diff --git a/R/class2tree.R b/R/class2tree.R index 5e5ce459..b19ce6a4 100644 --- a/R/class2tree.R +++ b/R/class2tree.R @@ -67,9 +67,13 @@ class2tree <- function(input, varstep = TRUE, check = TRUE, ...) { # Get rank and ID list rankList <- dt2df(lapply(input, get_rank), idcol = FALSE) nameList <- dt2df(lapply(input, get_name), idcol = FALSE) + strainIndex <- grep("norank", rankList$X1) + rankList$X1[strainIndex] <- "strain" + nameList$X1[strainIndex] <- + gsub("norank_[[:digit:]]+", "strain", nameList$X1[strainIndex]) # Create taxonomy matrix - df <- taxonomy_table_creator(nameList,rankList) + df <- taxonomy_table_creator(nameList, rankList) if (!inherits(df, "data.frame")) { stop("no taxon ranks in common - try different inputs") @@ -180,56 +184,63 @@ taxa2dist <- function(x, varstep = FALSE, check = TRUE, labels) { out } -############################################################################### -#################### GET LIST OF ALL TAXONOMY RANK AND IDs #################### -############################################################################### -get_rank <- function(x){ - rankDf <- x[, 'rank'] - names(rankDf) <- x[, 'rank'] - - idDf <- x[, 'id'] - joinedDf <- cbind(data.frame(rankDf,stringsAsFactors=FALSE), - data.frame(idDf,stringsAsFactors=FALSE)) - joinedDf <- within(joinedDf, - rankDf[rankDf=='no rank'] <- - paste0("norank_",idDf[rankDf=='no rank'])) - - df <- data.frame(t(data.frame(rev(joinedDf$rankDf))), - stringsAsFactors = FALSE) +#' Get full taxonomy ranks and IDs +#' @noRd +#' @author Vinh Tran {tran@bio.uni-frankfurt.de} +get_rank <- function (x) { + rank_df <- x[, 'rank'] + names(rank_df) <- x[, 'rank'] + + id_df <- x[, 'id'] + joined_df <- cbind( + data.frame(rank_df, stringsAsFactors = FALSE), + data.frame(id_df, stringsAsFactors = FALSE) + ) + joined_df <- within( + joined_df, + rank_df[rank_df=='no rank'] <- paste0("norank_", id_df[rank_df=='no rank']) + ) + df <- data.frame( + t(data.frame(rev(joined_df$rank_df))), stringsAsFactors = FALSE + ) outDf <- data.frame(tip = x[nrow(x), "name"], df, stringsAsFactors = FALSE) return(outDf) } -get_name <- function(x){ - rankDf <- x[, 'rank'] - names(rankDf) <- x[, 'rank'] +#' Get taxonomy names and IDs for all ranks +#' @noRd +#' @author Vinh Tran {tran@bio.uni-frankfurt.de} +get_name <- function (x) { + rank_df <- x[, 'rank'] + names(rank_df) <- x[, 'rank'] nameDf <- x[, 'name'] - idDf <- x[, 'id'] - - joinedDf <- cbind(data.frame(rankDf,stringsAsFactors=FALSE), - data.frame(nameDf,stringsAsFactors=FALSE)) - joinedDf <- within(joinedDf, - rankDf[rankDf=='no rank'] <- - paste0("norank_",idDf[rankDf=='no rank'])) - joinedDf$name <- paste0(joinedDf$nameDf,"##",joinedDf$rankDf) - - df <- data.frame(t(data.frame(rev(joinedDf$name))), stringsAsFactors = FALSE) + id_df <- x[, 'id'] + + joined_df <- cbind( + data.frame(rank_df,stringsAsFactors=FALSE), + data.frame(nameDf,stringsAsFactors=FALSE) + ) + joined_df <- within( + joined_df, + rank_df[rank_df=='no rank'] <- paste0("norank_",id_df[rank_df=='no rank']) + ) + joined_df$name <- paste0(joined_df$nameDf, "##", joined_df$rank_df) + + df <- data.frame(t(data.frame(rev(joined_df$name))), stringsAsFactors = FALSE) outDf <- data.frame(tip = x[nrow(x), "name"], df, stringsAsFactors = FALSE) return(outDf) } -############################################################################### -#################### INDEXING ALL AVAILABLE RANKS (INCLUDING NORANK) ########## -############################################################################### -rank_indexing <- function(rankList){ - ##### input is a dataframe, where each row is a rank list of a taxon - +#' Indexing all available ranks (including norank) +#' @noRd +#' @param rankList dataframe, whose each row is a rank list of a taxon +#' @return A dataframe containing a list of all possible ranks and their indexed +#' values. +#' @author Vinh Tran {tran@bio.uni-frankfurt.de} +rank_indexing <- function (rankList) { ### get all available ranks from input rankList - uList <- unlist(rankList) - # remove unique rank by replacing with NA - # (unique rank is uninformative for sorting taxa) - uList[!duplicated(uList)] <- NA + uList <- unlist(rankList[seq(2, length(rankList))]) # get final list of available ranks (remove NA items) allInputRank <- as.character(unique(uList)) allInputRank <- allInputRank[!is.na(allInputRank)] @@ -241,98 +252,136 @@ rank_indexing <- function(rankList){ "infraorder","suborder","order","superorder","infraclass", "subclass","class","superclass","subphylum","phylum", "superphylum","subkingdom","kingdom","superkingdom") - rank2Index <- new.env() - for(i in 1:length(mainRank)){ - rank2Index[[mainRank[i]]] = i - } + rank2index <- new.env(hash = TRUE) + getHash <- Vectorize(get, vectorize.args = "x") + assignHash <- Vectorize(assign, vectorize.args = c("x", "value")) + for (i in seq_len(length(mainRank))) rank2index[[mainRank[i]]] <- i ### the magic happens here - for(k in 1:nrow(rankList)){ - ### get subset of rank list for current taxon which - ### contains only ranks existing in allInputRank + for (k in seq_len(nrow(rankList))) { + ## get rank list for current taxon containing only ranks in allInputRank subList <- rankList[k,][!is.na(rankList[k,])] - filter <- sapply(subList, function(x) x %in% allInputRank) + filter <- vapply( + subList, function(x) x %in% allInputRank, FUN.VALUE = logical(1)) subList <- subList[filter] - - ### now go to each rank and check... - for(i in 1:length(subList)){ - ## if it has no index (probably only for norank), then... - if(is.null(rank2Index[[subList[i]]])){ - ## set index for this rank = the [available] index of previous rank + 1 - for(j in 1:length(subList)){ - if(!is.null(rank2Index[[subList[i-j]]])){ - rank2Index[[subList[i]]] = rank2Index[[subList[i-j]]] + 1 - break + ## indexing + tmpEnv <- new.env(hash = TRUE) + flag <- 0 + for (i in seq_len(length(subList))) { + iRank <- subList[i] + if (is.null(rank2index[[iRank]])) { + # for new rank: get index of prev avail from this taxon + for (j in seq_len(length(subList))) { + if (j < i) { + if (!is.null(tmpEnv[[subList[i - j]]])) { + tmpEnv[[iRank]] <- tmpEnv[[subList[i - j]]] + 1 + break + } + } else j = j - 1 + } + } else { + # for old rank + if (i > 1) { + if (flag == 0) { + currentIndex <- rank2index[[iRank]] } else { - j = j-1 + currentIndex <- tmpEnv[[iRank]] } - } - } - ## else, check if the current index is smaller than - ## the index of previous rank, - else { - if(i>1){ - preRank <- subList[i-1] - ## if so, increase index of this current rank - ## by (index of previous rank + 1) - if(rank2Index[[subList[i]]] <= rank2Index[[preRank]]){ - rank2Index[[subList[i]]] = rank2Index[[preRank]] + 1 + if (currentIndex <= tmpEnv[[subList[i-1]]]) { + if (flag == 0) { + tmpEnv[[iRank]] <- tmpEnv[[subList[i-1]]] + 1 + for ( + r in ls(rank2index)[!