brapiR2 0.2.0

Breaking changes

• brapi_get_marker_map() no longer reads position data from brapi_variants() (referenceName/start, which many servers - including the public test server - leave NA, since the BrAPI spec makes those fields optional on Variant). It now queries the Genome Maps entity’s /markerpositions endpoint instead, which places a marker on a named map (genetic or physical) rather than a variant on a reference assembly. Signature change: brapi_get_marker_map(con, variantSetDbId = NULL, mapDbId = NULL), requiring exactly one of the two identifiers. The returned tibble’s columns have changed to variantDbId, variantName, mapDbId, mapName, type, unit, linkageGroupName, position - referenceName/start are gone. Existing positional calls (brapi_get_marker_map(con, variantSetDbId)) still work, but code reading referenceName or start from the result will break.
• brapi_germplasm_pedigree() and brapi_germplasm_progeny() now query /pedigree?germplasmDbId= instead of the /germplasm/{germplasmDbId}/pedigree and /germplasm/{germplasmDbId}/progeny sub-resources, which BrAPI deprecated in v2.1. The returned columns have changed: 15 rather than 8, pedigree is now pedigreeString, and parents, siblings and progeny are list-columns of tidy tibbles rather than raw nested lists. The added fields are progeny, germplasmPUI, defaultDisplayName, breedingMethodName, breedingMethodDbId, additionalInfo and externalReferences (@dwaring87, ropensci/software-review#792).

Bug fixes

• brapi_study_data() no longer silently returns the wrong study’s observations on servers that don’t implement the studyDbId filter on /observations server-side (which triggers a client-side fallback that fetches all observations and filters locally). The filter used dplyr::filter(.data$studyDbId == studyDbId), which - because the function’s own argument is also named studyDbId - resolved the right-hand side to the data column itself, making the comparison always TRUE and returning every study’s observations rather than just the requested one. Fixed to .data$studyDbId == .env$studyDbId, which correctly disambiguates the data column from the function argument.
• brapi_study_data() no longer errors on studies where a trait is measured on only some observation units. pivot_wider() fills the absent combinations with zero-length elements, and the simplification step’s unlist() silently dropped them, returning a column shorter than the table and failing inside dplyr::across(). Unmeasured cells are now NA, and simplified columns are character throughout, which is how BrAPI returns observation values (@dwaring87, ropensci/software-review#792).
• Records that differ only in JSON object key order are no longer treated as distinct. Key order is not significant in JSON, and at least one server varies it between records in the same response; nested objects are now normalised as they are parsed. On the study used to reproduce this, 75 of 4,613 observations were affected, and brapi_study_data() additionally drops exact duplicate records before pivoting, reporting how many it removed (@dwaring87, ropensci/software-review#792).
• brapi_login() now builds its request the same way every other function does. It previously hardcoded /brapi/, so authentication was impossible on servers using a different path, and it sent neither the user agent nor the Accept header.
• con$timeout is now applied to requests. The argument has been accepted and documented since 0.1.0 but never took effect, leaving every request on curl’s own default.
• Observation values are trimmed of surrounding whitespace before being returned by brapi_study_data(), so values such as "80 " do not become NA on conversion to numeric. Reported by @dwaring87 from a development server; not reproducible across 21 studies on T3/Oat Sandbox, T3/Wheat Sandbox and Cassavabase, so the trim is defensive (ropensci/software-review#792).
• brapi_germplasm_pedigree() and brapi_germplasm_progeny() filter the response on germplasmDbId client-side. The public test server ignores that parameter on /pedigree, so a request for one germplasm returned another alongside it (@dwaring87, ropensci/software-review#792).
• A single-object response whose result carries a field named data is no longer mistaken for a collection. The parser treated any result$data as the record envelope, so /lists/{listDbId} returned only its members and discarded every other field. data is now treated as the envelope only when it is absent of scalars — that is, empty or holding objects.
• A collection whose records are bare strings is no longer mistaken for a single object. /commoncropnames returns its crop names that way, and the whole response came back as one row with a list-column.

Minor improvements

• Failed requests now report what the server said, not just the HTTP status. A 401 from a Breedbase server reads “You must login and have permission to access this BrAPI call” rather than a bare HTTP 401 Unauthorized, and a failed login reports the server’s reason — “Incorrect Password”, or “JSON array body required” — instead of “no access token returned”. Servers report errors in several different ways, and all of the forms seen across the test server, Breedbase, T3 and GRIN-Global are handled; an HTML error page is not shown, since it is never useful to a user (@dwaring87, ropensci/software-review#792).
• brapi_study_data() checks that the observations it received are really from the study asked for. A server may accept the studyDbId filter and ignore it — the public test server does exactly this on /pedigree — in which case every study’s observations would have been pivoted together. Extra studies are now filtered out, and the function says how many it found (@dwaring87, ropensci/software-review#792).

