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Fixed pylint errors

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This commit is contained in:
Nuwan Goonasekera
2017-08-19 00:38:07 +05:30
parent b04ccbe55b
commit cb1b086324
3 changed files with 37 additions and 46 deletions
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lib/galaxy/tools/parameters/basic.py
+5 -14
View File
@@ -631,21 +631,12 @@ class GenomespaceFileToolParameter(ToolParameter):
Parameter that takes one of two values.
"""
def __init__(self, tool, elem):
ToolParameter.__init__(self, tool, elem)
self.value = elem.get('value')
def __init__(self, tool, input_source):
input_source = ensure_input_source( input_source )
ToolParameter.__init__(self, tool, input_source)
self.value = input_source.get('value')
def get_html_field(self, trans=None, value=None, other_values={}):
return form_builder.GenomespaceFileField(self.name, value)
def to_string(self, value, app):
"""Convert a value to a string representation suitable for persisting"""
if value is None:
return ''
else:
return str(value)
def get_initial_value(self, trans, context, history=None):
def get_initial_value(self, trans, other_values):
return self.value
tools/genomespace/genomespace_exporter.py
+1 -1
View File
@@ -1,6 +1,6 @@
import argparse
import sys
import binascii
import sys
from genomespaceclient import GenomeSpaceClient
tools/genomespace/genomespace_importer.py
+31 -31
View File
@@ -1,17 +1,15 @@
import argparse
import logging
import sys
import binascii
import uuid
import json
import os
import sys
import uuid
from genomespaceclient import GenomeSpaceClient
import galaxy
from galaxy.datatypes import sniff
from galaxy.datatypes.registry import Registry
from genomespaceclient import GenomeSpaceClient
from genomespaceclient import util
import galaxy
# Mappings for known genomespace formats to galaxy formats
GENOMESPACE_EXT_TO_GALAXY_EXT = {'rifles': 'rifles',
@@ -50,6 +48,7 @@ def _prepare_json_list( param_list ):
rval.append( str( value ) )
return rval
def _prepare_json_param_dict( param_dict ):
"""
JSON serialization Support functions for exec_before_job hook
@@ -64,6 +63,7 @@ def _prepare_json_param_dict( param_dict ):
rval[ key ] = str( value )
return rval
def exec_before_job( app, inp_data, out_data, param_dict=None, tool=None ):
"""
Galaxy override hook
@@ -94,7 +94,8 @@ def exec_before_job( app, inp_data, out_data, param_dict=None, tool=None ):
out = open( json_filename, 'w' )
out.write( json.dumps( json_params ) )
out.close()
def get_galaxy_ext_from_genomespace_format(file_format):
return GENOMESPACE_EXT_TO_GALAXY_EXT.get(file_format, None)
@@ -103,11 +104,11 @@ def sniff_data_type(json_params, output_file):
try:
datatypes_registry = Registry()
datatypes_registry.load_datatypes(
root_dir=json_params['job_config']['GALAXY_ROOT_DIR'],
config=json_params['job_config']['GALAXY_DATATYPES_CONF_FILE'])
root_dir=json_params['job_config']['GALAXY_ROOT_DIR'],
config=json_params['job_config']['GALAXY_DATATYPES_CONF_FILE'])
file_type = sniff.handle_uploaded_dataset_file(
output_file,
datatypes_registry)
output_file,
datatypes_registry)
return file_type
except:
return None
@@ -120,14 +121,14 @@ def determine_output_filename(input_url, metadata, json_params, primary_dataset)
name
"""
output_filename = json_params['output_data'][0]['file_name']
if not primary_dataset or not output_filename:
hda_id = json_params['output_data'][0]['hda_id']
output_filename = 'primary_%i_%s_visible_%s' % (hda_id, metadata.name, uuid.uuid4())
return os.path.join(os.getcwd(), output_filename)
def determine_file_type(input_url, output_filename, metadata, json_params):
"""
Determine the Galaxy data format for this file.
@@ -152,7 +153,6 @@ def determine_file_type(input_url, output_filename, metadata, json_params):
return file_type
def save_result_metadata(output_filename, file_type, metadata, json_params,
primary_dataset=False):
"""
@@ -164,31 +164,31 @@ def save_result_metadata(output_filename, file_type, metadata, json_params,
with open( json_params['job_config']['TOOL_PROVIDED_JOB_METADATA_FILE'], 'ab' ) as metadata_parameter_file:
if primary_dataset:
metadata_parameter_file.write( "%s\n" % json.dumps( dict( type='dataset',
dataset_id=dataset_id,
ext=file_type,
name="GenomeSpace importer on %s" % ( metadata.name ) ) ) )
dataset_id=dataset_id,
ext=file_type,
name="GenomeSpace importer on %s" % ( metadata.name ) ) ) )
else:
metadata_parameter_file.write( "%s\n" % json.dumps( dict( type='new_primary_dataset',
base_dataset_id=dataset_id,
ext=file_type,
filename=output_filename,
name="GenomeSpace importer on %s" % ( metadata.name ) ) ) )
base_dataset_id=dataset_id,
ext=file_type,
filename=output_filename,
name="GenomeSpace importer on %s" % ( metadata.name ) ) ) )
def download_single_file(gs_client, input_url, json_params,
primary_dataset=False):
# 1. Get file metadata
metadata = gs_client.get_metadata(input_url)
# 2. Determine output file name
output_filename = determine_output_filename(input_url, metadata, json_params, primary_dataset)
output_filename = determine_output_filename(input_url, metadata, json_params, primary_dataset)
# 3. Download file
gs_client.copy(input_url, output_filename)
# 4. Determine file type from available metadata
file_type = determine_file_type(input_url, output_filename, metadata, json_params)
# 5. Write job output metadata
save_result_metadata(output_filename, file_type, metadata, json_params,
primary_dataset=primary_dataset)
@@ -201,7 +201,7 @@ def download_from_genomespace_importer(json_parameter_file, root, data_conf, cus
# Add in missing job config properties that could not be set in the exec_before_job hook
json_params['job_config']['GALAXY_ROOT_DIR'] = root
json_params['job_config']['GALAXY_DATATYPES_CONF_FILE'] = data_conf
# Extract input_urls and token (format is input_urls^token). If a custom_token is
# provided, use that instead.
url_with_token = json_params.get('param_dict', {}).get("URL", "")
@@ -216,7 +216,7 @@ def download_from_genomespace_importer(json_parameter_file, root, data_conf, cus
for idx, input_url in enumerate(input_url_list):
download_single_file(gs_client, input_url, json_params,
primary_dataset=(idx==0))
primary_dataset=(idx == 0))
def process_args(args):