a80296445bc7ed63ace99ae147b74..cb567c594c82f5e67351f3f03b0a6cf8a93a6612 100644
--- a/pathvisio/pom.xml
+++ b/pathvisio/pom.xml
@@ -1,145 +1,57 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>parent</artifactId>
- <version>1.0</version>
- </parent>
- <artifactId>pathvisio</artifactId>
- <name>Pathvisio plugin</name>
-
-<!-- <packaging>bundle</packaging>
-
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.felix</groupId>
- <artifactId>maven-bundle-plugin</artifactId>
- <version>4.0.0</version>
- <extensions>true</extensions>
-
- <configuration>
- <instructions>
- <Bundle-Activator>lcsb.mapviewer.wikipathway.Activator</Bundle-Activator>
- <Bundle-Name>CellDesigner plugin v.${svnversion}</Bundle-Name>
-
- <Embed-Transitive>true</Embed-Transitive>
- <Embed-Dependency>*;scope=compile|runtime;inline=false</Embed-Dependency>
- <Import-Package>!org.relaxng.datatype,
- !org.slf4j,
- !org.slf4j.spi,
- !com.fasterxml.classmate,
- !com.fasterxml.classmate.members,
- !com.ibm.uvm.tools,
- !com.sun.jdi,
- !com.sun.jdi.connect,
- !com.sun.jdi.event,
- !com.sun.jdi.request,
- !com.sun.jdmk.comm,
- !com.sun.msv.datatype,
- !com.sun.msv.datatype.xsd,
- !com.google.gson,
- !javax.imageio,
- !javax.jmdns,
- !javax.jms,
- !javax.mail,
- !javax.mail.internet,
- !javax.management,
- !javax.naming,
- !javax.naming.event,
- !javax.naming.spi,
- !javax.security.auth,
- !javax.security.jacc,
- !javax.sql,
- !javax.swing,
- !javax.swing.border,
- !javax.swing.event,
- !javax.swing.filechooser,
- !javax.swing.plaf,
- !javax.swing.table,
- !javax.swing.text,
- !javax.swing.text.html,
- !javax.swing.tree,
- !javax.validation,
- !javax.validation.constraints,
- !javax.validation.groups,
- !javax.validation.metadata,
- !javax.xml,
- !javax.xml.bind,
- !javax.xml.bind.annotation,
- !javax.xml.bind.annotation.adapters,
- !javax.xml.namespace,
- !javax.xml.parsers,
- !javax.xml.stream,
- !javax.xml.stream.events,
- !javax.xml.stream.util,
- !javax.xml.transform,
- !javax.xml.transform.dom,
- !javax.xml.transform.sax,
- !javax.xml.transform.stream,
- !javax.xml.validation,
- !oracle.xml.parser,
- !oracle.xml.parser.v2,
- !org.apache.batik.dom,
- !org.apache.batik.svggen,
- !org.apache.batik.transcoder,
- !org.apache.batik.transcoder.image,
- !org.apache.commons.math,
- !org.apache.commons.math.stat,
- !org.apache.commons.math.stat.inference,
- !org.apache.commons.vfs2,
- !org.apache.fop.svg,
- !org.apache.tools.ant,
- !org.apache.tools.ant.taskdefs,
- !org.apache.tools.ant.types,
- !org.bridgedb,
- !org.bridgedb.bio,
- !org.bridgedb.gui,
- !org.bridgedb.rdb.construct,
- !org.gjt.xpp,
- !org.jaxen,
- !org.jaxen.jdom,
- !org.jaxen.dom4j,
- !org.jaxen.pattern,
- !org.jaxen.saxpath,
- !org.jboss.jandex,
- !org.jboss.logmanager,
- !org.jdom,
- !org.jdom.input,
- !org.jdom.output,
- !org.pathvisio.data,
- !org.w3c.dom,
- !org.w3c.dom.events,
- !org.w3c.dom.ranges,
- !org.w3c.dom.traversal,
- !org.xml.sax,
- !org.xml.sax.ext,
- !org.xml.sax.helpers,
- !org.xmlpull.v1,
- !sun.io,
- !sun.misc,
- org.osgi.framework;version=1.3.0,*</Import-Package>
- <Require-Bundle>org.pathvisio.core;bundle-version=3.0.0,
- org.pathvisio.desktop;bundle-version=3.0.0,
- org.pathvisio.gui;bundle-version=3.0.0
- </Require-Bundle>
- </instructions>
- </configuration>
- </plugin>
- </plugins>
- </build>
--->
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>parent</artifactId>
+ <version>1.0</version>
+ </parent>
+ <artifactId>pathvisio</artifactId>
+ <name>Pathvisio plugin</name>
+
+ <!-- <packaging>bundle</packaging> <build> <plugins> <plugin> <groupId>org.apache.felix</groupId>
+ <artifactId>maven-bundle-plugin</artifactId> <version>4.0.0</version> <extensions>true</extensions>
+ <configuration> <instructions> <Bundle-Activator>lcsb.mapviewer.wikipathway.Activator</Bundle-Activator>
+ <Bundle-Name>CellDesigner plugin v.${svnversion}</Bundle-Name> <Embed-Transitive>true</Embed-Transitive>
+ <Embed-Dependency>*;scope=compile|runtime;inline=false</Embed-Dependency>
+ <Import-Package>!org.relaxng.datatype, !org.slf4j, !org.slf4j.spi, !com.fasterxml.classmate,
+ !com.fasterxml.classmate.members, !com.ibm.uvm.tools, !com.sun.jdi, !com.sun.jdi.connect,
+ !com.sun.jdi.event, !com.sun.jdi.request, !com.sun.jdmk.comm, !com.sun.msv.datatype,
+ !com.sun.msv.datatype.xsd, !com.google.gson, !javax.imageio, !javax.jmdns,
+ !javax.jms, !javax.mail, !javax.mail.internet, !javax.management, !javax.naming,
+ !javax.naming.event, !javax.naming.spi, !javax.security.auth, !javax.security.jacc,
+ !javax.sql, !javax.swing, !javax.swing.border, !javax.swing.event, !javax.swing.filechooser,
+ !javax.swing.plaf, !javax.swing.table, !javax.swing.text, !javax.swing.text.html,
+ !javax.swing.tree, !javax.validation, !javax.validation.constraints, !javax.validation.groups,
+ !javax.validation.metadata, !javax.xml, !javax.xml.bind, !javax.xml.bind.annotation,
+ !javax.xml.bind.annotation.adapters, !javax.xml.namespace, !javax.xml.parsers,
+ !javax.xml.stream, !javax.xml.stream.events, !javax.xml.stream.util, !javax.xml.transform,
+ !javax.xml.transform.dom, !javax.xml.transform.sax, !javax.xml.transform.stream,
+ !javax.xml.validation, !oracle.xml.parser, !oracle.xml.parser.v2, !org.apache.batik.dom,
+ !org.apache.batik.svggen, !org.apache.batik.transcoder, !org.apache.batik.transcoder.image,
+ !org.apache.commons.math, !org.apache.commons.math.stat, !org.apache.commons.math.stat.inference,
+ !org.apache.commons.vfs2, !org.apache.fop.svg, !org.apache.tools.ant, !org.apache.tools.ant.taskdefs,
+ !org.apache.tools.ant.types, !org.bridgedb, !org.bridgedb.bio, !org.bridgedb.gui,
+ !org.bridgedb.rdb.construct, !org.gjt.xpp, !org.jaxen, !org.jaxen.jdom, !org.jaxen.dom4j,
+ !org.jaxen.pattern, !org.jaxen.saxpath, !org.jboss.jandex, !org.jboss.logmanager,
+ !org.jdom, !org.jdom.input, !org.jdom.output, !org.pathvisio.data, !org.w3c.dom,
+ !org.w3c.dom.events, !org.w3c.dom.ranges, !org.w3c.dom.traversal, !org.xml.sax,
+ !org.xml.sax.ext, !org.xml.sax.helpers, !org.xmlpull.v1, !sun.io, !sun.misc,
+ org.osgi.framework;version=1.3.0,*</Import-Package> <Require-Bundle>org.pathvisio.core;bundle-version=3.0.0,
+ org.pathvisio.desktop;bundle-version=3.0.0, org.pathvisio.gui;bundle-version=3.0.0
+ </Require-Bundle> </instructions> </configuration> </plugin> </plugins> </build> -->
<repositories>
<repository>
- <id>repo</id>
- <releases>
- <enabled>true</enabled>
- <checksumPolicy>ignore</checksumPolicy>
- </releases>
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- <url>file://${project.basedir}/repo</url>
+ <id>repo</id>
+ <releases>
+ <enabled>true</enabled>
+ <checksumPolicy>ignore</checksumPolicy>
+ </releases>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <url>file://${project.basedir}/repo</url>
</repository>
</repositories>
@@ -149,39 +61,39 @@
<artifactId>core</artifactId>
<version>${pathvisio.version}</version>
</dependency>
-
+
<dependency>
<groupId>org.pathvisio</groupId>
<artifactId>desktop</artifactId>
<version>${pathvisio.version}</version>
</dependency>
-
+
<dependency>
<groupId>org.pathvisio</groupId>
<artifactId>gui</artifactId>
<version>${pathvisio.version}</version>
</dependency>
-
+
<dependency>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>model</artifactId>
- <version>1.0</version>
- </dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>model</artifactId>
+ <version>1.0</version>
+ </dependency>
<dependency>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>converter-CellDesigner</artifactId>
- <version>1.0</version>
- </dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>converter-CellDesigner</artifactId>
+ <version>1.0</version>
+ </dependency>
<dependency>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>converter-graphics</artifactId>
- <scope>test</scope>
- <version>1.0</version>
- </dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>converter-graphics</artifactId>
+ <scope>test</scope>
+ <version>1.0</version>
+ </dependency>
- <!-- Log4J2-->
+ <!-- Log4J2 -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
@@ -193,11 +105,11 @@
<version>${log4j2.version}</version>
</dependency>
- <dependency>
- <groupId>org.apache.felix</groupId>
- <artifactId>org.osgi.core</artifactId>
- <version>${osgi.version}</version>
- </dependency>
+ <dependency>
+ <groupId>org.apache.felix</groupId>
+ <artifactId>org.osgi.core</artifactId>
+ <version>${osgi.version}</version>
+ </dependency>
<dependency>
<groupId>junit</groupId>
@@ -206,5 +118,14 @@
<scope>test</scope>
</dependency>
+ <!-- mockito used for testing -->
+ <dependency>
+ <groupId>org.mockito</groupId>
+ <artifactId>mockito-core</artifactId>
+ <version>${mockito.version}</version>
+ <scope>test</scope>
+ </dependency>
+
+
</dependencies>
</project>
\ No newline at end of file
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/GpmlParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/GpmlParser.java
index 796d4a006eb3dff90a82508037b8d1b981ca0143..4b0bc2275fbd7273faa2e80deeab52b8e6e650c1 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/GpmlParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/GpmlParser.java
@@ -35,7 +35,7 @@ public class GpmlParser extends Converter {
@Override
public String model2String(Model model) throws InconsistentModelException, ConverterException {
- ModelToGPML modelToGPML = new ModelToGPML();
+ ModelToGPML modelToGPML = new ModelToGPML(model.getName());
return modelToGPML.getGPML(model);
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/ImportExport.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/ImportExport.java
index f9279eb532056c40d9add52ae74902249666b800..4e7649b14147168487f18e87c88709f408f6242c 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/ImportExport.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/ImportExport.java
@@ -112,7 +112,7 @@ public class ImportExport implements Plugin {
CellDesignerXmlParser parser = new CellDesignerXmlParser();
Model model = (Model) parser.createModel(new ConverterParams().filename(fileName).sizeAutoAdjust(false));
- String tmp = new ModelToGPML().getGPML(model);
+ String tmp = new ModelToGPML(model.getName()).getGPML(model);
InputStream stream = new ByteArrayInputStream(tmp.getBytes(StandardCharsets.UTF_8));
Boolean validate = false;
pathway.readFromXml(stream, validate);
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/BiopaxParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/BiopaxParser.java
index e1a3725b8d2e926e4da1ccfb2d798f3dbfcaa704..7479f5ad1b82b6df6b6e19e946b6f4d860e9cbcd 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/BiopaxParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/BiopaxParser.java
@@ -8,12 +8,14 @@ import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.model.LogMarker;
+import lcsb.mapviewer.model.ProjectLogEntryType;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.wikipathway.model.biopax.*;
/**
- * Parser of Biopax data from the gpml file.
