oceanproc 1.2.2__tar.gz → 1.3.1__tar.gz

{oceanproc-1.2.2 → oceanproc-1.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: oceanproc
-Version: 1.2.2
+Version: 1.3.1
 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-1.2.2 → oceanproc-1.3.1}/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-1.2.2 → oceanproc-1.3.1}/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-1.2.2 → oceanproc-1.3.1}/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-1.2.2 → oceanproc-1.3.1}/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",
@@ -74,10 +103,9 @@ 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 v1.3.1')
     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())
 
     session_args.add_argument("--subject", "-su", required=True,
                               help="The identifier of the subject to preprocess")
@@ -138,7 +166,7 @@ def main():
     config_args.add_argument("--dscans_path", type=ExistingDir,
                              help="""The path to the directory containing 'dscans' files for inserting dummy scans into bold runs. Must be named exactly as corresponding bold image except with 'dscans' as 
                              the suffix and '.tsv' as the extension. Contents of the file must be a column, titled 'dummy_scan', with ones and zeros. Ones denote which frames should be dummy scans.""")
-    config_args.add_argument("--precomputed_derivatives", "-pd", type="Full-Path", dest="derivatives", nargs="*",
+    config_args.add_argument("--precomputed_derivatives", "-pd", type=ExistingDir, dest="derivatives", nargs="+",
                              help="A list of paths to any BIDS-style precomputed derivatives that should be used in preprocessing. (Ex. /path/to/bibsnet)")
     config_args.add_argument("--work_dir", "-w", type=ExistingDir, required=True,
                              help="The path to the working directory used to store intermediate files")
@@ -155,19 +183,16 @@ 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 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 +200,12 @@ 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 +217,10 @@ 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 +233,11 @@ 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 +248,11 @@ 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 +298,11 @@ 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 +327,6 @@ 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 +386,7 @@ 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-1.2.2 → oceanproc-1.3.1}/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
@@ -85,10 +84,8 @@ def run_preprocessing(subject:str,
     if flags.apptainer:
         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 = []
@@ -122,16 +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,
@@ -356,7 +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,
@@ -367,8 +366,45 @@ 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:
+        if out_path.exists():
+            # 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-1.2.2 → oceanproc-1.3.1}/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 +124,30 @@ 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:
+        if out_path.exists():
+            # 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-1.2.2 → oceanproc-1.3.1}/oceanproc/utils.py

@@ -239,20 +239,24 @@ 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, quiet=False):
     split_cmd = shlex.split(cmd)
     logger.info(f"running '{title}' with the following command: \n{' '.join(split_cmd)}\n")
     prepare_subprocess_logging(logger)
+    ecode = 0
     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)
+        ecode = p.poll()
         p.kill()
-        if p.poll() != 0:
-            raise RuntimeError(f"process -'{title}'- has ended with a non-zero exit code.")
+        if (ecode != 0) and (not quiet):
+            raise RuntimeError(f"process -'{title}'- has ended with a non-zero exit code <{ecode}>.")
+    return ecode
 
 
 def log_linebreak():
@@ -389,3 +393,30 @@ 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, quiet=True)
+
+    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, quiet=True)

{oceanproc-1.2.2 → oceanproc-1.3.1}/pyproject.toml

@@ -34,7 +34,7 @@ dependencies = [
     "pybids>=0.16.3",
 ]
 name = "oceanproc"
-version = "1.2.2"
+version = "1.3.1"
 description = "MRI preprocessing for WUSTL Ocean labs"
 readme = "README.md"