From d8106f37ee33eeb09160e46654261b8dbe2809da Mon Sep 17 00:00:00 2001
From: gpawel <gpawel>
Date: Mon, 12 Dec 2011 08:58:57 +0000
Subject: [PATCH] LMS-2701 General Batch Import: still takes forever for 1K
wells and crashes for 100K wells
SVN: 23969
---
.../bo/samplelister/ISampleListingQuery.java | 16 ++++++++
.../bo/samplelister/SampleListingWorker.java | 40 ++++++++++++++++++-
.../basic/dto/ListOrSearchSampleCriteria.java | 19 ++++++++-
.../plugin/generic/server/GenericServer.java | 2 +-
.../server/SampleRegisterOrUpdateUtil.java | 12 +++++-
5 files changed, 85 insertions(+), 4 deletions(-)
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 31dfeab59c6..7b40831a49d 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
@@ -340,6 +340,14 @@ public interface ISampleListingQuery extends TransactionQuery, IPropertyListingQ
{ StringArrayMapper.class }, fetchSize = FETCH_SIZE)
public DataIterator<SampleRecord> getSamplesForCodes(String[] sampleCodes);
+ /**
+ * Returns the non-empty container samples for the given <var>sampleCodes</var>.
+ */
+ @Select(sql = SELECT_FROM_SAMPLES_S
+ + " where s.id in (select samp_id_part_of from samples where samp_id_part_of in (select id from samples where code = any(?{1})))", parameterBindings =
+ { StringArrayMapper.class }, fetchSize = FETCH_SIZE)
+ public DataIterator<SampleRecord> getContainerSamplesForCodes(String[] sampleCodes);
+
/**
* Returns the samples for the given <var>permIds</var>.
*/
@@ -347,6 +355,14 @@ public interface ISampleListingQuery extends TransactionQuery, IPropertyListingQ
{ StringArrayMapper.class }, fetchSize = FETCH_SIZE)
public DataIterator<SampleRecord> getSamplesForPermIds(String[] permIds);
+ /**
+ * Returns the non-empty container samples for the given <var>sampleCodes</var>.
+ */
+ @Select(sql = SELECT_FROM_SAMPLES_S
+ + " where s.id in (select samp_id_part_of from samples where samp_id_part_of in (select id from samples where permId = any(?{1})))", parameterBindings =
+ { StringArrayMapper.class }, fetchSize = FETCH_SIZE)
+ public DataIterator<SampleRecord> getContainerSamplesForPermIds(String[] permIds);
+
//
// Sample Properties
//
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 0426f4d24fa..6e797e6a5c6 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
@@ -44,10 +44,10 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.CodeConverter;
import ch.systemsx.cisd.openbis.generic.shared.basic.PermlinkUtilities;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Deletion;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Deletion;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
@@ -218,7 +218,9 @@ final class SampleListingWorker extends AbstractLister
loadSampleTypes();
retrievePrimaryBasicSamples(tryGetIteratorForSamplesByIds());
retrievePrimaryBasicSamples(tryGetIteratorForSamplesByCodes());
+ retrievePrimaryBasicSamples(tryGetIteratorForContainerSamplesByCodes());
retrievePrimaryBasicSamples(tryGetIteratorForSamplesByPermIds());
+ retrievePrimaryBasicSamples(tryGetIteratorForContainerSamplesByPermIds());
retrievePrimaryBasicSamples(tryGetIteratorForSpaceSamples());
retrievePrimaryBasicSamples(tryGetIteratorForSharedSamples());
retrievePrimaryBasicSamples(tryGetIteratorForExperimentSamples());
@@ -351,6 +353,10 @@ final class SampleListingWorker extends AbstractLister
private Iterable<SampleRecord> tryGetIteratorForSamplesByCodes()
{
+ if (criteria.isSearchForContainerSamplesOnly())
+ {
+ return null;
+ }
String[] codes = criteria.trySampleCodes();
if (codes == null)
{
@@ -359,8 +365,26 @@ final class SampleListingWorker extends AbstractLister
return query.getSamplesForCodes(codes);
}
+ private Iterable<SampleRecord> tryGetIteratorForContainerSamplesByCodes()
+ {
+ if (criteria.isSearchForContainerSamplesOnly())
+ {
+ return null;
+ }
+ String[] codes = criteria.trySampleCodes();
+ if (codes == null)
+ {
+ return null;
+ }
+ return query.getContainerSamplesForCodes(codes);
+ }
+
private Iterable<SampleRecord> tryGetIteratorForSamplesByPermIds()
{
+ if (criteria.isSearchForContainerSamplesOnly())
+ {
+ return null;
+ }
String[] permIds = criteria.trySamplePermIds();
if (permIds == null)
{
@@ -369,6 +393,20 @@ final class SampleListingWorker extends AbstractLister
return query.getSamplesForPermIds(permIds);
}
+ private Iterable<SampleRecord> tryGetIteratorForContainerSamplesByPermIds()
+ {
+ if (false == criteria.isSearchForContainerSamplesOnly())
+ {
+ return null;
+ }
+ String[] permIds = criteria.trySamplePermIds();
+ if (permIds == null)
+ {
+ return null;
+ }
