Merge branch 'update-frontend' into newmain

.gitignore

@@ -66,7 +66,7 @@ data/project_*
 .idea/
 
 # ignore this datafile, now too big
-data/initTable.hdf5
+data/initTable*.hdf5
 data/workTable.hdf5
 
 # ignore the data
@@ -78,6 +78,7 @@ data/meta_table.csv
 data/out/
 data/rawGWASfiles/
 projects/project_*
+projects/celery_results
 
 # Ignore MacOS Files
 **/.DS_Store

.gitlab-ci.yml

@@ -23,7 +23,7 @@ test-python:
 #          '3.9',
           '3.10',
 #          '3.11',
-      ]
+        ]
 
 
 test-docker-compose:

ansible/README.md

-# JASS ansible playbooks
-
-This repository contains the playbooks to manage a JASS instance with ansible
-
-- `system.yaml`: install system requirements
-- `deploy.yaml`: download/update JASS and perform required procedures to migrate and restart
-
-## how to use these ?
-
-```
-ansible-playbook -v -i ./hosts_system system.yaml --ask-become-pass --extra-vars "deploy_user_name=jass repo_api_token=XXXXXX"
-ansible-playbook -v -i ./hosts_deploy deploy.yaml --ask-become-pass --extra-vars "deploy_user_name=jass repo_api_token=XXXXXX"
-```

ansible/celery.service

-[Unit]
-Description=Celery Service
-After=network.target
-
-[Service]
-Type=forking
-User=jass
-Group=nginx
-EnvironmentFile=-/etc/default/celeryd
-WorkingDirectory=/var/jass_data
-ExecStart=/bin/sh -c '${CELERY_BIN} multi start ${CELERYD_NODES} \
-  -A ${CELERY_APP} --pidfile=${CELERYD_PID_FILE} \
-  --logfile=${CELERYD_LOG_FILE} --loglevel=${CELERYD_LOG_LEVEL} ${CELERYD_OPTS}'
-ExecStop=/bin/sh -c '${CELERY_BIN} multi stopwait ${CELERYD_NODES} \
-  --pidfile=${CELERYD_PID_FILE}'
-ExecReload=/bin/sh -c '${CELERY_BIN} multi restart ${CELERYD_NODES} \
-  -A ${CELERY_APP} --pidfile=${CELERYD_PID_FILE} \
-  --logfile=${CELERYD_LOG_FILE} --loglevel=${CELERYD_LOG_LEVEL} ${CELERYD_OPTS}'
-
-[Install]
-WantedBy=multi-user.target

ansible/celeryd

-CELERYD_NODES="worker"
-CELERY_BIN="celery"
-CELERY_APP="jass"
-CELERYD_CHDIR="/var/jass_data"
-CELERYD_OPTS="--time-limit=3000 --concurrency=1 --max-tasks-per-child=1"
-CELERYD_LOG_FILE="/var/jass_data/celery%N.log"
-CELERYD_PID_FILE="/var/jass_data/celery%N.pid"
-CELERYD_LOG_LEVEL="DEBUG"
-CELERYD_USER="jass"
-CELERYD_GROUP="nginx"
-CELERY_CREATE_DIRS=1

