Fix instance data links

.gitignore

@@ -70,3 +70,4 @@ tramp
 
 ## Would rather not have the minimal java stuff pollute.
 *.class
+.idea

external/db-xrefs.yaml

@@ -3233,22 +3233,28 @@
   entity_types:
     - type_name: gene
       type_id: SO:0000704
-      id_syntax: (WP:CE[0-9]{5})|(WB(Gene|Var|RNAi|Transgene)[0-9]{8})
-      url_syntax: http://www.wormbase.org/db/gene/gene?name=[example_id]
+      id_syntax: (WB(Gene|Transgene)[0-9]{8})
+      url_syntax: http://www.wormbase.org/get?name=[example_id]&class=Gene
       example_id: WB:WBGene00003001
-      example_url: http://www.wormbase.org/db/get?class=Gene;name=WBGene00003001
+      example_url: http://www.wormbase.org/get?name=WBGene00003001&class=Gene
+    - type_name: RNAi
+      type_id: SO:0000337
+      id_syntax: (WBRNAi[0-9]{8})
+      url_syntax: http://www.wormbase.org/get?name=[example_id]&class=RNAi
+      example_id: WB:WBRNAi00061231
+      example_url: http://www.wormbase.org/db/get?name=WBRNAi00061231;class=RNAi
     - type_name: variation
       type_id: VariO:0001
-      id_syntax: (WP:CE[0-9]{5})|(WB(Gene|Var|RNAi|Transgene)[0-9]{8})
-      url_syntax: http://www.wormbase.org/db/gene/gene?name=[example_id]
-      example_id: WB:WBGene00003001
-      example_url: http://www.wormbase.org/db/get?class=Gene;name=WBGene00003001
+      id_syntax: (WBVar[0-9]{8})
+      url_syntax: http://www.wormbase.org/get?name=[example_id]&class=Variation
+      example_id: WB:WBVar00249887
+      example_url: http://www.wormbase.org/get?name=WBVar00249887&class=Variation
     - type_name: protein
       type_id: PR:000000001
-      id_syntax: (WP:CE[0-9]{5})|(WB(Gene|Var|RNAi|Transgene)[0-9]{8})
-      url_syntax: http://www.wormbase.org/db/gene/gene?name=[example_id]
-      example_id: WB:WBGene00003001
-      example_url: http://www.wormbase.org/db/get?class=Gene;name=WBGene00003001
+      id_syntax: (WP:CE[0-9]{5})
+      url_syntax: http://www.wormbase.org/get?name=[example_id]&class=Protein
+      example_id: WP:CE01843&
+      example_url: http://www.wormbase.org/get?name=WP:CE01843&class=Protein
 - database: WB_REF
   name: WormBase database of nematode biology
   generic_urls:

javascript/npm/amigo2-instance-data/tests/linker.tests.js

@@ -47,7 +47,19 @@ describe('linker tests', function(){
     	assert.equal(l.url('XXXX:S000006169'),
     		     null,
     		     'linker: null');
-
+
+      assert.equal(l.url('WB:WBGene00003001'),
+		  'http://www.wormbase.org/get?name=WBGene00003001&class=Gene',
+		  'linker: wb gene');
+        assert.equal(l.url('WB:WBRNAi00061231'),
+            'http://www.wormbase.org/get?name=WBRNAi00061231&class=RNAi',
+            'linker: wb RNAi');
+      assert.equal(l.url('WB:WBVar00249887'),
+		  'http://www.wormbase.org/get?name=WBVar00249887&class=Variation',
+		   'linker: wb variation');
+      assert.equal(l.url('WP:CE01843'),
+		   'http://www.wormbase.org/get?name=WP:CE01843&class=Protein',
+	           'linker: wb protein');
     });
 
     it('internal edge cases', function(){
@@ -77,7 +89,7 @@ describe('linker tests', function(){
     	assert.isTrue(_ends_with(l.url('foo', 'grebe'), '/grebe'),
     		      'interlink: grebe not special (3): ' +
 		      l.url('foo', 'grebe'));
-	
+
     });
 
     it('synonyms', function(){
@@ -101,13 +113,13 @@ describe('linker tests', function(){
     	assert.isNull(l.url(null), 'null url');
     	assert.isNull(l.url(''), "'' url");
     	assert.isNull(l.anchor(null), 'null anchor');
-	
+
     	// And make sure that we can do things like PANTHER's double.
     	// url_syntax: http://www.geneontology.org/gene-associations/submission/paint/[example_id]/[example_id].txt
-    	assert.equal(l.url('PAINT_REF:PTHR10046'),
-    		     'http://www.geneontology.org/gene-associations/submission/paint/PTHR10046/PTHR10046.txt',
+    	assert.equal(l.url('PAINT_REF:10046'),
+    		     'http://www.pantherdb.org/panther/lookupId.jsp?id=PTHR10046',
     		     'linker: panther');
-	
+
     });
 
 });