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