From 86375d3711eb8bc6360a712822e5bc50153c1b4c Mon Sep 17 00:00:00 2001
From: brinn <brinn>
Date: Thu, 3 Feb 2011 21:21:26 +0000
Subject: [PATCH] [LMS-2044] HCS: Change Data Set Types [LMS-2040] Screening:
Provide Overlay data sets via the API
SVN: 19745
---
.../v1/IScreeningOpenbisServiceFacade.java | 18 ++-
.../client/api/v1/ScreeningClientApiTest.java | 2 +-
.../api/v1/ScreeningClientApiTester.java | 2 +-
.../api/v1/ScreeningOpenbisServiceFacade.java | 34 +++++-
.../screening/server/ScreeningServer.java | 12 ++
.../server/ScreeningServerLogger.java | 14 +++
.../server/logic/ImageDatasetLoader.java | 78 ++++++++++++-
.../server/logic/ScreeningApiImpl.java | 12 ++
.../server/logic/ScreeningUtils.java | 106 +++++++++++-------
.../shared/api/v1/IScreeningApiServer.java | 28 +++++
.../api/v1/dto/ImageDatasetReference.java | 30 ++++-
.../shared/basic/dto/ScreeningConstants.java | 14 ++-
.../server/logic/ScreeningApiImplTest.java | 104 +++++++++++++++++
13 files changed, 404 insertions(+), 50 deletions(-)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
index 603f95e69aa..2ad934bd649 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
@@ -91,10 +91,26 @@ public interface IScreeningOpenbisServiceFacade
List<? extends PlateIdentifier> plates);
/**
- * For a given set of plates provides the list of all connected data sets containing images.
+ * For a given set of plates provides the list of all connected data sets containing images
+ * which are not segmentation images.
+ *
+ * @deprecated Use {@link #listRawImageDatasets(List)} instead.
*/
+ @Deprecated
public List<ImageDatasetReference> listImageDatasets(List<? extends PlateIdentifier> plates);
+ /**
+ * For a given set of plates provides the list of all connected data sets containing raw images.
+ */
+ public List<ImageDatasetReference> listRawImageDatasets(List<? extends PlateIdentifier> plates);
+
+ /**
+ * For a given set of plates provides the list of all connected data sets containing
+ * segmentation images (overlays).
+ */
+ public List<ImageDatasetReference> listSegmentationImageDatasets(
+ List<? extends PlateIdentifier> plates);
+
/**
* For the given <var>experimentIdentifier</var> find all plate locations that are connected to
* the specified <var>materialIdentifier</var>. If <code>findDatasets == true</code>, find also
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningClientApiTest.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningClientApiTest.java
index fab871c1ff6..2956248f31f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningClientApiTest.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningClientApiTest.java
@@ -114,7 +114,7 @@ public class ScreeningClientApiTest
List<Plate> plates = facade.listPlates();
print("Plates: " + plates);
- List<ImageDatasetReference> imageDatasets = facade.listImageDatasets(plates);
+ List<ImageDatasetReference> imageDatasets = facade.listRawImageDatasets(plates);
Collections.sort(imageDatasets, new Comparator<ImageDatasetReference>()
{
public int compare(ImageDatasetReference r1, ImageDatasetReference r2)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningClientApiTester.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningClientApiTester.java
index 6caade42116..135f28e0036 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningClientApiTester.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningClientApiTester.java
@@ -220,7 +220,7 @@ public class ScreeningClientApiTester
private void loadImagesByDataSetCode()
{
Form form = new Form(this, "Parameters for Loading Images by Data Set");
- List<ImageDatasetReference> dataSets = facade.listImageDatasets(facade.listPlates());
+ List<ImageDatasetReference> dataSets = facade.listRawImageDatasets(facade.listPlates());
List<String> dataSetCodes = new ArrayList<String>();
for (ImageDatasetReference imageDataset : dataSets)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
index 044fca2be1c..5c52dbac014 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
@@ -8,6 +8,7 @@ import java.io.OutputStream;
import java.lang.reflect.Method;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
@@ -264,14 +265,45 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
}
/**
- * For a given set of plates provides the list of all connected data sets containing images.
