oceanproc 1.2.1__tar.gz → 1.3.0__tar.gz

{oceanproc-1.2.1 → oceanproc-1.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: oceanproc
-Version: 1.2.1
+Version: 1.3.0
 Summary: MRI preprocessing for WUSTL Ocean labs
 Author-Email: Ramone Agard <rhagard@wustl.edu>, Joey Scanga <joeyscanga92@gmail.com>
 Requires-Python: <3.13,>=3.10

{oceanproc-1.2.1 → oceanproc-1.3.0}/oceanproc/bids_wrapper.py

@@ -4,14 +4,12 @@ from argparse import ArgumentParser
 from pathlib import Path
 import json
 import os
-import re
 import shutil
-import subprocess
 from textwrap import dedent
 import xml.etree.ElementTree as et
-from .utils import exit_program_early, prompt_user_continue, prepare_subprocess_logging, debug_logging, log_linebreak, flags, run_subprocess
+from .utils import exit_program_early, prompt_user_continue, prepare_subprocess_logging, debug_logging, log_linebreak, flags, run_subprocess, update_permissions
 import logging
-from bids import BIDSLayout, BIDSLayoutIndexer
+from bids import BIDSLayout
 from bisect import bisect
 module_logger = logging.getLogger("fsspec")
 module_logger.setLevel(logging.CRITICAL)
@@ -136,16 +134,16 @@ def run_dcm2bids(subject:str,
                 logger.debug(f"deleting file: {f}")
                 os.remove(f)
 
-    except RuntimeError or subprocess.CalledProcessError as e:
+    except (Exception, KeyboardInterrupt) as e:
         prepare_subprocess_logging(logger, stop=True)
         logger.exception(e, stack_info=True)
-        exit_program_early(f"Problem running '{title}'.")
+        return False
 
+    return True
 
 @debug_logging
 def run_dcm2niix(source_dir:Path,
-                 tmp_nifti_dir:Path,
-                 clean_up_func=None):
+                 tmp_nifti_dir:Path):
     """
     Run dcm2niix with the given input and output directories.
 
@@ -176,11 +174,12 @@ def run_dcm2niix(source_dir:Path,
         log_linebreak()
         logger.info("####### Converting DICOM files into NIFTI #######\n")
         run_subprocess(helper_command, title=title)
-    except RuntimeError or subprocess.CalledProcessError as e:
+    except (Exception, KeyboardInterrupt) as e:
         prepare_subprocess_logging(logger, stop=True)
         logger.exception(e, stack_info=True)
-        exit_program_early(f"Problem running '{title}'.",
-                           exit_func=clean_up_func if clean_up_func else None)
+        return False
+    
+    return True
 
 
 def get_usability_from_file(usability_file:Path):
@@ -322,7 +321,8 @@ def dicom_to_bids(subject:str,
         if not p.exists():
             exit_program_early(f"Path {str(p)} does not exist.")
 
-    if (path_that_exists := bids_dir / f"sub-{subject}/ses-{session}").exists() and (not skip_prompt):
+    sub_ses_bids_dir = bids_dir / f"sub-{subject}/ses-{session}"
+    if sub_ses_bids_dir.exists() and (not skip_prompt):
         ans = prompt_user_continue(dedent("""
                                         A raw data bids path for this subject and session already exists.
                                         Would you like to delete its contents and rerun dcm2bids? If not,
@@ -330,7 +330,7 @@ def dicom_to_bids(subject:str,
                                             """))
         if ans:
             logger.debug("removing the old BIDS raw data directory and its contents")
-            shutil.rmtree(path_that_exists)
+            shutil.rmtree(sub_ses_bids_dir)
         else:
             return
 
@@ -345,16 +345,27 @@ def dicom_to_bids(subject:str,
                 logger.warning(f"There was a problem deleting the temporary directory at {tmp_nifti_path}")
 
     clean_up(quiet=True)
+    nii_success = True
     if not nifti:
-        run_dcm2niix(source_dir=source_dir,
-                     tmp_nifti_dir=tmp_nifti_path)
+        nii_success = run_dcm2niix(source_dir=source_dir,
+                                   tmp_nifti_dir=tmp_nifti_path)
     else:
         # copy current niftis to tmp_nifti_path 
         logger.info(f"copying the source NIFTI files to tmp directory, {tmp_nifti_path}")
         shutil.copytree(source_dir.resolve(), tmp_nifti_path.resolve())
 
-
-    # filter out know 'weird' files that can be created during conversion
+    # update the permissions on the nifti files
+    update_permissions(
+        permissions=flags.file_permissions,
+        path=tmp_nifti_path,
+        recursive=True,
+        group=flags.permissions_group
+    )
+    
+    if not nii_success:
+        exit_program_early(f"Problem running 'dcm2niix'")
+
+    # filter out known 'weird' files that can be created during conversion
     if not keep_all_niftis:
         files_to_remove = []
         short_runs = list(tmp_nifti_path.glob("[!.]*[a-z].nii*")) + list(tmp_nifti_path.glob("[!.]*[a-z].json"))
@@ -396,13 +407,24 @@ def dicom_to_bids(subject:str,
                                usability_file=usability_file,
                                session_number=session_index)
 
-    run_dcm2bids(subject=subject,
+    dcm2bids_success = run_dcm2bids(subject=subject,
                  session=session,
                  nifti_dir=tmp_nifti_path,
                  bids_output_dir=bids_dir,
                  config_file=bids_config,
                  nordic_config=nordic_config,
                  skip_validate=skip_validate)
+    
+    update_permissions(
+        permissions=flags.file_permissions,
+        path=sub_ses_bids_dir,
+        recursive=True,
+        group=flags.permissions_group,
+        quiet=True
+    )
+
+    if not dcm2bids_success:
+        exit_program_early(f"Problem running 'dcm2bids'")
 
     if not flags.debug:
         clean_up()

{oceanproc-1.2.1 → oceanproc-1.3.0}/oceanproc/events_long.py

@@ -2,7 +2,7 @@ import pandas as pd
 import numpy as np
 import nibabel as nib
 import json
-from .utils import exit_program_early, debug_logging, log_linebreak
+from .utils import exit_program_early, debug_logging, log_linebreak, update_permissions, flags
 from pathlib import Path
 import logging
 
@@ -162,6 +162,11 @@ def create_events_and_confounds(bids_path:Path, derivs_path:Path, sub:str, ses:s
                          output_file=event_file_out)
         append_to_confounds(confounds_file=confounds_file, 
                             fd_thresh=fd_thresh)
+        update_permissions(
+            permissions=flags.file_permissions,
+            path=event_file_out,
+            group=flags.permissions_group
+        )
         
 
 

{oceanproc-1.2.1 → oceanproc-1.3.0}/oceanproc/group_series.py

@@ -3,53 +3,20 @@
 import json
 from datetime import datetime, timedelta
 import argparse
-import re
 from pathlib import Path
-import xml.etree.ElementTree as et
 from bids import BIDSLayout
 import logging
 
 from bids.layout import BIDSFile
-from .utils import exit_program_early, debug_logging, log_linebreak, flags
+from .utils import exit_program_early, debug_logging, log_linebreak, flags, update_permissions
 import nibabel as nib
 import numpy as np
-import shutil
 
 module_logger = logging.getLogger("fsspec")
 module_logger.setLevel(logging.CRITICAL)
 
 logger = logging.getLogger(__name__)
 
-
-# @debug_logging
-# def get_locals_from_xml(xml_path: Path) -> tuple[set, str]:
-#     """
-#     Read in the xml file to find the localizers.
-
-#     :param xml_path: Path to XML generated by XNAT
-#     :type xml_path: pathlib.Path
-#     :return: Set containing all localizer IDs
-#     :rtype: set
-#     """
-#     tree = et.parse(xml_path)
-#     prefix = "{" + str(tree.getroot()).split("{")[-1].split("}")[0] + "}"
-#     scan_element_list = list(tree.iter(f"{prefix}scans"))
-#     exp_element_list = list(tree.iter(f"{prefix}experiments"))
-#     study_id = exp_element_list[0][0].get("study_id")
-
-#     if len(scan_element_list) != 1:
-#         exit_program_early(f"Error parsing the xml file provided. Found none or more than one scan groups")
-
-#     scans = scan_element_list[0]
-
-#     localizers = set()
-#     for s in scans:
-#         if re.match(r"Localizer.*", s.get("type")) and s.find(f'{prefix}quality').text == "usable":
-#             acq_time = datetime.strptime(s.find(f"{prefix}startTime").text, "%H:%M:%S")
-#             series_id = s.get("ID")
-#             localizers.add((acq_time, series_id))
-#     return (sorted(localizers), study_id)
-
 DEFAULT_LOCALIZER_LABEL = "00"
 EXTRACTED_ACQ_VALUE = "bestVol"
 
