diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreService.java
index 3621e331b362e491216eb868fbd73158bf500aa4..e48e373ea6f00c402a1acec51502e88cb498d9bd 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreService.java
@@ -63,7 +63,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.ISessionWorkspaceProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISequenceDatabase;
import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SequenceSearchResult;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomainSearchResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CustomImportFile;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatastoreServiceDescription;
@@ -514,7 +514,7 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
}
@Override
- public List<SequenceSearchResult> searchForDataSetsWithSequences(String sessionToken,
+ public List<SearchDomainSearchResult> searchForDataSetsWithSequences(String sessionToken,
String preferredSequenceDatabaseOrNull, String sequenceSnippet,
Map<String, String> optionalParametersOrNull)
{
@@ -522,15 +522,15 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
ISequenceDatabase sequenceDatabase = findSequenceDatabase(provider, preferredSequenceDatabaseOrNull);
if (sequenceDatabase != null)
{
- List<SequenceSearchResult> result = sequenceDatabase.search(sequenceSnippet, optionalParametersOrNull);
- for (SequenceSearchResult sequenceSearchResult : result)
+ List<SearchDomainSearchResult> result = sequenceDatabase.search(sequenceSnippet, optionalParametersOrNull);
+ for (SearchDomainSearchResult sequenceSearchResult : result)
{
- sequenceSearchResult.setSequenceDatabaseName(sequenceDatabase.getName());
+ sequenceSearchResult.setSearchDomain(sequenceDatabase.getName());
}
return result;
}
operationLog.warn("No available sequence database found.");
- return new ArrayList<SequenceSearchResult>();
+ return new ArrayList<SearchDomainSearchResult>();
}
private ISequenceDatabase findSequenceDatabase(PluginTaskProvider<ISequenceDatabase> provider,
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceLogger.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceLogger.java
index 1466957fab368b7466c8d53ce83835e631241990..906252f1d23101cca75e72a144a656eabdfc8a89 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceLogger.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceLogger.java
@@ -26,7 +26,7 @@ import ch.systemsx.cisd.common.resource.IInitializable;
import ch.systemsx.cisd.common.serviceconversation.ServiceMessage;
import ch.systemsx.cisd.openbis.common.spring.IInvocationLoggerContext;
import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SequenceSearchResult;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomainSearchResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CustomImportFile;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IDatasetLocation;
@@ -197,7 +197,7 @@ class DataStoreServiceLogger implements IDataStoreService, IInitializable
}
@Override
- public List<SequenceSearchResult> searchForDataSetsWithSequences(String sessionToken,
+ public List<SearchDomainSearchResult> searchForDataSetsWithSequences(String sessionToken,
String preferredSequenceDatabaseOrNull, String sequenceSnippet,
Map<String, String> optionalParametersOrNull)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v2/sequencedatabases/BlastDatabase.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v2/sequencedatabases/BlastDatabase.java
index 7e8dd0526039ada26a08e49b284ab5fe78adb614..e6f7a7a7a88fc5d177df3ebb8ce779caaa05ac9a 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v2/sequencedatabases/BlastDatabase.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v2/sequencedatabases/BlastDatabase.java
@@ -44,7 +44,8 @@ import ch.systemsx.cisd.common.process.ProcessResult;
import ch.systemsx.cisd.etlserver.plugins.BlastDatabaseCreationMaintenanceTask;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISequenceDatabase;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.BlastUtils;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SequenceSearchResult;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetFileSearchResultLocation;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomainSearchResult;
/**
* Implementation of {@link ISequenceDatabase} based on <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi">BLAST</a>.
@@ -135,14 +136,14 @@ public class BlastDatabase extends AbstractSequenceDatabase
}
@Override
- public List<SequenceSearchResult> search(String sequenceSnippet, Map<String, String> optionalParametersOrNull)
+ public List<SearchDomainSearchResult> search(String sequenceSnippet, Map<String, String> optionalParametersOrNull)
{
Map<String, String> parameters = new HashMap<String, String>();
if (optionalParametersOrNull != null)
{
parameters.putAll(optionalParametersOrNull);
}
- List<SequenceSearchResult> result = new ArrayList<SequenceSearchResult>();
+ List<SearchDomainSearchResult> result = new ArrayList<SearchDomainSearchResult>();
SequenceType sequenceType = FastaUtilities.determineSequenceType(sequenceSnippet);
String queryFileName = new MessageFormat(QUERY_FILE_NAME_TEMPLATE).format(
new Object[] {new Date(), counter.getAndIncrement()});
@@ -158,11 +159,13 @@ public class BlastDatabase extends AbstractSequenceDatabase
Matcher matcher = STITLE_PATTERN.matcher(row[0]);
if (matcher.matches())
{
- SequenceSearchResult sequenceSearchResult = new SequenceSearchResult();
- sequenceSearchResult.setSequenceIdentifier(matcher.group(1));
- sequenceSearchResult.setDataSetCode(matcher.group(2));
- sequenceSearchResult.setPathInDataSet(matcher.group(3));
- sequenceSearchResult.setPositionInSequence(parse(row[1]));
+ SearchDomainSearchResult sequenceSearchResult = new SearchDomainSearchResult();
+ DataSetFileSearchResultLocation resultLocation = new DataSetFileSearchResultLocation();
+ resultLocation.setSequenceIdentifier(matcher.group(1));
+ resultLocation.setDataSetCode(matcher.group(2));
+ resultLocation.setPathInDataSet(matcher.group(3));
+ resultLocation.setPositionInSequence(parse(row[1]));
+ sequenceSearchResult.setResultLocation(resultLocation);
result.add(sequenceSearchResult);
}
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v2/sequencedatabases/EchoDatabase.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v2/sequencedatabases/EchoDatabase.java
index e53451e969e40e6983050223e32c135031d8c7c2..c552078ed42108706204b90d6253039e40c83267 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v2/sequencedatabases/EchoDatabase.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v2/sequencedatabases/EchoDatabase.java
@@ -25,7 +25,7 @@ import java.util.Properties;
import com.fasterxml.jackson.databind.ObjectMapper;
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SequenceSearchResult;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomainSearchResult;
/**
* A test database that returns a search result that was stored in the parameters map under a key equal to the searched sequence snippet.
