Chore/python3

.github/main.workflow

@@ -0,0 +1,9 @@
+workflow "Run python formatter" {
+  on = "pull_request"
+  resolves = ["Run wool"]
+}
+
+action "Run wool" {
+  uses = "uc-cdis/wool@master"
+  secrets = ["GITHUB_TOKEN"]
+}

.travis.yml

@@ -2,7 +2,6 @@ dist: xenial
 language: python
 
 python:
-  - "2.7"
   - "3.6"
 
 sudo: false

Dockerfile

@@ -1,26 +1,39 @@
 # To run: docker run -v /path/to/wsgi.py:/var/www/indexd/wsgi.py --name=indexd -p 81:80 indexd
 # To check running container: docker exec -it indexd /bin/bash 
 
-FROM quay.io/cdis/py27base:pybase2-1.0.2
+FROM quay.io/cdis/python-nginx:pybase3-1.0.0
 
-MAINTAINER CDIS <cdissupport@opensciencedatacloud.org>
 
-RUN mkdir /var/www/indexd \
-	&& chown www-data /var/www/indexd
+ENV appname=indexd
 
-COPY . /indexd
-COPY ./deployment/uwsgi/uwsgi.ini /etc/uwsgi/uwsgi.ini
+RUN apk update \
+    && apk add postgresql-libs postgresql-dev libffi-dev libressl-dev \
+    && apk add linux-headers musl-dev gcc \
+    && apk add curl bash git vim
 
-WORKDIR /indexd
+COPY . /$appname
+COPY ./deployment/uwsgi/uwsgi.ini /etc/uwsgi/uwsgi.ini
+COPY ./deployment/uwsgi/wsgi.py /$appname/wsgi.py
+WORKDIR /$appname
 
-RUN python -m pip install -r requirements.txt
-RUN COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" >indexd/index/version_data.py
-RUN VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >>indexd/index/version_data.py
-RUN python setup.py install
+RUN python -m pip install --upgrade pip \
+    && python -m pip install --upgrade setuptools \
+    && pip install -r requirements.txt
 
+RUN mkdir -p /var/www/$appname \
+    && mkdir -p /var/www/.cache/Python-Eggs/ \
+    && mkdir /run/nginx/ \
+    && ln -sf /dev/stdout /var/log/nginx/access.log \
+    && ln -sf /dev/stderr /var/log/nginx/error.log \
+    && chown nginx -R /var/www/.cache/Python-Eggs/ \
+    && chown nginx /var/www/$appname
 
 EXPOSE 80
 
-WORKDIR /var/www/indexd
+RUN COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" >$appname/version_data.py \
+    && VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >>$appname/version_data.py \
+    && python setup.py install
+
+WORKDIR /var/www/$appname
 
 CMD /dockerrun.sh

bin/index_admin.py

@@ -2,7 +2,8 @@
 import sys
 from cdislogging import get_logger
 
-logger = get_logger('index_admin')
+logger = get_logger("index_admin")
+
 
 def main(path, action=None, username=None, password=None):
     sys.path.append(path)
@@ -11,45 +12,45 @@ def main(path, action=None, username=None, password=None):
     except ImportError:
         logger.info("Can't import local_settings, import from default")
         from indexd.default_settings import settings
-    driver = settings['auth']
-    index_driver = settings['config']['INDEX']['driver']
-    alias_driver = settings['config']['ALIAS']['driver']
-    if action == 'create':
+    driver = settings["auth"]
+    index_driver = settings["config"]["INDEX"]["driver"]
+    alias_driver = settings["config"]["ALIAS"]["driver"]
+    if action == "create":
         try:
             driver.add(username, password)
-            logger.info('User {} created'.format(username))
+            logger.info("User {} created".format(username))
         except Exception as e:
-            logger.error(e.message)
+            logger.error(e)
 
-    elif action == 'delete':
+    elif action == "delete":
         try:
             driver.delete(username)
-            logger.info('User {} deleted'.format(username))
+            logger.info("User {} deleted".format(username))
         except Exception as e:
-            logger.error(e.message)
+            logger.error(e)
 
-    elif action == 'migrate_database':
+    elif action == "migrate_database":
         try:
-            logger.info('Start database migration')
+            logger.info("Start database migration")
             alias_driver.migrate_alias_database()
             index_driver.migrate_index_database()
         except Exception as e:
-            logger.error(e.message)
-if __name__ == '__main__':
+            logger.error(e)
+
+
+if __name__ == "__main__":
 
     parser = argparse.ArgumentParser()
 
     parser.add_argument(
-        '--path',
-        default='/var/www/indexd/',
-        help='path to find local_settings.py',
+        "--path", default="/var/www/indexd/", help="path to find local_settings.py"
     )
-    subparsers = parser.add_subparsers(title='action', dest='action')
-    create = subparsers.add_parser('create')
-    delete = subparsers.add_parser('delete')
-    migrate = subparsers.add_parser('migrate_database')
-    create.add_argument('--username', required=True)
-    create.add_argument('--password', required=True)
-    delete.add_argument('--username', required=True)
+    subparsers = parser.add_subparsers(title="action", dest="action")
+    create = subparsers.add_parser("create")
+    delete = subparsers.add_parser("delete")
+    migrate = subparsers.add_parser("migrate_database")
+    create.add_argument("--username", required=True)
+    create.add_argument("--password", required=True)
+    delete.add_argument("--username", required=True)
     args = parser.parse_args()
     main(**args.__dict__)

deployment/uwsgi/uwsgi.ini

@@ -2,9 +2,11 @@
 protocol = uwsgi
 socket = /var/run/gen3/uwsgi.sock
 buffer-size = 32768
+uid = nginx
+gid = nginx
+chown-socket = nginx:nginx
 chmod-socket = 666
 master = true
-processes = 2
 harakiri-verbose = true
 # No global HARAKIRI, using only user HARAKIRI, because export overwrites it
 # Cannot overwrite global HARAKIRI with user's: https://git.io/fjYuD
@@ -16,13 +18,9 @@ reload-mercy = 45
 mule-reload-mercy = 45
 disable-logging = true
 wsgi-file=/indexd/wsgi.py
-plugins = python
+plugins = python3
 vacuum = true
-uid = www-data
-gid = www-data
-pythonpath = /var/www/indexd/
 pythonpath = /indexd/
-pythonpath = /usr/local/lib/python2.7/dist-packages/
 # Initialize application in worker processes, not master. This prevents the
 # workers from all trying to open the same database connections at startup.
 lazy = true

wsgi.py → deployment/uwsgi/wsgi.py

@@ -1,4 +1,5 @@
 from indexd import get_app
 import os
-os.environ['INDEXD_SETTINGS'] = '/var/www/indexd/'
+
+os.environ["INDEXD_SETTINGS"] = "/var/www/indexd/"
 application = get_app()

indexd/__init__.py

@@ -1 +1 @@
-from .app import get_app 
+from .app import get_app