Mercurial > repos > gga > apollo_list_organism
comparison json2iframe.py @ 9:f26ac3b582e1 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 49fe23e3fb330234900946352fbc3a86deeeb639
| author | gga |
|---|---|
| date | Mon, 29 Jul 2019 10:10:25 -0400 |
| parents | 1f2e360f7554 |
| children | 1cab73e6bf13 |
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| 8:2c749ed310da | 9:f26ac3b582e1 |
|---|---|
| 8 if __name__ == '__main__': | 8 if __name__ == '__main__': |
| 9 parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services') | 9 parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services') |
| 10 parser.add_argument('apollo', help='Complete Apollo URL') | 10 parser.add_argument('apollo', help='Complete Apollo URL') |
| 11 parser.add_argument('json', type=argparse.FileType("r"), help='JSON Data') | 11 parser.add_argument('json', type=argparse.FileType("r"), help='JSON Data') |
| 12 parser.add_argument('external_apollo_url') | 12 parser.add_argument('external_apollo_url') |
| 13 parser.add_argument('--tracklist', action='store_true') | |
| 13 | 14 |
| 14 args = parser.parse_args() | 15 args = parser.parse_args() |
| 15 | 16 |
| 16 # https://fqdn/apollo/annotator/loadLink?loc=NC_005880:0..148317&organism=326&tracks= | 17 # https://fqdn/apollo/annotator/loadLink?loc=NC_005880:0..148317&organism=326 |
| 17 data = json.load(args.json) | 18 data = json.load(args.json) |
| 18 | 19 |
| 19 # This is base64 encoded to get past the toolshed's filters. | 20 # This is base64 encoded to get past the toolshed's filters. |
| 20 HTML_TPL = """ | 21 HTML_TPL = """ |
| 21 <html> | 22 <html> |
| 22 <head> | 23 <head> |
| 23 <title>Embedded Apollo Access</title> | 24 <title>Embedded Apollo Access</title> |
| 24 <style type="text/css">body {{margin: 0;}} iframe {{border: 0;width: 100%;height: 100%}}</style> | 25 <style type="text/css">body {{margin: 0;}} iframe {{border: 0;width: 100%;height: 100%}}</style> |
| 25 </head> | 26 </head> |
| 26 <body> | 27 <body> |
| 27 <iframe src="{base_url}/annotator/loadLink?loc={chrom}&organism={orgId}&tracklist=1"></iframe> | 28 <iframe src="{base_url}/annotator/loadLink?loc={chrom}&organism={orgId}{tracklist}"></iframe> |
| 28 </body> | 29 </body> |
| 29 </html> | 30 </html> |
| 30 """ | 31 """ |
| 31 | 32 |
| 32 print(HTML_TPL.format(base_url=args.external_apollo_url, chrom="", orgId=data[0]['id'])) | 33 print(HTML_TPL.format(base_url=args.external_apollo_url, chrom="", orgId=data[0]['id'], tracklist='&tracklist=1' if args.tracklist else '')) |