diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbsoluteImageReference.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbsoluteImageReference.java
index df7ab282b3c048125eb9f53be8aee3211088d167..1adc6e9a4c3a8e4b8a896f983c9f749efc977c13 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbsoluteImageReference.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbsoluteImageReference.java
@@ -16,8 +16,8 @@
package ch.systemsx.cisd.openbis.dss.etl;
-import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.common.io.IContent;
+import ch.systemsx.cisd.openbis.dss.etl.dto.ImageTransfomationFactories;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.RequestedImageSize;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
@@ -35,9 +35,7 @@ public class AbsoluteImageReference extends AbstractImageReference
private final RequestedImageSize imageSize;
- private IImageTransformerFactory transformerFactory;
-
- private IImageTransformerFactory transformerFactoryForMergedChannels;
+ private final ImageTransfomationFactories imageTransfomationFactories;
// This is an artificial value which helps to keep coloring channels constant. Starts with 0.
// Unique for a given experiment or dataset (if channels are per dataset).
@@ -47,14 +45,18 @@ public class AbsoluteImageReference extends AbstractImageReference
* @param content the content before choosing the color component and the page
*/
public AbsoluteImageReference(IContent content, String uniqueId, Integer pageOrNull,
- ColorComponent colorComponentOrNull, RequestedImageSize imageSize, int channelIndex)
+ ColorComponent colorComponentOrNull, RequestedImageSize imageSize, int channelIndex,
+ ImageTransfomationFactories imageTransfomationFactories)
{
super(pageOrNull, colorComponentOrNull);
assert imageSize != null : "image size is null";
+ assert imageTransfomationFactories != null : "imageTransfomationFactories is null";
+
this.content = content;
this.uniqueId = uniqueId;
this.imageSize = imageSize;
this.channelIndex = channelIndex;
+ this.imageTransfomationFactories = imageTransfomationFactories;
}
/**
@@ -76,14 +78,9 @@ public class AbsoluteImageReference extends AbstractImageReference
return imageSize;
}
- public final IImageTransformerFactory getTransformerFactory()
- {
- return transformerFactory;
- }
-
- public final IImageTransformerFactory getTransformerFactoryForMergedChannels()
+ public ImageTransfomationFactories getImageTransfomationFactories()
{
- return transformerFactoryForMergedChannels;
+ return imageTransfomationFactories;
}
public int getChannelIndex()
@@ -91,26 +88,11 @@ public class AbsoluteImageReference extends AbstractImageReference
return channelIndex;
}
- public final void setTransformerFactoryForMergedChannels(
- IImageTransformerFactory transformerFactoryForMergedChannels)
- {
- this.transformerFactoryForMergedChannels = transformerFactoryForMergedChannels;
- }
-
- public final void setTransformerFactory(IImageTransformerFactory transformerFactory)
- {
- this.transformerFactory = transformerFactory;
- }
-
public AbsoluteImageReference createWithoutColorComponent()
{
ColorComponent colorComponent = null;
- AbsoluteImageReference ref =
- new AbsoluteImageReference(content, uniqueId, tryGetPage(), colorComponent,
- imageSize, channelIndex);
- ref.setTransformerFactory(transformerFactory);
- ref.setTransformerFactoryForMergedChannels(transformerFactoryForMergedChannels);
- return ref;
+ return new AbsoluteImageReference(content, uniqueId, tryGetPage(), colorComponent,
+ imageSize, channelIndex, imageTransfomationFactories);
}
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingDatasetLoader.java
index 6f07a138145a1895049916c414d2845383a0d6cc..c24810d9657f77db13f96cc407a0fd450dbf4f55 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingDatasetLoader.java
@@ -25,6 +25,7 @@ import ch.systemsx.cisd.common.io.IContent;
import ch.systemsx.cisd.openbis.dss.etl.AbsoluteImageReference;
import ch.systemsx.cisd.openbis.dss.etl.IContentRepository;
import ch.systemsx.cisd.openbis.dss.etl.IImagingDatasetLoader;
+import ch.systemsx.cisd.openbis.dss.etl.dto.ImageTransfomationFactories;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageChannelStackReference;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageChannelStackReference.HCSChannelStackByLocationReference;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageChannelStackReference.MicroscopyChannelStackByLocationReference;
@@ -91,20 +92,21 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
String path = imageDTO.getFilePath();
IContent content = contentRepository.getContent(path);
ColorComponent colorComponent = imageDTO.getColorComponent();
- AbsoluteImageReference imgRef =
- new AbsoluteImageReference(content, path, imageDTO.getPage(), colorComponent,
- imageSize, getChannelIndex(channel));
- imgRef.setTransformerFactoryForMergedChannels(tryGetImageTransformerFactoryForMergedChannels());
- imgRef.setTransformerFactory(channel.getImageTransformerFactory());
- return imgRef;
+ ImageTransfomationFactories imageTransfomationFactories = new ImageTransfomationFactories();
+ imageTransfomationFactories
+ .setForMergedChannels(tryGetImageTransformerFactoryForMergedChannels());
+ imageTransfomationFactories.setForChannel(channel.tryGetImageTransformerFactory());
+ imageTransfomationFactories.setForImage(imageDTO.tryGetImageTransformerFactory());
+ return new AbsoluteImageReference(content, path, imageDTO.getPage(), colorComponent,
+ imageSize, getChannelIndex(channel), imageTransfomationFactories);
}
private IImageTransformerFactory tryGetImageTransformerFactoryForMergedChannels()
{
- IImageTransformerFactory imageTransformerFactory = dataset.getImageTransformerFactory();
+ IImageTransformerFactory imageTransformerFactory = dataset.tryGetImageTransformerFactory();
if (imageTransformerFactory == null && experimentOrNull != null)
{
- imageTransformerFactory = experimentOrNull.getImageTransformerFactory();
+ imageTransformerFactory = experimentOrNull.tryGetImageTransformerFactory();
}
return imageTransformerFactory;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/ImageTransfomationFactories.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/ImageTransfomationFactories.java
new file mode 100644
index 0000000000000000000000000000000000000000..3a6aa9f26c661afaf8029fc3fc5d1546514ec10d
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/ImageTransfomationFactories.java
@@ -0,0 +1,62 @@
+/*
+ * 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.dss.etl.dto;
+
+import ch.systemsx.cisd.base.image.IImageTransformerFactory;
+
+/**
+ * Stores transformations defined for the image on different levels.
