# 创建共用网络
docker network create media-network

# 运行数据库容器
# docker run --name mediaMysql \
#   --network media-network \
#   -p 3306:3306 \
#   -v /vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/data/:/var/lib/mysql \
#   -e MYSQL_ROOT_PASSWORD='Gzy1234566.' \
#   -d my-media-mysql:v1
#   -v /vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/mysql/data/:/var/lib/mysql \
#   -v /vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/mysql/conf:/etc/mysql/conf.d \
#   -v /vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/log/:/var/log/mysql \
# docker volume create media-mysql-data
docker run --name mediaMysql \
    --network media-network \
    -e MYSQL_ROOT_PASSWORD='Gzy1234566.' \
    -v media-mysql-data:/var/lib/mysql \
    -p 3306:3306 \
    -d \
    media-mysql:v1 \
    mysqld

docker exec -it mediaMysql mysql -uroot -p
Gzy1234566.




# CREATE TABLE cultured_data ( 
#     `id` INT NOT NULL AUTO_INCREMENT PRIMARY KEY COMMENT 'Primary key', 
#     `species_dive_id` INT NOT NULL COMMENT 'species dive id', 
#     `pH` TEXT NULL COMMENT 'pH', 
#     `o2` TEXT NULL COMMENT 'o2', 
#     `microbial_name` TEXT NULL COMMENT 'species name', 
#     `media_name` TEXT NULL COMMENT 'media name', 
#     `media_source` TEXT NULL COMMENT 'media source', 
#     `mediadive_id` TEXT NULL COMMENT 'mediadive id', 
#     `nutrition` TEXT NULL COMMENT 'compounds list', 
#     `gram_stain` TEXT NULL COMMENT 'gram type', 
#     `temperature` TEXT NULL COMMENT 'temperature', 
#     `domain` TEXT NULL COMMENT 'domain', 
#     `phylum` TEXT NULL COMMENT 'phylum', 
#     `class` TEXT NULL COMMENT 'Class', 
#     `order` TEXT NULL COMMENT 'order', 
#     `family` TEXT NULL COMMENT 'family', 
#     `genus` TEXT NULL COMMENT 'genus', 
#     `species` TEXT NULL COMMENT 'species', 
#     `taxonomy` TEXT NULL COMMENT 'taxonomy', 
#     `synonym` TEXT NULL COMMENT 'synonym', 
#     `genome` VARCHAR(50) NULL COMMENT 'genome',
#     `predict_temperature` TEXT NULL COMMENT 'predict temperature', 
#     `predict_pH` TEXT NULL COMMENT 'predict pH', 
#     `predict_o2` TEXT NULL COMMENT 'predict o2', 
#     `cultured_type` TEXT NULL COMMENT 'culture type'
# ) COMMENT 'Cultured microbial data';
# `genome` VARCHAR(50) NULL COMMENT 'genome',
# `genome` TEXT NULL COMMENT 'genome',

# 赋予可读权限
# chown mysql:mysql /var/lib/mysql-files/cultured_dataLinux.csv
# chmod 644 /var/lib/mysql-files/cultured_dataLinux.csv

# LOAD DATA INFILE '/var/lib/mysql-files/cultured_dataLinux.csv'
# INTO TABLE cultured_data
# FIELDS TERMINATED BY ','
# OPTIONALLY ENCLOSED BY '"'
# LINES TERMINATED BY '\n'
# IGNORE 1 ROWS
# (species_dive_id,pH,o2,microbial_name,media_name,media_source,mediadive_id,nutrition,gram_stain,temperature,domain,phylum,Class,`order`,family,genus,species,taxonomy,synonym,genome,predict_temperature,predict_pH,predict_o2,cultured_type);

# UPDATE cultured_data 
# SET cultured_type = REPLACE(REPLACE(REPLACE(cultured_type, '\t', ''), '\r', ''), '\n', '');

# UPDATE cultured_data
# SET predict_o2 = 'aerobe'
# WHERE predict_o2 = 'aerotolerant';

# UPDATE cultured_data
# SET phylum = 'Thermotogota'
# WHERE phylum = 'Thermotogae';

# UPDATE cultured_data
# SET phylum = 'Aquificota'
# WHERE phylum = 'Aquificae';

# UPDATE cultured_data
# SET phylum = 'Thermodesulfobacteriales'
# WHERE phylum = 'Thermodesulfobacteria';

# UPDATE cultured_data
# SET class = 'Actinomycetes'
# WHERE class = 'Actinobacteria';




# 运行Web服务器容器
docker run -d \
  --name mediaNode \
  --network media-network \
  -p 3000:3000 \
  -v /var/run/docker.sock:/var/run/docker.sock \
  -v /usr/bin/docker:/usr/bin/docker \
  -v /vol1/1000/home/gzy/mediaDatabase/media-transformer/:/app \
  -w /app \
  media-node:v2 \
  nodemon server.js

docker exec -it mediaNode bash
npm install -g nodemon


# # prokka容器
# docker run -it --name prokka \
#   -v /vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/uploads/:/app/ \
#   -w /app \
#   media-prokka:v1 \
#   bash


