From 89c6624169af3f18b27c7bb7f4b93dedf5c549fc Mon Sep 17 00:00:00 2001
From: buczekp <buczekp>
Date: Fri, 12 Nov 2010 09:12:39 +0000
Subject: [PATCH] [LMS-1772] tests of registration/update of samples with many
parents
SVN: 18649
---
.../generic/shared/basic/dto/NewSample.java | 13 +-
.../web/server/GenericClientServiceTest.java | 171 +++++++++++++++++-
.../CinaBundleRegistrationTest.java | 3 +-
3 files changed, 176 insertions(+), 11 deletions(-)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewSample.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewSample.java
index 3ca2619cefa..9168598c802 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewSample.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewSample.java
@@ -152,8 +152,17 @@ public class NewSample extends Identifier<NewSample> implements Comparable<NewSa
@Deprecated
public final String getParentIdentifier()
{
- return getParentsOrNull() == null || getParentsOrNull().length == 0 ? null
- : getParentsOrNull()[0];
+ if (getParentsOrNull() == null || getParentsOrNull().length == 0)
+ {
+ return null;
+ } else if (getParentsOrNull().length > 1)
+ {
+ throw new IllegalStateException("Sample " + getIdentifier()
+ + " has more than one parent");
+ } else
+ {
+ return getParentsOrNull()[0];
+ }
}
/**
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientServiceTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientServiceTest.java
index 97161fc1917..8c0beb436de 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientServiceTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientServiceTest.java
@@ -80,18 +80,14 @@ public final class GenericClientServiceTest extends AbstractClientServiceTest
private GenericClientService genericClientService;
- @SuppressWarnings("deprecation")
private final static NewSample createNewSample(final String sampleIdentifier,
- final String sampleTypeCode, final IEntityProperty[] properties, final String parent,
- final String container)
+ final String sampleTypeCode, final IEntityProperty[] properties)
{
final NewSample newSample = new NewSample();
newSample.setIdentifier(sampleIdentifier);
final SampleType sampleType = createSampleType(sampleTypeCode);
newSample.setSampleType(sampleType);
newSample.setProperties(properties);
- newSample.setParentIdentifier(parent);
- newSample.setContainerIdentifier(container);
return newSample;
}
@@ -236,8 +232,7 @@ public final class GenericClientServiceTest extends AbstractClientServiceTest
{
final String sessionKey = "some-session-key";
final NewSample newSample =
- createNewSample("/group1/sample1", "MASTER_PLATE", IEntityProperty.EMPTY_ARRAY,
- null, null);
+ createNewSample("/group1/sample1", "MASTER_PLATE", IEntityProperty.EMPTY_ARRAY);
context.checking(new Expectations()
{
{
@@ -367,6 +362,89 @@ public final class GenericClientServiceTest extends AbstractClientServiceTest
context.assertIsSatisfied();
}
+ @Test
+ public final void testRegisterSamplesWithParents() throws IOException
+ {
+ final UploadedFilesBean uploadedFilesBean = new UploadedFilesBean();
+ final String sessionKey = "uploaded-files";
+ final NewSample newSample = new NewSample();
+ newSample.setIdentifier("MP");
+ newSample.setParentsOrNull(new String[]
+ { "MP_1", "MP_2" });
+ newSample.setProperties(new IEntityProperty[0]);
+ final SampleType sampleType = createSampleType("MASTER_PLATE");
+ final String fileName = "originalFileName.txt";
+
+ final List<NewSamplesWithTypes> samplesWithType = new ArrayList<NewSamplesWithTypes>();
