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Make some files compatible with Python3

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Also enlarge the set of files tested with flake8 under Python3
This commit is contained in:
Nicola Soranzo
2016-06-03 19:24:46 +01:00
parent 30fd1d679b
commit cc336f61c0
25 changed files with 325 additions and 242 deletions
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tools/data_source/microbial_import_code.py
+6 -4
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@@ -1,3 +1,5 @@
from __future__ import print_function
from shutil import copyfile
from galaxy import tools
@@ -88,17 +90,17 @@ def load_microbial_data( GALAXY_DATA_INDEX_DIR, sep='\t' ):
# post processing, set build for data and add additional data to history
def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
base_dataset = out_data.items()[0][1]
base_dataset = list(out_data.items())[0][1]
history = base_dataset.history
if history is None:
print "unknown history!"
print("unknown history!")
return
kingdom = param_dict.get( 'kingdom', None )
org = param_dict.get( 'org', None )
# if not (kingdom or group or org):
if not (kingdom or org):
print "Parameters are not available."
print("Parameters are not available.")
# workflow passes galaxy.tools.parameters.basic.UnvalidatedValue instead of values
if isinstance( kingdom, tools.parameters.basic.UnvalidatedValue ):
kingdom = kingdom.value
@@ -116,7 +118,7 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr
chr = fields[2]
dbkey = fields[3]
file_type = fields[4]
name, data = out_data.items()[0]
name, data = list(out_data.items())[0]
data.set_size()
basic_name = data.name
data.name = data.name + " (" + microbe_info[kingdom][org]['chrs'][chr]['data'][description]['feature'] + " for " + microbe_info[kingdom][org]['name'] + ":" + chr + ")"