From 370bd9a992d0a985b02245a59d05ae6a81ed57a7 Mon Sep 17 00:00:00 2001
From: felmer <franz-josef.elmer@id.ethz.ch>
Date: Tue, 21 Apr 2020 07:19:01 +0200
Subject: [PATCH] SSDM-9367: UpdateExperimentTest and DeleteExperimentTest
extended
---
.../asapi/v3/DeleteExperimentTest.java | 68 +++++-
.../asapi/v3/UpdateExperimentTest.java | 212 ++++++++++++++++++
2 files changed, 279 insertions(+), 1 deletion(-)
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/DeleteExperimentTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/DeleteExperimentTest.java
index 39b066f04b8..c5ec68864b3 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/DeleteExperimentTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/DeleteExperimentTest.java
@@ -29,16 +29,19 @@ import org.testng.annotations.Test;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.DataSetPermId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.deletion.id.IDeletionId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.id.EntityTypePermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.Experiment;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.create.ExperimentCreation;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.delete.ExperimentDeletionOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.fetchoptions.ExperimentFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.id.ExperimentPermId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.id.ProjectIdentifier;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.id.PropertyTypePermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.delete.SampleDeletionOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.SamplePermId;
import ch.ethz.sis.openbis.systemtest.asapi.v3.index.RemoveFromIndexState;
import ch.systemsx.cisd.common.action.IDelegatedAction;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.systemtest.authorization.ProjectAuthorizationUser;
-
import junit.framework.Assert;
/**
@@ -250,4 +253,67 @@ public class DeleteExperimentTest extends AbstractDeletionTest
"delete-experiments EXPERIMENT_IDS('[TEST-LOGGING-1, TEST-LOGGING-2]') DELETION_OPTIONS('ExperimentDeletionOptions[reason=test-reason]')");
}
+ @Test
+ public void testDeleteSampleOfASampleProperty()
+ {
+ // Given
+ String sessionToken = v3api.login(TEST_USER, PASSWORD);
+ PropertyTypePermId propertyType = createASamplePropertyType(sessionToken, null);
+ EntityTypePermId experimentType = createAnExperimentType(sessionToken, true, propertyType);
+ ExperimentCreation creation = new ExperimentCreation();
+ creation.setCode("EXPERIMENT_WITH_SAMPLE_PROPERTY");
+ creation.setTypeId(experimentType);
+ creation.setProjectId(new ProjectIdentifier("/TEST-SPACE/TEST-PROJECT"));
+ SamplePermId propertySamplePermId = createCisdSample(createCisdExperiment());
+ creation.setSampleProperty(propertyType.getPermId(), propertySamplePermId);
+ ExperimentPermId experimentPermId = v3api.createExperiments(sessionToken, Arrays.asList(creation)).get(0);
+ SampleDeletionOptions deletionOptions = new SampleDeletionOptions();
+ deletionOptions.setReason("a test");
+
+ // When
+ IDeletionId deletionId = v3api.deleteSamples(sessionToken, Arrays.asList(propertySamplePermId), deletionOptions);
+
+ // Then
+ ExperimentFetchOptions fetchOptions = new ExperimentFetchOptions();
+ fetchOptions.withProperties();
+ fetchOptions.withSampleProperties();
+ Experiment experiment = v3api.getExperiments(sessionToken, Arrays.asList(experimentPermId), fetchOptions).get(experimentPermId);
+ assertEquals(experiment.getSampleProperties().toString(), "{}");
+ assertEquals(experiment.getProperties().toString(), "{}");
+
+ v3api.confirmDeletions(sessionToken, Arrays.asList(deletionId));
+ experiment = v3api.getExperiments(sessionToken, Arrays.asList(experimentPermId), fetchOptions).get(experimentPermId);
+ assertEquals(experiment.getSampleProperties().toString(), "{}");
+ assertEquals(experiment.getProperties().toString(), "{}");
+ }
+
+ @Test
+ public void testDeleteSampleWithSampleProperty()
+ {
+ // Given
+ String sessionToken = v3api.login(TEST_USER, PASSWORD);
+ PropertyTypePermId propertyType = createASamplePropertyType(sessionToken, null);
+ EntityTypePermId experimentType = createAnExperimentType(sessionToken, true, propertyType);
+ ExperimentCreation creation = new ExperimentCreation();
+ creation.setCode("EXPERIMENT_WITH_SAMPLE_PROPERTY");
