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Expand repairs in convert_owl #213

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merged 1 commit into from
Mar 19, 2024
Merged

Expand repairs in convert_owl #213

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16 changes: 14 additions & 2 deletions kg_obo/robot_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -107,7 +107,7 @@ def convert_owl(robot_path: str, input_owl: str, output: str, robot_env: dict) -
success = True
except sh.ErrorReturnCode_1 as e: # If ROBOT runs but returns an error
print(f"ROBOT encountered an error: {e}")
print(f"Will try to repair...")
print("Will try to repair by removing object properties...")
try:
robot_command('remove',
'--input', input_owl,
Expand All @@ -118,6 +118,7 @@ def convert_owl(robot_path: str, input_owl: str, output: str, robot_env: dict) -
success = True
except sh.ErrorReturnCode_1 as e:
print(f"ROBOT encountered another error: {e}")
print("Will try to repair by removing comments..")
try:
robot_command('remove',
'--input', input_owl,
Expand All @@ -128,7 +129,18 @@ def convert_owl(robot_path: str, input_owl: str, output: str, robot_env: dict) -
success = True
except sh.ErrorReturnCode_1 as e:
print(f"ROBOT encountered yet another error: {e}")
success = False
print("Will try to repair by removing IAO:0000115...")
try:
robot_command('remove',
'--input', input_owl,
'--exclude-term', 'IAO:0000115',
'--output', output,
_env=robot_env,
)
success = True
except sh.ErrorReturnCode_1 as e:
print(f"ROBOT encountered yet a further error: {e}")
return False

# Neutralize invalid prefixes.
print("Replacing any invalid prefixes...")
Expand Down
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