New features

• New Genome Maps entity support (R/genome_maps.R): brapi_maps(), brapi_map(), brapi_map_linkage_groups(), brapi_marker_positions(), brapi_search_marker_positions().
• New Pedigree entity support (R/germplasm.R): brapi_pedigree() and brapi_search_pedigree() retrieve pedigree records across many germplasm in one call, via /pedigree and /search/pedigree. brapi_germplasm_pedigree() and brapi_germplasm_progeny() now delegate to brapi_pedigree() rather than calling the sub-resources BrAPI deprecated in v2.1. Each row is one pedigree node; parents, siblings and progeny, when requested, are list-columns of tidy per-node tibbles rather than raw nested lists, so a node with several relatives is never silently collapsed to one row.
• New Ontologies entity support (R/phenotyping.R): brapi_ontologies() and brapi_ontology(), cross-referenced from brapi_traits(), brapi_scales(), brapi_methods(), and brapi_observation_variables().
• brapiR2 now wraps 32 of the 37 BrAPI v2.1 entities across all four modules (49 of 138 retrieval endpoints); see DESIGN.md for the full coverage breakdown and which entities remain uncovered.
• brapi_connection() gains a path argument for servers that do not serve BrAPI under /brapi/. GRIN-Global instances use gringlobal/brapi and were previously unreachable; Germinate and GIGWA deployments commonly sit under their own prefixes too. Defaults to "brapi", so existing code is unaffected. print() shows the path only when it differs from the default, and the cache key now includes it, so two servers sharing a hostname no longer collide.
• Requests now send a user agent identifying brapiR2, its version, and the httr2 and R versions in use, so server operators can see what is calling them. Requests made on continuous integration are marked as such. brapi_connection() gains a user_agent argument to override it (@dwaring87, ropensci/software-review#792).
• New brapi_location() retrieves a single location by ID, so a user who knows a study’s locationDbId can fetch its coordinates without listing every location and filtering. Verified against the public test server, Cassavabase, T3/Oat Sandbox and USDA-GRIN (@dwaring87, ropensci/software-review#792).
• New brapi_list() retrieves a single list by ID together with its contents. brapi_lists() returns only metadata, so there was previously no way to reach a list’s members at all. The members come back as a character vector in the data list-column, ready to pass to another function (@dwaring87, ropensci/software-review#792).
• brapi_get() and brapi_post_search() are now exported, so an endpoint brapiR2 does not wrap, a server extension, or a query parameter no named function exposes can be reached without dropping to raw HTTP. Pagination, caching, authentication and error reporting work as they do for the named functions. Recommended by both reviewers and by the rOpenSci packaging guidelines (@dwaring87, @jmh579, ropensci/software-review#792).
• brapi_get() gains a max_pages argument. An unfiltered call against a production server walks every page: Cassavabase holds 8,539 studies and took 18 minutes to return them, and a germplasm listing on T3/Wheat ran for over an hour before being interrupted. There was no way to ask for just the first page. The default fetches everything as before, and a truncated result is never cached.

Deprecated

• brapi_fetch_parallel() no longer sets or restores a future plan itself. Per the future package’s best-practices vignette, the parallel backend is now the caller’s choice: call future::plan() before calling brapi_fetch_parallel() to fetch in parallel. The .workers argument is deprecated - supplying it now emits a warning and has no effect.

