From 4a4c89560f4a799f50fcb66b6b9d3c88e5c94e30 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 10 Sep 2018 15:11:34 +0200
Subject: [PATCH] speed up of unit test
---
.../api/projects/drugs/DrugRestImpl.java | 2 +
.../lcsb/mapviewer/api/RestTestFunctions.java | 2 +-
.../chemicals/ChemicalRestImplTest.java | 12 +--
.../api/projects/drugs/DrugRestImplTest.java | 4 +-
.../src/test/resources/test-dataSource.xml | 38 ++++++++
.../src/test/resources/test-db.properties | 3 +
rest-api/testFiles/model/drug_target.xml | 86 +++++++++++++++++++
7 files changed, 136 insertions(+), 11 deletions(-)
create mode 100644 rest-api/src/test/resources/test-dataSource.xml
create mode 100644 rest-api/src/test/resources/test-db.properties
create mode 100644 rest-api/testFiles/model/drug_target.xml
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
index 4881c9da07..f1b639add0 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
@@ -59,10 +59,12 @@ public class DrugRestImpl extends BaseRestImpl {
organism = TaxonomyBackend.HUMAN_TAXONOMY;
}
Drug drug = drugService.getByName(query, new DbSearchCriteria().project(project).organisms(organism).colorSet(0));
+ logger.debug(drug);
if (drug != null) {
List<Model> models = getModels(projectId, "*", token);
result.add(prepareDrug(drug, columnSet, models));
}
+ logger.debug(result);
return result;
}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java b/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java
index bf772d9828..9b9be9a835 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java
@@ -67,7 +67,7 @@ import lcsb.mapviewer.services.interfaces.IUserService;
"/applicationContext-service.xml", //
"/applicationContext-rest.xml", //
"/test-applicationContext.xml", //
- "/dataSource.xml", //
+ "/test-dataSource.xml", //
})
@RunWith(SpringJUnit4ClassRunner.class)
public abstract class RestTestFunctions {
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImplTest.java
index f93f323983..66d8d22784 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImplTest.java
@@ -21,19 +21,13 @@ import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.services.interfaces.IModelService;
-import lcsb.mapviewer.services.search.DbSearchCriteria;
-import lcsb.mapviewer.services.search.chemical.IChemicalService;
public class ChemicalRestImplTest extends RestTestFunctions {
Logger logger = Logger.getLogger(ChemicalRestImplTest.class);
@Autowired
-
private ChemicalRestImpl _drugRestImpl;
- @Autowired
- private IChemicalService chemicalService;
-
@AfterClass
public static void tearDownAfterClass() throws Exception {
}
@@ -63,8 +57,10 @@ public class ChemicalRestImplTest extends RestTestFunctions {
@Test
public void testPrepareChemicalWithProblematicMesh() throws Exception {
try {
- Chemical chemical = chemicalService.getByName("Tetrachlorodibenzodioxin",
- new DbSearchCriteria().disease(new MiriamData(MiriamType.MESH_2012, "D010300")));
+
+ Chemical chemical = new Chemical();
+ chemical.setChemicalId(new MiriamData(MiriamType.MESH_2012, "invalidID"));
+
Map<String, Object> result = _drugRestImpl.prepareChemical(chemical, _drugRestImpl.createChemicalColumnSet(""),
new ArrayList<>());
assertNotNull(result);
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/drugs/DrugRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/drugs/DrugRestImplTest.java
index 89e6026906..dc96c4953f 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/drugs/DrugRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/drugs/DrugRestImplTest.java
@@ -42,8 +42,8 @@ public class DrugRestImplTest extends RestTestFunctions {
@SuppressWarnings("unchecked")
public void testGetDrugsByQuery() throws Exception {
try {
- DrugRestImpl drugRestImpl = createMockProjectRest("testFiles/model/sample.xml");
- Map<String, Object> result = drugRestImpl.getDrugsByQuery(token, "sample", "", "nadh").get(0);
+ DrugRestImpl drugRestImpl = createMockProjectRest("testFiles/model/drug_target.xml");
