This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.tool_shed.tools.tool_validator

import logging

from galaxy.tool_shed.tools.data_table_manager import ShedToolDataTableManager
from galaxy.tool_shed.util import (
from galaxy.tool_util.fetcher import ToolLocationFetcher
from galaxy.tool_util.parser import get_tool_source
from galaxy.tools import (
from galaxy.tools.parameters import dynamic_options

log = logging.getLogger(__name__)

[docs]class ToolValidator:
[docs] def __init__(self, app): self.app = app self.stdtm = ShedToolDataTableManager(self.app)
[docs] def check_tool_input_params(self, repo_dir, tool_config_name, tool, sample_files): """ Check all of the tool's input parameters, looking for any that are dynamically generated using external data files to make sure the files exist. """ invalid_files_and_errors_tups = [] for input_param in tool.input_params: if isinstance(input_param, parameters.basic.SelectToolParameter) and input_param.is_dynamic: # If the tool refers to .loc files or requires an entry in the tool_data_table_conf.xml, # make sure all requirements exist. options = input_param.dynamic_options or input_param.options if options and isinstance(options, dynamic_options.DynamicOptions): if options.tool_data_table or options.missing_tool_data_table_name: # Make sure the repository contains a tool_data_table_conf.xml.sample file. sample_tool_data_table_conf = hg_util.get_config_from_disk( "tool_data_table_conf.xml.sample", repo_dir ) if sample_tool_data_table_conf: error, correction_msg = self.stdtm.handle_sample_tool_data_table_conf_file( sample_tool_data_table_conf, persist=False ) if error: invalid_files_and_errors_tups.append( ("tool_data_table_conf.xml.sample", correction_msg) ) else: correction_msg = "This file requires an entry in the tool_data_table_conf.xml file. " correction_msg += "Upload a file named tool_data_table_conf.xml.sample to the repository " correction_msg += "that includes the required entry to correct this error.<br/>" invalid_tup = (tool_config_name, correction_msg) if invalid_tup not in invalid_files_and_errors_tups: invalid_files_and_errors_tups.append(invalid_tup) if options.index_file or options.tool_data_table and options.tool_data_table.missing_index_file: # Make sure the repository contains the required xxx.loc.sample file. index_file = options.index_file or options.tool_data_table.missing_index_file index_file_name = basic_util.strip_path(index_file) sample_found = False for sample_file in sample_files: sample_file_name = basic_util.strip_path(sample_file) if sample_file_name == f"{index_file_name}.sample": options.index_file = index_file_name if options.tool_data_table: options.tool_data_table.missing_index_file = None sample_found = True break if not sample_found: correction_msg = f"This file refers to a file named <b>{str(index_file_name)}</b>. " correction_msg += ( "Upload a file named <b>%s.sample</b> to the repository to correct this error." % str(index_file_name) ) invalid_files_and_errors_tups.append((tool_config_name, correction_msg)) return invalid_files_and_errors_tups
[docs] def load_tool_from_config(self, repository_id, full_path): tool_source = get_tool_source( full_path, enable_beta_formats=getattr(self.app.config, "enable_beta_tool_formats", False), tool_location_fetcher=ToolLocationFetcher(), ) try: tool = create_tool_from_source( config_file=full_path, app=self.app, tool_source=tool_source, repository_id=repository_id, allow_code_files=False, ) valid = True error_message = None except KeyError as e: tool = None valid = False error_message = ( f'This file requires an entry for "{str(e)}" in the tool_data_table_conf.xml file. Upload a file ' ) error_message += ( "named tool_data_table_conf.xml.sample to the repository that includes the required entry to correct " ) error_message += "this error. " log.exception(error_message) except Exception as e: tool = None valid = False error_message = str(e) log.exception("Caught exception loading tool from %s:", full_path) return tool, valid, error_message