[2] | 1 | #!/usr/bin/env python |
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| 2 | |
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| 3 | # runs after the job (and after the default post-filter) |
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| 4 | import os |
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| 5 | from galaxy import eggs |
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| 6 | from galaxy import jobs |
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| 7 | from galaxy.tools.parameters import DataToolParameter |
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| 8 | # Older py compatibility |
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| 9 | try: |
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| 10 | set() |
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| 11 | except: |
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| 12 | from sets import Set as set |
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| 13 | |
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| 14 | def validate_input( trans, error_map, param_values, page_param_map ): |
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| 15 | dbkeys = set() |
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| 16 | data_param_names = set() |
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| 17 | data_params = 0 |
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| 18 | for name, param in page_param_map.iteritems(): |
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| 19 | if isinstance( param, DataToolParameter ): |
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| 20 | # for each dataset parameter |
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| 21 | if param_values.get(name, None) != None: |
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| 22 | dbkeys.add( param_values[name].dbkey ) |
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| 23 | data_params += 1 |
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| 24 | # check meta data |
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| 25 | try: |
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| 26 | param = param_values[name] |
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| 27 | startCol = int( param.metadata.startCol ) |
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| 28 | endCol = int( param.metadata.endCol ) |
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| 29 | chromCol = int( param.metadata.chromCol ) |
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| 30 | if param.metadata.strandCol is not None: |
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| 31 | strandCol = int ( param.metadata.strandCol ) |
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| 32 | else: |
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| 33 | strandCol = 0 |
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| 34 | except: |
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| 35 | error_msg = "The attributes of this dataset are not properly set. " + \ |
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| 36 | "Click the pencil icon in the history item to set the chrom, start, end and strand columns." |
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| 37 | error_map[name] = error_msg |
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| 38 | data_param_names.add( name ) |
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| 39 | if len( dbkeys ) > 1: |
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| 40 | for name in data_param_names: |
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| 41 | error_map[name] = "All datasets must belong to same genomic build, " \ |
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| 42 | "this dataset is linked to build '%s'" % param_values[name].dbkey |
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| 43 | if data_params != len(data_param_names): |
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| 44 | for name in data_param_names: |
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| 45 | error_map[name] = "A dataset of the appropriate type is required" |
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