From ec96ebc537b13cf8a74b2760f10b98456d163cbe Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 23 Nov 2018 09:57:00 +0100
Subject: [PATCH] proper recon element is used when annotating by name
---
.../services/annotators/ElementAnnotator.java | 5 +++
.../services/annotators/ReconAnnotator.java | 37 ++++++++++++++++++-
.../annotators/ReconAnnotatorTest.java | 15 ++++++++
.../lcsb/mapviewer/model/map/MiriamType.java | 9 ++++-
4 files changed, 63 insertions(+), 3 deletions(-)
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
index 520c32d4f3..909d574132 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
@@ -523,6 +523,11 @@ public abstract class ElementAnnotator extends CachableInterface {
element.addMiriamData(md);
}
+ protected void addRhea(BioEntity element, String value) {
+ MiriamData md = createMiriamData(MiriamType.RHEA, value);
+ element.addMiriamData(md);
+ }
+
/**
* Sets {@link BioEntity#getFormula()}.
*
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..110a1bab6d 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;
@@ -142,7 +143,7 @@ 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();
@@ -294,9 +295,18 @@ public class ReconAnnotator extends ElementAnnotator implements IExternalService
continue;
} else if (key.equals("casRegistry")) {
addCas(annotatedObject, value);
+ } else if (key.equals("rhea")) {
+ addRhea(annotatedObject, value);
} else if (key.equals("epa_id")) {
// for now we don't handle it
continue;
+ } else if (key.equals("biocyc")) {
+ // for now we don't handle it
+ continue;
+ } else if (key.equals("createdDate")) {
+ continue;
+ } else if (key.equals("updatedDate")) {
+ continue;
} else {
unknown = true;
}
@@ -316,6 +326,31 @@ public class ReconAnnotator extends ElementAnnotator implements IExternalService
}
}
+ private JsonObject getBestMatchForAbbreviation(String id, JsonArray asJsonArray) {
+ String match = null;
+ JsonObject result = null;
+ for (JsonElement element : asJsonArray) {
+ if (((JsonObject) element).get("abbreviation") != null) {
+ 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;
+ }
+ } else if (match == null) {
+ logger.warn("No abbreviation found for element: " + element);
+ result = (JsonObject) element;
+ }
+ }
+ return result;
+ }
+
+
@Override
public String getCommonName() {
return "Recon annotator";
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotatorTest.java
index 3fe3c8a56a..47f4ec4024 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotatorTest.java
@@ -189,6 +189,21 @@ public class ReconAnnotatorTest extends AnnotationTestFunctions {
}
}
+ @Test
+ public void testAnnotatingForOxygen() throws Exception {
+ try {
+ SimpleMolecule molecule = new SimpleMolecule("id");
+ molecule.setName("o2");
+ reconAnnotator.annotateElement(molecule);
+ assertTrue(molecule.getMiriamData().size() > 0);
+ assertEquals(0, getWarnings().size());
+ assertEquals("O2", molecule.getFormula());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testAnnotatingWithWhitespace() throws Exception {
try {
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
index 40a92c1e2d..ebd5dabeed 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
@@ -469,7 +469,7 @@ public enum MiriamType {
*/
VMH_METABOLITE("VMH metabolite", //
"https://vmh.uni.lu/", //
- "urn:miriam:vmhmetabolite", //
+ new String[] { "urn:miriam:vmhmetabolite", "http://identifiers.org/vmhmetabolite/" }, //
new Class<?>[] { Chemical.class }, "MIR:00000636"),
/**
@@ -477,7 +477,7 @@ public enum MiriamType {
*/
VMH_REACTION("VMH reaction", //
"https://vmh.uni.lu/", //
- "urn:miriam:vmhreaction", //
+ new String[] { "urn:miriam:vmhreaction", "http://identifiers.org/vmhreaction/" }, //
new Class<?>[] { Reaction.class }, "MIR:00000640"),
/**
@@ -741,6 +741,11 @@ public enum MiriamType {
foundType = type;
foundUri = uri;
}
+ } else if (miriamUri.startsWith(uri) && uri.endsWith("/")) {
+ if (uri.length() > foundUri.length()) {
+ foundType = type;
+ foundUri = uri;
+ }
}
}
}
--
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