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Commit a6e7ede8 authored by Piotr Gawron's avatar Piotr Gawron
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unit test for duplicate mirna by target

parent e0b15dbc
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1 merge request!75Resolve "MiRNA - Show all - duplicated entries"
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with 173 additions and 47 deletions
rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImpl.java
+ 4
− 47
View file @ a6e7ede8
......@@ -23,8 +23,6 @@ import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.IModelService;
import lcsb.mapviewer.services.interfaces.IUserService;
import lcsb.mapviewer.services.search.ElementMatcher;
import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
import lcsb.mapviewer.services.search.db.DbSearchCriteria;
......@@ -32,7 +30,6 @@ import lcsb.mapviewer.services.search.db.GeneRow;
import lcsb.mapviewer.services.search.db.TargetView;
import lcsb.mapviewer.services.search.db.mirna.IMiRNAService;
import lcsb.mapviewer.services.search.db.mirna.MiRNAView;
import lcsb.mapviewer.services.view.AnnotationView;
import lcsb.mapviewer.services.view.AuthenticationToken;
@Transactional(value = "txManager")
......@@ -47,18 +44,12 @@ public class MiRnaRestImpl extends BaseRestImpl {
@Autowired
private IMiRNAService miRnaService;
@Autowired
private IModelService modelService;
@Autowired
private IUserService userService;
@Autowired
private ElementMatcher elementMatcher;
public List<Map<String, Object>> getMiRnasByQuery(String token, String projectId, String columns, String query) throws SecurityException, QueryException {
AuthenticationToken authenticationToken = userService.getToken(token);
Model model = modelService.getLastModelByProjectId(projectId, authenticationToken);
AuthenticationToken authenticationToken = getUserService().getToken(token);
Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
}
......@@ -88,40 +79,6 @@ public class MiRnaRestImpl extends BaseRestImpl {
return models;
}
/**
* @return the userService
* @see #userService
*/
public IUserService getUserService() {
return userService;
}
/**
* @param userService
* the userService to set
* @see #userService
*/
public void setUserService(IUserService userService) {
this.userService = userService;
}
/**
* @return the modelService
* @see #modelService
*/
public IModelService getModelService() {
return modelService;
}
/**
* @param modelService
* the modelService to set
* @see #modelService
*/
public void setModelService(IModelService modelService) {
this.modelService = modelService;
}
private Map<String, Object> prepareMiRna(MiRNAView miRna, Set<String> columnsSet, List<Model> models) {
Map<String, Object> result = new HashMap<>();
for (String string : columnsSet) {
......@@ -221,8 +178,8 @@ public class MiRnaRestImpl extends BaseRestImpl {
public List<Map<String, Object>> getMiRnasByTarget(String token, String projectId, String targetType, String targetId, String columns)
throws SecurityException, QueryException {
AuthenticationToken authenticationToken = userService.getToken(token);
Model model = modelService.getLastModelByProjectId(projectId, authenticationToken);
AuthenticationToken authenticationToken = getUserService().getToken(token);
Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
}
......
rest-api/src/test/java/lcsb/mapviewer/api/projects/AllProjectTests.java
+ 2
− 0
View file @ a6e7ede8
......@@ -5,11 +5,13 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
import lcsb.mapviewer.api.projects.drugs.AllDrugTests;
import lcsb.mapviewer.api.projects.mirnas.AllMiRnaTests;
import lcsb.mapviewer.api.projects.models.AllModelsTests;
import lcsb.mapviewer.api.projects.overlays.AllOverlaysTests;
@RunWith(Suite.class)
@SuiteClasses({ AllDrugTests.class, //
AllMiRnaTests.class, //
AllModelsTests.class, //
AllOverlaysTests.class, //
ModelMetaDataTest.class, //
......
