[ENH] Add --refresh flag to dm_qc_report

bin/dm_qc_report.py

@@ -12,7 +12,11 @@
     <session>         Datman name of session to process e.g. DTI_CMH_H001_01_01
 
 Options:
-    --remake           Delete and recreate all QC metrics.
+    --refresh          Update dashboard metadata (e.g. header diffs, scan
+                       lengths) and generate missing metrics, if any. Note
+                       that existing QC metrics will not be modified.
+    --remake           Delete and recreate all QC metrics. Also force update
+                       of dashboard metadata (e.g. header diffs, scan lengths).
     --log-to-server    If set, all log messages will also be sent to the
                        configured logging server. This is useful when the
                        script is run on the queue, since it swallows logging.
@@ -22,7 +26,7 @@
 
 Requires:
     FSL/5.0.10
-    MATLAB/R2014a - qa-dti phantom pipeline
+    matlab/R2014a - qa-dti phantom pipeline
     AFNI/2014.12.16 - abcd_fmri phantom pipeline
 """
 
@@ -47,15 +51,18 @@
 logger = logging.getLogger(os.path.basename(__file__))
 
 REMAKE = False
+REFRESH = False
 
 
 def main():
     global REMAKE
+    global REFRESH
 
     arguments = docopt(__doc__)
     study = arguments["<study>"]
     session = arguments["<session>"]
     REMAKE = arguments["--remake"]
+    REFRESH = arguments["--refresh"]
     use_server = arguments["--log-to-server"]
     verbose = arguments["--verbose"]
     debug = arguments["--debug"]
@@ -141,7 +148,7 @@ def submit_subjects(config):
     subs = get_subids(config)
 
     for subject in subs:
-        if not (REMAKE or needs_qc(subject, config)):
+        if not (REMAKE or REFRESH or needs_qc(subject, config)):
             continue
 
         command = make_command(subject)
@@ -150,7 +157,7 @@ def submit_subjects(config):
         logger.info(f"Submitting QC job for {subject}.")
         datman.utils.submit_job(
             command, job_name, "/tmp", system=config.system,
-            argslist="--mem=3G"
+            argslist="--mem=5G"
         )
 
 
@@ -333,7 +340,7 @@ def update_dashboard(nii_path, header_ignore=None, header_tolerance=None):
     """
     db_record = datman.dashboard.get_scan(nii_path)
 
-    if REMAKE or db_record.is_outdated_header_diffs():
+    if REMAKE or REFRESH or db_record.is_outdated_header_diffs():
         try:
             db_record.update_header_diffs(
                 standard=db_record.gold_standards[0],
@@ -344,7 +351,7 @@ def update_dashboard(nii_path, header_ignore=None, header_tolerance=None):
                 f"exception: {e}"
             )
 
-    if REMAKE or not db_record.length:
+    if REMAKE or REFRESH or not db_record.length:
         add_scan_length(nii_path, db_record)
 
 
@@ -404,11 +411,16 @@ def add_scan_length(nii_path, scan):
 
 
 def remove_outputs(metric):
-    for item in metric.outputs:
-        try:
-            os.remove(item)
-        except FileNotFoundError:
-            pass
+    try:
+        os.remove(metric.manifest_path)
+    except FileNotFoundError:
+        pass
+    for command in metric.outputs:
+        for item in metric.outputs[command]:
+            try:
+                os.remove(item)
+            except FileNotFoundError:
+                pass
 
 
 if __name__ == "__main__":

datman/metrics.py

@@ -44,7 +44,7 @@ def write_manifest(self, overwrite=False):
         if os.path.exists(self.manifest_path):
             if not overwrite:
                 return
-            orig = self.read_json()
+            orig = self.read_manifest()
         else:
             orig = None