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Docker installation for oxigraph #4

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7497fe7
init
ch-sander Aug 10, 2024
35f26fa
custom setup works
ch-sander Aug 11, 2024
641358d
Update .gitignore
ch-sander Aug 11, 2024
8ab3a83
ss
ch-sander Aug 11, 2024
c71459b
Oxigraph
ch-sander Aug 21, 2024
0c3c362
oxigraph runs
ch-sander Aug 22, 2024
e05c4e1
Update docker-compose.yml
ch-sander Aug 25, 2024
9cfc505
prepare for PR
ch-sander Aug 28, 2024
d4c0ffb
Update .env
ch-sander Aug 28, 2024
77f253c
del data_oxigraph
ch-sander Aug 28, 2024
523ce5a
permission fix
ch-sander Aug 28, 2024
407a542
Update README.md
ch-sander Aug 28, 2024
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7 changes: 6 additions & 1 deletion .gitignore
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# runtime
blazegraph/
researchspace/
data_oxigraph/
basic/test.json
/basic/researchspace
/full-setup/researchspace
/custom/researchspace/runtime-data/data/repositories/tests/lock
/custom/researchspace/runtime-data/data/repositories/tests/lock
16 changes: 7 additions & 9 deletions full-setup/.env
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# (required). Hostname on which ResearchSpace instance should be available.
RESEARCHSPACE_HOST_NAME=
RESEARCHSPACE_HOST_NAME=localhost

# (required) your project name, to have nice container names in the docker-compose setup.
# see https://docs.docker.com/compose/reference/envvars/#compose_project_name
COMPOSE_PROJECT_NAME=
COMPOSE_PROJECT_NAME=graceful17

# (required) memory limits for docker containers

# Total amount of memory available for containers
RESEARCHSPACE_MEMORY=1g
BLAZEGRAPH_MEMORY=1g
RESEARCHSPACE_MEMORY=10g
DIGILIB_MEMORY=500m

OXIGRAPH_DATA=./data_oxigraph

# (optional) additional ReseearchSpace runtime options.
# By default increases jetty upload limit to ~100mb
RESEARCHSPACE_OPTS=-Dorg.eclipse.jetty.server.Request.maxFormContentSize=1000000

# (optional) additional JVM opts for various applications
# WARNING! Don't set Xmx here, use memory variables above. We use -XX:+UseContainerSupport, see https://merikan.com/2019/04/jvm-in-a-container/ for more details about memory management of Java apps inside docker.
RESEARCHSPACE_JAVA_OPTS=
BLAZEGRAPH_JAVA_OPTS=
DIGILIB_JAVA_OPTS=

# docker images
RESEARCHSPACE_IMAGE=researchspace/platform-ci:latest
BLAZEGRAPH_IMAGE=researchspace/blazegraph:latest
DIGILIB_IMAGE=robcast/digilib:latest

OXIGRAPH_IMAGE=oxigraph/oxigraph:latest
DIGILIB_IMAGE=researchspace/digilib:2.9.1-12m
56 changes: 22 additions & 34 deletions full-setup/docker-compose.yml
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Expand Up @@ -5,14 +5,16 @@ services:
restart: unless-stopped
mem_limit: ${RESEARCHSPACE_MEMORY}
mem_reservation: ${RESEARCHSPACE_MEMORY}
# ports:
# - "10214:8080" # routed via nginx to RESEARCHSPACE_HOST_NAME
environment:
# 1. Connect researchspace instance to blazegraph instance, in this case we use internal hostname available only inside docker-compose create network.
# 2. Set default logging profile to log4j2, other possible options are log4j2-debug.xml, log4j2-trace.xml
# 3-5. Create storage needed for image upload functionality
# 6-8. Create temp storage needed for image upload functionality
# 7. Additional options provided in .env file
PLATFORM_OPTS: >-
-Dconfig.environment.sparqlEndpoint=http://blazegraph:8080/blazegraph/sparql
-Dconfig.environment.sparqlEndpoint=http://oxigraph:7878/query
-Dlog4j.configurationFile=classpath:org/researchspace/logging/log4j2.xml
-Dconfig.storage.images.type=nonVersionedFile
-Dconfig.storage.images.mutable=true
Expand All @@ -34,42 +36,13 @@ services:
# mount folder where temporary files should be stored
- ./researchspace/data/tmp:/tmp-data:rw

