diff --git a/screening/etc/service.properties b/screening/etc/service.properties
index 3917b50cc88b7878e615d0b2fb852b5bcb51e4fe..f6b7f9d2bc1ced60a6da6f8e3fbfede97c3be455 100644
--- a/screening/etc/service.properties
+++ b/screening/etc/service.properties
@@ -159,7 +159,7 @@ screening-dss-api-exporter-servlet.path = /rmi-datastore-server-screening-api-v1
# ---------------------------------------------------------------------------
data-sources = imaging-db
-imaging-db.version-holder-class = ch.systemsx.cisd.openbis.plugin.screening.shared.ImagingDatabaseVersionHolder
+imaging-db.version-holder-class = ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImagingDatabaseVersionHolder
imaging-db.databaseEngineCode = postgresql
imaging-db.basicDatabaseName = imaging
imaging-db.databaseKind = dev
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractionResult.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractionResult.java
index e744d06bef95e1af705fbb0ccecd0df9a760881d..66b14cb63ea7daf38a01b9e624f7479165108775 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractionResult.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractionResult.java
@@ -17,6 +17,9 @@ package ch.systemsx.cisd.openbis.dss.etl;
import java.io.File;
import java.util.List;
+import java.util.Set;
+
+import ch.systemsx.cisd.bds.hcs.Channel;
/**
* Class which contains the image extraction process results.
@@ -31,10 +34,14 @@ public final class HCSImageFileExtractionResult
/** The invalid files found. */
private final List<File> invalidFiles;
- public HCSImageFileExtractionResult(List<AcquiredPlateImage> images, List<File> invalidFiles)
+ private final Set<Channel> channels;
+
+ public HCSImageFileExtractionResult(List<AcquiredPlateImage> images, List<File> invalidFiles,
+ Set<Channel> channels)
{
this.images = images;
this.invalidFiles = invalidFiles;
+ this.channels = channels;
}
public List<AcquiredPlateImage> getImages()
@@ -46,4 +53,9 @@ public final class HCSImageFileExtractionResult
{
return invalidFiles;
}
+
+ public Set<Channel> getChannels()
+ {
+ return channels;
+ }
}
\ 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 3325b90176f15a6962c5e2664ce678fccfaf20ed..30af1e46c3a1a6036f703aa102fa1b2a1396735a 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
@@ -22,6 +22,10 @@ import java.util.ArrayList;
import java.util.List;
import java.util.Properties;
+import javax.sql.DataSource;
+
+import net.lemnik.eodsql.QueryTool;
+
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang.time.DurationFormatUtils;
import org.apache.log4j.Logger;
@@ -50,6 +54,8 @@ import ch.systemsx.cisd.etlserver.ITypeExtractor;
import ch.systemsx.cisd.etlserver.PlateDimension;
import ch.systemsx.cisd.etlserver.PlateDimensionParser;
import ch.systemsx.cisd.etlserver.HCSImageCheckList.FullLocation;
+import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingUploadDAO;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
@@ -79,6 +85,10 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
private static final String DEPRECATED_FILE_EXTRACTOR_PROPERTY = "deprecated-file-extractor";
+ // -----------
+
+ private final DataSource dataSource;
+
private final Geometry spotGeometry;
private final int numberOfChannels;
@@ -88,6 +98,8 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
private final ch.systemsx.cisd.etlserver.IHCSImageFileExtractor deprecatedImageFileExtractor;
+ private IImagingUploadDAO currentTransaction;
+
public PlateStorageProcessor(final Properties properties)
{
super(properties);
@@ -110,6 +122,8 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
ClassUtils.create(ch.systemsx.cisd.etlserver.IHCSImageFileExtractor.class,
fileExtractorClass, properties);
}
+ this.dataSource = ServiceProvider.getDataSourceProvider().getDataSource(properties);
+ this.currentTransaction = null;
}
private int extractNumberOfChannels()
@@ -124,6 +138,11 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
return channels;
}
+ private IImagingUploadDAO createQuery()
+ {
+ return QueryTool.getQuery(dataSource, IImagingUploadDAO.class);
+ }
+
private final static void checkDataSetInformation(final DataSetInformation dataSetInformation)
{
assert dataSetInformation != null : "Unspecified data set information";