+ * Parser of Biopax data from the GPML file.
*
* @author Piotr Gawron
*
@@ -34,7 +36,13 @@ public class BiopaxParser {
* Mapping between {@link MiriamData} and hash value.
*/
private Map<MiriamData, String> miriamHash = new HashMap<>();
+
+ private String mapName;
+ public BiopaxParser(String mapName) {
+ this.mapName = mapName;
+ }
+
/**
* Creates data structure from BioPax xml node.
*
@@ -51,7 +59,7 @@ public class BiopaxParser {
if ("bp:PublicationXref".equalsIgnoreCase(node.getNodeName())) {
BiopaxPublication publication = parsePublication(node);
if (publication.getId() == null || publication.getId().isEmpty()) {
- logger.warn("No pubmed identifier defined for publication: title: " + publication.getTitle());
+ logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, publication.getId(), "BioPax", mapName), "No pubmed identifier defined for publication: title: " + publication.getTitle());
}
result.addPublication(publication);
} else if ("bp:openControlledVocabulary".equalsIgnoreCase(node.getNodeName())) {
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/CyclicEdgeException.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/CyclicEdgeException.java
index 1d2a3e863e19170b2b0146d0948d721012b21cdd..dd3c892074010c8bfba9a58ea35e166f571a4019 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/CyclicEdgeException.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/CyclicEdgeException.java
@@ -1,6 +1,8 @@
package lcsb.mapviewer.wikipathway.XML;
import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.model.LogMarker;
+import lcsb.mapviewer.wikipathway.model.Edge;
/**
* Exception that shold be thrown when edges create a cycle. Consider an example
@@ -25,14 +27,24 @@ public class CyclicEdgeException extends ConverterException {
*/
private static final long serialVersionUID = 1L;
+ private Edge edge;
+
/**
* Default constructor with message passed in the argument.
*
* @param string
* message of this exception
*/
- public CyclicEdgeException(String string) {
+ public CyclicEdgeException(String string, Edge edge) {
super(string);
+ this.edge = edge;
+ }
+
+ public LogMarker getLogMarker() {
+ if (edge != null) {
+ return edge.getLogMarker();
+ }
+ return null;
}
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/DataNodeParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/DataNodeParser.java
index 445bf4de09cc6690e7d0baff393d86ae49c8c56b..83c86d3a206194ee4c094f044bca365b6c90ed1c 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/DataNodeParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/DataNodeParser.java
@@ -24,21 +24,26 @@ import lcsb.mapviewer.wikipathway.model.*;
public class DataNodeParser extends GraphicalPathwayElementParser<DataNode> {
/**
- * Default claass logger.
+ * Default class logger.
*/
private final Logger logger = LogManager.getLogger(DataNodeParser.class);
/**
* PArser used to process references.
*/
- private final ReferenceParser referenceParser = new ReferenceParser();
+ private final ReferenceParser referenceParser;
+
+ public DataNodeParser(String mapName) {
+ super(mapName);
+ referenceParser = new ReferenceParser(mapName);
+ }
@Override
public DataNode parse(Element eElement) throws UnknownTypeException {
if (!eElement.getNodeName().equals("DataNode")) {
throw new InvalidArgumentException(ShapeParser.class.getSimpleName() + " can parse only DataNode xml nodes");
}
- DataNode node = new DataNode(eElement.getAttribute("GraphId"));
+ DataNode node = new DataNode(eElement.getAttribute("GraphId"), getMapName());
for (Pair<String, String> entry : getAttributes(eElement)) {
switch (entry.getLeft()) {
@@ -184,12 +189,12 @@ public class DataNodeParser extends GraphicalPathwayElementParser<DataNode> {
case ("org.pathvisio.model.GenMAPP-Xref"):
// skip it when it's empty
if (!value.isEmpty()) {
- logger.warn(shape.getWarningPrefix() + "Unknown attribute of node. Key: " + key + "; value: " + value);
+ logger.warn(shape.getLogMarker() + "Unknown attribute of node. Key: " + key + "; value: " + value);
break;
}
break;
default:
- logger.warn(shape.getWarningPrefix() + "Unknown attribute of node. Key: " + key + "; value: " + value);
+ logger.warn(shape.getLogMarker() + "Unknown attribute of node. Key: " + key + "; value: " + value);
break;
}
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeLineParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeLineParser.java
index 7a534a22728935567f347401b3096394d0dc2c6c..a3553184d0fcb1998a8585156578a2aab225755e 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeLineParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeLineParser.java
@@ -14,7 +14,7 @@ import lcsb.mapviewer.wikipathway.model.Edge;
/**
* Parser class that creates {@link Edge} objects from Xml {@link Element node}.
- * However the xml node is not typica edge node , but line node.
+ * However the xml node is not typical edge node , but line node.
*
* @author Piotr Gawron
*
@@ -24,12 +24,17 @@ public class EdgeLineParser extends ElementGpmlParser<Edge> {
/**
* Default class logger.
*/
- private final Logger logger = LogManager.getLogger(EdgeLineParser.class);
+ private final Logger logger = LogManager.getLogger();
/**
* Parser used to parse typical {@link Edge} xml nodes.
*/
- private final EdgeParser edgeParser = new EdgeParser();
+ private final EdgeParser edgeParser;
+
+ public EdgeLineParser(String mapName) {
+ super(mapName);
+ this.edgeParser = new EdgeParser(mapName);
+ }
/**
* Creates {@link Edge} from xml line node.
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeParser.java
index fe9739662e138fa4532dba0e273eff324e196ca1..eec580d9c26ce5bf339d9b8be006200a9536259c 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeParser.java
@@ -13,6 +13,7 @@ import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.model.LogMarker;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.wikipathway.model.*;
@@ -29,13 +30,13 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
*/
private static final int INITIAL_ID_VALUE = 10000;
/**
- * This is default lenght of lines when lines are drawn in
- * {@link GpmlLineConnectorType#ELBOW} mode, but without specifing coordinates.
+ * This is default length of lines when lines are drawn in
+ * {@link GpmlLineConnectorType#ELBOW} mode, but without specifying coordinates.
*/
private static final double DEFAULT_DISTNACE = 20;
/**
* Counter used for generating identifiers if identifiers aren't provided by the
- * gpml model.
+ * GPML model.
*/
private static int idCounter = INITIAL_ID_VALUE;
/**
@@ -46,11 +47,11 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
* Parser used for extracting {@link lcsb.mapviewer.model.map.MiriamData
* references} from GPML model.
*/
- private ReferenceParser referenceParser = new ReferenceParser();
+ private ReferenceParser referenceParser;
/**
* Parser used for extracting {@link PointData points} from GPML xml nodes.
*/
- private PointDataParser pointParser = new PointDataParser();
+ private PointDataParser pointParser;
/**
* This function get new id for interactions that don't have id.
@@ -62,6 +63,12 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
return "id" + idCounter;
}
+ public EdgeParser(String mapName) {
+ super(mapName);
+ pointParser = new PointDataParser(mapName);
+ referenceParser = new ReferenceParser(mapName);
+ }
+
/**
* Creates {@link Edge} from xml node.