+ *
+ * @author Tomasz Pylak
+ */
+public class ImageTransfomationFactories
+{
+ // applied when a single channel is displayed
+ private IImageTransformerFactory singleChannel;
+
+ // applied when all channels of the image are merged
+ private IImageTransformerFactory mergedChannels;
+
+ // individual transformation for the image
+ private IImageTransformerFactory image;
+
+ public IImageTransformerFactory tryGetForChannel(boolean areChannelsMerged)
+ {
+ return areChannelsMerged ? mergedChannels : singleChannel;
+ }
+
+ public void setForChannel(IImageTransformerFactory transformerFactoryForChannel)
+ {
+ this.singleChannel = transformerFactoryForChannel;
+ }
+
+ public void setForMergedChannels(IImageTransformerFactory transformerFactoryForMergedChannels)
+ {
+ this.mergedChannels = transformerFactoryForMergedChannels;
+ }
+
+ public IImageTransformerFactory tryGetForImage()
+ {
+ return image;
+ }
+
+ public void setForImage(IImageTransformerFactory transformerFactoryForImage)
+ {
+ this.image = transformerFactoryForImage;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtils.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtils.java
index 1f50bd38599f764c69e074b7f7a7a43684c78207..4348e6bfb240f222da0de87272e88af4e43b8a5d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtils.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtils.java
@@ -43,6 +43,7 @@ import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.openbis.dss.etl.AbsoluteImageReference;
import ch.systemsx.cisd.openbis.dss.etl.HCSImageDatasetLoaderFactory;
import ch.systemsx.cisd.openbis.dss.etl.IImagingDatasetLoader;
+import ch.systemsx.cisd.openbis.dss.etl.dto.ImageTransfomationFactories;
import ch.systemsx.cisd.openbis.dss.generic.server.ResponseContentStream;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.DatasetAcquiredImagesReference;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageChannelStackReference;
@@ -206,6 +207,8 @@ public class ImageChannelsUtils
return mergeChannels(imageContents, transform, mergeAllChannels);
}
+ // Check if all exiting channels of the image should be merged (and not a single one or a
+ // subset).
// We want to treat the case where merged channels were requested in the same way as the case
// where all channel names have been enumerated.
private boolean isMergeAllChannels(DatasetAcquiredImagesReference imageChannels)
@@ -420,14 +423,8 @@ public class ImageChannelsUtils
private static BufferedImage calculateAndTransformSingleImage(
AbsoluteImageReference imageReference, boolean transform, boolean allChannelsMerged)
{
- IImageTransformerFactory transformerFactory = null;
- if (transform)
- {
- transformerFactory =
- allChannelsMerged ? imageReference.getTransformerFactoryForMergedChannels()
- : imageReference.getTransformerFactory();
- }
- return transform(calculateSingleImage(imageReference), transformerFactory);
+ BufferedImage image = calculateSingleImage(imageReference);
+ return transform(image, imageReference, transform, allChannelsMerged);
}
private static BufferedImage calculateSingleImage(AbsoluteImageReference imageReference)
@@ -489,31 +486,48 @@ public class ImageChannelsUtils
private static BufferedImage mergeChannels(List<AbsoluteImageReference> imageReferences,
boolean transform, boolean allChannelsMerged)
{
+ AbsoluteImageReference singleImageReference = imageReferences.get(0);
if (imageReferences.size() == 1)
{
- AbsoluteImageReference imageReference = imageReferences.get(0);
- return calculateAndTransformSingleImage(imageReference, transform, allChannelsMerged);
+ return calculateAndTransformSingleImage(singleImageReference, transform,
+ allChannelsMerged);
} else
{
List<ImageWithReference> images = calculateSingleImages(imageReferences);
BufferedImage mergedImage = mergeImages(images);
// NOTE: even if we are not merging all the channels but just few of them we use the
// merged-channel transformation
- IImageTransformerFactory transformerFactory =
- transform ? imageReferences.get(0).getTransformerFactoryForMergedChannels()
- : null;
- return transform(mergedImage, transformerFactory);
+ return transform(mergedImage, singleImageReference, transform, true);
+ }
+ }
+
+ private static BufferedImage transform(BufferedImage image,
+ AbsoluteImageReference imageReference, boolean transform, boolean allChannelsMerged)
+ {
+ BufferedImage resultImage = image;
+ ImageTransfomationFactories transfomations =
+ imageReference.getImageTransfomationFactories();
+ // image level transformation is applied always, as it cannot be applied or changed in
+ // external image viewer
+ resultImage = applyImageTransformation(resultImage, transfomations.tryGetForImage());
+
+ if (transform == false)
+ {
+ return resultImage;
}
+ IImageTransformerFactory channelLevelTransformation =
+ transfomations.tryGetForChannel(allChannelsMerged);
+ return applyImageTransformation(resultImage, channelLevelTransformation);
}
- private static BufferedImage transform(BufferedImage input,
- IImageTransformerFactory factoryOrNull)
+ private static BufferedImage applyImageTransformation(BufferedImage image,
+ IImageTransformerFactory transformerFactoryOrNull)
{
- if (factoryOrNull == null)
+ if (transformerFactoryOrNull == null)
{
- return input;
+ return image;
}
- return factoryOrNull.createTransformer().transform(input);
+ return transformerFactoryOrNull.createTransformer().transform(image);
}
private static class ImageWithReference
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
index 1dc3538e0625960cee66135ba64faf850e8e134f..ee825310f453748da5ec15663e99dfcf35d83b24 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
@@ -127,8 +127,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
DssServiceRpcScreening(String storeRootDir, IImagingReadonlyQueryDAO dao,
IImagingTransformerDAO transformerDAO, IEncapsulatedOpenBISService service,
- IShareIdManager shareIdManager,
- boolean registerAtNameService)
+ IShareIdManager shareIdManager, boolean registerAtNameService)
{
super(service, shareIdManager);
this.dao = dao;
@@ -747,14 +746,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
+ dataSetIdentifiers);
}
String experimentPermID = experimentPermIDs.iterator().next();
