Trying to port BirdNET-stream to Docker

.gitignore

@@ -9,3 +9,5 @@ species_list.txt
 push.sh
 
 config/*.conf
+
+.vscode/

CHANGELOG.md

@@ -9,5 +9,6 @@
 - Extracts BirdNET bird contacts into SQL database
 - Add birdnet_stream icecast audio streaming and live spectrogram service https://birdnet/spectro
 - Add /today/species and /today/{date}/species/{id} endpoints
-- Add records deletion button
+- Add records deletion button and /records/delete endpoint as well as bulk deletion (select all button on /today/species/{id} endpoint)
 - Add systemd status page /status
+- Add i18n for webapp (not species name), en|fr only for the moment

CONTRIBUTING.md

@@ -22,6 +22,9 @@ BirdNET-stream webapp is written in PHP Symfony. The i18n files are stored in th
 
 Any help is welcome to translate the webapp into your language.
 
+Add your language code into [./www/bin/translate.sh](./www/bin/translate.sh) and run it to update the translation files.
+
+Then, edit generated files in [./www/translations](./www/translations).
 
 ## Filing a pull request
 

INSTALL.md

@@ -5,7 +5,7 @@ This guide allow you to install BirdNET-stream step by step on your debian based
 For a one-liner installation, you can use the following command:
 
 ```bash
-curl -sL https://raw.githubusercontent.com/birdnet-stream/birdnet-stream/master/install.sh | bash
+curl -sL https://raw.githubusercontent.com/UncleSamulus/BirdNET-stream/main/install.sh | bash
 ```
 
 ## Requirements
@@ -34,7 +34,7 @@ sudo apt-get install ffmpeg
 ### Clone BirdNET-stream repository
 
 ```bash
-git clone --recurse-submodules https://forge.chapril.org/UncleSamulus/BirdNET-stream.git
+git clone --recurse-submodules https://github.com/UncleSamulus/BirdNET-stream.git
 ```
 
 ### Setup python virtualenv and packages

TODO

@@ -1,2 +1,5 @@
 - Fix clean script
 - Fix service manager
+- Add docker support
+- Species i18n
+- File purge policy

daemon/birdnet_analyzis.sh

@@ -82,7 +82,11 @@ analyze_chunk() {
 # Perform audio chunk analysis on all recorded chunks
 analyze_chunks() {
     for chunk_name in $(get_chunk_list); do
-        analyze_chunk $chunk_name
+        if [[ -f "${CHUNK_FOLDER}/out/$chunk_name.d/model.out.csv" ]]; then
+            debug "Skipping $chunk_name, as it has already been analyzed"
+        else
+            analyze_chunk $chunk_name
+        fi
         chunk_path="${CHUNK_FOLDER}/in/$chunk_name"
         mv $chunk_path "${CHUNK_FOLDER}/out/$chunk_name"
     done

daemon/birdnet_clean.sh

@@ -3,6 +3,16 @@
 ## Clean up var folder from useless files
 ##
 
+set -e
+# set -x
+
+DEBUG=${DEBUG:-1}
+debug() {
+    if [[ $DEBUG -eq 1 ]]; then
+        echo "$1"
+    fi
+}
+
 config_filepath="./config/analyzer.conf"
 
 if [ -f "$config_filepath" ]; then
@@ -20,51 +30,61 @@ wav2dir_name() {
 
 # Clean out folder from empty audio
 clean() {
-    rm -rf $(junk)
+    for item in $(junk); do
+        debug "Removing: $item"
+        rm -rf "$CHUNK_FOLDER/out/$item"
+    done
+    empty_audios=$(find "$CHUNK_FOLDER/in" -type f -size 0)
+    for item in $empty_audios; do
+        rm -rf "$item"
+    done
 }
 
-# Check if string contains string
-mem() {
-    string=$2
-    substring=$1
-    if [[ "$string" == *"$substring"* ]]; then
-        echo "true"
-    else
-        echo "false"
-    fi
+dryclean() {
+    debug "Dry run mode"
+    debug "Script will remove the following files:"
+    for item in $(junk); do
+        debug "$item"
+    done
+    empty_audios=$(find "$CHUNK_FOLDER/in" -type f -size 0)
+    for item in $empty_audios; do
+        echo "$item"
+    done
 }
 
