From 3a6075c8f096e06ba635c76b9ee7c61b348beb57 Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Tue, 21 Jun 2011 13:02:03 +0000
Subject: [PATCH] LMS-2280 ranks in "gene in all assays" view
SVN: 21780
---
.../application/DisplayTypeIDGenerator.java | 6 +-
...aterialFeaturesFromAllExperimentsGrid.java | 2 +-
.../MaterialReplicaFeatureSummaryGrid.java | 2 +-
.../MaterialReplicaSummarySection.java | 2 +-
...tureVectorsFromAllExperimentsProvider.java | 21 +-
.../resultset/ScreeningProviderMessages.java | 2 +-
.../screening/server/ScreeningServer.java | 3 +-
.../BasicWellContentQueryResult.java | 36 +++
.../ExperimentReferenceQueryResult.java | 37 +++
.../server/dataaccess/IScreeningQuery.java | 58 ++++-
.../dataaccess/PatternMatchingUtils.java | 35 +++
.../dataaccess/WellContentQueryResult.java | 17 +-
.../ExperimentFeatureVectorSummaryLoader.java | 5 +-
...alAllAssaysFeatureVectorSummaryLoader.java | 230 +++++++++++-------
.../MaterialFeatureVectorSummaryLoader.java | 8 +-
.../server/logic/WellContentLoader.java | 18 +-
.../logic/WellFeatureCollectionLoader.java | 2 +
.../logic/WellReplicaSummaryCalculator.java | 66 +++--
.../dto/MaterialIdFeatureVectorSummary.java | 6 +-
.../dto/ExperimentFeatureVectorSummary.java | 1 +
.../dto/MaterialFeatureVectorSummary.java | 4 +-
...erialFeatureVectorSummaryParametrized.java | 16 +-
.../MaterialSimpleFeatureVectorSummary.java | 12 +-
.../basic/dto/MaterialSummarySettings.java | 12 +-
.../shared/basic/dto/ScreeningConstants.java | 3 -
.../server/dataaccess/ScreeningDAOTest.java | 15 ++
.../WellReplicaSummaryCalculatorTest.java | 6 +-
27 files changed, 451 insertions(+), 174 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/BasicWellContentQueryResult.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/ExperimentReferenceQueryResult.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/PatternMatchingUtils.java
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/DisplayTypeIDGenerator.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/DisplayTypeIDGenerator.java
index 43d41a1ff05..a0929d89762 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/DisplayTypeIDGenerator.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/DisplayTypeIDGenerator.java
@@ -35,17 +35,15 @@ public enum DisplayTypeIDGenerator implements IDisplayTypeIDGenerator
PLATE_LOCATIONS_MATERIAL_SECTION("plate-locations-material-section"),
- REPLICA_SUMMARY_MATERIAL_SECTION("replica-summary-material-section"),
-
EXPERIMENT_PLATE_LOCATIONS_SECTION("plate-locations-experiment-section"),
EXPERIMENT_WELL_MATERIALS_SECTION("experiment-well-materials-section"),
EXPERIMENT_FEATURE_VECTOR_SUMMARY_SECTION("experiment-feature-vector-summary-section"),
- MATERIAL_REPLICA_FEATURE_SUMMARY_SECTION("material-replica-feature-summary-section"),
+ MATERIAL_REPLICA_SUMMARY_SECTION("material-replica-summary-section"),
- MATERIAL_FEATURES_FROM_ALL_EXPERIMENTS_SECTION("material-features-from-all-experiments-section");
+ MATERIAL_FEATURES_FROM_ALL_EXPERIMENTS_SECTION("material-features-all-experiments-section");
private final String genericNameOrPrefix;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialFeaturesFromAllExperimentsGrid.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialFeaturesFromAllExperimentsGrid.java
index b133d560620..3202c0f4bec 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialFeaturesFromAllExperimentsGrid.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialFeaturesFromAllExperimentsGrid.java
@@ -76,7 +76,7 @@ public class MaterialFeaturesFromAllExperimentsGrid extends
ExperimentSearchByProjectCriteria experimentSearchCriteria)
{
super(viewContext.getCommonViewContext(), BROWSER_ID, true,
- DisplayTypeIDGenerator.MATERIAL_REPLICA_FEATURE_SUMMARY_SECTION);
+ DisplayTypeIDGenerator.MATERIAL_REPLICA_SUMMARY_SECTION);
this.screeningViewContext = viewContext;
this.material = material;
this.experimentSearchCriteria = experimentSearchCriteria;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaFeatureSummaryGrid.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaFeatureSummaryGrid.java
index 002728f9541..5824e787ae9 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaFeatureSummaryGrid.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaFeatureSummaryGrid.java
@@ -64,7 +64,7 @@ public class MaterialReplicaFeatureSummaryGrid extends
TechId experimentId, TechId materialId)
{
super(viewContext.getCommonViewContext(), BROWSER_ID, true,
- DisplayTypeIDGenerator.MATERIAL_REPLICA_FEATURE_SUMMARY_SECTION);
+ DisplayTypeIDGenerator.MATERIAL_REPLICA_SUMMARY_SECTION);
this.specificViewContext = viewContext;
this.experimentId = experimentId;
this.materialId = materialId;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaSummarySection.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaSummarySection.java
index b96b8c2a36a..7e6b9072041 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaSummarySection.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaSummarySection.java
@@ -39,7 +39,7 @@ class MaterialReplicaSummarySection extends TabContent
this.restrictGlobalScopeLinkToProject = restrictGlobalScopeLinkToProject;
setHeaderVisible(false);
- setIds(DisplayTypeIDGenerator.REPLICA_SUMMARY_MATERIAL_SECTION);
+ setIds(DisplayTypeIDGenerator.MATERIAL_REPLICA_SUMMARY_SECTION);
}
@Override
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/resultset/MaterialFeatureVectorsFromAllExperimentsProvider.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/resultset/MaterialFeatureVectorsFromAllExperimentsProvider.java
index c654ca05107..73bf0219c3d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/resultset/MaterialFeatureVectorsFromAllExperimentsProvider.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/resultset/MaterialFeatureVectorsFromAllExperimentsProvider.java
@@ -86,7 +86,11 @@ public class MaterialFeatureVectorsFromAllExperimentsProvider extends
{
for (CodeAndLabel codeAndLabel : summary.getFeatureDescriptions())
{
- columnGroup.column(codeAndLabel.getCode()).withTitle(codeAndLabel.getLabel());