- if (isMergedChannel(channel))
- {
- return getDAO().tryGetExperimentByPermId(experimentPermID).getImageTransformerFactory();
- } else
- {
- return getDAO().tryGetChannelForExperimentPermId(experimentPermID, channel)
- .getImageTransformerFactory();
- }
+ return tryGetImageTransformerFactoryForExperiment(experimentPermID, channel);
}
private Set<String> getExperimentPermIDs(String sessionToken,
@@ -781,11 +773,24 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
ImgDatasetDTO dataset = getImagingDataset(datasetIdentifier);
if (isMergedChannel(channel))
{
- return dataset.getImageTransformerFactory();
+ return dataset.tryGetImageTransformerFactory();
} else
{
return getDAO().tryGetChannelForDataset(dataset.getId(), channel)
- .getImageTransformerFactory();
+ .tryGetImageTransformerFactory();
+ }
+ }
+
+ private IImageTransformerFactory tryGetImageTransformerFactoryForExperiment(
+ String experimentPermID, String channel)
+ {
+ if (isMergedChannel(channel))
+ {
+ return getDAO().tryGetExperimentByPermId(experimentPermID).tryGetImageTransformerFactory();
+ } else
+ {
+ return getDAO().tryGetChannelForExperimentPermId(experimentPermID, channel)
+ .tryGetImageTransformerFactory();
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/AbstractImageTransformerFactoryHolder.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/AbstractImageTransformerFactoryHolder.java
index b4ad0f7adec2ddb44b5cd1fc7a345731cbc92e44..4eead6285eb9353de40a17d243849353e49f8d92 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/AbstractImageTransformerFactoryHolder.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/AbstractImageTransformerFactoryHolder.java
@@ -43,7 +43,7 @@ abstract class AbstractImageTransformerFactoryHolder extends AbstractHashable
this.serializedImageTransformerFactory = serializedImageTransformerFactory;
}
- public IImageTransformerFactory getImageTransformerFactory()
+ public IImageTransformerFactory tryGetImageTransformerFactory()
{
if (serializedImageTransformerFactory == null)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingTransformerDAO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingTransformerDAO.java
index 4e59a6dd10dc7829655c3059d5539b3e2191d72d..f08a89140afb2167a9ee472cd45558577ac3a4aa 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingTransformerDAO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingTransformerDAO.java
@@ -36,6 +36,10 @@ public interface IImagingTransformerDAO extends TransactionQuery
{ TransformerFactoryMapper.class, TypeMapper.class /* default */})
public void saveTransformerFactoryForDataset(long datasetId, IImageTransformerFactory factory);
+ @Update(sql = "update images set image_transformer_factory = ?{2} where id = ?{1}", parameterBindings =
+ { TransformerFactoryMapper.class, TypeMapper.class /* default */})
+ public void saveTransformerFactoryForImage(long imageId, IImageTransformerFactory factory);
+
@Update(sql = "update channels set image_transformer_factory = ?{3} "
+ "where code = ?{2} and exp_id = ?{1}", parameterBindings =
{ TransformerFactoryMapper.class, TypeMapper.class/* default */, TypeMapper.class /* default */})
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgImageDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgImageDTO.java
index 3c0d33c38e19dde1dfb22f43da9c58c2d58ac92c..b3ccb8a864939d6876adee4b3734121a8a6a083f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgImageDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgImageDTO.java
@@ -18,12 +18,10 @@ package ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess;
import net.lemnik.eodsql.ResultColumn;
-import ch.systemsx.cisd.common.utilities.AbstractHashable;
-
/**
* @author Tomasz Pylak
*/
-public class ImgImageDTO extends AbstractHashable
+public class ImgImageDTO extends AbstractImageTransformerFactoryHolder
{
@ResultColumn("id")
private long id;
@@ -36,7 +34,7 @@ public class ImgImageDTO extends AbstractHashable
@ResultColumn("COLOR")
private String colorComponentOrNull;
-
+
@SuppressWarnings("unused")
private ImgImageDTO()
{
diff --git a/screening/source/sql/postgresql/010/data.sql b/screening/source/sql/postgresql/010/data.sql
new file mode 100644
index 0000000000000000000000000000000000000000..f08222c48c2932180be40863f775e14dac5267bc
--- /dev/null
+++ b/screening/source/sql/postgresql/010/data.sql
@@ -0,0 +1,275 @@
+-- Note that these data has to be loaded manually into the openBIS Core database.
+
+-- TODO: this sql should be converted to a generic sql without refering to technical ids.
+-- Now the ids should be updated if some new records will be added in the generic data.
+
+--
+-- PostgreSQL database dump
+--
+
+SET statement_timeout = 0;
+SET client_encoding = 'UTF8';
+SET standard_conforming_strings = off;
+SET check_function_bodies = false;
+SET client_min_messages = warning;
+SET escape_string_warning = off;
+
+SET search_path = public, pg_catalog;
+
+--
+-- Data for Name: controlled_vocabularies; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY controlled_vocabularies (id, code, description, registration_timestamp, pers_id_registerer, is_managed_internally, is_internal_namespace, dbin_id, modification_timestamp, is_chosen_from_list, source_uri) FROM stdin;
+2 PLATE_GEOMETRY The geometry or dimensions of a plate 2008-06-17 16:38:30.723292+02 1 t t 1 2009-11-27 16:02:26.451046+01 t \N
+3 MICROSCOPE Microscope used in an experiment. 2009-11-29 23:55:18.978884+01 1 f f 1 2009-12-17 01:50:54.68+01 t \N
+\.
+
+
+--
+-- Data for Name: controlled_vocabulary_terms; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY controlled_vocabulary_terms (id, code, registration_timestamp, covo_id, pers_id_registerer, label, description, ordinal) FROM stdin;
+3 384_WELLS_16X24 2008-06-17 16:38:30.723292+02 2 1 384 Wells, 16x24 \N 1
+4 96_WELLS_8X12 2008-06-17 16:38:31.101031+02 2 1 96 Wells, 8x12 \N 2
+5 1536_WELLS_32X48 2008-06-17 16:38:31.101031+02 2 1 1536 Wells, 32x48 \N 3
+6 BD_PATHWAY_855 2009-11-29 23:55:18.978884+01 3 1 \N \N 1
+7 MD_IMAGEXPRESS_MICROLIVE 2009-11-29 23:55:18.978884+01 3 1 \N \N 2
+8 MD_IMAGEXPRESS_MICRO_2 2009-11-29 23:55:18.978884+01 3 1 \N \N 3
+\.
+
+
+--
+-- Data for Name: data_set_types; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY data_set_types (id, code, description, dbin_id, modification_timestamp) FROM stdin;
+3 HCS_IMAGE_ANALYSIS_DATA Data derived from analysis of HCS images 1 2009-11-27 16:02:26.451046+01
+2 HCS_IMAGE HCS raw images acquired by microscopes 1 2009-11-27 16:02:26.451046+01
+4 HCS_ANALYSIS_PER_GENE Image analysis data aggregated per gene. 1 2009-12-16 16:59:50.743029+01
+\.
+
+
+--
+-- Data for Name: material_types; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY material_types (id, code, description, dbin_id, modification_timestamp) FROM stdin;
+1 VIRUS Virus 1 2009-11-27 16:02:26.451046+01
+2 CELL_LINE Cell Line or Cell Culture. The growing of cells under controlled conditions. 1 2009-11-27 16:02:26.451046+01
+3 GENE Gene 1 2009-11-27 16:02:26.451046+01
+4 SIRNA siRNA nucleotide 1 2009-11-27 16:02:26.451046+01
+5 CONTROL Control of a control layout 1 2009-11-27 16:02:26.451046+01
+6 BACTERIUM Bacterium 1 2009-11-27 16:02:26.451046+01
+7 COMPOUND Compound 1 2009-11-27 16:02:26.451046+01
+\.
+
+
+--
+-- Data for Name: property_types; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY property_types (id, code, description, label, daty_id, registration_timestamp, pers_id_registerer, covo_id, is_managed_internally, is_internal_namespace, dbin_id, maty_prop_id) FROM stdin;
+3 NUCLEOTIDE_SEQUENCE A sequence of nucleotides Nucleotide Sequence 1 2008-02-28 13:03:03.358532+01 1 \N f f 1 \N
+4 REFSEQ NCBI Reference Sequence code, applicable to sequences of type: DNA, RNA, protein RefSeq 1 2008-02-28 13:03:03.358532+01 1 \N f f 1 \N
+13 MICROSCOPE Microscope 7 2009-11-29 23:57:05.85618+01 1 3 f f 1 \N
+7 INHIBITOR_OF Inhibitor Of Inhibitor Of 8 2009-11-27 16:02:45.060699+01 1 \N f f 1 3
+11 SIRNA siRNA siRNA 8 2009-11-29 23:56:19.39967+01 1 \N f f 1 4
+12 CONTROL Control Control 8 2009-11-29 23:56:37.355313+01 1 \N f f 1 5
+6 PLATE_GEOMETRY Plate Geometry Plate Geometry 7 2008-06-17 16:38:30.723292+02 1 2 t t 1 \N
+15 NUMBER_OF_CHANNEL Channels 3 2009-12-17 10:56:17.239319+01 1 \N f f 1 \N
+16 LIBRARY_ID Library id Id from the master plate library 1 2008-02-28 13:03:03.358532+01 1 \N f f 1 \N
+\.
+
+
+--
+-- Data for Name: data_set_type_property_types; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY data_set_type_property_types (id, dsty_id, prty_id, is_mandatory, is_managed_internally, pers_id_registerer, registration_timestamp, section, ordinal) FROM stdin;
+\.
+
+
+--
+-- Data for Name: experiment_types; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY experiment_types (id, code, description, dbin_id, modification_timestamp) FROM stdin;
+2 COMPOUND_HCS Compound High Content Screening 1 2009-11-27 16:02:26.451046+01
+1 SIRNA_HCS Small Interfering RNA High Content Screening 1 2009-11-27 16:02:26.451046+01
+\.
+
+
+--
+-- Data for Name: experiment_type_property_types; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY experiment_type_property_types (id, exty_id, prty_id, is_mandatory, is_managed_internally, pers_id_registerer, registration_timestamp, section, ordinal) FROM stdin;
+1 1 1 t t 1 2008-06-17 16:38:49.023295+02 \N 1
+2 2 1 t t 1 2008-06-17 16:38:49.301922+02 \N 1
+5 1 13 f f 1 2009-12-17 10:54:01.261178+01 \N 2
+\.
+
+
+--
+-- Data for Name: file_format_types; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY file_format_types (id, code, description, dbin_id) FROM stdin;
+7 PNG \N 1
+8 CSV files with values separated by comma or semicolon 1
+9 JPG \N 1
+\.
+
+
+--
+-- Data for Name: filters; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY filters (id, dbin_id, name, description, registration_timestamp, pers_id_registerer, modification_timestamp, expression, is_public, grid_id) FROM stdin;
+9 1 Infection index \N 2009-12-16 21:19:19.012657+01 1 2009-12-16 22:41:56.863+01 float(row.col('colIndex_5')) > float(${threshold}) t data-set-reporting-gridplate-image-analysis-merger
+8 1 Total number of cells \N 2009-12-16 21:18:05.161964+01 1 2009-12-16 22:42:31.707+01 int(row.col('colIndex_3')) > int(${threshold}) t data-set-reporting-gridplate-image-analysis-merger
+7 1 Number of infected cells \N 2009-12-16 21:17:40.765083+01 1 2009-12-16 22:42:46.052+01 int(row.col('colIndex_4')) > int(${threshold}) t data-set-reporting-gridplate-image-analysis-merger
+\.
+
+
+--
+-- Data for Name: material_type_property_types; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY material_type_property_types (id, maty_id, prty_id, is_mandatory, registration_timestamp, pers_id_registerer, is_managed_internally, section, ordinal) FROM stdin;
+10 4 7 t 2009-11-27 16:02:45.060699+01 1 f \N 4
+9 5 1 f 2008-02-28 13:03:03.358532+01 1 f \N 1
+8 4 1 f 2008-02-28 13:03:03.358532+01 1 f \N 3
+6 4 3 t 2008-02-28 13:03:03.358532+01 1 f \N 1
+12 4 16 f 2008-02-28 13:03:03.358532+01 1 f \N 1
+5 3 1 f 2008-02-28 13:03:03.358532+01 1 f \N 2
+3 7 1 t 2008-02-28 13:03:03.358532+01 1 f \N 1
+2 6 1 t 2008-02-28 13:03:03.358532+01 1 f \N 1
+1 1 1 t 2008-02-28 13:03:03.358532+01 1 f \N 1
+\.
+
+
+--
+-- Data for Name: sample_types; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY sample_types (id, code, description, dbin_id, is_listable, generated_from_depth, part_of_depth, modification_timestamp, is_auto_generated_code, generated_code_prefix) FROM stdin;
+3 PLATE Cell Plate 1 t 2 0 2009-11-27 16:02:26.451046+01 f S
+7 SIRNA_WELL \N 1 f 0 1 2009-11-27 19:42:03.483115+01 f O
+8 CONTROL_WELL \N 1 f 0 1 2009-11-27 19:42:25.791288+01 f C
+9 LIBRARY \N 1 f 0 0 2009-11-27 19:42:25.791288+01 f L
+\.
+
+
+--
+-- Data for Name: sample_type_property_types; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY sample_type_property_types (id, saty_id, prty_id, is_mandatory, is_managed_internally, pers_id_registerer, registration_timestamp, is_displayed, section, ordinal) FROM stdin;
+8 7 11 f f 1 2009-11-29 23:57:38.268212+01 t \N 1
+9 8 12 f f 1 2009-11-29 23:57:49.098187+01 t \N 1
+10 3 6 f f 1 2009-11-30 01:28:20.972263+01 t \N 1
+\.
+
+--
+-- PostgreSQL database dump complete
+--
+
+--------------------------------------------------
+-- update sequences values
+--------------------------------------------------
+
+select setval('controlled_vocabulary_id_seq', 100);
+select setval('cvte_id_seq', 100);
+select setval('property_type_id_seq', 100);
+select setval('file_format_type_id_seq', 100);
+select setval('filter_id_seq', 100);
+select setval('experiment_type_id_seq', 100);
+select setval('sample_type_id_seq', 100);
+select setval('data_set_type_id_seq', 100);
+select setval('material_type_id_seq', 100);
+select setval('etpt_id_seq', 100);
+select setval('stpt_id_seq', 100);
+select setval('mtpt_id_seq', 100);
+
+
+--------------------------------------------------
+-- create a gene property and assign it to sirna well
+--------------------------------------------------
+
+insert into property_types(
+ id,
+ code, description, label,
+ daty_id,
+ pers_id_registerer,
+ dbin_id,
+ maty_prop_id)
+values(
+ nextval('PROPERTY_TYPE_ID_SEQ'),
+ 'GENE','Inhibited gene','Gene',
+ (select id from data_types where code = 'MATERIAL'),
+ (select id from persons where user_id ='system'),
+ (select id from database_instances where is_original_source = 'T'),
+ (select id from material_types where code = 'GENE')
+ );
+
+insert into sample_type_property_types(
+ id,
+ saty_id,
+ prty_id,
+ is_mandatory,
+ pers_id_registerer,
+ ordinal
+) values(
+ nextval('stpt_id_seq'),
+ (select id from sample_types where code = 'SIRNA_WELL'),
+ (select id from property_types where code = 'GENE'),
+ false,
+ (select id from persons where user_id ='system'),
+ (select max(ordinal)+1 from sample_type_property_types
+ where saty_id = (select id from sample_types where code = 'SIRNA_WELL'))
+ );
+
+
+--------------------------------------------------
+-- Create gene property: gene_symbols
+--------------------------------------------------
+
+
+ insert into property_types
+ (id
+ ,code
+ ,description
+ ,label
+ ,daty_id
+ ,pers_id_registerer
+ ,dbin_id)
+ values
+ (nextval('PROPERTY_TYPE_ID_SEQ')
+ ,'GENE_SYMBOLS'
+ ,'Gene symbols'
+ ,'Gene symbols'
+ ,(select id from data_types where code ='VARCHAR')
+ ,(select id from persons where user_id ='system')
+ ,(select id from database_instances where is_original_source = 'T')
+ );
+
+ insert into material_type_property_types(
+ id,
+ maty_id,
+ prty_id,
+ is_mandatory,
+ pers_id_registerer,
+ ordinal
+ ) values(
+ nextval('mtpt_id_seq'),
+ (select id from material_types where code = 'GENE'),
+ (select id from property_types where code = 'GENE_SYMBOLS'),
