forked from linux/WebHosting_DMZ
tubylinxyz fix to solve neo4j enterprise edition errors (#80)
The previous version of the application was giving errors because it depended on an API only available in the Neo4j Enterprise Edition (see below.)
```
2026-09-10 13:56:45.771+0000 ERROR Client triggered an unexpected error [Neo.DatabaseError.Schema.ConstraintCreationFailed]: Unable to create Constraint( type='NODE KEY', schema=(:Entity {parent_rcsb_id, entity_id}) ):
Node Key constraint requires Neo4j Enterprise Edition. Note that only the first found violation is shown., reference 8954d204-b1d3-4966-afca-09e7639654ae.
2026-09-10 13:56:45.789+0000 ERROR Client triggered an unexpected error [Neo.DatabaseError.Schema.ConstraintCreationFailed]: Unable to create Constraint( type='NODE KEY', schema=(:Instance {parent_rcsb_id, asym_id}) ):
Node Key constraint requires Neo4j Enterprise Edition. Note that only the first found violation is shown., reference 31e54bfc-f60d-4e20-8f62-74b3648bf995.
```
The developer solved those issues and created new docker images that were replaced in this PR.
Reviewed-on: linux/WebHosting_DMZ#80
Reviewed-by: buchel_k <konrad.bucheli@psi.ch>
Co-authored-by: João Pedro Agostinho de Sousa <joao.agostinho-de-sousa@psi.ch>
This commit is contained in:
agosti_j authored and 
buchel_k committed
1 parent
3ce2f3bc31
commit
d4cd9ea1cf
1 file changed
+150
-162
+150
-162
@@ -512,168 +512,156 @@ services:
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networks:
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- backend
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# # João Pedro Agostinho de Sousa <joao.agostinho-de-sousa@psi.ch>
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# # tubulin.xyz
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# neo4j:
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# image: neo4j:5
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# environment:
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# NEO4J_AUTH: neo4j/${NEO4J_PASSWORD}
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# NEO4J_server_memory_heap_initial__size: 1G
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# NEO4J_server_memory_heap_max__size: 2G
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# NEO4J_server_memory_pagecache_size: 1G
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# volumes:
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# - /mount/webhosting_dmz_write/tubulin/neo4j/data:/data
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# - /mount/webhosting_dmz_write/tubulin/neo4j/logs:/logs
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# healthcheck:
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# test:
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# [
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# "CMD",
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# "cypher-shell",
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# "-u",
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# "neo4j",
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# "-p",
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# "${NEO4J_PASSWORD}",
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# "RETURN 1",
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# ]
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# interval: 10s
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# timeout: 5s
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# retries: 10
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# start_period: 30s
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# restart: always
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# networks:
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# - tubulinxyz_backend
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# stop_grace_period: 60s
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# logging:
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# driver: json-file
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# options:
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# max-size: "50m"
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# max-file: "5"
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# deploy:
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# resources:
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# limits:
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# memory: 4G
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#
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# bootstrap:
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# image: ghcr.io/rtviii/tubulinxyz:latest
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# pull_policy: always
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# environment:
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# NEO4J_URI: bolt://neo4j:7687
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# NEO4J_USER: neo4j
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# NEO4J_PASSWORD: ${NEO4J_PASSWORD}
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# NEO4J_CURRENTDB: neo4j
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# TUBXZ_ROOT: /app
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# TUBETL_DATA: /mnt/tubetl_data
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# NCBI_TAXA_SQLITE: /app/.etetoolkit/taxa.sqlite
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# volumes:
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# - /mount/webhosting_dmz_write/tubulin/data:/mnt/tubetl_data
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# - /mount/webhosting_dmz_write/tubulin/log:/var/log/tubxz
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# depends_on:
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# neo4j:
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# condition: service_healthy
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# entrypoint: ["/bin/sh", "/app/scripts/init_and_seed.sh"]
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# restart: always
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# networks:
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# - tubulinxyz_backend
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# logging:
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# driver: json-file
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# options:
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# max-size: "50m"
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# max-file: "3"
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# deploy:
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# resources:
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# limits:
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# memory: 4G
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#
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# backend:
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# image: ghcr.io/rtviii/tubulinxyz:latest
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# pull_policy: always
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# environment:
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# NEO4J_URI: bolt://neo4j:7687
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# NEO4J_USER: neo4j
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# NEO4J_PASSWORD: ${NEO4J_PASSWORD}
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# NEO4J_CURRENTDB: neo4j
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# SECRET_KEY: ${SECRET_KEY}
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# TUBXZ_ROOT: /app
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# TUBETL_DATA: /mnt/tubetl_data
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# NCBI_TAXA_SQLITE: /app/.etetoolkit/taxa.sqlite
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# volumes:
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# - /mount/webhosting_dmz_write/tubulin/data:/mnt/tubetl_data
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# - /mount/webhosting_dmz_write/tubulin/log:/var/log/tubxz:ro
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# depends_on:
