Merge branch 'master' of sissource.ethz.ch:sispub/openbis into master

commonbase/build.gradle

@@ -8,10 +8,10 @@ dependencies {
             'sis:sis-base:18.09.0',
 	        'rinn:restrictions:1.0.2',
 			// Removed libraries from JDK 11 used by many projects
-			'javax.activation:activation:1.1.1', // TODO: Add to ivy repository and remove mavenCentral() from repository.gradle
+			'javax.activation:activation:1.1.1',
 			'javax.annotation:javax.annotation-api:1.3.2',
 			'javax.xml.bind:jaxb-api:2.3.0',
-			'org.glassfish.jaxb:jaxb-runtime:2.3.0', // TODO: Add to ivy repository and remove mavenCentral() from repository.gradle
+			'org.glassfish.jaxb:jaxb-runtime:2.3.0',
 			'org.glassfish.main.javaee-api:javax.jws:3.1.2.2'
 
 	testCompile 'fjelmer:classycle:1.4.2',

datastore_server/dist/datastore_server.sh

@@ -160,7 +160,13 @@ CP=`echo $LIB_FOLDER/slf4j-log4j12-1.6.2.jar $LIB_FOLDER/datastore_server.jar $L
     | sed 's/ /:/g'`
 
 CMD="${JAVA_BIN}"
-COMMON_OPTIONS="${JAVA_OPTS} ${JAVA_MEM_OPTS} -Dnative.libpath=$LIB_FOLDER/native -classpath $CP ch.systemsx.cisd.openbis.dss.generic.DataStoreServer"
+version=$("${CMD}" -version 2>&1 | awk -F '"' '/version/ {print $2}'| cut -c1-3)
+JAVA_VERSION_OPTS=""
+if [[ "$version" != "1.8" ]]; then
+    JAVA_VERSION_OPTS="--add-exports java.xml/jdk.xml.internal=ALL-UNNAMED"
+fi
+COMMON_OPTIONS="${JAVA_OPTS} ${JAVA_MEM_OPTS} $JAVA_VERSION_OPTS -Dnative.libpath=$LIB_FOLDER/native -classpath $CP ch.systemsx.cisd.openbis.dss.generic.DataStoreServer"
+
 
 # ensure that we ignore a possible prefix "--" for any command 
 command="${command#--*}"

gradle/build.gradle

@@ -6,7 +6,6 @@ evaluationDependsOn(':authentication')
 evaluationDependsOn(':dbmigration')
 evaluationDependsOn(':openbis')
 evaluationDependsOn(':datastore_server')
-evaluationDependsOn(':rtd_phosphonetx')
 evaluationDependsOn(':screening')
 evaluationDependsOn(':rtd_yeastx')
 evaluationDependsOn(':deep_sequencing_unit')

gradle/repository.gradle

@@ -7,5 +7,4 @@ ext.repositoryConfig = {
         ivyPattern "http://svnsis.ethz.ch/repos/cisd/ivy-repository/trunk/[organisation]/[module]/[revision]/ivy.xml"
         artifactPattern "http://svnsis.ethz.ch/repos/cisd/ivy-repository/trunk/[organisation]/[module]/[revision]/[artifact]-[revision](-[classifier]).[ext]"
     }
-    mavenCentral() // TODO: remove after adding dependencies to Ivy repository
 }

gradle/settings.gradle

 includeFlat 'commonbase', 'common', 'openbis_api', 'openbis-common', 'authentication', 'dbmigration', 'openbis', 
-    'datastore_server', 'screening', 'rtd_phosphonetx', 'deep_sequencing_unit', 'rtd_yeastx', 
+    'datastore_server', 'screening', 'deep_sequencing_unit', 'rtd_yeastx', 
     'openbis_standard_technologies', 'installation', 'image_readers', 'ui-test', 'js-test', 'datamover', 
     'plasmid', 'rtd_cina', 'openbis_oai_pmh', 'big_data_link_server', 'openbis_ng_ui'