ansible/deploy.yaml

----
-- hosts: all
-  become: yes
-  gather_facts: yes
-  tasks:
-    # stop uwsgi service
-    - name: stop JASS service
-      systemd: state=stopped name=jass-uwsgi enabled=true
-      ignore_errors: yes
-      when: not docker
-    # stop nginx service
-    - name: stop nginx service
-      systemd: state=stopped name=nginx enabled=true
-      ignore_errors: yes
-      when: not docker
-    # stop celery service
-    - name: stop celery service
-      systemd: state=stopped name=celery enabled=true
-      ignore_errors: yes
-      when: not docker
-    - name: update yum
-      become: true
-      yum: name=* state=latest
-    - name: install yum utils
-      become: true
-      yum: name=yum-utils state=latest
-    - name: install the 'Development tools' package group
-      become: true
-      yum:
-        name: "@Development tools"
-        state: present
-    - name: add repo IUS
-      become: true
-      yum:
-        name: https://repo.ius.io/ius-release-el7.rpm
-        state: present
-    - name: install git
-      become: true
-      yum: name=git state=latest
-    - name: install python
-      become: true
-      yum: name=python36u state=latest
-    - name: install pip
-      become: true
-      yum: name=python36u-pip state=latest
-    - name: install python36u-devel
-      become: true
-      yum: name=python36u-devel state=latest
-    - name: pcre
-      become: true
-      yum: name=pcre state=latest
-    - name: pcre-devel
-      become: true
-      yum: name=pcre-devel state=latest
-    - name: install git
-      yum: name=git state=latest
-      become: true
-    - name: epel-release
-      become: true
-      yum: name=epel-release state=latest
-    - name: nginx
-      become: true
-      yum: name=nginx state=latest
-    - name: zlib-devel # required by Pillow
-      become: true
-      yum: name=zlib-devel state=latest
-    - name: libjpeg-turbo-devel # required by Pillow
-      become: true
-      yum: name=libjpeg-turbo-devel state=latest
-    - pip: 
-        name: wheel
-        executable: pip3.6
-    # install jass on server
-    - name: install jass from gitlab
-      pip: 
-        name: git+https://gitlab.pasteur.fr/statistical-genetics/jass.git
-        state: forcereinstall
-        executable: pip3.6
-      when: not docker
-    - name: download JASS frozen requirements file
-      get_url:
-        url: https://gitlab.pasteur.fr/statistical-genetics/jass/raw/master/requirements.txt
-        dest: /tmp/requirements.txt
-        force: yes
-      when: not docker
-    - pip:
-        requirements: /tmp/requirements.txt
-        state: forcereinstall
-        executable: pip3.6
-      when: not docker
-    # install jass on docker
-    - name: install jass from local
-      pip:
-        editable: true
-        name: file:///code/
-        state: forcereinstall
-        executable: pip3.6
-      when: docker
-    - name: install jass deps from local
-      pip:
-        requirements: /code/ansible/reqs-docker.txt
-        state: forcereinstall
-        executable: pip3.6
-      when: docker
-    # install python web deps
-    - name: install uwsgi
-      pip: 
-        name: uwsgi
-        executable: pip3.6
-      become: true
-    - name: copy nginx config       
-      become: true
-      copy:
-         src: nginx.conf
-         dest: /etc/nginx/nginx.conf
-    - name: copy systemd service file for JASS-web
-      copy: 
-        src: jass-uwsgi.service 
-        dest: /lib/systemd/system/jass-uwsgi.service
-        owner: root
-        group: root
-    - name: copy JASS uwsgi configuration file
-      copy: 
-        src: jass_uwsgi.ini
-        dest: /var/jass_data
-        owner: '{{ deploy_user_name }}'
-        group: nginx
-    - name: copy celeryd configuration file
-      copy: 
-        src: celeryd
-        dest: /etc/default
-        owner: root
-        group: root
-    - name: copy celery systemd service
-      copy: 
-        src: celery.service
-        dest: /lib/systemd/system/celery.service
-        owner: root
-        group: root
-    # start uwsgi service
-    - name: start JASS service if relevant
-      systemd: state=started name=jass-uwsgi enabled=true daemon_reload=true
-      when: not docker
-    # start nginx service
-    - name: start NGINX service if relevant
-      systemd: state=started name=nginx enabled=true daemon_reload=true
-      when: not docker
-    # start celery service
-    - name: start celery service if relevant
-      systemd: state=started name=celery enabled=true daemon_reload=true
-      when: not docker

ansible/hosts_deploy

-hub17.hosting.pasteur.fr   ansible_user=jass

ansible/hosts_local

-127.0.0.1 ansible_connection=local

ansible/hosts_system

-jass.pasteur.fr

ansible/jass-uwsgi.service

-[Unit]
-Description=uWSGI instance to serve JASS
-After=network.target
-
-[Service]
-User=jass
-Group=nginx
-WorkingDirectory=/var/jass_data
-ExecStart=/bin/uwsgi --ini jass_uwsgi.ini
-
-[Install]
-WantedBy=multi-user.target

ansible/jass-web.service

-[Unit]
-Description=JASS Web Server
-After=network.target remote-fs.target nss-lookup.target
-
-[Service]
-Type=oneshot
-RemainAfterExit=yes
-ExecStart=/etc/jass/apachectl start
-ExecStop=/etc/jass/apachectl stop
-
-[Install]
-WantedBy=multi-user.target

ansible/jass_uwsgi.ini

-[uwsgi]
-env = JASS_DATA_DIR=/var/jass_data
-module = jass.wsgi
-
-master = true
-processes = 5
-
-socket = jass_web.sock
-chmod-socket = 660
-vacuum = true
-
-die-on-term = true
-
-logto = /var/jass_data/uwsgi_error_log

