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Source code for galaxy.tools.parameters.input_translation

"""
Tool Input Translation.
"""

import logging

from galaxy.util.bunch import Bunch

log = logging.getLogger(__name__)


[docs]class ToolInputTranslator: """ Handles Tool input translation. This is used for data source tools >>> from galaxy.util import Params, XML >>> translator = ToolInputTranslator.from_element(XML( ... ''' ... <request_param_translation> ... <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /> ... <request_param galaxy_name="URL" remote_name="URL" missing="" > ... <append_param separator="&amp;" first_separator="?" join="="> ... <value name="_export" missing="1" /> ... <value name="GALAXY_URL" missing="0" /> ... </append_param> ... </request_param> ... <request_param galaxy_name="dbkey" remote_name="db" missing="?" /> ... <request_param galaxy_name="organism" remote_name="org" missing="unknown species" /> ... <request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" /> ... <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" /> ... <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="tabular" > ... <value_translation> ... <value galaxy_value="tabular" remote_value="primaryTable" /> ... <value galaxy_value="tabular" remote_value="selectedFields" /> ... <value galaxy_value="wig" remote_value="wigData" /> ... <value galaxy_value="interval" remote_value="tab" /> ... <value galaxy_value="html" remote_value="hyperlinks" /> ... <value galaxy_value="fasta" remote_value="sequence" /> ... </value_translation> ... </request_param> ... </request_param_translation> ... ''')) >>> params = Params({'db':'hg17', 'URL':'URL_value', 'org':'Human', 'hgta_outputType':'primaryTable'}) >>> translator.translate(params) >>> print(sorted(params.__dict__.keys())) ['URL', 'URL_method', 'data_type', 'db', 'dbkey', 'description', 'hgta_outputType', 'org', 'organism', 'table'] >>> params.get('URL', None) in ['URL_value?GALAXY_URL=0&_export=1', 'URL_value?_export=1&GALAXY_URL=0'] True """
[docs] @classmethod def from_element(cls, elem): """Loads the proper filter by the type attribute of elem""" rval = ToolInputTranslator() for req_param in elem.findall("request_param"): # req_param tags must look like <request_param galaxy_name="dbkey" remote_name="GENOME" missing="" /> # trans_list = [] remote_name = req_param.get("remote_name") galaxy_name = req_param.get("galaxy_name") missing = req_param.get("missing") value_trans = {} append_param = None value_trans_elem = req_param.find('value_translation') if value_trans_elem is not None: for value_elem in value_trans_elem.findall('value'): remote_value = value_elem.get("remote_value") galaxy_value = value_elem.get("galaxy_value") if None not in [remote_value, galaxy_value]: value_trans[remote_value] = galaxy_value append_param_elem = req_param.find("append_param") if append_param_elem is not None: separator = append_param_elem.get('separator', ',') first_separator = append_param_elem.get('first_separator', None) join_str = append_param_elem.get('join', '=') append_dict = {} for value_elem in append_param_elem.findall('value'): value_name = value_elem.get('name') value_missing = value_elem.get('missing') if None not in [value_name, value_missing]: append_dict[value_name] = value_missing append_param = Bunch(separator=separator, first_separator=first_separator, join_str=join_str, append_dict=append_dict) rval.param_trans_dict[remote_name] = Bunch(galaxy_name=galaxy_name, missing=missing, value_trans=value_trans, append_param=append_param) return rval
[docs] def __init__(self): self.param_trans_dict = {}
[docs] def translate(self, params): """ update params in-place """ for remote_name, translator in self.param_trans_dict.items(): galaxy_name = translator.galaxy_name # NB: if a param by name galaxy_name is provided, it is always thrown away unless galaxy_name == remote_name value = params.get(remote_name, translator.missing) # get value from input params, or use default value specified in tool config if translator.value_trans and value in translator.value_trans: value = translator.value_trans[value] if translator.append_param: for param_name, missing_value in translator.append_param.append_dict.items(): param_value = params.get(param_name, missing_value) if translator.append_param.first_separator and translator.append_param.first_separator not in value: sep = translator.append_param.first_separator else: sep = translator.append_param.separator value += f'{sep}{param_name}{translator.append_param.join_str}{param_value}' params.update({galaxy_name: value})