Skip to contents

Changelog

metasalmon 0.0.17

  • Improved measurement semantic query shaping for count-like fields:
    • split variable/property query behavior so NATURAL_SPAWNERS_TOTAL no longer defaults both roles to the same abundance concept,
    • added a count-like unit fallback query (count) for measurement columns that clearly represent totals/counts/abundance.
  • Added/updated regression tests for role-aware query behavior, count-like unit fallback, and unit-label backfill when applying unit suggestions.

metasalmon 0.0.16

  • Rewrote README-review.txt intro and checklist to be shorter, more first-time friendly, and more action-oriented.
  • create_sdp() now prints an explicit up-front note that semantic seeding may take a few minutes.
  • Improved column-level semantic query construction for measurement fields so placeholder text is not used as the query source.
  • Added role-aware query shaping that improves built-in sample suggestions for NATURAL_SPAWNERS_TOTAL (e.g., variable/property SpawnerAbundance, entity Population, constraint NaturalOrigin) and avoids the previous exploitation/mortality-rate mismatches.
  • Unit suggestions are now skipped when no unit context exists, and applying a unit suggestion now backfills unit_label when missing.

metasalmon 0.0.15

  • create_sdp() now tells users up front when online semantic seeding may take a few minutes and points to seed_semantics = FALSE for the fastest first pass.
  • Simplified README-review.txt into a shorter 7-step checklist so the review flow is easier to follow.

metasalmon 0.0.14

  • Simplified the package-creation surface so create_sdp() is the clear one-shot entrypoint, write_salmon_datapackage() is the advanced/manual writer, and the older create-from-data helper was removed.
  • Reworked create_sdp() output into a cleaner review layout with metadata/ and data/ subdirectories, package-root README-review.txt, package-root semantic_suggestions.csv (when present), and root datapackage.json.
  • Rewrote README-review.txt as a step-by-step checklist that explains the canonical Salmon Data Package, how to share the full package folder (or zip), and how to return to R for validation.
  • Tightened default semantic seeding so code-level semantic suggestions run only for factor/categorical source columns by default, while keeping column-level and table-level seeding available.
  • Added optional update notifications inside create_sdp() via check_updates, using the explicit check_for_updates() helper rather than package-attach network checks.
  • Refreshed README, vignettes, reference pages, generated documentation, tests, and pkgdown outputs to match the new workflow and layout.

metasalmon 0.0.13

  • Made edh_build_iso19139_xml() default to the richer North American Profile / HNAP-aware EDH export while keeping profile = "iso19139" available as an explicit fallback.
  • Expanded EDH export support for bilingual locale scaffolding, deterministic identifiers, legal constraints, maintenance/status, reference systems, bounding boxes, and distribution metadata, with regression coverage against the confirmed EDH sample shape.
  • Added apply_semantic_suggestions() for explicit opt-in merges of suggest_semantics() results into dictionaries.
  • Restored canonical Salmon Data Package CSVs (dataset.csv, tables.csv, column_dictionary.csv, optional codes.csv) as the source of truth in read_salmon_datapackage(), treating datapackage.json as derived/interoperability metadata.
  • Refreshed README, vignettes, pkgdown reference metadata, and GPT collaboration guidance to match the EDH default/export semantics and explicit dictionary-application workflow.
  • Rebuilt package documentation, tests, source tarball, and pkgdown site for the 0.0.13 release.

metasalmon 0.0.12

  • Added a GCDFO-backed find_terms() search backend that queries the DFO Salmon Ontology first via content negotiation against https://w3id.org/gcdfo/salmon.
  • For salmon-domain roles, find_terms() now prioritizes GCDFO results and only falls back to OLS/NVS when GCDFO returns no good label hit.
  • Updated suggest_semantics(), infer_dictionary(seed_semantics = TRUE), man pages, and vignettes to reflect the new GCDFO-first search behavior.
  • Rebuilt package documentation, tests, source tarball, and pkgdown site for the 0.0.12 release.

metasalmon 0.0.11

  • Added optional semantic seeding to infer_dictionary() via seed_semantics = TRUE, with optional source/max-per-role controls (semantic_sources, semantic_max_per_role).
    • This returns dictionary suggestions via attr(dict, "semantic_suggestions") without changing existing defaults.
  • Added guidance at the package README quick example that keeps the home-page flow short and links to 5-minute Quickstart + dedicated deep-dive articles.
  • Marked related vignettes as workflow-specific to avoid duplicating the Quickstart path; data-dictionary-publication and reusing-standards-salmon-data-terms now orient users to post-Quickstart use.

metasalmon 0.0.10

  • Changed validate_dictionary() and validate_semantics() non-strict semantics:
    • missing term_iri, property_iri, entity_iri, and unit_iri on column_role == "measurement" no longer block package creation by default;
    • missing fields now trigger a strong warning that calls out next steps and points to suggest_semantics() plus the standards guide.
  • Preserved strict validation when require_iris = TRUE so CI/high-assurance flows can still enforce full semantic coverage.
  • Updated README, man pages, and tests to document and verify the new behavior.
  • Added metasalmon package release metadata for version 0.0.10.

metasalmon 0.0.9

  • Added edh_build_iso19139_xml() to generate starter ISO 19139 metadata XML for DFO Enterprise Data Hub / GeoNetwork upload workflows.
  • Added tests and reference documentation for the EDH XML export helper.
  • Updated dataset metadata examples/templates to better support EDH workflows:
    • Expanded inst/extdata/dataset.csv with contact_org, contact_position, update_frequency, topic_categories, keywords, and security_classification.
    • Updated inst/extdata/custom-gpt-prompt.md to distinguish controlled topic_categories from free-text keywords and to note XML export support.
    • Refreshed README and vignette examples to include EDH-ready optional metadata and XML export guidance.

metasalmon 0.0.8

metasalmon 0.0.6

  • Added read_github_csv_dir() to read all CSV files from a GitHub directory into a named list, similar to using dir() with lapply() for local files.
  • Supports pattern matching, version pinning, and passes options to read_csv() for all files.
  • Added comprehensive test coverage for the new function.

metasalmon 0.0.5

metasalmon 0.0.4

  • Added ms_setup_github() to guide one-time PAT setup (git check, browser token creation, git credential storage) and verify access to the private Qualark data repository.
  • Added qualark_raw_url() and read_qualark_csv() to build stable raw GitHub URLs and read Qualark CSVs using the stored PAT (with SSO-aware error messages and retry logic).
  • New tests cover URL construction, blob/raw URL normalization, and an opt-in Qualark fetch when a token is configured.

metasalmon 0.0.3

  • Added find_terms() function for searching candidate terms across external vocabularies (OLS, NVS, BioPortal).
  • find_terms() now ranks results deterministically using I-ADOPT role hints from inst/extdata/iadopt-terminologies.csv (preferred vocabularies boosted; ties stable).
  • suggest_semantics() now returns best-effort suggestions (stored in attr(,'semantic_suggestions')) instead of a placeholder message.
  • Added I-ADOPT component fields (property_iri, entity_iri, constraint_iri, method_iri) to dictionary schema and package creation/reading.
  • Enhanced validation: measurement columns now require I-ADOPT components (term_iri, property_iri, entity_iri, unit_iri).
  • Updated table metadata: renamed entity_type/entity_iri to observation_unit/observation_unit_iri for clarity.
  • Added httr package dependency for vocabulary search functionality.
  • Dictionary validation now normalizes optional semantic columns and returns the normalized dictionary.
  • Vignettes now show end-to-end semantic enrichment (I-ADOPT-aware suggestions) and how to align with smn-gpt.

metasalmon 0.0.2

  • Unified semantic fields to term_iri + term_type and reserved concept_scheme_iri for code lists only.
  • Updated GPT collaboration guidance, schemas, and pkgdown outputs to match the new fields.
  • Refreshed vignettes, tests, and reference docs; bumped package version.

metasalmon 0.0.1

  • Initial development snapshot.