From fc92b70f2cc8440a11442c7a1d733bc2cabdb1df Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 17 Jan 2018 17:26:53 +0100
Subject: [PATCH] chemical connector uses api over ssl and due to change of
http response status error handling slightly changed
---
.../annotation/services/ChemicalParser.java | 12 ++++++------
.../annotation/services/ChemicalParserTest.java | 2 +-
2 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalParser.java
index df03d1175c..014346e376 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalParser.java
@@ -57,18 +57,18 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
/**
* Homepage of drugbank.
*/
- static final String URL = "http://ctdbase.org/";
+ static final String URL = "https://ctdbase.org/";
/**
* URL to get a list of chemicals by disease id.
*/
- public static final String DISEASE_URL = "http://ctdbase.org/detail.go?6578706f7274=1&d-1332398-e=5&view=chem&"
+ public static final String DISEASE_URL = "https://ctdbase.org/detail.go?6578706f7274=1&d-1332398-e=5&view=chem&"
+ "type=disease&acc=MESH%3A";
/**
* URL to get a list of chemicals by gene id.
*/
- public static final String DISEASE_GENE_URL = "http://ctdbase.org/detail.go?slimTerm=all&6578706f7274=1&qid=3464576&"
+ public static final String DISEASE_GENE_URL = "https://ctdbase.org/detail.go?slimTerm=all&6578706f7274=1&qid=3464576&"
+ "d-1332398-e=5&view=disease&type=gene&assnType=curated&acc=";
/**
@@ -218,7 +218,7 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
}
}
- } catch (FileNotFoundException e) {
+ } catch (WrongResponseCodeIOException e) {
// it means that there are no results for this query
} catch (IOException e) {
throw new ChemicalSearchException("ctdbase service unavailable", e);
@@ -447,14 +447,14 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
if (entrez == null) {
invalidHgnc.add(md);
} else {
- String query = "http://ctdbase.org/detail.go?type=gene&view=ixn&chemAcc=" + chemID.getResource() + "&acc=" + entrez.getResource();
+ String query = "https://ctdbase.org/detail.go?type=gene&view=ixn&chemAcc=" + chemID.getResource() + "&acc=" + entrez.getResource();
String referencesPage = getWebPageContent(query);
Matcher matcher = pattern.matcher(referencesPage);
while (matcher.find()) {
idx.add(matcher.group(1));
}
for (String string : idx) {
- String query2 = "http://ctdbase.org/detail.go?6578706f7274=1&d-1340579-e=5&type=relationship&ixnId=" + string;
+ String query2 = "https://ctdbase.org/detail.go?6578706f7274=1&d-1340579-e=5&type=relationship&ixnId=" + string;
String referencesPage2 = getWebPageContent(query2);
String[] lines = referencesPage2.split("\n");
for (int i = 1; i < lines.length; i++) {
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java
index f03eb92e17..38fa0393ed 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java
@@ -551,7 +551,7 @@ public class ChemicalParserTest extends AnnotationTestFunctions {
// remove info about single publication from cache (so we will have to
// download it)
chemicalParser.getCache().removeByQuery(
- "http://ctdbase.org/detail.go?6578706f7274=1&d-1340579-e=5&type=relationship&ixnId=4802115", chemicalParser.getCacheType());
+ "https://ctdbase.org/detail.go?6578706f7274=1&d-1340579-e=5&type=relationship&ixnId=4802115", chemicalParser.getCacheType());
// disallow to use cache for first query (it will be directly about drug),
// so parser will have to parse results taking data from cache (or
--
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