+ columnGroup.column(getFeatureValueColumnId(codeAndLabel)).withTitle(
+ codeAndLabel.getLabel());
+ columnGroup.column(getFeatureRankColumnId(codeAndLabel)).withTitle(
+ ScreeningProviderMessages.RANK_COLUMN_MSG);
+
}
}
}
@@ -100,11 +104,24 @@ public class MaterialFeatureVectorsFromAllExperimentsProvider extends
builder.column(EXPERIMENT).addString(experiment.getCode());
float[] features = row.getFeatureVectorSummary();
+ int[] ranks = row.getFeatureVectorRanks();
List<CodeAndLabel> descriptions = row.getFeatureDescriptions();
for (int i = 0; i < features.length; i++)
{
CodeAndLabel description = descriptions.get(i);
- builder.column(description.getCode()).addDouble((double) features[i]);
+ builder.column(getFeatureValueColumnId(description)).addDouble((double) features[i]);
+ builder.column(getFeatureRankColumnId(description)).addInteger(new Long(ranks[i]));
}
}
+
+ private String getFeatureValueColumnId(CodeAndLabel codeAndLabel)
+ {
+ return "value-" + codeAndLabel.getCode();
+ }
+
+ private String getFeatureRankColumnId(CodeAndLabel codeAndLabel)
+ {
+ return "rank-" + codeAndLabel.getCode();
+ }
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/resultset/ScreeningProviderMessages.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/resultset/ScreeningProviderMessages.java
index a0487553756..67d475733da 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/resultset/ScreeningProviderMessages.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/resultset/ScreeningProviderMessages.java
@@ -23,7 +23,7 @@ package ch.systemsx.cisd.openbis.plugin.screening.client.web.server.resultset;
*/
class ScreeningProviderMessages
{
- public static final String RANK_COLUMN_MSG = " Rank";
+ public static final String RANK_COLUMN_MSG = "Rank";
public static String getRankColumnHeader(int numberOfMaterialsInExperiment)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
index 953cfef8ebd..558b4df4dad 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
@@ -349,8 +349,9 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
MaterialSummarySettings settings = new MaterialSummarySettings();
settings.setAggregationType(MaterialReplicaSummaryAggregationType.MEDIAN);
settings.setFeatureCodes(new ArrayList<String>());
+ settings.setReplicaMatrialTypePatterns(new String[]
+ { "GENE", "CONTROL", "COMPOUND" });
settings.setMaterialDetailsPropertyType(ScreeningConstants.GENE_SYMBOLS);
- settings.setReplicaMatrialTypePatterns(ScreeningConstants.REPLICA_METERIAL_TYPE_PATTERN);
settings.setBiologicalReplicatePropertyTypeCodes("CONCENTRATION", "SIRNA");
return settings;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/BasicWellContentQueryResult.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/BasicWellContentQueryResult.java
new file mode 100644
index 00000000000..76182c72cab
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/BasicWellContentQueryResult.java
@@ -0,0 +1,36 @@
+/*
+ * Copyright 2011 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.plugin.screening.server.dataaccess;
+
+import ch.rinn.restrictions.Private;
+
+/**
+ * Basic information about well content which allows to compute rankings.
+ *
+ * @author Tomasz Pylak
+ */
+@Private
+public class BasicWellContentQueryResult
+{
+ public String well_code;
+
+ public String plate_perm_id;
+
+ public String exp_perm_id;
+
+ public long material_content_id;
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/ExperimentReferenceQueryResult.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/ExperimentReferenceQueryResult.java
new file mode 100644
index 00000000000..377299c9bed
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/ExperimentReferenceQueryResult.java
@@ -0,0 +1,37 @@
+/*
+ * Copyright 2011 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.plugin.screening.server.dataaccess;
+
+/**
+ * A pointer to the experiment.
+ *
+ * @author Tomasz Pylak
+ */
+public class ExperimentReferenceQueryResult
+{
+ public long exp_id;
+
+ public String exp_code;
+
+ public String exp_type_code;
+
+ public String exp_perm_id;
+
+ public String proj_code;
+
+ public String space_code;
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/IScreeningQuery.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/IScreeningQuery.java
index fc63e1dd5ee..8fbef51d14e 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/IScreeningQuery.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/IScreeningQuery.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess;
+import java.util.List;
+
import net.lemnik.eodsql.BaseQuery;
import net.lemnik.eodsql.DataIterator;
import net.lemnik.eodsql.Select;
@@ -32,7 +34,8 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.StringArrayMapper;
* @author Tomasz Pylak
*/
@Private
-@Friend(toClasses = WellContentQueryResult.class)
+@Friend(toClasses =
+ { WellContentQueryResult.class, BasicWellContentQueryResult.class })
public interface IScreeningQuery extends BaseQuery
{
@@ -61,7 +64,8 @@ public interface IScreeningQuery extends BaseQuery
+ " join samples pl on well.samp_id_part_of = pl.id"
+ " join experiments exp on pl.expe_id = exp.id "
+ " join experiment_types exp_type on exp.exty_id = exp_type.id "
- + " join projects on exp.proj_id = projects.id join spaces on projects.space_id = spaces.id "
+ + " join projects on exp.proj_id = projects.id "
+ + " join spaces on projects.space_id = spaces.id "
+ " join sample_types pl_type on pl.saty_id = pl_type.id "
+ " join sample_types well_type on well.saty_id = well_type.id "
+ " join material_types well_material_type on well_material.maty_id = well_material_type.id";
@@ -188,6 +192,27 @@ public interface IScreeningQuery extends BaseQuery
public DataIterator<WellContentQueryResult> getPlateMappingForMaterialType(String spaceCode,
String plateCode, String materialTypeCode);
+ /**
+ * @param materialTypesPattern only materials with a type matching to this pattern will be
+ * considered
+ * @return the material to well plate mapping for all the wells of the specified experiment.
