Fixed the seeded semantic-context warning path so seed_semantics = TRUE no longer crashes when mixed or previously unsupported llm_context_files trigger cli interpolation in package creation/review flows.
Expanded llm_context_files handling so HTML/HTM, DOCX, .R, .Rmd, and .qmd inputs are read or normalized cleanly during LLM review instead of failing on unsupported-file warnings.
Added Excel workbook context-file support for package-native LLM review, including .xls, .xlsx, and .xlsm inputs via the optional readxl package.
Hardened LLM assessment parsing so malformed accept responses without a selected candidate degrade to review, and falsey missing_context placeholders no longer pollute outputs.
Expanded LLM regression coverage with mixed-context bundle tests for the exact chapi + ollama2.mistral:7b configuration, including markdown, CSV, Excel, PDF, HTML, DOCX, and notebook/source context bundles across dataset.csv, tables.csv, column_dictionary.csv, and codes.csv targets.
Finished the scripts/llm-sanity-check.R harness into a richer end-to-end smoke tool: it now generates per-case context bundles, records context formats in the summaries, rebuilds EDH XML after a simulated review pass, and writes stable CSV outputs under artifacts/.
Added and linked a dedicated LLM review getting-started guide from the quickstart/setup docs so the package-native workflow is easier to discover.
metasalmon 0.1.1
Added a first-class chapi LLM provider preset for DFO’s internal Open WebUI endpoint. It defaults to ollama2.mistral:7b, uses https://chapi-dev.intra.azure.cloud.dfo-mpo.gc.ca/api, reads provider-specific overrides from CHAPI_API_KEY, CHAPI_MODEL, and CHAPI_BASE_URL, and now gives slower gpt-oss responses a longer effective timeout plus one retry.
Updated the quickstart/home-page docs so internal DFO users can opt into chapi directly from create_sdp(..., llm_assess = TRUE), while external users get parallel OpenRouter-free and OpenAI-credit setup paths.
Promoted create_sdp() and the Salmon Data Package workflow into a coherent release shape: single-table and multi-table package creation, semantic review artifacts, and post-review EDH rebuild are now aligned and documented as the primary path.
Hardened final-review behavior: validate_salmon_datapackage(..., require_iris = TRUE) now fails on unresolved metadata placeholders, blank table observation-unit IRIs, and lingering review sentinels so strict validation actually means review is finished.
Hardened table-level semantic review writes and EDH rebuilds: LLM-selected table suggestions now write back into metadata/tables.csv, and write_edh_xml_from_sdp() now refuses to rebuild from obviously unreviewed packages.
Improved package-native LLM review ergonomics: one-shot shortlist preservation now respects llm_top_n, shared llm_context_files are reused across targets, and non-interactive profile-scoped term requests now fail clearly instead of silently emitting junk defaults.
Fixed multi-table semantic seeding so later tables use their own context instead of borrowing semantic context from table 1.
Cleaned the release docs surface: refreshed the package description, fixed broken source-view links and vignette anchors, removed stale GPT-era remnants and orphaned assets, hid leaked internal helper pages from the public site, and rebuilt pkgdown from the integrated source.
Bundled a matching Fraser Coho 2023–2024 starter dictionary plus provenance link so the installed package has a realistic context-file demo for the package-native LLM workflow.
metasalmon 0.0.27
Fixed a deterministic semantic-query bug for spawner-style measurement columns: the property-slot query no longer hard-codes count for columns like natural_adult_spawners, and now prefers spawner abundance so the shortlist is more semantically sensible before LLM review.
Added one bounded LLM exploration round for weak semantic shortlists: when the first LLM pass comes back as review/propose-new-term or low-confidence, suggest_semantics(..., llm_assess = TRUE) may request 1–2 alternate plain-text search queries, rerun deterministic retrieval, merge/de-dupe candidates, and reassess once without letting the model mint raw IRIs.
metasalmon 0.0.26
Further tuned the OpenRouter free path for practicality: openrouter/free now uses smaller pair-sized batches and a smaller effective candidate shortlist per target so free-router prompts stay lighter on larger quickstart-style runs.
metasalmon 0.0.25
Made the OpenRouter free path more practical for full semantic review runs: live openrouter/free requests are now serially batched in pairs and use a smaller effective shortlist per target when using the built-in HTTP client, which trims request overhead without adding flaky parallel fan-out.
Added batch fallback safety: if a batched OpenRouter response is malformed or incomplete, metasalmon now falls back to per-target assessment instead of poisoning the whole run.
Retained the 0.0.24 hardening: longer effective timeout, one retry for transient failures, lighter context payloads, and downgrade-to-review handling for out-of-range candidate indexes.
metasalmon 0.0.24
Hardened package-native LLM review for flaky free-router behavior: OpenRouter free models now get a longer effective timeout, one automatic retry for transient HTTP/network failures, and fewer context chunks per request so prompts stay lighter.
Hardened invalid LLM candidate-index handling: out-of-range selected_candidate_index values no longer poison the whole target; they are downgraded to review with no auto-selection instead of surfacing as a hard LLM error.
metasalmon 0.0.23
Added package-native LLM semantic review on top of deterministic retrieval: suggest_semantics(..., llm_assess = TRUE) can now assess shortlisted candidates with OpenAI-compatible providers, attach llm_* review columns to semantic_suggestions, and expose target-level results via attr(dict, "semantic_llm_assessments").
Added local context-file support for LLM semantic review, including README/markdown/text-style files and optional PDF extraction via pdftools, with bounded chunking so reports are trimmed before prompting.
Added OpenRouter support for package-native LLM review, including pass-through model ids (so OpenRouter models ending in :free work without special branching).
Extended apply_semantic_suggestions() with strategy = "llm" and min_llm_confidence for explicit application of LLM-reviewed matches.
Updated README, GPT-collaboration vignette, entrypoint docs, tests, and generated documentation for the 0.0.23 feature release.
metasalmon 0.0.22
Simplified EDH XML support down to the single DFO Enterprise Data Hub HNAP export we actually use: edh_build_hnap_xml() is now the canonical helper, while edh_build_iso19139_xml() remains only as a deprecated compatibility alias.
Simplified create_sdp() EDH export behavior: include_edh_xml = TRUE now always writes metadata/metadata-edh-hnap.xml; legacy edh_profile / EDH_Profile / EDH_profile inputs are still accepted as deprecated compatibility shims, while edh_xml_path is deprecated and ignored.
Rebuilt reference docs, tests, package artifacts, and pkgdown site for the 0.0.22 patch release.
metasalmon 0.0.20
Hardened GitHub helper security: GitHub readers now reject non-GitHub remote URLs and avoid attaching GitHub auth headers to non-GitHub hosts; improved public/private auth behavior and related tests.
Hardened package writing + export reliability: create_sdp() now fails fast with an explicit overwrite = TRUE message when the target directory already exists, fixed DwC validator execution path, and improved ontology fetch robustness with explicit timeout handling and cache fallback behavior.
Surfaced clearer warning messages when online vocabulary API lookups time out, so empty find_terms() results are less opaque during semantic seeding.
Fixed submit_term_request_issues() batch routing so per-row ontology_repo values are honored instead of posting all rows to the first repo.
Clarified validate_semantics() API by explicitly deprecating ignored legacy arguments (entity_defaults, vocab_priority) with coverage for warning behavior.
Improved release/test hygiene: dependency bootstrap script hardening, tighter warning assertions in brittle tests, and refreshed package description wording.
metasalmon 0.0.19
Hardened table observation-unit auto-apply in create_sdp(): table-level observation-unit suggestions are now ignored when driven by placeholder review text and only auto-applied when lexical compatibility checks pass against non-placeholder table metadata.
Improved non-measurement term_iri auto-apply quality without disabling the feature: incompatible candidates are now filtered using role-hint mismatch checks, match-type/score guards, and token-level lexical compatibility with the target column context.
Strengthened infer_column_role() heuristics for NuSEDS-like fields: year-like columns are now classified as temporal more reliably, and NATURAL_ADULT_SPAWNERS-style quantity columns are inferred as measurement.
Tightened default code-level seeding gates to reduce free-text noise while preserving useful low-cardinality categorical/attribute suggestions: text-like field names and non-code-like all-unique short character values are excluded from the default factor-scope code seeding path.
Added regression coverage for the above hardening paths, including placeholder-driven table seeding prevention, bad non-measurement suggestion filtering, improved role inference for fuller examples, and free-text seeding guardrails.
Rebuilt reference docs, tests, package artifacts, and pkgdown site for the 0.0.19 patch release.
metasalmon 0.0.18
Reworked review placeholders so missing descriptions/metadata are labeled explicitly (MISSING DESCRIPTION: / MISSING METADATA:) instead of the more ambiguous generic review wording.
create_sdp() and related inference paths now seed table-level observation-unit review content and auto-apply the top table semantic suggestion into tables.csv, including observation_unit_iri and a backfilled observation_unit label when needed.
Broadened default semantic suggestion coverage beyond measurement columns in a conservative way: categorical and controlled low-cardinality attribute columns can now receive lighter term_iri suggestions, while identifier and temporal columns remain excluded from default non-measurement suggestion seeding.
Broadened default code-level semantic seeding so ordinary low-cardinality character columns from typical CSV imports are considered, rather than relying on R factor inputs.
Made inferred required flags less misleading by marking obvious identifier columns as required and leaving other columns unknown (NA) until reviewed, instead of defaulting everything to FALSE.
Improved auto-filled term_type values when term_iri suggestions are applied and kept the target_description vs column_description distinction explicit in suggestion outputs.
Added a second bundled official NuSEDS example dataset: nuseds-fraser-coho-2023-2024.csv (173 rows across 2023–2024), while keeping the existing 30-row demo sample intact.
Added reproducible provenance for bundled NuSEDS examples via data-raw/nuseds_fraser_coho_examples.R and documented the upstream Open Government Canada record/resource and licensing.
Updated README, vignettes, reference docs, and tests to reflect the broader semantic seeding behavior, required-flag review stance, observation-unit handling, and the tiny-vs-fuller example-data workflow.
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.
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.
Added reference documentation pages for both crosswalk helpers.
Refreshed README feature list to include the new NuSEDS crosswalk utilities.
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
Renamed the GitHub CSV helpers to generic names: github_raw_url() and read_github_csv(). repo is now required unless you provide a full URL.
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.