@@ -46,7 +46,7 @@ public class EchoDatabase extends AbstractSequenceDatabase
}
@Override
- public List<SequenceSearchResult> search(String sequenceSnippet, Map<String, String> optionalParametersOrNull)
+ public List<SearchDomainSearchResult> search(String sequenceSnippet, Map<String, String> optionalParametersOrNull)
{
String resultStr = optionalParametersOrNull.get(sequenceSnippet);
if (resultStr != null)
@@ -54,7 +54,7 @@ public class EchoDatabase extends AbstractSequenceDatabase
try
{
ObjectMapper mapper = new ObjectMapper();
- SequenceSearchResult result = mapper.readValue(resultStr, SequenceSearchResult.class);
+ SearchDomainSearchResult result = mapper.readValue(resultStr, SearchDomainSearchResult.class);
return Collections.singletonList(result);
} catch (Exception e)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v2/ISequenceDatabase.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v2/ISequenceDatabase.java
index 7055d2745406fe656349854daa7bffccab5a5984..1e5894fed4627598654231b9165611b6fb2a60ba 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v2/ISequenceDatabase.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v2/ISequenceDatabase.java
@@ -21,7 +21,7 @@ import java.util.List;
import java.util.Map;
import java.util.Properties;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SequenceSearchResult;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomainSearchResult;
/**
* Interface for a database for nucleotid or amonioacid sequences.
@@ -34,7 +34,7 @@ public interface ISequenceDatabase
{
/**
* Returns the name of this sequence database instance.
- * Will be used to populated {@link SequenceSearchResult} instances of the search result..
+ * Will be used to populated {@link SearchDomainSearchResult} instances of the search result..
*/
public String getName();
@@ -50,5 +50,5 @@ public interface ISequenceDatabase
* @param optionalParametersOrNull Optional parameters which might be used. Can be <code>null</code>.
* @return an empty list if nothing be found.
*/
- public List<SequenceSearchResult> search(String sequenceSnippet, Map<String, String> optionalParametersOrNull);
+ public List<SearchDomainSearchResult> search(String sequenceSnippet, Map<String, String> optionalParametersOrNull);
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceTest.java
index 126f3a3a737cb031cde13ce5c13456865061a52a..477b4d6e70f9d83ccdbf81255e84fdcf67ba3ebf 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceTest.java
@@ -47,7 +47,8 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISequenceData
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.PluginUtilTest;
import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
import ch.systemsx.cisd.openbis.generic.shared.IServiceForDataStoreServer;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SequenceSearchResult;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetFileSearchResultLocation;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomainSearchResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUploadContext;
import ch.systemsx.cisd.openbis.generic.shared.dto.builders.DatasetDescriptionBuilder;
@@ -117,12 +118,14 @@ public class DataStoreServiceTest extends AssertJUnit
}
@Override
- public List<SequenceSearchResult> search(String sequenceSnippet, Map<String, String> optionalParametersOrNull)
+ public List<SearchDomainSearchResult> search(String sequenceSnippet, Map<String, String> optionalParametersOrNull)
{
assertSame(SEQUENCE_SNIPPET, sequenceSnippet);
assertSame(OPTIONAL_PARAMETERS, optionalParametersOrNull);
- SequenceSearchResult sequenceSearchResult = new SequenceSearchResult();
- sequenceSearchResult.setDataSetCode(dataSetCode);
+ SearchDomainSearchResult sequenceSearchResult = new SearchDomainSearchResult();
+ DataSetFileSearchResultLocation resultLocation = new DataSetFileSearchResultLocation();
+ sequenceSearchResult.setResultLocation(resultLocation);
+ resultLocation.setDataSetCode(dataSetCode);
return Arrays.asList(sequenceSearchResult);
}
@@ -184,7 +187,7 @@ public class DataStoreServiceTest extends AssertJUnit
pluginTaskParameters = context.mock(IPluginTaskInfoProvider.class);
preparePluginTaskInfoProvider();
- List<SequenceSearchResult> result = createService().searchForDataSetsWithSequences(sessionToken,
+ List<SearchDomainSearchResult> result = createService().searchForDataSetsWithSequences(sessionToken,
null, SEQUENCE_SNIPPET, OPTIONAL_PARAMETERS);
assertEquals(0, result.size());
@@ -197,7 +200,7 @@ public class DataStoreServiceTest extends AssertJUnit
pluginTaskParameters = context.mock(IPluginTaskInfoProvider.class);
preparePluginTaskInfoProvider("-1", "-2");
- List<SequenceSearchResult> result = createService().searchForDataSetsWithSequences(sessionToken,
+ List<SearchDomainSearchResult> result = createService().searchForDataSetsWithSequences(sessionToken,
null, SEQUENCE_SNIPPET, OPTIONAL_PARAMETERS);
assertEquals(0, result.size());
@@ -210,10 +213,10 @@ public class DataStoreServiceTest extends AssertJUnit
pluginTaskParameters = context.mock(IPluginTaskInfoProvider.class);
preparePluginTaskInfoProvider("1", "2");
- List<SequenceSearchResult> result = createService().searchForDataSetsWithSequences(sessionToken,
+ List<SearchDomainSearchResult> result = createService().searchForDataSetsWithSequences(sessionToken,
null, SEQUENCE_SNIPPET, OPTIONAL_PARAMETERS);
- assertEquals("DS-1", result.get(0).getDataSetCode());
+ assertEquals("DS-1", ((DataSetFileSearchResultLocation) result.get(0).getResultLocation()).getDataSetCode());
assertEquals(1, result.size());
context.assertIsSatisfied();
}
@@ -224,10 +227,10 @@ public class DataStoreServiceTest extends AssertJUnit
pluginTaskParameters = context.mock(IPluginTaskInfoProvider.class);
preparePluginTaskInfoProvider("1", "2");
- List<SequenceSearchResult> result = createService().searchForDataSetsWithSequences(sessionToken,
+ List<SearchDomainSearchResult> result = createService().searchForDataSetsWithSequences(sessionToken,
"db-2", SEQUENCE_SNIPPET, OPTIONAL_PARAMETERS);
