From bd0d45368fcca84ffeec94daaa4bfc7b88167df8 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <p.gawron@atcomp.pl>
Date: Thu, 13 Mar 2025 12:59:08 +0100
Subject: [PATCH] add source data to data overlay entry
---
CHANGELOG | 5 ++
.../converter/ColorSchemaColumn.java | 61 +++++++++--------
.../converter/ColorSchemaReader.java | 67 +++++++++++--------
.../converter/ColorSchemaReaderTest.java | 50 ++++++++------
.../model/overlay/DataOverlayEntry.java | 10 +++
...0313__add_source_data_to_overlay_entry.sql | 2 +
...0313__add_source_data_to_overlay_entry.sql | 2 +
.../overlays/OverlayEntryDTOSerializer.java | 19 +++---
.../web/OverlayControllerIntegrationTest.java | 30 +++++++++
.../lcsb/mapviewer/web/api/NewApiDocs.java | 4 ++
10 files changed, 164 insertions(+), 86 deletions(-)
create mode 100644 persist/src/main/resources/db/migration/hsql/18.2.0/V18.0.8.20250313__add_source_data_to_overlay_entry.sql
create mode 100644 persist/src/main/resources/db/migration/postgres/18.2.0/V18.0.8.20250313__add_source_data_to_overlay_entry.sql
diff --git a/CHANGELOG b/CHANGELOG
index dd576dddf6..f741b55be8 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/converter/src/main/java/lcsb/mapviewer/converter/ColorSchemaColumn.java b/converter/src/main/java/lcsb/mapviewer/converter/ColorSchemaColumn.java
index 8ff5134345..109c1d7ba4 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 03c368cd93..f6eef6f01d 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 26653afab2..e6a507c1f9 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/model/src/main/java/lcsb/mapviewer/model/overlay/DataOverlayEntry.java b/model/src/main/java/lcsb/mapviewer/model/overlay/DataOverlayEntry.java
index ed60700108..db715cc745 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/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 0000000000..93bdf335b4
--- /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 0000000000..93bdf335b4
--- /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/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 64932af3e8..99fb059d98 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/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java
index 88fe296228..7733dc5cda 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 13293284c3..72b1da5f35 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()
--
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