Merge pull request #165 from dartmouth-pbs/bf-datalad-metadata

Use .repo.set_metadata to stay compatible with upcoming datalad 0.10

Author: yarikoptic

heudiconv/external/dlad.py

@@ -1,30 +1,34 @@
 import os
 import os.path as op
 import logging
+from glob import glob
+from os import path as op
 
-from ..utils import create_file_if_missing, mark_sensitive
+from ..utils import create_file_if_missing
 
 lgr = logging.getLogger(__name__)
 
 MIN_VERSION = '0.7'
 
+
 def prepare_datalad(studydir, outdir, sid, session, seqinfo, dicoms, bids):
     """ Prepare data for datalad """
+    from datalad.api import Dataset
     datalad_msg_suf = ' %s' % sid
     if session:
         datalad_msg_suf += ", session %s" % session
     if seqinfo:
         datalad_msg_suf += ", %d sequences" % len(seqinfo)
     datalad_msg_suf += ", %d dicoms" % (len(sum(seqinfo.values(), []))
                                         if seqinfo else len(dicoms))
-    from datalad.api import Dataset
     ds = Dataset(studydir)
     if not op.exists(outdir) or not ds.is_installed():
         add_to_datalad(outdir, studydir,
                        msg="Preparing for %s" % datalad_msg_suf,
                        bids=bids)
     return datalad_msg_suf
 
+
 def add_to_datalad(topdir, studydir, msg, bids):
     """Do all necessary preparations (if were not done before) and save
     """
@@ -33,7 +37,7 @@ def add_to_datalad(topdir, studydir, msg, bids):
     from datalad.support.annexrepo import AnnexRepo
     from datalad.support.external_versions import external_versions
     assert external_versions['datalad'] >= MIN_VERSION, (
-      "Need datalad >= {}".format(MIN_VERSION)) # add to reqs
+      "Need datalad >= {}".format(MIN_VERSION))  # add to reqs
 
     studyrelpath = op.relpath(studydir, topdir)
     assert not studyrelpath.startswith(op.pardir)  # so we are under
@@ -133,3 +137,25 @@ def add_to_datalad(topdir, studydir, msg, bids):
       http://git-annex.branchable.com/tips/automatically_adding_metadata/
     - possibly even make separate sub-datasets for originaldata, derivatives ?
     """
+
+
+def mark_sensitive(ds, path_glob):
+    """
+
+    Parameters
+    ----------
+    ds : Dataset to operate on
+    path_glob : str
+      glob of the paths within dataset to work on
+
+    Returns
+    -------
+    None
+    """
+    paths = glob(op.join(ds.path, path_glob))
+    if not paths:
+        return
+    ds.repo.set_metadata(
+        paths,
+        init=[('distribution-restrictions', 'sensitive')],
+        recursive=True)

heudiconv/utils.py

@@ -7,7 +7,6 @@
 import sys
 import shutil
 import copy
-import logging
 import stat
 import os.path as op
 from pathlib import Path
@@ -121,28 +120,6 @@ def create_file_if_missing(filename, content):
     return True
 
 
-def mark_sensitive(ds, path_glob=None):
-    """
-
-    Parameters
-    ----------
-    ds : Dataset to operate on
-    path_glob : str, optional
-      glob of the paths within dataset to work on
-    Returns
-    -------
-    None
-    """
-    sens_kwargs = dict(
-        init=[('distribution-restrictions', 'sensitive')]
-    )
-    if path_glob:
-        paths = glob(op.join(ds.path, path_glob))
-        if not paths:
-            return
-        sens_kwargs['path'] = paths
-    ds.metadata(recursive=True, **sens_kwargs)
-
 def read_config(infile):
     with open(infile, 'rt') as fp:
         info = eval(fp.read())