+ creation.setTypeId(experimentType);
+ creation.setProjectId(new ProjectIdentifier("/TEST-SPACE/TEST-PROJECT"));
+ SamplePermId propertySamplePermId = createCisdSample(createCisdExperiment());
+ creation.setSampleProperty(propertyType.getPermId(), propertySamplePermId);
+ ExperimentPermId experimentPermId = v3api.createExperiments(sessionToken, Arrays.asList(creation)).get(0);
+ ExperimentDeletionOptions deletionOptions = new ExperimentDeletionOptions();
+ deletionOptions.setReason("a test");
+
+ // When
+ IDeletionId deletionId = v3api.deleteExperiments(sessionToken, Arrays.asList(experimentPermId), deletionOptions);
+
+ // Then
+ ExperimentFetchOptions fetchOptions = new ExperimentFetchOptions();
+ fetchOptions.withProperties();
+ fetchOptions.withSampleProperties();
+ assertEquals(v3api.getExperiments(sessionToken, Arrays.asList(experimentPermId), fetchOptions).toString(), "{}");
+ v3api.confirmDeletions(sessionToken, Arrays.asList(deletionId));
+ assertEquals(v3api.getExperiments(sessionToken, Arrays.asList(experimentPermId), fetchOptions).toString(), "{}");
+ }
+
}
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/UpdateExperimentTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/UpdateExperimentTest.java
index d0722b2bde6..b1cb6e8107e 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/UpdateExperimentTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/UpdateExperimentTest.java
@@ -48,6 +48,7 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.update.ExperimentUpda
import ch.ethz.sis.openbis.generic.asapi.v3.dto.person.id.PersonPermId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.id.IProjectId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.id.ProjectIdentifier;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.id.PropertyTypePermId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.roleassignment.Role;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.roleassignment.create.RoleAssignmentCreation;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.Sample;
@@ -55,7 +56,9 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.create.SampleCreation;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.delete.SampleDeletionOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.fetchoptions.SampleFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.ISampleId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.SampleIdentifier;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.SamplePermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.update.SampleUpdate;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.id.SpacePermId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.tag.id.ITagId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.tag.id.TagCode;
@@ -994,6 +997,215 @@ public class UpdateExperimentTest extends AbstractExperimentTest
"update-experiments EXPERIMENT_UPDATES('[ExperimentUpdate[experimentId=/TEST-SPACE/TEST-PROJECT/EXP-SPACE-TEST], ExperimentUpdate[experimentId=200811050940555-1032]]')");
}
+ @Test
+ public void testUpdateWithUnknownPropertyOfTypeSample()
+ {
+ // Given
+ String sessionToken = v3api.login(TEST_USER, PASSWORD);
+ ExperimentCreation creation = new ExperimentCreation();
+ creation.setCode("EXPERIMENT_WITH_SAMPLE_PROPERTY");
+ creation.setTypeId(new EntityTypePermId("DELETION_TEST"));
+ creation.setProjectId(new ProjectIdentifier("/TEST-SPACE/TEST-PROJECT"));
+ ExperimentPermId experimentPermId = v3api.createExperiments(sessionToken, Arrays.asList(creation)).get(0);
+
+ ExperimentUpdate update = new ExperimentUpdate();
+ update.setExperimentId(experimentPermId);
+ update.setSampleProperty("PLATE", new SamplePermId("200811050924898-997"));
+
+ // When
+ assertUserFailureException(Void -> v3api.updateExperiments(sessionToken, Arrays.asList(update)),
+ // Then
+ "Not a property of data type SAMPLE: PLATE");
+ }
+
+ @Test
+ public void testUpdateWithPropertyOfTypeSampleWithUnknownSample()
+ {
+ // Given
+ String sessionToken = v3api.login(TEST_USER, PASSWORD);
+ PropertyTypePermId propertyType = createASamplePropertyType(sessionToken, null);
+ EntityTypePermId experimentType = createAnExperimentType(sessionToken, false, propertyType);
+ ExperimentCreation creation = new ExperimentCreation();
+ creation.setCode("EXPERIMENT_WITH_SAMPLE_PROPERTY");
+ creation.setTypeId(experimentType);
