Mercurial > repos > xuebing > sharplabtool
comparison tools/validation/validate.py @ 0:9071e359b9a3
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 #!/usr/bin/env python | |
| 2 | |
| 3 """ | |
| 4 Validate a dataset based on extension a metadata passed in on the | |
| 5 command line. Outputs a binhex'd representation of the exceptions. | |
| 6 | |
| 7 usage: %prog input output | |
| 8 -m, --metadata=N: base64 pickeled metadata | |
| 9 -x, --ext=N: extension as understood by galaxy | |
| 10 """ | |
| 11 | |
| 12 import pkg_resources; pkg_resources.require( "bx-python" ) | |
| 13 from bx.cookbook import doc_optparse | |
| 14 | |
| 15 from galaxy import model | |
| 16 from fileinput import FileInput | |
| 17 from galaxy import util | |
| 18 | |
| 19 def main(): | |
| 20 options, args = doc_optparse.parse( __doc__ ) | |
| 21 | |
| 22 try: | |
| 23 extension = options.ext | |
| 24 except: | |
| 25 doc_optparse.exception() | |
| 26 | |
| 27 # create datatype | |
| 28 data = model.Dataset( extension=extension, id=int( args[0] ) ) | |
| 29 data.file_path = "/home/ian/trunk/database/files/" | |
| 30 | |
| 31 if options.metadata: | |
| 32 data.metadata = util.string_to_object( options.metadata ) | |
| 33 | |
| 34 errors = data.datatype.validate( data ) | |
| 35 print util.object_to_string(errors) | |
| 36 | |
| 37 if __name__ == "__main__": | |
| 38 main() |