installation/build.gradle

@@ -6,7 +6,6 @@ evaluationDependsOn(':authentication')
 evaluationDependsOn(':dbmigration')
 evaluationDependsOn(':openbis')
 evaluationDependsOn(':datastore_server')
-evaluationDependsOn(':rtd_phosphonetx')
 evaluationDependsOn(':screening')
 evaluationDependsOn(':rtd_yeastx')
 evaluationDependsOn(':deep_sequencing_unit')
@@ -167,9 +166,6 @@ task createInstallerJar(type: Jar, dependsOn: [compileInstaller, jar]) {
     for (f in configurations.archives.files) {
         from zipTree(f)
     }
-    manifest {
-        attributes('Main-Class' : 'com.izforge.izpack.installer.bootstrap.Installer')
-    }
 }
 
 task createInstallerZip(type: Tar, dependsOn: createInstallerJar) {

installation/resource/tarball/run-console.sh

@@ -84,4 +84,4 @@ else
   readAdminPassword
 fi
 
-java -Djava.util.logging.config.file=$BASE/jul.config -DADMIN_PASSWORD=$ADMIN_PASSWORD -DCONSOLE=true -Dmerge.props.to.installation.vars=true -jar $BASE/openBIS-installer.jar -options-auto $BASE/console.properties
+java -Djava.util.logging.config.file=$BASE/jul.config -DADMIN_PASSWORD=$ADMIN_PASSWORD -DCONSOLE=true -Dmerge.props.to.installation.vars=true -cp $BASE/openBIS-installer.jar com.izforge.izpack.installer.bootstrap.Installer -options-auto $BASE/console.properties

installation/resource/tarball/run-ui.sh

-#!/bin/bash
-
-#Detect Java version
-
-if type -p java; then
-    _java=java
-else
-    echo "Java not available"
-	exit -1
-fi
-
-if [[ "$_java" ]]; then
-    version=$("$_java" -version 2>&1 | awk -F '"' '/version/ {print $2}'| cut -c1-3)
-    if [[ "$version" == "1.8" || "$version" == "11." ]]; then
-        echo Java version $version found.
-    else
-        echo Java version $version found is neither 1.8 or 11.
-        exit -1
-    fi
-fi
-
-#Continue installation
-
-BASE=`dirname "$0"`
-if [ ${BASE#/} == ${BASE} ]; then
-    BASE="`pwd`/${BASE}"
-fi
-
-java -Djava.util.logging.config.file=$BASE/jul.config -jar $BASE/openBIS-installer.jar
\ No newline at end of file

installation/settings.gradle

 includeFlat 'commonbase', 'common', 
     'openbis_api', 'openbis-common', 'authentication', 'dbmigration', 'openbis', 
-    'datastore_server', 'screening', 'rtd_yeastx', 'rtd_phosphonetx', 'deep_sequencing_unit', 'plasmid',
+    'datastore_server', 'screening', 'rtd_yeastx', 'deep_sequencing_unit', 'plasmid',
     'openbis_standard_technologies', 'big_data_link_server', 'openbis_ng_ui'

integration-tests/settings.py

@@ -5,8 +5,8 @@ import sys
 import os.path
 import time
 
-# Base URL of the CI server which hosts the artifacts.
-CI_BASE_URL = 'http://bs-ci01.ethz.ch:8090'
+# Default base URL of the CI server which hosts the artifacts.
+ci_base_url = 'http://bs-ci01.ethz.ch:8090'
 
 reuseRepository = False
 devMode = False
@@ -20,9 +20,12 @@ if len(sys.argv) > 1:
         devMode = True
     elif firstArgument == '-d':
         devMode = True
+    elif firstArgument == '-s':
+        ci_base_url = sys.argv[2]
     elif firstArgument == '-h':
-        print("Usage: %s [-h|-r|-d|-rd]\n-h: prints this help\n-r: reuses artifact repository\n"
-            + "-d: developing mode\n-rd: both options" % os.path.basename(cmd))
+        print(("Usage: %s [-h|-r|-d|-rd|-s <ci server>]\n-h: prints this help\n-r: reuses artifact repository\n"
+            + "-d: developing mode\n-rd: both options\n"
+            + "-s <ci server>: option for CI server host name") % os.path.basename(cmd))
         exit(1)
     else:
         print("Unknown option: %s. Use option '-h' to see usage." % firstArgument)
@@ -34,6 +37,6 @@ sys.path.append("%s/sourceTest" % dirname)
 
 from systemtest.artifactrepository import JenkinsArtifactRepository 
 
-REPOSITORY = JenkinsArtifactRepository(CI_BASE_URL, "%s/targets/artifact-repository" % dirname)
+REPOSITORY = JenkinsArtifactRepository(ci_base_url, "%s/targets/artifact-repository" % dirname)
 if not reuseRepository:
     REPOSITORY.clear()

js-test/build.gradle

@@ -8,7 +8,6 @@ evaluationDependsOn(':openbis')
 evaluationDependsOn(':datastore_server')
 evaluationDependsOn(':ui-test')
 evaluationDependsOn(':screening')
-evaluationDependsOn(':rtd_phosphonetx')
 
 
 apply from: '../gradle/javaproject.gradle'
@@ -43,13 +42,11 @@ dependencies {
 
 	testCompile project(path: ':ui-test', configuration: 'tests')
 	
-	testRuntime project(':screening'), project(':rtd_phosphonetx')
-	
 	testRuntimeFirst 'javax:servlet-api:3.1.0', 'reflections:reflections:0.9.10', 'apache:commons-lang3:3.7'
 	
 	testRuntimeSecond 'google:gwt-user:2.4'
 
-	externalDss project(':screening'), project(':rtd_phosphonetx')
+	externalDss project(':screening')
 } 
 
 sourceSets.test.runtimeClasspath = configurations.testRuntimeFirst + configurations.testRuntimeSecond + sourceSets.test.runtimeClasspath
@@ -62,7 +59,7 @@ task copyWar(type: Copy, dependsOn: project(':openbis_standard_technologies').wa
 
 test {
     useTestNG()
-    options.suites('source/java/tests.xml')    
+    options.suites('source/java/tests-dev.xml')    
 
     jvmArgs '-Xmx2048m', '-XX:MaxPermSize=256m', '-Dorg.eclipse.jetty.util.log.class=org.eclipse.jetty.util.log.StrErrLog', '-Duser.timezone=Europe/Zurich', '-Xdebug', '-Xrunjdwp:transport=dt_socket,address=20010,server=y,suspend=n'
     

js-test/settings.gradle

 includeFlat 'commonbase', 'common', 'openbis_api', 'openbis-common', 'authentication', 'dbmigration', 'openbis', 
-    'datastore_server', 'screening', 'rtd_yeastx', 'rtd_phosphonetx', 'deep_sequencing_unit', 'plasmid', 'openbis_standard_technologies',
-    'ui-test','screening', 'rtd_phosphonetx'
+    'datastore_server', 'screening', 'rtd_yeastx', 'deep_sequencing_unit', 'plasmid', 'openbis_standard_technologies',
+    'ui-test','screening'

openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/search/dao/PostgresSearchDAO.java

@@ -89,26 +89,35 @@ public class PostgresSearchDAO implements ISQLSearchDAO
 
     private void assertPropertyTypesConsistent(final TranslationContext translationContext)
     {
-        final String pt = "pt";
-        final String dt = "dt";
-        final String propertyTypeAlias = "propertytype";
-        final String dataTypeAlias = "datatype";
-        final String sql = SELECT + SP + pt + PERIOD + CODE_COLUMN + SP + propertyTypeAlias + COMMA
-                + SP + dt + PERIOD + CODE_COLUMN + SP + dataTypeAlias + NL
-                + FROM + SP + PROPERTY_TYPES_TABLE + SP + pt + NL
-                + INNER_JOIN + SP + DATA_TYPES_TABLE + SP + dt + SP
-                + ON + SP + pt + PERIOD + DATA_TYPE_COLUMN + SP + EQ + SP + dt + PERIOD + ID_COLUMN;
-
-        final List<Map<String, Object>> queryResultList = sqlExecutor.execute(sql, Collections.emptyList());
-        final Map<String, String> dataTypesOfPropertyTypes = queryResultList.stream().collect(Collectors.toMap(
-                (valueByColumnName) -> (String) valueByColumnName.get(propertyTypeAlias),
-                (valueByColumnName) -> (String) valueByColumnName.get(dataTypeAlias)));
+        final Map<String, String> dataTypeByPropertyCode;
+
+        if(translationContext.getDataTypeByPropertyCode() == null) {
+            final String pt = "pt";
+            final String dt = "dt";
+            final String propertyTypeAlias = "propertytype";
+            final String dataTypeAlias = "datatype";
+            final String isManagedInternallyAlias = "ismanagedinternally";
+            final String sql = SELECT + SP + pt + PERIOD + CODE_COLUMN + SP + propertyTypeAlias + COMMA
+                    + SP + pt + PERIOD + IS_MANAGED_INTERNALLY + SP + isManagedInternallyAlias + COMMA
+                    + SP + dt + PERIOD + CODE_COLUMN + SP + dataTypeAlias + NL
+                    + FROM + SP + PROPERTY_TYPES_TABLE + SP + pt + NL
+                    + INNER_JOIN + SP + DATA_TYPES_TABLE + SP + dt + SP
+                    + ON + SP + pt + PERIOD + DATA_TYPE_COLUMN + SP + EQ + SP + dt + PERIOD + ID_COLUMN;
+
+            final List<Map<String, Object>> queryResultList = sqlExecutor.execute(sql, Collections.emptyList());
+            dataTypeByPropertyCode = queryResultList.stream().collect(Collectors.toMap(
+                    (valueByColumnName) -> ((((Boolean) valueByColumnName.get(isManagedInternallyAlias)) ? "$" : "") + ((String) valueByColumnName.get(propertyTypeAlias))),
+                    (valueByColumnName) -> (String) valueByColumnName.get(dataTypeAlias)));
+            translationContext.setDataTypeByPropertyCode(dataTypeByPropertyCode);
+        } else {
+            dataTypeByPropertyCode = translationContext.getDataTypeByPropertyCode();
+        }
 
         translationContext.getCriteria().forEach(criterion ->
         {
             if (criterion instanceof NumberPropertySearchCriteria)
             {
-                final String dataType = dataTypesOfPropertyTypes.get(((NumberPropertySearchCriteria) criterion)
+                final String dataType = dataTypeByPropertyCode.get(((NumberPropertySearchCriteria) criterion)
                         .getFieldName());
                 if (!dataType.equals(DataTypeCode.INTEGER.toString())
                         && !dataType.equals(DataTypeCode.REAL.toString()))
@@ -117,7 +126,7 @@ public class PostgresSearchDAO implements ISQLSearchDAO
                 }
             } else if (criterion instanceof DatePropertySearchCriteria)
             {
-                final String dataType = dataTypesOfPropertyTypes.get(((DatePropertySearchCriteria) criterion)
+                final String dataType = dataTypeByPropertyCode.get(((DatePropertySearchCriteria) criterion)
                         .getFieldName());
                 if (!dataType.equals(DataTypeCode.TIMESTAMP.toString())
                         && !dataType.equals(DataTypeCode.DATE.toString()))

openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/search/planner/AbstractCompositeEntitySearchManager.java

@@ -75,10 +75,16 @@ public abstract class AbstractCompositeEntitySearchManager<CRITERIA extends Abst
                 authorisationInformation);
     }
 
-    protected Set<Long> doSearchForIDs(final Long userId, final Collection<ISearchCriteria> parentsCriteria,
-            final Collection<ISearchCriteria> childrenCriteria, final Collection<ISearchCriteria> mainCriteria,
-            final SearchOperator finalSearchOperator, final String idsColumnName, final TableMapper tableMapper, final AuthorisationInformation authorisationInformation)
+    protected Set<Long> doSearchForIDs(final Long userId,
+            final Collection<ISearchCriteria> upstreamRelationshipsCriteria,
+            final Collection<ISearchCriteria> downstreamRelationshipsCriteria,
+            final Collection<ISearchCriteria> mainCriteria,
+            final SearchOperator finalSearchOperator, final String idsColumnName, final TableMapper tableMapper,
+            final AuthorisationInformation authorisationInformation)
     {
+        // upstreamRelationshipsCriteria & downstreamRelationshipsCriteria are relationships from the relationships
+        // table, for datasets it is both the parent-child relationships and containers but for samples it is only the
+        // parent-child ones.
         final Set<Long> mainCriteriaIntermediateResults;
         if (!mainCriteria.isEmpty())
         {
@@ -92,45 +98,61 @@ public abstract class AbstractCompositeEntitySearchManager<CRITERIA extends Abst
         }
 
         final Set<Long> parentCriteriaIntermediateResults;
-        if (!parentsCriteria.isEmpty())
+        final Set<Long> containerCriteriaIntermediateResults;
+        if (!upstreamRelationshipsCriteria.isEmpty())
         {
-            parentCriteriaIntermediateResults = Arrays.stream(IGetRelationshipIdExecutor.RelationshipType.values())
-                    .flatMap(relationshipType ->
-                    {
-                        final Collection<ISearchCriteria> filteredParentsCriteria =
-                                getCriteriaByRelationshipType(parentsCriteria, relationshipType);
-
-                        // The parents criteria can be or not recursive, they are resolved by a recursive call
-                        final Set<Long> finalParentIds = findFinalRelationshipIds(userId, authorisationInformation,
-                                finalSearchOperator, filteredParentsCriteria, tableMapper);
-                        final Set<Long> finalParentIdsFiltered = filterIDsByUserRights(userId, authorisationInformation,
-                                finalParentIds);
-                        return getChildrenIdsOf(finalParentIdsFiltered, tableMapper,
-                                relationshipType).stream();
-
-                    }).collect(Collectors.toSet());
+            final Collection<ISearchCriteria> filteredParentsCriteria =
+                    getCriteriaByRelationshipType(upstreamRelationshipsCriteria,
+                            IGetRelationshipIdExecutor.RelationshipType.PARENT_CHILD);
+
+            if (!filteredParentsCriteria.isEmpty())
+            {
+                final Set<Long> finalParentIds = findFinalRelationshipIds(userId, authorisationInformation,
+                        finalSearchOperator, filteredParentsCriteria, tableMapper);
+                final Set<Long> finalParentIdsFiltered = filterIDsByUserRights(userId, authorisationInformation,
+                        finalParentIds);
+                parentCriteriaIntermediateResults = getChildrenIdsOf(finalParentIdsFiltered, tableMapper,
+                        IGetRelationshipIdExecutor.RelationshipType.PARENT_CHILD);
+            } else
+                {
+                parentCriteriaIntermediateResults = null;
+            }
+
+            final Collection<ISearchCriteria> filteredContainersCriteria =
+                    getCriteriaByRelationshipType(upstreamRelationshipsCriteria,
+                            IGetRelationshipIdExecutor.RelationshipType.CONTAINER_COMPONENT);
+
+            if (!filteredContainersCriteria.isEmpty())
+            {
+                final Set<Long> finalContainerIds = findFinalRelationshipIds(userId, authorisationInformation,
+                        finalSearchOperator, filteredContainersCriteria, tableMapper);
+                final Set<Long> finalContainerIdsFiltered = filterIDsByUserRights(userId, authorisationInformation,
+                        finalContainerIds);
+                containerCriteriaIntermediateResults = getChildrenIdsOf(finalContainerIdsFiltered, tableMapper,
+                        IGetRelationshipIdExecutor.RelationshipType.CONTAINER_COMPONENT);
+            } else
+            {
+                containerCriteriaIntermediateResults = null;
+            }
         } else
         {
             parentCriteriaIntermediateResults = null;
+            containerCriteriaIntermediateResults = null;
         }
 
