diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/remoteapitest/api/v1/GeneralInformationServiceAbstractTestCases.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/remoteapitest/api/v1/GeneralInformationServiceAbstractTestCases.java
deleted file mode 100644
index 3fbcd584d86a692473f0099cc6b47d75f1cb6be3..0000000000000000000000000000000000000000
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/remoteapitest/api/v1/GeneralInformationServiceAbstractTestCases.java
+++ /dev/null
@@ -1,594 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.remoteapitest.api.v1;
-
-import java.net.MalformedURLException;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.EnumSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.testng.AssertJUnit;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.common.utilities.ToStringComparator;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.Connections;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyType;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyTypeGroup;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Role;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseAttribute;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchSubCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SpaceWithProjectsAndRoleAssignments;
-
-/**
- * This class contains a set of generic tests cases for {@link IGeneralInformationService}. The test
- * cases require an instance of {@link IGeneralInformationService} to be injected from an external
- * source and thus cannot run on their own.
- *
- * @author Franz-Josef Elmer
- * @author Kaloyan Enimanev
- */
-// exclude from running directly as TestNG test.
-@Test(groups =
- { "abstract", "broken" })
-public class GeneralInformationServiceAbstractTestCases extends AssertJUnit
-{
- /**
- * Helps delaying the initialization of the {@link IGeneralInformationService} field until the
- * necessary infrastructure has been bootstrapped.
- */
- public static interface IGeneralInformationServiceFactory
- {
- IGeneralInformationService createService();
- }
-
- private final IGeneralInformationServiceFactory serviceHolder;
-
- private IGeneralInformationService generalInformationService;
-
- private String sessionToken;
-
- public GeneralInformationServiceAbstractTestCases(
- IGeneralInformationServiceFactory serviceHolder)
- {
- this.serviceHolder = serviceHolder;
- }
-
- @BeforeMethod
- public void beforeMethod() throws MalformedURLException
- {
- generalInformationService = serviceHolder.createService();
- sessionToken = generalInformationService.tryToAuthenticateForAllServices("test", "a");
- }
-
- @AfterMethod
- public void afterMethod() throws MalformedURLException
- {
- generalInformationService.logout(sessionToken);
- }
-
- @Test
- public void testListNamedRoleSets()
- {
- Map<String, Set<Role>> namedRoleSets =
- generalInformationService.listNamedRoleSets(sessionToken);
-
- assertEquals("[ADMIN(instance), ADMIN(space)]", namedRoleSets.get("SPACE_ADMIN").toString());
- }
-
- @Test
- public void testListSpacesWithProjectsAndRoleAssignments()
- {
- List<SpaceWithProjectsAndRoleAssignments> spaces =
- generalInformationService.listSpacesWithProjectsAndRoleAssignments(sessionToken,
- null);
-
- Collections.sort(spaces, new Comparator<SpaceWithProjectsAndRoleAssignments>()
- {
- public int compare(SpaceWithProjectsAndRoleAssignments s1,
- SpaceWithProjectsAndRoleAssignments s2)
- {
- return s1.getCode().compareTo(s2.getCode());
- }
- });
- checkSpace("CISD", "[/CISD/DEFAULT, /CISD/NEMO, /CISD/NOE]",
- "[ADMIN(instance), ADMIN(space), ETL_SERVER(instance), ETL_SERVER(space)]",
- spaces.get(0));
- checkSpace("TESTGROUP", "[/TESTGROUP/TESTPROJ]",
- "[ADMIN(instance), ADMIN(space), ETL_SERVER(instance)]", spaces.get(1));
- assertEquals(2, spaces.size());
- }
-
- @Test
- public void testListProjects()
- {
- List<Project> result = generalInformationService.listProjects(sessionToken);
- assertEquals(true, result.size() > 0);
- String expectedSampleIdentifier = "/TESTGROUP/TESTPROJ";
- for (Project project : result)
- {
- if (expectedSampleIdentifier.equals(project.toString()))
- {
- return;
- }
- }
- fail("result didn't contain project " + expectedSampleIdentifier);
- }
-
- @Test
- public void testSearchForSamples()
- {
- SearchCriteria sc = new SearchCriteria();
- sc.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, "*"));
- List<Sample> result = generalInformationService.searchForSamples(sessionToken, sc);
- assertEquals(true, result.size() > 0);
- String expectedSampleIdentifier = "/CISD/CL1";
- for (Sample sample : result)
- {
- if (expectedSampleIdentifier.equals(sample.getIdentifier()))
- {
- return;
- }
- }
- fail("result didn't contain sample " + expectedSampleIdentifier);
- }
-
- @Test(dependsOnMethods = "testSearchForSamples")
- public void testSearchForSamplesWithNoCriterion()
- {
- SearchCriteria sc = new SearchCriteria();
- sc.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, "*"));
- List<Sample> result = generalInformationService.searchForSamples(sessionToken, sc);
-
- // if no criterion was specified all samples should be returned as well
- SearchCriteria scWithNoCriterion = new SearchCriteria();
- List<Sample> resultWithNoCriterion =
- generalInformationService.searchForSamples(sessionToken, scWithNoCriterion);
- assertEquals(result, resultWithNoCriterion);
- }
-
- @Test
- public void testSearchForSamplesByProperty()
- {
- // Search for Samples first
- SearchCriteria sc = new SearchCriteria();
- sc.addMatchClause(MatchClause.createPropertyMatch("ORGANISM", "HUMAN"));
- List<Sample> result = generalInformationService.searchForSamples(sessionToken, sc);
- assertEquals(1, result.size());
- }
-
- @Test
- public void testSearchForSamplesByExperimentCode()
- {
- // Search for Samples with only experiment's code limiting the results
- SearchCriteria sc = new SearchCriteria();
