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compose.yml
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services:
db:
container_name: ${COMPOSE_PROJECT_NAME}_db # don't allow to scale the container
image: mysql:8.0
# MBSD-262
command: >
--default-authentication-plugin=mysql_native_password
--binlog_expire_logs_seconds=86400
--max-binlog-size=268435456
--secure-file-priv=""
--local-infile=1
--innodb_redo_log_capacity=1G
cap_add:
- SYS_NICE # CAP_SYS_NICE, fix error mbind: Operation not permitted
restart: unless-stopped
environment:
- MYSQL_DATABASE=mediawiki
- MYSQL_ROOT_HOST=%
- MYSQL_ROOT_PASSWORD=${MYSQL_ROOT_PASSWORD?Variable MYSQL_ROOT_PASSWORD not set}
volumes:
- ./__initdb:/docker-entrypoint-initdb.d
- db_data:/var/lib/mysql
matomo-db:
profiles:
- matomo
container_name: ${COMPOSE_PROJECT_NAME}_matomo_db # don't allow to scale the container
image: mysql:8.0
# MBSD-262
command: >
--default-authentication-plugin=mysql_native_password
--binlog_expire_logs_seconds=86400
--max-binlog-size=268435456
--secure-file-priv=""
--local-infile=1
cap_add:
- SYS_NICE # CAP_SYS_NICE, fix error mbind: Operation not permitted
restart: unless-stopped
environment:
- MYSQL_DATABASE=matomo
- MYSQL_ROOT_HOST=%
- MYSQL_ROOT_PASSWORD=${MATOMO_MYSQL_ROOT_PASSWORD?Variable MATOMO_MYSQL_ROOT_PASSWORD not set}
- MYSQL_USER=matomo
- MYSQL_PASSWORD=${MATOMO_MYSQL_PASSWORD?Variable MATOMO_MYSQL_PASSWORD not set}
volumes:
- /matomo/__initdb:/docker-entrypoint-initdb.d
- /matomo/data:/var/lib/mysql
web:
image: ghcr.io/wikiteq/taqasta:1.39.13-20251029-3c6664f # BEFORE upgrading to 1.4x, make sure the PR https://github.com/WikiTeq/Taqasta/pull/264 was merged or MW version >= 1.43.1
restart: unless-stopped
extra_hosts:
- "gateway.docker.internal:host-gateway"
depends_on:
- db
- redis
- elasticsearch
command: bash /entrypoint.sh
environment:
- MW_SITE_SERVER=https://bugsigdb.org
- MW_DB_NAME=mediawiki
- MW_DB_PASS=${MYSQL_ROOT_PASSWORD?Variable MYSQL_ROOT_PASSWORD not set}
- MW_NCBI_TAXONOMY_API_KEY=${MW_NCBI_TAXONOMY_API_KEY:-}
- MW_RECAPTCHA_SITE_KEY=${MW_RECAPTCHA_SITE_KEY:-}
- MW_RECAPTCHA_SECRET_KEY=${MW_RECAPTCHA_SECRET_KEY:-}
- MW_ADMIN_USER=admin
- MW_ADMIN_PASSWORD
- MW_SITE_NAME=BugSigDB
- MW_SITE_LANG=en
- MW_ENABLE_UPLOADS=1
- MW_MAIN_CACHE_TYPE=CACHE_REDIS
- MW_SEARCH_TYPE=CirrusSearch
- MW_PROXY_SERVERS=varnish:80
- MW_CACHE_PURGE_PAUSE=3600
- MW_CACHE_PURGE_PAGE=Main_Page
- PHP_MEMORY_LIMIT=4056M
- MW_JOB_RUNNER_MEMORY_LIMIT=1G
volumes:
- web_data:/mediawiki
- images:/mediawiki/images
- ./_logs/httpd:/var/log/apache2
- ./_logs/mediawiki:/var/log/mediawiki
- ./_settings/:/var/www/mediawiki/w/_settings
- ./_resources/favicon.ico:/var/www/mediawiki/w/favicon.ico
- ./_resources/logo.png:/var/www/mediawiki/w/logo.png
- ./_resources/chameleon:/var/www/mediawiki/w/skins/chameleon/custom
- ./_resources/footer_icons/cuny.png:/var/www/mediawiki/w/cuny.png
- ./_resources/footer_icons/mw.png:/var/www/mediawiki/w/mw.png
- ./_resources/footer_icons/smw.png:/var/www/mediawiki/w/smw.png
- ./_resources/footer_icons/ww.png:/var/www/mediawiki/w/ww.png
- ./_resources/footer_icons/bioc.png:/var/www/mediawiki/w/bioc.png
- ./_resources/extensions/CategoryLockdown:/var/www/mediawiki/w/extensions/CategoryLockdown
- ./_resources/extensions/SubpageWatchlist:/var/www/mediawiki/w/extensions/SubpageWatchlist
- ./_resources/extensions/SemanticScribunto:/var/www/mediawiki/w/extensions/SemanticScribunto
- ./_resources/extensions/SemanticDependencyUpdater:/var/www/mediawiki/w/extensions/SemanticDependencyUpdater
- ./_resources/googlef2273af339547660.html:/var/www/mediawiki/googlef2273af339547660.html
- ./_resources/updateQueryDependencies.php:/var/www/mediawiki/w/extensions/SemanticMediaWiki/maintenance/updateQueryDependencies.php
- ./entrypoint.sh:/entrypoint.sh
- ./cache_purge.sh:/cache_purge.sh
# csv reports with index enabled, MBSD-355
- ./export_csv.sh:/export_csv.sh
- ./csv_reports:/mediawiki/images/csv_reports
labels:
# cron
- cron.enabled=true
# studies export, MBSD-355, every hour performs export of studies, experiments and signatures CSVs
- "cron.report-export-csv.schedule=0 */1 * * *"
- 'cron.report-export-csv.command=bash /export_csv.sh'
redis:
container_name: ${COMPOSE_PROJECT_NAME}_redis # don't allow to scale the container
image: "redis:7.4.0-alpine3.20"
restart: unless-stopped
volumes:
- redis_data:/data
- ./_resources/redis.conf:/usr/local/etc/redis/redis.conf
command: ["redis-server", "/usr/local/etc/redis/redis.conf"]
elasticsearch:
container_name: ${COMPOSE_PROJECT_NAME}_elasticsearch # don't allow to scale the container
image: docker.elastic.co/elasticsearch/elasticsearch:7.10.2
restart: unless-stopped
environment:
- discovery.type=single-node
- bootstrap.memory_lock=true
- "ES_JAVA_OPTS=-Xms512m -Xmx512m"
- cluster.routing.allocation.disk.threshold_enabled=true
- cluster.routing.allocation.disk.watermark.flood_stage=1gb
- cluster.routing.allocation.disk.watermark.high=2gb
- cluster.routing.allocation.disk.watermark.low=3gb
ulimits:
memlock:
soft: -1
hard: -1
volumes:
- elasticsearch_data:/usr/share/elasticsearch/data
matomo:
profiles:
- matomo
image: matomo:5.1.1
restart: unless-stopped
networks:
- default
- traefik-public
depends_on:
- matomo-db
environment:
- MATOMO_DATABASE_HOST=matomo-db
- MATOMO_DATABASE_DBNAME=matomo
- MATOMO_DATABASE_USERNAME=matomo
- MATOMO_DATABASE_PASSWORD=${MATOMO_MYSQL_PASSWORD?Variable MATOMO_MYSQL_PASSWORD not set}
- PHP_MEMORY_LIMIT=2G
volumes:
- matomo_data:/var/www/html
- ./_resources/matomo-bootstrap.php:/var/www/html/bootstrap.php
labels:
# cron
- cron.enabled=true
- cron.maintenance-matomo.schedule=@daily
- cron.maintenance-matomo.command=./console core:archive --force-all-websites --url="http://matomo"
# Traefik
# (rule and middlewares are set in the override files, keep them synchronized)
# - traefik.http.routers.${COMPOSE_PROJECT_NAME}-matomo.rule=Host(`bugsigdb.org`) && PathPrefix(`/matomo/`)
# - traefik.http.routers.${COMPOSE_PROJECT_NAME}-matomo.middlewares=${COMPOSE_PROJECT_NAME}-matomo-stripprefix,${COMPOSE_PROJECT_NAME}-matomo-headers
- traefik.enable=true
- traefik.docker.network=traefik-public
- traefik.constraint-label=traefik-public
- traefik.http.routers.${COMPOSE_PROJECT_NAME}-matomo.entrypoints=websecure
- traefik.http.routers.${COMPOSE_PROJECT_NAME}-matomo.tls.certresolver=le
- traefik.http.middlewares.${COMPOSE_PROJECT_NAME}-matomo-stripprefix.stripprefix.prefixes=/matomo
- traefik.http.middlewares.${COMPOSE_PROJECT_NAME}-matomo-headers.headers.customrequestheaders.X-Forwarded-Uri=/matomo
varnish:
container_name: ${COMPOSE_PROJECT_NAME}_varnish # don't allow to scale the container
image: pastakhov/varnish:7.0
restart: unless-stopped
networks:
- default
- traefik-public
depends_on:
- web
tmpfs:
- /var/lib/varnish:exec
environment:
- VARNISH_SIZE=5G
- VARNISH_STORAGE_KIND=file
- VARNISH_LOG_DIR=/var/log/varnish
- VARNISH_LOG_FORMAT=X-Real-IP
- MATOMO_USER=admin
- MATOMO_PASSWORD=${MATOMO_PASSWORD?Variable MATOMO_PASSWORD not set}
volumes:
- ./_resources/varnish:/etc/varnish:ro
- varnish_data:/data
- ./_logs/varnish:/var/log/varnish
- matomo_data:/var/www/html
labels:
# cron
- cron.enabled=true
# Every hour at the 59th minute
- cron.import_logs_matomo.schedule=59 * * * *
- cron.import_logs_matomo.command=import_logs_matomo
# Traefik
# (rule and middlewares are set in the override files, keep them synchronized)
# - traefik.http.routers.${COMPOSE_PROJECT_NAME}-varnish.rule=Host(`bugsigdb.org`)
# - traefik.http.routers.${COMPOSE_PROJECT_NAME}-varnish.middlewares=crowdsec@file
- traefik.enable=true
- traefik.docker.network=traefik-public
- traefik.constraint-label=traefik-public
- traefik.http.routers.${COMPOSE_PROJECT_NAME}-varnish.entrypoints=websecure
- traefik.http.routers.${COMPOSE_PROJECT_NAME}-varnish.tls.certresolver=le
cron:
container_name: ${COMPOSE_PROJECT_NAME}_cron # don't allow to scale the container
image: ghcr.io/wikiteq/cron:20251103-11
restart: unless-stopped
environment:
- COMPOSE_PROJECT_NAME=${COMPOSE_PROJECT_NAME}
volumes:
- /var/run/docker.sock:/var/run/docker.sock:ro
- ./_logs/cron:/var/log/cron
labels:
# Enable cron scheduling for the cron container itself
- cron.enabled=true
# Log archiving job - runs daily and creates archives when a period accumulates 30 files
- cron.archive_cron_logs.schedule=@daily
- cron.archive_cron_logs.command=archive-cron-logs 30
networks:
traefik-public:
external: true
volumes:
db_data:
web_data:
images:
redis_data:
elasticsearch_data:
varnish_data:
matomo_data:
restic_data: