false positive validation error from queries:run

[aclum]

Describe the bug
I believe I'm getting a false positive validation error from queries:run, when I dump the document that runtime says is not valid, it in fact validates against the schema with linkml-validate

To Reproduce
Steps to reproduce the behavior:

1. curl command

   curl -X 'POST' \
     'https://api.microbiomedata.org/queries:run' \
     -H 'accept: application/json' \
     -H 'Authorization: Bearer $TOKEN' \
     -H 'Content-Type: application/json' \
     -d '
     {
      "update": "data_generation_set",
      "updates": [{"q": {"id": "nmdc:omprc-12-bk872674"}, "u": {"$set": {"has_input": ["nmdc:dobj-11-nxmk9429"]}}}]
    }'

Error is:

{
  "detail": "Schema document(s) would be invalid after proposed update: {'data_generation_set': [\"{'add_date': '2022-03-25', 'gold_sequencing_project_identifiers': ['gold:Gp0618285'], 'has_input': ['nmdc:dobj-11-nxmk9429'], 'id': 'nmdc:omprc-12-bk872674', 'mod_date': '2024-01-07', 'name': 'Soil microbial communities from pasture in Falmouth, Massachusetts, USA - PETF_TOP', 'ncbi_project_name': 'Soil microbial communities from pasture in Falmouth, Massachusetts, USA - PETF_TOP', 'principal_investigator': {'email': '[email protected]', 'has_raw_value': 'Nancy Hess', 'name': 'Nancy Hess', 'type': 'nmdc:PersonValue'}, 'processing_institution': 'JGI', 'type': 'nmdc:NucleotideSequencing', 'analyte_category': 'metagenome', 'associated_studies': ['nmdc:sty-11-28tm5d36'], 'instrument_used': ['nmdc:inst-14-xx07be40'], 'has_output': ['nmdc:dobj-11-nxmk9429', 'nmdc:dobj-11-x7tmms98', 'nmdc:dobj-11-b7kmr176', 'nmdc:dobj-11-fj64fw53']} is not valid under any of the given schemas\"]}"
}

copy the result, replace single with double quotes, convert to yaml and validate with

$ poetry run linkml-validate -C NucleotideSequencing -s src/schema/nmdc.yaml test2.yaml
No issues found

Expected behavior
A clear and concise description of what you expected to happen.
expected 200 response code

Screenshots
If applicable, add screenshots to help explain your problem.

Acceptance Criteria

• Clear to everyone involved
• Can be tested or verified
• Either passes or fails (cannot be 50% completed, for example)
• Focus on the outcome, not how the outcome is achieved
• As specific as possible (fast page load speed vs. 3-second page load speed)
• if multiple criteria, present as a bulleted list of short scenarios (see template below)

Example scenario-based template:
Given (some given context or precondition), when (I take this action), then (this will be the specific outcome).

Additional context
I need this to clean up some the issues from running import automation. blocks parts of microbiomedata/nmdc_automation#333

[eecavanna]

Here's a formatted version of the input JSON payload (from the curl command):

{
    "update": "data_generation_set",
    "updates": [
        {
            "q": {
                "id": "nmdc:omprc-12-bk872674"
            },
            "u": {
                "$set": {
                    "has_input": [
                        "nmdc:dobj-11-nxmk9429"
                    ]
                }
            }
        }
    ]
}

[dwinston]

@aclum the current (valid) document has nmdc:bsm-11-g06qhv26 in has_input. I notice you are updating the input to be a DataObject versus a Biosample. Is that intended?

[dwinston]

also, nmdc:dobj-11-nxmk9429 is currently an output of https://api.microbiomedata.org/nmdcschema/ids/nmdc:omprc-12-bk872674. do you want to $unset that as you $set it as an input?

[dwinston]

from discussion, it seems this update as expressed was not the intended update, so closing.

[eecavanna]

Thanks, @dwinston, and thanks for providing the reproduction steps, @aclum.