diff --git a/CHANGELOG b/CHANGELOG
index dd576dddf6813122411def05d053934c9670644f..f741b55be8c02f96bb149f3457e85661193933fa 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,8 @@
+minerva (18.2.0) stable; urgency=medium
+ * Small improvement: add source data to data overlay (#2228)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu> Thu, 13 Mar 2025 13:00:00 +0200
+
minerva (18.1.1) stable; urgency=medium
* Bug fix: SBGN-ML import/export should not use compartmentOrder for
non-compartment entities (#2193)
diff --git a/CellDesigner-plugin/pom.xml b/CellDesigner-plugin/pom.xml
index 8b4f056695b8fd90cce5ae6825286ee6de0f66b5..3acc9fd0e1731e72167955bf512b5e8d914c4455 100644
--- a/CellDesigner-plugin/pom.xml
+++ b/CellDesigner-plugin/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</parent>
<artifactId>CellDesigner-plugin</artifactId>
<!-- dependency from the MapViewer model -->
@@ -50,19 +50,19 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>commons</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<dependency>
diff --git a/annotation/pom.xml b/annotation/pom.xml
index 638da580c3ee78b2caa19bc82d88efe16357c410..369d15c30b394069af5e1669c47eff389b8eb85f 100644
--- a/annotation/pom.xml
+++ b/annotation/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</parent>
<artifactId>annotation</artifactId>
<name>Annotation module</name>
@@ -19,7 +19,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<!-- dependency from the MapViewer dao -->
@@ -27,7 +27,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>persist</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<!-- dependency from the MapViewer cell designer parser (we need access
@@ -35,13 +35,13 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<!-- Log4J2 -->
diff --git a/commons/pom.xml b/commons/pom.xml
index 2f6112442c1769a4b93bdd2e74730de78c06f8b3..d3fc7132a7314ee5bf6c721074223c8baa2850be 100644
--- a/commons/pom.xml
+++ b/commons/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</parent>
<artifactId>commons</artifactId>
<name>Mapviewer commons</name>
diff --git a/converter-CellDesigner/pom.xml b/converter-CellDesigner/pom.xml
index 38b05a88d2995936f20557e785dde0f507844033..85c3b2d5cca9f028c2a3a0c33784d26062279788 100644
--- a/converter-CellDesigner/pom.xml
+++ b/converter-CellDesigner/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</parent>
<artifactId>converter-CellDesigner</artifactId>
<name>CellDesigner converter</name>
@@ -17,13 +17,13 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<!-- Log4J2 -->
diff --git a/converter-SBGNML/pom.xml b/converter-SBGNML/pom.xml
index 78cf9295a016e5140fb766c994f2873fb4d7cfea..cb585d9ed400d284413156bcefa26e60253e9c47 100644
--- a/converter-SBGNML/pom.xml
+++ b/converter-SBGNML/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</parent>
<artifactId>converter-SBGNML</artifactId>
@@ -20,26 +20,26 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>persist</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<dependency>
diff --git a/converter-graphics/pom.xml b/converter-graphics/pom.xml
index e39210329eb33e7aa21b3655ca773b526f9d0ddd..eefcb9cd6f67274448ca2f1aa36cea951f80361a 100644
--- a/converter-graphics/pom.xml
+++ b/converter-graphics/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</parent>
<artifactId>converter-graphics</artifactId>
<name>MapViewer graphics converter</name>
@@ -18,13 +18,13 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model-command</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<!-- Log4J2 -->
diff --git a/converter-sbml/pom.xml b/converter-sbml/pom.xml
index d0c6e4105a9e9d6d03f91dbbbcbfe789a3d25e8a..5ad0853a701bf73e8d7cc0383b83ead66b64ec60 100644
--- a/converter-sbml/pom.xml
+++ b/converter-sbml/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</parent>
<artifactId>converter-sbml</artifactId>
<name>converter-sbml</name>
@@ -40,22 +40,22 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model-command</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<!-- Log4J2 -->
@@ -167,7 +167,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
<scope>test</scope>
</dependency>
diff --git a/converter/pom.xml b/converter/pom.xml
index f6e53dd58ab98742e450874329f9372773c17266..70eac0c67a063a330ba4382cf04d611d4166c750 100644
--- a/converter/pom.xml
+++ b/converter/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</parent>
<artifactId>converter</artifactId>
@@ -15,7 +15,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<dependency>
<groupId>xerces</groupId>
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ColorSchemaColumn.java b/converter/src/main/java/lcsb/mapviewer/converter/ColorSchemaColumn.java
index 8ff5134345db0facf9a156a4c713ad51a3e9955d..109c1d7ba4221d13035403962b4346b1c21c29e5 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ColorSchemaColumn.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ColorSchemaColumn.java
@@ -1,124 +1,123 @@
package lcsb.mapviewer.converter;
+import lcsb.mapviewer.model.overlay.DataOverlayType;
+
+import java.util.Collections;
import java.util.HashSet;
import java.util.Set;
-import lcsb.mapviewer.model.overlay.DataOverlayType;
-
/**
* This enum defines which columns are available for defining
* {@link lcsb.mapviewer.model.map.layout.ColorSchema}.
