diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/ISampleListingQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/ISampleListingQuery.java
index 3db8e1e751a7ad32c737410e17be91901dbf7d95..30a0d043196334c5e3b649a3d85c68525314b235 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/ISampleListingQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/ISampleListingQuery.java
@@ -41,9 +41,13 @@ public interface ISampleListingQuery extends BaseQuery
+ "s.registration_timestamp as s_registration_timestamp, "
+ "s.modification_timestamp as s_modification_timestamp, sp.code as sp_code, "
+ "st.id as st_id, st.code as st_code, pe.first_name as pe_first_name, "
- + "pe.last_name as pe_last_name, pe.user_id as pe_user_id, pe.email as pe_email "
+ + "pe.last_name as pe_last_name, pe.user_id as pe_user_id, pe.email as pe_email, "
+ + "e.code as exp_code, p.code as proj_code, ps.code as proj_space_code "
+ "from samples as s join sample_types as st on s.saty_id = st.id "
+ "left join spaces as sp on s.space_id = sp.id "
+ + "left join experiments as e on s.expe_id = e.id "
+ + "left join projects as p on e.proj_id = p.id "
+ + "left join spaces as ps on p.space_id = ps.id "
+ "join persons as pe on s.pers_id_registerer = pe.id where s.id = any(?{1}) ", parameterBindings =
{ LongSetMapper.class }, fetchSize = FETCH_SIZE)
public List<SampleRecord> listSamplesByIds(LongSet sampleIDs);
@@ -67,7 +71,7 @@ public interface ISampleListingQuery extends BaseQuery
public List<SampleRelationshipRecord> getDescendants(Long relationshipID, LongSet sampleIDs);
@Select(sql = "with recursive connected_relationships as (select * from sample_relationships "
- + "where relationship_id = ?{1} and sample_id_parent = any(?{2}) "
+ + "where relationship_id = ?{1} and sample_id_child = any(?{2}) "
+ "union select sr.* from connected_relationships as cr "
+ "join sample_relationships as sr on cr.sample_id_parent = sr.sample_id_child) "
+ "select * from connected_relationships", parameterBindings =
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/SampleLister.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/SampleLister.java
index 8389c544ac29e190cbf762b42527051a43bd66a9..53e28f8c2db5735cce07e4ed3ed95f334945609c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/SampleLister.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/SampleLister.java
@@ -108,9 +108,11 @@ public class SampleLister implements ISampleLister
{
descendants = query.getChildren(getRelationShipType(), rootSampleIdSet);
}
+ LongSet descendentIdSet = new LongOpenHashSet();
for (SampleRelationshipRecord relationShip : descendants)
{
sampleIdSet.add(relationShip.sample_id_child);
+ descendentIdSet.add(relationShip.sample_id_child);
}
List<SampleRelationshipRecord> ancestors = Collections.emptyList();
if (fetchOptions.contains(SampleFetchOption.ANCESTORS))
@@ -120,34 +122,72 @@ public class SampleLister implements ISampleLister
{
ancestors = query.getParents(getRelationShipType(), rootSampleIdSet);
}
+ LongSet ancestorIdSet = new LongOpenHashSet();
for (SampleRelationshipRecord relationShip : ancestors)
{
sampleIdSet.add(relationShip.sample_id_parent);
+ ancestorIdSet.add(relationShip.sample_id_parent);
}
- List<SampleRecord> list = query.listSamplesByIds(sampleIdSet);
TableMap<Long, SampleRecord> sampleRecords =
- new TableMap<Long, SampleRecord>(list, ID_EXTRACTOR);
+ getAllSamples(sampleIdSet, rootSampleIdSet, descendentIdSet, ancestorIdSet,
+ fetchOptions);
if (fetchOptions.contains(SampleFetchOption.PROPERTIES))
{
enrichWithProperties(sampleRecords, sampleIdSet);
}
- enrichWithDescendants(descendants, sampleRecords);
- enrichWithAncestors(ancestors, sampleRecords);
+ enrichWithDescendants(descendants, sampleRecords,
