From fd2b69b3c623df1e6f471daa1d093424b9930fda Mon Sep 17 00:00:00 2001
From: buczekp <buczekp>
Date: Fri, 25 Jun 2010 07:30:04 +0000
Subject: [PATCH] [LMS-1588] stop using reporting plugin in openBIS to fetch
image dataset metadata (ScreeningPlateImageParamsReportingPlugin)
SVN: 16733
---
.../dss/etl/HCSImageDatasetLoaderFactory.java | 77 -------------------
...eeningPlateImageParamsReportingPlugin.java | 1 +
.../dataaccess/db/ScreeningDAOFactory.java | 4 +-
.../server/logic/DatasetReportsLoader.java | 62 ++++++---------
.../logic/GenePlateLocationsLoader.java | 15 ++--
.../server/logic/PlateContentLoader.java | 14 +---
.../shared/basic/dto/ScreeningConstants.java | 3 -
.../shared/imaging/HCSDatasetLoader.java | 5 ++
.../shared/imaging/IHCSDatasetLoader.java | 2 +
9 files changed, 45 insertions(+), 138 deletions(-)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageDatasetLoaderFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageDatasetLoaderFactory.java
index ac0b35df322..82f7855d77b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageDatasetLoaderFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageDatasetLoaderFactory.java
@@ -17,20 +17,14 @@
package ch.systemsx.cisd.openbis.dss.etl;
import java.io.File;
-import java.util.ArrayList;
import java.util.HashMap;
-import java.util.List;
import java.util.Map;
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.common.io.FileBasedContent;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.HCSImageDatasetLoader;
-import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDatasetDownloadServlet.Size;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
@@ -64,7 +58,6 @@ public class HCSImageDatasetLoaderFactory
public static final IHCSImageDatasetLoader create(File datasetRootDir, String datasetCode)
{
return createImageDBLoader(datasetRootDir, datasetCode);
- // return createBDSLoader(datasetRootDir);
}
private static HCSImageDatasetLoader createImageDBLoader(File datasetRootDir, String datasetCode)
@@ -73,74 +66,4 @@ public class HCSImageDatasetLoaderFactory
return new HCSImageDatasetLoader(query, datasetCode, repository);
}
- // remove when not needed
- @SuppressWarnings("unused")
- private static IHCSImageDatasetLoader createBDSLoader(File datasetRootDir)
- {
- final ch.systemsx.cisd.bds.hcs.HCSDatasetLoader loader =
- new ch.systemsx.cisd.bds.hcs.HCSDatasetLoader(datasetRootDir);
- return adapt(loader);
- }
-
- private static IHCSImageDatasetLoader adapt(final ch.systemsx.cisd.bds.hcs.HCSDatasetLoader loader)
- {
- return new IHCSImageDatasetLoader()
- {
-
- 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(String chosenChannel,
- Location wellLocation, Location tileLocation, Size thumbnailSizeOrNull)
- {
- if (thumbnailSizeOrNull != null)
- {
- return null;
- }
- String absPath =
- loader.tryGetStandardNodeAt(convertToNumber(chosenChannel),
- wellLocation, tileLocation);
- return new AbsoluteImageReference(new FileBasedContent(new File(absPath)),
- null, null);
- }
-
- private int convertToNumber(String chosenChannel)
- {
- return Integer.parseInt(chosenChannel) - 1;
- }
-
- public List<String> getChannelsNames()
- {
- List<String> names = new ArrayList<String>();
- for (int i = 0; i < getChannelCount(); i++)
- {
- names.add(convertToName(i));
- }
- return names;
- }
-
- private String convertToName(int i)
- {
- return (i + 1) + "";
- }
-
- };
- }
}
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 e7273040dae..99108406ddb 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
@@ -41,6 +41,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
*
* @author Tomasz Pylak
*/
+// TODO 2010-06-25, Piotr Buczek: remove
public class ScreeningPlateImageParamsReportingPlugin extends AbstractDatastorePlugin implements
IReportingPluginTask
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/db/ScreeningDAOFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/db/ScreeningDAOFactory.java
index 9a8095fdcf5..5a7c72404d6 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/db/ScreeningDAOFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/db/ScreeningDAOFactory.java
@@ -58,8 +58,8 @@ public class ScreeningDAOFactory implements IScreeningDAOFactory
{
throw CheckedExceptionTunnel.wrapIfNecessary(ex);
}
- // TODO this is the same solution as in PhosphoNetX - is it ok to use connection here?