         final Set<Long> childrenCriteriaIntermediateResults;
-        if (!childrenCriteria.isEmpty())
+        if (!downstreamRelationshipsCriteria.isEmpty())
         {
-            childrenCriteriaIntermediateResults = Arrays.stream(IGetRelationshipIdExecutor.RelationshipType.values())
-                    .flatMap(relationshipType ->
-                    {
-                        final Collection<ISearchCriteria> filteredChildrenCriteria =
-                                getCriteriaByRelationshipType(childrenCriteria, relationshipType);
-
-                        // The children criteria can be or not recursive, they are resolved by a recursive call
-                        final Set<Long> finalChildrenIds = findFinalRelationshipIds(userId, authorisationInformation,
-                                finalSearchOperator, filteredChildrenCriteria, tableMapper);
-                        final Set<Long> finalChildrenIdsFiltered = filterIDsByUserRights(userId,
-                                authorisationInformation, finalChildrenIds);
-                        return getParentsIdsOf(finalChildrenIdsFiltered, tableMapper,
-                                relationshipType).stream();
-                    }).collect(Collectors.toSet());
+            final Collection<ISearchCriteria> filteredChildrenCriteria =
+                    getCriteriaByRelationshipType(downstreamRelationshipsCriteria,
+                            IGetRelationshipIdExecutor.RelationshipType.PARENT_CHILD);
+
+            final Set<Long> finalChildrenIds = findFinalRelationshipIds(userId, authorisationInformation,
+                    finalSearchOperator, filteredChildrenCriteria, tableMapper);
+            final Set<Long> finalChildrenIdsFiltered = filterIDsByUserRights(userId,
+                    authorisationInformation, finalChildrenIds);
+            childrenCriteriaIntermediateResults = getParentsIdsOf(finalChildrenIdsFiltered, tableMapper,
+                    IGetRelationshipIdExecutor.RelationshipType.PARENT_CHILD);
         } else
         {
             childrenCriteriaIntermediateResults = null;
@@ -138,15 +160,21 @@ public abstract class AbstractCompositeEntitySearchManager<CRITERIA extends Abst
 
         // Reaching this point we have the intermediate results of all recursive queries
         final Set<Long> results;
-        if (containsValues(mainCriteriaIntermediateResults) || containsValues(parentCriteriaIntermediateResults) ||
-                containsValues(childrenCriteriaIntermediateResults))
+        if (containsValues(mainCriteriaIntermediateResults) || containsValues(parentCriteriaIntermediateResults)
+                || containsValues(containerCriteriaIntermediateResults)
+                || containsValues(childrenCriteriaIntermediateResults))
         {
             // If we have results, we merge them
             results = mergeResults(finalSearchOperator,
-                    mainCriteriaIntermediateResults != null ? Collections.singleton(mainCriteriaIntermediateResults) : Collections.emptySet(),
-                    childrenCriteriaIntermediateResults != null ? Collections.singleton(childrenCriteriaIntermediateResults) : Collections.emptySet(),
-                    parentCriteriaIntermediateResults != null ? Collections.singleton(parentCriteriaIntermediateResults) : Collections.emptySet());
-        } else if (mainCriteria.isEmpty() && parentsCriteria.isEmpty() && childrenCriteria.isEmpty())
+                    mainCriteriaIntermediateResults != null
+                            ? Collections.singleton(mainCriteriaIntermediateResults) : Collections.emptySet(),
+                    childrenCriteriaIntermediateResults != null
+                            ? Collections.singleton(childrenCriteriaIntermediateResults) : Collections.emptySet(),
+                    parentCriteriaIntermediateResults != null
+                            ? Collections.singleton(parentCriteriaIntermediateResults) : Collections.emptySet(),
+                    containerCriteriaIntermediateResults != null
+                            ? Collections.singleton(containerCriteriaIntermediateResults) : Collections.emptySet());
+        } else if (mainCriteria.isEmpty() && upstreamRelationshipsCriteria.isEmpty() && downstreamRelationshipsCriteria.isEmpty())
         {
             // If we don't have results and criteria are empty, return all.
             results = getAllIds(userId, authorisationInformation, idsColumnName, tableMapper);

openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/search/planner/SampleContainerSearchManager.java