ansible/nginx.conf

-# For more information on configuration, see:
-#   * Official English Documentation: http://nginx.org/en/docs/
-#   * Official Russian Documentation: http://nginx.org/ru/docs/
-
-user nginx;
-worker_processes auto;
-error_log /var/log/nginx/error.log;
-pid /run/nginx.pid;
-
-# Load dynamic modules. See /usr/share/nginx/README.dynamic.
-include /usr/share/nginx/modules/*.conf;
-
-events {
-    worker_connections 1024;
-}
-
-http {
-    log_format  main  '$remote_addr - $remote_user [$time_local] "$request" '
-                      '$status $body_bytes_sent "$http_referer" '
-                      '"$http_user_agent" "$http_x_forwarded_for"';
-
-    access_log  /var/log/nginx/access.log  main;
-
-    sendfile            on;
-    tcp_nopush          on;
-    tcp_nodelay         on;
-    keepalive_timeout   65;
-    types_hash_max_size 2048;
-
-    include             /etc/nginx/mime.types;
-    default_type        application/octet-stream;
-
-    # Load modular configuration files from the /etc/nginx/conf.d directory.
-    # See http://nginx.org/en/docs/ngx_core_module.html#include
-    # for more information.
-    include /etc/nginx/conf.d/*.conf;
-
-    server {
-        listen       80 default_server;
-        listen       [::]:80 default_server;
-        server_name  _;
-        root         /usr/share/nginx/html;
-
-        # Load configuration files for the default server block.
-        include /etc/nginx/default.d/*.conf;
-
-        location / {
-            include uwsgi_params;
-            uwsgi_pass unix:/var/jass_data/jass_web.sock;
-            uwsgi_read_timeout 3600;
-            uwsgi_max_temp_file_size 10240m;
-
-            proxy_connect_timeout       3600;
-            proxy_send_timeout          3600;
-            proxy_read_timeout          3600;
-            send_timeout                3600;
-
-            proxy_http_version 1.1;
-            proxy_set_header Connection "";
-        }
-
-        error_page 404 /404.html;
-            location = /40x.html {
-        }
-
-        error_page 500 502 503 504 /50x.html;
-            location = /50x.html {
-        }
-    }
-
-}

ansible/params-docker.json

-{
-    "deploy_user_name":"root",
-    "docker":true,
-}

ansible/params-server.json

-{
-    "deploy_user_name":"jass",
-    "docker":false,
-    "repo_api_token":"$REPO_API_TOKEN"
-}

ansible/reqs-docker.txt

--r ../requirements.txt

ansible/ssh_key.json.j2

-{"id": "Statistical-Genetics/jass","title" : "jass_deploy_key","key": "{{ key_value.stdout }}"}

ansible/system.retry

-jass.pasteur.fr

ansible/system.yaml

----
-- hosts: all
-  gather_facts: no
-  tasks:
-    #
-    # User and Group configuration
-    #
-    # application user ({{deploy_user_name}}) is created
-    # in the wheel group, which has to be passwordless sudo
-    # and upload the key as a deploy key to gitlab
-    - name: Make sure we have a 'wheel' group
-      become: true
-      group:
-        name: wheel
-        state: present
-    - name: Allow 'wheel' group to have passwordless sudo
-      become: true
-      lineinfile:
-        dest: /etc/sudoers
-        state: present
-        regexp: '^%wheel'
-        line: '%wheel ALL=(ALL) NOPASSWD: ALL'
-    - name: Create {{ deploy_user_name }} user
-      user: name={{ deploy_user_name }} groups=wheel,nginx append=yes state=present createhome=yes generate_ssh_key=yes ssh_key_bits=2048 ssh_key_file=.ssh/id_rsa
-      become: true
-    - name: Cat deployer's user public key
-      shell: "cat /home/{{ deploy_user_name }}/.ssh/id_rsa.pub"
-      register: key_value
-      become: true
-    - name: Create ssh_key json
-      template: src=ssh_key.json.j2 dest=/home/{{ deploy_user_name }}/ssh_key.json group={{ deploy_user_name }} owner={{ deploy_user_name }} force=yes
-      become: true
-    - name: Cat deployer's user public key
-      shell: "cat /home/{{ deploy_user_name }}/ssh_key.json"
-      become: true
-    - name: Upload deploy keys to gitlab
-      shell: "curl -X POST -H 'Accept: application/json' -H 'Content-type: application/json' -H 'PRIVATE-TOKEN: {{ repo_api_token }}' --data-binary @/home/{{ deploy_user_name }}/ssh_key.json https://gitlab.pasteur.fr/api/v3/projects/251/keys"
-      become: true
-    #
-    # Security configuration
-    #
-    # disable SELinux, and open firewall to incoming http 
-    - name: disable SELinux
-      become: true
-      selinux:
-        state: disabled
-    - name: Open firewall to HTTP traffic
-      firewalld:
-        service: http
-        permanent: true
-        state: enabled
-      become: true

client/.eslintrc.js

@@ -18,6 +18,7 @@ module.exports = {
   // add your custom rules here
   rules: {
     "no-unused-vars": "off",
-    'no-console': 'off'
+    'no-console': 'off',
+    'vue/valid-v-slot': 'off'
   }
 }