From a7270a5434616e3f947b71878b4c1f6805cc4a92 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 20 Dec 2017 16:14:02 +0100
Subject: [PATCH] getModel method added to BioEntity
---
.../annotation/RestAnnotationParserTest.java | 818 ++++++++----------
.../lcsb/mapviewer/model/map/BioEntity.java | 298 ++++---
.../model/map/reaction/Reaction.java | 6 +-
.../mapviewer/model/map/species/Element.java | 5 +-
4 files changed, 513 insertions(+), 614 deletions(-)
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
index 7c68b06fff..2ed94bcb8f 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
@@ -6,8 +6,6 @@ import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
-import java.util.ArrayList;
-import java.util.Collection;
import java.util.List;
import java.util.Set;
@@ -16,6 +14,7 @@ import org.apache.xerces.dom.DocumentImpl;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import org.w3c.dom.Document;
import org.w3c.dom.Node;
@@ -34,465 +33,362 @@ import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Species;
public class RestAnnotationParserTest extends CellDesignerTestFunctions {
- Logger logger = Logger.getLogger(RestAnnotationParserTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void test() throws Exception {
-
- try {
- RestAnnotationParser rap = new RestAnnotationParser();
-
- String response = readFile("testFiles/annotation/sampleDescription.txt");
-
- List<String> synonyms = rap.getSynonyms(response);
- assertEquals(3, synonyms.size());
- assertTrue(synonyms.contains("CAMK"));
- assertTrue(synonyms.contains("CAMKIV"));
-
- List<String> formerSymbols = rap.getFormerSymbols(response);
- assertEquals(0, formerSymbols.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseNotes() throws Exception {
- try {
- RestAnnotationParser parser = new RestAnnotationParser();
- Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes.xml");
- Species proteinAlias = new GenericProtein("id");
- parser.processNotes(node.getFirstChild(), proteinAlias);
- String notes = proteinAlias.getNotes();
- assertNotNull(notes);
- assertFalse(notes.contains("body"));
- assertTrue(notes.contains("some"));
- // after redoing it should be the same
- parser.processNotes(node.getFirstChild(), proteinAlias);
- notes = proteinAlias.getNotes();
- assertNotNull(notes);
- assertFalse(notes.contains("body"));
- assertTrue(notes.contains("some"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseNotes2() throws Exception {
- try {
- RestAnnotationParser parser = new RestAnnotationParser();
- Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes3.xml");
- Species proteinAlias = new GenericProtein("id");
- parser.processNotes(node.getFirstChild(), proteinAlias);
- String notes = proteinAlias.getNotes();
- assertNotNull(notes);
- assertFalse(notes.contains("body"));
- assertTrue(notes.contains("some"));
- // after redoing it should be the same
- parser.processNotes(node.getFirstChild(), proteinAlias);
- notes = proteinAlias.getNotes();
- assertNotNull(notes);
- assertFalse(notes.contains("body"));
- assertTrue(notes.contains("some"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseNotes3() throws Exception {
- try {
- RestAnnotationParser parser = new RestAnnotationParser();
- Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes4.xml");
- Species proteinAlias = new GenericProtein("id");
- proteinAlias.setNotes("text");
- parser.processNotes(node.getFirstChild(), proteinAlias);
- String notes = proteinAlias.getNotes();
- assertNotNull(notes);
- assertFalse(notes.contains("body"));
- assertTrue(notes.contains("some"));
- // after redoing it should be the same
- parser.processNotes(node.getFirstChild(), proteinAlias);
- notes = proteinAlias.getNotes();
- assertNotNull(notes);
- assertFalse(notes.contains("body"));
- assertTrue(notes.contains("some"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseCollisionNotes() throws Exception {
- try {
- RestAnnotationParser parser = new RestAnnotationParser();
- Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes2.xml");
-
- GenericProtein protein = new GenericProtein("pr_id1");
- protein.addSynonym("a1");
- protein.addFormerSymbol("a1");