@@ -331,6 +298,13 @@ def extract_best_acqusition(fmap_file: str|BIDSFile, bids_layout: BIDSLayout) ->
     with open(best_acq_json, "w") as out_js:
         json.dump(jd, out_js, indent=4)
 
+    for fmap_out_path in [best_acq_fmap, best_acq_json]:
+        update_permissions(
+            permissions=flags.file_permissions,
+            path=fmap_out_path,
+            group=flags.permissions_group,
+        )
+
     return (BIDSFile(best_acq_fmap), BIDSFile(best_acq_json))
     
 

{oceanproc-1.2.1 → oceanproc-1.3.0}/oceanproc/ocean_proc.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python3
 
 import argparse
+from ast import arg
 import sys
 from pathlib import Path
 import logging
@@ -10,10 +11,12 @@ from oceanproc.group_series import map_fmap_to_func, map_fmap_to_func_with_pairi
 from oceanproc.preprocessing_wrapper import process_data, adult_defaults, infant_defaults, mount_opts, insert_dummy_frames
 from oceanproc.segmentation_wrapper import segmentation_args, segment_anatomical
 from oceanproc.events_long import create_events_and_confounds
-from oceanproc.utils import exit_program_early, prompt_user_continue, default_log_format, add_file_handler, export_args_to_file, flags, debug_logging, log_linebreak, extract_options, make_option
+from oceanproc.utils import *
 from oceanproc.oceanparse import OceanParser
 from bids import BIDSLayout, BIDSLayoutIndexer
 import shutil
+import grp
+import os
 from textwrap import dedent
 
 logging.basicConfig(level=logging.INFO,
@@ -65,6 +68,32 @@ def main():
                 f"path string <{path}> does not represent an existing file"
             )
         return p
+
+    def ValidPermissions(permissions):
+        try:
+            validate_permissions_string(permissions)
+        except ValueError:
+            raise argparse.ArgumentTypeError(
+                f"permissions string <{permissions}> does not represent a valid permissions string"
+            )
+        return permissions
+
+    def ValidGroup(group):
+        try:
+            group_id = grp.getgrnam(group).gr_gid
+            valid_groups = os.getgroups()
+            if group_id not in valid_groups:
+                raise argparse.ArgumentTypeError(
+                    f"current user does not belong to group <{group}>"
+                )
+        except KeyError:
+            raise argparse.ArgumentTypeError(
+                f"group name <{group}> is not a valid system user group"
+            )
+        return group
+
+    default_user_group = grp.getgrgid(os.getgid()).gr_name
+    default_file_permissions = "771"
     
     parser = OceanParser(
         prog="oceanproc",
@@ -74,7 +103,7 @@ def main():
         epilog="An arguments file can be accepted with @FILEPATH.\nAny additional arguments not listed in the help message will be passed to the preprocessing subprocess.",
         allow_abbrev=False
     )
-    parser.add_argument("--version", action="version", version='%(prog)s v1.1.8')
+    parser.add_argument("--version", action="version", version='%(prog)s v1.3.0')
     session_args = parser.add_argument_group("Session Specific")
     config_args = parser.add_argument_group("Configuration Arguments", "These arguments are saved to a file if the '--export_args' option is used")
     parser.register("type", "Full-Path", lambda p: Path(p).resolve())
@@ -155,19 +184,16 @@ def main():
                              help="Path to the BIBSnet apptainer image to use for segmentation. If provided, BIBSnet segmentation will be run and the outputs will be used for preprocessing. (Must be used with the '--infant' flag)")
     config_args.add_argument("--bibsnet_work", "-bw", type=ExistingDir,
                              help="The path to the working directory used to store intermediate files for BIBSnet")
+    config_args.add_argument("--permissions_group", "-g", type=ValidGroup, default=default_user_group,
+                             help=f"The user group that should own all of the created files. (Default is for the current user is '{default_user_group}'")
+    config_args.add_argument("--file_permissions", "-fp", type=ValidPermissions, default=default_file_permissions,
+                             help=f"The file permissions that all output files should have, represented in numeric format. (Default permissions is '{default_file_permissions}'")
     args, unknown_args = parser.parse_known_args()
 