@@ -37,26 +37,22 @@ import java.util.Set;
  * 
  * @author Viktor Kovtun
  */
-public class SampleContainerSearchManager extends AbstractCompositeEntitySearchManager<SampleContainerSearchCriteria, Sample, Long>
+public class SampleContainerSearchManager extends AbstractLocalSearchManager<SampleContainerSearchCriteria, Sample,
+        Long>
 {
 
-    public SampleContainerSearchManager(final ISQLSearchDAO searchDAO, final ISQLAuthorisationInformationProviderDAO authProvider,
+    public SampleContainerSearchManager(final ISQLSearchDAO searchDAO,
+            final ISQLAuthorisationInformationProviderDAO authProvider,
             final IID2PEMapper<Long, Long> idsMapper)
     {
         super(searchDAO, authProvider, idsMapper);
     }
 
-    @Override
-    protected Class<? extends AbstractCompositeSearchCriteria> getParentsSearchCriteriaClass()
-    {
-        return SampleParentsSearchCriteria.class;
-    }
-
     public Set<Long> searchForIDs(final Long userId, final AuthorisationInformation authorisationInformation,
             final SampleContainerSearchCriteria criteria,
             final AbstractCompositeSearchCriteria parentCriteria, final String idsColumnName)
     {
-        return doSearchForIDs(userId, authorisationInformation, criteria, null, idsColumnName, TableMapper.SAMPLE);
+        return super.searchForIDs(userId, authorisationInformation, criteria, idsColumnName, TableMapper.SAMPLE);
     }
 
     @Override
@@ -64,30 +60,10 @@ public class SampleContainerSearchManager extends AbstractCompositeEntitySearchM
         return doSortIDs(ids, sortOptions, TableMapper.SAMPLE);
     }
 
-    @Override
-    protected Class<? extends AbstractCompositeSearchCriteria> getChildrenSearchCriteriaClass()
-    {
-        return SampleChildrenSearchCriteria.class;
-    }
-
-    @Override
-    protected SampleContainerSearchCriteria createEmptyCriteria()
-    {
-        throw new UnsupportedOperationException("This method is not supposed to be called.");
-    }
-
     @Override
     protected Set<Long> doFilterIDsByUserRights(final Set<Long> ids, final AuthorisationInformation authorisationInformation)
     {
         return getAuthProvider().getAuthorisedSamples(ids, authorisationInformation);
     }
 
-    @Override
-    protected Set<Long> getAllIds(final Long userId, final AuthorisationInformation authorisationInformation, final String idsColumnName,
-            final TableMapper tableMapper)
-    {
-        return getSearchDAO().queryDBWithNonRecursiveCriteria(userId, new DummyCompositeSearchCriterion(), tableMapper,
-                idsColumnName, authorisationInformation);
-    }
-
 }

openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/search/translator/TranslationContext.java

@@ -50,6 +50,8 @@ public class TranslationContext
 
     private Map<String, String> dataTypeByPropertyName;
 
+    private Map<String, String> dataTypeByPropertyCode;
+
     private Collection<Long> ids;
 
     private SortOptions<?> sortOptions;
@@ -143,6 +145,14 @@ public class TranslationContext
         this.dataTypeByPropertyName = dataTypeByPropertyName;
     }
 
+    public Map<String, String> getDataTypeByPropertyCode() {
+        return dataTypeByPropertyCode;
+    }
+
+    public void setDataTypeByPropertyCode(Map<String, String> dataTypeByPropertyCode) {
+        this.dataTypeByPropertyCode = dataTypeByPropertyCode;
+    }
+
     public Collection<Long> getIds()
     {
         return ids;

openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/search/translator/condition/AnyPropertySearchConditionTranslator.java

