Merge branch 'master' of https://github.com/CATH-SWISSMODEL/cathsm-server

DEPLOY.md

 
+## Docker environment
+
+Remove any system docker software (if installed):
+
+```sh
+sudo yum remove docker docker-compose docker-common
+```
+
+Install latest `docker`:
+
+```sh
+# https://www.digitalocean.com/community/tutorials/how-to-install-and-use-docker-on-centos-7
+curl -fsSL https://get.docker.com/ | sh
+sudo systemctl start docker
+sudo systemctl enable docker
+```
+
+Install latest `docker-compose`:
+
+```sh
+# https://www.digitalocean.com/community/tutorials/how-to-install-and-use-docker-compose-on-centos-7
+sudo curl -L "https://github.com/docker/compose/releases/download/1.23.2/docker-compose-$(uname -s)-$(uname -m)" -o /usr/local/bin/docker-compose
+sudo chmod +x /usr/local/bin/docker-compose
+```
+
+Get the `cathsm-server` code:
+
+```sh
+CATHSM_BRANCH=v0.0.1
+CATHSM_ENV=production
+sudo mkdir cathsm-server-${CATHSM_ENV}
+sudo chown ucbcisi:users cathsm-server-${CATHSM_ENV}
+git clone --branch=${CATHSM_BRANCH} https://github.com/CATH-SWISSMODEL/cathsm-server.git cathsm-server-${CATHSM_ENV}
+```
+
+Build `docker-compose`:
+
+```sh
+cd cathsm-server-${CATHSM_ENV}
+cp .env.example .env
+vim .env
+sudo docker-compose -f docker-compose.yml build
+```
+
+Run `docker-compose`:
+
+```sh
+cd cathsm-server-${CATHSM_ENV}
+sudo docker-compose -f docker-compose.yml run
 ```
+
+## Post install
+
+* Add Django group `API User` with the following permissions:
+
+```
+admin | log entry | Can view log entry  
+auth | group | Can view group  
+auth | permission | Can view permission  
+auth | user | Can view user  
+authtoken | Token | Can add Token  
+authtoken | Token | Can change Token  
+authtoken | Token | Can delete Token  
+authtoken | Token | Can view Token  
+contenttypes | content type | Can view content type  
+select_template_api | select template alignment | Can add select template alignment  
+select_template_api | select template alignment | Can change select template alignment  
+select_template_api | select template alignment | Can delete select template alignment  
+select_template_api | select template alignment | Can view select template alignment  
+select_template_api | select template hit | Can add select template hit  
+select_template_api | select template hit | Can change select template hit  
+select_template_api | select template hit | Can delete select template hit  
+select_template_api | select template hit | Can view select template hit  
+select_template_api | select template task | Can add select template task  
+select_template_api | select template task | Can change select template task  
+select_template_api | select template task | Can delete select template task  
+select_template_api | select template task | Can view select template task  
+sessions | session | Can add session  
+sessions | session | Can change session  
+sessions | session | Can delete session  
+sessions | session | Can view session
+```
+
+* Add Django users for general functionality:
+  * `apitest` - see `cathsm-client/tests/api1_test.py`
+  * `apiuser` - see `cathsm-server/frontend/src/components/WorkFlow.js`
+
+## Manual deployment
+
+The following steps are now deprecated (since the deployment has been moved to `docker-compose`), however
+the notes are being left here for reference.
+
+```sh
 # https://www.digitalocean.com/community/tutorials/how-to-set-up-django-with-postgres-nginx-and-gunicorn-on-centos-7
 
 sudo yum install python36 git redis nginx postgresql  postgresql-contrib postgresql-devel

Docker/.env.template

+# password for the superuser of Postgres
+# (note: not the password of the Django user 
+# accessing the database)
+POSTGRES_PASSWORD=
+
+# name of the database that will be created for
+# the CATH-SM-API
+POSTGRES_DB=
+
+# dedicated datbase user for the Django app,
+# postgres will create it in the database on
+# first startup, Django uses it to log into the
+# database
+DJANGO_DB_USR=
+
+# Password for the dedicated database user as
+# scram-sha-256 hash. to generate a hash for a
+# password, set up a mock-up PostgreSQL database,
+# set encryption to scram-sha-256 and create a
+# user with DJANGO_DB_USR and DJANGO_DB_CLR_PW.
+# Then run
+# `select usename,passwd from PG_SHADOW;`.
+DJANGO_DB_PW=
+
+# cleartext password for the dedicated database user
+DJANGO_DB_CLR_PW=
+
+# the administrative user for Django, the
+# one which would normally go into
+# eg `manage.py createsuperuser`
+DJANGO_DB_ADMIN_USR=
+
+# password for django superuser 
+DJANGO_DB_ADMIN_PW=
+
+# mail address for the django superuser
+DJANGO_DB_ADMIN_ML=
+
+# source of code base:
+#   'fromlocal'   : local checkout of Git repo
+#   'fromgitrepo' : clones the repo during build 
+CATHSMAPI_CODEBASE=fromlocal
+
+# If CATHSMAPI_CODEBASE=fromgitrepo,
+# determines the branch/ tag to be used from
+# the Git repository
+CATHSMAPI_GITTAG=v0.0.1
+

Docker/docker-compose.yml

@@ -11,40 +11,14 @@ version: "3.5"
 # Please note: Environment variables used by this Docker Compose setup are
 #              spawned from a '.env' file. This file needs to be in the same
 #              directory as the docker-compose command is run. Variables in this
-#              file are defined by '<VARIABLE NAME>=<VALUE>'. Variables needed
-#              are:
-#                POSTGRES_PASSWORD - password for the superuser of Postgres, not
-#                                    the password of the Django user accessing
-#                                    the database
-#                POSTGRES_DB - name of the database that will be created for
-#                              the CATH-SM-API
-#                DJANGO_DB_USR - dedicated datbase user for the Django app,
-#                                postgres will create it in the database on
-#                                first startup, Django uses it to log into the
-#                                database
-#                DJANGO_DB_PW - Password for the dedicated database user as
-#                               scram-sha-256 hash. to generate a hash for a
-#                               password, set up a mock-up PostgreSQL database,
-#                               set encryption to scram-sha-256 and create a
-#                               user with DJANGO_DB_USR and DJANGO_DB_CLR_PW.
-#                               Then run
-#                               `select usename,passwd from PG_SHADOW;`.
-#                DJANGO_DB_CLR_PW - Cleartext password for the dedicated
-#                                   database user
-#                DJANGO_DB_ADMIN_USR - the administrative user for Django, the
-#                                      one which would normally go into
-#                                      `manage.py createsuperuser`
-#                DJANGO_DB_ADMIN_PW - password for the Django superuser
-#                DJANGO_DB_ADMIN_ML - mail address for the Django superuser
-#                CATHSMAPI_CODEBASE - there is a default for that one, it
-#                                     switches between using a local checkout
-#                                     of the Git repository or fetch a new one
-#                                     to build images; 'fromlocal' (the default)
-#                                     uses the local checkout, 'fromgitrepo'
-#                                     clones the repo during build.
-#                CATHSMAPI_GITTAG - If CATHSMAPI_CODEBASE=fromgitrepo,
-#                                   determines the branch/ tag to be used from
-#                                   the Git repository
+#              file are defined by '<VARIABLE NAME>=<VALUE>'.
+#             
+#              For convenience, a template `.env` file has been included in this
+#              repository (called `.env.template`). The easiest way to copy this
+#              template then change the values for each variable locally.
+#
+#              $ cp .env.template .env
+#              $ vi .env
 
 volumes:
   db-store: