| 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.
Input
A raw submission portal dict with a metadata_submission key.
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.
