From e05c823ea2f6ef4249bb82102bf02a1de3cdd6a3 Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Mon, 20 Dec 2010 12:18:01 +0000
Subject: [PATCH] LMS-1939 improve specific DSS uploading plugin
SVN: 19194
---
.../etl/AbstractImageStorageProcessor.java | 9 ++-
.../openbis/dss/etl/HCSImageCheckList.java | 69 ++--------------
.../dss/etl/UnparsedImageFileInfoLexer.java | 2 +-
.../biozentrum/BZDataSetInfoExtractor.java | 29 ++++---
.../BZDatasetDirectoryNameTokenizer.java | 32 +++++---
.../openbis/dss/etl/dto/ImageSeriesPoint.java | 81 +++++++++++++++++++
.../BZDatasetDirectoryNameTokenizerTest.java | 38 +++++++++
7 files changed, 171 insertions(+), 89 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/ImageSeriesPoint.java
create mode 100644 screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/BZDatasetDirectoryNameTokenizerTest.java
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageStorageProcessor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageStorageProcessor.java
index 9498a1d8914..bb5ae6b1252 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageStorageProcessor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageStorageProcessor.java
@@ -20,8 +20,10 @@ import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.HashSet;
import java.util.List;
import java.util.Properties;
+import java.util.Set;
import javax.sql.DataSource;
@@ -50,6 +52,7 @@ import ch.systemsx.cisd.etlserver.hdf5.Hdf5Container;
import ch.systemsx.cisd.etlserver.hdf5.HierarchicalStructureDuplicatorFileToHdf5;
import ch.systemsx.cisd.openbis.dss.Constants;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingQueryDAO;
+import ch.systemsx.cisd.openbis.dss.etl.dto.ImageSeriesPoint;
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.dto.StorageFormat;
@@ -711,15 +714,17 @@ abstract class AbstractImageStorageProcessor extends AbstractStorageProcessor
protected static boolean hasImageSeries(List<AcquiredSingleImage> images)
{
+ Set<ImageSeriesPoint> points = new HashSet<ImageSeriesPoint>();
for (AcquiredSingleImage image : images)
{
if (image.tryGetTimePoint() != null || image.tryGetDepth() != null
|| image.tryGetSeriesNumber() != null)
{
- return true;
+ points.add(new ImageSeriesPoint(image.tryGetTimePoint(), image.tryGetDepth(), image
+ .tryGetSeriesNumber()));
}
}
- return false;
+ return points.size() > 1;
}
}
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 05ebadacd74..564716c4b8b 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
@@ -25,6 +25,7 @@ import java.util.Set;
import ch.systemsx.cisd.bds.hcs.Geometry;
import ch.systemsx.cisd.common.utilities.AbstractHashable;
+import ch.systemsx.cisd.openbis.dss.etl.dto.ImageSeriesPoint;
import ch.systemsx.cisd.openbis.plugin.screening.shared.dto.PlateDimension;
/**
@@ -119,85 +120,25 @@ public final class HCSImageCheckList
// Helper classes
//
- private static final class CheckDimension
- {
- private final Float timeOrNull;
-
- private final Float depthOrNull;
-
- private final Integer seriesNumberOrNull;
-
- public CheckDimension(Float timeOrNull, Float depthOrNull, Integer seriesNumberOrNull)
- {
- this.timeOrNull = timeOrNull;
- this.depthOrNull = depthOrNull;
- this.seriesNumberOrNull = seriesNumberOrNull;
- }
-
- @Override
- public int hashCode()
- {
- final int prime = 31;
- int result = 1;
- result = prime * result + ((depthOrNull == null) ? 0 : depthOrNull.hashCode());
- result = prime * result + ((timeOrNull == null) ? 0 : timeOrNull.hashCode());
- result =
- prime * result
- + ((seriesNumberOrNull == null) ? 0 : seriesNumberOrNull.hashCode());
- return result;
- }
-
- @Override
- public boolean equals(Object obj)
- {
- if (this == obj)
- return true;
- if (obj == null)
- return false;
- if (getClass() != obj.getClass())
- return false;
- CheckDimension other = (CheckDimension) obj;
- if (depthOrNull == null)
- {
- if (other.depthOrNull != null)
- return false;
- } else if (!depthOrNull.equals(other.depthOrNull))
- return false;
- if (timeOrNull == null)
- {
