Mercurial > repos > devteam > cluster
diff operation_filter.py @ 0:45fb880ab3bf
Imported from capsule None
author | devteam |
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date | Tue, 01 Apr 2014 09:12:53 -0400 |
parents | |
children | 1e895b74f29f |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/operation_filter.py Tue Apr 01 09:12:53 2014 -0400 @@ -0,0 +1,99 @@ +# 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