Merge pull request #63 from camicroscope/develop

For 3.10.2

Dockerfile

@@ -1,9 +1,9 @@
-FROM python:3-stretch
+FROM python:3
 
 WORKDIR /var/www
 RUN apt-get update
 RUN apt-get -q update --fix-missing
-RUN apt-get -q install -y openslide-tools python-openslide vim
+RUN apt-get -q install -y openslide-tools python3-openslide vim openssl
 RUN apt-get -q install -y libvips libvips-dev
 
 RUN pip install pyvips
@@ -12,6 +12,8 @@ RUN pip install gunicorn
 RUN pip install greenlet
 RUN pip install gunicorn[eventlet]
 
+run openssl version -a
+
 ENV FLASK_ENV development
 
 RUN mkdir -p /images/uploading

NCISlideUtil.py

@@ -150,10 +150,16 @@ def addSpecialty(data):
         for collection in collections:
             # add specialty
             pid = addSpecialty({'text': collection['specialty']})
+
+            # add users
+            users = []
+            for user in collection['pathologists']:
+                users.append({'user': user})
+
             for sub in collection['subspecialties']:
                 # add specialty
                 cid = addSpecialty(
-                    {'text': sub, 'pid': pid})
+                    {'text': sub, 'pid': pid, 'users': users})
                 # save the token id and collection id as map
                 if cid is not None:
                     subspecialties_map[sub.lower()] = cid
@@ -163,7 +169,11 @@ def addSpecialty(data):
 with open(flat_file_path, 'r', encoding='utf-8-sig') as f:
     reader = csv.DictReader(f)
     for row in reader:
-        flat_map[row['tokenid'].lower()] = row
+        token = row['tokenid'] or row['token_id'] or None
+        if token:
+            flat_map[row['tokenid'].lower()] = row
+        else:
+            print('no token id in flat_file')
 
 # NCI DOE create a metadata dict END