From c1d5a3ca9e5468796ac9ca9ed69159a59a255d78 Mon Sep 17 00:00:00 2001 From: wkmor1 Date: Mon, 4 Nov 2024 16:22:06 +0200 Subject: [PATCH] Improve the way 'municipality' data is handled What a 'municipality' is, varies from country to country. Strictly speaking, a Finnish 'municipality', in the Darwin Core standard, is a 'county'. But in the USA for example a 'municipality' is a level of organisation below the county level. These changes account for these differences by adding a level below 'municipality' in the Finnish sense which is called 'local_area' (or 'municipality' in DwC). It is assumed that non-Finnish data will use the terms 'county' and and 'municipality' in the raw data (e.g., data coming from the Kotka CMS) in the sense they are outline in Darwin Core. And Finnish data will map 'municipality' to DwC 'county' lacking any true 'municipality' data. --- R/finbif_occurrence.R | 95 +++- R/finbif_records.R | 69 ++- R/sysdata.rda | Bin 20372 -> 20414 bytes R/utils.R | 8 + data-raw/variables.csv | 3 +- tests/fixtures/finbif_occurrence.yml | 601 +++++++++++---------- tests/testthat/_snaps/finbif_occurrence.md | 50 +- tests/testthat/test-finbif_occurrence.R | 2 +- 8 files changed, 482 insertions(+), 346 deletions(-) diff --git a/R/finbif_occurrence.R b/R/finbif_occurrence.R index 7de2441b..501b296f 100644 --- a/R/finbif_occurrence.R +++ b/R/finbif_occurrence.R @@ -292,6 +292,10 @@ occurrence <- function(fb_records_obj) { fb_occurrence_df <- compute_region(fb_occurrence_df) + fb_occurrence_df <- compute_municipality(fb_occurrence_df) + + fb_occurrence_df <- compute_local_area(fb_occurrence_df) + fb_occurrence_df <- compute_codes(fb_occurrence_df) fb_occurrence_df <- extract_facts(fb_occurrence_df) @@ -1436,6 +1440,91 @@ compute_region <- function(fb_occurrence_df) { #' @noRd +compute_municipality <- function(fb_occurrence_df) { + + dwc <- attr(fb_occurrence_df, "dwc", TRUE) + + vtype <- col_type_string(dwc) + + var_names <- sysdata(list(which = "var_names")) + + m_var <- var_names[["computed_var_municipality", vtype]] + + add <- attr(fb_occurrence_df, "include_new_cols", TRUE) + + if (add && m_var %in% attr(fb_occurrence_df, "column_names", TRUE)) { + + idv <- var_names[["gathering.interpretations.finnishMunicipality", vtype]] + + id <- basename(fb_occurrence_df[[idv]]) + + municipality <- finbif_metadata( + "municipality", + attr(fb_occurrence_df, "locale", TRUE), + attr(fb_occurrence_df, "cache", TRUE)[[2L]] + ) + + fact_names <- var_names[["gathering.facts.fact", vtype]] + + fact_values <- var_names[["gathering.facts.value", vtype]] + + which_county <- lapply( + fb_occurrence_df[[fact_names]], + match, + "http://tun.fi/MY.county", + nomatch = 0 + ) + + county <- mapply( + extract_fact, + fb_occurrence_df[[fact_values]], + lapply(which_county, as.logical), + SIMPLIFY = FALSE, + USE.NAMES = FALSE + ) + + fb_occurrence_df[[m_var]] <- ifelse( + is.na(id), unlist(county), municipality[id, "name"] + ) + + } + + fb_occurrence_df + +} + +#' @noRd + +compute_local_area <- function(fb_occurrence_df) { + + dwc <- attr(fb_occurrence_df, "dwc", TRUE) + + vtype <- col_type_string(dwc) + + var_names <- sysdata(list(which = "var_names")) + + la_var <- var_names[["computed_var_local_area", vtype]] + + add <- attr(fb_occurrence_df, "include_new_cols", TRUE) + + if (add && la_var %in% attr(fb_occurrence_df, "column_names", TRUE)) { + + idv <- var_names[["gathering.interpretations.finnishMunicipality", vtype]] + + lav <- var_names[["gathering.municipality", vtype]] + + fb_occurrence_df[[la_var]] <- ifelse( + is.na(fb_occurrence_df[[idv]]), fb_occurrence_df[[lav]], NA_character_ + ) + + } + + fb_occurrence_df + +} + +#' @noRd + multi_req <- function(fb_records_obj) { filters <- fb_records_obj[["filter"]] @@ -1662,10 +1751,14 @@ extract_facts <- function(fb_occurrence_df) { values_name <- var_names[[level_vls, vtype]] - fb_occurrence_df[[fact]] <- mapply( + fact_value <- mapply( extract_fact, fb_occurrence_df[[values_name]], is_fact ) + fb_occurrence_df[[fact]] <- mapply( + concat_two_strings, fb_occurrence_df[[fact]], fact_value + ) + } } diff --git a/R/finbif_records.R b/R/finbif_records.R index 1d7957d8..7dbc3062 100644 --- a/R/finbif_records.R +++ b/R/finbif_records.R @@ -607,28 +607,28 @@ infer_selection <- function(fb_records_obj) { infer_computed_vars <- function(fb_records_obj) { - l <- list( + computable_vars <- list( abundance = list( vars = c( - "abundance", "individualCount", "occurrence_status", "occurrenceStatus" + "computed_var_abundance", "computed_var_occurrence_status" ), - v_names = c( + select_names = c( "unit.interpretations.individualCount", "unit.abundanceString" ) ), cu = list( - vars = c("coordinates_uncertainty", "coordinateUncertaintyInMeters"), - v_names = c( + vars = "computed_var_coordinates_uncertainty", + select_names = c( "gathering.interpretations.coordinateAccuracy", "document.sourceId" ) ), citation = list( - vars = c("citation", "bibliographicCitation"), - v_names = c("document.documentId", "document.sourceId") + vars = "computed_var_citation", + select_names = c("document.documentId", "document.sourceId") ), sn = list( - vars = c("scientific_name", "scientificName"), - v_names = c( + vars = "computed_var_scientific_name", + select_names = c( "unit.linkings.taxon.scientificName", "unit.taxonVerbatim", "unit.linkings.taxon.scientificNameAuthorship", @@ -637,34 +637,49 @@ infer_computed_vars <- function(fb_records_obj) { ) ), red_list = list( - vars = c("red_list_status", "redListStatus"), - v_names = c( + vars = "computed_var_red_list_status", + select_names = c( "unit.linkings.taxon.latestRedListStatusFinland.status", "unit.linkings.taxon.latestRedListStatusFinland.year" ) ), region = list( - vars = c("region", "stateProvince"), - v_names = c( + vars = "computed_var_region", + select_names = c( "gathering.interpretations.finnishMunicipality", "gathering.province" ) ), institution_code = list( - vars = c("institution_code", "institutionCode"), - v_names = "document.collectionId" + vars = "computed_var_institution_code", + select_names = "document.collectionId" ), collection_code = list( - vars = c("collection_code", "collectionCode"), - v_names = "document.collectionId" + vars = "computed_var_institution_code", + select_names = "document.collectionId" ), country = list( - vars = "country", - v_names = c("gathering.interpretations.country", "gathering.country") + vars = "computed_var_country", + select_names = c("gathering.interpretations.country", "gathering.country") ), country_code = list( - vars = c("country_code", "countryCode"), - v_names = c("gathering.interpretations.country", "gathering.country") + vars = "computed_var_country_code", + select_names = c("gathering.interpretations.country", "gathering.country") + ), + municipality = list( + vars = "computed_var_municipality", + select_names = c( + "gathering.interpretations.finnishMunicipality", + "gathering.facts.fact", + "gathering.facts.value" + ) + ), + local_area = list( + "computed_var_local_area", + select_names = c( + "gathering.interpretations.finnishMunicipality", + "gathering.municipality" + ) ) ) @@ -674,13 +689,17 @@ infer_computed_vars <- function(fb_records_obj) { var_type <- fb_records_obj[["var_type"]] - for (i in l) { + for (i in computable_vars) { + + i_vars <- i[["vars"]] + + i_var_names <- var_names[i_vars, var_type] - if (any(i[["vars"]] %in% select)) { + if (any(i_var_names %in% select)) { - v_names_i <- i[["v_names"]] + select_names_i <- i[["select_names"]] - select <- c(select, var_names[v_names_i, var_type]) + select <- c(select, var_names[select_names_i, var_type]) } diff --git a/R/sysdata.rda b/R/sysdata.rda index 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unit.abundanceString,abundance_verbatim,verbatimAbundance,FALSE,FALSE,character,character,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE gathering.interpretations.countryDisplayname,country_interpreted,countryInterpreted,FALSE,FALSE,character,character,TRUE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE gathering.interpretations.biogeographicalProvinceDisplayname,bio_province_interpreted,bioStateProvinceInterpreted,FALSE,FALSE,character,character,TRUE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE -computed_var_from_id_municipality,municipality,county,FALSE,FALSE,character,character,TRUE,TRUE,FALSE,TRUE,TRUE,FALSE,TRUE,FALSE,FALSE +computed_var_municipality,municipality,county,FALSE,FALSE,character,character,TRUE,TRUE,FALSE,TRUE,TRUE,FALSE,TRUE,FALSE,FALSE +computed_var_local_area,local_area,municipality,FALSE,FALSE,character,character,TRUE,TRUE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE computed_var_region,region,stateProvince,FALSE,FALSE,character,character,TRUE,TRUE,FALSE,TRUE,TRUE,FALSE,TRUE,FALSE,FALSE gathering.conversions.wgs84WKT,footprint_wgs84,footprintWKT,FALSE,FALSE,character,character,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE gathering.conversions.linelengthInMeters,line_length_m,lineLengthMeters,FALSE,FALSE,integer,integer,TRUE,TRUE,FALSE,TRUE,TRUE,FALSE,TRUE,FALSE,FALSE diff --git a/tests/fixtures/finbif_occurrence.yml b/tests/fixtures/finbif_occurrence.yml index a4378989..cf37d30e 100644 --- a/tests/fixtures/finbif_occurrence.yml +++ b/tests/fixtures/finbif_occurrence.yml @@ -15,7 +15,7 @@ http_interactions: reason: OK message: 'Success: (200) OK' headers: - date: Tue, 01 Oct 2024 13:31:09 GMT + date: Mon, 04 Nov 2024 06:48:37 GMT content-type: application/json; charset=utf-8 content-length: '342' x-powered-by: Express @@ -35,7 +35,7 @@ http_interactions: file: no string: '[{"matchingName":"Plants","nameType":"MX.vernacularName","id":"MX.37601","scientificName":"Plantae","scientificNameAuthorship":"Haeckel","taxonRank":"MX.kingdom","cursiveName":false,"finnish":true,"species":false,"vernacularName":{"fi":"kasvit","sv":"egentliga växter","en":"Plants"},"kingdomScientificName":"Plantae","type":"exactMatches"}]' - recorded_at: 2024-10-01 13:31:25 GMT + recorded_at: 2024-11-04 06:49:05 GMT recorded_with: vcr/1.6.0, webmockr/1.0.0 - request: method: get @@ -53,7 +53,7 @@ http_interactions: reason: OK message: 'Success: (200) OK' headers: - date: Tue, 01 Oct 2024 13:31:09 GMT + date: Mon, 04 Nov 2024 06:48:38 GMT content-type: application/json;charset=utf-8 transfer-encoding: chunked access-control-allow-origin: '*' @@ -67,8 +67,8 @@ http_interactions: body: encoding: '' file: no - string: '{"total":37402}' - recorded_at: 2024-10-01 13:31:25 GMT + string: '{"total":40497}' + recorded_at: 2024-11-04 06:49:05 GMT recorded_with: vcr/1.6.0, webmockr/1.0.0 - request: method: get @@ -86,7 +86,7 @@ http_interactions: reason: OK message: 'Success: (200) OK' headers: - date: Tue, 01 Oct 2024 13:31:09 GMT + date: Mon, 04 Nov 2024 06:48:38 GMT content-type: application/json; charset=utf-8 content-length: '374' x-powered-by: Express @@ -105,7 +105,7 @@ http_interactions: encoding: '' file: no string: '[{"matchingName":"Birds","nameType":"MX.vernacularName","id":"MX.37580","scientificName":"Aves","taxonRank":"MX.class","cursiveName":false,"finnish":true,"species":false,"vernacularName":{"fi":"linnut","sv":"fåglar","en":"Birds"},"informalGroups":[{"id":"MVL.1","name":{"en":"Birds","sv":"Fåglar","fi":"Linnut"}}],"kingdomScientificName":"Animalia","type":"exactMatches"}]' - recorded_at: 2024-10-01 13:31:25 GMT + recorded_at: 2024-11-04 06:49:05 GMT recorded_with: vcr/1.6.0, webmockr/1.0.0 - request: method: get @@ -123,7 +123,7 @@ http_interactions: reason: OK message: 'Success: (200) OK' headers: - date: Tue, 01 Oct 2024 13:31:10 GMT + date: Mon, 04 Nov 2024 06:48:39 GMT content-type: application/json;charset=utf-8 transfer-encoding: chunked access-control-allow-origin: '*' @@ -137,17 +137,17 @@ http_interactions: body: encoding: '' file: no - string: '{"currentPage":1,"nextPage":2,"lastPage":3157,"pageSize":5,"total":15781,"results":[{"unit":{"abundanceString":"2","interpretations":{"individualCount":2,"needsCheck":false,"needsIdentification":false,"recordQuality":"NEUTRAL","reliability":"UNDEFINED"},"linkings":{"taxon":{"informalTaxonGroups":["http://tun.fi/MVL.1","http://tun.fi/MVL.1141","http://tun.fi/MVL.1162"],"latestRedListStatusFinland":{"status":"http://tun.fi/MX.iucnLC","year":2019},"primaryHabitat":{"habitat":"http://tun.fi/MKV.habitatVsr"},"scientificName":"Pandion - haliaetus","scientificNameAuthorship":"(Linnaeus, 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+ recorded_at: 2024-11-04 06:49:05 GMT recorded_with: vcr/1.6.0, webmockr/1.0.0 - request: method: get @@ -14295,14 +14310,14 @@ http_interactions: reason: OK message: 'Success: (200) OK' headers: - date: Tue, 01 Oct 2024 13:31:13 GMT + date: Mon, 04 Nov 2024 06:48:42 GMT content-type: application/json; charset=utf-8 transfer-encoding: chunked x-powered-by: Express access-control-allow-origin: '*' access-control-allow-credentials: 'true' x-download-options: noopen - etag: W/"3fdb-DrZvSTCHP2vkN5OCoHF9ssnyls4" + etag: W/"3fdb-ENAsjO3bNRHXnm5o3MiQE83AsBI" vary: Accept-Encoding content-encoding: gzip cache-control: public @@ -14331,8 +14346,8 @@ http_interactions: – tunturikoivikot (pois lukien tunturikoivulehdot)","sv":"Mt – fjällbjörkskogar (exkl. örtrika fjällbjörkskogar)"},"altParent":"MKV.habitatM"},{"id":"MKV.habitatMtl","value":{"fi":"Mtl – tunturikoivulehdot","en":"Mtl – herb-rich alpine birch forests","sv":"Mtl - – örtrika fjällbjörkskogar"},"altParent":"MKV.habitatM"},{"id":"MKV.habitatS","value":{"fi":"S - – Suot","en":"S – Mires","sv":"S – Myrmarker"}},{"id":"MKV.habitatSl","value":{"fi":"Sl + – örtrika fjällbjörkskogar"},"altParent":"MKV.habitatM"},{"id":"MKV.habitatS","value":{"en":"S + – Mires","fi":"S – Suot","sv":"S – Myrmarker"}},{"id":"MKV.habitatSl","value":{"fi":"Sl – letot","en":"Sl – rich fens","sv":"Sl – rikkärr"},"altParent":"MKV.habitatS"},{"id":"MKV.habitatSla","value":{"en":"Sla – open rich fens","fi":"Sla – avoletot","sv":"Sla – öppna kärr"},"altParent":"MKV.habitatSl"},{"id":"MKV.habitatSlr","value":{"sv":"Slr – rikkärrs-tallkär","en":"Slr – rich pine fens","fi":"Slr – lettorämeet"},"altParent":"MKV.habitatSl"},{"id":"MKV.habitatSlk","value":{"fi":"Slk @@ -14423,29 +14438,29 @@ http_interactions: – luolat ja halkeamat","en":"Kl – caves and crevices","sv":"Kl – grottor och skrevor"},"altParent":"MKV.habitatK"},{"id":"MKV.habitatKm","value":{"sv":"Km – silikatrika hällmarker","en":"Km – siliceous rock outcrops","fi":"Km – karut - ja keskiravinteiset kalliot"},"altParent":"MKV.habitatK"},{"id":"MKV.habitatT","value":{"en":"T - – Alpine habitats","fi":"T – Tunturipaljakat","sv":"T – Fjäll"}},{"id":"MKV.habitatTk","value":{"fi":"Tk - – tunturikankaat","en":"Tk – alpine heaths","sv":"Tk – fjällhedar"},"altParent":"MKV.habitatT"},{"id":"MKV.habitatTn","value":{"sv":"Tn - – fjällängar","en":"Tn – alpine meadows","fi":"Tn – tunturiniityt"},"altParent":"MKV.habitatT"},{"id":"MKV.habitatTu","value":{"sv":"Tu - – snölegor","en":"Tu – snowbeds","fi":"Tu – lumenviipymät"},"altParent":"MKV.habitatT"},{"id":"MKV.habitatTp","value":{"sv":"Tp - – fjällbuskmarker","en":"Tp – alpine heath scrubs","fi":"Tp – tunturikangaspensaikot"},"altParent":"MKV.habitatT"},{"id":"MKV.habitatTl","value":{"en":"Tl + ja keskiravinteiset kalliot"},"altParent":"MKV.habitatK"},{"id":"MKV.habitatT","value":{"fi":"T + – Tunturipaljakat","en":"T – Alpine habitats","sv":"T – Fjäll"}},{"id":"MKV.habitatTk","value":{"fi":"Tk + – tunturikankaat","en":"Tk – alpine heaths","sv":"Tk – fjällhedar"},"altParent":"MKV.habitatT"},{"id":"MKV.habitatTn","value":{"fi":"Tn + – tunturiniityt","en":"Tn – alpine meadows","sv":"Tn – fjällängar"},"altParent":"MKV.habitatT"},{"id":"MKV.habitatTu","value":{"sv":"Tu + – snölegor","en":"Tu – snowbeds","fi":"Tu – lumenviipymät"},"altParent":"MKV.habitatT"},{"id":"MKV.habitatTp","value":{"en":"Tp + – alpine heath scrubs","sv":"Tp – fjällbuskmarker","fi":"Tp – tunturikangaspensaikot"},"altParent":"MKV.habitatT"},{"id":"MKV.habitatTl","value":{"en":"Tl – alpine rock outcrops and boulder fields","fi":"Tl – paljakan kalliot ja - kivikot","sv":"Tl – hällmarker och stenjordar på fjäll"},"altParent":"MKV.habitatT"},{"id":"MKV.habitatTll","value":{"en":"Tll - – alpine siliceous rock outcrops and boulder fields","fi":"Tll – paljakan - karut ja keskiravinteiset kalliot ja kivikot","sv":"Tll – oligotrofa och mesotrofa - hällmarker och stenjordar på fjäll"},"altParent":"MKV.habitatTl"},{"id":"MKV.habitatTlk","value":{"en":"Tlk - – alpine calcareous rock outcrops and boulder fields","sv":"Tlk – kalkrika - hällmarker och stenjordar på fjäll","fi":"Tlk – paljakan kalkkikalliot ja - -kivikot"},"altParent":"MKV.habitatTl"},{"id":"MKV.habitatTls","value":{"sv":"Tls - – serpentinberg och -block på fjäll","fi":"Tls – paljakan serpentiinikalliot - ja -kivikot","en":"Tls – alpine serpentine rock outcrops and boulder fields"},"altParent":"MKV.habitatTl"},{"id":"MKV.habitatTlr","value":{"en":"Tlr + kivikot","sv":"Tl – hällmarker och stenjordar på fjäll"},"altParent":"MKV.habitatT"},{"id":"MKV.habitatTll","value":{"sv":"Tll + – oligotrofa och mesotrofa hällmarker och stenjordar på fjäll","en":"Tll – + alpine siliceous rock outcrops and boulder fields","fi":"Tll – paljakan karut + ja keskiravinteiset kalliot ja kivikot"},"altParent":"MKV.habitatTl"},{"id":"MKV.habitatTlk","value":{"en":"Tlk + – alpine calcareous rock outcrops and boulder fields","fi":"Tlk – paljakan + kalkkikalliot ja -kivikot","sv":"Tlk – kalkrika hällmarker och stenjordar + på fjäll"},"altParent":"MKV.habitatTl"},{"id":"MKV.habitatTls","value":{"en":"Tls + – alpine serpentine rock outcrops and boulder fields","sv":"Tls – serpentinberg + och -block på fjäll","fi":"Tls – paljakan serpentiinikalliot ja -kivikot"},"altParent":"MKV.habitatTl"},{"id":"MKV.habitatTlr","value":{"en":"Tlr – alpine gorges and canyons","fi":"Tlr – paljakan kalliorotkot, rotkolaaksot ja kurut","sv":"Tlr – klyftor och raviner på fjäll"},"altParent":"MKV.habitatTl"},{"id":"MKV.habitatTlä","value":{"en":"Tlä – alpine spring complexes and seepage areas","fi":"Tlä – paljakan lähteiköt - ja tihkupinnat","sv":"Tlä – källor och källpåverkade områden på fjäll"},"altParent":"MKV.habitatT"},{"id":"MKV.habitatTs","value":{"sv":"Ts - – myrmarker på fjäll","fi":"Ts – paljakan suot","en":"Ts – alpine mires"},"altParent":"MKV.habitatT"},{"id":"MKV.habitatTj","value":{"sv":"Tj - – sjöar och tjärnar på fjäll","en":"Tj – alpine ponds and lakes (shores included)","fi":"Tj - – paljakan järvet ja lammet (sis. rannat)"},"altParent":"MKV.habitatT"},{"id":"MKV.habitatTv","value":{"en":"Tv + ja tihkupinnat","sv":"Tlä – källor och källpåverkade områden på fjäll"},"altParent":"MKV.habitatT"},{"id":"MKV.habitatTs","value":{"en":"Ts + – alpine mires","sv":"Ts – myrmarker på fjäll","fi":"Ts – paljakan suot"},"altParent":"MKV.habitatT"},{"id":"MKV.habitatTj","value":{"fi":"Tj + – paljakan järvet ja lammet (sis. rannat)","sv":"Tj – sjöar och tjärnar på + fjäll","en":"Tj – alpine ponds and lakes (shores included)"},"altParent":"MKV.habitatT"},{"id":"MKV.habitatTv","value":{"en":"Tv – streams in fell area (incl. shores)","sv":"Tv – ström på fjäll (inkl. strand)","fi":"Tv – paljakan virtavedet (sis. rannat)"},"altParent":"MKV.habitatT"},{"id":"MKV.habitatTa","value":{"fi":"Ta – paljakan lampareet ja allikot","sv":"Ta – göl på fjäll","en":"Ta – puddles @@ -14469,7 +14484,7 @@ http_interactions: – rakennukset ja rakenteet","en":"Ir – buildings and constructions","sv":"Ir – byggnader och konstruktioner"},"altParent":"MKV.habitatI"},{"id":"MKV.habitatU","value":{"fi":"? – Elinympäristö tuntematon","sv":"? – Habitat okänt","en":"? – Habitat unknown"}}]' - recorded_at: 2024-10-01 13:31:25 GMT + recorded_at: 2024-11-04 06:49:05 GMT recorded_with: vcr/1.6.0, webmockr/1.0.0 - request: method: get @@ -14487,7 +14502,7 @@ http_interactions: reason: OK message: 'Success: (200) OK' headers: - date: Tue, 01 Oct 2024 13:31:13 GMT + date: Mon, 04 Nov 2024 06:48:42 GMT content-type: application/json; charset=utf-8 transfer-encoding: chunked x-powered-by: Express @@ -14527,7 +14542,7 @@ http_interactions: kalliot/kivikot","sv":"ke – intermediärä-basiska hällmarker samt sten- och blockfält"}},{"id":"MKV.habitatSpecificTypeCA","value":{"fi":"ca – kalkkivaikutteinen","en":"ca – calcareous effect","sv":"ca – kalkrik"}}]' - recorded_at: 2024-10-01 13:31:25 GMT + recorded_at: 2024-11-04 06:49:05 GMT recorded_with: vcr/1.6.0, webmockr/1.0.0 - request: method: get @@ -14545,14 +14560,14 @@ http_interactions: reason: OK message: 'Success: (200) OK' headers: - date: Tue, 01 Oct 2024 13:31:13 GMT + date: Mon, 04 Nov 2024 06:48:43 GMT content-type: application/json; charset=utf-8 transfer-encoding: chunked x-powered-by: Express access-control-allow-origin: '*' access-control-allow-credentials: 'true' x-download-options: noopen - etag: W/"531-gS47FAs+MwyrxNJbgc0CV/r/AUY" + etag: W/"531-5qkI0/7r87AQSpGfInQN4o71HcU" vary: Accept-Encoding content-encoding: gzip cache-control: public @@ -14570,14 +14585,14 @@ http_interactions: – Regionally Extinct","fi":"RE – Suomesta hävinneet","sv":"RE – Nationellt utdöd"}},{"id":"MX.iucnCR","value":{"fi":"CR – Äärimmäisen uhanalaiset","en":"CR – Critically Endangered","sv":"CR – Akut hotad"}},{"id":"MX.iucnEN","value":{"en":"EN - – Endangered","fi":"EN – Erittäin uhanalaiset","sv":"EN – Starkt hotad"}},{"id":"MX.iucnVU","value":{"sv":"VU - – Sårbar","en":"VU – Vulnerable","fi":"VU – Vaarantuneet"}},{"id":"MX.iucnNT","value":{"sv":"NT - – Nära hotad","en":"NT – Near Threatened","fi":"NT – Silmälläpidettävät"}},{"id":"MX.iucnLC","value":{"fi":"LC + – Endangered","fi":"EN – Erittäin uhanalaiset","sv":"EN – Starkt hotad"}},{"id":"MX.iucnVU","value":{"en":"VU + – Vulnerable","fi":"VU – Vaarantuneet","sv":"VU – Sårbar"}},{"id":"MX.iucnNT","value":{"en":"NT + – Near Threatened","fi":"NT – Silmälläpidettävät","sv":"NT – Nära hotad"}},{"id":"MX.iucnLC","value":{"fi":"LC – Elinvoimaiset","sv":"LC – Livskraftig","en":"LC – Least Concern"}},{"id":"MX.iucnDD","value":{"en":"DD - – Data Deficient","sv":"DD – Kunskapsbrist","fi":"DD – Puutteellisesti tunnetut"}},{"id":"MX.iucnNA","value":{"en":"NA - – Not Applicable","sv":"NA – Ej tillämplig","fi":"NA – Arviointiin soveltumattomat"}},{"id":"MX.iucnNE","value":{"fi":"NE - – Arvioimatta jätetyt","en":"NE – Not Evaluated","sv":"NE – Ej bedömd"}}]' - recorded_at: 2024-10-01 13:31:25 GMT + – Data Deficient","sv":"DD – Kunskapsbrist","fi":"DD – Puutteellisesti tunnetut"}},{"id":"MX.iucnNA","value":{"sv":"NA + – Ej tillämplig","fi":"NA – Arviointiin soveltumattomat","en":"NA – Not Applicable"}},{"id":"MX.iucnNE","value":{"en":"NE + – Not Evaluated","fi":"NE – Arvioimatta jätetyt","sv":"NE – Ej bedömd"}}]' + recorded_at: 2024-11-04 06:49:05 GMT recorded_with: vcr/1.6.0, webmockr/1.0.0 - request: method: get @@ -14595,7 +14610,7 @@ http_interactions: reason: OK message: 'Success: (200) OK' headers: - date: Tue, 01 Oct 2024 13:31:14 GMT + date: Mon, 04 Nov 2024 06:48:43 GMT content-type: application/json; charset=utf-8 transfer-encoding: chunked x-powered-by: Express @@ -14712,7 +14727,7 @@ http_interactions: endemiska ciklider"}},{"id":"MVL.1287","name":{"en":"Endemic cichlids of Lake Malawi","fi":"Malawijärven endeemiset kirjoahvenet","sv":"Malawisjöns endemiska ciklider"}}],"lastPage":1,"@context":"http://schema.laji.fi/context/informalTaxonGroup.jsonld"}' - recorded_at: 2024-10-01 13:31:25 GMT + recorded_at: 2024-11-04 06:49:05 GMT recorded_with: vcr/1.6.0, webmockr/1.0.0 - request: method: get @@ -14730,7 +14745,7 @@ http_interactions: reason: OK message: 'Success: (200) OK' headers: - date: Tue, 01 Oct 2024 13:31:14 GMT + date: Mon, 04 Nov 2024 06:48:43 GMT content-type: application/json; charset=utf-8 transfer-encoding: chunked x-powered-by: Express @@ -14877,7 +14892,7 @@ http_interactions: eggs or living young in the nest.","fi":"82 Varma pesintä: nähty pesässä munia tai poikasia.","sv":"82 Säker häckning; Direkt bevis på säker häckning konstaterat: sett i boet ägg eller ungar"}}]' - recorded_at: 2024-10-01 13:31:25 GMT + recorded_at: 2024-11-04 06:49:05 GMT recorded_with: vcr/1.6.0, webmockr/1.0.0 - request: method: get @@ -14895,7 +14910,7 @@ http_interactions: reason: OK message: 'Success: (200) OK' headers: - date: Tue, 01 Oct 2024 13:31:14 GMT + date: Mon, 04 Nov 2024 06:48:43 GMT content-type: application/json; charset=utf-8 content-length: '474' x-powered-by: Express @@ -14918,7 +14933,7 @@ http_interactions: breeding","fi":"Mahdollinen pesintä","sv":"Möjlig häckning"}},{"id":"MY.atlasClassEnumC","value":{"fi":"Todennäköinen pesintä","en":"Probable breeding","sv":"Sannolik häckning"}},{"id":"MY.atlasClassEnumD","value":{"fi":"Varma pesintä","en":"Confirmed breeding","sv":"Säker häckning"}}]' - recorded_at: 2024-10-01 13:31:25 GMT + recorded_at: 2024-11-04 06:49:05 GMT recorded_with: vcr/1.6.0, webmockr/1.0.0 - request: method: get @@ -14936,12 +14951,12 @@ http_interactions: reason: OK message: 'Success: (200) OK' headers: - date: Tue, 01 Oct 2024 13:31:14 GMT + date: Mon, 04 Nov 2024 06:48:43 GMT content-type: application/json; charset=utf-8 - content-length: '47900' + content-length: '40457' x-powered-by: Express access-control-allow-origin: '*' - etag: W/"bb1c-M6/VtH/5sMi3SRI1+sKDPX5L/5k" + etag: 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(kasvitiede)"}},{"id":"MX.variety","value":{"en":"variety","fi":"muunnos","sv":"varietet"}},{"id":"MX.subvariety","value":{"en":"subvariety","fi":"alamuunnos","sv":"subvarietet"}},{"id":"MX.form","value":{"en":"form","sv":"form","fi":"muoto"}},{"id":"MX.subform","value":{"en":"subform","fi":"alamuoto","sv":"subform"}},{"id":"MX.hybrid","value":{"en":"hybrid","fi":"risteymä","sv":"hybrid"}},{"id":"MX.anamorph","value":{"en":"anamorph","sv":"anamorf","fi":"anamorfisuus"}},{"id":"MX.ecotype","value":{"sv":"ekotyp","fi":"ekotyyppi","en":"ecotype"}},{"id":"MX.populationGroup","value":{"en":"population + group","sv":"population grupp","fi":"populaatioryhmä"}},{"id":"MX.intergenericHybrid","value":{"en":"intergeneric + hybrid","fi":"sukujenvälinen risteymä (kasvitiede)","sv":""}},{"id":"MX.infragenericHybrid","value":{"en":"infrageneric + hybrid","fi":"suvunsisäinen risteymä (kasvitiede)","sv":""}},{"id":"MX.cultivar","value":{"fi":"lajike","en":"cultivar","sv":""}},{"id":"MX.group","value":{"en":"Group","sv":"Grupp","fi":"viljelykasvien + Ryhmä"}},{"id":"MX.grex","value":{"sv":"grex","fi":"grex","en":"grex"}}]' + recorded_at: 