diff --git a/DESCRIPTION b/DESCRIPTION index 5536ba81..e518d1a6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -96,7 +96,7 @@ Imports: crayon, cli, phangorn, - conditionz + lifecycle Suggests: testthat, vegan, diff --git a/NAMESPACE b/NAMESPACE index 6510a82d..07c28a64 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -346,7 +346,6 @@ importFrom(bold,bold_tax_name) importFrom(cli,cat_line) importFrom(cli,rule) importFrom(cli,symbol) -importFrom(conditionz,ConditionKeeper) importFrom(crayon,style) importFrom(crul,AsyncVaried) importFrom(crul,HttpClient) diff --git a/R/bold_search.R b/R/bold_search.R index 4f957fab..373d6c9c 100644 --- a/R/bold_search.R +++ b/R/bold_search.R @@ -65,8 +65,11 @@ bold_search <- function(sci = NULL, id = NULL, fuzzy = FALSE, dataTypes = 'basic', includeTree=FALSE, response=FALSE, name = NULL, ...) { - pchk(name, "sci") - if (!is.null(name)) sci <- name + if (!is.null(name)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "bold_search(name)", with = "bold_search(sci)") + sci <- name + } + stopifnot(!is.null(sci) | !is.null(id)) type <- if (is.null(sci)) "id" else "sci" tmp <- switch(type, diff --git a/R/children.R b/R/children.R index 9a52b3da..6691c1f0 100644 --- a/R/children.R +++ b/R/children.R @@ -81,8 +81,11 @@ children <- function(...){ #' @rdname children children.default <- function(sci_id, db = NULL, rows = NA, x = NULL, ...) { nstop(db) - pchk(x, "sci_id") - if (!is.null(x)) sci_id <- x + if (!is.null(x)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "children(x)", with = "children(sci_id)") + sci_id <- x + } + results <- switch( db, itis = { diff --git a/R/classification.R b/R/classification.R index a7ddaed4..ba63c419 100644 --- a/R/classification.R +++ b/R/classification.R @@ -228,7 +228,11 @@ classification <- function(...){ classification.default <- function(sci_id, db = NULL, callopts = list(), return_id = TRUE, rows = NA, x = NULL, ...) { nstop(db) - pchk(x, "sci_id") + if (!is.null(x)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "classification(x)", with = "classification(sci_id)") + sci_id <- x + } + switch( db, itis = { diff --git a/R/comm2sci.R b/R/comm2sci.R index 35d87eb8..e8eb579e 100644 --- a/R/comm2sci.R +++ b/R/comm2sci.R @@ -63,8 +63,11 @@ comm2sci <- function(...) { #' @rdname comm2sci comm2sci.default <- function(com, db='ncbi', itisby='search', simplify=TRUE, commnames = NULL, ...) { - pchk(commnames, "com") - if (!is.null(commnames)) com <- commnames + if (!is.null(commnames)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "comm2sci(commnames)", with = "comm2sci(com)") + com <- commnames + } + assert(com, "character") assert(simplify, "logical") temp <- lapply(com, sci_from_comm, db = db, simplify = simplify, diff --git a/R/downstream.R b/R/downstream.R index 91c54776..b44a5dfd 100644 --- a/R/downstream.R +++ b/R/downstream.R @@ -115,7 +115,10 @@ downstream.default <- function(sci_id, db=NULL, downto=NULL, intermediate=FALSE, rows=NA, x=NULL, ...) { nstop(downto, "downto") nstop(db) - pchk(x, "sci_id") + if (!is.null(x)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "downstream(x)", with = "downstream(sci_id)") + sci_id <- x + } if (!is.null(x)) sci_id <- x switch( db, diff --git a/R/eol_search.R b/R/eol_search.R index 3488b2b4..25171b9e 100644 --- a/R/eol_search.R +++ b/R/eol_search.R @@ -40,7 +40,11 @@ eol_search <- function(sci, page=1, exact=NULL, filter_tid=NULL, filter_heid=NULL, filter_by_string=NULL, cache_ttl=NULL, terms = NULL, ...) { - pchk(terms, "sci") + if (!is.null(terms)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "eol_search(terms)", with = "eol_search(sci)") + sci = terms + } + query <- gsub("\\s", "+", sci) args <- tc(list(q = query, page = page, exact = exact, filter_by_taxon_concept_id = filter_tid, diff --git a/R/gbif_downstream.R b/R/gbif_downstream.R index a11c47fd..893d7855 100644 --- a/R/gbif_downstream.R +++ b/R/gbif_downstream.R @@ -66,9 +66,11 @@ gbif_downstream <- function(id, downto, intermediate = FALSE, limit = 100, start = NULL, key = NULL, ...) { - pchk(key, "id") - if (!is.null(key)) id <- key - + if (!is.null(key)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "gbif_downstream(key)", with = "gbif_downstream(id)") + id <- key + } + should_be('intermediate', intermediate, 'logical') downto <- tolower(downto) diff --git a/R/get_boldid.R b/R/get_boldid.R index 4144f9d3..cd49aa24 100644 --- a/R/get_boldid.R +++ b/R/get_boldid.R @@ -123,7 +123,11 @@ get_boldid <- function(sci, fuzzy = FALSE, dataTypes = 'basic', assert(division, "character") assert(parent, "character") assert_rows(rows) - pchk(searchterm, "sci") + if (!is.null(searchterm)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "get_boldid(searchterm)", with = "get_boldid(sci)") + sci <- searchterm + } + if (inherits(sci, "character")) { tstate <- taxon_state$new(class = "boldid", names = sci) @@ -352,7 +356,10 @@ check_boldid <- function(x){ get_boldid_ <- function(sci, messages = TRUE, fuzzy = FALSE, dataTypes='basic', includeTree=FALSE, rows = NA, searchterm = NULL, ...) { - pchk(searchterm, "sci") + if (!is.null(searchterm)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "get_boldid_(searchterm)", with = "get_boldid_(sci)") + sci <- searchterm + } stats::setNames(lapply(sci, get_boldid_help, messages = messages, fuzzy = fuzzy, dataTypes=dataTypes, includeTree=includeTree, rows = rows, ...), sci) diff --git a/R/get_eolid.R b/R/get_eolid.R index 351d0f7d..0eca0900 100644 --- a/R/get_eolid.R +++ b/R/get_eolid.R @@ -120,7 +120,11 @@ get_eolid <- function(sci_com, ask = TRUE, messages = TRUE, assert(rank, "character") assert(data_source, "character") assert_rows(rows) - pchk(sciname, "sci_com") + if (!is.null(sciname)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "get_eolid(sciname)", with = "get_eolid(sci_com)") + sci_com <- sciname + } + if (inherits(sci_com, "character")) { tstate <- taxon_state$new(class = "eolid", names = sci_com) @@ -391,7 +395,11 @@ get_eol_pageid <- function(x) { #' @rdname get_eolid get_eolid_ <- function(sci_com, messages = TRUE, rows = NA, sciname = NULL, ...) { - pchk(sciname, "sci_com") + if (!is.null(sciname)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "get_eolid_(sciname)", with = "get_eolid_(sci_com)") + sci_com <- sciname + } + stats::setNames(lapply(sci_com, get_eolid_help, messages = messages, rows = rows, ...), sci_com) } diff --git a/R/get_gbifid.R b/R/get_gbifid.R index 1c5ec57f..29e90799 100644 --- a/R/get_gbifid.R +++ b/R/get_gbifid.R @@ -140,8 +140,11 @@ get_gbifid <- function(sci, ask = TRUE, messages = TRUE, rows = NA, assert(rank, "character") assert(method, "character") assert_rows(rows) - pchk(sciname, "sci") - + if (!is.null(sciname)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "get_gbifid(sciname)", with = "get_gbifid(sci)") + sci <- sciname + } + if (inherits(sci, "character")) { tstate <- taxon_state$new(class = "gbifid", names = sci) items <- sci @@ -323,7 +326,10 @@ check_gbifid <- function(x){ get_gbifid_ <- function(sci, messages = TRUE, rows = NA, method = "backbone", sciname = NULL) { - pchk(sciname, "sci") + if (!is.null(sciname)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "get_gbifid_(sciname)", with = "get_gbifid_(sci)") + sci <- sciname + } stats::setNames(lapply(sci, get_gbifd_help, messages = messages, rows = rows, method = method), sci) } diff --git a/R/get_iucn.R b/R/get_iucn.R index 71c24f69..239e2a4b 100644 --- a/R/get_iucn.R +++ b/R/get_iucn.R @@ -56,7 +56,11 @@ get_iucn <- function(sci, messages = TRUE, key = NULL, x = NULL, ...) { assert(sci, c("character", "taxon_state")) assert(messages, "logical") - pchk(x, "sci") + if (!is.null(x)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "get_iucn(x)", with = "get_iucn(sci)") + sci <- x + } + if (inherits(sci, "character")) { tstate <- taxon_state$new(class = "iucn", names = sci) diff --git a/R/get_natservid.R b/R/get_natservid.R index c9d522e5..6f046069 100644 --- a/R/get_natservid.R +++ b/R/get_natservid.R @@ -80,7 +80,11 @@ get_natservid <- function(sci_com, searchtype = "scientific", ask = TRUE, assert(ask, "logical") assert(messages, "logical") assert_rows(rows) - pchk(query, "sci_com") + if (!is.null(commnames)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "get_natservid(query)", with = "get_natservid(sci_com)") + sci_com <- query + } + if (inherits(sci_com, "character")) { tstate <- taxon_state$new(class = "natservid", names = sci_com) @@ -266,7 +270,10 @@ check_natservid <- function(x){ get_natservid_ <- function(sci_com, searchtype = "scientific", messages = TRUE, rows = NA, query = NULL, ...) { - pchk(query, "sci_com") + if (!is.null(query)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "get_natservid_(query)", with = "get_natservid_(sci_com)") + sci_com <- query + } stats::setNames( lapply(sci_com, get_natservid_help, searchtype = searchtype, messages = messages, rows = rows, ...), diff --git a/R/get_nbnid.R b/R/get_nbnid.R index 6dc3b94f..a9d6f8d3 100644 --- a/R/get_nbnid.R +++ b/R/get_nbnid.R @@ -93,8 +93,11 @@ get_nbnid <- function(sci_com, ask = TRUE, messages = TRUE, rec_only = FALSE, assert(rank, "character") assert(messages, "logical") assert_rows(rows) - pchk(name, "sci_com") - + if (!is.null(name)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "get_nbnid(name)", with = "get_nbnid(sci_com)") + sci_com <- name + } + if (inherits(sci_com, "character")) { tstate <- taxon_state$new(class = "nbnid", names = sci_com) items <- sci_com @@ -283,7 +286,10 @@ check_nbnid <- function(x){ #' @rdname get_nbnid get_nbnid_ <- function(sci_com, messages = TRUE, rec_only = FALSE, rank = NULL, rows = NA, name = NULL, ...) { - pchk(name, "sci_com") + if (!is.null(name)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "get_nbnid_(name)", with = "get_nbnid_(sci_com)") + sci_com <- name + } stats::setNames(lapply(sci_com, get_nbnid_help, messages = messages, rec_only = rec_only, rank = rank, rows = rows, ...), sci_com) } diff --git a/R/get_pow.R b/R/get_pow.R index dd9dbb57..7495e5a1 100644 --- a/R/get_pow.R +++ b/R/get_pow.R @@ -104,8 +104,11 @@ get_pow <- function(sci_com, accepted = FALSE, ask = TRUE, messages = TRUE, assert(family_filter, "character") assert(rank_filter, "character") assert_rows(rows) - pchk(x, "sci_com") - + if (!is.null(x)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "get_pow(x)", with = "get_pow(sci_com)") + sci_com <- x + } + if (inherits(sci_com, "character")) { tstate <- taxon_state$new(class = "pow", names = sci_com) items <- sci_com @@ -286,7 +289,11 @@ check_pow <- function(x){ #' @export #' @rdname get_pow get_pow_ <- function(sci_com, messages = TRUE, rows = NA, x = NULL, ...) { - pchk(x, "sci_com") + if (!is.null(x)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "get_pow_(x)", with = "get_pow_(sci_com)") + sci_com <- x + } + stats::setNames(lapply(sci_com, get_pow_help, messages = messages, rows = rows, ...), sci_com) } diff --git a/R/get_tolid.R b/R/get_tolid.R index 0855672c..8b5850c6 100644 --- a/R/get_tolid.R +++ b/R/get_tolid.R @@ -73,7 +73,11 @@ get_tolid <- function(sci, ask = TRUE, messages = TRUE, rows = NA, assert(sci, c("character", "taxon_state")) assert(ask, "logical") assert(messages, "logical") - pchk(sciname, "sci") + if (!is.null(sciname)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "get_tolid(sciname)", with = "get_tolid(sci)") + sci <- sciname + } + if (!all(is.na(rows))) { assert(rows, c("numeric", "integer")) stopifnot(rows > 0) @@ -254,7 +258,10 @@ check_tolid <- function(x){ #' @export #' @rdname get_tolid get_tolid_ <- function(sci, messages = TRUE, rows = NA, sciname = NULL) { - pchk(sciname, "sci") + if (!is.null(sciname)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "get_tolid_(sciname)", with = "get_tolid_(sci)") + sci <- sciname + } stats::setNames( lapply(sci, get_tolid_help, messages = messages, rows = rows), sci diff --git a/R/get_tpsid.R b/R/get_tpsid.R index 2fc1525f..d037108a 100644 --- a/R/get_tpsid.R +++ b/R/get_tpsid.R @@ -106,11 +106,14 @@ get_tpsid <- function(sci, ask = TRUE, messages = TRUE, key = NULL, assert(sci, c("character", "taxon_state")) assert(ask, "logical") - assert(messages, "logical") assert(family, "character") assert(rank, "character") assert_rows(rows) - pchk(sciname, "sci") + if (!is.null(sciname)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "get_tpsid(sciname)", with = "get_tpsid(sci)") + sci <- sciname + } + if (inherits(sci, "character")) { tstate <- taxon_state$new(class = "tpsid", names = sci) @@ -283,7 +286,10 @@ check_tpsid <- function(x){ get_tpsid_ <- function(sci, messages = TRUE, key = NULL, rows = NA, sciname = NULL, ...) { - pchk(sciname, "sci") + if (!is.null(sciname)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "get_tpsid_(sciname)", with = "get_tpsid_(sci)") + sci <- sciname + } stats::setNames(lapply(sci, get_tpsid_help, messages = messages, key=key, rows = rows, ...), sci) } diff --git a/R/get_tsn.R b/R/get_tsn.R index 2a4fec85..5e111299 100644 --- a/R/get_tsn.R +++ b/R/get_tsn.R @@ -83,7 +83,11 @@ get_tsn <- function(sci_com, searchtype = "scientific", accepted = FALSE, assert(searchtype, "character") assert(accepted, "logical") assert_rows(rows) - pchk(searchterm, "sci_com") + if (!is.null(searchterm)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "get_tsn(searchterm)", with = "get_tsn(sci_com)") + sci_com <- searchterm + } + if (inherits(sci_com, "character")) { tstate <- taxon_state$new(class = "tsn", names = sci_com) @@ -269,7 +273,11 @@ check_tsn <- function(x){ #' @rdname get_tsn get_tsn_ <- function(sci_com, messages = TRUE, searchtype = "scientific", accepted = TRUE, rows = NA, searchterm = NULL, ...) { - pchk(searchterm, "sci_com") + if (!is.null(searchterm)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "get_tsn_(searchterm)", with = "get_tsn_(sci_com)") + sci_com <- searchterm + } + stats::setNames( lapply(sci_com, get_tsn_help, messages = messages, searchtype = searchtype, accepted = accepted, rows = rows, ...), diff --git a/R/get_uid.R b/R/get_uid.R index dbbcc227..ef25a8e4 100644 --- a/R/get_uid.R +++ b/R/get_uid.R @@ -174,7 +174,11 @@ get_uid <- function(sci_com, ask = TRUE, messages = TRUE, rows = NA, assert(rank_filter, "character") assert_rows(rows) key <- getkey(key, service = "entrez") - pchk(sciname, "sci_com") + if (!is.null(sciname)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "get_uid(sciname)", with = "get_uid(sci_com)") + sci_com <- sciname + } + if (inherits(sci_com, "character")) { tstate <- taxon_state$new(class = "uid", names = sci_com) @@ -406,7 +410,11 @@ get_uid_ <- function(sci_com, messages = TRUE, rows = NA, key = NULL, sciname = NULL, ...) { key <- getkey(key, "ENTREZ_KEY") - pchk(sciname, "sci_com") + if (!is.null(sciname)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "get_uid_(sciname)", with = "get_uid_(sci_com)") + sci_com <- sciname + } + stats::setNames(lapply(sci_com, get_uid_help, messages = messages, rows = rows, key = key, ...), sci_com) } diff --git a/R/get_wiki.R b/R/get_wiki.R index 9dc4eb05..3d07391f 100644 --- a/R/get_wiki.R +++ b/R/get_wiki.R @@ -56,7 +56,11 @@ get_wiki <- function(sci_com, wiki_site = "species", wiki = "en", ask = TRUE, assert(wiki, "character") assert(messages, "logical") assert_rows(rows) - pchk(x, "sci_com") + if (!is.null(x)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "get_wiki(x)", with = "get_wiki(sci_com)") + sci_com <- x + } + if (inherits(sci_com, "character")) { tstate <- taxon_state$new(class = "wiki", names = sci_com) diff --git a/R/get_wormsid.R b/R/get_wormsid.R index 40553c4b..a95cfa34 100644 --- a/R/get_wormsid.R +++ b/R/get_wormsid.R @@ -115,9 +115,12 @@ get_wormsid <- function(sci_com, searchtype = "scientific", marine_only = TRUE, assert(fuzzy, "logical") assert(accepted, "logical") assert(ask, "logical") - assert(messages, "logical") assert_rows(rows) - pchk(query, "sci_com") + if (!is.null(query)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "get_wormsid(query)", with = "get_wormsid(sci_com)") + sci_com <- query + } + if (inherits(sci_com, "character")) { tstate <- taxon_state$new(class = "wormsid", names = sci_com) @@ -318,7 +321,10 @@ get_wormsid_ <- function(sci_com, messages = TRUE, searchtype = "scientific", marine_only = TRUE, fuzzy = NULL, accepted = TRUE, rows = NA, query = NULL, ...) { - pchk(query, "sci_com") + if (!is.null(query)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "get_wormsid_(query)", with = "get_wormsid_(sci_com)") + sci_com <- query + } stats::setNames( lapply(sci_com, get_wormsid_help, messages = messages, searchtype = searchtype, marine_only = marine_only, fuzzy = fuzzy, diff --git a/R/gni_search.R b/R/gni_search.R index 4243aae8..adf0b1bd 100644 --- a/R/gni_search.R +++ b/R/gni_search.R @@ -52,7 +52,11 @@ gni_search <- function(sci, per_page = NULL, page = NULL, justtotal = FALSE, parse_names = FALSE, search_term = NULL, ...) { - pchk(search_term, "sci") + if (!is.null(search_term)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "gni_search(search_term)", with = "gni_search(sci)") + sci <- search_term + } + query <- tc(list(search_term = sci, per_page = per_page, page = page)) cli <- crul::HttpClient$new(paste0(gni_base(), "name_strings.json"), diff --git a/R/gnr_resolve.R b/R/gnr_resolve.R index a465fdf6..1a1e7b47 100644 --- a/R/gnr_resolve.R +++ b/R/gnr_resolve.R @@ -131,7 +131,11 @@ gnr_resolve <- function(sci, data_source_ids = NULL, resolve_once = FALSE, with_canonical_ranks = FALSE, http = "get", cap_first = TRUE, fields = "minimal", names = NULL, ...) { - pchk(names, "sci") + if (!is.null(names)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "gnr_resolve(names)", with = "gnr_resolve(sci)") + sci <- names + } + if (!is.null(names)) sci <- names fields <- match.arg(fields, c("minimal", "all")) http <- match.arg(http, c("get", "post")) diff --git a/R/id2name.R b/R/id2name.R index f3adec18..ea2ca72b 100644 --- a/R/id2name.R +++ b/R/id2name.R @@ -50,7 +50,11 @@ id2name <- function(id, db = NULL, x = NULL, ...) UseMethod("id2name") #' @rdname id2name id2name.default <- function(id, db = NULL, x = NULL, ...) { nstop(db) - pchk(x, "sci") + if (!is.null(x)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "id2name(x)", with = "id2name(sci)") + sci <- x + } + if (!is.null(x)) id <- x if (!db %in% id2name_sources) { stop("'db' must be one of ", paste(id2name_sources, collapse = ", ")) diff --git a/R/iplant_resolve.R b/R/iplant_resolve.R index 0e57894a..eadd87b0 100644 --- a/R/iplant_resolve.R +++ b/R/iplant_resolve.R @@ -15,8 +15,11 @@ #' iplant_resolve("Helianthusss", verbose = TRUE) #' } iplant_resolve <- function(sci, retrieve='all', query = NULL, ...) { - pchk(query, "sci") - if (!is.null(query)) sci <- query + if (!is.null(query)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "iplant_resolve(query)", with = "iplant_resolve(sci)") + sci <- query + } + url <- "http://tnrs.iplantc.org/tnrsm-svc/matchNames" sci <- paste(sci, collapse = ",") args <- tc(list(names = sci, retrieve = retrieve)) diff --git a/R/itis_downstream.R b/R/itis_downstream.R index f8a3d300..577da767 100644 --- a/R/itis_downstream.R +++ b/R/itis_downstream.R @@ -39,7 +39,11 @@ itis_downstream <- function(id, downto, intermediate = FALSE, tsns = NULL, ...) { - pchk(tsns, "id") + if (!is.null(tsns)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "itis_downstream(tsns)", with = "itis_downstream(id)") + id <- tsns + } + if (!is.null(tsns)) id <- tsns downto <- tolower(downto) downto2 <- taxize_ds$rank_ref[which_rank(downto), "rankid"] diff --git a/R/lowest_common.R b/R/lowest_common.R index c078e757..33bf1b01 100644 --- a/R/lowest_common.R +++ b/R/lowest_common.R @@ -110,7 +110,11 @@ lowest_common.default <- function(sci_id, db = NULL, rows = NA, class_list = NUL low_rank = NULL, x = NULL, ...) { if (is.null(db)) if (!is.null(class_list)) db <- attr(class_list, "db") nstop(db) - pchk(x, "sci_id") + if (!is.null(x)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "lowest_common(x)", with = "lowest_common(sci_id)") + sci_id <- x + } + if (!is.null(x)) sci_id <- x switch( db, diff --git a/R/nbn_search.R b/R/nbn_search.R index d1c34e16..368bdf5a 100644 --- a/R/nbn_search.R +++ b/R/nbn_search.R @@ -36,7 +36,11 @@ nbn_search <- function(sci_com, fq = NULL, order = NULL, sort = NULL, start = 0, rows = 25, facets = NULL, q = NULL, ...) { - pchk(q, "sci_com") + if (!is.null(q)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "nbn_search(q)", with = "nbn_search(sci_com)") + sci_com <- q + } + args <- tc(list( q = sci_com, fq = fq, pageSize = rows, startIndex = start, sort = sort, dir = order, facets = facets diff --git a/R/pow_search.R b/R/pow_search.R index bb909ffb..1c3003b8 100644 --- a/R/pow_search.R +++ b/R/pow_search.R @@ -42,7 +42,11 @@ pow_search <- function(sci_com, limit = 100, cursor = "*", sort = NULL, assert(limit, c("integer", "numeric")) assert(cursor, "character") assert(sort, "character") - pchk(q, "sci_com") + if (!is.null(q)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "pow_search(q)", with = "pow_search(sci_com)") + sci_com <- q + } + args <- tc(list(q = sci_com, perPage = limit, cursor = cursor, sort = sort)) pow_GET(file.path(pow_base(), "api/2", "search"), args, ...) } diff --git a/R/resolve.R b/R/resolve.R index a739417d..dd11aa80 100644 --- a/R/resolve.R +++ b/R/resolve.R @@ -36,7 +36,11 @@ #' resolve(sci="Qercuss", db = "iplant", verbose = TRUE) #' } resolve <- function(sci, db = 'gnr', query = NULL, ...) { - pchk(query, "sci") + if (!is.null(query)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "resolve(query)", with = "resolve(sci)") + sci <- query + } + if (!is.null(query)) sci <- query db <- match.arg(db, choices = c('iplant', 'gnr'), several.ok = TRUE) diff --git a/R/sci2comm.R b/R/sci2comm.R index a5b5a739..b660b60a 100644 --- a/R/sci2comm.R +++ b/R/sci2comm.R @@ -64,8 +64,11 @@ sci2comm <- function(...){ sci2comm.default <- function(sci, db='ncbi', simplify=TRUE, scinames = NULL, ...) { - pchk(scinames, "sci") - if (!is.null(scinames)) sci <- scinames + if (!is.null(scinames)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "sci2comm(scinames)", with = "sci2comm(sci)") + sci <- scinames + } + temp <- lapply(sci, getsci, db = db, simplify = simplify, ...) stats::setNames(temp, sci) } diff --git a/R/synonyms.R b/R/synonyms.R index 1ab291ff..8d1b92e5 100644 --- a/R/synonyms.R +++ b/R/synonyms.R @@ -114,7 +114,10 @@ synonyms <- function(...) { #' @rdname synonyms synonyms.default <- function(sci_id, db = NULL, rows = NA, x = NULL, ...) { nstop(db) - pchk(x, "sci") + if (!is.null(x)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "synonyms(x)", with = "synonyms(sci_id)") + sci_id <- x + } if (!is.null(x)) sci_id <- x switch( db, diff --git a/R/tax_name.R b/R/tax_name.R index a6e9bf03..889dd772 100644 --- a/R/tax_name.R +++ b/R/tax_name.R @@ -53,8 +53,11 @@ tax_name <- function(sci, get, db = "itis", pref = 'ncbi', messages = TRUE, query = NULL, ...) { - pchk(query, "sci") - if (!is.null(query)) sci <- query + if (!is.null(query)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "tax_name(query)", with = "tax_name(sci)") + sci <- query + } + if (missing(get)) stop("you must supply a 'get' value", call. = FALSE) db <- match.arg(db, c('itis', 'ncbi', 'both')) if (db == 'both' && !pref %in% c('ncbi', 'itis')) { diff --git a/R/tax_rank.R b/R/tax_rank.R index 24ce0949..645d0130 100644 --- a/R/tax_rank.R +++ b/R/tax_rank.R @@ -51,8 +51,11 @@ tax_rank.default <- function(sci_id, db = NULL, rows = NA, x = NULL, ...) { tax_rank.character <- function(sci_id, db = NULL, rows = NA, x = NULL, ...) { nstop(db) stopifnot(length(db) == 1) - pchk(x, "sci_id") - if (!is.null(x)) sci_id <- x + if (!is.null(x)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "tax_rank(x)", with = "tax_rank(sci_id)") + sci_id <- x + } + switch( db, bold = stats::setNames(tax_rank_(process_ids(sci_id, db, get_boldid, diff --git a/R/taxize-package.R b/R/taxize-package.R index fe04b965..9134f777 100644 --- a/R/taxize-package.R +++ b/R/taxize-package.R @@ -72,7 +72,6 @@ #' @importFrom R6 R6Class #' @importFrom crayon style #' @importFrom cli symbol cat_line rule -#' @importFrom conditionz ConditionKeeper #' @name taxize-package #' @aliases taxize #' @docType package diff --git a/R/tp_search.R b/R/tp_search.R index 7fffb207..5d367b90 100644 --- a/R/tp_search.R +++ b/R/tp_search.R @@ -33,10 +33,16 @@ tp_search <- function(sci=NULL, com=NULL, nameid=NULL, orderby=NULL, sortorder=NULL, pagesize=NULL, startrow=NULL, type=NULL, key=NULL, name=NULL, commonname=NULL, ...) { - pchk(name, "sci") - pchk(commonname, "com") - if (!is.null(name)) sci <- name - if (!is.null(commonname)) com <- commonname + if (!is.null(name)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "tp_search(name)", with = "tp_search(sci)") + sci <- name + } + if (!is.null(commonname)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "tp_search(commonname)", with = "tp_search(com)") + com <- commonname + } + + url = 'http://services.tropicos.org/Name/Search' key <- getkey(key, "TROPICOS_KEY") if (!is.null(sci)) { diff --git a/R/upstream.R b/R/upstream.R index 96eb9c92..122471ab 100644 --- a/R/upstream.R +++ b/R/upstream.R @@ -43,8 +43,11 @@ upstream.default <- function(sci_id, db = NULL, upto = NULL, rows = NA, nstop(upto, "upto") nstop(db) - pchk(x, "sci_id") - if (!is.null(x)) sci_id <- x + if (!is.null(x)) { + lifecycle::deprecate_warn(when = "v0.9.97", what = "upstream(x)", with = "upstream(sci_id)") + sci_id <- x + } + switch( db, itis = { diff --git a/R/zzz.R b/R/zzz.R index f5bacc91..95ae1e0d 100644 --- a/R/zzz.R +++ b/R/zzz.R @@ -286,24 +286,3 @@ ncbi_rate_limit_pause <- function(key) { } } -# foo <- function(x) { -# deparse(substitute(x)) -# } -# bar <- function(z) { -# foo(z) -# } -# bar(z = "adf") -taxize_ck <- conditionz::ConditionKeeper$new(times = 1, condition = "warning") -pchk <- function(from, to, pkg_version = "v0.9.97") { - assert(deparse(substitute(from)), "character") - assert(to, "character") - assert(pkg_version, "character") - # & will be removed in a future version - param_mssg <- "`%s` param is deprecated as of taxize %s, use `%s` instead." - parms_help <- "\nSee `?taxize-params` for more information." - once_per <- "\nThis warning will be thrown once per R session." - mssg <- c(sprintf(param_mssg, deparse(substitute(from)), pkg_version, to), - parms_help, once_per) - if (!is.null(from)) - taxize_ck$handle_conditions(warning(mssg)) -} diff --git a/codemeta.json b/codemeta.json index 29553e4c..90fde208 100644 --- a/codemeta.json +++ b/codemeta.json @@ -14,7 +14,7 @@ "name": "R", "url": "https://r-project.org" }, - "runtimePlatform": "R version 4.1.2 (2021-11-01)", + "runtimePlatform": "R version 4.2.2 Patched (2022-11-10 r83330)", "provider": { "@id": "https://cran.r-project.org", "@type": "Organization", @@ -426,22 +426,22 @@ }, "25": { "@type": "SoftwareApplication", - "identifier": "conditionz", - "name": "conditionz", + "identifier": "lifecycle", + "name": "lifecycle", "provider": { "@id": "https://cran.r-project.org", "@type": "Organization", "name": "Comprehensive R Archive Network (CRAN)", "url": "https://cran.r-project.org" }, - "sameAs": "https://CRAN.R-project.org/package=conditionz" + "sameAs": "https://CRAN.R-project.org/package=lifecycle" }, "SystemRequirements": null }, "applicationCategory": "Taxonomy", "isPartOf": "https://ropensci.org", "keywords": ["taxonomy", "biology", "nomenclature", "JSON", "API", "web", "api-client", "identifiers", "species", "names", "data", "api", "biodiversity", "rstats", "darwincore", "taxize", "api-wrapper", "r", "r-package"], - "fileSize": "11363.214KB", + "fileSize": "11368.156KB", "citation": [ { "@type": "ScholarlyArticle", @@ -559,6 +559,6 @@ ], "releaseNotes": "https://github.com/ropensci/taxize/blob/master/NEWS.md", "readme": "https://github.com/ropensci/taxize/blob/master/README.md", - "contIntegration": ["https://github.com/ropensci/taxize/actions/", "https://codecov.io/gh/ropensci/taxize"], + "contIntegration": ["https://github.com/ropensci/taxize/actions/", "https://app.codecov.io/gh/ropensci/taxize"], "developmentStatus": "https://www.repostatus.org/#active" } diff --git a/tests/fixtures/children_no_results_structure_ncbi_x.yml b/tests/fixtures/children_no_results_structure_ncbi_x.yml index 50420dcc..92dfcc38 100644 --- a/tests/fixtures/children_no_results_structure_ncbi_x.yml +++ b/tests/fixtures/children_no_results_structure_ncbi_x.yml @@ -6,9 +6,10 @@ http_interactions: encoding: '' string: '' headers: - User-Agent: libcurl/7.54.0 r-curl/3.3 crul/0.7.0.9100 Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -16,29 +17,31 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 29 Jan 2019 19:50:48 GMT + date: Thu, 09 Mar 2023 21:23:42 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '8' - ncbi-phid: 939B131039D6F975000026C382A243BD.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: 099C7BF95B0D3C90_3E50SID + ncbi-phid: 322C2D2E52F0459500002DD44E4F57A0.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - l5d-success-class: '1.0' - ncbi-sid: 7770C5D297EE2A63_A310SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '9' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=7770C5D297EE2A63_A310SID; domain=.nih.gov; path=/; expires=Wed, - 29 Jan 2020 19:50:49 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=099C7BF95B0D3C90_3E50SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:23:43 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' + file: no string: | 000(23424234234[All Names])23424234234No items found. - recorded_at: 2019-01-29 19:50:47 GMT - recorded_with: vcr/0.2.2, webmockr/0.3.0 + recorded_at: 2023-03-09 21:23:43 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 diff --git a/tests/fixtures/children_warn_on_db_mismatch.yml b/tests/fixtures/children_warn_on_db_mismatch.yml index 9bf51ec2..fa0d9fb3 100644 --- a/tests/fixtures/children_warn_on_db_mismatch.yml +++ b/tests/fixtures/children_warn_on_db_mismatch.yml @@ -8,8 +8,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.92) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.92) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -17,25 +17,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Fri, 06 Mar 2020 16:42:27 GMT + date: Thu, 09 Mar 2023 21:23:44 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '9' - ncbi-phid: 939B6CBF14E4C84500002DB7B1A2DD86.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: 4411ECD8DA923CC5_F6B3SID + ncbi-phid: 322C2D2E52F0459500005CD458452038.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 997E676B85280B92_DCA0SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '9' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=997E676B85280B92_DCA0SID; domain=.nih.gov; path=/; expires=Sat, - 06 Mar 2021 16:42:27 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=4411ECD8DA923CC5_F6B3SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:23:45 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -43,8 +45,8 @@ http_interactions: 110 315576 Chironomus+riparius[All Names] All Names 1 N GROUP Chironomus+riparius[All Names] - recorded_at: 2020-03-06 16:42:28 GMT - recorded_with: vcr/0.5.0, webmockr/0.6.0 + recorded_at: 2023-03-09 21:23:47 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&ID=315576&api_key=<> @@ -52,7 +54,7 @@ http_interactions: encoding: '' string: '' headers: - User-Agent: libcurl/7.54.0 r-curl/4.3 crul/0.9.0 + User-Agent: libcurl/7.81.0 r-curl/4.3.3 crul/1.3 Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* response: @@ -62,25 +64,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Fri, 06 Mar 2020 16:42:27 GMT + date: Thu, 09 Mar 2023 21:23:45 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '8' - ncbi-phid: 939B6CBF14E4C84500003EB7B2F26F75.1.1.m_3 + referrer-policy: origin-when-cross-origin + ncbi-sid: CED34A3432AFD9B1_2DA0SID + ncbi-phid: 322C2D2E52F0459500004DD45BA99C7C.1.1.m_5 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: CBAD0795B323D535_30CCSID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=CBAD0795B323D535_30CCSID; domain=.nih.gov; path=/; expires=Sat, - 06 Mar 2021 16:42:28 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=CED34A3432AFD9B1_2DA0SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:23:46 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: |- @@ -88,6 +92,12 @@ http_interactions: 315576 Chironomus riparius + + + authority + Chironomus riparius Meigen, 1804 + + 1165752 species Invertebrates @@ -99,7 +109,7 @@ http_interactions: 5 Invertebrate Mitochondrial - cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Diptera; Nematocera; Culicomorpha; Chironomoidea; Chironomidae; Chironominae; Chironomini; Chironomus; Chironomus incertae sedis + cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Culicomorpha; Chironomoidea; Chironomidae; Chironominae; Chironomini; Chironomus; Chironomus incertae sedis 131567 @@ -114,7 +124,7 @@ http_interactions: 33154 Opisthokonta - no rank + clade 33208 @@ -124,27 +134,27 @@ http_interactions: 6072 Eumetazoa - no rank + clade 33213 Bilateria - no rank + clade 33317 Protostomia - no rank + clade 1206794 Ecdysozoa - no rank + clade 88770 Panarthropoda - no rank + clade 6656 @@ -154,12 +164,12 @@ http_interactions: 197563 Mandibulata - no rank + clade 197562 Pancrustacea - no rank + clade 6960 @@ -174,7 +184,7 @@ http_interactions: 85512 Dicondylia - no rank + clade 7496 @@ -188,7 +198,7 @@ http_interactions: 33392 - Holometabola + Endopterygota cohort @@ -243,8 +253,8 @@ http_interactions: - recorded_at: 2020-03-06 16:42:28 GMT - recorded_with: vcr/0.5.0, webmockr/0.6.0 + recorded_at: 2023-03-09 21:23:47 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Chironomus%20riparius%5BNext%20Level%5D%20AND%20Chironomus%20incertae%20sedis%5Bsubtree%5D&RetMax=1000&RetStart=0&api_key=<> @@ -254,8 +264,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.92) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.92) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -263,29 +273,31 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Fri, 06 Mar 2020 16:42:28 GMT + date: Thu, 09 Mar 2023 21:23:46 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '8' - ncbi-phid: 939B6CBF14E4C84500005EB7B3AA7FAE.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: 14CB22FE87ED67F9_2701SID + ncbi-phid: 322C2D2E52F0459500003CD45EEF12AF.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: E99BAE18B4652C89_66CASID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=E99BAE18B4652C89_66CASID; domain=.nih.gov; path=/; expires=Sat, - 06 Mar 2021 16:42:28 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=14CB22FE87ED67F9_2701SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:23:46 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | 000Chironomus riparius[Next Level] AND Chironomus incertae sedis[subtree]Chironomus riparius[Next Level]No items found. - recorded_at: 2020-03-06 16:42:28 GMT - recorded_with: vcr/0.5.0, webmockr/0.6.0 + recorded_at: 2023-03-09 21:23:47 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 diff --git a/tests/fixtures/class2tree_classification_call.yml b/tests/fixtures/class2tree_classification_call.yml index 33c83901..ef0eee6b 100644 --- a/tests/fixtures/class2tree_classification_call.yml +++ b/tests/fixtures/class2tree_classification_call.yml @@ -8,8 +8,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -17,25 +17,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:15:09 GMT + date: Thu, 09 Mar 2023 21:24:04 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '9' - ncbi-phid: 322C7ECC5D85ECB500003349CF942D1C.