+ List<NewSample> newSamples = new ArrayList<NewSample>();
+ newSamples.add(newSample);
+ samplesWithType.add(new NewSamplesWithTypes(sampleType, newSamples));
+ context.checking(new Expectations()
+ {
+ {
+ prepareGetHttpSession(this);
+ prepareGetSessionToken(this);
+
+ allowing(httpSession).getAttribute(sessionKey);
+ will(returnValue(uploadedFilesBean));
+
+ allowing(httpSession).removeAttribute(sessionKey);
+
+ exactly(1).of(multipartFile).getOriginalFilename();
+ will(returnValue(fileName));
+
+ one(multipartFile).transferTo(with(any(File.class)));
+ will(new CustomAction("copy content")
+ {
+ public Object invoke(Invocation invocation) throws Throwable
+ {
+ final File target = (File) invocation.getParameter(0);
+ FileUtilities.writeToFile(target,
+ "identifier\tparents\nMP\tMP_1,MP_2");
+ return null;
+ }
+ });
+
+ one(genericServer).registerSamples(with(equal(SESSION_TOKEN)),
+ with(newSampleWithTypesList()));
+ will(new CustomAction("check sample")
+ {
+
+ @SuppressWarnings(
+ { "unchecked" })
+ public Object invoke(Invocation invocation) throws Throwable
+ {
+ final List<NewSamplesWithTypes> samplesSecions =
+ (List<NewSamplesWithTypes>) invocation.getParameter(1);
+ assertEquals(1, samplesSecions.size());
+ final NewSamplesWithTypes samples = samplesSecions.get(0);
+ // Do not compare sampleType, as the registration code doesn't set
+ // the database instance.
+ assertEquals(sampleType.getCode(), samples.getSampleType()
+ .getCode());
+ assertEquals(1, samples.getNewSamples().size());
+ final NewSample sample = samples.getNewSamples().get(0);
+ assertEquals("MP", sample.getIdentifier());
+ assertEquals(2, sample.getParentsOrNull().length);
+ assertEquals("MP_1", sample.getParentsOrNull()[0]);
+ assertEquals("MP_2", sample.getParentsOrNull()[1]);
+ assertEquals(0, sample.getProperties().length);
+ return null;
+ }
+ });
+ }
+ });
+ uploadedFilesBean.addMultipartFile(multipartFile);
+ final List<BatchRegistrationResult> result =
+ genericClientService.registerSamples(sampleType, sessionKey, null);
+ assertEquals(1, result.size());
+ final BatchRegistrationResult batchRegistrationResult = result.get(0);
+ assertEquals(fileName, batchRegistrationResult.getFileName());
+ assertEquals("Registration of 1 sample(s) is complete.",
+ batchRegistrationResult.getMessage());
+ context.assertIsSatisfied();
+ }
+
@Test
public final void testUpdateSamples() throws IOException
{
@@ -424,7 +502,7 @@ public final class GenericClientServiceTest extends AbstractClientServiceTest
final NewSample sample1 = samples.getNewSamples().get(0);
assertEquals("/G1/MP1", sample1.getIdentifier());
assertEquals("/G1/MP2", sample1.getContainerIdentifier());
- assertEquals(0, sample1.getParentsOrNull().length);
+ assertEquals(null, sample1.getParentIdentifier());
assertEquals("EXP1", sample1.getExperimentIdentifier());
assertEquals(1, sample1.getProperties().length);
final IEntityProperty prop1 = sample1.getProperties()[0];
@@ -454,6 +532,83 @@ public final class GenericClientServiceTest extends AbstractClientServiceTest
context.assertIsSatisfied();
}
+ @Test
+ public final void testUpdateSamplesWithParents() throws IOException
+ {
+ final UploadedFilesBean uploadedFilesBean = new UploadedFilesBean();
+ final String sessionKey = "uploaded-files";
+
+ final SampleType sampleType = createSampleType("MASTER_PLATE");
+ final String defaultGroupIdentifier = "/G1";
+ final String fileName = "fileName.txt";
+
+ context.checking(new Expectations()
+ {
+ {
