Mercurial > repos > gga > apollo_feat_from_gff3

comparison json2iframe.py @ 9:09dacc7c6a21 draft

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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 10:11:02 -0400
parents 5aa3bc8d0253
children 18217f8862ef
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8:922dd0b252c8 9:09dacc7c6a21
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 ''))