rfair 0.2.0

Scores can differ from rfair 0.1.0: several fixes below change what counts as evidence, and new metadata sources find evidence that was missed before. Rerun assessments before comparing them with 0.1.0 results. Agreement with the reference F-UJI 4.0.0 service (metrics v0.8, five fixture DOIs, 85 metric comparisons) rose from 91.8% to 97.6%; see tests/conformance/README.md.

Scoring fixes

• id_parse() no longer treats a plain URL with a numeric path segment (for example https://figshare.com/articles/dataset/foo/12345/1) as a Handle. Such URLs were marked persistent and resolved through hdl.handle.net instead of their own page. The Handle pattern is now anchored at the start, as in F-UJI’s verify_handle().
• An identifier that does not resolve is no longer reported or scored as resolved. resolved_url is NA, the new resolution element records the attempt (URL, HTTP status, error), and print() shows it as unresolved. FsF-A1-02MD-1 (metadata retrievable) now requires a harvested metadata record, as F-UJI’s testMetadataRetrievable does; a page that resolves but offers no extractable metadata no longer earns it. A nonexistent DOI dropped from 17.3% to 13.5%; the remaining points (identifier scheme, HTTP protocol) are the ones F-UJI also awards.
• FsF-A1-02MD-2 (data retrievable) now requires a data link that answers with a 2xx status, as in F-UJI. Up to five links are probed with a GET that is closed once the headers arrive; HEAD hung on repositories that build files on request.
• schema.org isAccessibleForFree is read as an access statement, as F-UJI does (FsF-A1-01M, classify_access()).
• RDF graph metadata (Turtle, RDF/XML) was never harvested: the query used SPARQL 1.1 property paths, which librdf rejects. Triples are now mapped in R, creator nodes resolve to names, and predicate namespaces feed the semantic vocabulary and community standard metrics. Scores can rise for repositories that serve RDF.
• Metadata sources that fail are recorded in the new harvest_errors element. API rate limits (GitHub, GitLab, Codeberg, repository APIs) are also raised as an rfair_rate_limit warning and stop further calls to that API for the assessment, instead of silently lowering software scores.
• license_reuse() recognizes the OGL, Etalab, CDLA, DL-DE, and NLOD open data licenses, and classes MPL as copyleft.
• Link headers split only between links, so URLs containing commas survive.
• FsF-I2-01M (semantic vocabularies) checks namespaces against F-UJI’s full linked-vocabulary index (5,160 registered namespaces from LOV, BioPortal, Bioregistry, SeaDataNet, and others) instead of a curated list of 20, and also counts vocabulary terms used as metadata values (for example an SPDX license URL), as F-UJI does. XML metadata keeps its declared namespaces.
• Assessments record the version of the bundled reference data in reference_data.

New metadata sources

• DOIs registered outside DataCite (Crossref, mEDRA, JaLC, KISTI) are harvested through CSL JSON content negotiation: title, authors, publisher, dates, abstract, subjects, licenses, Crossref text-mining links, and relations. The registration agency is looked up (bundled prefix table, then https://doi.org/ra/), and the DataCite requests are skipped for DOIs registered elsewhere. CSL metadata does not satisfy FsF-F4-01M-2, which is specific to DataCite.
• When no data links were found, the file list is read from the repository API: Zenodo, figshare, Dataverse, and Dryad.
• schema.org metadata embedded as microdata or RDFa is harvested, next to JSON-LD, and counts as embedded metadata for FsF-F4-01M and FsF-I1-01M. As in F-UJI, only CreativeWork types count (not Organization or BreadcrumbList).

Software assessment

• Code repositories on GitLab (API v4, nested groups) and Codeberg or any Forgejo/Gitea instance (API v1) are harvested, next to GitHub. Tokens are read from GITHUB_PAT (then GITHUB_TOKEN), GITLAB_PAT, and CODEBERG_TOKEN, and sent as a Bearer Authorization header, which libcurl does not forward when a redirect leaves the host.
• Under the software metrics, a DOI whose metadata links a repository (for example Zenodo’s IsSupplementTo link to GitHub) is bridged to it: the repository supplies the software signals and the DOI counts as the registry DOI. rfair’s own Zenodo concept DOI rose from 2.2% to 100%.
• Archiving is checked against Software Heritage and the language package registry (CRAN from DESCRIPTION, PyPI from pyproject.toml or setup.cfg), not only against text mentions.
• The harvested repository signals are returned as a$software.
• FRSM results are labeled evidence_type = "heuristic", and print() says so: the scores come from repository signals that have not been validated against expert judgement. frsm_agreement() compares them with expert ratings (percent agreement and Cohen’s kappa per test, plus agreement between raters), and inst/extdata/frsm_validation_template.csv is a rating sheet for all 45 FRSM tests. The validation study itself is still to be done.

Guidance

• fair_recommendations() lists every failed test with one concrete action, largest score gain first (the gain allows for each metric’s cap). The Shiny app shows it in a “How to improve” tab.
• fair_compare() reports per-metric or per-test changes between two assessments.

Machine-readable results

• as_rdf() adds one DQV quality measurement per metric and one FAIR Test Result per metric test in the OSTrails FAIR Testing Resource vocabulary (https://w3id.org/ftr/, version 1.3.0): pass or fail, completion, the evidence as a log, and for failed tests the fair_recommendations() action as a suggestion. Turtle output now checks for the jsonld package it needs.

