From ff10cfc8fb24a537ea5369399a776fc11aad2208 Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Tue, 9 Mar 2010 09:11:18 +0000
Subject: [PATCH] LMS-1398 Work on CINA ETL + new tests
SVN: 15072
---
.../cisd/cina/dss/StorageProcessor.java | 11 +-
.../dss/info/CinaDataSetInfoExtractor.java | 6 +-
.../info/EntityRegistrationSuccessEmail.java | 240 ++++++++++++++++++
.../dss/info/ExperimentMetadataExtractor.java | 8 +-
.../cisd/cina/dss/info/FolderOracle.java | 8 +-
.../dss/info/SampleMetadataExtractor.java | 70 ++---
.../info/CinaDataSetInfoExtractorTest.java | 125 +++++++++
.../cisd/cina/dss/info/FolderOracleTest.java | 82 ++++++
.../ambiguous-data-folder/dataset.properties | 3 +
.../ambiguous-data-folder/sample.properties | 3 +
.../dataset-data-folder/dataset.properties | 3 +
.../dss/info/empty-data-folder/.gitignore | 0
.../experiment.properties | 3 +
.../info/sample-data-folder/sample.properties | 3 +
14 files changed, 519 insertions(+), 46 deletions(-)
create mode 100644 rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/EntityRegistrationSuccessEmail.java
create mode 100644 rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/CinaDataSetInfoExtractorTest.java
create mode 100644 rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/FolderOracleTest.java
create mode 100644 rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/ambiguous-data-folder/dataset.properties
create mode 100644 rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/ambiguous-data-folder/sample.properties
create mode 100644 rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/dataset-data-folder/dataset.properties
create mode 100644 rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/empty-data-folder/.gitignore
create mode 100644 rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/experiment-data-folder/experiment.properties
create mode 100644 rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/sample-data-folder/sample.properties
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/StorageProcessor.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/StorageProcessor.java
index e0245ac168f..1c319511cc7 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/StorageProcessor.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/StorageProcessor.java
@@ -19,6 +19,7 @@ package ch.systemsx.cisd.cina.dss;
import java.io.File;
import java.util.Properties;
+import ch.systemsx.cisd.cina.dss.info.EntityRegistrationSuccessEmail;
import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.etlserver.AbstractDelegatingStorageProcessor;
import ch.systemsx.cisd.etlserver.IStorageProcessor;
@@ -58,6 +59,11 @@ public class StorageProcessor extends AbstractDelegatingStorageProcessor
final ITypeExtractor typeExtractor, final IMailClient mailClient,
final File incomingDataSetDirectory, final File rootDir)
{
+ // Create the email first because the email looks into the directory to determine its
+ // content.
+ EntityRegistrationSuccessEmail successEmail =
+ new EntityRegistrationSuccessEmail(dataSetInformation, incomingDataSetDirectory);
+
File answer =
super.storeData(dataSetInformation, typeExtractor, mailClient,
incomingDataSetDirectory, rootDir);
@@ -68,9 +74,8 @@ public class StorageProcessor extends AbstractDelegatingStorageProcessor
emailAddress = defaultEmailAddress;
}
- mailClient.sendMessage("[CINA] Registered Experiment",
- "Experment was successfully registered. Use the following properties file : experiment.code="
- + dataSetInformation.getExperimentIdentifier(), null, null, emailAddress);
+ mailClient.sendMessage(successEmail.getSubject(), successEmail.getContent(), null, null,
+ emailAddress);
return answer;
}
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 976ff280cec..753b7b8ab2e 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 +70,14 @@ public class CinaDataSetInfoExtractor implements IDataSetInfoExtractor
switch (folderType)
{
case DATA_SET:
- processDataSetFolder(metadata.tryMetadataFile(), dataSetInformation, openbisService);
