nathandunn / apolloconvertedgrails3server Goto Github PK

-- Broken and important

• annotations:
  • single-level feature
  • ncRNA top
  • get_features: use with to do a further embedded: https://stackoverflow.com/a/21900438/1739366
  • set labels explicitly to ALWAYS include Feature: #19 , http://gorm.grails.org/snapshot/neo4j/manual/index.html#labelStrategy
  • add features multiple times with the same GFF3 (naming collision currently) (only does one add current)
  • ncRNA gene top
  • gene (MRNA top)!
  • MRNA top?

(test bootstrap)

-- blocked from testing

• io: need features to download
• remote: sequence interaction methods . . . probably working, but need to be able to add fasta, etc. . . . doesn't to work quite right
• delete features from organisms (if other tess are good)
• export GFF3 (if other tests are good)

--- Working

• canned comments: add_comment, delete_comment, get_comments, update_comments all works all works
• users (especially load_users)
• canned keys, works, though we can probably get rid of some methods
• canned values, works, though we can probably get rid of some methods
• metrics
• groups (very weird error)
• status
• organisms: works, but some issues with the features, have not yet tested, because of IO

https://github.com/nathandunn/apollo-performance/projects/1

• collapse feature locations into an edge property pointing to a sequence
• collapse feature relationship into a part_of property / single edge
• use biolink properties / https://biolink.github.io/biolink-model/docs/Gene.html / https://biolink.github.io/biolink-model/docs/TranscriptToGeneRelationship.html / https://biolink.github.io/biolink-model/docs/GenomicSequenceLocalization.html and potentially RDF to Scheccle, or JSON to JSONSchema

2020-06-02 12:44:28.990 ERROR --- [nio-8080-exec-2] o.b.apollo.FeatureRelationshipService    : More than one child feature relationships found for Feature{id=22026, symbol='null', description='null', name='dpyn-00001', uniqueName='e9a2de42-5081-49f3-bcea-489da1707d0e', sequenceLength=null, status=nullg

during add transcript of addfeature

• this is something that couldn't be done within an RDBMS . .
• locations could be collapsed within the node, but that is a speedup that could be done in both places

http://gorm.grails.org/snapshot/neo4j/manual/index.html#labelStrategy

Set explicitly to cycle though ALL of the inheritance heirarchy to eventually include feature

• availableStatus
• canned comment
• canned key
• canned value
• featureEvent (report?)
• featureType
• jbrowse / chooseOrganism
• organism
• proxy
• sequence
• suggestedName
• webServices
• index
• menu
• web_services?
• others (in admin, etc.)
• reports
• home (remove metrics)
• auth
• annotator