-    # try:
-    #     assert args.derivs_path.is_dir(), "Derivatives directory must exist but it cannot be found"
-    #     assert args.bids_path.is_dir(), "Raw Bids directory must exist but it cannot be found"
-    #     if not args.skip_dcm2bids:
-    #         assert args.source_data.is_dir(), "Source data directory must exist but it cannot be found"
-    #     assert args.work_dir.is_dir(), "Work directroy must exist but it cannot be found"
-    # except AssertionError as e:
-    #     logger.exception(e)
-    #     parser.error(e)
-
-    defaults = infant_defaults if args.infant else adult_defaults
+    if args.infant:
+        flags.infant = True
+
+    defaults = infant_defaults if flags.infant else adult_defaults
     for k,v in defaults.__dict__.items():
         if k in args.__dict__ and args.__dict__[k] is None:
             args.__dict__[k] = v
@@ -175,15 +201,12 @@ def main():
     unknown_args = extract_options(unknown_args)
 
     bibsnet_path = (args.derivs_path / "bibsnet").resolve()
-    if args.infant and args.bibsnet_image_path:
+    if flags.infant and args.bibsnet_image_path:
         if args.derivatives is None:
             args.derivatives = [bibsnet_path]
         elif bibsnet_path not in args.derivatives:
             args.derivatives.append(bibsnet_path)
 
-    # if args.bibsnet_work and (not args.bibsnet_work.exists()):
-    #     parser.error("BIBSnet working directory must exist but it cannot be found")
-
     if args.longitudinal:
         for lg_group in args.longitudinal:
             if not lg_group[0].is_dir():
@@ -195,11 +218,10 @@ def main():
                     parser.error(f"usability file must be a .xml or .json file, and it must exist: {lg_group[1]}")
             else:
                 parser.error(f"longitudinal argument cannot have more than 2 elements: {lg_group}")
+        flags.longitudinal = True
 
     preproc_image = f"{defaults.image_name}:{args.image_version}"
     if args.preproc_image_path:
-        # if not args.preproc_image_path.exists():
-        #     parser.error(f"Cannot find the preprocessing apptainer image at the path: {args.preproc_image_path}")
         flags.apptainer = True
         preproc_image = args.preproc_image_path
 
@@ -212,6 +234,11 @@ def main():
     if args.debug_mode:
         flags.debug = True
         logger.setLevel(logging.DEBUG)
+    
+    flags.file_permissions = args.file_permissions
+    flags.permissions_group = args.permissions_group
+    flags.gid = grp.getgrnam(flags.permissions_group).gr_gid
+    flags.uid = os.getuid()
 
     logger.info("Starting oceanproc...")
     logger.info(f"Log will be stored at {log_path}")
@@ -222,14 +249,11 @@ def main():
             assert args.export_args.parent.exists() and args.export_args.suffix, "Argument export path must be a file path in a directory that exists"
             logger.info(f"####### Exporting Configuration Arguments to: '{args.export_args}' #######")
             export_args_to_file(args, config_args, args.export_args, extra_args=unknown_args)
+            update_permissions(permissions=flags.file_permissions, path=args.export_args, group=flags.permissions_group)
         except Exception as e:
             logger.exception(e)
             exit_program_early(e)
 
-    if args.longitudinal:
-        flags.longitudinal = True
-    if args.infant:
-        flags.infant = True
 
     # log the input arguments
     for k,v in (dict(args._get_kwargs())).items():
@@ -275,6 +299,11 @@ def main():
         with open(bids_path / ".bidsignore", "r") as f:
             ignore_list.extend(f.readlines())
     ignore_list = list(set(ignore_list))
+    other_sub_paths = [
+      p.name for p in bids_path.glob("sub-*") 
+      if not f"sub-{args.subject}".startswith(p.name) and p.is_dir()  # 'startswith' to account for pybids regexifying after the end of subject name
+    ]
+    ignore_list.extend(other_sub_paths)
     bids_layout = BIDSLayout(args.bids_path, validate=False, indexer=BIDSLayoutIndexer(ignore=ignore_list, validate=False))
 