# mount folder where apps should be stored
- ./researchspace/apps:/apps:rw

# runtime data folder with config files and ad-hoc templates
- ./researchspace/runtime-data:/runtime-data
depends_on:
- blazegraph
- digilib
logging:
driver: json-file
options:
max-size: "200k"
max-file: "10"

blazegraph:
image: ${BLAZEGRAPH_IMAGE}
restart: unless-stopped
mem_limit: ${BLAZEGRAPH_MEMORY}
mem_reservation: ${BLAZEGRAPH_MEMORY}
environment:
JAVA_OPTS: ${BLAZEGRAPH_JAVA_OPTS}
volumes:
- ./blazegraph/:/blazegraph-data
logging:
driver: json-file
options:
max-size: "200k"
max-file: "10"

digilib:
image: ${DIGILIB_IMAGE}
restart: unless-stopped
mem_limit: ${DIGILIB_MEMORY}
mem_reservation: ${DIGILIB_MEMORY}
environment:
BASEDIR_LIST: /var/lib/images
IIIF_IMAGE_BASE_URL: "https://${RESEARCHSPACE_HOST_NAME}/proxy/IIIF/"
volumes:
- ./researchspace/data/images/file:/var/lib/images:rw
- oxigraph
logging:
driver: json-file
options:
Expand Down Expand Up @@ -119,3 +92,18 @@ services:
max-size: "200k"
max-file: "10"

digilib:
image: ${DIGILIB_IMAGE}
restart: unless-stopped
mem_limit: ${DIGILIB_MEMORY}
mem_reservation: ${DIGILIB_MEMORY}
environment:
BASEDIR_LIST: /var/lib/images
IIIF_IMAGE_BASE_URL: "http://localhost:10214/proxy/IIIF/"
volumes:
- ./researchspace/data/images/file:/var/lib/images:rw
logging:
driver: json-file
options:
max-size: "200k"
max-file: "10"
16 changes: 8 additions & 8 deletions full-setup/fix-folder-permissions.sh
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Expand Up @@ -4,7 +4,7 @@
set -e

RUNTIME_DATA=./researchspace
BLAZEGRAPH_DATA=./blazegraph
OXIGRAPH_DATA=./data_oxigraph

echo "Creating storage folders"

Expand All @@ -14,19 +14,19 @@ mkdir -p ${RUNTIME_DATA}/data/tmp/file
echo "Changing ownership of the ResearchSpace runtime-data folder: ${RUNTIME_DATA}"

# change ownership of the runtime-data folder to uid/guid that is used inside researchspace docker container
chown -R 100:0 ${RUNTIME_DATA}
sudo chown -R 100:0 ${RUNTIME_DATA}

# make sure that folder has correct write permissions and new files that are created inside the folder inherit ownership
chmod -R g+ws ${RUNTIME_DATA}
sudo chmod -R g+ws ${RUNTIME_DATA}

echo "Creating blazegraph journal folder: ${BLAZEGRAPH_DATA}"
echo "Creating oxigraph store folder: ${OXIGRAPH_DATA}"

# create folder for blazegraph journal file
mkdir -p ${BLAZEGRAPH_DATA}
mkdir -p ${OXIGRAPH_DATA}

# change ownership of the blazegraph data folder to uid/guid that is used inside blazegraph docker container
chown -R 999:999 ${BLAZEGRAPH_DATA}
sudo chown -R $USER:$USER ${OXIGRAPH_DATA}
sudo chmod -R 775 ${OXIGRAPH_DATA}

