Simsbiohub 471 Taxon -> ITIS Migration

[MacQSL]

Taxon -> ITIS Migration

Description of changes:

1. Created migration for dropping taxon table and associated taxon_id fields.
2. Added new columns for itis_tsn + itis_scientific_name (scientific name only exists in the critter table)
3. Created new ItisService / CritterService / MarkingServices / XrefService
4. Migration handles the translation of previous taxon_ids -> itis_tsn values.
5. Updated seed data.
6. Updated endpoints / routers / services / repositories that handle taxon_id
7. Removed old dead code / unused endpoints
8. General refactoring of code to be more similar to SIMS
9. Updated swagger documentation

Important Features

Migration (prisma/migrations/taxon_to_itis)

• Drops unused taxon fields
• Drops taxon table
• Converts old taxon_id -> ITIS tsn's
• Drops unused / old development views
• Drops triggers relating to previous taxon table

ItisService

• Handles querying ITIS for hierarchy
• Conversion of scientific name -> tsn / tsn -> scientific name
• Patches objects to sync tsn / scientific name

XrefService / XrefRepository

• Converted the endpoints from taxon_id queries -> tsn queries
• Formatted the complex prisma queries / formatters to raw sql
• Including qualitative options in qualitative options response

CritterService / CritterRepository

• Formatted the complex prisma queries / formatters to raw sql

[MacQSL]

Critter

/api/critter/create

• swagger docs says it needs an ID as a parameter it just needs the payload

Im unable to reproduce this. Are you making a post request to this endpoint?

Xref

Probably just a data issue but this is the TSN I used: /api/xref/taxon-qualitative-measurements?tsn=180701

• no measurements responds with an error

/api/xref/taxon-quantitative-measurements?tsn=180701

• no measurements responds with an error

/api/xref/taxon-measurements?tsn=180701

• no measurements responds with an error

I've updated these endpoints to respond empty but succeed if no xref values for provided tsn (and tsn value is real tsn). You can test with tsn=180596

Lookup Endpoints

/api/lookups/enum/frequency-unit

endpoint changed to api/lookups/enum/frequency-units updated swagger

• route not found

/api/lookups/enum/measurement-unit

endpoint changed to api/lookups/enum/measurement-units updated swagger

Access

/api

• swggaer docs return object with message, endpoint just returns strings

updated swagger

/api/types/{model}

• returns an array not a string

updated the swagger for types/{model} endpoint.