     ##### Remove the scans marked as 'unusable' #####
@@ -299,7 +328,6 @@ def main():
                 subject=args.subject,
                 session=args.session,
                 layout=bids_layout,
-                # xml_path=xml_data_path,
                 allow_uneven_fmap_groups=args.allow_uneven_fmap_groups,
                 extract_best_fmap=args.extract_best_fmap
             )
@@ -359,7 +387,7 @@ def main():
         )
 
     ##### Create long formatted event files #####
-    if not args.skip_event_files:
+    if not args.skip_event_files and not args.anat_only:
         create_events_and_confounds(
             bids_path=args.bids_path,
             derivs_path=preproc_derivs_path,

{oceanproc-1.2.1 → oceanproc-1.3.0}/oceanproc/preprocessing_wrapper.py

@@ -3,9 +3,8 @@
 from pathlib import Path
 import logging
 from bids import BIDSLayout
-from .utils import exit_program_early, make_option, prepare_subprocess_logging, flags, debug_logging, log_linebreak, run_subprocess
+from .utils import exit_program_early, make_option, prepare_subprocess_logging, flags, debug_logging, log_linebreak, run_subprocess, update_permissions
 import shutil
-from subprocess import Popen, PIPE
 from matplotlib import pyplot as plt
 from bs4 import BeautifulSoup as bsoup
 import pandas as pd
@@ -76,14 +75,17 @@ def run_preprocessing(subject:str,
         exit_program_early(f"Bids path {bids_path} does not exist.")
     elif not derivs_path.exists():
         exit_program_early(f"Derivatives path {derivs_path} does not exist.")
+
+    license_mount = "/opt/freesurfer/license.txt"
+    bids_mount = "/data"
+    derivs_mount = "/out"
+    work_mount = "/work"
     
     if flags.apptainer:
-        cmd_prelude = "apptainer run --nv --cleanenv --no-mount cwd"
+        cmd_prelude = f"apptainer run --nv --cleanenv --no-mount cwd --pwd {work_mount}"
         mount_flag = "-B"
-    else:
-        uid = Popen(["id", "-u"], stdout=PIPE).stdout.read().decode("utf-8").strip()
-        gid = Popen(["id", "-g"], stdout=PIPE).stdout.read().decode("utf-8").strip()
-        cmd_prelude = f"docker run --rm -i -u {uid}:{gid}"
+    else: 
+        cmd_prelude = f"docker run --rm -i -u {flags.uid}:{flags.gid}"
         mount_flag = "-v"
 
     additional_mount_paths = []
@@ -104,10 +106,6 @@ def run_preprocessing(subject:str,
     additional_mount_paths = " ".join(additional_mount_paths)
     additional_mount_args = " ".join(additional_mount_args)
 
-    license_mount = "/opt/freesurfer/license.txt"
-    bids_mount = "/data"
-    derivs_mount = "/out"
-    work_mount = "/work"
     preproc_command = f"""{cmd_prelude}
                             {mount_flag} {license_file.resolve()}:{license_mount}:ro
                             {mount_flag} {bids_path.resolve()}:{bids_mount}:ro
@@ -121,16 +119,18 @@ def run_preprocessing(subject:str,
                             {additional_mount_args}
                             {option_chain}"""
     
+    success = True
     try:
         run_subprocess(preproc_command, title=title)
-    except RuntimeError as e:
+    except (Exception, KeyboardInterrupt) as e:
         prepare_subprocess_logging(logger, stop=True)
         logger.exception(e, stack_info=True)
-        exit_program_early(f"Program '{title}' has run into an error.",
-                           None if flags.debug else clean_up)
+        success = False
+
     if not flags.debug:
         clean_up()
 
