update doc and run script

comex-run.sh

 #! /bin/bash
 
+
+usage() { echo -e "Usage: $0 [-d|-p]\n    -d  dev mode (app bind point is 0.0.0.0:9090)\n    -p prod mode (app bind point is /tmp/comex.sock)" 1>&2; exit 1; }
+
+unset COMEX_BIND_POINT
+while getopts dph run_mode; do
+    case $run_mode in
+    d)
+        # debug mode: run on TCP socket 0.0.0.0:9090
+        export COMEX_BIND_POINT=0.0.0.0:9090
+        echo "binding gunicorn to tcp socket: $COMEX_BIND_POINT"
+        ;;
+    p)
+        # production mode: run on fs socket
+        export COMEX_BIND_POINT='unix:/tmp/comex.sock'
+        echo "binding gunicorn to fs socket: $COMEX_BIND_POINT"
+
+        # POSS in-memory socket ?
+        # export COMEX_BIND_POINT='unix:/run/shm/comex.sock'
+        ;;
+    *)
+        usage
+    esac
+done
+
+# production mode is the default
+if [ -z "$COMEX_BIND_POINT" ]
+then
+    echo "(no mode was specified: using production mode)"
+    export COMEX_BIND_POINT='unix:/tmp/comex.sock'
+    echo "binding gunicorn to fs socket: $COMEX_BIND_POINT"
+fi
+
 # if we're inside a docker (we're used as entrypoint)...
 if grep --quiet docker /proc/1/cgroup
   then
     # ... then we're also in charge of the inner nginx
     #     (to package the php with the services below)
-    export REAL_DOCKER_HOST=$(hostname -i)
-    echo "starting nginx on $REAL_DOCKER_HOST"
+    export COMEX_DOCKER_HOST_IP=$(hostname -i)
+    echo "starting nginx on docker (available at http://$COMEX_DOCKER_HOST_IP)"
     service nginx start
 
     echo "starting php 7 with clear_env = no"
     /etc/init.d/php7.0-fpm start
-    # NB if we started it with the "service" command
-    #    all our env vars would be intercepted by it
-    #    even though we set "clear_env=no" in www.conf
+    # NB if we started php-fpm with the "service" command
+    #    then all our env vars would be intercepted by it
+    #    even though we set "clear_env=no" in www.conf !
 fi
 
 # anyway we always need a simple web server to run the services
 export COMEX_NWORKERS=$(grep -oP '(?<=COMEX_NWORKERS=).*' config/parametres_comex.ini)
 
-echo "binding gunicorn to unix:/tmp/comex.sock"
-gunicorn -b unix:/tmp/comex.sock services.main:app --workers $COMEX_NWORKERS --worker-class gevent
-
-
-# export COMEX_HOST=$(grep -oP '(?<=COMEX_HOST=).*' config/parametres_comex.ini)
-# export COMEX_PORT=$(grep -oP '(?<=COMEX_PORT=).*' config/parametres_comex.ini)
-# echo "binding gunicorn to $COMEX_HOST:$COMEX_PORT"
-# gunicorn -b $COMEX_HOST:$COMEX_PORT services.main:app --workers $COMEX_NWORKERS
+gunicorn -b $COMEX_BIND_POINT services.main:app --workers $COMEX_NWORKERS --worker-class gevent

doc/dev_setup.md

@@ -8,7 +8,7 @@ comex app contains:
     - the services views are in `services/main.py`
     - the main templates are `base_layout.html` and `rootindex.html`
     - main and `services/user.py` handle DB add/modify/remove scholars
-    - `services/db_to_tina_api` contains a custom python extraction function for tinawebJS
+    - `services/dbdatapi.py` contains a facet agregation API and custom python extraction function to create bipartite graphs for tinawebJS display
   - a copy of tinawebJS in `static/tinawebJS` to explore the data in graph view
     - the twjs is in a legacy version, downloadable [via this subtree](https://github.com/moma/tinawebJS/tree/comex_wip)
 
@@ -19,9 +19,9 @@ comex app contains:
 In development, it is more natural to run the app *without* the docker wrapper.
 This way one can see the effects of changes without the bother of committing them, pulling them in the image and rebuilding the image.
 
-Another difference is that without the docker wrapper, the app will be available on COMEX_HOST:9090 instead of 8080.
+Another difference is that without the docker wrapper, the app will be available on 0.0.0.0:9090 instead of 8080.
 