- *
+ *
* @author Piotr Gawron
- *
*/
public enum ColorSchemaColumn {
/**
* Name of the element.
*/
- NAME(new DataOverlayType[] { DataOverlayType.GENERIC }),
+ NAME(new DataOverlayType[]{DataOverlayType.GENERIC}),
- GENE_NAME(new DataOverlayType[] { DataOverlayType.GENETIC_VARIANT }),
+ GENE_NAME(new DataOverlayType[]{DataOverlayType.GENETIC_VARIANT}),
/**
* Name of the map.
*/
- MAP_NAME(new DataOverlayType[] { DataOverlayType.GENERIC, DataOverlayType.GENETIC_VARIANT }),
+ MAP_NAME(new DataOverlayType[]{DataOverlayType.GENERIC, DataOverlayType.GENETIC_VARIANT}),
+
+ SOURCE_DATA(new DataOverlayType[]{DataOverlayType.GENERIC}),
/**
* Value that will be transformed into new color.
- *
+ *
* @see ColorSchemaColumn#COLOR
*/
- VALUE(new DataOverlayType[] { DataOverlayType.GENERIC }),
+ VALUE(new DataOverlayType[]{DataOverlayType.GENERIC}),
/**
* In which compartment the element should be located.
*/
- COMPARTMENT(new DataOverlayType[] { DataOverlayType.GENERIC, DataOverlayType.GENETIC_VARIANT }),
+ COMPARTMENT(new DataOverlayType[]{DataOverlayType.GENERIC, DataOverlayType.GENETIC_VARIANT}),
/**
* Class type of the element.
*/
- TYPE(new DataOverlayType[] { DataOverlayType.GENERIC }),
+ TYPE(new DataOverlayType[]{DataOverlayType.GENERIC}),
/**
* New element/reaction color.
*/
- COLOR(new DataOverlayType[] { DataOverlayType.GENERIC, DataOverlayType.GENETIC_VARIANT }),
+ COLOR(new DataOverlayType[]{DataOverlayType.GENERIC, DataOverlayType.GENETIC_VARIANT}),
/**
* Identifier of the element.
*/
- IDENTIFIER(new DataOverlayType[] { DataOverlayType.GENERIC, DataOverlayType.GENETIC_VARIANT }),
+ IDENTIFIER(new DataOverlayType[]{DataOverlayType.GENERIC, DataOverlayType.GENETIC_VARIANT}),
/**
* Element identifier.
*/
- ELEMENT_IDENTIFIER(new DataOverlayType[] { DataOverlayType.GENERIC }),
+ ELEMENT_IDENTIFIER(new DataOverlayType[]{DataOverlayType.GENERIC}),
/**
* New line width of the reaction.
*/
- LINE_WIDTH(new DataOverlayType[] { DataOverlayType.GENERIC }),
+ LINE_WIDTH(new DataOverlayType[]{DataOverlayType.GENERIC}),
/**
* Position where gene variants starts.
*/
- POSITION(new DataOverlayType[] { DataOverlayType.GENETIC_VARIANT }),
+ POSITION(new DataOverlayType[]{DataOverlayType.GENETIC_VARIANT}),
/**
* Original DNA of the variant.
*/
- ORIGINAL_DNA(new DataOverlayType[] { DataOverlayType.GENETIC_VARIANT }),
+ ORIGINAL_DNA(new DataOverlayType[]{DataOverlayType.GENETIC_VARIANT}),
/**
* Alternative DNA of the variant.
*/
- ALTERNATIVE_DNA(new DataOverlayType[] { DataOverlayType.GENETIC_VARIANT }),
+ ALTERNATIVE_DNA(new DataOverlayType[]{DataOverlayType.GENETIC_VARIANT}),
/**
* Short description of the entry.
*/
- DESCRIPTION(new DataOverlayType[] { DataOverlayType.GENETIC_VARIANT, DataOverlayType.GENERIC }),
+ DESCRIPTION(new DataOverlayType[]{DataOverlayType.GENETIC_VARIANT, DataOverlayType.GENERIC}),
/**
* Contig where variant was observed.
*/
- CONTIG(new DataOverlayType[] { DataOverlayType.GENETIC_VARIANT }),
+ CONTIG(new DataOverlayType[]{DataOverlayType.GENETIC_VARIANT}),
- CHROMOSOME(new DataOverlayType[] { DataOverlayType.GENETIC_VARIANT }),
+ CHROMOSOME(new DataOverlayType[]{DataOverlayType.GENETIC_VARIANT}),
- ALLELE_FREQUENCY(new DataOverlayType[] { DataOverlayType.GENETIC_VARIANT }),
+ ALLELE_FREQUENCY(new DataOverlayType[]{DataOverlayType.GENETIC_VARIANT}),
- VARIANT_IDENTIFIER(new DataOverlayType[] { DataOverlayType.GENETIC_VARIANT }),
+ VARIANT_IDENTIFIER(new DataOverlayType[]{DataOverlayType.GENETIC_VARIANT}),
/**
* Should the direction of reaction be reversed.
*/
- REVERSE_REACTION(new DataOverlayType[] { DataOverlayType.GENERIC }),
+ REVERSE_REACTION(new DataOverlayType[]{DataOverlayType.GENERIC}),
/**
* Optional amino acid change in the variant.
*/
- AMINO_ACID_CHANGE(new DataOverlayType[] { DataOverlayType.GENETIC_VARIANT });
+ AMINO_ACID_CHANGE(new DataOverlayType[]{DataOverlayType.GENETIC_VARIANT});
/**
* Set of types where column is allowed.
*/
- private Set<DataOverlayType> types = new HashSet<>();
+ private final Set<DataOverlayType> types = new HashSet<>();
/**
* Default constructor that creates enum entry.
*
- * @param types
- * list of {@link DataOverlayType types} where this column is allowed
+ * @param types list of {@link DataOverlayType types} where this column is allowed
*/
ColorSchemaColumn(final DataOverlayType[] types) {
- for (final DataOverlayType colorSchemaType : types) {
- this.types.add(colorSchemaType);
- }
+ Collections.addAll(this.types, types);
}
public String getColumnName() {
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ColorSchemaReader.java b/converter/src/main/java/lcsb/mapviewer/converter/ColorSchemaReader.java
index 03c368cd9387a50eaf58581e92520cbd37b611e4..f6eef6f01d1544e20b11d254420ac3c4c4bbaaf5 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ColorSchemaReader.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ColorSchemaReader.java
@@ -52,9 +52,9 @@ import lcsb.mapviewer.model.overlay.InvalidDataOverlayException;
/**
* Class that reads information about set of {@link DataOverlayEntry color
* schemas} from the input file.
- *
+ *
* @author Piotr Gawron
- *
+ *
*/
public class ColorSchemaReader {
@@ -104,7 +104,7 @@ public class ColorSchemaReader {
/**
* Reads information about set of {@link DataOverlayEntry color schemas} from
* the input stream.
- *
+ *
* @param colorInputStream
* input stream with {@link DataOverlayEntry}
* @param params
@@ -150,7 +150,7 @@ public class ColorSchemaReader {
/**
* Reads information about set of {@link DataOverlayEntry color schemas} from
* the filename.
- *
+ *
* @param filename
* file with {@link DataOverlayEntry}
* @return list of coloring schemas
@@ -172,7 +172,7 @@ public class ColorSchemaReader {
/**
* Reads information about set of {@link DataOverlayEntry color schemas} from
* the input stream represented as byte array.
- *
+ *
* @param inputData
* source in form of byte array
* @return list of coloring schemas
@@ -198,7 +198,7 @@ public class ColorSchemaReader {
/**
* Reads information about set of {@link GeneVariantDataOverlayEntry gene
* variant color schemas} from the input stream.
