From b5b1738397d5d1e8dc5179e91725591a4d797ea3 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 7 Jun 2019 14:02:13 +0200
Subject: [PATCH] model_name renamed to map_name
---
CHANGELOG | 2 +
.../services/impl/LayoutService.java | 4 +-
.../services/utils/ColorSchemaReader.java | 6 +--
.../services/utils/ColorSchemaXlsxReader.java | 4 +-
.../utils/data/ColorSchemaColumn.java | 4 +-
.../services/utils/ColorSchemaReaderTest.java | 37 +++++++++++++++++++
6 files changed, 48 insertions(+), 9 deletions(-)
diff --git a/CHANGELOG b/CHANGELOG
index bd089b970b..8ffa5ce732 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 f3379ed425..a6ba78e935 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 40a7e31684..fb49f55ff8 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 1437bd3795..631a20734a 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 5cbcc2e705..045198598e 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 2f02c86852..7041b25dfc 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;
+ }
+ }
+
+
}
--
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