From 5eaef346f2dfe3618e24964103bc5801abb469a4 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 7 Jun 2019 15:00:11 +0200
Subject: [PATCH] some columns are marked as deprecated
---
CHANGELOG | 5 +++++
.../mapviewer/services/utils/ColorSchemaReader.java | 11 ++++++++++-
.../services/utils/data/ColorSchemaColumn.java | 6 ++++--
3 files changed, 19 insertions(+), 3 deletions(-)
diff --git a/CHANGELOG b/CHANGELOG
index 8b544c0a48..484adae3d3 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,6 +1,11 @@
minerva (12.3.1~beta.1) unstable; urgency=low
* Small improvement: model_name renamed to map_name in data overlay columns
(#827)
+ * Small improvement: name, type, reference_genome_type and
+ reference_genome_version column in genetic variant data overlay are
+ deprecated (#827)
+ * Bug fix: deprecated columns in data overlay are not visible to the end user
+ (#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/utils/ColorSchemaReader.java b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
index 2471473e53..e9f8739556 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
@@ -7,6 +7,7 @@ import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
+import java.lang.reflect.Field;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
@@ -720,7 +721,15 @@ public class ColorSchemaReader {
} else {
String columnNames = "";
for (ColorSchemaColumn schemaColumn : ColorSchemaColumn.values()) {
- if (schemaColumn.getTypes().contains(type)) {
+ boolean deprecated = false;
+ try {
+ Field f = ColorSchemaColumn.class.getField(schemaColumn.name());
+ if (f.isAnnotationPresent(Deprecated.class))
+ deprecated = true;
+ } catch (NoSuchFieldException | SecurityException e) {
+ }
+
+ if (schemaColumn.getTypes().contains(type) && !deprecated) {
columnNames += schemaColumn.getColumnName() + ", ";
}
}
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 045198598e..fd9e213116 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
@@ -19,7 +19,7 @@ public enum ColorSchemaColumn {
/**
* Name of the element.
*/
- NAME(new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
+ NAME(new ColorSchemaType[] { ColorSchemaType.GENERIC}),
GENE_NAME(new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
@@ -43,7 +43,7 @@ public enum ColorSchemaColumn {
/**
* Class type of the element.
*/
- TYPE(new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
+ TYPE(new ColorSchemaType[] { ColorSchemaType.GENERIC}),
/**
* New element/reaction color.
@@ -99,11 +99,13 @@ public enum ColorSchemaColumn {
/**
* What's the {@link ReferenceGenomeType}.
*/
+ @Deprecated
REFERENCE_GENOME_TYPE(new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
/**
* {@link ReferenceGenome#version Version} of the reference genome.
*/
+ @Deprecated
REFERENCE_GENOME_VERSION(new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
/**
--
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