# make sure that folder has correct write permissions and new files that are created inside the folder inherit ownership
chmod -R g+ws ${RUNTIME_DATA}

sudo chmod -R g+ws ${RUNTIME_DATA}
87 changes: 87 additions & 0 deletions full-setup/nginx/conf.d/default.conf
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# If we receive X-Forwarded-Proto, pass it through; otherwise, pass along the
# scheme used to connect to this server
map $http_x_forwarded_proto $proxy_x_forwarded_proto {
default $http_x_forwarded_proto;
'' $scheme;
}
# If we receive X-Forwarded-Port, pass it through; otherwise, pass along the
# server port the client connected to
map $http_x_forwarded_port $proxy_x_forwarded_port {
default $http_x_forwarded_port;
'' $server_port;
}
# If we receive Upgrade, set Connection to "upgrade"; otherwise, delete any
# Connection header that may have been passed to this server
map $http_upgrade $proxy_connection {
default upgrade;
'' close;
}
# Apply fix for very long server names
server_names_hash_bucket_size 128;
# Default dhparam
# Set appropriate X-Forwarded-Ssl header
map $scheme $proxy_x_forwarded_ssl {
default off;
https on;
}
gzip_types text/plain text/css application/javascript application/json application/x-javascript text/xml application/xml application/xml+rss text/javascript;
log_format vhost '$host $remote_addr - $remote_user [$time_local] '
'"$request" $status $body_bytes_sent '
'"$http_referer" "$http_user_agent"';
access_log off;
ssl_protocols TLSv1.2 TLSv1.3;
ssl_ciphers 'ECDHE-ECDSA-AES128-GCM-SHA256:ECDHE-RSA-AES128-GCM-SHA256:ECDHE-ECDSA-AES256-GCM-SHA384:ECDHE-RSA-AES256-GCM-SHA384:ECDHE-ECDSA-CHACHA20-POLY1305:ECDHE-RSA-CHACHA20-POLY1305:DHE-RSA-AES128-GCM-SHA256:DHE-RSA-AES256-GCM-SHA384';
ssl_prefer_server_ciphers off;
# HTTP 1.1 support
proxy_http_version 1.1;
proxy_buffering off;
proxy_set_header Host $http_host;
proxy_set_header Upgrade $http_upgrade;
proxy_set_header Connection $proxy_connection;
proxy_set_header X-Real-IP $remote_addr;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
proxy_set_header X-Forwarded-Proto $proxy_x_forwarded_proto;
proxy_set_header X-Forwarded-Ssl $proxy_x_forwarded_ssl;
proxy_set_header X-Forwarded-Port $proxy_x_forwarded_port;
# Mitigate httpoxy attack (see README for details)
proxy_set_header Proxy "";
server {
server_name _; # This is just an invalid value which will never trigger on a real hostname.
listen 80;
access_log /var/log/nginx/access.log vhost;
return 503;
}
# localhost
upstream localhost {
## Can be connected with "graceful17_default" network
# graceful17-researchspace-1
server 172.21.0.5:8080;
}
server {
server_name localhost;
listen 80 default_server;
access_log /var/log/nginx/access.log vhost;
location / {
proxy_pass http://localhost;
}
}
server {
server_name localhost;
listen 7878;
rewrite ^/(.*) /$1 break;
proxy_ignore_client_abort on;
proxy_set_header X-Real-IP $remote_addr;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
proxy_set_header Host $http_host;
proxy_set_header Access-Control-Allow-Origin "*";
location ~ ^(/|/query)$ {
proxy_pass http://oxigraph:7878;
proxy_pass_request_headers on;
}
location ~ ^(/update|/store)$ {
auth_basic "Oxigraph Administrator's Area";
auth_basic_user_file /etc/nginx/.htpasswd;
proxy_pass http://oxigraph:7878;
proxy_pass_request_headers on;
}
}
23 changes: 23 additions & 0 deletions oxigraph/.env
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# (required) your project name, to have nice container names in the docker-compose setup.
# see https://docs.docker.com/compose/reference/envvars/#compose_project_name
COMPOSE_PROJECT_NAME=

# (required) memory limits for docker containers

# Total amount of memory available for containers
RESEARCHSPACE_MEMORY=1g
DIGILIB_MEMORY=500m

# (optional) additional ReseearchSpace runtime options.
# By default increases jetty upload limit to ~100mb
RESEARCHSPACE_OPTS=-Dorg.eclipse.jetty.server.Request.maxFormContentSize=1000000

