From 67c456b07377f6229374d412696e8fefa87148a2 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 15 Jan 2018 19:07:54 +0100
Subject: [PATCH] chemical contains synonyms
---
.../lcsb/mapviewer/annotation/data/Chemical.java | 4 ++++
.../annotation/services/ChemicalParser.java | 13 ++++++++++++-
2 files changed, 16 insertions(+), 1 deletion(-)
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/data/Chemical.java b/annotation/src/main/java/lcsb/mapviewer/annotation/data/Chemical.java
index 651cecb2df..89186f8b2c 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/Chemical.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/Chemical.java
@@ -304,4 +304,8 @@ public class Chemical implements Serializable, TargettingStructure {
return getInferenceNetwork();
}
+ public void addSynonyms(List<String> synonyms) {
+ this.synonyms.addAll(synonyms);
+ }
+
}
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 c6d51b90ab..20f97ebc08 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalParser.java
@@ -26,6 +26,7 @@ import lcsb.mapviewer.annotation.cache.WebPageDownloader;
import lcsb.mapviewer.annotation.cache.XmlSerializer;
import lcsb.mapviewer.annotation.data.Chemical;
import lcsb.mapviewer.annotation.data.ChemicalDirectEvidence;
+import lcsb.mapviewer.annotation.data.MeSH;
import lcsb.mapviewer.annotation.data.Target;
import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
@@ -168,6 +169,9 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
@Autowired
private ProjectDao projectDao;
+ @Autowired
+ private MeSHParser meshParser;
+
/**
*
*/
@@ -349,7 +353,7 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
}
List<String> list = getSuggestedQueryListWithoutCache(project, diseaseId);
result = StringUtils.join(list, "\n");
- } else {
+ } else {
result = super.refreshCacheQuery(query);
}
} else {
@@ -396,8 +400,15 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
result = getChemicalFromChemicalLine(lineValues, chemID);
}
}
+ if (result != null) {
+ MeSH mesh = meshParser.getMeSH(result.getChemicalId());
+ result.addSynonyms(mesh.getSynonyms());
+ }
+
} catch (IOException e) {
throw new ChemicalSearchException("ctdbase service unavailable", e);
+ } catch (AnnotatorException e) {
+ throw new ChemicalSearchException("problem with accessing mesh db", e);
}
// put them in cache
--
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