# HG changeset patch
# User nathandunn
# Date 1498660028 14400
# Node ID 66ece4fd024f50cfcc390c4ddf11b4350fdf1990
# Parent 028a3ffc17b45be351e0c9654cee1fce1c729f0a
planemo upload commit 20eeb677e99874173440a365f2db04e315e7ebed
diff -r 028a3ffc17b4 -r 66ece4fd024f README.md
--- a/README.md Fri Jun 23 15:04:12 2017 -0400
+++ b/README.md Wed Jun 28 10:27:08 2017 -0400
@@ -1,12 +1,13 @@
# Biolink-planteome
[![Build Status](https://travis-ci.org/nathandunn/biolink-planteome.svg?branch=master)](https://travis-ci.org/nathandunn/biolink-planteome)
-[![DOI](https://zenodo.org/badge/94568425.svg)](https://zenodo.org/badge/latestdoi/94568425)
+[![DOI](https://zenodo.org/badge/94568147.svg)](https://zenodo.org/badge/latestdoi/94568147)
+
Wrapper around the [planteome Iniatitive Biolink API](https://biolink.planteome.org/api/).
-Available on the [Galaxy Toolshed](https://toolshed.g2.bx.psu.edu/repository?repository_id=c46e72ccdb506940).
+Available on the [Galaxy Toolshed](https://toolshed.g2.bx.psu.edu/repository?repository_id=6a4f55387fe48fbd).
The [planteome Intiative](http://planteome.org/) is a warehouse that integrates, aligns, and re-distributes cross-species gene, genotype, variant, disease, and phenotype data using ontology associations.
diff -r 028a3ffc17b4 -r 66ece4fd024f associations.xml
--- a/associations.xml Fri Jun 23 15:04:12 2017 -0400
+++ b/associations.xml Wed Jun 28 10:27:08 2017 -0400
@@ -5,18 +5,18 @@
$output
+ curl --silent -X GET --header 'Accept: application/json' 'http://biolink.planteome.org/api/association/$type/?rows=$rows&fetch_objects=true&subject=$subject' > $output
#else if $type == 'from'
- curl --silent -X GET --header 'Accept: application/json' 'http://biolink.planteome.org/apiapi/association/$type/$subject?rows=$rows&fetch_objects=true' > $output
+ curl --silent -X GET --header 'Accept: application/json' 'http://biolink.planteome.org/api/association/$type/$subject?rows=$rows&fetch_objects=true' > $output
#else if $type == 'to'
- curl --silent -X GET --header 'Accept: application/json' 'http://biolink.planteome.org/apiapi/association/$type/$object?rows=$rows&fetch_objects=true' > $output
+ curl --silent -X GET --header 'Accept: application/json' 'http://biolink.planteome.org/api/association/$type/$object?rows=$rows&fetch_objects=true' > $output
#else if $type == 'between'
- curl --silent -X GET --header 'Accept: application/json' 'http://biolink.planteome.org/apiapi/association/$type/$subject/$object?rows=$rows&fetch_objects=true' > $output
+ curl --silent -X GET --header 'Accept: application/json' 'http://biolink.planteome.org/api/association/$type/$subject/$object?rows=$rows&fetch_objects=true' > $output
#end if
]]>
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diff -r 028a3ffc17b4 -r 66ece4fd024f bioentity-associations.xml
--- a/bioentity-associations.xml Fri Jun 23 15:04:12 2017 -0400
+++ b/bioentity-associations.xml Wed Jun 28 10:27:08 2017 -0400
@@ -4,16 +4,16 @@
$output
+curl --silent -X GET --header 'Accept: application/json' 'http://biolink.planteome.org/api/bioentity/$input/associations/?rows=$rows&fetch_objects=true' > $output
]]>
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diff -r 028a3ffc17b4 -r 66ece4fd024f bulk-operations.xml
--- a/bulk-operations.xml Fri Jun 23 15:04:12 2017 -0400
+++ b/bulk-operations.xml Wed Jun 28 10:27:08 2017 -0400
@@ -4,17 +4,17 @@
$output
+curl --silent -X GET --header 'Accept: application/json' 'http://biolink.planteome.org/api/mart/$association/$object_category/$taxon?rows=$rows&fetch_objects=true' > $output
]]>
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diff -r 028a3ffc17b4 -r 66ece4fd024f disease-associations.xml
--- a/disease-associations.xml Fri Jun 23 15:04:12 2017 -0400
