diff --git a/.gitignore b/.gitignore index 6eedf7c2e..ddee16936 100644 --- a/.gitignore +++ b/.gitignore @@ -70,3 +70,4 @@ tramp ## Would rather not have the minimal java stuff pollute. *.class +.idea diff --git a/external/db-xrefs.yaml b/external/db-xrefs.yaml index 5a1d5b7a4..ea44d906f 100644 --- a/external/db-xrefs.yaml +++ b/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: diff --git a/javascript/npm/amigo2-instance-data/tests/linker.tests.js b/javascript/npm/amigo2-instance-data/tests/linker.tests.js index 53f8ac6c0..ef49c7f47 100644 --- a/javascript/npm/amigo2-instance-data/tests/linker.tests.js +++ b/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'); - + }); });