diff --git a/screening/etc/service.properties b/screening/etc/service.properties
index 7f7a322157ba0688a5e5a1c0492aecf1b2c7a571..32409fbca4b575a15d9028978454ad3df55bb7ea 100644
--- a/screening/etc/service.properties
+++ b/screening/etc/service.properties
@@ -79,25 +79,7 @@ quiet-period = 3
# ---------------------------------------------------------------------------
# Comma separated names of reporting plugins. Each plugin should have configuration properties prefixed with its name.
-reporting-plugins = plate-image-reporter, plate-image-params-reporter, default-plate-image-analysis-merger, plate-image-analysis-graph, demo-reporter
-
-# Label of the plugin which will be shown for the users.
-demo-reporter.label = Show Dataset Size
-# Comma separated list of dataset type codes which can be handled by this plugin.
-demo-reporter.dataset-types = UNKNOWN
-# Plugin class specification (together with the list of packages this class belongs to).
-demo-reporter.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.demo.DemoReportingPlugin
-# The property file. Its content will be passed as a parameter to the plugin.
-demo-reporter.properties-file =
-
-# Label of the plugin which will be shown for the users.
-plate-image-reporter.label = Show Plate Images
-# Comma separated list of dataset type codes which can be handled by this plugin.
-plate-image-reporter.dataset-types = HCS_IMAGE
-# Plugin class specification (together with the list of packages this class belongs to).
-plate-image-reporter.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.ScreeningImageReportingPlugin
-# The property file. Its content will be passed as a parameter to the plugin.
-plate-image-reporter.properties-file =
+reporting-plugins = plate-image-params-reporter, default-plate-image-analysis-merger, plate-image-analysis-graph
# Label of the plugin which will be shown for the users.
plate-image-params-reporter.label = Show Plate Image Parameters
@@ -169,7 +151,7 @@ imaging-db.scriptFolder = source/sql
# Comma separated names of processing threads. Each thread should have configuration properties prefixed with its name.
# E.g. 'code-extractor' property for the thread 'my-etl' should be specified as 'my-etl.code-extractor'
-inputs=raw-data, plate-analysis-data, lmc-raw-data, lmc-jpg-data, lmc-segmented-jpg-data, image-db-data
+inputs=raw-data, plate-analysis-data, lmc-raw-data, lmc-jpg-data, lmc-segmented-jpg-data, image-db-data, pelk-raw-img-db, lmc-raw-img-db
# ---------------------------------------------------------------------------
# 'raw-data' thread configuration
@@ -377,6 +359,62 @@ image-db-data.storage-processor.well_geometry = 1x1
image-db-data.storage-processor.deprecated-file-extractor = ch.systemsx.cisd.openbis.dss.etl.genedata.HCSImageFileExtractor
image-db-data.storage-processor.data-source = imaging-db
+# ---------------------------------------------------------------------------
+
+# The directory to watch for incoming data.
+pelk-raw-img-db.incoming-dir = targets/raw-images-pelk-db
+pelk-raw-img-db.incoming-data-completeness-condition = auto-detection
+
+# The extractor class to use for code extraction
+pelk-raw-img-db.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor
+pelk-raw-img-db.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator}
+pelk-raw-img-db.data-set-info-extractor.index-of-sample-code = -1
+pelk-raw-img-db.data-set-info-extractor.index-of-data-producer-code = 1
+pelk-raw-img-db.data-set-info-extractor.index-of-data-production-date = 0
+pelk-raw-img-db.data-set-info-extractor.space-code = DEMO
+
+# The extractor class to use for type extraction
+pelk-raw-img-db.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
+pelk-raw-img-db.type-extractor.file-format-type = PNG
+pelk-raw-img-db.type-extractor.locator-type = RELATIVE_LOCATION
+pelk-raw-img-db.type-extractor.data-set-type = HCS_IMAGE
+pelk-raw-img-db.type-extractor.is-measured = true
+
+pelk-raw-img-db.storage-processor = ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor
+pelk-raw-img-db.storage-processor.channel-names = blue, green
+pelk-raw-img-db.storage-processor.well_geometry = 3x3
+pelk-raw-img-db.storage-processor.deprecated-file-extractor = ch.systemsx.cisd.etlserver.imsb.HCSImageFileExtractor
+pelk-raw-img-db.storage-processor.data-source = imaging-db
+
+
+# ---------------------------------------------------------------------------
+
+# The directory to watch for incoming data.
+lmc-raw-img-db.incoming-dir = targets/raw-images-lmc-db
+lmc-raw-img-db.incoming-data-completeness-condition = auto-detection
+
+# The extractor class to use for code extraction
+lmc-raw-img-db.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor
+lmc-raw-img-db.data-set-info-extractor.entity-separator = .
+lmc-raw-img-db.data-set-info-extractor.index-of-sample-code = 0
+lmc-raw-img-db.data-set-info-extractor.index-of-data-producer-code =
+lmc-raw-img-db.data-set-info-extractor.space-code = DEMO
+
+# The extractor class to use for type extraction
+lmc-raw-img-db.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
+lmc-raw-img-db.type-extractor.file-format-type = JPG
+lmc-raw-img-db.type-extractor.locator-type = RELATIVE_LOCATION
+lmc-raw-img-db.type-extractor.data-set-type = HCS_IMAGE
+lmc-raw-img-db.type-extractor.is-measured = true
+
+lmc-raw-img-db.storage-processor = ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor
+lmc-raw-img-db.storage-processor.channel-names = dapi, gfp
+lmc-raw-img-db.storage-processor.well_geometry = 3x3
+lmc-raw-img-db.storage-processor.deprecated-file-extractor = ch.systemsx.cisd.openbis.dss.etl.lmc.HCSImageFileExtractor
+lmc-raw-img-db.storage-processor.data-source = imaging-db
+#lmc-raw-img-db.storage-processor.
+#lmc-raw-img-db.storage-processor.compute_file_checksums = false
+
# ---------------------------------------------------------------------------
# (optional) archiver configuration
# ---------------------------------------------------------------------------
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
new file mode 100644
index 0000000000000000000000000000000000000000..0d225fa9feccd6beac8c15101949fb3fe03a0570
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbsoluteImageReference.java
@@ -0,0 +1,55 @@
+/*
+ * Copyright 2010 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;
+
+import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgImageDTO.ColorComponent;
+
+/**
+ * @author Tomasz Pylak
+ */
+public class AbsoluteImageReference
+{
+ private final String imageAbsolutePath;
+
+ private final Integer pageOrNull;
+
+ private final ColorComponent colorComponentOrNull;
+
+ public AbsoluteImageReference(String imageAbsolutePath, Integer pageOrNull,
+ ColorComponent colorComponentOrNull)
+ {
+ this.imageAbsolutePath = imageAbsolutePath;
+ this.pageOrNull = pageOrNull;
+ this.colorComponentOrNull = colorComponentOrNull;
+ }
+
+ public String getImageAbsolutePath()
+ {
+ return imageAbsolutePath;
+ }
+
+ public Integer tryGetPage()
+ {
+ return pageOrNull;
+ }
+
+ public ColorComponent tryGetColorComponent()
+ {
+ return colorComponentOrNull;
+ }
+
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSDatasetLoaderFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSDatasetLoaderFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..a7568cbf59e6378bc8b92893777cb506a6f1838d
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSDatasetLoaderFactory.java
@@ -0,0 +1,100 @@
+/*
+ * Copyright 2010 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;
+
+import java.io.File;
+
+import javax.sql.DataSource;
+
+import net.lemnik.eodsql.QueryTool;
+
+import ch.systemsx.cisd.bds.hcs.Geometry;
+import ch.systemsx.cisd.bds.hcs.Location;
+import ch.systemsx.cisd.openbis.dss.etl.dataaccess.HCSDatasetLoader;
+import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingUploadDAO;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
+
+/**
+ * @author Tomasz Pylak
+ */
+public class HCSDatasetLoaderFactory
+{
+ private static final IImagingUploadDAO query = createQuery();
+
+ private static IImagingUploadDAO createQuery()
+ {
+ DataSource dataSource =
+ ServiceProvider.getDataSourceProvider().getDataSource(
+ ScreeningConstants.IMAGING_DATA_SOURCE);
+ return QueryTool.getQuery(dataSource, IImagingUploadDAO.class);
+ }
+
+ public static final IHCSDatasetLoader create(File datasetRootDir, String datasetCode)
+ {
+ return createImageDBLoader(datasetRootDir, datasetCode);
+ // return createBDSLoader(datasetRootDir);
+ }
+
+ private static HCSDatasetLoader createImageDBLoader(File datasetRootDir, String datasetCode)
+ {
+ return new HCSDatasetLoader(query, datasetCode, datasetRootDir);
+ }
+
