Fixes for Docker build. Added explicit installs for major python3 pac…

…kage dependencies
jmtyszka · Dec 20, 2019 · 765049b · 765049b
1 parent 3e328f8
commit 765049b
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Showing 9 changed files with 13 additions and 195 deletions.
diff --git a/bidskit/organize.py b/bidskit/organize.py
@@ -26,8 +26,8 @@
 
 import os
 import shutil
-import bidskit.translate as btr
-import bidskit.io as bio
+from . import translate as btr
+from . import io as bio
 import copy
 
 

diff --git a/bidskit/translate.py b/bidskit/translate.py
@@ -29,7 +29,6 @@
 import json
 import re
 import subprocess
-import datetime as dt
 import numpy as np
 
 from glob import glob
@@ -392,7 +391,17 @@ def auto_run_no(file_list, prot_dict):
 
         # Parse dcm2niix filename into relevant keys, including suffix
         info = parse_dcm2niix_fname(fname)
-        _, bids_suffix, _ = prot_dict[info['SerDesc']]
+
+        ser_desc = info['SerDesc']
+
+        if ser_desc in prot_dict:
+            _, bids_suffix, _ = prot_dict[info['SerDesc']]
+        else:
+            print('')
+            print('* Series description {} missing from code/Protocol_Translator.json'.format(ser_desc))
+            print('* Please use EXCLUDE_BIDS_Directory and EXCLUDE_BIDS_Name instead of deleting a series entry')
+            print('* Exiting')
+            sys.exit(1)
 
         # Construct a unique series description using multirecon suffix
         ser_suffix = bids_suffix + '_' + info['Suffix']

diff --git a/venv/bin/activate b/venv/bin/activate
diff --git a/venv/bin/activate.csh b/venv/bin/activate.csh
diff --git a/venv/bin/activate.fish b/venv/bin/activate.fish
diff --git a/venv/bin/python b/venv/bin/python
diff --git a/venv/bin/python3 b/venv/bin/python3
diff --git a/venv/bin/python3.7 b/venv/bin/python3.7
diff --git a/venv/pyvenv.cfg b/venv/pyvenv.cfg