+ return query.getContainerSamplesForPermIds(permIds);
+ }
+
private Iterable<SampleRecord> tryGetIteratorForSpaceSamples()
{
if (criteria.isIncludeSpace() == false)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ListOrSearchSampleCriteria.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ListOrSearchSampleCriteria.java
index cdcd0b8d8a9..65152963b77 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ListOrSearchSampleCriteria.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ListOrSearchSampleCriteria.java
@@ -48,6 +48,8 @@ public final class ListOrSearchSampleCriteria extends ListSampleCriteria
private final String[] permIds;
+ private final boolean searchForContainerSamplesOnly;
+
private boolean enrichDependentSamplesWithProperties = false;
/** Creates criteria that delegates to given {@link ListSampleCriteria}. */
@@ -57,6 +59,7 @@ public final class ListOrSearchSampleCriteria extends ListSampleCriteria
this.listCriteria = listCriteria;
this.sampleCodes = null;
this.permIds = null;
+ this.searchForContainerSamplesOnly = false;
}
/** Creates criteria that delegates to given {@link TrackingSampleCriteria}. */
@@ -66,6 +69,7 @@ public final class ListOrSearchSampleCriteria extends ListSampleCriteria
this.newTrackingCriteria = newTrackingCriteria;
this.sampleCodes = null;
this.permIds = null;
+ this.searchForContainerSamplesOnly = false;
}
/** Creates criteria for detailed search of samples with given ids. */
@@ -75,19 +79,27 @@ public final class ListOrSearchSampleCriteria extends ListSampleCriteria
this.sampleIds = sampleIds;
this.sampleCodes = null;
this.permIds = null;
+ this.searchForContainerSamplesOnly = false;
}
/** Creates criteria for detailed search of samples with codes. */
public ListOrSearchSampleCriteria(final String[] codes, final boolean codesArePermIds)
+ {
+ this(codes, codesArePermIds, false);
+ }
+
+ /** Creates criteria for detailed search of samples with codes. */
+ public ListOrSearchSampleCriteria(String[] codes, boolean codesArePermIds,
+ boolean searchForContainerSamplesOnly)
{
// Need to add the type to disambiguate method signatures for erased generic types.
assert codes != null;
+ this.searchForContainerSamplesOnly = searchForContainerSamplesOnly;
if (codesArePermIds)
{
this.sampleCodes = null;
this.permIds = codes;
-
} else
{
this.sampleCodes = codes;
@@ -104,6 +116,7 @@ public final class ListOrSearchSampleCriteria extends ListSampleCriteria
this.sampleCodes = codes;
this.permIds = permIds;
+ this.searchForContainerSamplesOnly = false;
}
// search
@@ -232,4 +245,8 @@ public final class ListOrSearchSampleCriteria extends ListSampleCriteria
this.enrichDependentSamplesWithProperties = enrichDependentSamplesWithProperties;
}
+ public boolean isSearchForContainerSamplesOnly()
+ {
+ return searchForContainerSamplesOnly;
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
index 2690a9f265a..0848420fe86 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
@@ -322,7 +322,7 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
// for contained samples add container samples codes
codes = SampleRegisterOrUpdateUtil.extractContainerCodes(newSamples);
ListOrSearchSampleCriteria criteria =
- SampleRegisterOrUpdateUtil.createListSamplesByCodeCriteria(codes);
+ SampleRegisterOrUpdateUtil.createListContainerSamplesByCodeCriteria(codes);
List<Sample> existingContainers = sampleLister.list(criteria);
for (Sample s : existingContainers)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/SampleRegisterOrUpdateUtil.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/SampleRegisterOrUpdateUtil.java
index a8c450f4c76..f1f56d39afb 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/SampleRegisterOrUpdateUtil.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/SampleRegisterOrUpdateUtil.java
@@ -228,8 +228,18 @@ public class SampleRegisterOrUpdateUtil
return extractCode(sampleIdentifier.getSampleCode());
} else
{
- SampleIdentifier parsedContainerIdentifier = SampleIdentifierFactory.parse(containerIdentifier);
+ SampleIdentifier parsedContainerIdentifier =
+ SampleIdentifierFactory.parse(containerIdentifier);
return extractCode(parsedContainerIdentifier.getSampleCode());
}
}
+
+ public static ListOrSearchSampleCriteria createListContainerSamplesByCodeCriteria(
+ List<String> codes)
+ {
+ String[] codesAsArray = codes.toArray(new String[0]);
+ ListOrSearchSampleCriteria criteria =
+ new ListOrSearchSampleCriteria(codesAsArray, false, true);
+ return criteria;
+ }
}
--
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