- SearchCriteria ec = new SearchCriteria();
- ec.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, "EXP-TEST-1"));
- sc.addSubCriteria(SearchSubCriteria.createExperimentCriteria(ec));
- List<Sample> result = generalInformationService.searchForSamples(sessionToken, sc);
- assertEquals(1, result.size());
- assertEquals("/CISD/NEMO/EXP-TEST-1", result.get(0).getExperimentIdentifierOrNull());
- }
-
- @Test
- public void testSearchForSamplesByExperimentProperty()
- {
- // Search for Samples with only experiment's property limiting the results
- SearchCriteria sc = new SearchCriteria();
- SearchCriteria ec = new SearchCriteria();
- ec.addMatchClause(MatchClause.createPropertyMatch("DESCRIPTION", "A simple experiment"));
- sc.addSubCriteria(SearchSubCriteria.createExperimentCriteria(ec));
- List<Sample> result = generalInformationService.searchForSamples(sessionToken, sc);
- assertEquals(2, result.size());
- }
-
- @Test
- public void testSearchForSamplesByParentCode()
- {
- // Search for Samples with only parent's code limiting the results
- SearchCriteria sc = new SearchCriteria();
- sc.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, "*"));
- SearchCriteria pc = new SearchCriteria();
- pc.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, "MP002-1"));
- sc.addSubCriteria(SearchSubCriteria.createSampleParentCriteria(pc));
- List<Sample> result = generalInformationService.searchForSamples(sessionToken, sc);
- assertEquals(2, result.size());
- }
-
- @Test
- public void testSearchForSamplesByChildCode()
- {
- // Search for Samples with only child's code limiting the results
- SearchCriteria sc = new SearchCriteria();
- sc.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, "*"));
- SearchCriteria cc = new SearchCriteria();
- cc.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, "3VCP*"));
- sc.addSubCriteria(SearchSubCriteria.createSampleChildCriteria(cc));
- List<Sample> result = generalInformationService.searchForSamples(sessionToken, sc);
- assertEquals(2, result.size());
- }
-
- @Test
- public void testSearchForSamplesByContainerCode()
- {
- // Search for Samples with only container's code limiting the results
- SearchCriteria sc = new SearchCriteria();
- SearchCriteria cc = new SearchCriteria();
- cc.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, "CL1"));
- sc.addSubCriteria(SearchSubCriteria.createSampleContainerCriteria(cc));
- List<Sample> result = generalInformationService.searchForSamples(sessionToken, sc);
- assertEquals(2, result.size());
- for (Sample s : result)
- {
- assertTrue(s.getCode() + "doesn't start with 'CL1:'", s.getCode().startsWith("CL1:"));
- }
- }
-
- @Test
- public void testSearchForSamplesByExperimentAndParentCode()
- {
- // Search for Samples first
- SearchCriteria sc = new SearchCriteria();
- List<Sample> result = generalInformationService.searchForSamples(sessionToken, sc);
- assertEquals(true, result.size() > 600);
- // Add experiment criteria limiting results to 7
- SearchCriteria ec = new SearchCriteria();
- ec.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, "EXP-REUSE"));
- sc.addSubCriteria(SearchSubCriteria.createExperimentCriteria(ec));
- List<Sample> result2 = generalInformationService.searchForSamples(sessionToken, sc);
- assertEquals(7, result2.size());
- // Add parent criteria limiting results to only 2
- SearchCriteria pc = new SearchCriteria();
- pc.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, "DP1-A"));
- sc.addSubCriteria(SearchSubCriteria.createSampleParentCriteria(pc));
- List<Sample> result3 = generalInformationService.searchForSamples(sessionToken, sc);
- assertEquals(2, result3.size());
- }
-
- @Test
- public void testListDataSetsForAllSamples()
- {
- // Search for Samples first
- SearchCriteria sc = new SearchCriteria();
- List<Sample> samples = generalInformationService.searchForSamples(sessionToken, sc);
- List<DataSet> result = generalInformationService.listDataSets(sessionToken, samples);
- assertEquals(true, result.size() > 0);
- }
-
- @Test
- public void testListDataSetsWithParentsForAllSamples()
- {
- // Search for Samples first
- SearchCriteria sc = new SearchCriteria();
- List<Sample> samples = generalInformationService.searchForSamples(sessionToken, sc);
- List<DataSet> result =
- generalInformationService.listDataSets(sessionToken, samples,
- EnumSet.of(Connections.PARENTS));
- assertEquals(true, result.size() > 0);
- // See if some sample has parents
- boolean parentCodesFound = false;
- for (DataSet dataSet : result)
- {
- if (false == dataSet.getParentCodes().isEmpty())
- {
- parentCodesFound = true;
- break;
- }
- }
-
- assertTrue("No parent codes should have been found", (false == parentCodesFound));
- }
-
- @Test
- public void testListDataSetsForSample()
- {
- // Search for Samples first
- SearchCriteria sc = new SearchCriteria();
- sc.addMatchClause(MatchClause.createPropertyMatch("ORGANISM", "HUMAN"));
- List<Sample> samples = generalInformationService.searchForSamples(sessionToken, sc);
- List<DataSet> result =
- generalInformationService.listDataSetsForSample(sessionToken, samples.get(0), true);
- assertEquals(true, result.size() > 0);
- }
-
- @Test
- public void testListDataSetsForEmptySampleList()
- {
- List<Sample> samples = new ArrayList<Sample>();
- List<DataSet> result = generalInformationService.listDataSets(sessionToken, samples);
- assertEquals(true, result.size() == 0);
- }
-
- private static final String DEFAULT_PLATE_GEOMETRY_VALUE = "384_WELLS_16X24";
-
- @Test
- public void testSearchForDataSetsByProperty()
- {
- // Search for Samples first
- SearchCriteria sc = new SearchCriteria();
- sc.addMatchClause(MatchClause.createPropertyMatch("$PLATE_GEOMETRY",
- DEFAULT_PLATE_GEOMETRY_VALUE));
- List<Sample> samples = generalInformationService.searchForSamples(sessionToken, sc);
- assertEquals(true, samples.size() > 0);
- List<DataSet> result = generalInformationService.listDataSets(sessionToken, samples);
- assertEquals(true, result.size() == 0);
- }
-
- private void checkSpace(String expectedCode, String expectedProjects, String expectedRoles,
- SpaceWithProjectsAndRoleAssignments space)
- {
- assertEquals(expectedCode, space.getCode());
- List<Project> projects = space.getProjects();
- Collections.sort(projects, new Comparator<Project>()
- {
- public int compare(Project p1, Project p2)
- {
- return p1.getCode().compareTo(p2.getCode());
- }
- });
- assertEquals(expectedProjects, projects.toString());
- List<Role> roles = new ArrayList<Role>(space.getRoles("test"));
- Collections.sort(roles, new Comparator<Role>()
- {
- public int compare(Role r1, Role r2)
- {
- return r1.toString().compareTo(r2.toString());
- }
- });
- assertEquals(expectedRoles, roles.toString());
- }
-
- @Test
- public void testListExperiments()
- {
- List<SpaceWithProjectsAndRoleAssignments> spaces =
- generalInformationService.listSpacesWithProjectsAndRoleAssignments(sessionToken,
- null);
- ArrayList<Project> projects = new ArrayList<Project>();
- for (SpaceWithProjectsAndRoleAssignments space : spaces)
- {
- projects.addAll(space.getProjects());
- }
- List<Experiment> result =
- generalInformationService.listExperiments(sessionToken, projects, "SIRNA_HCS");
- assertEquals(true, result.size() > 0);
- Experiment resultExperiment = result.get(0);
- boolean identifierIsOk = "/CISD/DEFAULT/EXP-REUSE".equals(resultExperiment.getIdentifier());
- identifierIsOk |= "/CISD/NEMO/EXP-TEST-2".equals(resultExperiment.getIdentifier());
- assertEquals("Experiment should be: " + resultExperiment.getIdentifier(), true,
- identifierIsOk);
- }
-
- @Test
- public void testListExperimentsByIdentifier()
- {
- List<SpaceWithProjectsAndRoleAssignments> spaces =
- generalInformationService.listSpacesWithProjectsAndRoleAssignments(sessionToken,
- null);
- ArrayList<Project> projects = new ArrayList<Project>();
- for (SpaceWithProjectsAndRoleAssignments space : spaces)
- {
- projects.addAll(space.getProjects());
- }
- List<Experiment> experimentsByProject =
- generalInformationService.listExperiments(sessionToken, projects, "SIRNA_HCS");
- assertEquals(true, experimentsByProject.size() > 0);
-
- List<String> experimentIdentifiers = new ArrayList<String>();
- for (Experiment exp : experimentsByProject)
- {
- experimentIdentifiers.add(exp.getIdentifier());
- }
-
- List<Experiment> results =
- generalInformationService.listExperiments(sessionToken, experimentIdentifiers);
- Comparator<Experiment> experimentCompare = new Comparator<Experiment>()
- {
-
- public int compare(Experiment o1, Experiment o2)
- {
- return o1.getIdentifier().compareTo(o2.getIdentifier());
- }
- };
- Collections.sort(experimentsByProject, experimentCompare);
- Collections.sort(results, experimentCompare);
- assertEquals(experimentsByProject, results);
- }
-
- @Test
- public void testListDataSetTypes()
- {
- List<DataSetType> dataSetTypes = generalInformationService.listDataSetTypes(sessionToken);
- assertEquals(4, dataSetTypes.size());
-
- Collections.sort(dataSetTypes, new ToStringComparator());
- DataSetType dataSetType = dataSetTypes.get(1);
- assertEquals("HCS_IMAGE", dataSetType.getCode());
-
- List<PropertyTypeGroup> propertyTypeGroups = dataSetType.getPropertyTypeGroups();
- assertEquals(1, propertyTypeGroups.size());
-
- PropertyTypeGroup propertyTypeGroup = propertyTypeGroups.get(0);
- assertEquals(null, propertyTypeGroup.getName());
-
- List<PropertyType> propertyTypes = propertyTypeGroup.getPropertyTypes();
- assertEquals(4, propertyTypes.size());
-
- PropertyType propertyType;
- propertyType = propertyTypes.get(0);
- assertEquals("COMMENT", propertyType.getCode());
- assertEquals("Comment", propertyType.getLabel());
- assertEquals("Any other comments", propertyType.getDescription());
-
- propertyType = propertyTypes.get(1);
- assertEquals("ANY_MATERIAL", propertyType.getCode());
- assertEquals("any_material", propertyType.getLabel());
- assertEquals("any_material", propertyType.getDescription());
- }
-
- @Test
- public void testSearchForDataSetsByCode()
- {
- SearchCriteria sc = new SearchCriteria();
- sc.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, "*"));
- List<DataSet> result = generalInformationService.searchForDataSets(sessionToken, sc);
- assertTrue(result.size() > 0);
- String expectedDataSetCode = "20081105092159188-3";
- for (DataSet dataSet : result)
- {
- if (expectedDataSetCode.equals(dataSet.getCode()))
- {
- return;
- }
- }
- fail("result didn't contain data set" + expectedDataSetCode);
- }
-
- @Test
- public void testSearchForDataSetsByExperiments()
- {
- SearchCriteria searchCriteria = new SearchCriteria();
- SearchCriteria expCriteria = new SearchCriteria();
- expCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE,
- "EXP-TEST-1"));
- searchCriteria.addSubCriteria(SearchSubCriteria.createExperimentCriteria(expCriteria));
- List<DataSet> result =
- generalInformationService.searchForDataSets(sessionToken, searchCriteria);
- assertEquals(1, result.size());
-
- DataSet dataSet = result.get(0);
- assertEquals("20081105092159111-1", dataSet.getCode());
- assertEquals("/CISD/NEMO/EXP-TEST-1", dataSet.getExperimentIdentifier());
-
- }
-
- @Test
- public void testSearchForDataSetsBySamples()
- {
- SearchCriteria searchCriteria = new SearchCriteria();
- SearchCriteria sampleCriteria = new SearchCriteria();
- sampleCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE,
- "CP-TEST-1"));
- searchCriteria.addSubCriteria(SearchSubCriteria.createSampleCriteria(sampleCriteria));
- List<DataSet> result =
- generalInformationService.searchForDataSets(sessionToken, searchCriteria);
- assertEquals(1, result.size());
-
- DataSet dataSet = result.get(0);
- assertEquals("20081105092159111-1", dataSet.getCode());
- assertEquals("/CISD/NEMO/EXP-TEST-1", dataSet.getExperimentIdentifier());
- assertEquals("/CISD/CP-TEST-1", dataSet.getSampleIdentifierOrNull());
- }
-
- @Test
- public void testSearchForDataSetsByParent()
- {
- SearchCriteria searchCriteria = new SearchCriteria();
-
- SearchCriteria parentCriteria = new SearchCriteria();
- parentCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE,
- "20081105092159333-3"));
- searchCriteria
- .addSubCriteria(SearchSubCriteria.createDataSetParentCriteria(parentCriteria));
-
- List<DataSet> result =
- generalInformationService.searchForDataSets(sessionToken, searchCriteria);
-
- assertEquals(2, result.size());
- assertEquals(
- "[DataSet[20081105092259000-8,/CISD/DEFAULT/EXP-REUSE,<null>,HCS_IMAGE,{COMMENT=no comment}], "
- + "DataSet[20081105092259000-9,/CISD/DEFAULT/EXP-REUSE,<null>,HCS_IMAGE,{COMMENT=no comment}]]",
- result.toString());
- }
-
- @Test
- public void testSearchForDataSetsByChild()
- {
- SearchCriteria searchCriteria = new SearchCriteria();
- SearchCriteria childCriteria = new SearchCriteria();
- childCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE,
- "20081105092259000-9"));
- searchCriteria.addSubCriteria(SearchSubCriteria.createDataSetChildCriteria(childCriteria));
-
- List<DataSet> result =
- generalInformationService.searchForDataSets(sessionToken, searchCriteria);
- assertEquals(3, result.size());
- assertEquals(
- "[DataSet[20081105092159111-1,/CISD/NEMO/EXP-TEST-1,/CISD/CP-TEST-1,HCS_IMAGE,{ANY_MATERIAL=null, BACTERIUM=null, COMMENT=no comment, GENDER=null}], "
- + "DataSet[20081105092159222-2,/CISD/NOE/EXP-TEST-2,/CISD/CP-TEST-2,HCS_IMAGE,{COMMENT=no comment}], "
- + "DataSet[20081105092159333-3,/CISD/NEMO/EXP-TEST-2,/CISD/CP-TEST-3,HCS_IMAGE,{COMMENT=no comment}]]",
- result.toString());
- }
-
- @Test
- public void testSearchForDataSetsByParentAndChild()
- {
- SearchCriteria searchCriteria = new SearchCriteria();
-
- SearchCriteria parentCriteria = new SearchCriteria();
- parentCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE,
- "20081105092159333-3"));
- searchCriteria
- .addSubCriteria(SearchSubCriteria.createDataSetParentCriteria(parentCriteria));
-
- SearchCriteria childCriteria = new SearchCriteria();
- childCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE,
- "20081105092259900-1"));
- searchCriteria.addSubCriteria(SearchSubCriteria.createDataSetChildCriteria(childCriteria));
-
- List<DataSet> result =
- generalInformationService.searchForDataSets(sessionToken, searchCriteria);
- assertEquals(1, result.size());
- assertEquals(
- "[DataSet[20081105092259000-9,/CISD/DEFAULT/EXP-REUSE,<null>,HCS_IMAGE,{COMMENT=no comment}]]",
- result.toString());
- }
-
- @Test
- public void testSearchForDataSetsByContainer()
- {
- SearchCriteria searchCriteria = new SearchCriteria();
- SearchCriteria containerCriteria = new SearchCriteria();
-
- containerCriteria.addMatchClause(MatchClause.createAttributeMatch(
- MatchClauseAttribute.CODE, "20110509092359990-10"));
- searchCriteria.addSubCriteria(SearchSubCriteria
- .createDataSetContainerCriteria(containerCriteria));
-
- List<DataSet> result =
- generalInformationService.searchForDataSets(sessionToken, searchCriteria);
- assertEquals(2, result.size());
- assertEquals(
- "[DataSet[20110509092359990-11,/CISD/DEFAULT/EXP-REUSE,<null>,HCS_IMAGE,{COMMENT=non-virtual comment}], "
- + "DataSet[20110509092359990-12,/CISD/DEFAULT/EXP-REUSE,<null>,HCS_IMAGE,{COMMENT=non-virtual comment}]]",
- result.toString());
- }
-
-}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/remoteapitest/api/v1/GeneralInformationServiceHttpInvokerApiTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/remoteapitest/api/v1/GeneralInformationServiceHttpInvokerApiTest.java
index 103b9669a08352b223fbafc696240199f1c7b55e..8d5978855a2c8bb86a20b9e4ced971710629f8de 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/remoteapitest/api/v1/GeneralInformationServiceHttpInvokerApiTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/remoteapitest/api/v1/GeneralInformationServiceHttpInvokerApiTest.java
@@ -25,9 +25,6 @@ import java.util.List;
import java.util.Map;
import org.springframework.remoting.httpinvoker.HttpInvokerServiceExporter;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Factory;
import org.testng.annotations.Test;
import ch.systemsx.cisd.common.api.client.ServiceFinder;
@@ -42,8 +39,6 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseAttribute;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
-import ch.systemsx.cisd.openbis.remoteapitest.RemoteApiTestCase;
-import ch.systemsx.cisd.openbis.remoteapitest.api.v1.GeneralInformationServiceAbstractTestCases.IGeneralInformationServiceFactory;
/**
* Verifies that an instance of {@link IGeneralInformationService} is published via
@@ -53,64 +48,52 @@ import ch.systemsx.cisd.openbis.remoteapitest.api.v1.GeneralInformationServiceAb
*/
@Test(groups =
{ "remote api" })
-public class GeneralInformationServiceHttpInvokerApiTest extends RemoteApiTestCase implements
- IGeneralInformationServiceFactory
+public class GeneralInformationServiceHttpInvokerApiTest extends
+ GeneralInformationServiceJsonApiTest
{
private static final String SERVICE_URL = "http://localhost:8888/";
- private IGeneralInformationService service;
-
- private String sessionToken;
-
- @BeforeMethod
- public void beforeMethod()
- {
- service = createService();
- sessionToken = service.tryToAuthenticateForAllServices("test", "a");
- }
-
- @AfterMethod
- public void afterMethod()
+ @Override
+ protected IGeneralInformationService createService()
{
- service.logout(sessionToken);
- }
-
- @Factory
- public Object[] createTestCases()
- {
- return new Object[]
- { new GeneralInformationServiceAbstractTestCases(this) };
+ ServiceFinder generalInformationServiceFinder =
+ new ServiceFinder("openbis", IGeneralInformationService.SERVICE_URL);
+ return generalInformationServiceFinder.createService(IGeneralInformationService.class,
+ SERVICE_URL, 5000);
}
@Test
public void testRegistrationDetailsAvailable()