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: 3F9E7D833862D6F6_DD26SID + ncbi-phid: 939B640887F4D8E500005400B24D08DE.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 7826E6290826BD04_FBFASID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=7826E6290826BD04_FBFASID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:15:09 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=3F9E7D833862D6F6_DD26SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:05 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -43,8 +45,8 @@ http_interactions: 110 152733 Klattia+flava[All Names] All Names 1 N GROUP Klattia+flava[All Names] - recorded_at: 2020-05-05 00:15:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:20 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Trollius%2Bsibiricus&api_key=<> @@ -54,8 +56,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -63,25 +65,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:15:09 GMT + date: Thu, 09 Mar 2023 21:24:05 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '8' - ncbi-phid: 322C7ECC5D85ECB500003F49D01C47C0.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: 3DE81F381B164D9A_913ESID + ncbi-phid: 939B640887F4D8E500005100B4E87F3D.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 5EBD1AA1453DB058_A908SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=5EBD1AA1453DB058_A908SID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:15:10 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=3DE81F381B164D9A_913ESID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:06 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -89,8 +93,8 @@ http_interactions: 110 944286 Trollius+sibiricus[All Names] All Names 1 N GROUP Trollius+sibiricus[All Names] - recorded_at: 2020-05-05 00:15:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:20 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Arachis%2Bparaguariensis&api_key=<> @@ -100,8 +104,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -109,25 +113,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:15:10 GMT + date: Thu, 09 Mar 2023 21:24:07 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '7' - ncbi-phid: 322C7ECC5D85ECB500002049D084A581.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: 0178A90DD02F9A25_987ASID + ncbi-phid: 939B640887F4D8E500004200B78B840F.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 2633ADA65D2DF29D_DCFASID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '9' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=2633ADA65D2DF29D_DCFASID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:15:10 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=0178A90DD02F9A25_987ASID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:07 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -135,8 +141,8 @@ http_interactions: 110 224337 Arachis+paraguariensis[All Names] All Names 1 N GROUP Arachis+paraguariensis[All Names] - recorded_at: 2020-05-05 00:15:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:20 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Tanacetum%2Bboreale&api_key=<> @@ -146,8 +152,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -155,25 +161,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:15:10 GMT + date: Thu, 09 Mar 2023 21:24:07 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 322C7ECC5D85ECB500004B49D0EBB496.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: D08A9C3321BFCC45_511ASID + ncbi-phid: 939B640887F4D8E500003800BA25829B.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 37ABB3878133CC96_5B3FSID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '9' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=37ABB3878133CC96_5B3FSID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:15:10 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=D08A9C3321BFCC45_511ASID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:08 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -181,8 +189,8 @@ http_interactions: 110 128002 Tanacetum+boreale[All Names] All Names 1 N GROUP Tanacetum+boreale[All Names] - recorded_at: 2020-05-05 00:15:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:20 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Gentiana%2Byakushimensis&api_key=<> @@ -192,8 +200,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -201,25 +209,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:15:10 GMT + date: Thu, 09 Mar 2023 21:24:08 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 322C7ECC5D85ECB500001449D15669B9.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: 5494CC94403F0EA4_0B61SID + ncbi-phid: 939B640887F4D8E500003E00BB9954D4.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 4878D33BCFC583E6_C37BSID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=4878D33BCFC583E6_C37BSID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:15:11 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=5494CC94403F0EA4_0B61SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:09 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -227,8 +237,8 @@ http_interactions: 110 553063 Gentiana+yakushimensis[All Names] All Names 1 N GROUP Gentiana+yakushimensis[All Names] - recorded_at: 2020-05-05 00:15:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:20 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Sesamum%2Bschinzianum&api_key=<> @@ -238,8 +248,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -247,25 +257,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:15:10 GMT + date: Thu, 09 Mar 2023 21:24:09 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 322C7ECC5D85ECB500002B49D1ADA5AA.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: 11446A439D4A17A5_7496SID + ncbi-phid: 939B640887F4D8E500002700BD97B983.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 0005551744197F8E_544ESID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=0005551744197F8E_544ESID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:15:11 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=11446A439D4A17A5_7496SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:09 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -273,8 +285,8 @@ http_interactions: 110 768545 Sesamum+schinzianum[All Names] All Names 1 N GROUP Sesamum+schinzianum[All Names] - recorded_at: 2020-05-05 00:15:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:20 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Pilea%2Bverrucosa&api_key=<> @@ -284,8 +296,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -293,25 +305,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:15:10 GMT + date: Thu, 09 Mar 2023 21:24:10 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 322C7ECC5D85ECB500004849D2123E23.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: C4436A4A082F6542_6536SID + ncbi-phid: D0BD29F778F3A205000030FA2A2659F5.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: A67100960CB69D26_E012SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=A67100960CB69D26_E012SID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:15:11 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=C4436A4A082F6542_6536SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:10 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -319,8 +333,8 @@ http_interactions: 110 1399730 Pilea+verrucosa[All Names] All Names 1 N GROUP Pilea+verrucosa[All Names] - recorded_at: 2020-05-05 00:15:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:20 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Tibouchina%2Bstriphnocalyx&api_key=<> @@ -330,8 +344,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -339,25 +353,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:15:11 GMT + date: Thu, 09 Mar 2023 21:24:10 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 322C7ECC5D85ECB500005449D26A615B.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: 80FF91ED90D2E294_8809SID + ncbi-phid: D0BD29F778F3A20500004CFA2C5D7F38.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 6DD9B4069D8B7176_2066SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=6DD9B4069D8B7176_2066SID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:15:11 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=80FF91ED90D2E294_8809SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:11 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -365,8 +381,8 @@ http_interactions: 110 1160690 Tibouchina+striphnocalyx[All Names] All Names 1 N GROUP Tibouchina+striphnocalyx[All Names] - recorded_at: 2020-05-05 00:15:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:20 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Lycium%2Bdasystemum&api_key=<> @@ -376,8 +392,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -385,25 +401,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:15:11 GMT + date: Thu, 09 Mar 2023 21:24:10 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 322C7ECC5D85ECB500003549D2CC1495.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: 3F8CA4E80BB0A3AE_9729SID + ncbi-phid: D0BD29F778F3A205000035FA2EAB6D3A.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 3BF57BCE57E412F8_1724SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=3BF57BCE57E412F8_1724SID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:15:12 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=3F8CA4E80BB0A3AE_9729SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:11 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -411,8 +429,8 @@ http_interactions: 110 942185 Lycium+dasystemum[All Names] All Names 1 N GROUP Lycium+dasystemum[All Names] - recorded_at: 2020-05-05 00:15:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:20 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Berkheya%2Bechinacea&api_key=<> @@ -422,8 +440,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -431,25 +449,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:15:12 GMT + date: Thu, 09 Mar 2023 21:24:12 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 322C7ECC5D85ECB500004849D332A8D5.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: DB5D199D54E283AF_760BSID + ncbi-phid: D0BD29F778F3A20500004CFA309C78AB.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 19A1E6C305F6A0AF_5439SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=19A1E6C305F6A0AF_5439SID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:15:12 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=DB5D199D54E283AF_760BSID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:12 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -457,8 +477,8 @@ http_interactions: 110 527996 Berkheya+echinacea[All Names] All Names 1 N GROUP Berkheya+echinacea[All Names] - recorded_at: 2020-05-05 00:15:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:20 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Androcymbium%2Bvillosum&api_key=<> @@ -468,8 +488,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -477,25 +497,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:15:12 GMT + date: Thu, 09 Mar 2023 21:24:12 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 322C7ECC5D85ECB500004849D3A6199A.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: 0E20449612D800EF_943CSID + ncbi-phid: D0BD29F778F3A20500005DFA32B56516.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: A80611092FFCAD04_E2B5SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=A80611092FFCAD04_E2B5SID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:15:12 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=0E20449612D800EF_943CSID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:13 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -503,8 +525,8 @@ http_interactions: 110 279457 Androcymbium+villosum[All Names] All Names 1 N GROUP Androcymbium+villosum[All Names] - recorded_at: 2020-05-05 00:15:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:20 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Helianthus%2Bannuus&api_key=<> @@ -514,8 +536,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -523,25 +545,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:15:12 GMT + date: Thu, 09 Mar 2023 21:24:13 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 322C7ECC5D85ECB500004B49D3F8898A.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: F41CB39A4905538B_F957SID + ncbi-phid: D0BD29F778F3A205000047FA351153D1.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: DAD369ED4B6ED94E_4A13SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=DAD369ED4B6ED94E_4A13SID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:15:12 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=F41CB39A4905538B_F957SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:14 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -549,8 +573,8 @@ http_interactions: 110 4232 Helianthus+annuus[All Names] All Names 1 N GROUP Helianthus+annuus[All Names] - recorded_at: 2020-05-05 00:15:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:20 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Madia%2Belegans&api_key=<> @@ -560,8 +584,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -569,25 +593,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:15:13 GMT + date: Thu, 09 Mar 2023 21:24:14 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 939B0CD3340CCB750000215B6F47EFFD.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: A375846A682C0C76_C7ECSID + ncbi-phid: D0BD29F778F3A205000057FA387DB46A.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 4111DDA58B8532D3_91B9SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=4111DDA58B8532D3_91B9SID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:15:13 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=A375846A682C0C76_C7ECSID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:14 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -595,8 +621,8 @@ http_interactions: 110 4255 Madia+elegans[All Names] All Names 1 N GROUP Madia+elegans[All Names] - recorded_at: 2020-05-05 00:15:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:20 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Lupinus%2Balbicaulis&api_key=<> @@ -606,8 +632,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -615,25 +641,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:15:13 GMT + date: Thu, 09 Mar 2023 21:24:14 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 939B0CD3340CCB750000525B6F67A1E7.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: F7ADEB7F0B1D0D1B_E39ESID + ncbi-phid: D0BD29F778F3A205000048FA3ABE52FB.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 10214F10FABFC944_A4B8SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=10214F10FABFC944_A4B8SID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:15:13 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=F7ADEB7F0B1D0D1B_E39ESID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:15 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -641,8 +669,8 @@ http_interactions: 110 377318 Lupinus+albicaulis[All Names] All Names 1 N GROUP Lupinus+albicaulis[All Names] - recorded_at: 2020-05-05 00:15:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:20 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Pinus%2Blambertiana&api_key=<> @@ -652,8 +680,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -661,25 +689,28 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:15:13 GMT + date: Thu, 09 Mar 2023 21:24:15 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 939B0CD3340CCB7500004B5B6F8E560C.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: A120AF42E0F54039_3D54SID + ncbi-phid: D0BD29F778F3A20500003CFA3D0E31E7.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 09874115786D48BC_2C81SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=09874115786D48BC_2C81SID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:15:13 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=A120AF42E0F54039_3D54SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:16 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block + connection: close transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -687,8 +718,8 @@ http_interactions: 110 3343 Pinus+lambertiana[All Names] All Names 1 N GROUP Pinus+lambertiana[All Names] - recorded_at: 2020-05-05 00:15:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:20 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Haloarcula%2Bamylolytica%2BJCM%2B13557&api_key=<> @@ -698,8 +729,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -707,25 +738,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:15:13 GMT + date: Thu, 09 Mar 2023 21:24:17 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 939B0CD3340CCB7500001C5B6FCA7B8E.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: E819E5D2F4B9B4AF_4AB7SID + ncbi-phid: D0BD29F778F3A205000035FA460297B2.