+ private static IHCSDatasetLoader createBDSLoader(File datasetRootDir)
+ {
+ final ch.systemsx.cisd.bds.hcs.HCSDatasetLoader loader =
+ new ch.systemsx.cisd.bds.hcs.HCSDatasetLoader(datasetRootDir);
+ return adapt(loader);
+ }
+
+ private static IHCSDatasetLoader adapt(final ch.systemsx.cisd.bds.hcs.HCSDatasetLoader loader)
+ {
+ return new IHCSDatasetLoader()
+ {
+
+ public void close()
+ {
+ loader.close();
+ }
+
+ public int getChannelCount()
+ {
+ return loader.getChannelCount();
+ }
+
+ public Geometry getPlateGeometry()
+ {
+ return loader.getPlateGeometry();
+ }
+
+ public Geometry getWellGeometry()
+ {
+ return loader.getWellGeometry();
+ }
+
+ public AbsoluteImageReference tryGetImage(int chosenChannel, Location wellLocation,
+ Location tileLocation)
+ {
+ String absPath =
+ loader.tryGetStandardNodeAt(chosenChannel, wellLocation, tileLocation);
+ return new AbsoluteImageReference(absPath, null, null);
+ }
+
+ };
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSDatasetUploader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSDatasetUploader.java
index 07603feebe67fd071c55b83e34b6f1d204fb0f31..6bb1120e83769a1b2e5def7063deeebe124d4efa 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSDatasetUploader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSDatasetUploader.java
@@ -24,6 +24,7 @@ import java.util.Set;
import java.util.Map.Entry;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.dss.etl.HCSImageFileExtractionResult.Channel;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingUploadDAO;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgAcquiredImageDTO;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgChannelDTO;
@@ -66,17 +67,45 @@ class HCSDatasetUploader
private Map<String, Long> getOrCreateChannels(long expId,
Set<HCSImageFileExtractionResult.Channel> channels)
{
- Map<String/* name */, ImgChannelDTO> existingChannels =
- asNameMap(dao.getChannelsByExperimentId(expId));
+ List<ImgChannelDTO> allChannels = dao.getChannelsByExperimentId(expId);
+ if (allChannels.size() == 0)
+ {
+ return createChannels(expId, channels);
+ } else
+ {
+ return updateChannels(expId, channels, allChannels);
+ }
+ }
+
+ private Map<String, Long> updateChannels(long expId, Set<Channel> channels,
+ List<ImgChannelDTO> allChannels)
+ {
+ Map<String/* name */, ImgChannelDTO> existingChannels = asNameMap(allChannels);
+ Map<String, Long> map = new HashMap<String, Long>();
+ for (HCSImageFileExtractionResult.Channel channel : channels)
+ {
+ ImgChannelDTO channelDTO = updateChannel(channel, expId, existingChannels);
+ addChannel(map, channelDTO);
+ }
+ return map;
+ }
+
+ private Map<String, Long> createChannels(long expId, Set<Channel> channels)
+ {
Map<String, Long> map = new HashMap<String, Long>();
for (HCSImageFileExtractionResult.Channel channel : channels)
{
- ImgChannelDTO channelDTO = getOrCreateChannel(channel, expId, existingChannels);
- map.put(channelDTO.getName(), channelDTO.getId());
+ ImgChannelDTO channelDTO = createChannel(expId, channel);
+ addChannel(map, channelDTO);
}
return map;
}
+ private static void addChannel(Map<String, Long> map, ImgChannelDTO channelDTO)
+ {
+ map.put(channelDTO.getName(), channelDTO.getId());
+ }
+
private static Map<String, ImgChannelDTO> asNameMap(List<ImgChannelDTO> channels)
{
Map<String, ImgChannelDTO> nameMap = new HashMap<String, ImgChannelDTO>();
@@ -87,37 +116,51 @@ class HCSDatasetUploader
return nameMap;
}
- private ImgChannelDTO getOrCreateChannel(HCSImageFileExtractionResult.Channel channel,
- long expId, Map<String, ImgChannelDTO> existingChannels)
+ private ImgChannelDTO updateChannel(HCSImageFileExtractionResult.Channel channel, long expId,
+ Map<String, ImgChannelDTO> existingChannels)
{
- ImgChannelDTO channelDTO = createChannelDTO(channel, expId);
- ImgChannelDTO existingChannel = existingChannels.get(channelDTO.getName());
- if (existingChannel != null)
+ ImgChannelDTO channelDTO = makeChannelDTO(channel, expId);
+ String channelName = channelDTO.getName();
+ ImgChannelDTO existingChannel = existingChannels.get(channelName);
+ if (existingChannel == null)
{
- // if a channel with a specified name already exists for an experiment, its description
- // will be updated
- if (existingChannel.getWavelength() != channelDTO.getWavelength())
- {
- throw UserFailureException
- .fromTemplate(
- "There are already datasets registered for the experiment "
- + "which use the same channel name, but with a different wavelength! "
- + "Channel %s, old wavelength %d, new wavelength %d.",
- channelDTO.getName(), existingChannel.getWavelength(), channelDTO
- .getWavelength());
- }
- channelDTO.setId(existingChannel.getId());
- dao.updateChannel(channelDTO);
- } else
+ throw createInvalidNewChannelException(expId, existingChannels, channelName);
+ }
+ // a channel with a specified name already exists for an experiment, its description
+ // will be updated
+ if (existingChannel.getWavelength().equals(channelDTO.getWavelength()) == false)
{
- // if a channel with a specified name does not exists for an experiment, it's created
- long channelId = dao.addChannel(channelDTO);
- channelDTO.setId(channelId);
+ throw UserFailureException.fromTemplate(
+ "There are already datasets registered for the experiment "
+ + "which use the same channel name, but with a different wavelength! "
+ + "Channel %s, old wavelength %d, new wavelength %d.", channelName,
+ existingChannel.getWavelength(), channelDTO.getWavelength());
}
+ channelDTO.setId(existingChannel.getId());
+ dao.updateChannel(channelDTO);
+ return channelDTO;
+ }
+
+ private static UserFailureException createInvalidNewChannelException(long expId,
+ Map<String, ImgChannelDTO> existingChannels, String channelName)
+ {
+ return UserFailureException.fromTemplate(
+ "Experiment with id '%d' has already some channels registered "
+ + "and does not have a channel with a name '%s'. "
+ + "Register a new experiment to use new channels. "
+ + "Available channel names in this experiment: %s.", expId, channelName,
+ existingChannels.keySet());
+ }
+
+ private ImgChannelDTO createChannel(long expId, HCSImageFileExtractionResult.Channel channel)
+ {
+ ImgChannelDTO channelDTO = makeChannelDTO(channel, expId);
+ long channelId = dao.addChannel(channelDTO);
+ channelDTO.setId(channelId);
return channelDTO;
}
- private static ImgChannelDTO createChannelDTO(HCSImageFileExtractionResult.Channel channel,
+ private static ImgChannelDTO makeChannelDTO(HCSImageFileExtractionResult.Channel channel,
long expId)
{
return ImgChannelDTO.createExperimentChannel(channel.getName(), channel.getDescription(),
@@ -156,7 +199,7 @@ class HCSDatasetUploader
createImages(stackImagesMap, channelsMap);
}
- private Map<ImgChannelStackDTO, List<AcquiredImageInStack>> makeStackImagesMap(
+ private static Map<ImgChannelStackDTO, List<AcquiredImageInStack>> makeStackImagesMap(
List<AcquiredPlateImage> images, Long[][] spotIds, long datasetId)
{
Map<ImgChannelStackDTO, List<AcquiredImageInStack>> map =
@@ -260,8 +303,8 @@ class HCSDatasetUploader
return newSpots;
}
- private Boolean[][] extractNewSpots(int rows, int columns, List<AcquiredPlateImage> images,
- List<ImgSpotDTO> existingSpots)
+ private static Boolean[][] extractNewSpots(int rows, int columns,
+ List<AcquiredPlateImage> images, List<ImgSpotDTO> existingSpots)
{
Boolean[][] spots = extractExistingSpots(rows, columns, images);
unmarkSpots(existingSpots, spots);
@@ -312,15 +355,15 @@ class HCSDatasetUploader
{
for (ImgSpotDTO existingSpot : existingSpots)
{
- spotMatrix[existingSpot.getRow()][existingSpot.getColumn()] = false;
+ spotMatrix[existingSpot.getRow() - 1][existingSpot.getColumn() - 1] = false;
}
}
private long createDataset(long contId, ScreeningContainerDatasetInfo info)
{
ImgDatasetDTO dataset =
- new ImgDatasetDTO(info.getDatasetPermId(), info.getTileRows(), info
- .getTileColumns(), contId);
+ new ImgDatasetDTO(info.getDatasetPermId(), info.getRelativeImagesDirectory(), info
+ .getTileRows(), info.getTileColumns(), contId);
return dao.addDataset(dataset);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageCheckList.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageCheckList.java
index 70b6872723a9490090b889088d7d2cdbd1cd62ad..7ee65431e9f9cab8b0cfe244cde7fbef94fd390b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageCheckList.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageCheckList.java
@@ -23,6 +23,7 @@ import java.util.Map;
import ch.systemsx.cisd.bds.hcs.Geometry;
import ch.systemsx.cisd.common.utilities.AbstractHashable;
+import ch.systemsx.cisd.etlserver.PlateDimension;
/**
* Helper class to set the <code>is_complete</code> flag in the <i>BDS</i> library.