- // shouldn't it be a data source passed here in constructor?
+ // TODO 2010-06-25, Piotr Buczek: this is the same solution as in PhosphoNetX - is it ok to
+ // use connection here? shouldn't it be a data source passed here in constructor?
imagingQueryDAO = QueryTool.getQuery(connection, IImagingQueryDAO.class);
if (operationLog.isInfoEnabled())
{
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 f9c1c782696..4123343ed38 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
@@ -21,13 +21,13 @@ import java.util.List;
import org.apache.commons.lang.StringEscapeUtils;
+import ch.systemsx.cisd.bds.hcs.Geometry;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataTable;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable;
-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.server.IScreeningBusinessObjectFactory;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImageParameters;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.IHCSDatasetLoader;
/**
* Loads content of datasets by contacting DSS.
@@ -43,52 +43,40 @@ public class DatasetReportsLoader
ScreeningConstants.PLATE_IMAGE_ANALYSIS_REPORT_KEY, datastoreCode, datasets);
}
- public static List<PlateImageParameters> loadPlateImageParameters(List<String> datasets,
- String datastoreCode, IExternalDataTable externalDataTable)
- {
- TableModel imageParamsReport =
- externalDataTable.createReportFromDatasets(
- ScreeningConstants.PLATE_IMAGE_PARAMS_REPORT_KEY, datastoreCode, datasets);
- return asImageParams(imageParamsReport);
- }
-
- private static List<PlateImageParameters> asImageParams(TableModel imageParamsReport)
+ public static List<PlateImageParameters> loadPlateImageParameters(List<String> datasetCodes,
+ IScreeningBusinessObjectFactory boFactory)
{
List<PlateImageParameters> paramsList = new ArrayList<PlateImageParameters>();
- for (TableModelRow tableModelRow : imageParamsReport.getRows())
+
+ for (String datasetCode : datasetCodes)
{
- paramsList.add(asImageParams(tableModelRow));
+ final IHCSDatasetLoader loader = boFactory.createHCSDatasetLoader(datasetCode);
+ paramsList.add(createImageParameters(loader));
}
return paramsList;
}
- private static PlateImageParameters asImageParams(TableModelRow tableModelRow)
+ // TODO 2010-06-25, Piotr Buczek: move
+ public static PlateImageParameters createImageParameters(IHCSDatasetLoader loader)
{
+ final String datasetCode = loader.getDatasetPermId();
+ final Geometry plateGeometry = loader.getPlateGeometry();
+ final Geometry wellGeometry = loader.getWellGeometry();
+ final List<String> channelsNames = loader.getChannelsNames();
+
PlateImageParameters params = new PlateImageParameters();
- List<ISerializableComparable> values = tableModelRow.getValues();
- params.setDatasetCode(asText(values.get(0)));
- params.setRowsNum(asNum(values.get(1)));
- params.setColsNum(asNum(values.get(2)));
- params.setTileRowsNum(asNum(values.get(3)));
- params.setTileColsNum(asNum(values.get(4)));
- String channelsNamesCsv = asText(values.get(5));
- String[] splittedChannelsNames = channelsNamesCsv.split(",");
- List<String> channelNames = new ArrayList<String>();
- for (String val : splittedChannelsNames)
+ params.setDatasetCode(datasetCode);
+ params.setRowsNum(plateGeometry.getRows());
+ params.setColsNum(plateGeometry.getColumns());
+ params.setTileRowsNum(wellGeometry.getRows());
+ params.setTileColsNum(wellGeometry.getColumns());
+ List<String> escapedChannelNames = new ArrayList<String>();
+ for (String name : channelsNames)
{
- channelNames.add(StringEscapeUtils.escapeCsv(val));
+ escapedChannelNames.add(StringEscapeUtils.escapeCsv(name));
}
- params.setChannelsNames(channelNames);
+ params.setChannelsNames(escapedChannelNames);
return params;
}
- private static String asText(ISerializableComparable serializableComparable)
- {
- return serializableComparable.toString();
- }
-
- private static int asNum(ISerializableComparable serializableComparable)
- {
- return (int) ((IntegerTableCell) serializableComparable).getNumber();
- }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/GenePlateLocationsLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/GenePlateLocationsLoader.java
index 4b329d1e26f..9dc330f9c6d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/GenePlateLocationsLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/GenePlateLocationsLoader.java