- if (other.timeOrNull != null)
- return false;
- } else if (!timeOrNull.equals(other.timeOrNull))
- return false;
- if (seriesNumberOrNull == null)
- {
- if (other.seriesNumberOrNull != null)
- return false;
- } else if (!seriesNumberOrNull.equals(other.seriesNumberOrNull))
- return false;
- return true;
- }
- }
-
private static final class Check
{
private boolean checkedOff;
- private final Set<CheckDimension> dimensions = new HashSet<CheckDimension>();
+ private final Set<ImageSeriesPoint> dimensions = new HashSet<ImageSeriesPoint>();
final void checkOff(Float timepointOrNull, Float depthOrNull, Integer seriesNumberOrNull)
{
- dimensions.add(new CheckDimension(timepointOrNull, depthOrNull, seriesNumberOrNull));
+ dimensions.add(new ImageSeriesPoint(timepointOrNull, depthOrNull, seriesNumberOrNull));
checkedOff = true;
}
final boolean isCheckedOff(Float timepointOrNull, Float depthOrNull,
Integer seriesNumberOrNull)
{
- CheckDimension dim = null;
+ ImageSeriesPoint dim = null;
if (timepointOrNull != null || depthOrNull != null || seriesNumberOrNull != null)
{
- dim = new CheckDimension(timepointOrNull, depthOrNull, seriesNumberOrNull);
+ dim = new ImageSeriesPoint(timepointOrNull, depthOrNull, seriesNumberOrNull);
}
return checkedOff && (dim == null || dimensions.contains(dim));
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/UnparsedImageFileInfoLexer.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/UnparsedImageFileInfoLexer.java
index f7b3521f22c..ef708fb3c93 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/UnparsedImageFileInfoLexer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/UnparsedImageFileInfoLexer.java
@@ -121,7 +121,7 @@ public class UnparsedImageFileInfoLexer
return info;
}
- private static Map<Character, String> extractTokensMap(String text)
+ public static Map<Character, String> extractTokensMap(String text)
{
Map<Character, String> tokensMap = new HashMap<Character, String>();
String[] tokens = StringUtils.split(text, TOKENS_SEPARATOR);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/BZDataSetInfoExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/BZDataSetInfoExtractor.java
index bab4a42c23e..b45fe0113f0 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/BZDataSetInfoExtractor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/BZDataSetInfoExtractor.java
@@ -66,17 +66,22 @@ public class BZDataSetInfoExtractor implements IDataSetInfoExtractor
static final String PLATE_GEOMETRY = "plate-geometry";
+ static final String SEPARATOR = "separator";
+
private final String spaceCode;
private final String projectCode;
private final String defaultPlateGeometryOrNull;
+ private final String separatorOrNull;
+
public BZDataSetInfoExtractor(final Properties properties)
{
spaceCode = PropertyUtils.getMandatoryProperty(properties, SPACE_CODE);
projectCode = PropertyUtils.getMandatoryProperty(properties, PROJECT_CODE);
defaultPlateGeometryOrNull = properties.getProperty(PLATE_GEOMETRY);
+ separatorOrNull = properties.getProperty(SEPARATOR);
}
public DataSetInformation getDataSetInformation(File incomingDataSetPath,
@@ -84,9 +89,16 @@ public class BZDataSetInfoExtractor implements IDataSetInfoExtractor
EnvironmentFailureException
{
- BZDatasetDirectoryNameTokenizer tokens =
- new BZDatasetDirectoryNameTokenizer(FilenameUtils.getBaseName(incomingDataSetPath
- .getPath()));
+ String fileBaseName = FilenameUtils.getBaseName(incomingDataSetPath.getPath());
+ if (separatorOrNull != null)
+ {
+ int separatorIndex = fileBaseName.indexOf(separatorOrNull);
+ if (separatorIndex != -1)
+ {
+ fileBaseName = fileBaseName.substring(0, separatorIndex);
+ }
+ }
+ BZDatasetDirectoryNameTokenizer tokens = new BZDatasetDirectoryNameTokenizer(fileBaseName);
String sampleCode = getSampleCode(tokens);
String experimentCode = getExperiment(tokens);
ExperimentIdentifier experimentIdentifier =
@@ -155,12 +167,6 @@ public class BZDataSetInfoExtractor implements IDataSetInfoExtractor
if (experimentOrNull == null)