+ fetchOptions.contains(SampleFetchOption.DESCENDANTS));
+ enrichWithAncestors(ancestors, sampleRecords,
+ fetchOptions.contains(SampleFetchOption.ANCESTORS));
List<Sample> samples = new ArrayList<Sample>();
for (Long rootSampleID : sampleIDs)
{
SampleRecord sampleRecord = sampleRecords.tryGet(rootSampleID);
if (sampleRecord != null)
{
- samples.add(createSample(sampleRecord, fetchOptions));
+ samples.add(createSample(sampleRecord));
}
}
Collections.sort(samples, SAMPLE_COMPARATOR);
return samples;
}
+ public TableMap<Long, SampleRecord> getAllSamples(LongSet sampleIdSet, LongSet rootSampleIdSet,
+ LongSet descendentIdSet, LongSet ancestorIdSet, EnumSet<SampleFetchOption> fetchOptions)
+ {
+ List<SampleRecord> list = query.listSamplesByIds(sampleIdSet);
+ TableMap<Long, SampleRecord> sampleRecords =
+ new TableMap<Long, SampleRecord>(list, ID_EXTRACTOR);
+ for (SampleRecord sampleRecord : sampleRecords)
+ {
+ sampleRecord.fetchOptions = createAppropriateFetchOptions(fetchOptions);
+ if (rootSampleIdSet.contains(sampleRecord.s_id))
+ {
+ if (fetchOptions.contains(SampleFetchOption.CHILDREN)
+ || fetchOptions.contains(SampleFetchOption.DESCENDANTS))
+ {
+ sampleRecord.fetchOptions.add(SampleFetchOption.CHILDREN);
+ }
+ if (fetchOptions.contains(SampleFetchOption.PARENTS)
+ || fetchOptions.contains(SampleFetchOption.ANCESTORS))
+ {
+ sampleRecord.fetchOptions.add(SampleFetchOption.PARENTS);
+ }
+ } else if (fetchOptions.contains(SampleFetchOption.ANCESTORS)
+ && ancestorIdSet.contains(sampleRecord.s_id))
+ {
+ sampleRecord.fetchOptions.add(SampleFetchOption.PARENTS);
+ } else if (fetchOptions.contains(SampleFetchOption.DESCENDANTS)
+ && descendentIdSet.contains(sampleRecord.s_id))
+ {
+ sampleRecord.fetchOptions.add(SampleFetchOption.CHILDREN);
+ }
+ }
+ return sampleRecords;
+ }
+
public void enrichWithAncestors(List<SampleRelationshipRecord> ancestors,
- TableMap<Long, SampleRecord> sampleRecords)
+ TableMap<Long, SampleRecord> sampleRecords, boolean allAncestors)
{
for (SampleRelationshipRecord ancestor : ancestors)
{
@@ -158,6 +198,10 @@ public class SampleLister implements ISampleLister
if (child.parents == null)
{
child.parents = new LinkedList<SampleRecord>();
+ if (allAncestors)
+ {
+ child.fetchOptions.add(SampleFetchOption.PARENTS);
+ }
}
child.parents.add(parent);
}
@@ -165,7 +209,7 @@ public class SampleLister implements ISampleLister
}
public void enrichWithDescendants(List<SampleRelationshipRecord> descendants,
- TableMap<Long, SampleRecord> sampleRecords)
+ TableMap<Long, SampleRecord> sampleRecords, boolean allDescendants)
{
for (SampleRelationshipRecord descendant : descendants)
{
@@ -176,15 +220,20 @@ public class SampleLister implements ISampleLister
if (parent.children == null)
{
parent.children = new LinkedList<SampleRecord>();
+ if (allDescendants)
+ {
+ parent.fetchOptions.add(SampleFetchOption.CHILDREN);
+ }
}
parent.children.add(child);
}
}
}
- private void enrichWithProperties(TableMap<Long, SampleRecord> sampleRecords, LongSet sampleIDs)
+ private void enrichWithProperties(TableMap<Long, SampleRecord> sampleRecords,
+ LongSet sampleIdSet)
{
- List<PropertyRecord> properties = query.getProperties(sampleIDs);
+ List<PropertyRecord> properties = query.getProperties(sampleIdSet);
for (PropertyRecord propertyRecord : properties)
{
SampleRecord sampleRecord = sampleRecords.tryGet(propertyRecord.entity_id);
@@ -199,7 +248,7 @@ public class SampleLister implements ISampleLister
}
}
- private Sample createSample(SampleRecord sampleRecord, EnumSet<SampleFetchOption> fetchOptions)
+ private Sample createSample(SampleRecord sampleRecord)
{
Sample.SampleInitializer initializer = new Sample.SampleInitializer();
initializer.setId(sampleRecord.s_id);
