API extension for Support for Retsynth#63
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rkrishnasanka wants to merge 31 commits intobebop:devfrom
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* renamed pkg/insert to pkg/init. * add CreateTestDB function for init package. * backing up and checking out new branch. * added personal fork of surrealdb driver to go.mod and go.sum. * added config to use surrealdb websocket default url. * added config defaults for admin user and password. * added DB name to config. * insert, upsert, and retrieval working for genbank. * got basic uniprot insert working. * updated testdev config db namespace to allbaseTest * CreateTestDB now clobbers old testdbs. * changed create to upsert like logic. * got compound insertion for rhea working. * commented out and added TODOs for things that cause tests to fail. Will add issues.
…rresponding queries. TODO: 1. Update with the sql queries with the builder API queries 2. Add the GraphQL structures 3. Add the testcases for `queries.go`
TODO: - There's a need to collapse all the queries for specific types of queries. Perhaps do this once the datamodels have been joined together. - We can reduce the number of potential bugs for mistyping, we need to tie in the types for all the subfields away from base types. It's necessary to wrapper these datafields to have the static type safety in the long run
TODO: - Refactor VCS to be more of an object like so that we can reduce dependenies . - Create workthrough tests to make sure we are able to do - Flesh out the full extent of the retsynth tests now that we have the minimal database
TODO: Need to update this with the more specific API calls as needed by RetSynth.
…phql files for both a retsynth specific API to use as a stand-in replacement with the current public version of retsynth. Additionally started creating the synbiodb.graphql that should be the convergence API
…ng project - Added and ran the baseline gqlgen package and generated the implementations - Need to figure out how to have multiple graphql schemas and have separate resolvers for them
…es. Additionally, this is the first prototype of the graphql engine
Baseline querying works for the organisms and compounds API
- Cleaned up resolver code - Moved the server start code into main.go - Updated the makefile with clean, run playground and build functions that chain
- Moved all the parameters into the `parameters` package
…reduces the overall code repeat.
Currently working on the rest of the test cases.
…ests to verify if the sql is correct.
… for a large subset of queries. These are unresolved problems.
…ly assumed that they would just return None types / nil values
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This is a draft pull request for an API integration that adds support for retsynth data dumps. This PR reflects the baseline support for incorporating
allbasewithin Upp BioTODO:
allbasedata models