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58 refactor re id tools ingest records to not use deprecated v1workflowsactivities endpoint #59

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mbthornton-lbl
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This PR provides validate_record and submit_record methods on the NmdcRuntimeUserApi client, and updates the ingest-records command to use them

This PR can also close #56

The delete-old-records code already does this:

    for record in old_db_records:
        for set_name, object_record in record.items():
            if set_name == "omics_processing_set":
                continue

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@aclum aclum left a comment

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We discussed during 1x1 but the json:submit endpoint is not working on napa. For testing we'll use Eric's wrapper to validate with json:validate and submit w/pymongo directly.

…nsert_many

Successfully tested on my local system - still need MongoDB uri/credentials for Napa DB instance
@mbthornton-lbl mbthornton-lbl requested a review from aclum February 15, 2024 20:02
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@Michal-Babins Michal-Babins left a comment

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Added validate record against json:validate endpoint. Added submit record against json:submit endpoint. Use pymongo directly for ingest.

@mbthornton-lbl mbthornton-lbl merged commit 5758c6c into main Feb 15, 2024
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@mbthornton-lbl mbthornton-lbl deleted the 58-refactor-re_id_tools-ingest-records-to-not-use-deprecated-v1workflowsactivities-endpoint branch February 15, 2024 21:50
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