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 0CEE370B0DECB22B_6EB0SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '9' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=0CEE370B0DECB22B_6EB0SID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:15:14 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=E819E5D2F4B9B4AF_4AB7SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:17 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -733,8 +766,8 @@ http_interactions: 110 1227452 Haloarcula+amylolytica+JCM+13557[All Names] All Names 1 N GROUP Haloarcula+amylolytica+JCM+13557[All Names] - recorded_at: 2020-05-05 00:15:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:20 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Halomonas%2Bsp.%2B%27Soap%2BLake%2B%236%27&api_key=<> @@ -744,8 +777,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -753,25 +786,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:15:13 GMT + date: Thu, 09 Mar 2023 21:24:18 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 939B0CD3340CCB750000535B7017DC27.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: 8945A5EFDE213F05_FE1ASID + ncbi-phid: D0BD29F778F3A20500005BFA4895A696.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 48695AF160DB2F4D_F167SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=48695AF160DB2F4D_F167SID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:15:14 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=8945A5EFDE213F05_FE1ASID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:18 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -779,8 +814,8 @@ http_interactions: 110 1949203 Halomonas+sp.+'Soap+Lake+#6'[All Names] All Names 1 N GROUP Halomonas+sp.+'Soap+Lake+#6'[All Names] - recorded_at: 2020-05-05 00:15:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:20 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&ID=152733%2C944286%2C224337%2C128002%2C553063%2C768545%2C1399730%2C1160690%2C942185%2C527996%2C279457%2C4232%2C4255%2C377318%2C3343%2C1227452%2C1949203&api_key=<> @@ -788,7 +823,7 @@ http_interactions: encoding: '' string: '' headers: - User-Agent: libcurl/7.64.1 r-curl/4.3 crul/0.9.0 + User-Agent: libcurl/7.81.0 r-curl/4.3.3 crul/1.3 Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* response: @@ -798,25 +833,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:15:14 GMT + date: Thu, 09 Mar 2023 21:24:19 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '7' - ncbi-phid: 939B0CD3340CCB7500003B5B7082BDF2.1.1.m_3 + referrer-policy: origin-when-cross-origin + ncbi-sid: FE583F53D68D7DC7_D8ACSID + ncbi-phid: D0BD29F778F3A20500005BFA4BB8AA30.1.1.m_5 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: ACE78F281549B13D_A087SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=ACE78F281549B13D_A087SID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:15:14 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=FE583F53D68D7DC7_D8ACSID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:19 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: |- @@ -871,22 +908,22 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 3398 @@ -896,12 +933,12 @@ http_interactions: 1437183 Mesangiospermae - no rank + clade 4447 Liliopsida - no rank + clade 1437197 @@ -989,22 +1026,22 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 3398 @@ -1014,7 +1051,7 @@ http_interactions: 1437183 Mesangiospermae - no rank + clade 41768 @@ -1110,22 +1147,22 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 3398 @@ -1135,32 +1172,32 @@ http_interactions: 1437183 Mesangiospermae - no rank + clade 71240 eudicotyledons - no rank + clade 91827 Gunneridae - no rank + clade 1437201 Pentapetalae - no rank + clade 71275 rosids - no rank + clade 91835 fabids - no rank + clade 72025 @@ -1180,12 +1217,12 @@ http_interactions: 2231393 50 kb inversion clade - no rank + clade 2231387 dalbergioids sensu lato - no rank + clade 163725 @@ -1195,7 +1232,7 @@ http_interactions: 2231390 Pterocarpus clade - no rank + clade 3817 @@ -1274,22 +1311,22 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 3398 @@ -1299,32 +1336,32 @@ http_interactions: 1437183 Mesangiospermae - no rank + clade 71240 eudicotyledons - no rank + clade 91827 Gunneridae - no rank + clade 1437201 Pentapetalae - no rank + clade 71274 asterids - no rank + clade 91882 campanulids - no rank + clade 4209 @@ -1417,22 +1454,22 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 3398 @@ -1442,32 +1479,32 @@ http_interactions: 1437183 Mesangiospermae - no rank + clade 71240 eudicotyledons - no rank + clade 91827 Gunneridae - no rank + clade 1437201 Pentapetalae - no rank + clade 71274 asterids - no rank + clade 91888 lamiids - no rank + clade 4055 @@ -1559,22 +1596,22 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 3398 @@ -1584,32 +1621,32 @@ http_interactions: 1437183 Mesangiospermae - no rank + clade 71240 eudicotyledons - no rank + clade 91827 Gunneridae - no rank + clade 1437201 Pentapetalae - no rank + clade 71274 asterids - no rank + clade 91888 lamiids - no rank + clade 4143 @@ -1687,22 +1724,22 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 3398 @@ -1712,32 +1749,32 @@ http_interactions: 1437183 Mesangiospermae - no rank + clade 71240 eudicotyledons - no rank + clade 91827 Gunneridae - no rank + clade 1437201 Pentapetalae - no rank + clade 71275 rosids - no rank + clade 91835 fabids - no rank + clade 3744 @@ -1815,22 +1852,22 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 3398 @@ -1840,32 +1877,32 @@ http_interactions: 1437183 Mesangiospermae - no rank + clade 71240 eudicotyledons - no rank + clade 91827 Gunneridae - no rank + clade 1437201 Pentapetalae - no rank + clade 71275 rosids - no rank + clade 91836 malvids - no rank + clade 41944 @@ -1953,22 +1990,22 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 3398 @@ -1978,32 +2015,32 @@ http_interactions: 1437183 Mesangiospermae - no rank + clade 71240 eudicotyledons - no rank + clade 91827 Gunneridae - no rank + clade 1437201 Pentapetalae - no rank + clade 71274 asterids - no rank + clade 91888 lamiids - no rank + clade 4069 @@ -2061,7 +2098,7 @@ http_interactions: 1 Standard - cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliopsida; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; campanulids; Asterales; Asteraceae; Cichorioideae; Arctotideae; Gorteriinae; Berkheya + cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliopsida; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; campanulids; Asterales; Asteraceae; Vernonioideae; Arctotideae; Gorteriinae; Berkheya 131567 @@ -2091,22 +2128,22 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 3398 @@ -2116,32 +2153,32 @@ http_interactions: 1437183 Mesangiospermae - no rank + clade 71240 eudicotyledons - no rank + clade 91827 Gunneridae - no rank + clade 1437201 Pentapetalae - no rank + clade 71274 asterids - no rank + clade 91882 campanulids - no rank + clade 4209 @@ -2154,8 +2191,8 @@ http_interactions: family - 219120 - Cichorioideae + 2758482 + Vernonioideae subfamily @@ -2234,22 +2271,22 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 3398 @@ -2259,12 +2296,12 @@ http_interactions: 1437183 Mesangiospermae - no rank + clade 4447 Liliopsida - no rank + clade 1437197 @@ -2360,22 +2397,22 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 3398 @@ -2385,32 +2422,32 @@ http_interactions: 1437183 Mesangiospermae - no rank + clade 71240 eudicotyledons - no rank + clade 91827 Gunneridae - no rank + clade 1437201 Pentapetalae - no rank + clade 71274 asterids - no rank + clade 91882 campanulids - no rank + clade 4209 @@ -2430,7 +2467,7 @@ http_interactions: 911341 Heliantheae alliance - no rank + clade 102814 @@ -2504,22 +2541,22 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 3398 @@ -2529,32 +2566,32 @@ http_interactions: 1437183 Mesangiospermae - no rank + clade 71240 eudicotyledons - no rank + clade 91827 Gunneridae - no rank + clade 1437201 Pentapetalae - no rank + clade 71274 asterids - no rank + clade 91882 campanulids - no rank + clade 4209 @@ -2574,7 +2611,7 @@ http_interactions: 911341 Heliantheae alliance - no rank + clade 219128 @@ -2652,22 +2689,22 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 3398 @@ -2677,32 +2714,32 @@ http_interactions: 1437183 Mesangiospermae - no rank + clade 71240 eudicotyledons - no rank + clade 91827 Gunneridae - no rank + clade 1437201 Pentapetalae - no rank + clade 71275 rosids - no rank + clade 91835 fabids - no rank + clade 72025 @@ -2722,17 +2759,17 @@ http_interactions: 2231393 50 kb inversion clade - no rank + clade 2231384 genistoids sensu lato - no rank + clade 2231385 core genistoids - no rank + clade 163729 @@ -2776,7 +2813,7 @@ http_interactions: 1 Standard - cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Acrogymnospermae; Pinopsida; Pinidae; Pinales; Pinaceae; Pinus; Strobus + cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Acrogymnospermae; Pinopsida; Pinidae; Conifers I; Pinales; Pinaceae; Pinus; Pinus subgen. Strobus 131567 @@ -2806,27 +2843,27 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 1437180 Acrogymnospermae - no rank + clade 58019 @@ -2838,6 +2875,11 @@ http_interactions: Pinidae subclass + + 2821352 + Conifers I + clade + 1446380 Pinales @@ -2855,7 +2897,7 @@ http_interactions: 139272 - Strobus + Pinus subgen. Strobus subgenus @@ -2873,7 +2915,7 @@ http_interactions: 1227452 Haloarcula amylolytica JCM 13557 396317 - no rank + strain Bacteria 11 @@ -2903,7 +2945,7 @@ http_interactions: 2290931 Stenosarchaea group - no rank + clade 183963 @@ -2949,7 +2991,7 @@ http_interactions: 0 Unspecified - cellular organisms; Bacteria; Proteobacteria; Gammaproteobacteria; Oceanospirillales; Halomonadaceae; Halomonas; unclassified Halomonas + cellular organisms; Bacteria; Pseudomonadota; Gammaproteobacteria; Oceanospirillales; Halomonadaceae; Halomonas; unclassified Halomonas 131567 @@ -2963,7 +3005,7 @@ http_interactions: 1224 - Proteobacteria + Pseudomonadota phylum @@ -2998,5 +3040,5 @@ http_interactions: - recorded_at: 2020-05-05 00:15:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:20 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 diff --git a/tests/fixtures/class2tree_classification_dup_call.yml b/tests/fixtures/class2tree_classification_dup_call.yml index 8f00657f..a9f3b38c 100644 --- a/tests/fixtures/class2tree_classification_dup_call.yml +++ b/tests/fixtures/class2tree_classification_dup_call.yml @@ -8,8 +8,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -17,25 +17,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:14:26 GMT + date: Thu, 09 Mar 2023 21:24:20 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '9' - ncbi-phid: D0BD1587C1A60415000021533F013544.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: 35EB91C275D08731_234BSID + ncbi-phid: D0BD29F778F3A20500005DFA510C904E.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: B5DFFAF54F8566DA_486FSID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '9' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=B5DFFAF54F8566DA_486FSID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:14:27 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=35EB91C275D08731_234BSID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:20 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -43,8 +45,8 @@ http_interactions: 110 10090 Mus+musculus[All Names] All Names 1 N GROUP Mus+musculus[All Names] - recorded_at: 2020-05-05 00:14:29 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:23 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Escherichia%2Bcoli&api_key=<> @@ -54,8 +56,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -63,25 +65,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:14:27 GMT + date: Thu, 09 Mar 2023 21:24:21 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '8' - ncbi-phid: D0BD1587C1A60415000025533F875462.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: 14752C8D11304036_602CSID + ncbi-phid: D0BD29F778F3A20500002AFA54DFA318.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 209C7E0582C12BB0_F125SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=209C7E0582C12BB0_F125SID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:14:27 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=14752C8D11304036_602CSID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:21 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -89,8 +93,8 @@ http_interactions: 110 562 Escherichia+coli[All Names] All Names 1 N GROUP Escherichia+coli[All Names] - recorded_at: 2020-05-05 00:14:29 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:23 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Haloferax%2Bdenitrificans&api_key=<> @@ -100,8 +104,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -109,25 +113,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:14:27 GMT + date: Thu, 09 Mar 2023 21:24:21 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '7' - ncbi-phid: D0BD1587C1A6041500003F53406EE192.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: 6BE029F0E8D3D618_19C4SID + ncbi-phid: D0BD29F778F3A205000053FA566D1558.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: EB0D1E3A7589794F_D9D0SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=EB0D1E3A7589794F_D9D0SID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:14:28 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=6BE029F0E8D3D618_19C4SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:21 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -135,8 +141,8 @@ http_interactions: 110 35745 Haloferax+denitrificans[All Names] All Names 1 N GROUP Haloferax+denitrificans[All Names] - recorded_at: 2020-05-05 00:14:29 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:23 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Mus%2Bmusculus&api_key=<> @@ -146,8 +152,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -155,25 +161,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:14:27 GMT + date: Thu, 09 Mar 2023 21:24:22 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: D0BD1587C1A604150000565340F72C87.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: D2CF1B0CCBCB0F94_F838SID + ncbi-phid: D0BD29F778F3A205000042FA593D0B08.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: D7E5F3733D051035_F384SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=D7E5F3733D051035_F384SID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:14:28 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=D2CF1B0CCBCB0F94_F838SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:22 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -181,8 +189,8 @@ http_interactions: 110 10090 Mus+musculus[All Names] All Names 1 N GROUP Mus+musculus[All Names] - recorded_at: 2020-05-05 00:14:29 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:23 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&ID=10090%2C562%2C35745%2C10090&api_key=<> @@ -190,7 +198,7 @@ http_interactions: encoding: '' string: '' headers: - User-Agent: libcurl/7.64.1 r-curl/4.3 crul/0.9.0 + User-Agent: libcurl/7.81.0 r-curl/4.3.3 crul/1.3 Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* response: @@ -200,25 +208,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:14:28 GMT + date: Thu, 09 Mar 2023 21:24:22 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: D0BD1587C1A60415000061534185FBDC.1.1.m_3 + referrer-policy: origin-when-cross-origin + ncbi-sid: 957BA5689E72B0CA_871FSID + ncbi-phid: D0BD29F778F3A205000053FA5B7B6CDA.1.1.m_3 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: E3B2CE53074578D8_80DESID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=E3B2CE53074578D8_80DESID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:14:28 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=957BA5689E72B0CA_871FSID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:23 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: |- @@ -268,7 +278,7 @@ http_interactions: 33154 Opisthokonta - no rank + clade 33208 @@ -278,17 +288,17 @@ http_interactions: 6072 Eumetazoa - no rank + clade 33213 Bilateria - no rank + clade 33511 Deuterostomia - no rank + clade 7711 @@ -303,22 +313,22 @@ http_interactions: 7742 Vertebrata - no rank + clade 7776 Gnathostomata - no rank + clade 117570 Teleostomi - no rank + clade 117571 Euteleostomi - no rank + clade 8287 @@ -328,17 +338,17 @@ http_interactions: 1338369 Dipnotetrapodomorpha - no rank + clade 32523 Tetrapoda - no rank + clade 32524 Amniota - no rank + clade 40674 @@ -348,17 +358,17 @@ http_interactions: 32525 Theria - no rank + clade 9347 Eutheria - no rank + clade 1437010 Boreoeutheria - no rank + clade 314146 @@ -368,7 +378,7 @@ http_interactions: 314147 Glires - no rank + clade 9989 @@ -383,7 +393,7 @@ http_interactions: 337687 Muroidea - no rank + clade 10066 @@ -419,6 +429,7 @@ http_interactions: Bacterium coli commune Enterococcus coli E. coli + Achromobacter sp. ATCC 35328 Escherichia sp. 3_2_53FAA Escherichia sp. MAR bacterium 10a @@ -532,6 +543,14 @@ http_interactions: type material NCTC:9001 + + type material + personal::U5/41 + + + type material + strain U5/41 + misspelling Escherchia coli @@ -552,7 +571,7 @@ http_interactions: 0 Unspecified - cellular organisms; Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia + cellular organisms; Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia 131567 @@ -566,7 +585,7 @@ http_interactions: 1224 - Proteobacteria + Pseudomonadota phylum @@ -591,7 +610,7 @@ http_interactions: 1995/02/27 09:24:00 - 2018/11/23 18:09:58 + 2022/12/05 17:02:38 1993/06/11 01:00:00 @@ -683,7 +702,7 @@ http_interactions: 2290931 Stenosarchaea group - no rank + clade 183963 @@ -755,7 +774,7 @@ http_interactions: 33154 Opisthokonta - no rank + clade 33208 @@ -765,17 +784,17 @@ http_interactions: 6072 Eumetazoa - no rank + clade 33213 Bilateria - no rank + clade 33511 Deuterostomia - no rank + clade 7711 @@ -790,22 +809,22 @@ http_interactions: 7742 Vertebrata - no rank + clade 7776 Gnathostomata - no rank + clade 117570 Teleostomi - no rank + clade 117571 Euteleostomi - no rank + clade 8287 @@ -815,17 +834,17 @@ http_interactions: 1338369 Dipnotetrapodomorpha - no rank + clade 32523 Tetrapoda - no rank + clade 32524 Amniota - no rank + clade 40674 @@ -835,17 +854,17 @@ http_interactions: 32525 Theria - no rank + clade 9347 Eutheria - no rank + clade 1437010 Boreoeutheria - no rank + clade 314146 @@ -855,7 +874,7 @@ http_interactions: 314147 Glires - no rank + clade 9989 @@ -870,7 +889,7 @@ http_interactions: 337687 Muroidea - no rank + clade 10066 @@ -899,5 +918,5 @@ http_interactions: - recorded_at: 2020-05-05 00:14:29 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:23 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 diff --git a/tests/fixtures/class2tree_internal_fxns.yml b/tests/fixtures/class2tree_internal_fxns.yml index 983b0a35..49073746 100644 --- a/tests/fixtures/class2tree_internal_fxns.yml +++ b/tests/fixtures/class2tree_internal_fxns.yml @@ -8,8 +8,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -17,25 +17,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:13:08 GMT + date: Thu, 09 Mar 2023 21:23:47 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '9' - ncbi-phid: 322C7ECC5D85ECB500003F4936FF0737.