+ */
+ @Select(sql = "select "
+ + " well.code as well_code, "
+ + " pl.perm_id as plate_perm_id, "
+ + " exp.perm_id as exp_perm_id, "
+ + " well_props.mate_prop_id as material_content_id "
+ + "from experiments exp "
+ + " join samples pl on pl.expe_id = exp.id "
+ + " join samples well on well.samp_id_part_of = pl.id "
+ + " join sample_properties well_props on well_props.samp_id = well.id "
+ + " join materials well_material on well_props.mate_prop_id = well_material.id "
+ + " join material_types well_material_type on well_material.maty_id = well_material_type.id "
+ + "where pl.samp_id_part_of is null and exp.id = ?{1} "
+ + " and well_material_type.code similar to ?{2}", fetchSize = FETCH_SIZE)
+ public List<BasicWellContentQueryResult> getPlateLocationsForExperiment(long experimentId,
+ String materialTypesPattern);
+
/**
* @return the material to well plate mapping for the given <var>spaceCode</var> and
* <var>plateCode</var>. Consider all material types. Only fills <var>well_code</var>,
@@ -249,4 +274,33 @@ public interface IScreeningQuery extends BaseQuery
+ " AND well_material.maty_id = ?{2}", fetchSize = FETCH_SIZE)
public DataIterator<Long> getMaterialsForExperimentWells(long experimentId, long materialTypeId);
+ static final String EXPERIMENTS_WITH_MATERIAL_SELECT =
+ " select distinct "
+ + " exp.id as exp_id, "
+ + " exp.code as exp_code, "
+ + " exp.perm_id as exp_perm_id, "
+ + " exp_type.code as exp_type_code, "
+ + " projects.code as proj_code, "
+ + " spaces.code as space_code "
+ + " from materials well_material"
+ + " join sample_properties well_props on well_props.mate_prop_id = well_material.id "
+ + " join samples well on well_props.samp_id = well.id"
+ + " join experiments exp on well.expe_id = exp.id "
+ + " join experiment_types exp_type on exp.exty_id = exp_type.id "
+ + " join projects on exp.proj_id = projects.id "
+ + " join spaces on projects.space_id = spaces.id ";
+
+ /** @returns experiments in which a given material has been screened */
+ @Select(sql = EXPERIMENTS_WITH_MATERIAL_SELECT + " where well_material.id = ?{1}")
+ public List<ExperimentReferenceQueryResult> getExperimentsWithMaterial(long materialId);
+
+ /**
+ * @returns experiments restricted to the specified project in which a given material has been
+ * screened
+ */
+ @Select(sql = EXPERIMENTS_WITH_MATERIAL_SELECT
+ + " where well_material.id = ?{1} and exp.proj_id = ?{2}")
+ public List<ExperimentReferenceQueryResult> getExperimentsWithMaterial(long materialId,
+ long projectId);
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/PatternMatchingUtils.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/PatternMatchingUtils.java
new file mode 100644
index 00000000000..f42b962f3d1
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/PatternMatchingUtils.java
@@ -0,0 +1,35 @@
+/*
+ * Copyright 2011 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.plugin.screening.server.dataaccess;
+
+import ch.systemsx.cisd.openbis.plugin.screening.server.logic.ScreeningUtils;
+
+/**
+ * @author Tomasz Pylak
+ */
+public class PatternMatchingUtils
+{
+ /**
+ * Changes a list into a regular expression which matches in 'SIMILAR TO' postgres constructions
+ * with texts which contains any element of the list as a prefix.
+ */
+ public static String asPostgresSimilarExpression(String[] substrings)
+ {
+ return ScreeningUtils.asSubstringExpression(substrings, "%");
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/WellContentQueryResult.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/WellContentQueryResult.java
index 5bfbe41b4f1..e20ef78e867 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/WellContentQueryResult.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/WellContentQueryResult.java
@@ -22,7 +22,7 @@ import ch.rinn.restrictions.Private;
* @author Tomasz Pylak
*/
@Private
-public class WellContentQueryResult
+public class WellContentQueryResult extends ExperimentReferenceQueryResult
{
// well pointer
@@ -44,21 +44,8 @@ public class WellContentQueryResult
public String plate_perm_id;
- // a pointer to the experiment of the plate
-
- public long exp_id;
-
- public String exp_code;
-
- public String exp_type_code;
-
- public String exp_perm_id;
-
- public String proj_code;
-
- public String space_code;
-
// a pointer to a material which was being searched for inside a well
+
// NOTE: this information is filled just in few queries.
@Deprecated
public long material_content_id;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ExperimentFeatureVectorSummaryLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ExperimentFeatureVectorSummaryLoader.java
index edaab707f70..07baa2ae640 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ExperimentFeatureVectorSummaryLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ExperimentFeatureVectorSummaryLoader.java
@@ -113,7 +113,7 @@ public class ExperimentFeatureVectorSummaryLoader extends AbstractContentLoader
List<? extends IWellData> wellDataList)
{
return WellReplicaSummaryCalculator.calculateReplicasFeatureVectorSummaries(wellDataList,
- settings.getAggregationType());
+ settings.getAggregationType(), false);
}
private static List<MaterialFeatureVectorSummary> enrichWithMaterial(
@@ -270,7 +270,8 @@ public class ExperimentFeatureVectorSummaryLoader extends AbstractContentLoader
private static Material tryFindReplicaMaterial(Sample well, MaterialSummarySettings settings)
{
- String replicaMatrialTypePattern = settings.getReplicaMatrialTypePattern();
+ String replicaMatrialTypePattern =
+ ScreeningUtils.asJavaRegExpr(settings.getReplicaMatrialTypeSubstrings());
if (replicaMatrialTypePattern == null)
{
return null;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialAllAssaysFeatureVectorSummaryLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialAllAssaysFeatureVectorSummaryLoader.java
index 90cf9b3dc54..2710fc71240 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialAllAssaysFeatureVectorSummaryLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialAllAssaysFeatureVectorSummaryLoader.java
@@ -23,22 +23,27 @@ import java.util.List;
import java.util.Map;
import java.util.Set;
+import org.apache.commons.lang.time.StopWatch;
+
import ch.systemsx.cisd.common.collections.CollectionUtils;
import ch.systemsx.cisd.common.collections.CollectionUtils.ICollectionMappingFunction;
-import ch.systemsx.cisd.common.collections.GroupByMap;
-import ch.systemsx.cisd.common.collections.IKeyExtractor;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.plugin.screening.server.IScreeningBusinessObjectFactory;
+import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.BasicWellContentQueryResult;
+import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.ExperimentReferenceQueryResult;
+import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.IScreeningQuery;