@@ -250,7 +269,8 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
{
throw new UserFailureException("Experiment unknown for data set " + dataSetInformation);
}
- ScreeningContainerDatasetInfo info = createScreeningDatasetInfo(experiment, dataSetInformation);
+ ScreeningContainerDatasetInfo info =
+ createScreeningDatasetInfo(experiment, dataSetInformation);
HCSImageFileExtractionResult extractionResult =
extractImages(dataSetInformation, incomingDataSetDirectory);
@@ -332,14 +352,29 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
@Override
public void commit()
{
- // FIXME 2010--, Tomasz Pylak: implement me
+ commitDatabaseChanges();
+ }
+
+ private void commitDatabaseChanges()
+ {
+ if (currentTransaction == null)
+ {
+ throw new IllegalStateException("there is no transaction to commit");
+ }
+ try
+ {
+ currentTransaction.close(true);
+ } finally
+ {
+ currentTransaction = null;
+ }
}
public UnstoreDataAction rollback(File incomingDataSetDirectory, File storedDataDirectory,
Throwable exception)
{
unstoreFiles(incomingDataSetDirectory, storedDataDirectory);
- unstoreFromDatabase();
+ rollbackDatabaseChanges();
return UnstoreDataAction.MOVE_TO_ERROR;
}
@@ -385,12 +420,28 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
private void storeInDatabase(ScreeningContainerDatasetInfo info, List<AcquiredPlateImage> images)
{
+ if (currentTransaction != null)
+ {
+ throw new IllegalStateException("previous transaction has not been commited!");
+ }
+ currentTransaction = createQuery();
// FIXME 2010--, Tomasz Pylak: implement me
}
- private void unstoreFromDatabase()
+ private void rollbackDatabaseChanges()
{
- // FIXME 2010-05-14, Tomasz Pylak: delete the whle dataset from the screening database
+ if (currentTransaction == null)
+ {
+ throw new IllegalStateException("there is no transaction to rollback");
+ }
+ try
+ {
+ currentTransaction.rollback();
+ } finally
+ {
+ currentTransaction.close();
+ currentTransaction = null;
+ }
}
/**
@@ -514,7 +565,8 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
.createDirectoryNode(incomingDataSetDirectory),
dataSetInformation, accepter);
return new HCSImageFileExtractionResult(accepter.getImages(),
- asRelativePaths(originalResult.getInvalidFiles()));
+ asRelativePaths(originalResult.getInvalidFiles()), originalResult
+ .getChannels());
}
private List<File> asRelativePaths(List<IFile> files)
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
new file mode 100644
index 0000000000000000000000000000000000000000..cee7e3814491f721aab83fb8d42aebd61d5b9d1c
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IImagingUploadDAO.java
@@ -0,0 +1,36 @@
+/*
+ * 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.dataaccess;
+
+import net.lemnik.eodsql.Select;
+import net.lemnik.eodsql.TransactionQuery;
+
+/**
+ * @author Tomasz Pylak
+ */
+public interface IImagingUploadDAO extends TransactionQuery
+{
+ @Select("select ID from EXPERIMENTS where PERM_ID = ?{1}")
+ public Long tryGetExperimentIdByPermId(String experimentPermId);
+
+ @Select("insert into EXPERIMENTS (PERM_ID) values (?{1}) returning ID")
+ public long addExperiment(String experimentPermId);
+
+ @Select("select * from CONTAINERS where PERM_ID = ?{1}")
+ public ImgContainerDTO tryGetContainerByPermId(String containerPermId);
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/ScreeningDatabaseVersionHolder.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingDatabaseVersionHolder.java
similarity index 75%
rename from screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/ScreeningDatabaseVersionHolder.java
rename to screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingDatabaseVersionHolder.java
index ecffb28e669ecaa9b04ee0d88b8bd4158bfd6a69..21acd307892bfb55ae8c339ea2dac709c31da39e 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/ScreeningDatabaseVersionHolder.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingDatabaseVersionHolder.java
@@ -14,15 +14,16 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.plugin.screening.shared;
+package ch.systemsx.cisd.openbis.dss.etl.dataaccess;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IDatabaseVersionHolder;
/**
- * Stores current version of special purpose screening database.
+ * Stores current version of special purpose imaging database.