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: 78442BAD678A46F4_19C0SID + ncbi-phid: 322C2D2E52F0459500002CD464DBA541.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: AE369EDDD1CFB77D_4610SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '9' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=AE369EDDD1CFB77D_4610SID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:13:08 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=78442BAD678A46F4_19C0SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:23:48 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -43,8 +45,8 @@ http_interactions: 110 152733 Klattia+flava[All Names] All Names 1 N GROUP Klattia+flava[All Names] - recorded_at: 2020-05-05 00:13:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:01 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Trollius%2Bsibiricus&api_key=<> @@ -54,8 +56,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -63,25 +65,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:13:08 GMT + date: Thu, 09 Mar 2023 21:23:48 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '8' - ncbi-phid: D0BD1587C1A6041500004252D4557933.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: 33E012E59022C47C_ED50SID + ncbi-phid: 322C2D2E52F0459500002BD46986B378.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: CE13F25CA9261FE7_2AC8SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=CE13F25CA9261FE7_2AC8SID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:13:09 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=33E012E59022C47C_ED50SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:23:49 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -89,8 +93,8 @@ http_interactions: 110 944286 Trollius+sibiricus[All Names] All Names 1 N GROUP Trollius+sibiricus[All Names] - recorded_at: 2020-05-05 00:13:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:01 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Arachis%2Bparaguariensis&api_key=<> @@ -100,8 +104,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -109,25 +113,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:13:09 GMT + date: Thu, 09 Mar 2023 21:23:49 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '8' - ncbi-phid: D0BD1587C1A6041500003E52D4A96B4D.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: A77F718F06443E9E_7B56SID + ncbi-phid: 322C2D2E52F04595000059D46DD9E93B.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: C0FA28B2498143E8_0A77SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=C0FA28B2498143E8_0A77SID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:13:09 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=A77F718F06443E9E_7B56SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:23:50 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -135,8 +141,8 @@ http_interactions: 110 224337 Arachis+paraguariensis[All Names] All Names 1 N GROUP Arachis+paraguariensis[All Names] - recorded_at: 2020-05-05 00:13:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:01 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Tanacetum%2Bboreale&api_key=<> @@ -146,8 +152,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -155,25 +161,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:13:09 GMT + date: Thu, 09 Mar 2023 21:23:49 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '7' - ncbi-phid: D0BD1587C1A6041500003852D4F94735.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: 115B49704F57A481_D7F2SID + ncbi-phid: 322C2D2E52F0459500004DD4714C0230.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 07282D45C8039367_8E89SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=07282D45C8039367_8E89SID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:13:10 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=115B49704F57A481_D7F2SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:23:50 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -181,8 +189,8 @@ http_interactions: 110 128002 Tanacetum+boreale[All Names] All Names 1 N GROUP Tanacetum+boreale[All Names] - recorded_at: 2020-05-05 00:13:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:01 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Gentiana%2Byakushimensis&api_key=<> @@ -192,8 +200,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -201,25 +209,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:13:09 GMT + date: Thu, 09 Mar 2023 21:23:50 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: D0BD1587C1A6041500003552D54F0411.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: A340B4B03F751AAE_AB1CSID + ncbi-phid: 322C2D2E52F04595000038D47542210B.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 8F1A2ECE76F44208_F585SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=8F1A2ECE76F44208_F585SID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:13:10 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=A340B4B03F751AAE_AB1CSID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:23:51 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -227,8 +237,8 @@ http_interactions: 110 553063 Gentiana+yakushimensis[All Names] All Names 1 N GROUP Gentiana+yakushimensis[All Names] - recorded_at: 2020-05-05 00:13:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:01 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Sesamum%2Bschinzianum&api_key=<> @@ -238,8 +248,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -247,25 +257,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:13:10 GMT + date: Thu, 09 Mar 2023 21:23:51 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: D0BD1587C1A6041500004A52D5B0FBD6.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: DEC8BA31E7772D94_25F4SID + ncbi-phid: 322C2D2E52F04595000034D478984040.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 24C9B34A92D6C5DD_0640SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=24C9B34A92D6C5DD_0640SID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:13:10 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=DEC8BA31E7772D94_25F4SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:23:52 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -273,8 +285,8 @@ http_interactions: 110 768545 Sesamum+schinzianum[All Names] All Names 1 N GROUP Sesamum+schinzianum[All Names] - recorded_at: 2020-05-05 00:13:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:01 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Pilea%2Bverrucosa&api_key=<> @@ -284,8 +296,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -293,25 +305,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:13:10 GMT + date: Thu, 09 Mar 2023 21:23:52 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '7' - ncbi-phid: 939B0CD3340CCB750000465B0DFBCB53.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: 5370EF7291568FC6_F956SID + ncbi-phid: 322C2D2E52F0459500003CD47B9AC3C7.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 70545EF51D174653_F7ACSID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=70545EF51D174653_F7ACSID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:13:11 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=5370EF7291568FC6_F956SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:23:53 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -319,8 +333,8 @@ http_interactions: 110 1399730 Pilea+verrucosa[All Names] All Names 1 N GROUP Pilea+verrucosa[All Names] - recorded_at: 2020-05-05 00:13:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:01 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Tibouchina%2Bstriphnocalyx&api_key=<> @@ -330,8 +344,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -339,25 +353,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:13:11 GMT + date: Thu, 09 Mar 2023 21:23:53 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '7' - ncbi-phid: 939B0CD3340CCB750000605B0E69D961.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: C82A8E4B4BC5D0DA_0E13SID + ncbi-phid: 322C2D2E52F04595000016D47DF05F67.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: FDE962CBF527337B_5FC4SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=FDE962CBF527337B_5FC4SID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:13:11 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=C82A8E4B4BC5D0DA_0E13SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:23:53 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -365,8 +381,8 @@ http_interactions: 110 1160690 Tibouchina+striphnocalyx[All Names] All Names 1 N GROUP Tibouchina+striphnocalyx[All Names] - recorded_at: 2020-05-05 00:13:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:01 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Lycium%2Bdasystemum&api_key=<> @@ -376,8 +392,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -385,25 +401,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:13:11 GMT + date: Thu, 09 Mar 2023 21:23:54 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '7' - ncbi-phid: 939B0CD3340CCB750000645B0F5F9CE1.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: 5D54A6869BCADFF9_65C2SID + ncbi-phid: 322C2D2E52F04595000041D48022CBE6.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 7592EDB808F16E29_25EASID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=7592EDB808F16E29_25EASID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:13:12 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=5D54A6869BCADFF9_65C2SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:23:54 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -411,8 +429,8 @@ http_interactions: 110 942185 Lycium+dasystemum[All Names] All Names 1 N GROUP Lycium+dasystemum[All Names] - recorded_at: 2020-05-05 00:13:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:01 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Berkheya%2Bechinacea&api_key=<> @@ -422,8 +440,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -431,25 +449,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:13:11 GMT + date: Thu, 09 Mar 2023 21:23:54 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '7' - ncbi-phid: 939B0CD3340CCB750000615B0FBA1E4E.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: F14C58EAF9CE56F3_CBA4SID + ncbi-phid: 939B640887F4D8E500005F008FE98E46.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: A5741D60EF5AD9CF_7C70SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=A5741D60EF5AD9CF_7C70SID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:13:12 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=F14C58EAF9CE56F3_CBA4SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:23:55 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -457,8 +477,8 @@ http_interactions: 110 527996 Berkheya+echinacea[All Names] All Names 1 N GROUP Berkheya+echinacea[All Names] - recorded_at: 2020-05-05 00:13:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:01 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Androcymbium%2Bvillosum&api_key=<> @@ -468,8 +488,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -477,25 +497,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:13:12 GMT + date: Thu, 09 Mar 2023 21:23:55 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '7' - ncbi-phid: 939B0CD3340CCB750000645B10230E91.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: 02843695A84E8653_2437SID + ncbi-phid: 939B640887F4D8E500003C0092C396F6.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: B4A5BEAB053F4C56_FBAESID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=B4A5BEAB053F4C56_FBAESID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:13:12 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=02843695A84E8653_2437SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:23:56 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -503,8 +525,8 @@ http_interactions: 110 279457 Androcymbium+villosum[All Names] All Names 1 N GROUP Androcymbium+villosum[All Names] - recorded_at: 2020-05-05 00:13:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:01 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Helianthus%2Bannuus&api_key=<> @@ -514,8 +536,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -523,25 +545,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:13:12 GMT + date: Thu, 09 Mar 2023 21:23:55 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 939B0CD3340CCB750000245B1087289F.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: D24C9241D4021F3E_2B17SID + ncbi-phid: 939B640887F4D8E500003A00954D1AA7.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 867B41AF97F82EA0_791ASID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=867B41AF97F82EA0_791ASID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:13:12 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=D24C9241D4021F3E_2B17SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:23:56 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -549,8 +573,8 @@ http_interactions: 110 4232 Helianthus+annuus[All Names] All Names 1 N GROUP Helianthus+annuus[All Names] - recorded_at: 2020-05-05 00:13:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:01 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Madia%2Belegans&api_key=<> @@ -560,8 +584,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -569,25 +593,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:13:12 GMT + date: Thu, 09 Mar 2023 21:23:56 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 939B0CD3340CCB7500004E5B1134C91C.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: 1179749BD7595DCE_53E2SID + ncbi-phid: 939B640887F4D8E500003E00977B78B1.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: FD619DC14D179F73_6759SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=FD619DC14D179F73_6759SID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:13:13 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=1179749BD7595DCE_53E2SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:23:57 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -595,8 +621,8 @@ http_interactions: 110 4255 Madia+elegans[All Names] All Names 1 N GROUP Madia+elegans[All Names] - recorded_at: 2020-05-05 00:13:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:01 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Lupinus%2Balbicaulis&api_key=<> @@ -606,8 +632,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -615,25 +641,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:13:13 GMT + date: Thu, 09 Mar 2023 21:23:57 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 939B0CD3340CCB750000395B11B75BF7.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: 86F377F5AA39A3AC_DF9FSID + ncbi-phid: 939B640887F4D8E500004F009A42D564.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 1FAC390772283ECB_5E1CSID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=1FAC390772283ECB_5E1CSID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:13:13 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=86F377F5AA39A3AC_DF9FSID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:23:58 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -641,8 +669,8 @@ http_interactions: 110 377318 Lupinus+albicaulis[All Names] All Names 1 N GROUP Lupinus+albicaulis[All Names] - recorded_at: 2020-05-05 00:13:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:01 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Pinus%2Blambertiana&api_key=<> @@ -652,8 +680,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -661,25 +689,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:13:13 GMT + date: Thu, 09 Mar 2023 21:23:58 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '7' - ncbi-phid: 939B0CD3340CCB750000585B12562151.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: 30184A6273FE36EE_06F7SID + ncbi-phid: 939B640887F4D8E500002E009DE3E1DE.