@@ -38,7 +39,7 @@ public final class HCSImageCheckList
private final Map<FullLocation, Check> imageMap;
- public HCSImageCheckList(final String[] channelNames, final Geometry plateGeometry,
+ public HCSImageCheckList(final String[] channelNames, final PlateDimension plateGeometry,
final Geometry wellGeometry)
{
if (channelNames.length < 1)
@@ -56,9 +57,9 @@ public final class HCSImageCheckList
imageMap = new HashMap<FullLocation, Check>();
for (String channelName : channelNames)
{
- for (int wellCol = 1; wellCol <= plateGeometry.getColumns(); wellCol++)
+ for (int wellCol = 1; wellCol <= plateGeometry.getColsNum(); wellCol++)
{
- for (int wellRow = 1; wellRow <= plateGeometry.getRows(); wellRow++)
+ for (int wellRow = 1; wellRow <= plateGeometry.getRowsNum(); wellRow++)
{
for (int tileCol = 1; tileCol <= wellGeometry.getColumns(); tileCol++)
{
@@ -71,8 +72,8 @@ public final class HCSImageCheckList
}
}
}
- assert imageMap.size() == channelNames.length * plateGeometry.getColumns()
- * plateGeometry.getRows() * wellGeometry.getColumns() * wellGeometry.getRows() : "Wrong map size";
+ assert imageMap.size() == channelNames.length * plateGeometry.getColsNum()
+ * plateGeometry.getRowsNum() * wellGeometry.getColumns() * wellGeometry.getRows() : "Wrong map size";
}
public final void checkOff(AcquiredPlateImage image)
@@ -147,7 +148,7 @@ public final class HCSImageCheckList
private final static String toString(final int row, final int col, final String type)
{
- return type + "= (" + row + ", " + col + ")";
+ return type + "=(" + row + "," + col + ")";
}
//
@@ -157,7 +158,7 @@ public final class HCSImageCheckList
@Override
public final String toString()
{
- return "[ channel = " + channelName + "," + toString(wellRow, wellCol, "well") + ","
+ return "[channel=" + channelName + ", " + toString(wellRow, wellCol, "well") + ", "
+ toString(tileRow, tileCol, "tile") + "]";
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IHCSDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IHCSDatasetLoader.java
new file mode 100644
index 0000000000000000000000000000000000000000..fb3fab8b5a9c27a35b5980589c32ca5e23d2eca3
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IHCSDatasetLoader.java
@@ -0,0 +1,43 @@
+/*
+ * Copyright 2010 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;
+
+import ch.systemsx.cisd.bds.hcs.Geometry;
+import ch.systemsx.cisd.bds.hcs.Location;
+
+/**
+ * @author Tomasz Pylak
+ */
+public interface IHCSDatasetLoader
+{
+
+ /** has to be called at the end */
+ void close();
+
+ Geometry getPlateGeometry();
+
+ Geometry getWellGeometry();
+
+ int getChannelCount();
+
+ /**
+ * @param chosenChannel start from 1
+ * @return image (with absolute path, page and color)
+ */
+ AbsoluteImageReference tryGetImage(int chosenChannel, Location wellLocation,
+ Location tileLocation);
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateStorageProcessor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateStorageProcessor.java
index 37f1f3eb844631bb6200da552cd6b2254b714214..72b8be9eaf574e62dd91ce94f8c1701caf41970f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateStorageProcessor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateStorageProcessor.java
@@ -35,7 +35,6 @@ import org.apache.log4j.Logger;
import ch.systemsx.cisd.bds.hcs.Channel;
import ch.systemsx.cisd.bds.hcs.Geometry;
import ch.systemsx.cisd.bds.hcs.Location;
-import ch.systemsx.cisd.bds.hcs.PlateGeometry;
import ch.systemsx.cisd.bds.storage.IFile;
import ch.systemsx.cisd.bds.storage.filesystem.NodeFactory;
import ch.systemsx.cisd.common.collections.CollectionUtils;
@@ -168,8 +167,8 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
// ---------------------------------
- private ScreeningContainerDatasetInfo createScreeningDatasetInfo(final Experiment experiment,
- final DataSetInformation dataSetInformation)
+ private ScreeningContainerDatasetInfo createScreeningDatasetInfo(Experiment experiment,
+ DataSetInformation dataSetInformation, String relativeImagesDirectory)
{
ScreeningContainerDatasetInfo info = new ScreeningContainerDatasetInfo();
info.setExperimentPermId(experiment.getPermId());
@@ -179,19 +178,21 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
info.setContainerPermId(sample.getPermId());
info.setDatasetPermId(dataSetInformation.getDataSetCode());
- Geometry plateGeometry = getPlateGeometry(dataSetInformation);
- int plateRows = plateGeometry.getRows();
- int plateCols = plateGeometry.getColumns();
+ PlateDimension plateGeometry = getPlateGeometry(dataSetInformation);
+ int plateRows = plateGeometry.getRowsNum();
+ int plateCols = plateGeometry.getColsNum();
info.setContainerRows(plateRows);
info.setContainerColumns(plateCols);
info.setTileRows(spotGeometry.getRows());
info.setTileColumns(spotGeometry.getColumns());
+ info.setRelativeImagesDirectory(relativeImagesDirectory);
+
return info;
}
- private Geometry getPlateGeometry(final DataSetInformation dataSetInformation)
+ private PlateDimension getPlateGeometry(final DataSetInformation dataSetInformation)
{
final IEntityProperty[] sampleProperties = dataSetInformation.getProperties();
final PlateDimension plateDimension =
@@ -202,9 +203,7 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
"Missing plate geometry for the plate registered for sample identifier '"
+ dataSetInformation.getSampleIdentifier() + "'.");
}
- final Geometry plateGeometry =
- new PlateGeometry(plateDimension.getRowsNum(), plateDimension.getColsNum());
- return plateGeometry;
+ return plateDimension;
}
// ---------------------------------
@@ -275,22 +274,33 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
HCSImageFileExtractionResult extractionResult =
extractImages(dataSetInformation, incomingDataSetDirectory);
- ScreeningContainerDatasetInfo info =
- createScreeningDatasetInfo(experiment, dataSetInformation);
+ validateImages(dataSetInformation, mailClient, incomingDataSetDirectory, extractionResult);
- validateImages(dataSetInformation, mailClient, incomingDataSetDirectory, info,
- extractionResult);
+ File imagesInStoreFolder = moveFileToDirectory(incomingDataSetDirectory, originalFolder);
+ String relativeImagesDirectory =
+ getRelativeImagesDirectory(rootDirectory, imagesInStoreFolder);
- moveFileToDirectory(incomingDataSetDirectory, originalFolder);
- storeInDatabase(info, extractionResult.getImages(), extractionResult.getChannels());
+ storeInDatabase(experiment, dataSetInformation, extractionResult, relativeImagesDirectory);
return rootDirectory;
}
+ private String getRelativeImagesDirectory(File rootDirectory, File imagesInStoreFolder)
+ {
+ String root = rootDirectory.getAbsolutePath();
+ String imgDir = imagesInStoreFolder.getAbsolutePath();
+ if (imgDir.startsWith(root) == false)
+ {
+ throw UserFailureException.fromTemplate(
+ "Directory %s should be a subdirectory of directory %s.", imgDir, root);
+ }
+ return imgDir.substring(root.length());
+ }
+
private void validateImages(final DataSetInformation dataSetInformation,
final IMailClient mailClient, final File incomingDataSetDirectory,
- ScreeningContainerDatasetInfo info, HCSImageFileExtractionResult extractionResult)
+ HCSImageFileExtractionResult extractionResult)
{
- HCSImageCheckList imageCheckList = createImageCheckList(info);
+ HCSImageCheckList imageCheckList = createImageCheckList(dataSetInformation);
checkImagesForDuplicates(extractionResult, imageCheckList);
if (extractionResult.getInvalidFiles().size() > 0)
{
@@ -318,12 +328,10 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
}
}
- private HCSImageCheckList createImageCheckList(ScreeningContainerDatasetInfo info)
+ private HCSImageCheckList createImageCheckList(DataSetInformation dataSetInformation)
{
- Geometry plateGeometry = getPlateGeometry(info);
- HCSImageCheckList imageCheckList =
- new HCSImageCheckList(channelNames, plateGeometry, spotGeometry);
- return imageCheckList;
+ PlateDimension plateGeometry = getPlateGeometry(dataSetInformation);
+ return new HCSImageCheckList(channelNames, plateGeometry, spotGeometry);
}
private HCSImageFileExtractionResult extractImages(final DataSetInformation dataSetInformation,
@@ -386,6 +394,12 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
checkParameters(incomingDataSetDirectory, storedDataDirectory);
final File originalDataFile = tryGetProprietaryData(storedDataDirectory);
+ if (originalDataFile == null)
+ {
+ // nothing has been stored in the file system yet,
+ // e.g. because images could not be validated
+ return;
+ }
// Move the data from the 'original' directory back to the 'incoming' directory.
final File incomingDirectory = incomingDataSetDirectory.getParentFile();
try
@@ -420,22 +434,27 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
}
}
- private void storeInDatabase(ScreeningContainerDatasetInfo info,
- List<AcquiredPlateImage> images, Set<HCSImageFileExtractionResult.Channel> channels)
+ private void storeInDatabase(Experiment experiment, DataSetInformation dataSetInformation,
+ HCSImageFileExtractionResult extractionResult, String relativeImagesDirectory)
{
+ ScreeningContainerDatasetInfo info =
+ createScreeningDatasetInfo(experiment, dataSetInformation, relativeImagesDirectory);
+
if (currentTransaction != null)
{
throw new IllegalStateException("previous transaction has not been commited!");
}
currentTransaction = createQuery();
- HCSDatasetUploader.upload(currentTransaction, info, images, channels);
+
+ HCSDatasetUploader.upload(currentTransaction, info, extractionResult.getImages(),
+ extractionResult.getChannels());
}
private void rollbackDatabaseChanges()
{
if (currentTransaction == null)
{
- throw new IllegalStateException("there is no transaction to rollback");
+ return; // storing in the imaging db has not started
}
try
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfo.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfo.java
index 46a5705dbdf843bfd5a03f051543d31d1adc41ba..8c2de3f9987c3f2ca76926c96028eba4e978c0da 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfo.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfo.java
@@ -33,6 +33,10 @@ class ScreeningContainerDatasetInfo
private int tileRows, tileColumns;
+ // All images paths are relative to the IMAGES_DIRECTORY folder.
+ // The folder path itself is relative to the dataset root directory.
+ private String relativeImagesDirectory;
+
public String getExperimentPermId()
{
return experimentPermId;
@@ -103,4 +107,13 @@ class ScreeningContainerDatasetInfo
this.tileColumns = tileColumns;
}
+ public String getRelativeImagesDirectory()
+ {
+ return relativeImagesDirectory;
+ }
+
+ public void setRelativeImagesDirectory(String relativeImagesDirectory)
+ {
+ this.relativeImagesDirectory = relativeImagesDirectory;
+ }
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/HCSDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/HCSDatasetLoader.java
index c4742d1454a76c272ed0285deb757638d51da7a0..14210b9c8e72360d3aa15f77f3a2969a759eae4d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/HCSDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/HCSDatasetLoader.java
@@ -16,14 +16,12 @@
package ch.systemsx.cisd.openbis.dss.etl.dataaccess;
-import java.sql.Connection;
-import java.sql.SQLException;
-
-import net.lemnik.eodsql.QueryTool;
+import java.io.File;
import ch.systemsx.cisd.bds.hcs.Geometry;
import ch.systemsx.cisd.bds.hcs.Location;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.dss.etl.AbsoluteImageReference;
+import ch.systemsx.cisd.openbis.dss.etl.IHCSDatasetLoader;
/**
* Helper class for easy handling of HCS image dataset standard structure.
@@ -31,26 +29,26 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
* @author Tomasz Pylak
* @author Piotr Buczek
*/
-public class HCSDatasetLoader
+public class HCSDatasetLoader implements IHCSDatasetLoader
{
+ private final File datasetRootDir;
+
private final IImagingUploadDAO query;
private final ImgDatasetDTO dataset;
private ImgContainerDTO container;
- private Long channelCount;
+ private Integer channelCount;
- /**
- * @exception SQLException if a database access error occurs
- */
- public HCSDatasetLoader(Connection connection, String datasetPermId) throws SQLException
+ public HCSDatasetLoader(IImagingUploadDAO query, String datasetPermId, File datasetRootDir)
{
- this.query = QueryTool.getQuery(connection, IImagingUploadDAO.class);
+ this.datasetRootDir = datasetRootDir;
+ this.query = query;
this.dataset = query.tryGetDatasetByPermId(datasetPermId);
if (dataset == null)
{
- throw UserFailureException.fromTemplate("Dataset '%s' not found", datasetPermId);
+ throw new IllegalStateException(String.format("Dataset '%s' not found", datasetPermId));
}
}
@@ -85,7 +83,7 @@ public class HCSDatasetLoader
.getFieldNumberOfColumns());
}
- public long getChannelCount()
+ public int getChannelCount()
{
if (channelCount == null)
{
@@ -100,7 +98,7 @@ public class HCSDatasetLoader
* @param chosenChannel start from 1
* @return image (with absolute path, page and color)
*/
- public ImgImageDTO tryGetStandardNodeAt(int chosenChannel, Location wellLocation,
+ public AbsoluteImageReference tryGetImage(int chosenChannel, Location wellLocation,
Location tileLocation)
{
assert chosenChannel > 0;
@@ -116,6 +114,23 @@ public class HCSDatasetLoader
long chosenChannelId = channelIds[chosenChannel - 1];
- return query.getImage(chosenChannelId, getDataset().getId(), tileLocation, wellLocation);
+ ImgImageDTO imageDTO =
+ query
+ .tryGetImage(chosenChannelId, getDataset().getId(), tileLocation,
+ wellLocation);
+ if (imageDTO != null)
+ {
+ return new AbsoluteImageReference(getAbsolutePath(imageDTO), imageDTO.getPage(),
+ imageDTO.getColorComponent());
+ } else
+ {
+ return null;
+ }
+ }
+
+ private String getAbsolutePath(ImgImageDTO imageDTO)
+ {
+ File imgDir = new File(datasetRootDir, dataset.getImagesDirectoryPath());
+ return new File(imgDir, imageDTO.getFilePath()).getAbsolutePath();
}
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IImagingUploadDAO.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IImagingUploadDAO.java
index 299b774adea26d6ea9950bb95f286a8b69e9ab62..54ece75b656834d9629a8d429dd960d2d930af5f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IImagingUploadDAO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IImagingUploadDAO.java
@@ -31,8 +31,7 @@ public interface IImagingUploadDAO extends TransactionQuery
{
public static final int FETCH_SIZE = 1000;
- // select acquired_images.images.*
- // from acquired_images
+ // select acquired_images.images.* from acquired_images
@Select("select i.* from IMAGES i, ACQUIRED_IMAGES ai, CHANNEL_STACKS cs, SPOTS s "
+ "where "
// where acquired_images.channel.id = ?{channelId}
@@ -45,8 +44,7 @@ public interface IImagingUploadDAO extends TransactionQuery
+ "cs.x = ?{3.x} and cs.y = ?{3.y} and s.x = ?{4.x} and s.y = ?{4.y} and "
// joins
+ "ai.IMG_ID = i.ID and ai.CHANNEL_STACK_ID = cs.ID and cs.SPOT_ID = s.ID")
- // TODO 2010-05-19, Tomasz Pylak: add unit tests
- public ImgImageDTO getImage(long channelId, long datasetId, Location tileLocation,
+ public ImgImageDTO tryGetImage(long channelId, long datasetId, Location tileLocation,
Location wellLocation);
// simple getters
@@ -64,7 +62,7 @@ public interface IImagingUploadDAO extends TransactionQuery
public ImgContainerDTO getContainerById(long containerId);
@Select("select count(*) from CHANNELS where DS_ID = ?{1} or EXP_ID = ?{2}")
- public long countChannelByDatasetIdOrExperimentId(long datasetId, long experimentId);
+ public int countChannelByDatasetIdOrExperimentId(long datasetId, long experimentId);
@Select(sql = "select id from CHANNELS where DS_ID = ?{1} or EXP_ID = ?{2} order by name", fetchSize = FETCH_SIZE)
public long[] getChannelIdsByDatasetIdOrExperimentId(long datasetId, long experimentId);
@@ -96,8 +94,9 @@ public interface IImagingUploadDAO extends TransactionQuery
+ "(?{1.permId}, ?{1.numberOfColumns}, ?{1.numberOfRows}, ?{1.experimentId}) returning ID")
public long addContainer(ImgContainerDTO container);
- @Select("insert into DATA_SETS (PERM_ID, FIELDS_WIDTH, FIELDS_HEIGHT, CONT_ID) values "
- + "(?{1.permId}, ?{1.fieldNumberOfColumns}, ?{1.fieldNumberOfRows}, ?{1.containerId}) returning ID")
+ @Select("insert into DATA_SETS (PERM_ID, IMAGES_DIRECTORY, FIELDS_WIDTH, FIELDS_HEIGHT, CONT_ID) values "
+ + "(?{1.permId}, ?{1.imagesDirectoryPath}, ?{1.fieldNumberOfColumns}, "
+ + "?{1.fieldNumberOfRows}, ?{1.containerId}) returning ID")
public long addDataset(ImgDatasetDTO dataset);
@Select("insert into IMAGES (PATH, PAGE, COLOR) values "
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgDatasetDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgDatasetDTO.java
index 18a1ee6d1090b95769835af1ab91297690146f5f..f53826a611d55ada0bd909c8d37a3ed6f16b5372 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgDatasetDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgDatasetDTO.java
@@ -32,6 +32,9 @@ public class ImgDatasetDTO extends AbstractHashable
@ResultColumn("PERM_ID")
private String permId;
+ @ResultColumn("IMAGES_DIRECTORY")
+ private String imagesDirectoryPath;
+
@ResultColumn("FIELDS_WIDTH")
private Integer fieldNumberOfColumnsOrNull;
@@ -47,10 +50,11 @@ public class ImgDatasetDTO extends AbstractHashable
// All Data-Object classes must have a default constructor.
