i #275 remove unaltered_file_path and fix auth

Reorganized the condition surrounding this file.
The logic was already using it as a saved_folder_path.

Renamed the `contents` variable to something more clear.

A lot of the code surrounding auth was also fixed and
expanded on.

At the stage of this commit, the downloaders work
for date range and issue range, and the refresher
also works (the refresher was tested on Kaiaulu
JIRA where I have more control over the timestamps).

Signed-off-by: Carlos Paradis <carlosviansi@gmail.com>

R/jira.R

@@ -385,7 +385,6 @@ download_jira_issues_by_issue_key <- function(domain,
 #' @param max_total_downloads Maximum downloads per function call.
 #' This value specifies how many issues should be extracted and API calls will cease if a subsequent
 #' API call would reach or surpass this value.
-#' @param unaltered_file_path the path to the directory that contains the files
 #' @param verbose boolean flag to specify printing operational
 #' messages or not. These messages will describe errors or successes in executing code.
 #' And example may be declaring the file name of a successfully downloaded file or printing
@@ -406,94 +405,93 @@ refresh_jira_issues <- function(domain,
                                 save_folder_path,
                                 max_results,
                                 max_total_downloads,
-                                unaltered_file_path,
                                 verbose){
 
-  # Check if the file exists
-  if(file.exists(unaltered_file_path)) {
-    # Check if the file is empty by checking its size
-    # List all files and subdirectories in the directory
-    contents <- list.files(path = unaltered_file_path)
+  # List all files and subdirectories in the directory
+  existing_issues <- list.files(path = save_folder_path)
 
-    # If the file is empty, download all issues
-    if(length(contents) == 0) {
-      if(verbose){
-        message("The file is empty.Downloading all\n")
-      }
-      download_jira_issues(domain = domain,
-                           jql_query = jql_query,
-                           fields = fields,
-                           username = username,
-                           password = password,
-                           save_folder_path = save_folder_path,
-                           max_results = max_results,
-                           max_total_downloads = max_total_downloads,
-                           search_query = NULL,
-                           verbose = verbose)
+  # If the folder is empty, then start by downloading all issues.
+  if(length(existing_issues) == 0) {
+    if(verbose){
+      message("The folder is empty. Downloading all issues. \n")
+    }
+    download_jira_issues(domain = domain,
+                         jql_query = jql_query,
+                         fields = fields,
+                         username = username,
+                         password = password,
+                         save_folder_path = save_folder_path,
+                         max_results = max_results,
+                         max_total_downloads = max_total_downloads,
+                         search_query = NULL,
+                         verbose = verbose)
+  } else {
+    # If folder is not empty, find the highest issue key, and resume download after it.
+    # First, get the file name with the last downloaded 'issueKey' value
+    file_name_with_greatest_issue_key <- parse_jira_latest_date(save_folder_path)
+
+    # Prepare the path and filename
+    issue_refresh <- file.path(save_folder_path, file_name_with_greatest_issue_key)
+
+    # Check if the file exists
+    if(file.exists(issue_refresh)) {
+    # Check if the file is empty by checking its size
     } else {
-      # If file is not empty, run the refresh function
-      # Get the file name with the latest 'issueKey' value
-      file_name_with_greatest_issue_key <- parse_jira_latest_date(unaltered_file_path)
       if(verbose){
-        message("Filename with latest date: ", file_name_with_greatest_issue_key)
+        stop("The file does not exist.\n")
       }
+    }
+    if(verbose){
+      message("Filename with highest date (and therefore latest issue key is inside): ", issue_refresh)
+    }
 
-      # Prep the path and filename
-      issue_refresh <- paste0(unaltered_file_path, file_name_with_greatest_issue_key)
-
-      # Read the JSON file
-      json_data <- jsonlite::fromJSON(txt = issue_refresh, simplifyVector = FALSE)
-
-      # Extract the Maximum issue key value
-      # Start with a low value assuming no negative numbers
-      max_numeric_part <- -1
-      max_key <- ""
-
-      for (issue in json_data$issues) {
-        # Extract the key for the current issue
-        current_key <- issue$key
+    # Read the JSON file
+    json_data <- jsonlite::fromJSON(txt = issue_refresh, simplifyVector = FALSE)
 
-        # Extract the numeric part of the key
-        # Assuming the key format is "PROJECTNAME-NUMBER"
-        numeric_part <- as.numeric(sub("^[^-]+-", "", current_key))
+    # Extract the Maximum issue key value
+    # Start with a low value assuming no negative numbers
+    max_numeric_part <- -1
+    max_key <- ""
 
-        # Check if the numeric part is greater than the current maximum
-        if (numeric_part > max_numeric_part) {
-          # Update the maximum numeric part and the corresponding key
-          max_numeric_part <- numeric_part
-          max_key <- current_key
-        }
-      }
+    for (issue in json_data$issues) {
+      # Extract the key for the current issue
+      current_key <- issue$key
 
-      # Print the key with the maximum numeric part
-      if(verbose){
-        message("The greatest issue key value is ", max_key)
-      }
+      # Extract the numeric part of the key
+      # Assuming the key format is "PROJECTNAME-NUMBER"
+      numeric_part <- as.numeric(sub("^[^-]+-", "", current_key))
 
-      # Construct the search query to append to the JIRA API request
-      search_query <- paste0("AND issueKey > ", max_key)
-      if(verbose){
-        message("Appending ", search_query, " to JQL query")
+      # Check if the numeric part is greater than the current maximum
+      if (numeric_part > max_numeric_part) {
+        # Update the maximum numeric part and the corresponding key
+        max_numeric_part <- numeric_part
+        max_key <- current_key
       }
+    }
 
-      # Call the downloader with appended query
-      download_jira_issues(domain = domain,
-                          jql_query = jql_query,
-                          fields = fields,
-                          username = username,
-                          password =password,
-                          save_folder_path = save_folder_path,
-                          max_results = max_results,
-                          max_total_downloads = max_total_downloads,
-                          search_query = search_query,
-                          verbose = verbose)
+    # Print the key with the maximum numeric part
+    if(verbose){
+      message("The greatest issue key value is ", max_key)
     }
-  } else {
+
+    # Construct the search query to append to the JIRA API request
+    search_query <- paste0("AND issueKey > ", max_key)
     if(verbose){
-      message("The file does not exist.\n")
+      message("Appending ", search_query, " to JQL query")
     }
-  }
 
+    # Call the downloader with appended query
+    download_jira_issues(domain = domain,
+                        jql_query = jql_query,
+                        fields = fields,
+                        username = username,
+                        password = password,
+                        save_folder_path = save_folder_path,
+                        max_results = max_results,
+                        max_total_downloads = max_total_downloads,
+                        search_query = search_query,
+                        verbose = verbose)
+  }
 }