- *
+ *
* @param colorInputStream
* input stream with {@link GeneVariantDataOverlayEntry}
* @param params
@@ -372,7 +372,7 @@ public class ColorSchemaReader {
/**
* Sets proper value of identifier to {@link DataOverlayEntry} from cell
* content.
- *
+ *
* @param schema
* {@link DataOverlayEntry} where name should be set
* @param type
@@ -388,7 +388,7 @@ public class ColorSchemaReader {
/**
* Sets proper name to {@link DataOverlayEntry} from cell content.
- *
+ *
* @param schema
* {@link DataOverlayEntry} where name should be set
* @param content
@@ -406,10 +406,17 @@ public class ColorSchemaReader {
}
}
+
+ private void processSourceDataColumn(final DataOverlayEntry schema, final String content) {
+ if (!content.isEmpty()) {
+ schema.setSourceData(content);
+ }
+ }
+
/**
* Sets proper compartment names to {@link DataOverlayEntry} from cell
* content.
- *
+ *
* @param schema
* {@link DataOverlayEntry} where name should be set
* @param content
@@ -425,7 +432,7 @@ public class ColorSchemaReader {
/**
* Transforms string into {@link ReferenceGenomeType}.
- *
+ *
* @param referenceGenomeStr
* type as a string
* @return {@link ReferenceGenomeType} obtained from input string
@@ -450,13 +457,13 @@ public class ColorSchemaReader {
/**
* Merges collection of {@link DataOverlayEntry} that might contain duplicate
* names into collection that doesn't have duplicate names.
- *
+ *
* @param schemas
* {@link Collection} of {@link DataOverlayEntry} that might contain
* duplicate name
* @return {@link Collection} of {@link DataOverlayEntry} that doesn't contain
* duplicate names
- *
+ *
*/
private Collection<DataOverlayEntry> mergeSchemas(final Collection<DataOverlayEntry> schemas) {
Map<String, DataOverlayEntry> schemasByName = new HashMap<>();
@@ -500,7 +507,7 @@ public class ColorSchemaReader {
/**
* Gets color that should be assigned to {@link GeneVariantDataOverlayEntry}.
- *
+ *
* @param geneVariations
* list of variants
* @return {@link Color} that should be assigned to
@@ -519,7 +526,7 @@ public class ColorSchemaReader {
/**
* Reads information about set of {@link GenericDataOverlayEntry generic color
* schemas} from the input stream.
- *
+ *
* @param colorInputStream
* input stream with {@link GenericDataOverlayEntry}
* @return list of coloring schemas
@@ -549,17 +556,18 @@ public class ColorSchemaReader {
Map<ColorSchemaColumn, Integer> schemaColumns = new HashMap<>();
List<Pair<MiriamType, Integer>> customIdentifiers = parseColumns(columns, schemaColumns, DataOverlayType.GENERIC);
- Integer valueColumn = schemaColumns.get(ColorSchemaColumn.VALUE);
- Integer colorColumn = schemaColumns.get(ColorSchemaColumn.COLOR);
- Integer nameColumn = schemaColumns.get(ColorSchemaColumn.NAME);
- Integer modelNameColumn = schemaColumns.get(ColorSchemaColumn.MAP_NAME);
- Integer identifierColumn = schemaColumns.get(ColorSchemaColumn.IDENTIFIER);
- Integer elementIdentifierColumn = schemaColumns.get(ColorSchemaColumn.ELEMENT_IDENTIFIER);
- Integer compartmentColumn = schemaColumns.get(ColorSchemaColumn.COMPARTMENT);
- Integer typeColumn = schemaColumns.get(ColorSchemaColumn.TYPE);
- Integer lineWidthColumn = schemaColumns.get(ColorSchemaColumn.LINE_WIDTH);
- Integer reverseReactionColumn = schemaColumns.get(ColorSchemaColumn.REVERSE_REACTION);
- Integer descriptionColumn = schemaColumns.get(ColorSchemaColumn.DESCRIPTION);
+ final Integer valueColumn = schemaColumns.get(ColorSchemaColumn.VALUE);
+ final Integer colorColumn = schemaColumns.get(ColorSchemaColumn.COLOR);
+ final Integer nameColumn = schemaColumns.get(ColorSchemaColumn.NAME);
+ final Integer modelNameColumn = schemaColumns.get(ColorSchemaColumn.MAP_NAME);
+ final Integer sourceDataColumn = schemaColumns.get(ColorSchemaColumn.SOURCE_DATA);
+ final Integer identifierColumn = schemaColumns.get(ColorSchemaColumn.IDENTIFIER);
+ final Integer elementIdentifierColumn = schemaColumns.get(ColorSchemaColumn.ELEMENT_IDENTIFIER);
+ final Integer compartmentColumn = schemaColumns.get(ColorSchemaColumn.COMPARTMENT);
+ final Integer typeColumn = schemaColumns.get(ColorSchemaColumn.TYPE);