+import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.PatternMatchingUtils;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.IWellData;
+import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.MaterialIdFeatureVectorSummary;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.WellData;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ExperimentReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.FeatureVectorValues;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialSimpleFeatureVectorSummary;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialSummarySettings;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.FeatureVectorLoader.WellFeatureCollection;
@@ -55,146 +60,191 @@ public class MaterialAllAssaysFeatureVectorSummaryLoader extends AbstractContent
IDAOFactory daoFactory, TechId materialId, TechId projectTechIdOrNull,
MaterialSummarySettings settings)
{
- List<WellContent> assayWellsForMaterial = null;
+ IScreeningQuery dao = createDAO(daoFactory);
+ List<ExperimentReference> experiments =
+ fetchExperiments(materialId, projectTechIdOrNull, dao);
+
+ return new MaterialAllAssaysFeatureVectorSummaryLoader(session, businessObjectFactory,
+ daoFactory, dao, settings).loadMaterialFeatureVectorsFromAllAssays(materialId,
+ experiments);
+ }
+
+ private static List<ExperimentReference> fetchExperiments(TechId materialId,
+ TechId projectTechIdOrNull, IScreeningQuery dao)
+ {
+ List<ExperimentReferenceQueryResult> experimentRefs;
if (projectTechIdOrNull == null)
{
- // load results from all experiments
- assayWellsForMaterial =
- WellContentLoader.loadOnlyMetadata(session, businessObjectFactory, daoFactory,
- materialId);
+ experimentRefs = dao.getExperimentsWithMaterial(materialId.getId());
} else
{
// load results only for experiments within a given project
- assayWellsForMaterial =
- WellContentLoader.loadOnlyMetadataForProject(session, businessObjectFactory,
- daoFactory, materialId, projectTechIdOrNull);
+ experimentRefs =
+ dao.getExperimentsWithMaterial(materialId.getId(), projectTechIdOrNull.getId());
}
- return new MaterialAllAssaysFeatureVectorSummaryLoader(session, businessObjectFactory,
- daoFactory, settings).loadMaterialFeatureVectorsFromAllAssays(materialId,
- assayWellsForMaterial);
+ return asExperimentReferences(experimentRefs);
+ }
+
+ private static List<ExperimentReference> asExperimentReferences(
+ List<ExperimentReferenceQueryResult> experiments)
+ {
+ return CollectionUtils
+ .map(experiments,
+ new ICollectionMappingFunction<ExperimentReference, ExperimentReferenceQueryResult>()
+ {
+ public ExperimentReference map(
+ ExperimentReferenceQueryResult experiment)
+ {
+ return createExperimentReference(experiment);
+ }
+ });
+ }
+
+ private static ExperimentReference createExperimentReference(ExperimentReferenceQueryResult exp)
+ {
+ return new ExperimentReference(exp.exp_id, exp.exp_perm_id, exp.exp_code,
+ exp.exp_type_code, exp.proj_code, exp.space_code);
}
private final MaterialSummarySettings settings;
+ private final IScreeningQuery screeningQuery;
+
private MaterialAllAssaysFeatureVectorSummaryLoader(Session session,
IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory,
- MaterialSummarySettings settings)
+ IScreeningQuery screeningQuery, MaterialSummarySettings settings)
{
super(session, businessObjectFactory, daoFactory);
this.settings = settings;
+ this.screeningQuery = screeningQuery;
+ }
+
+ private List<BasicWellContentQueryResult> fetchWellLocations(ExperimentReference experiment)
+ {
+ String materialTypePattern =
+ PatternMatchingUtils.asPostgresSimilarExpression(settings
+ .getReplicaMatrialTypeSubstrings());
+ return screeningQuery.getPlateLocationsForExperiment(experiment.getId(),
+ materialTypePattern);
}
/**
* Note that different experiments can have different set of features!
*/
private List<MaterialSimpleFeatureVectorSummary> loadMaterialFeatureVectorsFromAllAssays(
- TechId materialId, List<WellContent> allAssayWellsForMaterial)
+ TechId materialId, List<ExperimentReference> experiments)
{
- Set<PlateIdentifier> plates = extractPlates(allAssayWellsForMaterial);
- WellFeatureCollection<FeatureVectorValues> allWellFeaturesOrNull =
- tryLoadWellSingleFeatureVectors(plates);
-
- Map<ExperimentReference, Set<WellReference>> wellsForExperimentMap =
- groupWellsByExperiment(allAssayWellsForMaterial);
-
List<MaterialSimpleFeatureVectorSummary> summaries =
new ArrayList<MaterialSimpleFeatureVectorSummary>();
- for (ExperimentReference experiment : wellsForExperimentMap.keySet())
+ StopWatch watch = new StopWatch();
+ watch.start();
+ for (ExperimentReference experiment : experiments)
{
- Set<WellReference> experimentWells = wellsForExperimentMap.get(experiment);
+ operationLog.info("Fetching analysis summary for experiment " + experiment);
+ List<BasicWellContentQueryResult> allWells = fetchWellLocations(experiment);
- MaterialSimpleFeatureVectorSummary summary =
- calculateExperimentFeatureVectorSummary(materialId, experiment,
- experimentWells, allWellFeaturesOrNull);
- summaries.add(summary);
+ Set<PlateIdentifier> plates = extractPlates(allWells);
+ WellFeatureCollection<FeatureVectorValues> allWellFeaturesOrNull =
+ tryLoadWellSingleFeatureVectors(plates);
+ if (allWellFeaturesOrNull == null)
+ {
+ summaries.add(new MaterialSimpleFeatureVectorSummary(experiment));
+ } else
+ {
+
+ Map<WellReference, Long/* material id */> wellToMaterialMap =
+ createWellToMaterialMap(allWells);
+
+ MaterialSimpleFeatureVectorSummary summary =
+ calculateExperimentFeatureVectorSummary(materialId, experiment,
+ allWellFeaturesOrNull, wellToMaterialMap);
+ summaries.add(summary);
+ }
}
+ operationLog.info(String.format(
+ "Fetching all experiment analysis summary for material %d took %d msec",
+ materialId.getId(), watch.getTime()));
return summaries;
}
- private MaterialSimpleFeatureVectorSummary calculateExperimentFeatureVectorSummary(
- TechId materialId, ExperimentReference experiment, Set<WellReference> experimentWells,
- WellFeatureCollection<FeatureVectorValues> allWellFeaturesOrNull)
+ private static Map<WellReference, Long/* material id */> createWellToMaterialMap(
+ List<BasicWellContentQueryResult> wells)
{
- if (allWellFeaturesOrNull == null)
+ Map<WellReference, Long> wellToMaterialMap = new HashMap<WellReference, Long>();
+ for (BasicWellContentQueryResult well : wells)
{
- return new MaterialSimpleFeatureVectorSummary(experiment);
+ WellReference wellReference = createWellReference(well);
+ wellToMaterialMap.put(wellReference, well.material_content_id);
}
+ return wellToMaterialMap;
+ }
+ private static WellReference createWellReference(BasicWellContentQueryResult well)
+ {
+ WellLocation wellLocation = WellLocation.parseLocationStr(well.well_code);
+ return new WellReference(wellLocation, well.plate_perm_id);
