From 9d92a9260977ecee10f596fe40028bf5e22f68e5 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 22 Nov 2018 15:20:15 +0100
Subject: [PATCH] some drugs didn't have mechanism target defined
---
.../annotation/services/ChEMBLParser.java | 26 ++++++++++++-------
.../api/projects/drugs/DrugRestImplTest.java | 13 ++++++++++
2 files changed, 29 insertions(+), 10 deletions(-)
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 cedc92718e..ea67d90cda 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
@@ -153,6 +153,9 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
throw new InvalidArgumentException(
"Target must be of a type: " + MiriamType.CHEMBL_TARGET + ". But found: " + md.getDataType());
}
+ if (md.getResource().isEmpty()) {
+ throw new InvalidArgumentException("Invalid target id" + md);
+ }
try {
Target target = new Target();
target.setSource(md);
@@ -261,13 +264,13 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
}
/**
- * REturns list of targes for given drug.
+ * Returns list of targets for given drug.
*
* @param drugId
* identifier of a drug for which targets are looked
* @throws DrugSearchException
* thrown when there are problems with connection to ChEMBL database
- * @return list of targes for given drug
+ * @return list of targets for given drug
*/
List<Target> getTargetsByDrugId(MiriamData drugId) throws DrugSearchException {
if (!MiriamType.CHEMBL_COMPOUND.equals(drugId.getDataType())) {
@@ -275,8 +278,8 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
}
List<Target> targets = new ArrayList<>();
try {
-
- String page = getWebPageContent(TARGET_MECHANISM_BY_DRUG_ID_API_URL + drugId.getResource());
+ String url = TARGET_MECHANISM_BY_DRUG_ID_API_URL + drugId.getResource();
+ String page = getWebPageContent(url);
Document document = getXmlDocumentFromString(page);
Node response = getNode("response", document);
@@ -287,14 +290,17 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
if (node.getNodeType() == Node.ELEMENT_NODE) {
if (node.getNodeName().equalsIgnoreCase("mechanism")) {
Node chemblTargetIdNode = getNode("target_chembl_id", node);
- MiriamData targetMiriam = new MiriamData(MiriamType.CHEMBL_TARGET, chemblTargetIdNode.getTextContent());
+ String chemblTargetId = chemblTargetIdNode.getTextContent();
+ if (chemblTargetId != null && !chemblTargetId.isEmpty()) {
+ MiriamData targetMiriam = new MiriamData(MiriamType.CHEMBL_TARGET, chemblTargetId);
- Target target = getTargetFromId(targetMiriam);
- Node referenceNode = getNode("mechanism_refs", node);
+ Target target = getTargetFromId(targetMiriam);
+ Node referenceNode = getNode("mechanism_refs", node);
- Set<MiriamData> references = parseReferences(referenceNode);
- target.addReferences(references);
- targets.add(target);
+ Set<MiriamData> references = parseReferences(referenceNode);
+ target.addReferences(references);
+ targets.add(target);
+ }
}
}
}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/drugs/DrugRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/drugs/DrugRestImplTest.java
index 89e6026906..515b299b95 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/drugs/DrugRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/drugs/DrugRestImplTest.java
@@ -53,6 +53,19 @@ public class DrugRestImplTest extends RestTestFunctions {
throw e;
}
}
+ @Test
+ public void test() throws Exception {
+ try {
+ DrugRestImpl drugRestImpl = createMockProjectRest("testFiles/model/sample.xml");
+ Map<String, Object> result = drugRestImpl.getDrugsByQuery(token, "sample", "", "Picato").get(0);
+ assertNotNull(result);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
private DrugRestImpl createMockProjectRest(String string) throws Exception {
Model model = super.getModelForFile(string, true);
--
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