Refactor nmdc_database_tools to use nmdcschema GET endpoints and fix data truncation

microbiomedata / nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

https://microbiomedata.github.io/nmdc-schema/

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Closed mbthornton-lbl closed 9 months ago

mbthornton-lbl commented 9 months ago

Formerly: queries:run endpoint truncates data in response The queries:run endpoint is only returning the first 100 results of a query

Query: { "find": "omics_processing_set", "filter": {"part_of": "nmdc:sty-11-aygzgv51"} } Response: response_1704828951248.json

Note at the end of the response JSON that it claims partialResultsReturned: null

mbthornton-lbl commented 9 months ago

Proposed Fix:

refactor to not rely on the queries:run POST endpoint; Use the nmdcschema/{collection_name} GET endpoint instead
Simplify / refactor API client to be GET only w/o authentication / token etc.