-#### Minimal config
+#### Minimal run commands
 
 ```
 # get the code
@@ -33,24 +33,37 @@ cd $INSTALL_DIR
 sudo pip3 install -r setup/requirements.txt
 ```
 
-Then to run the comex2 server just do:
+Then to run the comex2 server for development just do:
 ```
-bash comex-run.sh
+bash comex-run.sh -d
 ```
 
-Check the parameters in `config/parametres_comex.ini`
-
-Finally, simply configure the serving of your php|www documentroot in nginx (cf [detailed doc](https://github.com/moma/comex2/blob/master/doc/nginx_conf.md) for real-life conf).
-
+At this point you're running a python gunicorn webserver pointing to the files in `/services`. You can connect to `0.0.0.0:9090` and checkout the app, but you won't have the php, DB access and authentication elements working yet.
 
 -------
 
 #### Full dev config
-  1. external mysql database
-  2. external doors (or simulated by docker)
-  3. gunicorn webserver (linked to 1 & 2 via `$SQL_HOST` and `$DOORS_HOST`)
+  1. php serving
+  2. mysql database
+  3. doors authentication server
+  4. gunicorn webserver (linked to 1 & 2 via `$SQL_HOST` and `$DOORS_HOST`)
+
+##### 1) Set up your php
+Configure the serving of our php documents in your nginx with something like this:
+
+```
+location ~ \.php$ {
+    include snippets/fastcgi-php.conf;
+    fastcgi_pass unix:/run/php/php7.0-fpm.sock;
+    # here adapt documentroot to your real path to comex
+    fastcgi_param SCRIPT_FILENAME /home/romain/comex2$fastcgi_script_name;
+    #                             -------------------
+    #                                 documentroot
+}
+```
 
-##### 1) Set up your mysql database
+
+##### 2) Set up your mysql database
 
 ###### If you have your own local mysql
 ```
@@ -77,7 +90,7 @@ docker inspect comex_db | jq -r '.[0].NetworkSettings.IPAddress'
 nano config/parametres_comex.ini
 ```
 
-##### 2) Set up a doors connection
+##### 3) Set up a doors connection
 Again, the environment variable `DOORS_HOST` must simply be set to the doors server's hostname or IP, and `DOORS_PORT` to the doors server's exposed port.
 
 ###### If you have a doors server
@@ -88,16 +101,19 @@ nano config/parametres_comex.ini
 
 ###### If you have no doors server
 
-For tests you can use a self-deployed doors container, available on [this repository](https://github.com/ISCPIF/doors-docker)
+For tests you can use a self-deployed doors container, available from ISCPIF on [this repository](https://github.com/ISCPIF/doors-docker)
 
 
-##### 3) Run the regomex app with gunicorn
+##### 4) Run the regomex app with gunicorn
 ```
-bash comex-run.sh
+bash comex-run.sh -d
 ```
 
-The form server is then accessible locally on `0.0.0.0:9090/services/user/register`
+The user DB service is then accessible locally on `0.0.0.0:9090/services/user`
+
+The API server is then accessible locally on `0.0.0.0:9090/services/api`
+(for instance `services/api/aggs?field=keywords&like=biol`)
 
-**Remark:** the prefix `/services` and the user route `/user` can both be changed in the config file
+**Remark:** the prefix `/services` and the routes `/user` and `/api` can both be changed in the config file
 
 -------

setup/dockers/comex2_services/Dockerfile

@@ -44,16 +44,12 @@ RUN git clone https://github.com/moma/comex2.git
 # main CMD to start the app
 WORKDIR /comex2
 
-# flask dev server
-# CMD python3 server_comex_registration.py
-
 # start nginx inner wrapper and gunicorn production server
-CMD bash comex-run.sh
+CMD bash comex-run.sh -p
 
 # ports -----------------------------------------------------------------------
 
 # nginx server (redirecting to php AND services)
 EXPOSE 80
 
-# https test
-EXPOSE 443
+# https is actually handled outside by proxy layer

setup/dockers/docker-compose.yml

@@ -11,8 +11,8 @@
          - ../../data/shared_mysql_data:/var/lib/mysql
 
       comex_test:
-        container_name: comex_test
-        image: comex2_services:testing
+        container_name: comex_services
+        image: comex2_services:latest
         build: ./comex2_services
         # logs will show all that's printed to STDOUT with tty:true
         tty: true