RF: Deprecate create-study and replace with a respective procedure. (C…

…loses psychoinformatics-de#46)

datalad_hirni/commands/create_study.py

@@ -44,6 +44,12 @@ def __call__(
         from datalad.distribution.dataset import Dataset
         from datalad.distribution.install import Install
         from datalad.distribution.siblings import Siblings
+        from datalad.support.exceptions import DeprecatedError
+
+        raise DeprecatedError(new="use 'datalad create' and 'datalad "
+                                  "run-procedure setup_study_dataset' instead "
+                                  "to setup a HIRNI study dataset.",
+                              msg="'hirni-create-study is deprecated.")
 
         import os
 

datalad_hirni/resources/procedures/setup_study_dataset.py

@@ -0,0 +1,54 @@
+"""Procedure to apply a sensible default setup to a study dataset
+"""
+
+import sys
+from datalad.distribution.dataset import require_dataset
+
+# bound dataset methods
+import datalad.distribution.add
+import datalad.distribution.save
+from datalad.plugin.add_readme import AddReadme
+
+ds = require_dataset(
+    sys.argv[1],
+    check_installed=True,
+    purpose='study dataset setup')
+
+
+force_in_git = [
+    'README',
+    'CHANGES',
+    'dataset_description.json',
+    '**/{}'.format(ds.config.get("datalad.hirni.studyspec.filename",
+                                 "studyspec.json")),
+]
+
+# except for hand-picked global metadata, we want anything
+# to go into the annex to be able to retract files after
+# publication
+ds.repo.set_gitattributes([('**', {'annex.largefiles': 'anything'})])
+ds.repo.set_gitattributes([(p, {'annex.largefiles': 'nothing'})
+                           for p in force_in_git])
+
+
+# TODO:
+# Note: This default is using the DICOM's PatientID as the acquisition ID
+# (directory name in the study dataset). That approach works for values
+# accessible via the DICOM metadata directly. We probably want a way to apply
+# more sophisticated rules, which could be achieved by a String Formatter
+# providing more sophisticated operations like slicing (prob. to be shared with
+# datalad's --output-format logic) or by apply specification rules prior to
+# determining final location of the imported subdataset. The latter might lead
+# to a mess, since import and specification routines would then be quite
+# twisted.
+ds.config.add('datalad.hirni.import.acquisition-format',
+              "{PatientID}", where='dataset')
+
+ds.save(message='[HIRNI] Default study dataset setup')
+
+# Include the most basic README to prevent heudiconv from adding one
+ds.add_readme(filename='README', existing='fail')
+
+
+# TODO: Reconsider using an import container and if so, link it herein. See
+# now-deprecated hirni-create-study command