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Ignore user data table errors for now
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Fixes #17822
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mvdbeek committed Apr 2, 2024
1 parent 3669cae commit dee8278
Showing 1 changed file with 6 additions and 1 deletion.
7 changes: 6 additions & 1 deletion lib/galaxy/tools/parameters/dynamic_options.py
Original file line number Diff line number Diff line change
Expand Up @@ -766,7 +766,12 @@ def get_user_options(self, user: User):
hdas = user.get_user_data_tables(self.tool_data_table_name)
by_dbkey = {}
for hda in hdas:
by_dbkey.update(self.hda_to_table_entries(hda, self.tool_data_table_name))
try:
by_dbkey.update(self.hda_to_table_entries(hda, self.tool_data_table_name))
except Exception as e:
# This is a bug, `hda_to_table_entries` is not generic enough for certain loc file
# structures, such as for the dada2_species, which doesn't have a dbkey column
log.warning("Failed to read data table bundle entries: %s", e)
for data_table_entry in by_dbkey.values():
field_entry = []
for column_key in self.tool_data_table.columns.keys():
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