From 807c07c882c79467893c75b2148d62c25660bebe Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Thu, 27 May 2010 07:38:05 +0000
Subject: [PATCH] LMS-1544 Added ability to search for samples by sample codes.
SVN: 16132
---
.../bo/samplelister/ISampleListingQuery.java | 26 +++--
.../bo/samplelister/SampleListingWorker.java | 11 +++
.../dataaccess/db/SimpleSQLStringArray.java | 98 +++++++++++++++++++
.../db/SimpleSQLStringArrayString.java | 53 ++++++++++
.../dataaccess/db/StringArrayMapper.java | 54 ++++++++++
.../basic/dto/ListOrSearchSampleCriteria.java | 20 +++-
6 files changed, 255 insertions(+), 7 deletions(-)
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SimpleSQLStringArray.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SimpleSQLStringArrayString.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/StringArrayMapper.java
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 ba087160e66..54eae526952 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
@@ -38,6 +38,7 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.common.MaterialEntity
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.VocabularyTermRecord;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.entity.ExperimentProjectGroupCodeRecord;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.LongSetMapper;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.StringArrayMapper;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
/**
@@ -151,8 +152,7 @@ public interface ISampleListingQuery extends TransactionQuery, IPropertyListingQ
+ " 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 "
- + " where s.expe_id is not null and g.dbin_id=?{1} "
- + " order by s.code", fetchSize = FETCH_SIZE)
+ + " where s.expe_id is not null and g.dbin_id=?{1} " + " order by s.code", fetchSize = FETCH_SIZE)
public DataIterator<SampleRecord> getAllGroupSamplesWithExperiment(long dbInstanceId);
/**
@@ -162,8 +162,7 @@ public interface ISampleListingQuery extends TransactionQuery, IPropertyListingQ
+ " 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 "
- + " where g.dbin_id=?{1} and s.saty_id=?{2}"
- + " order by s.code", fetchSize = FETCH_SIZE)
+ + " where g.dbin_id=?{1} and s.saty_id=?{2}" + " order by s.code", fetchSize = FETCH_SIZE)
public DataIterator<SampleRecord> getAllGroupSamplesForSampleType(long dbInstanceId,
long sampleTypeId);
@@ -222,8 +221,7 @@ public interface ISampleListingQuery extends TransactionQuery, IPropertyListingQ
+ " select samp_id from sample_properties sp where sp.stpt_id in ("
+ " select id from sample_type_property_types stpt where stpt.prty_id = "
+ " (select id from property_types where code=?{2})"
- + " ) and value=?{3}"
- + " ) and not id = any(?{4})", parameterBindings =
+ + " ) and value=?{3}" + " ) and not id = any(?{4})", parameterBindings =
{ TypeMapper.class, TypeMapper.class, TypeMapper.class, LongSetMapper.class }, fetchSize = FETCH_SIZE)
public DataIterator<SampleRecord> getSamplesWithPropertyValue(long sampleTypeId,
String propertyTypeCode, String propertyValue, LongSet sampleIds);
@@ -299,6 +297,22 @@ public interface ISampleListingQuery extends TransactionQuery, IPropertyListingQ
{ LongSetMapper.class }, fetchSize = FETCH_SIZE)
public DataIterator<SampleRecord> getSamples(LongSet sampleIds);
+ /**
+ * Returns the samples for the given <var>sampleCodes</var>.
+ */
+ @Select(sql = "select s.id, s.perm_id, s.code, s.expe_id, s.grou_id, s.dbin_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.code = any(?{1})", parameterBindings =
+ { StringArrayMapper.class }, fetchSize = FETCH_SIZE)
+ public DataIterator<SampleRecord> getSamplesForCodes(String[] sampleCodes);
+
+ @Select(sql = "select s.id, s.perm_id, s.code, s.expe_id, s.grou_id, s.dbin_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.code in (?{1})", fetchSize = FETCH_SIZE)
+ public DataIterator<SampleRecord> getSamples(String sampleCodesString);
+
//
// 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 0fc6ce7eb91..bcce95c1723 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
@@ -209,6 +209,7 @@ final class SampleListingWorker
loadGroups();
loadSampleTypes();
retrievePrimaryBasicSamples(tryGetIteratorForSamplesByIds());
+ retrievePrimaryBasicSamples(tryGetIteratorForSamplesByCodes());
retrievePrimaryBasicSamples(tryGetIteratorForGroupSamples());
retrievePrimaryBasicSamples(tryGetIteratorForSharedSamples());
retrievePrimaryBasicSamples(tryGetIteratorForExperimentSamples());
@@ -335,6 +336,16 @@ final class SampleListingWorker
return query.getSamples(new LongOpenHashSet(ids));
}
+ private Iterable<SampleRecord> tryGetIteratorForSamplesByCodes()
+ {
+ String[] codes = criteria.trySampleCodes();
+ if (codes == null)
+ {
+ return null;
+ }
+ return query.getSamplesForCodes(codes);
+ }
+
private Iterable<SampleRecord> tryGetIteratorForGroupSamples()
{
if (criteria.isIncludeSpace() == false)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SimpleSQLStringArray.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SimpleSQLStringArray.java
new file mode 100644
index 00000000000..1734fb13f8f
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SimpleSQLStringArray.java
@@ -0,0 +1,98 @@
+/*
+ * Copyright 2009 ETH Zuerich, CISD
+ *
+ * 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.server.dataaccess.db;
+
+import java.sql.SQLException;
+import java.sql.Types;
+
+/**
+ * A simple implementation of {@link java.sql.Array} for <code>String[]</code>.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+class SimpleSQLStringArray extends AbstractSQLArray
+{
+
+ private final String[] value;
+
+ SimpleSQLStringArray(String[] array)
+ {
+ value = array;
+ }
+
+ /**
+ * Get the object array.
+ *
+ * @return the object array
+ */
+ public Object getArray()
+ {
+ return value;
+ }
+
+ /**
+ * Get the base type of this array.
+ *
+ * @return VARCHAR
+ */
+ public int getBaseType()
+ {
+ return Types.VARCHAR;
+ }
+
+ /**
+ * Get the base type name of this array.
+ *
+ * @return "varchar"
+ */
+ public String getBaseTypeName()
+ {
+ return "varchar";
+ }
+
+ @Override
+ public void free() throws SQLException
+ {
+ // do nothing
+ }
+
+ @Override
+ /*
+ * * For the PostgreSQL JDBC driver to work with this class, this method needs to return
+ * '{x,y,z,...}'.
+ */
+ public String toString()
+ {
+ final StringBuilder builder = new StringBuilder();
+ builder.append("{");
+ for (String v : value)
+ {
+ builder.append("\"");
+ builder.append(v);
+ builder.append("\"");
+ builder.append(',');
+ }
+ // Remove the trailing ','
+ if (value.length > 0)
+ {
+ builder.setLength(builder.length() - 1);
+ }
+ builder.append("}");
+ return builder.toString();
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SimpleSQLStringArrayString.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SimpleSQLStringArrayString.java
new file mode 100644
index 00000000000..116cf71a474
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SimpleSQLStringArrayString.java
@@ -0,0 +1,53 @@
+/*
+ * Copyright 2009 ETH Zuerich, CISD
+ *
+ * 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.server.dataaccess.db;
+
+
+/**
+ * A helper class for converting a <code>String[]</code> to a valid array String in SQL.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class SimpleSQLStringArrayString
+{
+
+ private final String[] value;
+
+ public SimpleSQLStringArrayString(String[] array)
+ {
+ value = array;
+ }
+
+ @Override
+ public String toString()
+ {
+ final StringBuilder builder = new StringBuilder();
+ for (String v : value)
+ {
+ builder.append("\'");
+ builder.append(v);
+ builder.append("\'");
+ builder.append(',');
+ }
+ if (value.length > 0)
+ {
+ builder.setLength(builder.length() - 1);
+ }
+ return builder.toString();
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/StringArrayMapper.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/StringArrayMapper.java
new file mode 100644
index 00000000000..f63528433b6
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/StringArrayMapper.java
@@ -0,0 +1,54 @@
+/*
+ * Copyright 2009 ETH Zuerich, CISD
+ *
+ * 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.server.dataaccess.db;
+
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.sql.Types;
+
+import net.lemnik.eodsql.TypeMapper;
+
+/**
+ * A class for mapping <code>String[]</code> to {@link java.sql.Array}.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class StringArrayMapper implements TypeMapper<String[]>
+{
+ public String[] get(ResultSet results, int column) throws SQLException
+ {
+ return (String[]) results.getArray(column).getArray();
+ }
+
+ public void set(PreparedStatement statement, int column, String[] obj) throws SQLException
+ {
+ if (obj != null)
+ {
+ statement.setArray(column, new SimpleSQLStringArray(obj));
+ } else
+ {
+ statement.setNull(column, Types.ARRAY);
+ }
+ }
+
+ public void set(ResultSet results, int column, String[] obj) throws SQLException
+ {
+ results.updateArray(column, new SimpleSQLStringArray(obj));
+ }
+
+}
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 422357613c3..3cd6c6b8740 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
@@ -43,6 +43,8 @@ public final class ListOrSearchSampleCriteria extends ListSampleCriteria
private Collection<Long> sampleIds;
+ private final String[] sampleCodes;
+
private boolean enrichDependentSamplesWithProperties = false;
/** Creates criteria that delegates to given {@link ListSampleCriteria}. */
@@ -50,6 +52,7 @@ public final class ListOrSearchSampleCriteria extends ListSampleCriteria
{
assert listCriteria != null;
this.listCriteria = listCriteria;
+ this.sampleCodes = null;
}
/** Creates criteria that delegates to given {@link TrackingSampleCriteria}. */
@@ -57,6 +60,7 @@ public final class ListOrSearchSampleCriteria extends ListSampleCriteria
{
assert newTrackingCriteria != null;
this.newTrackingCriteria = newTrackingCriteria;
+ this.sampleCodes = null;
}
/** Creates criteria for detailed search of samples with given ids. */
@@ -64,6 +68,16 @@ public final class ListOrSearchSampleCriteria extends ListSampleCriteria
{
assert sampleIds != null;
this.sampleIds = sampleIds;
+ this.sampleCodes = null;
+ }
+
+ /** Creates criteria for detailed search of samples with codes. */
+ public ListOrSearchSampleCriteria(final String[] sampleCodes)
+ {
+ // Need to add the type to disambiguate method signatures for erased generic types.
+ assert sampleCodes != null;
+
+ this.sampleCodes = sampleCodes;
}
// search
@@ -73,6 +87,11 @@ public final class ListOrSearchSampleCriteria extends ListSampleCriteria
return sampleIds;
}
+ public String[] trySampleCodes()
+ {
+ return sampleCodes;
+ }
+
// delegation to NewTrackingSampleCriteria
public String getSampleTypeCode()
@@ -149,5 +168,4 @@ public final class ListOrSearchSampleCriteria extends ListSampleCriteria
{
this.enrichDependentSamplesWithProperties = enrichDependentSamplesWithProperties;
}
-
}
--
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