Merge pull request #27 from NCI-GDC/release/py3

chore(release): Sam-I-Am Release

Dockerfile

@@ -1,23 +1,23 @@
-FROM quay.io/ncigdc/apache-base:1.0.3 as build
+FROM quay.io/ncigdc/apache-base:1.0.3-py3.5 as build
 
 
 COPY . /indexd
 WORKDIR /indexd
 
 RUN apt-get update \
  && apt-get install -y --no-install-recommends \
-    python2.7 \
-    python-dev \
-    python-pip \
-    python-setuptools \
+    python3 \
+    python3-dev \
+    python3-pip \
+    python3-setuptools \
     libpq-dev \
     libpq5 \
     gcc \
- && pip install wheel \
- && pip install -r build/requirements.txt \
- && python setup.py install 
+ && pip3 install wheel \
+ && pip3 install -r build/requirements.txt \
+ && python3 setup.py install
 
-FROM quay.io/ncigdc/apache-base:1.0.3
+FROM quay.io/ncigdc/apache-base:1.0.3-py3.5
 
 LABEL org.label-schema.name="indexd" \
       org.label-schema.description="indexd container image" \
@@ -33,7 +33,7 @@ RUN mkdir -p /var/www/indexd/ \
 
 COPY wsgi.py /var/www/indexd/ 
 COPY bin/indexd /var/www/indexd/ 
-COPY --from=build /usr/local/lib/python2.7/dist-packages /usr/local/lib/python2.7/dist-packages
+COPY --from=build /usr/local/lib/python3.5/dist-packages /usr/local/lib/python3.5/dist-packages
 COPY . /indexd
 
 WORKDIR /var/www/indexd

dockerrun.bash

@@ -14,5 +14,5 @@ if [[ -f ./wsgi.py && "$GEN3_DEBUG" == "True" ]]; then
   echo -e "\napplication.debug=True\n" >> ./wsgi.py
 fi  
 
-sudo -u www-data python wsgi.py
+sudo -u www-data python3 wsgi.py
 /usr/sbin/apache2ctl -D FOREGROUND

indexd/index/drivers/alchemy.py

@@ -20,7 +20,7 @@
     or_,
     select,
 )
-from sqlalchemy.dialects.postgres import JSONB
+from sqlalchemy.dialects.postgresql import JSONB
 from sqlalchemy.exc import IntegrityError, ProgrammingError
 from sqlalchemy.ext.declarative import declarative_base
 from sqlalchemy.orm import joinedload, relationship, sessionmaker

requirements.txt

@@ -1,10 +1,10 @@
-flask==0.12.4
+flask==1.1.1
 jsonschema==2.5.1
-sqlalchemy==1.0.8
+sqlalchemy==1.3.3
 sqlalchemy-utils>=0.32.21
 psycopg2>=2.7
-future>=0.16.0,<1.0.0
--e git+https://github.com/NCI-GDC/[email protected].8#egg=indexclient
+future==0.18.1
+-e git+https://github.com/NCI-GDC/[email protected].10#egg=indexclient
 -e git+https://github.com/uc-cdis/[email protected]#egg=cdislogging
 -e git+https://github.com/uc-cdis/[email protected]#egg=doiclient
 -e git+https://github.com/uc-cdis/[email protected]#egg=dosclient

setup.py

@@ -2,29 +2,27 @@
 
 setup(
     name='indexd',
-    version='2.2.0',
+    version='2.3.0',
     packages=find_packages(),
     package_data={
         'index': [
             'schemas/*',
         ]
     },
     install_requires=[
-        'flask==0.12.4',
-        'jsonschema==2.5.1',
-        'sqlalchemy==1.0.8',
-        'sqlalchemy-utils>=0.32.21',
+        'flask<2',
+        'jsonschema<3',
+        'sqlalchemy==1.3.3',
+        'sqlalchemy-utils<1',
         'psycopg2>=2.7',
-        'future>=0.16.0,<1.0.0',
         'cdislogging',
         'indexclient',
         'doiclient',
         'dosclient',
+        'future<1'
     ],
     dependency_links=[
         "git+https://github.com/uc-cdis/[email protected]#egg=cdislogging",
-        "git+https://github.com/uc-cdis/[email protected]#egg=indexclient",
-        "git+https://github.com/uc-cdis/[email protected]#egg=doiclient",
-        "git+https://github.com/uc-cdis/[email protected]#egg=dosclient",
+        "git+https://github.com/NCI-GDC/[email protected]#egg=indexclient",
     ],
 )