+ * For a given set of plates provides the list of all connected data sets containing raw images.
+ *
+ * @deprecated Use {@link #listRawImageDatasets(List)} instead.
*/
+ @Deprecated
public List<ImageDatasetReference> listImageDatasets(List<? extends PlateIdentifier> plates)
{
checkASMinimalMinorVersion("listImageDatasets", List.class);
return openbisScreeningServer.listImageDatasets(sessionToken, plates);
}
+ /**
+ * For a given set of plates provides the list of all connected data sets containing raw images.
+ */
+ public List<ImageDatasetReference> listRawImageDatasets(List<? extends PlateIdentifier> plates)
+ {
+ if (hasASMethod("listRawImageDatasets", List.class))
+ {
+ return openbisScreeningServer.listRawImageDatasets(sessionToken, plates);
+ } else
+ {
+ checkASMinimalMinorVersion("listImageDatasets", List.class);
+ return openbisScreeningServer.listImageDatasets(sessionToken, plates);
+ }
+ }
+
+ /**
+ * For a given set of plates provides the list of all connected data sets containing images.
+ */
+ public List<ImageDatasetReference> listSegmentationImageDatasets(
+ List<? extends PlateIdentifier> plates)
+ {
+ if (hasASMethod("listSegmentationImageDatasets", List.class))
+ {
+ return openbisScreeningServer.listSegmentationImageDatasets(sessionToken, plates);
+ }
+ return Collections.emptyList();
+ }
+
/**
* For the given <var>experimentIdentifier</var> find all plate locations that are connected to
* the specified <var>materialIdentifier</var>. If <code>findDatasets == true</code>, find also
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 ccbc902c869..b29383c6c46 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
@@ -244,6 +244,18 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
return createScreeningApiImpl(sessionToken).listImageDatasets(plates);
}
+ public List<ImageDatasetReference> listRawImageDatasets(String sessionToken,
+ List<? extends PlateIdentifier> plates)
+ {
+ return createScreeningApiImpl(sessionToken).listRawImageDatasets(plates);
+ }
+
+ public List<ImageDatasetReference> listSegmentationImageDatasets(String sessionToken,
+ List<? extends PlateIdentifier> plates)
+ {
+ return createScreeningApiImpl(sessionToken).listSegmentationImageDatasets(plates);
+ }
+
public List<PlateWellReferenceWithDatasets> listPlateWells(
String sessionToken,
ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentIdentifier experimentIdentifer,
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java
index 912bedb6f79..c52278ce06a 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java
@@ -180,6 +180,20 @@ final class ScreeningServerLogger extends AbstractServerLogger implements IScree
return null;
}
+ public List<ImageDatasetReference> listRawImageDatasets(String sessionToken,
+ List<? extends PlateIdentifier> plates) throws IllegalArgumentException
+ {
+ logAccess(sessionToken, "listRawImageDatasets", "#plates: %s", plates.size());
+ return null;
+ }
+
+ public List<ImageDatasetReference> listSegmentationImageDatasets(String sessionToken,
+ List<? extends PlateIdentifier> plates) throws IllegalArgumentException
+ {
+ logAccess(sessionToken, "listSegmentationImageDatasets", "#plates: %s", plates.size());
+ return null;
+ }
+
public List<PlateWellReferenceWithDatasets> listPlateWells(
String sessionToken,
ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentIdentifier experimentIdentifer,
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ImageDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ImageDatasetLoader.java
index 714fb8e8004..5dcd63527f0 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ImageDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ImageDatasetLoader.java
@@ -55,6 +55,24 @@ class ImageDatasetLoader extends PlateDatasetLoader
return filterImageDatasets();
}
+ /**
+ * Return the raw image datasets for the specified plates.
+ */
+ private List<ExternalData> getRawImageDatasets()
+ {
+ load();
+ return filterRawImageDatasets();
+ }
+
+ /**
+ * Return the segmentation image datasets (overlays) for the specified plates.
+ */
+ private List<ExternalData> getSegmentationImageDatasets()
+ {
+ load();
+ return filterSegmententationImageDatasets();
+ }
+
/**
* Return the image datasets references for the specified plates.