(ls(rank2index) %in% ls(tmpEnv))] + ) { + if (rank2index[[r]] >= currentIndex) { + tmpEnv[[r]] <- + rank2index[[r]] + (tmpEnv[[iRank]] - rank2index[[iRank]]) + flag <- 1 + } + } + } else { + step <- tmpEnv[[subList[i-1]]] - currentIndex + 1 + for (n in ls(rank2index)) { + if (rank2index[[n]] >= currentIndex) { + tmpEnv[[n]] <- rank2index[[n]] + step + } + } + } + assignHash(ls(tmpEnv), getHash(ls(tmpEnv), tmpEnv), rank2index) + } else { + if (is.null(tmpEnv[[iRank]])) { + tmpEnv[[iRank]] <- rank2index[[iRank]] + } } + } else { + tmpEnv[[iRank]] <- rank2index[[iRank]] } } } + assignHash(ls(tmpEnv), getHash(ls(tmpEnv), tmpEnv), rank2index) } - - ### output a list of indexed ranks - index2RankDf <- data.frame("index"=character(), - "rank"=character(), - stringsAsFactors=FALSE) - for(i in 1:length(allInputRank)){ - index2RankDf[i,] = c(rank2Index[[allInputRank[i]]],allInputRank[i]) - } - - index2RankDf$index <- as.numeric(index2RankDf$index) + + # convert env into dataframe and return + index2RankList <- lapply( + seq_len(length(allInputRank)), function (x) { + data.frame( + index = rank2index[[allInputRank[x]]], + rank = allInputRank[x], stringsAsFactors = FALSE + ) + } + ) + index2RankDf <- do.call(rbind, index2RankList) index2RankDf <- index2RankDf[with(index2RankDf, order(index2RankDf$index)),] - return(index2RankDf) } -############################################################################### -#################### ARRANGE RANK IDs INTO SORTED RANK LIST (index2RankDf) #### -############################################################################### -taxonomy_table_creator <- function(nameList,rankList){ +#' Align NCBI taxonomy IDs of list of taxa into a sorted rank list +#' @noRd +#' @param nameList a dataframe whose each row is a rank+ID list of a taxon +#' @param rankList a dataframe whose each row is a rank list of a taxon +#' @return An aligned taxonomy dataframe which contains all the available +#' taxonomy ranks from the id list and rank list +#' @author Vinh Tran {tran@bio.uni-frankfurt.de} +taxonomy_table_creator <- function (nameList, rankList) { colnames(nameList)[1] <- "tip" - - ### get indexed rank list + # get indexed rank list index2RankDf <- rank_indexing(rankList) - - ### get ordered rank list + # get ordered rank list orderedRank <- factor(index2RankDf$rank, levels = index2RankDf$rank) - - ### create a dataframe containing ordered ranks - full_rank_name_df <- data.frame("rank"=matrix(unlist(orderedRank), - nrow=length(orderedRank), - byrow=TRUE), - stringsAsFactors=FALSE) + # create a dataframe containing ordered ranks + full_rank_name_df <- data.frame( + "rank"= matrix(unlist(orderedRank), nrow = length(orderedRank), byrow=TRUE), + stringsAsFactors = FALSE + ) full_rank_name_df$index <- as.numeric(rownames(full_rank_name_df)) + + fullRankIDdf <- data.frame( + rank = matrix( + unlist(orderedRank), nrow = length(orderedRank), byrow = TRUE + ), stringsAsFactors = FALSE) + fullRankIDdf$index <- as.numeric(rownames(fullRankIDdf)) - for(i in 1:nrow(nameList)){ + for (i in 1:nrow(nameList)) { ### get list of all IDs for this taxon taxonDf <- data.frame(nameList[i,]) - taxonName <- unlist(strsplit(as.character(nameList[i,]$tip), - "##", - fixed = TRUE)) + taxonName <- unlist( + strsplit(as.character(nameList[i,]$tip), "##", fixed = TRUE) + ) ### convert into long format # mTaxonDf <- suppressWarnings(melt(taxonDf,id = "tip")) - mTaxonDf <- setDF(suppressWarnings(data.table::melt(as.data.table(taxonDf), - id = "tip"))) + mTaxonDf <- data.table::setDF( + suppressWarnings( + data.table::melt(data.table::as.data.table(taxonDf), id = "tip") + ) + ) ### get rank names and corresponding IDs - splitCol <- data.frame(do.call('rbind', - strsplit(as.character(mTaxonDf$value), - "##", - fixed=TRUE))) + splitCol <- data.frame( + do.call( + 'rbind', strsplit(as.character(mTaxonDf$value), "##", fixed=TRUE) + ) + ) mTaxonDf <- cbind(mTaxonDf,splitCol) ### remove NA cases @@ -342,22 +391,24 @@ taxonomy_table_creator <- function(nameList,rankList){ mTaxonDf <- mTaxonDf[,c("X1","X2")] if(mTaxonDf$X2[1] != index2RankDf$rank[1] && !index2RankDf$rank[1] %in% mTaxonDf$X2){ - mTaxonDf <- rbind(data.frame("X1"=mTaxonDf$X1[1], - "X2"=index2RankDf$rank[1]), - mTaxonDf) + mTaxonDf <- rbind( + data.frame("X1"=mTaxonDf$X1[1], "X2"=index2RankDf$rank[1]), mTaxonDf + ) } ### rename columns colnames(mTaxonDf) <- c(taxonName[1],"rank") ### merge with index2RankDf (Df contains all available ranks of input data) - full_rank_name_df <- merge(full_rank_name_df,mTaxonDf, by=c("rank"), all.x = TRUE) + full_rank_name_df <- merge( + full_rank_name_df,mTaxonDf, by=c("rank"), all.x = TRUE + ) ### reorder ranks full_rank_name_df <- full_rank_name_df[order(full_rank_name_df$index),] ### replace NA id by id of previous rank - full_rank_name_df <- na.locf(full_rank_name_df) + full_rank_name_df <- zoo::na.locf(full_rank_name_df) } ### remove index column @@ -372,7 +423,8 @@ taxonomy_table_creator <- function(nameList,rankList){ ### replace NA values in the dataframe t_full_rank_name_df if(nrow(t_full_rank_name_df[is.na(t_full_rank_name_df),]) > 0){ - t_full_rank_name_dfTMP <- t_full_rank_name_df[complete.cases(t_full_rank_name_df),] + t_full_rank_name_dfTMP <- + t_full_rank_name_df[complete.cases(t_full_rank_name_df),] t_full_rank_name_dfEdit <- t_full_rank_name_df[is.na(t_full_rank_name_df),] for(i in 1:nrow(t_full_rank_name_dfEdit)){ diff --git a/tests/fixtures/class2tree_classification_call.yml b/tests/fixtures/class2tree_classification_call.yml index e2a6db78..431d5cc8 100644 --- a/tests/fixtures/class2tree_classification_call.yml +++ b/tests/fixtures/class2tree_classification_call.yml @@ -1,15 +1,15 @@ http_interactions: - request: method: get - uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Klattia%2Bflava&api_key=<> + uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Klattia%2Bflava 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/0.9.92.92) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.92) + User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) + X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) response: status: status_code: '200' @@ -17,20 +17,20 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Fri, 06 Mar 2020 01:28:24 GMT + date: Tue, 17 Mar 2020 08:48:58 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '9' - ncbi-phid: D0BD321EAD513EE500003F4C3F34ECDE.1.1.m_1 + x-ratelimit-remaining: '2' + ncbi-phid: 939B870A2F8619D50000243EE4C78F2D.1.1.m_1 cache-control: private - ncbi-sid: ECCE7B8080C31EF6_97C4SID + ncbi-sid: E527634F7AEEBD65_A461SID content-encoding: gzip - x-ratelimit-limit: '10' + x-ratelimit-limit: '3' access-control-allow-origin: '*' content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=ECCE7B8080C31EF6_97C4SID; domain=.nih.gov; path=/; expires=Sat, - 06 Mar 2021 01:28:25 GMT + set-cookie: ncbi_sid=E527634F7AEEBD65_A461SID; domain=.nih.gov; path=/; expires=Wed, + 17 Mar 2021 08:48:58 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked @@ -43,19 +43,19 @@ http_interactions: 110 152733 Klattia+flava[All Names] All Names 1 N GROUP Klattia+flava[All Names] - recorded_at: 2020-03-06 01:28:30 GMT + recorded_at: 2020-03-17 08:49:12 GMT recorded_with: vcr/0.5.0, webmockr/0.6.0 - request: method: get - uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Trollius%2Bsibiricus&api_key=<> + uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Trollius%2Bsibiricus 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/0.9.92.92) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.92) + User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) + X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) response: status: status_code: '200' @@ -63,20 +63,20 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Fri, 06 Mar 2020 01:28:25 GMT + date: Tue, 17 Mar 2020 08:48:59 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '8' - ncbi-phid: 939B359643F5AE9500005C47555CF697.1.1.m_1 + x-ratelimit-remaining: '1' + ncbi-phid: 939B870A2F8619D50000423EE62B21F5.1.1.m_1 cache-control: private - ncbi-sid: AEB8BD4C361CC2D6_BABFSID + ncbi-sid: E2D62A80B9AA5371_48ADSID content-encoding: gzip - x-ratelimit-limit: '10' + x-ratelimit-limit: '3' access-control-allow-origin: '*' content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=AEB8BD4C361CC2D6_BABFSID; domain=.nih.gov; path=/; expires=Sat, - 06 Mar 2021 01:28:26 GMT + set-cookie: ncbi_sid=E2D62A80B9AA5371_48ADSID; domain=.nih.gov; path=/; expires=Wed, + 17 Mar 2021 08:48:59 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked @@ -89,19 +89,19 @@ http_interactions: 110 944286 Trollius+sibiricus[All Names] All Names 1 N GROUP Trollius+sibiricus[All Names] - recorded_at: 2020-03-06 01:28:30 GMT + recorded_at: 2020-03-17 08:49:12 GMT recorded_with: vcr/0.5.0, webmockr/0.6.0 - request: method: get - uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Arachis%2Bparaguariensis&api_key=<> + uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Arachis%2Bparaguariensis 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/0.9.92.92) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.92) + User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) + X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) response: status: status_code: '200' @@ -109,20 +109,20 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Fri, 06 Mar 2020 01:28:25 GMT + date: Tue, 17 Mar 2020 08:49:00 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '7' - ncbi-phid: 939B359643F5AE950000544755A3D57A.1.1.m_1 + x-ratelimit-remaining: '1' + ncbi-phid: 939B870A2F8619D50000223EE85AE057.1.1.m_1 cache-control: private - ncbi-sid: C222F7F9528082E2_E5F8SID + ncbi-sid: 675101529BA56C75_9BEFSID content-encoding: gzip - x-ratelimit-limit: '10' + x-ratelimit-limit: '3' access-control-allow-origin: '*' content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=C222F7F9528082E2_E5F8SID; domain=.nih.gov; path=/; expires=Sat, - 06 Mar 2021 01:28:26 GMT + set-cookie: ncbi_sid=675101529BA56C75_9BEFSID; domain=.nih.gov; path=/; expires=Wed, + 17 Mar 2021 08:49:00 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked @@ -135,19 +135,19 @@ http_interactions: 110 224337 Arachis+paraguariensis[All Names] All Names 1 N GROUP Arachis+paraguariensis[All Names] - recorded_at: 2020-03-06 01:28:30 GMT + recorded_at: 2020-03-17 08:49:12 GMT recorded_with: vcr/0.5.0, webmockr/0.6.0 - request: method: get - uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Tanacetum%2Bboreale&api_key=<> + uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Tanacetum%2Bboreale 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/0.9.92.92) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.92) + User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) + X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) response: status: status_code: '200' @@ -155,20 +155,20 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Fri, 06 Mar 2020 01:28:25 GMT + date: Tue, 17 Mar 2020 08:49:00 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '7' - ncbi-phid: 939B359643F5AE950000224755F57AAA.1.1.m_1 + x-ratelimit-remaining: '1' + ncbi-phid: 939B870A2F8619D50000593EEA4C0C2A.1.1.m_1 cache-control: private - ncbi-sid: C8EF0FB9F68B361F_74C9SID + ncbi-sid: 9AD72DAA4B0961E8_54B1SID content-encoding: gzip - x-ratelimit-limit: '10' + x-ratelimit-limit: '3' access-control-allow-origin: '*' content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=C8EF0FB9F68B361F_74C9SID; domain=.nih.gov; path=/; expires=Sat, - 06 Mar 2021 01:28:26 GMT + set-cookie: ncbi_sid=9AD72DAA4B0961E8_54B1SID; domain=.nih.gov; path=/; expires=Wed, + 