[2] | 1 | # runs after the job (and after the default post-filter) |
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| 2 | import os |
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| 3 | from galaxy import eggs |
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| 4 | from galaxy import jobs |
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| 5 | from galaxy.tools.parameters import DataToolParameter |
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| 6 | # Older py compatibility |
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| 7 | try: |
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| 8 | set() |
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| 9 | except: |
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| 10 | from sets import Set as set |
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| 11 | |
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| 12 | #def exec_before_process(app, inp_data, out_data, param_dict, tool=None): |
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| 13 | # """Sets the name of the data""" |
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| 14 | # dbkeys = sets.Set( [data.dbkey for data in inp_data.values() ] ) |
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| 15 | # if len(dbkeys) != 1: |
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| 16 | # raise Exception, '<p><font color="yellow">Both Queries must be from the same genome build</font></p>' |
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| 17 | |
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| 18 | def validate_input( trans, error_map, param_values, page_param_map ): |
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| 19 | dbkeys = set() |
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| 20 | data_param_names = set() |
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| 21 | data_params = 0 |
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| 22 | for name, param in page_param_map.iteritems(): |
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| 23 | if isinstance( param, DataToolParameter ): |
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| 24 | # for each dataset parameter |
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| 25 | if param_values.get(name, None) != None: |
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| 26 | dbkeys.add( param_values[name].dbkey ) |
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| 27 | data_params += 1 |
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| 28 | # check meta data |
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| 29 | try: |
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| 30 | param = param_values[name] |
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| 31 | if isinstance( param.datatype, trans.app.datatypes_registry.get_datatype_by_extension( 'gff' ).__class__ ): |
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| 32 | # TODO: currently cannot validate GFF inputs b/c they are not derived from interval. |
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| 33 | pass |
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| 34 | else: # Validate interval datatype. |
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| 35 | startCol = int( param.metadata.startCol ) |
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| 36 | endCol = int( param.metadata.endCol ) |
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| 37 | chromCol = int( param.metadata.chromCol ) |
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| 38 | if param.metadata.strandCol is not None: |
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| 39 | strandCol = int ( param.metadata.strandCol ) |
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| 40 | else: |
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| 41 | strandCol = 0 |
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| 42 | except: |
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| 43 | error_msg = "The attributes of this dataset are not properly set. " + \ |
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| 44 | "Click the pencil icon in the history item to set the chrom, start, end and strand columns." |
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| 45 | error_map[name] = error_msg |
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| 46 | data_param_names.add( name ) |
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| 47 | if len( dbkeys ) > 1: |
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| 48 | for name in data_param_names: |
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| 49 | error_map[name] = "All datasets must belong to same genomic build, " \ |
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| 50 | "this dataset is linked to build '%s'" % param_values[name].dbkey |
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| 51 | if data_params != len(data_param_names): |
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| 52 | for name in data_param_names: |
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| 53 | error_map[name] = "A dataset of the appropriate type is required" |
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| 54 | |
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| 55 | # Commented out by INS, 5/30/2007. What is the PURPOSE of this? |
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| 56 | def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None): |
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| 57 | """Verify the output data after each run""" |
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| 58 | items = out_data.items() |
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| 59 | |
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| 60 | for name, data in items: |
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| 61 | try: |
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| 62 | if stderr and len( stderr ) > 0: |
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| 63 | raise Exception( stderr ) |
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| 64 | |
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| 65 | except Exception, exc: |
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| 66 | data.blurb = jobs.JOB_ERROR |
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| 67 | data.state = jobs.JOB_ERROR |
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| 68 | |
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| 69 | ## def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None): |
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| 70 | ## pass |
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| 71 | |
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| 72 | |
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| 73 | def exec_after_merge(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None): |
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| 74 | exec_after_process( |
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| 75 | app, inp_data, out_data, param_dict, tool=tool, stdout=stdout, stderr=stderr) |
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| 76 | |
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| 77 | # strip strand column if clusters were merged |
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| 78 | items = out_data.items() |
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| 79 | for name, data in items: |
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| 80 | if param_dict['returntype'] == True: |
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| 81 | data.metadata.chromCol = 1 |
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| 82 | data.metadata.startCol = 2 |
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| 83 | data.metadata.endCol = 3 |
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| 84 | # merge always clobbers strand |
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| 85 | data.metadata.strandCol = None |
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| 86 | |
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| 87 | |
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| 88 | def exec_after_cluster(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None): |
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| 89 | exec_after_process( |
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| 90 | app, inp_data, out_data, param_dict, tool=tool, stdout=stdout, stderr=stderr) |
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| 91 | |
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| 92 | # strip strand column if clusters were merged |
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| 93 | if param_dict["returntype"] == '1': |
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| 94 | items = out_data.items() |
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| 95 | for name, data in items: |
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| 96 | data.metadata.strandCol = None |
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