- assertEquals("DS-2", result.get(0).getDataSetCode());
+ assertEquals("DS-2", ((DataSetFileSearchResultLocation) result.get(0).getResultLocation()).getDataSetCode());
assertEquals(1, result.size());
context.assertIsSatisfied();
}
@@ -238,10 +241,10 @@ public class DataStoreServiceTest extends AssertJUnit
pluginTaskParameters = context.mock(IPluginTaskInfoProvider.class);
preparePluginTaskInfoProvider("-1", "2", "-3", "4");
- List<SequenceSearchResult> result = createService().searchForDataSetsWithSequences(sessionToken,
+ List<SearchDomainSearchResult> result = createService().searchForDataSetsWithSequences(sessionToken,
"db-3", SEQUENCE_SNIPPET, OPTIONAL_PARAMETERS);
- assertEquals("DS-2", result.get(0).getDataSetCode());
+ assertEquals("DS-2", ((DataSetFileSearchResultLocation) result.get(0).getResultLocation()).getDataSetCode());
assertEquals(1, result.size());
context.assertIsSatisfied();
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
index 48d4adc7c275e2683a617fc6ba96893a7b906c09..363a4bdf374728c3d9a1adf5de4786311507bfca 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
@@ -86,7 +86,7 @@ import ch.systemsx.cisd.openbis.generic.server.authorization.validator.ExternalD
import ch.systemsx.cisd.openbis.generic.server.authorization.validator.MatchingEntityValidator;
import ch.systemsx.cisd.openbis.generic.server.authorization.validator.ProjectValidator;
import ch.systemsx.cisd.openbis.generic.server.authorization.validator.SampleValidator;
-import ch.systemsx.cisd.openbis.generic.server.authorization.validator.SequenceSearchResultValidator;
+import ch.systemsx.cisd.openbis.generic.server.authorization.validator.SearchDomainSearchResultValidator;
import ch.systemsx.cisd.openbis.generic.server.authorization.validator.SpaceValidator;
import ch.systemsx.cisd.openbis.generic.server.business.IPropertiesBatchManager;
import ch.systemsx.cisd.openbis.generic.server.business.bo.DataAccessExceptionTranslator;
@@ -1615,15 +1615,14 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
@Override
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
- @ReturnValueFilter(validatorClass = SequenceSearchResultValidator.class)
- public List<SequenceSearchResultWithFullDataSet> searchForDataSetsWithSequences(String sessionToken,
- String preferredSequenceDatabaseOrNull, String sequenceSnippet,
- Map<String, String> optionalParametersOrNull)
+ @ReturnValueFilter(validatorClass = SearchDomainSearchResultValidator.class)
+ public List<SearchDomainSearchResultWithFullDataSet> searchOnSearchDomain(String sessionToken,
+ String preferredSearchDomainOrNull, String searchString, Map<String, String> optionalParametersOrNull)
{
Session session = getSession(sessionToken);
IDataSetTable dataSetTable = businessObjectFactory.createDataSetTable(session);
- return dataSetTable.searchForDataSetsWithSequences(preferredSequenceDatabaseOrNull, sequenceSnippet,
+ return dataSetTable.searchForDataSetsWithSequences(preferredSearchDomainOrNull, searchString,
optionalParametersOrNull);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServerLogger.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServerLogger.java
index 4c5b2d1a5340c82167f197cc1bca5b576d3fddde..819d6968cae6936f90b4325664bb458c100ba947 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServerLogger.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServerLogger.java
@@ -109,7 +109,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleUpdateResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Script;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ScriptType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ScriptUpdateResult;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SequenceSearchResultWithFullDataSet;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SearchDomainSearchResultWithFullDataSet;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
@@ -697,12 +697,11 @@ final class CommonServerLogger extends AbstractServerLogger implements ICommonSe
}
@Override
- public List<SequenceSearchResultWithFullDataSet> searchForDataSetsWithSequences(String sessionToken,
- String preferredSequenceDatabaseOrNull, String sequenceSnippet,
- Map<String, String> optionalParametersOrNull)
+ public List<SearchDomainSearchResultWithFullDataSet> searchOnSearchDomain(String sessionToken,
+ String preferredSearchDomainOrNull, String searchString, Map<String, String> optionalParametersOrNull)
{
- logAccess(sessionToken, "search_for_datasets_with_sequences", "preferred_database(%s) sequence_snippet(%s)",
- preferredSequenceDatabaseOrNull, sequenceSnippet);
+ logAccess(sessionToken, "search_on_search_domain", "preferred_search_domain(%s) seerch_string(%s)",
+ preferredSearchDomainOrNull, searchString);
return null;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java
index a3d377ebfc265806c594cf2a452b880976485129..ef3ad1162b1ffaf70c11c7a7510f4537352703f5 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java
@@ -93,8 +93,8 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleFetchOption;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomainSearchResult;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchableEntityKind;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SequenceSearchResult;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SpaceWithProjectsAndRoleAssignments;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Vocabulary;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.IObjectId;
@@ -114,7 +114,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListMaterialCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SequenceSearchResultWithFullDataSet;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SearchDomainSearchResultWithFullDataSet;
import ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentHolderPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.AuthorizationGroupPE;
@@ -951,22 +951,22 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
// There is no @ReturnValueFilter because commonServer.searchForDataSetsWithSequences() does already the filtering.
