🔥 Remove deprecated --disable_file_logging CLI flag (#1809)

Author: shnizzedy

CHANGELOG.md

@@ -35,6 +35,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Added data-config-specific hash string to C-PAC-generated config files
 - Updated `rbc-options` preconfig to use `fmriprep-options` preprocessing
 - Changed minimized pipeline base from `default` to `blank`
+- Removed deprecated `--disable_file_logging` CLI flag
 
 ### Fixed
 - Fixed [a bug](https://github.com/FCP-INDI/C-PAC/issues/1779) in which generated pipeline configs were not 100% accurate. The only affected configurable option discovered in testing was seed-based correlation analysis always reverting to the default configuration.

CPAC/resources/configs/pipeline_config_anat-only.yml

@@ -77,15 +77,15 @@ registration_workflows:
       FSL-FNIRT:
 
         # Reference mask for FSL registration.
-        ref_mask: $$$FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask_dil.nii.gz
+        ref_mask: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask_dil.nii.gz
 
     # Template to be used during registration.
     # It is not necessary to change this path unless you intend to use a non-standard template.
-    T1w_brain_template: $$$FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain.nii.gz
+    T1w_brain_template: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain.nii.gz
 
     # Template to be used during registration.
     # It is not necessary to change this path unless you intend to use a non-standard template.
-    T1w_template: $$$FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}.nii.gz
+    T1w_template: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}.nii.gz
 
     # Register skull-on anatomical image to a template.
     reg_with_skull: Off
@@ -112,11 +112,11 @@ registration_workflows:
 
           # Standard Skull Stripped Template. Used as a reference image for functional registration.
           # This can be different than the template used as the reference/fixed for T1-to-template registration.
-          T1w_brain_template_funcreg: $$$FSLDIR/data/standard/MNI152_T1_${func_resolution}_brain.nii.gz
+          T1w_brain_template_funcreg: $FSLDIR/data/standard/MNI152_T1_${func_resolution}_brain.nii.gz
 
           # Standard Anatomical Brain Image with Skull.
           # This can be different than the template used as the reference/fixed for T1-to-template registration.
-          T1w_template_funcreg: $$$FSLDIR/data/standard/MNI152_T1_${func_resolution}.nii.gz
+          T1w_template_funcreg: $FSLDIR/data/standard/MNI152_T1_${func_resolution}.nii.gz
 
     EPI_registration:
       ANTs:
@@ -129,7 +129,7 @@ registration_workflows:
 
         # Identity matrix used during FSL-based resampling of BOLD-space data throughout the pipeline.
         # It is not necessary to change this path unless you intend to use a different template.
-        identity_matrix: $$$FSLDIR/etc/flirtsch/ident.mat
+        identity_matrix: $FSLDIR/etc/flirtsch/ident.mat
 
 functional_preproc:
   run: Off

CPAC/resources/configs/pipeline_config_rbc-options.yml

@@ -35,15 +35,15 @@ registration_workflows:
 
     # Template to be used during registration.
     # It is not necessary to change this path unless you intend to use a non-standard template.
-    T1w_brain_template: $$$FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain.nii.gz
+    T1w_brain_template: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain.nii.gz
 
     # Template to be used during registration.
     # It is not necessary to change this path unless you intend to use a non-standard template.
-    T1w_template: $$$FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}.nii.gz
+    T1w_template: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}.nii.gz
 
     # Template to be used during registration.
     # It is not necessary to change this path unless you intend to use a non-standard template.
-    T1w_brain_template_mask: $$$FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask.nii.gz
+    T1w_brain_template_mask: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask.nii.gz
 
   functional_registration:
     func_registration_to_template:
@@ -69,18 +69,18 @@ registration_workflows:
 
           # Standard Skull Stripped Template. Used as a reference image for functional registration.
           # This can be different than the template used as the reference/fixed for T1-to-template registration.
-          T1w_brain_template_funcreg: $$$FSLDIR/data/standard/MNI152_T1_${func_resolution}_brain.nii.gz
+          T1w_brain_template_funcreg: $FSLDIR/data/standard/MNI152_T1_${func_resolution}_brain.nii.gz
 
           # Standard Anatomical Brain Image with Skull.
           # This can be different than the template used as the reference/fixed for T1-to-template registration.
-          T1w_template_funcreg: $$$FSLDIR/data/standard/MNI152_T1_${func_resolution}.nii.gz
+          T1w_template_funcreg: $FSLDIR/data/standard/MNI152_T1_${func_resolution}.nii.gz
 
           # Template to be used during registration.
           # It is not necessary to change this path unless you intend to use a non-standard template.
-          T1w_brain_template_mask_funcreg: $$$FSLDIR/data/standard/MNI152_T1_${func_resolution}_brain_mask.nii.gz
+          T1w_brain_template_mask_funcreg: $FSLDIR/data/standard/MNI152_T1_${func_resolution}_brain_mask.nii.gz
 
           # a standard template for resampling if using float resolution
-          T1w_template_for_resample: $$$FSLDIR/data/standard/MNI152_T1_${func_resolution}_brain.nii.gz
+          T1w_template_for_resample: $FSLDIR/data/standard/MNI152_T1_${func_resolution}_brain.nii.gz
 
 functional_preproc:
   distortion_correction:

CPAC/utils/configuration/yaml_template.py

@@ -164,7 +164,8 @@ def dump(self, new_dict, parents=None):
                 # SSOT FSLDIR
                 if (isinstance(value, str) and fsldir in value and
                         key != 'FSLDIR'):
-                    value = value.replace(fsldir, '$FSLDIR')
+                    value = re.sub(r'\$*FSLDIR', '$FSLDIR',
+                                   value.replace(fsldir, '$FSLDIR'))
                 if isinstance(value, dict):
                     _dump += [indented_key, self.dump(new_dict, keys)]
                 elif isinstance(value, list):

dev/docker_data/run.py

@@ -247,10 +247,6 @@ def run_main():
     parser.add_argument('--save_working_dir', nargs='?',
                         help='Save the contents of the working directory.',
                         default=False)
-    parser.add_argument('--disable_file_logging', action='store_true',
-                        help='Disable file logging, this is useful for '
-                             'clusters that have disabled file locking.',
-                        default=False)
 
     parser.add_argument('--participant_label',
                         help='The label of the participant that should be '
@@ -595,8 +591,6 @@ def run_main():
             c['pipeline_setup']['system_config']['observed_usage'][
                 'buffer'] = args.runtime_buffer
 
-        c['disable_log'] = args.disable_file_logging
-
         if args.save_working_dir is not False:
             c['pipeline_setup']['working_directory'][
                 'remove_working_dir'] = False