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Commit 9a91f723 authored by Piotr Gawron's avatar Piotr Gawron
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ElementDao tests merged

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1 merge request!782Resolve "Replace deprecated APIs"
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persist/src/test/java/lcsb/mapviewer/persist/PersistTestFunctions.java
+ 0
− 5
View file @ 9a91f723
......@@ -26,9 +26,7 @@ import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.persist.dao.ProjectDao;
import lcsb.mapviewer.persist.dao.cache.CacheTypeDao;
import lcsb.mapviewer.persist.dao.map.CommentDao;
import lcsb.mapviewer.persist.dao.map.ModelDao;
import lcsb.mapviewer.persist.dao.map.species.ElementDao;
import lcsb.mapviewer.persist.dao.user.UserDao;
@Transactional
......@@ -56,9 +54,6 @@ public abstract class PersistTestFunctions {
@Autowired
protected DbUtils dbUtils;
@Autowired
protected ElementDao elementDao;
@Autowired
protected CacheTypeDao cacheTypeDao;
......
persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest.java deleted 100644 → 0
+ 0
− 149
View file @ cd0e66bd
package lcsb.mapviewer.persist.dao.map.layout.alias;
import static org.junit.Assert.assertEquals;
import java.util.ArrayList;
import java.util.List;
import org.apache.logging.log4j.*;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.SearchIndex;
import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.model.SubmodelType;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.Structure;
import lcsb.mapviewer.model.map.species.field.UniprotRecord;
import lcsb.mapviewer.persist.PersistTestFunctions;
public class AliasDaoTest extends PersistTestFunctions {
Logger logger = LogManager.getLogger(AliasDaoTest.class);
private Project project;
String projectId = "Some_id";
int identifierCounter = 0;
int zIndex = 0;
@Before
public void setUp() throws Exception {
project = projectDao.getProjectByProjectId(projectId);
if (project != null) {
projectDao.delete(project);
}
project = new Project();
project.setProjectId(projectId);
projectDao.add(project);
}
@After
public void tearDown() throws Exception {
projectDao.delete(project);
}
@Test
public void anotherSaveDaoTest() throws Exception {
try {
Model model = createModel();
project.addModel(model);
Element element = model.getElementByElementId("sa2");
element.getSearchIndexes().add(new SearchIndex("blabla"));
modelDao.add(model);
Model model2 = new ModelFullIndexed(modelDao.getById(model.getId()));
Element element2 = elementDao.getById(model2.getElementByElementId("sa2").getId());
assertEquals(1, element2.getSearchIndexes().size());
modelDao.delete(model);
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
private Model createModel() {
Model model = new ModelFullIndexed(null);
model.addElement(createProtein(264.8333333333335, 517.75, 86.0, 46.0, "sa2"));
model.addElement(createProtein(267.6666666666665, 438.75, 80.0, 40.0, "sa1117"));
model.addElement(createProtein(261.6666666666665, 600.75, 92.0, 52.0, "sa1119"));
model.addElement(createProtein(203.666666666667, 687.75, 98.0, 58.0, "sa1121"));
Species alias = createProtein(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
Species alias2 = createProtein(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
Complex alias3 = createComplex(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
alias3.addSpecies(alias);
alias3.addSpecies(alias2);
alias.setComplex(alias3);
alias2.setComplex(alias3);
model.addElement(alias);
model.addElement(alias2);
model.addElement(alias3);
model.addElement(createCompartment(380.0, 416.0, 1893.0, 1866.0, "ca1"));
model.setWidth(2000);
model.setHeight(2000);
return model;
}
@Test
public void saveAliasWithSubmodelTest() throws Exception {
try {
long count = modelDao.getCount();
Model model = createModel();
Model model1 = createModel();
Element element = model.getElementByElementId("sa2");
ElementSubmodelConnection submodel = new ElementSubmodelConnection(model1, SubmodelType.UNKNOWN);
element.setSubmodel(submodel);
project.addModel(model);
projectDao.add(project);
projectDao.flush();
long count2 = modelDao.getCount();
assertEquals(count + 2, count2);
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void saveWithUniprotData() throws Exception {
try {
Model model = createModel();
project.addModel(model);
Species element = model.getElementByElementId("sa2");
UniprotRecord uniprotRecord = new UniprotRecord();
Structure s = new Structure();
s.setPdbId("x");
s.setChainId("y");
List<Structure> list = new ArrayList<>();
list.add(s);
s.setUniprot(uniprotRecord);
uniprotRecord.addStructures(list);
uniprotRecord.setSpecies(element);
element.getUniprots().add(uniprotRecord);
modelDao.add(model);
modelDao.delete(model);
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
}
persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AllAliasTests.java
+ 3
− 4
View file @ 9a91f723
......@@ -5,10 +5,9 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ AliasDaoTest.class,
AliasDaoTest2.class,
AntisenseRnaTest.class,
RnaTest.class,
@SuiteClasses({ AntisenseRnaTest.class,
ElementDaoTest.class,
RnaTest.class,
})
public class AllAliasTests {
......
persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest2.java → persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/ElementDaoTest.java
+ 132
− 4
View file @ 9a91f723
......@@ -5,18 +5,30 @@ import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import java.awt.geom.Point2D;
import java.util.ArrayList;
import java.util.List;
import org.apache.logging.log4j.*;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.SearchIndex;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.model.SubmodelType;
import lcsb.mapviewer.model.map.species.AntisenseRna;
import lcsb.mapviewer.model.map.species.Chemical;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Ion;
import lcsb.mapviewer.model.map.species.Phenotype;
......@@ -26,10 +38,20 @@ import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.ModificationSite;
import lcsb.mapviewer.model.map.species.field.ModificationState;
import lcsb.mapviewer.model.map.species.field.Residue;
import lcsb.mapviewer.model.map.species.field.Structure;
import lcsb.mapviewer.model.map.species.field.UniprotRecord;
import lcsb.mapviewer.persist.PersistTestFunctions;
import lcsb.mapviewer.persist.dao.map.species.ElementDao;
public class AliasDaoTest2 extends PersistTestFunctions {
static Logger logger = LogManager.getLogger(AliasDaoTest.class);
public class ElementDaoTest extends PersistTestFunctions {
@SuppressWarnings("unused")
private Logger logger = LogManager.getLogger(ElementDaoTest.class);
@Autowired
private ElementDao elementDao;
private Project project;
private String projectId = "Some_id";
private Integer testChargeVal = 1;
private String testIdAlias = "a";
......@@ -41,10 +63,116 @@ public class AliasDaoTest2 extends PersistTestFunctions {
@Before
public void setUp() throws Exception {
project = projectDao.getProjectByProjectId(projectId);
if (project != null) {
projectDao.delete(project);
}
project = new Project();
project.setProjectId(projectId);
projectDao.add(project);
}
@After
public void tearDown() throws Exception {
projectDao.delete(project);
}
@Test
public void anotherSaveDaoTest() throws Exception {
try {
Model model = createModel();
project.addModel(model);
Element element = model.getElementByElementId("sa2");
element.getSearchIndexes().add(new SearchIndex("blabla"));
modelDao.add(model);
Model model2 = new ModelFullIndexed(modelDao.getById(model.getId()));
Element element2 = elementDao.getById(model2.getElementByElementId("sa2").getId());
assertEquals(1, element2.getSearchIndexes().size());
modelDao.delete(model);
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
private Model createModel() {
Model model = new ModelFullIndexed(null);
model.addElement(createProtein(264.8333333333335, 517.75, 86.0, 46.0, "sa2"));
model.addElement(createProtein(267.6666666666665, 438.75, 80.0, 40.0, "sa1117"));
model.addElement(createProtein(261.6666666666665, 600.75, 92.0, 52.0, "sa1119"));
model.addElement(createProtein(203.666666666667, 687.75, 98.0, 58.0, "sa1121"));
Species alias = createProtein(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
Species alias2 = createProtein(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
Complex alias3 = createComplex(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
alias3.addSpecies(alias);
alias3.addSpecies(alias2);
alias.setComplex(alias3);
alias2.setComplex(alias3);
model.addElement(alias);
model.addElement(alias2);
model.addElement(alias3);
model.addElement(createCompartment(380.0, 416.0, 1893.0, 1866.0, "ca1"));
model.setWidth(2000);
model.setHeight(2000);
return model;
}
@Test
public void saveAliasWithSubmodelTest() throws Exception {
try {
long count = modelDao.getCount();
Model model = createModel();
Model model1 = createModel();
Element element = model.getElementByElementId("sa2");
ElementSubmodelConnection submodel = new ElementSubmodelConnection(model1, SubmodelType.UNKNOWN);
element.setSubmodel(submodel);
project.addModel(model);
projectDao.add(project);
projectDao.flush();
long count2 = modelDao.getCount();
assertEquals(count + 2, count2);
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void saveWithUniprotData() throws Exception {
try {
Model model = createModel();
project.addModel(model);
Species element = model.getElementByElementId("sa2");
UniprotRecord uniprotRecord = new UniprotRecord();
Structure s = new Structure();
s.setPdbId("x");
s.setChainId("y");
List<Structure> list = new ArrayList<>();
list.add(s);
s.setUniprot(uniprotRecord);
uniprotRecord.addStructures(list);
uniprotRecord.setSpecies(element);
element.getUniprots().add(uniprotRecord);
modelDao.add(model);
modelDao.delete(model);
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
......@@ -174,7 +302,7 @@ public class AliasDaoTest2 extends PersistTestFunctions {
try {
AntisenseRna sp = createAntisenseRna(testIdAlias);
ModificationSite mr = new ModificationSite();
mr.setName("name");
sp.addModificationSite(mr);
......
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