+ }
+
+ private MaterialSimpleFeatureVectorSummary calculateExperimentFeatureVectorSummary(
+ TechId materialId, ExperimentReference experiment,
+ WellFeatureCollection<FeatureVectorValues> experimentFeatures,
+ Map<WellReference, Long> wellToMaterialMap)
+ {
+ // we have to calculate summaries for all materials in the experiment to get the right
+ // ranking of the specified material
List<IWellData> experimentWellData =
- selectExperimentWellData(experimentWells, allWellFeaturesOrNull, materialId);
- float[] summaryFeatureVector =
- WellReplicaSummaryCalculator.calculateSummaryFeatureVector(experimentWellData,
- settings.getAggregationType());
+ createWellData(wellToMaterialMap, experimentFeatures.getFeatures());
+ List<MaterialIdFeatureVectorSummary> experimentSummaries =
+ WellReplicaSummaryCalculator.calculateReplicasFeatureVectorSummaries(
+ experimentWellData, settings.getAggregationType(), false);
+
+ // select the summary of the right material
+ MaterialIdFeatureVectorSummary materialSummary =
+ findMaterialSummary(materialId, experimentSummaries);
return new MaterialSimpleFeatureVectorSummary(experiment,
- allWellFeaturesOrNull.getFeatureCodesAndLabels(), summaryFeatureVector);
+ experimentFeatures.getFeatureCodesAndLabels(),
+ materialSummary.getFeatureVectorSummary(), materialSummary.getFeatureVectorRanks());
}
- private static List<IWellData> selectExperimentWellData(Set<WellReference> experimentWells,
- WellFeatureCollection<FeatureVectorValues> allWellFeatures, TechId materialId)
+ private MaterialIdFeatureVectorSummary findMaterialSummary(TechId materialId,
+ List<MaterialIdFeatureVectorSummary> summaries)
{
- List<IWellData> experimentWellDataList = new ArrayList<IWellData>();
- List<FeatureVectorValues> features = allWellFeatures.getFeatures();
- for (FeatureVectorValues feature : features)
+ for (MaterialIdFeatureVectorSummary summary : summaries)
{
- if (experimentWells.contains(feature.getWellReference()))
+ if (summary.getMaterial().equals(materialId.getId()))
{
- float[] values = WellFeatureCollectionLoader.asFeatureVectorValues(feature);
- IWellData wellData = new WellData(materialId.getId(), values);
- experimentWellDataList.add(wellData);
+ return summary;
}
}
- return experimentWellDataList;
+ throw new IllegalStateException("It should not happen: no summary found for material "
+ + materialId);
}
- private static Map<ExperimentReference, Set<WellReference>> groupWellsByExperiment(
- List<WellContent> allAssayWellsForMaterial)
+ // connects each well with a material with its feature vector
+ private static List<IWellData> createWellData(
+ Map<WellReference, Long/* material id */> wellToMaterialMap,
+ List<FeatureVectorValues> features)
{
- GroupByMap<ExperimentReference, WellContent> expToWellContentMap =
- GroupByMap.create(allAssayWellsForMaterial,
- new IKeyExtractor<ExperimentReference, WellContent>()
- {
- public ExperimentReference getKey(WellContent wellContent)
- {
- return wellContent.getExperiment();
- }
- });
- return convertToWellReferences(expToWellContentMap);
- }
-
- private static Map<ExperimentReference, Set<WellReference>> convertToWellReferences(
- GroupByMap<ExperimentReference, WellContent> expToWellContentMap)
- {
- Map<ExperimentReference, Set<WellReference>> map =
- new HashMap<ExperimentReference, Set<WellReference>>();
- for (ExperimentReference exp : expToWellContentMap.getKeys())
+ List<IWellData> experimentWellDataList = new ArrayList<IWellData>();
+ for (FeatureVectorValues feature : features)
{
- List<WellContent> wellContents = expToWellContentMap.getOrDie(exp);
- map.put(exp, asWellReferences(wellContents));
+ Long materialId = wellToMaterialMap.get(feature.getWellReference());
+ if (materialId != null)
+ {
+ float[] values = WellFeatureCollectionLoader.asFeatureVectorValues(feature);
+ IWellData wellData = new WellData(materialId, values);
+ experimentWellDataList.add(wellData);
+ }
}
- return map;
- }
-
- private static Set<WellReference> asWellReferences(List<WellContent> wellContents)
- {
- List<WellReference> wells =
- CollectionUtils.map(wellContents,
- new ICollectionMappingFunction<WellReference, WellContent>()
- {
- public WellReference map(WellContent wellContent)
- {
- return new WellReference(wellContent.tryGetLocation(),
- wellContent.getPlate().getPermId());
- }
- });
- return new HashSet<WellReference>(wells);
+ return experimentWellDataList;
}
- private static Set<PlateIdentifier> extractPlates(List<WellContent> wells)
+ private static Set<PlateIdentifier> extractPlates(List<BasicWellContentQueryResult> allWells)
{
Set<PlateIdentifier> plates = new HashSet<PlateIdentifier>();
- for (WellContent well : wells)
+ for (BasicWellContentQueryResult well : allWells)
{
- String platePermId = well.getPlate().getPermId();
+ String platePermId = well.plate_perm_id;
PlateIdentifier plateIdent = PlateIdentifier.createFromPermId(platePermId);
plates.add(plateIdent);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoader.java
index 09604792a2d..e0eb9b912cf 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoader.java
@@ -86,7 +86,7 @@ public class MaterialFeatureVectorSummaryLoader extends ExperimentFeatureVectorS
}
MaterialIdFeatureVectorSummary generalSummary = backendResult.getGeneralSummary();
- float[] featureVectorDeviatons = generalSummary.getFeatureVectorDeviations();
+ float[] featureVectorDeviatons = generalSummary.tryGetFeatureVectorDeviations();
float[] featureVectorSummaries = generalSummary.getFeatureVectorSummary();
int[] featureVectorRanks = generalSummary.getFeatureVectorRanks();
@@ -98,7 +98,9 @@ public class MaterialFeatureVectorSummaryLoader extends ExperimentFeatureVectorS
MaterialReplicaFeatureSummary replicaRow = new MaterialReplicaFeatureSummary();
replicaRows.add(replicaRow);
- replicaRow.setFeatureVectorDeviation(featureVectorDeviatons[i]);
+ double deviation =
+ featureVectorDeviatons == null ? Double.NaN : featureVectorDeviatons[i];
+ replicaRow.setFeatureVectorDeviation(deviation);
replicaRow.setFeatureVectorSummary(featureVectorSummaries[i]);
replicaRow.setFeatureVectorRank(featureVectorRanks[i]);
replicaRow.setFeatureDescription(featureDescriptions.get(i));
@@ -261,7 +263,7 @@ public class MaterialFeatureVectorSummaryLoader extends ExperimentFeatureVectorS
{
List<MaterialIdFeatureVectorSummary> featureSummaries =
WellReplicaSummaryCalculator.calculateReplicasFeatureVectorSummaries(
- experimentWellDataList, settings.getAggregationType());
+ experimentWellDataList, settings.getAggregationType(), true);
return tryFindMaterialSummary(materialId, featureSummaries);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellContentLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellContentLoader.java