- protein.setFullName("yyy");
- protein.setAbbreviation("aaaa");
- protein.setCharge(9);
- protein.setSymbol("D");
- parser.processNotes(node.getFirstChild(), protein);
- assertEquals(1, protein.getSynonyms().size());
- assertEquals(1, protein.getFormerSymbols().size());
-
- assertEquals(6, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidNotes1() throws Exception {
- try {
- RestAnnotationParser parser = new RestAnnotationParser();
- Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes_invalid_charge.xml");
-
- Species proteinAlias = new GenericProtein("id");
- parser.processNotes(node.getFirstChild(), proteinAlias);
-
- assertEquals(1, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseCollisionNotes2() throws Exception {
- try {
- RestAnnotationParser parser = new RestAnnotationParser();
- Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes2.xml");
- Reaction reaction = new Reaction();
- reaction.addSynonym("a1");
- reaction.setAbbreviation("aaaa");
- reaction.setSubsystem("sss");
- reaction.setGeneProteinReaction("str");
- reaction.setFormula("xxx");
- reaction.setMechanicalConfidenceScore(-45);
- reaction.setUpperBound(4.5);
- reaction.setLowerBound(4.5);
-
- parser.processNotes(node.getFirstChild(), reaction);
-
- assertEquals(8, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testMoveAnnotationsFromNotes() throws Exception {
- try {
- Model model = getModelForFile("testFiles/copyingAnnotationModel.xml");
-
- Set<Element> elements = model.getElements();
- for (Element element : elements) {
- if (element.getName().equals("blabla")) {
- assertEquals(2, element.getMiriamData().size());
- element.getMiriamData().add(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, "12345"));
- element.getMiriamData().add(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, "333666"));
- assertEquals(2, element.getMiriamData().size());
- }
- assertFalse(element.getNotes().contains("rdf:RDF"));
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProcessRdfDescription() throws Exception {
- try {
- RestAnnotationParser rap = new RestAnnotationParser();
- Species speciesAlias = new GenericProtein("id");
- speciesAlias.setNotes(
- "begining\n" + "<rdf:RDF>" + "<rdf:Description rdf:about=\"#s2157\">\n" + "<bqmodel:is>\n" + "<rdf:Bag>\n"
- + "<rdf:li rdf:resource=\"urn:miriam:obo.chebi:CHEBI%3A17515\"/>\n" + "</rdf:Bag>\n" + "</bqmodel:is>\n" + "</rdf:Description>\n" + "</rdf:RDF>"
- + "\nend ending");
- rap.processRdfDescription(speciesAlias);
- assertEquals("begining\n\nend ending", speciesAlias.getNotes());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetMiriamDataFromAnnotation() throws Exception {
- try {
- RestAnnotationParser rap = new RestAnnotationParser();
- String response = readFile("testFiles/annotation/sampleDescription.txt");
-
- Set<MiriamData> set = rap.getMiriamData(response);
- for (MiriamData miriamData : set) {
- if (miriamData.getDataType().equals(MiriamType.KEGG_GENES)) {
- assertTrue(miriamData.getResource().contains("hsa"));
- }
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetMiriamDataFromEmpty() throws Exception {
- try {
- RestAnnotationParser rap = new RestAnnotationParser();
-
- Set<MiriamData> set = rap.getMiriamData(null);
- assertEquals(0, set.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testCreateAnnotationString() throws Exception {
- try {
- RestAnnotationParser rap = new RestAnnotationParser();
-
- String former1 = "form1";
- String former2 = "form2";
- GenericProtein element = new GenericProtein("id");
- element.addFormerSymbol(former1);
- element.addFormerSymbol(former2);
- element.setCharge(1);
- String str = rap.createAnnotationString(element, true);
- assertTrue(str.contains(former1));
- assertTrue(str.contains(former2));
-
- for (NoteField field : NoteField.values()) {
- if (field.getClazz().isAssignableFrom(element.getClass()) || CellDesignerElement.class.isAssignableFrom(field.getClazz())) {
- assertTrue("Export string doesn't contain info about: " + field.getCommonName(), str.indexOf(field.getCommonName()) >= 0);
- }
-
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetFormerSymbolsFromInvalidStr() throws Exception {
- try {
- RestAnnotationParser rap = new RestAnnotationParser();
-
- assertEquals(0, rap.getFormerSymbols(null).size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetNotesInvalid() throws Exception {
- try {
- RestAnnotationParser rap = new RestAnnotationParser();
-
- Document xmlDoc = new DocumentImpl();
- Node node = xmlDoc.createElement("bla");
-
- rap.getNotes(node);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testProcessNotesForInvalidElement() throws Exception {
- try {
- RestAnnotationParser parser = new RestAnnotationParser();
- Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes4.xml");
- parser.processNotes(node.getFirstChild(), new BioEntity() {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- @Override
- public void setSynonyms(List<String> synonyms) {
- }
-
- @Override
- public void setSymbol(String symbol) {
- }
-
- @Override
- public void setNotes(String notes) {
- }
-
- @Override
- public void setName(String name) {
- }
-
- @Override
- public void setFormula(String formula) {
- }
-
- @Override
- public void setAbbreviation(String abbreviation) {
- }
-
- @Override
- public List<String> getSynonyms() {
- return new ArrayList<>();
- }
-
- @Override
- public String getSymbol() {
- return "";
- }
-
- @Override
- public String getNotes() {
- return "";
- }
-
- @Override
- public String getName() {
- return "";
- }
-
- @Override
- public Collection<MiriamData> getMiriamData() {
- return null;
- }
-
- @Override
- public String getFormula() {
- return null;
- }
-
- @Override
- public String getAbbreviation() {
- return null;
- }
-
- @Override
- public void addMiriamData(MiriamData md) {
- }
-
- @Override
- public void addMiriamData(Collection<MiriamData> miriamData) {
- }
-
- @Override
- public int getId() {
- // TODO Auto-generated method stub
- return 0;
- }
-
- @Override
- public String getStringType() {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public void setVisibilityLevel(String zoomLevelVisibility) {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public String getVisibilityLevel() {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public void setVisibilityLevel(Integer zoomLevelVisibility) {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public String getElementId() {
- // TODO Auto-generated method stub
- return null;
+ Logger logger = Logger.getLogger(RestAnnotationParserTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void test() throws Exception {
+
+ try {
+ RestAnnotationParser rap = new RestAnnotationParser();
+
+ String response = readFile("testFiles/annotation/sampleDescription.txt");
+
+ List<String> synonyms = rap.getSynonyms(response);
+ assertEquals(3, synonyms.size());
+ assertTrue(synonyms.contains("CAMK"));
+ assertTrue(synonyms.contains("CAMKIV"));
+
+ List<String> formerSymbols = rap.getFormerSymbols(response);
+ assertEquals(0, formerSymbols.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseNotes() throws Exception {
+ try {
+ RestAnnotationParser parser = new RestAnnotationParser();
+ Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes.xml");
+ Species proteinAlias = new GenericProtein("id");
+ parser.processNotes(node.getFirstChild(), proteinAlias);
+ String notes = proteinAlias.getNotes();
+ assertNotNull(notes);
+ assertFalse(notes.contains("body"));
+ assertTrue(notes.contains("some"));
+ // after redoing it should be the same
+ parser.processNotes(node.getFirstChild(), proteinAlias);
+ notes = proteinAlias.getNotes();
+ assertNotNull(notes);
+ assertFalse(notes.contains("body"));
+ assertTrue(notes.contains("some"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseNotes2() throws Exception {
+ try {
+ RestAnnotationParser parser = new RestAnnotationParser();
+ Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes3.xml");
+ Species proteinAlias = new GenericProtein("id");
+ parser.processNotes(node.getFirstChild(), proteinAlias);
+ String notes = proteinAlias.getNotes();
+ assertNotNull(notes);
+ assertFalse(notes.contains("body"));
+ assertTrue(notes.contains("some"));
+ // after redoing it should be the same
+ parser.processNotes(node.getFirstChild(), proteinAlias);