+ processDataSetFolder(metadata.tryGetMetadataFile(), dataSetInformation, openbisService);
break;
case EXPERIMENT:
- processExperimentFolder(metadata.tryMetadataFile(), dataSetInformation,
+ processExperimentFolder(metadata.tryGetMetadataFile(), dataSetInformation,
openbisService);
break;
case SAMPLE:
- processSampleFolder(metadata.tryMetadataFile(), dataSetInformation, openbisService);
+ processSampleFolder(metadata.tryGetMetadataFile(), dataSetInformation, openbisService);
break;
case UNKNOWN:
break;
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/EntityRegistrationSuccessEmail.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/EntityRegistrationSuccessEmail.java
new file mode 100644
index 00000000000..ace867bee77
--- /dev/null
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/EntityRegistrationSuccessEmail.java
@@ -0,0 +1,240 @@
+/*
+ * 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.cina.dss.info;
+
+import java.io.File;
+
+import ch.systemsx.cisd.cina.dss.info.FolderOracle.FolderType;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+
+/**
+ * Create the subject and content for an email that is sent when an experiment or sample is
+ * registered.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class EntityRegistrationSuccessEmail
+{
+ private final DataSetInformation dataSetInformation;
+
+ private final EntityEmailDetails entityEmailDetails;
+
+ private static final String EMAIL_SUBJECT_PREFIX = "[CINA]";
+
+ private static final String SAMPLE_CODE_PREFIX = "S";
+
+ public EntityRegistrationSuccessEmail(DataSetInformation dataSetInformation,
+ File incomingDataSetDirectory)
+ {
+ this.dataSetInformation = dataSetInformation;
+
+ FolderType folderType = new FolderOracle().getTypeForFolder(incomingDataSetDirectory);
+ switch (folderType)
+ {
+ case DATA_SET:
+ entityEmailDetails = new DatasetEmailDetails();
+ break;
+ case EXPERIMENT:
+ entityEmailDetails = new ExperimentEmailDetails();
+ break;
+ case SAMPLE:
+ entityEmailDetails = new SampleEmailDetails();
+ break;
+ case UNKNOWN:
+ entityEmailDetails = new UnknownEmailDetails();
+ break;
+ default:
+ entityEmailDetails = new UnknownEmailDetails();
+ break;
+ }
+ }
+
+ public boolean shouldSendEmail()
+ {
+ return entityEmailDetails.shouldSendEmail();
+ }
+
+ public String getSubject()
+ {
+ StringBuffer subject = new StringBuffer();
+ subject.append(EMAIL_SUBJECT_PREFIX);
+ subject.append(" Registered ");
+ entityEmailDetails.appendEntityName(subject);
+ subject.append(" ");
+ entityEmailDetails.appendSubjectDetails(subject);
+ return subject.toString();
+ }
+
+ public String getContent()
+ {
+ StringBuffer content = new StringBuffer();
+ entityEmailDetails.appendEntityName(content);
+ content.append(" was successfully registered. Use the following metadata file to register");
+ entityEmailDetails.appendFollowOnEntityName(content);
+ content.append(":\n");
+ content.append("------");
+ entityEmailDetails.appendMetadataFileName(content);
+ content.append("------");
+ content.append("\n");
+ entityEmailDetails.appendMetadataFileContent(content);
+
+ return content.toString();
+ }
+
+ private abstract class EntityEmailDetails
+ {
+ boolean shouldSendEmail()
+ {
+ return false;
+ }
+
+ abstract void appendEntityName(StringBuffer sb);
+
+ void appendFollowOnEntityName(StringBuffer sb)
+ {
+ }
+
+ void appendSubjectDetails(StringBuffer subject)
+ {
+ }
+
+ void appendMetadataFileName(StringBuffer sb)
+ {
+ }
+
+ void appendMetadataFileContent(StringBuffer sb)
+ {
+
+ }
+ }
+
+ private class ExperimentEmailDetails extends EntityEmailDetails
+ {
+ @Override
+ boolean shouldSendEmail()
+ {
+ return true;
+ }
+
+ @Override
+ void appendEntityName(StringBuffer sb)
+ {
+ sb.append("Experiment");
+ }
+
+ @Override
+ void appendFollowOnEntityName(StringBuffer sb)
+ {
+ sb.append("Samples");
+ }
+
+ @Override
+ void appendSubjectDetails(StringBuffer subject)
+ {
+ subject.append(dataSetInformation.getExperimentIdentifier());
+ }
+
+ @Override