*
@@ -76,7 +83,7 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
if (graphId == null || graphId.equals("")) {
graphId = getNewId();
}
- Edge edge = new Edge(graphId);
+ Edge edge = new Edge(graphId, getMapName());
for (Pair<String, String> entry : getAttributes(eElement)) {
switch (entry.getLeft()) {
@@ -120,13 +127,13 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
parseAttribute(element, edge);
break;
default:
- logger.warn(edge.getWarningPrefix() + "Unknown edge node: " + node.getNodeName() + ".");
+ logger.warn(edge.getLogMarker(), "Unknown edge node: " + node.getNodeName() + ".");
break;
}
}
}
if (!graphicsParsed) {
- throw new ConverterException(edge.getWarningPrefix() + "No Graphics information found for edge.");
+ throw new ConverterException(edge.getLogMarker() + "No Graphics information found for edge.");
}
return edge;
}
@@ -191,7 +198,7 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
} else if ("Anchor".equalsIgnoreCase(node.getNodeName())) {
anchors.add((Element) node);
} else {
- logger.warn(edge.getWarningPrefix() + "Unknown graphics edge node: " + node.getNodeName() + ".");
+ logger.warn(edge.getLogMarker(), "Unknown graphics edge node: " + node.getNodeName() + ".");
}
}
}
@@ -216,17 +223,17 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
}
edge.setReversibleReaction(pointDataList.get(0).getType() == GpmlInteractionType.ARROW);
- edge.getLine().setPoints(getPoints(edge.getWarningPrefix(), pointDataList, connectorType));
+ edge.getLine().setPoints(getPoints(edge.getLogMarker(), pointDataList, connectorType));
if (edge.getLine().getPoints().size() < 2) {
throw new ConverterException(
- edge.getWarningPrefix() + "Contains too less points. At least two points are required in a line.");
+ edge.getLogMarker() + "Contains too less points. At least two points are required in a line.");
}
double lineLength = 0;
for (Line2D line : edge.getLine().getLines()) {
lineLength += line.getP1().distance(line.getP2());
}
if (lineLength <= Configuration.EPSILON) {
- throw new ConverterException(edge.getWarningPrefix() + "Line cannot have 0 length.");
+ throw new ConverterException(edge.getLogMarker() + "Line cannot have 0 length.");
}
// anchors
@@ -268,7 +275,7 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
* @throws UnknownTypeException
* throw when connector type is invalid
*/
- List<Point2D> getPoints(String warningPrefix, List<PointData> pointDataList,
+ List<Point2D> getPoints(LogMarker warningPrefix, List<PointData> pointDataList,
GpmlLineConnectorType connectorType)
throws InvalidElbowConnectorException, UnknownTypeException {
List<Point2D> result = new ArrayList<>();
@@ -371,7 +378,7 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
// if line is curved then inform user that we don't support it and create
// a default one
case CURVED:
- logger.warn(warningPrefix + "Curved connections are not supported.");
+ logger.warn(warningPrefix, "Curved connections are not supported.");
for (PointData pointData : pointDataList) {
result.add(pointData.toPoint());
}
@@ -397,7 +404,7 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
* @throws InvalidElbowConnectorException
* thrown when output cannot be computed because input data is invalid
*/
- private int computeNumberOfPerpendicularSegments(String warningPrefix, PointData start, PointData end)
+ private int computeNumberOfPerpendicularSegments(LogMarker warningPrefix, PointData start, PointData end)
throws InvalidElbowConnectorException {
Point2D fromPoint = start.toPoint();
Point2D toPoint = end.toPoint();
@@ -548,7 +555,7 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
* @return new {@link Edge} object with unique identifier
*/
public Edge createEmpty() {
- return new Edge(getNewId());
+ return new Edge(getNewId(), getMapName());
}
/**
@@ -564,13 +571,13 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
String value = eTmp.getAttribute("Value");
switch (key) {
case ("org.pathvisio.core.ds"):
- // skip for now (no idea what des it mean)
+ // skip for now (no idea what does it mean)
break;
case ("org.pathvisio.core.id"):
- // skip for now (no idea what des it mean)
+ // skip for now (no idea what does it mean)
break;
default:
- logger.warn(edge.getWarningPrefix() + "Unknown attribute of node. Key: " + key + "; value: " + value);
+ logger.warn(edge.getLogMarker(), "Unknown attribute of node. Key: " + key + "; value: " + value);
break;
}
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ElementGpmlParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ElementGpmlParser.java
index d1e6398aaa09d738eebf0b4742a124551c424073..5f98517be9979f31628a3861bc93e579a87afa2b 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ElementGpmlParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ElementGpmlParser.java
@@ -1,8 +1,7 @@
package lcsb.mapviewer.wikipathway.XML;
-import java.awt.*;
+import java.awt.Color;
import java.util.*;
-import java.util.List;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -18,7 +17,7 @@ import lcsb.mapviewer.converter.ConverterException;
* @author Piotr Gawron
*
* @param <T>
- * class for which this parser aplies
+ * class for which this parser applies
*/
public abstract class ElementGpmlParser<T> {
@@ -32,6 +31,12 @@ public abstract class ElementGpmlParser<T> {
@SuppressWarnings("unused")
private final Logger logger = LogManager.getLogger(ElementGpmlParser.class);
+ private String mapName;
+
+ public ElementGpmlParser(String mapName) {
+ this.mapName = mapName;
+ }
+
/**
* Creates object from xml node given in parameter.
*
@@ -44,7 +49,7 @@ public abstract class ElementGpmlParser<T> {
public abstract T parse(Element node) throws ConverterException;
/**
- * Converts object into xml string (in gpml format).
+ * Converts object into xml string (in GPML format).
*
* @param object
* object to transform
@@ -55,7 +60,7 @@ public abstract class ElementGpmlParser<T> {
public abstract String toXml(T object) throws ConverterException;
/**
- * Converts list of objects into xml string (in gpml format) representing this
+ * Converts list of objects into xml string (in GPML format) representing this
* list.
*
* @param list
@@ -131,4 +136,7 @@ public abstract class ElementGpmlParser<T> {
return result;
}
+ public String getMapName() {
+ return mapName;
+ }
}
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 8b14d6f2a5bc6c30c5819c56936cb7d9b795a7cb..917c4bb9252a7ab5244686e02cce00da12d0e6c9 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GPMLToModel.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GPMLToModel.java
@@ -15,11 +15,11 @@ import lcsb.mapviewer.wikipathway.model.Graph;
public class GPMLToModel {
/**
- * This function creates model from gpml input stream.
+ * This function creates model from GPML input stream.
*
* @param stream
- * input stream that contains gpml data
- * @return {@link Model} created from gpml file
+ * input stream that contains GPML data
+ * @return {@link Model} created from GPML file
* @throws IOException
* thrown when there is a problem with input file
* @throws ConverterException
@@ -27,7 +27,7 @@ public class GPMLToModel {
*/
public Model getModel(InputStream stream) throws IOException, ConverterException {
Graph graph = new GpmlParser().createGraph(stream);
- Model model = new ModelContructor().getModel(graph);
+ Model model = new ModelContructor(graph.getMapName()).getModel(graph);
return model;
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GpmlParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GpmlParser.java
index 43be3375771c9693b150f15205de2b7df1f839ed..a089df90776080c771fe617d3d12e215a8a848d2 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GpmlParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GpmlParser.java
@@ -11,6 +11,7 @@ import org.apache.logging.log4j.Logger;
import org.w3c.dom.*;
import org.xml.sax.SAXException;
+import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.ConverterException;
@@ -30,44 +31,44 @@ public class GpmlParser {
/**
* Default class logger.
*/
- private Logger logger = LogManager.getLogger(GpmlParser.class);
+ private Logger logger = LogManager.getLogger();
/**
* Parser used for creating {@link Shape shapes}.
*/
- private ShapeParser shapeParser = new ShapeParser();
+ private ShapeParser shapeParser;
/**
* Parser used for creating {@link lcsb.mapviewer.wikipathway.model.DataNode
* data nodes}.
*/
- private DataNodeParser dataNodeParser = new DataNodeParser();
+ private DataNodeParser dataNodeParser;
/**
* Parser used for creating {@link Label labels}.
*/
- private LabelParser labelParser = new LabelParser();
+ private LabelParser labelParser;
/**
* Parser used for creating {@link Edge edges}.
*/
- private EdgeParser edgeParser = new EdgeParser();
+ private EdgeParser edgeParser;
/**
* Parser used for creating {@link lcsb.mapviewer.wikipathway.model.State
* states}.
*/
- private StateParser stateParser = new StateParser();
+ private StateParser stateParser;
/**
* Parser used for creating {@link Edge edges} from line xml nodes.
*/
- private EdgeLineParser edgeLineParser = new EdgeLineParser();
+ private EdgeLineParser edgeLineParser;
/**
* Parser used for creating {@link PointData points} from line xml nodes.
*/
- private PointDataParser pointParser = new PointDataParser();
+ private PointDataParser pointParser;
/**
* This function returns parent interaction for edge that has anchor at one end.
@@ -98,7 +99,7 @@ public class GpmlParser {
edge = graph.getEdgeByAnchor(anchor);
// when we have cycle then return null
if (processedEdges.contains(edge)) {
- throw new CyclicEdgeException(edge.getWarningPrefix() + " edge is a part of invalid, cyclic edge");
+ throw new CyclicEdgeException("Edge is a part of invalid, cyclic edge", edge);
}
processedEdges.add(edge);
}
@@ -121,61 +122,62 @@ public class GpmlParser {
graph.setBoardHeight(Math.ceil(Double.parseDouble(boardHeight)));
}
- /**
- * This function adds groups to graph and nest them.
- *
- * @param groups
- * xml nodes
- * @param graph
- * object where data is stored
- * @throws UnknownAttributeValueException
- * thrown when there is a problem with xml attributes
- */
- protected void addGroups(List<Node> groups, Graph graph) throws UnknownAttributeValueException {
- // Adding Groups to graph
- for (Node nNode : groups) {
- if (nNode.getNodeType() == Node.ELEMENT_NODE) {
- Element eElement = (Element) nNode;
- String graphId = eElement.getAttribute("GraphId");
- String groupId = eElement.getAttribute("GroupId");
- if (graphId.equals("") || graphId == null) {
- graphId = groupId;
- }
- String style = eElement.getAttribute("Style");
- if ("".equals(style)) {
- style = null;
- }
- if (style != null &&
- !"Complex".equalsIgnoreCase(style) &&
- !"Group".equalsIgnoreCase(style)) {
- throw new UnknownAttributeValueException(
- "Unknown value of \"style\" attribute for group node: " + style + ". Only null, Complex, Group are supported.");
- }
- Group group = new Group(graphId, groupId);
- group.setStyle(style);
-
- String zIndex = eElement.getAttribute("ZOrder");
- if (zIndex!=null && !zIndex.isEmpty()) {
- group.setzOrder(Integer.valueOf(zIndex));
- }
- graph.addGroup(group);
- }
- }
- // Handling nested groups
- Group gr1, gr2;
- for (Node nNode : groups) {
- if (nNode.getNodeType() == Node.ELEMENT_NODE) {
- Element eElement = (Element) nNode;
- String groupRef = eElement.getAttribute("GroupRef");
- String groupId = eElement.getAttribute("GroupId");
- if (groupRef != null && !groupRef.equals("")) {
- gr1 = graph.getGroupByGroupId(groupRef);
- gr2 = graph.getGroupByGroupId(groupId);
- gr1.addNode(gr2);
- }
- }
- }
- }
+ /**
+ * This function adds groups to graph and nest them.
+ *
+ * @param groups
+ * xml nodes
+ * @param graph
+ * object where data is stored
+ * @throws UnknownAttributeValueException
+ * thrown when there is a problem with xml attributes
+ */
+ protected void addGroups(List<Node> groups, Graph graph) throws UnknownAttributeValueException {
+ // Adding Groups to graph
+ for (Node nNode : groups) {
+ if (nNode.getNodeType() == Node.ELEMENT_NODE) {
+ Element eElement = (Element) nNode;
+ String graphId = eElement.getAttribute("GraphId");
+ String groupId = eElement.getAttribute("GroupId");
+ if (graphId.equals("") || graphId == null) {
+ graphId = groupId;
+ }
+ String style = eElement.getAttribute("Style");
+ if ("".equals(style)) {
+ style = null;
+ }
+ if (style != null &&
+ !"Complex".equalsIgnoreCase(style) &&
+ !"Group".equalsIgnoreCase(style)) {
+ throw new UnknownAttributeValueException(
+ "Unknown value of \"style\" attribute for group node: " + style
+ + ". Only null, Complex, Group are supported.");
+ }
+ Group group = new Group(graphId, groupId, graph.getMapName());
+ group.setStyle(style);
+
+ String zIndex = eElement.getAttribute("ZOrder");
+ if (zIndex != null && !zIndex.isEmpty()) {
+ group.setzOrder(Integer.valueOf(zIndex));
+ }
+ graph.addGroup(group);
+ }
+ }
+ // Handling nested groups
+ Group gr1, gr2;
+ for (Node nNode : groups) {
+ if (nNode.getNodeType() == Node.ELEMENT_NODE) {
+ Element eElement = (Element) nNode;
+ String groupRef = eElement.getAttribute("GroupRef");
+ String groupId = eElement.getAttribute("GroupId");
+ if (groupRef != null && !groupRef.equals("")) {
+ gr1 = graph.getGroupByGroupId(groupRef);
+ gr2 = graph.getGroupByGroupId(groupId);
+ gr1.addNode(gr2);
+ }
+ }
+ }
+ }
/**
* This function adds edges to graph. It ignores edges that have no connection
@@ -184,7 +186,7 @@ public class GpmlParser {
* @param nodes
* xml nodes
* @param graph
- * object where data is sotred
+ * object where data is sorted
*/
private void prepareEdges(List<Node> nodes, Graph graph) {
for (Node nNode : nodes) {
@@ -211,7 +213,7 @@ public class GpmlParser {
shape.setTreatAsNode(true);
}
if (edge.getStart() == null || edge.getEnd() == null) {
- logger.warn(edge.getWarningPrefix() + "Interaction is not connected");
+ logger.warn(edge.getLogMarker(), "Interaction is not connected");
} else {
graph.addEdge(edge);
@@ -244,11 +246,11 @@ public class GpmlParser {
InteractionMapping mapping = InteractionMapping.getInteractionMapping(edge.getType(), edge.getLine().getType());
if (mapping != null) {
if (mapping.isInteractionWarning()) {
- logger.warn(edge.getWarningPrefix() + "Invalid interaction type.");
+ logger.warn(edge.getLogMarker(), "Invalid interaction type.");
}
} else {
throw new InvalidXmlSchemaException(
- edge.getWarningPrefix() + "Unknown interaction type: " + edge.getType() + " and line type: "
+ edge.getLogMarker() + "Unknown interaction type: " + edge.getType() + " and line type: "
+ edge.getLine().getType());
}
}
@@ -256,7 +258,7 @@ public class GpmlParser {
for (Edge edge : graph.getEdges()) {
try {
if (graph.getEdgeByAnchor(edge.getEnd()) != null && graph.getEdgeByAnchor(edge.getStart()) != null) {
- logger.warn(edge.getWarningPrefix() + "Interaction can not connect two anchors.");
+ logger.warn(edge.getLogMarker(), "Interaction can not connect two anchors.");
} else if (graph.getEdgeByAnchor(edge.getEnd()) != null && graph.getNodeByGraphId(edge.getStart()) != null) {
Interaction tmp = getParentInteraction(graph, edge);
if (tmp != null) {
@@ -264,7 +266,7 @@ public class GpmlParser {
edge.getLine().getType());
if (mapping != null) {
if (mapping.isInputWarning()) {
- logger.warn(edge.getWarningPrefix() + "Invalid interaction type as an input to reaction.");
+ logger.warn(edge.getLogMarker(), "Invalid interaction type as an input to reaction.");
}
if (Modifier.class.isAssignableFrom(mapping.getModelInputReactionNodeType())) {
tmp.addModifier(edge);
@@ -281,7 +283,7 @@ public class GpmlParser {
throw new InvalidXmlSchemaException("Unknown interaction type: " + edge.getType());
}
} else {
- logger.warn(edge.getWarningPrefix() + "Interaction is disconnected.");
+ logger.warn(edge.getLogMarker(), "Interaction is disconnected.");
}
} else if (graph.getEdgeByAnchor(edge.getStart()) != null && graph.getNodeByGraphId(edge.getEnd()) != null) {
Interaction tmp = getParentInteraction(graph, edge);
@@ -290,7 +292,7 @@ public class GpmlParser {
edge.getLine().getType());
if (mapping != null) {
if (mapping.isOutputWarning()) {
- logger.warn(edge.getWarningPrefix() + "Invalid interaction type \"" + edge.getType()
+ logger.warn(edge.getLogMarker(), "Invalid interaction type \"" + edge.getType()
+ "\" as an output from reaction.");
}
if (Modifier.class.isAssignableFrom(mapping.getModelOutputReactionNodeType())) {
@@ -308,13 +310,13 @@ public class GpmlParser {
throw new InvalidXmlSchemaException("Unknown interaction type: " + edge.getType());
}
} else {
- logger.warn(edge.getWarningPrefix() + "Interaction is disconnected.");
+ logger.warn(edge.getLogMarker(), "Interaction is disconnected.");
}
} else if (graph.getNodeByGraphId(edge.getEnd()) == null || graph.getNodeByGraphId(edge.getStart()) == null) {
- logger.warn(edge.getWarningPrefix() + "Interaction edge is invalid (one end is not connected).");
+ logger.warn(edge.getLogMarker(), "Interaction edge is invalid (one end is not connected).");
}
} catch (CyclicEdgeException e) {
- logger.warn(e, e);
+ logger.warn(e.getLogMarker(), e.getMessage(), e);
}
}
}
@@ -372,6 +374,15 @@ public class GpmlParser {
Node biopax = null;
Graph graph = new Graph();
+ graph.setMapName(XmlParser.getNodeAttr("Name", root.item(0)));
+ edgeLineParser = new EdgeLineParser(graph.getMapName());
+ edgeParser = new EdgeParser(graph.getMapName());
+ dataNodeParser = new DataNodeParser(graph.getMapName());
+ labelParser = new LabelParser(graph.getMapName());
+ shapeParser = new ShapeParser(graph.getMapName());
+ stateParser = new StateParser(graph.getMapName());
+ pointParser = new PointDataParser(graph.getMapName());
+
for (int x = 0; x < nodes.getLength(); x++) {
Node node = nodes.item(x);
if (node.getNodeType() == Node.ELEMENT_NODE) {
@@ -432,7 +443,7 @@ public class GpmlParser {
addInteractions(graph);
if (biopax != null) {
- graph.setBiopaxData(new BiopaxParser().parse(biopax));
+ graph.setBiopaxData(new BiopaxParser(graph.getMapName()).parse(biopax));
}
Map<String, String> attributesMap = new HashMap<String, String>();
for (Element attribute : attributes) {
@@ -498,7 +509,7 @@ public class GpmlParser {
}
List<Edge> howExtend = extendable.get(anchor);
if (howExtend == null) {
- logger.warn(edge.getWarningPrefix() + " Should be connected with another element, but nothing found.");
+ logger.warn(edge.getLogMarker(), " Should be connected with another element, but nothing found.");
if (edge.getStart().equals(anchor)) {
edge.setStart(null);
} else if (edge.getEnd().equals(anchor)) {
@@ -514,7 +525,7 @@ public class GpmlParser {
toRemove.add(edge);
toRemove.add(howExtend.get(0));
- logger.warn(exception, exception);
+ logger.warn(edge.getLogMarker(), exception.getMessage(), exception);
}
}
}
@@ -549,8 +560,7 @@ public class GpmlParser {
mapping = MergeMapping.getMergeMappingByInteractions(edge1.getType(), false, edge2.getType(), true);
}
if (mapping == null) {
- String message = edge1.getWarningPrefix() + edge2.getWarningPrefix() + "Don't know how to merge interactions";
- throw new UnknownMergingMethodException(message);
+ throw new UnknownMergingMethodException("Don't know how to merge interactions");
}
Edge first;
if (mapping.isReversed1()) {
@@ -567,10 +577,9 @@ public class GpmlParser {
first.extend(second);
if (!first.getLine().getType().equals(second.getLine().getType())) {
- logger.warn(
- first.getWarningPrefix() + second.getWarningPrefix() + " merging edges with different line types: "
- + first.getLine().getType() + ", "
- + second.getLine().getType());
+ logger.warn(first.getLogMarker(), "Merging edges with different line types: "
+ + first.getLine().getType() + ", "
+ + second.getLine().getType());
}
first.setType(mapping.getResultType());
if (mapping.isResultReversed()) {
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GraphicalPathwayElementParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GraphicalPathwayElementParser.java
index bfb0819c05ac56df547e47e9bbacfec43d82eb91..3d623ba886a4138888e42ae0a18af4b004331e90 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GraphicalPathwayElementParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GraphicalPathwayElementParser.java
@@ -22,7 +22,11 @@ public abstract class GraphicalPathwayElementParser<T extends GraphicalPathwayEl
/**
* Default class logger.
*/
- private final Logger logger = LogManager.getLogger(GraphicalPathwayElementParser.class);
+ private final Logger logger = LogManager.getLogger();
+
+ public GraphicalPathwayElementParser(String mapName) {
+ super(mapName);
+ }
/**
* Parse font attributes that might appear.
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/LabelParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/LabelParser.java
index 383d5a3718c70f9cc009c5b7fbcc0b8425d37940..cf8be530028c2909f6472118f453b50a843062be 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/LabelParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/LabelParser.java
@@ -29,14 +29,19 @@ public class LabelParser extends GraphicalPathwayElementParser<Label> {
*/
private final Logger logger = LogManager.getLogger();
- private ReferenceParser referenceParser = new ReferenceParser();
+ private ReferenceParser referenceParser;
+
+ public LabelParser(String mapName) {
+ super(mapName);
+ referenceParser = new ReferenceParser(mapName);
+ }
@Override
public Label parse(Element eElement) throws UnknownTypeException {
if (!eElement.getNodeName().equals("Label")) {
throw new InvalidArgumentException(ShapeParser.class.getSimpleName() + " can parse only Label xml nodes");
}
- Label label = new Label(eElement.getAttribute("GraphId"));
+ Label label = new Label(eElement.getAttribute("GraphId"), getMapName());
for (Pair<String, String> entry : getAttributes(eElement)) {
switch (entry.getLeft()) {
@@ -176,12 +181,12 @@ public class LabelParser extends GraphicalPathwayElementParser<Label> {
case ("org.pathvisio.model.GenMAPP-Xref"):
// skip it when it's empty
if (!value.isEmpty()) {
- logger.warn(shape.getWarningPrefix() + "Unknown attribute of node. Key: " + key + "; value: " + value);
+ logger.warn(shape.getLogMarker() + "Unknown attribute of node. Key: " + key + "; value: " + value);
break;
}
break;
default:
- logger.warn(shape.getWarningPrefix() + "Unknown attribute of node. Key:" + key + "; value: " + value);
+ logger.warn(shape.getLogMarker() + "Unknown attribute of node. Key:" + key + "; value: " + value);
break;
}
}
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 b464424687cb37690b025e0cce8339ff67ee7836..2e05f6fa89e7a4fec44b43e00f4f293aea0c83ea 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
@@ -10,13 +10,16 @@ import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.*;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.PolylineDataFactory;
import lcsb.mapviewer.converter.model.celldesigner.reaction.ReactionLineData;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierTypeUtils;
+import lcsb.mapviewer.model.LogMarker;
+import lcsb.mapviewer.model.ProjectLogEntryType;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.Drawable;
import lcsb.mapviewer.model.map.MiriamData;
@@ -77,11 +80,16 @@ public class ModelContructor {
/**
* Default class logger.
*/
- private Logger logger = LogManager.getLogger(ModelContructor.class);
+ private Logger logger = LogManager.getLogger();
+
/**
* Parser used for extracting {@link MiriamData references} from GPML model.
