Feat/error logs (#16)

* added list of tasks to achieve

* update deps

* update elixir version in CI/CD pipeline

* update todo with branch push checks

* underscores separation of large numbers

* update elixir version and deps

* add basic module  docs

* remove IO.inspect call

* check if list is empty rather than traversing list for length

* revert empty list code

* duration tests

* add mime type tests

* use logger instread of inspect, remove todos

* replace list length check with Enum.empty

* replace list length check with !Enum.empty?

* numbers readability fix by using underscores on large numbers

* iucn parser replaced case with multiclause function and added test

* replace map and join with map_join

* fix multiple spec issues where map() must be inside a list

lib/application.ex

@@ -1,4 +1,5 @@
 defmodule PlantIdDiscordBot.Application do
+  @moduledoc false
   use Application
 
   @impl true

lib/commands.ex

@@ -1,4 +1,7 @@
 defmodule PlantIdDiscordBot.Consumer.Commands do
+  @moduledoc """
+  Application commands.
+  """
   def global_application_commands do
     [
       %{

lib/metrics/message.ex

@@ -1,4 +1,7 @@
 defmodule PlantIdDiscordBot.Metrics.Message do
+  @moduledoc """
+  Metrics messaging.
+  """
   def send() do
     PlantIdDiscordBot.Metrics.requests()
     |> format_message()

lib/metrics/requests.ex

@@ -1,4 +1,7 @@
 defmodule PlantIdDiscordBot.Metrics.Requests do
+  @moduledoc """
+  Basic metrics with usage count per guild.
+  """
   use Agent
   alias PlantIdDiscordBot.Metrics.Requests
   alias PlantIdDiscordBot.ProcessRegistry

lib/mocks/nostrum_api.ex

@@ -6,7 +6,7 @@ defmodule PlantIdDiscordBotTest.Mocks.Nostrum.Api do
   # def create_message(_channel_id, content), do: {:ok, content}
 
   def create_message(_channel_id, content) do
-    send(self(), {:create_message, 123456, content})
+    send(self(), {:create_message, 123_456, content})
     {:ok, content}
   end
 

lib/plantid_discord_bot.ex

@@ -26,10 +26,15 @@ defmodule PlantIdDiscordBot.Consumer do
   end
 
   def handle_event({:MESSAGE_CREATE, %{attachments: attachments} = message, _ws_state}) do
-    if length(attachments) > 0 do
-      # deprecated -> Nostrum.Api.Channel.start_typing/1 in v1.0
+    if !Enum.empty?(attachments) do
       Api.start_typing!(message.channel_id)
       Cog.PlantNetMessage.id(message)
     end
+
+    # if length(attachments) > 0 do
+    #   # deprecated -> Nostrum.Api.Channel.start_typing/1 in v1.0
+    #   Api.start_typing!(message.channel_id)
+    #   Cog.PlantNetMessage.id(message)
+    # end
   end
 end

lib/plantid_discord_bot/cogs/info.ex

@@ -1,4 +1,9 @@
 defmodule PlantIdDiscordBot.Cog.Info do
+  @moduledoc """
+  Functions for using the /info application command.
+
+  Returns a message embed of application commands available to the user.
+  """
   use Nostrum.Consumer
   import Nostrum.Struct.Embed
   alias PlantIdDiscordBot.Utils

lib/plantid_discord_bot/cogs/plantnet_message.ex

@@ -1,4 +1,7 @@
 defmodule PlantIdDiscordBot.Cog.PlantNetMessage do
+  @moduledoc """
+  Functions for sending and receiving data from PLantNet
+  """
   require Logger
 
   use Nostrum.Consumer
@@ -49,7 +52,6 @@ defmodule PlantIdDiscordBot.Cog.PlantNetMessage do
           nil
       end
 
