From 642ebbccc83644a142725cbf2e3884f6a6f511c1 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 30 Jun 2017 14:51:23 +0200
Subject: [PATCH] test files modified due to changes in reactome db data
---
.../xml/ReactomeBlackBoxEventParserTest.java | 10 ++--
.../xml/ReactomeCandidateSetParserTest.java | 47 +++++++++--------
.../ReactomeCatalystActivityParserTest.java | 23 ++++----
.../xml/ReactomeDefinedSetParserTest.java | 14 ++---
...ReactomeGenomeEncodedEntityParserTest.java | 32 ++++++------
.../xml/ReactomeOtherEntityParserTest.java | 32 ++++++------
...eactomeReferenceGeneProductParserTest.java | 2 +-
.../ReactomeReferenceIsoformParserTest.java | 2 +-
.../testFiles/reactome/candidateSet.out.xml | 0
reactome/testFiles/reactome/candidateSet.xml | 2 +-
.../testFiles/reactome/catalystActivity.xml | 2 +-
reactome/testFiles/reactome/definedSet.xml | 52 +------------------
reactome/testFiles/reactome/reaction.xml | 2 +-
.../reactome/referenceGeneProduct.xml | 2 +-
.../testFiles/reactome/referenceIsoform.xml | 2 +-
15 files changed, 88 insertions(+), 136 deletions(-)
delete mode 100644 reactome/testFiles/reactome/candidateSet.out.xml
diff --git a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeBlackBoxEventParserTest.java b/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeBlackBoxEventParserTest.java
index 188e2ba612..7302ad9740 100644
--- a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeBlackBoxEventParserTest.java
+++ b/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeBlackBoxEventParserTest.java
@@ -2,10 +2,6 @@ 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.ReactomeBlackBoxEvent;
-import lcsb.mapviewer.reactome.model.ReactomeStatus;
import org.apache.log4j.Logger;
import org.junit.After;
@@ -14,8 +10,12 @@ import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
import org.w3c.dom.Document;
+import lcsb.mapviewer.reactome.ReactomeTestFunctions;
+import lcsb.mapviewer.reactome.model.ReactomeBlackBoxEvent;
+import lcsb.mapviewer.reactome.model.ReactomeStatus;
+
public class ReactomeBlackBoxEventParserTest extends ReactomeTestFunctions {
- Logger logger = Logger.getLogger(ReactomeBlackBoxEventParserTest.class);
+ Logger logger = Logger.getLogger(ReactomeBlackBoxEventParserTest.class);
@Autowired
ReactomeBlackBoxEventParser parser;
diff --git a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeCandidateSetParserTest.java b/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeCandidateSetParserTest.java
index b2cd3015e8..c882c0cdab 100644
--- a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeCandidateSetParserTest.java
+++ b/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeCandidateSetParserTest.java
@@ -2,10 +2,6 @@ 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.ReactomeCandidateSet;
-import lcsb.mapviewer.reactome.model.ReactomeStatus;
import org.apache.log4j.Logger;
import org.junit.After;
@@ -14,11 +10,16 @@ import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
import org.w3c.dom.Document;
-public class ReactomeCandidateSetParserTest extends ReactomeTestFunctions{
- Logger logger = Logger.getLogger(ReactomeCandidateSetParserTest.class);
+import lcsb.mapviewer.reactome.ReactomeTestFunctions;
+import lcsb.mapviewer.reactome.model.ReactomeCandidateSet;
+import lcsb.mapviewer.reactome.model.ReactomeStatus;
+
+public class ReactomeCandidateSetParserTest extends ReactomeTestFunctions {
+ Logger logger = Logger.getLogger(ReactomeCandidateSetParserTest.class);
@Autowired
- ReactomeCandidateSetParser parser ;
+ ReactomeCandidateSetParser parser;
+
@Before
public void setUp() throws Exception {
}
@@ -33,20 +34,20 @@ public class ReactomeCandidateSetParserTest extends ReactomeTestFunctions{
Document document = getXmlDocumentFromFile("testFiles/reactome/candidateSet.xml");
ReactomeCandidateSet res = parser.parseObject(document.getChildNodes().item(0));
assertNotNull(res);
- assertEquals((Integer)549096,res.getCreated().getDbId());
- assertEquals((Integer)549113,res.getDbId());
