diff --git a/CHANGELOG b/CHANGELOG index bd089b970b397bdee8eaf649977ad39b1c2c18d1..8ffa5ce7328701a207dc540da79ac340a74f9152 100644 --- a/CHANGELOG +++ b/CHANGELOG @@ -1,4 +1,6 @@ minerva (12.3.1~beta.1) unstable; urgency=low + * Small improvement: model_name renamed to map_name in data overlay columns + (#827) * Bug fix: invalid color in data overlay provides proper feedback to the user (#822) * Bug fix: genetic variant overlay without name caused problems (#832) diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java index f3379ed425efc9d7d5684a84c8f0068b3dd5091f..a6ba78e9357d37e2478adc17036891c6022fabc8 100644 --- a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java +++ b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java @@ -672,7 +672,7 @@ public class LayoutService implements ILayoutService { sb.append("\t"); } else if (column.equals(ColorSchemaColumn.NAME)) { sb.append(schema.getName() + "\t"); - } else if (column.equals(ColorSchemaColumn.MODEL_NAME)) { + } else if (column.equals(ColorSchemaColumn.MAP_NAME)) { sb.append(schema.getModelName() + "\t"); } else if (column.equals(ColorSchemaColumn.VALUE)) { sb.append(schema.getValue() + "\t"); @@ -727,7 +727,7 @@ public class LayoutService implements ILayoutService { sb.append("\t"); } else if (column.equals(ColorSchemaColumn.NAME)) { sb.append(schema.getName() + "\t"); - } else if (column.equals(ColorSchemaColumn.MODEL_NAME)) { + } else if (column.equals(ColorSchemaColumn.MAP_NAME)) { sb.append(schema.getModelName() + "\t"); } else if (column.equals(ColorSchemaColumn.VALUE)) { sb.append(schema.getValue() + "\t"); diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java index 40a7e3168491692e113689db0005b9085d4aa903..fb49f55ff8d20c0799cead5ccda144125431765d 100644 --- a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java +++ b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java @@ -166,7 +166,7 @@ public class ColorSchemaReader { throw new InvalidColorSchemaException(ColorSchemaColumn.GENE_NAME + " and " + ColorSchemaColumn.NAME + " column cannot appear in the same dataset"); } - Integer modelNameColumn = schemaColumns.get(ColorSchemaColumn.MODEL_NAME); + Integer modelNameColumn = schemaColumns.get(ColorSchemaColumn.MAP_NAME); Integer identifierColumn = schemaColumns.get(ColorSchemaColumn.IDENTIFIER); Integer variantIdentifierColumn = schemaColumns.get(ColorSchemaColumn.VARIANT_IDENTIFIER); Integer allelFrequencyColumn = schemaColumns.get(ColorSchemaColumn.ALLEL_FREQUENCY); @@ -493,7 +493,7 @@ public class ColorSchemaReader { Integer valueColumn = schemaColumns.get(ColorSchemaColumn.VALUE); Integer colorColumn = schemaColumns.get(ColorSchemaColumn.COLOR); Integer nameColumn = schemaColumns.get(ColorSchemaColumn.NAME); - Integer modelNameColumn = schemaColumns.get(ColorSchemaColumn.MODEL_NAME); + Integer modelNameColumn = schemaColumns.get(ColorSchemaColumn.MAP_NAME); Integer identifierColumn = schemaColumns.get(ColorSchemaColumn.IDENTIFIER); Integer elementIdentifierColumn = schemaColumns.get(ColorSchemaColumn.ELEMENT_IDENTIFIER); if (elementIdentifierColumn == null) { @@ -789,7 +789,7 @@ public class ColorSchemaReader { result.add(ColorSchemaColumn.NAME); } if (schema.getModelName() != null) { - result.add(ColorSchemaColumn.MODEL_NAME); + result.add(ColorSchemaColumn.MAP_NAME); } if (schema.getElementId() != null) { result.add(ColorSchemaColumn.ELEMENT_IDENTIFIER); diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java index 1437bd37958dfe69f61f9d6886aae3127730de7e..631a20734afe26a0e1662fdc68cd6d17c2766eee 100644 --- a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java +++ b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java @@ -156,7 +156,7 @@ public class ColorSchemaXlsxReader { valueColumn = foundSchemaColumns.get(ColorSchemaColumn.VALUE); colorColumn = foundSchemaColumns.get(ColorSchemaColumn.COLOR); nameColumn = foundSchemaColumns.get(ColorSchemaColumn.NAME); - modelNameColumn = foundSchemaColumns.get(ColorSchemaColumn.MODEL_NAME); + modelNameColumn = foundSchemaColumns.get(ColorSchemaColumn.MAP_NAME); identifierColumn = foundSchemaColumns.get(ColorSchemaColumn.IDENTIFIER); elementIdentifierColumn = foundSchemaColumns.get(ColorSchemaColumn.ELEMENT_IDENTIFIER); if (elementIdentifierColumn == null) { @@ -326,7 +326,7 @@ public class ColorSchemaXlsxReader { result.add(ColorSchemaColumn.NAME); } if (schema.getModelName() != null) { - result.add(ColorSchemaColumn.MODEL_NAME); + result.add(ColorSchemaColumn.MAP_NAME); } if (schema.getElementId() != null) { result.add(ColorSchemaColumn.ELEMENT_IDENTIFIER); diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java b/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java index 5cbcc2e705d9551376089163c832de4a38150096..045198598e771100ee9939a54feee51d4a560485 100644 --- a/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java +++ b/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java @@ -24,9 +24,9 @@ public enum ColorSchemaColumn { GENE_NAME(new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), /** - * Name of the element. + * Name of the map. */ - MODEL_NAME(new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), + MAP_NAME("model_name",new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), /** * Value that will be transformed into new color. diff --git a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java index 2f02c86852f2a79df97599b83620a90b323fe335..7041b25dfcf88cb4a916bb30620b491811b21009 100644 --- a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java +++ b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java @@ -444,4 +444,41 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions { assertEquals(0, classes.size()); } + @Test + public void testColoringWithModelName() throws Exception { + try { + String input = "name\tcolor\tmodel_name\n" + + "s1\t#ff0000\txxx\n" ; + Map<String, String> params = new HashMap<>(); + params.put(TextFileUtils.COLUMN_COUNT_PARAM, "3"); + + Collection<ColorSchema> schemas = reader + .readColorSchema(new ByteArrayInputStream(input.getBytes(StandardCharsets.UTF_8)), params); + assertEquals(1, schemas.size()); + assertNotNull(schemas.iterator().next().getModelName()); + } catch (Exception e) { + e.printStackTrace(); + throw e; + } + } + + @Test + public void testColoringWithMapName() throws Exception { + try { + String input = "name\tcolor\tmap_name\n" + + "s1\t#ff0000\txxx\n" ; + Map<String, String> params = new HashMap<>(); + params.put(TextFileUtils.COLUMN_COUNT_PARAM, "3"); + + Collection<ColorSchema> schemas = reader + .readColorSchema(new ByteArrayInputStream(input.getBytes(StandardCharsets.UTF_8)), params); + assertEquals(1, schemas.size()); + assertNotNull(schemas.iterator().next().getModelName()); + } catch (Exception e) { + e.printStackTrace(); + throw e; + } + } + + }