rest-api/src/test/java/lcsb/mapviewer/api/projects/mirnas/AllMiRnaTests.java 0 → 100644
+ 11
− 0
View file @ a6e7ede8
package lcsb.mapviewer.api.projects.mirnas;
import org.junit.runner.RunWith;
import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ MiRnaRestImplTest.class })
public class AllMiRnaTests {
}
rest-api/src/test/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImplTest.java 0 → 100644
+ 67
− 0
View file @ a6e7ede8
package lcsb.mapviewer.api.projects.mirnas;
import static org.junit.Assert.assertFalse;
import static org.mockito.Matchers.any;
import static org.mockito.Matchers.anyString;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.apache.log4j.Logger;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
import org.mockito.Mockito;
import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.api.RestTestFunctions;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.services.interfaces.IModelService;
public class MiRnaRestImplTest extends RestTestFunctions {
Logger logger = Logger.getLogger(MiRnaRestImplTest.class);
@Autowired
MiRnaRestImpl _miRnaRestImpl;
@AfterClass
public static void tearDownAfterClass() throws Exception {
}
@Before
public void setUp() throws Exception {
}
@After
public void tearDown() throws Exception {
}
@Test
public void testGetMiRnasByTarget() throws Exception {
try {
MiRnaRestImpl miRnaRestImpl = createMockProjectRest("testFiles/model/mi_rna_target.xml");
List<Map<String, Object>> result = miRnaRestImpl.getMiRnasByTarget(token.getId(), "mi_rna_target", "ALIAS", "0", "");
Set<String> names = new HashSet<>();
for (Map<String, Object> miRna : result) {
assertFalse("Duplicate miRna found: " + miRna.get("name"), names.contains(miRna.get("name")));
names.add((String)miRna.get("name"));
}
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
private MiRnaRestImpl createMockProjectRest(String string) throws Exception {
Model model = super.getModelForFile(string, true);
IModelService mockModelService = Mockito.mock(IModelService.class);
Mockito.when(mockModelService.getLastModelByProjectId(anyString(), any())).thenReturn(model);
_miRnaRestImpl.setModelService(mockModelService);
return _miRnaRestImpl;
}
}
rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
+ 3
− 0
View file @ a6e7ede8
......@@ -88,6 +88,7 @@ public class ElementRestImplTest extends RestTestFunctions {
}
}
@SuppressWarnings("unchecked")
@Test
public void testGetModificationsForProtein() throws Exception {
try {
......@@ -109,6 +110,7 @@ public class ElementRestImplTest extends RestTestFunctions {
}
}
@SuppressWarnings("unchecked")
@Test
public void testGetModificationsForRna() throws Exception {
try {
......@@ -130,6 +132,7 @@ public class ElementRestImplTest extends RestTestFunctions {
}
}
@SuppressWarnings("unchecked")
@Test
public void testGetModificationsForAntisenseRna() throws Exception {
try {
......
rest-api/testFiles/model/mi_rna_target.xml 0 → 100644
+ 86
− 0
View file @ a6e7ede8
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
<model metaid="untitled" id="untitled">
<annotation>
<celldesigner:extension>
<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
<celldesigner:listOfCompartmentAliases/>
<celldesigner:listOfComplexSpeciesAliases/>
<celldesigner:listOfSpeciesAliases>
<celldesigner:speciesAlias id="sa1" species="s1">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="150.0" y="167.0" w="80.0" h="40.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="40.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffccffcc" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="0.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
</celldesigner:listOfSpeciesAliases>
<celldesigner:listOfGroups/>
<celldesigner:listOfProteins>
<celldesigner:protein id="pr1" name="BCL2" type="GENERIC"/>
</celldesigner:listOfProteins>
<celldesigner:listOfGenes/>
<celldesigner:listOfRNAs/>
<celldesigner:listOfAntisenseRNAs/>
<celldesigner:listOfLayers/>
<celldesigner:listOfBlockDiagrams/>
</celldesigner:extension>
</annotation>
<listOfUnitDefinitions>
<unitDefinition metaid="substance" id="substance" name="substance">
<listOfUnits>
<unit metaid="CDMT00001" kind="mole"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="volume" id="volume" name="volume">
<listOfUnits>
<unit metaid="CDMT00002" kind="litre"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="area" id="area" name="area">
<listOfUnits>
<unit metaid="CDMT00003" kind="metre" exponent="2"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="length" id="length" name="length">
<listOfUnits>
<unit metaid="CDMT00004" kind="metre"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="time" id="time" name="time">
<listOfUnits>
<unit metaid="CDMT00005" kind="second"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment metaid="default" id="default" size="1" units="volume"/>
</listOfCompartments>
<listOfSpecies>
<species metaid="s1" id="s1" name="BCL2" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
</listOfSpecies>
</model>
</sbml>
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