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Fix moving of data manager output for entries

Browse Source 
https://github.com/galaxyproject/galaxy/pull/8250 introduced the
add and remove keys for removing items from a data table.
If there is a single data table definition incoming (meaning a
dictionary) that does not specify the `add` key the new code would
just ignore that entry and not move it.

Fixes https://github.com/galaxyproject/tools-iuc/issues/2783?
This commit is contained in:
mvdbeek
2020-01-20 17:36:12 +01:00
parent 47c5a0e108
commit f327189c2b
1 changed files with 10 additions and 20 deletions
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lib/galaxy/tools/data_manager/manager.py
+10 -20
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@@ -266,28 +266,18 @@ class DataManager(object):
data_tables_dict = data_manager_dict.get('data_tables', {})
for data_table_name in self.data_tables.keys():
data_table_values = None
data_table_remove_values = None
# Add/Remove option for data tables
if isinstance(data_tables_dict.get(data_table_name), dict):
data_table_data = data_tables_dict.get(data_table_name, None)
# Validate results
if not data_table_data:
log.warning('Data table seems invalid: "%s".' % data_table_name)
continue
data_table_values = data_table_data.pop('add', None)
data_table_remove_values = data_table_data.pop('remove', None)
# Remove it as well here
data_tables_dict.pop(data_table_name, None)
else:
data_table_values = data_tables_dict.pop(data_table_name, None)
if not data_table_values and not data_table_remove_values:
data_table_values = data_tables_dict.pop(data_table_name, None)
if not data_table_values:
log.warning('No values for data table "%s" were returned by the data manager "%s".' % (data_table_name, self.id))
continue # next data table
data_table_remove_values = None
if isinstance(data_table_values, dict):
values_to_add = data_table_values.get('add')
data_table_remove_values = data_table_values.get('remove')
if values_to_add or data_table_remove_values:
# 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)
if data_table is None:
log.error('The data manager "%s" returned an unknown data table "%s" with new entries "%s". These entries will not be created. Please confirm that an entry for "%s" exists in your "%s" file.' % (self.id, data_table_name, data_table_values, data_table_name, 'tool_data_table_conf.xml'))