*/
- private BiopaxFactory biopaxFactory = new BiopaxFactory();
+ private BiopaxFactory biopaxFactory;
+
+ public ModelContructor(String mapName) {
+ biopaxFactory = new BiopaxFactory(mapName);
+ }
/**
* This function creates Species from DataNode.
@@ -242,7 +250,7 @@ public class ModelContructor {
((Gene) species).addModificationSite((ModificationSite) mr);
} else {
logger.warn(
- state.getWarningPrefix() + "state for " + species.getClass().getSimpleName() + " is not supported.");
+ state.getLogMarker(), "state for " + species.getClass().getSimpleName() + " is not supported.");
}
if (mr != null) {
mr.setIdModificationResidue(state.getGraphId());
@@ -259,10 +267,10 @@ public class ModelContructor {
if (protein.getStructuralState() == null) {
protein.setStructuralState(createStructuralState(state, protein));
} else {
- logger.warn(state.getWarningPrefix() + " tries to override another state: " + protein.getStructuralState());
+ logger.warn(state.getLogMarker(), " tries to override another state: " + protein.getStructuralState());
}
} else {
- logger.warn(state.getWarningPrefix() + "structural state for " + species.getClass().getSimpleName()
+ logger.warn(state.getLogMarker(), "structural state for " + species.getClass().getSimpleName()
+ " is not supported.");
}
}
@@ -321,7 +329,7 @@ public class ModelContructor {
public LayerRect createRectangle(Shape shape) {
LayerRect rect = new LayerRect();
Rectangle2D rec;
- if (shouldRotate90degrees(shape.getRotation())) {
+ if (shouldRotate90degrees(shape)) {
rec = rotate90degrees(shape.getRectangle());
} else {
rec = shape.getRectangle();
@@ -339,7 +347,15 @@ public class ModelContructor {
rectangle.getCenterY() - rectangle.getWidth() / 2, rectangle.getHeight(), rectangle.getWidth());
}
+ boolean shouldRotate90degrees(Shape shape) {
+ return shouldRotate90degrees(shape.getRotation(), shape);
+ }
+
boolean shouldRotate90degrees(Double rot) {
+ return shouldRotate90degrees(rot, null);
+ }
+
+ boolean shouldRotate90degrees(Double rot, Shape shape) {
if (rot == null) {
return false;
}
@@ -352,12 +368,20 @@ public class ModelContructor {
}
if (Math.abs(rotation) < Math.PI / 4) {
if (Math.abs(rotation) > Configuration.EPSILON) {
- logger.warn("Rotation of objects is not supported. Rotation=" + rot);
+ LogMarker marker = null;
+ if (shape != null) {
+ marker = shape.getLogMarker();
+ }
+ logger.warn(marker, "Rotation of objects is not supported. Rotation=" + rot);
}
return false;
}
if ((Math.PI / 2 - Math.abs(rotation)) > Configuration.EPSILON) {
- logger.warn("Rotation of objects is not supported. Rotation=" + rot);
+ LogMarker marker = null;
+ if (shape != null) {
+ marker = shape.getLogMarker();
+ }
+ logger.warn(marker, "Rotation of objects is not supported. Rotation=" + rot);
}
return true;
}
@@ -483,7 +507,7 @@ public class ModelContructor {
* @return {@link Unknown} object created from input {@link Label}
*/
private Species createSpecies(Label label) {
- logger.warn(label.getWarningPrefix() + " Label cannot be part of reaction. Tranforming to Unknown");
+ logger.warn(label.getLogMarker(), " Label cannot be part of reaction. Tranforming to Unknown");
Species res = new Unknown(label.getGraphId());
res.addMiriamData(label.getReferences());
@@ -504,7 +528,7 @@ public class ModelContructor {
* @return {@link Unknown} object created from input {@link Label}
*/
private Species createSpecies(Shape shape) {
- logger.warn(shape.getWarningPrefix() + " Shape can not be part of reaction. Tranforming to Unknown");
+ logger.warn(shape.getLogMarker(), " Shape can not be part of reaction. Tranforming to Unknown");
Species res = new Unknown(shape.getGraphId());
StringBuilder notes = new StringBuilder();
@@ -550,7 +574,7 @@ public class ModelContructor {
} else if (graph.getShapeByGraphId(pe.getGraphId()) != null) {
Shape shape = graph.getShapeByGraphId(pe.getGraphId());
if (INALID_COMPLEX_SHAPE_CHILDREN.contains(shape.getShape())) {
- logger.warn(shape.getWarningPrefix() + shape.getShape() + " cannot be part of a complex. Skipping.");
+ logger.warn(shape.getLogMarker(), shape.getShape() + " cannot be part of a complex. Skipping.");
} else {
throw new UnknownChildClassException("Unknown class type with id \"" + pe.getGraphId() + "\": "
+ shape.getShape() + ". Group id: " + group.getGraphId());
@@ -653,7 +677,7 @@ public class ModelContructor {
reaction.addNode(splitOperator);
} else {
PolylineData operatorLine = lines.get(SplitOperator.class);
- for (int i = 0; i < operatorLine.getPoints().size()-1; i++) {
+ for (int i = 0; i < operatorLine.getPoints().size() - 1; i++) {
productLine.addPoint(i, operatorLine.getPoints().get(i));
}
product.setLine(PolylineDataFactory.removeCollinearPoints(productLine));
@@ -664,12 +688,14 @@ public class ModelContructor {
reaction.addModifier(mod);
}
if (reaction instanceof TwoReactantReactionInterface && reaction.getReactants().size() < 2) {
- logger.warn("Reaction should contain at least 2 reactants. GraphId: " + interaction.getGraphId());
+ logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, reaction),
+ "Reaction should contain at least 2 reactants. GraphId: " + interaction.getGraphId());
reaction = new UnknownTransitionReaction(reaction);
}
if (reaction instanceof ReducedNotation && ((reaction.getReactants().size() > 1)
|| reaction.getProducts().size() > 1 || reaction.getModifiers().size() > 0)) {
- logger.warn("Reaction should contain only one reactant and one product. GraphId: " + interaction.getGraphId());
+ logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, reaction),
+ "Reaction should contain only one reactant and one product. GraphId: " + interaction.getGraphId());
reaction = new UnknownTransitionReaction(reaction);
}
ReactionLineData rld = ReactionLineData.getByReactionType(reaction.getClass());
@@ -891,7 +917,7 @@ public class ModelContructor {
notes = StringEscapeUtils.unescapeHtml4(notes);
}
model.setNotes(notes);
- model.addMiriamData(new BiopaxFactory().getMiriamData(graph.getBiopaxData(), graph.getBiopaxReferences()));
+ model.addMiriamData(biopaxFactory.getMiriamData(graph.getBiopaxData(), graph.getBiopaxReferences()));
data.layer.addLayerLines(createLines(graph));
@@ -999,15 +1025,16 @@ public class ModelContructor {
}
List<Element> toRemove = new ArrayList<>();
ElementUtils eu = new ElementUtils();
- for (Element alias : model.getElements()) {
- if (alias instanceof Complex) {
- Complex cAlias = (Complex) alias;
- if (cAlias.getSize() <= EPSILON && cAlias.getAllChildren().size() == 0) {
- if (aliasesInReaction.contains(alias)) {
- logger.warn(eu.getElementTag(alias) + "Empty element is invalid, but it's a part of reaction.");
+ for (Element element : model.getElements()) {
+ if (element instanceof Complex) {
+ Complex complex = (Complex) element;
+ if (complex.getSize() <= EPSILON && complex.getAllChildren().size() == 0) {
+ if (aliasesInReaction.contains(element)) {
+ logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, element),
+ "Empty element is invalid, but it's a part of reaction.");
} else {
- toRemove.add(alias);
- logger.warn(eu.getElementTag(alias) + "Empty element is invalid");
+ toRemove.add(element);
+ logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, element), "Empty element is invalid");
}
}
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java
index ffc86624258d3625c019e9c343faf3f08215cce0..859d56b2ec650a2c42ff26508bd8309f39fef8ef 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java
@@ -54,22 +54,26 @@ public class ModelToGPML {
private final Logger logger = LogManager.getLogger(ModelToGPML.class);
/**
* Counter used for generating identifiers if identifiers aren't provided by the
- * gpml model.
+ * GPML model.
*/
private int idCounter = INITIAL_ID_VALUE;
/**
* Parser used to convert from/to xml {@link MiriamData} annotations.
*/
- private ReferenceParser referenceParser = new ReferenceParser();
+ private ReferenceParser referenceParser;
/**
- * Parser used to convert from/to xml (in biopax format) {@link MiriamData}
+ * Parser used to convert from/to xml (in BioPAX format) {@link MiriamData}
* annotations.
*/
- private BiopaxParser biopaxParser = new BiopaxParser();
+ private BiopaxParser biopaxParser;
private ColorParser colorParser = new ColorParser();
+ public ModelToGPML(String mapName) {
+ referenceParser = new ReferenceParser(mapName);
+ }
+
/**
* Returns new unique identifier for the model.
*
@@ -587,6 +591,8 @@ public class ModelToGPML {
*/
public String getGPML(Model model) throws ConverterException {
+ biopaxParser = new BiopaxParser(model.getName());
+
StringBuilder gpml = new StringBuilder("");
gpml.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
gpml.append("<Pathway xmlns=\"http://pathvisio.org/GPML/2013a\" Name=\"Generated\">\n");
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/PointDataParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/PointDataParser.java
index 614829c67033e05d2441c2da4b1ef2ff402baf12..784c707898a596636f9cff136c3b612326879eca 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/PointDataParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/PointDataParser.java
@@ -23,11 +23,15 @@ public class PointDataParser extends ElementGpmlParser<PointData> {
/**
* Default class logger.
*/
- private final Logger logger = LogManager.getLogger(PointDataParser.class);
+ private final Logger logger = LogManager.getLogger();
+
+ public PointDataParser(String mapName) {
+ super(mapName);
+ }
@Override
public PointData parse(Element element) throws UnknownTypeException {
- PointData result = new PointData();
+ PointData result = new PointData(getMapName());
for (Pair<String, String> entry : getAttributes(element)) {
switch (entry.getLeft()) {
case ("X"):
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ReferenceParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ReferenceParser.java
index 3439c7fd94af2f96f509d2be4fb996f1ecac68de..4615a3980ff914f4cf2ee6917877b22c870406fc 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ReferenceParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ReferenceParser.java
@@ -28,6 +28,10 @@ public class ReferenceParser extends ElementGpmlParser<MiriamData> {
*/
private final Logger logger = LogManager.getLogger(ReferenceParser.class);
+ public ReferenceParser(String mapName) {
+ super(mapName);
+ }
+
/**
* This function creates MiriamData from database name and id.
*
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ShapeParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ShapeParser.java
index cd1834340f271c4eb07094a2c2b4de658193e6fe..6bade4543815e4943f1ae431d5a73a56623bd95d 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ShapeParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ShapeParser.java
@@ -28,14 +28,18 @@ public class ShapeParser extends GraphicalPathwayElementParser<Shape> {
/**
* Default class logger.
*/
- private final Logger logger = LogManager.getLogger(ShapeParser.class);
+ private final Logger logger = LogManager.getLogger();
+
+ public ShapeParser(String mapName) {
+ super(mapName);
+ }
@Override
public Shape parse(Element eElement) throws ConverterException {
if (!eElement.getNodeName().equals("Shape")) {
throw new InvalidArgumentException(ShapeParser.class.getSimpleName() + " can parse only Shape xml nodes");
}
- Shape shape = new Shape(eElement.getAttribute("GraphId"));
+ Shape shape = new Shape(eElement.getAttribute("GraphId"), getMapName());
for (Pair<String, String> entry : getAttributes(eElement)) {
switch (entry.getLeft()) {
case ("GraphId"):
@@ -111,12 +115,12 @@ public class ShapeParser extends GraphicalPathwayElementParser<Shape> {
shape.setCompartment(true);
break;
default:
- logger.warn(shape.getWarningPrefix() + "Unknown line type: " + value);
+ logger.warn(shape.getLogMarker() + "Unknown line type: " + value);
break;
}
break;
default:
- logger.warn(shape.getWarningPrefix() + "Unknown attribute of node. Key:" + key + "; value: " + value);
+ logger.warn(shape.getLogMarker() + "Unknown attribute of node. Key:" + key + "; value: " + value);
break;
}
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/StateParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/StateParser.java
index 99deb50bad55b8e2962de3db7e9559d3fbe0614f..7c9d7d7f7addcf77e8177205bc5d37e229097951 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/StateParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/StateParser.java
@@ -31,14 +31,19 @@ public class StateParser extends ElementGpmlParser<State> {
* Parser used for extracting {@link lcsb.mapviewer.model.map.MiriamData
* references} from GPML model.
*/
- private ReferenceParser referenceParser = new ReferenceParser();
+ private ReferenceParser referenceParser;
+
+ public StateParser(String mapName) {
+ super(mapName);
+ referenceParser = new ReferenceParser(mapName);
+ }
@Override
public State parse(Element eElement) throws ConverterException {
if (!eElement.getNodeName().equals("State")) {
throw new InvalidArgumentException(StateParser.class.getSimpleName() + " can parse only State xml nodes");
}
- State state = new State(eElement.getAttribute("GraphId"));
+ State state = new State(eElement.getAttribute("GraphId"), getMapName());
for (Pair<String, String> entry : getAttributes(eElement)) {
switch (entry.getLeft()) {
case ("GraphId"):
@@ -159,7 +164,7 @@ public class StateParser extends ElementGpmlParser<State> {
String value = eTmp.getAttribute("Value");
switch (key) {
default:
- logger.warn(state.getWarningPrefix() + "Unknown attribute of node. Key:" + key + "; value: " + value);
+ logger.warn(state.getLogMarker() + "Unknown attribute of node. Key:" + key + "; value: " + value);
break;
}
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/DataNode.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/DataNode.java
index e3262048f1d0cc409965b29382c4f296152de8ff..b0443a560c5b329b48ea777d1eeca9d50b37a998 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/DataNode.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/DataNode.java
@@ -60,8 +60,8 @@ public class DataNode extends GraphicalPathwayElement {
* @param graphId
* {@link PathwayElement#graphId}
*/
- public DataNode(String graphId) {
- super(graphId);
+ public DataNode(String graphId, String mapName) {
+ super(graphId, mapName);
}
/**
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Edge.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Edge.java
index 7b9d4d2f11d897d61265afce38ae96254c1bf4f0..73f05db593ef63245e3b42ea54db1c0e46f9d4a6 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Edge.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Edge.java
@@ -10,6 +10,8 @@ import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.LogMarker;
+import lcsb.mapviewer.model.ProjectLogEntryType;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.MiriamData;
@@ -36,7 +38,7 @@ public class Edge implements Serializable {
/**
* Default class logger.
*/
- private final transient Logger logger = LogManager.getLogger(Edge.class);
+ private final transient Logger logger = LogManager.getLogger();
/**
* Identifier in GPML model.
@@ -72,7 +74,7 @@ public class Edge implements Serializable {
* GPML interaction type (arrow).
*/
private GpmlInteractionType type = GpmlInteractionType.LINE;
-
+
private boolean reversibleReaction = false;
/**
@@ -94,7 +96,9 @@ public class Edge implements Serializable {
* List of identifiers used by BioPax nodes that are inside GPML. These BioPax
* nodes contain annotations.
*/
- private List<String> biopaxReferences = new ArrayList<String>();
+ private List<String> biopaxReferences = new ArrayList<>();
+
+ private String mapName;
/**
* Default constructor.
@@ -102,8 +106,9 @@ public class Edge implements Serializable {
* @param graphId
* {@link #graphId}
*/
- public Edge(String graphId) {
+ public Edge(String graphId, String mapName) {
this.graphId = graphId;
+ this.mapName = mapName;
}
/**
@@ -127,6 +132,7 @@ public class Edge implements Serializable {
this.biopaxReferences.addAll(original.getBiopaxReferences());
this.zOrder = original.getzOrder();
this.reversibleReaction = original.isReversibleReaction();
+ this.mapName = original.getMapName();
}
/**
@@ -280,8 +286,12 @@ public class Edge implements Serializable {
*
* @return string that identifies element in logs
*/
- public String getWarningPrefix() {
- return "[" + getType() + ", id: " + getGraphId() + "]\t";
+ public LogMarker getLogMarker() {
+ return new LogMarker(ProjectLogEntryType.PARSING_ISSUE, getType().toString(), getGraphId(), getMapName());
+ }
+
+ private String getMapName() {
+ return mapName;
}
/**
@@ -356,16 +366,14 @@ public class Edge implements Serializable {
public void extend(Edge edge2) {
// check if extension make sense (they should point to the same identifier)
if (!getEnd().equals(edge2.getStart())) {
- throw new InvalidArgumentException(
- getWarningPrefix() + edge2.getWarningPrefix() + " Cannot merge - anchor points doesn't match: " + getEnd()
- + "," + edge2.getStart());
+ throw new InvalidArgumentException(" Cannot merge - anchor points doesn't match: " + getEnd()
+ + "," + edge2.getStart());
}
if (line.getEndPoint().distance(edge2.getLine().getBeginPoint()) > EPSILON) {
- throw new InvalidArgumentException(
- getWarningPrefix() + edge2.getWarningPrefix() + " Cannot merge - edges are far from each other: "
- + line.getEndPoint() + ","
- + edge2.getLine().getBeginPoint());
+ throw new InvalidArgumentException(" Cannot merge - edges are far from each other: "
+ + line.getEndPoint() + ","
+ + edge2.getLine().getBeginPoint());
}
// graphId should be the same
@@ -397,8 +405,7 @@ public class Edge implements Serializable {
// color should be skipped
if (!getColor().equals(edge2.getColor())) {
- logger
- .warn(getWarningPrefix() + edge2.getWarningPrefix() + " Problem with merging. Edges have different colors.");
+ logger.warn(getLogMarker(), "Problem with merging. Edges have different colors.");
}
// add biopax references
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlInteractionType.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlInteractionType.java
index 3775bf5f8ebe4af95f395b592b13d23fd7850aa7..959c12f16fae848de625e27bf38840851877d27f 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlInteractionType.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlInteractionType.java
@@ -104,11 +104,11 @@ public enum GpmlInteractionType {
}
/**
- * Returns a type identified by the gpml string.
+ * Returns a type identified by the GPML string.
*
* @param gpmlString
- * string in GPML represetning type
- * @return type identified by the gpml string
+ * string in GPML representing type
+ * @return type identified by the GPML string
* @throws UnknownTypeException
* thrown when type cannot be resolved
*/
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Graph.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Graph.java
index 69efb26c026e0bc9b0e100bb524689d2db250303..2bb964bff65b2cb52cef44ca50b83f98482998d9 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Graph.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Graph.java
@@ -132,6 +132,8 @@ public class Graph implements Serializable {
*/
private List<State> states = new ArrayList<State>();
+ private String mapName;;
+
/**
* Default constructor.
*/
@@ -172,7 +174,7 @@ public class Graph implements Serializable {
nodes.put(node.getGraphId(), node);
if (node.getGroupRef() != null && !node.getGroupRef().equals("")) {
if (groupsByGroupId.get(node.getGroupRef()) == null) {
- logger.warn(node.getWarningPrefix() + "Missing group: " + node.getGroupRef());
+ logger.warn(node.getLogMarker(), "Missing group: " + node.getGroupRef());
} else {
groupsByGroupId.get(node.getGroupRef()).addNode(node);
}
@@ -580,4 +582,12 @@ public class Graph implements Serializable {
this.states = states;
}
+ public String getMapName() {
+ return mapName;
+ }
+
+ public void setMapName(String mapName) {
+ this.mapName = mapName;
+ }
+
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GraphicalPathwayElement.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GraphicalPathwayElement.java
index 76174f80a8b0b4023b599d6b07d7b149671e4ee0..4092a9d744aff442d6a386c1eac76521188c7a15 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GraphicalPathwayElement.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GraphicalPathwayElement.java
@@ -81,8 +81,8 @@ public abstract class GraphicalPathwayElement extends PathwayElement {
* @param graphId
* {@link PathwayElement#graphId}
*/
- public GraphicalPathwayElement(String graphId) {
- super(graphId);
+ public GraphicalPathwayElement(String graphId, String mapName) {
+ super(graphId, mapName);
}
/**
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Group.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Group.java
index 16160000c56f46d53e5d2db443bf0d3c01585c68..98050cb259c6957c510c5af8ad755e3e78b5e85a 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Group.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Group.java
@@ -46,8 +46,8 @@ public class Group extends PathwayElement {
* @param groupId
* {@link #groupId}
*/
- public Group(String graphId, String groupId) {
- super(graphId);
+ public Group(String graphId, String groupId, String mapName) {
+ super(graphId, mapName);
this.groupId = groupId;
nodes = new HashSet<PathwayElement>();
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Label.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Label.java
index 9a59e192093576db4004662ebea56770d1d1d840..ecd0c164a3304b1836255a59b344b3b7e3a0cc1f 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Label.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Label.java
@@ -61,8 +61,8 @@ public class Label extends GraphicalPathwayElement {
* @param graphId
* {@link PathwayElement#graphId}
*/
- public Label(String graphId) {
- super(graphId);
+ public Label(String graphId, String mapName) {
+ super(graphId, mapName);
setTextLabel(null);
setGroupRef(null);
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PathwayElement.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PathwayElement.java
index ad817852bfa0ba1bc8a4a68043ca8105376c6715..ffd1988a00b5b17ccc206d9dce89cdf8b49b99e8 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PathwayElement.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PathwayElement.java
@@ -5,6 +5,9 @@ import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
+import lcsb.mapviewer.model.LogMarker;
+import lcsb.mapviewer.model.ProjectLogEntryType;
+
/**
* Abstract class for pathway elements. It defines common functionalities for
* all elements in the model. There are two known subclasses:
@@ -45,14 +48,17 @@ public abstract class PathwayElement implements Serializable {
*/
private List<String> biopaxReferences = new ArrayList<>();
+ private String mapName;
+
/**
* Default constructor.
*
* @param graphId
* {@link #graphId} value
*/
- public PathwayElement(String graphId) {
+ public PathwayElement(String graphId, String mapName) {
this.graphId = graphId;
+ this.mapName = mapName;
}
/**
@@ -93,13 +99,8 @@ public abstract class PathwayElement implements Serializable {
*/
abstract Rectangle2D getRectangle();
- /**
- * Returns prefix that should be used in logger for warnings about this element.
- *
- * @return prefix that should be used in logger for warnings about this element
- */
- public String getWarningPrefix() {
- return "[" + this.getClass().getSimpleName() + ", " + getGraphId() + "]\t";
+ public LogMarker getLogMarker() {
+ return new LogMarker(ProjectLogEntryType.PARSING_ISSUE, this.getClass().getSimpleName(), getGraphId(), getMapName());
}
/**
@@ -162,4 +163,12 @@ public abstract class PathwayElement implements Serializable {
public void addComment(String comment) {
this.comments.add(comment);
}
+
+ public String getMapName() {
+ return mapName;
+ }
+
+ public void setMapName(String mapName) {
+ this.mapName = mapName;
+ }
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PointData.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PointData.java
index bff65363b8b948998d165a48faf8826744b669a4..aba876c1253aa9f757628af95bfdf29d5e9af001 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PointData.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PointData.java
@@ -6,6 +6,9 @@ import java.io.Serializable;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
+import lcsb.mapviewer.model.LogMarker;
+import lcsb.mapviewer.model.ProjectLogEntryType;
+
/**
* Class that defines information about point stored in GPML structures.
*
@@ -56,6 +59,12 @@ public class PointData implements Serializable {
*/
private GpmlInteractionType type;
+ private String mapName;
+
+ public PointData(String mapName) {
+ this.mapName = mapName;
+ }
+
/**
* @return the x
* @see #x
@@ -183,7 +192,7 @@ public class PointData implements Serializable {
} else if (relX.equals("0.0") && relY.equals("0.0")) {
return Direction.NONE;
} else {
- logger.warn("[" + graphRef + "]\t" +
+ logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, null, null, getMapName()),
"Cannot determine connection direction from values: relX=" + relX + "; relY=" + relY + ". Estimating...");
double xVal = Double.valueOf(relX);
double yVal = Double.valueOf(relY);
@@ -208,4 +217,12 @@ public class PointData implements Serializable {
return "[" + this.getClass().getSimpleName() + " x=" + x + "; y=" + y + "; graphRef=" + graphRef + "; relX=" + relX
+ "; relY=" + relY + "; type=" + type + "]";
}
+
+ public String getMapName() {
+ return mapName;
+ }
+
+ public void setMapName(String mapName) {
+ this.mapName = mapName;
+ }
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Shape.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Shape.java
index 4f5c2a2e490482e2b0ce2017efd8ca1e2abced72..d54bf0f4eeb06a981c7453a0752078c78ea4bc37 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Shape.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Shape.java
@@ -2,6 +2,9 @@ package lcsb.mapviewer.wikipathway.model;
import java.awt.Color;
+import lcsb.mapviewer.model.LogMarker;
+import lcsb.mapviewer.model.ProjectLogEntryType;
+
/**
* Class used to store data from Shape from GPML.
*
@@ -61,8 +64,8 @@ public class Shape extends GraphicalPathwayElement {
* @param graphId
* {@link PathwayElement#graphId}
*/
- public Shape(String graphId) {
- super(graphId);
+ public Shape(String graphId, String mapName) {
+ super(graphId, mapName);
setRectangle(null);
setShape(null);
setTextLabel(null);
@@ -84,8 +87,8 @@ public class Shape extends GraphicalPathwayElement {
}
@Override
- public String getWarningPrefix() {
- return "[" + getShape() + " " + getGraphId() + "]\t";
+ public LogMarker getLogMarker() {
+ return new LogMarker(ProjectLogEntryType.PARSING_ISSUE, getShape(), getGraphId(), getMapName());
}
/**
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/State.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/State.java
index 23bdb2e65336694ddc0e3082220901b7cd4df546..610dd36a5e8961ef92d2b04ba7fdd562b421ec79 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/State.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/State.java
@@ -64,7 +64,7 @@ public class State extends GraphicalPathwayElement {
private Double width;
/**
- * Heightof the element.
+ * Height of the element.
*/
private Double height;
@@ -74,8 +74,8 @@ public class State extends GraphicalPathwayElement {
* @param graphId
* {@link PathwayElement#graphId}
*/
- public State(String graphId) {
- super(graphId);
+ public State(String graphId, String mapName) {
+ super(graphId, mapName);
}
/**
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxFactory.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxFactory.java
index ac63f06475c24a885664eb3b058fd75b6dd80655..50e450d8c5ae6690db5d0760ea314b0929f22075 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxFactory.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxFactory.java
@@ -6,10 +6,17 @@ import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.LogMarker;
+import lcsb.mapviewer.model.ProjectLogEntryType;
import lcsb.mapviewer.model.map.*;
public class BiopaxFactory {
private Logger logger = LogManager.getLogger();
+ private String mapName;
+
+ public BiopaxFactory(String mapName) {
+ this.mapName = mapName;
+ }
/**
* Creates {@link MiriamData annotation} from {@link BiopaxPublication}.
@@ -52,15 +59,26 @@ public class BiopaxFactory {
if (md != null) {
result.add(md);
} else {
- logger.warn("[" + string + "]\tBiopax publication is invalid.");
+ logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, "BiopaxReference", string, getMapName()),
+ "Publication is invalid.");
}
} else {
- logger.warn("[" + string + "]\tBiopax publication doesn't exist.");
+ logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, "BiopaxReference", string, getMapName()),
+ "Biopax publication doesn't exist.");
}
} else {
- logger.warn("[Biopax, " + string + "]\tInvalid BioPax reference.");
+ logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, "BiopaxReference", string, getMapName()),
+ "Invalid BioPax reference.");
}
}
return result;
}
+
+ public String getMapName() {
+ return mapName;
+ }
+
+ public void setMapName(String mapName) {
+ this.mapName = mapName;
+ }
}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/WikipathwaysTestFunctions.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/WikipathwaysTestFunctions.java
index c263cc8a5dabcf43a1a001e125cf02256a4007f6..0d6b120a1e87318d319428bba9c3ef9cbe62e31c 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/WikipathwaysTestFunctions.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/WikipathwaysTestFunctions.java
@@ -1,5 +1,7 @@
package lcsb.mapviewer.wikipathway;
+import static org.junit.Assert.assertTrue;
+
import java.awt.Color;
import java.io.*;
import java.net.URL;
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BiopaxParserTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BiopaxParserTest.java
index 2b25b91443bca4bea099d22cffea6bcf7e81c6c5..91306b3dbf8e0d50284e0a7de12f865e4373e10e 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BiopaxParserTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BiopaxParserTest.java
@@ -11,8 +11,11 @@ import lcsb.mapviewer.wikipathway.model.biopax.BiopaxPublication;
public class BiopaxParserTest extends WikipathwaysTestFunctions {
+ BiopaxParser parser ;
+
@Before
public void setUp() throws Exception {
+ parser = new BiopaxParser("mapName");
}
@After
@@ -21,7 +24,6 @@ public class BiopaxParserTest extends WikipathwaysTestFunctions {
@Test
public void testParse() throws Exception {
- BiopaxParser parser = new BiopaxParser();
Document document = getXmlDocumentFromFile("testFiles/biopax/small.xml");
BiopaxData data = parser.parse(document.getFirstChild());
assertNotNull(data);
@@ -38,7 +40,6 @@ public class BiopaxParserTest extends WikipathwaysTestFunctions {
@Test
public void testIncorrectPumeds() throws Exception {
- BiopaxParser parser = new BiopaxParser();
Document document = getXmlDocumentFromFile("testFiles/biopax/invalid_pubmed_reference.xml");
BiopaxData data = parser.parse(document.getFirstChild());
assertNotNull(data);
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/DataNodeParserTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/DataNodeParserTest.java
index 12e619ba5db29888c4e12671be3152c520e7d1e6..98a4ba41923a0d5f0cb7dfbebc667628d60cdda1 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/DataNodeParserTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/DataNodeParserTest.java
@@ -14,10 +14,11 @@ import lcsb.mapviewer.wikipathway.model.DataNode;
public class DataNodeParserTest extends WikipathwaysTestFunctions {
Logger logger = LogManager.getLogger(DataNodeParserTest.class);
- DataNodeParser parser = new DataNodeParser();
+ DataNodeParser parser ;
@Before
public void setUp() throws Exception {
+ parser = new DataNodeParser("mapName");
}
@After
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/EdgeLineParserTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/EdgeLineParserTest.java
index 3b51b1f8d9f875a581cbd9c5ede41c6708f7ddc7..3ebefd525ba7f663a90b7b8ded442f0cf2e50b78 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/EdgeLineParserTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/EdgeLineParserTest.java
@@ -12,10 +12,11 @@ import lcsb.mapviewer.wikipathway.model.Edge;
public class EdgeLineParserTest extends WikipathwaysTestFunctions {
- EdgeLineParser parser = new EdgeLineParser();
+ private EdgeLineParser parser;
@Before
public void setUp() throws Exception {
+ parser = new EdgeLineParser("mapName");
}
@After
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/EdgeParserTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/EdgeParserTest.java
index e59195edd55a88e15401db9d874ad768d3256a44..ef6088f6200f60fa4d378fec062597428567b88d 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/EdgeParserTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/EdgeParserTest.java
@@ -8,6 +8,7 @@ import java.util.List;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
+import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.Configuration;
@@ -17,12 +18,17 @@ public class EdgeParserTest {
Logger logger = LogManager.getLogger();
- EdgeParser parser = new EdgeParser();
+ EdgeParser parser ;
+ @Before
+ public void setUp() {
+ parser = new EdgeParser("mapName");
+ }
+
@Test
public void testGetPointsWithoutTargetDirection() throws Exception {
List<PointData> gpmlPoints = new ArrayList<>();
- PointData pointData = new PointData();
+ PointData pointData = new PointData("mapName");
pointData.setX(370.0);
pointData.setY(506.9845153753351);
pointData.setRelX("0.0");
@@ -30,12 +36,12 @@ public class EdgeParserTest {
pointData.setGraphRef("db29a");
gpmlPoints.add(pointData);
- pointData = new PointData();
+ pointData = new PointData("mapName");
pointData.setX(337.9360555506242);
pointData.setY(558.2089552238806);
gpmlPoints.add(pointData);
- pointData = new PointData();
+ pointData = new PointData("mapName");
pointData.setX(305.8721111012484);
pointData.setY(587.6687409348253);
pointData.setRelX("0.0");
@@ -59,7 +65,7 @@ public class EdgeParserTest {
@Test