*
* @author Tomasz Pylak
*/
-public class ScreeningDatabaseVersionHolder
+public class ImagingDatabaseVersionHolder implements IDatabaseVersionHolder
{
/** Current version of the database. */
static final String DATABASE_VERSION = "001";
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgAcquiredImageDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgAcquiredImageDTO.java
new file mode 100644
index 0000000000000000000000000000000000000000..ff3268fb5d5c96cf5ad45dacd15ed6ab8d4b841f
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgAcquiredImageDTO.java
@@ -0,0 +1,93 @@
+/*
+ * 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.dataaccess;
+
+import net.lemnik.eodsql.AutoGeneratedKeys;
+import net.lemnik.eodsql.ResultColumn;
+
+/**
+ * @author Tomasz Pylak
+ */
+public class ImgAcquiredImageDTO
+{
+ @AutoGeneratedKeys
+ private long id;
+
+ @ResultColumn("IMG_ID")
+ private long imageId;
+
+ // can be null if there is no thumbnail
+ @ResultColumn("THUMBNAIL_ID")
+ private Long thumbnailId;
+
+ @ResultColumn("CHANNEL_STACK_ID")
+ private long channelStackId;
+
+ @ResultColumn("CHANNEL_ID")
+ private long channelId;
+
+ public long getId()
+ {
+ return id;
+ }
+
+ public void setId(long id)
+ {
+ this.id = id;
+ }
+
+ public long getImageId()
+ {
+ return imageId;
+ }
+
+ public void setImageId(long imageId)
+ {
+ this.imageId = imageId;
+ }
+
+ public Long getThumbnailId()
+ {
+ return thumbnailId;
+ }
+
+ public void setThumbnailId(Long thumbnailId)
+ {
+ this.thumbnailId = thumbnailId;
+ }
+
+ public long getChannelStackId()
+ {
+ return channelStackId;
+ }
+
+ public void setChannelStackId(long channelStackId)
+ {
+ this.channelStackId = channelStackId;
+ }
+
+ public long getChannelId()
+ {
+ return channelId;
+ }
+
+ public void setChannelId(long channelId)
+ {
+ this.channelId = channelId;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgChannelDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgChannelDTO.java
new file mode 100644
index 0000000000000000000000000000000000000000..df8812dbe4e4d009beba992e20d8f813389e4db2
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgChannelDTO.java
@@ -0,0 +1,137 @@
+/*
+ * 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.dataaccess;
+
+import net.lemnik.eodsql.AutoGeneratedKeys;
+import net.lemnik.eodsql.ResultColumn;
+
+/**
+ * @author Tomasz Pylak
+ */
+// CREATE TABLE CHANNELS (
+// ID BIGSERIAL NOT NULL,
+//
+// NAME NAME NOT NULL,
+// DESCRIPTION DESCRIPTION,
+// WAVELENGTH INTEGER,
+//
+// 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))
+// );
+public class ImgChannelDTO
+{
+ @AutoGeneratedKeys
+ private long id;
+
+ @ResultColumn("NAME")
+ private String name;
+
+ @ResultColumn("DESCRIPTION")
+ private String descriptionOrNull;
+
+ @ResultColumn("WAVELENGTH")
+ private Integer wavelengthOrNull;
+
+ // can be null if experimentId is not null
+ @ResultColumn("DS_ID")
+ private Long datasetIdOrNull;
+
+ // can be null if datasetId is not null
+ @ResultColumn("EXP_ID")
+ private Long experimentIdOrNull;
+
+ public ImgChannelDTO(String name, String descriptionOrNull, Integer wavelengthOrNull,
+ Long datasetIdOrNull, Long experimentIdOrNull)
+ {
+ assert (datasetIdOrNull == null && experimentIdOrNull != null)
+ || (datasetIdOrNull != null && experimentIdOrNull == null);
+ this.name = name;
+ this.descriptionOrNull = descriptionOrNull;
+ this.wavelengthOrNull = wavelengthOrNull;
+ this.datasetIdOrNull = datasetIdOrNull;
+ this.experimentIdOrNull = experimentIdOrNull;
+ }
+
