diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/model/ReactomeReactionCoordinates.java b/reactome/src/main/java/lcsb/mapviewer/reactome/model/ReactomeReactionCoordinates.java
deleted file mode 100644
index 3a351f38a1f2719af37c33a4e52a610654d110f1..0000000000000000000000000000000000000000
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/model/ReactomeReactionCoordinates.java
+++ /dev/null
@@ -1,102 +0,0 @@
-package lcsb.mapviewer.reactome.model;
-
-/**
- * Object representing Reactome <a href=
- * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=ReactionCoordinates"
- * >ReactionCoordinates</a> object.
- *
- * @author Piotr Gawron
- *
- */
-public class ReactomeReactionCoordinates extends ReactomeDatabaseObject {
-
- /**
- * Source x param in reactome model. More information can be found <a
- * href="http://wiki.reactome.org/index.php/Glossary_Data_Model">here</a>.
- */
- private Integer sourceX;
- /**
- * Source y param in reactome model. More information can be found <a
- * href="http://wiki.reactome.org/index.php/Glossary_Data_Model">here</a>.
- */
- private Integer sourceY;
- /**
- * Target x param in reactome model. More information can be found <a
- * href="http://wiki.reactome.org/index.php/Glossary_Data_Model">here</a>.
- */
- private Integer targetX;
- /**
- * Target x param in reactome model. More information can be found <a
- * href="http://wiki.reactome.org/index.php/Glossary_Data_Model">here</a>.
- */
- private Integer targetY;
-
- /**
- * @return the sourceX
- * @see #sourceX
- */
- public Integer getSourceX() {
- return sourceX;
- }
-
- /**
- * @param sourceX
- * the sourceX to set
- * @see #sourceX
- */
- public void setSourceX(Integer sourceX) {
- this.sourceX = sourceX;
- }
-
- /**
- * @return the sourceY
- * @see #sourceY
- */
- public Integer getSourceY() {
- return sourceY;
- }
-
- /**
- * @param sourceY
- * the sourceY to set
- * @see #sourceY
- */
- public void setSourceY(Integer sourceY) {
- this.sourceY = sourceY;
- }
-
- /**
- * @return the targetX
- * @see #targetX
- */
- public Integer getTargetX() {
- return targetX;
- }
-
- /**
- * @param targetX
- * the targetX to set
- * @see #targetX
- */
- public void setTargetX(Integer targetX) {
- this.targetX = targetX;
- }
-
- /**
- * @return the targetY
- * @see #targetY
- */
- public Integer getTargetY() {
- return targetY;
- }
-
- /**
- * @param targetY
- * the targetY to set
- * @see #targetY
- */
- public void setTargetY(Integer targetY) {
- this.targetY = targetY;
- }
-
-}
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReactionCoordinatesParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReactionCoordinatesParser.java
deleted file mode 100644
index c6082bbd1df4ab8969be746151b1f8b82d34ed4c..0000000000000000000000000000000000000000
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/ReactomeReactionCoordinatesParser.java
+++ /dev/null
@@ -1,24 +0,0 @@
-package lcsb.mapviewer.reactome.xml;
-
-import lcsb.mapviewer.reactome.model.ReactomeReactionCoordinates;
-import lcsb.mapviewer.reactome.xml.columnParser.ReactionCoordinatesColumnParser;
-
-/**
- * Parser for reactome xml retrieved from <a href=
- * "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html"
- * >Reactome API</a> for <a href=
- * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=ReactionCoordinates"
- * >ReactionCoordinates</a> object.
- *
- * @author Piotr Gawron
- *
- */
-public class ReactomeReactionCoordinatesParser extends ReactomeNodeParser<ReactomeReactionCoordinates> {
-
- /**
- * Default constructor.