 # Get list of junk files
 junk() {
     # Get all empty files from treatement folder
-    find "${CHUNK_FOLDER}/out" -type f -name '*.wav' -size 0
+    junk=$(find "${CHUNK_FOLDER}/out" -type f -name '*.wav' -size 0)
     for file in $junk; do
         folder=$(wav2dir_name "$file")
         if [[ -d $folder ]]; then
             junk="$junk $folder"
         fi
     done
-    # Get all empty files from record folder
-    junk=$(find "${CHUNK_FOLDER}/in" -type f -name '*.wav' -exec basename {} \; ! -size 0)
     # Get all empty treatment directories
-    junk="$junk $(find ${CHUNK_FOLDER}/out -type d -empty)"
-    # Get all empty record directories
-    treatement_folder=$(find -wholename "${CHUNK_FOLDER}/out/*" -type d ! -empty)
-    if [[ ! -z ${treatement_folder} ]]; then
-        for folder in $treatement_folder; do
-            echo $folder
-            if [[ ! $(mem $folder $junk) = "true" ]] && $(no_bird_in_model_output $folder); then
-                junk="$junk $folder"
-            fi
-        done
-    fi
+    junk="$junk $(find ${CHUNK_FOLDER}/out/* -type d -empty)"
+    # Get all no birdcontact directories
+    treatement_folders=$(find ${CHUNK_FOLDER}/out/* -type d ! -empty)
+    for folder in $treatement_folders; do
+        folder_basename=$(basename "$folder")
+        if [[ $(no_bird_in_model_output $folder_basename) = "true" ]]; then
+            # Add model output file to junk list
+            junk="$junk $folder_basename/model.out.csv"
+            junk="$junk $folder_basename"
+        fi
+    done
     echo "$junk"
 }
 
 no_bird_in_model_output() {
     folder=$1
-    output="${folder}/model.out.csv"
-    lines=$(wc -l < "$output")
+    output="$CHUNK_FOLDER/out/$folder/model.out.csv"
+    if [[ -f $output ]]; then
+        lines=$(wc -l <"$output")
+    else
+        lines=0
+    fi
     if [[ $lines -eq 1 ]]; then
         echo "true"
     else
@@ -72,8 +92,8 @@ no_bird_in_model_output() {
     fi
 }
 
-main() {
+if [[ $1 = "dry" ]]; then
+    dryclean
+else
     clean
-}
-
-main
+fi

daemon/database/migrations/.gitignore

@@ -0,0 +1 @@
+.

daemon/database/migrations/migrate.sh

@@ -0,0 +1,34 @@
+#! /usr/bin/bash
+
+DEBUG=${DEBUG:-1}
+debug() {
+    if [ "$DEBUG" -eq 1 ]; then
+        echo "$1"
+    fi
+}
+
+# Load config file
+config_filepath="./config/analyzer.conf"
+
+if [ -f "$config_filepath" ]; then
+    source "$config_filepath"
+else
+    echo "Config file not found: $config_filepath"
+    exit 1
+fi
+
+# Check if database location is specified
+if [ -z "$DATABASE" ]; then
+    echo "DATABASE location not specified"
+    echo "Defaults to ./var/db.sqlite"
+    DATABASE="./var/db.sqlite"
+fi
+
+if [[ ! -f "$DATABASE" ]]; then
+    echo "Database file not found: $DATABASE"
+    exit 1
+fi
+
+source ./daemon/database/scripts/database.sh
+
+sqlite3 "$DATABASE" "ALTER TABLE observation ADD COLUMN verified BOOLEAN CHECK (verified IN (0, 1)) DEFAULT 0;"

daemon/database/structure.sql

@@ -25,6 +25,7 @@ CREATE TABLE IF NOT EXISTS observation (
     `date` TEXT NOT NULL,
     `notes` TEXT,
     `confidence` REAL NOT NULL,
+    `verified` BOOLEAN NOT NULL CHECK (`verified` IN (0, 1)) DEFAULT 0,
     FOREIGN KEY(taxon_id) REFERENCES taxon(taxon_id),
     FOREIGN KEY(location_id) REFERENCES location(location_id)
 );