+++ b/disease-associations.xml Wed Jun 28 10:27:08 2017 -0400
@@ -4,10 +4,10 @@
$output
+curl --silent -X GET --header 'Accept: application/json' 'http://biolink.planteome.org/api/bioentity/disease/$input/$association/?rows=$rows&fetch_objects=true' > $output
]]>
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diff -r 028a3ffc17b4 -r 66ece4fd024f gene-associations.xml
--- a/gene-associations.xml Fri Jun 23 15:04:12 2017 -0400
+++ b/gene-associations.xml Wed Jun 28 10:27:08 2017 -0400
@@ -4,43 +4,43 @@
$output
+curl --silent -X GET --header 'Accept: application/json' 'http://biolink.planteome.org/api/bioentity/gene/$input/$association/?rows=$rows&fetch_objects=true' > $output
]]>
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diff -r 028a3ffc17b4 -r 66ece4fd024f genotype-associations.xml
--- a/genotype-associations.xml Fri Jun 23 15:04:12 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
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diff -r 028a3ffc17b4 -r 66ece4fd024f get-object.xml
--- a/get-object.xml Fri Jun 23 15:04:12 2017 -0400
+++ b/get-object.xml Wed Jun 28 10:27:08 2017 -0400
@@ -4,14 +4,14 @@
$output
+curl --silent -X GET --header 'Accept: application/json' 'http://biolink.planteome.org/api/bioentity/$type$input$associations?rows=$rows&fetch_objects=true' > $output
]]>
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diff -r 028a3ffc17b4 -r 66ece4fd024f macros.xml
--- a/macros.xml Fri Jun 23 15:04:12 2017 -0400
+++ b/macros.xml Wed Jun 28 10:27:08 2017 -0400
@@ -9,11 +9,11 @@
- doi:10.5281/zenodo.815635
+ doi:10.5281/zenodo.817595
diff -r 028a3ffc17b4 -r 66ece4fd024f phenotype-gene-associations.xml
--- a/phenotype-gene-associations.xml Fri Jun 23 15:04:12 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
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diff -r 028a3ffc17b4 -r 66ece4fd024f run_server.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/run_server.sh Wed Jun 28 10:27:08 2017 -0400
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+planemo s `cat tools.txt`
+
+
diff -r 028a3ffc17b4 -r 66ece4fd024f run_tests.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/run_tests.sh Wed Jun 28 10:27:08 2017 -0400
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+planemo t `cat tools.txt`
+
+
diff -r 028a3ffc17b4 -r 66ece4fd024f search-operations.xml
--- a/search-operations.xml Fri Jun 23 15:04:12 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,30 +0,0 @@
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diff -r 028a3ffc17b4 -r 66ece4fd024f substance-associations.xml
--- a/substance-associations.xml Fri Jun 23 15:04:12 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,39 +0,0 @@
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diff -r 028a3ffc17b4 -r 66ece4fd024f test-data/associations-for-variant.json
--- a/test-data/associations-for-variant.json Fri Jun 23 15:04:12 2017 -0400
+++ b/test-data/associations-for-variant.json Wed Jun 28 10:27:08 2017 -0400
@@ -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": ":.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": "shha/shha [n.s.]", "id": "ZFIN:ZDB-FISH-150901-6607"}], "edges": [{"sub": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8", "pred": "GENO:0000382", "obj": "ZFIN:ZDB-ALT-010427-8"}, {"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-150901-6607", "pred": "GENO:0000382", "obj": "ZFIN:ZDB-FISH-150901-6607"}, {"sub": "ZFIN:ZDB-FISH-150901-19342", "pred": "GENO:0000382", "obj": "ZFIN:ZDB-FISH-150901-6607"}, {"sub": "ZFIN:ZDB-FISH-150901-6607", "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": "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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