+ final Integer lineWidthColumn = schemaColumns.get(ColorSchemaColumn.LINE_WIDTH);
+ final Integer reverseReactionColumn = schemaColumns.get(ColorSchemaColumn.REVERSE_REACTION);
+ final Integer descriptionColumn = schemaColumns.get(ColorSchemaColumn.DESCRIPTION);
if (nameColumn == null && identifierColumn == null && customIdentifiers.size() == 0
&& elementIdentifierColumn == null) {
@@ -594,6 +602,9 @@ public class ColorSchemaReader {
if (modelNameColumn != null) {
processModelNameColumn(schema, values[modelNameColumn]);
}
+ if (sourceDataColumn != null) {
+ processSourceDataColumn(schema, values[sourceDataColumn]);
+ }
if (valueColumn != null) {
schema.setValue(parseValueColumn(values[valueColumn], errorPrefix));
}
@@ -715,7 +726,7 @@ public class ColorSchemaReader {
/**
* Sets proper reaction identifier to {@link DataOverlayEntry} from cell
* content.
- *
+ *
* @param schema
* {@link DataOverlayEntry} where name should be set
* @param content
@@ -731,7 +742,7 @@ public class ColorSchemaReader {
/**
* Transform headers of columns into map with {@link ColorSchemaColumn column
* types} to column number.
- *
+ *
* @param columns
* headers of columns
* @param schemaColumns
@@ -787,7 +798,7 @@ public class ColorSchemaReader {
/**
* Returns list of columns that should be printed for given coloring schemas.
- *
+ *
* @param schemas
* list of schemas
* @return list of columns that should be printed (were set in the coloring
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/ColorSchemaReaderTest.java b/converter/src/test/java/lcsb/mapviewer/converter/ColorSchemaReaderTest.java
index 26653afab2446c851c69f1181a529a5972bc4ed1..e6a507c1f951a3c15d8c77e171780d5333a426a8 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/ColorSchemaReaderTest.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/ColorSchemaReaderTest.java
@@ -1,15 +1,22 @@
package lcsb.mapviewer.converter;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.TextFileUtils;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.overlay.DataOverlayEntry;
+import lcsb.mapviewer.model.overlay.GeneVariant;
+import lcsb.mapviewer.model.overlay.GeneVariantDataOverlayEntry;
+import lcsb.mapviewer.model.overlay.InvalidDataOverlayException;
+import org.apache.commons.io.output.ByteArrayOutputStream;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
import java.awt.Color;
import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.FileInputStream;
-import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
@@ -18,19 +25,10 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
-import org.apache.commons.io.output.ByteArrayOutputStream;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.TextFileUtils;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.overlay.DataOverlayEntry;
-import lcsb.mapviewer.model.overlay.GeneVariant;
-import lcsb.mapviewer.model.overlay.GeneVariantDataOverlayEntry;
-import lcsb.mapviewer.model.overlay.InvalidDataOverlayException;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
public class ColorSchemaReaderTest extends ConverterTestFunctions {
@@ -89,7 +87,7 @@ public class ColorSchemaReaderTest extends ConverterTestFunctions {
assertEquals(1, schemas.size());
}
- private byte[] fileToByteArray(final File f) throws FileNotFoundException, IOException {
+ private byte[] fileToByteArray(final File f) throws IOException {
InputStream in = new FileInputStream(f);
byte[] buff = new byte[8000];
@@ -124,6 +122,7 @@ public class ColorSchemaReaderTest extends ConverterTestFunctions {
for (final GeneVariant geneVariant : schema.getGeneVariants()) {
if (geneVariant.getAminoAcidChange() != null && !geneVariant.getAminoAcidChange().trim().isEmpty()) {
aaChangeFound = true;
+ break;
}
}
assertTrue("Amino acid are not present in parsed data", aaChangeFound);
@@ -362,4 +361,17 @@ public class ColorSchemaReaderTest extends ConverterTestFunctions {
assertEquals(2, schemas.size());
}
+ @Test
+ public void testColoringWithSourceData() throws Exception {
+ String input = "name\tcolor\tsource_data\n"
+ + "s1\t#ff0000\txxx\n";
+ Map<String, String> params = new HashMap<>();
