diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleListingQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleListingQuery.java
index efbe72b17a0b5fdf47786220cf16a16d2f070abf..aa74188c8a01b176d014c39e19e6285e4c0118db 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleListingQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleListingQuery.java
@@ -87,7 +87,7 @@ public interface ISampleListingQuery extends TransactionQuery, IPropertyListingQ
/**
* Returns the samples for the given <var>groupCode</var>.
*/
- @Select(sql = "select s.id, s.perm_id, s.code, s.expe_id, "
+ @Select(sql = "select s.id, s.perm_id, s.code, s.expe_id, s.grou_id, "
+ " s.registration_timestamp, s.pers_id_registerer, "
+ " s.samp_id_generated_from, s.samp_id_part_of, s.saty_id, s.inva_id "
+ " from samples s join sample_types st on s.saty_id=st.id"
@@ -98,7 +98,7 @@ public interface ISampleListingQuery extends TransactionQuery, IPropertyListingQ
/**
* Returns the samples for the given <var>groupCode</var> that are assigned to an experiment.
*/
- @Select(sql = "select s.id, s.perm_id, s.code, s.saty_id, s.expe_id, "
+ @Select(sql = "select s.id, s.perm_id, s.code, s.saty_id, s.expe_id, s.grou_id, "
+ " s.samp_id_generated_from, s.registration_timestamp, s.modification_timestamp, "
+ " s.pers_id_registerer, s.samp_id_part_of, s.inva_id "
+ " from samples s join groups g on s.grou_id=g.id "
@@ -110,7 +110,7 @@ public interface ISampleListingQuery extends TransactionQuery, IPropertyListingQ
/**
* Returns the samples for the given <var>groupCode</var> and <var>sampleTypeId</var>
*/
- @Select(sql = "select s.id, s.perm_id, s.code, s.expe_id, "
+ @Select(sql = "select s.id, s.perm_id, s.code, s.expe_id, s.grou_id, "
+ " s.registration_timestamp, s.pers_id_registerer, "
+ " s.samp_id_generated_from, s.samp_id_part_of, s.saty_id, s.inva_id "
+ " from samples s join groups g on s.grou_id=g.id "
@@ -123,7 +123,7 @@ public interface ISampleListingQuery extends TransactionQuery, IPropertyListingQ
* Returns the samples for the given <var>groupCode</var> and <var>sampleTypeId</var> that are
* assigned to an experiment.
*/
- @Select(sql = "select s.id, s.perm_id, s.code, s.saty_id, s.expe_id, "
+ @Select(sql = "select s.id, s.perm_id, s.code, s.saty_id, s.expe_id, s.grou_id, "
+ " s.samp_id_generated_from, s.registration_timestamp, s.modification_timestamp, "
+ " s.pers_id_registerer, s.samp_id_part_of, s.inva_id "
+ " from samples s join groups g on s.grou_id=g.id "
@@ -139,7 +139,7 @@ public interface ISampleListingQuery extends TransactionQuery, IPropertyListingQ
/**
* Returns the samples for the given <var>experimentId</var>.
*/
- @Select(sql = "select s.id, s.perm_id, s.code, s.expe_id, "
+ @Select(sql = "select s.id, s.perm_id, s.code, s.expe_id, s.grou_id, "
+ " s.registration_timestamp, s.pers_id_registerer, "
+ " s.samp_id_generated_from, s.samp_id_part_of, s.saty_id, s.inva_id "
+ " from samples s where s.expe_id=?{1}", fetchSize = FETCH_SIZE)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListingWorker.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListingWorker.java
index 1b0a2a56c56d1e221cda62b9093047dcfc77cf18..df836798727163d9994e9b52fd1523193445c487 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListingWorker.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListingWorker.java
@@ -200,19 +200,13 @@ final class SampleListingWorker
{
final StopWatch watch = new StopWatch();
watch.start();
- final Experiment expOrNull = tryLoadExperiment();
- final boolean oneGroupPerSample = isOneGroupPerSamples();
- final Group groupOrNull = oneGroupPerSample ? null : tryLoadGroup(expOrNull);
- loadGroups(); // all groups are needed for parent samples identifiers
+ loadGroups();
loadSampleTypes();
- retrievePrimaryBasicSamples(tryGetIteratorForSamplesByIds(), groupOrNull, oneGroupPerSample);
- retrievePrimaryBasicSamples(tryGetIteratorForGroupSamples(), groupOrNull, oneGroupPerSample);
- retrievePrimaryBasicSamples(tryGetIteratorForSharedSamples(), groupOrNull,
- oneGroupPerSample);
- retrievePrimaryBasicSamples(tryGetIteratorForExperimentSamples(), groupOrNull,
- oneGroupPerSample);
- retrievePrimaryBasicSamples(tryGetIteratorForContainedSamples(), groupOrNull,
- oneGroupPerSample);
+ retrievePrimaryBasicSamples(tryGetIteratorForSamplesByIds());
+ retrievePrimaryBasicSamples(tryGetIteratorForGroupSamples());
+ retrievePrimaryBasicSamples(tryGetIteratorForSharedSamples());
+ retrievePrimaryBasicSamples(tryGetIteratorForExperimentSamples());
+ retrievePrimaryBasicSamples(tryGetIteratorForContainedSamples());
if (operationLog.isDebugEnabled())
{
watch.stop();
@@ -255,6 +249,7 @@ final class SampleListingWorker
private void loadGroups()
{
+ // all groups are needed for parent samples identifiers
final Group[] groups = referencedEntityDAO.getAllGroups(databaseInstanceId);
for (Group group : groups)
{
@@ -263,52 +258,6 @@ final class SampleListingWorker
}
}
- private Experiment tryLoadExperiment()
- {
- final TechId experimentTechId = criteria.getExperimentId();
- if (experimentTechId == null)
- {
- return null;
- }
- return createAndSaveExperiment(experimentTechId.getId(), null);
- }
-
- private Experiment createAndSaveExperiment(final long experimentId, final Group groupOrNull)
- {
- final Experiment experiment = referencedEntityDAO.getExperiment(experimentId);
- experiments.put(experimentId, experiment);
- return experiment;
- }
-
- private boolean isOneGroupPerSamples()
- {
- return criteria.getContainerSampleId() != null || criteria.getSampleIds() != null;
- }
-
- private Group tryLoadGroup(final Experiment expOrNull)
- {
- if (criteria.isIncludeGroup() == false && expOrNull == null)
- {
- return null;
- }
- if (criteria.getGroupCode() != null)
- {
- final Group group = new Group();
- group.setCode(StringEscapeUtils.escapeHtml(criteria.getGroupCode()));
- group.setInstance(databaseInstance);
- group.setId(referencedEntityDAO.getGroupIdForCode(group.getCode()));
- return group;
- } else if (expOrNull != null)
- {
- final Group group = expOrNull.getProject().getGroup();
- group.setId(referencedEntityDAO.getGroupIdForCode(group.getCode()));
- return group;
- } else
- {
- throw new IllegalStateException("No group definition available.");
- }
- }
-
private void loadSampleTypes()
{
final SampleType sampleTypeOrNull = tryGetSingleModeSampleType();
@@ -338,6 +287,13 @@ final class SampleListingWorker
}
+ private Experiment createAndSaveExperiment(final long experimentId)