+ false,
+ (select id from persons where user_id ='system'),
+ (select max(ordinal)+1 from material_type_property_types
+ where maty_id = (select id from material_types where code = 'GENE'))
+ );
+
diff --git a/screening/source/sql/postgresql/010/schema-010.sql b/screening/source/sql/postgresql/010/schema-010.sql
new file mode 100644
index 0000000000000000000000000000000000000000..681a48e7475b37745e2c199da0d840ea246cb176
--- /dev/null
+++ b/screening/source/sql/postgresql/010/schema-010.sql
@@ -0,0 +1,273 @@
+
+/* ---------------------------------------------------------------------- */
+/* Domains */
+/* ---------------------------------------------------------------------- */
+
+CREATE DOMAIN TECH_ID AS BIGINT;
+
+CREATE DOMAIN CODE AS VARCHAR(40);
+
+CREATE DOMAIN NAME AS VARCHAR(80);
+
+CREATE DOMAIN DESCRIPTION AS VARCHAR(200);
+
+CREATE DOMAIN FILE_PATH as VARCHAR(1000);
+
+CREATE DOMAIN COLOR_COMPONENT AS VARCHAR(40) CHECK (VALUE IN ('RED', 'GREEN', 'BLUE'));
+
+CREATE DOMAIN BOOLEAN_CHAR AS BOOLEAN DEFAULT FALSE;
+
+/* ---------------------------------------------------------------------- */
+/* Tables */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE EXPERIMENTS (
+ ID BIGSERIAL NOT NULL,
+ PERM_ID CODE NOT NULL,
+ IMAGE_TRANSFORMER_FACTORY BYTEA,
+
+ PRIMARY KEY (ID),
+ UNIQUE (PERM_ID)
+);
+
+CREATE TABLE CONTAINERS (
+ ID BIGSERIAL NOT NULL,
+ PERM_ID CODE NOT NULL,
+
+ SPOTS_WIDTH INTEGER,
+ SPOTS_HEIGHT INTEGER,
+
+ EXPE_ID TECH_ID NOT NULL,
+
+ PRIMARY KEY (ID),
+ UNIQUE (PERM_ID),
+ CONSTRAINT FK_SAMPLE_1 FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+CREATE INDEX CONTAINERS_EXPE_IDX ON CONTAINERS(EXPE_ID);
+
+CREATE TABLE SPOTS (
+ ID BIGSERIAL NOT NULL,
+
+ -- position in the container, one-based
+ X INTEGER,
+ Y INTEGER,
+ CONT_ID TECH_ID NOT NULL,
+
+ PRIMARY KEY (ID),
+ CONSTRAINT FK_SPOT_1 FOREIGN KEY (CONT_ID) REFERENCES CONTAINERS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+CREATE INDEX SPOTS_CONT_IDX ON SPOTS(CONT_ID);
+-- allows to select one spot of the container quicker
+CREATE INDEX SPOTS_COORDS_IDX ON SPOTS(CONT_ID, X, Y);
+
+CREATE TABLE DATA_SETS (
+ ID BIGSERIAL NOT NULL,
+ PERM_ID CODE NOT NULL,
+
+ FIELDS_WIDTH INTEGER,
+ FIELDS_HEIGHT INTEGER,
+
+ CONT_ID TECH_ID,
+ -- a redundant information if there are timepoint or depth stack data for any spots in this dataset
+ IS_MULTIDIMENSIONAL BOOLEAN_CHAR NOT NULL,
+ -- transformation for merged channels on the dataset level, overrides experiment level transformation
+ IMAGE_TRANSFORMER_FACTORY BYTEA,
+
+ PRIMARY KEY (ID),
+ UNIQUE (PERM_ID),
+ CONSTRAINT FK_DATA_SET_1 FOREIGN KEY (CONT_ID) REFERENCES CONTAINERS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+CREATE INDEX DATA_SETS_CONT_IDX ON DATA_SETS(CONT_ID);
+
+CREATE TABLE CHANNELS (
+ ID BIGSERIAL NOT NULL,
+
+ CODE NAME NOT NULL,
+ LABEL NAME NOT NULL,
+ DESCRIPTION DESCRIPTION,
+ WAVELENGTH INTEGER,
+ IMAGE_TRANSFORMER_FACTORY BYTEA,
+
+ DS_ID TECH_ID,
+ EXP_ID TECH_ID,
+
+ PRIMARY KEY (ID),
+ CONSTRAINT FK_CHANNELS_1 FOREIGN KEY (DS_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+ CONSTRAINT FK_CHANNELS_2 FOREIGN KEY (EXP_ID) REFERENCES EXPERIMENTS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+ CONSTRAINT CHANNELS_DS_EXP_ARC_CK CHECK ((DS_ID IS NOT NULL AND EXP_ID IS NULL) OR (DS_ID IS NULL AND EXP_ID IS NOT NULL)),
+
+ CONSTRAINT CHANNELS_UK_1 UNIQUE(CODE, DS_ID),
+ CONSTRAINT CHANNELS_UK_2 UNIQUE(CODE, EXP_ID)
+);
+
+CREATE INDEX CHANNELS_DS_IDX ON CHANNELS(DS_ID);
+
+CREATE TABLE CHANNEL_STACKS (
+ ID BIGSERIAL NOT NULL,
+
+ -- x and y are kind of a two dimensional sequence number, some use case may only use x and leave y alone
+ X INTEGER,
+ Y INTEGER,
+ -- We use the fixed dimension meters here.
+ Z_in_M REAL,
+ -- We use the fixed dimension seconds here.
+ T_in_SEC REAL,
+ SERIES_NUMBER INTEGER,
+
+ -- For all channel stacks of a well (HCS) or image dataset (microscopy) there should be exactly
+ -- one record with is_representative = true
+ is_representative BOOLEAN_CHAR NOT NULL DEFAULT 'F',
+
+ DS_ID TECH_ID NOT NULL,
+ SPOT_ID TECH_ID,
+
+ PRIMARY KEY (ID),
+ CONSTRAINT FK_CHANNEL_STACKS_1 FOREIGN KEY (SPOT_ID) REFERENCES SPOTS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+ CONSTRAINT FK_CHANNEL_STACKS_2 FOREIGN KEY (DS_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+CREATE INDEX CHANNEL_STACKS_DS_IDX ON CHANNEL_STACKS(DS_ID);
+CREATE INDEX CHANNEL_STACKS_SPOT_IDX ON CHANNEL_STACKS(SPOT_ID);
+CREATE INDEX CHANNEL_STACKS_DIM_IDX ON CHANNEL_STACKS(X, Y, Z_in_M, T_in_SEC);
+
+CREATE TABLE IMAGES (
+ ID BIGSERIAL NOT NULL,
+
+ PATH FILE_PATH NOT NULL,
+ PAGE INTEGER,
+ COLOR COLOR_COMPONENT,
+ IMAGE_TRANSFORMER_FACTORY BYTEA,
+
+ PRIMARY KEY (ID)
+);
+
+CREATE TABLE ACQUIRED_IMAGES (
+ ID BIGSERIAL NOT NULL,
+
+ IMG_ID TECH_ID NOT NULL,
+ THUMBNAIL_ID TECH_ID,
+
+ CHANNEL_STACK_ID TECH_ID NOT NULL,
+ CHANNEL_ID TECH_ID NOT NULL,
+
+ PRIMARY KEY (ID),
+ CONSTRAINT FK_IMAGES_1 FOREIGN KEY (CHANNEL_STACK_ID) REFERENCES CHANNEL_STACKS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+ CONSTRAINT FK_IMAGES_2 FOREIGN KEY (CHANNEL_ID) REFERENCES CHANNELS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+ CONSTRAINT FK_IMAGES_3 FOREIGN KEY (IMG_ID) REFERENCES IMAGES (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+ CONSTRAINT FK_IMAGES_4 FOREIGN KEY (THUMBNAIL_ID) REFERENCES IMAGES (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+CREATE INDEX IMAGES_CHANNEL_STACK_IDX ON ACQUIRED_IMAGES(CHANNEL_STACK_ID);
+CREATE INDEX IMAGES_CHANNEL_IDX ON ACQUIRED_IMAGES(CHANNEL_ID);
+CREATE INDEX IMAGES_IMG_IDX ON ACQUIRED_IMAGES(IMG_ID);
+CREATE INDEX IMAGES_THUMBNAIL_IDX ON ACQUIRED_IMAGES(THUMBNAIL_ID);
+
+CREATE TABLE EVENTS (
+ LAST_SEEN_DELETION_EVENT_ID TECH_ID NOT NULL
+);
+
+/* ---------------------------------------------------------------------- */
+/* FEATURE VECTORS */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE FEATURE_DEFS (
+ ID BIGSERIAL NOT NULL,
+
+ CODE NAME NOT NULL,
+ LABEL NAME NOT NULL,
+ DESCRIPTION DESCRIPTION,
+
+ DS_ID TECH_ID NOT NULL,
+
+ PRIMARY KEY (ID),
+ CONSTRAINT FK_FEATURE_DEFS_1 FOREIGN KEY (DS_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+ CONSTRAINT FEATURE_DEFS_UK_1 UNIQUE(CODE, DS_ID)
+);
+
+CREATE INDEX FEATURE_DEFS_DS_IDX ON FEATURE_DEFS(DS_ID);
+
+CREATE TABLE FEATURE_VOCABULARY_TERMS (
+ ID BIGSERIAL NOT NULL,
+
+ CODE NAME NOT NULL,
+ SEQUENCE_NUMBER INTEGER NOT NULL,
+ FD_ID TECH_ID NOT NULL,
+
+ PRIMARY KEY (ID),
+ CONSTRAINT FK_FEATURE_VOCABULARY_TERMS_1 FOREIGN KEY (FD_ID) REFERENCES FEATURE_DEFS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+CREATE INDEX FEATURE_VOCABULARY_TERMS_FD_IDX ON FEATURE_VOCABULARY_TERMS(FD_ID);
+
+CREATE TABLE FEATURE_VALUES (
+ ID BIGSERIAL NOT NULL,
+
+ -- we use the fixed dimension meters here
+ Z_in_M REAL,
+ -- we use the fixed dimension seconds here
+ T_in_SEC REAL,
+ -- Serialized 2D matrix with values for each spot.
+ -- Contains floats which can be NaN.
+ -- It is never a case that the whole matrix contains NaN - in such a case we save nothing.
+ -- If feature definition has some connected vocabulary terms then the matrix
+ -- stores FEATURE_VOCABULARY_TERMS.SEQUENCE_NUMBER of the terms (should be casted from float to int).
+ -- If the term is null the Float.NaN is stored.
+ VALUES BYTEA NOT NULL,
+
+ FD_ID TECH_ID NOT NULL,
+
+ PRIMARY KEY (ID),
+ CONSTRAINT FK_FEATURE_VALUES_1 FOREIGN KEY (FD_ID) REFERENCES FEATURE_DEFS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+ -- This constaint does not make any sense. Leave it out for now.
+ -- CONSTRAINT FEATURE_VALUES_UK_1 UNIQUE(Z_in_M, T_in_SEC)
+);
+
+CREATE INDEX FEATURE_VALUES_FD_IDX ON FEATURE_VALUES(FD_ID);
+CREATE INDEX FEATURE_VALUES_Z_AND_T_IDX ON FEATURE_VALUES(Z_in_M, T_in_SEC);
+
+
+/* ---------------------------------------------------------------------- */
+/* FUNCTIONS AND TRIGGERS */
+/* ---------------------------------------------------------------------- */
+
+CREATE OR REPLACE FUNCTION DELETE_UNUSED_IMAGES() RETURNS trigger AS $$
+BEGIN
+ delete from images where id = OLD.img_id or id = OLD.thumbnail_id;
+ RETURN NEW;
+END;
+$$ LANGUAGE 'plpgsql';
+
+CREATE TRIGGER UNUSED_IMAGES AFTER DELETE ON ACQUIRED_IMAGES
+ FOR EACH ROW EXECUTE PROCEDURE DELETE_UNUSED_IMAGES();
+
+------------------------------------------------------------------------------------
+-- Purpose: Create trigger CHANNEL_STACKS_CHECK which checks if both spot_id and dataset.cont_id
+-- are both null or not null.