+ Map<String, Object> result = drugRestImpl.getDrugsByQuery(token, "drug_target", "", "Selisistat").get(0);
List<Map<String, Object>> references = (List<Map<String, Object>>) result.get("references");
Map<String, Object> reference = references.get(0);
assertNotNull(reference.get("type"));
diff --git a/rest-api/src/test/resources/test-dataSource.xml b/rest-api/src/test/resources/test-dataSource.xml
new file mode 100644
index 0000000000..85af9016f8
--- /dev/null
+++ b/rest-api/src/test/resources/test-dataSource.xml
@@ -0,0 +1,38 @@
+<beans xmlns="http://www.springframework.org/schema/beans"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:tx="http://www.springframework.org/schema/tx"
+ xmlns:context="http://www.springframework.org/schema/context"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans-4.0.xsd
+ http://www.springframework.org/schema/tx
+ http://www.springframework.org/schema/tx/spring-tx-4.0.xsd
+ http://www.springframework.org/schema/context
+ http://www.springframework.org/schema/context/spring-context-4.0.xsd">
+
+ <context:property-placeholder location="classpath:test-db.properties" />
+
+
+ <!-- Data Source Declaration -->
+ <bean id="DataSource"
+ class="com.mchange.v2.c3p0.ComboPooledDataSource"
+ destroy-method="close">
+ <property name="driverClass" value="org.postgresql.Driver" />
+ <property name="jdbcUrl" value="${database.uri}" />
+ <property name="user" value="${database.username}" />
+ <property name="password" value="${database.password}" />
+ <property name="maxPoolSize" value="90" />
+ <property name="maxStatements" value="5" />
+ <property name="minPoolSize" value="5" />
+ </bean>
+
+ <bean id="DbInit" class="lcsb.mapviewer.persist.CustomDatabasePopulator">
+ <property name="dataSource"><ref bean="DataSource"/></property>
+ </bean>
+
+ <bean id="startupScripts" class="org.springframework.jdbc.datasource.init.DataSourceInitializer">
+ <property name="dataSource"><ref bean="DataSource"/></property>
+ <property name="databasePopulator"><ref bean="DbInit"/></property>
+ <property name="enabled" value="true"/>
+ </bean>
+
+</beans>
diff --git a/rest-api/src/test/resources/test-db.properties b/rest-api/src/test/resources/test-db.properties
new file mode 100644
index 0000000000..8e0d1e79f3
--- /dev/null
+++ b/rest-api/src/test/resources/test-db.properties
@@ -0,0 +1,3 @@
+database.uri=jdbc:postgresql://localhost:5432/map_viewer-test
+database.username=map_viewer
+database.password=123qweasdzxc
\ No newline at end of file
diff --git a/rest-api/testFiles/model/drug_target.xml b/rest-api/testFiles/model/drug_target.xml
new file mode 100644
index 0000000000..6500fc3ff4
--- /dev/null
+++ b/rest-api/testFiles/model/drug_target.xml
@@ -0,0 +1,86 @@
+<?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="1308" sizeY="600"/>
+<celldesigner:listOfCompartmentAliases/>
+<celldesigner:listOfComplexSpeciesAliases/>
+<celldesigner:listOfSpeciesAliases>
+<celldesigner:speciesAlias id="sa15" species="s16">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="328.0" y="248.0" w="119.0" h="63.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="119.0" height="63.0"/>
+<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="1.0"/>
+<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="pr7" name="SIRT1" 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="CDMT00069" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00070" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00071" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00072" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00073" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+</listOfCompartments>
+<listOfSpecies>
+<species metaid="s16" id="s16" name="SIRT1" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr7</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+</listOfSpecies>
+</model>
+</sbml>
--
GitLab