- assertEquals((Integer)549119,res.getModified().get(0).getDbId());
- assertEquals((Integer)1106869,res.getStableIdentifier().getDbId());
- assertEquals((Integer)17906,res.getCompartments().get(0).getDbId());
- assertEquals((Integer)162843,res.getInferredTos().get(0).getDbId());
- assertEquals((Integer)61855,res.getHasMembers().get(0).getDbId());
- assertEquals((Integer)549076,res.getHasCandidates().get(0).getDbId());
- assertEquals((Integer)48887,res.getSpecies().get(0).getDbId());
- assertEquals((Integer)3508822,res.getEdited().get(0).getDbId());
-
- assertEquals("GPAM or GPAT2",res.getNames().get(0));
- assertEquals("GPAM or GPAT2 [mitochondrial outer membrane]",res.getDisplayName());
-
+ assertEquals((Integer) 549096, res.getCreated().getDbId());
+ assertEquals((Integer) 549113, res.getDbId());
+ assertEquals((Integer) 549119, res.getModified().get(0).getDbId());
+ assertEquals((Integer) 1106869, res.getStableIdentifier().getDbId());
+ assertEquals((Integer) 17906, res.getCompartments().get(0).getDbId());
+ assertEquals((Integer) 198809, res.getInferredTos().get(0).getDbId());
+ assertEquals((Integer) 61855, res.getHasMembers().get(0).getDbId());
+ assertEquals((Integer) 549076, res.getHasCandidates().get(0).getDbId());
+ assertEquals((Integer) 48887, res.getSpecies().get(0).getDbId());
+ assertEquals((Integer) 3508822, res.getEdited().get(0).getDbId());
+
+ assertEquals("GPAM or GPAT2", res.getNames().get(0));
+ assertEquals("GPAM or GPAT2 [mitochondrial outer membrane]", res.getDisplayName());
+
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -58,7 +59,7 @@ public class ReactomeCandidateSetParserTest extends ReactomeTestFunctions{
try {
Document document = getXmlDocumentFromFile("testFiles/reactome/candidateSet.xml");
ReactomeCandidateSet res = parser.parseObject(document.getChildNodes().item(0));
-
+
rc.updateOnlyIdFields(res);
assertEquals(ReactomeStatus.FULL, res.getCreated().getStatus());
assertEquals(ReactomeStatus.FULL, res.getStableIdentifier().getStatus());
@@ -69,7 +70,7 @@ public class ReactomeCandidateSetParserTest extends ReactomeTestFunctions{
assertEquals(ReactomeStatus.FULL, res.getHasCandidates().get(0).getStatus());
assertEquals(ReactomeStatus.FULL, res.getEdited().get(0).getStatus());
assertEquals(ReactomeStatus.FULL, res.getSpecies().get(0).getStatus());
-
+
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeCatalystActivityParserTest.java b/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeCatalystActivityParserTest.java
index e4d80756f6..e3bb92a7f2 100644
--- a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeCatalystActivityParserTest.java
+++ b/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeCatalystActivityParserTest.java
@@ -2,10 +2,6 @@ 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.ReactomeCatalystActivity;
-import lcsb.mapviewer.reactome.model.ReactomeStatus;
import org.apache.log4j.Logger;
import org.junit.After;
@@ -14,11 +10,16 @@ import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
import org.w3c.dom.Document;
-public class ReactomeCatalystActivityParserTest extends ReactomeTestFunctions{
- Logger logger = Logger.getLogger(ReactomeCatalystActivityParserTest.class);
+import lcsb.mapviewer.reactome.ReactomeTestFunctions;
+import lcsb.mapviewer.reactome.model.ReactomeCatalystActivity;
+import lcsb.mapviewer.reactome.model.ReactomeStatus;
+
+public class ReactomeCatalystActivityParserTest extends ReactomeTestFunctions {
+ Logger logger = Logger.getLogger(ReactomeCatalystActivityParserTest.class);
@Autowired
- ReactomeCatalystActivityParser parser ;
+ ReactomeCatalystActivityParser parser;
+
@Before
public void setUp() throws Exception {
}
@@ -33,8 +34,8 @@ public class ReactomeCatalystActivityParserTest extends ReactomeTestFunctions{
Document document = getXmlDocumentFromFile("testFiles/reactome/catalystActivity.xml");
ReactomeCatalystActivity res = parser.parseObject(document.getChildNodes().item(0));
assertNotNull(res);
- assertEquals((Integer)8347,res.getActivity().getDbId());
