5.1.0.4 model changes

[alancleary]

@sammyjava has a 5.1.0.4-model-changes branch that adds support for Intermine version 5.1.0.4, which is required to integrate the trait association search web component into the LIS site, among other things. I'm opening this issue to serve as a reference for things related to this work that are located in different repos. Edit: Sam has left the project so this issue is being repurposed to keep track of the work that needs to be done to finish implementing support for InterMine version 5.1.0.4.

• [x] #50
• [x] Add types missing from has-stuff-interfaces branch
  • [x] DataSource
  • [x] OntologyRelation
  • [x] OntologyTermSynonym
• [x] Add implementations for new types
  • [x] CDS
  • [x] DataSource (has-stuff-interfaces)
  • [x] Exon
  • [x] GeneFlankingRegion
  • [x] IntergenicRegion
  • [x] Intron
  • [x] OntologyRelation (has-stuff-interfaces)
  • [x] OntologyTermSynonym (has-stuff-interfaces)
  • [x] PanGeneSet
  • [x] ProteinMatch
  • [x] Sequence
  • [x] SOTerm
  • [x] Transcript
  • [x] UTR
• [ ] Make sure all types are up-to-date between with both the 5.1.0.4-model-changes and has-stuff-interfaces branches
  • [x] Annotatable.graphql
  • [x] Author.graphql
  • [x] BioEntity.graphql
  • [x] CDS.graphql
  • [x] Chromosome.graphql
  • [x] DataSet.graphql
  • [x] DataSource.graphql
  • [x] Exon.graphql
  • [x] ExpressionSample.graphql
  • [x] ExpressionSource.graphql
  • [x] ExpressionValue.graphql See issue #154
  • [x] GeneFamilyAssignment.graphql
  • [x] GeneFamily.graphql
  • [x] GeneFamilyTally.graphql
  • [x] GeneFlankingRegion.graphql
  • [ ] Gene.graphql
  • [x] GeneticMap.graphql
  • [x] GeneticMarker.graphql
  • [x] GenotypingPlatform.graphql
  • [x] GWAS.graphql
  • [x] GWASResult.graphql
  • [x] IntergenicRegion.graphql
  • [x] Intron.graphql
  • [x] LinkageGroup.graphql
  • [x] LinkageGroupPosition.graphql
  • [ ] Linkout.graphql
  • [x] Location.graphql Excluding feature field
  • [x] MRNA.graphql
  • [x] OntologyAnnotation.graphql Excluding subject field
  • [x] Ontology.graphql
  • [x] OntologyRelation.graphql
  • [x] OntologyTerm.graphql
  • [x] OntologyTermSynonym.graphql
  • [x] Organism.graphql
  • [x] PanGeneSet.graphql
  • [x] Pathway.graphql
  • [x] Phylonode.graphql
  • [x] Phylotree.graphql
  • [x] ProteinDomain.graphql
  • [x] Protein.graphql
  • [x] ProteinMatch.graphql
  • [x] Publication.graphql
  • [x] QTL.graphql
  • [ ] QTLStudy.graphql
  • [ ] Query.graphql
  • [x] SequenceFeature.graphql See issue #154
  • [ ] Sequence.graphql
  • [x] SOTerm.graphql SequenceOntologyTerm
  • [ ] Strain.graphql
  • [ ] Supercontig.graphql
  • [x] SyntenicRegion.graphql
  • [ ] SyntenyBlock.graphql
  • [ ] Trait.graphql
  • [x] Transcript.graphql
  • [ ] UTR.graphql
• [ ] Do all bio entities need the bio entity joins (see protein for an example)? And do transitive types, i.e. sequences and transcripts, need them as well? For example, there's a sequenceFeatureJoinsFactory that doesn't contain any of the joins from the bioEntityJoinsFactory...
• [ ] Update every interface type to have the suffix Interface
• [ ] Update every interface resolver factory to have the prefix is
• [ ] Make sure all type implementations include every field in the type
• [ ] Make sure all types are imported/exported in src/data-sources/intermine/models/index.ts
• [ ] Make sure all search-<type> files are implemented and up to date
• [ ] Make sure all API functions that support multiple types use a generic internal function
• [ ] Make sure all API functions are listed in src/data-sources/intermine/api/index.ts
• [ ] Make sure all resolvers are listed in src/resolvers/intermine/index.ts
• [ ] Remove InterMine comments
  • [ ] src/types/
  • [ ] src/data-sources/intermine/api/
  • [ ] src/data-sources/intermine/models/
  • [ ] src/resolvers/intermine/
• [ ] Make sure new types are in top-level Query
• [ ] Merge main
• [ ] Make sure all InterMine API functions use jsoncount instead of summaryPath
• [ ] Make sure generic types (annotatable, bio-entity, sequence-feature, and transcript) union types are complete
• [ ] Add generic resolvers; see the generic-resolvers branch for an example. This will basically be any resolver in an interface's resolver factory and any resolver that calls a getTypeForOtherType function.
  • [x] Annotatable
  • [x] BioEntity
  • [ ] CDSs
  • [ ] CrossReference
  • [x] DataSets
  • [ ] Exons
  • [x] GeneticMarkers
  • [x] GenotypingPlatform
  • [ ] Introns
  • [x] OntologyAnnotation
  • [x] OntologyTermInterface
  • [x] PanGeneSets
  • [x] Phylotree
  • [x] Publications
  • [x] SequenceFeature
  • [x] Transcripts
  • [ ] UTRs
• [x] #155
• [ ] #153
• [ ] Remove the HasStuff interfaces from the GraphQL API because the interfaces have no external function; i.e. keep the internal hasStuffFactory resolvers.

[sammyjava]

I've done some housekeeping/streamlining of the 5.1.0.4 model. It's not that much different, but note to self to double-check all the types and resolvers and queries against 5.1.0.4.

[sammyjava]

I've renamed the interfaces to FooInterface with a resolvable type Foo that implements it. I've added a boatload of types that hadn't been added yet.

Generally, if a field like locatedFeatures originates in a class like BioEntity (it does), then the resolver will treat the object as a BioEntity for resolution. This helps simplify some things like resolving locatedFeatures, which was missing before.

[sammyjava]

I've done the final updates to the types in the 5.1.0.4-model-changes branch. However, work needs to be done with resolvers to handle a few late things, if one wants to get 5.1.0.4 going with the old code base in this repo, rather than rolling out the big has-stuff-interfaces branch, which has all of the below done plus a helluva lot more. I may be able to get that work done next Thursday so 5.1.0.4 is tested and ready to go.

• [ ] Annotatable now has the dataSets collection, removed from BioEntity. So, everything that implements Annotatable should pick up populated dataSets in their resolver.
• [ ] Remove dataSets population from BioEntity (see above)
• [ ] DataSet.entities replaces bioEntities - but that isn't implemented in this branch, anyway, so that needs to be added.
• [ ] SyntenyBlock now implements Annotatable