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added fixes #12

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8 changes: 6 additions & 2 deletions hallmonitor/app.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@
datadict_has_changes,
file_last_modified_date,
get_args,
get_deviation_files,
get_deviation_string,
get_eeg_errors,
get_expected_combination_rows,
Expand Down Expand Up @@ -112,6 +113,7 @@ def validate_data(
joint_rows = get_joint_root_vars(dataset)
logger.debug("Joint rows: %s", joint_rows)
combo_rows = get_expected_combination_rows(dataset)
logger.debug("Combination rows: %s", combo_rows)
combo_variables = set()
for combo in combo_rows:
combo_variables.update(combo.variables)
Expand All @@ -124,8 +126,6 @@ def validate_data(
len(missing_ids),
)



# raise errors for missing identifiers without a no-data.txt
for id in missing_ids:
# if appropriate option is set, skip "missing" errors when identifier is in pending-qa
Expand Down Expand Up @@ -326,6 +326,7 @@ def validate_data(
no_data_file = get_no_data_file(dir_filenames, id, joint_rows,logger)
has_no_data = True if no_data_file else False

joint_deviation_files = get_deviation_files(dir_filenames, id, joint_rows,logger)

logger.debug("has_deviation=%s, has_no_data=%s", has_deviation, has_no_data)
if has_deviation and has_no_data:
Expand Down Expand Up @@ -367,10 +368,13 @@ def validate_data(

misnamed_files = []
dir_filepaths = [os.path.join(id_dir, f) for f in dir_filenames]
# Solution: Create all possible known deviation.txt that could be located within as long as it iis in joint/ combination and enable it
for file_path in dir_filepaths:
file_name = os.path.basename(file_path)
if file_name == deviation_file:
continue
elif file_name in joint_deviation_files:
continue
elif file_name == "issue.txt":
pending.append(
new_error_record(
Expand Down
21 changes: 21 additions & 0 deletions hallmonitor/hmutils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -997,6 +997,27 @@ def get_deviation_file(dir_filenames, identifier, joint_rows, logger):
logger.debug("Found joint deviation file %s for identifier %s", joint_deviation_file, identifier)
return joint_deviation_file
return None

def get_deviation_files(dir_filenames, identifier, joint_rows, logger):
"""
Return a list of deviation files for the given identifier and joint rows.
"""
joint_deviation_files = []
if not any(f.endswith("deviation.txt") for f in dir_filenames):
return []
for joint_row in joint_rows:
if identifier.variable in joint_row.variables:
logger.debug("Identifier %s is part of joint row %s", identifier, joint_row.name)
# check for deviation/no-data files for joint root variable
#joint_deviation_file = f"{joint_row.name}_deviation.txt"
#joint_no_data_file = f"{joint_row.name}_no-data.txt"
for var in joint_row.variables:
joint_id = Identifier(
identifier.subject, var, identifier.session, identifier.run, identifier.event
)
joint_deviation_file = f"{joint_id}_deviation.txt"
joint_deviation_files.append(joint_deviation_file)
return joint_deviation_files

def get_no_data_file(dir_filenames, identifier, joint_rows, logger):
"""
Expand Down