Current and custom MLST package contract, version 2
This additive package format uses the existing seven-locus ungapped typing engine. It makes no new accuracy claim. Historical schema 1 and its frozen cutoff remain unchanged; the historical contract still applies to it.
manifest.json is authenticated by an independently supplied SHA-256 or a trusted
catalogue’s component pin. Version 2 requires these fields:
| Field | Requirement |
|---|---|
schema, schema_version | pterobacter.mlst-scheme/2, integer 2 |
package_id, scheme | Nonempty source-specific identity |
package_scope | custom or current_snapshot |
loci | Exactly dnaA, fusA, gyrB, leuS, pyrG, rplB, rpoB, in that order |
retrieved_utc | Valid UTC YYYY-MM-DDTHH:MM:SSZ timestamp |
sequence_state, currency_statement | Nonempty description and coverage limitation |
source | Nonempty name and nonempty HTTPS urls array |
rights | Nonempty statement, access, HTTPS terms_url; redistribution is permitted, restricted or unknown |
submission_coverage | {"kind":"unknown","through":null} or {"kind":"through_submission_date","through":"YYYY-MM-DD"} |
data_root, profiles_file | Safe relative directory and a single filename |
data_sha256 | Exact mapping of all eight data paths to lowercase SHA-256 |
allele_counts, profile_count | Counts matching the verified data |
Each locus file is data_root/LOCUS.tfa. The profile table is
data_root/profiles_file, with the same columns and allele/ST rules as schema 1.
The package inventory must contain exactly those eight files and manifest.json.
Paths use ASCII letters, digits, dots, underscores and hyphens in nonempty segments;
. and .. segments, absolute paths and links are refused.
Version 2 refuses the historical fields submission_cutoff,
complete_through_cutoff_independently_established and cutoff_evidence.
Reports carry the declared coverage separately from retrieval time, plus source,
rights, currency statement and package hashes. A dated coverage declaration is
reported as source-declared and not independently established. Unknown coverage
has a null report cutoff. No metadata field changes the typing or taxonomy rules.
current_snapshot describes the source’s snapshot claim. It does not prove that
all submissions are present, confer redistribution rights or authorize downloads.
Current PubMLST provisioning is unavailable until source-specific access and
rights are settled. Synthetic tests cover this contract without fetching a new
scheme; users remain responsible for obtaining a permitted, authenticated package.