+ void appendMetadataFileContent(StringBuffer sb)
+ {
+ sb.append(SampleMetadataExtractor.EXPERIMENT_IDENTIFIER_KEY);
+ sb.append("=");
+ sb.append(dataSetInformation.getExperimentIdentifier());
+ sb.append("\n");
+
+ sb.append(SampleMetadataExtractor.EXPERIMENT_OWNER_EMAIL_KEY);
+ sb.append("=");
+ sb.append(dataSetInformation.tryGetUploadingUserEmail());
+ sb.append("\n");
+
+ sb.append(SampleMetadataExtractor.SAMPLE_CODE_PREFIX_KEY);
+ sb.append("=");
+ sb.append(SAMPLE_CODE_PREFIX);
+ sb.append("\n");
+ }
+
+ @Override
+ void appendMetadataFileName(StringBuffer sb)
+ {
+ sb.append(FolderOracle.SAMPLE_METADATA_FILENAME);
+
+ }
+ }
+
+ private class SampleEmailDetails extends EntityEmailDetails
+ {
+ @Override
+ boolean shouldSendEmail()
+ {
+ return true;
+ }
+
+ @Override
+ void appendEntityName(StringBuffer sb)
+ {
+ sb.append("Sample");
+ }
+
+ @Override
+ void appendFollowOnEntityName(StringBuffer sb)
+ {
+ sb.append("Data Sets");
+ }
+
+ @Override
+ void appendSubjectDetails(StringBuffer subject)
+ {
+ subject.append(dataSetInformation.getSampleIdentifier());
+ }
+
+ @Override
+ void appendMetadataFileContent(StringBuffer sb)
+ {
+ }
+
+ @Override
+ void appendMetadataFileName(StringBuffer sb)
+ {
+ sb.append(FolderOracle.DATA_SET_METADATA_FILENAME);
+
+ }
+ }
+
+ private class DatasetEmailDetails extends EntityEmailDetails
+ {
+ @Override
+ void appendEntityName(StringBuffer sb)
+ {
+ sb.append("Data Set");
+ }
+
+ @Override
+ void appendSubjectDetails(StringBuffer subject)
+ {
+ subject.append(dataSetInformation.getDataSetCode());
+ }
+ }
+
+ private class UnknownEmailDetails extends EntityEmailDetails
+ {
+ @Override
+ void appendEntityName(StringBuffer sb)
+ {
+ sb.append("Unknown");
+ }
+ }
+}
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/ExperimentMetadataExtractor.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/ExperimentMetadataExtractor.java
index a73ee64970f..003b5bf2b70 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/ExperimentMetadataExtractor.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/ExperimentMetadataExtractor.java
@@ -53,7 +53,7 @@ class ExperimentMetadataExtractor
// Internal state used during extraction
private String projectCode;
- private String experimentCode;
+ private String experimentCodePrefix;
private String emailAddress;
@@ -97,7 +97,7 @@ class ExperimentMetadataExtractor
private void extractMetadata()
{
projectCode = experimentMetadata.get(PROJECT_CODE_KEY);
- experimentCode = experimentMetadata.get(EXPERIMENT_CODE_KEY);
+ experimentCodePrefix = experimentMetadata.get(EXPERIMENT_CODE_KEY);
emailAddress = experimentMetadata.get(EXPERIMENT_OWNER_EMAIL_KEY);
}
@@ -107,7 +107,7 @@ class ExperimentMetadataExtractor
private ExperimentIdentifier createExperiment() throws EnvironmentFailureException
{
ExperimentIdentifier identifier =
- new ExperimentIdentifier(null, SPACE_CODE, projectCode, experimentCode + "-"
+ new ExperimentIdentifier(null, SPACE_CODE, projectCode, experimentCodePrefix + "-"
+ experimentCodeSuffix);
// Check that the identifier is unique
@@ -136,7 +136,7 @@ class ExperimentMetadataExtractor
"A project code must be specified to register an experiment.");
}
- if (null == experimentCode)
+ if (null == experimentCodePrefix)
{
throw new UserFailureException(
"An experiment code must be specified to register an experiment.");
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/FolderOracle.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/FolderOracle.java
index 9eccab4a2ef..9d66c6abfd6 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/FolderOracle.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/FolderOracle.java
@@ -65,7 +65,7 @@ class FolderOracle
return type;
}
- File tryMetadataFile()
+ File tryGetMetadataFile()
{
return metadataFileOrNull;
}
@@ -73,11 +73,11 @@ class FolderOracle
// The known conventions for naming metadata files. If a new metadata file is created, cases
// should be added to getFilenameFilter() and getFolderMetadataForFile() as well.