+ notes = proteinAlias.getNotes();
+ assertNotNull(notes);
+ assertFalse(notes.contains("body"));
+ assertTrue(notes.contains("some"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseNotes3() throws Exception {
+ try {
+ RestAnnotationParser parser = new RestAnnotationParser();
+ Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes4.xml");
+ Species proteinAlias = new GenericProtein("id");
+ proteinAlias.setNotes("text");
+ parser.processNotes(node.getFirstChild(), proteinAlias);
+ String notes = proteinAlias.getNotes();
+ assertNotNull(notes);
+ assertFalse(notes.contains("body"));
+ assertTrue(notes.contains("some"));
+ // after redoing it should be the same
+ parser.processNotes(node.getFirstChild(), proteinAlias);
+ notes = proteinAlias.getNotes();
+ assertNotNull(notes);
+ assertFalse(notes.contains("body"));
+ assertTrue(notes.contains("some"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseCollisionNotes() throws Exception {
+ try {
+ RestAnnotationParser parser = new RestAnnotationParser();
+ Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes2.xml");
+
+ GenericProtein protein = new GenericProtein("pr_id1");
+ protein.addSynonym("a1");
+ protein.addFormerSymbol("a1");
+ protein.setFullName("yyy");
+ protein.setAbbreviation("aaaa");
+ protein.setCharge(9);
+ protein.setSymbol("D");
+ parser.processNotes(node.getFirstChild(), protein);
+ assertEquals(1, protein.getSynonyms().size());
+ assertEquals(1, protein.getFormerSymbols().size());
+
+ assertEquals(6, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidNotes1() throws Exception {
+ try {
+ RestAnnotationParser parser = new RestAnnotationParser();
+ Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes_invalid_charge.xml");
+
+ Species proteinAlias = new GenericProtein("id");
+ parser.processNotes(node.getFirstChild(), proteinAlias);
+
+ assertEquals(1, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseCollisionNotes2() throws Exception {
+ try {
+ RestAnnotationParser parser = new RestAnnotationParser();
+ Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes2.xml");
+ Reaction reaction = new Reaction();
+ reaction.addSynonym("a1");
+ reaction.setAbbreviation("aaaa");
+ reaction.setSubsystem("sss");
+ reaction.setGeneProteinReaction("str");
+ reaction.setFormula("xxx");
+ reaction.setMechanicalConfidenceScore(-45);
+ reaction.setUpperBound(4.5);
+ reaction.setLowerBound(4.5);
+
+ parser.processNotes(node.getFirstChild(), reaction);
+
+ assertEquals(8, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testMoveAnnotationsFromNotes() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/copyingAnnotationModel.xml");
+
+ Set<Element> elements = model.getElements();
+ for (Element element : elements) {
+ if (element.getName().equals("blabla")) {
+ assertEquals(2, element.getMiriamData().size());
+ element.getMiriamData()
+ .add(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, "12345"));
+ element.getMiriamData()
+ .add(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, "333666"));
+ assertEquals(2, element.getMiriamData().size());
}
- });
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProcessInvalidNotes() throws Exception {
- try {
- RestAnnotationParser parser = new RestAnnotationParser();
- String str = super.readFile("testFiles/xmlNodeTestExamples/notes5.xml");
-
- parser.processNotes(str, new GenericProtein("id"));
-
- assertEquals(1, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProcessNotes() throws Exception {
- try {
- String newNotes = "new notes";
- String oldNotes = "old notes";
- RestAnnotationParser parser = new RestAnnotationParser();
- String str = "Description: " + newNotes + "\n" + oldNotes;
- GenericProtein protein = new GenericProtein("id");
- parser.processNotes(str, protein);
-
- assertTrue(protein.getNotes().contains(newNotes));
- assertTrue(protein.getNotes().contains(oldNotes));
- assertFalse(protein.getNotes().contains("Description"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertFalse(element.getNotes().contains("rdf:RDF"));
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProcessRdfDescription() throws Exception {
+ try {
+ RestAnnotationParser rap = new RestAnnotationParser();