+    return success
 
 @debug_logging
 def add_fd_plot_to_report(subject:str,
@@ -355,7 +355,7 @@ def process_data(subject:str,
     option_chain = " ".join([make_option(v, key=k, delimeter=" ", convert_underscore=True) for k,v in kwargs.items()])
     preproc_title = "NiBabies" if flags.infant else "fMRIPrep"
 
-    run_preprocessing(subject=subject,
+    preproc_success = run_preprocessing(subject=subject,
                       session=session if flags.infant else None,
                       bids_path=bids_path,
                       derivs_path=derivs_path,
@@ -366,8 +366,44 @@ def process_data(subject:str,
                       option_chain=option_chain,
                       additional_mounts=additional_mounts,
                       remove_work_folder=remove_work_folder)
-
-    add_fd_plot_to_report(subject=subject,
-                          session=session,
-                          derivs_path=derivs_path,
-                          title=preproc_title)
+    
+    if preproc_success:
+        add_fd_plot_to_report(subject=subject,
+                            session=session,
+                            derivs_path=derivs_path,
+                            title=preproc_title)
+    
+    paths_to_update = []
+    paths_to_update.extend(sorted(derivs_path.glob(f"sub-{subject}*")))
+    paths_to_update.extend(sorted(derivs_path.glob(f"sourcedata/*/sub-{subject}*")))
+    for out_path in paths_to_update:
+        # update file permissions for preprocessing outputs
+        update_permissions(
+            permissions=flags.file_permissions, 
+            path=out_path, 
+            recursive=True,
+            group=flags.permissions_group
+        )
+        
+    # check other top-level files
+    other_paths = [derivs_path/"dataset_description.json", derivs_path/"logs"]
+    for op in other_paths:
+        if op.exists() and (op.stat().st_uid == flags.uid):
+            update_permissions(
+                permissions=flags.file_permissions,
+                path=op,
+                recursive=True,
+                group=flags.permissions_group
+            )
+            
+    # update file permisions for working directory files
+    update_permissions(
+        permissions=flags.file_permissions, 
+        path=work_path, 
+        recursive=True,
+        group=flags.permissions_group,
+        quiet=True
+    )
+    
+    if not preproc_success:
+        exit_program_early(f"Program '{preproc_title}' has run into an error.")

{oceanproc-1.2.1 → oceanproc-1.3.0}/oceanproc/segmentation_wrapper.py

@@ -2,7 +2,8 @@
 
 from pathlib import Path
 import logging
-from .utils import exit_program_early, make_option, prepare_subprocess_logging, flags, debug_logging, log_linebreak, run_subprocess
+from sre_constants import SUCCESS
+from .utils import exit_program_early, make_option, prepare_subprocess_logging, flags, debug_logging, log_linebreak, run_subprocess, update_permissions
 import shutil
 from pathlib import Path
 
@@ -59,9 +60,6 @@ def run_bibsnet(subject:str,
     elif not bibsnet_image.exists():
         exit_program_early(f"BIBSnet image path {derivs_path} does not exist.")
 
-    # uid = Popen(["id", "-u"], stdout=PIPE).stdout.read().decode("utf-8").strip()
-    # gid = Popen(["id", "-g"], stdout=PIPE).stdout.read().decode("utf-8").strip()
-
     bids_mount = "/data"
     derivs_mount = "/out"
     work_mount = "/work"
@@ -75,16 +73,18 @@ def run_bibsnet(subject:str,
                             -w {work_mount} --verbose
                             {option_chain}"""
     
+    success = True
     try:
         run_subprocess(bibsnet_command, title="BIBSnet")
-    except RuntimeError as e:
+    except (Exception, KeyboardInterrupt) as e:
         prepare_subprocess_logging(logger, stop=True)
         logger.exception(e, stack_info=True)
-        exit_program_early(f"Program 'BIBSnet' has run into an error.",
-                           None if flags.debug else clean_up)
+        success = False
+
     if not flags.debug:
         clean_up()
 
+    return success
 
 @debug_logging
 def segment_anatomical(subject:str,
@@ -116,7 +116,7 @@ def segment_anatomical(subject:str,
     """
     option_chain = " ".join([make_option(v, key=k, delimeter=" ", convert_underscore=True) for k,v in kwargs.items()])
 
