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Commit ca3f245d authored by Piotr Gawron's avatar Piotr Gawron
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speed up of chemical unit test

parent 5cf7061b
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2 merge requests!630WIP: Resolve "The privileges of a new user are not saved in some cases",!386Resolve "Continous integration tests"
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annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java
+ 24
− 57
View file @ ca3f245d
......@@ -42,6 +42,13 @@ public class ChemicalParserTest extends AnnotationTestFunctions {
Logger logger = Logger.getLogger(ChemicalParserTest.class);
final MiriamData parkinsonDiseaseId = new MiriamData(MiriamType.MESH_2012, "D010300");
final MiriamData dystoniaDisease = new MiriamData(MiriamType.MESH_2012, "C538007");
MiriamData glutathioneDisulfideChemicalId = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "D019803");
MiriamData stilbeneOxideChemicalId = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "C025906");
// lazabemide with one Gene MAOB and therapeutic and 3 publications
MiriamData lazabemideChemicalId = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "C059303");
@Autowired
private ChemicalParser chemicalParser;
......@@ -130,34 +137,13 @@ public class ChemicalParserTest extends AnnotationTestFunctions {
@Test
public void testFindByIDFromChemicalList() throws Exception {
try {
// Parkinson disease
Map<MiriamData, String> listFromDB = chemicalParser.getChemicalsForDisease(parkinsonDiseaseId);
assertNotNull(listFromDB);
assertTrue(!listFromDB.isEmpty());
Map.Entry<MiriamData, String> entry = listFromDB.entrySet().iterator().next();
assertNotNull(entry);
// Get the first entry
String chemicalName1 = entry.getValue();
assertTrue((chemicalName1 != null) && !chemicalName1.trim().isEmpty());
chemicalName1 = chemicalName1.trim().toLowerCase();
MiriamData chemicalId1 = entry.getKey();
assertTrue(
(chemicalId1 != null) && (chemicalId1.getResource() != null) && !chemicalId1.getResource().trim().isEmpty());
// Dopamine with 23 Gens and 60 publication and one marker/mechanism and
// 60 publications
MiriamData chemicalId2 = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "D019803");
// lazabemide with one Gene MAOB and therapeutic and 3 publications
MiriamData chemicalId3 = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "C059303");
// caramiphen with no genes and one therapeutic
MiriamData chemicalId4 = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "C004519");
List<MiriamData> idsList = new ArrayList<MiriamData>();
idsList.add(chemicalId1);
idsList.add(chemicalId2);
idsList.add(chemicalId3);
idsList.add(chemicalId4);
List<MiriamData> idsList = new ArrayList<>();
idsList.add(stilbeneOxideChemicalId);
idsList.add(lazabemideChemicalId);
List<Chemical> chemcials = chemicalParser.getChemicals(parkinsonDiseaseId, idsList);
assertEquals(idsList.size(), chemcials.size());
for (Chemical chem : chemcials) {
assertNotNull(chem);
for (Target t : chem.getInferenceNetwork()) {
......@@ -177,10 +163,9 @@ public class ChemicalParserTest extends AnnotationTestFunctions {
@Test
public void testGetGlutathioneDisulfideData() throws Exception {
try {
MiriamData glutathioneDisulfideId = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "D019803");
List<MiriamData> idsList = new ArrayList<>();
idsList.add(glutathioneDisulfideId);
idsList.add(glutathioneDisulfideChemicalId);
List<Chemical> chemicals = chemicalParser.getChemicals(parkinsonDiseaseId, idsList);
assertEquals(1, chemicals.size());
......@@ -197,12 +182,13 @@ public class ChemicalParserTest extends AnnotationTestFunctions {
@Test
public void testGetChemicalBySynonym() throws Exception {
try {
List<Chemical> chemicals = chemicalParser.getChemicalsBySynonym(parkinsonDiseaseId, "MPTP");
String glutathioneDisulfideSynonym = "GSSG";
List<Chemical> chemicals = chemicalParser.getChemicalsBySynonym(parkinsonDiseaseId, glutathioneDisulfideSynonym);
