Organism & Analysis Migration

[Ferrisx4]

Content Migration and Beautification - Stage 1

Stage 1 commences with migrating the Organism and Analysis content types to be 100% pure Tripal 3 and to customize them per i5k requirements.

Original Review Document

Organism

• [x] List of organisms (/organisms/)
• [x] Links (Internal - Tripal)
• [ ] Links (External)
  • for external links that are to NCBI - create another issue to migrate these, but AFTER the first release (not a dealbreaker)
• [x] Tripal Node aliases (/Drosophila_biarmipes/ -> Tripal 3 entity page)
• [x] Images
  • [x] Credits/Attribution
  • [x] Where to store Organism images (research) (do default - sites/default/files)
  • [x] [Automated] Migrated Tripal 3 organisms retain the image field (via script that extracts the URL from file_managed table)
• [ ] Remove Tripal 2 content (final step)
• [x] [Automated] Strip HTML out of chado.organism's abbreviation, possibly other fields
  • Ignoring chado.organism's comment field for now.

Analysis

• [ ] Check if assembly stats that are now in organism page get migrated to corresponding genome assembly analysis
  • if not - create another issue to migrate these, but AFTER the first release (not a dealbreaker)
• [ ] Associated publications into the pub table - create another issue to migrate these, but AFTER the first release (not a dealbreaker)

Migration automation

• [ ] If possible and not too onerous - automate display customization (which fields to show and where) for each content type.
• [x] Disable "date performed" field - not useful
• [ ] Analysis content type - disable all panes EXCEPT Summary

[mpoelchau]

Still need to remove Tripal2 content. Publication info is in separate issue. Assembly stats migrated to analysis - this is not a high priority, let's table this for now. External links - they work, need to verify that this isn't a problem Disable date performed field - done External links - they work