Mercurial > repos > stevecassidy > alveoimport

annotate alveo_get_item_list.py @ 14:a38315ecf593 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
author stevecassidy
date Wed, 01 Nov 2017 01:18:15 -0400
parents 56fda3d161f0
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
56fda3d161f0 planemo upload commit 0203cb3a0b40d9348674b2b098af805e2986abca-dirty
stevecassidy
parents:
diff changeset
1 from __future__ import print_function
56fda3d161f0 planemo upload commit 0203cb3a0b40d9348674b2b098af805e2986abca-dirty
stevecassidy
parents:
diff changeset
2 import argparse
56fda3d161f0 planemo upload commit 0203cb3a0b40d9348674b2b098af805e2986abca-dirty
stevecassidy
parents:
diff changeset
3 import pyalveo
56fda3d161f0 planemo upload commit 0203cb3a0b40d9348674b2b098af805e2986abca-dirty
stevecassidy
parents:
diff changeset
4 import sys
14
a38315ecf593 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
parents: 6
diff changeset
5 from util import API_URL
6
56fda3d161f0 planemo upload commit 0203cb3a0b40d9348674b2b098af805e2986abca-dirty
stevecassidy
parents:
diff changeset
6
56fda3d161f0 planemo upload commit 0203cb3a0b40d9348674b2b098af805e2986abca-dirty
stevecassidy
parents:
diff changeset
7
56fda3d161f0 planemo upload commit 0203cb3a0b40d9348674b2b098af805e2986abca-dirty
stevecassidy
parents:
diff changeset
8 def parser():
14
a38315ecf593 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
parents: 6
diff changeset
9 p = argparse.ArgumentParser(description="Downloads documents in an Alveo Item List")
a38315ecf593 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
parents: 6
diff changeset
10 p.add_argument('--api_key', required=True, action="store", type=str, help="Alveo API key")
a38315ecf593 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
parents: 6
diff changeset
11 p.add_argument('--item_list_url', required=True, action="store", type=str, help="Item List to download")
a38315ecf593 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
parents: 6
diff changeset
12 p.add_argument('--output', required=True, action="store", type=str, help="output file name")
a38315ecf593 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
parents: 6
diff changeset
13 return p.parse_args()
a38315ecf593 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
parents: 6
diff changeset
14
6
56fda3d161f0 planemo upload commit 0203cb3a0b40d9348674b2b098af805e2986abca-dirty
stevecassidy
parents:
diff changeset
15
56fda3d161f0 planemo upload commit 0203cb3a0b40d9348674b2b098af805e2986abca-dirty
stevecassidy
parents:
diff changeset
16 def main():
56fda3d161f0 planemo upload commit 0203cb3a0b40d9348674b2b098af805e2986abca-dirty
stevecassidy
parents:
diff changeset
17 args = parser()
56fda3d161f0 planemo upload commit 0203cb3a0b40d9348674b2b098af805e2986abca-dirty
stevecassidy
parents:
diff changeset
18 try:
56fda3d161f0 planemo upload commit 0203cb3a0b40d9348674b2b098af805e2986abca-dirty
stevecassidy
parents:
diff changeset
19 api_key = open(args.api_key, 'r').read().strip()
56fda3d161f0 planemo upload commit 0203cb3a0b40d9348674b2b098af805e2986abca-dirty
stevecassidy
parents:
diff changeset
20
56fda3d161f0 planemo upload commit 0203cb3a0b40d9348674b2b098af805e2986abca-dirty
stevecassidy
parents:
diff changeset
21 client = pyalveo.Client(api_key=api_key, api_url=API_URL, use_cache=False)
56fda3d161f0 planemo upload commit 0203cb3a0b40d9348674b2b098af805e2986abca-dirty
stevecassidy
parents:
diff changeset
22 item_list = client.get_item_list(args.item_list_url)
56fda3d161f0 planemo upload commit 0203cb3a0b40d9348674b2b098af805e2986abca-dirty
stevecassidy
parents:
diff changeset
23
56fda3d161f0 planemo upload commit 0203cb3a0b40d9348674b2b098af805e2986abca-dirty
stevecassidy
parents:
diff changeset
24 with open(args.output, 'w') as out:
56fda3d161f0 planemo upload commit 0203cb3a0b40d9348674b2b098af805e2986abca-dirty
stevecassidy
parents:
diff changeset
25 out.write("ItemURL\n")
56fda3d161f0 planemo upload commit 0203cb3a0b40d9348674b2b098af805e2986abca-dirty
stevecassidy
parents:
diff changeset
26 for item in item_list:
56fda3d161f0 planemo upload commit 0203cb3a0b40d9348674b2b098af805e2986abca-dirty
stevecassidy
parents:
diff changeset
27 out.write(item + "\n")
56fda3d161f0 planemo upload commit 0203cb3a0b40d9348674b2b098af805e2986abca-dirty
stevecassidy
parents:
diff changeset
28
56fda3d161f0 planemo upload commit 0203cb3a0b40d9348674b2b098af805e2986abca-dirty
stevecassidy
parents:
diff changeset
29 except pyalveo.APIError as e:
56fda3d161f0 planemo upload commit 0203cb3a0b40d9348674b2b098af805e2986abca-dirty
stevecassidy
parents:
diff changeset
30 print("ERROR: " + str(e), file=sys.stderr)
56fda3d161f0 planemo upload commit 0203cb3a0b40d9348674b2b098af805e2986abca-dirty
stevecassidy
parents:
diff changeset
31 sys.exit(1)
56fda3d161f0 planemo upload commit 0203cb3a0b40d9348674b2b098af805e2986abca-dirty
stevecassidy
parents:
diff changeset
32
14
a38315ecf593 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
parents: 6
diff changeset
33
6
56fda3d161f0 planemo upload commit 0203cb3a0b40d9348674b2b098af805e2986abca-dirty
stevecassidy
parents:
diff changeset
34 if __name__ == '__main__':
56fda3d161f0 planemo upload commit 0203cb3a0b40d9348674b2b098af805e2986abca-dirty
stevecassidy
parents:
diff changeset
35 main()