From 33a16f7d993580ce417392cc238d6a81f700b892 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 6 Sep 2018 18:20:50 +0200
Subject: [PATCH] recon returns unsorted data entries for query - fix on best
match
---
.../services/annotators/ReconAnnotator.java | 32 ++++++++++++++++++-
1 file changed, 31 insertions(+), 1 deletion(-)
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java
index 8cf0fd072e..731bd37306 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java
@@ -7,6 +7,7 @@ import java.util.Map.Entry;
import org.apache.log4j.Logger;
+import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
import com.google.gson.JsonParser;
@@ -133,6 +134,7 @@ public class ReconAnnotator extends ElementAnnotator implements IExternalService
logger.warn("Unknown class type: " + annotatedObject.getClass());
return;
}
+ logger.debug(url);
try {
String content = getWebPageContent(url);
@@ -142,7 +144,7 @@ public class ReconAnnotator extends ElementAnnotator implements IExternalService
JsonElement jelement = new JsonParser().parse(content);
JsonObject jobject = jelement.getAsJsonObject();
if (jobject.get("results").getAsJsonArray().size() > 0) {
- jobject = jobject.get("results").getAsJsonArray().get(0).getAsJsonObject();
+ jobject = getBestMatchForAbbreviation(id, jobject.get("results").getAsJsonArray());
for (Entry<String, JsonElement> entry : jobject.entrySet()) {
String key = entry.getKey();
@@ -297,6 +299,15 @@ public class ReconAnnotator extends ElementAnnotator implements IExternalService
} else if (key.equals("epa_id")) {
// for now we don't handle it
continue;
+ } else if (key.equals("createdDate")) {
+ // for now we don't handle it
+ continue;
+ } else if (key.equals("updatedDate")) {
+ // for now we don't handle it
+ continue;
+ } else if (key.equals("biocyc")) {
+ // for now we don't handle it
+ continue;
} else {
unknown = true;
}
@@ -316,6 +327,25 @@ public class ReconAnnotator extends ElementAnnotator implements IExternalService
}
}
+ private JsonObject getBestMatchForAbbreviation(String id, JsonArray asJsonArray) {
+ String match = null;
+ JsonObject result = null;
+ for (JsonElement element : asJsonArray) {
+ String objAbreviation = ((JsonObject) element).get("abbreviation").getAsString();
+ if (match == null) {
+ match = objAbreviation;
+ result = (JsonObject) element;
+ } else if (match.length() > objAbreviation.length()) {
+ match = objAbreviation;
+ result = (JsonObject) element;
+ } else if (id.equalsIgnoreCase(objAbreviation)) {
+ match = objAbreviation;
+ result = (JsonObject) element;
+ }
+ }
+ return result;
+ }
+
@Override
public String getCommonName() {
return "Recon annotator";
--
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