From 5d252147ecc48dd4d80dcd4630c3409ad8bc3bb5 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 6 Jun 2019 20:03:50 +0200
Subject: [PATCH] genetic variant overlay without name caused problems
---
CHANGELOG | 1 +
.../services/utils/ColorSchemaReader.java | 2 +-
.../services/utils/ColorSchemaReaderTest.java | 97 ++++++++-----------
.../testFiles/coloring/gene_variants_id.txt | 5 +
4 files changed, 48 insertions(+), 57 deletions(-)
create mode 100644 service/testFiles/coloring/gene_variants_id.txt
diff --git a/CHANGELOG b/CHANGELOG
index 90f4e97461..71510373a8 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,6 +1,7 @@
minerva (12.3.1~beta.1) unstable; urgency=low
* Bug fix: invalid color in data overlay provides proper feedback to the user
(#822)
+ * Bug fix: genetic variant overlay without name caused problems (#832)
* Bug fix: tair locus identifiers were used improperly - instead of id the
name was used
* Bug fix: plugin tab header wasn't properly resized after adding plugins
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 87b27aa822..93f0517170 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
@@ -292,7 +292,7 @@ public class ColorSchemaReader {
gv.setContig(values[contigColumn]);
schema.addGeneVariation(gv);
- if (schema.getName().contains(";")) {
+ if (schema.getName()!=null && schema.getName().contains(";")) {
String[] names = schema.getName().split(";");
for (String string : names) {
if (!string.trim().isEmpty()) {
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 20d037fa24..119fb25312 100644
--- a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
@@ -11,6 +11,8 @@ 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;
import java.util.Collection;
@@ -75,21 +77,27 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
public void testReadGeneVariantsSchema() throws Exception {
try {
File f = new File("testFiles/coloring/gene_variants.txt");
- InputStream in = new FileInputStream(f);
+ byte[] data = fileToByteArray(f);
- byte[] buff = new byte[8000];
-
- int bytesRead = 0;
+ ByteArrayInputStream bin = new ByteArrayInputStream(data);
- ByteArrayOutputStream bao = new ByteArrayOutputStream();
+ ColorSchemaReader reader = new ColorSchemaReader();
- while ((bytesRead = in.read(buff)) != -1) {
- bao.write(buff, 0, bytesRead);
- }
- in.close();
- bao.close();
+ Collection<ColorSchema> schemas = reader.readColorSchema(bin,
+ TextFileUtils.getHeaderParametersFromFile(new ByteArrayInputStream(data)));
+ assertNotNull(schemas);
+ assertEquals(3, schemas.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- byte[] data = bao.toByteArray();
+ @Test
+ public void testReadGeneVariantByIdSchema() throws Exception {
+ try {
+ File f = new File("testFiles/coloring/gene_variants_id.txt");
+ byte[] data = fileToByteArray(f);
ByteArrayInputStream bin = new ByteArrayInputStream(data);
@@ -98,32 +106,37 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
Collection<ColorSchema> schemas = reader.readColorSchema(bin,
TextFileUtils.getHeaderParametersFromFile(new ByteArrayInputStream(data)));
assertNotNull(schemas);
- assertEquals(3, schemas.size());
+ assertEquals(1, schemas.size());
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
- @Test
- public void testReadGeneVariantsWithAminoAcidChange() throws Exception {
- try {
- File f = new File("testFiles/coloring/gene_variants_aa_change.txt");
- InputStream in = new FileInputStream(f);
+ private byte[] fileToByteArray(File f) throws FileNotFoundException, IOException {
+ InputStream in = new FileInputStream(f);
- byte[] buff = new byte[8000];
+ byte[] buff = new byte[8000];
- int bytesRead = 0;
+ int bytesRead = 0;
- ByteArrayOutputStream bao = new ByteArrayOutputStream();
+ ByteArrayOutputStream bao = new ByteArrayOutputStream();
- while ((bytesRead = in.read(buff)) != -1) {
- bao.write(buff, 0, bytesRead);
- }
- in.close();
- bao.close();
+ while ((bytesRead = in.read(buff)) != -1) {
+ bao.write(buff, 0, bytesRead);
+ }
+ in.close();
+ bao.close();
- byte[] data = bao.toByteArray();
+ byte[] data = bao.toByteArray();
+ return data;
+ }
+
+ @Test
+ public void testReadGeneVariantsWithAminoAcidChange() throws Exception {
+ try {
+ File f = new File("testFiles/coloring/gene_variants_aa_change.txt");
+ byte[] data = fileToByteArray(f);
ByteArrayInputStream bin = new ByteArrayInputStream(data);
@@ -151,21 +164,7 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
public void testReadGeneVariantsWithNewNamingSchema() throws Exception {
try {
File f = new File("testFiles/coloring/gene_variants_new_naming.txt");
- InputStream in = new FileInputStream(f);
-
- byte[] buff = new byte[8000];
-
- int bytesRead = 0;
-
- ByteArrayOutputStream bao = new ByteArrayOutputStream();
-
- while ((bytesRead = in.read(buff)) != -1) {
- bao.write(buff, 0, bytesRead);
- }
- in.close();
- bao.close();
-
- byte[] data = bao.toByteArray();
+ byte[] data = fileToByteArray(f);
ByteArrayInputStream bin = new ByteArrayInputStream(data);
@@ -185,21 +184,7 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
public void testReadGeneVariantsSchemaWithAF() throws Exception {
try {
File f = new File("testFiles/coloring/gene_variants_all_freq.txt");
- InputStream in = new FileInputStream(f);
-
- byte[] buff = new byte[8000];
-
- int bytesRead = 0;
-
- ByteArrayOutputStream bao = new ByteArrayOutputStream();
-
- while ((bytesRead = in.read(buff)) != -1) {
- bao.write(buff, 0, bytesRead);
- }
- in.close();
- bao.close();
-
- byte[] data = bao.toByteArray();
+ byte[] data = fileToByteArray(f);
ByteArrayInputStream bin = new ByteArrayInputStream(data);
diff --git a/service/testFiles/coloring/gene_variants_id.txt b/service/testFiles/coloring/gene_variants_id.txt
new file mode 100644
index 0000000000..d2ee602490
--- /dev/null
+++ b/service/testFiles/coloring/gene_variants_id.txt
@@ -0,0 +1,5 @@
+#TYPE=GENETIC_VARIANT
+#GENOME_TYPE=UCSC
+#GENOME_VERSION=hg38
+position original_dna alternative_dna Entrez gene description color contig
+10146 AC A 123456 upstream #ff0000 chr1
--
GitLab