- */
- public ReactomeReactionCoordinatesParser() {
- super(ReactomeReactionCoordinates.class, ReactionCoordinatesColumnParser.class);
- }
-}
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/columnParser/ReactionCoordinatesColumnParser.java b/reactome/src/main/java/lcsb/mapviewer/reactome/xml/columnParser/ReactionCoordinatesColumnParser.java
deleted file mode 100644
index 3e2c99edfaa4f38a91bd417d08a61f05cf952dc2..0000000000000000000000000000000000000000
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/xml/columnParser/ReactionCoordinatesColumnParser.java
+++ /dev/null
@@ -1,38 +0,0 @@
-package lcsb.mapviewer.reactome.xml.columnParser;
-
-import lcsb.mapviewer.reactome.model.ReactomeReactionCoordinates;
-
-import org.w3c.dom.Node;
-
-/**
- * Parser for properties of Reactome <a href=
- * "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=ReactionCoordinates"
- * >ReactionCoordinates</a> object.
- *
- * @author Piotr Gawron
- *
- */
-public class ReactionCoordinatesColumnParser extends ColumnParser<ReactomeReactionCoordinates> {
- /**
- * Default constructor. Defines parser for super class of ReactionCoordinates.
- */
- protected ReactionCoordinatesColumnParser() {
- super(DatabaseObjectColumnParser.class);
- }
-
- @Override
- public void updateColumnFromNode(ReactomeReactionCoordinates object, Node node) {
- if (node.getNodeName().equalsIgnoreCase("sourceX")) {
- object.setSourceX(Integer.parseInt(node.getTextContent()));
- } else if (node.getNodeName().equalsIgnoreCase("sourceY")) {
- object.setSourceY(Integer.parseInt(node.getTextContent()));
- } else if (node.getNodeName().equalsIgnoreCase("targetX")) {
- object.setTargetX(Integer.parseInt(node.getTextContent()));
- } else if (node.getNodeName().equalsIgnoreCase("targetY")) {
- object.setTargetY(Integer.parseInt(node.getTextContent()));
- } else {
- getParentParser().updateColumnFromNode(object, node);
- }
- }
-
-}
diff --git a/reactome/src/main/resources/applicationContext-reactome.xml b/reactome/src/main/resources/applicationContext-reactome.xml
index a1fa4c3cc819b628bde2c33140b79462d139fc4d..a7422cb31e82d6dd1293b6872e626fd3100ffe2c 100644
--- a/reactome/src/main/resources/applicationContext-reactome.xml
+++ b/reactome/src/main/resources/applicationContext-reactome.xml
@@ -110,7 +110,6 @@
<bean id="ReactomePublicationParser" class="lcsb.mapviewer.reactome.xml.ReactomePublicationParser"/>
<bean id="ReactomeReactionlikeEventParser" class="lcsb.mapviewer.reactome.xml.ReactomeReactionlikeEventParser"/>
<bean id="ReactomeReactionParser" class="lcsb.mapviewer.reactome.xml.ReactomeReactionParser"/>
- <bean id="ReactomeReactionCoordinatesParser" class="lcsb.mapviewer.reactome.xml.ReactomeReactionCoordinatesParser"/>
<bean id="ReactomeReactionVertexParser" class="lcsb.mapviewer.reactome.xml.ReactomeReactionVertexParser"/>
<bean id="ReactomeReferenceDatabaseParser" class="lcsb.mapviewer.reactome.xml.ReactomeReferenceDatabaseParser"/>
<bean id="ReactomeReferenceDNASequenceParser" class="lcsb.mapviewer.reactome.xml.ReactomeReferenceDNASequenceParser"/>
diff --git a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/GeneralTests.java b/reactome/src/test/java/lcsb/mapviewer/reactome/xml/GeneralTests.java
index 24b750d1f2d6b33ef0fc448be23e2191b81d5b36..19daa9c94ff6a1dafcbcb5445610aa48797149eb 100644
--- a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/GeneralTests.java
+++ b/reactome/src/test/java/lcsb/mapviewer/reactome/xml/GeneralTests.java
@@ -11,555 +11,544 @@ import org.junit.Ignore;
import org.junit.Test;
public class GeneralTests extends ReactomeTestFunctions {
- Logger logger = Logger.getLogger(GeneralTests.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testFragmentInsertionModification() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(2318717);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFragmentDeletionModification() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(2063905);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInterChainCrosslinkedResidue() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(4419898);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testIntraChainCrosslinkedResidue() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(3777079);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGroupModifiedResidue() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(2396027);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testModifiedResidue() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(140630);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- @Ignore("Reactome server returns Internal Server error")
