From 1b678cd3746aec8a9524fb0c1f4a79911ebc143f Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 10 Sep 2018 13:04:09 +0200
Subject: [PATCH] new implementation for resolving miriam resources fixed
---
.../annotation/services/MiriamConnector.java | 19 +++++--------------
1 file changed, 5 insertions(+), 14 deletions(-)
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnector.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnector.java
index 00b97432ce..af5982d3d0 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnector.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnector.java
@@ -1,14 +1,11 @@
package lcsb.mapviewer.annotation.services;
import java.io.IOException;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
import org.apache.log4j.Logger;
import org.hibernate.AnnotationException;
-
-import com.google.gson.Gson;
+import org.w3c.dom.Document;
+import org.w3c.dom.Node;
import lcsb.mapviewer.annotation.cache.CachableInterface;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
@@ -219,19 +216,13 @@ public final class MiriamConnector extends CachableInterface implements IExterna
*/
protected String getUrlString2(MiriamData md) throws AnnotationException {
try {
- String result = null;
String queryUri = md.getDataType().getUris().get(0) + ":" + md.getResource();
String query = "https://www.ebi.ac.uk/miriamws/main/rest/resolve/" + queryUri;
String page = getWebPageContent(query);
- Gson gson = new Gson();
-
- Map<?, ?> gsonObject = new HashMap<String, Object>();
- gsonObject = (Map<?, ?>) gson.fromJson(page, gsonObject.getClass());
- Object uris = gsonObject.get("uri");
- Map<?, ?> entry = (Map<?, ?>) ((List<?>) uris).get(0);
- result = (String) entry.get("$");
+ Document document = getXmlDocumentFromString(page);
+ Node uri = getNode("uri", document.getChildNodes());
+ return getNodeValue(uri);
- return result;
} catch (Exception e) {
throw new AnnotationException("Problem with accessing miriam REST API", e);
}
--
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