diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvToCanonicalFeatureVector.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvToCanonicalFeatureVector.java
index 417e713fef57c97660585f47a951225b93588ce1..321b5f50b64f84266ed85d93efae4d8ce5987cab 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvToCanonicalFeatureVector.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvToCanonicalFeatureVector.java
@@ -23,7 +23,7 @@ import java.util.List;
import ch.systemsx.cisd.common.utilities.Counters;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLines;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndTitle;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndLabel;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.dto.PlateFeatureValues;
@@ -132,7 +132,7 @@ public class CsvToCanonicalFeatureVector
FeatureColumn column, Counters<String> counters)
{
CanonicalFeatureVector featureVector = new CanonicalFeatureVector();
- CodeAndTitle codeAndTitle = new CodeAndTitle(column.name);
+ CodeAndLabel codeAndTitle = new CodeAndLabel(column.name);
ImgFeatureDefDTO featureDef = new ImgFeatureDefDTO();
featureDef.setLabel(codeAndTitle.getTitle());
featureDef.setDescription(codeAndTitle.getTitle());
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFormatToCanonicalFeatureVector.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFormatToCanonicalFeatureVector.java
index cb311c96f62d7abd7977b1ff90cb91a859f7a342..3badf24bd05cf7c7f2fc1f2df4925f2f1bacff85 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFormatToCanonicalFeatureVector.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFormatToCanonicalFeatureVector.java
@@ -27,7 +27,7 @@ import org.apache.commons.lang.StringUtils;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.utilities.Counters;
import ch.systemsx.cisd.openbis.dss.etl.featurevector.CanonicalFeatureVector;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndTitle;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndLabel;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.dto.PlateFeatureValues;
@@ -82,7 +82,7 @@ public class GenedataFormatToCanonicalFeatureVector
CanonicalFeatureVector featureVector = new CanonicalFeatureVector();
String name = feature.name;
- String code = CodeAndTitle.normalize(name);
+ String code = CodeAndLabel.normalize(name);
int count = counters.count(code);
ImgFeatureDefDTO featureDef = new ImgFeatureDefDTO();
featureDef.setCode(count == 1 ? code : code + count);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilder.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilder.java
index bdc5d700342fdeb7d5a40eea5872aa65119f0289..4ed16beba83164054e70e085738ff32f26c2c225 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilder.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilder.java
@@ -29,7 +29,7 @@ import java.util.Map.Entry;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndTitle;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndLabel;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetWellReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
@@ -64,7 +64,7 @@ public class FeatureTableBuilder
private final List<Bundle> bundles;
- private final Map<CodeAndTitle, Integer> featureCodeLabelToIndexMap;
+ private final Map<CodeAndLabel, Integer> featureCodeLabelToIndexMap;
private final Set<String> featureCodes;
@@ -89,7 +89,7 @@ public class FeatureTableBuilder
this.dao = dao;
this.service = service;
bundles = new ArrayList<Bundle>();
- featureCodeLabelToIndexMap = new LinkedHashMap<CodeAndTitle, Integer>();
+ featureCodeLabelToIndexMap = new LinkedHashMap<CodeAndLabel, Integer>();
this.featureCodes = new LinkedHashSet<String>(featureCodes);
this.useAllFeatures = featureCodes.isEmpty();
}
@@ -135,7 +135,7 @@ public class FeatureTableBuilder
final ImgFeatureDefDTO featureDefinition = featureCodeToDefMap.get(featureCode);
if (featureDefinition != null)
{
- CodeAndTitle codeAndLabel = getCodeAndLabel(featureDefinition);
+ CodeAndLabel codeAndLabel = getCodeAndLabel(featureDefinition);
if (featureCodeLabelToIndexMap.containsKey(codeAndLabel) == false)
{
featureCodeLabelToIndexMap.put(codeAndLabel,
@@ -158,9 +158,9 @@ public class FeatureTableBuilder
* Returns all feature codes/labels found. If the feature code list in the constructor is not empty the
* result will a list where the codes are a subset of this list.