- public void testSequenceDomain() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(173802);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testEntityFunctionalStatus() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(3080617);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testPathway() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(168276);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testBlackBoxEvent() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(2454113);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDepolymerisation() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(173642);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testPolymerisation() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(936986);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReaction() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(71593);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testEvidenceType() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(4546411);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCellType() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(2473605);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDisease() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(1625206);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testPsiMod() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(448185);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSequenceOntology() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(2318494);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testEntityCompartment() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(1470028);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGO_MolecularFunction() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(77954);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- @Ignore("In reactome there is no object of this type")
- public void testPathwayCoordinates() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(5477003);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFigure() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(157815);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFrontPage() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(4545014);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFunctionalStatusType() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(2426108);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInstanceEdit() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(1598217);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testPathwayDiagram() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(2162173);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testPathwayVertex() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(10834395);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReactionVertex() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(10834441);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCandidateSet() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(198809);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testOpenSet() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(162704);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDefinedSet() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(453350);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testOtherEntity() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(162704);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testPolymer() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(2160866);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSimpleEntity() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(868632);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testLiteratureReference() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(182836);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testURL() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(1170534);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReferenceDatabase() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(1385634);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReactionCoordinates() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(142110);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReferenceGroup() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(164405);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReferenceMolecule() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(142110);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReferenceIsoform() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(59007);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReferenceRNASequence() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(188854);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testNegativeRegulation() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(5229351);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRequirement() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(72781);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testPositiveRegulation() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(5623897);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSummation() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(143360);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testTaxon() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(72968);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReferenceDNASequence() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(10030875);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSpecies() throws Exception {
- try {
- ReactomeDatabaseObject object = rc.getFullObjectForDbId(181384);
- assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Logger logger = Logger.getLogger(GeneralTests.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testFragmentInsertionModification() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(2318717);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFragmentDeletionModification() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(2063905);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInterChainCrosslinkedResidue() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(4419898);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testIntraChainCrosslinkedResidue() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(3777079);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGroupModifiedResidue() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(2396027);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testModifiedResidue() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(140630);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ @Ignore("Reactome server returns Internal Server error")
+ public void testSequenceDomain() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(173802);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testEntityFunctionalStatus() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(3080617);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testPathway() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(168276);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testBlackBoxEvent() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(2454113);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDepolymerisation() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(173642);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testPolymerisation() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(936986);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReaction() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(71593);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testEvidenceType() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(4546411);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCellType() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(2473605);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDisease() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(1625206);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testPsiMod() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(448185);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSequenceOntology() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(2318494);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testEntityCompartment() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(1470028);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGO_MolecularFunction() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(77954);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ @Ignore("In reactome there is no object of this type")
+ public void testPathwayCoordinates() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(5477003);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFigure() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(157815);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFrontPage() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(4545014);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFunctionalStatusType() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(2426108);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInstanceEdit() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(1598217);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testPathwayDiagram() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(2162173);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testPathwayVertex() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(10834395);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionVertex() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(10834441);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCandidateSet() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(198809);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testOpenSet() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(162704);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDefinedSet() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(453350);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testOtherEntity() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(162704);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testPolymer() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(2160866);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSimpleEntity() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(868632);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testLiteratureReference() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(182836);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testURL() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(1170534);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReferenceDatabase() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(1385634);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReferenceGroup() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(164405);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReferenceMolecule() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(33265);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReferenceIsoform() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(59007);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReferenceRNASequence() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(188854);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testNegativeRegulation() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(5229351);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRequirement() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(72781);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testPositiveRegulation() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(5623897);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSummation() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(143360);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTaxon() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(72968);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReferenceDNASequence() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(10030875);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSpecies() throws Exception {
