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matentzn
changed the title
linkml-map 0.5.3 requires Python >=3.10, and 3.9 is past end of life.
linkml 1.11 removed linkml.validators.jsonschemavalidator.
docs/schema/fair_mappings_schema.yaml is regenerated by gen-doc on every docs deploy, so the committed copy was never what got published - it only went stale. Matches how docs/elements is already handled.
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Turns the repo from a schema definition into something you can point at a real mapping set. A
fair-mappingscommand parses SSSOM and LinkML-Map documents into FAIR Mappings Schema instances andvalidates them against the schema.
parsetransforms a source document into a.fms.ymlinstance, driven by declarative LinkML-Maptransformation specs (
sssom-to-fair,linkmlmap-to-fair) rather than hand-written field mapping.validatechecks an instance against the schema and exits non-zero with the errors on stderr.-I/--mapping-typetakes its permissible values fromMappingSpecificationTypeEnumread out of theschema at runtime, so the CLI's accepted types cannot drift from the model.
parse_sssom_tsvaccepts an iterable of lines as well as a path, so it can read the#-commentedheader off a streamed HTTP response without downloading the whole mapping set.
schema.pyresolves the bundled schema, the SSSOM and LinkML-Map schemas from their installedpackages, and the bundled transformation specs through
importlib.resources, so everything works froman installed wheel and not just a checkout.
Adds
linkml_maptoMappingSpecificationTypeEnum. That is the only change to the published data modelin this PR.
The distribution is renamed to
fair-mappingsand gains a console script of the same name. 55 testscover parsing, the CLI, validation, schema resource resolution and the package API.
What is not here
An earlier version of this branch carried a FAIR scoring system:
fair_weightannotations on every slot,a
scorecommand, and a 0-1 score per specification. That has been removed — a single score invitesleague tables and implies an authority over what FAIRness is that this schema should not claim. The
per-slot breakdown was the genuinely useful part of it, and I will open a separate issue proposing a
metadata completeness checker that keeps that and drops the grade.