From fc90157f4e0d948b5101bc52d169a6c90d111245 Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Tue, 9 Mar 2010 15:11:34 +0000
Subject: [PATCH] LMS-1398 Made the properties files more uniform between
experiment registration and sample registration. Fixed problems with sample
registration.
SVN: 15086
---
.../dss/info/CinaDataSetInfoExtractor.java | 4 +--
.../dss/info/ExperimentMetadataExtractor.java | 32 +++++++++++--------
.../dss/info/SampleMetadataExtractor.java | 13 ++++----
.../info/ExperimentMetadataExtractorTest.java | 32 ++++++++++++-------
.../dss/info/SampleMetadataExtractorTest.java | 16 ++++++----
.../experiment.properties | 4 +--
6 files changed, 57 insertions(+), 44 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 d7a7ec8ec11..3ddd1f239b9 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
@@ -147,8 +147,8 @@ public class CinaDataSetInfoExtractor implements IDataSetInfoExtractor
Calendar now = GregorianCalendar.getInstance();
StringBuffer sb = new StringBuffer();
sb.append(now.get(Calendar.YEAR));
- sb.append(now.get(Calendar.MONTH));
- sb.append(now.get(Calendar.DAY_OF_MONTH));
+ sb.append(String.format("%02d", now.get(Calendar.MONTH) + 1));
+ sb.append(String.format("%02d", now.get(Calendar.DAY_OF_MONTH)));
sb.append(now.get(Calendar.HOUR_OF_DAY));
sb.append(now.get(Calendar.MINUTE));
return sb.toString();
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 132ec1004ac..963cf597578 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
@@ -25,6 +25,8 @@ 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.dto.identifier.ExperimentIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifierFactory;
/**
* Package-visible helper class to extract information from the XML metadata file and register a new
@@ -35,9 +37,9 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifi
class ExperimentMetadataExtractor
{
// Keys expected in metadata properties file
- public static final String PROJECT_CODE_KEY = "project.code";
+ public static final String PROJECT_IDENTIFIER_KEY = "project.identifier";
- public static final String EXPERIMENT_CODE_KEY = "experiment.code";
+ public static final String EXPERIMENT_CODE_KEY = "experiment.code-prefix";
public static final String EXPERIMENT_OWNER_EMAIL_KEY = "experiment.owner-email";
@@ -51,14 +53,12 @@ class ExperimentMetadataExtractor
private final IEncapsulatedOpenBISService openbisService;
// Internal state used during extraction
- private String projectCode;
+ private ProjectIdentifier projectIdentifier;
private String experimentCodePrefix;
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";
@@ -96,7 +96,11 @@ class ExperimentMetadataExtractor
private void extractMetadata()
{
- projectCode = experimentMetadata.get(PROJECT_CODE_KEY);
+ String projectIdString = experimentMetadata.get(PROJECT_IDENTIFIER_KEY);
+ if (projectIdString != null)
+ {
+ projectIdentifier = new ProjectIdentifierFactory(projectIdString).createIdentifier();
+ }
experimentCodePrefix = experimentMetadata.get(EXPERIMENT_CODE_KEY);
emailAddress = experimentMetadata.get(EXPERIMENT_OWNER_EMAIL_KEY);
}
@@ -106,22 +110,22 @@ class ExperimentMetadataExtractor
*/
private ExperimentIdentifier createExperiment() throws EnvironmentFailureException
{
- ExperimentIdentifier identifier =
- new ExperimentIdentifier(null, SPACE_CODE, projectCode, experimentCodePrefix + "-"
+ ExperimentIdentifier experimentIdentifier =
+ new ExperimentIdentifier(projectIdentifier, experimentCodePrefix + "-"
+ experimentCodeSuffix);
// Check that the identifier is unique
- Experiment experiment = openbisService.tryToGetExperiment(identifier);
+ Experiment experiment = openbisService.tryToGetExperiment(experimentIdentifier);
if (experiment != null)
{
throw new EnvironmentFailureException(
"The generated experiment identifer, which must be unique, is already in the database. This should not happen: Please contact the administrator.");
}
- openbisService.registerExperiment(new NewExperiment(identifier.toString(),
+ openbisService.registerExperiment(new NewExperiment(experimentIdentifier.toString(),
EXPERIMENT_TYPE_CODE));
- return identifier;
+ return experimentIdentifier;
}
/**
@@ -130,16 +134,16 @@ class ExperimentMetadataExtractor
*/
private void verifyRequiredMetadataDataHasBeenProvided() throws UserFailureException
{
- if (null == projectCode)
+ if (null == projectIdentifier)
{
throw new UserFailureException(
- "A project code must be specified to register an experiment.");
+ "A project identifier must be specified to register an experiment.");
}
if (null == experimentCodePrefix)
{
throw new UserFailureException(
- "An experiment code must be specified to register an experiment.");
+ "An experiment code prefix must be specified to register an experiment.");
}
if (null == emailAddress)
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 6e5e96bab78..b147ce7ed99 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
@@ -28,8 +28,8 @@ 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.ExperimentIdentifierFactory;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
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
@@ -43,8 +43,6 @@ class SampleMetadataExtractor
{
// Keys expected in metadata properties file
- 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 =
@@ -98,6 +96,7 @@ class SampleMetadataExtractor
SampleIdentifier sampleId = this.createSample();
dataSetInformation.setExperimentIdentifier(experimentIdentifier);
+ dataSetInformation.setGroupCode(sampleId.getGroupLevel().getGroupCode());
dataSetInformation.setSampleCode(sampleId.getSampleCode());
dataSetInformation.setUploadingUserEmail(emailAddress);
}
@@ -134,8 +133,8 @@ class SampleMetadataExtractor
}
SampleIdentifier sampleId =
- SampleIdentifier.createOwnedBy(new SampleOwnerIdentifier(experimentIdentifier),
- sampleCodePrefix + "-" + sampleCodeSuffix);
+ new SampleIdentifier(new GroupIdentifier((String) null, experimentIdentifier
+ .getGroupCode()), sampleCodePrefix + "-" + sampleCodeSuffix);
NewSample sample = new NewSample();
SampleType sampleType = new SampleType();
@@ -165,13 +164,13 @@ class SampleMetadataExtractor
if (null == experimentIdentifier)
{
throw new UserFailureException(
- "An experiment code must be specified to register an experiment.");
+ "An experiment identifier must be specified to register an experiment.");
}
if (null == sampleCodePrefix)
{
throw new UserFailureException(
- "An sample code must be specified to register an experiment.");
+ "An sample code prefix must be specified to register an experiment.");
}
if (null == emailAddress)
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/ExperimentMetadataExtractorTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/ExperimentMetadataExtractorTest.java
index 911086f0428..8fcee75876f 100644
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/ExperimentMetadataExtractorTest.java
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/ExperimentMetadataExtractorTest.java
@@ -32,6 +32,8 @@ 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.dto.identifier.ExperimentIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifierFactory;
/**
* @author Chandrasekhar Ramakrishnan
@@ -66,18 +68,21 @@ public class ExperimentMetadataExtractorTest extends AssertJUnit
@Test
public void testSuccessfulExperimentRegistration()
{
- final String projectCode = "CINA1";
- final String experimentCode = "EXP";
+ final String projectIdString = "/CINA/CINA1";
+ final String experimentCodePrefix = "EXP";
final String experimentCodeSuffix = "SUFFIX";
final String ownerEmail = "no-one@nowhere.ch";
final HashMap<String, String> experimentMetadata = new HashMap<String, String>();
- experimentMetadata.put("project.code", projectCode);
- experimentMetadata.put("experiment.code", experimentCode);
+ experimentMetadata.put("project.identifier", projectIdString);
+ experimentMetadata.put("experiment.code-prefix", experimentCodePrefix);
experimentMetadata.put("experiment.owner-email", ownerEmail);
+ final ProjectIdentifier projectIdentifier =
+ new ProjectIdentifierFactory(projectIdString).createIdentifier();
+
final ExperimentIdentifier identifier =
- new ExperimentIdentifier(null, "CINA", projectCode, experimentCode + "-"
+ new ExperimentIdentifier(projectIdentifier, experimentCodePrefix + "-"
+ experimentCodeSuffix);
final NewExperiment newExperiment =
new NewExperiment(identifier.toString(), "CINA_EXP_TYPE");
@@ -94,7 +99,7 @@ public class ExperimentMetadataExtractorTest extends AssertJUnit
new ExperimentMetadataExtractor(dataSetInformation, experimentMetadata,
experimentCodeSuffix, openbisService);
extractor.processMetadataAndFillDataSetInformation();
- assertTrue(ownerEmail.equals(dataSetInformation.tryGetUploadingUserEmail()));
+ assertEquals(ownerEmail, dataSetInformation.tryGetUploadingUserEmail());
context.assertIsSatisfied();
}
@@ -106,18 +111,21 @@ public class ExperimentMetadataExtractorTest extends AssertJUnit
@Test
public void testDuplicateExperimentRegistration()
{
- final String projectCode = "CINA1";
- final String experimentCode = "EXP";
+ final String projectIdString = "/CINA/CINA1";
+ final String experimentCodePrefix = "EXP";
final String experimentCodeSuffix = "SUFFIX";
final String ownerEmail = "no-one@nowhere.ch";
final HashMap<String, String> experimentMetadata = new HashMap<String, String>();
- experimentMetadata.put("project.code", projectCode);
- experimentMetadata.put("experiment.code", experimentCode);
+ experimentMetadata.put("project.identifier", projectIdString);
+ experimentMetadata.put("experiment.code-prefix", experimentCodePrefix);
experimentMetadata.put("experiment.owner-email", ownerEmail);
+ final ProjectIdentifier projectIdentifier =
+ new ProjectIdentifierFactory(projectIdString).createIdentifier();
+
final ExperimentIdentifier identifier =
- new ExperimentIdentifier(null, "CINA", projectCode, experimentCode + "-"
+ new ExperimentIdentifier(projectIdentifier, experimentCodePrefix + "-"
+ experimentCodeSuffix);
final Experiment existingExperiment = new Experiment();
context.checking(new Expectations()
@@ -139,7 +147,7 @@ public class ExperimentMetadataExtractorTest extends AssertJUnit
{
// this should happen
}
- assertTrue(ownerEmail.equals(dataSetInformation.tryGetUploadingUserEmail()));
+ assertEquals(ownerEmail, dataSetInformation.tryGetUploadingUserEmail());
context.assertIsSatisfied();
}
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/SampleMetadataExtractorTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/SampleMetadataExtractorTest.java
index 1b334fadc18..491e2775934 100644
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/SampleMetadataExtractorTest.java
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/info/SampleMetadataExtractorTest.java
@@ -35,6 +35,7 @@ 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.ExperimentIdentifierFactory;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleOwnerIdentifier;
@@ -87,8 +88,8 @@ public class SampleMetadataExtractorTest extends AssertJUnit
experiment.setIdentifier(experimentIdentifier.toString());
final SampleIdentifier sampleIdentifier =
- SampleIdentifier.createOwnedBy(new SampleOwnerIdentifier(experimentIdentifier),
- sampleCodePrefix + "-" + sampleCodeSuffix);
+ new SampleIdentifier(new GroupIdentifier((String) null, "CINA"), sampleCodePrefix
+ + "-" + sampleCodeSuffix);
final NewSample newSample = new NewSample();
SampleType sampleType = new SampleType();
@@ -111,7 +112,8 @@ public class SampleMetadataExtractorTest extends AssertJUnit
new SampleMetadataExtractor(dataSetInformation, sampleMetadata, sampleCodeSuffix,
openbisService);
extractor.processMetadataAndFillDataSetInformation();
- assertTrue(ownerEmail.equals(dataSetInformation.tryGetUploadingUserEmail()));
+ assertEquals(ownerEmail, dataSetInformation.tryGetUploadingUserEmail());
+ assertEquals("/CINA/S-SUFFIX", dataSetInformation.getSampleIdentifier().toString());
context.assertIsSatisfied();
}
@@ -139,8 +141,8 @@ public class SampleMetadataExtractorTest extends AssertJUnit
experiment.setIdentifier(experimentIdentifier.toString());
final SampleIdentifier sampleIdentifier =
- SampleIdentifier.createOwnedBy(new SampleOwnerIdentifier(experimentIdentifier),
- sampleCodePrefix + "-" + sampleCodeSuffix);
+ new SampleIdentifier(new GroupIdentifier((String) null, "CINA"), sampleCodePrefix
+ + "-" + sampleCodeSuffix);
final Sample existingSample = new Sample();
context.checking(new Expectations()
@@ -165,7 +167,7 @@ public class SampleMetadataExtractorTest extends AssertJUnit
{
// this should happen
}
- assertTrue(ownerEmail.equals(dataSetInformation.tryGetUploadingUserEmail()));
+ assertEquals(ownerEmail, dataSetInformation.tryGetUploadingUserEmail());
context.assertIsSatisfied();
}
@@ -274,7 +276,7 @@ public class SampleMetadataExtractorTest extends AssertJUnit
{
// This should happen
}
- assertTrue(ownerEmail.equals(dataSetInformation.tryGetUploadingUserEmail()));
+ assertEquals(ownerEmail, dataSetInformation.tryGetUploadingUserEmail());
context.assertIsSatisfied();
}
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
index 124fde3eff7..f15a939bc1b 100644
--- 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
@@ -1,3 +1,3 @@
-project.code = CINA1
-experiment.code = EXP
+project.identifier = /CINA/CINA1
+experiment.code-prefix = EXP
experiment.owner-email = no-one@nowhere.ch
\ No newline at end of file
--
GitLab