2024-11-04 06:49:05 GMT recorded_with: vcr/1.6.0, webmockr/1.0.0 - request: method: get @@ -15608,7 +15623,7 @@ http_interactions: reason: OK message: 'Success: (200) OK' headers: - date: Tue, 01 Oct 2024 13:31:21 GMT + date: Mon, 04 Nov 2024 06:48:54 GMT content-type: application/json; charset=utf-8 content-length: '2' x-powered-by: Express @@ -15627,5 +15642,5 @@ http_interactions: encoding: '' file: no string: '[]' - recorded_at: 2024-10-01 13:31:25 GMT + recorded_at: 2024-11-04 06:49:05 GMT recorded_with: vcr/1.6.0, webmockr/1.0.0 diff --git a/tests/testthat/_snaps/finbif_occurrence.md b/tests/testthat/_snaps/finbif_occurrence.md index 1e71ba62..e629df9d 100644 --- a/tests/testthat/_snaps/finbif_occurrence.md +++ b/tests/testthat/_snaps/finbif_occurrence.md @@ -9,16 +9,16 @@ [4] "Records available: 15781 + 728" [5] "A data.frame [20 x 26]" [6] " scientific_name abundance lat_wgs84 lon_wgs84 date_time" - [7] "1 Buteo buteo (Linnae… 1 62.872 21.7856 2023-01-01 10:00:00" - [8] "2 Haliaeetus albicill… 1 63.22185 21.52314 2023-01-01 10:00:00" - [9] "3 Pandion haliaetus (… 2 62.24648 21.89424 2023-01-01 10:00:00" - [10] "4 Pandion haliaetus (… 2 60.05948 23.85433 2023-01-01 10:00:00" - [11] "5 Turdus pilaris Linn… 1 66.55132 25.75795 2023-01-01 10:00:00" - [12] "6 Falco peregrinus Tu… 1 NA NA 2023-01-01 10:00:00" - [13] "7 Falco tinnunculus L… 1 62.22979 24.59263 2023-01-01 10:00:00" - [14] "8 Pyrrhula pyrrhula (… NA 60.23555 25.00538 2023-12-27 10:00:00" - [15] "9 Accipiter nisus (Li… 1 62.06566 28.23997 2023-01-01 10:00:00" - [16] "10 Pandion haliaetus (… 2 NA NA 2023-01-01 10:00:00" + [7] "1 Ficedula hypoleuca … 5 64.0057 23.62257 2023-01-01 10:00:00" + [8] "2 Pica pica (Linnaeus… NA 61.12005 26.31582 2023-01-23 10:00:00" + [9] "3 Pandion haliaetus (… 1 60.69503 24.15879 2023-01-01 10:00:00" + [10] "4 Parus major Linnaeu… 9 60.90207 26.16773 2023-01-01 10:00:00" + [11] "5 Pandion haliaetus (… 1 63.23659 21.91926 2023-01-01 10:00:00" + [12] "6 Passer montanus (Li… 4 60.54187 25.99479 2023-01-01 10:00:00" + [13] "7 Haliaeetus albicill… 1 59.71766 18.98764 2023-01-01 11:00:00" + [14] "8 Apus apus (Linnaeus… 1 60.54187 25.99479 2023-01-01 10:00:00" + [15] "9 Dryocopus martius (… 1 62.5697 22.13113 2023-01-01 10:00:00" + [16] "10 Phoenicurus phoenic… 1 67.7927 29.48489 2023-01-01 09:00:00" [17] "...with 10 more records and 21 more variables:" [18] "coordinates_uncertainty, any_issues, requires_verification," [19] "requires_identification, record_reliability, record_quality, duration," @@ -48,8 +48,8 @@ Output Records downloaded: 0 + 0 Records available: 0 + 0 - A data.frame [0 x 2] - [1] municipality set + A data.frame [0 x 3] + [1] municipality local_area set <0 rows> (or 0-length row.names) --- @@ -57,21 +57,21 @@ Code plants Output - Records downloaded: 35 - Records available: 35 - A data.frame [35 x 2] + Records downloaded: 34 + Records available: 34 + A data.frame [34 x 2] threatened_status orig_taxon_rank - 1 Near Threatened species - 2 Threatened species - 3 species + 1 genus + 2 genus + 3 Statutory species 4 species - 5 species - 6 species - 7 species - 8 species - 9 family - 10 Threatened species - ...with 25 more records + 5 Near Threatened species + 6 Statutory species + 7 genus + 8 Statutory species + 9 species + 10 species + ...with 24 more records --- diff --git a/tests/testthat/test-finbif_occurrence.R b/tests/testthat/test-finbif_occurrence.R index c271f53f..4b4d2849 100644 --- a/tests/testthat/test-finbif_occurrence.R +++ b/tests/testthat/test-finbif_occurrence.R @@ -80,7 +80,7 @@ test_that("fetching occurrences works", { set1 = c(collection = "HR.778"), set2 = c(collection = "HR.778") ), - select = "municipality", + select = c("municipality", "local_area"), filter_col = "set", quiet = TRUE )