index 2fd5caa4e82..4b3eb9c3c6e 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellContentLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellContentLoader.java
@@ -738,12 +738,11 @@ public class WellContentLoader extends AbstractContentLoader
MaterialSearchCriteria materialSearchCriteria =
materialCriteria.getMaterialSearchCriteria();
- ExperimentSearchCriteria experimentCriteria =
- materialCriteria.getExperimentCriteria();
+ ExperimentSearchCriteria experimentCriteria = materialCriteria.getExperimentCriteria();
SingleExperimentSearchCriteria experimentOrNull = experimentCriteria.tryGetExperiment();
BasicProjectIdentifier projectOrNull = experimentCriteria.tryGetProjectIdentifier();
- IScreeningQuery dao = createDAO(daoFactory);
+ IScreeningQuery dao = createDAO();
if (materialSearchCriteria.tryGetMaterialCodesOrProperties() != null)
{
MaterialSearchCodesCriteria codesCriteria =
@@ -882,7 +881,7 @@ public class WellContentLoader extends AbstractContentLoader
private List<WellContent> loadLocations(TechId geneMaterialId, TechId experimentId)
{
DataIterator<WellContentQueryResult> locations =
- createDAO(daoFactory).getPlateLocationsForMaterialId(geneMaterialId.getId(),
+ createDAO().getPlateLocationsForMaterialId(geneMaterialId.getId(),
experimentId.getId());
return convert(locations);
@@ -891,18 +890,23 @@ public class WellContentLoader extends AbstractContentLoader
private List<WellContent> loadLocations(TechId geneMaterialId)
{
DataIterator<WellContentQueryResult> locations =
- createDAO(daoFactory).getPlateLocationsForMaterialId(geneMaterialId.getId());
+ createDAO().getPlateLocationsForMaterialId(geneMaterialId.getId());
return convert(locations);
}
private List<WellContent> loadLocationsForProject(TechId geneMaterialId, TechId projectId)
{
DataIterator<WellContentQueryResult> locations =
- createDAO(daoFactory).getPlateLocationsForMaterialAndProjectIds(
- geneMaterialId.getId(), projectId.getId());
+ createDAO().getPlateLocationsForMaterialAndProjectIds(geneMaterialId.getId(),
+ projectId.getId());
return convert(locations);
}
+ private IScreeningQuery createDAO()
+ {
+ return createDAO(daoFactory);
+ }
+
private List<WellContent> convert(Iterable<WellContentQueryResult> queryResults)
{
List<WellContent> wellContents = convertAndRemoveDuplicateWells(queryResults);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellFeatureCollectionLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellFeatureCollectionLoader.java
index 73cb2b26159..12081462f8b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellFeatureCollectionLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellFeatureCollectionLoader.java
@@ -190,6 +190,8 @@ public class WellFeatureCollectionLoader extends AbstractContentLoader
}
}
+ // TODO 2011-06-21, Tomasz Pylak: this looks pretty unefficient. Could we do this erlier,
+ // avoiding converting these objects?
public static float[] asFeatureVectorValues(FeatureVectorValues featureVector)
{
FeatureValue[] featureValues = featureVector.getFeatureValues();
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellReplicaSummaryCalculator.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellReplicaSummaryCalculator.java
index 518f0d53227..317f6f47b78 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellReplicaSummaryCalculator.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellReplicaSummaryCalculator.java
@@ -41,20 +41,26 @@ public class WellReplicaSummaryCalculator
/**
* Calculates summaries and ranks for each group of well replicas (biological or technical).
* Usually a replica is determined by the material in the well, e.g. gene or compound.
+ *
+ * @param calculateDeviations if true then deviations for each aggregation will be calculated as
+ * well
*/
public static List<MaterialIdFeatureVectorSummary> calculateReplicasFeatureVectorSummaries(
List<? extends IWellData> wellDataList,
- MaterialReplicaSummaryAggregationType aggregationType)
+ MaterialReplicaSummaryAggregationType aggregationType, boolean calculateDeviations)
{
validate(wellDataList);
WellReplicaSummaryCalculator calculator =
new WellReplicaSummaryCalculator(wellDataList, aggregationType);
List<MaterialIdFeatureVectorSummary> summaries =
- calculator.calculateReplicasFeatureVectorSummaries();
+ calculator.calculateReplicasFeatureVectorSummaries(calculateDeviations);
return summaries;
}
- /** Calculates one aggregated number for each feature, taking all specified wells into account. */
+ /**
+ * Calculates one aggregated number for each feature, taking all specified wells (which should b
+ * technical replicates) into account.
+ */
public static float[] calculateSummaryFeatureVector(
List<? extends IWellData> techicalReplicaWells,
MaterialReplicaSummaryAggregationType aggregationType)
@@ -62,7 +68,7 @@ public class WellReplicaSummaryCalculator
validate(techicalReplicaWells);
int numberOfFeatures = getNumberOfFeatures(techicalReplicaWells);
return calculateSummaryFeatureVector(techicalReplicaWells, aggregationType,
- numberOfFeatures).getAggregates();
+ numberOfFeatures, false).getAggregates();
}
private static void validate(List<? extends IWellData> wellDataList)
@@ -108,10 +114,11 @@ public class WellReplicaSummaryCalculator
});
}
- private List<MaterialIdFeatureVectorSummary> calculateReplicasFeatureVectorSummaries()
+ private List<MaterialIdFeatureVectorSummary> calculateReplicasFeatureVectorSummaries(
+ boolean calculateDeviations)
{
Map<Long/* replica id */, SummaryFeatureVector> replicaToSummaryMap =
- calculateSummaryFeatures();
+ calculateSummaryFeatures(calculateDeviations);
Map<Long/* replica id */, int[]/* ranks for each feature */> ranks =
calculateRanks(replicaToSummaryMap, numberOfFeatures);
@@ -125,7 +132,8 @@ public class WellReplicaSummaryCalculator
// array not empty, all materials are the same
MaterialIdFeatureVectorSummary summary =
new MaterialIdFeatureVectorSummary(replicaId, summaryFeatures.getAggregates(),
- summaryFeatures.getDeviation(), ranks.get(replicaId), numberOfReplicas);
+ summaryFeatures.tryGetDeviations(), ranks.get(replicaId),
+ numberOfReplicas);
summaries.add(summary);
}
return summaries;
@@ -206,7 +214,7 @@ public class WellReplicaSummaryCalculator
return ranks;
}
- private Map<Long, SummaryFeatureVector> calculateSummaryFeatures()
+ private Map<Long, SummaryFeatureVector> calculateSummaryFeatures(boolean calculateDeviations)
{
Map<Long/* replica id */, SummaryFeatureVector> replicaToSummaryMap =
new HashMap<Long, SummaryFeatureVector>();
@@ -215,7 +223,8 @@ public class WellReplicaSummaryCalculator
{
List<IWellData> replicaWells = replicaToWellDataMap.getOrDie(replicaId);
SummaryFeatureVector summary =
- calculateSummaryFeatureVector(replicaWells, aggregationType, numberOfFeatures);
+ calculateSummaryFeatureVector(replicaWells, aggregationType, numberOfFeatures,
+ calculateDeviations);
