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Refactor to make app access a bit clearer.

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This commit is contained in:
John Chilton
2022-12-20 10:35:17 -05:00
parent 70a0a814dc
commit d484ec006b
1 changed files with 3 additions and 2 deletions
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lib/galaxy/tools/data_manager/manager.py
+3 -2
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@@ -288,6 +288,7 @@ class DataManager:
return tool
def process_result(self, out_data: Dict[str, OutputDataset]) -> None:
tool_data_tables = self.data_managers.app.tool_data_tables
data_manager_dicts: Dict[str, Any] = {}
data_manager_dict: Dict[str, Any] = {}
# TODO: fix this merging below
@@ -320,7 +321,7 @@ class DataManager:
# We don't have an old style data table definition
data_table_values = values_to_add
data_table = self.data_managers.app.tool_data_tables.get(data_table_name, None)
data_table = tool_data_tables.get(data_table_name, None)
if data_table is None:
log.error(
f'The data manager "{self.id}" returned an unknown data table "{data_table_name}" with new entries "{data_table_values}". These entries will not be created. Please confirm that an entry for "{data_table_name}" exists in your "tool_data_table_conf.xml" file.'
@@ -372,7 +373,7 @@ class DataManager:
util.move_merge(ref_file.extra_files_path, self._data_manager_path)
path_column_names = ["path"]
for data_table_name, data_table_values in data_tables_dict.items():
data_table = self.data_managers.app.tool_data_tables.get(data_table_name, None)
data_table = tool_data_tables.get(data_table_name, None)
if not isinstance(data_table_values, list):
data_table_values = [data_table_values]
for data_table_row in data_table_values: