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CI tests

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dr. M.S. (Matthijs) Berends
2019-05-13 12:21:57 +02:00
parent 38a4421450
commit 0dc0715dc6
21 changed files with 137 additions and 68 deletions
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32
R/mo.R
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@ -557,22 +557,22 @@ exec_as.mo <- function(x,
if (nchar(gsub("[^a-zA-Z]", "", x_trimmed[i])) < 3
& !x_backup_without_spp[i] %like% "O?(26|103|104|104|111|121|145|157)") {
# check if search term was like "A. species", then return first genus found with ^A
if (x_backup[i] %like% "[a-z]+ species" | x_backup[i] %like% "[a-z] spp[.]?") {
# get mo code of first hit
found <- microorganismsDT[fullname %like% x_withspaces_start_only[i], mo]
if (length(found) > 0) {
mo_code <- found[1L] %>% strsplit("_") %>% unlist() %>% .[1:2] %>% paste(collapse = "_")
found <- microorganismsDT[mo == mo_code, ..property][[1]]
# return first genus that begins with x_trimmed, e.g. when "E. spp."
if (length(found) > 0) {
x[i] <- found[1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
}
next
}
}
}
# if (x_backup[i] %like% "[a-z]+ species" | x_backup[i] %like% "[a-z] spp[.]?") {
# # get mo code of first hit
# found <- microorganismsDT[fullname %like% x_withspaces_start_only[i], mo]
# if (length(found) > 0) {
# mo_code <- found[1L] %>% strsplit("_") %>% unlist() %>% .[1:2] %>% paste(collapse = "_")
# found <- microorganismsDT[mo == mo_code, ..property][[1]]
# # return first genus that begins with x_trimmed, e.g. when "E. spp."
# if (length(found) > 0) {
# x[i] <- found[1L]
# if (initial_search == TRUE) {
# set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
# }
# next
# }
# }
# }
# fewer than 3 chars and not looked for species, add as failure
x[i] <- microorganismsDT[mo == "UNKNOWN", ..property][[1]]
if (initial_search == TRUE) {