+ params.put(TextFileUtils.COLUMN_COUNT_PARAM, "3");
+
+ Collection<DataOverlayEntry> schemas = reader
+ .readColorSchema(new ByteArrayInputStream(input.getBytes(StandardCharsets.UTF_8)), params);
+ assertEquals(1, schemas.size());
+ assertNotNull(schemas.iterator().next().getSourceData());
+ }
+
}
diff --git a/frontend-js/pom.xml b/frontend-js/pom.xml
index daec87d496ea05af35838ed4180cec4270145617..86beb1b4b44f8666d993f1f7e8e8c853368a94be 100644
--- a/frontend-js/pom.xml
+++ b/frontend-js/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</parent>
<artifactId>frontend-js</artifactId>
<name>frontend-js</name>
diff --git a/model-command/pom.xml b/model-command/pom.xml
index 0ea553bece32b80c7ba215b0b907fd3ebf21acd4..6c6d2bfd59e6c2e8ee9e44716bdadf7de6b98352 100644
--- a/model-command/pom.xml
+++ b/model-command/pom.xml
@@ -3,7 +3,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</parent>
<artifactId>model-command</artifactId>
<name>Model commands</name>
@@ -16,7 +16,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
@@ -24,7 +24,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<!-- Log4J2-->
diff --git a/model/pom.xml b/model/pom.xml
index 5cbdcfe395d865a17f0faf0a8739ae9778f6255b..41c41790d11a23e4db072e9098898bf1ac7cae3e 100644
--- a/model/pom.xml
+++ b/model/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</parent>
<artifactId>model</artifactId>
<name>model MapViewer</name>
@@ -15,7 +15,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>commons</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<!-- Java xml serialization -->
diff --git a/model/src/main/java/lcsb/mapviewer/model/overlay/DataOverlayEntry.java b/model/src/main/java/lcsb/mapviewer/model/overlay/DataOverlayEntry.java
index ed607001086bebfdd6c96d6192fe9b238680900d..db715cc745a7862ef1eafeb7ef314b41dc574f15 100644
--- a/model/src/main/java/lcsb/mapviewer/model/overlay/DataOverlayEntry.java
+++ b/model/src/main/java/lcsb/mapviewer/model/overlay/DataOverlayEntry.java
@@ -60,6 +60,8 @@ public abstract class DataOverlayEntry implements Serializable {
*/
private String modelName = null;
+ private String sourceData = null;
+
/**
* Original identifier of the {@link BioEntity} to change the color.
*/
@@ -415,4 +417,12 @@ public abstract class DataOverlayEntry implements Serializable {
public void setDataOverlay(final DataOverlay dataOverlay) {
this.dataOverlay = dataOverlay;
}
+
+ public String getSourceData() {
+ return sourceData;
+ }
+
+ public void setSourceData(final String sourceData) {
+ this.sourceData = sourceData;
+ }
}
diff --git a/pathvisio/pom.xml b/pathvisio/pom.xml
index db2cc0845e8c7fb53eae2b60d550c018b9fbfdf6..13ac79c89e5873575b3e9b8cdc5afffc17c9c6d9 100644
--- a/pathvisio/pom.xml
+++ b/pathvisio/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</parent>
<artifactId>pathvisio</artifactId>
<name>Pathvisio plugin</name>
@@ -77,26 +77,26 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
<scope>test</scope>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model-command</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<!-- Log4J2 -->
diff --git a/persist/pom.xml b/persist/pom.xml
index 9d4f4f2f6ed517234f83f1691d1968490e307b6e..ed46065d06b37f9a16b3e5b739768dbd6966ce93 100644
--- a/persist/pom.xml
+++ b/persist/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</parent>
<artifactId>persist</artifactId>
@@ -26,7 +26,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<!-- Hibernate -->
diff --git a/persist/src/main/resources/db/migration/hsql/18.2.0/V18.0.8.20250313__add_source_data_to_overlay_entry.sql b/persist/src/main/resources/db/migration/hsql/18.2.0/V18.0.8.20250313__add_source_data_to_overlay_entry.sql
new file mode 100644
index 0000000000000000000000000000000000000000..93bdf335b425a96afa88944f55f26861edd085f4
--- /dev/null
+++ b/persist/src/main/resources/db/migration/hsql/18.2.0/V18.0.8.20250313__add_source_data_to_overlay_entry.sql
@@ -0,0 +1,2 @@
+alter table data_overlay_entry_table
+ add column source_data character varying(255);
