v2023.1.26 Fix Flywheel folder handling for Web vs CLI downloads

jmtyszka · Jan 26, 2023 · 5f7f3db · 5f7f3db
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,11 @@
 # BIDSKIT Changelog
 
+## Version 2023.1.26
+- Fixed folder name handling for Web vs CLI Flywheel DICOM downloads
+
+## Version 2023.1.12
+- Add support for Flywheel DICOM download curation
+
 ## Version 2022.2.1
 - Added support for complex-valued, bias corrected and multiecho image types
 - Added command line control for rec-, echo- and part- keys in BIDS filenames

diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # BIDSKIT
 
-### Version 2023.1.12
+### Version 2023.1.26
 Python utilities for converting from DICOM to BIDS neuroimaging formats.
 
 The *bidskit* console command takes a directory tree containing imaging series from one or more subjects (eg T1w MPRAGE, BOLD EPI, Fieldmaps), converts the imaging data to Nifti-1 format with JSON metadata files (sidecars) and populates a directory tree according to the latest BIDS specification.

diff --git a/bidskit/flywheel.py b/bidskit/flywheel.py
@@ -36,7 +36,7 @@ def unpack(dataset_dir):
     src_dir = op.join(dataset_dir, 'sourcedata')
     os.makedirs(src_dir, exist_ok=True)
 
-    # Look for one or more flywheel tarballs
+    # Look for one or more flywheel tarballs in the BIDS dataset root folder
     fw_tarball_list = sorted(glob(op.join(dataset_dir, 'flywheel_*.tar')))
 
     if len(fw_tarball_list) < 1:
@@ -50,12 +50,24 @@ def unpack(dataset_dir):
             subprocess.run(['tar', 'xf', tb_fname, '-C', src_dir])
 
             # bidskit uses sourcedata/<SUBJECT>/<SESSION> organization
-            # Flywheel uses sourcedata/flywheel/<GROUP>/<PROJECT>/<SUBJECT>/SESSION>
+            # Flywheel uses sourcedata/<FWDIRNAME>/<GROUP>/<PROJECT>/<SUBJECT>/SESSION>
             # so move <SUBJECT> folder up three levels within sourcedata and
-            # delete sourcedata/flywheel folder tree
+            # delete sourcedata/<FWDIRNAME> folder tree
+            # Currently FWDIRNAME can be either 'flywheel' for web downloads or 'scitran'
+            # for CLI downloads
+
+            # Check for existence of sourcedata/flywheel or sourcedata/scitran folders
+            # following untarring
+            fw_web_dir = op.join(src_dir, 'flywheel')
+            fw_cli_dir = op.join(src_dir, 'scitran')
+            if op.isdir(fw_web_dir):
+                fw_dir = fw_web_dir
+            elif op.isdir(fw_cli_dir):
+                fw_dir = fw_cli_dir
+            else:
+                raise Exception(f'Neither sourcedata/flywheel or sourcedata/scitran exist following tar extraction')
 
             # Assume only one group/project present in sourcedata following tarball unpacking
-            fw_dir = op.join(src_dir, 'flywheel')
             subj_dir_list = sorted(glob(op.join(fw_dir, '*', '*', '*')))
             for subj_dir in subj_dir_list:
                 print(f'  Moving {subj_dir} to {src_dir}')

diff --git a/docs/Flywheel.md b/docs/Flywheel.md
@@ -4,7 +4,7 @@ Flywheel allows export of all DICOM data from a project, subject or session from
 The data exports to an uncompressed tar archive (*tarball*) with the following example folder organization:
 
 ```
-flywheel
+flywheel or scitran
 └── odoherty
     └── OLEL
         └── JOD_OLEL_031

diff --git a/setup.py b/setup.py
@@ -45,7 +45,7 @@
     # For a discussion on single-sourcing the version across setup.py and the
     # project code, see
     # https://packaging.python.org/en/latest/single_source_version.html
-    version='2023.1.12',  # Required
+    version='2023.1.26',  # Required
 
     # This is a one-line description or tagline of what your project does. This
     # corresponds to the "Summary" metadata field: