Fixed Otoliths#5

Now search_cas() returns a message for matches not found
mattiaghilardi · Mar 1, 2024 · 9a0585e · 9a0585e
1 parent 60f4337
commit 9a0585e
Showing 1 changed file with 52 additions and 47 deletions.
diff --git a/R/search_catalog.R b/R/search_catalog.R
@@ -87,58 +87,63 @@ get_cas <- function(query,type){
   if (httr::status_code(res) == 200){
     result = res %>%
       xml2::read_html() %>%
-      xml2::xml_find_all("//p[@class='result']") %>%
-      xml2::xml_text() %>%
-      tibble::enframe() %>%
-      dplyr::mutate(value = stringr::str_squish(value)) %>%
-      dplyr::filter(value != "") %>%
-      dplyr::mutate(
-        query = stringr::str_extract(value, "[a-z]+, [A-Za-z]+"),
-        content = stringr::str_extract(value, "(?<=Current status: ).*"),
-        species = stringr::str_split(content,"\\. ",simplify = T)[,1],
-        family = stringr::str_split(content,"\\. ",simplify = T)[,2],
-        species_author = stringr::str_trim(ifelse(grepl("Valid as",species),gsub("Valid as ","",species),
-                                                  ifelse(grepl("Synonym of",species),gsub("Synonym of ","",species),
-                                                         ifelse(grepl("Uncertain as",species),gsub("Uncertain as ","",species),species)))),
-        status = ifelse(grepl("Valid as",species),"Validation",
-                        ifelse(grepl("Synonym of",species),"Synonym",
-                               ifelse(grepl("Uncertain as",species),"Uncertainty",NA)))
-      ) %>%
-      na.omit() %>%
-      dplyr::select(query,species_author,family,status)
+      xml2::xml_find_all("//p[@class='result']")
+    if (length(result) == 0) {
+      message(paste("No match found for", query))
+    } else {
+      result = result %>%
+        xml2::xml_text() %>%
+        tibble::enframe() %>%
+        dplyr::mutate(value = stringr::str_squish(value)) %>%
+        dplyr::filter(value != "") %>%
+        dplyr::mutate(
+          query = stringr::str_extract(value, "[a-z]+, [A-Za-z]+"),
+          content = stringr::str_extract(value, "(?<=Current status: ).*"),
+          species = stringr::str_split(content,"\\. ",simplify = T)[,1],
+          family = stringr::str_split(content,"\\. ",simplify = T)[,2],
+          species_author = stringr::str_trim(ifelse(grepl("Valid as",species),gsub("Valid as ","",species),
+                                                    ifelse(grepl("Synonym of",species),gsub("Synonym of ","",species),
+                                                           ifelse(grepl("Uncertain as",species),gsub("Uncertain as ","",species),species)))),
+          status = ifelse(grepl("Valid as",species),"Validation",
+                          ifelse(grepl("Synonym of",species),"Synonym",
+                                 ifelse(grepl("Uncertain as",species),"Uncertainty",NA)))
+        ) %>%
+        na.omit() %>%
+        dplyr::select(query,species_author,family,status)
 
-    dd = stringr::str_locate_all(result$species_author, " ")
-    end = c()
-    switch(type, `genus_family` = {
-      for (i in 1:length(dd)) {
-        end[i] = dd[[i]][1]
+      dd = stringr::str_locate_all(result$species_author, " ")
+      end = c()
+      switch(type, `genus_family` = {
+        for (i in 1:length(dd)) {
+          end[i] = dd[[i]][1]
+        }
+      }, `species_family` = {
+        for (i in 1:length(dd)) {
+          end[i] = dd[[i]][2]
+        }
+      }, `species_genus` = {
+        for (i in 1:length(dd)) {
+          end[i] = dd[[i]][2]
+        }
+      },`species` = {
+        for (i in 1:length(dd)) {
+          end[i] = dd[[i]][2]
+        }
       }
-    }, `species_family` = {
-      for (i in 1:length(dd)) {
-        end[i] = dd[[i]][2]
-      }
-    }, `species_genus` = {
-      for (i in 1:length(dd)) {
-        end[i] = dd[[i]][2]
-      }
-    },`species` = {
-      for (i in 1:length(dd)) {
-        end[i] = dd[[i]][2]
-      }
-    }
-    )
-    result$species = stringr::str_sub(result$species_author, 1, end - 1)
-    result$author = stringr::str_sub(result$species_author, end + 1)
-    #result$family = gsub(":.*","",result$family)
-    result$family = gsub(": ","_",result$family)
-    if(type == "genus_family"){
-      names(result)[2] = "genus_author"
-      names(result)[5] = "genus"
-      result$family = gsub("\\.","",result$family)
+      )
+      result$species = stringr::str_sub(result$species_author, 1, end - 1)
+      result$author = stringr::str_sub(result$species_author, end + 1)
       #result$family = gsub(":.*","",result$family)
       result$family = gsub(": ","_",result$family)
+      if(type == "genus_family"){
+        names(result)[2] = "genus_author"
+        names(result)[5] = "genus"
+        result$family = gsub("\\.","",result$family)
+        #result$family = gsub(":.*","",result$family)
+        result$family = gsub(": ","_",result$family)
+      }
+      return(tibble::as_tibble(result[,c(1,2,5,6,3,4)]))
     }
-    return(tibble::as_tibble(result[,c(1,2,5,6,3,4)]))
   }else{
     cat("Error request - the parameter query is not valid")
     browseURL(baseurl)