From 1be1214555e9885530ba55618ff7a8cfa61b3119 Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Tue, 9 Mar 2010 10:25:54 +0000
Subject: [PATCH] LMS-1398 Hook up the SampleMetadatExtractor to the
CinaDataSetInfoExtractor and add tests.
SVN: 15078
---
.../dss/info/CinaDataSetInfoExtractor.java | 20 ++++++--
.../info/CinaDataSetInfoExtractorTest.java | 46 +++++++++++--------
.../info/sample-data-folder/sample.properties | 6 +--
3 files changed, 47 insertions(+), 25 deletions(-)
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/CinaDataSetInfoExtractor.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/CinaDataSetInfoExtractor.java
index 753b7b8ab2e..d7a7ec8ec11 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/CinaDataSetInfoExtractor.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/CinaDataSetInfoExtractor.java
@@ -70,14 +70,16 @@ public class CinaDataSetInfoExtractor implements IDataSetInfoExtractor
switch (folderType)
{
case DATA_SET:
- processDataSetFolder(metadata.tryGetMetadataFile(), dataSetInformation, openbisService);
+ processDataSetFolder(metadata.tryGetMetadataFile(), dataSetInformation,
+ openbisService);
break;
case EXPERIMENT:
processExperimentFolder(metadata.tryGetMetadataFile(), dataSetInformation,
openbisService);
break;
case SAMPLE:
- processSampleFolder(metadata.tryGetMetadataFile(), dataSetInformation, openbisService);
+ processSampleFolder(metadata.tryGetMetadataFile(), dataSetInformation,
+ openbisService);
break;
case UNKNOWN:
break;
@@ -114,7 +116,19 @@ public class CinaDataSetInfoExtractor implements IDataSetInfoExtractor
private void processSampleFolder(final File metadataFile,
final DataSetInformation dataSetInformation, IEncapsulatedOpenBISService openbisService)
{
-
+ try
+ {
+ HashMap<String, String> sampleMetadata = convertMetadataFileToMap(metadataFile);
+ SampleMetadataExtractor extractor =
+ new SampleMetadataExtractor(dataSetInformation, sampleMetadata,
+ getEntityCodeSuffix(), openbisService);
+ extractor.processMetadataAndFillDataSetInformation();
+ } catch (IOException ex)
+ {
+ UserFailureException userFailure =
+ new UserFailureException("Could not register sample", ex);
+ throw userFailure;
+ }
}
/**
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/CinaDataSetInfoExtractorTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/CinaDataSetInfoExtractorTest.java
index a223bf275e5..047286c2edc 100644
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/CinaDataSetInfoExtractorTest.java
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/CinaDataSetInfoExtractorTest.java
@@ -29,8 +29,11 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
/**
* @author Chandrasekhar Ramakrishnan
@@ -79,25 +82,30 @@ public class CinaDataSetInfoExtractorTest extends AssertJUnit
assertTrue("no-one@nowhere.ch".equals(dataSetInformation.tryGetUploadingUserEmail()));
}
- // @Test
- // public void testRegisterSample()
- // {
- // context.checking(new Expectations()
- // {
- // {
- // one(openbisService).tryToGetExperiment(with(any(ExperimentIdentifier.class)));
- // will(returnValue(null));
- // one(openbisService).registerExperiment(with(any(NewExperiment.class)));
- // }
- // });
- //
- // File sampleFolder =
- // new File("sourceTest/java/ch/systemsx/cisd/cina/dss/info/sample-data-folder");
- // DataSetInformation dataSetInformation =
- // extractor.getDataSetInformation(sampleFolder, openbisService);
- //
- // assertTrue("no-one@nowhere.ch".equals(dataSetInformation.tryGetUploadingUserEmail()));
- // }
+ @Test
+ public void testRegisterSample()
+ {
+ final Experiment existingExperiment = new Experiment();
+ context.checking(new Expectations()
+ {
+ {
+ one(openbisService).tryToGetExperiment(with(any(ExperimentIdentifier.class)));
+ will(returnValue(existingExperiment));
+ one(openbisService).tryGetSampleWithExperiment(
+ with(any(SampleIdentifier.class)));
+ will(returnValue(null));
+ one(openbisService).registerSample(with(any(NewSample.class)),
+ with(aNull(String.class)));
+ }
+ });
+
+ File sampleFolder =
+ new File("sourceTest/java/ch/systemsx/cisd/cina/dss/info/sample-data-folder");
+ DataSetInformation dataSetInformation =
+ extractor.getDataSetInformation(sampleFolder, openbisService);
+
+ assertTrue("no-one@nowhere.ch".equals(dataSetInformation.tryGetUploadingUserEmail()));
+ }
@Test
public void testRegisterAmbiguousFolder()
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/sample-data-folder/sample.properties b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/sample-data-folder/sample.properties
index 124fde3eff7..80ba74bf10f 100644
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/sample-data-folder/sample.properties
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/sample-data-folder/sample.properties
@@ -1,3 +1,3 @@
-project.code = CINA1
-experiment.code = EXP
-experiment.owner-email = no-one@nowhere.ch
\ No newline at end of file
+experiment.identifier = /CINA/CINA1/EXP1
+experiment.owner-email = no-one@nowhere.ch
+sample.code-prefix = S
\ No newline at end of file
--
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