# ./prokka_batch.sh --input /app/input_data --output /app/output_results --threads 4 --force





# pH预测容器运行测试
# docker run --rm \
#     -v /vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/uploads/prokka_annotation/:/app/prokka_annotation \
#     -v "/vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/results":/app/results \
#     -v "/vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/scripts":/app/scripts \
#     -w /app \
#     ph-pred:v4 \
#     bash -c "conda run -n ph_model_jupyter  bash /app/scripts/pHPredict.sh /app/prokka_annotation /app/results/ph_predict"

# docker run -d \
#     --name phpredict \
#     -v /vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/uploads/prokka_annotation/:/app/prokka_annotation \
#     -v "/vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/results":/app/results \
#     -v "/vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/scripts":/app/scripts \
#     -w /app \
#     media-ph-pred:v1 \
#     tail -f /dev/null
# docker exec -it phpredict bash

# 温度氧气预测容器运行测试
# docker run --rm \
#     -v /vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/uploads/prokka_annotation/:/app/prokka_annotation \
#     -v "/vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/results":/app/results \
#     -v "/vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/scripts":/app/scripts \
#     -w /app \
#     bacdive-ai:v1 \
#     bash -c "source /etc/profile && source /opt/conda/etc/profile.d/conda.sh && conda activate bacdiveai && pip install --root-user-action=ignore tqdm && bash /app/scripts/TempO2Predict.sh /app/prokka_annotation /app/results/tempo2predict"

# docker run -d \
#     --name tempo2predict \
#     -v /vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/uploads/prokka_annotation/:/app/prokka_annotation \
#     -v "/vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/results":/app/results \
#     -v "/vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/scripts":/app/scripts \
#     -w /app \
#     bacdive-ai:v1 \
#     tail -f /dev/null
# docker exec -it tempo2predict bash

# 最大生长速率预测容器运行测试
# docker run --rm \
#     -v /vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/uploads/prokka_annotation/:/app/prokka_annotation \
#     -v "/vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/results":/app/results \
#     -v "/vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/scripts":/app/scripts \
#     -w /app \
#     shengwei/grodon2:latest \
#     bash -c "bash /app/scripts/GrowthPredict.sh /app/prokka_annotation /app/results/growth_predict"
# docker run -d \
#     --name growthpredict \
#     -e PATH='/usr/local/bin:/usr/bin:/bin:/opt/conda/lib/R/bin' \
#     -v /vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/uploads/prokka_annotation/:/app/prokka_annotation \
#     -v "/vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/results":/app/results \
#     -v "/vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/scripts":/app/scripts \
#     -w /app \
#     media-grodon2:v1 \
#     tail -f /dev/null
# docker exec -it growthpredict bash

# 远程调用GPU服务器进行培养基预测
# 将用户加入doker用户组
sudo usermod -aG docker gzy

# 检查是否安装nvidia-docker2


docker run --rm \
    -v /vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/uploads/prokka_annotation/:/app/prokka_annotation \
    -v "/vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/results":/app/results \
    -v "/vol1/1000/home/gzy/mediaDatabase/mediaTransformer":/app/scripts \
    -w /app \
    media-trasnformer:v2 \
    bash -c "source /opt/conda/etc/profile.d/conda.sh && conda activate uncultured_pytorch && pip install sentencepiece && bash /app/scripts/mediaPredict.sh /app/prokka_annotation /app/results/media_predict"

docker run -d \
    --name mediapredict \
    -v /vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/uploads/prokka_annotation/:/app/prokka_annotation \
    -v "/vol1/1000/home/gzy/mediaDatabase/htmlMediaDatabase/results":/app/results \
    -v "/vol1/1000/home/gzy/mediaDatabase/mediaTransformer":/app/scripts \
    -w /app \
    media-trasnformer:v2 \
    tail -f /dev/null
docker exec -it mediapredict bash