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# neo4j:
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# condition: service_healthy
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# healthcheck:
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# test: ["CMD", "curl", "-f", "http://localhost:8000/health"]
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# interval: 30s
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# timeout: 5s
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# retries: 3
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# start_period: 15s
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# restart: always
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# networks:
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# - backend
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# - tubulinxyz_backend
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# stop_grace_period: 30s
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# logging:
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# driver: json-file
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# options:
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# max-size: "50m"
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# max-file: "5"
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# deploy:
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# resources:
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# limits:
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# memory: 2G
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#
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# scheduler:
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# image: ghcr.io/rtviii/tubulinxyz:latest
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# pull_policy: always
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# environment:
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# NEO4J_URI: bolt://neo4j:7687
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# NEO4J_USER: neo4j
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# NEO4J_PASSWORD: ${NEO4J_PASSWORD}
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# NEO4J_CURRENTDB: neo4j
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# TUBXZ_ROOT: /app
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# TUBETL_DATA: /mnt/tubetl_data
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# NCBI_TAXA_SQLITE: /app/.etetoolkit/taxa.sqlite
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# volumes:
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# - /mount/webhosting_dmz_write/tubulin/data:/mnt/tubetl_data
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# - /mount/webhosting_dmz_write/tubulin/log:/var/log/tubxz
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# depends_on:
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# neo4j:
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# condition: service_healthy
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# entrypoint: ["/bin/sh", "/app/scripts/start_scheduler.sh"]
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# restart: always
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# networks:
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# - tubulinxyz_backend
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# logging:
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# driver: json-file
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# options:
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# max-size: "50m"
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# max-file: "5"
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# deploy:
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# resources:
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# limits:
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# memory: 4G
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#
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# frontend:
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# image: ghcr.io/rtviii/tubulinxyz-frontend:latest
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# pull_policy: always
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# depends_on:
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# backend:
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# condition: service_healthy
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# restart: always
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# networks:
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# - backend
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# - tubulinxyz_backend
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# logging:
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# driver: json-file
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# options:
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# max-size: "50m"
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# max-file: "3"
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# deploy:
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# resources:
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# limits:
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# memory: 512M
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#
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# João Pedro Agostinho de Sousa <joao.agostinho-de-sousa@psi.ch>
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# tubulin.xyz
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neo4j:
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image: neo4j:5.26-community
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environment:
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NEO4J_AUTH: neo4j/${NEO4J_PASSWORD}
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NEO4J_server_memory_heap_initial__size: 1G
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NEO4J_server_memory_heap_max__size: 2G
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NEO4J_server_memory_pagecache_size: 1G
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volumes:
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- /mount/webhosting_dmz_write/tubulin/neo4j/data:/data
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- /mount/webhosting_dmz_write/tubulin/neo4j/logs:/logs
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healthcheck:
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test: ["CMD", "cypher-shell", "-u", "neo4j", "-p", "${NEO4J_PASSWORD}", "RETURN 1"]
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interval: 10s
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timeout: 5s
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retries: 10
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start_period: 30s
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restart: always
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networks:
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- tubulinxyz_backend
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stop_grace_period: 60s
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logging:
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driver: json-file
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options:
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max-size: "50m"
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max-file: "5"
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deploy:
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resources:
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limits:
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memory: 4G
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bootstrap:
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image: ghcr.io/rtviii/tubulinxyz:0.2.1
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pull_policy: always
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environment:
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NEO4J_URI: bolt://neo4j:7687
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NEO4J_USER: neo4j
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NEO4J_PASSWORD: ${NEO4J_PASSWORD}
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TUBXZ_ROOT: /app
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TUBETL_DATA: /mnt/tubetl_data
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NCBI_TAXA_SQLITE: /app/.etetoolkit/taxa.sqlite
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volumes:
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- /mount/webhosting_dmz_write/tubulin/data:/mnt/tubetl_data
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- /mount/webhosting_dmz_write/tubulin/log:/var/log/tubxz
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depends_on:
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neo4j:
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condition: service_healthy
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entrypoint: ["/bin/sh", "/app/scripts/init_and_seed.sh"]
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restart: always
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networks:
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- tubulinxyz_backend
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logging:
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driver: json-file
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options:
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max-size: "50m"
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max-file: "3"
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deploy:
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resources:
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limits:
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memory: 4G
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backend:
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image: ghcr.io/rtviii/tubulinxyz:0.2.1
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pull_policy: always
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environment:
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NEO4J_URI: bolt://neo4j:7687
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NEO4J_USER: neo4j
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NEO4J_PASSWORD: ${NEO4J_PASSWORD}
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SECRET_KEY: ${SECRET_KEY}
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TUBXZ_ROOT: /app
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TUBETL_DATA: /mnt/tubetl_data
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NCBI_TAXA_SQLITE: /app/.etetoolkit/taxa.sqlite
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volumes:
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- /mount/webhosting_dmz_write/tubulin/data:/mnt/tubetl_data
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- /mount/webhosting_dmz_write/tubulin/log:/var/log/tubxz:ro
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depends_on:
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neo4j:
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condition: service_healthy
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healthcheck:
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test: ["CMD", "curl", "-f", "http://localhost:8000/health"]
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interval: 30s
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timeout: 5s
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retries: 3
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start_period: 15s
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restart: always
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networks:
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- backend
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- tubulinxyz_backend
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stop_grace_period: 30s
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logging:
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driver: json-file
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options:
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max-size: "50m"
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max-file: "5"
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deploy:
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resources:
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limits:
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memory: 2G
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scheduler:
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image: ghcr.io/rtviii/tubulinxyz:0.2.1
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pull_policy: always
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environment:
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NEO4J_URI: bolt://neo4j:7687
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NEO4J_USER: neo4j
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NEO4J_PASSWORD: ${NEO4J_PASSWORD}
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TUBXZ_ROOT: /app
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TUBETL_DATA: /mnt/tubetl_data
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NCBI_TAXA_SQLITE: /app/.etetoolkit/taxa.sqlite
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volumes:
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- /mount/webhosting_dmz_write/tubulin/data:/mnt/tubetl_data
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- /mount/webhosting_dmz_write/tubulin/log:/var/log/tubxz
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depends_on:
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neo4j:
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condition: service_healthy
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entrypoint: ["/bin/sh", "/app/scripts/start_scheduler.sh"]
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restart: always
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networks:
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- tubulinxyz_backend
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logging:
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driver: json-file
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options:
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max-size: "50m"
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max-file: "5"
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deploy:
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resources:
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limits:
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memory: 4G
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frontend:
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image: ghcr.io/rtviii/tubulinxyz-frontend:0.2.0
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pull_policy: always
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depends_on:
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backend:
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condition: service_healthy
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restart: always
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networks:
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- backend
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- tubulinxyz_backend
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logging:
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driver: json-file
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options:
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max-size: "50m"
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max-file: "3"
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deploy:
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resources:
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limits:
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memory: 512M
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networks:
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public:
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backend:
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Block a user