Commit 5eaef346 authored by Piotr Gawron's avatar Piotr Gawron
Browse files

some columns are marked as deprecated

parent d04da2a3
minerva (12.3.1~beta.1) unstable; urgency=low minerva (12.3.1~beta.1) unstable; urgency=low
* Small improvement: model_name renamed to map_name in data overlay columns * Small improvement: model_name renamed to map_name in data overlay columns
(#827) (#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 * Bug fix: invalid color in data overlay provides proper feedback to the user
(#822) (#822)
* Bug fix: genetic variant overlay without name caused problems (#832) * Bug fix: genetic variant overlay without name caused problems (#832)
......
...@@ -7,6 +7,7 @@ import java.io.FileInputStream; ...@@ -7,6 +7,7 @@ import java.io.FileInputStream;
import java.io.IOException; import java.io.IOException;
import java.io.InputStream; import java.io.InputStream;
import java.io.InputStreamReader; import java.io.InputStreamReader;
import java.lang.reflect.Field;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Collection; import java.util.Collection;
import java.util.HashMap; import java.util.HashMap;
...@@ -720,7 +721,15 @@ public class ColorSchemaReader { ...@@ -720,7 +721,15 @@ public class ColorSchemaReader {
} else { } else {
String columnNames = ""; String columnNames = "";
for (ColorSchemaColumn schemaColumn : ColorSchemaColumn.values()) { 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() + ", "; columnNames += schemaColumn.getColumnName() + ", ";
} }
} }
......
...@@ -19,7 +19,7 @@ public enum ColorSchemaColumn { ...@@ -19,7 +19,7 @@ public enum ColorSchemaColumn {
/** /**
* Name of the element. * Name of the element.
*/ */
NAME(new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), NAME(new ColorSchemaType[] { ColorSchemaType.GENERIC}),
GENE_NAME(new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), GENE_NAME(new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
...@@ -43,7 +43,7 @@ public enum ColorSchemaColumn { ...@@ -43,7 +43,7 @@ public enum ColorSchemaColumn {
/** /**
* Class type of the element. * Class type of the element.
*/ */
TYPE(new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), TYPE(new ColorSchemaType[] { ColorSchemaType.GENERIC}),
/** /**
* New element/reaction color. * New element/reaction color.
...@@ -99,11 +99,13 @@ public enum ColorSchemaColumn { ...@@ -99,11 +99,13 @@ public enum ColorSchemaColumn {
/** /**
* What's the {@link ReferenceGenomeType}. * What's the {@link ReferenceGenomeType}.
*/ */
@Deprecated
REFERENCE_GENOME_TYPE(new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), REFERENCE_GENOME_TYPE(new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
/** /**
* {@link ReferenceGenome#version Version} of the reference genome. * {@link ReferenceGenome#version Version} of the reference genome.
*/ */
@Deprecated
REFERENCE_GENOME_VERSION(new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), REFERENCE_GENOME_VERSION(new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
/** /**
......
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