Roadmap

This is the roadmap for GenoRing releases.

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• GenoRing platform (PERL script)
  • Module install
  • Module uninstall
  • Support for module not providing services
  • Support for service alternatives
  • Support to replace containerized services into local/external ones
  • Complete support for (GenoRing) module upgrade (ie. not managed app or data)
  • Support to run shell in running services
  • Support to run shell in offline services
  • Manage module dependencies with version (eg. having a separate MongoDB service required by Gigwa)
  • Support for services only need to perform install or backend actions
  • Support for multiple GenoRing instances (container/volume/network prefix)
  • Support for multi-site (same GenoRing instance, multiple target sites with separate data/database)
  • Data versioning system
  • Fix ARM compatibility
  • Support for non-exposed volumes (-no-exposed-volumes, Windows compatibility): how module hooks could access to not exposed volumes? Provide a wrapper script for file operations that could use a FS container when needed?
  • Improve exposed volumes access permission/owner
  • Support for profiles "prod", "staging", "dev", "backend" and "offline" in "genoring" CMS/php image to select modules to enable
  • Backup volume only writable during backup operations (or for "backend" profile?)
  • Automated tests scaffold
  • Tests
    • GenoRing without any services (ex.: all "localized")
    • Service "localization"
    • HTTPd alternative
    • A basic CMS replacement
• GenoRing core API ("genoring" script in "genoring" CMS/PHP container)
  • Implement a wrapper script to handle composer and drush commands
  • Design a GenoRing core API to allow CMS replacement
  • Manage drush commands in a separate PHP script
  • Document how to create an alternative CMS
• Modules
  • GenoRing
    • Change Docker image USER to non-root
  • Gigwa
    • Fix site integration issue (error on front page)
    • Rework Gigwa integration: create a Drupal module for Gigwa to manage account bridge, data loading, site integration,...
    • Consider MongoDB as a separate module and a dependency
  • JBrowse
    • Generate a JBrowse file structure using JBrowse Docker container or create a packagist library?
    • integrate Drupal module for JBrowse (tripal_jbrowse)
  • Galaxy
    • Create GenoRing module
  • DIAMOND/BLAST
    • Create GenoRing module
  • BrAPI Mapper
    • Create GenoRing module
    • Document (use, configure, ...)
  • Heatmap gene expression (heatmap visualization analysis expression module) Tripal module
    • Create GenoRing module
    • See what's up with the existing Tripal module
  • Apollo
    • Create GenoRing module
  • Artemis
    • Create GenoRing module
  • EBI export
    • Create GenoRing module
  • Let's Encypt module
• Web Interface (GenoRing Drupal distribution, module and theme)
  • GenorRing base theme
    • Change header banner to end in half circle and be full width
    • Change Olivero "Drupal" background with a "DNA" background
    • Option to set a header background image
    • Investigate how to manage a single page site and provide that option
    • Identify fontawesome-like free icons to use
  • GenoRing module
    • Drupal UI "tours" for GenoRing
    • Dataset creation page
    • Module data loading page
    • Dashboard
    • Design and implement a "data model" aggregator for external entities
    • Design and implement a UI for data search
  • GenoRing distribution
    • Review list of modules to enable (including core modules)
    • Generate a new config to install
  • External entity FASTA storage client
  • External entity Newick storage client
  • External entity SPARQL storage client
  • External entity XML response decoder
  • Design and implement a biological material ordering and tracking Drupal module
  • Investigate tool execution (from Drupal UI): based on Symfony process component, see how to allow switching between a local execution, a galaxy execution or a container execution.
• Data types and models (design)
  • Define data types and models we want to handle
    • Pangenome?
    • Breeding data types: a study data type?
  • Genome data type
    • Field list and Metadata (Genome name, version, author, data file or directory,...)
  • Genebank data type
    • Field list and Metadata (Genome name, version, author, data file or directory,...)
  • Gene model
  • Species model
  • Germplasm model
  • Discuss what is needed to have data models "AI ready"
• Documentation (global)
  • TEMPLATE module: review documentation to avoid duplicates in multiple readmes
  • Document alternatives
    • Apache 2 HTTPd proxy
    • How to create a CMS replacement
  • Document "to local" for services
    • Nginx proxy to local
    • PostgreSQL to local
    • Drupal CMS + PHP-FPM to local
    • Gigwa to local
  • Document backup system
    • How backup are managed and structured
    • How to implement backup management in modules
  • Document data management system
    • Architecture (dataset --> xntt types)
    • How to generate data releases
    • How to load data into modules
• GenoRing portal (genoring.net)
  • Setup GenoRing official portal site
  • GenoRing contact emails
  • Add graphical elements and schemas
  • Biological data portal comparison table
  • Setup a service for GenoRing site registration