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: F05AF123D464260D_7578SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '9' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=F05AF123D464260D_7578SID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:13:14 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=30184A6273FE36EE_06F7SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:23:59 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -687,8 +717,8 @@ http_interactions: 110 3343 Pinus+lambertiana[All Names] All Names 1 N GROUP Pinus+lambertiana[All Names] - recorded_at: 2020-05-05 00:13:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:01 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Haloarcula%2Bamylolytica%2BJCM%2B13557&api_key=<> @@ -698,8 +728,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -707,25 +737,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:13:13 GMT + date: Thu, 09 Mar 2023 21:23:59 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '7' - ncbi-phid: 939B0CD3340CCB7500002E5B12D0E604.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: 3AEFBE65A96A2B3D_6B7FSID + ncbi-phid: 939B640887F4D8E5000041009FE91274.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: C9E699776B49055F_9ADBSID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=C9E699776B49055F_9ADBSID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:13:14 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=3AEFBE65A96A2B3D_6B7FSID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:00 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -733,8 +765,8 @@ http_interactions: 110 1227452 Haloarcula+amylolytica+JCM+13557[All Names] All Names 1 N GROUP Haloarcula+amylolytica+JCM+13557[All Names] - recorded_at: 2020-05-05 00:13:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:01 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Halomonas%2Bsp.%2B%27Soap%2BLake%2B%236%27&api_key=<> @@ -744,8 +776,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -753,25 +785,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:13:14 GMT + date: Thu, 09 Mar 2023 21:24:00 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 939B0CD3340CCB750000305B133085A9.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: E6F52523A4A092B7_8651SID + ncbi-phid: 939B640887F4D8E500002D00A20455D2.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: B1226D859B8382BA_9732SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=B1226D859B8382BA_9732SID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:13:14 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=E6F52523A4A092B7_8651SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:00 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -779,8 +813,8 @@ http_interactions: 110 1949203 Halomonas+sp.+'Soap+Lake+#6'[All Names] All Names 1 N GROUP Halomonas+sp.+'Soap+Lake+#6'[All Names] - recorded_at: 2020-05-05 00:13:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:01 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&ID=152733%2C944286%2C224337%2C128002%2C553063%2C768545%2C1399730%2C1160690%2C942185%2C527996%2C279457%2C4232%2C4255%2C377318%2C3343%2C1227452%2C1949203&api_key=<> @@ -788,7 +822,7 @@ http_interactions: encoding: '' string: '' headers: - User-Agent: libcurl/7.64.1 r-curl/4.3 crul/0.9.0 + User-Agent: libcurl/7.81.0 r-curl/4.3.3 crul/1.3 Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* response: @@ -798,25 +832,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:13:15 GMT + date: Thu, 09 Mar 2023 21:24:00 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 939B0CD3340CCB7500005B5B13E196CA.1.1.m_3 + referrer-policy: origin-when-cross-origin + ncbi-sid: 489FAC210130BE02_7809SID + ncbi-phid: 939B640887F4D8E500005C00A3698DB7.1.1.m_3 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 3097097599BD941C_EA93SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=3097097599BD941C_EA93SID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:13:15 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=489FAC210130BE02_7809SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:01 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: |- @@ -871,22 +907,22 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 3398 @@ -896,12 +932,12 @@ http_interactions: 1437183 Mesangiospermae - no rank + clade 4447 Liliopsida - no rank + clade 1437197 @@ -989,22 +1025,22 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 3398 @@ -1014,7 +1050,7 @@ http_interactions: 1437183 Mesangiospermae - no rank + clade 41768 @@ -1110,22 +1146,22 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 3398 @@ -1135,32 +1171,32 @@ http_interactions: 1437183 Mesangiospermae - no rank + clade 71240 eudicotyledons - no rank + clade 91827 Gunneridae - no rank + clade 1437201 Pentapetalae - no rank + clade 71275 rosids - no rank + clade 91835 fabids - no rank + clade 72025 @@ -1180,12 +1216,12 @@ http_interactions: 2231393 50 kb inversion clade - no rank + clade 2231387 dalbergioids sensu lato - no rank + clade 163725 @@ -1195,7 +1231,7 @@ http_interactions: 2231390 Pterocarpus clade - no rank + clade 3817 @@ -1274,22 +1310,22 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 3398 @@ -1299,32 +1335,32 @@ http_interactions: 1437183 Mesangiospermae - no rank + clade 71240 eudicotyledons - no rank + clade 91827 Gunneridae - no rank + clade 1437201 Pentapetalae - no rank + clade 71274 asterids - no rank + clade 91882 campanulids - no rank + clade 4209 @@ -1417,22 +1453,22 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 3398 @@ -1442,32 +1478,32 @@ http_interactions: 1437183 Mesangiospermae - no rank + clade 71240 eudicotyledons - no rank + clade 91827 Gunneridae - no rank + clade 1437201 Pentapetalae - no rank + clade 71274 asterids - no rank + clade 91888 lamiids - no rank + clade 4055 @@ -1559,22 +1595,22 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 3398 @@ -1584,32 +1620,32 @@ http_interactions: 1437183 Mesangiospermae - no rank + clade 71240 eudicotyledons - no rank + clade 91827 Gunneridae - no rank + clade 1437201 Pentapetalae - no rank + clade 71274 asterids - no rank + clade 91888 lamiids - no rank + clade 4143 @@ -1687,22 +1723,22 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 3398 @@ -1712,32 +1748,32 @@ http_interactions: 1437183 Mesangiospermae - no rank + clade 71240 eudicotyledons - no rank + clade 91827 Gunneridae - no rank + clade 1437201 Pentapetalae - no rank + clade 71275 rosids - no rank + clade 91835 fabids - no rank + clade 3744 @@ -1815,22 +1851,22 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 3398 @@ -1840,32 +1876,32 @@ http_interactions: 1437183 Mesangiospermae - no rank + clade 71240 eudicotyledons - no rank + clade 91827 Gunneridae - no rank + clade 1437201 Pentapetalae - no rank + clade 71275 rosids - no rank + clade 91836 malvids - no rank + clade 41944 @@ -1953,22 +1989,22 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 3398 @@ -1978,32 +2014,32 @@ http_interactions: 1437183 Mesangiospermae - no rank + clade 71240 eudicotyledons - no rank + clade 91827 Gunneridae - no rank + clade 1437201 Pentapetalae - no rank + clade 71274 asterids - no rank + clade 91888 lamiids - no rank + clade 4069 @@ -2061,7 +2097,7 @@ http_interactions: 1 Standard - cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliopsida; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; campanulids; Asterales; Asteraceae; Cichorioideae; Arctotideae; Gorteriinae; Berkheya + cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliopsida; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; campanulids; Asterales; Asteraceae; Vernonioideae; Arctotideae; Gorteriinae; Berkheya 131567 @@ -2091,22 +2127,22 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 3398 @@ -2116,32 +2152,32 @@ http_interactions: 1437183 Mesangiospermae - no rank + clade 71240 eudicotyledons - no rank + clade 91827 Gunneridae - no rank + clade 1437201 Pentapetalae - no rank + clade 71274 asterids - no rank + clade 91882 campanulids - no rank + clade 4209 @@ -2154,8 +2190,8 @@ http_interactions: family - 219120 - Cichorioideae + 2758482 + Vernonioideae subfamily @@ -2234,22 +2270,22 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 3398 @@ -2259,12 +2295,12 @@ http_interactions: 1437183 Mesangiospermae - no rank + clade 4447 Liliopsida - no rank + clade 1437197 @@ -2360,22 +2396,22 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 3398 @@ -2385,32 +2421,32 @@ http_interactions: 1437183 Mesangiospermae - no rank + clade 71240 eudicotyledons - no rank + clade 91827 Gunneridae - no rank + clade 1437201 Pentapetalae - no rank + clade 71274 asterids - no rank + clade 91882 campanulids - no rank + clade 4209 @@ -2430,7 +2466,7 @@ http_interactions: 911341 Heliantheae alliance - no rank + clade 102814 @@ -2504,22 +2540,22 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 3398 @@ -2529,32 +2565,32 @@ http_interactions: 1437183 Mesangiospermae - no rank + clade 71240 eudicotyledons - no rank + clade 91827 Gunneridae - no rank + clade 1437201 Pentapetalae - no rank + clade 71274 asterids - no rank + clade 91882 campanulids - no rank + clade 4209 @@ -2574,7 +2610,7 @@ http_interactions: 911341 Heliantheae alliance - no rank + clade 219128 @@ -2652,22 +2688,22 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 3398 @@ -2677,32 +2713,32 @@ http_interactions: 1437183 Mesangiospermae - no rank + clade 71240 eudicotyledons - no rank + clade 91827 Gunneridae - no rank + clade 1437201 Pentapetalae - no rank + clade 71275 rosids - no rank + clade 91835 fabids - no rank + clade 72025 @@ -2722,17 +2758,17 @@ http_interactions: 2231393 50 kb inversion clade - no rank + clade 2231384 genistoids sensu lato - no rank + clade 2231385 core genistoids - no rank + clade 163729 @@ -2776,7 +2812,7 @@ http_interactions: 1 Standard - cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Acrogymnospermae; Pinopsida; Pinidae; Pinales; Pinaceae; Pinus; Strobus + cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Acrogymnospermae; Pinopsida; Pinidae; Conifers I; Pinales; Pinaceae; Pinus; Pinus subgen. Strobus 131567 @@ -2806,27 +2842,27 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 1437180 Acrogymnospermae - no rank + clade 58019 @@ -2838,6 +2874,11 @@ http_interactions: Pinidae subclass + + 2821352 + Conifers I + clade + 1446380 Pinales @@ -2855,7 +2896,7 @@ http_interactions: 139272 - Strobus + Pinus subgen. Strobus subgenus @@ -2873,7 +2914,7 @@ http_interactions: 1227452 Haloarcula amylolytica JCM 13557 396317 - no rank + strain Bacteria 11 @@ -2903,7 +2944,7 @@ http_interactions: 2290931 Stenosarchaea group - no rank + clade 183963 @@ -2949,7 +2990,7 @@ http_interactions: 0 Unspecified - cellular organisms; Bacteria; Proteobacteria; Gammaproteobacteria; Oceanospirillales; Halomonadaceae; Halomonas; unclassified Halomonas + cellular organisms; Bacteria; Pseudomonadota; Gammaproteobacteria; Oceanospirillales; Halomonadaceae; Halomonas; unclassified Halomonas 131567 @@ -2963,7 +3004,7 @@ http_interactions: 1224 - Proteobacteria + Pseudomonadota phylum @@ -2998,5 +3039,5 @@ http_interactions: - recorded_at: 2020-05-05 00:13:15 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:01 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 diff --git a/tests/fixtures/classification.yml b/tests/fixtures/classification.yml index c091dbd2..dec0df2d 100644 --- a/tests/fixtures/classification.yml +++ b/tests/fixtures/classification.yml @@ -8,8 +8,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -17,25 +17,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Mon, 10 Feb 2020 22:15:54 GMT + date: Thu, 09 Mar 2023 21:24:26 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '9' - ncbi-phid: D0BD591C6591225500002D238ED73FD2.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: DE4EDAE919D40D95_C013SID + ncbi-phid: D0BD29F778F3A205000058FA6B1FD83E.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 5D84CDA0A6D7C404_CC39SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '9' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=5D84CDA0A6D7C404_CC39SID; domain=.nih.gov; path=/; expires=Wed, - 10 Feb 2021 22:15:55 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=DE4EDAE919D40D95_C013SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:26 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -43,8 +45,8 @@ http_interactions: 110 315576 Chironomus+riparius[All Names] All Names 1 N GROUP Chironomus+riparius[All Names] - recorded_at: 2020-02-10 22:16:00 GMT - recorded_with: vcr/0.4.1.94, webmockr/0.5.1.98 + recorded_at: 2023-03-09 21:24:32 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=aaa%2Bvva&api_key=<> @@ -54,8 +56,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -63,32 +65,34 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Mon, 10 Feb 2020 22:15:54 GMT + date: Thu, 09 Mar 2023 21:24:27 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '8' - ncbi-phid: D0BD591C6591225500004C238FEFEE66.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: BE3B7E4040CBDFB8_EBDFSID + ncbi-phid: D0BD29F778F3A205000033FA6D41608A.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: A7701634E646D8C0_813ESID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=A7701634E646D8C0_813ESID; domain=.nih.gov; path=/; expires=Wed, - 10 Feb 2021 22:15:55 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=BE3B7E4040CBDFB8_EBDFSID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:27 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | 000(aaa+vva[All Names])aaa+vvaNo items found. - recorded_at: 2020-02-10 22:16:00 GMT - recorded_with: vcr/0.4.1.94, webmockr/0.5.1.98 + recorded_at: 2023-03-09 21:24:32 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&ID=315576&api_key=<> @@ -96,7 +100,7 @@ http_interactions: encoding: '' string: '' headers: - User-Agent: libcurl/7.54.0 r-curl/4.3 crul/0.9.0 + User-Agent: libcurl/7.81.0 r-curl/4.3.3 crul/1.3 Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* response: @@ -106,25 +110,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Mon, 10 Feb 2020 22:15:55 GMT + date: Thu, 09 Mar 2023 21:24:27 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '7' - ncbi-phid: D0BD591C659122550000422390B28C0C.1.1.m_3 + referrer-policy: origin-when-cross-origin + ncbi-sid: E9AECD406233AE76_34D2SID + ncbi-phid: D0BD29F778F3A20500004DFA704F5838.1.1.m_5 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: CF92CBA5D8B74ABB_B42ESID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=CF92CBA5D8B74ABB_B42ESID; domain=.nih.gov; path=/; expires=Wed, - 10 Feb 2021 22:15:55 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=E9AECD406233AE76_34D2SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:28 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: |- @@ -132,6 +138,12 @@ http_interactions: 315576 Chironomus riparius + + + authority + Chironomus riparius Meigen, 1804 + + 1165752 species Invertebrates @@ -143,7 +155,7 @@ http_interactions: 5 Invertebrate Mitochondrial - cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Diptera; Nematocera; Culicomorpha; Chironomoidea; Chironomidae; Chironominae; Chironomini; Chironomus; Chironomus incertae sedis + cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Culicomorpha; Chironomoidea; Chironomidae; Chironominae; Chironomini; Chironomus; Chironomus incertae sedis 131567 @@ -158,7 +170,7 @@ http_interactions: 33154 Opisthokonta - no rank + clade 33208 @@ -168,27 +180,27 @@ http_interactions: 6072 Eumetazoa - no rank + clade 33213 Bilateria - no rank + clade 33317 Protostomia - no rank + clade 1206794 Ecdysozoa - no rank + clade 88770 Panarthropoda - no rank + clade 6656 @@ -198,12 +210,12 @@ http_interactions: 197563 Mandibulata - no rank + clade 197562 Pancrustacea - no rank + clade 6960 @@ -218,7 +230,7 @@ http_interactions: 85512 Dicondylia - no rank + clade 7496 @@ -232,7 +244,7 @@ http_interactions: 33392 - Holometabola + Endopterygota cohort @@ -287,8 +299,8 @@ http_interactions: - recorded_at: 2020-02-10 22:16:00 GMT - recorded_with: vcr/0.4.1.94, webmockr/0.5.1.98 + recorded_at: 2023-03-09 21:24:32 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://www.itis.gov/ITISWebService/jsonservice/getITISTermsFromScientificName?srchKey=Chironomus%20riparius @@ -296,7 +308,7 @@ http_interactions: encoding: '' string: '' headers: - User-Agent: libcurl/7.54.0 r-curl/4.3 crul/0.9.0 + User-Agent: libcurl/7.81.0 r-curl/4.3.3 crul/1.3 Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* response: @@ -305,24 +317,19 @@ http_interactions: message: OK explanation: Request fulfilled, document follows headers: - connection: keep-alive - content-length: '287' + status: 'HTTP/2 200 ' + date: Thu, 09 Mar 2023 21:24:30 GMT content-type: text/json;charset=ISO-8859-1 - date: Mon, 10 Feb 2020 22:15:58 GMT - status: 'HTTP/1.1 200 ' - strict-transport-security: - - max-age=63072000; includeSubdomains; preload - - max-age=63072000; includeSubdomains; preload - x-application: itis_webservices - x-node-name: not shown - x-upstream-member: not shown + content-length: '287' + x-frame-options: SAMEORIGIN + strict-transport-security: max-age=63072000; includeSubdomains; preload body: - encoding: UTF-8 + encoding: '' file: no string: | {"class":"gov.usgs.itis.itis_service.data.SvcItisTermList","itisTerms":[{"author":"Meigen, 1804","class":"gov.usgs.itis.itis_service.data.SvcItisTerm","commonNames":[null],"nameUsage":"valid","scientificName":"Chironomus riparius","tsn":"129313"}],"requestedName":"Chironomus riparius"} - recorded_at: 2020-02-10 22:16:00 GMT - recorded_with: vcr/0.4.1.94, webmockr/0.5.1.98 + recorded_at: 2023-03-09 21:24:32 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://www.itis.gov/ITISWebService/jsonservice/getITISTermsFromScientificName?srchKey=aaa%20vva @@ -330,7 +337,7 @@ http_interactions: encoding: '' string: '' headers: - User-Agent: libcurl/7.54.0 r-curl/4.3 crul/0.9.0 + User-Agent: libcurl/7.81.0 r-curl/4.3.3 crul/1.3 Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* response: @@ -339,24 +346,19 @@ http_interactions: message: OK explanation: Request fulfilled, document follows headers: - connection: keep-alive - content-length: '105' + status: 'HTTP/2 200 ' + date: Thu, 09 Mar 2023 21:24:31 GMT content-type: text/json;charset=ISO-8859-1 - date: Mon, 10 Feb 2020 22:15:59 GMT - status: 'HTTP/1.1 200 ' - strict-transport-security: - - max-age=63072000; includeSubdomains; preload - - max-age=63072000; includeSubdomains; preload - x-application: itis_webservices - x-node-name: not shown - x-upstream-member: not shown + content-length: '105' + x-frame-options: SAMEORIGIN + strict-transport-security: max-age=63072000; includeSubdomains; preload body: - encoding: UTF-8 + encoding: '' file: no string: | {"class":"gov.usgs.itis.itis_service.data.SvcItisTermList","itisTerms":[null],"requestedName":"aaa vva"} - recorded_at: 2020-02-10 22:16:00 GMT - recorded_with: vcr/0.4.1.94, webmockr/0.5.1.98 + recorded_at: 2023-03-09 21:24:32 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://www.itis.gov/ITISWebService/jsonservice/getFullHierarchyFromTSN?tsn=129313 @@ -364,7 +366,7 @@ http_interactions: encoding: '' string: '' headers: - User-Agent: libcurl/7.54.0 r-curl/4.3 crul/0.9.0 + User-Agent: libcurl/7.81.0 r-curl/4.3.3 crul/1.3 Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* response: @@ -373,21 +375,16 @@ http_interactions: message: OK explanation: Request fulfilled, document follows headers: - connection: keep-alive - content-length: '3475' + status: 'HTTP/2 200 ' + date: Thu, 09 Mar 2023 21:24:32 GMT content-type: text/json;charset=ISO-8859-1 - date: Mon, 10 Feb 2020 22:16:00 GMT - status: 'HTTP/1.1 200 ' - strict-transport-security: - - max-age=63072000; includeSubdomains; preload - - max-age=63072000; includeSubdomains; preload - x-application: itis_webservices - x-node-name: not shown - x-upstream-member: not shown + content-length: '3475' + x-frame-options: SAMEORIGIN + strict-transport-security: max-age=63072000; includeSubdomains; preload body: - encoding: UTF-8 + encoding: '' file: no string: | {"author":"","class":"gov.usgs.itis.itis_service.data.SvcHierarchyRecordList","hierarchyList":[{"author":null,"class":"gov.usgs.itis.itis_service.data.SvcHierarchyRecord","parentName":"","parentTsn":"","rankName":"Kingdom","taxonName":"Animalia","tsn":"202423"},{"author":null,"class":"gov.usgs.itis.itis_service.data.SvcHierarchyRecord","parentName":"Animalia","parentTsn":"202423","rankName":"Subkingdom","taxonName":"Bilateria","tsn":"914154"},{"author":null,"class":"gov.usgs.itis.itis_service.data.SvcHierarchyRecord","parentName":"Bilateria","parentTsn":"914154","rankName":"Infrakingdom","taxonName":"Protostomia","tsn":"914155"},{"author":null,"class":"gov.usgs.itis.itis_service.data.SvcHierarchyRecord","parentName":"Protostomia","parentTsn":"914155","rankName":"Superphylum","taxonName":"Ecdysozoa","tsn":"914158"},{"author":null,"class":"gov.usgs.itis.itis_service.data.SvcHierarchyRecord","parentName":"Ecdysozoa","parentTsn":"914158","rankName":"Phylum","taxonName":"Arthropoda","tsn":"82696"},{"author":null,"class":"gov.usgs.itis.itis_service.data.SvcHierarchyRecord","parentName":"Arthropoda","parentTsn":"82696","rankName":"Subphylum","taxonName":"Hexapoda","tsn":"563886"},{"author":null,"class":"gov.usgs.itis.itis_service.data.SvcHierarchyRecord","parentName":"Hexapoda","parentTsn":"563886","rankName":"Class","taxonName":"Insecta","tsn":"99208"},{"author":null,"class":"gov.usgs.itis.itis_service.data.SvcHierarchyRecord","parentName":"Insecta","parentTsn":"99208","rankName":"Subclass","taxonName":"Pterygota","tsn":"100500"},{"author":null,"class":"gov.usgs.itis.itis_service.data.SvcHierarchyRecord","parentName":"Pterygota","parentTsn":"100500","rankName":"Infraclass","taxonName":"Neoptera","tsn":"563890"},{"author":null,"class":"gov.usgs.itis.itis_service.data.SvcHierarchyRecord","parentName":"Neoptera","parentTsn":"563890","rankName":"Superorder","taxonName":"Holometabola","tsn":"914213"},{"author":null,"class":"gov.usgs.itis.itis_service.data.SvcHierarchyRecord","parentName":"Holometabola","parentTsn":"914213","rankName":"Order","taxonName":"Diptera","tsn":"118831"},{"author":null,"class":"gov.usgs.itis.itis_service.data.SvcHierarchyRecord","parentName":"Diptera","parentTsn":"118831","rankName":"Suborder","taxonName":"Nematocera","tsn":"118832"},{"author":null,"class":"gov.usgs.itis.itis_service.data.SvcHierarchyRecord","parentName":"Nematocera","parentTsn":"118832","rankName":"Infraorder","taxonName":"Culicomorpha","tsn":"125808"},{"author":null,"class":"gov.usgs.itis.itis_service.data.SvcHierarchyRecord","parentName":"Culicomorpha","parentTsn":"125808","rankName":"Family","taxonName":"Chironomidae","tsn":"127917"},{"author":null,"class":"gov.usgs.itis.itis_service.data.SvcHierarchyRecord","parentName":"Chironomidae","parentTsn":"127917","rankName":"Subfamily","taxonName":"Chironominae","tsn":"129228"},{"author":null,"class":"gov.usgs.itis.itis_service.data.SvcHierarchyRecord","parentName":"Chironominae","parentTsn":"129228","rankName":"Tribe","taxonName":"Chironomini","tsn":"129229"},{"author":null,"class":"gov.usgs.itis.itis_service.data.SvcHierarchyRecord","parentName":"Chironomini","parentTsn":"129229","rankName":"Genus","taxonName":"Chironomus","tsn":"129254"},{"author":"Meigen, 1804","class":"gov.usgs.itis.itis_service.data.SvcHierarchyRecord","parentName":"Chironomus","parentTsn":"129254","rankName":"Species","taxonName":"Chironomus riparius","tsn":"129313"}],"rankName":"","sciName":"","tsn":"129313"} - recorded_at: 2020-02-10 22:16:00 GMT - recorded_with: vcr/0.4.1.94, webmockr/0.5.1.98 + recorded_at: 2023-03-09 21:24:32 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 diff --git a/tests/fixtures/classification_cbind_rbind.yml b/tests/fixtures/classification_cbind_rbind.yml index ce229f1c..c8bcd304 100644 --- a/tests/fixtures/classification_cbind_rbind.yml +++ b/tests/fixtures/classification_cbind_rbind.yml @@ -8,8 +8,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -17,25 +17,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Mon, 24 Feb 2020 23:37:56 GMT + date: Thu, 09 Mar 2023 21:24:35 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '9' - ncbi-phid: D0BD57157EF9A68500001F37C383BDD6.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: F210CD16A481D728_0E05SID + ncbi-phid: 322C2D2E52F04595000032D5053BBAD8.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: C4DC67FCA4F90483_E73ASID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '9' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=C4DC67FCA4F90483_E73ASID; domain=.nih.gov; path=/; expires=Wed, - 24 Feb 2021 23:37:57 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=F210CD16A481D728_0E05SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:35 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -43,8 +45,8 @@ http_interactions: 110 9696 Puma+concolor[All Names] All Names 1 N GROUP Puma+concolor[All Names] - recorded_at: 2020-02-24 23:37:58 GMT - recorded_with: vcr/0.4.2.91, webmockr/0.5.1.98 + recorded_at: 2023-03-09 21:24:37 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Accipiter%2Bstriatus&api_key=<> @@ -54,8 +56,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -63,25 +65,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Mon, 24 Feb 2020 23:37:56 GMT + date: Thu, 09 Mar 2023 21:24:35 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '8' - ncbi-phid: D0BD57157EF9A68500005337C3C444C1.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: A508854AB1AE24BC_3267SID + ncbi-phid: 322C2D2E52F04595000042D507838E37.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 33BDD96E6E3DA45F_BF8CSID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=33BDD96E6E3DA45F_BF8CSID; domain=.nih.gov; path=/; expires=Wed, - 24 Feb 2021 23:37:57 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=A508854AB1AE24BC_3267SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:36 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -89,8 +93,8 @@ http_interactions: 110 56330 Accipiter+striatus[All Names] All Names 1 N GROUP Accipiter+striatus[All Names] - recorded_at: 2020-02-24 23:37:58 GMT - recorded_with: vcr/0.4.2.91, webmockr/0.5.1.98 + recorded_at: 2023-03-09 21:24:37 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&ID=9696%2C56330&api_key=<> @@ -98,7 +102,7 @@ http_interactions: encoding: '' string: '' headers: - User-Agent: libcurl/7.47.0 r-curl/4.3 crul/0.9.0 + User-Agent: libcurl/7.81.0 r-curl/4.3.3 crul/1.3 Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* response: @@ -108,25 +112,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Mon, 24 Feb 2020 23:37:57 GMT + date: Thu, 09 Mar 2023 21:24:36 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '7' - ncbi-phid: 939B1ADCACB471850000283A42EBE925.1.1.m_3 + referrer-policy: origin-when-cross-origin + ncbi-sid: 662199E97AFB3266_E7D3SID + ncbi-phid: 322C2D2E52F04595000050D50A5C7ECE.1.1.m_5 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: C6E1829CE36CACB0_4A6ESID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=C6E1829CE36CACB0_4A6ESID; domain=.nih.gov; path=/; expires=Wed, - 24 Feb 2021 23:37:58 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=662199E97AFB3266_E7D3SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:37 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: |- @@ -138,6 +144,10 @@ http_interactions: puma Felis concolor Panthera concolor + + authority + Felis concolor Linnaeus, 1771 + 146712 species @@ -165,7 +175,7 @@ http_interactions: 33154 Opisthokonta - no rank + clade 33208 @@ -175,17 +185,17 @@ http_interactions: 6072 Eumetazoa - no rank + clade 33213 Bilateria - no rank + clade 33511 Deuterostomia - no rank + clade 7711 @@ -200,22 +210,22 @@ http_interactions: 7742 Vertebrata - no rank + clade 7776 Gnathostomata - no rank + clade 117570 Teleostomi - no rank + clade 117571 Euteleostomi - no rank + clade 8287 @@ -225,17 +235,17 @@ http_interactions: 1338369 Dipnotetrapodomorpha - no rank + clade 32523 Tetrapoda - no rank + clade 32524 Amniota - no rank + clade 40674 @@ -245,17 +255,17 @@ http_interactions: 32525 Theria - no rank + clade 9347 Eutheria - no rank + clade 1437010 Boreoeutheria - no rank + clade 314145 @@ -297,6 +307,10 @@ http_interactions: Accipiter striatus Sharp-shinned hawk + + authority + Accipiter striatus Vieillot, 1807 + authority Accipiter striatus Vieillot, 1808 @@ -328,7 +342,7 @@ http_interactions: 33154 Opisthokonta - no rank + clade 33208 @@ -338,17 +352,17 @@ http_interactions: 6072 Eumetazoa - no rank + clade 33213 Bilateria - no rank + clade 33511 Deuterostomia - no rank + clade 7711 @@ -363,22 +377,22 @@ http_interactions: 7742 Vertebrata - no rank + clade 7776 Gnathostomata - no rank + clade 117570 Teleostomi - no rank + clade 117571 Euteleostomi - no rank + clade 8287 @@ -388,57 +402,57 @@ http_interactions: 1338369 Dipnotetrapodomorpha - no rank + clade 32523 Tetrapoda - no rank + clade 32524 Amniota - no rank + clade 8457 Sauropsida - no rank + clade 32561 Sauria - no rank + clade 1329799 Archelosauria - no rank + clade 8492 Archosauria - no rank + clade 436486 Dinosauria - no rank + clade 436489 Saurischia - no rank + clade 436491 Theropoda - no rank + clade 436492 Coelurosauria - no rank + clade 8782 @@ -472,10 +486,10 @@ http_interactions: 1997/01/23 17:31:00 - 2017/06/14 10:56:24 + 2020/09/23 15:46:16 1997/07/02 01:00:00 - recorded_at: 2020-02-24 23:37:58 GMT - recorded_with: vcr/0.4.2.91, webmockr/0.5.1.98 + recorded_at: 2023-03-09 21:24:37 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 diff --git a/tests/fixtures/classification_variety_of_names.yml b/tests/fixtures/classification_variety_of_names.yml index d05faf86..1e550195 100644 --- a/tests/fixtures/classification_variety_of_names.yml +++ b/tests/fixtures/classification_variety_of_names.yml @@ -8,8 +8,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.97) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.97) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -17,25 +17,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 09 Jun 2020 01:45:41 GMT + date: Thu, 09 Mar 2023 21:24:37 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '9' - ncbi-phid: 939B5C81F6EEE0D500005A30917E6D2A.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: EB03103224018CF5_CA8DSID + ncbi-phid: 322C2D2E52F04595000056D50D170834.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 2B821E0BEBE4AC06_C1F7SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=2B821E0BEBE4AC06_C1F7SID; domain=.nih.gov; path=/; expires=Wed, - 09 Jun 2021 01:45:41 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=EB03103224018CF5_CA8DSID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:37 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -43,8 +45,8 @@ http_interactions: 110 992823 Regmatodon+orthostegius[All Names] All Names 1 N GROUP Regmatodon+orthostegius[All Names] - recorded_at: 2020-06-09 01:45:43 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:41 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&ID=992823&api_key=<> @@ -52,7 +54,7 @@ http_interactions: encoding: '' string: '' headers: - User-Agent: libcurl/7.70.0 r-curl/4.3 crul/0.9.0 + User-Agent: libcurl/7.81.0 r-curl/4.3.3 crul/1.3 Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* response: @@ -62,25 +64,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 09 Jun 2020 01:45:41 GMT + date: Thu, 09 Mar 2023 21:24:37 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '8' - ncbi-phid: 939B5C81F6EEE0D50000253091B072F8.1.1.m_3 + referrer-policy: origin-when-cross-origin + ncbi-sid: 8DFD1A1E79ECAC31_2877SID + ncbi-phid: 322C2D2E52F04595000030D50FBA3C1C.1.1.m_5 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 55BEDAE65289073B_98FBSID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=55BEDAE65289073B_98FBSID; domain=.nih.gov; path=/; expires=Wed, - 09 Jun 2021 01:45:42 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=8DFD1A1E79ECAC31_2877SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:38 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: |- @@ -91,7 +95,7 @@ http_interactions: authority - Regmatodon orthostegius Mont. + Regmatodon orthostegius Mont., 1842 324116 @@ -135,17 +139,17 @@ http_interactions: 3193 Embryophyta - no rank + clade 3208 Bryophyta - no rank + clade 404260 Bryophytina - no rank + clade 3214 @@ -190,8 +194,8 @@ http_interactions: - recorded_at: 2020-06-09 01:45:43 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:41 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Fagraea%2Bfragrans&api_key=<> @@ -201,8 +205,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.97) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.97) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -210,25 +214,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 09 Jun 2020 01:45:42 GMT + date: Thu, 09 Mar 2023 21:24:39 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '7' - ncbi-phid: 939B5C81F6EEE0D500003E309221D2C3.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: 322A4DBD61E5FCFA_F174SID + ncbi-phid: 322C2D2E52F04595000059D5140BF856.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 9B801FC7AB799015_1E45SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=9B801FC7AB799015_1E45SID; domain=.nih.gov; path=/; expires=Wed, - 09 Jun 2021 01:45:42 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=322A4DBD61E5FCFA_F174SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:39 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -236,8 +242,8 @@ http_interactions: 110 84942 Fagraea+fragrans[All Names] All Names 1 N GROUP Fagraea+fragrans[All Names] - recorded_at: 2020-06-09 01:45:43 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:41 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&ID=84942&api_key=<> @@ -245,7 +251,7 @@ http_interactions: encoding: '' string: '' headers: - User-Agent: libcurl/7.70.0 r-curl/4.3 crul/0.9.0 + User-Agent: libcurl/7.81.0 r-curl/4.3.3 crul/1.3 Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* response: @@ -255,39 +261,46 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 09 Jun 2020 01:45:42 GMT + date: Thu, 09 Mar 2023 21:24:40 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 939B5C81F6EEE0D500001430926495FF.1.1.m_3 + referrer-policy: origin-when-cross-origin + ncbi-sid: 0F92931871DD9CAA_EE12SID + ncbi-phid: 322C2D2E52F04595000029D516D09095.1.1.m_3 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: ABEC4FDA1944FCF5_FF19SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=ABEC4FDA1944FCF5_FF19SID; domain=.nih.gov; path=/; expires=Wed, - 09 Jun 2021 01:45:42 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=0F92931871DD9CAA_EE12SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:40 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: |- 84942 - Fagraea fragrans + Cyrtophyllum fragrans + Fagraea fragrans + + authority + Cyrtophyllum fragrans (Roxb.) DC., 1845 + authority - Fagraea fragrans Roxb. + Fagraea fragrans Roxb., 1824 - 26476 + 2546024 species Plants and Fungi @@ -298,7 +311,7 @@ http_interactions: 1 Standard - cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliopsida; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Gentianales; Gentianaceae; Potalieae; Potaliinae; Fagraea + cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliopsida; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Gentianales; Gentianaceae; Potalieae; Potaliinae; Cyrtophyllum 131567 @@ -328,22 +341,22 @@ http_interactions: 3193 Embryophyta - no rank + clade 58023 Tracheophyta - no rank + clade 78536 Euphyllophyta - no rank + clade 58024 Spermatophyta - no rank + clade 3398 @@ -353,32 +366,32 @@ http_interactions: 1437183 Mesangiospermae - no rank + clade 71240 eudicotyledons - no rank + clade 91827 Gunneridae - no rank + clade 1437201 Pentapetalae - no rank + clade 71274 asterids - no rank + clade 91888 lamiids - no rank + clade 4055 @@ -401,8 +414,8 @@ http_interactions: subtribe - 26476 - Fagraea + 2546024 + Cyrtophyllum genus @@ -413,10 +426,10 @@ http_interactions: 1998/11/19 17:47:00 - 2005/01/19 15:15:00 + 2021/10/12 17:40:04 1999/01/01 00:00:00 - recorded_at: 2020-06-09 01:45:43 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:41 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 diff --git a/tests/fixtures/classification_warn_on_db_mismatch.yml b/tests/fixtures/classification_warn_on_db_mismatch.yml index 65444fa4..4d4bd731 100644 --- a/tests/fixtures/classification_warn_on_db_mismatch.yml +++ b/tests/fixtures/classification_warn_on_db_mismatch.yml @@ -8,8 +8,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.92) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.92) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -17,25 +17,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Fri, 06 Mar 2020 01:30:50 GMT + date: Thu, 09 Mar 2023 21:24:42 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '9' - ncbi-phid: 322C9E4055AFCB5500003B3B9FE206B9.