From ee316a1547292525b62db7214ffa24864063e961 Mon Sep 17 00:00:00 2001
From: Nan Li <nan.li@emory.edu>
Date: Sun, 26 Feb 2023 20:26:04 -0600
Subject: [PATCH 1/3] read the 'pathologists' from flat_file.csv to assign
 users to collections.

---
 NCISlideUtil.py | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/NCISlideUtil.py b/NCISlideUtil.py
index b33e17a..78fc370 100644
--- a/NCISlideUtil.py
+++ b/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
 

From d8274e0b30c5dd4ac8c8cc32ef80f4f12c6a644e Mon Sep 17 00:00:00 2001
From: Ryan Birmingham <birm@rbirm.us>
Date: Wed, 3 May 2023 13:56:48 -0400
Subject: [PATCH 2/3] update dockerfile

---
 Dockerfile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 9b80f6b..2142b95 100644
--- a/Dockerfile
+++ b/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
 RUN apt-get -q install -y libvips libvips-dev
 
 RUN pip install pyvips

From ed4637408c529df29fedb7900243135bd18c998d Mon Sep 17 00:00:00 2001
From: Ryan Birmingham <birm@rbirm.us>
Date: Wed, 3 May 2023 14:43:28 -0400
Subject: [PATCH 3/3] openssl update

---
 Dockerfile | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 2142b95..d97ef8c 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -3,7 +3,7 @@ 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 python3-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