Warning

This document is for an old release 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 (
    basic_util,
    hg_util,
)
from galaxy.tool_util.fetcher import ToolLocationFetcher
from galaxy.tool_util.parser import get_tool_source
from galaxy.tools import (
    create_tool_from_source,
    parameters,
)
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, ) tool.assert_finalized(raise_if_invalid=True) 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