*/
- public List<CodeAndTitle> getCodesAndLabels()
+ public List<CodeAndLabel> getCodesAndLabels()
{
- return new ArrayList<CodeAndTitle>(featureCodeLabelToIndexMap.keySet());
+ return new ArrayList<CodeAndLabel>(featureCodeLabelToIndexMap.keySet());
}
/**
@@ -234,9 +234,9 @@ public class FeatureTableBuilder
return row;
}
- private CodeAndTitle getCodeAndLabel(final ImgFeatureDefDTO featureDefinition)
+ private CodeAndLabel getCodeAndLabel(final ImgFeatureDefDTO featureDefinition)
{
- return new CodeAndTitle(featureDefinition.getCode(), featureDefinition.getLabel());
+ return new CodeAndLabel(featureDefinition.getCode(), featureDefinition.getLabel());
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java
index 338890fae790a4e0d13bc4650f863a87f8e0896d..5cc2e6a3d31e82fb304cf7bde1b4fe8dc11d42ab 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java
@@ -23,7 +23,7 @@ import java.util.List;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.ITabularData;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndTitle;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndLabel;
import ch.systemsx.cisd.openbis.dss.shared.DssScreeningUtils;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.PlateUtils;
@@ -86,19 +86,19 @@ public class TabularDataGraphServlet extends AbstractTabularDataGraphServlet
final FeatureTableBuilder tableBuilder = new FeatureTableBuilder(dao, service);
tableBuilder.addFeatureVectorsOfDataSet(dataSetCode);
- List<CodeAndTitle> featureCodeAndLabels = tableBuilder.getCodesAndLabels();
+ List<CodeAndLabel> featureCodeAndLabels = tableBuilder.getCodesAndLabels();
int headerTokensLength = featureCodeAndLabels.size() + 3;
headerLabels = new String[headerTokensLength];
headerLabels[0] = WELL_NAME_COLUMN;
headerLabels[1] = WELL_ROW_COLUMN;
headerLabels[2] = WELL_COLUMN_COLUMN;
headerCodes = new String[headerTokensLength];
- headerCodes[0] = CodeAndTitle.normalize(WELL_NAME_COLUMN);
- headerCodes[1] = CodeAndTitle.normalize(WELL_NAME_COLUMN);
- headerCodes[2] = CodeAndTitle.normalize(WELL_NAME_COLUMN);
+ headerCodes[0] = CodeAndLabel.normalize(WELL_NAME_COLUMN);
+ headerCodes[1] = CodeAndLabel.normalize(WELL_NAME_COLUMN);
+ headerCodes[2] = CodeAndLabel.normalize(WELL_NAME_COLUMN);
int i = 1;
- for (CodeAndTitle featureCodeAndLabel : featureCodeAndLabels)
+ for (CodeAndLabel featureCodeAndLabel : featureCodeAndLabels)
{
headerCodes[i] = featureCodeAndLabel.getCode();
headerLabels[i++] = featureCodeAndLabel.getTitle();
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/AbstractTabularDataGraph.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/AbstractTabularDataGraph.java
index dc3955f1de5bc0e9e828acd26399fd9b769cc2f6..399ee259a15d683122e6213568632b22a27ddef8 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/AbstractTabularDataGraph.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/AbstractTabularDataGraph.java
@@ -33,6 +33,7 @@ import org.jfree.data.general.Dataset;
import org.jfree.data.xy.DefaultXYDataset;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.ITabularData;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndLabel;
/**
* Abstract superclass for the different kinds of graphs.
@@ -139,15 +140,17 @@ abstract class AbstractTabularDataGraph<T extends TabularDataGraphConfiguration>
}
/**
- * Return the column number for the column header or -1 if none was found
+ * Return the column number for the column header or -1 if none was found. Argument will
+ * be first normalized.
*/
protected int tryColumnNumberForHeader(String columnHeaderCode)
{
+ String normalizedCode = CodeAndLabel.normalize(columnHeaderCode);
String[] headers = fileLines.getHeaderCodes();
int i = 0;
for (String header : headers)
{
- if (columnHeaderCode.equals(header))
+ if (normalizedCode.equals(header))
{
return i;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisMergedRowsReportingPlugin.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisMergedRowsReportingPlugin.java
index 2129aa7eaadec67530dd3977982580de802ebfb1..0b80cfc9e95b546f0ec3aa0f9353ea5a9cc4fb8e 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisMergedRowsReportingPlugin.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisMergedRowsReportingPlugin.java
@@ -28,7 +28,7 @@ import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IReportingPlugi
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.SimpleTableModelBuilder;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndTitle;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndLabel;
import ch.systemsx.cisd.openbis.dss.shared.DssScreeningUtils;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DoubleTableCell;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable;
@@ -85,14 +85,14 @@ public class ImageAnalysisMergedRowsReportingPlugin extends AbstractDatastorePlu
String dataSetCode = datasetDescription.getDatasetCode();
featureTableBuilder.addFeatureVectorsOfDataSet(dataSetCode);
}
- List<CodeAndTitle> codeAndLabels = featureTableBuilder.getCodesAndLabels();
+ List<CodeAndLabel> codeAndLabels = featureTableBuilder.getCodesAndLabels();
List<FeatureTableRow> rows = featureTableBuilder.createFeatureTableRows();