docker-compose.yml

@@ -0,0 +1,36 @@
+version: '3.8'
+
+networks:
+  birdnet_network:
+
+services:
+  # database:
+  #   container_name: birdnet_database
+  #   image:
+
+  php:
+    container_name: birdnet_php
+    image: php:8.1-fpm
+    ports:
+      - "${PHP_FPM_PORT:-9001}:9000"
+
+
+  nginx:
+    container_name: birdnet_nginx
+    build:
+      context: ./docker/
+    environment:
+      SERVER_NAME: ${SERVER_NAME:-birdnet.local}
+      PHP_FPM_PORT: ${PHP_FPM_PORT:-9001}
+    restart: unless-stopped
+    volumes:
+      - ./www:/var/www/birdnet/
+      - ./www/nginx.conf:/etc/nginx/conf.d/birdnet.conf
+    ports:
+      - "81:80"
+    dependends_on:
+      - php
+
+  birdnet:
+    container_name: birdnet_analyzer
+    image: 

docker/all/Dockerfile

@@ -0,0 +1,20 @@
+# All in One BirdNET docker image
+FROM debian:bullseye
+
+ENV REPOSITORY=${REPOSITORY:-https://github.com/UncleSamulus/BirdNET-stream.git}
+# DEBUG defaults to 1 for descriptive DEBUG logs, 0 for error logs only 
+ENV DEBUG=${DEBUG:-1} 
+RUN useradd birdnet
+WORKDIR /home/birdnet
+
+# Upgrade system
+RUN apt-get update && apt-get upgrade -y
+
+# Install curl
+RUN apt-get install -y \
+    curl \
+    sudo
+
+RUN curl -sL https://raw.githubusercontent.com/UncleSamulus/BirdNET-stream/master/install.sh | bash
+
+USER birdnet

docker/all/README.md

@@ -0,0 +1,27 @@
+# All in One Docker Container for BirdNET-stream application
+
+## Requirements
+
+- docker
+
+## Quick start
+
+```bash
+git clone https://github.com/UncleSamulus/BirdNET-stream.git
+cd ./BirdNET-stream/docker/all
+docker build -t "birdnet_all:latest" .
+```
+
+If `docker` command does not work because of unsufficient permissions, you could add your user to `docker` group:
+
+```bash
+sudo usermod -aG docker $USER
+```
+
+Then logout, reconnect and try again.
+
+Then, docker container should be run this way:
+
+```bash
+docker run -it birdnet_all --restart unless-stopped
+```

docker/recording/Dockerfile

@@ -0,0 +1,16 @@
+# Recording container for BirdNET-stream
+# Reference: https://leimao.github.io/blog/Docker-Container-Audio/
+
+FROM debian:bullseye
+
+ENV DEBIAN_FRONTEND noninteractive
+
+# Install packages dependencies
+
+RUN apt-get update && \
+    apt-get install apt-utils \
+    && apt-get install -y --no-install-recommends \
+    libasound2 \
+    alsa-utils \
+    libsndfile1-dev \
+    && apt-get clean

install.sh

@@ -1,19 +1,12 @@
 #! /usr/bin/env bash
+# Standard Installation Script for BirdNET-stream for Debian Based Linux distros
 # set -x
 set -e
 
 DEBUG=${DEBUG:-0}
 
-# Standard Installation Script for BirdNET-stream for Debian Based Linux distros
-
 REQUIREMENTS="git ffmpeg python3-pip python3-dev"
-REPOSITORY="https://github.com/UncleSamulus/BirdNET-stream.git"
-
-# Update system
-update() {
-    sudo apt-get update
-    sudo apt-get upgrade -y
-}
+REPOSITORY=${REPOSITORY:-https://github.com/UncleSamulus/BirdNET-stream.git}
 
 debug() {
     if [ $DEBUG -eq 1 ]; then
@@ -32,7 +25,7 @@ install_requirements() {
     done
     if [ -n "$missing_requirements" ]; then
         debug "Installing missing requirements: $missing_requirements"
-        sudo apt-get install $missing_requirements
+        sudo apt-get install -y $missing_requirements
     fi
 }
 

utils/fix_permissions.sh

@@ -0,0 +1,25 @@
+#! /usr/bin/env bash
+
+set -e
+
+DEBUG=${DEBUG:-1}
+debug() {
+    if [ $DEBUG -eq 1 ]; then
+        echo "$1"
+    fi
+}
+
+config_filepath="./config/analyzer.conf"
+
+if [ -f "$config_filepath" ]; then
+    source "$config_filepath"
+else
+    echo "Config file not found: $config_filepath"
+    exit 1
+fi
+
+
+GROUP=birdnet
+
+sudo chown -R $USER:$GROUP $CHUNK_FOLDER
+sudo chmod -R 775 $CHUNK_FOLDER