+------------------------------------------------------------------------------------
+
+CREATE OR REPLACE FUNCTION CHANNEL_STACKS_CHECK() RETURNS trigger AS $$
+DECLARE
+ v_cont_id CODE;
+BEGIN
+
+ select cont_id into v_cont_id from data_sets where id = NEW.ds_id;
+
+ -- Check that if there is no spot than there is no dataset container as well
+ if v_cont_id IS NULL then
+ if NEW.spot_id IS NOT NULL then
+ RAISE EXCEPTION 'Insert/Update of CHANNEL_STACKS failed, as the dataset container is not set, but spot is (spot id = %).',NEW.spot_id;
+ end if;
+ else
+ if NEW.spot_id IS NULL then
+ RAISE EXCEPTION 'Insert/Update of CHANNEL_STACKS failed, as the dataset container is set (id = %), but spot is not set.',v_cont_id;
+ end if;
+ end if;
+ RETURN NEW;
+END;
+$$ LANGUAGE 'plpgsql';
+
+CREATE TRIGGER CHANNEL_STACKS_CHECK BEFORE INSERT OR UPDATE ON CHANNEL_STACKS
+ FOR EACH ROW EXECUTE PROCEDURE CHANNEL_STACKS_CHECK();
\ No newline at end of file
diff --git a/screening/source/sql/postgresql/010/upload-screening-metadata.sh b/screening/source/sql/postgresql/010/upload-screening-metadata.sh
new file mode 100755
index 0000000000000000000000000000000000000000..1a8a1969f1ef9d83fafdeb766696b9c5eef14fe7
--- /dev/null
+++ b/screening/source/sql/postgresql/010/upload-screening-metadata.sh
@@ -0,0 +1,2 @@
+DB=$1
+psql -U postgres -d openbis_$DB -f data.sql
diff --git a/screening/source/sql/postgresql/migration/migration-009-010.sql b/screening/source/sql/postgresql/migration/migration-009-010.sql
new file mode 100644
index 0000000000000000000000000000000000000000..db3cf424f7c9734a1cbd670781f515b4eb433799
--- /dev/null
+++ b/screening/source/sql/postgresql/migration/migration-009-010.sql
@@ -0,0 +1,3 @@
+-- Migration from 009 to 010
+
+ALTER TABLE images ADD COLUMN image_transformer_factory BYTEA;
\ No newline at end of file
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtilsTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtilsTest.java
index db7cc1938fe1c4c4fc7454668f8314875506ba7b..bf3ada2540fd3e42d441d5c7e3ad022eba8bf3af 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtilsTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtilsTest.java
@@ -39,6 +39,7 @@ import ch.systemsx.cisd.common.io.FileBasedContent;
import ch.systemsx.cisd.common.io.IContent;
import ch.systemsx.cisd.openbis.dss.etl.AbsoluteImageReference;
import ch.systemsx.cisd.openbis.dss.etl.IImagingDatasetLoader;
+import ch.systemsx.cisd.openbis.dss.etl.dto.ImageTransfomationFactories;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.DatasetAcquiredImagesReference;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageChannelStackReference;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.RequestedImageSize;
@@ -123,8 +124,7 @@ public class ImageChannelsUtilsTest extends AssertJUnit
public void testGetTiffImage()
{
AbsoluteImageReference absoluteImageReference =
- new AbsoluteImageReference(image("img1.tiff"), "id42", null, null,
- RequestedImageSize.createOriginal(), 0);
+ createAbsoluteImageReference("img1.tiff", RequestedImageSize.createOriginal());
performTest(absoluteImageReference, getImageContentDescription(image("img1.png")), null);
context.assertIsSatisfied();
}
@@ -134,8 +134,7 @@ public class ImageChannelsUtilsTest extends AssertJUnit
{
Size size = new Size(4, 2);
AbsoluteImageReference absoluteImageReference =
- new AbsoluteImageReference(image("img1.jpg"), "id42", null, null,
- new RequestedImageSize(size, false), 0);
+ createAbsoluteImageReference("img1.jpg", new RequestedImageSize(size, false));
performTest(absoluteImageReference, "cde cde\ncde cde\n", size);
context.assertIsSatisfied();
}
@@ -191,9 +190,8 @@ public class ImageChannelsUtilsTest extends AssertJUnit
{
final DatasetAcquiredImagesReference imageRef = createDatasetAcquiredImagesReference();
AbsoluteImageReference imgRef =
- new AbsoluteImageReference(image("img1.gif"), "id42", null, null,
- RequestedImageSize.createOriginal(), 0);
- imgRef.setTransformerFactory(transformerFactory);
+ createAbsoluteImageReference("img1.gif", RequestedImageSize.createOriginal());
+ imgRef.getImageTransfomationFactories().setForChannel(transformerFactory);
prepareExpectations(imgRef, imageRef);
context.checking(new Expectations()
@@ -211,6 +209,13 @@ public class ImageChannelsUtilsTest extends AssertJUnit
context.assertIsSatisfied();
}
+ private static AbsoluteImageReference createAbsoluteImageReference(String fileName,
+ RequestedImageSize imageSize)
+ {
+ return new AbsoluteImageReference(image(fileName), "id42", null, null, imageSize, 0,
+ new ImageTransfomationFactories());
+ }
+
private ImageChannelsUtils createImageChannelsUtils(Size thumbnailSizeOrNull)
{
return new ImageChannelsUtils(loader, new RequestedImageSize(thumbnailSizeOrNull, false));
@@ -235,7 +240,7 @@ public class ImageChannelsUtilsTest extends AssertJUnit
}
}
- private IContent image(String fileName)
+ private static IContent image(String fileName)
{
return new FileBasedContent(new File(TEST_IMAGE_FOLDER, fileName));
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
index 03230353b2cb16b8ccf281813a88f4fb973ed621..cbba754fbb7f453825a9443fbe4aca3712a0ac48 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
@@ -50,6 +50,7 @@ import ch.systemsx.cisd.common.io.FileBasedContent;
import ch.systemsx.cisd.common.io.IContent;
import ch.systemsx.cisd.openbis.dss.etl.AbsoluteImageReference;
import ch.systemsx.cisd.openbis.dss.etl.IImagingDatasetLoader;
+import ch.systemsx.cisd.openbis.dss.etl.dto.ImageTransfomationFactories;
import ch.systemsx.cisd.openbis.dss.generic.server.DatasetSessionAuthorizer;
import ch.systemsx.cisd.openbis.dss.generic.server.DssServiceRpcAuthorizationAdvisor;
import ch.systemsx.cisd.openbis.dss.generic.server.DssServiceRpcAuthorizationAdvisor.DssServiceRpcAuthorizationMethodInterceptor;
@@ -324,13 +325,13 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
ImageChannelStackReference.createHCSFromLocations(new Location(3, 1),
new Location(1, 1)), thumbnailSize);
will(returnValue(new AbsoluteImageReference(image("img1.jpg"), "img1", null,
- null, thumbnailSize, 0)));
+ null, thumbnailSize, 0, new ImageTransfomationFactories())));
one(imageLoader).tryGetImage(
channel,
ImageChannelStackReference.createHCSFromLocations(new Location(3, 1),
new Location(2, 1)), thumbnailSize);
will(returnValue(new AbsoluteImageReference(image("img1.gif"), "img1", null,
- null, thumbnailSize, 0)));
+ null, thumbnailSize, 0, new ImageTransfomationFactories())));
}
});
@@ -703,7 +704,7 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
}
});
}
-
+
private FeatureVectorDatasetReference createFeatureVectorDatasetReference(String dataSetCode)
{
return new FeatureVectorDatasetReference(dataSetCode, "", null, null, null, null, null,