{
// project
- List<Project> projects = service.listProjects(sessionToken);
+ List<Project> projects = generalInformationService.listProjects(sessionToken);
assertTrue(projects.size() > 0);
checkRegistrationDetails(projects.get(0).getRegistrationDetails());
// experiment
- List<Experiment> experiments = service.listExperiments(sessionToken, projects, "SIRNA_HCS");
+ List<Experiment> experiments =
+ generalInformationService.listExperiments(sessionToken, projects, "SIRNA_HCS");
assertTrue(experiments.size() > 0);
checkRegistrationDetails(experiments.get(0).getRegistrationDetails());
// sample
SearchCriteria sc = new SearchCriteria();
sc.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, "CP-TEST-1"));
- List<Sample> samples = service.searchForSamples(sessionToken, sc);
+ List<Sample> samples = generalInformationService.searchForSamples(sessionToken, sc);
assertTrue(samples.size() > 0);
Sample sample = samples.get(0);
checkRegistrationDetails(sample.getRegistrationDetails());
// data set
- List<DataSet> dataSets = service.listDataSetsForSample(sessionToken, sample, false);
+ List<DataSet> dataSets =
+ generalInformationService.listDataSetsForSample(sessionToken, sample, false);
assertTrue(dataSets.size() > 0);
assertNotNull(dataSets.get(0).getRegistrationDetails().getRegistrationDate());
// vocabularies
- Map<Vocabulary, List<VocabularyTerm>> termMap = service.getVocabularyTermsMap(sessionToken);
+ Map<Vocabulary, List<VocabularyTerm>> termMap =
+ generalInformationService.getVocabularyTermsMap(sessionToken);
ArrayList<Vocabulary> vocabs = new ArrayList<Vocabulary>(termMap.keySet().size());
vocabs.addAll(termMap.keySet());
List<VocabularyTerm> terms = termMap.get(vocabs.get(0));
@@ -130,11 +113,4 @@ public class GeneralInformationServiceHttpInvokerApiTest extends RemoteApiTestCa
}
- public IGeneralInformationService createService()
- {
- ServiceFinder generalInformationServiceFinder =
- new ServiceFinder("openbis", IGeneralInformationService.SERVICE_URL);
- return generalInformationServiceFinder.createService(IGeneralInformationService.class,
- SERVICE_URL, 5000);
- }
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/remoteapitest/api/v1/GeneralInformationServiceJsonApiTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/remoteapitest/api/v1/GeneralInformationServiceJsonApiTest.java
index 1a18f404b5acd0a0c03aaa9d428511c52ffe6d82..3a3f6e5e2e962f2a77a6ca4ba1d7e6402e1d8c16 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/remoteapitest/api/v1/GeneralInformationServiceJsonApiTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/remoteapitest/api/v1/GeneralInformationServiceJsonApiTest.java
@@ -16,18 +16,44 @@
package ch.systemsx.cisd.openbis.remoteapitest.api.v1;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.AssertJUnit.fail;
+
import java.net.MalformedURLException;
import java.net.URL;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.EnumSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
-import org.testng.annotations.Factory;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import com.googlecode.jsonrpc4j.JsonRpcHttpClient;
import com.googlecode.jsonrpc4j.ProxyUtil;
+import ch.systemsx.cisd.common.utilities.ToStringComparator;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.Connections;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyType;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyTypeGroup;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Role;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseAttribute;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchSubCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SpaceWithProjectsAndRoleAssignments;
import ch.systemsx.cisd.openbis.remoteapitest.RemoteApiTestCase;
-import ch.systemsx.cisd.openbis.remoteapitest.api.v1.GeneralInformationServiceAbstractTestCases.IGeneralInformationServiceFactory;
/**
* Verifies that an instance of {@link IGeneralInformationService} is published via JSON-RPC and
@@ -37,20 +63,16 @@ import ch.systemsx.cisd.openbis.remoteapitest.api.v1.GeneralInformationServiceAb
*/
@Test(groups =
{ "remote api" })
-public class GeneralInformationServiceJsonApiTest extends RemoteApiTestCase implements
- IGeneralInformationServiceFactory
+public class GeneralInformationServiceJsonApiTest extends RemoteApiTestCase
{
private static final String SERVICE_URL = "http://localhost:8888/openbis/"
+ IGeneralInformationService.JSON_SERVICE_URL;
- @Factory
- public Object[] createTestCases()
- {
- return new Object[]
- { new GeneralInformationServiceAbstractTestCases(this) };
- }
+ protected IGeneralInformationService generalInformationService;
- public IGeneralInformationService createService()
+ protected String sessionToken;
+
+ protected IGeneralInformationService createService()
{
try
{
@@ -64,4 +86,514 @@ public class GeneralInformationServiceJsonApiTest extends RemoteApiTestCase impl
}
}
+ @BeforeMethod
+ public void beforeMethod() throws MalformedURLException
+ {
+ generalInformationService = createService();
+ sessionToken = generalInformationService.tryToAuthenticateForAllServices("test", "a");
+ }
+
+ @AfterMethod
+ public void afterMethod() throws MalformedURLException
+ {
+ generalInformationService.logout(sessionToken);
+ }
+
+ @Test
+ public void testListNamedRoleSets()
+ {
+ Map<String, Set<Role>> namedRoleSets =
+ generalInformationService.listNamedRoleSets(sessionToken);
+
+ assertEquals("[ADMIN(instance), ADMIN(space)]", namedRoleSets.get("SPACE_ADMIN").toString());
+ }
+
+ @Test
+ public void testListSpacesWithProjectsAndRoleAssignments()
+ {
+ List<SpaceWithProjectsAndRoleAssignments> spaces =
+ generalInformationService.listSpacesWithProjectsAndRoleAssignments(sessionToken,
+ null);
+
+ Collections.sort(spaces, new Comparator<SpaceWithProjectsAndRoleAssignments>()
+ {
+ public int compare(SpaceWithProjectsAndRoleAssignments s1,
