Mercurial > repos > gga > apollo_export

annotate list_organisms.py @ 14:0d4234488bd0 draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 7f274d9deece87f6837ffb0a22d9231671be4542"
author gga
date Wed, 19 Aug 2020 06:55:33 -0400
parents c3b5bc8b4080
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b4a85d0c85b8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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1 #!/usr/bin/env python
b4a85d0c85b8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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2 from __future__ import print_function
b4a85d0c85b8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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b4a85d0c85b8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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4 import argparse
b4a85d0c85b8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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5 import json
b4a85d0c85b8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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c3b5bc8b4080 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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7 from apollo import accessible_organisms
c3b5bc8b4080 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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c3b5bc8b4080 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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9 from arrow.apollo import get_apollo_instance
c3b5bc8b4080 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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c3b5bc8b4080 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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11 from webapollo import UserObj, handle_credentials
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b4a85d0c85b8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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13 if __name__ == '__main__':
b4a85d0c85b8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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14 parser = argparse.ArgumentParser(description='List all organisms available in an Apollo instance')
b4a85d0c85b8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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15 parser.add_argument('email', help='User Email')
b4a85d0c85b8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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16 args = parser.parse_args()
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c3b5bc8b4080 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
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18 wa = get_apollo_instance()
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20 gx_user = UserObj(**wa.users._assert_or_create_user(args.email))
c3b5bc8b4080 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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21 handle_credentials(gx_user)
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23 all_orgs = wa.organisms.get_organisms()
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b4a85d0c85b8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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25 orgs = accessible_organisms(gx_user, all_orgs)
b4a85d0c85b8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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b4a85d0c85b8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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27 print(json.dumps(orgs, indent=2))