From d640638088c64966639472135574ccede816c8c5 Mon Sep 17 00:00:00 2001
From: pkupczyk <pkupczyk>
Date: Tue, 6 Aug 2013 14:21:26 +0000
Subject: [PATCH] SP-781 / BIS-496: data-set-uploader fails to start on
biozentrum - fix a bug where listing experiments didn't work properly with a
mixture of project identifiers with and without database instance codes
SVN: 29606
---
.../server/business/bo/ExperimentTable.java | 7 +--
.../server/dataaccess/db/ProjectDAO.java | 7 +--
.../dto/identifier/IdentifierHelper.java | 50 ++++++++++++++-----
.../api/v1/GeneralInformationServiceTest.java | 2 +-
4 files changed, 47 insertions(+), 19 deletions(-)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentTable.java
index 029b661a1e5..8a871f4dca1 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentTable.java
@@ -50,6 +50,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
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.IdentifierHelper;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
@@ -174,7 +175,7 @@ public final class ExperimentTable extends AbstractBusinessObject implements IEx
private void checkNotNull(final List<ProjectIdentifier> projectIdentifiers, final List<ProjectPE> projects)
{
- Set<String> unknownProjectIdentifiers = new HashSet<String>();
+ Set<ProjectIdentifier> unknownProjectIdentifiers = new HashSet<ProjectIdentifier>();
if (projectIdentifiers != null)
{
@@ -182,7 +183,7 @@ public final class ExperimentTable extends AbstractBusinessObject implements IEx
{
if (projectIdentifier != null)
{
- unknownProjectIdentifiers.add(projectIdentifier.toString());
+ unknownProjectIdentifiers.add(IdentifierHelper.createFullProjectIdentifier(projectIdentifier, getHomeDatabaseInstance()));
}
}
}
@@ -193,7 +194,7 @@ public final class ExperimentTable extends AbstractBusinessObject implements IEx
{
if (project != null)
{
- unknownProjectIdentifiers.remove(project.getIdentifier());
+ unknownProjectIdentifiers.remove(IdentifierHelper.createFullProjectIdentifier(project));
}
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ProjectDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ProjectDAO.java
index 2bb80380db2..b06f5cd49c9 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ProjectDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ProjectDAO.java
@@ -39,6 +39,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.IdentifierHelper;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
/**
@@ -129,15 +130,15 @@ public class ProjectDAO extends AbstractGenericEntityDAO<ProjectPE> implements I
List<ProjectPE> allProjects = listProjects();
List<ProjectPE> matchingProjects = new LinkedList<ProjectPE>();
- Set<String> projectIdentifiersSet = new HashSet<String>();
+ Set<ProjectIdentifier> projectIdentifiersSet = new HashSet<ProjectIdentifier>();
for (ProjectIdentifier projectIdentifier : projectIdentifiers)
{
- projectIdentifiersSet.add(projectIdentifier.toString());
+ projectIdentifiersSet.add(IdentifierHelper.createFullProjectIdentifier(projectIdentifier, getDatabaseInstance()));
}
for (ProjectPE project : allProjects)
{
- if (projectIdentifiersSet.contains(project.getIdentifier()))
+ if (projectIdentifiersSet.contains(IdentifierHelper.createFullProjectIdentifier(project)))
{
matchingProjects.add(project);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/IdentifierHelper.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/IdentifierHelper.java
index 3a99377113f..015f68afadd 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/IdentifierHelper.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/IdentifierHelper.java
@@ -192,8 +192,8 @@ public final class IdentifierHelper
}
/**
- * Extracts "sub" code from {@link SamplePE} that is in exactly the same as the one kept in DB
- * (so the same one that is mapped with {@link SamplePE#getCode()}).
+ * Extracts "sub" code from {@link SamplePE} that is in exactly the same as the one kept in DB (so the same one that is mapped with
+ * {@link SamplePE#getCode()}).
*/
public final static String extractSubCode(SamplePE samplePE)
{
@@ -201,8 +201,7 @@ public final class IdentifierHelper
}
/**
- * Converts "sub" code from <var>sampleCode</var> that is in exactly the same as the one kept in
- * DB.
+ * Converts "sub" code from <var>sampleCode</var> that is in exactly the same as the one kept in DB.
*/
public final static String convertSubCode(String sampleCode)
{
@@ -210,9 +209,8 @@ public final class IdentifierHelper
}
/**
- * Extracts "full" sample code from {@link SamplePE}. For contained samples has a prefix
- * consisting of container sample DB code and a colon, otherwise it is just sample DB code,
- * where by "sample DB code" is the code kept in the DB.
+ * Extracts "full" sample code from {@link SamplePE}. For contained samples has a prefix consisting of container sample DB code and a colon,
+ * otherwise it is just sample DB code, where by "sample DB code" is the code kept in the DB.
*/
public final static String extractCode(SamplePE samplePE)
{
@@ -232,11 +230,9 @@ public final class IdentifierHelper
}
/**
- * Converts "full" sample code from the <var>sampleCode</var> and
- * <var>containerCodeOrNull</var>. For contained samples (i.e.
- * <code>containerCodeOrNull != null</code>) has a prefix consisting of container sample DB code
- * and a colon, otherwise it is just sample DB code, where by "sample DB code" is the code kept
- * in the DB.
+ * Converts "full" sample code from the <var>sampleCode</var> and <var>containerCodeOrNull</var>. For contained samples (i.e.
+ * <code>containerCodeOrNull != null</code>) has a prefix consisting of container sample DB code and a colon, otherwise it is just sample DB code,
+ * where by "sample DB code" is the code kept in the DB.
*/
public final static String convertCode(String sampleCode, String containerCodeOrNull)
{
@@ -269,6 +265,36 @@ public final class IdentifierHelper
return identifier;
}
+ /**
+ * Creates a full {@link ProjectIdentifier} (i.e. identifier with database instance, space and project codes specified) from given
+ * <var>project</var>.
+ */
+ public final static ProjectIdentifier createFullProjectIdentifier(final ProjectPE project)
+ {
+ assert project != null : "Unspecified project";
+ return new ProjectIdentifier(project.getSpace().getDatabaseInstance().getCode(), project.getSpace().getCode(), project.getCode());
+ }
+
+ /**
+ * Creates a full {@link ProjectIdentifier} (i.e. identifier with database instance, space and project codes specified) from given
+ * <var>projectIdentifier</var> and <var>homeDatabaseInstance</var>.
+ */
+ public final static ProjectIdentifier createFullProjectIdentifier(final ProjectIdentifier projectIdentifier,
+ DatabaseInstancePE homeDatabaseInstance)
+ {
+ assert projectIdentifier != null : "Unspecified project identifier";
+ assert homeDatabaseInstance != null : "Unspecified home database instance";
+
+ if (projectIdentifier.isHomeDatabase())
+ {
+ return new ProjectIdentifier(homeDatabaseInstance.getCode(), projectIdentifier.getSpaceCode(), projectIdentifier.getProjectCode());
+ } else
+ {
+ return new ProjectIdentifier(projectIdentifier.getDatabaseInstanceCode(), projectIdentifier.getSpaceCode(),
+ projectIdentifier.getProjectCode());
+ }
+ }
+
/**
* Creates a {@link ExperimentIdentifier} from given <var>experiment</var>.
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceTest.java
index bdc13d4c94c..33590cb25c4 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceTest.java
@@ -581,7 +581,7 @@ public class GeneralInformationServiceTest extends AbstractServerTestCase
ProjectIdentifier projectIdentifier =
new ProjectIdentifier("SPACE-1", "PROJECT-1");
one(commonServer).listExperiments(SESSION_TOKEN, returnExperimentType,
- projectIdentifier);
+ Collections.singletonList(projectIdentifier));
Person registrator = new Person();
registrator.setEmail("mail@mail.com");
--
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