@@ -221,6 +270,11 @@ public class SampleLister implements ISampleLister
initializer.setRegistrationDetails(new EntityRegistrationDetails(detailsInitializer));
initializer.setSampleTypeId(sampleRecord.st_id);
initializer.setSampleTypeCode(sampleRecord.st_code);
+ if (sampleRecord.exp_code != null)
+ {
+ initializer.setExperimentIdentifierOrNull("/" + sampleRecord.proj_space_code + "/"
+ + sampleRecord.proj_code + "/" + sampleRecord.exp_code);
+ }
Map<String, String> properties = sampleRecord.properties;
if (properties != null)
{
@@ -229,36 +283,14 @@ public class SampleLister implements ISampleLister
initializer.putProperty(entry.getKey(), entry.getValue());
}
}
- EnumSet<SampleFetchOption> rootFetchOptions = createAppropriateFetchOptions(fetchOptions);
- if (fetchOptions.contains(SampleFetchOption.CHILDREN)
- || fetchOptions.contains(SampleFetchOption.DESCENDANTS))
- {
- rootFetchOptions.add(SampleFetchOption.CHILDREN);
- }
- if (fetchOptions.contains(SampleFetchOption.PARENTS)
- || fetchOptions.contains(SampleFetchOption.ANCESTORS))
- {
- rootFetchOptions.add(SampleFetchOption.PARENTS);
- }
- initializer.setRetrievedFetchOptions(rootFetchOptions);
+ initializer.setRetrievedFetchOptions(sampleRecord.fetchOptions);
if (sampleRecord.children != null)
{
- EnumSet<SampleFetchOption> childrenOptions =
- createAppropriateFetchOptions(fetchOptions);
- if (fetchOptions.contains(SampleFetchOption.DESCENDANTS))
- {
- childrenOptions.add(SampleFetchOption.CHILDREN);
- }
- initializer.setChildren(createChildren(sampleRecord.children, childrenOptions));
+ initializer.setChildren(createChildren(sampleRecord.children));
}
if (sampleRecord.parents != null)
{
- EnumSet<SampleFetchOption> parentsOptions = createAppropriateFetchOptions(fetchOptions);
- if (fetchOptions.contains(SampleFetchOption.ANCESTORS))
- {
- parentsOptions.add(SampleFetchOption.PARENTS);
- }
- initializer.setParents(createParents(sampleRecord.parents, parentsOptions));
+ initializer.setParents(createParents(sampleRecord.parents));
}
return new Sample(initializer);
}
@@ -271,25 +303,23 @@ public class SampleLister implements ISampleLister
: SampleFetchOption.BASIC);
}
- private List<Sample> createChildren(List<SampleRecord> childRecords,
- EnumSet<SampleFetchOption> fetchOptions)
+ private List<Sample> createChildren(List<SampleRecord> childRecords)
{
List<Sample> children = new ArrayList<Sample>();
for (SampleRecord childRecord : childRecords)
{
- children.add(createSample(childRecord, fetchOptions));
+ children.add(createSample(childRecord));
}
Collections.sort(children, SAMPLE_COMPARATOR);
return children;
}
- private List<Sample> createParents(List<SampleRecord> parentRecords,
- EnumSet<SampleFetchOption> fetchOptions)
+ private List<Sample> createParents(List<SampleRecord> parentRecords)
{
List<Sample> parents = new ArrayList<Sample>();
for (SampleRecord parentRecord : parentRecords)
{
- parents.add(createSample(parentRecord, fetchOptions));
+ parents.add(createSample(parentRecord));
}
Collections.sort(parents, SAMPLE_COMPARATOR);
return parents;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/SampleRecord.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/SampleRecord.java
index c66cec766fcd28ef2b80cea4500ee047e69e5450..717e4a743b0432f0776165e3521272addbb53b22 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/SampleRecord.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/SampleRecord.java
@@ -17,9 +17,12 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo.fetchoptions.samplelister;
import java.util.Date;
+import java.util.EnumSet;
import java.util.List;
import java.util.Map;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleFetchOption;
+
/**
* @author Franz-Josef Elmer
*/