}
- public ImgDatasetDTO(String permId, Integer fieldNumberOfRowsOrNull,
- Integer fieldNumberOfColumnsOrNull, long containerId)
+ public ImgDatasetDTO(String permId, String imagesDirectoryPath,
+ Integer fieldNumberOfRowsOrNull, Integer fieldNumberOfColumnsOrNull, long containerId)
{
this.permId = permId;
+ this.imagesDirectoryPath = imagesDirectoryPath;
this.fieldNumberOfColumnsOrNull = fieldNumberOfColumnsOrNull;
this.fieldNumberOfRowsOrNull = fieldNumberOfRowsOrNull;
this.containerId = containerId;
@@ -106,4 +110,14 @@ public class ImgDatasetDTO extends AbstractHashable
this.containerId = containerId;
}
+ public String getImagesDirectoryPath()
+ {
+ return imagesDirectoryPath;
+ }
+
+ public void setImagesDirectoryPath(String imagesDirectoryPath)
+ {
+ this.imagesDirectoryPath = imagesDirectoryPath;
+ }
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractImagesDownloadServlet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractImagesDownloadServlet.java
index dc7dfbb46460f146566ffe723741858016d2549e..0a8ff8c0f5381a7b6c261d2dbe8d2f39f222975d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractImagesDownloadServlet.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractImagesDownloadServlet.java
@@ -43,7 +43,7 @@ abstract class AbstractImagesDownloadServlet extends AbstractDatasetDownloadServ
* @throw EnvironmentFailureException if image does not exist
*/
protected abstract ResponseContentStream createImageResponse(TileImageReference params,
- File datasetRoot) throws IOException, EnvironmentFailureException;
+ File datasetRoot, String datasetCode) throws IOException, EnvironmentFailureException;
protected static class RequestParams extends TileImageReference
{
@@ -151,7 +151,7 @@ abstract class AbstractImagesDownloadServlet extends AbstractDatasetDownloadServ
ResponseContentStream responseStream;
try
{
- responseStream = createImageResponse(params, datasetRoot);
+ responseStream = createImageResponse(params, datasetRoot, params.getDatasetCode());
} catch (EnvironmentFailureException e)
{
operationLog.warn(e.getMessage());
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/MergingImagesDownloadServlet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/MergingImagesDownloadServlet.java
index a2f4ee4a544f5164a057981ebd5f8cde4d1509cd..6b389338437e6d1d25eb1b27440865a19e66771d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/MergingImagesDownloadServlet.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/MergingImagesDownloadServlet.java
@@ -42,9 +42,9 @@ public class MergingImagesDownloadServlet extends AbstractImagesDownloadServlet
**/
@Override
protected final ResponseContentStream createImageResponse(TileImageReference params,
- File datasetRoot) throws IOException, EnvironmentFailureException
+ File datasetRoot, String datasetCode) throws IOException, EnvironmentFailureException
{
- List<File> imageFiles = ImageChannelsUtils.getImagePaths(datasetRoot, params);
+ List<File> imageFiles = ImageChannelsUtils.getImagePaths(datasetRoot, datasetCode, params);
BufferedImage image = ImageChannelsUtils.mergeImageChannels(params, imageFiles);
File singleFileOrNull = imageFiles.size() == 1 ? imageFiles.get(0) : null;
return createResponseContentStream(image, singleFileOrNull);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/SplittingImagesDownloadServlet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/SplittingImagesDownloadServlet.java
index 82739794b59e9f341e52130b3620bbb8bc563b67..0da94aff87d4eec92ea8af9461d2b4c794d2ca7d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/SplittingImagesDownloadServlet.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/SplittingImagesDownloadServlet.java
@@ -20,9 +20,10 @@ import java.awt.image.BufferedImage;
import java.io.File;
import java.io.IOException;
-import ch.systemsx.cisd.bds.hcs.HCSDatasetLoader;
import ch.systemsx.cisd.bds.hcs.Location;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.openbis.dss.etl.HCSDatasetLoaderFactory;
+import ch.systemsx.cisd.openbis.dss.etl.IHCSDatasetLoader;
import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelsUtils;
import ch.systemsx.cisd.openbis.dss.generic.server.images.TileImageReference;
@@ -38,10 +39,10 @@ public class SplittingImagesDownloadServlet extends AbstractImagesDownloadServle
private static final long serialVersionUID = 1L;
/** throws {@link EnvironmentFailureException} when image does not exist */
- private File getImagePath(File datasetRoot, TileImageReference params)
+ private File getImagePath(File datasetRoot, String datasetCode, TileImageReference params)
throws EnvironmentFailureException
{
- HCSDatasetLoader imageAccessor = new HCSDatasetLoader(datasetRoot);
+ IHCSDatasetLoader imageAccessor = HCSDatasetLoaderFactory.create(datasetRoot, datasetCode);
Location wellLocation = params.getWellLocation();
Location tileLocation = params.getTileLocation();
int channel = 1; // NOTE: we assume that there is only one channel
@@ -56,9 +57,9 @@ public class SplittingImagesDownloadServlet extends AbstractImagesDownloadServle
**/
@Override
protected final ResponseContentStream createImageResponse(TileImageReference params,
- File datasetRoot) throws IOException, EnvironmentFailureException
+ File datasetRoot, String datasetCode) throws IOException, EnvironmentFailureException
{
- File imageFile = getImagePath(datasetRoot, params);
+ File imageFile = getImagePath(datasetRoot, datasetCode, params);
BufferedImage image = ImageChannelsUtils.mergeImageChannels(params, imageFile);
return createResponseContentStream(image, imageFile);
}
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 a78d64eb95b1b63af69b859762d8dab16b31dfd0..3ae25a3a1087a40460720a36274c2731ddbb0549 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
@@ -22,9 +22,11 @@ import java.io.File;
import java.util.ArrayList;
import java.util.List;
-import ch.systemsx.cisd.bds.hcs.HCSDatasetLoader;
import ch.systemsx.cisd.bds.hcs.Location;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.openbis.dss.etl.AbsoluteImageReference;
+import ch.systemsx.cisd.openbis.dss.etl.HCSDatasetLoaderFactory;
+import ch.systemsx.cisd.openbis.dss.etl.IHCSDatasetLoader;
import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDatasetDownloadServlet.Size;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
@@ -57,9 +59,10 @@ public class ImageChannelsUtils
* be merged.
* @throw {@link EnvironmentFailureException} when image does not exist
*/
- public static List<File> getImagePaths(File datasetRoot, TileImageReference params)
+ public static List<File> getImagePaths(File datasetRoot, String datasetCode,
+ TileImageReference params)
{
- HCSDatasetLoader imageAccessor = new HCSDatasetLoader(datasetRoot);
+ IHCSDatasetLoader imageAccessor = HCSDatasetLoaderFactory.create(datasetRoot, datasetCode);
Location wellLocation = params.getWellLocation();
Location tileLocation = params.getTileLocation();
List<File> paths = new ArrayList<File>();
@@ -152,14 +155,16 @@ public class ImageChannelsUtils
* @param chosenChannel starts from 1
* @throw {@link EnvironmentFailureException} when image does not exist
*/
- public static File getImagePath(HCSDatasetLoader imageAccessor, Location wellLocation,
+ public static File getImagePath(IHCSDatasetLoader imageAccessor, Location wellLocation,
Location tileLocation, int chosenChannel)
{
- String imagePath =
- imageAccessor.tryGetStandardNodeAt(chosenChannel, wellLocation, tileLocation);
- if (imagePath != null)
+ AbsoluteImageReference image =
+ imageAccessor.tryGetImage(chosenChannel, wellLocation, tileLocation);
+ if (image != null)
{
- return new File(imagePath);
+ // TODO 2010-05-31, Tomasz Pylak: add support for tiff paged images and channels
+ // splitting
+ return new File(image.getImageAbsolutePath());
} else
{
throw EnvironmentFailureException.fromTemplate(
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ScreeningImageReportingPlugin.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ScreeningImageReportingPlugin.java
deleted file mode 100644
index 0d41b216824912a5031e8a4159c39cd6c032b395..0000000000000000000000000000000000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ScreeningImageReportingPlugin.java
+++ /dev/null
@@ -1,206 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.dss.generic.server.plugins;
-
-import static ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.SimpleTableModelBuilder.asNum;
-import static ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.SimpleTableModelBuilder.asText;
-
-import java.io.File;
-import java.util.Arrays;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Properties;
-
-import ch.systemsx.cisd.bds.DataStructureLoader;
-import ch.systemsx.cisd.bds.IDataStructure;
-import ch.systemsx.cisd.bds.hcs.Geometry;
-import ch.systemsx.cisd.bds.hcs.IHCSImageFormattedData;
-import ch.systemsx.cisd.bds.hcs.Location;
-import ch.systemsx.cisd.bds.storage.INode;
-import ch.systemsx.cisd.bds.v1_0.IDataStructureV1_0;
-import ch.systemsx.cisd.common.exceptions.NotImplementedException;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractDatastorePlugin;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IReportingPluginTask;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.SimpleTableModelBuilder;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ImageTableCell;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.StringTableCell;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
-
-/**
- * Reporting plugin which shows all images in wells of a plate dataset.
