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Formatting and linting fixes for GenomeSpace tool

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This commit is contained in:
Nuwan Goonasekera
2017-08-19 00:38:07 +05:30
parent 517fd23fc8
commit b73e21b584
3 changed files with 39 additions and 37 deletions
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lib/galaxy/tools/parameters/basic.py
+1 -1
View File
@@ -632,7 +632,7 @@ class GenomespaceFileToolParameter(ToolParameter):
"""
def __init__(self, tool, input_source):
input_source = ensure_input_source( input_source )
input_source = ensure_input_source(input_source)
ToolParameter.__init__(self, tool, input_source)
self.value = input_source.get('value')
lib/galaxy/web/form_builder.py
+1 -1
View File
@@ -224,7 +224,7 @@ class GenomespaceFileField(BaseField):
' $(selector).val(config.destination + \'^\' + config.token); }} }});">'
'Browse</a>'.format(prefix, self.name, escape(str(self.value), quote=True)))
def to_dict( self ):
def to_dict(self):
return dict(name=self.name,
token_field=self.token_field)
tools/genomespace/genomespace_importer.py
+37 -35
View File
@@ -34,37 +34,37 @@ GENOMESPACE_EXT_TO_GALAXY_EXT = {'rifles': 'rifles',
'gct': 'gct'}
def _prepare_json_list( param_list ):
def _prepare_json_list(param_list):
"""
JSON serialization Support functions for exec_before_job hook
"""
rval = []
for value in param_list:
if isinstance( value, dict ):
rval.append( _prepare_json_param_dict( value ) )
elif isinstance( value, list ):
rval.append( _prepare_json_list( value ) )
if isinstance(value, dict):
rval.append(_prepare_json_param_dict(value))
elif isinstance(value, list):
rval.append(_prepare_json_list(value))
else:
rval.append( str( value ) )
rval.append(str(value))
return rval
def _prepare_json_param_dict( param_dict ):
def _prepare_json_param_dict(param_dict):
"""
JSON serialization Support functions for exec_before_job hook
"""
rval = {}
for key, value in param_dict.iteritems():
if isinstance( value, dict ):
rval[ key ] = _prepare_json_param_dict( value )
elif isinstance( value, list ):
rval[ key ] = _prepare_json_list( value )
if isinstance(value, dict):
rval[key] = _prepare_json_param_dict(value)
elif isinstance(value, list):
rval[key] = _prepare_json_list(value)
else:
rval[ key ] = str( value )
rval[key] = str(value)
return rval
def exec_before_job( app, inp_data, out_data, param_dict=None, tool=None ):
def exec_before_job(app, inp_data, out_data, param_dict=None, tool=None):
"""
Galaxy override hook
See: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccode.3E_tag_set
@@ -77,22 +77,24 @@ def exec_before_job( app, inp_data, out_data, param_dict=None, tool=None ):
if param_dict is None:
param_dict = {}
json_params = {}
json_params[ 'param_dict' ] = _prepare_json_param_dict( param_dict )
json_params[ 'output_data' ] = []
json_params[ 'job_config' ] = dict( GALAXY_DATATYPES_CONF_FILE=param_dict.get( 'GALAXY_DATATYPES_CONF_FILE' ), GALAXY_ROOT_DIR=param_dict.get( 'GALAXY_ROOT_DIR' ), TOOL_PROVIDED_JOB_METADATA_FILE=galaxy.jobs.TOOL_PROVIDED_JOB_METADATA_FILE )
json_params['param_dict'] = _prepare_json_param_dict(param_dict)
json_params['output_data'] = []
json_params['job_config'] = dict(GALAXY_DATATYPES_CONF_FILE=param_dict.get('GALAXY_DATATYPES_CONF_FILE'),
GALAXY_ROOT_DIR=param_dict.get('GALAXY_ROOT_DIR'),
TOOL_PROVIDED_JOB_METADATA_FILE=galaxy.jobs.TOOL_PROVIDED_JOB_METADATA_FILE)
json_filename = None
for i, ( out_name, data ) in enumerate( out_data.iteritems() ):
for i, (out_name, data) in enumerate(out_data.iteritems()):
file_name = data.get_file_name()
data_dict = dict( out_data_name=out_name,
ext=data.ext,
dataset_id=data.dataset.id,
hda_id=data.id,
file_name=file_name )
json_params[ 'output_data' ].append( data_dict )
data_dict = dict(out_data_name=out_name,
ext=data.ext,
dataset_id=data.dataset.id,
hda_id=data.id,
file_name=file_name)
json_params['output_data'].append(data_dict)
if json_filename is None:
json_filename = file_name
with open( json_filename, 'w' ) as out:
out.write( json.dumps( json_params ) )
with open(json_filename, 'w') as out:
out.write(json.dumps(json_params))
def get_galaxy_ext_from_genomespace_format(format):
@@ -172,18 +174,18 @@ def save_result_metadata(output_filename, file_type, metadata, json_params,
and associated metadata
"""
dataset_id = json_params['output_data'][0]['dataset_id']
with open( json_params['job_config']['TOOL_PROVIDED_JOB_METADATA_FILE'], 'ab' ) as metadata_parameter_file:
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 ) ) ) )
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))))
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 ) ) ) )
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))))
def download_single_file(gs_client, input_url, json_params,