@@ -50,10 +53,18 @@ public class SampleRecord
public String pe_email;
+ public String exp_code;
+
+ public String proj_code;
+
+ public String proj_space_code;
+
public List<SampleRecord> children;
public List<SampleRecord> parents;
public Map<String, String> properties;
+ public EnumSet<SampleFetchOption> fetchOptions;
+
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/v1/GeneralInformationServiceTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/v1/GeneralInformationServiceTest.java
index 449004d45b1dea2d98ba6c6aaec32a2b5c70de8f..91b3e8dfbbd95157ca8e2ed9c4ac0d3e9088435f 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/v1/GeneralInformationServiceTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/v1/GeneralInformationServiceTest.java
@@ -191,6 +191,149 @@ public class GeneralInformationServiceTest extends SystemTestCase
assertEntities("[]", samples);
}
+ @Test
+ public void testSearchForSamplesWithParents()
+ {
+ SearchCriteria searchCriteria = new SearchCriteria();
+ searchCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.TYPE,
+ "DILUTION_PLATE"));
+
+ EnumSet<SampleFetchOption> fetchOptions =
+ EnumSet.of(SampleFetchOption.PROPERTIES, SampleFetchOption.PARENTS);
+ List<Sample> samples =
+ generalInformationService.searchForSamples(sessionToken, searchCriteria,
+ fetchOptions);
+
+ assertEntities("[/CISD/3V-125, /CISD/3V-126, /CISD/DP1-A, /CISD/DP1-B, /CISD/DP2-A, /DP]",
+ samples);
+ assertEquals(fetchOptions, samples.get(0).getRetrievedFetchOptions());
+ List<Sample> parents = samples.get(0).getParents();
+ assertEntities("[/CISD/MP002-1]", parents);
+ assertEquals("MP002-1", parents.get(0).getCode());
+ assertEquals(EnumSet.of(SampleFetchOption.PROPERTIES), parents.get(0)
+ .getRetrievedFetchOptions());
+ assertEquals("{PLATE_GEOMETRY=384_WELLS_16X24}", parents.get(0).getProperties().toString());
+ }
+
+ @Test
+ public void testSearchForSamplesWithParentsButNoProperties()
+ {
+ SearchCriteria searchCriteria = new SearchCriteria();
+ searchCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.TYPE,
+ "DILUTION_PLATE"));
+
+ EnumSet<SampleFetchOption> fetchOptions = EnumSet.of(SampleFetchOption.PARENTS);
+ List<Sample> samples =
+ generalInformationService.searchForSamples(sessionToken, searchCriteria,
+ fetchOptions);
+
+ assertEntities("[/CISD/3V-125, /CISD/3V-126, /CISD/DP1-A, /CISD/DP1-B, /CISD/DP2-A, /DP]",
+ samples);
+ assertEquals(EnumSet.of(SampleFetchOption.BASIC, SampleFetchOption.PARENTS), samples.get(0)
+ .getRetrievedFetchOptions());
+ assertEquals(null, samples.get(0).getExperimentIdentifierOrNull());
+ assertEquals("{}", samples.get(0).getProperties().toString());
+ List<Sample> parents = samples.get(0).getParents();
+ assertEntities("[/CISD/MP002-1]", parents);
+ assertEquals("MP002-1", parents.get(0).getCode());
+ assertEquals(EnumSet.of(SampleFetchOption.BASIC), parents.get(0).getRetrievedFetchOptions());
+ assertEquals("{}", parents.get(0).getProperties().toString());
+ }
+
+ @Test
+ public void testSearchForSamplesWithParentsAndDescendentsButNoProperties()
+ {
+ SearchCriteria searchCriteria = new SearchCriteria();
+ searchCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.TYPE,
+ "DILUTION_PLATE"));
+
+ EnumSet<SampleFetchOption> fetchOptions =
+ EnumSet.of(SampleFetchOption.PARENTS, SampleFetchOption.DESCENDANTS);
+ List<Sample> samples =
+ generalInformationService.searchForSamples(sessionToken, searchCriteria,
+ fetchOptions);
+
+ assertEntities("[/CISD/3V-125, /CISD/3V-126, /CISD/DP1-A, /CISD/DP1-B, /CISD/DP2-A, /DP]",
+ samples);
+ assertEquals(EnumSet.of(SampleFetchOption.BASIC, SampleFetchOption.PARENTS,
+ SampleFetchOption.CHILDREN), samples.get(0).getRetrievedFetchOptions());
+ assertEquals(null, samples.get(0).getExperimentIdentifierOrNull());