+ public long getId()
+ {
+ return id;
+ }
+
+ public void setId(long id)
+ {
+ this.id = id;
+ }
+
+ public String getName()
+ {
+ return name;
+ }
+
+ public void setName(String name)
+ {
+ this.name = name;
+ }
+
+ public String getDescription()
+ {
+ return descriptionOrNull;
+ }
+
+ public void setDescription(String description)
+ {
+ this.descriptionOrNull = description;
+ }
+
+ public Integer getWavelength()
+ {
+ return wavelengthOrNull;
+ }
+
+ public void setWavelength(Integer wavelength)
+ {
+ this.wavelengthOrNull = wavelength;
+ }
+
+ public Long getDatasetId()
+ {
+ return datasetIdOrNull;
+ }
+
+ public void setDatasetId(Long datasetId)
+ {
+ this.datasetIdOrNull = datasetId;
+ }
+
+ public Long getExperimentId()
+ {
+ return experimentIdOrNull;
+ }
+
+ public void setExperimentId(Long experimentId)
+ {
+ this.experimentIdOrNull = experimentId;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgChannelStackDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgChannelStackDTO.java
new file mode 100644
index 0000000000000000000000000000000000000000..d92339eb5028a12d28f77bc2fc831a79ba97b499
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgChannelStackDTO.java
@@ -0,0 +1,131 @@
+/*
+ * 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.dataaccess;
+
+import net.lemnik.eodsql.AutoGeneratedKeys;
+import net.lemnik.eodsql.ResultColumn;
+
+/**
+ * @author Tomasz Pylak
+ */
+public class ImgChannelStackDTO
+{
+ @AutoGeneratedKeys
+ private long id;
+
+ // x and y are kind of a two dimensional sequence number, (e.g. tile column)
+ @ResultColumn("X")
+ private Integer x;
+
+ // x and y are kind of a two dimensional sequence number, (e.g. tile row, 1 is the first row)
+ // Some use case may only use x and leave y alone.
+ @ResultColumn("Y")
+ private Integer y;
+
+ // can be null
+ @ResultColumn("Z_in_M")
+ private Float z;
+
+ // can be null
+ @ResultColumn("T_in_SEC")
+ private Float t;
+
+ @ResultColumn("DS_ID")
+ private long datasetId;
+
+ @ResultColumn("SPOT_ID")
+ private long spotId;
+
+ public ImgChannelStackDTO(int x, int y, long datasetId, long spotId)
+ {
+ this.x = x;
+ this.y = y;
+ this.datasetId = datasetId;
+ this.spotId = spotId;
+ }
+
+ public long getId()
+ {
+ return id;
+ }
+
+ public void setId(long id)
+ {
+ this.id = id;
+ }
+
+ public Integer getX()
+ {
+ return x;
+ }
+
+ public void setX(Integer x)
+ {
+ this.x = x;
+ }
+
+ public Integer getY()
+ {
+ return y;
+ }
+
+ public void setY(Integer y)
+ {
+ this.y = y;
+ }
+
+ public Float getZ()
+ {
+ return z;
+ }
+
+ public void setZ(Float z)
+ {
+ this.z = z;
+ }
+
+ public Float getT()
+ {
+ return t;
+ }
+
+ public void setT(Float t)
+ {
+ this.t = t;
+ }
+
+ public long getDatasetId()
+ {
+ return datasetId;
+ }
+
+ public void setDatasetId(long datasetId)
+ {
+ this.datasetId = datasetId;
+ }
+
+ public long getSpotId()
+ {
+ return spotId;
+ }
+
+ public void setSpotId(long spotId)
+ {
+ this.spotId = spotId;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgContainerDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgContainerDTO.java
new file mode 100644
index 0000000000000000000000000000000000000000..c2b824b5e500ddcf7806b659db48f3f2362202c4
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgContainerDTO.java
@@ -0,0 +1,94 @@
+/*
+ * 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.dataaccess;
+
+import net.lemnik.eodsql.AutoGeneratedKeys;
+import net.lemnik.eodsql.ResultColumn;
+
+/**
+ * DTO holding information about the container in the imaging database.
+ *
+ * @author Tomasz Pylak
+ */
+public class ImgContainerDTO
+{
+ @AutoGeneratedKeys
+ private long id;
+
+ @ResultColumn("PERM_ID")
+ private String permId;
+
+ @ResultColumn("SPOTS_WIDTH")
+ private Integer spotWidth;
+
+ @ResultColumn("SPOTS_HEIGHT")
+ private Integer spotHeight;
+
+ @ResultColumn("EXPE_ID")
+ private long experimentId;
+
+ public long getId()
+ {
+ return id;
+ }
+
+ public void setId(long id)
+ {
+ this.id = id;
+ }
+
+ public String getPermId()
+ {
+ return permId;
+ }
+
+ public void setPermId(String permId)
+ {
+ this.permId = permId;
+ }
+
+ public Integer getSpotWidth()
+ {
+ return spotWidth;
+ }
+
+ public void setSpotWidth(Integer spotWidth)
+ {
+ this.spotWidth = spotWidth;
+ }
+
+ public Integer getSpotHeight()
+ {
+ return spotHeight;
+ }
+
+ public void setSpotHeight(Integer spotHeight)
+ {
+ this.spotHeight = spotHeight;
+ }
+
+ public long getExperimentId()
+ {
+ return experimentId;
+ }
+
+ public void setExperimentId(long experimentId)
+ {
+ this.experimentId = experimentId;
+ }
+
+}
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
new file mode 100644
index 0000000000000000000000000000000000000000..c12c34bf6513b25724947a5981dbdee392914447
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgDatasetDTO.java
@@ -0,0 +1,101 @@
+/*
+ * 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.dataaccess;
+
+import net.lemnik.eodsql.AutoGeneratedKeys;
+import net.lemnik.eodsql.ResultColumn;
+
+/**
+ * @author Tomasz Pylak
+ */
+public class ImgDatasetDTO
+{
+ @AutoGeneratedKeys
+ private long id;
+
+ @ResultColumn("PERM_ID")
+ private String permId;
+
+ @ResultColumn("FIELDS_WIDTH")
+ private Integer fieldsWidthOrNull;
+
+ @ResultColumn("FIELDS_HEIGHT")
+ private Integer fieldsHeightOrNull;
+
+ @ResultColumn("CONT_ID")
+ private long containerId;
+
+ public ImgDatasetDTO(String permId, Integer fieldsWidthOrNull, Integer fieldsHeightOrNull,
+ long containerId)
+ {
+ this.permId = permId;
+ this.fieldsWidthOrNull = fieldsWidthOrNull;
+ this.fieldsHeightOrNull = fieldsHeightOrNull;
+ this.containerId = containerId;
+ }
+
+ public long getId()
+ {
+ return id;
+ }
+
+ public void setId(long id)
+ {
+ this.id = id;
+ }
+
+ public String getPermId()
+ {
+ return permId;
+ }
+
+ public void setPermId(String permId)
+ {
+ this.permId = permId;
+ }
+
+ public Integer getFieldsWidth()
+ {
+ return fieldsWidthOrNull;
+ }
+
+ public void setFieldsWidth(Integer fieldsWidth)
+ {
+ this.fieldsWidthOrNull = fieldsWidth;
+ }
+
+ public Integer getFieldsHeight()
+ {
+ return fieldsHeightOrNull;
+ }
+
+ public void setFieldsHeight(Integer fieldsHeight)
+ {
+ this.fieldsHeightOrNull = fieldsHeight;
+ }
+
+ public long getContainerId()
+ {
+ return containerId;
+ }
+
+ public void setContainerId(long containerId)
+ {
+ this.containerId = containerId;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgImageDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgImageDTO.java
new file mode 100644
index 0000000000000000000000000000000000000000..d82d5ca4c0bccb9259e8a3ee2d26cbf7268d19fc
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgImageDTO.java
@@ -0,0 +1,96 @@
+/*
+ * 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.dataaccess;
+
+import net.lemnik.eodsql.AutoGeneratedKeys;
+import net.lemnik.eodsql.ResultColumn;
+
+/**
+ * @author Tomasz Pylak
+ */
+public class ImgImageDTO
+{
+ @AutoGeneratedKeys
+ private long id;
+
+ @ResultColumn("PATH")
+ private String filePath;
+
+ @ResultColumn("PAGE")
+ private Integer pathOrNull;
+
+ @ResultColumn("COLOR")
