Changed trans->app.

tools/data_source/biomart_filter.py

@@ -5,7 +5,7 @@ import urllib
 from galaxy import datatypes, config
 import tempfile, shutil
 
-def exec_before_job( trans, inp_data, out_data, param_dict, tool=None):
+def exec_before_job( app, inp_data, out_data, param_dict, tool=None):
     """Sets the name of the data"""
     data_name = param_dict.get( 'name', 'Biomart query' )
     data_type = param_dict.get( 'type', 'text' )

tools/data_source/encodedb_filter.py

@@ -5,10 +5,10 @@ def validate(incoming):
     #raise Exception, 'not quite right'
     pass
 
-def exec_before_job( trans, inp_data, out_data, param_dict, tool=None):
+def exec_before_job( app, inp_data, out_data, param_dict, tool=None):
     """Sets the name of the data"""
     dataid = param_dict.get( 'dataid', None )
-    data = trans.model.Dataset.get( dataid )
+    data = app.model.Dataset.get( dataid )
     if data:
         data.info = data.states.RUNNING
         data.flush()

tools/data_source/hbvar_filter.py

@@ -4,7 +4,7 @@ import urllib
 from galaxy import datatypes, config
 import tempfile, shutil
 
-def exec_before_job( trans, inp_data, out_data, param_dict, tool=None):
+def exec_before_job( app, inp_data, out_data, param_dict, tool=None):
     """Sets the name of the data"""
     data_name = param_dict.get( 'name', 'HbVar query' )
     data_type = param_dict.get( 'type', 'text' )

tools/data_source/ucsc_filter.py

@@ -6,7 +6,7 @@ def validate(incoming):
     #raise Exception, 'not quite right'
     pass
 
-def exec_before_job( trans, inp_data, out_data, param_dict, tool=None):
+def exec_before_job( app, inp_data, out_data, param_dict, tool=None):
     """Sets the name of the data"""
     outputType = param_dict.get( 'hgta_outputType', None )
     if isinstance(outputType, list) and len(outputType)>0: outputType = outputType[-1]

tools/data_source/ucsc_tablebrowser_code.py

@@ -1,7 +1,7 @@
 #Code for direct connection to UCSC
 from galaxy import datatypes
 
-def exec_before_job( trans, inp_data, out_data, param_dict, tool=None):
+def exec_before_job( app, inp_data, out_data, param_dict, tool=None):
     """Sets the name of the data"""
     outputType = param_dict.get( 'hgta_outputType', "interval" ).lower() #assume all data is interval, we will fix later if not the case
     #list for converting ucsc to galaxy exts, if not in following dictionary, use provided datatype

tools/encode/random_intervals_code.py

@@ -35,6 +35,6 @@ def get_available_data( build ):
         return [('No data available for this build','None',True)]
 
 
-#def exec_before_job(inp_data, out_data, param_dict, tool):
+#def exec_before_job(app, inp_data, out_data, param_dict, tool):
 #    for name, data in out_data.items():
 #        data.name = data.name + " [" + maf_sets[param_dict['mafType']]['description'] + "]"

tools/extract/genebed_maf_to_fasta_code.py

@@ -45,6 +45,6 @@ def get_available_species( maf_uid ):
         available_sets.append(('No data available for this configuration','None',True))
     return available_sets
 
-def exec_before_job(trans,inp_data, out_data, param_dict, tool):
+def exec_before_job(app,inp_data, out_data, param_dict, tool):
     for name, data in out_data.items():
         data.name = data.name + " [" + maf_sets[param_dict['mafSource']]['description'] + "]"

tools/extract/interval2maf_code.py

@@ -38,6 +38,6 @@ def get_available_data( build ):
     return available_sets
 
 
-def exec_before_job(trans,inp_data, out_data, param_dict, tool):
+def exec_before_job(app,inp_data, out_data, param_dict, tool):
     for name, data in out_data.items():
         data.name = data.name + " [" + maf_sets[param_dict['mafType']]['description'] + "]"

tools/extract/interval2maf_pairwise_code.py

@@ -38,6 +38,6 @@ def get_available_data( build ):
     return available_sets
 
 
-def exec_before_job(trans,inp_data, out_data, param_dict, tool):
+def exec_before_job(app,inp_data, out_data, param_dict, tool):
     for name, data in out_data.items():
         data.name = data.name + " [" + maf_sets[param_dict['mafType']]['description'] + "]"

tools/extract/interval_maf_to_merged_fasta_code.py

@@ -45,6 +45,6 @@ def get_available_species( maf_uid ):
         available_sets.append(('No data available for this configuration','None',True))
     return available_sets
 
-def exec_before_job(trans,inp_data, out_data, param_dict, tool):
+def exec_before_job(app,inp_data, out_data, param_dict, tool):
     for name, data in out_data.items():
         data.name = data.name + " [" + maf_sets[param_dict['mafSource']]['description'] + "]"

tools/validation/fix_errors_code.py

@@ -14,7 +14,7 @@ def validate(incoming):
     #raise Exception, 'not quite right'
     pass
 
-def exec_before_job( trans, inp_data, out_data, param_dict, tool=None):
+def exec_before_job( app, inp_data, out_data, param_dict, tool=None):
     """Build a temp file with errors in it"""
     errors = []
     for name, data in inp_data.items():