diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/FullSampleIdentifier.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/FullSampleIdentifier.java
new file mode 100644
index 0000000000000000000000000000000000000000..bd76b7ea549a452086ea8ebee0c18c5c69124e8c
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/FullSampleIdentifier.java
@@ -0,0 +1,92 @@
+/*
+ * Copyright 2015 ETH Zuerich, SIS
+ *
+ * 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.ethz.sis.openbis.generic.server.api.v3.executor.sample;
+
+import org.apache.commons.lang.StringUtils;
+
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.SampleIdentifier;
+
+/**
+ * Helper class which parses a sample identifier string.
+ *
+ * @author Franz-Josef Elmer
+ */
+class FullSampleIdentifier
+{
+ private SampleIdentifierParts sampleIdentifierParts;
+ private String sampleCode;
+
+ FullSampleIdentifier(String sampleIdentifier)
+ {
+ if (StringUtils.isBlank(sampleIdentifier))
+ {
+ throw new IllegalArgumentException("Unspecified sample identifier.");
+ }
+ if (sampleIdentifier.startsWith("/") == false)
+ {
+ throw new IllegalArgumentException("Sample identifier has to start with a '/': " + sampleIdentifier);
+ }
+ String[] parts = sampleIdentifier.split("/");
+ String spaceCode = null;
+ String projectCode = null;
+ if (parts.length > 4)
+ {
+ throw new IllegalArgumentException("Sample identifier can not contain more than three '/': " + sampleIdentifier);
+ } else if (parts.length == 3)
+ {
+ spaceCode = parts[1];
+ } else if (parts.length == 4)
+ {
+ spaceCode = parts[1];
+ projectCode = parts[2];
+ }
+ String code = parts[parts.length - 1];
+ String[] splittedCode = code.split(":");
+ String containerCode = null;
+ String plainSampleCode = code;
+ if (splittedCode.length > 2)
+ {
+ throw new IllegalArgumentException("Sample code can not contain more than one ':': " + sampleIdentifier);
+ } else if (splittedCode.length == 2)
+ {
+ containerCode = splittedCode[0];
+ plainSampleCode = splittedCode[1];
+ }
+ sampleCode = plainSampleCode;
+ sampleIdentifierParts = new SampleIdentifierParts(spaceCode, projectCode, containerCode);
+
+ }
+
+ SampleIdentifierParts getParts()
+ {
+ return sampleIdentifierParts;
+ }
+
+ String getSampleCode()
+ {
+ return sampleCode;
+ }
+
+ @Override
+ public String toString()
+ {
+ return new SampleIdentifier(sampleIdentifierParts.getSpaceCodeOrNull(),
+ sampleIdentifierParts.getProjectCodeOrNull(), sampleIdentifierParts.getContainerCodeOrNull(),
+ sampleCode).toString();
+ }
+
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ListSampleTechIdByIdentifier.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ListSampleTechIdByIdentifier.java
index 730b9dc28e9568caa979adf02097afa66e7dd260..366cf9f11f03d5bd502d6870bac01be42b0fc8ff 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ListSampleTechIdByIdentifier.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ListSampleTechIdByIdentifier.java
@@ -49,11 +49,11 @@ public class ListSampleTechIdByIdentifier extends AbstractListTechIdById<SampleI
{
return SampleIdentifier.class;
}
-
+
@Override
protected Map<Long, SampleIdentifier> createIdsByTechIdsMap(List<SampleIdentifier> ids)
{
- Map<Key, Map<String, SampleIdentifier>> groupedIdentifiers = new HashMap<>();
+ Map<SampleIdentifierParts, Map<String, SampleIdentifier>> groupedIdentifiers = new HashMap<>();
for (SampleIdentifier sampleIdentifier : ids)
{
ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier sampleIdentifier2
@@ -75,7 +75,7 @@ public class ListSampleTechIdByIdentifier extends AbstractListTechIdById<SampleI