17 Mar 2021 08:49:01 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked @@ -181,19 +181,19 @@ http_interactions: 110 128002 Tanacetum+boreale[All Names] All Names 1 N GROUP Tanacetum+boreale[All Names] - recorded_at: 2020-03-06 01:28:30 GMT + recorded_at: 2020-03-17 08:49:12 GMT recorded_with: vcr/0.5.0, webmockr/0.6.0 - request: method: get - uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Gentiana%2Byakushimensis&api_key=<> + uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Gentiana%2Byakushimensis 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/0.9.92.92) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.92) + User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) + X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) response: status: status_code: '200' @@ -201,20 +201,20 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Fri, 06 Mar 2020 01:28:26 GMT + date: Tue, 17 Mar 2020 08:49:00 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 939B359643F5AE9500002F475623CDAD.1.1.m_1 + x-ratelimit-remaining: '1' + ncbi-phid: 939B870A2F8619D500003F3EEBC2B77C.1.1.m_1 cache-control: private - ncbi-sid: DECF44A10D4A50A3_E7B6SID + ncbi-sid: CE1A71CA16D25119_F6B0SID content-encoding: gzip - x-ratelimit-limit: '10' + x-ratelimit-limit: '3' access-control-allow-origin: '*' content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=DECF44A10D4A50A3_E7B6SID; domain=.nih.gov; path=/; expires=Sat, - 06 Mar 2021 01:28:26 GMT + set-cookie: ncbi_sid=CE1A71CA16D25119_F6B0SID; domain=.nih.gov; path=/; expires=Wed, + 17 Mar 2021 08:49:01 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked @@ -227,19 +227,19 @@ http_interactions: 110 553063 Gentiana+yakushimensis[All Names] All Names 1 N GROUP Gentiana+yakushimensis[All Names] - recorded_at: 2020-03-06 01:28:30 GMT + recorded_at: 2020-03-17 08:49:12 GMT recorded_with: vcr/0.5.0, webmockr/0.6.0 - request: method: get - uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Sesamum%2Bschinzianum&api_key=<> + uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Sesamum%2Bschinzianum 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/0.9.92.92) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.92) + User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) + X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) response: status: status_code: '200' @@ -247,20 +247,20 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Fri, 06 Mar 2020 01:28:26 GMT + date: Tue, 17 Mar 2020 08:49:01 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 939B359643F5AE9500004547565787BD.1.1.m_1 + x-ratelimit-remaining: '1' + ncbi-phid: 939B870A2F8619D50000373EECD577D8.1.1.m_1 cache-control: private - ncbi-sid: 1249B5A889F50C1D_D4F9SID + ncbi-sid: AB51D9837A0A5E8E_93FESID content-encoding: gzip - x-ratelimit-limit: '10' + x-ratelimit-limit: '3' access-control-allow-origin: '*' content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=1249B5A889F50C1D_D4F9SID; domain=.nih.gov; path=/; expires=Sat, - 06 Mar 2021 01:28:27 GMT + set-cookie: ncbi_sid=AB51D9837A0A5E8E_93FESID; domain=.nih.gov; path=/; expires=Wed, + 17 Mar 2021 08:49:02 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked @@ -273,19 +273,19 @@ http_interactions: 110 768545 Sesamum+schinzianum[All Names] All Names 1 N GROUP Sesamum+schinzianum[All Names] - recorded_at: 2020-03-06 01:28:30 GMT + recorded_at: 2020-03-17 08:49:12 GMT recorded_with: vcr/0.5.0, webmockr/0.6.0 - request: method: get - uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Pilea%2Bverrucosa&api_key=<> + uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Pilea%2Bverrucosa 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/0.9.92.92) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.92) + User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) + X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) response: status: status_code: '200' @@ -293,20 +293,20 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Fri, 06 Mar 2020 01:28:26 GMT + date: Tue, 17 Mar 2020 08:49:01 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 939B359643F5AE9500002747569267BA.1.1.m_1 + x-ratelimit-remaining: '1' + ncbi-phid: 939B870A2F8619D500004B3EEE090160.1.1.m_1 cache-control: private - ncbi-sid: 11610C6021113FFF_18FFSID + ncbi-sid: 318BF9F584B3FD4E_1101SID content-encoding: gzip - x-ratelimit-limit: '10' + x-ratelimit-limit: '3' access-control-allow-origin: '*' content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=11610C6021113FFF_18FFSID; domain=.nih.gov; path=/; expires=Sat, - 06 Mar 2021 01:28:27 GMT + set-cookie: ncbi_sid=318BF9F584B3FD4E_1101SID; domain=.nih.gov; path=/; expires=Wed, + 17 Mar 2021 08:49:02 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked @@ -319,19 +319,19 @@ http_interactions: 110 1399730 Pilea+verrucosa[All Names] All Names 1 N GROUP Pilea+verrucosa[All Names] - recorded_at: 2020-03-06 01:28:30 GMT + recorded_at: 2020-03-17 08:49:12 GMT recorded_with: vcr/0.5.0, webmockr/0.6.0 - request: method: get - uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Tibouchina%2Bstriphnocalyx&api_key=<> + uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Tibouchina%2Bstriphnocalyx 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/0.9.92.92) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.92) + User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) + X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) response: status: status_code: '200' @@ -339,20 +339,20 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Fri, 06 Mar 2020 01:28:27 GMT + date: Tue, 17 Mar 2020 08:49:02 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 939B359643F5AE950000384756C27B1B.1.1.m_1 + x-ratelimit-remaining: '1' + ncbi-phid: 939B870A2F8619D50000373EEF77E3BD.1.1.m_1 cache-control: private - ncbi-sid: F284482E7734610C_2F1DSID + ncbi-sid: 4C47175352B2434D_B57CSID content-encoding: gzip - x-ratelimit-limit: '10' + x-ratelimit-limit: '3' access-control-allow-origin: '*' content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=F284482E7734610C_2F1DSID; domain=.nih.gov; path=/; expires=Sat, - 06 Mar 2021 01:28:27 GMT + set-cookie: ncbi_sid=4C47175352B2434D_B57CSID; domain=.nih.gov; path=/; expires=Wed, + 17 Mar 2021 08:49:03 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked @@ -365,19 +365,19 @@ http_interactions: 110 1160690 Tibouchina+striphnocalyx[All Names] All Names 1 N GROUP Tibouchina+striphnocalyx[All Names] - recorded_at: 2020-03-06 01:28:30 GMT + recorded_at: 2020-03-17 08:49:12 GMT recorded_with: vcr/0.5.0, webmockr/0.6.0 - request: method: get - uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Lycium%2Bdasystemum&api_key=<> + uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Lycium%2Bdasystemum 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/0.9.92.92) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.92) + User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) + X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) response: status: status_code: '200' @@ -385,20 +385,20 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Fri, 06 Mar 2020 01:28:27 GMT + date: Tue, 17 Mar 2020 08:49:02 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 939B359643F5AE9500005947572E966A.1.1.m_1 + x-ratelimit-remaining: '1' + ncbi-phid: 939B870A2F8619D50000223EF0BB2457.1.1.m_1 cache-control: private - ncbi-sid: 0AFFB85E479D7310_B586SID + ncbi-sid: 3C63143D0DFB7B5F_9882SID content-encoding: gzip - x-ratelimit-limit: '10' + x-ratelimit-limit: '3' access-control-allow-origin: '*' content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=0AFFB85E479D7310_B586SID; domain=.nih.gov; path=/; expires=Sat, - 06 Mar 2021 01:28:28 GMT + set-cookie: ncbi_sid=3C63143D0DFB7B5F_9882SID; domain=.nih.gov; path=/; expires=Wed, + 17 Mar 2021 08:49:03 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked @@ -411,19 +411,19 @@ http_interactions: 110 942185 Lycium+dasystemum[All Names] All Names 1 N GROUP Lycium+dasystemum[All Names] - recorded_at: 2020-03-06 01:28:30 GMT + recorded_at: 2020-03-17 08:49:12 GMT recorded_with: vcr/0.5.0, webmockr/0.6.0 - request: method: get - uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Berkheya%2Bechinacea&api_key=<> + uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Berkheya%2Bechinacea 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/0.9.92.92) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.92) + User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) + X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) response: status: status_code: '200' @@ -431,20 +431,20 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Fri, 06 Mar 2020 01:28:27 GMT + date: Tue, 17 Mar 2020 08:49:04 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 939B359643F5AE9500004547579FE5EB.1.1.m_1 + x-ratelimit-remaining: '1' + ncbi-phid: 939B870A2F8619D500005D3EF2159497.1.1.m_1 cache-control: private - ncbi-sid: 759671CDD9191091_DF00SID + ncbi-sid: 4087853D8AA6AB90_65ACSID content-encoding: gzip - x-ratelimit-limit: '10' + x-ratelimit-limit: '3' access-control-allow-origin: '*' content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=759671CDD9191091_DF00SID; domain=.nih.gov; path=/; expires=Sat, - 06 Mar 2021 01:28:28 GMT + set-cookie: ncbi_sid=4087853D8AA6AB90_65ACSID; domain=.nih.gov; path=/; expires=Wed, + 17 Mar 2021 08:49:04 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked @@ -457,19 +457,19 @@ http_interactions: 110 527996 Berkheya+echinacea[All Names] All Names 1 N GROUP Berkheya+echinacea[All Names] - recorded_at: 2020-03-06 01:28:30 GMT + recorded_at: 2020-03-17 08:49:12 GMT recorded_with: vcr/0.5.0, webmockr/0.6.0 - request: method: get - uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Androcymbium%2Bvillosum&api_key=<> + uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Androcymbium%2Bvillosum 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/0.9.92.92) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.92) + User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) + X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) response: status: status_code: '200' @@ -477,20 +477,20 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Fri, 06 Mar 2020 01:28:28 GMT + date: Tue, 17 Mar 2020 08:49:04 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 939B359643F5AE95000055475802E003.1.1.m_1 + x-ratelimit-remaining: '1' + ncbi-phid: 939B870A2F8619D50000393EF36869C4.1.1.m_1 cache-control: private - ncbi-sid: 6C0593350F5B7858_B531SID + ncbi-sid: 5C0F72873D4812AE_ADBESID content-encoding: gzip - x-ratelimit-limit: '10' + x-ratelimit-limit: '3' access-control-allow-origin: '*' content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=6C0593350F5B7858_B531SID; domain=.nih.gov; path=/; expires=Sat, - 06 Mar 2021 01:28:28 GMT + set-cookie: ncbi_sid=5C0F72873D4812AE_ADBESID; domain=.nih.gov; path=/; expires=Wed, + 17 Mar 2021 08:49:04 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked @@ -503,19 +503,19 @@ http_interactions: 110 279457 Androcymbium+villosum[All Names] All Names 1 N GROUP Androcymbium+villosum[All Names] - recorded_at: 2020-03-06 01:28:30 GMT + recorded_at: 2020-03-17 08:49:12 GMT recorded_with: vcr/0.5.0, webmockr/0.6.0 - request: method: get - uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Helianthus%2Bannuus&api_key=<> + uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Helianthus%2Bannuus 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/0.9.92.92) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.92) + User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) + X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) response: status: status_code: '200' @@ -523,20 +523,20 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Fri, 06 Mar 2020 01:28:28 GMT + date: Tue, 17 Mar 2020 08:49:04 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 939B359643F5AE950000294758B7C6D9.1.1.m_1 + x-ratelimit-remaining: '1' + ncbi-phid: 939B870A2F8619D50000583EF4436196.1.1.m_1 cache-control: private - ncbi-sid: 9AD7ADDF9535CF91_365FSID + ncbi-sid: F0CDB922D1BCDB01_C5E3SID content-encoding: gzip - x-ratelimit-limit: '10' + x-ratelimit-limit: '3' access-control-allow-origin: '*' content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=9AD7ADDF9535CF91_365FSID; domain=.nih.gov; path=/; expires=Sat, - 