- assertEquals((Integer)162843,res.getPhysicalEntity().getDbId());
+ assertEquals((Integer) 8347, res.getActivity().getDbId());
+ assertEquals((Integer) 2160866, res.getPhysicalEntity().getDbId());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -46,12 +47,12 @@ public class ReactomeCatalystActivityParserTest extends ReactomeTestFunctions{
try {
Document document = getXmlDocumentFromFile("testFiles/reactome/catalystActivity.xml");
ReactomeCatalystActivity res = parser.parseObject(document.getChildNodes().item(0));
-
+
rc.updateOnlyIdFields(res);
assertEquals(ReactomeStatus.FULL, res.getActivity().getStatus());
assertEquals(ReactomeStatus.FULL, res.getPhysicalEntity().getStatus());
assertEquals(ReactomeStatus.FULL, res.getCreated().getStatus());
-
+
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeDefinedSetParserTest.java b/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeDefinedSetParserTest.java
index a8923e80b3..08ea34aa2b 100644
--- a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeDefinedSetParserTest.java
+++ b/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeDefinedSetParserTest.java
@@ -2,10 +2,6 @@ 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.ReactomeDefinedSet;
-import lcsb.mapviewer.reactome.model.ReactomeStatus;
import org.apache.log4j.Logger;
import org.junit.After;
@@ -14,11 +10,15 @@ import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
import org.w3c.dom.Document;
+import lcsb.mapviewer.reactome.ReactomeTestFunctions;
+import lcsb.mapviewer.reactome.model.ReactomeDefinedSet;
+import lcsb.mapviewer.reactome.model.ReactomeStatus;
+
public class ReactomeDefinedSetParserTest extends ReactomeTestFunctions {
- Logger logger = Logger.getLogger(ReactomeDefinedSetParserTest.class);
+ Logger logger = Logger.getLogger(ReactomeDefinedSetParserTest.class);
@Autowired
- ReactomeDefinedSetParser parser;
+ ReactomeDefinedSetParser parser;
@Before
public void setUp() throws Exception {
@@ -39,7 +39,7 @@ public class ReactomeDefinedSetParserTest extends ReactomeTestFunctions {
assertEquals((Integer) 453376, res.getModified().get(0).getDbId());
assertEquals((Integer) 1107637, res.getStableIdentifier().getDbId());
assertEquals((Integer) 70101, res.getCompartments().get(0).getDbId());
- assertEquals((Integer) 162843, res.getInferredTos().get(0).getDbId());
+ assertEquals((Integer) 9178869, res.getInferredTos().get(0).getDbId());
assertEquals((Integer) 453360, res.getHasMembers().get(0).getDbId());
assertEquals((Integer) 48887, res.getSpecies().get(0).getDbId());
assertEquals((Integer) 445353, res.getAuthored().getDbId());
diff --git a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeGenomeEncodedEntityParserTest.java b/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeGenomeEncodedEntityParserTest.java
index 97b012230b..5207b1d290 100644
--- a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeGenomeEncodedEntityParserTest.java
+++ b/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeGenomeEncodedEntityParserTest.java
@@ -2,10 +2,6 @@ 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.ReactomeGenomeEncodedEntity;
-import lcsb.mapviewer.reactome.model.ReactomeStatus;
import org.apache.log4j.Logger;
import org.junit.After;
@@ -14,11 +10,15 @@ import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
import org.w3c.dom.Document;
-public class ReactomeGenomeEncodedEntityParserTest extends ReactomeTestFunctions{
- Logger logger = Logger.getLogger(ReactomeGenomeEncodedEntityParserTest.class);
+import lcsb.mapviewer.reactome.ReactomeTestFunctions;
+import lcsb.mapviewer.reactome.model.ReactomeGenomeEncodedEntity;
+import lcsb.mapviewer.reactome.model.ReactomeStatus;
+
+public class ReactomeGenomeEncodedEntityParserTest extends ReactomeTestFunctions {
+ Logger logger = Logger.getLogger(ReactomeGenomeEncodedEntityParserTest.class);
@Autowired
- ReactomeGenomeEncodedEntityParser parser = new ReactomeGenomeEncodedEntityParser();
+ ReactomeGenomeEncodedEntityParser parser = new ReactomeGenomeEncodedEntityParser();
@Before
