WebApollo Embed

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Work in progress: come back later

Description of setting up WebApollo as an embedded web application

Use case

  1. Run WebApollo as an integrated component of a web application
  2. Support multiple species
  3. Support multiple users with private editing session
    • Users can have multiple projects/species
  4. Jump straight to edit mode without user login

Installation

  1. Use the regular installation/configuration procedure
  2. Use exemplar species sequence annotations, we will add multiple species support below

Unsorted odds and ends

The key thing that must be done for multiple species/users/sessions on one server is creating multiple tomcat webapps by cloning the WebApollo Directory tree.

Demo user.png Refseqs.png Refseqs in db.png


Anatomy of a WebApollo clone

  • The clone of the webapp is almost entirely symbolic links, except where otherwise noted.
  • We can't just create a symbolic link to the base WebApollo installation because some of the internal components are real files
WebApollo_clone
 |-- META-INF -> symlink
 |-- WEB-INF -> symlink
 |-- annotations
 |-- config
 |   |-- blat_config.xml -> symlink
 |   |-- canned_comments.xml -> symlink
 |   |-- chado_config.xml -> symlink
 |   |-- config.xml
 |   |-- gff3_config.xml -> symlink
 |   |-- hibernate.xml -> symlink
 |   |-- mapping.xml -> symlink
 |   |-- track_name_comparator.js -> symlink
 |   `-- translation_tables -> symlink
 |-- images -> symlink
 |-- index.html -> symlink
 |-- jbrowse
 |   |-- bin -> symlink
 |   |-- combination_tracks.css -> symlink
 |   |-- data
 |   |   |-- names -> symlink
 |   |   |-- seq -> symlink
 |   |   |-- trackList.json
 |   |   `-- tracks
 |   |       `-- EG -> symlink 
 |   |-- export_dialog.css -> symlink
 |   |-- faceted_track_selector.css -> symlink
 |   |-- file_dialog.css -> symlink
 |   |-- genome.css -> symlink
 |   |-- icons.css -> symlink
 |   |-- img -> symlink
 |   |-- index.html -> symlink
 |   |-- jbrowse_conf.json -> symlink
 |   |-- main.css -> symlink
 |   |-- maker.css -> symlink
 |   |-- menubar.css -> symlink
 |   |-- plugins -> symlink
 |   |-- sample_data -> symlink
 |   |-- src -> symlink
 |   `-- track_styles.css -> symlink
 |-- js -> symlink
 |-- jslib -> symlink
 |-- selectTrack.jsp -> symlink
 |-- styles -> symlink
 |-- tmp
 |-- userPermissions.jsp -> symlink
 `-- user_interfaces -> symlink