- public List<SequenceSearchResult> searchForDataSetsWithSequences(String sessionToken,
- String preferredSequenceDatabaseOrNull, String sequenceSnippet,
- Map<String, String> optionalParametersOrNull)
+ public List<SearchDomainSearchResult> searchOnSearchDomain(String sessionToken, String preferredSearchDomainOrNull,
+ String searchString, Map<String, String> optionalParametersOrNull)
{
checkSession(sessionToken);
- List<SequenceSearchResult> result = new ArrayList<SequenceSearchResult>();
- List<SequenceSearchResultWithFullDataSet> list = commonServer.searchForDataSetsWithSequences(sessionToken,
- preferredSequenceDatabaseOrNull, sequenceSnippet, optionalParametersOrNull);
- for (SequenceSearchResultWithFullDataSet sequenceSearchResult : list)
+ List<SearchDomainSearchResult> result = new ArrayList<SearchDomainSearchResult>();
+ List<SearchDomainSearchResultWithFullDataSet> list = commonServer.searchOnSearchDomain(sessionToken,
+ preferredSearchDomainOrNull, searchString, optionalParametersOrNull);
+ for (SearchDomainSearchResultWithFullDataSet sequenceSearchResult : list)
{
result.add(sequenceSearchResult.getSearchResult());
}
return result;
}
+
@Override
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceLogger.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceLogger.java
index 8c810eeab6fe2ec71d004146ad95e763d0f8db29..d8affd3285e803cd6ef80e7831a4f79b781b0709 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceLogger.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceLogger.java
@@ -46,7 +46,7 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleFetchOption;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SequenceSearchResult;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomainSearchResult;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SpaceWithProjectsAndRoleAssignments;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.experiment.IExperimentId;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.metaproject.IMetaprojectId;
@@ -296,12 +296,11 @@ class GeneralInformationServiceLogger extends AbstractServerLogger implements
}
@Override
- public List<SequenceSearchResult> searchForDataSetsWithSequences(String sessionToken,
- String preferredSequenceDatabaseOrNull, String sequenceSnippet,
- Map<String, String> optionalParametersOrNull)
+ public List<SearchDomainSearchResult> searchOnSearchDomain(String sessionToken, String preferredSearchDomainOrNull,
+ String searchString, Map<String, String> optionalParametersOrNull)
{
- logAccess(sessionToken, "search-for-data-sets-with-sequences", "PREFERRED_DATABASE(%s) SEQUENCE_SNIPPET(%s)",
- preferredSequenceDatabaseOrNull, sequenceSnippet);
+ logAccess(sessionToken, "search-on-search-domain", "PREFERRED_SEARCH_DOMAIN(%s) SEARCH_STRING(%s)",
+ preferredSearchDomainOrNull, searchString);
return null;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/SequenceSearchResultValidator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/SearchDomainSearchResultValidator.java
similarity index 72%
rename from openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/SequenceSearchResultValidator.java
rename to openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/SearchDomainSearchResultValidator.java
index 694c157557f014f2dcfc7fa08ab832d7a13c3a50..0b70d7dc4221391a4f1c0b4c1bd78ed7dde5296e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/SequenceSearchResultValidator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/SearchDomainSearchResultValidator.java
@@ -16,20 +16,20 @@
package ch.systemsx.cisd.openbis.generic.server.authorization.validator;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SequenceSearchResultWithFullDataSet;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SearchDomainSearchResultWithFullDataSet;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
/**
- * Validator of @SequenceSearchResult.
+ * Validator of @SearchdoquenceSearchResult.
*
* @author Franz-Josef Elmer
*/
-public class SequenceSearchResultValidator extends AbstractValidator<SequenceSearchResultWithFullDataSet>
+public class SearchDomainSearchResultValidator extends AbstractValidator<SearchDomainSearchResultWithFullDataSet>
{
private final ExternalDataValidator validator = new ExternalDataValidator();
@Override
- public boolean doValidation(PersonPE person, SequenceSearchResultWithFullDataSet value)
+ public boolean doValidation(PersonPE person, SearchDomainSearchResultWithFullDataSet value)
{
return validator.isValid(person, value.getDataSet());
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java
index c6611cc505c20e3d11d60c4e73adc7dc17395bb0..effdb604904a17348661ec0bce830dc28305c0b2 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java
@@ -61,7 +61,9 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.event.DeleteDataSetEve
import ch.systemsx.cisd.openbis.generic.server.dataaccess.util.KeyExtractorFactory;
import ch.systemsx.cisd.openbis.generic.shared.Constants;
import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SequenceSearchResult;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetFileSearchResultLocation;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ISearchDomainResultLocation;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomainSearchResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
import ch.systemsx.cisd.openbis.generic.shared.basic.TableModelAppender;
import ch.systemsx.cisd.openbis.generic.shared.basic.TableModelAppender.TableModelWithDifferentColumnCountException;
@@ -75,7 +77,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetBatchUpdateDetai
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.LinkModel;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SequenceSearchResultWithFullDataSet;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SearchDomainSearchResultWithFullDataSet;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetBatchUpdatesDTO;
@@ -276,26 +278,31 @@ public final class DataSetTable extends AbstractDataSetBusinessObject implements
}
@Override
- public List<SequenceSearchResultWithFullDataSet> searchForDataSetsWithSequences(String preferredSequenceDatabaseOrNull,
+ public List<SearchDomainSearchResultWithFullDataSet> searchForDataSetsWithSequences(String preferredSequenceDatabaseOrNull,
String sequenceSnippet, Map<String, String> optionalParametersOrNull)
{
- List<SequenceSearchResult> result = askAllDataStoreServers(preferredSequenceDatabaseOrNull,
+ List<SearchDomainSearchResult> result = askAllDataStoreServers(preferredSequenceDatabaseOrNull,
sequenceSnippet, optionalParametersOrNull);
TableMap<String, AbstractExternalData> fullDataSetsByCode = listFullDataSets(result);
return filterSearchResultAndInjectFullDataSets(result, fullDataSetsByCode);
}
- private List<SequenceSearchResultWithFullDataSet> filterSearchResultAndInjectFullDataSets(List<SequenceSearchResult> result,
+ private List<SearchDomainSearchResultWithFullDataSet> filterSearchResultAndInjectFullDataSets(List<SearchDomainSearchResult> result,
TableMap<String, AbstractExternalData> fullDataSetsByCode)
{
- List<SequenceSearchResultWithFullDataSet> filteredResult = new ArrayList<SequenceSearchResultWithFullDataSet>();
- for (SequenceSearchResult sequenceSearchResult : result)
+ List<SearchDomainSearchResultWithFullDataSet> filteredResult = new ArrayList<SearchDomainSearchResultWithFullDataSet>();
+ for (SearchDomainSearchResult sequenceSearchResult : result)
{
- String dataSetCode = sequenceSearchResult.getDataSetCode();
+ ISearchDomainResultLocation resultLocation = sequenceSearchResult.getResultLocation();
+ if (resultLocation instanceof DataSetFileSearchResultLocation == false)
+ {
+ continue;
+ }
+ String dataSetCode = ((DataSetFileSearchResultLocation) resultLocation).getDataSetCode();
AbstractExternalData fullDataSet = fullDataSetsByCode.tryGet(dataSetCode);
if (fullDataSet != null)
{
- SequenceSearchResultWithFullDataSet resultWithFullDataSet = new SequenceSearchResultWithFullDataSet();
+ SearchDomainSearchResultWithFullDataSet resultWithFullDataSet = new SearchDomainSearchResultWithFullDataSet();
resultWithFullDataSet.setDataSet(fullDataSet);
resultWithFullDataSet.setSearchResult(sequenceSearchResult);
filteredResult.add(resultWithFullDataSet);
@@ -304,7 +311,7 @@ public final class DataSetTable extends AbstractDataSetBusinessObject implements
return filteredResult;
}
- private TableMap<String, AbstractExternalData> listFullDataSets(List<SequenceSearchResult> result)
+ private TableMap<String, AbstractExternalData> listFullDataSets(List<SearchDomainSearchResult> result)
{
IKeyExtractor<String, AbstractExternalData> codeKeyExtractor = KeyExtractorFactory.<AbstractExternalData> createCodeKeyExtractor();
if (result.isEmpty())
@@ -312,9 +319,14 @@ public final class DataSetTable extends AbstractDataSetBusinessObject implements
return new TableMap<String, AbstractExternalData>(codeKeyExtractor);
}
Set<String> codes = new LinkedHashSet<String>();
- for (SequenceSearchResult sequenceSearchResult : result)
+ for (SearchDomainSearchResult sequenceSearchResult : result)
{
- codes.add(sequenceSearchResult.getDataSetCode());
+ ISearchDomainResultLocation resultLocation = sequenceSearchResult.getResultLocation();
+ if (resultLocation instanceof DataSetFileSearchResultLocation == false)
+ {
+ continue;
+ }
+ codes.add(((DataSetFileSearchResultLocation) resultLocation).getDataSetCode());
}
List<DataPE> fullDataSetPEs = getDataDAO().tryToFindFullDataSetsByCodes(codes, false, false);
List<AbstractExternalData> fullDataSets = DataSetTranslator.translate(fullDataSetPEs, "?", "?",
@@ -322,10 +334,10 @@ public final class DataSetTable extends AbstractDataSetBusinessObject implements
return new TableMap<String, AbstractExternalData>(fullDataSets, codeKeyExtractor);
}
- private List<SequenceSearchResult> askAllDataStoreServers(String preferredSequenceDatabaseOrNull,
+ private List<SearchDomainSearchResult> askAllDataStoreServers(String preferredSequenceDatabaseOrNull,
String sequenceSnippet, Map<String, String> optionalParametersOrNull)
{
- List<SequenceSearchResult> result = new ArrayList<SequenceSearchResult>();
+ List<SearchDomainSearchResult> result = new ArrayList<SearchDomainSearchResult>();
List<DataStorePE> stores = getDataStoreDAO().listDataStores();
for (DataStorePE dataStore : stores)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IDataSetTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IDataSetTable.java
index 714ba7e419d025600d0b29abdf3003dfecb40451..36d6cc6112335fe9c628b115e89881e36469bc83 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IDataSetTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IDataSetTable.java
@@ -21,7 +21,7 @@ import java.util.Map;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.LinkModel;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SequenceSearchResultWithFullDataSet;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SearchDomainSearchResultWithFullDataSet;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetBatchUpdatesDTO;
@@ -39,7 +39,7 @@ public interface IDataSetTable
/**
* Searchs for data sets with sequences.