Documentation

• Added LICENSE.md with the full MIT licence text, which was missing from the repository, so GitHub had no licence to detect and anyone opening LICENSE found no grant of rights. The copyright holder is now named explicitly rather than “brapiR2 authors” (@dwaring87, ropensci/software-review#792).
• @dwaring87 and @jmh579 are recorded in DESCRIPTION with the rev role for their rOpenSci reviews (ropensci/software-review#792).
• Corrected a misspelling in the QBMS comparison table in the getting-started vignette (@jmh579, ropensci/software-review#792).
• The getting-started vignette’s “Caching and Parallel Fetching” section now explains what each feature does and when to reach for it, rather than describing the future package at length. The design rationale for why brapi_fetch_parallel() does not set a plan has moved to DESIGN.md (@jmh579, ropensci/software-review#792).
• The “Connecting to a Server” section now links to Authentication and to Handling Credentials Safely, which most users need before anything else on the page (@jmh579, ropensci/software-review#792).
• The recommendation on when to choose QBMS and when to choose brapiR2 now sits with the comparison it belongs to, rather than after the references (@jmh579, ropensci/software-review#792).
• The vignette’s parallel-fetching chunks are guarded on furrr and future being installed, so the vignette builds where suggested packages are absent.
• DESCRIPTION now declares Language: en-GB, and the package’s prose has been made consistent with it. Six American spellings were corrected, and inst/WORDLIST has been extended with the domain vocabulary and package names the spellchecker cannot know (@jmh579, ropensci/software-review#792).
• The README installs with pak::pak() rather than remotes::install_github(), which now warns (@jmh579, ropensci/software-review#792), and notes that remotes and devtools need build_vignettes = TRUE for the vignette to be installed at all (@dwaring87, ropensci/software-review#792).
• The README leads with what brapiR2 does and which BrAPI modules it covers. The QBMS comparison table and the notes on other BrAPI clients have moved into Related Packages, and Authentication now comes before the extended examples (@jmh579, ropensci/software-review#792).
• The genomic selection article no longer fits the same trait with BGLR and sommer as well as rrBLUP. The comparison of when to reach for each package stays; the code that fitted them is shown rather than run, since neither result was used and both added a heavy dependency to the build (@jmh579, ropensci/software-review#792).
• Every wrapper’s help page now has a “BrAPI endpoint” section naming the endpoint it calls, linking to that endpoint’s definition in the v2.1 specification, and listing the query parameters the specification defines for it. brapi_studies() documented only trialDbId while the specification defines nine; the same gap existed across the package (@dwaring87, @jmh579, ropensci/software-review#792).
• The coverage figures are now derived from the specification rather than stated from memory. dev/brapi-spec.R reads the pinned V2.1 tag of the BrAPI specification repository and writes the endpoint inventory that the documentation is generated from. Correcting against it: the specification defines 37 top-level entities rather than 36, brapiR2 wraps 49 retrieval endpoints rather than 56, and Planned Crosses was missing from the list of uncovered entities.
• New ?brapi_coverage lists every BrAPI endpoint brapiR2 wraps, grouped by module, with the function that wraps each one, and names the entities that have no wrapper. Asked for by @jmh579 and @dwaring87 (ropensci/software-review#792).
• DESCRIPTION no longer names specific BrAPI implementations. It claimed compatibility with Breedbase, BMS, EBS, GIGWA and Germinate, of which only Breedbase had been tested; it now claims the specification instead. The README records which servers brapiR2 has actually been exercised against — eight, across three implementations — and which it has not (@jmh579, ropensci/software-review#792).
• DESIGN.md no longer lists four packages of mine as brapiR2’s downstream pipeline. Two are unreleased and two are at early versions, so the pipeline was described as though it were established.
• The vignette’s credentials section now says that the token is held in the connection object, so it is written to disk by saveRDS() and printed by str(), while print() shows only whether the connection is authenticated.
• Examples now check that the test server is reachable before running, so they report the server being down rather than failing. Every example makes live requests, and CRAN runs \donttest{} examples on some check flavours.

Testing

• Substantially expanded the mocked and live-server test suites alongside the features above: argument-capturing tests for every new thin wrapper, dedicated tests for the pedigree relative-list parsing (nodes with parents, with progeny, and with neither), and guarded integration tests against the public BrAPI test server for every new function.
• Added tests for the work done in response to review: URL construction and cache keys under a non-default path, the user agent as sent and as overridden, login reaching a non-standard path, JSON key-order normalisation, unmeasured traits filling with NA rather than shortening the column, whitespace trimming, the client-side studyDbId and germplasmDbId filters, the three response shapes the parser must tell apart, and the error-message extraction for each form a server uses.

brapiR2 0.1.0

New features

• Initial release covering the BrAPI v2.1 specification’s Core, Germplasm, Phenotyping, and Genotyping modules.
• Core module: brapi_programs(), brapi_trials(), brapi_studies(), brapi_locations(), brapi_seasons(), brapi_lists(), brapi_people(), brapi_server_info().
• Germplasm module: brapi_germplasm(), brapi_germplasm_pedigree(), brapi_germplasm_progeny(), brapi_crosses(), brapi_crossing_projects(), brapi_seed_lots(), brapi_search_germplasm().
• Phenotyping module: brapi_observation_units(), brapi_observations(), brapi_observation_variables(), brapi_traits(), brapi_scales(), brapi_methods(), brapi_images(), brapi_events(), brapi_search_observations(), brapi_search_variables().
• Genotyping module: brapi_samples(), brapi_variants(), brapi_variant_sets(), brapi_calls(), brapi_call_sets(), brapi_references(), brapi_reference_sets(), brapi_allele_matrix(), brapi_search_variants(), brapi_search_calls().
• Convenience functions: brapi_study_data() (wide-format phenotype table), brapi_get_dosage_matrix(), brapi_get_marker_map().
• Stateless brapi_connection() — no global state or side effects.
• Automatic pagination for all GET endpoints.
• Async search handling (202 status + polling).
• Built-in response caching with brapi_cache_enable().
• Parallel batch fetching with brapi_fetch_parallel().

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