+ creation.setProjectId(new ProjectIdentifier("/TEST-SPACE/TEST-PROJECT"));
+ creation.setSampleProperty(propertyType.getPermId(), new SampleIdentifier("/CISD/CL1"));
+ ExperimentPermId experimentPermId = v3api.createExperiments(sessionToken, Arrays.asList(creation)).get(0);
+
+ ExperimentUpdate update = new ExperimentUpdate();
+ update.setExperimentId(experimentPermId);
+ update.setSampleProperty(propertyType.getPermId(), new SampleIdentifier("/CISD/UNKNOWN"));
+
+ // When
+ assertUserFailureException(Void -> v3api.updateExperiments(sessionToken, Arrays.asList(update)),
+ // Then
+ "Unknown sample: /CISD/UNKNOWN");
+ }
+
+ @Test
+ public void testUpdateWithPropertyOfTypeSampleWithSampleOfWrongType()
+ {
+ // Given
+ String sessionToken = v3api.login(TEST_USER, PASSWORD);
+ PropertyTypePermId propertyType = createASamplePropertyType(sessionToken,
+ new EntityTypePermId("WELL", EntityKind.SAMPLE));
+ EntityTypePermId experimentType = createAnExperimentType(sessionToken, false, propertyType);
+ ExperimentCreation creation = new ExperimentCreation();
+ creation.setCode("EXPERIMENT_WITH_SAMPLE_PROPERTY");
+ creation.setTypeId(experimentType);
+ creation.setProjectId(new ProjectIdentifier("/TEST-SPACE/TEST-PROJECT"));
+ creation.setSampleProperty(propertyType.getPermId(), new SamplePermId("200811050917877-438"));
+ ExperimentPermId experimentPermId = v3api.createExperiments(sessionToken, Arrays.asList(creation)).get(0);
+
+ ExperimentUpdate update = new ExperimentUpdate();
+ update.setExperimentId(experimentPermId);
+ update.setSampleProperty(propertyType.getPermId(), new SamplePermId("200811050919915-8"));
+
+ // When
+ assertUserFailureException(Void -> v3api.updateExperiments(sessionToken, Arrays.asList(update)),
+ // Then
+ "Property " + propertyType.getPermId() + " is not a sample of type WELL but of type CONTROL_LAYOUT");
+ }
+
+ @Test
+ public void testUpdateWithPropertyOfTypeSampleWithSampleNotAccessable()
+ {
+ // Given
+ String adminSessionToken = v3api.login(TEST_USER, PASSWORD);
+ PropertyTypePermId propertyType = createASamplePropertyType(adminSessionToken, null);
+ EntityTypePermId experimentType = createAnExperimentType(adminSessionToken, false, propertyType);
+ ExperimentCreation creation = new ExperimentCreation();
+ creation.setCode("EXPERIMENT_WITH_SAMPLE_PROPERTY");
+ creation.setTypeId(experimentType);
+ creation.setProjectId(new ProjectIdentifier("/TEST-SPACE/TEST-PROJECT"));
+ creation.setSampleProperty(propertyType.getPermId(), new SampleIdentifier("/CISD/CL1"));
+ ExperimentPermId experimentPermId = v3api.createExperiments(adminSessionToken, Arrays.asList(creation)).get(0);
+
+ String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
+ ExperimentUpdate update = new ExperimentUpdate();
+ update.setExperimentId(experimentPermId);
+ update.setSampleProperty(propertyType.getPermId(), new SampleIdentifier("/CISD/CL1"));
+
+ // When
+ assertUserFailureException(Void -> v3api.updateExperiments(sessionToken, Arrays.asList(update)),
+ // Then
+ "Unknown sample: /CISD/CL1");
+ }
+
+ @Test
+ public void testUpdateAddSampleProperty()
+ {
+ // Given
+ String sessionToken = v3api.login(TEST_USER, PASSWORD);
+ PropertyTypePermId propertyType = createASamplePropertyType(sessionToken, null);
+ EntityTypePermId experimentType = createAnExperimentType(sessionToken, false, propertyType);
+ ExperimentCreation creation = new ExperimentCreation();
+ creation.setCode("EXPERIMENT_WITH_SAMPLE_PROPERTY");
+ creation.setTypeId(experimentType);
+ creation.setProjectId(new ProjectIdentifier("/TEST-SPACE/TEST-PROJECT"));
+ ExperimentPermId experimentPermId = v3api.createExperiments(sessionToken, Arrays.asList(creation)).get(0);
+
+ ExperimentUpdate update = new ExperimentUpdate();
+ update.setExperimentId(experimentPermId);
+ update.setSampleProperty(propertyType.getPermId(), new SamplePermId("200811050924898-997"));
+
+ // When
+ v3api.updateExperiments(sessionToken, Arrays.asList(update));
+
+ // Then
+ ExperimentFetchOptions fetchOptions = new ExperimentFetchOptions();
+ fetchOptions.withProperties();
+ fetchOptions.withSampleProperties();
+ Experiment experiment = v3api.getExperiments(sessionToken, Arrays.asList(experimentPermId), fetchOptions).get(experimentPermId);
+ assertEquals(experiment.getProperties().toString(), "{" + propertyType.getPermId() + "=200811050924898-997}");