}
String sampleSubCode = CodeConverter.tryToDatabase(sampleIdentifier2.getSampleSubCode());
String containerCode = CodeConverter.tryToDatabase(sampleIdentifier2.tryGetContainerCode());
- Key key = new Key(spaceCode, containerCode);
+ SampleIdentifierParts key = new SampleIdentifierParts(spaceCode, null, containerCode);
Map<String, SampleIdentifier> identifiersByCode = groupedIdentifiers.get(key);
if (identifiersByCode == null)
{
@@ -87,9 +87,9 @@ public class ListSampleTechIdByIdentifier extends AbstractListTechIdById<SampleI
Map<Long, SampleIdentifier> result = new HashMap<>();
SampleQuery query = QueryTool.getManagedQuery(SampleQuery.class);
- for (Entry<Key, Map<String, SampleIdentifier>> entry : groupedIdentifiers.entrySet())
+ for (Entry<SampleIdentifierParts, Map<String, SampleIdentifier>> entry : groupedIdentifiers.entrySet())
{
- Key key = entry.getKey();
+ SampleIdentifierParts key = entry.getKey();
Map<String, SampleIdentifier> identifiersByCode = entry.getValue();
List<TechIdStringIdentifierRecord> records = list(query, key, identifiersByCode.keySet());
for (TechIdStringIdentifierRecord record : records)
@@ -101,11 +101,11 @@ public class ListSampleTechIdByIdentifier extends AbstractListTechIdById<SampleI
return result;
}
- private List<TechIdStringIdentifierRecord> list(SampleQuery query, Key key, Collection<String> codes)
+ private List<TechIdStringIdentifierRecord> list(SampleQuery query, SampleIdentifierParts key, Collection<String> codes)
{
String[] codesArray = codes.toArray(new String[codes.size()]);
- String spaceCode = key.spaceCodeOrNull;
- String containerCode = key.containerCodeOrNull;
+ String spaceCode = key.getSpaceCodeOrNull();
+ String containerCode = key.getContainerCodeOrNull();
if (spaceCode == null)
{
if (containerCode == null)
@@ -121,48 +121,4 @@ public class ListSampleTechIdByIdentifier extends AbstractListTechIdById<SampleI
return query.listSpaceSampleTechIdsByContainerCodeAndCodes(spaceCode, containerCode, codesArray);
}
- private static final class Key
- {
- private String spaceCodeOrNull;
- private String containerCodeOrNull;
-
- Key(String spaceCodeOrNull, String containerCodeOrNull)
- {
- this.spaceCodeOrNull = spaceCodeOrNull;
- this.containerCodeOrNull = containerCodeOrNull;
- }
-
- @Override
- public boolean equals(Object obj)
- {
- if (obj == this)
- {
- return true;
- }
- if (obj instanceof Key == false)
- {
- return false;
- }
- Key key = (Key) obj;
- return isEqual(spaceCodeOrNull, key.spaceCodeOrNull)
- && isEqual(containerCodeOrNull, key.containerCodeOrNull);
- }
-
- private boolean isEqual(String str1, String str2)
- {
- return str1 == null ? str1 == str2 : str1.equals(str2);
- }
-
- @Override
- public int hashCode()
- {
- return 37 * calcHashCode(spaceCodeOrNull) + calcHashCode(containerCodeOrNull);
- }
-
- private int calcHashCode(String str)
- {
- return str == null ? 0 : str.hashCode();
- }
- }
-
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SampleIdentifierParts.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SampleIdentifierParts.java
new file mode 100644
index 0000000000000000000000000000000000000000..61302519b06e6ba661900518a0ddad2ac413fd82
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SampleIdentifierParts.java
@@ -0,0 +1,87 @@
+/*
+ * Copyright 2015 ETH Zuerich, SIS
+ *
+ * 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.ethz.sis.openbis.generic.server.api.v3.executor.sample;
+
+final class SampleIdentifierParts
+{
+ private String spaceCodeOrNull;
+ private String projectCodeOrNull;
+ private String containerCodeOrNull;
+
+ SampleIdentifierParts(String spaceCodeOrNull, String projectCodeOrNull, String containerCodeOrNull)
+ {
+ this.spaceCodeOrNull = spaceCodeOrNull;
+ this.projectCodeOrNull = projectCodeOrNull;
+ this.containerCodeOrNull = containerCodeOrNull;
+ }
+
+ public String getSpaceCodeOrNull()
+ {
+ return spaceCodeOrNull;
+ }
+
+ public String getProjectCodeOrNull()
+ {
+ return projectCodeOrNull;
+ }
+
+ public String getContainerCodeOrNull()
+ {
+ return containerCodeOrNull;
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof SampleIdentifierParts == false)
+ {
+ return false;
+ }
+ SampleIdentifierParts key = (SampleIdentifierParts) obj;
+ return isEqual(spaceCodeOrNull, key.spaceCodeOrNull)
+ && isEqual(projectCodeOrNull, key.projectCodeOrNull)
+ && isEqual(containerCodeOrNull, key.containerCodeOrNull);
+ }
+
+ private boolean isEqual(String str1, String str2)
+ {
+ return str1 == null ? str1 == str2 : str1.equals(str2);
+ }
+
+ @Override
+ public int hashCode()
+ {
+ return 37 * (37 * calcHashCode(spaceCodeOrNull) + calcHashCode(projectCodeOrNull))
+ + calcHashCode(containerCodeOrNull);
+ }
+
+ @Override
+ public String toString()
+ {
+ // TODO Auto-generated method stub
+ return super.toString();
+ }
+
+ private int calcHashCode(String str)
+ {
+ return str == null ? 0 : str.hashCode();
+ }
+}
\ No newline at end of file
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/entity/sample/SampleBaseRecord.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/entity/sample/SampleBaseRecord.java
index 2760bddbb3ca3522b74f06e34a458fae5e9bc4e8..49fa50b50122fbaecf03dc021c3481e5ce3a0c8f 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/entity/sample/SampleBaseRecord.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/entity/sample/SampleBaseRecord.java
@@ -30,6 +30,8 @@ public class SampleBaseRecord extends ObjectBaseRecord
public String spaceCode;
+ public String projectCode;
+
public String containerCode;
public String permId;
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/entity/sample/SampleQuery.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/entity/sample/SampleQuery.java
index 798f6198f3260e2cd2d0f109a2a760d2acc16b5b..bd87d642c458c6664b5f8985b98d7e837c5176ef 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/entity/sample/SampleQuery.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/entity/sample/SampleQuery.java
@@ -41,8 +41,11 @@ public interface SampleQuery extends ObjectQuery
+ "where s.id = any(?{1})", parameterBindings = { LongSetMapper.class }, fetchSize = FETCH_SIZE)
public List<SampleAuthorizationRecord> getAuthorizations(LongSet sampleIds);
- @Select(sql = "select s.id, s.code, s.perm_id as permId, sp.code as spaceCode, sc.code as containerCode, s.registration_timestamp as registrationDate, s.modification_timestamp as modificationDate "
+ @Select(sql = "select s.id, s.code, s.perm_id as permId, sp.code as spaceCode, p.code as projectCode, "
+ + "sc.code as containerCode, s.registration_timestamp as registrationDate, "
+ + "s.modification_timestamp as modificationDate "
+ "from samples s left join spaces sp on s.space_id = sp.id "
+ + "left join projects p on s.proj_id = p.id "
+ "left join samples sc on s.samp_id_part_of = sc.id "
+ "where s.id = any(?{1})", parameterBindings = { LongSetMapper.class }, fetchSize = FETCH_SIZE)
public List<SampleBaseRecord> getSamples(LongSet sampleIds);
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/entity/sample/SampleTranslator.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/entity/sample/SampleTranslator.java
index 888af5f9247fbddd9a9d550813d190785e831518..33e0ea3ae6df187795f8928bf624aade9662100b 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/entity/sample/SampleTranslator.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/entity/sample/SampleTranslator.java
@@ -208,7 +208,8 @@ public class SampleTranslator extends AbstractCachingTranslator<Long, Sample, Sa
result.setPermId(new SamplePermId(baseRecord.permId));
result.setCode(baseRecord.code);
- result.setIdentifier(new SampleIdentifier(baseRecord.spaceCode, baseRecord.containerCode, baseRecord.code));
+ result.setIdentifier(new SampleIdentifier(baseRecord.spaceCode, baseRecord.projectCode,
+ baseRecord.containerCode, baseRecord.code));
result.setModificationDate(baseRecord.modificationDate);
result.setRegistrationDate(baseRecord.registrationDate);
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/FullSampleIdentifierTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/FullSampleIdentifierTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..4feb0e8aefa4aed8fabc72bb9b8482b40f70daa5
--- /dev/null
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/FullSampleIdentifierTest.java
@@ -0,0 +1,69 @@
+/*
+ * Copyright 2015 ETH Zuerich, SIS
+ *
+ * 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.ethz.sis.openbis.generic.server.api.v3.executor.sample;
+
+import static junit.framework.Assert.assertEquals;
+import static junit.framework.Assert.fail;
+
+import org.testng.annotations.Test;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class FullSampleIdentifierTest
+{
+
+ @Test
+ public void testHappyCases()
+ {
+ assertSampId("/S1");
+ assertSampId("/SPACE1/S2");
+ assertSampId("/SPACE1/S2:A02");
+ assertSampId("/SPACE1/PROJECT1/S1");
+ assertSampId("/SPACE1/PROJECT1/S1:A02");
+ }
+
+ @Test
+ public void testFailingCases()
+ {
+ assertInvalidSampId("Unspecified sample identifier.", null);
+ assertInvalidSampId("Unspecified sample identifier.", "");
+ assertInvalidSampId("Sample identifier has to start with a '/': A/BC", "A/BC");
+ assertInvalidSampId("Sample identifier can not contain more than three '/': /A/B/C/D", "/A/B/C/D");
+ assertInvalidSampId("Sample code can not contain more than one ':': /A/B:C:D", "/A/B:C:D");
+ }
+
+ private void assertInvalidSampId(String expectedErrorMsg, String identifier)
+ {
+ try
+ {
+ new FullSampleIdentifier(identifier);
+ fail("IllegalArgumentException expected");
+ } catch (IllegalArgumentException ex)
+ {
+ assertEquals(expectedErrorMsg, ex.getMessage());
+ }
+ }
+
+ private void assertSampId(String identifier)
+ {
+ assertEquals(new FullSampleIdentifier(identifier).toString(), identifier);
+ }
+
+}
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/ProjectSampleTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/ProjectSampleTest.java
index a4e75b18e9ff0a8e2bc9192ae25d726f79cfacf1..0a8f05a6754429136cff918ade6cca0f97792fdd 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/ProjectSampleTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/ProjectSampleTest.java
@@ -367,7 +367,7 @@ public class ProjectSampleTest extends AbstractTest
SearchResult<Sample> result = v3api.searchSamples(systemSessionToken, searchCriteria, fetchOptions);
- assertEquals(result.getObjects().get(0).getIdentifier().getIdentifier(), "/CISD/3VCP5");
+ assertEquals(result.getObjects().get(0).getIdentifier().getIdentifier(), "/CISD/NEMO/3VCP5");
assertEquals(result.getObjects().get(0).getProject().getIdentifier().getIdentifier(), "/CISD/NEMO");