+ private ColorComponent colorComponentOrNull;
+
+ public static enum ColorComponent
+ {
+ RED, GREEN, BLUE
+ }
+
+ public ImgImageDTO(String filePath)
+ {
+ this(filePath, null, null);
+ }
+
+ public ImgImageDTO(String filePath, Integer pathOrNull, ColorComponent colorComponentOrNull)
+ {
+ this.filePath = filePath;
+ this.pathOrNull = pathOrNull;
+ this.colorComponentOrNull = colorComponentOrNull;
+ }
+
+ public long getId()
+ {
+ return id;
+ }
+
+ public void setId(long id)
+ {
+ this.id = id;
+ }
+
+ public String getFilePath()
+ {
+ return filePath;
+ }
+
+ public void setFilePath(String filePath)
+ {
+ this.filePath = filePath;
+ }
+
+ public Integer getPath()
+ {
+ return pathOrNull;
+ }
+
+ public void setPath(Integer path)
+ {
+ this.pathOrNull = path;
+ }
+
+ public ColorComponent getColorComponent()
+ {
+ return colorComponentOrNull;
+ }
+
+ public void setColorComponent(ColorComponent colorComponent)
+ {
+ this.colorComponentOrNull = colorComponent;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgSpotDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgSpotDTO.java
new file mode 100644
index 0000000000000000000000000000000000000000..e2cb4cbcd7c32ed401ffe5ef3e8151af4873d914
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgSpotDTO.java
@@ -0,0 +1,103 @@
+/*
+ * 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.dataaccess;
+
+import net.lemnik.eodsql.AutoGeneratedKeys;
+import net.lemnik.eodsql.ResultColumn;
+
+/**
+ * @author Tomasz Pylak
+ */
+public class ImgSpotDTO
+{
+ @AutoGeneratedKeys
+ private long id;
+
+ @ResultColumn("PERM_ID")
+ private String permId;
+
+ // position in the container, one-based (e.g. well column)
+ @ResultColumn("X")
+ private Integer x;
+
+ // position in the container, one-based (e.g. well row, 1 is the first row)
+ @ResultColumn("Y")
+ private Integer y;
+
+ @ResultColumn("CONT_ID")
+ private long containerId;
+
+ public ImgSpotDTO(long id, String permId, Integer x, Integer y, long containerId)
+ {
+ this.id = id;
+ this.permId = permId;
+ this.x = x;
+ this.y = y;
+ this.containerId = containerId;
+ }
+
+ public long getId()
+ {
+ return id;
+ }
+
+ public void setId(long id)
+ {
+ this.id = id;
+ }
+
+ public String getPermId()
+ {
+ return permId;
+ }
+
+ public void setPermId(String permId)
+ {
+ this.permId = permId;
+ }
+
+ public Integer getX()
+ {
+ return x;
+ }
+
+ public void setX(Integer x)
+ {
+ this.x = x;
+ }
+
+ public Integer getY()
+ {
+ return y;
+ }
+
+ public void setY(Integer y)
+ {
+ this.y = y;
+ }
+
+ public long getContainerId()
+ {
+ return containerId;
+ }
+
+ public void setContainerId(long containerId)
+ {
+ this.containerId = containerId;
+ }
+
+}
diff --git a/screening/source/sql/postgresql/001/schema-001.sql b/screening/source/sql/postgresql/001/schema-001.sql
index 90b6b2a5ddcb21563e1537151abce28ac8b5f180..a0858f746149df7a7422fe045d6a45496b857e77 100644
--- a/screening/source/sql/postgresql/001/schema-001.sql
+++ b/screening/source/sql/postgresql/001/schema-001.sql
@@ -149,6 +149,8 @@ CREATE TABLE IMAGES (
/* FEATURE VECTORS */
/* ---------------------------------------------------------------------- */
+/* --- UNUSED YET ---------------------------------------
+
CREATE TABLE FEATURE_DEFS (
ID BIGSERIAL NOT NULL,
@@ -187,3 +189,4 @@ CREATE INDEX FEATURE_VALUES_FD_IDX ON FEATURE_VALUES(FD_ID);
CREATE INDEX FEATURE_VALUES_DS_IDX ON FEATURE_VALUES(DS_ID);
CREATE INDEX FEATURE_VALUES_Z_AND_T_IDX ON FEATURE_VALUES(Z_in_M, T_in_SEC);
+ --- END UNUSED YET --------------------------------------- */