From 864d2fd293fe223fc1748800e54d7813693af2c8 Mon Sep 17 00:00:00 2001
From: kaloyane <kaloyane>
Date: Fri, 1 Apr 2011 14:08:23 +0000
Subject: [PATCH] [LMS-2163] refactor feature vector loading out of
WellContentLoader, make the implementation of WellContentLoader.loadXXXX a
bit more verbose and easy to read
SVN: 20625
---
.../screening/server/ScreeningServer.java | 7 ++-
.../logic/FeatureVectorValuesLoader.java | 60 ++++++++++++++++++
.../server/logic/WellContentLoader.java | 61 +++++--------------
3 files changed, 79 insertions(+), 49 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorValuesLoader.java
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 ba3c28560d0..e904d46ccbc 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
@@ -66,6 +66,7 @@ import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.VocabularyTranslator;
import ch.systemsx.cisd.openbis.plugin.generic.shared.IGenericServer;
import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.IScreeningQuery;
+import ch.systemsx.cisd.openbis.plugin.screening.server.logic.FeatureVectorValuesLoader;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.PlateContentLoader;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.ScreeningApiImpl;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.WellContentLoader;
@@ -205,9 +206,9 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
public FeatureVectorValues getWellFeatureVectorValues(String sessionToken, String datasetCode,
String datastoreCode, WellLocation wellLocation)
{
- Session session = getSession(sessionToken);
- return WellContentLoader.loadFeatureVectorValues(session, businessObjectFactory,
- getDAOFactory(), datasetCode, datastoreCode, wellLocation);
+ getSession(sessionToken);
+ return FeatureVectorValuesLoader.loadFeatureVectorValues(businessObjectFactory,
+ datasetCode, datastoreCode, wellLocation);
}
public LogicalImageInfo getImageDatasetInfo(String sessionToken, String datasetCode,
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorValuesLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorValuesLoader.java
new file mode 100644
index 00000000000..79eaa38b29f
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorValuesLoader.java
@@ -0,0 +1,60 @@
+/*
+ * 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.logic;
+
+import java.util.Arrays;
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.plugin.screening.server.IScreeningBusinessObjectFactory;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.FeatureVectorValues;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellFeatureVectorReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.FeatureVectorLoader.WellFeatureCollection;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.IHCSFeatureVectorLoader;
+
+/**
+ * @author Kaloyan Enimanev
+ */
+public class FeatureVectorValuesLoader
+{
+
+ public static FeatureVectorValues loadFeatureVectorValues(
+ IScreeningBusinessObjectFactory businessObjectFactory,
+ String datasetCode, String datastoreCode, WellLocation wellLocation)
+ {
+ IHCSFeatureVectorLoader loader =
+ businessObjectFactory.createHCSFeatureVectorLoader(datastoreCode);
+
+ List<WellFeatureVectorReference> wellReferences =
+ Arrays.asList(new WellFeatureVectorReference(datasetCode, wellLocation));
+ WellFeatureCollection<FeatureVectorValues> featureVectors =
+ loader.fetchWellFeatureValuesIfPossible(wellReferences);
+
+ List<FeatureVectorValues> features = featureVectors.getFeatures();
+ if (features.size() == 0)
+ {
+ // Because of the way we are storing the features it can happen only if dataset contains
+ // no features (NaN are stored in the plate matrix for the wells which have no value
+ // specified).
+ return null;
+ } else
+ {
+ return featureVectors.getFeatures().get(0);
+ }
+ }
+
+}
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 b56b6aa5cb8..3c09d44d421 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
@@ -100,8 +100,11 @@ public class WellContentLoader
IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory,
TechId geneMaterialId, String experimentPermId)
{
- return new WellContentLoader(session, businessObjectFactory, daoFactory).loadLocations(
- geneMaterialId, experimentPermId);
+ WellContentLoader loader =
+ new WellContentLoader(session, businessObjectFactory, daoFactory);
+
+ List<WellContent> contents = loader.loadLocations(geneMaterialId, experimentPermId);
+ return loader.enrichWithWellProperties(contents);
}
/** loads wells metadata, but no information about image or image analysis datasets */
@@ -109,8 +112,9 @@ public class WellContentLoader
IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory,
TechId geneMaterialId)
{
- return new WellContentLoader(session, businessObjectFactory, daoFactory)
- .loadLocations(geneMaterialId);
+ final WellContentLoader loader = new WellContentLoader(session, businessObjectFactory, daoFactory);
+ List<WellContent> contents = loader.loadLocations(geneMaterialId);
+ return loader.enrichWithWellProperties(contents);
}
/**
@@ -122,16 +126,14 @@ public class WellContentLoader
IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory,
WellSearchCriteria materialCriteria)
{
- return new WellContentLoader(session, businessObjectFactory, daoFactory)
- .loadLocationsAndEnrich(materialCriteria);
- }
+ WellContentLoader loader =
+ new WellContentLoader(session, businessObjectFactory, daoFactory);
- public static FeatureVectorValues loadFeatureVectorValues(Session session,
- IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory,
- String datasetCode, String datastoreCode, WellLocation wellLocation)
- {
- return new WellContentLoader(session, businessObjectFactory, daoFactory)
- .getFeatureVectorValues(datasetCode, datastoreCode, wellLocation);
+ List<WellContent> locations = loader.loadLocations(materialCriteria);
+ List<WellContent> uniqueLocations = loader.filterWellDuplicates(locations);
+ List<WellContent> withProperties = loader.enrichWithWellProperties(uniqueLocations);
+ List<WellContent> withPropsAndDataSets = loader.enrichWithDatasets(withProperties);
+ return loader.enrichWithFeatureVectors(withPropsAndDataSets);
}
/**
@@ -174,39 +176,6 @@ public class WellContentLoader
this.daoFactory = daoFactory;
}
- private FeatureVectorValues getFeatureVectorValues(String dataSetCode, String datastoreCode,
- WellLocation wellLocation)
- {
- IHCSFeatureVectorLoader loader =
- businessObjectFactory.createHCSFeatureVectorLoader(datastoreCode);
-
- List<WellFeatureVectorReference> wellReferences =
- Arrays.asList(new WellFeatureVectorReference(dataSetCode, wellLocation));
- WellFeatureCollection<FeatureVectorValues> featureVectors =
- loader.fetchWellFeatureValuesIfPossible(wellReferences);
-
- List<FeatureVectorValues> features = featureVectors.getFeatures();
- if (features.size() == 0)
- {
- // Because of the way we are storing the features it can happen only if dataset contains
- // no features (NaN are stored in the plate matrix for the wells which have no value
- // specified).
- return null;
- } else
- {
- return featureVectors.getFeatures().get(0);
- }
- }
-
- private List<WellContent> loadLocationsAndEnrich(WellSearchCriteria materialCriteria)
- {
- List<WellContent> locations = loadLocations(materialCriteria);
- List<WellContent> uniqueLocations = filterWellDuplicates(locations);
- List<WellContent> withProperties = enrichWithWellProperties(uniqueLocations);
- List<WellContent> withPropsAndDataSets = enrichWithDatasets(withProperties);
- return enrichWithFeatureVectors(withPropsAndDataSets);
- }
-
private List<WellContent> filterWellDuplicates(List<WellContent> wellContents)
{
Set<String> seenPermIds = new HashSet<String>();
--
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