-    # TODO improve composition
     if saved_images do
       try do
         prepare_images(saved_images)

lib/plantid_discord_bot/file_server.ex

@@ -1,4 +1,7 @@
 defmodule PlantIdDiscordBot.FileServer do
+  @moduledoc """
+  File server for temporary storage of images until a response is made.
+  """
   use Plug.Builder
 
   plug(Plug.Logger)

lib/plantid_discord_bot/file_server/file.ex

@@ -2,6 +2,8 @@ defmodule PlantIdDiscordBot.FileServer.File do
   @moduledoc """
   File utilities
   """
+  require Logger
+
   alias PlantIdDiscordBot.FileServer.ImageConverter
 
   @image_path Application.compile_env(:plantid_discord_bot, :image_path)
@@ -56,7 +58,6 @@ defmodule PlantIdDiscordBot.FileServer.File do
     |> File.read()
   end
 
-  # TODO make into a task for async deletion and deal with errors
   @spec delete_files!([String.t()]) :: :ok
   def delete_files!(filenames) do
     tasks =
@@ -65,8 +66,7 @@ defmodule PlantIdDiscordBot.FileServer.File do
           try do
             File.rm!(Path.join(@image_path, filename))
           rescue
-            # TODO Logger
-            e -> IO.inspect(e)
+            e -> Logger.error(e)
           end
         end)
       end)

lib/plantid_discord_bot/guild.ex

@@ -1,4 +1,7 @@
 defmodule PlantIdDiscordBot.Guild do
+  @moduledoc """
+  Guild related functions.
+  """
   alias Nostrum.Cache.GuildCache
 
   def get_guild_name!(guild_id) do

lib/plantid_discord_bot/process_registry.ex

@@ -1,4 +1,7 @@
 defmodule PlantIdDiscordBot.ProcessRegistry do
+  @moduledoc """
+  Process registry.
+  """
   def start_link do
     Registry.start_link(keys: :unique, name: __MODULE__)
   end

lib/plantid_discord_bot/rate_limiter.ex

@@ -1,4 +1,10 @@
 defmodule PlantIdDiscordBot.RateLimiter do
+  @moduledoc """
+  Basic rate limiter to prevent one guild from calling too many requests in 24 hours.
+
+  Custom limits have been set for some guilds that are trusted.
+  """
+
   use GenServer
   require Logger
 

lib/plantid_discord_bot/utils.ex

@@ -1,4 +1,7 @@
 defmodule PlantIdDiscordBot.Utils do
+  @moduledoc """
+  Bot related utility functions.
+  """
   def get_uptime() do
     start_time = Application.get_env(:plantid_discord_bot, :start_time)
 

lib/plantnet/parser.ex

@@ -33,7 +33,7 @@ defmodule PlantIdDiscordBot.PlantNet.Parser do
   @doc """
   Parses the response from the PlantNet API into a map.
   """
-  @spec parse(String.t()) :: map()
+  @spec parse(String.t()) :: String.t()
   def parse(response) do
     response
     |> to_map!()
@@ -85,7 +85,7 @@ defmodule PlantIdDiscordBot.PlantNet.Parser do
     "My best guess is **#{best_guess_name}** with a confidence of **#{score}%**.#{get_common_names(best_result)}\n\nSpecies info from plant databases:\n[GBIF](<#{best_result["gbif_url"]}>) | [PFAF](<#{best_result["pfaf_url"]}>) | [POWO](<#{best_result["powo_url"]}>)#{if best_result_iucn_category, do: "\n\nConservation status: #{iucn_parser(best_result_iucn_category)}"}#{get_alternatives(other_results)}"
   end
 
-  @spec generate_gbif_url(map()) :: map()
+  @spec generate_gbif_url([map()]) :: [map()]
   defp generate_gbif_url(data) do
     Enum.map(data, fn result ->
       gbif_id = result["gbif"]["id"]
@@ -93,7 +93,7 @@ defmodule PlantIdDiscordBot.PlantNet.Parser do
     end)
   end
 
