rescuing files for git annex

Author: daeh

.gitignore

@@ -1 +1,35 @@
-/annex/objects/SHA256E-s1164--c0074611d4178ba7bf603159c93e65f7ee7aa7c2c339a30098a9cd7e20db4547.py
+import os
+import os.path as op
+
+import logging
+
+lgr = logging.getLogger(__name__)
+
+# start with SLURM but extend past that #TODO
+def queue_conversion(progname, queue, outdir, heuristic, dicoms, sid,
+                     anon_cmd, converter, session,with_prov, bids):
+
+        # Rework this...
+        convertcmd = ' '.join(['python', progname,
+                               '-o', outdir,
+                               '-f', heuristic,
+                               '-s', sid,
+                               '--anon-cmd', anon_cmd,
+                               '-c', converter])
+        if session:
+            convertcmd += " --ses '%s'" % session
+        if with_prov:
+            convertcmd += " --with-prov"
+        if bids:
+            convertcmd += " --bids"
+        if dicoms:
+            convertcmd += " --files"
+            convertcmd += [" '%s'" % f for f in dicoms]
+
+        script_file = 'dicom-%s.sh' % sid
+        with open(script_file, 'wt') as fp:
+            fp.writelines(['#!/bin/bash\n', convertcmd])
+        outcmd = 'sbatch -J dicom-%s -p %s -N1 -c2 --mem=20G %s' \
+                 % (sid, queue, script_file)
+
+        os.system(outcmd)

heudiconv/queue.py

@@ -1 +1,19 @@
-/annex/objects/SHA256E-s305--d13f986ddc4e3ba2a9fdea076834eb9861cddd365380d5675ebdf1177281f352.py
+#! /usr/bin/env python 
+
+import sys
+import re
+import ctypes
+
+
+def bids_id_(sid):
+    parsed_id = re.compile(r"^(?:sub-|)(.+)$").search(sid).group(1)
+    return str(ctypes.c_size_t(hash(parsed_id)).value)
+
+
+def main():
+    sid = sys.argv[1]
+    return bids_id_(sid)
+
+
+if __name__ == '__main__':
+    main()