+ Species speciesAlias = new GenericProtein("id");
+ speciesAlias.setNotes("begining\n" + "<rdf:RDF>" + "<rdf:Description rdf:about=\"#s2157\">\n" + "<bqmodel:is>\n"
+ + "<rdf:Bag>\n" + "<rdf:li rdf:resource=\"urn:miriam:obo.chebi:CHEBI%3A17515\"/>\n" + "</rdf:Bag>\n"
+ + "</bqmodel:is>\n" + "</rdf:Description>\n" + "</rdf:RDF>" + "\nend ending");
+ rap.processRdfDescription(speciesAlias);
+ assertEquals("begining\n\nend ending", speciesAlias.getNotes());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetMiriamDataFromAnnotation() throws Exception {
+ try {
+ RestAnnotationParser rap = new RestAnnotationParser();
+ String response = readFile("testFiles/annotation/sampleDescription.txt");
+
+ Set<MiriamData> set = rap.getMiriamData(response);
+ for (MiriamData miriamData : set) {
+ if (miriamData.getDataType().equals(MiriamType.KEGG_GENES)) {
+ assertTrue(miriamData.getResource().contains("hsa"));
+ }
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetMiriamDataFromEmpty() throws Exception {
+ try {
+ RestAnnotationParser rap = new RestAnnotationParser();
+
+ Set<MiriamData> set = rap.getMiriamData(null);
+ assertEquals(0, set.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testCreateAnnotationString() throws Exception {
+ try {
+ RestAnnotationParser rap = new RestAnnotationParser();
+
+ String former1 = "form1";
+ String former2 = "form2";
+ GenericProtein element = new GenericProtein("id");
+ element.addFormerSymbol(former1);
+ element.addFormerSymbol(former2);
+ element.setCharge(1);
+ String str = rap.createAnnotationString(element, true);
+ assertTrue(str.contains(former1));
+ assertTrue(str.contains(former2));
+
+ for (NoteField field : NoteField.values()) {
+ if (field.getClazz().isAssignableFrom(element.getClass())
+ || CellDesignerElement.class.isAssignableFrom(field.getClazz())) {
+ assertTrue("Export string doesn't contain info about: " + field.getCommonName(),
+ str.indexOf(field.getCommonName()) >= 0);
+ }
+
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetFormerSymbolsFromInvalidStr() throws Exception {
+ try {
+ RestAnnotationParser rap = new RestAnnotationParser();
+
+ assertEquals(0, rap.getFormerSymbols(null).size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetNotesInvalid() throws Exception {
+ try {
+ RestAnnotationParser rap = new RestAnnotationParser();
+
+ Document xmlDoc = new DocumentImpl();
+ Node node = xmlDoc.createElement("bla");
+
+ rap.getNotes(node);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testProcessNotesForInvalidElement() throws Exception {
+ try {
+ RestAnnotationParser parser = new RestAnnotationParser();
+ Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes4.xml");
+ BioEntity bioEntity = Mockito.mock(BioEntity.class);
+ Mockito.when(bioEntity.getNotes()).thenReturn("");
+ parser.processNotes(node.getFirstChild(), bioEntity);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProcessInvalidNotes() throws Exception {
+ try {
+ RestAnnotationParser parser = new RestAnnotationParser();
+ String str = super.readFile("testFiles/xmlNodeTestExamples/notes5.xml");
+
+ parser.processNotes(str, new GenericProtein("id"));
+
+ assertEquals(1, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProcessNotes() throws Exception {
+ try {
+ String newNotes = "new notes";
+ String oldNotes = "old notes";
+ RestAnnotationParser parser = new RestAnnotationParser();
+ String str = "Description: " + newNotes + "\n" + oldNotes;
+ GenericProtein protein = new GenericProtein("id");
+ parser.processNotes(str, protein);
+
+ assertTrue(protein.getNotes().contains(newNotes));
+ assertTrue(protein.getNotes().contains(oldNotes));
+ assertFalse(protein.getNotes().contains("Description"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java b/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java
index 8361b25af4..70319d5914 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java
@@ -4,6 +4,8 @@ import java.io.Serializable;
import java.util.Collection;
import java.util.List;
+import lcsb.mapviewer.model.map.model.Model;
+
/**
* Interface that describes bio entity on the map (like Protein or Reaction).