public void testGetPointsWithoutSourceDirection() throws Exception {
List<PointData> gpmlPoints = new ArrayList<>();
- PointData pointData = new PointData();
+ PointData pointData = new PointData("mapName");
pointData.setX(418.1490729057133);
pointData.setY(421.3813636363637);
pointData.setRelX("0.0");
@@ -67,17 +73,17 @@ public class EdgeParserTest {
pointData.setGraphRef("f78da");
gpmlPoints.add(pointData);
- pointData = new PointData();
+ pointData = new PointData("mapName");
pointData.setX(506.83491062039946);
pointData.setY(396.35686597839583);
gpmlPoints.add(pointData);
- pointData = new PointData();
+ pointData = new PointData("mapName");
pointData.setX(506.83491062039946);
pointData.setY(369.3819137749735);
gpmlPoints.add(pointData);
- pointData = new PointData();
+ pointData = new PointData("mapName");
pointData.setX(718.8015247108307);
pointData.setY(343.0727655099894);
pointData.setRelX("0.0");
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ElementGpmlParserTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ElementGpmlParserTest.java
index 2f44e6873d579629891d37edbd8dac912f154412..fb2f8d0e2ba4e518c1935c363c004fe45d7f0690 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ElementGpmlParserTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ElementGpmlParserTest.java
@@ -1,35 +1,18 @@
package lcsb.mapviewer.wikipathway.XML;
import static org.junit.Assert.assertNotNull;
+import static org.mockito.Mockito.CALLS_REAL_METHODS;
-import java.awt.*;
-import java.util.Collection;
+import java.awt.Color;
import org.junit.*;
-import org.w3c.dom.Element;
+import org.mockito.Mockito;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
public class ElementGpmlParserTest extends WikipathwaysTestFunctions {
- ElementGpmlParser<Object> parser = new ElementGpmlParser<Object>() {
- @Override
- public Object parse(Element node) throws ConverterException {
- throw new NotImplementedException();
- }
-
- @Override
- public String toXml(Object object) throws ConverterException {
- throw new NotImplementedException();
- }
-
- @Override
- public String toXml(Collection<Object> list) throws ConverterException {
- throw new NotImplementedException();
- }
- };
+ ElementGpmlParser<?> parser = Mockito.mock(ElementGpmlParser.class, CALLS_REAL_METHODS);
@Before
public void setUp() throws Exception {
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/LabelParserTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/LabelParserTest.java
index aa346f17ef07767653f3a8f4312c37269aea867e..eb9e33368f1fe43b30b89759b9d482e38596f2fa 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/LabelParserTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/LabelParserTest.java
@@ -11,7 +11,7 @@ import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
import lcsb.mapviewer.wikipathway.model.Label;
public class LabelParserTest extends WikipathwaysTestFunctions {
- LabelParser parser = new LabelParser();
+ LabelParser parser = new LabelParser("mapName");
@Before
public void setUp() throws Exception {
@@ -57,7 +57,7 @@ public class LabelParserTest extends WikipathwaysTestFunctions {
public void testParseGraphics() throws Exception {
Element node = fileToNode("testFiles/elements/label_graphics.xml");
- Label label = new Label("test");
+ Label label = new Label("test", "mapName");
parser.parseGraphics(node, label);
assertNotNull(label);
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelContructorTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelContructorTest.java
index acb69da6375af10472e03df7a029ac0652ed50ec..a9b43c1bb71d2ba9e0c343b68fb57f8c8ea8cc73 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelContructorTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelContructorTest.java
@@ -19,11 +19,13 @@ public class ModelContructorTest extends WikipathwaysTestFunctions {
Logger logger = LogManager.getLogger(ModelContructorTest.class);
ModelComparator comparator = new ModelComparator();
+ ModelContructor mc ;
private int elementCounter = 0;
@Before
public void setUp() throws Exception {
+ mc = new ModelContructor("mapName");
}
@After
@@ -32,9 +34,9 @@ public class ModelContructorTest extends WikipathwaysTestFunctions {
@Test
public void testZIndexForElement() throws Exception {
- ModelToGPML parser = new ModelToGPML();
Model model = createEmptyModel();
model.addElement(createProtein());
+ ModelToGPML parser = new ModelToGPML(model.getName());
String xml = parser.getGPML(model);
assertNotNull(xml);
@@ -61,17 +63,15 @@ public class ModelContructorTest extends WikipathwaysTestFunctions {
@Test
public void testShouldRotate90degreesWithNoAsAnswer() {
- ModelContructor mc = new ModelContructor();
assertFalse(mc.shouldRotate90degrees(0.0));
assertFalse(mc.shouldRotate90degrees(Math.PI));
assertFalse(mc.shouldRotate90degrees(15 * Math.PI));
assertFalse(mc.shouldRotate90degrees(-Math.PI));
- assertFalse(mc.shouldRotate90degrees(null));
+ assertFalse(mc.shouldRotate90degrees((Double)null));
}
@Test
public void testShouldRotate90degrees() {
- ModelContructor mc = new ModelContructor();
assertTrue(mc.shouldRotate90degrees(Math.PI / 2));
assertTrue(mc.shouldRotate90degrees(15 * Math.PI / 2));
assertTrue(mc.shouldRotate90degrees(-Math.PI / 2));
@@ -79,7 +79,6 @@ public class ModelContructorTest extends WikipathwaysTestFunctions {
@Test
public void testShouldRotate90degreesWithWarnings() {
- ModelContructor mc = new ModelContructor();
assertFalse(mc.shouldRotate90degrees(0.0 + 0.5));
assertEquals(1, super.getWarnings().size());
assertFalse(mc.shouldRotate90degrees(Math.PI + 0.5));
@@ -98,7 +97,6 @@ public class ModelContructorTest extends WikipathwaysTestFunctions {
@Test
public void testRotate90degrees() {
- ModelContructor mc = new ModelContructor();
Rectangle2D result = mc.rotate90degrees(new Rectangle2D.Double(10, 20, 30, 40));
assertEquals(5, result.getX(), Configuration.EPSILON);
assertEquals(25, result.getY(), Configuration.EPSILON);
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 be945f0b5b4667a1cae0de5d5bbb3a79f213df03..a0e8cb5ed09a7e32f2b494baa9b0571fe18c2539 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelToGPMLTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelToGPMLTest.java
@@ -32,10 +32,10 @@ public class ModelToGPMLTest extends WikipathwaysTestFunctions {
@Test
public void test() throws Exception {
- ModelToGPML parser = new ModelToGPML();
CellDesignerXmlParser cellDesignerXmlParser = new CellDesignerXmlParser();
Model model = cellDesignerXmlParser
.createModel(new ConverterParams().filename("testFiles/other_full/GSTP1 subnetwork_220214.xml"));
+ ModelToGPML parser = new ModelToGPML(model.getName());
String xml = parser.getGPML(model);
assertNotNull(xml);
assertEquals(10, getWarnings().size());
@@ -46,7 +46,6 @@ public class ModelToGPMLTest extends WikipathwaysTestFunctions {
@Test
public void testAnnotations() throws Exception {
- ModelToGPML parser = new ModelToGPML();
Model model = new ModelFullIndexed(null);
model.setWidth(1000);
@@ -59,6 +58,7 @@ public class ModelToGPMLTest extends WikipathwaysTestFunctions {
model.addElement(alias);
+ ModelToGPML parser = new ModelToGPML(model.getName());
String xml = parser.getGPML(model);
assertNotNull(xml);
assertEquals(0, getWarnings().size());
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ReactionLayoutFinderTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ReactionLayoutFinderTest.java
index 0dc4747db50c4a46497978b09be33d9c4053c452..4f4e364a54c9840a2dee65f5aaad6ab2bf6f0309 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ReactionLayoutFinderTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ReactionLayoutFinderTest.java
@@ -136,7 +136,7 @@ public class ReactionLayoutFinderTest extends WikipathwaysTestFunctions {
}
private Edge createEdge(String id, Point2D p1, Point2D p2) {
- Edge modifierEdge = new Edge(id);
+ Edge modifierEdge = new Edge(id, null);
modifierEdge.setLine(new PolylineData(p1, p2));
return modifierEdge;
}
@@ -204,7 +204,7 @@ public class ReactionLayoutFinderTest extends WikipathwaysTestFunctions {
@Test
public void testNodeLinesInteractionWithTwoReactants() {
- Edge edge = new Edge("id");
+ Edge edge = new Edge("id", null);
PolylineData line = new PolylineData(Arrays.asList(
new Point2D.Double(0, 0),
new Point2D.Double(100, 0),
@@ -220,7 +220,7 @@ public class ReactionLayoutFinderTest extends WikipathwaysTestFunctions {
@Test
public void testNodeLinesInteractionWithTwoProducts() {
- Edge edge = new Edge("id");
+ Edge edge = new Edge("id", null);
PolylineData line = new PolylineData(Arrays.asList(
new Point2D.Double(0, 0),
new Point2D.Double(100, 0),
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ReferenceParserTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ReferenceParserTest.java
index 385d524ffe417d5fbdd12f5d3a92b8b740e05c08..2a3d7dfb7aecb2e1fb57151a7f4b1a5a87396750 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ReferenceParserTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ReferenceParserTest.java
@@ -16,7 +16,7 @@ import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
public class ReferenceParserTest extends WikipathwaysTestFunctions {
Logger logger = LogManager.getLogger(ReferenceParserTest.class);
- ReferenceParser mc = new ReferenceParser();
+ ReferenceParser mc = new ReferenceParser("mapName");
@Before
public void setUp() throws Exception {
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ShapeParserTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ShapeParserTest.java
index 11c6fb1cf41b174451bca55504b6f1a6c3acf336..5cc4e8f274423756f40502f91ca5ada44e377d0a 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ShapeParserTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ShapeParserTest.java
@@ -14,7 +14,7 @@ import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
import lcsb.mapviewer.wikipathway.model.Shape;
public class ShapeParserTest extends WikipathwaysTestFunctions {
- ShapeParser parser = new ShapeParser();
+ ShapeParser parser = new ShapeParser("mapName");
@After
public void tearDown() throws Exception {
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/StateParserTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/StateParserTest.java
index 4f8a696a79a1d4ead521e7c4dee63f7fff007a26..cfb051908b9ff7e90cdd33808b526deed90ad6c8 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/StateParserTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/StateParserTest.java
@@ -13,7 +13,7 @@ import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
import lcsb.mapviewer.wikipathway.model.State;
public class StateParserTest extends WikipathwaysTestFunctions {
- StateParser parser = new StateParser();
+ StateParser parser = new StateParser("mapName");
@After
public void tearDown() throws Exception {
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/PointDataTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/PointDataTest.java
index b42102350fcda3b28e7684d87e4977a5c71470b3..9612a7125808af9984f5f060fe449f93090186ee 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/PointDataTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/PointDataTest.java
@@ -17,7 +17,7 @@ public class PointDataTest extends WikipathwaysTestFunctions {
@Test
public void testSeialization() {
- SerializationUtils.serialize(new PointData());
+ SerializationUtils.serialize(new PointData("mapName"));
}
}