replicaToSummaryMap.put(replicaId, summary);
}
return replicaToSummaryMap;
@@ -226,12 +235,12 @@ public class WellReplicaSummaryCalculator
{
private final float[] aggregate;
- private final float[] deviation;
+ private final float[] deviationsOrNull;
- public SummaryFeatureVector(float[] aggregate, float[] deviation)
+ public SummaryFeatureVector(float[] aggregate, float[] deviationsOrNull)
{
this.aggregate = aggregate;
- this.deviation = deviation;
+ this.deviationsOrNull = deviationsOrNull;
}
public float[] getAggregates()
@@ -239,38 +248,55 @@ public class WellReplicaSummaryCalculator
return aggregate;
}
- public float[] getDeviation()
+ /** null if not calculated */
+ public float[] tryGetDeviations()
{
- return deviation;
+ return deviationsOrNull;
}
}
private static SummaryFeatureVector calculateSummaryFeatureVector(
List<? extends IWellData> replicaWells,
- MaterialReplicaSummaryAggregationType aggregationType, int numberOfFeatures)
+ MaterialReplicaSummaryAggregationType aggregationType, int numberOfFeatures,
+ boolean calculateDeviations)
{
switch (aggregationType)
{
case MEDIAN:
- return calculateMedianVector(replicaWells, numberOfFeatures);
+ return calculateMedianVector(replicaWells, numberOfFeatures, calculateDeviations);
default:
throw new IllegalStateException("Unhandled aggregation type: " + aggregationType);
}
}
private static SummaryFeatureVector calculateMedianVector(
- List<? extends IWellData> replicaWells, int numberOfFeatures)
+ List<? extends IWellData> replicaWells, int numberOfFeatures,
+ boolean calculateDeviations)
{
float[] medians = new float[numberOfFeatures];
+ for (int featureIx = 0; featureIx < numberOfFeatures; featureIx++)
+ {
+ medians[featureIx] = calculateMedian(replicaWells, featureIx);
+ }
+ float[] deviations = null;
+ if (calculateDeviations)
+ {
+ deviations = calculateDeviations(replicaWells, numberOfFeatures, medians);
+ }
+ return new SummaryFeatureVector(medians, deviations);
+ }
+
+ private static float[] calculateDeviations(List<? extends IWellData> replicaWells,
+ int numberOfFeatures, float[] medians)
+ {
float[] deviations = new float[numberOfFeatures];
for (int featureIx = 0; featureIx < numberOfFeatures; featureIx++)
{
- float median = calculateMedian(replicaWells, featureIx);
- medians[featureIx] = median;
+ float median = medians[featureIx];
deviations[featureIx] =
calculateMedianAbsoluteDeviation(median, replicaWells, featureIx);
}
- return new SummaryFeatureVector(medians, deviations);
+ return deviations;
}
private static void sortBySelectedFeature(List<IWellData> replicaWells, int featureIx)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/MaterialIdFeatureVectorSummary.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/MaterialIdFeatureVectorSummary.java
index 669f265961e..58312443c95 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/MaterialIdFeatureVectorSummary.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/MaterialIdFeatureVectorSummary.java
@@ -32,17 +32,17 @@ public class MaterialIdFeatureVectorSummary extends MaterialFeatureVectorSummary
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
public MaterialIdFeatureVectorSummary(Long materialId, float[] featureVectorSummary,
- float[] featureVectorDeviations, int[] featureVectorRanks,
+ float[] featureVectorDeviationsOrNull, int[] featureVectorRanks,
int numberOfMaterialsInExperiment)
{
- super(materialId, featureVectorSummary, featureVectorDeviations, featureVectorRanks,
+ super(materialId, featureVectorSummary, featureVectorDeviationsOrNull, featureVectorRanks,
numberOfMaterialsInExperiment);
}
public MaterialFeatureVectorSummary createWithMaterial(Material material)
{
return new MaterialFeatureVectorSummary(material, getFeatureVectorSummary(),
- getFeatureVectorDeviations(), getFeatureVectorRanks(),
+ tryGetFeatureVectorDeviations(), getFeatureVectorRanks(),
getNumberOfMaterialsInExperiment());
}
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ExperimentFeatureVectorSummary.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ExperimentFeatureVectorSummary.java
index ce32a28209f..2b8033f6d47 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ExperimentFeatureVectorSummary.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ExperimentFeatureVectorSummary.java
@@ -33,6 +33,7 @@ public class ExperimentFeatureVectorSummary implements ISerializable
private ExperimentReference experiment;
+ // summaries without computed deviation
private List<MaterialFeatureVectorSummary> materialsSummary;
// has the same length as feature vectors in all material summaries
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialFeatureVectorSummary.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialFeatureVectorSummary.java
index 0edf2bd23b5..400dcbcfab3 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialFeatureVectorSummary.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialFeatureVectorSummary.java
@@ -36,10 +36,10 @@ public class MaterialFeatureVectorSummary extends
}
public MaterialFeatureVectorSummary(Material material, float[] featureVectorSummary,
- float[] featureVectorDeviations, int[] featureVectorRanks,
+ float[] featureVectorDeviationsOrNull, int[] featureVectorRanks,
int numberOfMaterialsInExperiment)
{
- super(material, featureVectorSummary, featureVectorDeviations, featureVectorRanks,
+ super(material, featureVectorSummary, featureVectorDeviationsOrNull, featureVectorRanks,
numberOfMaterialsInExperiment);
}
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialFeatureVectorSummaryParametrized.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialFeatureVectorSummaryParametrized.java
index f5270fe8886..1fd6ce82f9a 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialFeatureVectorSummaryParametrized.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialFeatureVectorSummaryParametrized.java
@@ -31,13 +31,17 @@ public class MaterialFeatureVectorSummaryParametrized<T> implements ISerializabl
private T material;
+ private int numberOfMaterialsInExperiment;
+
+ // --- one element for each feature: summary, deviation and rank
+
private float[] featureVectorSummary;
- private float[] featureVectorDeviations;
+ private float[] featureVectorDeviationsOrNull;
private int[] featureVectorRanks;
- private int numberOfMaterialsInExperiment;
+ // ---
// GTW
protected MaterialFeatureVectorSummaryParametrized()
@@ -45,12 +49,12 @@ public class MaterialFeatureVectorSummaryParametrized<T> implements ISerializabl
}
public MaterialFeatureVectorSummaryParametrized(T material, float[] featureVectorSummary,
- float[] featureVectorDeviations, int[] featureVectorRanks,
+ float[] featureVectorDeviationsOrNull, int[] featureVectorRanks,
int numberOfMaterialsInExperiment)
{
this.material = material;
this.featureVectorSummary = featureVectorSummary;