assertEquals(result.getTotalCount(), 1);
}
@@ -383,7 +383,7 @@ public class ProjectSampleTest extends AbstractTest
SearchResult<Sample> result = v3api.searchSamples(systemSessionToken, searchCriteria, fetchOptions);
- assertEquals(result.getObjects().get(0).getIdentifier().getIdentifier(), "/CISD/3VCP5");
+ assertEquals(result.getObjects().get(0).getIdentifier().getIdentifier(), "/CISD/NEMO/3VCP5");
assertEquals(result.getObjects().get(0).getProject().getIdentifier().getIdentifier(), "/CISD/NEMO");
assertEquals(result.getTotalCount(), 1);
}
@@ -398,7 +398,7 @@ public class ProjectSampleTest extends AbstractTest
SearchResult<Sample> result = v3api.searchSamples(systemSessionToken, searchCriteria, fetchOptions);
- assertEquals(result.getObjects().get(0).getIdentifier().getIdentifier(), "/CISD/3VCP5");
+ assertEquals(result.getObjects().get(0).getIdentifier().getIdentifier(), "/CISD/NEMO/3VCP5");
assertEquals(result.getObjects().get(0).getProject().getIdentifier().getIdentifier(), "/CISD/NEMO");
assertEquals(result.getTotalCount(), 1);
}
@@ -413,7 +413,7 @@ public class ProjectSampleTest extends AbstractTest
SearchResult<Sample> result = v3api.searchSamples(systemSessionToken, searchCriteria, fetchOptions);
- assertEquals(result.getObjects().get(0).getIdentifier().getIdentifier(), "/CISD/3VCP5");
+ assertEquals(result.getObjects().get(0).getIdentifier().getIdentifier(), "/CISD/NEMO/3VCP5");
assertEquals(result.getObjects().get(0).getProject().getIdentifier().getIdentifier(), "/CISD/NEMO");
assertEquals(result.getTotalCount(), 1);
}
diff --git a/openbis_api/source/java/ch/ethz/sis/openbis/generic/shared/api/v3/dto/id/sample/SampleIdentifier.java b/openbis_api/source/java/ch/ethz/sis/openbis/generic/shared/api/v3/dto/id/sample/SampleIdentifier.java
index 90fe47d68de6c23c272fc5effcbbdc05cc0ec283..e029e57e7f8832695e1f378b4f8a1dcacbde01db 100644
--- a/openbis_api/source/java/ch/ethz/sis/openbis/generic/shared/api/v3/dto/id/sample/SampleIdentifier.java
+++ b/openbis_api/source/java/ch/ethz/sis/openbis/generic/shared/api/v3/dto/id/sample/SampleIdentifier.java
@@ -40,14 +40,31 @@ public class SampleIdentifier extends ObjectIdentifier implements ISampleId
public SampleIdentifier(String spaceCodeOrNull, String containerCodeOrNull, String sampleCode)
{
- this(createIdentifier(spaceCodeOrNull, containerCodeOrNull, sampleCode));
+ this(spaceCodeOrNull, null, containerCodeOrNull, sampleCode);
}
- private static String createIdentifier(String spaceCodeOrNull, String containerCodeOrNull, String sampleCode)
+ public SampleIdentifier(String spaceCodeOrNull, String projectCodeOrNull, String containerCodeOrNull, String sampleCode)
{
- String spaceCode = spaceCodeOrNull != null ? "/" + spaceCodeOrNull : "";
- String containerCode = containerCodeOrNull != null ? containerCodeOrNull + ":" : "";
- return spaceCode + "/" + containerCode + sampleCode;
+ this(createIdentifier(spaceCodeOrNull, projectCodeOrNull, containerCodeOrNull, sampleCode));
+ }
+
+ private static String createIdentifier(String spaceCodeOrNull, String projectCodeOrNull,
+ String containerCodeOrNull, String sampleCode)
+ {
+ StringBuilder builder = new StringBuilder("/");
+ if (spaceCodeOrNull != null)
+ {
+ builder.append(spaceCodeOrNull).append("/");
+ }
+ if (projectCodeOrNull != null)
+ {
+ builder.append(projectCodeOrNull).append("/");
+ }
+ if (containerCodeOrNull != null)
+ {
+ builder.append(containerCodeOrNull).append(":");
+ }
+ return builder.append(sampleCode).toString();
}
//