add procedure for batch-importing dicoms

procedures/import_subjects.py

@@ -0,0 +1,70 @@
+"""
+Procedure to import subjects based on a subjects.json
+
+The procedure should be called with the following arguments:
+    datalad run-procedure import_subjects subjects.json /path/to/source
+
+The subjects.json file should be a valid json array of objects, like:
+
+[
+    {"anon-sub": "007", "acq": "jb68_0007"},
+    {"anon-sub": "007", "acq": "jb68_0008"}
+]
+
+In our specific use-case, inside the source directory is there is a subfolder
+called `jb68_0007` inside which the relevant .tar-file also starts with that
+string.  This script automatically fills out that part for us, using the
+following template:
+
+datalad --pbs-runner condor hirni-import-dcm \
+    --anon-subject {anon-sub} {source}/{acq}/{acq}*.tar {acq}
+
+"""
+
+import sys
+from datalad.distribution.dataset import require_dataset
+import os
+import json
+
+# define expected keys:
+key_anon = "anon-sub"
+key_acq = "acq"
+
+ds = require_dataset(
+    sys.argv[1],
+    check_installed=True,
+    purpose='adding custom rule')
+
+file_subject = sys.argv[2]
+source_dir = sys.argv[3]
+
+if not os.path.isdir(source_dir):
+    sys.exit("source directory not valid")
+if not os.path.isfile(file_subject):
+    sys.exit("json-file not found")
+
+f = open(file_subject, "r")
+list = json.load(f)
+
+for item in list:
+    if key_anon in item and key_acq in item:
+
+        # check whether the target dicoms have already been imported, if yes,
+        # skip now
+        if os.path.isdir("{ds_path}/{acq}".format(
+            ds_path=ds.path,
+            acq=item[key_acq])):
+
+            print("[Hirni ADDONS] Acquisition {} "
+                "already present - skipping".format(item[key_acq]))
+            continue
+
+        cmd = ("datalad --pbs-runner condor hirni-import-dcm "
+            "--anon-subject {anon} {s}/{acq}/{acq}*.tar {acq}".format(
+            anon=item[key_anon],
+            s=source_dir,
+            acq=item[key_acq]
+            ))
+        print("[Hirni ADDONS] Running following command:")
+        print("[Hirni ADDONS] {}".format(cmd))
+        os.system(cmd)