feat: adding nginx for serving track data (#15) (#20)

.ci/config/nginx/nginx.conf

@@ -0,0 +1,35 @@
+user                  nginx;
+worker_processes      auto;
+
+error_log             /var/log/nginx/error.log notice;
+pid                   /var/run/nginx.pid;
+
+events {
+  worker_connections  1024;
+}
+
+http {
+  include             /etc/nginx/mime.types;
+  default_type        application/octet-stream;
+
+  log_format  main    '$remote_addr - $remote_user [$time_local] "$request" '
+                      '$status $body_bytes_sent "$http_referer" '
+                      '"$http_user_agent" "$http_x_forwarded_for"';
+
+  access_log          /var/log/nginx/access.log main;
+
+  sendfile            on;
+  keepalive_timeout   65;
+
+  gzip                on;
+
+  # The full static data directory is mounted into the container but we only
+  # serve the "nginx" sub directory (with indices in the default
+  # configuration).
+  server {
+    location / {
+      root /data/nginx;
+      autoindex on;
+    }
+  }
+}

.editorconfig

@@ -12,6 +12,10 @@ trim_trailing_whitespace = true
 indent_style = space
 indent_size = 4
 
+[*.conf]
+indent_style = space
+indent_size = 2
+
 [*.py]
 line_length=120
 known_first_party=varfish

.env.ci

@@ -61,6 +61,11 @@
 
 # -- General Container Configuration -----------------------------------------
 
+# Base directory for configuration.
+# config_basedir: ./.dev/config
+## In CI: set to directory with appropriate config.
+config_basedir=./.ci/config
+
 # Base directory for volumes.
 # volumes_basedir: ./volumes
 ## In CI: set to a directory with minimal data for spinning up the containers.

README.md

@@ -223,6 +223,30 @@ ln -Tsr .dev/volumes/varfish-static/data/download/worker/masked-repeat-grch38-*/
   .dev/volumes/varfish-static/data/worker/grch38/features/masked_repeat.bin
 ln -Tsr .dev/volumes/varfish-static/data/download/worker/masked-segdup-grch38-*/masked-segdup.bin \
   .dev/volumes/varfish-static/data/worker/grch38/features/masked_seqdup.bin
+
+##
+## tracks
+##
+
+mkdir -p .dev/volumes/varfish-static/data/nginx/grch3{7,8}
+
+paths_37=$(find .dev/volumes/varfish-static/data/download/tracks/ -type f -name '*.bed' -or -name '*.bed.gz' | sort | grep grch37)
+for path in $paths_37; do
+  if [[ -e ${path}.tbi ]]; then
+    ln -sr $path ${path}.tbi .dev/volumes/varfish-static/data/nginx/grch37
+  else
+    ln -sr $path .dev/volumes/varfish-static/data/nginx/grch37
+  fi
+done
+
+paths_38=$(find .dev/volumes/varfish-static/data/download/tracks/ -type f -name '*.bed' -or -name '*.bed.gz' | sort | grep grch38)
+for path in $paths_38; do
+  if [[ -e ${path}.tbi ]]; then
+    ln -sr $path ${path}.tbi .dev/volumes/varfish-static/data/nginx/grch38
+  else
+    ln -sr $path .dev/volumes/varfish-static/data/nginx/grch38
+  fi
+done
 ```
 
 To create an in-house database:
@@ -238,6 +262,14 @@ varfish-server-worker db to-bin \
   --path-output-bin .dev/volumes/varfish-static/data/worker/grch37/strucvars/inhouse.bin
 ```
 
+### Setup Configuration
+
+The next step step is to create the configuration files in `.dev/config`.
+
+```bash session
+mkdir -p .dev/config/nginx
+cp utils/nginx/nginx.conf .dev/config/nginx
+```
 
 ### Startup and Check
 

docker-compose.override.yml-dev

@@ -10,6 +10,7 @@
 #   - `3001` -- annonars
 #   - `3002` -- mehari
 #   - `3003` -- viguno
+#   - `3004` -- nginx
 #   - `3010` -- minio
 #   - `3011` -- minio console
 
@@ -29,6 +30,11 @@ services:
     ports:
       - "3003:8080"
 
+  # map nginx to port 3004
+  nginx:
+    ports:
+      - "3004:80"
+
   # map Minio S3 to port 9000 and console to 9001
   minio:
     ports:

docker-compose.yml

@@ -58,6 +58,23 @@ services:
       # Mount Docker socket into container so traefik can react to events.
       - "/var/run/docker.sock:/var/run/docker.sock:ro"
 
+  # -- nginx -----------------------------------------------------------------
+  #
+  # We serve static files such as browser tracks with nginx.
+
+  nginx:
+    container_name: nginx
+    hostname: nginx
+    image: ${image_nginx_name:-nginx}:${image_nginx_version:-1}
+    volumes:
+      - type: bind
+        source: ${volumes_basedir:-./.dev/volumes}/varfish-static/data
+        target: /data
+        read_only: true
+      - type: bind
+        source: ${config_basedir:-./.dev/config}/nginx/nginx.conf
+        target: /etc/nginx/nginx.conf
+
   # -- Mehari ----------------------------------------------------------------
   #
   # Mehari provides the transcript-related information.

env.tpl

@@ -59,8 +59,17 @@
 # Version of the "mc" (Minio client) image to use.
 # image_mc_version=latest
 
+# Name of the nginx image to use.
+# image_nginx_name=nginx
+
+# Version of the nginx image to use.
+# image_nginx_version=1
+
 # -- General Container Configuration -----------------------------------------
 
+# Base directory for configuration.
+# config_basedir: ./.dev/config
+
 # Base directory for volumes.
 # volumes_basedir: ./.dev/volumes
 

utils/nginx/nginx.conf

@@ -0,0 +1,35 @@
+user                  nginx;
+worker_processes      auto;
+
+error_log             /var/log/nginx/error.log notice;
+pid                   /var/run/nginx.pid;
+
+events {
+  worker_connections  1024;
+}
+
+http {
+  include             /etc/nginx/mime.types;
+  default_type        application/octet-stream;
+
+  log_format  main    '$remote_addr - $remote_user [$time_local] "$request" '
+                      '$status $body_bytes_sent "$http_referer" '
+                      '"$http_user_agent" "$http_x_forwarded_for"';
+
+  access_log          /var/log/nginx/access.log main;
+
+  sendfile            on;
+  keepalive_timeout   65;
+
+  gzip                on;
+
+  # The full static data directory is mounted into the container but we only
+  # serve the "nginx" sub directory (with indices in the default
+  # configuration).
+  server {
+    location / {
+      root /data/nginx;
+      autoindex on;
+    }
+  }
+}