forked from cytomine/Cytomine-community-edition
-
Notifications
You must be signed in to change notification settings - Fork 1
/
cytomine.template
226 lines (203 loc) · 5.94 KB
/
cytomine.template
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
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
# -------------------------------------------------- #
# Update these to configure your instance
global:
urls:
constant:
CORE: cytomine.local
IMAGE_SERVER: ims.cytomine.local
UPLOAD: upload.cytomine.local
urls_with_scheme:
constant:
CORE: http://cytomine.local
IMAGE_SERVER: http://ims.cytomine.local
UPLOAD: http://upload.cytomine.local
host_paths:
constant:
PROJECT_DATA_PATH: ./data
smtp:
constant:
HOST: mail.smtp
PORT: 587
USER: user
PASS: password
# -------------------------------------------------- #
# Only update variables below if you know what you are doing
versions:
constant:
CYTOMINE_COMMERCIAL: CE2023.1
images:
constant:
BIOFORMAT: cytomineuliege/bioformat:v3.1.0
CORE: cytomineuliege/core:4.0.0
MONGO: mongo:4.4.18-focal
NGINX: cytomineuliege/nginx:1.22.1-1.0.0
PIMS: cytomineuliege/pims:0.13.0-community-plugins
PIMS_CACHE: redis:7.0.8
POSTGIS: cytomineuliege/postgis:15-3.3-alpine-1.0.0
RABBITMQ: rabbitmq:3.10
WEB_UI: cytomineuliege/web_ui:2.0.0
internal_docker_urls: # must match respective container hostnames from compose file
constant:
WEB_UI: web_ui
CORE: core:8080
PIMS: pims:5000
RABBITMQ: rabbitmq
BIOFORMAT: bioformat
MONGO: mongo
NGINX: nginx
PIMS_CACHE: pims_cache
POSTGIS: postgis
container_paths:
constant:
IMAGES: /data/images
UPLOADED: /tmp/uploaded
javamelody:
constant:
DATA_PATH: /javamelody-core # inside container
USER: admin
auto:
PASS:
type: openssl
length: 32
postgres:
constant:
PORT: 5432
DB_NAME: docker
USER: docker
auto:
PASS:
type: openssl
length: 32
mongodb:
constant:
USER: mongoadmin
DB_NAME: cytomine
PORT: 27017
auto:
PASS:
type: openssl
length: 32
keys:
auto:
IMAGE_SERVER_PRIVATE: random_uuid
IMAGE_SERVER_PUBLIC: random_uuid
image_metadata:
constant:
PREFIXES: |-
APERIO=APERIO.
TIFF=TIFF.
HAMAMATSU=HAMAMATSU.
OPENSLIDE=OPENSLIDE.
EXIF=EXIF.
LEICA=LEICA.
JFIF=JFIF.
FILE=FILE.
PNG=PNG.
XMP=XMP.
VENTANA=VENTANA.
DICOM=DICOM.
MIRAX=MIRAX.
ICC_PROFILE=ICC_PROFILE.