diff --git a/persist/src/main/resources/db/migration/postgres/18.2.0/V18.0.8.20250313__add_source_data_to_overlay_entry.sql b/persist/src/main/resources/db/migration/postgres/18.2.0/V18.0.8.20250313__add_source_data_to_overlay_entry.sql
new file mode 100644
index 0000000000000000000000000000000000000000..93bdf335b425a96afa88944f55f26861edd085f4
--- /dev/null
+++ b/persist/src/main/resources/db/migration/postgres/18.2.0/V18.0.8.20250313__add_source_data_to_overlay_entry.sql
@@ -0,0 +1,2 @@
+alter table data_overlay_entry_table
+ add column source_data character varying(255);
diff --git a/pom.xml b/pom.xml
index 918085bc04c4b33d27c5d506e7d95139bf0dc57a..1da2a839dcab9de69dc066e8977a8e1e125ea99c 100644
--- a/pom.xml
+++ b/pom.xml
@@ -6,7 +6,7 @@
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
<packaging>pom</packaging>
<name>parent MapViewer</name>
diff --git a/rest-api/pom.xml b/rest-api/pom.xml
index f92e224b3f69c46cc3add662e599ff4eb2b1811a..2924cf6bbfdb21c8391feff86509462297143d5d 100644
--- a/rest-api/pom.xml
+++ b/rest-api/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</parent>
<artifactId>rest-api</artifactId>
<name>rest-api</name>
@@ -19,19 +19,19 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>service</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>pathvisio</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<dependency>
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayEntryDTOSerializer.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayEntryDTOSerializer.java
index 64932af3e8c3c408d625fbda919bcaca764744af..99fb059d98ea877aeac93eddf75b336e8cd1401b 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayEntryDTOSerializer.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayEntryDTOSerializer.java
@@ -1,27 +1,26 @@
package lcsb.mapviewer.api.projects.overlays;
-import java.io.IOException;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Objects;
-
import com.fasterxml.jackson.core.JsonGenerator;
import com.fasterxml.jackson.databind.JsonSerializer;
import com.fasterxml.jackson.databind.SerializerProvider;
import com.fasterxml.jackson.databind.ser.FilterProvider;
import com.fasterxml.jackson.databind.ser.PropertyFilter;
-
import lcsb.mapviewer.api.projects.overlays.OverlayController.OverlayEntryDTO;
import lcsb.mapviewer.model.overlay.DataOverlayType;
import lcsb.mapviewer.model.overlay.GeneVariantDataOverlayEntry;
import lcsb.mapviewer.modelutils.serializer.CustomExceptFilter;
import lcsb.mapviewer.modelutils.serializer.model.map.ElementIdentifierType;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Objects;
+
public class OverlayEntryDTOSerializer extends JsonSerializer<OverlayEntryDTO> {
@Override
public void serialize(final OverlayEntryDTO entry, final JsonGenerator gen,
- final SerializerProvider serializers)
+ final SerializerProvider serializers)
throws IOException {
PropertyFilter filter = null;
@@ -60,6 +59,9 @@ public class OverlayEntryDTOSerializer extends JsonSerializer<OverlayEntryDTO> {
case "description":
value = entry.getEntry().getDescription();
break;
+ case "sourcedata":
+ value = entry.getEntry().getSourceData();
+ break;
case "width":
if (Objects.equals(entry.getType(), ElementIdentifierType.REACTION)) {
value = entry.getEntry().getLineWidth();
@@ -78,7 +80,7 @@ public class OverlayEntryDTOSerializer extends JsonSerializer<OverlayEntryDTO> {
if (entry.getEntry() instanceof GeneVariantDataOverlayEntry) {
value = ((GeneVariantDataOverlayEntry) entry.getEntry()).getGeneVariants();
} else {
- value = new Object[] {};
+ value = new Object[]{};
}
break;
default:
@@ -102,6 +104,7 @@ public class OverlayEntryDTOSerializer extends JsonSerializer<OverlayEntryDTO> {
"type",
"geneVariations",
"uniqueId",
+ "sourceData",
"width");
}
diff --git a/service/pom.xml b/service/pom.xml
index b1131cba882e95d958b840e48b6484ee1c9aa6cd..16fb7b20328bb6062b39c379b929ac40b5df8651 100644
--- a/service/pom.xml
+++ b/service/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</parent>
<artifactId>service</artifactId>
@@ -19,7 +19,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<!-- dependency from the MapViewer dao -->
