def __init__(self, app):
self.app = app
self.stdtm = ShedToolDataTableManager(self.app)
class ToolValidator:
def __init__(self, app):
self.app = app
self.stdtm = ShedToolDataTableManager(self.app)
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
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