services:
default:
core:
constant:
METADATA_PREFIXES_FILE_URI: /app/metaPrefix.properties
auto:
SERVER_ID: random_uuid
JWT_SECRET:
type: secret
length: 256
whitelist: abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789'+.;^_~
ADMIN_PASSWORD:
type: openssl
length: 32
ADMIN_PRIVATE_KEY: random_uuid
ADMIN_PUBLIC_KEY: random_uuid
SUPER_ADMIN_PRIVATE_KEY: random_uuid
SUPER_ADMIN_PUBLIC_KEY: random_uuid
RABBITMQ_PRIVATE_KEY: random_uuid
RABBITMQ_PUBLIC_KEY: random_uuid
global:
IMAGE_SERVER_PRIVATE_KEY: keys.IMAGE_SERVER_PRIVATE
IMAGE_SERVER_PUBLIC_KEY: keys.IMAGE_SERVER_PUBLIC
POSTGIS_HOST: internal_docker_urls.POSTGIS
POSTGIS_PORT: postgres.PORT
POSTGIS_DB_NAME: postgres.DB_NAME
POSTGIS_USER: postgres.USER
POSTGIS_PASS: postgres.PASS
SMTP_HOST: smtp.HOST
SMTP_PORT: smtp.PORT
SMTP_USER: smtp.USER
SMTP_PASS: smtp.PASS
MONGO_HOST: internal_docker_urls.MONGO
MONGO_PORT: mongodb.PORT
MONGO_USER: mongodb.USER
MONGO_PASS: mongodb.PASS
MONGO_DB_NAME: mongodb.DB_NAME
JAVAMELODY_PATH: javamelody.DATA_PATH
JAVAMELODY_USER: javamelody.USER
JAVAMELODY_PASS: javamelody.PASS
SERVER_URL: urls_with_scheme.CORE
REVERSE_PROXY_URL: internal_docker_urls.NGINX
IMAGE_SERVER_URL: urls_with_scheme.IMAGE_SERVER
URL_CORE: urls.CORE
URL_IMS1: urls.IMAGE_SERVER
INSTANCE_HOST_WEBSITE_URL: urls_with_scheme.CORE
STORAGE_PATH: container_paths.IMAGES
METADATA_PREFIXES: image_metadata.PREFIXES
mongo:
global:
MONGO_INITDB_ROOT_USERNAME: mongodb.USER
MONGO_INITDB_ROOT_PASSWORD: mongodb.PASS
MONGO_INIT_DATABASE: mongodb.DB_NAME
bioformat:
constant:
BIOFORMAT_PORT: 4321
pims:
constant:
WEB_CONCURRENCY: 16
MAX_REQUESTS: 0
LOG_CONFIG_FILE: /app/logging.yml
DEFAULT_IMAGE_SIZE_SAFETY_MODE: SAFE_REJECT
DEFAULT_ANNOTATION_ORIGIN: LEFT_TOP
OUTPUT_SIZE_LIMIT: 10000
task_queue_enabled: false
cache_enabled: true
global:
CYTOMINE_PUBLIC_KEY: keys.IMAGE_SERVER_PUBLIC
CYTOMINE_PRIVATE_KEY: keys.IMAGE_SERVER_PRIVATE
ROOT: container_paths.IMAGES
PENDING_PATH: container_paths.UPLOADED
PIMS_URL: urls_with_scheme.IMAGE_SERVER
REVERSE_PROXY_URL: internal_docker_urls.NGINX
URL_CORE: urls.CORE
URL_IMAGE_SERVER: urls.IMAGE_SERVER
URL_UPLOAD: urls.UPLOAD
web_ui:
global:
URL_CORE: urls_with_scheme.CORE
URL_UPLOAD: urls_with_scheme.UPLOAD
CYTOMINE_COMMERCIAL_VERSION: versions.CYTOMINE_COMMERCIAL
METADATA_PREFIXES: image_metadata.PREFIXES
postgis:
global:
POSTGRES_USER: postgres.USER
POSTGRES_PASSWORD: postgres.PASS
POSTGRES_DB: postgres.DB_NAME
nginx:
global:
INTERNAL_URLS_WEB_UI: internal_docker_urls.WEB_UI
INTERNAL_URLS_CORE: internal_docker_urls.CORE
INTERNAL_URLS_IMS: internal_docker_urls.PIMS
URLS_CORE: urls.CORE
URLS_IMAGE_SERVER: urls.IMAGE_SERVER
URLS_UPLOAD: urls.UPLOAD
UPLOAD_PATH: container_paths.UPLOADED
etc_hosts_rewriter:
constant:
PROXY_HOSTNAME: nginx
global:
URL_CORE: urls.CORE
URL_IMS1: urls.IMAGE_SERVER
URL_UPLOAD: urls.UPLOAD