*
@@ -11,149 +13,149 @@ import java.util.List;
*
*/
public interface BioEntity extends Serializable {
- /**
- * Returns list of {@link MiriamData annotations} for the object.
- *
- * @return list of {@link MiriamData annotations} for the object
- */
- Collection<MiriamData> getMiriamData();
-
- /**
- * Adds miriam annotations to the element.
- *
- * @param miriamData
- * set of miriam annotations to be added
- */
- void addMiriamData(Collection<MiriamData> miriamData);
-
- /**
- * Adds miriam annotation to the element.
- *
- * @param md
- * miriam annotation to be added
- */
- void addMiriamData(MiriamData md);
-
- /**
- * Returns the name of the object.
- *
- * @return the name of the object
- */
- String getName();
-
- /**
- * Returns notes about the object.
- *
- * @return notes about the object
- */
- String getNotes();
-
- /**
- * Sets notes about the object.
- *
- * @param notes
- * new notes
- */
- void setNotes(String notes);
-
- /**
- * Returns the symbol of the element.
- *
- * @return the symbol of the element
- */
- String getSymbol();
-
- /**
- * Sets symbol of the element.
- *
- * @param symbol
- * new symbol
- */
- void setSymbol(String symbol);
-
- /**
- * Get list of synonyms.
- *
- * @return list of synonyms
- */
- List<String> getSynonyms();
-
- /**
- * Sets list of synonyms to the element.
- *
- * @param synonyms
- * new list
- */
- void setSynonyms(List<String> synonyms);
-
- /**
- * Returns the abbreviation.
- *
- * @return the abbreviation
- */
- String getAbbreviation();
-
- /**
- * Sets abbreviation.
- *
- * @param abbreviation
- * new abbreviation
- */
- void setAbbreviation(String abbreviation);
-
- /**
- * Sets formula.
- *
- * @param formula
- * new formula
- */
- void setFormula(String formula);
-
- /**
- * Returns the formula.
- *
- * @return the formula
- */
- String getFormula();
-
- /**
- * Sets the name to the object.
- *
- * @param name
- * name of the object
- *
- */
- void setName(String name);
-
- /**
- * Returns database identifier of the object.
- *
- * @return database identifier of the object
- */
- int getId();
-
- /**
- * Return human readable {@link String} representing class.
- *
- * @return human readable {@link String} representing class
- */
- String getStringType();
-
- /**
- * Sets semantic zoom level visibility.
- *
- * @param zoomLevelVisibility
- * semantic zoom level visibility
- */
- void setVisibilityLevel(String zoomLevelVisibility);
-
- /**
- * Sets semantic zoom level visibility.
- *
- * @param zoomLevelVisibility
- * semantic zoom level visibility
- */
- void setVisibilityLevel(Integer zoomLevelVisibility);
+ /**
+ * Returns list of {@link MiriamData annotations} for the object.