-  @spec generate_pfaf_url(map()) :: map()
+  @spec generate_pfaf_url([map()]) :: [map()]
   defp generate_pfaf_url(data) do
     Enum.map(data, fn result ->
       pfaf_slug = String.replace(result["species"]["scientificNameWithoutAuthor"], " ", "+")
@@ -104,7 +104,7 @@ defmodule PlantIdDiscordBot.PlantNet.Parser do
     end)
   end
 
-  @spec generate_powo_url(map()) :: map()
+  @spec generate_powo_url([map()]) :: [map()]
   defp generate_powo_url(data) do
     Enum.map(data, fn result ->
       powo_id = result["powo"]["id"]
@@ -123,29 +123,40 @@ defmodule PlantIdDiscordBot.PlantNet.Parser do
   end
 
   @spec iucn_parser(String.t()) :: String.t()
-  defp iucn_parser(abbreviation) do
-    case abbreviation do
-      "DD" -> "Data Deficient"
-      "LC" -> "Least Concern"
-      "NT" -> "Near Threatened"
-      "VU" -> "Vulnerable"
-      "EN" -> "Endangered"
-      "CR" -> "Critically Endangered"
-      "EW" -> "Extinct in the Wild"
-      "EX" -> "Extinct"
-      "NE" -> "Not Evaluated"
-      _ -> "Unknown"
-    end
-  end
+  def iucn_parser("DD"), do: "Data Deficient"
+  def iucn_parser("LC"), do: "Least Concern"
+  def iucn_parser("NT"), do: "Near Threatened"
+  def iucn_parser("VU"), do: "Vulnerable"
+  def iucn_parser("EN"), do: "Endangered"
+  def iucn_parser("CR"), do: "Critically Endangered"
+  def iucn_parser("EW"), do: "Extinct in the Wild"
+  def iucn_parser("EX"), do: "Extinct"
+  def iucn_parser("NE"), do: "Not Evaluated"
+  def iucn_parser(_), do: "Unknown"
 
   @spec get_alternatives(map()) :: String.t()
   defp get_alternatives(data) do
-    if length(data) > 0 do
+    if !Enum.empty?(data) do
       alternatives =
-        Enum.map(data, & &1["species"]["scientificNameWithoutAuthor"])
-        |> Enum.join(", ")
+        Enum.map_join(data, ", ", & &1["species"]["scientificNameWithoutAuthor"])
 
       "\n\nAlternatives include **#{alternatives}**."
     end
+
+    # if !Enum.empty?(data) do
+    #   alternatives =
+    #     Enum.map(data, & &1["species"]["scientificNameWithoutAuthor"])
+    #     |> Enum.join(", ")
+
+    #   "\n\nAlternatives include **#{alternatives}**."
+    # end
+
+    # if length(data) > 0 do
+    #   alternatives =
+    #     Enum.map(data, & &1["species"]["scientificNameWithoutAuthor"])
+    #     |> Enum.join(", ")
+
+    #   "\n\nAlternatives include **#{alternatives}**."
+    # end
   end
 end

lib/scheduler.ex

@@ -1,3 +1,6 @@
 defmodule PlantIdDiscordBot.Scheduler do
+  @moduledoc """
+  CRON job scheduler.
+  """
   use Quantum, otp_app: :plantid_discord_bot
 end

lib/utils/duration.ex

@@ -1,11 +1,21 @@
-# https://rosettacode.org/wiki/Convert_seconds_to_compound_duration
 defmodule PlantIdDiscordBot.Utils.Duration do
+  @moduledoc """
+  Duration conversion functions.
+  """
   @minute 60
   @hour @minute * 60
   @day @hour * 24
   @week @day * 7
   @divisor [@week, @day, @hour, @minute, 1]
 
+  @doc """
+  Convert seconds to a time string.
+  # https://rosettacode.org/wiki/Convert_seconds_to_compound_duration
+
+  ## Examples
+      iex> PlantIdDiscordBot.Utils.Duration.sec_to_str(65)
+      iex> "1m 5s"
+  """
   def sec_to_str(sec) do
     {_, [s, m, h, d, w]} =
       Enum.reduce(@divisor, {sec, []}, fn divisor, {n, acc} ->