*/
- List<SequenceSearchResultWithFullDataSet> searchForDataSetsWithSequences(String preferredSequenceDatabaseOrNull,
+ List<SearchDomainSearchResultWithFullDataSet> searchForDataSetsWithSequences(String preferredSequenceDatabaseOrNull,
String sequenceSnippet, Map<String, String> optionalParametersOrNull);
/**
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java
index 3f371a0afbaef74a0c91fab0c9540c6f0305141d..1c50d89ca71267866fb0097441a2a46a08e61b3b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java
@@ -104,7 +104,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleUpdateResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Script;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ScriptType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ScriptUpdateResult;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SequenceSearchResultWithFullDataSet;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SearchDomainSearchResultWithFullDataSet;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
@@ -659,12 +659,11 @@ public interface ICommonServer extends IServer
DetailedSearchCriteria criteria);
/**
- * Searches for data sets which have nucleotid or aminoacid sequences in there files.
+ * Searches on a search domain.
*/
@Transactional(readOnly = true)
- public List<SequenceSearchResultWithFullDataSet> searchForDataSetsWithSequences(String sessionToken,
- String preferredSequenceDatabaseOrNull, String sequenceSnippet,
- Map<String, String> optionalParametersOrNull);
+ public List<SearchDomainSearchResultWithFullDataSet> searchOnSearchDomain(String sessionToken,
+ String preferredSearchDomainOrNull, String searchString, Map<String, String> optionalParametersOrNull);
/**
* Searches for data sets that fulfill the specified search criteria.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IDataStoreService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IDataStoreService.java
index 566fa5ae5ce92c7f76ee3ac923aecb4dfd4d5f14..5ec24e9c623e6abdd571d846f0953d171a9c211b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IDataStoreService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IDataStoreService.java
@@ -22,7 +22,7 @@ import java.util.Map;
import ch.systemsx.cisd.common.exceptions.InvalidAuthenticationException;
import ch.systemsx.cisd.openbis.common.conversation.annotation.Conversational;
import ch.systemsx.cisd.openbis.common.conversation.annotation.Progress;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SequenceSearchResult;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomainSearchResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CustomImportFile;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IDatasetLocation;
@@ -175,7 +175,7 @@ public interface IDataStoreService
* @since 10
*/
@Conversational(progress = Progress.AUTOMATIC)
- public List<SequenceSearchResult> searchForDataSetsWithSequences(String sessionToken,
+ public List<SearchDomainSearchResult> searchForDataSetsWithSequences(String sessionToken,
String preferredSequenceDatabaseOrNull, String sequenceSnippet,
Map<String, String> optionalParametersOrNull);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SequenceSearchResultWithFullDataSet.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SearchDomainSearchResultWithFullDataSet.java
similarity index 76%
rename from openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SequenceSearchResultWithFullDataSet.java
rename to openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SearchDomainSearchResultWithFullDataSet.java
index a796500f26e34e0653098fa1e5f96d461fe471ae..7d504b3c4db3b059ac3cabe3457eb87db62d6c14 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SequenceSearchResultWithFullDataSet.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SearchDomainSearchResultWithFullDataSet.java
@@ -18,20 +18,20 @@ package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
import java.io.Serializable;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SequenceSearchResult;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomainSearchResult;
/**
- * Result of a sequence search.
+ * Result of a search in a search domain.