public void setUp() throws Exception {
@@ -34,13 +34,13 @@ public class ReactomeGenomeEncodedEntityParserTest extends ReactomeTestFunctions
Document document = getXmlDocumentFromFile("testFiles/reactome/genomeEncodedEntity.xml");
ReactomeGenomeEncodedEntity res = parser.parseObject(document.getChildNodes().item(0));
assertNotNull(res);
- assertEquals((Integer)500674,res.getDbId());
- assertEquals((Integer)500675,res.getCreated().getDbId());
- assertEquals((Integer)500696,res.getModified().get(0).getDbId());
- assertEquals((Integer)1106207,res.getStableIdentifier().getDbId());
- assertEquals((Integer)876,res.getCompartments().get(0).getDbId());
- assertEquals((Integer)48887,res.getSpecies().getDbId());
- assertEquals("unidentified caspase acting on ZO-2",res.getNames().get(0));
+ assertEquals((Integer) 500674, res.getDbId());
+ assertEquals((Integer) 500675, res.getCreated().getDbId());
+ assertEquals((Integer) 500696, res.getModified().get(0).getDbId());
+ assertEquals((Integer) 1106207, res.getStableIdentifier().getDbId());
+ assertEquals((Integer) 876, res.getCompartments().get(0).getDbId());
+ assertEquals((Integer) 48887, res.getSpecies().getDbId());
+ assertEquals("unidentified caspase acting on ZO-2", res.getNames().get(0));
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -52,14 +52,14 @@ public class ReactomeGenomeEncodedEntityParserTest extends ReactomeTestFunctions
try {
Document document = getXmlDocumentFromFile("testFiles/reactome/genomeEncodedEntity.xml");
ReactomeGenomeEncodedEntity res = parser.parseObject(document.getChildNodes().item(0));
-
+
rc.updateOnlyIdFields(res);
assertEquals(ReactomeStatus.FULL, res.getCreated().getStatus());
assertEquals(ReactomeStatus.FULL, res.getModified().get(0).getStatus());
assertEquals(ReactomeStatus.FULL, res.getStableIdentifier().getStatus());
assertEquals(ReactomeStatus.FULL, res.getCompartments().get(0).getStatus());
assertEquals(ReactomeStatus.FULL, res.getSpecies().getStatus());
-
+
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeOtherEntityParserTest.java b/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeOtherEntityParserTest.java
index befdce0974..ebffa145ef 100644
--- a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeOtherEntityParserTest.java
+++ b/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeOtherEntityParserTest.java
@@ -2,10 +2,6 @@ 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.ReactomeOtherEntity;
-import lcsb.mapviewer.reactome.model.ReactomeStatus;
import org.apache.log4j.Logger;
import org.junit.After;
@@ -14,11 +10,15 @@ import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
import org.w3c.dom.Document;
-public class ReactomeOtherEntityParserTest extends ReactomeTestFunctions{
- Logger logger = Logger.getLogger(ReactomeOtherEntityParserTest.class);
+import lcsb.mapviewer.reactome.ReactomeTestFunctions;
+import lcsb.mapviewer.reactome.model.ReactomeOtherEntity;
+import lcsb.mapviewer.reactome.model.ReactomeStatus;
+
+public class ReactomeOtherEntityParserTest extends ReactomeTestFunctions {
+ Logger logger = Logger.getLogger(ReactomeOtherEntityParserTest.class);
@Autowired
- ReactomeOtherEntityParser parser ;
+ ReactomeOtherEntityParser parser;
@Before
public void setUp() throws Exception {
@@ -34,15 +34,15 @@ public class ReactomeOtherEntityParserTest extends ReactomeTestFunctions{
Document document = getXmlDocumentFromFile("testFiles/reactome/otherEntity.xml");
ReactomeOtherEntity res = parser.parseObject(document.getChildNodes().item(0));
assertNotNull(res);
-
- assertEquals((Integer)29428, res.getDbId());
+
+ assertEquals((Integer) 29428, res.getDbId());
assertEquals("DNA [nucleoplasm]", res.getDisplayName());
- assertEquals((Integer)77027, res.getCreated().getDbId());
- assertEquals((Integer)368619, res.getStableIdentifier().getDbId());
- assertEquals((Integer)7660, res.getCompartments().get(0).getDbId());
- assertEquals((Integer)212290, res.getCrossReferences().get(0).getDbId());
+ assertEquals((Integer) 77027, res.getCreated().getDbId());
+ assertEquals((Integer) 368619, res.getStableIdentifier().getDbId());
+ assertEquals((Integer) 7660, res.getCompartments().get(0).getDbId());
+ assertEquals((Integer) 212290, res.getCrossReferences().get(0).getDbId());
assertEquals(2, res.getNames().size());
-
+
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -54,14 +54,14 @@ public class ReactomeOtherEntityParserTest extends ReactomeTestFunctions{
try {
Document document = getXmlDocumentFromFile("testFiles/reactome/otherEntity.xml");
ReactomeOtherEntity res = parser.parseObject(document.getChildNodes().item(0));
-
+
rc.updateOnlyIdFields(res);
assertEquals(ReactomeStatus.FULL, res.getStableIdentifier().getStatus());
assertEquals(ReactomeStatus.FULL, res.getCompartments().get(0).getStatus());
assertEquals(ReactomeStatus.FULL, res.getCrossReferences().get(0).getStatus());
assertEquals(ReactomeStatus.FULL, res.getModified().get(0).getStatus());
assertEquals(ReactomeStatus.FULL, res.getCreated().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 968b26e27d..826e059e5d 100644
--- a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceGeneProductParserTest.java
+++ b/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceGeneProductParserTest.java
@@ -51,7 +51,7 @@ public class ReactomeReferenceGeneProductParserTest extends ReactomeTestFunction
assertEquals((Integer) 2, res.getReferenceDatabase().getDbId());
assertEquals((Integer) 48895, res.getSpecies().getDbId());
- assertEquals((Integer) 7493873, res.getReferenceGenes().get(0).getDbId());
+ assertEquals((Integer) 10030875, 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 036abdd22a..2f3fba1e98 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) 7493873, res.getReferenceGenes().get(0).getDbId());
+ assertEquals((Integer) 10030875, 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/candidateSet.out.xml b/reactome/testFiles/reactome/candidateSet.out.xml
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/reactome/testFiles/reactome/candidateSet.xml b/reactome/testFiles/reactome/candidateSet.xml
index 5189f9ef86..c19156e7e9 100644
--- a/reactome/testFiles/reactome/candidateSet.xml
+++ b/reactome/testFiles/reactome/candidateSet.xml
@@ -24,7 +24,7 @@
<schemaClass>EntityCompartment</schemaClass>
</compartment>
<inferredTo xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="candidateSet">
- <dbId>162843</dbId>
+ <dbId>198809</dbId>
<displayName>GPAM or GPAT2 [intracellular]</displayName>
<schemaClass>CandidateSet</schemaClass>
</inferredTo>
diff --git a/reactome/testFiles/reactome/catalystActivity.xml b/reactome/testFiles/reactome/catalystActivity.xml
index 958153c07f..32897e931c 100644
--- a/reactome/testFiles/reactome/catalystActivity.xml
+++ b/reactome/testFiles/reactome/catalystActivity.xml
@@ -14,7 +14,7 @@
<schemaClass>GO_MolecularFunction</schemaClass>
</activity>
<physicalEntity xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="genomeEncodedEntity">
- <dbId>162843</dbId>
+ <dbId>2160866</dbId>
<displayName>AGL [cytosol]</displayName>
<schemaClass>EntityWithAccessionedSequence</schemaClass>
</physicalEntity>
diff --git a/reactome/testFiles/reactome/definedSet.xml b/reactome/testFiles/reactome/definedSet.xml
index e447c5775a..10a7f419c2 100644
--- a/reactome/testFiles/reactome/definedSet.xml
+++ b/reactome/testFiles/reactome/definedSet.xml
@@ -24,57 +24,7 @@
<schemaClass>EntityCompartment</schemaClass>
</compartment>
<inferredTo xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="definedSet">
- <dbId>162843</dbId>
- <displayName>((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl)glycogenin dimer [cytosol]</displayName>
- <schemaClass>DefinedSet</schemaClass>
- </inferredTo>
- <inferredTo xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="definedSet">
- <dbId>3675056</dbId>
- <displayName>((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl)glycogenin dimer [cytosol]</displayName>
- <schemaClass>DefinedSet</schemaClass>
- </inferredTo>
- <inferredTo>
- <dbId>3698315</dbId>