{
openbisService.registerExperiment(createExperimentSIRNAHCS(experimentIdentifier));
- experimentOrNull = openbisService.tryToGetExperiment(experimentIdentifier);
- if (experimentOrNull == null)
- {
- throw new UserFailureException(String.format("Experiment '%s' could not be found",
- experimentIdentifier));
- }
}
openbisService.registerSample(
createPlate(sampleIdentifier, experimentIdentifier, plateGeometry), null);
@@ -173,7 +179,7 @@ public class BZDataSetInfoExtractor implements IDataSetInfoExtractor
private static String getSampleCode(BZDatasetDirectoryNameTokenizer tokens)
{
- return "P_" + tokens.getExperimentToken() + "_" + tokens.getTimestampToken();
+ return "PLATE_" + tokens.getPlateBarcodeToken();
}
private static IEntityProperty[] createVocabularyProperty(String propertyTypeCode,
@@ -231,7 +237,8 @@ public class BZDataSetInfoExtractor implements IDataSetInfoExtractor
for (File imageFile : imageFiles)
{
UnparsedImageFileInfo imageInfo =
- UnparsedImageFileInfoLexer.tryExtractHCSImageFileInfo(imageFile, incomingDataSetPath);
+ UnparsedImageFileInfoLexer.tryExtractHCSImageFileInfo(imageFile,
+ incomingDataSetPath);
if (imageInfo != null)
{
String wellLocationToken = imageInfo.getWellLocationToken();
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/BZDatasetDirectoryNameTokenizer.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/BZDatasetDirectoryNameTokenizer.java
index 30e90f38f78..ca2763be302 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/BZDatasetDirectoryNameTokenizer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/BZDatasetDirectoryNameTokenizer.java
@@ -16,7 +16,9 @@
package ch.systemsx.cisd.openbis.dss.etl.biozentrum;
-import org.apache.commons.lang.StringUtils;
+import java.util.Map;
+
+import ch.systemsx.cisd.openbis.dss.etl.UnparsedImageFileInfoLexer;
/**
* Extracts useful information from dataset directory name specific to iBrain2.
@@ -25,9 +27,17 @@ import org.apache.commons.lang.StringUtils;
*/
public class BZDatasetDirectoryNameTokenizer
{
+ private static final char EXPERIMENT_MARKER = 'i';
+
+ private static final char MICROSCOPE_MARKER = 'm';
+
+ private static final char PLATE_BARCODE_MARKER = 'b';
+
+ private static final char UNIQUE_ID_MARKER = 'u';
+
private final String experimentToken;
- private final String plateToken;
+ private final String microscopeToken;
private final String barcodeToken;
@@ -35,11 +45,11 @@ public class BZDatasetDirectoryNameTokenizer
BZDatasetDirectoryNameTokenizer(String identifier)
{
- String[] namedParts = StringUtils.split(identifier, "_");
- experimentToken = StringUtils.split(namedParts[0], "-")[1];
- plateToken = StringUtils.split(namedParts[1], "-")[1];
- barcodeToken = StringUtils.split(namedParts[2], "-")[1];
- timestampToken = StringUtils.split(namedParts[3], "-")[1];
+ Map<Character, String> tokensMap = UnparsedImageFileInfoLexer.extractTokensMap(identifier);
+ experimentToken = tokensMap.get(EXPERIMENT_MARKER);
+ microscopeToken = tokensMap.get(MICROSCOPE_MARKER);
+ barcodeToken = tokensMap.get(PLATE_BARCODE_MARKER);
+ timestampToken = tokensMap.get(UNIQUE_ID_MARKER);
}
public String getExperimentToken()
@@ -47,17 +57,17 @@ public class BZDatasetDirectoryNameTokenizer
return experimentToken;
}
- public String getPlateToken()
+ public String getMicroscopeToken()
{
- return plateToken;
+ return microscopeToken;
}
- public String getBarcodeToken()
+ public String getPlateBarcodeToken()
{
return barcodeToken;
}
- public String getTimestampToken()
+ public String getUniqueIdToken()
{
return timestampToken;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/ImageSeriesPoint.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/ImageSeriesPoint.java
new file mode 100644
index 00000000000..813d74b6df0
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/ImageSeriesPoint.java
@@ -0,0 +1,81 @@
+/*
+ * 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.dto;
+
+/**
+ * DTO which stores time, depth and series number (all optional).