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: 7364432BE8D6AAEE_4B62SID + ncbi-phid: 322C2D2E52F04595000052D521807C75.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 7A0E2781C6707FB1_4A73SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '9' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=7A0E2781C6707FB1_4A73SID; domain=.nih.gov; path=/; expires=Sat, - 06 Mar 2021 01:30:51 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=7364432BE8D6AAEE_4B62SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:42 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -43,8 +45,8 @@ http_interactions: 110 315576 Chironomus+riparius[All Names] All Names 1 N GROUP Chironomus+riparius[All Names] - recorded_at: 2020-03-06 01:30:52 GMT - recorded_with: vcr/0.5.0, webmockr/0.6.0 + recorded_at: 2023-03-09 21:24:43 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&ID=315576&api_key=<> @@ -52,7 +54,7 @@ http_interactions: encoding: '' string: '' headers: - User-Agent: libcurl/7.54.0 r-curl/4.3 crul/0.9.0 + User-Agent: libcurl/7.81.0 r-curl/4.3.3 crul/1.3 Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* response: @@ -62,25 +64,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Fri, 06 Mar 2020 01:30:52 GMT + date: Thu, 09 Mar 2023 21:24:42 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '8' - ncbi-phid: D0BD321EAD513EE50000294CC30563B0.1.1.m_3 + referrer-policy: origin-when-cross-origin + ncbi-sid: E9587B9F07D501E6_4128SID + ncbi-phid: 322C2D2E52F0459500004FD5236AB7AA.1.1.m_3 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 90F67BE391C2AD4E_63B0SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=90F67BE391C2AD4E_63B0SID; domain=.nih.gov; path=/; expires=Sat, - 06 Mar 2021 01:30:52 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=E9587B9F07D501E6_4128SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:43 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: |- @@ -88,6 +92,12 @@ http_interactions: 315576 Chironomus riparius + + + authority + Chironomus riparius Meigen, 1804 + + 1165752 species Invertebrates @@ -99,7 +109,7 @@ http_interactions: 5 Invertebrate Mitochondrial - cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Diptera; Nematocera; Culicomorpha; Chironomoidea; Chironomidae; Chironominae; Chironomini; Chironomus; Chironomus incertae sedis + cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Culicomorpha; Chironomoidea; Chironomidae; Chironominae; Chironomini; Chironomus; Chironomus incertae sedis 131567 @@ -114,7 +124,7 @@ http_interactions: 33154 Opisthokonta - no rank + clade 33208 @@ -124,27 +134,27 @@ http_interactions: 6072 Eumetazoa - no rank + clade 33213 Bilateria - no rank + clade 33317 Protostomia - no rank + clade 1206794 Ecdysozoa - no rank + clade 88770 Panarthropoda - no rank + clade 6656 @@ -154,12 +164,12 @@ http_interactions: 197563 Mandibulata - no rank + clade 197562 Pancrustacea - no rank + clade 6960 @@ -174,7 +184,7 @@ http_interactions: 85512 Dicondylia - no rank + clade 7496 @@ -188,7 +198,7 @@ http_interactions: 33392 - Holometabola + Endopterygota cohort @@ -243,5 +253,5 @@ http_interactions: - recorded_at: 2020-03-06 01:30:52 GMT - recorded_with: vcr/0.5.0, webmockr/0.6.0 + recorded_at: 2023-03-09 21:24:43 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 diff --git a/tests/fixtures/comm2sci.yml b/tests/fixtures/comm2sci.yml index cff62932..97966797 100644 --- a/tests/fixtures/comm2sci.yml +++ b/tests/fixtures/comm2sci.yml @@ -8,8 +8,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.97) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.97) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -17,29 +17,40 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 09 Jun 2020 01:42:40 GMT + date: Thu, 09 Mar 2023 21:24:43 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '9' - ncbi-phid: 322C4109F0E1CE950000552585A1FD1F.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: 7511E427228B7251_FDFBSID + ncbi-phid: 322C2D2E52F04595000048D5291783FB.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 5D270936A2F6418C_4717SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '9' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=5D270936A2F6418C_4717SID; domain=.nih.gov; path=/; expires=Wed, - 09 Jun 2021 01:42:41 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=7511E427228B7251_FDFBSID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:44 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block 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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&ID=9643&api_key=<> @@ -49,8 +60,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.97) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.97) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -58,29 +69,120 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 09 Jun 2020 01:42:41 GMT + date: Thu, 09 Mar 2023 21:24:44 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '8' - ncbi-phid: 322C4109F0E1CE950000362586158972.1.1.m_5 + referrer-policy: origin-when-cross-origin + ncbi-sid: 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ICAgIDxUYXhvbj4KICAgICAgICAgICAgPFRheElkPjk2MzI8L1RheElkPgogICAgICAgICAgICA8U2Np + ZW50aWZpY05hbWU+VXJzaWRhZTwvU2NpZW50aWZpY05hbWU+CiAgICAgICAgICAgIDxSYW5rPmZhbWls + eTwvUmFuaz4KICAgICAgICA8L1RheG9uPgogICAgICAgIDxUYXhvbj4KICAgICAgICAgICAgPFRheElk + Pjk2Mzk8L1RheElkPgogICAgICAgICAgICA8U2NpZW50aWZpY05hbWU+VXJzdXM8L1NjaWVudGlmaWNO + YW1lPgogICAgICAgICAgICA8UmFuaz5nZW51czwvUmFuaz4KICAgICAgICA8L1RheG9uPgogICAgPC9M + aW5lYWdlRXg+CiAgICA8Q3JlYXRlRGF0ZT4xOTk1LzAyLzI3IDA5OjI0OjAwPC9DcmVhdGVEYXRlPgog + ICAgPFVwZGF0ZURhdGU+MjAyMC8wNC8yOCAyMjozMDowNjwvVXBkYXRlRGF0ZT4KICAgIDxQdWJEYXRl + PjE5OTMvMTEvMTkgMDA6MDA6MDA8L1B1YkRhdGU+CjwvVGF4b24+Cgo8L1RheGFTZXQ+ + recorded_at: 2023-03-09 21:24:48 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: http://services.tropicos.org/Name/Search?format=json&commonname=annual%20blue%20grass&apikey=<> @@ -90,8 +192,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.97) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.97) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -100,18 +202,22 @@ http_interactions: headers: status: HTTP/1.1 200 OK cache-control: private - content-length: '297' content-type: application/json; charset=utf-8 - server: Microsoft-IIS/7.5 + server: Microsoft-IIS/10.0 x-aspnet-version: 4.0.30319 x-powered-by: ASP.NET - date: Tue, 09 Jun 2020 01:42:41 GMT + date: Thu, 09 Mar 2023 21:24:47 GMT + content-length: '297' body: - encoding: ASCII-8BIT + encoding: '' file: no - string: W3siTmFtZUlkIjoyNTUwOTg4MSwiU2NpZW50aWZpY05hbWUiOiJQb2EgYW5udWEiLCJTY2llbnRpZmljTmFtZVdpdGhBdXRob3JzIjoiUG9hIGFubnVhIEwuIiwiRmFtaWx5IjoiUG9hY2VhZSIsIlJhbmtBYmJyZXZpYXRpb24iOiJzcC4iLCJOb21lbmNsYXR1cmVTdGF0dXNJRCI6MSwiTm9tZW5jbGF0dXJlU3RhdHVzTmFtZSI6IkxlZ2l0aW1hdGUiLCJTeW1ib2wiOiIhIiwiQXV0aG9yIjoiTC4iLCJEaXNwbGF5UmVmZXJlbmNlIjoiU3AuIFBsLiAxOiA2OCIsIkRpc3BsYXlEYXRlIjoiMTc1MyIsIlRvdGFsUm93cyI6MX1d - recorded_at: 2020-06-09 01:42:43 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + base64_string: W3siTmFtZUlkIjoyNTUwOTg4MSwiU2NpZW50aWZpY05hbWUiOiJQb2EgYW5udWEiLCJTY2llbnRpZmlj + TmFtZVdpdGhBdXRob3JzIjoiUG9hIGFubnVhIEwuIiwiRmFtaWx5IjoiUG9hY2VhZSIsIlJhbmtBYmJy + ZXZpYXRpb24iOiJzcC4iLCJOb21lbmNsYXR1cmVTdGF0dXNJRCI6MSwiTm9tZW5jbGF0dXJlU3RhdHVz + TmFtZSI6IkxlZ2l0aW1hdGUiLCJTeW1ib2wiOiIhIiwiQXV0aG9yIjoiTC4iLCJEaXNwbGF5UmVmZXJl + bmNlIjoiU3AuIFBsLiAxOiA2OCIsIkRpc3BsYXlEYXRlIjoiMTc1MyIsIlRvdGFsUm93cyI6MX1d + recorded_at: 2023-03-09 21:24:48 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: http://services.tropicos.org/Name/Search?format=json&commonname=black%20bear&apikey=<> @@ -121,8 +227,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.97) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.97) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -131,99 +237,20 @@ http_interactions: headers: status: HTTP/1.1 200 OK cache-control: private - content-length: '320' content-type: application/json; charset=utf-8 - server: Microsoft-IIS/7.5 + server: Microsoft-IIS/10.0 x-aspnet-version: 4.0.30319 x-powered-by: ASP.NET - date: Tue, 09 Jun 2020 01:42:41 GMT - body: - encoding: ASCII-8BIT - file: no - string: W3siTmFtZUlkIjoxMjMwMjQ0NiwiU2NpZW50aWZpY05hbWUiOiJBcmN0b3N0YXBoeWxvcyBhbHBpbmEiLCJTY2llbnRpZmljTmFtZVdpdGhBdXRob3JzIjoiQXJjdG9zdGFwaHlsb3MgYWxwaW5hIChMLikgU3ByZW5nLiIsIkZhbWlseSI6IkVyaWNhY2VhZSIsIlJhbmtBYmJyZXZpYXRpb24iOiJzcC4iLCJOb21lbmNsYXR1cmVTdGF0dXNOYW1lIjoiTm8gb3BpbmlvbiIsIkF1dGhvciI6IihMLikgU3ByZW5nLiIsIkRpc3BsYXlSZWZlcmVuY2UiOiJTeXN0LiBWZWcuIFtTcHJlbmdlbF0gMjogMjg3IiwiRGlzcGxheURhdGUiOiIxODI1IiwiVG90YWxSb3dzIjoxfV0= - recorded_at: 2020-06-09 01:42:43 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 -- request: - method: get - uri: https://eol.org/api/search/1.0.json?q=black%2Bbear&page=1 - body: - encoding: '' - string: '' - headers: - Accept-Encoding: gzip, deflate - Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.97) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.97) - response: - status: - status_code: '200' - message: OK - explanation: Request fulfilled, document follows - headers: - status: HTTP/1.1 200 OK - date: Tue, 09 Jun 2020 01:42:42 GMT - content-type: application/json; charset=utf-8 - content-length: '871' - connection: keep-alive - x-frame-options: ALLOWALL - x-robots-tag: noindex - etag: W/"24ef7e358fe86bc477c7a814cbf65e12" - cache-control: max-age=0, private, must-revalidate - x-request-id: 965315e3-8a23-405d-8c2e-c21ca79b2687 - x-runtime: '0.089491' - access-control-allow-origin: '*' - access-control-allow-methods: GET, POST, OPTIONS - access-control-allow-headers: DNT,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range - access-control-expose-headers: Content-Length,Content-Range - age: '0' - x-cache: MISS - x-cache-hits: '0' - accept-ranges: bytes - body: - encoding: ASCII-8BIT - file: no - string: 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 - recorded_at: 2020-06-09 01:42:43 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 -- request: - method: get - uri: https://eol.org/api/search/1.0.json?q=roe%2Bdeer&page=1 + date: Thu, 09 Mar 2023 21:24:47 GMT + content-length: '320' body: encoding: '' - string: '' - headers: - Accept-Encoding: gzip, deflate - Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.97) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.97) - response: - status: - status_code: '200' - message: OK - explanation: Request fulfilled, document follows - headers: - status: HTTP/1.1 200 OK - date: Tue, 09 Jun 2020 01:42:43 GMT - content-type: application/json; charset=utf-8 - content-length: '483' - connection: keep-alive - x-frame-options: ALLOWALL - x-robots-tag: noindex - etag: W/"bba140ef578e4ec60dedd9b4aa746f73" - cache-control: max-age=0, private, must-revalidate - x-request-id: 51f76fac-5e99-48be-8c42-1521cb6d3cd5 - x-runtime: '0.073592' - access-control-allow-origin: '*' - access-control-allow-methods: GET, POST, OPTIONS - access-control-allow-headers: DNT,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range - access-control-expose-headers: Content-Length,Content-Range - age: '0' - x-cache: MISS - x-cache-hits: '0' - accept-ranges: bytes - body: - encoding: ASCII-8BIT file: no - string: 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 - recorded_at: 2020-06-09 01:42:43 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + base64_string: W3siTmFtZUlkIjoxMjMwMjQ0NiwiU2NpZW50aWZpY05hbWUiOiJBcmN0b3N0YXBoeWxvcyBhbHBpbmEi + LCJTY2llbnRpZmljTmFtZVdpdGhBdXRob3JzIjoiQXJjdG9zdGFwaHlsb3MgYWxwaW5hIChMLikgU3By + ZW5nLiIsIkZhbWlseSI6IkVyaWNhY2VhZSIsIlJhbmtBYmJyZXZpYXRpb24iOiJzcC4iLCJOb21lbmNs + YXR1cmVTdGF0dXNOYW1lIjoiTm8gb3BpbmlvbiIsIkF1dGhvciI6IihMLikgU3ByZW5nLiIsIkRpc3Bs + YXlSZWZlcmVuY2UiOiJTeXN0LiBWZWcuIFtTcHJlbmdlbF0gMjogMjg3IiwiRGlzcGxheURhdGUiOiIx + ODI1IiwiVG90YWxSb3dzIjoxfV0= + recorded_at: 2023-03-09 21:24:48 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 diff --git a/tests/fixtures/comm2sci_warn_on_db_mismatch.yml b/tests/fixtures/comm2sci_warn_on_db_mismatch.yml index 606c9ca1..b54db3b1 100644 --- a/tests/fixtures/comm2sci_warn_on_db_mismatch.yml +++ b/tests/fixtures/comm2sci_warn_on_db_mismatch.yml @@ -8,8 +8,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -17,25 +17,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:17:50 GMT + date: Thu, 09 Mar 2023 21:24:48 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '9' - ncbi-phid: D0BD1587C1A6041500004D541787E32D.1.1.m_1 + referrer-policy: origin-when-cross-origin + ncbi-sid: B76A7F448C5A4A15_049ASID + ncbi-phid: D0BD29F778F3A20500005AFA91FA4B4C.1.1.m_1 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: CEE1B66F0C9D3900_2D47SID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '9' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=CEE1B66F0C9D3900_2D47SID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:17:50 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=B76A7F448C5A4A15_049ASID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:48 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: | @@ -43,8 +45,8 @@ http_interactions: 110 315576 Chironomus+riparius[All Names] All Names 1 N GROUP Chironomus+riparius[All Names] - recorded_at: 2020-05-05 00:17:51 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:50 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2 - request: method: get uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&ID=315576&api_key=<> @@ -54,8 +56,8 @@ http_interactions: headers: Accept-Encoding: gzip, deflate Accept: application/json, text/xml, application/xml, */* - User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.95.91) + User-Agent: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) + X-USER-AGENT: r-curl/4.3.3 crul/1.3 rOpenSci(taxize/0.9.100) response: status: status_code: '200' @@ -63,25 +65,27 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Tue, 05 May 2020 00:17:50 GMT + date: Thu, 09 Mar 2023 21:24:48 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '8' - ncbi-phid: D0BD1587C1A604150000265418CA46C4.1.1.m_3 + referrer-policy: origin-when-cross-origin + ncbi-sid: 485056E6C9A3EB59_9D66SID + ncbi-phid: D0BD29F778F3A205000046FA9349360D.1.1.m_3 + content-type: text/xml; charset=UTF-8 cache-control: private - ncbi-sid: 48323D7EE2FB8A95_333FSID content-encoding: gzip x-ratelimit-limit: '10' + x-ratelimit-remaining: '8' access-control-allow-origin: '*' - content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=48323D7EE2FB8A95_333FSID; domain=.nih.gov; path=/; expires=Wed, - 05 May 2021 00:17:51 GMT + access-control-expose-headers: X-RateLimit-Limit,X-RateLimit-Remaining + set-cookie: ncbi_sid=485056E6C9A3EB59_9D66SID; domain=.nih.gov; path=/; expires=Sat, + 09 Mar 2024 21:24:49 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked body: - encoding: UTF-8 + encoding: '' file: no string: |- @@ -89,6 +93,12 @@ http_interactions: 315576 Chironomus riparius + + + authority + Chironomus riparius Meigen, 1804 + + 1165752 species Invertebrates @@ -100,7 +110,7 @@ http_interactions: 5 Invertebrate Mitochondrial - cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Diptera; Nematocera; Culicomorpha; Chironomoidea; Chironomidae; Chironominae; Chironomini; Chironomus; Chironomus incertae sedis + cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Culicomorpha; Chironomoidea; Chironomidae; Chironominae; Chironomini; Chironomus; Chironomus incertae sedis 131567 @@ -115,7 +125,7 @@ http_interactions: 33154 Opisthokonta - no rank + clade 33208 @@ -125,27 +135,27 @@ http_interactions: 6072 Eumetazoa - no rank + clade 33213 Bilateria - no rank + clade 33317 Protostomia - no rank + clade 1206794 Ecdysozoa - no rank + clade 88770 Panarthropoda - no rank + clade 6656 @@ -155,12 +165,12 @@ http_interactions: 197563 Mandibulata - no rank + clade 197562 Pancrustacea - no rank + clade 6960 @@ -175,7 +185,7 @@ http_interactions: 85512 Dicondylia - no rank + clade 7496 @@ -189,7 +199,7 @@ http_interactions: 33392 - Holometabola + Endopterygota cohort @@ -244,5 +254,5 @@ http_interactions: - recorded_at: 2020-05-05 00:17:51 GMT - recorded_with: vcr/0.5.4, webmockr/0.6.2 + recorded_at: 2023-03-09 21:24:50 GMT + recorded_with: vcr/1.2.0, webmockr/0.8.2