-    run_bibsnet(subject=subject,
+    segment_success = run_bibsnet(subject=subject,
                       session=session,
                       bids_path=bids_path,
                       derivs_path=derivs_path,
@@ -124,5 +124,29 @@ def segment_anatomical(subject:str,
                       bibsnet_image=bibsnet_image,
                       option_chain=option_chain,
                       remove_work_folder=remove_work_folder)
+    
+    paths_to_update = sorted(derivs_path.glob(f"bibsnet/sub-{subject}*"))
+    paths_to_update.extend(sorted(work_path.glob(f"*/sub-{subject}*")))
+    for out_path in paths_to_update:
+        # update file permissions for segmentation outputs and working files
+        update_permissions(
+            permissions=flags.file_permissions, 
+            path=out_path, 
+            recursive=True,
+            group=flags.permissions_group)
+        
+    # check other top-level files
+    other_paths = [derivs_path/"dataset_description.json"]
+    for op in other_paths:
+        if op.exists() and (op.stat().st_uid == flags.uid):
+            update_permissions(
+                permissions=flags.file_permissions,
+                path=op,
+                recursive=True,
+                group=flags.permissions_group
+            )
+        
+    if not segment_success:
+        exit_program_early(f"Program 'BIBSnet' has run into an error.")
 
 

{oceanproc-1.2.1 → oceanproc-1.3.0}/oceanproc/utils.py

@@ -239,20 +239,21 @@ def prepare_subprocess_logging(this_logger,
 
 
 @debug_logging
-def run_subprocess(cmd: str, title: str):
+def run_subprocess(cmd: str, title: str, log_output=True):
     split_cmd = shlex.split(cmd)
     logger.info(f"running '{title}' with the following command: \n{' '.join(split_cmd)}\n")
     prepare_subprocess_logging(logger)
     with Popen(split_cmd, stdout=PIPE, stderr=PIPE) as p:
         while p.poll() == None:
-            for line in p.stdout:
-                logger.info(line.decode("utf-8", "ignore"))
-            for line in p.stderr:
-                logger.info(line.decode("utf-8", "ignore"))
+            if log_output:
+                for line in p.stdout:
+                    logger.info(line.decode("utf-8", "ignore"))
+                for line in p.stderr:
+                    logger.info(line.decode("utf-8", "ignore"))
         prepare_subprocess_logging(logger, stop=True)
         p.kill()
-        if p.poll() != 0:
-            raise RuntimeError(f"process -'{title}'- has ended with a non-zero exit code.")
+        if (ecode:=p.poll()) != 0:
+            raise RuntimeError(f"process -'{title}'- has ended with a non-zero exit code <{ecode}>.")
 
 
 def log_linebreak():
@@ -389,3 +390,30 @@ def parcellate_dtseries(dtseries_path: Path,
         exit_program_early(f"Program '{title}' has run into an error.")
 
     return ptseries_path
+
+def validate_permissions_string(permissions:str):
+    valid = True
+    if (len(permissions) != 3) or not permissions.isnumeric():
+        valid = False
+    if valid:
+        for character in permissions:
+            if int(character) > 7 or int(character) < 0:
+                valid = False
+
+    if not valid:
+        raise ValueError(f"Did not receive a valid permissions string: <{permissions}>")
+    
+
+def update_permissions(permissions:str, path:Path, recursive=False, group=None, quiet=False):
+    validate_permissions_string(permissions)
+    if not path.exists():
+        if quiet:
+            return
+        raise ValueError(f"Did not receive a valid path: <{path}>")
+    
+    chmod_cmd = f"chmod {'-R' if recursive else ''} {permissions} {path.resolve()}"
+    run_subprocess(cmd=chmod_cmd, title="chmod", log_output=False)
+
+    if group is not None:
+        chgrp_cmd = f"chgrp {'-R' if recursive else ''} {group} {path.resolve()}"
+        run_subprocess(cmd=chgrp_cmd, title="chgrp", log_output=False)

{oceanproc-1.2.1 → oceanproc-1.3.0}/pyproject.toml

@@ -34,7 +34,7 @@ dependencies = [
     "pybids>=0.16.3",
 ]
 name = "oceanproc"
-version = "1.2.1"
+version = "1.3.0"
 description = "MRI preprocessing for WUSTL Ocean labs"
 readme = "README.md"