submission-parser

name	submission-parser
description	Use this skill to extract structured fields (DOIs, study name, description, protocol info, MIxS extensions) from a raw NMDC submission portal object. Called at the start of metadata-suggestion-pipeline and env-triad when a submission_object is present.

Submission Parser Skill

Use this skill to extract structured fields from a raw NMDC submission portal object. Called at the start of both metadata-suggestion-pipeline and env-triad when a submission_object is present.

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Input

A raw submission portal dict with a metadata_submission key.

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What to extract

Parse the following fields from metadata_submission:

Output field	Source path
study_name	studyForm.studyName
description	studyForm.description
notes	studyForm.notes
gold_study_id	studyForm.GOLDStudyId
jgi_study_id	multiOmicsForm.JGIStudyId
dois	Merge and deduplicate studyForm.dataDois, studyForm.publicationDois, multiOmicsForm.awardDois — each entry is {"value": "10.x/y", "provider": "osti" | null}
protocol_descs	All externalProtocol.description values across mpProtocols, mbProtocols, mbGcProtocols, lipProtocols, nomProtocols, nomLcProtocols
protocol_names	All externalProtocol.name values from same sections
mixs_extensions	Interface class names derived from the sampleData keys or declared extensions (e.g. ["SoilInterface"])

Deduplication

Deduplicate DOIs by (value, provider) pair. Preserve original order.

Protocol extraction

For each protocol section in multiOmicsForm:

for section in [mpProtocols, mbProtocols, mbGcProtocols, lipProtocols, nomProtocols, nomLcProtocols]:
    protocols = multiOmicsForm.get(section) or {}
    for protocol in protocols values:
        external = protocol.get("externalProtocol", {})
        collect external.description and external.name if present

---

Output

A structured dict:

{
  "study_name": "Soil metabolome response...",
  "description": "In this study...",
  "notes": "",
  "gold_study_id": "",
  "jgi_study_id": "510963",
  "dois": [
    {"value": "10.1073/pnas.2004192118", "provider": "osti"},
    {"value": "10.46936/10.25585/60013043", "provider": "jgi"}
  ],
  "protocol_descs": ["Proteomics samples were separated..."],
  "protocol_names": ["proteomics lc", "metabolome lc"
   

Pass this structured dict to the build-study-context skill.