From b73e21b584dc13716460f550ed80108634adca37 Mon Sep 17 00:00:00 2001 From: Nuwan Goonasekera Date: Fri, 18 Aug 2017 02:11:40 +0530 Subject: [PATCH] Formatting and linting fixes for GenomeSpace tool --- lib/galaxy/tools/parameters/basic.py | 2 +- lib/galaxy/web/form_builder.py | 2 +- tools/genomespace/genomespace_importer.py | 72 ++++++++++++----------- 3 files changed, 39 insertions(+), 37 deletions(-) diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py index b53cb6dfb1c..8235b3e8fa8 100644 --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -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') diff --git a/lib/galaxy/web/form_builder.py b/lib/galaxy/web/form_builder.py index 4875a22771d..ffb9cbbdb0d 100644 --- a/lib/galaxy/web/form_builder.py +++ b/lib/galaxy/web/form_builder.py @@ -224,7 +224,7 @@ class GenomespaceFileField(BaseField): ' $(selector).val(config.destination + \'^\' + config.token); }} }});">' 'Browse'.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) diff --git a/tools/genomespace/genomespace_importer.py b/tools/genomespace/genomespace_importer.py index a69236198e2..8201bd5392a 100644 --- a/tools/genomespace/genomespace_importer.py +++ b/tools/genomespace/genomespace_importer.py @@ -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,