*
* @author Franz-Josef Elmer
*/
-public class SequenceSearchResultWithFullDataSet implements Serializable
+public class SearchDomainSearchResultWithFullDataSet implements Serializable
{
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
private AbstractExternalData dataSet;
- private SequenceSearchResult searchResult;
+ private SearchDomainSearchResult searchResult;
public AbstractExternalData getDataSet()
{
@@ -43,12 +43,12 @@ public class SequenceSearchResultWithFullDataSet implements Serializable
this.dataSet = dataSet;
}
- public SequenceSearchResult getSearchResult()
+ public SearchDomainSearchResult getSearchResult()
{
return searchResult;
}
- public void setSearchResult(SequenceSearchResult searchResult)
+ public void setSearchResult(SearchDomainSearchResult searchResult)
{
this.searchResult = searchResult;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/js/openbis.js b/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/js/openbis.js
index 6f88786baf584ef75507173c6210f2b14946ade1..158e9b2eea8a9a6ea99132e152fd3025b9bf0f8f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/js/openbis.js
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/js/openbis.js
@@ -861,16 +861,16 @@ openbis.prototype.searchForDataSetsOnBehalfOfUser = function(searchCriteria, use
}
/**
- * @see IGeneralInformationService.searchForDataSetsWithSequences(String, String, String, Map<String, String>)
+ * @see IGeneralInformationService.searchOnSearchDomain(String, String, String, Map<String, String>)
* @method
*/
-openbis.prototype.searchForDataSetsWithSequences = function(preferredSequenceDatabaseOrNull, sequenceSnippet, optionalParametersOrNull, action) {
+openbis.prototype.searchOnSearchDomain = function(preferredSearchDomainOrNull, searchString, optionalParametersOrNull, action) {
this._internal.ajaxRequest({
url: this._internal.generalInfoServiceUrl,
- data: { "method" : "searchForDataSetsWithSequences",
+ data: { "method" : "searchOnSearchDomain",
"params" : [ this.getSession(),
- preferredSequenceDatabaseOrNull,
- sequenceSnippet, optionalParametersOrNull ] },
+ preferredSearchDomainOrNull,
+ searchString, optionalParametersOrNull ] },
success: action
});
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTableTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTableTest.java
index 849953c59b21e12ac5a17bd1fff45c89929d5f79..b13e6887d3289ed78b411793e353b246aba37927 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTableTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTableTest.java
@@ -47,14 +47,15 @@ import ch.systemsx.cisd.openbis.generic.server.business.ManagerTestTool;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.event.DeleteDataSetEventBuilder;
import ch.systemsx.cisd.openbis.generic.shared.CommonTestUtils;
import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SequenceSearchResult;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetFileSearchResultLocation;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomainSearchResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Code;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetArchivingStatus;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SequenceSearchResultWithFullDataSet;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SearchDomainSearchResultWithFullDataSet;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUploadContext;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
@@ -186,18 +187,21 @@ public final class DataSetTableTest extends AbstractBOTest
}
});
- List<SequenceSearchResultWithFullDataSet> results =
+ List<SearchDomainSearchResultWithFullDataSet> results =
createDataSetTable().searchForDataSetsWithSequences(SEQUENCE_DATABASE, SEQUENCE_SNIPPET, OPTIONAL_PARAMETERS);
- assertEquals("Database: test-db, Data set: ds1, path: ds1/path, identifier: [id-ds1], position: 42",
+ assertEquals("Search Domain: test-db, Result location: [Data set: ds1, path: ds1/path, "
+ + "identifier: [id-ds1], position: 42]",
results.get(0).getSearchResult().toString());
assertEquals(ds1.getCode(), results.get(0).getDataSet().getCode());
assertEquals("/G1/P1/exp1", results.get(0).getDataSet().getExperiment().getIdentifier());
- assertEquals("Database: test-db, Data set: ds3, path: ds3/path, identifier: [id-ds3], position: 42",
+ assertEquals("Search Domain: test-db, Result location: [Data set: ds3, path: ds3/path, "
+ + "identifier: [id-ds3], position: 42]",
results.get(1).getSearchResult().toString());
assertEquals(ds3.getCode(), results.get(1).getDataSet().getCode());
assertEquals("/G1/P1/exp1", results.get(1).getDataSet().getExperiment().getIdentifier());
- assertEquals("Database: test-db, Data set: ds3, path: ds3/path, identifier: [id-ds3], position: 42",
+ assertEquals("Search Domain: test-db, Result location: [Data set: ds3, path: ds3/path, "
+ + "identifier: [id-ds3], position: 42]",
results.get(2).getSearchResult().toString());
assertEquals(ds3.getCode(), results.get(2).getDataSet().getCode());
assertEquals("/G1/P1/exp1", results.get(2).getDataSet().getExperiment().getIdentifier());
@@ -227,15 +231,17 @@ public final class DataSetTableTest extends AbstractBOTest
one(service).searchForDataSetsWithSequences(dataStore.getSessionToken(),
SEQUENCE_DATABASE, SEQUENCE_SNIPPET, OPTIONAL_PARAMETERS);
- List<SequenceSearchResult> results = new ArrayList<SequenceSearchResult>();
+ List<SearchDomainSearchResult> results = new ArrayList<SearchDomainSearchResult>();
for (String foundDataSet : foundDataSets)
{
- SequenceSearchResult result = new SequenceSearchResult();
- result.setSequenceDatabaseName("test-db");
- result.setDataSetCode(foundDataSet);
- result.setPathInDataSet(foundDataSet + "/path");
- result.setPositionInSequence(42);
- result.setSequenceIdentifier("id-" + foundDataSet);
+ SearchDomainSearchResult result = new SearchDomainSearchResult();
+ result.setSearchDomain("test-db");
+ DataSetFileSearchResultLocation resultLocation = new DataSetFileSearchResultLocation();
+ resultLocation.setDataSetCode(foundDataSet);
+ resultLocation.setPathInDataSet(foundDataSet + "/path");
+ resultLocation.setPositionInSequence(42);
+ resultLocation.setSequenceIdentifier("id-" + foundDataSet);
+ result.setResultLocation(resultLocation);
results.add(result);
}
will(returnValue(results));
diff --git a/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/IGeneralInformationService.java b/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/IGeneralInformationService.java
index 75153ba64d53ec09b8e87fd9d37b72524ff028d9..6ba9353657ccee4e693710707ee19c1205b9e542 100644
--- a/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/IGeneralInformationService.java
+++ b/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/IGeneralInformationService.java
@@ -44,7 +44,7 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleFetchOption;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SequenceSearchResult;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomainSearchResult;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SpaceWithProjectsAndRoleAssignments;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.experiment.IExperimentId;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.metaproject.IMetaprojectId;
@@ -398,18 +398,17 @@ public interface IGeneralInformationService extends IRpcService
EnumSet<DataSetFetchOption> fetchOptions);
/**
- * Searches for data sets which have nucleotid or amoniacid sequences in there files.