- *
- * @author Tomasz Pylak
- */
-public class ScreeningImageReportingPlugin extends AbstractDatastorePlugin implements
- IReportingPluginTask
-{
- // -------- column headers used to describe images for a plate
-
- private static final String IMAGE = "Thumbnail";
-
- private static final String CHANNEL = "Channel";
-
- private static final String TILE = "Tile";
-
- private static final String COLUMN = "Column";
-
- private static final String ROW = "Row";
-
- private static final String DATASET_CODE = "Dataset Code";
-
- private static final String IMAGE_PATH = "Image Path";
-
- // ----------
-
- private static final long serialVersionUID = 1L;
-
- public ScreeningImageReportingPlugin(Properties properties, File storeRoot)
- {
- super(properties, storeRoot);
- }
-
- public TableModel createReport(List<DatasetDescription> datasets)
- {
- SimpleTableModelBuilder builder = new SimpleTableModelBuilder();
- addReportHeaders(builder);
- DataStructureLoader loader = new DataStructureLoader(storeRoot);
- for (DatasetDescription dataset : datasets)
- {
- IDataStructureV1_0 structure = createDatasetAccessor(loader, dataset);
- IHCSImageFormattedData imageAccessor = getImageAccessor(structure);
- addReportRows(builder, dataset, imageAccessor);
- structure.close();
- }
- return builder.getTableModel();
- }
-
- private void addReportHeaders(SimpleTableModelBuilder builder)
- {
- // Note: we rely on that column order at the openBIS server side!
- builder.addHeader(DATASET_CODE);
- builder.addHeader(ROW);
- builder.addHeader(COLUMN);
- builder.addHeader(TILE);
- builder.addHeader(CHANNEL);
- builder.addHeader(IMAGE);
- builder.addHeader(IMAGE_PATH);
- }
-
- private void addReportRows(SimpleTableModelBuilder builder, DatasetDescription dataset,
- IHCSImageFormattedData imageAccessor)
- {
- Geometry plateGeometry = imageAccessor.getPlateGeometry();
- Geometry wellGeometry = imageAccessor.getWellGeometry();
- for (int channel = 1; channel <= imageAccessor.getChannelCount(); channel++)
- {
- for (Location wellLocation : new GeometryIterable(plateGeometry))
- {
- for (Location tileLocation : new GeometryIterable(wellGeometry))
- {
- INode img =
- imageAccessor.tryGetStandardNodeAt(channel, wellLocation, tileLocation);
- if (img != null)
- {
-
- String imageStoreRelativePath = getStoreRelativePath(img.getPath());
- ISerializableComparable image =
- createImageCell(dataset, new File(img.getPath()));
- String datasetCode = dataset.getDatasetCode();
- int tileNumber =
- tileLocation.getX() + (tileLocation.getY() - 1)
- * wellGeometry.getColumns();
- List<ISerializableComparable> row =
- Arrays.<ISerializableComparable> asList(asText(datasetCode),
- asNum(wellLocation.getY()), asNum(wellLocation.getX()),
- asNum(tileNumber), asNum(channel), image,
- asText(imageStoreRelativePath));
- builder.addRow(row);
- }
- }
- }
- }
- }
-
- private static class GeometryIterable implements Iterable<Location>
- {
- private final Geometry geometry;
-
- public GeometryIterable(Geometry geometry)
- {
- this.geometry = geometry;
- }
-
- public Iterator<Location> iterator()
- {
- return new Iterator<Location>()
- {
- private int x = 0;
-
- private int y = 1;
-
- public boolean hasNext()
- {
- return x < geometry.getColumns() || y < geometry.getRows();
- }
-
- public Location next()
- {
- if (x < geometry.getColumns())
- {
- x++;
- } else
- {
- x = 1;
- y++;
- }
- return new Location(x, y);
- }
-
- public void remove()
- {
- throw new NotImplementedException();
- }
- };
- }
- }
-
- private IHCSImageFormattedData getImageAccessor(IDataStructureV1_0 structure)
- {
- return (IHCSImageFormattedData) structure.getFormattedData();
- }
-
- private IDataStructureV1_0 createDatasetAccessor(DataStructureLoader loader,
- DatasetDescription dataset)
- {
- IDataStructure dataStructure = loader.load(dataset.getDataSetLocation(), false);
- return (IDataStructureV1_0) dataStructure;
- }
-
- private static ISerializableComparable createImageCell(DatasetDescription dataset, File file)
- {
- if (ImageUtil.isImageFile(file))
- {
- String code = dataset.getDatasetCode();
- String location = dataset.getDataSetLocation();
- return new ImageTableCell(code, location, file.getPath(), 100, 60);
- }
- return new StringTableCell(file.getName());
- }
-}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ScreeningPlateImageParamsReportingPlugin.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ScreeningPlateImageParamsReportingPlugin.java
index 0af088f7920fdb593eb6b32bab52f07c1e5af41b..4ea9ea4d3fcf049f02461d47ee4c625633e9bf9d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ScreeningPlateImageParamsReportingPlugin.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ScreeningPlateImageParamsReportingPlugin.java
@@ -25,7 +25,8 @@ import java.util.List;
import java.util.Properties;
import ch.systemsx.cisd.bds.hcs.Geometry;
-import ch.systemsx.cisd.bds.hcs.HCSDatasetLoader;
+import ch.systemsx.cisd.openbis.dss.etl.HCSDatasetLoaderFactory;
+import ch.systemsx.cisd.openbis.dss.etl.IHCSDatasetLoader;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractDatastorePlugin;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IReportingPluginTask;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.SimpleTableModelBuilder;
@@ -71,7 +72,8 @@ public class ScreeningPlateImageParamsReportingPlugin extends AbstractDatastoreP
for (DatasetDescription dataset : datasets)
{
File datasetFile = new File(storeRoot, dataset.getDataSetLocation());
- HCSDatasetLoader imageAccessor = new HCSDatasetLoader(datasetFile);
+ IHCSDatasetLoader imageAccessor =
+ HCSDatasetLoaderFactory.create(datasetFile, dataset.getDatasetCode());
addReportRows(builder, dataset, imageAccessor);
imageAccessor.close();
}
@@ -90,7 +92,7 @@ public class ScreeningPlateImageParamsReportingPlugin extends AbstractDatastoreP
}
private void addReportRows(SimpleTableModelBuilder builder, DatasetDescription dataset,
- HCSDatasetLoader imageAccessor)
+ IHCSDatasetLoader imageAccessor)
{
Geometry plateGeometry = imageAccessor.getPlateGeometry();
Geometry wellGeometry = imageAccessor.getWellGeometry();
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 57b039f014d23561a9afaf48d54df3587d0cf8e8..89215b2f40e1cb2b61100a975c27ad669a60383c 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
@@ -32,13 +32,15 @@ import org.springframework.remoting.httpinvoker.HttpInvokerServiceExporter;
import com.csvreader.CsvReader;
import ch.systemsx.cisd.bds.hcs.Geometry;
-import ch.systemsx.cisd.bds.hcs.HCSDatasetLoader;
import ch.systemsx.cisd.bds.hcs.Location;
import ch.systemsx.cisd.common.api.RpcServiceInterfaceVersionDTO;
import ch.systemsx.cisd.common.api.server.RpcServiceNameServer;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.io.ConcatenatedFileInputStream;
+import ch.systemsx.cisd.openbis.dss.etl.AbsoluteImageReference;
+import ch.systemsx.cisd.openbis.dss.etl.HCSDatasetLoaderFactory;
+import ch.systemsx.cisd.openbis.dss.etl.IHCSDatasetLoader;
import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDssServiceRpc;
import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelsUtils;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLines;
@@ -75,8 +77,9 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
// Register the service with the name server
RpcServiceInterfaceVersionDTO ifaceVersion =
- new RpcServiceInterfaceVersionDTO("screening-dss", "/rmi-datastore-server-screening-api-v1",
- getMajorVersion(), getMinorVersion());
+ new RpcServiceInterfaceVersionDTO("screening-dss",
+ "/rmi-datastore-server-screening-api-v1", getMajorVersion(),
+ getMinorVersion());
HttpInvokerServiceExporter nameServiceExporter =
ServiceProvider.getRpcNameServiceExporter();
RpcServiceNameServer nameServer = (RpcServiceNameServer) nameServiceExporter.getService();
@@ -166,7 +169,8 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
private static ImageDatasetMetadata extractImageMetadata(IImageDatasetIdentifier dataset,
File datasetRoot)
{
- HCSDatasetLoader imageAccessor = new HCSDatasetLoader(datasetRoot);
+ IHCSDatasetLoader imageAccessor =
+ HCSDatasetLoaderFactory.create(datasetRoot, dataset.getDatasetCode());
File imageFile = getAnyImagePath(imageAccessor, dataset);
Geometry wellGeometry = imageAccessor.getWellGeometry();
int channelsNumber = imageAccessor.getChannelCount();
@@ -176,7 +180,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
image.getHeight());
}