+ try {
+ ReactomeDatabaseObject object = rc.getFullObjectForDbId(181384);
+ assertFalse(object.getClass().getName().contains(ReactomeDatabaseObject.class.getName()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomePathwayParserTest.java b/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomePathwayParserTest.java
index a1cdbb63a3eb5e8e47e2be78d78d5c34d251c4ac..39ccd8999b067c2c1b112350d281f3c28f038a78 100644
--- a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomePathwayParserTest.java
+++ b/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomePathwayParserTest.java
@@ -3,9 +3,6 @@ package lcsb.mapviewer.reactome.xml;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.fail;
-import lcsb.mapviewer.reactome.ReactomeTestFunctions;
-import lcsb.mapviewer.reactome.model.ReactomePathway;
-import lcsb.mapviewer.reactome.model.ReactomeStatus;
import org.apache.log4j.Logger;
import org.junit.After;
@@ -14,78 +11,82 @@ import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
import org.w3c.dom.Document;
-public class ReactomePathwayParserTest extends ReactomeTestFunctions{
- Logger logger = Logger.getLogger(ReactomePathwayParserTest.class);
+import lcsb.mapviewer.reactome.ReactomeTestFunctions;
+import lcsb.mapviewer.reactome.model.ReactomePathway;
+import lcsb.mapviewer.reactome.model.ReactomeStatus;
+
+public class ReactomePathwayParserTest extends ReactomeTestFunctions {
+ Logger logger = Logger.getLogger(ReactomePathwayParserTest.class);
+
+ @Autowired
+ ReactomePathwayParser parser;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParseObject() throws Exception {
+ try {
+ Document document = getXmlDocumentFromFile("testFiles/reactome/pathway.xml");
+ ReactomePathway res = parser.parseObject(document.getChildNodes().item(0));
+ assertNotNull(res);
+ assertEquals((Integer) 111451, res.getCreated().getDbId());
+ assertEquals((Integer) 360839, res.getStableIdentifier().getDbId());
+ assertEquals((Integer) 70101, res.getCompartments().get(0).getDbId());
+ assertEquals(false, res.getIsInDisease());
+ assertEquals(false, res.getIsInferred());
+ assertEquals(false, res.getHasDiagram());
+ assertEquals(true, res.getDoRelease());
+ assertEquals((Integer) 141212, res.getLiteratureReferences().get(0).getDbId());
+ assertEquals((Integer) 450358, res.getOrthologousEvents().get(0).getDbId());
+ assertEquals((Integer) 71593, res.getPrecedingEvents().get(0).getDbId());
+ assertEquals((Integer) 48887, res.getSpecies().getDbId());
+ assertEquals((Integer) 212974, res.getSummations().get(0).getDbId());
+ assertEquals((Integer) 114254, res.getHasEvents().get(0).getDbId());
+ assertEquals("Formation of apoptosome", res.getDisplayName());
- @Autowired
- ReactomePathwayParser parser ;
- @Before
- public void setUp() throws Exception {
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @Test
+ public void testAnotherObject() {
+ try {
+ rc.getFullObjectForDbId(71336);
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
- @Test
- public void testParseObject() throws Exception {
- try {
- Document document = getXmlDocumentFromFile("testFiles/reactome/pathway.xml");
- ReactomePathway res = parser.parseObject(document.getChildNodes().item(0));
- assertNotNull(res);
- assertEquals((Integer)111451,res.getCreated().getDbId());
- assertEquals((Integer)360839,res.getStableIdentifier().getDbId());
- assertEquals((Integer)70101,res.getCompartments().get(0).getDbId());
- assertEquals(false,res.getIsInDisease());
- assertEquals(false,res.getIsInferred());
- assertEquals(false,res.getHasDiagram());
- assertEquals(true,res.getDoRelease());
- assertEquals((Integer)141212,res.getLiteratureReferences().get(0).getDbId());
- assertEquals((Integer)450358,res.getOrthologousEvents().get(0).getDbId());
- assertEquals((Integer)71593,res.getPrecedingEvents().get(0).getDbId());
- assertEquals((Integer)48887,res.getSpecies().getDbId());
- assertEquals((Integer)212974,res.getSummations().get(0).getDbId());
- assertEquals((Integer)114254,res.getHasEvents().get(0).getDbId());
- assertEquals("Formation of apoptosome", res.getDisplayName());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAnotherObject(){
- try {
- rc.getFullObjectForDbId(71336);
- } catch (Exception e){
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
+ @Test
+ public void testUpdateObjectFromDb() throws Exception {
+ try {
+ Document document = getXmlDocumentFromFile("testFiles/reactome/pathway.xml");
+ ReactomePathway res = parser.parseObject(document.getChildNodes().item(0));
- @Test
- public void testUpdateObjectFromDb() throws Exception {
- try {
- Document document = getXmlDocumentFromFile("testFiles/reactome/pathway.xml");
- ReactomePathway res = parser.parseObject(document.getChildNodes().item(0));
