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 4123343ed380955a1cae0a1ce0ad9e84c520afa6..47c46903b3a4e90953928ea9764bb2e69564cf8d 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 @@ -16,18 +16,11 @@ package ch.systemsx.cisd.openbis.plugin.screening.server.logic; -import java.util.ArrayList; 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.TableModel; -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. @@ -43,40 +36,4 @@ public class DatasetReportsLoader ScreeningConstants.PLATE_IMAGE_ANALYSIS_REPORT_KEY, datastoreCode, datasets); } - public static List<PlateImageParameters> loadPlateImageParameters(List<String> datasetCodes, - IScreeningBusinessObjectFactory boFactory) - { - List<PlateImageParameters> paramsList = new ArrayList<PlateImageParameters>(); - - for (String datasetCode : datasetCodes) - { - final IHCSDatasetLoader loader = boFactory.createHCSDatasetLoader(datasetCode); - paramsList.add(createImageParameters(loader)); - } - return paramsList; - } - - // 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(); - 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) - { - escapedChannelNames.add(StringEscapeUtils.escapeCsv(name)); - } - params.setChannelsNames(escapedChannelNames); - return params; - } - } 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 9dc330f9c6dd840b40249f2f971c363efd1a228f..b942f45924f5bbeff7e31f5c1be2e7c02d58e3fc 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 @@ -205,7 +205,7 @@ public class GenePlateLocationsLoader { final IHCSDatasetLoader loader = businessObjectFactory.createHCSDatasetLoader(datasetCode); - imageParameters.add(DatasetReportsLoader.createImageParameters(loader)); + imageParameters.add(PlateImageParametersFactory.create(loader)); } 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 e223a89032234e9fc4495534bc264bca00a546d1..08f94ca9fb703d10eddbe2c66fa3049c31b44ad0 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 @@ -274,7 +274,7 @@ public class PlateContentLoader { final IHCSDatasetLoader loader = businessObjectFactory.createHCSDatasetLoader(dataset.getCode()); - return DatasetReportsLoader.createImageParameters(loader); + return PlateImageParametersFactory.create(loader); } private static List<WellMetadata> createWells(List<Sample> wellSamples) diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateImageParametersFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateImageParametersFactory.java new file mode 100644 index 0000000000000000000000000000000000000000..87f34c1e82861b71eabd8cdc6533cb4505b1a8fd --- /dev/null +++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateImageParametersFactory.java @@ -0,0 +1,56 @@ +/* + * 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.server.logic; + +import java.util.ArrayList; +import java.util.List; + +import org.apache.commons.lang.StringEscapeUtils; + +import ch.systemsx.cisd.bds.hcs.Geometry; +import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImageParameters; +import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.IHCSDatasetLoader; + +/** + * Creates {@link PlateImageParameters} using {@link IHCSDatasetLoader}. + * + * @author Piotr Buczek + */ +public class PlateImageParametersFactory +{ + public static PlateImageParameters create(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(); + 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) + { + escapedChannelNames.add(StringEscapeUtils.escapeCsv(name)); + } + params.setChannelsNames(escapedChannelNames); + return params; + } +}