- private static File getAnyImagePath(HCSDatasetLoader imageAccessor,
+ private static File getAnyImagePath(IHCSDatasetLoader imageAccessor,
IImageDatasetIdentifier dataset)
{
Geometry plateGeometry = imageAccessor.getPlateGeometry();
@@ -184,12 +188,11 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
{
for (int col = 1; col <= plateGeometry.getColumns(); col++)
{
- String imagePath =
- imageAccessor.tryGetStandardNodeAt(1, new Location(col, row), new Location(
- 1, 1));
- if (imagePath != null)
+ AbsoluteImageReference image =
+ imageAccessor.tryGetImage(1, new Location(col, row), new Location(1, 1));
+ if (image != null)
{
- return new File(imagePath);
+ return new File(image.getImageAbsolutePath());
}
}
}
@@ -223,14 +226,14 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
public InputStream loadImages(String sessionToken, List<PlateImageReference> imageReferences)
{
- Map<String, HCSDatasetLoader> imageLoadersMap =
+ Map<String, IHCSDatasetLoader> imageLoadersMap =
getImageDatasetsMap(sessionToken, imageReferences);
List<File> imageFiles = new ArrayList<File>();
try
{
for (PlateImageReference imageReference : imageReferences)
{
- HCSDatasetLoader imageAccessor =
+ IHCSDatasetLoader imageAccessor =
imageLoadersMap.get(imageReference.getDatasetCode());
assert imageAccessor != null : "imageAccessor not found for: " + imageReference;
File imageFile = tryGetImageFile(imageAccessor, imageReference);
@@ -243,20 +246,20 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
return new ConcatenatedFileInputStream(true, imageFiles);
}
- private static void closeDatasetLoaders(Collection<HCSDatasetLoader> loaders)
+ private static void closeDatasetLoaders(Collection<IHCSDatasetLoader> loaders)
{
- for (HCSDatasetLoader loader : loaders)
+ for (IHCSDatasetLoader loader : loaders)
{
loader.close();
}
}
// throws exception if some datasets cannot be found
- private Map<String/* image or feature vector dataset code */, HCSDatasetLoader> getImageDatasetsMap(
+ private Map<String/* image or feature vector dataset code */, IHCSDatasetLoader> getImageDatasetsMap(
String sessionToken, List<PlateImageReference> imageReferences)
{
- Map<String/* dataset code */, HCSDatasetLoader> imageDatasetsMap =
- new HashMap<String, HCSDatasetLoader>();
+ Map<String/* dataset code */, IHCSDatasetLoader> imageDatasetsMap =
+ new HashMap<String, IHCSDatasetLoader>();
for (PlateImageReference imageReference : imageReferences)
{
if (imageDatasetsMap.containsKey(imageReference.getDatasetCode()) == false)
@@ -265,7 +268,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
tryFindImageDataset(sessionToken, imageReference.getDatasetCode());
if (imageDataset != null)
{
- HCSDatasetLoader imageAccessor = createImageLoader(imageDataset.getCode());
+ IHCSDatasetLoader imageAccessor = createImageLoader(imageDataset.getCode());
imageDatasetsMap.put(imageReference.getDatasetCode(), imageAccessor);
} else
{
@@ -277,7 +280,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
return imageDatasetsMap;
}
- private File tryGetImageFile(HCSDatasetLoader imageAccessor, PlateImageReference imageRef)
+ private File tryGetImageFile(IHCSDatasetLoader imageAccessor, PlateImageReference imageRef)
{
Location wellLocation = asLocation(imageRef.getWellPosition());
Location tileLocation =
@@ -310,12 +313,10 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
return new Location(wellPosition.getWellColumn(), wellPosition.getWellRow());
}
- private HCSDatasetLoader createImageLoader(String datasetCode)
+ private IHCSDatasetLoader createImageLoader(String datasetCode)
{
- HCSDatasetLoader loader;
File datasetRoot = getRootDirectoryForDataSet(datasetCode);
- loader = new HCSDatasetLoader(datasetRoot);
- return loader;
+ return HCSDatasetLoaderFactory.create(datasetRoot, datasetCode);
}
private ExternalData tryFindImageDataset(String sessionToken, String datasetCode)
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 8c8f91858cecde34ddb2c0442f653c12191b1667..dc5aa32e0e11d336f1db7c6feb316b8c77e12c51 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
@@ -58,7 +58,6 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateSingleImageReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
/**
@@ -138,12 +137,6 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
geneMaterialId, experimentIdentifier);
}
- public List<PlateSingleImageReference> listPlateImages(String sessionToken, TechId plateId)
- {
- Session session = getSession(sessionToken);
- return PlateContentLoader.listPlateImages(session, businessObjectFactory, plateId);
- }
-
public TableModel loadImageAnalysisForExperiment(String sessionToken, TechId experimentId)
{
Session session = getSession(sessionToken);
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 537045c43db1bfca6c3ac9d387e8a88303007d31..a8b44548a209a753c22e576af84c3e60ae25dee5 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
@@ -41,7 +41,6 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateSingleImageReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
/**
@@ -98,12 +97,6 @@ final class ScreeningServerLogger extends AbstractServerLogger implements IScree
return null;
}
- public List<PlateSingleImageReference> listPlateImages(String sessionToken, TechId plateId)
- {
- logAccess(sessionToken, "loadAllImages", "PLATE(%s)", plateId.getId());
- return null;
- }
-
public TableModel loadImageAnalysisForExperiment(String sessionToken, TechId experimentId)
{
logAccess(sessionToken, "loadImageAnalysisForExperiment", "EXPERIMENT(%s)", experimentId
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/DatasetReportsLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/DatasetReportsLoader.java
index 0c31b7d73a80f1a6ba875ed5dd9d56472230c294..abde749fb22b5e2dd29283b3fc8d5f863c9039f0 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/DatasetReportsLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/DatasetReportsLoader.java
@@ -25,7 +25,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IntegerTableCell;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRow;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImageParameters;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateSingleImageReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
/**
@@ -42,40 +41,6 @@ public class DatasetReportsLoader
ScreeningConstants.PLATE_IMAGE_ANALYSIS_REPORT_KEY, datastoreCode, datasets);
}
- public static List<PlateSingleImageReference> loadPlateImages(List<String> datasets,
- String datastoreCode, IExternalDataTable externalDataTable)
- {
- TableModel imageParamsReport =
- externalDataTable.createReportFromDatasets(
- ScreeningConstants.PLATE_IMAGE_REPORT_KEY, datastoreCode, datasets);
- return asPlateImages(imageParamsReport);
- }
-
- private static List<PlateSingleImageReference> asPlateImages(TableModel imagePathsReport)
- {
- List<PlateSingleImageReference> paths = new ArrayList<PlateSingleImageReference>();
- List<TableModelRow> rows = imagePathsReport.getRows();
- for (TableModelRow row : rows)
- {
- paths.add(asImagePath(row.getValues()));
- }
- return paths;
- }
-
- private static PlateSingleImageReference asImagePath(List<ISerializableComparable> values)
- {
- PlateSingleImageReference path = new PlateSingleImageReference();
- int col = 0;
- path.setDatasetCode(asText(values.get(col++)));
- path.setWellRow(asNum(values.get(col++)));
- path.setWellCol(asNum(values.get(col++)));
- path.setTile(asNum(values.get(col++)));
- path.setChannel(asNum(values.get(col++)));
- path.setImageUrl(asText(values.get(col++)));
- path.setImagePath(asText(values.get(col++)));
- return path;
- }
-
public static List<PlateImageParameters> loadPlateImageParameters(List<String> datasets,
String datastoreCode, IExternalDataTable externalDataTable)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java
index 26050512c808437ab9df3055d4f1f5ad80ac19e1..b94e4c7bcb33cbe80fd14f8c915fe51846b25bfc 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java
@@ -45,7 +45,6 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReferen
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImageParameters;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateSingleImageReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellMetadata;
@@ -57,15 +56,6 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellMetadata;
*/
public class PlateContentLoader
{
- /**
- * loads all images from all existing image datasets for the specified plate.