*/
@@ -63,6 +81,22 @@ class ImageDatasetLoader extends PlateDatasetLoader
return asImageDatasetReferences(getImageDatasets());
}
+ /**
+ * Return the raw image datasets references for the specified plates.
+ */
+ public List<ImageDatasetReference> getRawImageDatasetReferences()
+ {
+ return asImageDatasetReferences(getRawImageDatasets());
+ }
+
+ /**
+ * Return the segmentation image datasets references for the specified plates.
+ */
+ public List<ImageDatasetReference> getSegmentationImageDatasetReferences()
+ {
+ return asImageDatasetReferences(getSegmentationImageDatasets());
+ }
+
private List<ExternalData> filterImageDatasets()
{
List<ExternalData> result = new ArrayList<ExternalData>();
@@ -76,6 +110,32 @@ class ImageDatasetLoader extends PlateDatasetLoader
return result;
}
+ private List<ExternalData> filterRawImageDatasets()
+ {
+ List<ExternalData> result = new ArrayList<ExternalData>();
+ for (ExternalData externalData : getDatasets())
+ {
+ if (ScreeningUtils.isRawHcsImageDataset(externalData))
+ {
+ result.add(externalData);
+ }
+ }
+ return result;
+ }
+
+ private List<ExternalData> filterSegmententationImageDatasets()
+ {
+ List<ExternalData> result = new ArrayList<ExternalData>();
+ for (ExternalData externalData : getDatasets())
+ {
+ if (ScreeningUtils.isSegmentationHcsImageDataset(externalData))
+ {
+ result.add(externalData);
+ }
+ }
+ return result;
+ }
+
private List<ImageDatasetReference> asImageDatasetReferences(List<ExternalData> imageDatasets)
{
List<ImageDatasetReference> references = new ArrayList<ImageDatasetReference>();
@@ -86,12 +146,28 @@ class ImageDatasetLoader extends PlateDatasetLoader
return references;
}
+ private ExternalData tryGetParent(ExternalData externalData)
+ {
+ if (externalData.getParents() != null && externalData.getParents().size() == 1)
+ {
+ return externalData.getParents().iterator().next();
+ } else
+ {
+ return null;
+ }
+ }
+
protected ImageDatasetReference asImageDataset(ExternalData externalData)
{
+ if (externalData == null || ScreeningUtils.isHcsImageDataset(externalData) == false)
+ {
+ return null;
+ }
DataStore dataStore = externalData.getDataStore();
return new ImageDatasetReference(externalData.getCode(),
getDataStoreUrlFromDataStore(dataStore), createPlateIdentifier(externalData),
createExperimentIdentifier(externalData), extractPlateGeometry(externalData),
- externalData.getRegistrationDate(), extractProperties(externalData));
+ externalData.getRegistrationDate(), extractProperties(externalData),
+ asImageDataset(tryGetParent(externalData)));
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
index 6a14234f7b6..e6d6a54029b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
@@ -125,6 +125,18 @@ public class ScreeningApiImpl
session.tryGetHomeGroupCode(), plates).getImageDatasetReferences();
}
+ public List<ImageDatasetReference> listRawImageDatasets(List<? extends PlateIdentifier> plates)
+ {
+ return new ImageDatasetLoader(session, businessObjectFactory,
+ session.tryGetHomeGroupCode(), plates).getRawImageDatasetReferences();
+ }
+
+ public List<ImageDatasetReference> listSegmentationImageDatasets(List<? extends PlateIdentifier> plates)
+ {
+ return new ImageDatasetLoader(session, businessObjectFactory,
+ session.tryGetHomeGroupCode(), plates).getSegmentationImageDatasetReferences();
+ }
+
public List<Plate> listPlates()
{
final ISampleLister sampleLister = businessObjectFactory.createSampleLister(session);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningUtils.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningUtils.java
index aef25719c48..a47b4f94216 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningUtils.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningUtils.java