+ prepareGetHttpSession(this);
+ prepareGetSessionToken(this);
+
+ allowing(httpSession).getAttribute(sessionKey);
+ will(returnValue(uploadedFilesBean));
+
+ allowing(httpSession).removeAttribute(sessionKey);
+
+ exactly(1).of(multipartFile).getOriginalFilename();
+ will(returnValue(fileName));
+
+ one(multipartFile).transferTo(with(any(File.class)));
+ will(new CustomAction("copy content")
+ {
+ public Object invoke(Invocation invocation) throws Throwable
+ {
+ final File target = (File) invocation.getParameter(0);
+ FileUtilities.writeToFile(target, "identifier\tparents\n"
+ + "MP_1\t/G1/MP_11, /G1/MP_12\n" + "/G2/MP_2\t/G2/MP_21");
+ return null;
+ }
+ });
+
+ one(genericServer).updateSamples(with(equal(SESSION_TOKEN)),
+ with(newSampleWithTypesList()));
+ will(new CustomAction("check sample")
+ {
+
+ @SuppressWarnings("unchecked")
+ public Object invoke(Invocation invocation) throws Throwable
+ {
+ final List<NewSamplesWithTypes> samplesSecions =
+ (List<NewSamplesWithTypes>) invocation.getParameter(1);
+ assertEquals(1, samplesSecions.size());
+ final NewSamplesWithTypes samples = samplesSecions.get(0);
+ // Do not compare sampleType, as the update code doesn't check it
+ assertEquals(2, samples.getNewSamples().size());
+
+ final NewSample sample1 = samples.getNewSamples().get(0);
+ assertEquals("/G1/MP_1", sample1.getIdentifier());
+ assertEquals(2, sample1.getParentsOrNull().length);
+ assertEquals("/G1/MP_11", sample1.getParentsOrNull()[0]);
+ assertEquals("/G1/MP_12", sample1.getParentsOrNull()[1]);
+
+ final NewSample sample2 = samples.getNewSamples().get(1);
+ assertEquals("/G2/MP_2", sample2.getIdentifier());
+ assertEquals(1, sample2.getParentsOrNull().length);
+ assertEquals("/G2/MP_21", sample2.getParentsOrNull()[0]);
+
+ return null;
+ }
+ });
+ }
+ });
+ uploadedFilesBean.addMultipartFile(multipartFile);
+ final List<BatchRegistrationResult> result =
+ genericClientService.updateSamples(sampleType, sessionKey, defaultGroupIdentifier);
+ assertEquals(1, result.size());
+ final BatchRegistrationResult batchRegistrationResult = result.get(0);
+ assertEquals(fileName, batchRegistrationResult.getFileName());
+ assertEquals("Update of 2 sample(s) is complete.", batchRegistrationResult.getMessage());
+ context.assertIsSatisfied();
+ }
+
@Test
public void testUpdateMaterials() throws IOException
{
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/registrators/CinaBundleRegistrationTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/registrators/CinaBundleRegistrationTest.java
index 4ca8165ea20..36d8c8f7507 100644
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/registrators/CinaBundleRegistrationTest.java
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/registrators/CinaBundleRegistrationTest.java
@@ -434,7 +434,7 @@ public abstract class CinaBundleRegistrationTest extends AbstractFileSystemTestC
assertEquals(GRID_SAMPLE_IDENTIFIER, newSample.getIdentifier());
assertEquals(EXPERIMENT_IDENTIFIER.toString(),
newSample.getExperimentIdentifier());
- assertEquals(null, newSample.getParentIdentifier());
+ assertEquals(null, newSample.getParentsOrNull());
return true;
}
return false;
@@ -455,6 +455,7 @@ public abstract class CinaBundleRegistrationTest extends AbstractFileSystemTestC
// Create the Replica
one(openbisService).registerSample(with(new MatcherNoDesc<NewSample>()
{
+ @SuppressWarnings("deprecation")
public boolean matches(Object item)
{
if (item instanceof NewSample)
--
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