- this.featureVectorDeviations = featureVectorDeviations;
+ this.featureVectorDeviationsOrNull = featureVectorDeviationsOrNull;
this.featureVectorRanks = featureVectorRanks;
this.numberOfMaterialsInExperiment = numberOfMaterialsInExperiment;
}
@@ -65,9 +69,9 @@ public class MaterialFeatureVectorSummaryParametrized<T> implements ISerializabl
return featureVectorSummary;
}
- public float[] getFeatureVectorDeviations()
+ public float[] tryGetFeatureVectorDeviations()
{
- return featureVectorDeviations;
+ return featureVectorDeviationsOrNull;
}
public int[] getFeatureVectorRanks()
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialSimpleFeatureVectorSummary.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialSimpleFeatureVectorSummary.java
index f9094b78fd7..09850659f3b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialSimpleFeatureVectorSummary.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialSimpleFeatureVectorSummary.java
@@ -41,6 +41,8 @@ public class MaterialSimpleFeatureVectorSummary implements ISerializable
private float[] featureVectorSummary;
+ private int[] featureVectorRanks;
+
// GTW
@SuppressWarnings("unused")
private MaterialSimpleFeatureVectorSummary()
@@ -53,15 +55,17 @@ public class MaterialSimpleFeatureVectorSummary implements ISerializable
*/
public MaterialSimpleFeatureVectorSummary(ExperimentReference experiment)
{
- this(experiment, new ArrayList<CodeAndLabel>(), new float[0]);
+ this(experiment, new ArrayList<CodeAndLabel>(), new float[0], new int[0]);
}
public MaterialSimpleFeatureVectorSummary(ExperimentReference experiment,
- List<CodeAndLabel> featureDescriptions, float[] featureVectorSummary)
+ List<CodeAndLabel> featureDescriptions, float[] featureVectorSummary,
+ int[] featureVectorRanks)
{
this.experiment = experiment;
this.featureDescriptions = featureDescriptions;
this.featureVectorSummary = featureVectorSummary;
+ this.featureVectorRanks = featureVectorRanks;
}
public ExperimentReference getExperiment()
@@ -79,4 +83,8 @@ public class MaterialSimpleFeatureVectorSummary implements ISerializable
return featureVectorSummary;
}
+ public int[] getFeatureVectorRanks()
+ {
+ return featureVectorRanks;
+ }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialSummarySettings.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialSummarySettings.java
index aeb36e868e5..3c05eae5d5a 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialSummarySettings.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialSummarySettings.java
@@ -37,8 +37,10 @@ public class MaterialSummarySettings implements ISerializable
private List<String> featureCodes;
- private String replicaMatrialTypePattern;
+ private String[] replicaMatrialTypeSubstrings;
+ // well property codes which links to the material which determins which biological replicate it
+ // is, e.g. siRNA or compound
private List<String> biologicalReplicatePropertyTypeCodes;
private MaterialReplicaSummaryAggregationType aggregationType;
@@ -53,14 +55,14 @@ public class MaterialSummarySettings implements ISerializable
this.featureCodes = featureCodes;
}
- public String getReplicaMatrialTypePattern()
+ public String[] getReplicaMatrialTypeSubstrings()
{
- return replicaMatrialTypePattern;
+ return replicaMatrialTypeSubstrings;
}
- public void setReplicaMatrialTypePatterns(String replicaMatrialTypePattern)
+ public void setReplicaMatrialTypePatterns(String[] replicaMatrialTypeSubstrings)
{
- this.replicaMatrialTypePattern = replicaMatrialTypePattern;
+ this.replicaMatrialTypeSubstrings = replicaMatrialTypeSubstrings;
}
public List<String> getBiologicalReplicatePropertyTypeCodes()
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ScreeningConstants.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ScreeningConstants.java
index 576e5d0fafb..14accb1d7b2 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ScreeningConstants.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ScreeningConstants.java
@@ -131,9 +131,6 @@ public class ScreeningConstants
/** Used to import Qiagen siRNA libraries. */
public static final String LIBRARY_PLUGIN_TYPE_CODE = "LIBRARY";
- /** Types of materials which should be for grouping the analysis results */
- public static final String REPLICA_METERIAL_TYPE_PATTERN = ".*GENE.*|.*CONTROL.*|.*COMPOUND.*";
-
// --- !!!!!! It's discouraged to use this constant, try hard not to do that !!!!!!!! ---
/** It's discouraged to use this constant, use {@link #HCS_PLATE_SAMPLE_TYPE_PATTERN} instead. */
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/ScreeningDAOTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/ScreeningDAOTest.java
index f589680be44..08a2026c2b8 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/ScreeningDAOTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/ScreeningDAOTest.java
@@ -173,4 +173,19 @@ public class ScreeningDAOTest extends AbstractScreeningDAOTest
}
+ @Test
+ public void testGetGlobalBasicPlateLocations()
+ {
+ List<BasicWellContentQueryResult> locations =
+ EntityListingTestUtils.asList(query.getPlateLocationsForExperiment(1, "%GENE%"));
+ AssertJUnit.assertEquals(0, locations.size());
+
+ List<ExperimentReferenceQueryResult> experiments = query.getExperimentsWithMaterial(1);
+ AssertJUnit.assertEquals(0, experiments.size());
+
+ experiments = query.getExperimentsWithMaterial(1, 1);
+ AssertJUnit.assertEquals(0, experiments.size());
+
+ }
+
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellReplicaSummaryCalculatorTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellReplicaSummaryCalculatorTest.java
index 739e1be813f..93b89f8be44 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellReplicaSummaryCalculatorTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellReplicaSummaryCalculatorTest.java
@@ -66,13 +66,13 @@ public class WellReplicaSummaryCalculatorTest extends AssertJUnit
assertArraysEqual(new float[]
{ 1.5f, 6 }, repl1.getFeatureVectorSummary());
assertArraysEqual(new float[]
- { 0.5f, 2 }, repl1.getFeatureVectorDeviations());
+ { 0.5f, 2 }, repl1.tryGetFeatureVectorDeviations());
MaterialIdFeatureVectorSummary repl2 = summary.get(1 - replica1Ix);
assertArraysEqual(new float[]
{ 1, 100 }, repl2.getFeatureVectorSummary());
assertArraysEqual(new float[]
- { 0, 90 }, repl2.getFeatureVectorDeviations());
+ { 0, 90 }, repl2.tryGetFeatureVectorDeviations());
assertArraysEqual(new int[]
{ 1, 2 }, repl1.getFeatureVectorRanks());
@@ -212,6 +212,6 @@ public class WellReplicaSummaryCalculatorTest extends AssertJUnit
private List<MaterialIdFeatureVectorSummary> calculate(List<IWellData> wellDataList)
{
return WellReplicaSummaryCalculator.calculateReplicasFeatureVectorSummaries(wellDataList,
- MaterialReplicaSummaryAggregationType.MEDIAN);
+ MaterialReplicaSummaryAggregationType.MEDIAN, true);
}
}
--
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