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Add parse_retrieved_files option for the PP plugin. #1029

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7 changes: 4 additions & 3 deletions src/aiida_quantumespresso/calculations/pp.py
Original file line number Diff line number Diff line change
Expand Up @@ -83,6 +83,7 @@ def define(cls, spec):
spec.input('metadata.options.parser_name', valid_type=str, default='quantumespresso.pp')
spec.input('metadata.options.withmpi', valid_type=bool, default=True)
spec.input('metadata.options.keep_plot_file', valid_type=bool, default=False)
spec.input('metadata.options.parse_retrieved_files', valid_type=bool, default=True)

spec.output('output_parameters', valid_type=orm.Dict)
spec.output('output_data', valid_type=orm.ArrayData)
Expand Down Expand Up @@ -218,10 +219,10 @@ def prepare_for_submission(self, folder): # pylint: disable=too-many-branches,t
# distinguish them from one another. The `fileout` filename will be the full data filename with the `fileout`
# value as a suffix.
retrieve_tuples = [self._FILEOUT, (f'{self._FILPLOT}_*{self._FILEOUT}', '.', 0)]

if self.inputs.metadata.options.keep_plot_file:
calcinfo.retrieve_list.extend(retrieve_tuples)
else:
# If we do not want to parse the retrieved files, temporary retrieval is meaningless
elif self.inputs.metadata.options.parse_retrieved_files:
calcinfo.retrieve_temporary_list.extend(retrieve_tuples)

return calcinfo
return calcinfo
58 changes: 29 additions & 29 deletions src/aiida_quantumespresso/parsers/pp.py
Original file line number Diff line number Diff line change
Expand Up @@ -117,35 +117,35 @@ def get_key_from_filename(filename):
matches = re.search(pattern, filename)
return matches.group(1)

for filename in filenames:
# Directly parse the retrieved files after reading them to memory (`data_raw`). The raw data
# of each file is released from memory after parsing, to improve memory usage.
if filename.endswith(filename_suffix):
# Read the file to memory
try:
with file_opener(filename) as handle:
data_raw = handle.read()
except OSError:
return self.exit_codes.ERROR_OUTPUT_DATAFILE_READ.format(filename=filename)
# Parse the file
try:
key = get_key_from_filename(filename)
data_parsed.append((key, parsers[iflag](data_raw, self.units_dict[parsed_data['plot_num']])))
del data_raw
except Exception as exception: # pylint: disable=broad-except
return self.exit_codes.ERROR_OUTPUT_DATAFILE_PARSE.format(filename=filename, exception=exception)

# If we don't have any parsed files, we exit. Note that this will not catch the case where there should be more
# than one file, but the engine did not retrieve all of them. Since often we anyway don't know how many files
# should be retrieved there really is no way to check this explicitly.
if not data_parsed:
return self.exit_codes.ERROR_OUTPUT_DATAFILE_MISSING.format(filename=filename_prefix)

# Create output nodes
if len(data_parsed) == 1:
self.out('output_data', data_parsed[0][1])
else:
self.out('output_data_multiple', dict(data_parsed))
if self.node.inputs.metadata.options.parse_retrieved_files:
for filename in filenames:
# Directly parse the retrieved files after reading them to memory (`data_raw`). The raw data
# of each file is released from memory after parsing, to improve memory usage.
if filename.endswith(filename_suffix):
# Read the file to memory
try:
with file_opener(filename) as handle:
data_raw = handle.read()
except OSError:
return self.exit_codes.ERROR_OUTPUT_DATAFILE_READ.format(filename=filename)
# Parse the file
try:
key = get_key_from_filename(filename)
data_parsed.append((key, parsers[iflag](data_raw, self.units_dict[parsed_data['plot_num']])))
del data_raw
except Exception as exception: # pylint: disable=broad-except
return self.exit_codes.ERROR_OUTPUT_DATAFILE_PARSE.format(filename=filename, exception=exception)

# If we don't have any parsed files, we exit. Note that this will not catch the case where there should be more
# than one file, but the engine did not retrieve all of them. Since often we anyway don't know how many files
# should be retrieved there really is no way to check this explicitly.
if not data_parsed:
return self.exit_codes.ERROR_OUTPUT_DATAFILE_MISSING.format(filename=filename_prefix)

if len(data_parsed) == 1:
self.out('output_data', data_parsed[0][1])
else:
self.out('output_data_multiple', dict(data_parsed))

return self.exit(logs=logs)

Expand Down
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