assertEquals(1, chemicals.size());
Chemical mptp = chemicals.get(0);
assertTrue(mptp.getSynonyms().contains("MPTP"));
assertTrue(mptp.getSynonyms().contains(glutathioneDisulfideSynonym));
} catch (Exception e) {
e.printStackTrace();
throw e;
......@@ -252,9 +238,8 @@ public class ChemicalParserTest extends AnnotationTestFunctions {
Map<MiriamData, String> listFromDB = chemicalParser.getChemicalsForDisease(parkinsonDiseaseId);
assertNotNull(listFromDB);
assertTrue(!listFromDB.isEmpty());
MiriamData chemicalId = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "D015039");
List<MiriamData> idsList = new ArrayList<MiriamData>();
idsList.add(chemicalId);
List<MiriamData> idsList = new ArrayList<>();
idsList.add(stilbeneOxideChemicalId);
List<Chemical> chemcials = chemicalParser.getChemicals(parkinsonDiseaseId, idsList);
assertNotNull(chemcials);
assertTrue(chemcials.size() > 0);
......@@ -285,10 +270,11 @@ public class ChemicalParserTest extends AnnotationTestFunctions {
@Test
public void testGetByTarget() throws Exception {
try {
MiriamData target = new MiriamData(MiriamType.HGNC_SYMBOL, "TNF");
MiriamData target = new MiriamData(MiriamType.HGNC_SYMBOL, "GCH1");
List<MiriamData> targets = new ArrayList<>();
targets.add(target);
List<Chemical> list = chemicalParser.getChemicalListByTarget(targets, parkinsonDiseaseId);
List<Chemical> list = chemicalParser.getChemicalListByTarget(targets, dystoniaDisease);
assertNotNull(list);
assertFalse(list.isEmpty());
......@@ -356,11 +342,10 @@ public class ChemicalParserTest extends AnnotationTestFunctions {
@Test
public void testGetByEntrezTarget() throws Exception {
try {
// Parkinson disease
MiriamData target = new MiriamData(MiriamType.ENTREZ, "6647");
MiriamData target = new MiriamData(MiriamType.ENTREZ, "2643");
List<MiriamData> targets = new ArrayList<>();
targets.add(target);
List<Chemical> list = chemicalParser.getChemicalListByTarget(targets, parkinsonDiseaseId);
List<Chemical> list = chemicalParser.getChemicalListByTarget(targets, dystoniaDisease);
assertTrue(list.size() > 0);
} catch (Exception e) {
e.printStackTrace();
......@@ -371,7 +356,6 @@ public class ChemicalParserTest extends AnnotationTestFunctions {
@Test
public void testGetByTarget2() throws Exception {
try {
// Parkinson disease
MiriamData target = new MiriamData(MiriamType.HGNC_SYMBOL, "GALM");
List<MiriamData> targets = new ArrayList<>();
targets.add(target);
......@@ -406,22 +390,6 @@ public class ChemicalParserTest extends AnnotationTestFunctions {
}
}
@Test
public void testGetByTargetXXX() throws Exception {
try {
// Parkinson disease
MiriamData target = new MiriamData(MiriamType.HGNC_SYMBOL, "SOD1");
List<MiriamData> targets = new ArrayList<>();
targets.add(target);
List<Chemical> list = chemicalParser.getChemicalListByTarget(targets, parkinsonDiseaseId);
assertNotNull(list);
assertTrue(!list.isEmpty());
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testRefreshInvalidCacheQuery() throws Exception {
try {
......@@ -533,7 +501,7 @@ public class ChemicalParserTest extends AnnotationTestFunctions {
// count
assertEquals(2, getErrors().size());
// there are no genes (we have one that is invalid and should be
// discarderd)
// discarded)
assertEquals(0, result.getInferenceNetwork().size());
assertEquals(ChemicalDirectEvidence.THERAPEUTIC, result.getDirectEvidence());
......@@ -632,10 +600,9 @@ public class ChemicalParserTest extends AnnotationTestFunctions {
Model model = getModelForFile("testFiles/target_chemical/target.xml", false);
project.addModel(model);
List<String> result = chemicalParser.getSuggestedQueryList(project, parkinsonDiseaseId);
List<String> result = chemicalParser.getSuggestedQueryList(project, dystoniaDisease);
assertTrue(result.size() > 0);
logger.debug(result);
} catch (Exception e) {
e.printStackTrace();
......
annotation/testFiles/target_chemical/target.xml
+ 7
− 2336
View file @ ca3f245d
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