+ SpaceWithProjectsAndRoleAssignments s2)
+ {
+ return s1.getCode().compareTo(s2.getCode());
+ }
+ });
+ checkSpace("CISD", "[/CISD/DEFAULT, /CISD/NEMO, /CISD/NOE]",
+ "[ADMIN(instance), ADMIN(space), ETL_SERVER(instance), ETL_SERVER(space)]",
+ spaces.get(0));
+ checkSpace("TESTGROUP", "[/TESTGROUP/TESTPROJ]",
+ "[ADMIN(instance), ADMIN(space), ETL_SERVER(instance)]", spaces.get(1));
+ assertEquals(2, spaces.size());
+ }
+
+ @Test
+ public void testListProjects()
+ {
+ List<Project> result = generalInformationService.listProjects(sessionToken);
+ assertEquals(true, result.size() > 0);
+ String expectedSampleIdentifier = "/TESTGROUP/TESTPROJ";
+ for (Project project : result)
+ {
+ if (expectedSampleIdentifier.equals(project.toString()))
+ {
+ return;
+ }
+ }
+ fail("result didn't contain project " + expectedSampleIdentifier);
+ }
+
+ @Test
+ public void testSearchForSamples()
+ {
+ SearchCriteria sc = new SearchCriteria();
+ sc.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, "*"));
+ List<Sample> result = generalInformationService.searchForSamples(sessionToken, sc);
+ assertEquals(true, result.size() > 0);
+ String expectedSampleIdentifier = "/CISD/CL1";
+ for (Sample sample : result)
+ {
+ if (expectedSampleIdentifier.equals(sample.getIdentifier()))
+ {
+ return;
+ }
+ }
+ fail("result didn't contain sample " + expectedSampleIdentifier);
+ }
+
+ @Test(dependsOnMethods = "testSearchForSamples")
+ public void testSearchForSamplesWithNoCriterion()
+ {
+ SearchCriteria sc = new SearchCriteria();
+ sc.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, "*"));
+ List<Sample> result = generalInformationService.searchForSamples(sessionToken, sc);
+
+ // if no criterion was specified all samples should be returned as well
+ SearchCriteria scWithNoCriterion = new SearchCriteria();
+ List<Sample> resultWithNoCriterion =
+ generalInformationService.searchForSamples(sessionToken, scWithNoCriterion);
+ assertEquals(result, resultWithNoCriterion);
+ }
+
+ @Test
+ public void testSearchForSamplesByProperty()
+ {
+ // Search for Samples first
+ SearchCriteria sc = new SearchCriteria();
+ sc.addMatchClause(MatchClause.createPropertyMatch("ORGANISM", "HUMAN"));
+ List<Sample> result = generalInformationService.searchForSamples(sessionToken, sc);
+ assertEquals(1, result.size());
+ }
+
+ @Test
+ public void testSearchForSamplesByExperimentCode()
+ {
+ // Search for Samples with only experiment's code limiting the results
+ SearchCriteria sc = new SearchCriteria();
+ SearchCriteria ec = new SearchCriteria();
+ ec.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, "EXP-TEST-1"));
+ sc.addSubCriteria(SearchSubCriteria.createExperimentCriteria(ec));
+ List<Sample> result = generalInformationService.searchForSamples(sessionToken, sc);
+ assertEquals(1, result.size());
+ assertEquals("/CISD/NEMO/EXP-TEST-1", result.get(0).getExperimentIdentifierOrNull());
+ }
+
+ @Test
+ public void testSearchForSamplesByExperimentProperty()
+ {
+ // Search for Samples with only experiment's property limiting the results
+ SearchCriteria sc = new SearchCriteria();
+ SearchCriteria ec = new SearchCriteria();
+ ec.addMatchClause(MatchClause.createPropertyMatch("DESCRIPTION", "A simple experiment"));
+ sc.addSubCriteria(SearchSubCriteria.createExperimentCriteria(ec));
+ List<Sample> result = generalInformationService.searchForSamples(sessionToken, sc);
+ assertEquals(2, result.size());
+ }
+
+ @Test
+ public void testSearchForSamplesByParentCode()
+ {
+ // Search for Samples with only parent's code limiting the results
+ SearchCriteria sc = new SearchCriteria();
+ sc.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, "*"));
+ SearchCriteria pc = new SearchCriteria();
+ pc.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, "MP002-1"));
+ sc.addSubCriteria(SearchSubCriteria.createSampleParentCriteria(pc));
+ List<Sample> result = generalInformationService.searchForSamples(sessionToken, sc);
+ assertEquals(2, result.size());
+ }
+
+ @Test
+ public void testSearchForSamplesByChildCode()
+ {
+ // Search for Samples with only child's code limiting the results
+ SearchCriteria sc = new SearchCriteria();
+ sc.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, "*"));
+ SearchCriteria cc = new SearchCriteria();
+ cc.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, "3VCP*"));
+ sc.addSubCriteria(SearchSubCriteria.createSampleChildCriteria(cc));
+ List<Sample> result = generalInformationService.searchForSamples(sessionToken, sc);
+ assertEquals(2, result.size());
+ }
+
+ @Test
+ public void testSearchForSamplesByContainerCode()
+ {
+ // Search for Samples with only container's code limiting the results
+ SearchCriteria sc = new SearchCriteria();
+ SearchCriteria cc = new SearchCriteria();
+ cc.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, "CL1"));
+ sc.addSubCriteria(SearchSubCriteria.createSampleContainerCriteria(cc));
+ List<Sample> result = generalInformationService.searchForSamples(sessionToken, sc);
+ assertEquals(2, result.size());
+ for (Sample s : result)
+ {
+ assertTrue(s.getCode() + "doesn't start with 'CL1:'", s.getCode().startsWith("CL1:"));
+ }
+ }
+
+ @Test
+ public void testSearchForSamplesByExperimentAndParentCode()
+ {
+ // Search for Samples first
+ SearchCriteria sc = new SearchCriteria();
+ List<Sample> result = generalInformationService.searchForSamples(sessionToken, sc);
+ assertEquals(true, result.size() > 600);
+ // Add experiment criteria limiting results to 7
+ SearchCriteria ec = new SearchCriteria();
+ ec.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, "EXP-REUSE"));
+ sc.addSubCriteria(SearchSubCriteria.createExperimentCriteria(ec));
+ List<Sample> result2 = generalInformationService.searchForSamples(sessionToken, sc);
+ assertEquals(7, result2.size());
+ // Add parent criteria limiting results to only 2
+ SearchCriteria pc = new SearchCriteria();
