# HG changeset patch
# User nathandunn
# Date 1512250894 18000
# Node ID d40860663861323595ccae6d24dda36ea99b1e55
# Parent 88e1bd76b069f1c0bec24567e91f0c4fb3486055
planemo upload commit 1a35e82b210719d58263c618f9a67801db26d391
diff -r 88e1bd76b069 -r d40860663861 bioentityset-overrepresentation.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bioentityset-overrepresentation.xml Sat Dec 02 16:41:34 2017 -0500
@@ -0,0 +1,69 @@
+
+
+ macros.xml
+
+
+ $output
+*#
+#set $subject_string = ''
+#set $subject = $subject.replace(' ', '')
+#set $subject = $subject.replace(',', ' ')
+#for $word in $subject.split(' ')
+#set $subject_string += '&subject='+str($word)
+#end for
+
+#set $background_string = ''
+#set $background = $background.replace(' ', '')
+#set $background = $background.replace(',', ' ')
+#for $word in $background.split(' ')
+#set $background_string += '&background='+str($word)
+#end for
+
+curl --silent -X GET --header 'Accept: application/json' 'https://api-dev.monarchinitiative.org/api/bioentityset/overrepresentation/?object_category=$object_category$subject_string&background=$background_string&ontology=$ontology&subject_category=$subject_category&taxon=$taxon&object_category=$object_category&max_p_value=$max_p_value' > $output
+ ]]>
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diff -r 88e1bd76b069 -r d40860663861 test-data/associations-for-variant.json
--- a/test-data/associations-for-variant.json Thu Jun 22 15:28:43 2017 -0400
+++ b/test-data/associations-for-variant.json Sat Dec 02 16:41:34 2017 -0500
@@ -1,1 +1,1 @@
-{"associations": [{"subject_extension": null, "slim": null, "publications": null, "object": {"xrefs": null, "taxon": {"label": "Danio rerio", "id": "NCBITaxon:7955"}, "types": null, "categories": null, "replaced_by": null, "synonyms": null, "label": "fgf8a/fgf8a; shha/shha [n.s.]", "deprecated": null, "id": "ZFIN:ZDB-FISH-150901-25704", "description": null, "consider": null}, "id": "3fe46d0c-e666-48fd-a95e-7b3591d40f57", "type": null, "evidence_graph": {"nodes": [{"lbl": "tbx392", "id": "ZFIN:ZDB-ALT-010427-8"}, {"lbl": "fgf8a/fgf8a; shha/shha", "id": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8-ZDB-ALT-010427-8-_ZDB-GENE-990415-72-ZDB-ALT-980203-1091-ZDB-ALT-980203-1091"}, {"lbl": "shha", "id": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8"}, {"lbl": "shha/shha", "id": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8-ZDB-ALT-010427-8"}, {"lbl": "fgf8a/fgf8a; shha/shha [n.s.]", "id": "ZFIN:ZDB-FISH-150901-25704"}], "edges": [{"sub": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8", "pred": "GENO:0000382", "obj": "ZFIN:ZDB-ALT-010427-8"}, {"sub": "ZFIN:ZDB-FISH-150901-25704", "pred": "GENO:0000382", "obj": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8-ZDB-ALT-010427-8-_ZDB-GENE-990415-72-ZDB-ALT-980203-1091-ZDB-ALT-980203-1091"}, {"sub": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8-ZDB-ALT-010427-8", "pred": "GENO:0000382", "obj": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8"}, {"sub": "ZFIN:ZDB-FISH-150901-25704", "pred": "GENO:0000382", "obj": "ZFIN:ZDB-FISH-150901-25704"}, {"sub": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8-ZDB-ALT-010427-8-_ZDB-GENE-990415-72-ZDB-ALT-980203-1091-ZDB-ALT-980203-1091", "pred": "GENO:0000382", "obj": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8-ZDB-ALT-010427-8"}]}, "subject": {"xrefs": null, "taxon": {"label": null, "id": null}, "types": null, "categories": null, "replaced_by": null, "synonyms": null, "label": "tbx392", "deprecated": null, "id": "ZFIN:ZDB-ALT-010427-8", "description": null, "consider": null}, "provided_by": ["http://data.monarchinitiative.org/ttl/zfin.ttl"], "relation": {"types": null, "categories": null, "replaced_by": null, "synonyms": null, "label": null, "deprecated": null, "id": null, "description": null, "consider": null}, "qualifiers": null, "object_extension": null, "evidence_types": null}, {"subject_extension": null, "slim": null, "publications": null, "object": {"xrefs": null, "taxon": {"label": "Danio rerio", "id": "NCBITaxon:7955"}, "types": null, "categories": null, "replaced_by": null, "synonyms": null, "label": "shha/shha [n.s.]; myog", "deprecated": null, "id": "ZFIN:ZDB-FISH-150901-19342", "description": null, "consider": null}, "id": "ea094031-5086-478a-baf1-3297c258a429", "type": null, "evidence_graph": {"nodes": [{"lbl": "tbx392", "id": "ZFIN:ZDB-ALT-010427-8"}, {"lbl": "shha/shha [n.s.]; myog", "id": "ZFIN:ZDB-FISH-150901-19342"}, {"lbl": "shha", "id": 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null, "synonyms": null, "label": "tbx392", "deprecated": null, "id": "ZFIN:ZDB-ALT-010427-8", "description": null, "consider": null}, "provided_by": ["http://data.monarchinitiative.org/ttl/zfin.ttl"], "relation": {"types": null, "categories": null, "replaced_by": null, "synonyms": null, "label": null, "deprecated": null, "id": null, "description": null, "consider": null}, "qualifiers": null, "object_extension": null, "evidence_types": null}, {"subject_extension": null, "slim": null, "publications": null, "object": {"xrefs": null, "taxon": {"label": "Danio rerio", "id": "NCBITaxon:7955"}, "types": null, "categories": null, "replaced_by": null, "synonyms": null, "label": "ndr2/ndr2; shha/shha [n.s.]", "deprecated": null, "id": "ZFIN:ZDB-FISH-150901-12204", "description": null, "consider": null}, "id": "c0883e4f-2925-478f-bfae-621a2164fff5", "type": null, "evidence_graph": {"nodes": [{"lbl": "ndr2/ndr2; shha/shha [n.s.]", "id": "ZFIN:ZDB-FISH-150901-12204"}, {"lbl": "tbx392", "id": 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