- Move run_command() to __init__()

- Rename updatemetadata() to poolmetadata()
- Add/update documentation

Author: marcelzwiers

bidscoin/__init__.py

@@ -24,9 +24,11 @@
 import shutil
 import warnings
 import tempfile
+import subprocess
 from pathlib import Path
 from importlib import metadata
 from typing import Tuple, Union, List
+from logging import getLogger
 from .due import due, Doi
 try:
     import tomllib
@@ -40,6 +42,8 @@
     with open(Path(__file__).parents[1]/'pyproject.toml', 'rb') as fid:
         __version__ = tomllib.load(fid)['project']['version']
 
+LOGGER = getLogger(__name__)
+
 # Add license metadata
 __license__    = 'GNU General Public License v3.0 or later (GPLv3+)'
 __copyright__  = f"2018-{datetime.date.today().year}, Marcel Zwiers"
@@ -142,6 +146,25 @@ def lsdirs(folder: Path, wildcard: str='*') -> List[Path]:
     return sorted([item for item in sorted(folder.glob(wildcard)) if item.is_dir() and not is_hidden(item.relative_to(folder))])
 
 
+def run_command(command: str, success: tuple=(0,None)) -> int:
+    """
+    Runs a command in a shell using subprocess.run(command, ..)
+
+    :param command: The command that is executed
+    :param success: The return codes for successful operation (e,g, for dcm2niix it is (0,3))
+    :return:        The return code (e.g. 0 if the command was successfully executed (no errors), > 0 otherwise)
+    """
+
+    LOGGER.verbose(f"Command:\n{command}")
+    process = subprocess.run(command, shell=True, capture_output=True, text=True)
+    if process.stderr or process.returncode not in success:
+        LOGGER.error(f"Failed to run:\n{command}\nErrorcode {process.returncode}:\n{process.stdout}\n{process.stderr}")
+    else:
+        LOGGER.verbose(f"Output:\n{process.stdout}")
+
+    return process.returncode
+
+
 def trackusage(event: str, dryrun: bool=False) -> dict:
     """Sends a url GET request with usage data parameters (if tracking is allowed and we are not asleep)
 

bidscoin/bcoin.py

@@ -8,10 +8,8 @@
 import os
 import types
 import coloredlogs
-import inspect
 import logging
 import shutil
-import subprocess
 import sys
 import urllib.request
 import time
@@ -221,25 +219,6 @@ def reporterrors() -> str:
     return errors
 
 
-def run_command(command: str, success: tuple=(0,None)) -> int:
-    """
-    Runs a command in a shell using subprocess.run(command, ..)
-
-    :param command: The command that is executed
-    :param success: The return codes for successful operation (e,g, for dcm2niix it is (0,3))
-    :return:        The return code (e.g. 0 if the command was successfully executed (no errors), > 0 otherwise)
-    """
-
-    LOGGER.verbose(f"Command:\n{command}")
-    process = subprocess.run(command, shell=True, capture_output=True, text=True)
-    if process.stderr or process.returncode not in success:
-        LOGGER.error(f"Failed to run:\n{command}\nErrorcode {process.returncode}:\n{process.stdout}\n{process.stderr}")
-    else:
-        LOGGER.verbose(f"Output:\n{process.stdout}")
-
-    return process.returncode
-
-
 def list_executables(show: bool=False) -> list:
     """
     :param show:    Print the installed console scripts if True
@@ -454,8 +433,7 @@ def test_plugin(plugin: Union[Path,str], options: dict) -> int:
 
     # First test to see if we can import the plugin
     module = import_plugin(plugin, ('bidsmapper_plugin','bidscoiner_plugin'))
-    if not inspect.ismodule(module):
-        LOGGER.error(f"Invalid plugin: '{plugin}'")
+    if module is None:
         return 1
 
     # Then run the plugin's own 'test' routine (if implemented)

bidscoin/bids.py

@@ -2530,7 +2530,7 @@ def addmetadata(bidsses: Path):
                     json.dump(jsondata, sidecar, indent=4)
 
 
-def updatemetadata(datasource: DataSource, targetmeta: Path, usermeta: Meta, extensions: Iterable, sourcemeta: Path=Path()) -> Meta:
+def poolmetadata(datasource: DataSource, targetmeta: Path, usermeta: Meta, extensions: Iterable, sourcemeta: Path=Path()) -> Meta:
     """
     Load the metadata from the target (json sidecar), then add metadata from the source (json sidecar) and finally add
     the user metadata (meta table). Source metadata other than json sidecars are copied over to the target folder. Special

bidscoin/bidsapps/fixmeta.py

@@ -87,7 +87,7 @@ def fixmeta(bidsfolder: str, pattern: str, metadata: dict, participant: list, bi
 
                     # Load/copy over the source meta-data
                     jsonfile = target.with_suffix('').with_suffix('.json')
-                    jsondata = bids.updatemetadata(datasource, jsonfile, bids.Meta({}), ['.json'])
+                    jsondata = bids.poolmetadata(datasource, jsonfile, bids.Meta({}), ['.json'])
                     for key, value in metadata.items():
                         if isinstance(value, list):
                             for n in range(0, len(value), 2):

bidscoin/bidsapps/skullstrip.py

@@ -20,7 +20,7 @@
 from importlib.util import find_spec
 if find_spec('bidscoin') is None:
     sys.path.append(str(Path(__file__).parents[2]))
-from bidscoin import bcoin, bids, lsdirs, trackusage, DEBUG
+from bidscoin import bcoin, bids, lsdirs, trackusage, run_command, DEBUG
 from bidscoin.due import due, Doi
 
 
@@ -141,7 +141,7 @@ def skullstrip(bidsfolder: str, pattern: str, participant: list, masked: str, ou
                             jt.outputPath = f"{os.getenv('HOSTNAME')}:{Path.cwd() if DEBUG else tempfile.gettempdir()}/{jt.jobName}.out"
                             jobids.append(pbatch.runJob(jt))
                             LOGGER.info(f"Your skullstrip job has been submitted with ID: {jobids[-1]}")
-                        elif bcoin.run_command(f"mri_synthstrip -i {srcimg} -o {outputimg} -m {maskimg} {args}"):
+                        elif run_command(f"mri_synthstrip -i {srcimg} -o {outputimg} -m {maskimg} {args}"):
                             continue
 
                         # Add a json sidecar-file with the "SkullStripped" field