+ pc.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, "DP1-A"));
+ sc.addSubCriteria(SearchSubCriteria.createSampleParentCriteria(pc));
+ List<Sample> result3 = generalInformationService.searchForSamples(sessionToken, sc);
+ assertEquals(2, result3.size());
+ }
+
+ @Test
+ public void testListDataSetsForAllSamples()
+ {
+ // Search for Samples first
+ SearchCriteria sc = new SearchCriteria();
+ List<Sample> samples = generalInformationService.searchForSamples(sessionToken, sc);
+ List<DataSet> result = generalInformationService.listDataSets(sessionToken, samples);
+ assertEquals(true, result.size() > 0);
+ }
+
+ @Test
+ public void testListDataSetsWithParentsForAllSamples()
+ {
+ // Search for Samples first
+ SearchCriteria sc = new SearchCriteria();
+ List<Sample> samples = generalInformationService.searchForSamples(sessionToken, sc);
+ List<DataSet> result =
+ generalInformationService.listDataSets(sessionToken, samples,
+ EnumSet.of(Connections.PARENTS));
+ assertEquals(true, result.size() > 0);
+ // See if some sample has parents
+ boolean parentCodesFound = false;
+ for (DataSet dataSet : result)
+ {
+ if (false == dataSet.getParentCodes().isEmpty())
+ {
+ parentCodesFound = true;
+ break;
+ }
+ }
+
+ assertTrue("No parent codes should have been found", (false == parentCodesFound));
+ }
+
+ @Test
+ public void testListDataSetsForSample()
+ {
+ // Search for Samples first
+ SearchCriteria sc = new SearchCriteria();
+ sc.addMatchClause(MatchClause.createPropertyMatch("ORGANISM", "HUMAN"));
+ List<Sample> samples = generalInformationService.searchForSamples(sessionToken, sc);
+ List<DataSet> result =
+ generalInformationService.listDataSetsForSample(sessionToken, samples.get(0), true);
+ assertEquals(true, result.size() > 0);
+ }
+
+ @Test
+ public void testListDataSetsForEmptySampleList()
+ {
+ List<Sample> samples = new ArrayList<Sample>();
+ List<DataSet> result = generalInformationService.listDataSets(sessionToken, samples);
+ assertEquals(true, result.size() == 0);
+ }
+
+ private static final String DEFAULT_PLATE_GEOMETRY_VALUE = "384_WELLS_16X24";
+
+ @Test
+ public void testSearchForDataSetsByProperty()
+ {
+ // Search for Samples first
+ SearchCriteria sc = new SearchCriteria();
+ sc.addMatchClause(MatchClause.createPropertyMatch("$PLATE_GEOMETRY",
+ DEFAULT_PLATE_GEOMETRY_VALUE));
+ List<Sample> samples = generalInformationService.searchForSamples(sessionToken, sc);
+ assertEquals(true, samples.size() > 0);
+ List<DataSet> result = generalInformationService.listDataSets(sessionToken, samples);
+ assertEquals(true, result.size() == 0);
+ }
+
+ private void checkSpace(String expectedCode, String expectedProjects, String expectedRoles,
+ SpaceWithProjectsAndRoleAssignments space)
+ {
+ assertEquals(expectedCode, space.getCode());
+ List<Project> projects = space.getProjects();
+ Collections.sort(projects, new Comparator<Project>()
+ {
+ public int compare(Project p1, Project p2)
+ {
+ return p1.getCode().compareTo(p2.getCode());
+ }
+ });
+ assertEquals(expectedProjects, projects.toString());
+ List<Role> roles = new ArrayList<Role>(space.getRoles("test"));
+ Collections.sort(roles, new Comparator<Role>()
+ {
+ public int compare(Role r1, Role r2)
+ {
+ return r1.toString().compareTo(r2.toString());
+ }
+ });
+ assertEquals(expectedRoles, roles.toString());
+ }
+
+ @Test
+ public void testListExperiments()
+ {
+ List<SpaceWithProjectsAndRoleAssignments> spaces =
+ generalInformationService.listSpacesWithProjectsAndRoleAssignments(sessionToken,
+ null);
+ ArrayList<Project> projects = new ArrayList<Project>();
+ for (SpaceWithProjectsAndRoleAssignments space : spaces)
+ {
+ projects.addAll(space.getProjects());
+ }
+ List<Experiment> result =
+ generalInformationService.listExperiments(sessionToken, projects, "SIRNA_HCS");
+ assertEquals(true, result.size() > 0);
+ Experiment resultExperiment = result.get(0);
+ boolean identifierIsOk = "/CISD/DEFAULT/EXP-REUSE".equals(resultExperiment.getIdentifier());
+ identifierIsOk |= "/CISD/NEMO/EXP-TEST-2".equals(resultExperiment.getIdentifier());
+ assertEquals("Experiment should be: " + resultExperiment.getIdentifier(), true,
+ identifierIsOk);
+ }
+
+ @Test
+ public void testListExperimentsByIdentifier()
+ {
+ List<SpaceWithProjectsAndRoleAssignments> spaces =
+ generalInformationService.listSpacesWithProjectsAndRoleAssignments(sessionToken,
+ null);
+ ArrayList<Project> projects = new ArrayList<Project>();
+ for (SpaceWithProjectsAndRoleAssignments space : spaces)
+ {
+ projects.addAll(space.getProjects());
+ }
+ List<Experiment> experimentsByProject =
+ generalInformationService.listExperiments(sessionToken, projects, "SIRNA_HCS");
+ assertEquals(true, experimentsByProject.size() > 0);
+
+ List<String> experimentIdentifiers = new ArrayList<String>();
+ for (Experiment exp : experimentsByProject)
+ {
+ experimentIdentifiers.add(exp.getIdentifier());
+ }
+
+ List<Experiment> results =
+ generalInformationService.listExperiments(sessionToken, experimentIdentifiers);
+ Comparator<Experiment> experimentCompare = new Comparator<Experiment>()
+ {
+
+ public int compare(Experiment o1, Experiment o2)
+ {
+ return o1.getIdentifier().compareTo(o2.getIdentifier());
+ }
+ };
+ Collections.sort(experimentsByProject, experimentCompare);
+ Collections.sort(results, experimentCompare);
+ assertEquals(experimentsByProject, results);
+ }
+
+ @Test
+ public void testListDataSetTypes()
+ {
+ List<DataSetType> dataSetTypes = generalInformationService.listDataSetTypes(sessionToken);
+ assertEquals(4, dataSetTypes.size());
+
+ Collections.sort(dataSetTypes, new ToStringComparator());
+ DataSetType dataSetType = dataSetTypes.get(1);
+ assertEquals("HCS_IMAGE", dataSetType.getCode());
+
+ List<PropertyTypeGroup> propertyTypeGroups = dataSetType.getPropertyTypeGroups();
+ assertEquals(1, propertyTypeGroups.size());
+
+ PropertyTypeGroup propertyTypeGroup = propertyTypeGroups.get(0);
