The following must be available on your server:
- wheel
- pymongo
- httpie
- jsonref
- jsonschema
- Node.js and npm
- docker
After cloning this repo, you will need to set the paramters given in api/conf/config.json and app/conf/config.json
Visit https://data.glygen.org/ftp/ to see what data release/version $VER you want to download (for example 2.0.2), and go to the "api" subdirectory to run the python script to download from that release. Since this will take long, use nohup as shown below.
nohup python3 download_data.py -s $SER -v $VER > logfile.log &
where $SER is your deployment server which can be dev, tst, beta or prd. It is also important that you download all legacy releases since the application allows access to datasets from older releases.
From the "api" subdirectory, run the python script given to build and start a mongodb container:
python3 create_mongodb_container.py -s $SER
docker ps --all
The last command should list docker all containers and you should see the container
you created running_glyds_mongo_$SER. To start this container, the best way is
to create a service file (/usr/lib/systemd/system/docker-glyds-mongo-$SER.service),
and place the following content in it.
[Unit]
Description=Glyds MONGODB Container
Requires=docker.service
After=docker.service
[Service]
Restart=always
ExecStart=/usr/bin/docker start -a running_glyds_mongo_$SER
ExecStop=/usr/bin/docker stop -t 2 running_glyds_mongo_$SER
[Install]
WantedBy=default.target
This will allow you to start/stop the container with the following commands, and ensure that the container will start on server reboot.
$ sudo systemctl daemon-reload
$ sudo systemctl enable docker-glyds-mongo-$SER.service
$ sudo systemctl start docker-glyds-mongo-$SER.service
$ sudo systemctl stop docker-glyds-mongo-$SER.service
To init your mongodb, go to the "api" subdirectory and run (this should be done only one time):
python3 init_mongodb.py -s $SER
You can load data from the most recent release you have downloaded using the following command:
cd api
python3 load_current_release.py -s $SER -v $VER
To load data from downloaded legacy releases:
cd api
python3 load_legacy_release.py -s $SER -v $VER -m full
From the "api" subdirectory, run the python script given to build and start container:
python3 create_api_container.py -s $SER
docker ps --all
The last command should list docker all containers and you should see the container
you created running_glyds_api_$SER. To start this container, the best way is
to create a service file (/usr/lib/systemd/system/docker-glyds-api-$SER.service),
and place the following content in it.
[Unit]
Description=Glyds API Container
Requires=docker.service
After=docker.service
[Service]
Restart=always
ExecStart=/usr/bin/docker start -a running_glyds_api_$SER
ExecStop=/usr/bin/docker stop -t 2 running_glyds_api_$SER
[Install]
WantedBy=default.target
This will allow you to start/stop the container with the following commands, and ensure that the container will start on server reboot.
$ sudo systemctl daemon-reload
$ sudo systemctl enable docker-glyds-api-$SER.service
$ sudo systemctl start docker-glyds-api-$SER.service
$ sudo systemctl stop docker-glyds-api-$SER.service
From the "api" subdirectory, run the following to test the APIs
http POST http://localhost:$API_PORT/misc/info
http POST http://localhost:$API_PORT/dataset/search < queries/dataset_search.json
http POST http://localhost:$API_PORT/dataset/detail < queries/dataset_detail.json
http POST http://localhost:$API_PORT/dataset/historylist < queries/dataset_historylist.json
http POST http://localhost:$API_PORT/dataset/historydetail < queries/dataset_historydetail.json
http POST http://localhost:$API_PORT/dataset/submit < queries/dataset_submit.json
http POST http://localhost:$API_PORT/gsd/submit < queries/gsd_submit.json
http POST http://localhost:$API_PORT/dataset/glycan_finder < queries/dataset_glycan_finder.json
where $API_PORT the API port specified in the api/conf/config.json file.
After cloning this repo, you will need to set the paramters given in conf/config.json. The "app_port" is the port in the host that should map to docker container for the app.
From the "app" subdirectory, run the python script given to build and start container:
python3 create_app_container.py -s $SER
docker ps --all
The last command should list docker all containers and you should see the container
you created running_glyds_app_$SER. To start this container, the best way is
to create a service file (/usr/lib/systemd/system/docker-glyds-app-$SER.service),
and place the following content in it.
[Unit]
Description=Glyds APP Container
Requires=docker.service
After=docker.service
[Service]
Restart=always
ExecStart=/usr/bin/docker start -a running_glyds_app_$SER
ExecStop=/usr/bin/docker stop -t 2 running_glyds_app_$SER
[Install]
WantedBy=default.target
This will allow you to start/stop the container with the following commands, and ensure that the container will start on server reboot.
$ sudo systemctl daemon-reload
$ sudo systemctl enable docker-glyds-app-$SER.service
$ sudo systemctl start docker-glyds-app-$SER.service
$ sudo systemctl stop docker-glyds-app-$SER.service
To map the APP and API containers to public domains (e.g. www.glyds.org and api.glyds.org), add apache VirtualHost directives. This VirtualHost directive can be in a new f ile (e.g. /etc/httpd/conf.d/glyds.conf).
<VirtualHost *:443>
ServerName www.glyds.org
ProxyPass / http://127.0.0.1:$APP_PORT/
ProxyPassReverse / http://127.0.0.1:$APP_PORT/
</VirtualHost>
<VirtualHost *:443>
ServerName api.glyds.org
ProxyPass / http://127.0.0.1:$API_PORT/
ProxyPassReverse / http://127.0.0.1:$API_PORT/
</VirtualHost>
where $APP_PORT and $API_PORT are your port for the APP and API ports in conf/config.json file. You need to restart apache after this changes using the following command:
$ sudo apachectl restart