- */
- public static List<PlateSingleImageReference> listPlateImages(Session session,
- IScreeningBusinessObjectFactory businessObjectFactory, TechId plateId)
- {
- return new PlateContentLoader(session, businessObjectFactory).loadAllImages(plateId);
- }
-
public static TableModel loadImageAnalysisForPlate(Session session,
IScreeningBusinessObjectFactory businessObjectFactory, TechId plateId)
{
@@ -160,24 +150,6 @@ public class PlateContentLoader
externalDataTable);
}
- private List<PlateSingleImageReference> loadAllImages(TechId plateId)
- {
- IExternalDataTable externalDataTable = createExternalDataTable();
- List<ExternalDataPE> datasets = loadDatasets(plateId, externalDataTable);
- List<ExternalDataPE> imageDatasets = ScreeningUtils.filterImageDatasets(datasets);
- List<PlateSingleImageReference> imagePaths = new ArrayList<PlateSingleImageReference>();
- if (imageDatasets.size() > 0)
- {
- List<String> datasetCodes = extractCodes(imageDatasets);
- // NOTE: we assume that all datasets for one plate come from the same datastore
- String dataStoreCode = extractDataStoreCode(imageDatasets);
- imagePaths =
- DatasetReportsLoader.loadPlateImages(datasetCodes, dataStoreCode,
- externalDataTable);
- }
- return imagePaths;
- }
-
private String extractDataStoreCode(List<ExternalDataPE> imageDatasets)
{
assert imageDatasets.size() > 0;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/IScreeningServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/IScreeningServer.java
index 88adf7a5d942405ed0e71b1591d892b0bdde7434..e10407ac39a6d0420d445b6ec96288f7f9edbc25 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/IScreeningServer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/IScreeningServer.java
@@ -38,7 +38,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateSingleImageReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
/**
@@ -73,15 +72,6 @@ public interface IScreeningServer extends IServer
TechId geneMaterialId,
@AuthorizationGuard(guardClass = SpaceIdentifierPredicate.class) ExperimentIdentifier experimentIdentifier);
- /**
- * loads all images from all existing image datasets (in BDS-HCS format) for the specified
- * plate.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<PlateSingleImageReference> listPlateImages(String sessionToken,
- @AuthorizationGuard(guardClass = SampleTechIdPredicate.class) TechId plateId);
-
/**
* Loads all analysis results from all existing image-analysis datasets connected with the
* specified experiment. It is assumed that all datasets are CSV files with the same headers.
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateSingleImageReference.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateSingleImageReference.java
deleted file mode 100644
index 484331f65f08c6fcf7705ece01fec1b08a8c00eb..0000000000000000000000000000000000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateSingleImageReference.java
+++ /dev/null
@@ -1,117 +0,0 @@
-/*
- * Copyright 2010 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.shared.basic.dto;
-
-import java.io.Serializable;
-
-import com.google.gwt.user.client.rpc.IsSerializable;
-
-/**
- * Reference to a single image acquired for a plate.
- *
- * @author Tomasz Pylak
- */
-public class PlateSingleImageReference implements IsSerializable, Serializable
-{
- private static final long serialVersionUID = 1L;
-
- private String datasetCode;
-
- private int wellRow;
-
- private int wellCol;
-
- private int tile;
-
- private int channel;
-
- // url to fetch the image from DSS using HTTP, the hostname and servlet name is not included
- private String imageUrl;
-
- // path in the DSS store
- private String imagePath;
-
- public int getWellRow()
- {
- return wellRow;
- }
-
- public void setWellRow(int wellRow)
- {
- this.wellRow = wellRow;
- }
-
- public int getWellCol()
- {
- return wellCol;
- }
-
- public void setWellCol(int wellCol)
- {
- this.wellCol = wellCol;
- }
-
- public int getTile()
- {
- return tile;
- }
-
- public void setTile(int tile)
- {
- this.tile = tile;
- }
-
- public int getChannel()
- {
- return channel;
- }
-
- public void setChannel(int channel)
- {
- this.channel = channel;
- }
-
- public String getDatasetCode()
- {
- return datasetCode;
- }
-
- public void setDatasetCode(String datasetCode)
- {
- this.datasetCode = datasetCode;
- }
-
- public String getImageUrl()
- {
- return imageUrl;
- }
-
- public void setImageUrl(String imageUrl)
- {
- this.imageUrl = imageUrl;
- }
-
- public String getImagePath()
- {
- return imagePath;
- }
-
- public void setImagePath(String imagePath)
- {
- this.imagePath = imagePath;
- }
-}
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 e626d39f107f1e98e0155a08e785ce7bca7a175c..40d8d451d4fe92ba5b3cfbed259ab3081052d0c6 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
@@ -27,14 +27,14 @@ package ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto;
*/
public class ScreeningConstants
{
+ // name of the data source (configured in service.properties) which allows to access imaging db
+ public static final String IMAGING_DATA_SOURCE = "imaging-db";
+
// name of the property which stores material (gene) inhibited by the material stored in a well
public static final String INHIBITOR_PROPERTY_CODE = "INHIBITOR_OF";
// ---- required DSS plugins
- // id of the DSS screening reporting plugin to get the images
- public static final String PLATE_IMAGE_REPORT_KEY = "plate-image-reporter";
-
// id of the DSS screening reporting plugin to get the images parameters
public static final String PLATE_IMAGE_PARAMS_REPORT_KEY = "plate-image-params-reporter";
diff --git a/screening/source/sql/postgresql/001/schema-001.sql b/screening/source/sql/postgresql/001/schema-001.sql
index 11f5df79d0cd95e60481487e8f984723a84c1975..5385d12e09badaa1cb0c295aa6186671d329f463 100644
--- a/screening/source/sql/postgresql/001/schema-001.sql
+++ b/screening/source/sql/postgresql/001/schema-001.sql
@@ -59,7 +59,10 @@ CREATE INDEX SPOTS_CONT_IDX ON SPOTS(CONT_ID);
CREATE TABLE DATA_SETS (
ID BIGSERIAL NOT NULL,
- PERM_ID CODE NOT NULL,
+ PERM_ID CODE NOT NULL,
+ -- All images paths are relative to the IMAGES_DIRECTORY folder.
+ -- The folder path itself is relative to the dataset root directory.
+ IMAGES_DIRECTORY FILE_PATH,
FIELDS_WIDTH INTEGER,
FIELDS_HEIGHT INTEGER,
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingUploadDAOTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingUploadDAOTest.java
index 1d94d01c45116ea9ced5a15671d067e436a752ce..9f7992d56c9233232222d6e6333303490b47cef3 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingUploadDAOTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingUploadDAOTest.java
@@ -109,13 +109,13 @@ public class ImagingUploadDAOTest extends AbstractDBTest
private void testGetImage(final long datasetId, final long channelId1, final long channelId2)
{
ImgImageDTO image1 =
- dao.getImage(channelId1, datasetId, new Location(X_WELL_COLUMN, Y_WELL_ROW),
+ dao.tryGetImage(channelId1, datasetId, new Location(X_WELL_COLUMN, Y_WELL_ROW),
new Location(X_TILE_COLUMN, Y_TILE_ROW));
assertEquals(PATH1, image1.getFilePath());
assertEquals(ColorComponent.BLUE, image1.getColorComponent());
ImgImageDTO image2 =
- dao.getImage(channelId2, datasetId, new Location(X_WELL_COLUMN, Y_WELL_ROW),
+ dao.tryGetImage(channelId2, datasetId, new Location(X_WELL_COLUMN, Y_WELL_ROW),
new Location(X_TILE_COLUMN, Y_TILE_ROW));
assertEquals(PATH2, image2.getFilePath());
assertEquals(ColorComponent.RED, image2.getColorComponent());
@@ -186,7 +186,7 @@ public class ImagingUploadDAOTest extends AbstractDBTest
final Integer fieldsWidth = 1;
final Integer fieldsHeight = 2;
final ImgDatasetDTO dataset =
- new ImgDatasetDTO(permId, fieldsHeight, fieldsWidth, containerId);
+ new ImgDatasetDTO(permId, ".", fieldsHeight, fieldsWidth, containerId);
final long datasetId = dao.addDataset(dataset);
final ImgDatasetDTO loadedDataset = dao.tryGetDatasetByPermId(DS_PERM_ID);