Batch runs and HTTP

• assess_fair() gains max_time, a time budget for the whole assessment.
• assess_fair_batch() and assess_data_code() gain workers (parallel assessment by forking; serial on Windows), keep (the full assessments in the "assessments" attribute), and previous (resume an interrupted run), plus resolved and http_status columns.
• All requests share one policy: retry on 429 and 503 with capped waits, a per-host rate limit (options(rfair.rate_per_host)), and an optional HTTP cache (options(rfair.cache_dir)). Bodies are decoded from their declared charset to UTF-8.

Security

• options(rfair.block_private_hosts = TRUE) refuses non-http(s) URLs and hosts that resolve to loopback, private, link-local, or cloud metadata addresses. The request connects to the address that was checked (libcurl’s CURLOPT_RESOLVE), so DNS rebinding cannot swap it, and every redirect hop is checked, with credentials dropped when a redirect changes scheme, host, or port. The bundled Plumber API and Shiny app turn it on, since both fetch visitor-supplied URLs. Headless rendering (use_headless) runs in a browser outside this guard.
• The Plumber API refuses headless rendering unless the server sets RFAIR_API_ALLOW_HEADLESS=true.

Package metadata and tests

• CITATION.cff, codemeta.json, .zenodo.json, and ro-crate-metadata.json are generated from DESCRIPTION by data-raw/07-build-metadata.R, so title, authors, contributors, and dependencies agree. citation("rfair") reads the title and version from the package metadata. The CRAN DOI is recorded.
• The FAIR principles links point to the GO FAIR Foundation’s new address.
• Removed the unused suggested packages httptest2, jqr, wand, and covr. The documentation no longer mentions libmagic file sniffing, which was never implemented.
• The harvesters are tested end to end offline, with canned responses served through httr2::local_mocked_responses().
• A scheduled workflow compares rfair with the F-UJI Docker image monthly.

rfair 0.1.0

First release. rfair is a native R implementation of the F-UJI / FAIRsFAIR research data object assessment metrics and the FRSM (FAIR for Research Software) metrics. It performs the entire assessment in R, with no external server.

Assessment

• assess_fair() resolves a DOI, persistent identifier, URL, or code repository, harvests its metadata, and scores it against the FAIR metrics, returning a fair_assessment object.
• Multiple metric sets, listed by rfair_metric_versions(): the current F-UJI data metrics (v0.8) by default, several legacy and domain-specific versions (0.2-0.8, plus social-science and environmental variants), and the FRSM research-software metrics (0.7).
• Metadata harvesting from registries (DataCite, Crossref, GitHub), landing-page embedded metadata (schema.org JSON-LD, Dublin Core, OpenGraph, Highwire), signposting and typed links, content-negotiated XML (DataCite XML, MODS, EML, ISO 19139) and RDF / JSON-LD, and optional user-supplied metadata-service endpoints (OAI-PMH, OGC CSW, SPARQL, DCAT, schema.org, RO-Crate, CKAN).
• Software FAIR: pass a GitHub repository with metric_version = "0.7_software" to score it against the FRSM metrics from its repository signals (license, README, citation/codemeta, tests, CI, dependencies, coverage, releases, contributors). The FRSM metrics operationalize the FAIR Principles for Research Software (FAIR4RS; Chue Hong et al. 2022, doi:10.15497/RDA00068).
• id_parse() recognizes DOI, Handle, ARK, URN, UUID, identifiers.org / w3id, and compact prefix:accession identifiers.

Working with the result

• The fair_assessment object has print(), summary(), as.data.frame(), and plot() methods. plot() draws a category scorecard, a per-metric breakdown, or a concentric FAIR "sunburst".
• as_fuji_json() exports the assessment in the F-UJI FAIRResults JSON schema; as_rdf() exports W3C DQV quality measurements plus a schema.org Rating (JSON-LD or, with rdflib, Turtle).
• A bundled example assessment, fair_example, is provided for offline use.

Beyond F-UJI

• license_reuse() judges whether a license actually permits reuse, using the (Re)usable Data Project taxonomy; reusabledata_rating() looks up curated repository ratings.
• classify_access() flags controlled-access and sensitive data (which are not FAIR failures).
• identifier_hygiene() checks identifiers for layered or non-persistent forms.
• fair_tlc() reports the FAIR-TLC (Traceable, Licensed, Connected) indicators.
• fair_principles() and principle_definition() provide the canonical FAIR principle definitions; fair4rs_principles() provides the FAIR4RS principles for research software, and principle_definition() resolves FRSM software metrics to their FAIR4RS statement.

Batch assessment and rtransparent

• assess_fair_batch() scores a vector of identifiers into one tidy row each.
• assess_data_code() ingests the data and code identifiers that the rtransparent package extracts from articles (its open_data_links and open_code_links) and scores each (FsF for data, FRSM for code).
• split_identifiers() parses the " ; "-joined identifier strings.

Interfaces

• launch_rfair() opens a bslib Shiny app for interactive assessment.
• A no-install browser version is published at https://choxos.github.io/rfair/app/.
• A Plumber API scaffold and an OpenAPI contract are installed under system.file("plumber", package = "rfair") and system.file("openapi", package = "rfair").

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