Data integrations: bidirectional importers and exporters

[sorenwacker]

Umbrella for metaseed as a two-way bridge to scientific data repositories. Each integration is an optional extra (metaseed[<name>]), maps spec-driven against the relevant profile, and follows one seam.

Exporters — metaseed dataset -> repository format (existing epics)

• DCAT Add DCAT (Data Catalog Vocabulary) support #24 (done: JSON-LD/Turtle)
• FAIRDOM-SEEK FAIRDOM-SEEK interoperability #33
• PRIDE Support for export of PRIDE submission file #21
• MetaboLights MetaboLights submission export (ISA-Tab + MAF) #43

Importers — repository data -> metaseed dataset (new)

Importers epic #76 — sub-issues: #77 ENA (reference), #78 BrAPI, #79 PRIDE, #80 MetaboLights.

Shared principles

• Optional extras; network deps install only on opt-in (mirrors metaseed[dcat]).
• Spec-driven mapping; the profiles are the contract.
• Reuse the OLS network-client pattern (services/ontology.py: httpx + rate-limit + User-Agent + timeouts).
• Metadata, not raw data — reference data files (URLs), do not download reads/spectra.
• Hermetic tests: map from recorded fixtures; live calls marked @network.

Several repos get both an importer and an exporter (PRIDE, MetaboLights, eventually BrAPI), making metaseed a round-trip bridge.

[sorenwacker]

Status (260628): first step taken — all untested

The bidirectional bridge now exists in code, with an honest caveat: first step only, not yet properly tested.

Importers (merged): ENA, BrAPI, PRIDE, MetaboLights — accession/server → metadata → validated profile dataset, metadata-only (files referenced).
Exporters: ENA (submission XML, merged); BrAPI (JSON, #86), PRIDE (submission.px, #87), MetaboLights (ISA-Tab + MAF, #88). Plus a reusable metaseed.isatab writer (also serves isa and SEEK #33).

What 'tested' means here — and doesn't:

• Each adapter was smoke-tested against one live record (MTBLS1, PXD000001, a BrAPI test server, one ENA run). Useful sanity, not validation.
• That smoke test did catch one real bug (MetaboLights dropped study-level contributors/publications) — now fixed and guarded.
• Not done: comprehensive/edge-case coverage, multiple datasets per repo, verification that exports are actually accepted by the repositories' submission systems, auth/rate-limit/error-path hardening. Several mappings are partial (documented per adapter).

Bottom line: the seam and all eight adapters are in place — a real foundation — but this is proof-of-concept, not production-ready. Next: hardening + real-coverage testing.