06 Mar 2021 01:28:28 GMT + set-cookie: ncbi_sid=F0CDB922D1BCDB01_C5E3SID; domain=.nih.gov; path=/; expires=Wed, + 17 Mar 2021 08:49:05 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked @@ -549,19 +549,19 @@ http_interactions: 110 4232 Helianthus+annuus[All Names] All Names 1 N GROUP Helianthus+annuus[All Names] - recorded_at: 2020-03-06 01:28:30 GMT + recorded_at: 2020-03-17 08:49:12 GMT recorded_with: vcr/0.5.0, webmockr/0.6.0 - request: method: get - uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Madia%2Belegans&api_key=<> + uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Madia%2Belegans 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/0.9.92.92) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.92) + User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) + X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) response: status: status_code: '200' @@ -569,20 +569,20 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Fri, 06 Mar 2020 01:28:28 GMT + date: Tue, 17 Mar 2020 08:49:05 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 939B359643F5AE9500005847594B2F99.1.1.m_1 + x-ratelimit-remaining: '1' + ncbi-phid: 939B870A2F8619D50000333EF4CE164B.1.1.m_1 cache-control: private - ncbi-sid: 162E82F3052337CB_413FSID + ncbi-sid: D5658C7F3EE3050C_510ASID content-encoding: gzip - x-ratelimit-limit: '10' + x-ratelimit-limit: '3' access-control-allow-origin: '*' content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=162E82F3052337CB_413FSID; domain=.nih.gov; path=/; expires=Sat, - 06 Mar 2021 01:28:29 GMT + set-cookie: ncbi_sid=D5658C7F3EE3050C_510ASID; domain=.nih.gov; path=/; expires=Wed, + 17 Mar 2021 08:49:05 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked @@ -595,19 +595,19 @@ http_interactions: 110 4255 Madia+elegans[All Names] All Names 1 N GROUP Madia+elegans[All Names] - recorded_at: 2020-03-06 01:28:30 GMT + recorded_at: 2020-03-17 08:49:12 GMT recorded_with: vcr/0.5.0, webmockr/0.6.0 - request: method: get - uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Lupinus%2Balbicaulis&api_key=<> + uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Lupinus%2Balbicaulis 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/0.9.92.92) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.92) + User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) + X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) response: status: status_code: '200' @@ -615,20 +615,20 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Fri, 06 Mar 2020 01:28:29 GMT + date: Tue, 17 Mar 2020 08:49:06 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '7' - ncbi-phid: 939B359643F5AE9500002B475A23D250.1.1.m_1 + x-ratelimit-remaining: '1' + ncbi-phid: 939B870A2F8619D50000583EF592E934.1.1.m_1 cache-control: private - ncbi-sid: D218272CFC192FE1_6920SID + ncbi-sid: 7150EBAB010974BD_8C4FSID content-encoding: gzip - x-ratelimit-limit: '10' + x-ratelimit-limit: '3' access-control-allow-origin: '*' content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=D218272CFC192FE1_6920SID; domain=.nih.gov; path=/; expires=Sat, - 06 Mar 2021 01:28:29 GMT + set-cookie: ncbi_sid=7150EBAB010974BD_8C4FSID; domain=.nih.gov; path=/; expires=Wed, + 17 Mar 2021 08:49:06 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked @@ -641,19 +641,19 @@ http_interactions: 110 377318 Lupinus+albicaulis[All Names] All Names 1 N GROUP Lupinus+albicaulis[All Names] - recorded_at: 2020-03-06 01:28:30 GMT + recorded_at: 2020-03-17 08:49:12 GMT recorded_with: vcr/0.5.0, webmockr/0.6.0 - request: method: get - uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Pinus%2Blambertiana&api_key=<> + uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Pinus%2Blambertiana 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/0.9.92.92) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.92) + User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) + X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) response: status: status_code: '200' @@ -661,20 +661,20 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Fri, 06 Mar 2020 01:28:28 GMT + date: Tue, 17 Mar 2020 08:49:06 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 939B359643F5AE95000052475AB3F629.1.1.m_1 + x-ratelimit-remaining: '1' + ncbi-phid: 939B870A2F8619D500002A3EF64F0617.1.1.m_1 cache-control: private - ncbi-sid: 51966F5062331BE3_CC6BSID + ncbi-sid: EC53FBCF77FCF756_EE5CSID content-encoding: gzip - x-ratelimit-limit: '10' + x-ratelimit-limit: '3' access-control-allow-origin: '*' content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=51966F5062331BE3_CC6BSID; domain=.nih.gov; path=/; expires=Sat, - 06 Mar 2021 01:28:29 GMT + set-cookie: ncbi_sid=EC53FBCF77FCF756_EE5CSID; domain=.nih.gov; path=/; expires=Wed, + 17 Mar 2021 08:49:06 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked @@ -687,19 +687,19 @@ http_interactions: 110 3343 Pinus+lambertiana[All Names] All Names 1 N GROUP Pinus+lambertiana[All Names] - recorded_at: 2020-03-06 01:28:30 GMT + recorded_at: 2020-03-17 08:49:12 GMT recorded_with: vcr/0.5.0, webmockr/0.6.0 - request: method: get - uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Haloarcula%2Bamylolytica%2BJCM%2B13557&api_key=<> + uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Haloarcula%2Bamylolytica%2BJCM%2B13557 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/0.9.92.92) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.92) + User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) + X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) response: status: status_code: '200' @@ -707,20 +707,20 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Fri, 06 Mar 2020 01:28:30 GMT + date: Tue, 17 Mar 2020 08:49:07 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '7' - ncbi-phid: 939B359643F5AE9500004E475BA31C11.1.1.m_1 + x-ratelimit-remaining: '1' + ncbi-phid: 939B870A2F8619D50000293EF6F09E94.1.1.m_1 cache-control: private - ncbi-sid: 1AC351952FEDC5B9_D630SID + ncbi-sid: 39C31512586EA74D_C29CSID content-encoding: gzip - x-ratelimit-limit: '10' + x-ratelimit-limit: '3' access-control-allow-origin: '*' content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=1AC351952FEDC5B9_D630SID; domain=.nih.gov; path=/; expires=Sat, - 06 Mar 2021 01:28:30 GMT + set-cookie: ncbi_sid=39C31512586EA74D_C29CSID; domain=.nih.gov; path=/; expires=Wed, + 17 Mar 2021 08:49:07 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked @@ -733,19 +733,19 @@ http_interactions: 110 1227452 Haloarcula+amylolytica+JCM+13557[All Names] All Names 1 N GROUP Haloarcula+amylolytica+JCM+13557[All Names] - recorded_at: 2020-03-06 01:28:30 GMT + recorded_at: 2020-03-17 08:49:12 GMT recorded_with: vcr/0.5.0, webmockr/0.6.0 - 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=<> + uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Halomonas%2Bsp.