From fcaf43ab48eb6840e8665cca2031119d9156d581 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 1 Jul 2019 21:26:08 +0200
Subject: [PATCH] search for drugs with rna components didn't work
---
CHANGELOG | 2 ++
.../annotation/services/ChEMBLParser.java | 15 +++++++++------
.../annotation/services/ChEMBLParserTest.java | 13 +++++++++++++
3 files changed, 24 insertions(+), 6 deletions(-)
diff --git a/CHANGELOG b/CHANGELOG
index 3ceaad7be8..e7624beee3 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -3,6 +3,8 @@ minerva (13.1.1) stable; urgency=medium
* Bug fix: "Terms of Use" change to "Terms of Service" in all places (#843)
* Bug fix: upgrade to 13.1.0 crashed on machines where every element was
inside compartment (#856)
+ * Bug fix: searching for some drugs in chembl didn't provide any results even
+ though that data exists, for instance 'DORLIMOMAB ARITOX' (#842)
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 28 Jun 2019 17:00:00 +0200
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
index 9b7e329224..3a7519a5f3 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
@@ -256,12 +256,15 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
MiriamData result = null;
Node uniprotAccessionId = XmlParser.getNode("accession", targetComponent.getChildNodes());
if (uniprotAccessionId != null) {
- try {
- result = uniprotAnnotator
- .uniProtToHgnc(new MiriamData(MiriamType.UNIPROT, uniprotAccessionId.getTextContent()));
- result.setAnnotator(null);
- } catch (UniprotSearchException e) {
- throw new DrugSearchException(e);
+ String uniprotId = uniprotAccessionId.getTextContent();
+ if (uniprotId != null && !uniprotId.isEmpty()) {
+ try {
+ result = uniprotAnnotator
+ .uniProtToHgnc(new MiriamData(MiriamType.UNIPROT, uniprotId));
+ result.setAnnotator(null);
+ } catch (UniprotSearchException e) {
+ throw new DrugSearchException(e);
+ }
}
}
return result;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
index 0b4f0d4dd5..8fa920f651 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
@@ -273,6 +273,19 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
}
+ @Test
+ public void testGetTargetWithRnaComponent() throws Exception {
+ try {
+ Target test = chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "CHEMBL2363135"));
+
+ assertEquals(test.getSource().getResource(), "CHEMBL2363135");
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
@Test
public void testGetTargetFromInvalidId() throws Exception {
try {
--
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