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unit tests
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20
R/mo.R
20
R/mo.R
@ -325,7 +325,8 @@ as.mo <- function(x,
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result_mo <- NA_character_
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} else {
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result_mo <- AMR_env$MO_lookup$mo[match(top_hits[1], AMR_env$MO_lookup$fullname)]
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AMR_env$mo_uncertainties <- rbind2(AMR_env$mo_uncertainties,
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AMR_env$mo_uncertainties <- rbind2(
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AMR_env$mo_uncertainties,
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data.frame(
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original_input = x_search,
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input = x_search_cleaned,
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@ -335,14 +336,17 @@ as.mo <- function(x,
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minimum_matching_score = ifelse(is.null(minimum_matching_score), "NULL", minimum_matching_score),
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keep_synonyms = keep_synonyms,
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stringsAsFactors = FALSE
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))
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)
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)
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# save to package env to save time for next time
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AMR_env$mo_previously_coerced <- unique(rbind2(AMR_env$mo_previously_coerced,
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AMR_env$mo_previously_coerced <- unique(rbind2(
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AMR_env$mo_previously_coerced,
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data.frame(
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x = paste(x_search, minimum_matching_score),
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mo = result_mo,
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stringsAsFactors = FALSE
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)))
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)
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))
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}
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# the actual result:
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as.character(result_mo)
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@ -797,14 +801,14 @@ print.mo_uncertainties <- function(x, ...) {
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}
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cat(word_wrap("Matching scores are based on the resemblance between the input and the full taxonomic name, and the pathogenicity in humans. See `?mo_matching_score`.\n\n", add_fn = font_blue))
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add_MO_lookup_to_AMR_env()
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col_red <- function(x) font_rose_bg(font_black(x, collapse = NULL), collapse = NULL)
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col_orange <- function(x) font_orange_bg(font_black(x, collapse = NULL), collapse = NULL)
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col_yellow <- function(x) font_yellow_bg(font_black(x, collapse = NULL), collapse = NULL)
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col_green <- function(x) font_green_bg(font_black(x, collapse = NULL), collapse = NULL)
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if (has_colour()) {
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cat(word_wrap("Colour keys: ",
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col_red(" 0.000-0.499 "),
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@ -814,7 +818,7 @@ print.mo_uncertainties <- function(x, ...) {
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add_fn = font_blue
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), font_green_bg(" "), "\n", sep = "")
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}
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score_set_colour <- function(text, scores) {
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# set colours to scores
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text[scores >= 0.7] <- col_green(text[scores >= 0.7])
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