# (optional) additional JVM opts for various applications
# WARNING! Don't set Xmx here, use memory variables above. We use -XX:+UseContainerSupport, see https://merikan.com/2019/04/jvm-in-a-container/ for more details about memory management of Java apps inside docker.
RESEARCHSPACE_JAVA_OPTS=
DIGILIB_JAVA_OPTS=

# docker images
RESEARCHSPACE_IMAGE=researchspace/platform-ci:oxigraph-fix
DIGILIB_IMAGE=robcast/digilib:latest
OXIGRAPH_IMAGE=ghcr.io/oxigraph/oxigraph:main
15 changes: 15 additions & 0 deletions oxigraph/README.md
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# oxigraph replacing blazegraph

A docker installation if you want [oxigraph](https://github.com/oxigraph/oxigraph) instead of blazegraph to serve ResearchSpace.

## Why?

- blazegraph development is abandoned
- oxigraph is a performant in-development graph database implementing the SPARQL standard. It come with many supplementary libraries and packages to integrate it into various frameworks.

## Prerequisites

- Currently only works with ResearchSpace image `researchspace/platform-ci:oxigraph-fix`
- Make sure to enable the `--union-default-graph` flag at CLI startup
- you must create a `\researchspace\runtime-data\config\repositories\default.ttl`
- if you need to have the oxigraph service proxied (as for `full-setup`), add your nginx config at the end of `full-setup\nginx\nginx.tmpl` (see also https://github.com/oxigraph/oxigraph/tree/main/cli#run-the-web-server-with-basic-authentication)
71 changes: 71 additions & 0 deletions oxigraph/docker-compose.yml
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version: "2.2"
services:
researchspace:
image: ${RESEARCHSPACE_IMAGE}
restart: unless-stopped
mem_limit: ${RESEARCHSPACE_MEMORY}
mem_reservation: ${RESEARCHSPACE_MEMORY}
ports:
- "10214:8080"
environment:
# 1. Connect researchspace instance to blazegraph instance, in this case we use internal hostname available only inside docker-compose create network.
# 2. Set default logging profile to log4j2, other possible options are log4j2-debug.xml, log4j2-trace.xml
# 3-5. Create storage needed for image upload functionality
# 6-8. Create temp storage needed for image upload functionality
# 7. Additional options provided in .env file
# -Dlog4j.configurationFile=file:/runtime-data/log4j2-trace.xml
PLATFORM_OPTS: >-
-Dconfig.environment.sparqlEndpoint=http://oxigraph:7878/query
-Dlog4j.configurationFile=classpath:org/researchspace/logging/log4j2-debug.xml
-Dconfig.storage.images.type=nonVersionedFile
-Dconfig.storage.images.mutable=true
-Dconfig.storage.images.root=/images
-Dconfig.storage.tmp.type=nonVersionedFile
-Dconfig.storage.tmp.mutable=true
-Dconfig.storage.tmp.root=/tmp-data
${RESEARCHSPACE_OPTS}
JAVA_OPTS: ${RESEARCHSPACE_JAVA_OPTS}
volumes:
# mount folder where uploaded images should be stored
- ./researchspace/data/images:/images:rw

# mount folder where temporary files should be stored
- ./researchspace/data/tmp:/tmp-data:rw

# mount folder where apps should be stored
- ./researchspace/apps:/apps:rw

# runtime data folder with config files and ad-hoc templates
- ./researchspace/runtime-data:/runtime-data
depends_on:
- oxigraph
- digilib
logging:
driver: json-file
options:
max-size: "200k"
max-file: "10"

oxigraph:
image: ${OXIGRAPH_IMAGE}
ports:
- "7878:7878"
volumes:
- ./data_oxigraph:/data
command: ["serve", "--location", "/data", "--bind", "0.0.0.0:7878", "--union-default-graph", "--cors"]

digilib:
image: ${DIGILIB_IMAGE}
restart: unless-stopped
mem_limit: ${DIGILIB_MEMORY}
mem_reservation: ${DIGILIB_MEMORY}
environment:
BASEDIR_LIST: /var/lib/images
IIIF_IMAGE_BASE_URL: "http://localhost:10214/proxy/IIIF/"
volumes:
- ./researchspace/data/images/file:/var/lib/images:rw
logging:
driver: json-file
options:
max-size: "200k"
max-file: "10"
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