- * If no preferred sequence database is specified the first available one will be used. If the
- * preferred sequence database doesn't exist or isn't available also the first available database will be used.
+ * Searches on a search domain. If no preferred search domain is specified the first available one will be used.
+ * If the preferred sequence search domain doesn't exist or isn't available also the first available one will be used.
*
- * @param preferredSequenceDatabaseOrNull The key of the preferred sequence database or <code>null</code>.
- * @param sequenceSnippet A snippet of a sequence to search for.
+ * @param preferredSearchDomainOrNull The key of the preferred search domain or <code>null</code>.
+ * @param searchString The search string.
* @param optionalParametersOrNull Optional parameters. Can be <code>null</code>.
- * The semantics depends on the type of the used sequence database.
+ * The semantics depends on the type of search domain.
* @since 1.29
*/
- public List<SequenceSearchResult> searchForDataSetsWithSequences(String sessionToken,
- String preferredSequenceDatabaseOrNull, String sequenceSnippet,
+ public List<SearchDomainSearchResult> searchOnSearchDomain(String sessionToken,
+ String preferredSearchDomainOrNull, String searchString,
Map<String, String> optionalParametersOrNull);
/**
diff --git a/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/SequenceSearchResult.java b/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSetFileSearchResultLocation.java
similarity index 72%
rename from openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/SequenceSearchResult.java
rename to openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSetFileSearchResultLocation.java
index bec456d9040047cdcb482fa411cafd3f7b912fb0..f8af6ad5beb101b66cacfc6d0676376a0fc739ad 100644
--- a/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/SequenceSearchResult.java
+++ b/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSetFileSearchResultLocation.java
@@ -16,23 +16,18 @@
package ch.systemsx.cisd.openbis.generic.shared.api.v1.dto;
-import java.io.Serializable;
-
import ch.systemsx.cisd.base.annotation.JsonObject;
/**
- * Result of a sequence search. Returns the code of the data set where the sequence has been found,
- * the path of the file inside the data set which has the found sequence, and the sequence identifier.
+ * Result location for a search in a sequence in a file in data set.
*
* @author Franz-Josef Elmer
*/
-@JsonObject("SequenceSearchResult")
-public class SequenceSearchResult implements Serializable
+@JsonObject("DataSetFileSearchResultLocation")
+public class DataSetFileSearchResultLocation implements ISearchDomainResultLocation
{
private static final long serialVersionUID = 1L;
- private String sequenceDatabaseName;
-
private String dataSetCode;
private String pathInDataSet;
@@ -41,16 +36,6 @@ public class SequenceSearchResult implements Serializable
private int positionInSequence;
- public String getSequenceDatabaseName()
- {
- return sequenceDatabaseName;
- }
-
- public void setSequenceDatabaseName(String sequenceDatabaseKey)
- {
- this.sequenceDatabaseName = sequenceDatabaseKey;
- }
-
public String getDataSetCode()
{
return dataSetCode;
@@ -94,8 +79,9 @@ public class SequenceSearchResult implements Serializable
@Override
public String toString()
{
- return "Database: " + sequenceDatabaseName + ", Data set: " + dataSetCode + ", path: " + pathInDataSet
+ return "Data set: " + dataSetCode + ", path: " + pathInDataSet
+ ", identifier: [" + sequenceIdentifier + "], position: " + positionInSequence;
}
+
}
diff --git a/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/ISearchDomainResultLocation.java b/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/ISearchDomainResultLocation.java
new file mode 100644
index 0000000000000000000000000000000000000000..276bacfce0d47af0fe570ca58ec91db30857f0af
--- /dev/null
+++ b/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/ISearchDomainResultLocation.java
@@ -0,0 +1,29 @@
+/*
+ * Copyright 2014 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.systemsx.cisd.openbis.generic.shared.api.v1.dto;
+
+import java.io.Serializable;
+
+/**
+ * Marker interface specifying the location of search result on a search domain.
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface ISearchDomainResultLocation extends Serializable
+{
+
+}
diff --git a/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/SearchDomainSearchResult.java b/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/SearchDomainSearchResult.java
new file mode 100644
index 0000000000000000000000000000000000000000..868ee97cec5f89df13464bdff526c6a34d4bc715
--- /dev/null
+++ b/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/SearchDomainSearchResult.java
@@ -0,0 +1,63 @@
+/*
+ * Copyright 2014 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.systemsx.cisd.openbis.generic.shared.api.v1.dto;
+
+import java.io.Serializable;
+
+import ch.systemsx.cisd.base.annotation.JsonObject;
+
+/**
+ * Result of a search on a search domain.
+ *
+ * @author Franz-Josef Elmer
+ */
+@JsonObject("SearchDomainSearchResult")
+public class SearchDomainSearchResult implements Serializable
+{
+ private static final long serialVersionUID = 1L;
+
+ private String searchDomain;
+
+ private ISearchDomainResultLocation resultLocation;
+
+ public String getSearchDomain()
+ {
+ return searchDomain;
+ }
+
+ public void setSearchDomain(String searchDomain)
+ {
+ this.searchDomain = searchDomain;
+ }
+
+ public ISearchDomainResultLocation getResultLocation()
+ {
+ return resultLocation;
+ }
+
+ public void setResultLocation(ISearchDomainResultLocation resultLocation)
+ {
+ this.resultLocation = resultLocation;
+ }
+
+ @Override
+ public String toString()
+ {
+ return "Search Domain: " + getSearchDomain() + ", Result location: [" + resultLocation + "]";
+ }
+
+}