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annotate write_db_summary.py @ 0:35bcefc9176b draft default tip

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planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit dbd9af1e941e35ec9ca2a9f75af02edea67a5981
author sanbi-uwc
date Thu, 15 Jun 2017 07:41:38 -0400
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35bcefc9176b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit dbd9af1e941e35ec9ca2a9f75af02edea67a5981
sanbi-uwc
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diff changeset
1 #!/usr/bin/env python
35bcefc9176b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit dbd9af1e941e35ec9ca2a9f75af02edea67a5981
sanbi-uwc
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diff changeset
2 from __future__ import print_function
35bcefc9176b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit dbd9af1e941e35ec9ca2a9f75af02edea67a5981
sanbi-uwc
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35bcefc9176b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit dbd9af1e941e35ec9ca2a9f75af02edea67a5981
sanbi-uwc
parents:
diff changeset
4 import argparse
35bcefc9176b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit dbd9af1e941e35ec9ca2a9f75af02edea67a5981
sanbi-uwc
parents:
diff changeset
5 import os
35bcefc9176b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit dbd9af1e941e35ec9ca2a9f75af02edea67a5981
sanbi-uwc
parents:
diff changeset
6 import os.path
35bcefc9176b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit dbd9af1e941e35ec9ca2a9f75af02edea67a5981
sanbi-uwc
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35bcefc9176b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit dbd9af1e941e35ec9ca2a9f75af02edea67a5981
sanbi-uwc
parents:
diff changeset
8 parser = argparse.ArgumentParser(
35bcefc9176b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit dbd9af1e941e35ec9ca2a9f75af02edea67a5981
sanbi-uwc
parents:
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9 description="Write HTML summary from neostore datatype")
35bcefc9176b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit dbd9af1e941e35ec9ca2a9f75af02edea67a5981
sanbi-uwc
parents:
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10 parser.add_argument('basepath')
35bcefc9176b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit dbd9af1e941e35ec9ca2a9f75af02edea67a5981
sanbi-uwc
parents:
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11 parser.add_argument('label')
35bcefc9176b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit dbd9af1e941e35ec9ca2a9f75af02edea67a5981
sanbi-uwc
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12
35bcefc9176b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit dbd9af1e941e35ec9ca2a9f75af02edea67a5981
sanbi-uwc
parents:
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13 args = parser.parse_args()
35bcefc9176b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit dbd9af1e941e35ec9ca2a9f75af02edea67a5981
sanbi-uwc
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35bcefc9176b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit dbd9af1e941e35ec9ca2a9f75af02edea67a5981
sanbi-uwc
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15 output = """<html><head><title>Files for Composite Dataset ({})</title></head>
35bcefc9176b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit dbd9af1e941e35ec9ca2a9f75af02edea67a5981
sanbi-uwc
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16 <p/>This composite dataset is composed of
35bcefc9176b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit dbd9af1e941e35ec9ca2a9f75af02edea67a5981
sanbi-uwc
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17 the following files:<p/><ul>\n""".format(args.label)
35bcefc9176b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit dbd9af1e941e35ec9ca2a9f75af02edea67a5981
sanbi-uwc
parents:
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18 db_path = args.basepath + '/neo4jdb/databases/graph.db'
35bcefc9176b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit dbd9af1e941e35ec9ca2a9f75af02edea67a5981
sanbi-uwc
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19 for filename in os.listdir(db_path):
35bcefc9176b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit dbd9af1e941e35ec9ca2a9f75af02edea67a5981
sanbi-uwc
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20 if filename.startswith('.'):
35bcefc9176b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit dbd9af1e941e35ec9ca2a9f75af02edea67a5981
sanbi-uwc
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21 continue
35bcefc9176b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit dbd9af1e941e35ec9ca2a9f75af02edea67a5981
sanbi-uwc
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22 path = db_path + '/' + filename
35bcefc9176b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit dbd9af1e941e35ec9ca2a9f75af02edea67a5981
sanbi-uwc
parents:
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23 if os.path.isdir(path):
35bcefc9176b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit dbd9af1e941e35ec9ca2a9f75af02edea67a5981
sanbi-uwc
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24 continue
35bcefc9176b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit dbd9af1e941e35ec9ca2a9f75af02edea67a5981
sanbi-uwc
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25 output += "<li>{}</li>\n".format(filename)
35bcefc9176b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit dbd9af1e941e35ec9ca2a9f75af02edea67a5981
sanbi-uwc
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26 output += '</ul></html>\b'
35bcefc9176b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit dbd9af1e941e35ec9ca2a9f75af02edea67a5981
sanbi-uwc
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27 print(output)