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Table of Contents

  1. cellxgene proxy backstory
  2. cellxgene proxy setup
    1. etc/cellxgene_templates
      1. group_to_port.map defines group to port location
      2. mkcellxgene_config.pl
      3. apache2 template
      4. systemd.service template:
    2. var/www/
    3. etc/apache2 - apache2 configs
    4. cellxgene && cellxgene-gateway
    5. Basic usage
    6. links
  3. Demo

cellxgene proxy backstory

CZ CELLxGENE is an interactive data explorer for single-cell datasets. Leveraging modern web development techniques to enable fast visualizations allowing computational researchers to explore their data.

The Cellxgene Gateway enables users to utilize the Cellxgene Server offered by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) for multiple datasets. It presents an index of accessible h5ad (anndata) files. When a user selects a file, it initiates a Cellxgene Server instance to load the specific data file and subsequently proxies requests to that server.

Now imagine a scenario where multiple groups are interested in utilizing Cellxgene on their respective datasets.

One possible approach is to establish separate instances of cellxgene-gateway for each group. However, a more optimal solution would be to have a unified instance that incorporates some form of authentication specifically designed for different datasets/cellgene-gateway instances. Cellxgene-gateway proxy serves exatcly this purpose.

The global overview:

A research group maintains a directory containing multiple h5ad files.

For each group, a cellxgene-gateway instance is in place, which listens on a designated TCP port and serves the specific group directory containing h5ad files. Thus, there is a straightforward correspondence between a group, its respective directory, and a network port. This arrangement is configured using cellxgene-gateway variables, such as CELLXGENE_DATA and GATEWAY_PORT. To enhance this configuration, we can implement a reverse proxy that acts as an intermediary layer. By creating separate configurations, we can direct requests originating from specific group URLs to the corresponding cellxgene-gateway instances. Ultimately, this approach provides a unified interface for all groups. Additionally, we have the option to enable authentication for the group URLs, granting controlled access to the data based on group membership.

This repository offers templates and scripts. These resources facilitate the creation of configuration files for both the cellxgene-gateway and Apache2 reverse proxy components.

cellxgene proxy setup

This setup offers sample files and a brief explanation for configuring Apache2 reverse proxy with authentication using mod_auth_form for cellxgene_gateway processes. The setup can be implemented for processes running on the local or remote hosts.

etc/cellxgene_templates

group_to_port.map defines group to port location

mkcellxgene_config.pl

  • script which reads etc/cellxgene/group_to_port.map file and templates and generates systemd, apache2 configs and updates html page for apache's mod_auth_form module
  • deletetion is not implemented
  • runs in root context, since it will write systemd and apache configs

apache2 template

  • Ldap auth part is optional, this setup is using Openldap and groups with memberUid attribute. The <RequireAny/RequireAll> stanza allows users from different groups access only their cellxgene locations. The group sysop and defined users can access any resource.
  • See etc/apache2/sites-available/public.conf for the simplest config without authentication.

systemd.service template:

  • needs properly defined user and a number of ENV variables.
  • <group> and <port> will be updated by the mkcellxgene_config.pl script
  • One might need to call systemctl enable cellxgene_<group> to make services start on boot

var/www/

  • html and css files for mod_auth_form
  • contains the main index.html updated by mkcellxgene_config.pl

etc/apache2 - apache2 configs

  • list of enabled modules (in addition to the default ones) ( you might have different preferences!) ssl,rewrite,headers,ldap,session,authnz_ldap,request,session_cookie,session_crypto,proxy,proxy_http,proxy_html
  • sites-available/cellxgene.conf - the main config for http and https virtualhosts, also handles the logout action includes cellxgene/* dir with group configs generated by mkcellxgene_config.pl
  • public.conf for the public section

cellxgene && cellxgene-gateway

  • it is assumed that cellxgene and cellxgene-gateway are installed in the cellxgeneUser home dir

Basic usage

  1. Create the data directory for the new group and set appropirate permissions. (see the CELLXGENE_DATA var in the systemd template)
  2. Update /etc/cellxgene_templates/group_to_port.map
  3. Call /etc/cellxgene_templates/mkcellxgene_config.pl <group> to setup systemd, apache2 config and /var/www/index.html
  4. Start the new systemd service: service cellxgene_<group> start
  5. Reload apache2 config: service apache2 reload
  6. Navigate to the url and test the application
  7. Debug errors with journalctl -xe and (or) apache2 error log files

Links

Demo

Demo setup with Docker: https://github.com/mestia/cellxgene-proxy-docker-demo