SimpleTableModelBuilder builder = new SimpleTableModelBuilder(true);
builder.addHeader(DATA_SET_CODE_TITLE);
builder.addHeader(PLATE_IDENTIFIER_TITLE);
builder.addHeader(ROW_TITLE);
builder.addHeader(COLUMN_TITLE);
- for (CodeAndTitle codeAndLabel : codeAndLabels)
+ for (CodeAndLabel codeAndLabel : codeAndLabels)
{
builder.addHeader(codeAndLabel.getTitle(), codeAndLabel.getCode());
}
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 5168ceb069eecef77139957ffb14b6c93b5776f7..13c55a8815b060627207462e364c7d43b15e6221 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
@@ -44,7 +44,7 @@ import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelStackRefer
import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelsUtils;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndTitle;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndLabel;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
import ch.systemsx.cisd.openbis.dss.screening.shared.api.v1.IDssServiceRpcScreening;
import ch.systemsx.cisd.openbis.dss.shared.DssScreeningUtils;
@@ -250,9 +250,9 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
private List<String> getCodes(FeatureTableBuilder builder)
{
- List<CodeAndTitle> featureCodesAndLabels = builder.getCodesAndLabels();
+ List<CodeAndLabel> featureCodesAndLabels = builder.getCodesAndLabels();
List<String> codes = new ArrayList<String>();
- for (CodeAndTitle codeAndTitle : featureCodesAndLabels)
+ for (CodeAndLabel codeAndTitle : featureCodesAndLabels)
{
codes.add(codeAndTitle.getCode());
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilderTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilderTest.java
index 6f742a637c058541d5f0908a3503fa30820feb89..1388de771fb0dead8e5afb8e0ec1e78a9a2b7c8f 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilderTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilderTest.java
@@ -28,7 +28,7 @@ import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndTitle;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndLabel;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
@@ -85,7 +85,7 @@ public class FeatureTableBuilderTest extends AssertJUnit
builder.addFeatureVectorsOfDataSet(DATA_SET_CODE1);
builder.addFeatureVectorsOfDataSet(DATA_SET_CODE2);
builder.addFeatureVectorsOfDataSet(DATA_SET_CODE3);
- List<CodeAndTitle> codesAndLabels = builder.getCodesAndLabels();
+ List<CodeAndLabel> codesAndLabels = builder.getCodesAndLabels();
List<FeatureTableRow> rows = builder.createFeatureTableRows();
assertEquals("[<A> a, <B> b, <B> beta, <C> c]", codesAndLabels.toString());
@@ -110,7 +110,7 @@ public class FeatureTableBuilderTest extends AssertJUnit
builder.addFeatureVectorsOfDataSet(DATA_SET_CODE1);
builder.addFeatureVectorsOfDataSet(DATA_SET_CODE2);
builder.addFeatureVectorsOfDataSet(DATA_SET_CODE3);
- List<CodeAndTitle> codesAndLabels = builder.getCodesAndLabels();
+ List<CodeAndLabel> codesAndLabels = builder.getCodesAndLabels();
List<FeatureTableRow> rows = builder.createFeatureTableRows();
assertEquals("[<B> b, <B> beta]", codesAndLabels.toString());
@@ -142,7 +142,7 @@ public class FeatureTableBuilderTest extends AssertJUnit
for (int i = 0; i < featureCodesAndLabels.length; i++)
{
String codeAndLabels = featureCodesAndLabels[i];
- CodeAndTitle codeAndTitle = new CodeAndTitle(codeAndLabels);
+ CodeAndLabel codeAndTitle = new CodeAndLabel(codeAndLabels);
String title = codeAndTitle.getTitle();
String code = codeAndTitle.getCode();
if (filteredCodeOrNull == null || filteredCodeOrNull.equals(code))
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/FeatureVectorDAOTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/FeatureVectorDAOTest.java
index 6fd54fcb3479605b352558d3f71400e87edcf652..023d94d8efceefa92ed47f5dfa71c14cca50314d 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/FeatureVectorDAOTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/FeatureVectorDAOTest.java
@@ -26,7 +26,7 @@ import net.lemnik.eodsql.QueryTool;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndTitle;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndLabel;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
import ch.systemsx.cisd.openbis.plugin.screening.shared.dto.PlateFeatureValues;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
@@ -106,7 +106,7 @@ public class FeatureVectorDAOTest extends AbstractDBTest
ImgFeatureDefDTO featureDef = featureDefs.get(0);
assertEquals(TEST_FEATURE_LABEL, featureDef.getLabel());
- assertEquals(CodeAndTitle.normalize(TEST_FEATURE_LABEL), featureDef.getCode());
+ assertEquals(CodeAndLabel.normalize(TEST_FEATURE_LABEL), featureDef.getCode());
createFeatureValues(featureDef);
List<ImgFeatureValuesDTO> featureValuesList = dao.getFeatureValues(featureDef);
@@ -150,7 +150,7 @@ public class FeatureVectorDAOTest extends AbstractDBTest
// Attach a feature def to it
ImgFeatureDefDTO featureDef =
new ImgFeatureDefDTO(TEST_FEATURE_LABEL,
- CodeAndTitle.normalize(TEST_FEATURE_LABEL), "Test", dataSet.getId());
+ CodeAndLabel.normalize(TEST_FEATURE_LABEL), "Test", dataSet.getId());
return dao.addFeatureDef(featureDef);
}
}