+ *
+ * @return list of {@link MiriamData annotations} for the object
+ */
+ Collection<MiriamData> getMiriamData();
+
+ /**
+ * Adds miriam annotations to the element.
+ *
+ * @param miriamData
+ * set of miriam annotations to be added
+ */
+ void addMiriamData(Collection<MiriamData> miriamData);
+
+ /**
+ * Adds miriam annotation to the element.
+ *
+ * @param md
+ * miriam annotation to be added
+ */
+ void addMiriamData(MiriamData md);
+
+ /**
+ * Returns the name of the object.
+ *
+ * @return the name of the object
+ */
+ String getName();
+
+ /**
+ * Returns notes about the object.
+ *
+ * @return notes about the object
+ */
+ String getNotes();
+
+ /**
+ * Sets notes about the object.
+ *
+ * @param notes
+ * new notes
+ */
+ void setNotes(String notes);
+
+ /**
+ * Returns the symbol of the element.
+ *
+ * @return the symbol of the element
+ */
+ String getSymbol();
+
+ /**
+ * Sets symbol of the element.
+ *
+ * @param symbol
+ * new symbol
+ */
+ void setSymbol(String symbol);
+
+ /**
+ * Get list of synonyms.
+ *
+ * @return list of synonyms
+ */
+ List<String> getSynonyms();
+
+ /**
+ * Sets list of synonyms to the element.
+ *
+ * @param synonyms
+ * new list
+ */
+ void setSynonyms(List<String> synonyms);
+
+ /**
+ * Returns the abbreviation.
+ *
+ * @return the abbreviation
+ */
+ String getAbbreviation();
+
+ /**
+ * Sets abbreviation.
+ *
+ * @param abbreviation
+ * new abbreviation
+ */
+ void setAbbreviation(String abbreviation);
+
+ /**
+ * Sets formula.
+ *
+ * @param formula
+ * new formula
+ */
+ void setFormula(String formula);
+
+ /**
+ * Returns the formula.
+ *
+ * @return the formula
+ */
+ String getFormula();
+
+ /**
+ * Sets the name to the object.
+ *
+ * @param name
+ * name of the object
+ *
+ */
+ void setName(String name);
+
+ /**
+ * Returns database identifier of the object.
+ *
+ * @return database identifier of the object
+ */
+ int getId();
+
+ /**
+ * Return human readable {@link String} representing class.
+ *
+ * @return human readable {@link String} representing class
+ */
+ String getStringType();
+
+ /**
+ * Sets semantic zoom level visibility.
+ *
+ * @param zoomLevelVisibility
+ * semantic zoom level visibility
+ */
+ void setVisibilityLevel(String zoomLevelVisibility);
+
+ /**
+ * Sets semantic zoom level visibility.
+ *
+ * @param zoomLevelVisibility
+ * semantic zoom level visibility
+ */
+ void setVisibilityLevel(Integer zoomLevelVisibility);
/**
* Returns semantic zoom level visibility.
@@ -161,6 +163,14 @@ public interface BioEntity extends Serializable {
* @return semantic zoom level visibility
*/
String getVisibilityLevel();
-
+
String getElementId();
+
+ /**
+ * Returns the {@link Model} where BioEntity is located.
+ *
+ * @return the model
+ */
+ Model getModel();
+
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
index e3c6c3187f..5d04e7781c 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
@@ -727,12 +727,8 @@ public class Reaction implements BioEntity {
this.model = model2.getModelData();
}
- /**
- * Returns model where reaction is locacted.
- *
- * @return model where reaction is locacted.
- */
@XmlTransient
+ @Override
public Model getModel() {
return model.getModel();
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
index b6a16ea78d..a7e4a20b82 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
@@ -767,11 +767,8 @@ public abstract class Element implements BioEntity, Serializable {
this.transparencyLevel = transparencyLevel;
}
- /**
- * @return the model
- * @see #model
- */
@XmlTransient
+ @Override
public Model getModel() {
return model.getModel();
}
--
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