%2B%27Soap%2BLake%2B%236%27 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/0.9.92.92) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.92) + User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) + X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) response: status: status_code: '200' @@ -753,20 +753,20 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Fri, 06 Mar 2020 01:28:29 GMT + date: Tue, 17 Mar 2020 08:49:07 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 939B359643F5AE9500002C475C315E6D.1.1.m_1 + x-ratelimit-remaining: '1' + ncbi-phid: 939B870A2F8619D500003D3EF7D553F8.1.1.m_1 cache-control: private - ncbi-sid: FD3EAF4E0FDFA628_60C3SID + ncbi-sid: AD5E65163EC7D2A8_B2A3SID content-encoding: gzip - x-ratelimit-limit: '10' + x-ratelimit-limit: '3' access-control-allow-origin: '*' content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=FD3EAF4E0FDFA628_60C3SID; domain=.nih.gov; path=/; expires=Sat, - 06 Mar 2021 01:28:30 GMT + set-cookie: ncbi_sid=AD5E65163EC7D2A8_B2A3SID; domain=.nih.gov; path=/; expires=Wed, + 17 Mar 2021 08:49:08 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked @@ -779,11 +779,11 @@ 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: 2020-03-06 01:28:30 GMT + recorded_at: 2020-03-17 08:49:12 GMT recorded_with: vcr/0.5.0, webmockr/0.6.0 - 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=<> + 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 body: encoding: '' string: '' @@ -798,20 +798,20 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Fri, 06 Mar 2020 01:28:30 GMT + date: Tue, 17 Mar 2020 08:49:08 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 939B359643F5AE9500004F475CF4FF1C.1.1.m_3 + x-ratelimit-remaining: '1' + ncbi-phid: 939B870A2F8619D500001F3EF8687152.1.1.m_5 cache-control: private - ncbi-sid: 520BA015C2313677_D06ASID + ncbi-sid: EF942809A706CA3D_9162SID content-encoding: gzip - x-ratelimit-limit: '10' + x-ratelimit-limit: '3' access-control-allow-origin: '*' content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=520BA015C2313677_D06ASID; domain=.nih.gov; path=/; expires=Sat, - 06 Mar 2021 01:28:30 GMT + set-cookie: ncbi_sid=EF942809A706CA3D_9162SID; domain=.nih.gov; path=/; expires=Wed, + 17 Mar 2021 08:49:08 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked @@ -2998,5 +2998,5 @@ http_interactions: - recorded_at: 2020-03-06 01:28:30 GMT + recorded_at: 2020-03-17 08:49:12 GMT recorded_with: vcr/0.5.0, webmockr/0.6.0 diff --git a/tests/fixtures/class2tree_classification_dup_call.yml b/tests/fixtures/class2tree_classification_dup_call.yml index a05b7f21..6b02156b 100644 --- a/tests/fixtures/class2tree_classification_dup_call.yml +++ b/tests/fixtures/class2tree_classification_dup_call.yml @@ -1,15 +1,15 @@ http_interactions: - request: method: get - uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Mus%2Bmusculus&api_key=<> + uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Mus%2Bmusculus 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/0.9.92.92) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.92) + User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) + X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) response: status: status_code: '200' @@ -17,20 +17,20 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Fri, 06 Mar 2020 01:28:31 GMT + date: Tue, 17 Mar 2020 08:49:10 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '8' - ncbi-phid: 939B359643F5AE95000042475F0CC912.1.1.m_1 + x-ratelimit-remaining: '2' + ncbi-phid: 939B870A2F8619D50000303EFAD0E714.1.1.m_1 cache-control: private - ncbi-sid: C3055F8DB5E8EE69_B3C3SID + ncbi-sid: FA6E03631F40D124_B86ESID content-encoding: gzip - x-ratelimit-limit: '10' + x-ratelimit-limit: '3' access-control-allow-origin: '*' content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=C3055F8DB5E8EE69_B3C3SID; domain=.nih.gov; path=/; expires=Sat, - 06 Mar 2021 01:28:31 GMT + set-cookie: ncbi_sid=FA6E03631F40D124_B86ESID; domain=.nih.gov; path=/; expires=Wed, + 17 Mar 2021 08:49:10 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked @@ -43,19 +43,19 @@ http_interactions: 110 10090 Mus+musculus[All Names] All Names 1 N GROUP Mus+musculus[All Names] - recorded_at: 2020-03-06 01:28:32 GMT + recorded_at: 2020-03-17 08:49:15 GMT recorded_with: vcr/0.5.0, webmockr/0.6.0 - request: method: get - uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Escherichia%2Bcoli&api_key=<> + uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Escherichia%2Bcoli 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/0.9.92.92) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.92) + User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) + X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) response: status: status_code: '200' @@ -63,20 +63,20 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Fri, 06 Mar 2020 01:28:31 GMT + date: Tue, 17 Mar 2020 08:49:10 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '8' - ncbi-phid: 939B359643F5AE9500005B475F989A6B.1.1.m_1 + x-ratelimit-remaining: '1' + ncbi-phid: 939B870A2F8619D50000403EFB54EB54.1.1.m_1 cache-control: private - ncbi-sid: 0AD624F39A874AA4_0B40SID + ncbi-sid: 957F3E6DC3A8C595_24ADSID content-encoding: gzip - x-ratelimit-limit: '10' + x-ratelimit-limit: '3' access-control-allow-origin: '*' content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=0AD624F39A874AA4_0B40SID; domain=.nih.gov; path=/; expires=Sat, - 