-
Notifications
You must be signed in to change notification settings - Fork 0
/
docker-compose.yml
executable file
·113 lines (104 loc) · 3.65 KB
/
docker-compose.yml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
version: '3'
# Docs: https://docs.stardog.com/get-started/install-stardog/docker
services:
# Deploy a Stardog server
stardog:
image: stardog/stardog:8.2.2-java11-preview
restart: unless-stopped
volumes:
- /data/stardog:/var/opt/stardog
- ./drivers:/var/opt/stardog-ext
ports:
- 5820:5820
environment:
- "STARDOG_SERVER_JAVA_ARGS=-Xmx8g -Xms8g -XX:MaxDirectMemorySize=12g"
- "JAVA_OPTIONS=-Djava.net.preferIPv4Stack=true"
- STARDOG_EXT=/var/opt/stardog-ext
- LETSENCRYPT_HOST=stardog.137.120.31.102.nip.io
- VIRTUAL_HOST=stardog.137.120.31.102.nip.io
- VIRTUAL_PORT=5820
# Make sure system metadata and databases are properly upgraded:
# command: --upgrade
# Deploy 3 SQL databases for the MIMIC-IV dataset
postgres-mimic-iv:
image: postgres:15.3
restart: unless-stopped
environment:
- POSTGRES_USER=postgres
- POSTGRES_PASSWORD=${PASSWORD:-passwordtochange}
- LETSENCRYPT_HOST=mimic4.postgres.137.120.31.102.nip.io
- VIRTUAL_HOST=mimic4.postgres.137.120.31.102.nip.io
- VIRTUAL_PORT=5432
# - POSTGRES_DB=heart_failure_db
# ports:
# - 5432:5432
volumes:
# Copy the sql script to create tables
- ./virtual-kg/postgres_mimic_iv.sql:/docker-entrypoint-initdb.d/postgres_mimic_iv.sql
- ./virtual-kg/mimic-iv-2.2:/data
# - ./data/postgres:/var/lib/postgresql/data
postgres-mimic-iv-2:
image: postgres:15.3
restart: unless-stopped
environment:
- POSTGRES_USER=postgres
- POSTGRES_PASSWORD=${PASSWORD:-passwordtochange}
volumes:
- ./virtual-kg/postgres_mimic_iv_2.sql:/docker-entrypoint-initdb.d/postgres_mimic_iv_2.sql
- ./virtual-kg/mimic-iv-2.2:/data
mariadb-mimic-iv:
restart: unless-stopped
image: mariadb:11.0-rc
volumes:
- ./virtual-kg/mariadb_mimic_iv.sql:/docker-entrypoint-initdb.d/mariadb_mimic_iv.sql
- ./virtual-kg/mimic-iv-2.2:/data
# - ./data/mariadb:/var/lib/mysql
environment:
MARIADB_ROOT_PASSWORD: ${PASSWORD-passwordtochange}
MARIADB_USER: user
# ports:
# - 3306:3306
# command: --max-allowed-packet=16M --local_infile=1
# ontop:
# image: ontop/ontop
# restart: unless-stopped
# volumes:
# - ./:/data
# # - ./drill-override.conf:/opt/drill/conf/drill-override.conf
# # ports:
# # - 8047:8047 # web and REST
# # - 31010:31010 # JDBC
# stdin_open: true
# environment:
# - ONTOP_MAPPING_FILE=/data/ontop.rml.ttl
# - ONTOP_ONTOLOGY_FILE=/data/ontop.rdf
# - ONTOP_DB_USER=postgres
# - ONTOP_DB_PASSWORD=${PASSWORD:-passwordtochange}
# # - ONTOP_PROPERTIES_FILE=/data/ontop.properties
# # https://ontop-vkg.org/guide/advanced/configuration.html
# NOTE: To serve CSV files directly as SQL, we could also use LakeFS
# drill:
# image: apache/drill
# restart: unless-stopped
# volumes:
# - ./:/data
# # - ./drill-override.conf:/opt/drill/conf/drill-override.conf
# # ports:
# # - 8047:8047 # web and REST
# # - 31010:31010 # JDBC
# stdin_open: true
# environment:
# - DRILLBIT_MAX_PROC_MEM=8G
# - DRILL_HEAP=4G
# - DRILL_MAX_DIRECT_MEMORY=8G
# - DRILLBIT_CODE_CACHE_SIZE=1G
# NOTE: could be useful if we want to use our own SSO login instead of google
# stardog-studio:
# image: stardog/stardog-studio:current
# container_name: stardog-studio
# restart: unless-stopped
# environment:
# - LETSENCRYPT_HOST=studio.stardog.137.120.31.102.nip.io
# - VIRTUAL_HOST=studio.stardog.137.120.31.102.nip.io
# - VIRTUAL_PORT=8080
# network_mode: bridge