+ *
+ * @author Tomasz Pylak
+ */
+public final class ImageSeriesPoint
+{
+ private final Float timeOrNull;
+
+ private final Float depthOrNull;
+
+ private final Integer seriesNumberOrNull;
+
+ public ImageSeriesPoint(Float timeOrNull, Float depthOrNull, Integer seriesNumberOrNull)
+ {
+ this.timeOrNull = timeOrNull;
+ this.depthOrNull = depthOrNull;
+ this.seriesNumberOrNull = seriesNumberOrNull;
+ }
+
+ @Override
+ public int hashCode()
+ {
+ final int prime = 31;
+ int result = 1;
+ result = prime * result + ((depthOrNull == null) ? 0 : depthOrNull.hashCode());
+ result = prime * result + ((timeOrNull == null) ? 0 : timeOrNull.hashCode());
+ result =
+ prime * result + ((seriesNumberOrNull == null) ? 0 : seriesNumberOrNull.hashCode());
+ return result;
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (this == obj)
+ return true;
+ if (obj == null)
+ return false;
+ if (getClass() != obj.getClass())
+ return false;
+ ImageSeriesPoint other = (ImageSeriesPoint) obj;
+ if (depthOrNull == null)
+ {
+ if (other.depthOrNull != null)
+ return false;
+ } else if (!depthOrNull.equals(other.depthOrNull))
+ return false;
+ if (timeOrNull == null)
+ {
+ if (other.timeOrNull != null)
+ return false;
+ } else if (!timeOrNull.equals(other.timeOrNull))
+ return false;
+ if (seriesNumberOrNull == null)
+ {
+ if (other.seriesNumberOrNull != null)
+ return false;
+ } else if (!seriesNumberOrNull.equals(other.seriesNumberOrNull))
+ return false;
+ return true;
+ }
+}
\ No newline at end of file
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/BZDatasetDirectoryNameTokenizerTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/BZDatasetDirectoryNameTokenizerTest.java
new file mode 100644
index 00000000000..e03b91f3f2d
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/BZDatasetDirectoryNameTokenizerTest.java
@@ -0,0 +1,38 @@
+/*
+ * 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.biozentrum;
+
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+/**
+ * @author Tomasz Pylak
+ */
+public class BZDatasetDirectoryNameTokenizerTest extends AssertJUnit
+{
+ @Test
+ public void test()
+ {
+ BZDatasetDirectoryNameTokenizer tokenizer =
+ new BZDatasetDirectoryNameTokenizer(
+ "iBrucellaInfectionWF10_mBS-IX2_bRCB024_u0265626F");
+ assertEquals("BrucellaInfectionWF10", tokenizer.getExperimentToken());
+ assertEquals("BS-IX2", tokenizer.getMicroscopeToken());
+ assertEquals("RCB024", tokenizer.getPlateBarcodeToken());
+ assertEquals("0265626F", tokenizer.getUniqueIdToken());
+ }
+}
--
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