- private static String EXPERIMENT_METADATA_FILENAME = "experiment.properties";
+ static String EXPERIMENT_METADATA_FILENAME = "experiment.properties";
- private static String SAMPLE_METADATA_FILENAME = "sample.properties";
+ static String SAMPLE_METADATA_FILENAME = "sample.properties";
- private static String DATA_SET_METADATA_FILENAME = "dataset.properties";
+ static String DATA_SET_METADATA_FILENAME = "dataset.properties";
FolderOracle()
{
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/SampleMetadataExtractor.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/SampleMetadataExtractor.java
index 13bf4fa314f..d4fbb1d4343 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/SampleMetadataExtractor.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/SampleMetadataExtractor.java
@@ -25,47 +25,55 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleOwnerIdentifier;
/**
* Package-visible helper class to extract information from the XML metadata file and register a new
* sample using this data.
+ * <p>
+ * This class assumes that the sample type CINA_SAMPLE_TYPE has been registered.
*
* @author Chandrasekhar Ramakrishnan
*/
class SampleMetadataExtractor
{
// Keys expected in metadata properties file
- public static final String SAMPLE_CODE_KEY = "sample";
+
+ public static final String PROJECT_CODE_KEY = ExperimentMetadataExtractor.PROJECT_CODE_KEY;
+
+ public static final String EXPERIMENT_IDENTIFIER_KEY = "experiment.identifier";
+
+ public static final String EXPERIMENT_OWNER_EMAIL_KEY =
+ ExperimentMetadataExtractor.EXPERIMENT_OWNER_EMAIL_KEY;
+
+ public static final String SAMPLE_CODE_PREFIX_KEY = "sample.code-prefix";
// Instance state
private final DataSetInformation dataSetInformation;
private final Map<String, String> sampleMetadata;
- private final IEncapsulatedOpenBISService openbisService;
+ private final String sampleCodeSuffix;
- // Internal state used during extraction
- private String projectCode;
+ private final IEncapsulatedOpenBISService openbisService;
- private String experimentCode;
+ private ExperimentIdentifier experimentIdentifier;
- private String sampleCode;
+ private String sampleCodePrefix;
private String emailAddress;
- static final String SPACE_CODE = "CINA";
-
- static final String EXPERIMENT_TYPE_CODE = "CINA_EXP_TYPE";
-
- static final String SAMPLE_TYPE_CODE = "CINA_SAMPLE_TYPE";
+ private static final String SAMPLE_TYPE_CODE = "CINA_SAMPLE_TYPE";
SampleMetadataExtractor(DataSetInformation dataSetInformation,
- Map<String, String> sampleMetadata, IEncapsulatedOpenBISService openbisService)
+ Map<String, String> sampleMetadata, String sampleCodeSuffix,
+ IEncapsulatedOpenBISService openbisService)
{
this.dataSetInformation = dataSetInformation;
this.sampleMetadata = sampleMetadata;
+ this.sampleCodeSuffix = sampleCodeSuffix;
this.openbisService = openbisService;
}
@@ -79,20 +87,26 @@ class SampleMetadataExtractor
{
extractMetadata();
+ // Set the email address as early as possible because it will be used later to notify the
+ // user.
+ dataSetInformation.setUploadingUserEmail(emailAddress);
+
// Check that that the required data was specified in the properties file.
verifyRequiredMetadataDataHasBeenProvided();
- this.createSample();
- dataSetInformation.setSampleCode(sampleCode);
+ SampleIdentifier sampleId = this.createSample();
+ dataSetInformation.setExperimentIdentifier(experimentIdentifier);
+ dataSetInformation.setSampleCode(sampleId.getSampleCode());
dataSetInformation.setUploadingUserEmail(emailAddress);
}
private void extractMetadata()
{
- projectCode = sampleMetadata.get(ExperimentMetadataExtractor.PROJECT_CODE_KEY);
- experimentCode = sampleMetadata.get(ExperimentMetadataExtractor.EXPERIMENT_CODE_KEY);
- sampleCode = sampleMetadata.get(SAMPLE_CODE_KEY);
- emailAddress = sampleMetadata.get(ExperimentMetadataExtractor.EXPERIMENT_OWNER_EMAIL_KEY);
+ experimentIdentifier =
+ new ExperimentIdentifierFactory(sampleMetadata.get(EXPERIMENT_IDENTIFIER_KEY))
+ .createIdentifier();
+ sampleCodePrefix = sampleMetadata.get(SAMPLE_CODE_PREFIX_KEY);
+ emailAddress = sampleMetadata.get(EXPERIMENT_OWNER_EMAIL_KEY);
}
/**
@@ -101,17 +115,15 @@ class SampleMetadataExtractor
*/
private SampleIdentifier createSample()
{
- ExperimentIdentifier experimentId =
- new ExperimentIdentifier(null, SPACE_CODE, projectCode, experimentCode);
-
SampleIdentifier sampleId =
- new SampleIdentifier(new GroupIdentifier((String) null, SPACE_CODE), sampleCode);
+ SampleIdentifier.createOwnedBy(new SampleOwnerIdentifier(experimentIdentifier),
+ sampleCodePrefix + "-" + sampleCodeSuffix);
NewSample sample = new NewSample();
SampleType sampleType = new SampleType();
sampleType.setCode(SAMPLE_TYPE_CODE);
sample.setSampleType(sampleType);
- sample.setExperimentIdentifier(experimentId.toString());
+ sample.setExperimentIdentifier(experimentIdentifier.toString());
sample.setIdentifier(sampleId.toString());
Sample dbSample = openbisService.tryGetSampleWithExperiment(sampleId);
@@ -128,19 +140,13 @@ class SampleMetadataExtractor
*/
private void verifyRequiredMetadataDataHasBeenProvided() throws UserFailureException
{
- if (null == projectCode)
- {
- throw new UserFailureException(
- "A project code must be specified to register an experiment.");
- }
-
- if (null == experimentCode)
+ if (null == experimentIdentifier)
{
throw new UserFailureException(
"An experiment code must be specified to register an experiment.");
}
- if (null == sampleCode)
+ if (null == sampleCodePrefix)
{
throw new UserFailureException(
"An sample code must be specified to register an experiment.");
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
new file mode 100644
index 00000000000..a223bf275e5
--- /dev/null
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/CinaDataSetInfoExtractorTest.java
@@ -0,0 +1,125 @@
+/*
+ * 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.cina.dss.info;
+
+import java.io.File;
+import java.util.Properties;
+
+import org.jmock.Expectations;
+import org.jmock.Mockery;
+import org.testng.AssertJUnit;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+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.NewExperiment;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class CinaDataSetInfoExtractorTest extends AssertJUnit
+{
+ Mockery context;
+
+ IEncapsulatedOpenBISService openbisService;
+
+ CinaDataSetInfoExtractor extractor;
+
+ @BeforeMethod
+ public void beforeMethod()
+ {
+ context = new Mockery();
+ openbisService = context.mock(IEncapsulatedOpenBISService.class);
+ extractor = new CinaDataSetInfoExtractor(new Properties());
+ }
+
+ @AfterMethod
+ public void afterMethod()
+ {
+ // To following line of code should also be called at the end of each test method.
+ // Otherwise one do not known which test failed.
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testRegisterExperiment()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(openbisService).tryToGetExperiment(with(any(ExperimentIdentifier.class)));
+ will(returnValue(null));
+ one(openbisService).registerExperiment(with(any(NewExperiment.class)));
+ }
+ });
+
+ File experimentFolder =
+ new File("sourceTest/java/ch/systemsx/cisd/cina/dss/info/experiment-data-folder");
+ DataSetInformation dataSetInformation =
+ extractor.getDataSetInformation(experimentFolder, openbisService);
+
+ 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 testRegisterAmbiguousFolder()
+ {
+ File ambiguousDataFolder =
+ new File("sourceTest/java/ch/systemsx/cisd/cina/dss/info/ambiguous-data-folder");
+
+ try
+ {
+ extractor.getDataSetInformation(ambiguousDataFolder, openbisService);
+ fail("An ambiguous data folder should result in a UserFailureException.");
+ } catch (UserFailureException ex)
+ {
+
+ }
+ }
+
+ @Test
+ public void testRegisterEmptyFolder()
+ {
+ File emptyDataFolder =
+ new File("sourceTest/java/ch/systemsx/cisd/cina/dss/info/empty-data-folder");
+ extractor.getDataSetInformation(emptyDataFolder, openbisService);
+ }
+}
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/FolderOracleTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/FolderOracleTest.java
new file mode 100644
index 00000000000..0288e64fc34
--- /dev/null
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/FolderOracleTest.java
@@ -0,0 +1,82 @@
+/*
+ * 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.cina.dss.info;
+
+import java.io.File;
+
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.cina.dss.info.FolderOracle.FolderMetadata;
+import ch.systemsx.cisd.cina.dss.info.FolderOracle.FolderType;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class FolderOracleTest extends AssertJUnit
+{
+
+ @Test
+ public void testExperimentFolder()
+ {
+ FolderOracle folderOracle = new FolderOracle();
+ File experimentFolder =
+ new File("sourceTest/java/ch/systemsx/cisd/cina/dss/info/experiment-data-folder");
+ FolderMetadata metadata = folderOracle.getMetadataForFolder(experimentFolder);
+ assertTrue(metadata.getType() == FolderType.EXPERIMENT);
+ assertTrue("experiment.properties".equals(metadata.tryGetMetadataFile().getName()));
+ }
+
+ @Test
+ public void testSampleFolder()
+ {
+ FolderOracle folderOracle = new FolderOracle();
+ File sampleFolder =
+ new File("sourceTest/java/ch/systemsx/cisd/cina/dss/info/sample-data-folder");
+ FolderMetadata metadata = folderOracle.getMetadataForFolder(sampleFolder);
+ assertTrue(metadata.getType() == FolderType.SAMPLE);
+ assertTrue("sample.properties".equals(metadata.tryGetMetadataFile().getName()));
+ }
+
+ @Test
+ public void testDataSetFolder()
+ {
+ FolderOracle folderOracle = new FolderOracle();
+ File datasetFolder =
+ new File("sourceTest/java/ch/systemsx/cisd/cina/dss/info/dataset-data-folder");
+ FolderMetadata metadata = folderOracle.getMetadataForFolder(datasetFolder);
+ assertTrue(metadata.getType() == FolderType.DATA_SET);
+ assertTrue("dataset.properties".equals(metadata.tryGetMetadataFile().getName()));
+ }
+
+ @Test
+ public void testAmbiguousFolder()
+ {
+ FolderOracle folderOracle = new FolderOracle();
+ File ambiguousFolder =
+ new File("sourceTest/java/ch/systemsx/cisd/cina/dss/info/ambiguous-data-folder");
+ try
+ {
+ folderOracle.getMetadataForFolder(ambiguousFolder);
+ fail("The method getMetadataForFolder should throw an error on folder ambiguous-data-folder.");
+ } catch (UserFailureException ex)
+ {
+ // This should happen
+ }
+ }
+}
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/ambiguous-data-folder/dataset.properties b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/ambiguous-data-folder/dataset.properties
new file mode 100644
index 00000000000..124fde3eff7
--- /dev/null
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/ambiguous-data-folder/dataset.properties
@@ -0,0 +1,3 @@
+project.code = CINA1
+experiment.code = EXP
+experiment.owner-email = no-one@nowhere.ch
\ No newline at end of file
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/ambiguous-data-folder/sample.properties b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/ambiguous-data-folder/sample.properties
new file mode 100644
index 00000000000..124fde3eff7
--- /dev/null
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/ambiguous-data-folder/sample.properties
@@ -0,0 +1,3 @@
+project.code = CINA1
+experiment.code = EXP
+experiment.owner-email = no-one@nowhere.ch
\ No newline at end of file
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/dataset-data-folder/dataset.properties b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/dataset-data-folder/dataset.properties
new file mode 100644
index 00000000000..124fde3eff7
--- /dev/null
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/dataset-data-folder/dataset.properties
@@ -0,0 +1,3 @@
+project.code = CINA1
+experiment.code = EXP
+experiment.owner-email = no-one@nowhere.ch
\ No newline at end of file
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/empty-data-folder/.gitignore b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/empty-data-folder/.gitignore
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/experiment-data-folder/experiment.properties b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/experiment-data-folder/experiment.properties
new file mode 100644
index 00000000000..124fde3eff7
--- /dev/null
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/experiment-data-folder/experiment.properties
@@ -0,0 +1,3 @@
+project.code = CINA1
+experiment.code = EXP
+experiment.owner-email = no-one@nowhere.ch
\ No newline at end of file
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
new file mode 100644
index 00000000000..124fde3eff7
--- /dev/null
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/sample-data-folder/sample.properties
@@ -0,0 +1,3 @@
+project.code = CINA1
+experiment.code = EXP
+experiment.owner-email = no-one@nowhere.ch
\ No newline at end of file
--
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