def handle_sample_files_and_load_tool_from_tmp_config(
self, repo, repository_id, changeset_revision,
tool_config_filename, work_dir):
tool = None
message = ''
ctx = hg_util.get_changectx_for_changeset(repo, changeset_revision)
# We're not currently doing anything with the returned list of deleted_sample_files here. It is
# intended to help handle sample files that are in the manifest, but have been deleted from disk.
sample_files, deleted_sample_files = self.get_list_of_copied_sample_files(
repo, ctx, dir=work_dir)
if sample_files:
self.app.config.tool_data_path = work_dir
if 'tool_data_table_conf.xml.sample' in sample_files:
# Load entries into the tool_data_tables if the tool requires them.
tool_data_table_config = os.path.join(
work_dir, 'tool_data_table_conf.xml')
if tool_data_table_config:
error, message = self.tdtm.handle_sample_tool_data_table_conf_file(
tool_data_table_config, persist=False)
if error:
log.debug(message)
manifest_ctx, ctx_file = hg_util.get_ctx_file_path_from_manifest(
tool_config_filename, repo, changeset_revision)
if manifest_ctx and ctx_file:
tool, message2 = self.load_tool_from_tmp_config(
repo, repository_id, manifest_ctx, ctx_file, work_dir)
message = self.concat_messages(message, message2)
return tool, message, sample_files
def handle_sample_files_and_load_tool_from_tmp_config(
self, repo, repository_id, changeset_revision, tool_config_filename, work_dir
):
tool = None
message = ""
ctx = hg_util.get_changectx_for_changeset(repo, changeset_revision)
# We're not currently doing anything with the returned list of deleted_sample_files here. It is
# intended to help handle sample files that are in the manifest, but have been deleted from disk.
sample_files, deleted_sample_files = self.get_list_of_copied_sample_files(repo, ctx, dir=work_dir)
if sample_files:
self.app.config.tool_data_path = work_dir
if "tool_data_table_conf.xml.sample" in sample_files:
# Load entries into the tool_data_tables if the tool requires them.
tool_data_table_config = os.path.join(work_dir, "tool_data_table_conf.xml")
if tool_data_table_config:
error, message = self.tdtm.handle_sample_tool_data_table_conf_file(
tool_data_table_config, persist=False
)
if error:
log.debug(message)
manifest_ctx, ctx_file = hg_util.get_ctx_file_path_from_manifest(tool_config_filename, repo, changeset_revision)
if manifest_ctx and ctx_file:
tool, message2 = self.load_tool_from_tmp_config(repo, repository_id, manifest_ctx, ctx_file, work_dir)
message = self.concat_messages(message, message2)
return tool, message, sample_files