+ assertEquals("{}", samples.get(0).getProperties().toString());
+ List<Sample> parents = samples.get(0).getParents();
+ assertEntities("[/CISD/MP002-1]", parents);
+ assertEquals("MP002-1", parents.get(0).getCode());
+ assertEquals(EnumSet.of(SampleFetchOption.BASIC), parents.get(0).getRetrievedFetchOptions());
+ assertEquals("{}", parents.get(0).getProperties().toString());
+ List<Sample> children = samples.get(0).getChildren();
+ assertEntities("[/CISD/3VCP5, /CISD/3VCP6, /CISD/3VCP7, /CISD/3VCP8]", children);
+ assertEquals("3VCP5", children.get(0).getCode());
+ assertEquals(EnumSet.of(SampleFetchOption.BASIC, SampleFetchOption.CHILDREN),
+ children.get(0).getRetrievedFetchOptions());
+ assertEquals("{}", children.get(0).getProperties().toString());
+ assertEntities("[]", children.get(0).getChildren());
+ }
+
+ @Test
+ public void testSearchForSamplesWithAncestors()
+ {
+ SearchCriteria searchCriteria = new SearchCriteria();
+ searchCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE,
+ "3VCP*"));
+
+ EnumSet<SampleFetchOption> fetchOptions =
+ EnumSet.of(SampleFetchOption.PROPERTIES, SampleFetchOption.ANCESTORS);
+ List<Sample> samples =
+ generalInformationService.searchForSamples(sessionToken, searchCriteria,
+ fetchOptions);
+
+ assertEntities("[/CISD/3VCP5, /CISD/3VCP6, /CISD/3VCP7, /CISD/3VCP8]", samples);
+ assertEquals(EnumSet.of(SampleFetchOption.PROPERTIES, SampleFetchOption.PARENTS), samples
+ .get(0).getRetrievedFetchOptions());
+ assertEquals("/CISD/NEMO/EXP10", samples.get(0).getExperimentIdentifierOrNull());
+ List<Sample> parents = samples.get(0).getParents();
+ assertEntities("[/CISD/3V-125]", parents);
+ assertEquals("3V-125", parents.get(0).getCode());
+ assertEquals(EnumSet.of(SampleFetchOption.PROPERTIES, SampleFetchOption.PARENTS), parents
+ .get(0).getRetrievedFetchOptions());
+ List<Sample> grandParents = parents.get(0).getParents();
+ assertEntities("[/CISD/MP002-1]", grandParents);
+ assertEquals("MP002-1", grandParents.get(0).getCode());
+ assertEquals(EnumSet.of(SampleFetchOption.PROPERTIES, SampleFetchOption.PARENTS),
+ grandParents.get(0).getRetrievedFetchOptions());
+ assertEquals("{PLATE_GEOMETRY=384_WELLS_16X24}", grandParents.get(0).getProperties()
+ .toString());
+ assertEntities("[]", grandParents.get(0).getParents());
+ }
+
+ @Test
+ public void testSearchForSamplesWithDescendants()
+ {
+ SearchCriteria searchCriteria = new SearchCriteria();
+ searchCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE,
+ "MP002-1 "));
+
+ EnumSet<SampleFetchOption> fetchOptions =
+ EnumSet.of(SampleFetchOption.PROPERTIES, SampleFetchOption.DESCENDANTS);
+ List<Sample> samples =
+ generalInformationService.searchForSamples(sessionToken, searchCriteria,
+ fetchOptions);
+
+ assertEntities("[/CISD/MP002-1]", samples);
+ assertEquals(EnumSet.of(SampleFetchOption.PROPERTIES, SampleFetchOption.CHILDREN), samples
+ .get(0).getRetrievedFetchOptions());
+ List<Sample> children = samples.get(0).getChildren();
+ assertEntities("[/CISD/3V-125, /CISD/3V-126]", children);
+ assertEquals(EnumSet.of(SampleFetchOption.PROPERTIES, SampleFetchOption.CHILDREN), children
+ .get(0).getRetrievedFetchOptions());
+ List<Sample> grandChildren = children.get(0).getChildren();
+ assertEntities("[/CISD/3VCP5, /CISD/3VCP6, /CISD/3VCP7, /CISD/3VCP8]", grandChildren);
+ assertEquals("3VCP5", grandChildren.get(0).getCode());
+ assertEquals(EnumSet.of(SampleFetchOption.PROPERTIES, SampleFetchOption.CHILDREN),
+ grandChildren.get(0).getRetrievedFetchOptions());
+ assertEquals("{}", grandChildren.get(0).getProperties().toString());
+ assertEntities("[]", grandChildren.get(0).getChildren());
+ }
+
@Test
public void testListSamplesForExperiment()
{