rebuild. remove special characters from project names.

ABbiodiversity · Jan 11, 2024 · 04414a8 · 04414a8
1 parent 027f29f
commit 04414a8
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Showing 27 changed files with 46 additions and 73 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,6 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export("%>%")
 export(wt_audio_scanner)
 export(wt_auth)
 export(wt_chop)
@@ -51,4 +50,3 @@ import(tools)
 import(tuneR)
 import(unmarked)
 import(utils)
-importFrom(magrittr,"%>%")
diff --git a/R/api.R b/R/api.R
@@ -108,7 +108,7 @@ wt_get_download_summary <- function(sensor_id) {
 #'  \item main
 #'  \item project
 #'  \item location
-#'  \item point count
+#'  \item point_count
 #'  \item definitions
 #' }
 #'
@@ -138,11 +138,19 @@ wt_download_report <- function(project_id, sensor_id, reports, weather_cols = TR
     stop("Please authenticate with wt_auth().", call. = FALSE)
 
   # Check if the project_id is valid:
-  i <- wt_get_download_summary(sensor_id = sensor_id)
-  i <- unlist(i$project_id)
+  i <- wt_get_download_summary(sensor = sensor_id) %>%
+    tibble::as_tibble() %>%
+    dplyr::select(project_id, sensor)
 
-  if (!project_id %in% i) {
+  sensor_value <- i %>%
+    rename('id' = 1) %>%
+    dplyr::filter(id == project_id) %>%
+    dplyr::pull(sensor)
+
+  if (!project_id %in% i$project_id) {
     stop("The project_id you specified is not among the projects you are able to download for.", call. = TRUE)
+  } else if (sensor_value == 'ARU' & sensor_id == 'PC'){
+    stop('You will not be able to convert a PC project to ARU since the data does not contain media.', call. = TRUE)
   }
 
   # Make sure report is specified
@@ -213,6 +221,7 @@ wt_download_report <- function(project_id, sensor_id, reports, weather_cols = TR
   if ("megadetector" %in% reports) query_list$megaDetectorReport <- TRUE
   if ("megaclassifier" %in% reports) query_list$megaClassifierReport <- TRUE
 
+  # Include metadata
   query_list$includeMetaData <- TRUE
   query_list$splitLocation <- TRUE
 
@@ -221,7 +230,7 @@ wt_download_report <- function(project_id, sensor_id, reports, weather_cols = TR
   # tmp directory
   td <- tempdir()
 
-  # Create POST request
+  # Create GET request
   r <- httr::GET(
     httr::modify_url("https://www-api.wildtrax.ca", path = "/bis/download-report"),
     query = query_list,
@@ -232,7 +241,6 @@ wt_download_report <- function(project_id, sensor_id, reports, weather_cols = TR
     httr::progress()
     )
 
-
   # Stop if an error or bad request occurred
   if (httr::http_error(r))
     stop(sprintf(
@@ -248,11 +256,13 @@ wt_download_report <- function(project_id, sensor_id, reports, weather_cols = TR
   abstract <- list.files(td, pattern = "*_abstract.csv", full.names = TRUE, recursive = TRUE)
   file.remove(abstract)
 
-  # List data files, read into R as a list
-  files <- gsub(".csv", "", list.files(td, pattern = ".csv", recursive = TRUE))
-  files.full <- list.files(td, pattern = ".csv", full.names = TRUE, recursive = TRUE)
+  # Remove special characters
+  list.files(td, pattern = "*.csv", full.names = TRUE) %>%
+    purrr::map(~file.rename(.x, gsub("[:()?!~;]", "", .x)))
+  files.full <- list.files(td, pattern= "*.csv", full.names = TRUE)
+  files.less <- basename(files.full)
   x <- purrr::map(.x = files.full, .f = ~ readr::read_csv(., show_col_types = F, skip_empty_rows = T)) %>%
-    purrr::set_names(files)
+    purrr::set_names(files.less)
 
   # Remove weather columns, if desired
   if(weather_cols) {

diff --git a/R/utils-pipe.R b/R/utils-pipe.R
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/CODE_OF_CONDUCT.html b/docs/CODE_OF_CONDUCT.html
diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/SUPPORT.html b/docs/SUPPORT.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -9,7 +9,7 @@ articles:
   camera-data-wrangling: camera-data-wrangling.html
   introduction: introduction.html
   tutorials: tutorials.html
-last_built: 2024-01-09T19:58Z
+last_built: 2024-01-10T02:19Z
 urls:
   reference: https://abbiodiversity.github.io/wildRtrax/reference
   article: https://abbiodiversity.github.io/wildRtrax/articles

diff --git a/docs/reference/dot-wt_api_pr.html b/docs/reference/dot-wt_api_pr.html
diff --git a/docs/reference/dot-wt_auth.html b/docs/reference/dot-wt_auth.html
diff --git a/docs/reference/dot-wt_auth_expired.html b/docs/reference/dot-wt_auth_expired.html
diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/docs/reference/wildRtrax.html b/docs/reference/wildRtrax.html
diff --git a/docs/reference/wt_audio_scanner.html b/docs/reference/wt_audio_scanner.html
diff --git a/docs/reference/wt_auth.html b/docs/reference/wt_auth.html
diff --git a/docs/reference/wt_download_report.html b/docs/reference/wt_download_report.html
diff --git a/docs/reference/wt_get_download_summary.html b/docs/reference/wt_get_download_summary.html
diff --git a/docs/reference/wt_run_ap.html b/docs/reference/wt_run_ap.html
diff --git a/docs/reference/wt_signal_level.html b/docs/reference/wt_signal_level.html
diff --git a/docs/reference/wt_wac_info.html b/docs/reference/wt_wac_info.html
diff --git a/man/pipe.Rd b/man/pipe.Rd
diff --git a/vignettes/tutorials.Rmd b/vignettes/tutorials.Rmd
@@ -56,7 +56,6 @@ data <- wt_download_report(605,'ARU',c('birdnet','main'))
 The results from the `main` report can then be anti-joined against the `birdnet` report to determine if any species were detected than a human did not find. It's recommended to use high threshold values from BirdNET and species that should occur or be allowed in the project.
 
 ```{r}
-
 birdnet_report <- data[[1]] %>%
   dplyr::filter(is_species_allowed_in_project == 't',
          confidence > 50) %>%