-
- rc.updateOnlyIdFields(res);
- assertEquals(ReactomeStatus.FULL, res.getCreated().getStatus());
- assertEquals(ReactomeStatus.FULL, res.getStableIdentifier().getStatus());
- assertEquals(ReactomeStatus.FULL, res.getCompartments().get(0).getStatus());
- assertEquals(ReactomeStatus.FULL, res.getLiteratureReferences().get(0).getStatus());
- assertEquals(ReactomeStatus.FULL, res.getOrthologousEvents().get(0).getStatus());
- assertEquals(ReactomeStatus.FULL, res.getPrecedingEvents().get(0).getStatus());
- assertEquals(ReactomeStatus.FULL, res.getSpecies().getStatus());
- assertEquals(ReactomeStatus.FULL, res.getSummations().get(0).getStatus());
- assertEquals(ReactomeStatus.FULL, res.getHasEvents().get(0).getStatus());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ rc.updateOnlyIdFields(res);
+ assertEquals(ReactomeStatus.FULL, res.getCreated().getStatus());
+ assertEquals(ReactomeStatus.FULL, res.getStableIdentifier().getStatus());
+ assertEquals(ReactomeStatus.FULL, res.getCompartments().get(0).getStatus());
+ assertEquals(ReactomeStatus.FULL, res.getLiteratureReferences().get(0).getStatus());
+ assertEquals(ReactomeStatus.FULL, res.getOrthologousEvents().get(0).getStatus());
+ assertEquals(ReactomeStatus.FULL, res.getPrecedingEvents().get(0).getStatus());
+ assertEquals(ReactomeStatus.FULL, res.getSpecies().getStatus());
+ assertEquals(ReactomeStatus.FULL, res.getSummations().get(0).getStatus());
+ assertEquals(ReactomeStatus.FULL, res.getHasEvents().get(0).getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceGeneProductParserTest.java b/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceGeneProductParserTest.java
index 96dafd1036ffd21e9fbdb30bd82f4c5fbf7e5c1c..5412d92cafa5ca788bd8e42436993a411517d073 100644
--- a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceGeneProductParserTest.java
+++ b/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceGeneProductParserTest.java
@@ -53,7 +53,7 @@ public class ReactomeReferenceGeneProductParserTest extends ReactomeTestFunction
assertEquals((Integer) 2, res.getReferenceDatabase().getDbId());
assertEquals((Integer) 48895, res.getSpecies().getDbId());
- assertEquals((Integer) 11867801, res.getReferenceGenes().get(0).getDbId());
+ assertEquals((Integer) 11373937, res.getReferenceGenes().get(0).getDbId());
} catch (Exception e) {
e.printStackTrace();
diff --git a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceIsoformParserTest.java b/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceIsoformParserTest.java
index e3d882c27ad2baac56974113119a2b413107166b..1cfb460fdd0e475b183fc36a0f44ef9cf4880bc6 100644
--- a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceIsoformParserTest.java
+++ b/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceIsoformParserTest.java
@@ -39,7 +39,7 @@ public class ReactomeReferenceIsoformParserTest extends ReactomeTestFunctions {
assertEquals((Integer) 2, res.getReferenceDatabase().getDbId());
assertEquals("false", res.getIsSequenceChanged());
assertEquals((Integer) 48887, res.getSpecies().getDbId());
- assertEquals((Integer) 11867801, res.getReferenceGenes().get(0).getDbId());
+ assertEquals((Integer) 11373937, res.getReferenceGenes().get(0).getDbId());
assertEquals((Integer) 192971, res.getReferenceTranscripts().get(0).getDbId());
assertEquals((Integer) 402286, res.getIsoformParents().get(0).getDbId());
assertEquals("UniProt:P02545-1 LMNA", res.getDisplayName());
diff --git a/reactome/testFiles/reactome/pathway.xml b/reactome/testFiles/reactome/pathway.xml
index aed576fa7191ff3d964abe234b50ea27cea42b71..44b00bf41c848565b74cebae596d017248c2d3ab 100644
--- a/reactome/testFiles/reactome/pathway.xml
+++ b/reactome/testFiles/reactome/pathway.xml
@@ -152,18 +152,4 @@
<isInDisease>false</isInDisease>
<isInferred>false</isInferred>
</hasEvent>
- <hasEvent>
- <dbId>114256</dbId>
- <displayName>Cytochrome C:Apaf-1 binds Procaspase-9</displayName>
- <schemaClass>Reaction</schemaClass>
- <isInDisease>false</isInDisease>
- <isInferred>false</isInferred>
- </hasEvent>
- <hasEvent>
- <dbId>114259</dbId>
- <displayName>Cleavage of Procaspase-9 to Caspase-9</displayName>
- <schemaClass>Reaction</schemaClass>
- <isInDisease>false</isInDisease>
- <isInferred>false</isInferred>
- </hasEvent>
</pathway>
\ No newline at end of file
diff --git a/reactome/testFiles/reactome/referenceGeneProduct.xml b/reactome/testFiles/reactome/referenceGeneProduct.xml
index 82a6159dea46e82a9321082fa289d6c5d6d6124d..502894eef6af22255c140af50ca417422668445a 100644
--- a/reactome/testFiles/reactome/referenceGeneProduct.xml
+++ b/reactome/testFiles/reactome/referenceGeneProduct.xml
@@ -20,7 +20,7 @@
<schemaClass>Species</schemaClass>
</species>
<referenceGene>
- <dbId>11867801</dbId>
+ <dbId>11373937</dbId>
<displayName>BioGPS Gene:1 A1BG</displayName>
<schemaClass>ReferenceDNASequence</schemaClass>
</referenceGene>
diff --git a/reactome/testFiles/reactome/referenceIsoform.xml b/reactome/testFiles/reactome/referenceIsoform.xml
index 041a5cf24ef6acadbdb59b84fc1256c8d2d908dd..8d08e978b194355ce6d27192a52b759c8a67989c 100644
--- a/reactome/testFiles/reactome/referenceIsoform.xml
+++ b/reactome/testFiles/reactome/referenceIsoform.xml
@@ -382,7 +382,7 @@
<schemaClass>Species</schemaClass>
</species>
<referenceGene>
- <dbId>11867801</dbId>
+ <dbId>11373937</dbId>
<displayName>BioGPS Gene:1 A1BG</displayName>
<schemaClass>ReferenceDNASequence</schemaClass>
</referenceGene>