@@ -78,7 +78,7 @@ public class AnyPropertySearchConditionTranslator implements IConditionTranslato
         final String entityTypesSubTableAlias = joinInformation.getSubTableAlias();
 
         sqlBuilder.append(entityTypesSubTableAlias).append(PERIOD).append(joinInformation.getSubTableIdField())
-                .append(SP).append(IS_NOT_NULL).append(SP).append(AND).append(SP);
+                .append(SP).append(IS_NOT_NULL).append(SP).append(AND).append(SP).append(LP);
 
         if (value.getClass() != AnyStringValue.class)
         {
@@ -104,6 +104,8 @@ public class AnyPropertySearchConditionTranslator implements IConditionTranslato
         {
             sqlBuilder.append(TRUE);
         }
+
+        sqlBuilder.append(RP);
     }
 
     private static void appendSamplePropertyComparison(final StringBuilder sqlBuilder,

openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/search/translator/condition/BooleanFieldSearchConditionTranslator.java

@@ -97,7 +97,7 @@ public class BooleanFieldSearchConditionTranslator implements IConditionTranslat
         final String entityTypesSubTableAlias = joinInformation.getSubTableAlias();
 
         sqlBuilder.append(entityTypesSubTableAlias).append(PERIOD).append(joinInformation.getSubTableIdField())
-                .append(SP).append(IS_NOT_NULL).append(SP).append(AND).append(SP);
+                .append(SP).append(IS_NOT_NULL).append(SP).append(AND).append(SP).append(LP);
 
         if (value != null)
         {
@@ -118,6 +118,8 @@ public class BooleanFieldSearchConditionTranslator implements IConditionTranslat
                     .append(BOOLEAN).append(SP).append(EQ).append(SP).append(QU).append(SP).append(END);
             args.add(value);
         }
+
+        sqlBuilder.append(RP);
     }
 
 }

openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/search/translator/condition/DateFieldSearchConditionTranslator.java

@@ -112,7 +112,7 @@ public class DateFieldSearchConditionTranslator implements IConditionTranslator<
                 final String entityTypesSubTableAlias = joinInformation.getSubTableAlias();
 
                 sqlBuilder.append(entityTypesSubTableAlias).append(PERIOD).append(joinInformation.getSubTableIdField())
-                        .append(SP).append(IS_NOT_NULL).append(SP).append(AND).append(SP);
+                        .append(SP).append(IS_NOT_NULL).append(SP).append(AND).append(SP).append(LP);
 
                 sqlBuilder.append(CASE);
                 String casting = dataTypeByPropertyName.get(propertyName);
@@ -139,7 +139,7 @@ public class DateFieldSearchConditionTranslator implements IConditionTranslator<
                     throw new UserFailureException("Property " + propertyName + " is neither of data type "
                             + DataType.DATE + " nor " + DataType.TIMESTAMP + ".");
                 }
-                sqlBuilder.append(SP).append(ELSE).append(SP).append(false).append(SP).append(END);
+                sqlBuilder.append(SP).append(ELSE).append(SP).append(false).append(SP).append(END).append(RP);
 
                 break;
             }

openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/search/translator/condition/NumberFieldSearchConditionTranslator.java

@@ -133,7 +133,7 @@ public class NumberFieldSearchConditionTranslator implements IConditionTranslato
         final String entityTypesSubTableAlias = joinInformation.getSubTableAlias();
 
         sqlBuilder.append(entityTypesSubTableAlias).append(PERIOD).append(joinInformation.getSubTableIdField())
-                .append(SP).append(IS_NOT_NULL).append(SP).append(AND).append(SP);
+                .append(SP).append(IS_NOT_NULL).append(SP).append(AND).append(SP).append(LP);
 
         if (value != null)
         {
@@ -171,6 +171,7 @@ public class NumberFieldSearchConditionTranslator implements IConditionTranslato
 
             sqlBuilder.append(SP).append(ELSE).append(SP).append(false).append(SP).append(END);
         }
+        sqlBuilder.append(RP);
     }
 
 }