@@ -52,6 +52,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateMaterials
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.IHCSDatasetLoader;
/**
* @author Tomasz Pylak
@@ -90,7 +91,6 @@ public class GenePlateLocationsLoader
this.businessObjectFactory = businessObjectFactory;
this.daoFactory = daoFactory;
this.externalDataTable = businessObjectFactory.createExternalDataTable(session);
-
}
private List<WellContent> getPlateLocations(PlateMaterialsSearchCriteria materialCriteria)
@@ -200,16 +200,13 @@ public class GenePlateLocationsLoader
List<ExternalDataPE> usedDatasets)
{
List<String> datasetCodes = extractDatasetCodes(usedDatasets);
- if (datasetCodes.size() == 0)
+ List<PlateImageParameters> imageParameters = new ArrayList<PlateImageParameters>();
+ for (String datasetCode : datasetCodes)
{
- return new HashMap<String, PlateImageParameters>();
+ final IHCSDatasetLoader loader =
+ businessObjectFactory.createHCSDatasetLoader(datasetCode);
+ imageParameters.add(DatasetReportsLoader.createImageParameters(loader));
}
-
- // NOTE: assumes that all datasets are from the same datastore
- String datastoreCode = usedDatasets.get(0).getDataStore().getCode();
- List<PlateImageParameters> imageParameters =
- DatasetReportsLoader.loadPlateImageParameters(datasetCodes, datastoreCode,
- externalDataTable);
return asDatasetToParamsMap(imageParameters);
}
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 b94e4c7bcb3..e223a890322 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
@@ -17,7 +17,6 @@
package ch.systemsx.cisd.openbis.plugin.screening.server.logic;
import java.util.ArrayList;
-import java.util.Arrays;
import java.util.List;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
@@ -33,7 +32,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCrite
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
@@ -48,6 +46,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
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;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.IHCSDatasetLoader;
/**
* Loads content of the plate.
@@ -273,14 +272,9 @@ public class PlateContentLoader
private PlateImageParameters loadImageParams(ExternalDataPE dataset,
IExternalDataTable externalDataTable)
{
- DataStorePE dataStore = dataset.getDataStore();
- String datasetCode = dataset.getCode();
- List<String> datasets = Arrays.asList(datasetCode);
- List<PlateImageParameters> imageParamsReports =
- DatasetReportsLoader.loadPlateImageParameters(datasets, dataStore.getCode(),
- externalDataTable);
- assert imageParamsReports.size() == 1;
- return imageParamsReports.get(0);
+ final IHCSDatasetLoader loader =
+ businessObjectFactory.createHCSDatasetLoader(dataset.getCode());
+ return DatasetReportsLoader.createImageParameters(loader);
}
private static List<WellMetadata> createWells(List<Sample> wellSamples)
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 a54cb3e547a..f28f5180052 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
@@ -35,9 +35,6 @@ public class ScreeningConstants
// ---- required DSS plugins
- // 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";
-
// id of the DSS screening reporting plugin to get the images of the plate
public static final String PLATE_IMAGE_ANALYSIS_REPORT_KEY =
"default-plate-image-analysis-merger";
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java
index 11b03d9d39b..5b27abff787 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java
@@ -79,6 +79,11 @@ public class HCSDatasetLoader implements IHCSDatasetLoader
return dataset;
}
+ public String getDatasetPermId()
+ {
+ return dataset.getPermId();
+ }
+
public Geometry getWellGeometry()
{
return new Geometry(getDataset().getFieldNumberOfRows(), getDataset()
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/IHCSDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/IHCSDatasetLoader.java
index 80756fb4bde..16fa7369b7d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/IHCSDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/IHCSDatasetLoader.java
@@ -29,6 +29,8 @@ public interface IHCSDatasetLoader
/** has to be called at the end */
void close();
+ String getDatasetPermId();
+
Geometry getPlateGeometry();
Geometry getWellGeometry();
--
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