@@ -72,67 +72,57 @@ public class ScreeningUtils
public static <T extends DataPE> List<T> filterImageOverlayDatasets(Collection<T> datasets)
{
return filterDatasetsByTypePattern(datasets,
- ScreeningConstants.IMAGE_OVERLAY_DATASET_TYPE_PATTERN);
+ ScreeningConstants.IMAGE_OVERLAY_DATASET_TYPE_PATTERN,
+ ScreeningConstants.HCS_SEGMENTATION_IMAGE_DATASET_TYPE_PATTERN);
}
- /** excludes overlays even if they match to the image dataset pattern */
+ /** excludes overlay image data sets even when they match to the image dataset pattern */
public static List<ExternalDataPE> filterImageDatasets(List<ExternalDataPE> datasets)
{
- List<ExternalDataPE> allDatasets = new ArrayList<ExternalDataPE>();
- List<ExternalDataPE> hcsDatasets =
- filterDatasetsByTypePattern(datasets,
- ScreeningConstants.HCS_IMAGE_DATASET_TYPE_PATTERN);
- List<ExternalDataPE> micDatasets =
+ List<ExternalDataPE> allDatasets =
filterDatasetsByTypePattern(datasets,
+ ScreeningConstants.HCS_IMAGE_DATASET_TYPE_PATTERN,
ScreeningConstants.MICROSCOPY_IMAGE_DATASET_TYPE_PATTERN);
- allDatasets.addAll(hcsDatasets);
- allDatasets.addAll(micDatasets);
-
allDatasets =
excludeDatasetsByTypePattern(allDatasets,
- ScreeningConstants.IMAGE_OVERLAY_DATASET_TYPE_PATTERN);
+ ScreeningConstants.IMAGE_OVERLAY_DATASET_TYPE_PATTERN,
+ ScreeningConstants.HCS_SEGMENTATION_IMAGE_DATASET_TYPE_PATTERN);
return allDatasets;
}
/** chooses datasets of unknown types */
public static List<ExternalDataPE> filterUnknownDatasets(List<ExternalDataPE> datasets)
{
- List<ExternalDataPE> chosenDatasets = new ArrayList<ExternalDataPE>();
- for (ExternalDataPE dataset : datasets)
- {
- if (isTypeMatching(dataset, ScreeningConstants.HCS_IMAGE_ANALYSIS_DATASET_TYPE_PATTERN) == false
- && isTypeMatching(dataset, ScreeningConstants.HCS_IMAGE_DATASET_TYPE_PATTERN) == false
- && isTypeMatching(dataset,
- ScreeningConstants.MICROSCOPY_IMAGE_DATASET_TYPE_PATTERN) == false
- && isTypeMatching(dataset,
- ScreeningConstants.IMAGE_OVERLAY_DATASET_TYPE_PATTERN) == false)
- {
- chosenDatasets.add(dataset);
- }
- }
- return chosenDatasets;
+ return excludeDatasetsByTypePattern(datasets,
+ ScreeningConstants.HCS_IMAGE_ANALYSIS_DATASET_TYPE_PATTERN,
+ ScreeningConstants.HCS_IMAGE_DATASET_TYPE_PATTERN,
+ ScreeningConstants.HCS_RAW_IMAGE_DATASET_TYPE_PATTERN,
+ ScreeningConstants.HCS_RAW_IMAGE_LEGACY_DATASET_TYPE,
+ ScreeningConstants.IMAGE_OVERLAY_DATASET_TYPE_PATTERN,
+ ScreeningConstants.HCS_SEGMENTATION_IMAGE_DATASET_TYPE_PATTERN,
+ ScreeningConstants.MICROSCOPY_IMAGE_DATASET_TYPE_PATTERN);
}
private static <T extends DataPE> List<T> excludeDatasetsByTypePattern(List<T> datasets,
- String datasetTypeCodePattern)
+ String... datasetTypeCodePatterns)
{
- return filterDatasetsByTypePattern(datasets, datasetTypeCodePattern, false);
+ return filterDatasetsByTypePattern(datasets, false, datasetTypeCodePatterns);
}
public static <T extends DataPE> List<T> filterDatasetsByTypePattern(Collection<T> datasets,
- String datasetTypeCodePattern)
+ String... datasetTypeCodePatterns)
{
- return filterDatasetsByTypePattern(datasets, datasetTypeCodePattern, true);
+ return filterDatasetsByTypePattern(datasets, true, datasetTypeCodePatterns);
}
private static <T extends DataPE> List<T> filterDatasetsByTypePattern(Collection<T> datasets,
- String datasetTypeCodePattern, boolean shouldMatch)
+ boolean doesMatch, String... datasetTypeCodePatterns)
{
- List<T> chosenDatasets = new ArrayList<T>();
+ final List<T> chosenDatasets = new ArrayList<T>();
for (T dataset : datasets)
{
- if (isTypeMatching(dataset, datasetTypeCodePattern) == shouldMatch)
+ if (isOneOfTypesMatching(dataset, datasetTypeCodePatterns) == doesMatch)
{
chosenDatasets.add(dataset);
}
@@ -140,22 +130,50 @@ public class ScreeningUtils
return chosenDatasets;
}
+ private static boolean isOneOfTypesMatching(DataPE dataset, String... datasetTypeCodePatterns)
+ {
+ for (String datasetTypeCodePattern : datasetTypeCodePatterns)
+ {
+ if (isTypeMatching(dataset, datasetTypeCodePattern))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
private static boolean isTypeMatching(DataPE dataset, String datasetTypeCodePattern)
{
return dataset.getDataSetType().getCode().matches(datasetTypeCodePattern);
}
- public static boolean isBasicHcsImageDataset(ExternalData externalData)
+ public static boolean isHcsImageDataset(ExternalData externalData)
{
- return ScreeningUtils.isTypeMatching(externalData,
- ScreeningConstants.HCS_IMAGE_DATASET_TYPE_PATTERN)
- && isTypeMatching(externalData,
- ScreeningConstants.IMAGE_OVERLAY_DATASET_TYPE_PATTERN) == false;
+ return isOneOfTypesMatching(externalData,
+ ScreeningConstants.HCS_IMAGE_DATASET_TYPE_PATTERN,
+ ScreeningConstants.HCS_RAW_IMAGE_DATASET_TYPE_PATTERN,
+ ScreeningConstants.HCS_RAW_IMAGE_LEGACY_DATASET_TYPE,
+ ScreeningConstants.HCS_SEGMENTATION_IMAGE_DATASET_TYPE_PATTERN);
}
- public static boolean isTypeMatching(ExternalData dataset, String datasetTypeCodePattern)
+ public static boolean isRawHcsImageDataset(ExternalData externalData)
{
- return dataset.getDataSetType().getCode().matches(datasetTypeCodePattern);
+ return isTypeMatching(externalData, ScreeningConstants.HCS_RAW_IMAGE_DATASET_TYPE_PATTERN)
+ || ScreeningConstants.HCS_RAW_IMAGE_LEGACY_DATASET_TYPE.equals(externalData
+ .getDataSetType().getCode());
+ }
+
+ public static boolean isSegmentationHcsImageDataset(ExternalData externalData)
+ {
+ return isOneOfTypesMatching(externalData,
+ ScreeningConstants.IMAGE_OVERLAY_DATASET_TYPE_PATTERN,
+ ScreeningConstants.HCS_SEGMENTATION_IMAGE_DATASET_TYPE_PATTERN);
+ }
+
+ public static boolean isBasicHcsImageDataset(ExternalData externalData)
+ {
+ return isHcsImageDataset(externalData)
+ && isSegmentationHcsImageDataset(externalData) == false;
}
public static List<ExternalData> filterExternalDataByTypePattern(
@@ -164,7 +182,7 @@ public class ScreeningUtils
List<ExternalData> chosenDatasets = new ArrayList<ExternalData>();
for (ExternalData dataset : datasets)
{
- if (isTypeMatching(dataset, datasetTypeCodePatterns))
+ if (isOneOfTypesMatching(dataset, datasetTypeCodePatterns))
{
chosenDatasets.add(dataset);
}
@@ -172,7 +190,13 @@ public class ScreeningUtils
return chosenDatasets;
}
- private static boolean isTypeMatching(ExternalData dataset, String... datasetTypeCodePatterns)
+ public static boolean isTypeMatching(ExternalData dataset, String datasetTypeCodePattern)
+ {
+ return dataset.getDataSetType().getCode().matches(datasetTypeCodePattern);
+ }
+
+ private static boolean isOneOfTypesMatching(ExternalData dataset,
+ String... datasetTypeCodePatterns)
{
for (String datasetTypeCodePattern : datasetTypeCodePatterns)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/IScreeningApiServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/IScreeningApiServer.java
index 1ac2abf7a39..0201927d04b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/IScreeningApiServer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/IScreeningApiServer.java
@@ -141,6 +141,34 @@ public interface IScreeningApiServer extends IRpcService
@AuthorizationGuard(guardClass = ScreeningPlateListReadOnlyPredicate.class) List<? extends PlateIdentifier> plates)
throws IllegalArgumentException;
+ /**
+ * For a given set of plates provide the list of all data sets containing raw images for each of
+ * these plates.
+ *
+ * @since 1.6
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
+ @MinimalMinorVersion(6)
+ List<ImageDatasetReference> listRawImageDatasets(
+ String sessionToken,
+ @AuthorizationGuard(guardClass = ScreeningPlateListReadOnlyPredicate.class) List<? extends PlateIdentifier> plates)
+ throws IllegalArgumentException;
+
+ /**
+ * For a given set of plates provide the list of all data sets containing segmentation images
+ * for each of these plates.
+ *
+ * @since 1.6
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
+ @MinimalMinorVersion(6)
+ List<ImageDatasetReference> listSegmentationImageDatasets(
+ String sessionToken,
+ @AuthorizationGuard(guardClass = ScreeningPlateListReadOnlyPredicate.class) List<? extends PlateIdentifier> plates)
+ throws IllegalArgumentException;
+
/**
* Converts a given list of dataset codes to dataset identifiers.
*/
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageDatasetReference.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageDatasetReference.java
index 1a2b6f9d7f0..a6311acb17e 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageDatasetReference.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageDatasetReference.java
@@ -28,25 +28,51 @@ public class ImageDatasetReference extends DatasetReference implements IImageDat
{
private static final long serialVersionUID = 1L;
+ private final ImageDatasetReference parentImageDatasetReference;
+
@Deprecated
public ImageDatasetReference(String datasetCode, String datastoreServerUrl,
PlateIdentifier plate)
{
- super(datasetCode, datastoreServerUrl, plate);
+ this(datasetCode, datastoreServerUrl, plate, null, null, null, null, null);
}
@Deprecated
public ImageDatasetReference(String datasetCode, String datastoreServerUrl,
PlateIdentifier plate, Geometry plateGemoetry, Date registrationDate)
{
- super(datasetCode, datastoreServerUrl, plate, plateGemoetry, registrationDate);
+ this(datasetCode, datastoreServerUrl, plate, null, plateGemoetry, registrationDate, null,
+ null);
}
+ @Deprecated
public ImageDatasetReference(String datasetCode, String datastoreServerUrl,
PlateIdentifier plate, ExperimentIdentifier experimentIdentifier,
Geometry plateGemoetry, Date registrationDate, Map<String, String> propertiesOrNull)
+ {
+ this(datasetCode, datastoreServerUrl, plate, experimentIdentifier, plateGemoetry,
+ registrationDate, propertiesOrNull, null);
+ }
+
+ public ImageDatasetReference(String datasetCode, String datastoreServerUrl,
+ PlateIdentifier plate, ExperimentIdentifier experimentIdentifier,
+ Geometry plateGemoetry, Date registrationDate, Map<String, String> propertiesOrNull,
+ ImageDatasetReference parentImageSetsetReference)
{
super(datasetCode, datastoreServerUrl, plate, experimentIdentifier, plateGemoetry,
registrationDate, propertiesOrNull);
+ this.parentImageDatasetReference = parentImageSetsetReference;
}
+
+ /**
+ * Returns the image parent dataset of this data set, or <code>null</code>, if this data set
+ * doesn't have a parent image dataset or the server version is too old (< 1.6) to fill it.
+ *
+ * @since 1.6
+ */
+ public ImageDatasetReference getParentImageDatasetReference()
+ {
+ return parentImageDatasetReference;
+ }
+
}
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 f7713abe4f4..8d12db8fdf4 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
@@ -42,10 +42,20 @@ public class ScreeningConstants
// type of the dataset which stores plate image overlays
public static final String IMAGE_OVERLAY_DATASET_TYPE_PATTERN = ".*OVERLAY.*";
+ // type of the dataset which stores plate image overlays
+ public static final String HCS_SEGMENTATION_IMAGE_DATASET_TYPE_PATTERN =
+ "HCS_IMAGE_SEGMENTATION.*";
+
+ // Type of the dataset which stores raw plate images.
+ public static final String HCS_RAW_IMAGE_DATASET_TYPE_PATTERN = "HCS_IMAGE_RAW.*";
+
+ // The plain old legacy type for raw image data sets.
+ public static final String HCS_RAW_IMAGE_LEGACY_DATASET_TYPE = "HCS_IMAGE";
+
// Type of the dataset which stores plate images.
// We do not want old analysis data to match to this pattern.
public static final String HCS_IMAGE_DATASET_TYPE_PATTERN =
- ".*HCS_IMAGE($|[^_].*|_[^A].*|_A[^N].*|_AN[^A].*)";
+ ".*" + HCS_RAW_IMAGE_LEGACY_DATASET_TYPE + "($|[^_].*|_[^A].*|_A[^N].*|_AN[^A].*)";
public static final String HCS_PLATE_SAMPLE_TYPE_PATTERN = ".*PLATE.*";
@@ -80,7 +90,7 @@ public class ScreeningConstants
/** It's discouraged to use this constant. Code of the siRNA material type. */
public static final String SIRNA_PLUGIN_TYPE_NAME = "SIRNA";
-
+
public static final String SIRNA_WELL_TYPE_CODE = "SIRNA_WELL";
/** It's discouraged to use this constant. */
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImplTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImplTest.java
index 82a135cf92d..4b29c5d2238 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImplTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImplTest.java
@@ -18,6 +18,7 @@ package ch.systemsx.cisd.openbis.plugin.screening.server.logic;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Collections;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
@@ -171,6 +172,7 @@ public class ScreeningApiImplTest extends AbstractServerTestCase
});
List<ImageDatasetReference> dataSets = screeningApi.listImageDatasets(Arrays.asList(pi1));
+ assertEquals(1, dataSets.size());
assertEquals("1", dataSets.get(0).getDatasetCode());
assertEquals(Geometry.createFromRowColDimensions(16, 24), dataSets.get(0)
.getPlateGeometry());
@@ -179,7 +181,87 @@ public class ScreeningApiImplTest extends AbstractServerTestCase
// FIXME this check doesn't work because of space code (as well as 2 other cases below)
// assertEquals(pi1, dataSets.get(0).getPlate());
assertEquals(pi1.getPlateCode(), dataSets.get(0).getPlate().getPlateCode());
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testListRawImageDatasets()
+ {
+ final PlateIdentifier pi1 = createSharedPlate("p1");
+ context.checking(new Expectations()
+ {
+ {
+ one(screeningBOFactory).createSampleLister(SESSION);
+ will(returnValue(sampleLister));
+ one(sampleLister).list(with(any(ListOrSearchSampleCriteria.class)));
+ Sample p1 = plateSample(pi1, "384_WELLS_16X24");
+ will(returnValue(Arrays.asList(p1)));
+
+ one(screeningBOFactory).createDatasetLister(SESSION);
+ will(returnValue(datasetLister));
+ one(datasetLister).listBySampleIds(with(Arrays.asList((long) 1)));
+ will(returnValue(Arrays.asList(imageRawDataSet(p1, "1", 1),
+ imageRawDataSet(p1, "2", 2), imageAnalysisDataSet(p1, "3", 3))));
+ }
+ });
+
+ List<ImageDatasetReference> dataSets =
+ screeningApi.listRawImageDatasets(Arrays.asList(pi1));
+ assertEquals(2, dataSets.size());
+ assertEquals("1", dataSets.get(0).getDatasetCode());
