Mercurial > repos > devteam > basecoverage
view operation_filter.py @ 1:d00c8ea7792c
Corrected version string.
author | devteam <devteam@galaxyproject.org> |
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date | Thu, 10 Apr 2014 13:47:13 -0400 |
parents | 3755ee8a74d7 |
children | c929b6540d07 |
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# runs after the job (and after the default post-filter) import os from galaxy import eggs from galaxy import jobs from galaxy.tools.parameters import DataToolParameter from galaxy.jobs.handler import JOB_ERROR # Older py compatibility try: set() except: from sets import Set as set #def exec_before_process(app, inp_data, out_data, param_dict, tool=None): # """Sets the name of the data""" # dbkeys = sets.Set( [data.dbkey for data in inp_data.values() ] ) # if len(dbkeys) != 1: # raise Exception, '<p><font color="yellow">Both Queries must be from the same genome build</font></p>' def validate_input( trans, error_map, param_values, page_param_map ): dbkeys = set() data_param_names = set() data_params = 0 for name, param in page_param_map.iteritems(): if isinstance( param, DataToolParameter ): # for each dataset parameter if param_values.get(name, None) != None: dbkeys.add( param_values[name].dbkey ) data_params += 1 # check meta data try: param = param_values[name] if isinstance( param.datatype, trans.app.datatypes_registry.get_datatype_by_extension( 'gff' ).__class__ ): # TODO: currently cannot validate GFF inputs b/c they are not derived from interval. pass else: # Validate interval datatype. startCol = int( param.metadata.startCol ) endCol = int( param.metadata.endCol ) chromCol = int( param.metadata.chromCol ) if param.metadata.strandCol is not None: strandCol = int ( param.metadata.strandCol ) else: strandCol = 0 except: error_msg = "The attributes of this dataset are not properly set. " + \ "Click the pencil icon in the history item to set the chrom, start, end and strand columns." error_map[name] = error_msg data_param_names.add( name ) if len( dbkeys ) > 1: for name in data_param_names: error_map[name] = "All datasets must belong to same genomic build, " \ "this dataset is linked to build '%s'" % param_values[name].dbkey if data_params != len(data_param_names): for name in data_param_names: error_map[name] = "A dataset of the appropriate type is required" # Commented out by INS, 5/30/2007. What is the PURPOSE of this? def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None): """Verify the output data after each run""" items = out_data.items() for name, data in items: try: if stderr and len( stderr ) > 0: raise Exception( stderr ) except Exception, exc: data.blurb = JOB_ERROR data.state = JOB_ERROR ## def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None): ## pass def exec_after_merge(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None): exec_after_process( app, inp_data, out_data, param_dict, tool=tool, stdout=stdout, stderr=stderr) # strip strand column if clusters were merged items = out_data.items() for name, data in items: if param_dict['returntype'] == True: data.metadata.chromCol = 1 data.metadata.startCol = 2 data.metadata.endCol = 3 # merge always clobbers strand data.metadata.strandCol = None def exec_after_cluster(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None): exec_after_process( app, inp_data, out_data, param_dict, tool=tool, stdout=stdout, stderr=stderr) # strip strand column if clusters were merged if param_dict["returntype"] == '1': items = out_data.items() for name, data in items: data.metadata.strandCol = None