From a40a534b4ea74126463948e577290d8791c29712 Mon Sep 17 00:00:00 2001 From: Marcel Zwiers Date: Wed, 5 Feb 2025 11:12:04 +0100 Subject: [PATCH] Minor doctweaks --- bidscoin/bidseditor.py | 2 +- bidscoin/cli/_bidsmapper.py | 2 +- docs/workflow.rst | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/bidscoin/bidseditor.py b/bidscoin/bidseditor.py index 9094dd80..2880828a 100755 --- a/bidscoin/bidseditor.py +++ b/bidscoin/bidseditor.py @@ -341,7 +341,7 @@ def samples_menu(self, pos): datatype = table.item(index, 2).text() provenance = table.item(index, 5).text() if not Path(provenance).is_file(): - QMessageBox.warning(self, 'Edit BIDS mapping', f"Cannot reliably change the data type and/or suffix because the source file '{provenance}' can no longer be found.\n\nPlease restore the source data or use the `bidsmapper -s` option to solve this issue") + QMessageBox.warning(self, 'Edit BIDS mapping', f"Cannot reliably change the data type and/or suffix because the source file '{provenance}' can no longer be found.\n\nPlease restore the source data or use the `bidsmapper -s -f` options to solve this issue") continue # Get the new run from the template diff --git a/bidscoin/cli/_bidsmapper.py b/bidscoin/cli/_bidsmapper.py index ef35e6f3..1d814e9f 100755 --- a/bidscoin/cli/_bidsmapper.py +++ b/bidscoin/cli/_bidsmapper.py @@ -40,7 +40,7 @@ def get_parser() -> argparse.ArgumentParser: parser.add_argument('-n','--subprefix', help="The prefix common for all the source subject-folders (e.g. 'Pt' is the subprefix if subject folders are named 'Pt018', 'Pt019', ...). Use '*' when your subject folders do not have a prefix. Default: the value of the study/template bidsmap, e.g. 'sub-'", metavar='PREFIX') parser.add_argument('-m','--sesprefix', help="The prefix common for all the source session-folders (e.g. 'M_' is the subprefix if session folders are named 'M_pre', 'M_post', ..). Use '*' when your session folders do not have a prefix. Default: the value of the study/template bidsmap, e.g. 'ses-'", metavar='PREFIX') parser.add_argument('-u','--unzip', help='Wildcard pattern to unpack tarball/zip-files in the sub/ses sourcefolder that need to be unzipped (in a tempdir) to make the data readable. Default: the value of the study/template bidsmap', metavar='PATTERN') - parser.add_argument('-s','--store', help='Store provenance data samples in the bidsfolder/code/provenance folder (useful for inspecting e.g. zipped or transferred datasets)', action='store_true') + parser.add_argument('-s','--store', help='Store newly discovered data samples in the bidsfolder/code/provenance folder (useful for editing e.g. zipped or transferred datasets)', action='store_true') parser.add_argument('-a','--automated', help='Save the automatically generated bidsmap to disk and without interactively tweaking it with the bidseditor', action='store_true') parser.add_argument('-f','--force', help='Discard the previously saved bidsmap and logfile', action='store_true') parser.add_argument('--no-update', help="Do not update any sub-/ses-prefixes in or prepend the sourcefolder name to the <> expression that extracts the subject/session labels. This is normally done to make the extraction more robust, but could cause problems for certain use cases", action='store_true') diff --git a/docs/workflow.rst b/docs/workflow.rst index 9cc51a32..b62cf950 100644 --- a/docs/workflow.rst +++ b/docs/workflow.rst @@ -76,8 +76,8 @@ Here is how to run the bidsmapper command: Wildcard pattern to unpack tarball/zip-files in the sub/ses sourcefolder that need to be unzipped (in a tempdir) to make the data readable. Default: the value of the study/template bidsmap - -s, --store Store provenance data samples in the bidsfolder/code/provenance folder - (useful for inspecting e.g. zipped or transferred datasets) + -s, --store Store newly discovered data samples in the bidsfolder/code/provenance folder + (useful for editing e.g. zipped or transferred datasets) -a, --automated Save the automatically generated bidsmap to disk and without interactively tweaking it with the bidseditor -f, --force Discard the previously saved bidsmap and log file