@@ -27,47 +27,47 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>persist</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model-command</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>annotation</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<!-- dependency from the MapViewer cell designer parser -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<!-- dependency from the MapViewer SBGN-ML parser -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-SBGNML</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<!-- dependency from the MapViewer graphics converter -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<!-- dependency from the SBML parser -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-sbml</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<!-- Log4J2 -->
diff --git a/web/pom.xml b/web/pom.xml
index a7feec46e84d6994eefafd9bd66e7f97b7d29c98..fb8565aa8a1911d81b959b1cce63e798baca6dcb 100644
--- a/web/pom.xml
+++ b/web/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</parent>
<artifactId>web</artifactId>
<packaging>jar</packaging>
@@ -36,19 +36,19 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>service</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>rest-api</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>frontend-js</artifactId>
- <version>18.1.1</version>
+ <version>18.2.0</version>
</dependency>
<dependency>
diff --git a/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java
index 88fe296228dcc102ceab4486103ee1e7187c397a..7733dc5cda6abcf1169f810314697f48a2061388 100644
--- a/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java
@@ -631,6 +631,32 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
assertEquals(1, dataOverlayService.getDataOverlaysByProject(project).size());
}
+ @Test
+ public void testAdminCreateOverlayWithSourceData() throws Exception {
+ final User admin = userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN);
+
+ final UploadedFileEntry file = createFile("element_identifier\tvalue\tsource_data\n\t-1\txxx", admin);
+
+ final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
+
+ final String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
+ new BasicNameValuePair("fileId", String.valueOf(file.getId())),
+ new BasicNameValuePair("name", "overlay name"),
+ new BasicNameValuePair("description", "overlay name"),
+ new BasicNameValuePair("filename", "overlay name"),
+ new BasicNameValuePair("type", "GENERIC"))));
+
+ final RequestBuilder request = post("/minerva/api/projects/{projectId}/overlays/", TEST_PROJECT)
+ .contentType(MediaType.APPLICATION_FORM_URLENCODED)
+ .content(body)
+ .session(session);
+
+ mockMvc.perform(request)
+ .andExpect(status().is2xxSuccessful());
+
+ assertEquals(1, dataOverlayService.getDataOverlaysByProject(project).size());
+ }
+
@Test
public void testAdminCreateOverlayFromContent() throws Exception {
final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
@@ -1448,6 +1474,10 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
.description("description assigned to the bioEntity from overlay")
.type(JsonFieldType.STRING)
.optional(),
+ fieldWithPath("overlayContent.sourceData")
+ .description("source data")
+ .type(JsonFieldType.STRING)
+ .optional(),
fieldWithPath("overlayContent.geneVariations")
.description("list of gene variants assigned to the bioEntity from overlay")
.type(JsonFieldType.ARRAY)
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/NewApiDocs.java b/web/src/test/java/lcsb/mapviewer/web/api/NewApiDocs.java
index 13293284c354ec1fc344b6bc9ffeb45cc6b82ea9..72b1da5f351aa75e06aa7df5df1ecf3b130f170e 100644
--- a/web/src/test/java/lcsb/mapviewer/web/api/NewApiDocs.java
+++ b/web/src/test/java/lcsb/mapviewer/web/api/NewApiDocs.java
@@ -129,6 +129,10 @@ public class NewApiDocs {
fieldWithPath(prefix + "name")
.description("bioEntity name that should match")
.type(JsonFieldType.STRING),
+ fieldWithPath(prefix + "sourceData")
+ .description("source data")
+ .optional()
+ .type(JsonFieldType.STRING),
fieldWithPath(prefix + "modelName")
.description("bioEntity model name that should match")
.optional()