06 Mar 2021 01:28:31 GMT + set-cookie: ncbi_sid=957F3E6DC3A8C595_24ADSID; domain=.nih.gov; path=/; expires=Wed, + 17 Mar 2021 08:49:11 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked @@ -89,19 +89,19 @@ http_interactions: 110 562 Escherichia+coli[All Names] All Names 1 N GROUP Escherichia+coli[All Names] - recorded_at: 2020-03-06 01:28:32 GMT + recorded_at: 2020-03-17 08:49:15 GMT recorded_with: vcr/0.5.0, webmockr/0.6.0 - request: method: get - uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Haloferax%2Bdenitrificans&api_key=<> + uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Haloferax%2Bdenitrificans 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/0.9.92.92) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.92) + User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) + X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) response: status: status_code: '200' @@ -109,20 +109,20 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Fri, 06 Mar 2020 01:28:31 GMT + date: Tue, 17 Mar 2020 08:49:11 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '7' - ncbi-phid: 939B359643F5AE9500002647601D2C56.1.1.m_1 + x-ratelimit-remaining: '0' + ncbi-phid: 939B870A2F8619D500003D3EFBC8835F.1.1.m_1 cache-control: private - ncbi-sid: 0BF628704916A2C2_56A2SID + ncbi-sid: C52918AD6F84FA2A_A035SID content-encoding: gzip - x-ratelimit-limit: '10' + x-ratelimit-limit: '3' access-control-allow-origin: '*' content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=0BF628704916A2C2_56A2SID; domain=.nih.gov; path=/; expires=Sat, - 06 Mar 2021 01:28:32 GMT + set-cookie: ncbi_sid=C52918AD6F84FA2A_A035SID; domain=.nih.gov; path=/; expires=Wed, + 17 Mar 2021 08:49:11 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked @@ -135,19 +135,19 @@ http_interactions: 110 35745 Haloferax+denitrificans[All Names] All Names 1 N GROUP Haloferax+denitrificans[All Names] - recorded_at: 2020-03-06 01:28:32 GMT + recorded_at: 2020-03-17 08:49:15 GMT recorded_with: vcr/0.5.0, webmockr/0.6.0 - request: method: get - uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Mus%2Bmusculus&api_key=<> + uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Mus%2Bmusculus 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/0.9.92.92) - X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.92) + User-Agent: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) + X-USER-AGENT: r-curl/4.3 crul/0.9.0 rOpenSci(taxize/0.9.92.95) response: status: status_code: '200' @@ -155,20 +155,20 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Fri, 06 Mar 2020 01:28:32 GMT + date: Tue, 17 Mar 2020 08:49:11 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 939B359643F5AE950000424760D895F4.1.1.m_1 + x-ratelimit-remaining: '1' + ncbi-phid: 939B870A2F8619D500005C3EFC2C905B.1.1.m_1 cache-control: private - ncbi-sid: 9FA824582CDC1E26_82EESID + ncbi-sid: 5AFC736DE882444B_26B0SID content-encoding: gzip - x-ratelimit-limit: '10' + x-ratelimit-limit: '3' access-control-allow-origin: '*' content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=9FA824582CDC1E26_82EESID; domain=.nih.gov; path=/; expires=Sat, - 06 Mar 2021 01:28:32 GMT + set-cookie: ncbi_sid=5AFC736DE882444B_26B0SID; domain=.nih.gov; path=/; expires=Wed, + 17 Mar 2021 08:49:12 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked @@ -181,11 +181,11 @@ http_interactions: 110 10090 Mus+musculus[All Names] All Names 1 N GROUP Mus+musculus[All Names] - recorded_at: 2020-03-06 01:28:32 GMT + recorded_at: 2020-03-17 08:49:15 GMT recorded_with: vcr/0.5.0, webmockr/0.6.0 - request: method: get - uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&ID=10090%2C562%2C35745%2C10090&api_key=<> + uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&ID=10090%2C562%2C35745%2C10090 body: encoding: '' string: '' @@ -200,20 +200,20 @@ http_interactions: explanation: Request fulfilled, document follows headers: status: HTTP/1.1 200 OK - date: Fri, 06 Mar 2020 01:28:31 GMT + date: Tue, 17 Mar 2020 08:49:12 GMT server: Finatra strict-transport-security: max-age=31536000; includeSubDomains; preload content-security-policy: upgrade-insecure-requests - x-ratelimit-remaining: '6' - ncbi-phid: 939B359643F5AE9500004A47618007F0.1.1.m_5 + x-ratelimit-remaining: '1' + ncbi-phid: 939B870A2F8619D50000523EFC79168A.1.1.m_3 cache-control: private - ncbi-sid: 4E72EFEB6F50BBCF_0DD5SID + ncbi-sid: F6BEB181A3E5EB83_E615SID content-encoding: gzip - x-ratelimit-limit: '10' + x-ratelimit-limit: '3' access-control-allow-origin: '*' content-type: text/xml; charset=UTF-8 - set-cookie: ncbi_sid=4E72EFEB6F50BBCF_0DD5SID; domain=.nih.gov; path=/; expires=Sat, - 06 Mar 2021 01:28:32 GMT + set-cookie: ncbi_sid=F6BEB181A3E5EB83_E615SID; domain=.nih.gov; path=/; expires=Wed, + 17 Mar 2021 08:49:13 GMT x-ua-compatible: IE=Edge x-xss-protection: 1; mode=block transfer-encoding: chunked @@ -899,5 +899,5 @@ http_interactions: - recorded_at: 2020-03-06 01:28:32 GMT + recorded_at: 2020-03-17 08:49:15 GMT recorded_with: vcr/0.5.0, webmockr/0.6.0 diff --git a/tests/testthat/test-class2tree.R b/tests/testthat/test-class2tree.R index bf25e62d..c803bb61 100644 --- a/tests/testthat/test-class2tree.R +++ b/tests/testthat/test-class2tree.R @@ -1,12 +1,13 @@ context("class2tree") spnames <- c("Klattia flava", "Trollius sibiricus", "Arachis paraguariensis", - "Tanacetum boreale", "Gentiana yakushimensis", "Sesamum schinzianum", - "Pilea verrucosa", "Tibouchina striphnocalyx", "Lycium dasystemum", - "Berkheya echinacea", "Androcymbium villosum", - "Helianthus annuus", "Madia elegans", "Lupinus albicaulis", - "Pinus lambertiana", "Haloarcula amylolytica JCM 13557", - "Halomonas sp. 'Soap Lake #6'") + "Tanacetum boreale", "Gentiana yakushimensis", "Sesamum schinzianum", + "Pilea verrucosa", "Tibouchina striphnocalyx", "Lycium dasystemum", + "Berkheya echinacea", "Androcymbium villosum", + "Helianthus annuus", "Madia elegans", "Lupinus albicaulis", + "Pinus lambertiana", "Haloarcula amylolytica JCM 13557", + "Halomonas sp. 'Soap Lake #6'") + dupnames <- c("Mus musculus", "Escherichia coli", "Haloferax denitrificans", "Mus musculus")