+ {
+ final Experiment experiment = referencedEntityDAO.getExperiment(experimentId);
+ experiments.put(experimentId, experiment);
+ return experiment;
+ }
+
private SampleType tryGetSingleModeSampleType()
{
final SampleType sampleTypeOrNull = criteria.getSampleType();
@@ -430,23 +386,20 @@ final class SampleListingWorker
}
}
- private void retrievePrimaryBasicSamples(final Iterable<SampleRecord> sampleIteratorOrNull,
- final Group groupOrNull, final boolean oneGroupPerSample)
+ private void retrievePrimaryBasicSamples(final Iterable<SampleRecord> sampleIteratorOrNull)
{
assert sampleList != null;
- retrieveBasicSamples(sampleIteratorOrNull, groupOrNull, baseIndexURL, sampleList,
- oneGroupPerSample);
+ retrieveBasicSamples(sampleIteratorOrNull, baseIndexURL, sampleList);
}
private void retrieveDependentBasicSamples(final Iterable<SampleRecord> sampleIteratorOrNull)
{
- retrieveBasicSamples(sampleIteratorOrNull, null, null, null, true);
+ retrieveBasicSamples(sampleIteratorOrNull, null, null);
}
private void retrieveBasicSamples(final Iterable<SampleRecord> sampleIteratorOrNull,
- final Group groupOrNull, final String baseIndexURLOrNull,
- final List<Sample> sampleListOrNull, final boolean oneGroupPerSample)
+ final String baseIndexURLOrNull, final List<Sample> sampleListOrNull)
{
if (sampleIteratorOrNull == null)
{
@@ -455,9 +408,7 @@ final class SampleListingWorker
final boolean primarySample = (sampleListOrNull != null);
for (SampleRecord row : sampleIteratorOrNull)
{
- final Sample sample =
- createSample(row, groupOrNull, oneGroupPerSample, baseIndexURLOrNull,
- primarySample);
+ final Sample sample = createSample(row, baseIndexURLOrNull, primarySample);
sampleMap.put(sample.getId(), sample);
if (sampleListOrNull != null)
{
@@ -466,8 +417,7 @@ final class SampleListingWorker
}
}
- private Sample createSample(SampleRecord row, final Group groupOrNull,
- final boolean oneGroupPerSample, final String baseIndexURLOrNull,
+ private Sample createSample(SampleRecord row, final String baseIndexURLOrNull,
final boolean primarySample)
{
final Sample sample = new Sample();
@@ -475,23 +425,15 @@ final class SampleListingWorker
sample.setCode(IdentifierHelper.convertCode(row.code, null));
sample.setSubCode(IdentifierHelper.convertSubCode(row.code));
sample.setSampleType(sampleTypes.get(row.saty_id));
- if (oneGroupPerSample)
- {
- if (row.grou_id == null)
- {
- setDatabaseInstance(sample);
- } else
- {
- System.err.println(groupOrNull + " " + groupMap.get(row.grou_id));
- setGroup(sample, groupMap.get(row.grou_id));
- }
- } else if (groupOrNull != null)
+ // set group or instance
+ if (row.grou_id == null)
{
- setGroup(sample, groupOrNull);
+ setDatabaseInstance(sample);
} else
{
- setDatabaseInstance(sample);
+ setGroup(sample, groupMap.get(row.grou_id));
}
+ // set properties needed for primary samples
if (primarySample)
{
sample.setPermId(StringEscapeUtils.escapeHtml(row.perm_id));
@@ -507,9 +449,10 @@ final class SampleListingWorker
sample.setRegistrator(getOrCreateRegistrator(row));
if (row.expe_id != null)
{
- sample.setExperiment(getOrCreateExperiment(row, groupOrNull));
+ sample.setExperiment(getOrCreateExperiment(row));
}
}
+ // prepare loading related samples
if (row.samp_id_generated_from != null & maxSampleParentResolutionDepth > 0)
{
if (samplesAwaitingParentResolution.containsKey(row.id) == false)
@@ -566,12 +509,12 @@ final class SampleListingWorker
}
}
- private Experiment getOrCreateExperiment(SampleRecord row, final Group groupOrNull)
+ private Experiment getOrCreateExperiment(SampleRecord row)
{
Experiment experiment = experiments.get(row.expe_id);
if (experiment == null)
{
- experiment = createAndSaveExperiment(row.expe_id, groupOrNull);
+ experiment = createAndSaveExperiment(row.expe_id);
}
return experiment;
}