- <displayName>((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl)glycogenin-1 dimer (name copied from entity in Homo sapiens) [cytosol]</displayName>
- <schemaClass>Complex</schemaClass>
- </inferredTo>
- <inferredTo xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="definedSet">
- <dbId>3745417</dbId>
- <displayName>((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl)glycogenin dimer [cytosol]</displayName>
- <schemaClass>DefinedSet</schemaClass>
- </inferredTo>
- <inferredTo xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="definedSet">
- <dbId>3794661</dbId>
- <displayName>((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl)glycogenin dimer [cytosol]</displayName>
- <schemaClass>DefinedSet</schemaClass>
- </inferredTo>
- <inferredTo>
- <dbId>3841962</dbId>
- <displayName>((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl)glycogenin-1 dimer (name copied from entity in Homo sapiens) [cytosol]</displayName>
- <schemaClass>Complex</schemaClass>
- </inferredTo>
- <inferredTo>
- <dbId>3896793</dbId>
- <displayName>((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl)glycogenin-1 dimer (name copied from entity in Homo sapiens) [cytosol]</displayName>
- <schemaClass>Complex</schemaClass>
- </inferredTo>
- <inferredTo xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="definedSet">
- <dbId>3946296</dbId>
- <displayName>((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl)glycogenin dimer [cytosol]</displayName>
- <schemaClass>DefinedSet</schemaClass>
- </inferredTo>
- <inferredTo xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="definedSet">
- <dbId>3992073</dbId>
- <displayName>((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl)glycogenin dimer [cytosol]</displayName>
- <schemaClass>DefinedSet</schemaClass>
- </inferredTo>
- <inferredTo xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="definedSet">
- <dbId>4028294</dbId>
- <displayName>((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl)glycogenin dimer [cytosol]</displayName>
- <schemaClass>DefinedSet</schemaClass>
- </inferredTo>
- <inferredTo xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="definedSet">
- <dbId>4076351</dbId>
+ <dbId>9178869</dbId>
<displayName>((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl)glycogenin dimer [cytosol]</displayName>
<schemaClass>DefinedSet</schemaClass>
</inferredTo>
diff --git a/reactome/testFiles/reactome/reaction.xml b/reactome/testFiles/reactome/reaction.xml
index 1f3cc150a2..0566cadb34 100644
--- a/reactome/testFiles/reactome/reaction.xml
+++ b/reactome/testFiles/reactome/reaction.xml
@@ -73,7 +73,7 @@
<schemaClass>CatalystActivity</schemaClass>
</catalystActivity>
<input xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="complex">
- <dbId>162843</dbId>
+ <dbId>434005</dbId>
<displayName>((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl)glycogenin-1 dimer (name copied from entity in Homo sapiens) [cytosol]</displayName>
<schemaClass>Complex</schemaClass>
</input>
diff --git a/reactome/testFiles/reactome/referenceGeneProduct.xml b/reactome/testFiles/reactome/referenceGeneProduct.xml
index c025d910f3..e60c7b6e11 100644
--- a/reactome/testFiles/reactome/referenceGeneProduct.xml
+++ b/reactome/testFiles/reactome/referenceGeneProduct.xml
@@ -20,7 +20,7 @@
<schemaClass>Species</schemaClass>
</species>
<referenceGene>
- <dbId>7493873</dbId>
+ <dbId>10030875</dbId>
<displayName>ENSEMBL:DDB_G0292748</displayName>
<schemaClass>ReferenceDNASequence</schemaClass>
</referenceGene>
diff --git a/reactome/testFiles/reactome/referenceIsoform.xml b/reactome/testFiles/reactome/referenceIsoform.xml
index 213c168a9d..f5286c171f 100644
--- a/reactome/testFiles/reactome/referenceIsoform.xml
+++ b/reactome/testFiles/reactome/referenceIsoform.xml
@@ -382,7 +382,7 @@
<schemaClass>Species</schemaClass>
</species>
<referenceGene>
- <dbId>7493873</dbId>
+ <dbId>10030875</dbId>
<displayName>ENSEMBL:ENSG00000160789</displayName>
<schemaClass>ReferenceDNASequence</schemaClass>
</referenceGene>
--
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