+ assertEquals(experiment.getSampleProperties().toString(), "{" + propertyType.getPermId() + "=Sample 200811050924898-997}");
+ }
+
+ @Test
+ public void testUpdateChangeSampleProperty()
+ {
+ // Given
+ String sessionToken = v3api.login(TEST_USER, PASSWORD);
+ PropertyTypePermId propertyType = createASamplePropertyType(sessionToken, null);
+ EntityTypePermId experimentType = createAnExperimentType(sessionToken, false, propertyType);
+ ExperimentCreation creation = new ExperimentCreation();
+ creation.setCode("EXPERIMENT_WITH_SAMPLE_PROPERTY");
+ creation.setTypeId(experimentType);
+ creation.setProjectId(new ProjectIdentifier("/TEST-SPACE/TEST-PROJECT"));
+ creation.setSampleProperty(propertyType.getPermId(), new SamplePermId("200811050919915-8"));
+ ExperimentPermId experimentPermId = v3api.createExperiments(sessionToken, Arrays.asList(creation)).get(0);
+
+ ExperimentUpdate update = new ExperimentUpdate();
+ update.setExperimentId(experimentPermId);
+ update.setSampleProperty(propertyType.getPermId(), new SamplePermId("200811050924898-997"));
+
+ // When
+ v3api.updateExperiments(sessionToken, Arrays.asList(update));
+
+ // Then
+ ExperimentFetchOptions fetchOptions = new ExperimentFetchOptions();
+ fetchOptions.withProperties();
+ fetchOptions.withSampleProperties();
+ Experiment experiment = v3api.getExperiments(sessionToken, Arrays.asList(experimentPermId), fetchOptions).get(experimentPermId);
+ assertEquals(experiment.getProperties().toString(), "{" + propertyType.getPermId() + "=200811050924898-997}");
+ assertEquals(experiment.getSampleProperties().toString(), "{" + propertyType.getPermId() + "=Sample 200811050924898-997}");
+ }
+
+ @Test
+ public void testUpdateRemoveSampleProperty()
+ {
+ // Given
+ String sessionToken = v3api.login(TEST_USER, PASSWORD);
+ PropertyTypePermId propertyType = createASamplePropertyType(sessionToken, null);
+ EntityTypePermId experimentType = createAnExperimentType(sessionToken, false, propertyType);
+ ExperimentCreation creation = new ExperimentCreation();
+ creation.setCode("EXPERIMENT_WITH_SAMPLE_PROPERTY");
+ creation.setTypeId(experimentType);
+ creation.setProjectId(new ProjectIdentifier("/TEST-SPACE/TEST-PROJECT"));
+ creation.setSampleProperty(propertyType.getPermId(), new SamplePermId("200811050919915-8"));
+ ExperimentPermId experimentPermId = v3api.createExperiments(sessionToken, Arrays.asList(creation)).get(0);
+
+ ExperimentUpdate update = new ExperimentUpdate();
+ update.setExperimentId(experimentPermId);
+ update.setSampleProperty(propertyType.getPermId(), null);
+
+ // When
+ v3api.updateExperiments(sessionToken, Arrays.asList(update));
+
+ // Then
+ ExperimentFetchOptions fetchOptions = new ExperimentFetchOptions();
+ fetchOptions.withProperties();
+ fetchOptions.withSampleProperties();
+ Experiment experiment = v3api.getExperiments(sessionToken, Arrays.asList(experimentPermId), fetchOptions).get(experimentPermId);
+ assertEquals(experiment.getProperties().toString(), "{}");
+ assertEquals(experiment.getSampleProperties().toString(), "{}");
+ }
+
+ @Test
+ public void testUpdateRemoveMandatorySampleProperty()
+ {
+ // Given
+ String sessionToken = v3api.login(TEST_USER, PASSWORD);
+ PropertyTypePermId propertyType = createASamplePropertyType(sessionToken, null);
+ EntityTypePermId experimentType = createAnExperimentType(sessionToken, true, propertyType);
+ ExperimentCreation creation = new ExperimentCreation();
+ creation.setCode("EXPERIMENT_WITH_SAMPLE_PROPERTY");
+ creation.setTypeId(experimentType);
+ creation.setProjectId(new ProjectIdentifier("/TEST-SPACE/TEST-PROJECT"));
+ creation.setSampleProperty(propertyType.getPermId(), new SamplePermId("200811050919915-8"));
+ ExperimentPermId experimentPermId = v3api.createExperiments(sessionToken, Arrays.asList(creation)).get(0);
+
+ ExperimentUpdate update = new ExperimentUpdate();
+ update.setExperimentId(experimentPermId);
+ update.setSampleProperty(propertyType.getPermId(), null);
+
+ // When
+ assertUserFailureException(Void -> v3api.updateExperiments(sessionToken, Arrays.asList(update)),
+ "Property " + propertyType + " of entity type " + experimentType.getPermId()
+ + " can not be deleted because it is mandatory.");
+ }
+
+ @Test
private ExperimentPermId createExperimentWithoutAttachments()
{
final String sessionToken = v3api.login(TEST_USER, PASSWORD);
--
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