+ assertEquals(null, propertyTypeGroup.getName());
+
+ List<PropertyType> propertyTypes = propertyTypeGroup.getPropertyTypes();
+ assertEquals(4, propertyTypes.size());
+
+ PropertyType propertyType;
+ propertyType = propertyTypes.get(0);
+ assertEquals("COMMENT", propertyType.getCode());
+ assertEquals("Comment", propertyType.getLabel());
+ assertEquals("Any other comments", propertyType.getDescription());
+
+ propertyType = propertyTypes.get(1);
+ assertEquals("ANY_MATERIAL", propertyType.getCode());
+ assertEquals("any_material", propertyType.getLabel());
+ assertEquals("any_material", propertyType.getDescription());
+ }
+
+ @Test
+ public void testSearchForDataSetsByCode()
+ {
+ SearchCriteria sc = new SearchCriteria();
+ sc.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, "*"));
+ List<DataSet> result = generalInformationService.searchForDataSets(sessionToken, sc);
+ assertTrue(result.size() > 0);
+ String expectedDataSetCode = "20081105092159188-3";
+ for (DataSet dataSet : result)
+ {
+ if (expectedDataSetCode.equals(dataSet.getCode()))
+ {
+ return;
+ }
+ }
+ fail("result didn't contain data set" + expectedDataSetCode);
+ }
+
+ @Test
+ public void testSearchForDataSetsByExperiments()
+ {
+ SearchCriteria searchCriteria = new SearchCriteria();
+ SearchCriteria expCriteria = new SearchCriteria();
+ expCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE,
+ "EXP-TEST-1"));
+ searchCriteria.addSubCriteria(SearchSubCriteria.createExperimentCriteria(expCriteria));
+ List<DataSet> result =
+ generalInformationService.searchForDataSets(sessionToken, searchCriteria);
+ assertEquals(1, result.size());
+
+ DataSet dataSet = result.get(0);
+ assertEquals("20081105092159111-1", dataSet.getCode());
+ assertEquals("/CISD/NEMO/EXP-TEST-1", dataSet.getExperimentIdentifier());
+
+ }
+
+ @Test
+ public void testSearchForDataSetsBySamples()
+ {
+ SearchCriteria searchCriteria = new SearchCriteria();
+ SearchCriteria sampleCriteria = new SearchCriteria();
+ sampleCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE,
+ "CP-TEST-1"));
+ searchCriteria.addSubCriteria(SearchSubCriteria.createSampleCriteria(sampleCriteria));
+ List<DataSet> result =
+ generalInformationService.searchForDataSets(sessionToken, searchCriteria);
+ assertEquals(1, result.size());
+
+ DataSet dataSet = result.get(0);
+ assertEquals("20081105092159111-1", dataSet.getCode());
+ assertEquals("/CISD/NEMO/EXP-TEST-1", dataSet.getExperimentIdentifier());
+ assertEquals("/CISD/CP-TEST-1", dataSet.getSampleIdentifierOrNull());
+ }
+
+ @Test
+ public void testSearchForDataSetsByParent()
+ {
+ SearchCriteria searchCriteria = new SearchCriteria();
+
+ SearchCriteria parentCriteria = new SearchCriteria();
+ parentCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE,
+ "20081105092159333-3"));
+ searchCriteria
+ .addSubCriteria(SearchSubCriteria.createDataSetParentCriteria(parentCriteria));
+
+ List<DataSet> result =
+ generalInformationService.searchForDataSets(sessionToken, searchCriteria);
+
+ assertEquals(2, result.size());
+ assertEquals(
+ "[DataSet[20081105092259000-8,/CISD/DEFAULT/EXP-REUSE,<null>,HCS_IMAGE,{COMMENT=no comment}], "
+ + "DataSet[20081105092259000-9,/CISD/DEFAULT/EXP-REUSE,<null>,HCS_IMAGE,{COMMENT=no comment}]]",
+ result.toString());
+ }
+
+ @Test
+ public void testSearchForDataSetsByChild()
+ {
+ SearchCriteria searchCriteria = new SearchCriteria();
+ SearchCriteria childCriteria = new SearchCriteria();
+ childCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE,
+ "20081105092259000-9"));
+ searchCriteria.addSubCriteria(SearchSubCriteria.createDataSetChildCriteria(childCriteria));
+
+ List<DataSet> result =
+ generalInformationService.searchForDataSets(sessionToken, searchCriteria);
+ assertEquals(3, result.size());
+ assertEquals(
+ "[DataSet[20081105092159111-1,/CISD/NEMO/EXP-TEST-1,/CISD/CP-TEST-1,HCS_IMAGE,{ANY_MATERIAL=null, BACTERIUM=null, COMMENT=no comment, GENDER=null}], "
+ + "DataSet[20081105092159222-2,/CISD/NOE/EXP-TEST-2,/CISD/CP-TEST-2,HCS_IMAGE,{COMMENT=no comment}], "
+ + "DataSet[20081105092159333-3,/CISD/NEMO/EXP-TEST-2,/CISD/CP-TEST-3,HCS_IMAGE,{COMMENT=no comment}]]",
+ result.toString());
+ }
+
+ @Test
+ public void testSearchForDataSetsByParentAndChild()
+ {
+ SearchCriteria searchCriteria = new SearchCriteria();
+
+ SearchCriteria parentCriteria = new SearchCriteria();
+ parentCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE,
+ "20081105092159333-3"));
+ searchCriteria
+ .addSubCriteria(SearchSubCriteria.createDataSetParentCriteria(parentCriteria));
+
+ SearchCriteria childCriteria = new SearchCriteria();
+ childCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE,
+ "20081105092259900-1"));
+ searchCriteria.addSubCriteria(SearchSubCriteria.createDataSetChildCriteria(childCriteria));
+
+ List<DataSet> result =
+ generalInformationService.searchForDataSets(sessionToken, searchCriteria);
+ assertEquals(1, result.size());
+ assertEquals(
+ "[DataSet[20081105092259000-9,/CISD/DEFAULT/EXP-REUSE,<null>,HCS_IMAGE,{COMMENT=no comment}]]",
+ result.toString());
+ }
+
+ @Test
+ public void testSearchForDataSetsByContainer()
+ {
+ SearchCriteria searchCriteria = new SearchCriteria();
+ SearchCriteria containerCriteria = new SearchCriteria();
+
+ containerCriteria.addMatchClause(MatchClause.createAttributeMatch(
+ MatchClauseAttribute.CODE, "20110509092359990-10"));
+ searchCriteria.addSubCriteria(SearchSubCriteria
+ .createDataSetContainerCriteria(containerCriteria));
+
+ List<DataSet> result =
+ generalInformationService.searchForDataSets(sessionToken, searchCriteria);
+ assertEquals(2, result.size());
+ assertEquals(
+ "[DataSet[20110509092359990-11,/CISD/DEFAULT/EXP-REUSE,<null>,HCS_IMAGE,{COMMENT=non-virtual comment}], "
+ + "DataSet[20110509092359990-12,/CISD/DEFAULT/EXP-REUSE,<null>,HCS_IMAGE,{COMMENT=non-virtual comment}]]",
+ result.toString());
+ }
+
}