+ assertEquals("2", dataSets.get(1).getDatasetCode());
+ assertEquals(Geometry.createFromRowColDimensions(16, 24), dataSets.get(0)
+ .getPlateGeometry());
+ assertEquals(Geometry.createFromRowColDimensions(16, 24), dataSets.get(1)
+ .getPlateGeometry());
+ assertEquals(new Date(100), dataSets.get(0).getRegistrationDate());
+ assertEquals(new Date(200), dataSets.get(1).getRegistrationDate());
+ assertEquals(SERVER_URL, dataSets.get(0).getDatastoreServerUrl());
+ assertEquals(SERVER_URL, dataSets.get(1).getDatastoreServerUrl());
+ // FIXME this check doesn't work because of space code (as well as 2 other cases below)
+ // assertEquals(pi1, dataSets.get(0).getPlate());
+ assertEquals(pi1.getPlateCode(), dataSets.get(0).getPlate().getPlateCode());
+ assertEquals(pi1.getPlateCode(), dataSets.get(1).getPlate().getPlateCode());
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testListSegmentationImageDatasets()
+ {
+ final PlateIdentifier pi1 = createSharedPlate("p1");
+ context.checking(new Expectations()
+ {
+ {
+ one(screeningBOFactory).createSampleLister(SESSION);
+ will(returnValue(sampleLister));
+ one(sampleLister).list(with(any(ListOrSearchSampleCriteria.class)));
+ Sample p1 = plateSample(pi1, "384_WELLS_16X24");
+ will(returnValue(Arrays.asList(p1)));
+
+ one(screeningBOFactory).createDatasetLister(SESSION);
+ will(returnValue(datasetLister));
+ one(datasetLister).listBySampleIds(with(Arrays.asList((long) 1)));
+ final ExternalData rawImage = imageRawDataSet(p1, "2", 2);
+ will(returnValue(Arrays.asList(imageDataSet(p1, "1", 1), rawImage,
+ imageSegmentationDataSet(p1, "3", 3, rawImage),
+ imageAnalysisDataSet(p1, "4", 4))));
+ }
+ });
+
+ List<ImageDatasetReference> dataSets =
+ screeningApi.listSegmentationImageDatasets(Arrays.asList(pi1));
assertEquals(1, dataSets.size());
+ assertEquals("3", dataSets.get(0).getDatasetCode());
+ assertEquals(Geometry.createFromRowColDimensions(16, 24), dataSets.get(0)
+ .getPlateGeometry());
+ assertEquals(new Date(300), dataSets.get(0).getRegistrationDate());
+ assertEquals(SERVER_URL, dataSets.get(0).getDatastoreServerUrl());
+ assertEquals("2", dataSets.get(0).getParentImageDatasetReference().getDatasetCode());
+ assertEquals(SERVER_URL, dataSets.get(0).getParentImageDatasetReference()
+ .getDatastoreServerUrl());
+ // FIXME this check doesn't work because of space code (as well as 2 other cases below)
+ // assertEquals(pi1, dataSets.get(0).getPlate());
+ assertEquals(pi1.getPlateCode(), dataSets.get(0).getPlate().getPlateCode());
context.assertIsSatisfied();
}
@@ -368,6 +450,28 @@ public class ScreeningApiImplTest extends AbstractServerTestCase
return dataSet;
}
+ private ExternalData imageRawDataSet(Sample sample, String code, long id)
+ {
+ ExternalData dataSet = createDataSet(sample, code, id);
+ dataSet.setDataSetType(dataSetType("HCS_IMAGE_RAW"));
+ dataSet.setExperiment(new Experiment());
+ dataSet.getExperiment().setProject(new Project());
+ dataSet.getExperiment().getProject().setSpace(new Space());
+ return dataSet;
+ }
+
+ private ExternalData imageSegmentationDataSet(Sample sample, String code, long id,
+ ExternalData parent)
+ {
+ ExternalData dataSet = createDataSet(sample, code, id);
+ dataSet.setDataSetType(dataSetType("HCS_IMAGE_SEGMENTATION"));
+ dataSet.setParents(Collections.singleton(parent));
+ dataSet.setExperiment(new Experiment());
+ dataSet.getExperiment().setProject(new Project());
+ dataSet.getExperiment().getProject().setSpace(new Space());
+ return dataSet;
+ }
+
private ExternalData imageAnalysisDataSet(Sample sample, String code, long id)
{
ExternalData dataSet = createDataSet(sample, code, id);
--
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