Merge branch '246-add-doi-in-miriam-types' into 'master'

Resolve "add doi in miriam types"

Closes #246

See merge request piotr.gawron/minerva!165

annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java

@@ -208,6 +208,21 @@ public class MiriamConnectorTest extends AnnotationTestFunctions {
     }
   }
 
+  @Test
+  public void testGetUrlForDoi() throws Exception {
+    try {
+      // exclude first cached value
+      MiriamData md = new MiriamData(MiriamType.DOI, "10.1038/npjsba.2016.20");
+
+      String url = miriamConnector.getUrlString(md);
+      assertNotNull(url);
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
   @Test
   public void testMiriamDataToUri() throws Exception {
     try {

annotation/src/test/resources/log4j.properties

@@ -14,6 +14,8 @@ log4j.appender.R.File=${catalina.home}/logs/MapViewer.log
 log4j.appender.R.layout=org.apache.log4j.PatternLayout
 log4j.appender.R.layout.ConversionPattern=%d %5p [%t] (%F:%L) - %m%n
 
+#Silence miriam debug logs 
+log4j.logger.uk.ac.ebi.miriam.lib=warn
 
 log4j.logger.org.springframework=warn
 log4j.logger.org.hibernate=warn

frontend-js/src/main/js/gui/leftPanel/GuiUtils.js

@@ -119,7 +119,8 @@ GuiUtils.prototype.createAnnotationLink = function (annotation, showType) {
     type = "PUBMED";
     name = article.getId();
   } else {
-    name = annotation.getResource();
+    //replace encoded parts of uri (like %2F - > "/")
+    name = decodeURIComponent(annotation.getResource());
     var miriamType = self.getConfiguration().getMiriamTypeByName(annotation.getType());
     if (miriamType === null) {
       logger.warn("Unknown miriam type: " + annotation.getType());

frontend-js/src/test/js/gui/leftPanel/GuiUtils-test.js

@@ -3,6 +3,7 @@
 require('../../mocha-config.js');
 
 var Alias = require('../../../../main/js/map/data/Alias');
+var Annotation = require('../../../../main/js/map/data/Annotation');
 var GuiUtils = require('../../../../main/js/gui/leftPanel/GuiUtils');
 
 var chai = require('chai');
@@ -11,7 +12,7 @@ var logger = require('../../logger');
 
 describe('GuiUtils', function () {
 
-  it('constructor', function() {
+  it('constructor', function () {
     var map = helper.createCustomMap();
     helper.createSearchDbOverlay(map);
 
@@ -21,19 +22,19 @@ describe('GuiUtils', function () {
 
   it('default', function () {
     var aliasObj = {
-      symbol : "S1_SYMBOL",
-      formerSymbols : [],
-      modelId : 15781,
-      synonyms : [ "syn44" ],
-      description : "DESCRIPTION",
-      type : "Simple molecule",
-      abbreviation : "ABBREVIATION",
-      name : "s1",
-      bounds : {
-        x : 170.0,
-        y : 171.5,
-        width : 70.0,
-        height : 25.0
+      symbol: "S1_SYMBOL",
+      formerSymbols: [],
+      modelId: 15781,
+      synonyms: ["syn44"],
+      description: "DESCRIPTION",
+      type: "Simple molecule",
+      abbreviation: "ABBREVIATION",
+      name: "s1",
+      bounds: {
+        x: 170.0,
+        y: 171.5,
+        width: 70.0,
+        height: 25.0
       },
       formula: "FORMULA",
       id: 380217,
@@ -152,5 +153,21 @@ describe('GuiUtils', function () {
       assert.ok(logger.getWarnings().length > 0);
     });
   });
+  describe('createAnnotationLink', function () {
+    it('with encoded part in resource', function () {
+      // noinspection SpellCheckingInspection
+      var annotation = new Annotation({
+        resource: "10.1038%2Fnpjsba.2016.20",
+        link: "http://doi.org/10.1038%2Fnpjsba.2016.20",
+        id: 1116748,
+        type: "DOI"
+      });
+      var guiUtils = new GuiUtils(helper.getConfiguration());
+      var link = guiUtils.createAnnotationLink(annotation);
+      assert.ok(link);
+      assert.equal(0, logger.getWarnings().length);
+      assert.ok(link.innerHTML.indexOf("%2F") < 0, "url contains encoded %2F part of id");
+    });
 
+  });
 });

web/src/main/webapp/WEB-INF/resources/log4j.properties

@@ -33,3 +33,6 @@ log4j.logger.lcsb.mapviewer.db.model.map.reaction.ReactionComparator=warn
 log4j.logger.lcsb.mapviewer.db.model.map.species.ProteinComparator=warn
 log4j.logger.lcsb.mapviewer.db.model.map.layout.alias.ComplexAliasComparator=warn
 log4j.logger.lcsb.mapviewer.db.model.map.Element=info
+
+#Silence miriam debug logs 
+log4j.logger.uk.ac.ebi.miriam.lib=warn