Timeout when loading new knowledgebase

[scp93ch]

When using SPYDERISK via system-modeller-deployment, if I upload a new knowledgebase in the knowledgebase manager page then I get an error shown in the browser relating to a timeout. The knowledgebase does actually get uploaded correctly (that can be seen by a manual page refresh) but it appears not to have been.

From the logs it seems that there's a timeout on the Tomcat side, so I've added the issue here as the Tomcat config of the production image is created by the Dockerfile.

The knowledgebase version was 6a1-2-13.

Relevant log lines:

ssm         | 13:38:10.914 DEBUG u.a.s.i.s.s.s.StoreModelManager:169: Loaded model domain-network into graph <http://it-innovation.soton.ac.uk/ontologies/trustworthiness/domain-network>: INSERT DATA {
ssm         |   GRAPH <http://it-innovation.soton.ac.uk/model-management> {
ssm         |     <http://it-innovation.soton.ac.uk/ontologies/trustworthiness/domain-network> a void:Dataset ;
ssm         |       dcterms:title "domain-network" ;
ssm         |       dcterms:modified "2023-05-31T13:38:10Z"^^xsd:date .
ssm         |   }
ssm         | }
ssm         |
ssm         | 13:38:10.915 DEBUG u.a.s.i.s.s.r.DomainModelController:232: Loading icon mappings from file: /var/lib/tomcat/temp/domain4847609640534879168/icon-mapping.json
ssm         | 13:38:10.916 DEBUG u.a.s.i.s.s.u.PaletteGenerator:119: Getting icons for http://it-innovation.soton.ac.uk/ontologies/trustworthiness/domain-network
ssm         | 13:38:10.918  INFO u.a.s.i.s.s.u.PaletteGenerator:430: createPalette: calling build()
ssm         | 13:38:10.919  INFO u.a.s.i.s.s.u.PaletteGenerator:419: build started
ssm         | 13:38:10.920  INFO u.a.s.i.s.s.u.PaletteGenerator:421: build getAssets
ssm         | 13:38:10.921 DEBUG u.a.s.i.s.s.u.PaletteGenerator:204: Getting assets for domain: domain-network
ssm         | 13:38:11.945  INFO u.a.s.i.s.s.u.PaletteGenerator:211: Located 164 assets
ssm         | 13:38:11.982  INFO u.a.s.i.s.s.u.PaletteGenerator:423: build getLinks
ssm-proxy   | 172.22.0.1 - - [31/May/2023:13:38:42 +0000] "GET /auth/admin/realms/ssm-realm/users?username=testadmin HTTP/1.1" 200 392 "-" "Apache-HttpClient/4.5.12 (Java/1.8.0_275)" "host.docker.internal:8089"
ssm-proxy   | 172.22.0.1 - - [31/May/2023:13:38:42 +0000] "GET /auth/admin/realms/ssm-realm/users/b32c55ab-43f0-41d0-b983-e4992d488015 HTTP/1.1" 200 390 "-" "Apache-HttpClient/4.5.12 (Java/1.8.0_275)" "host.docker.internal:8089"
ssm-proxy   | 172.22.0.1 - - [31/May/2023:13:38:42 +0000] "GET /auth/admin/realms/ssm-realm/users/b32c55ab-43f0-41d0-b983-e4992d488015/role-mappings HTTP/1.1" 200 1454 "-" "Apache-HttpClient/4.5.12 (Java/1.8.0_275)" "host.docker.internal:8089"
ssm-proxy   | 172.22.0.1 - - [31/May/2023:13:38:42 +0000] "GET /system-modeller/auth/me HTTP/1.1" 200 183 "http://localhost:8089/system-modeller/domain-manager" "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/113.0.0.0 Safari/537.36" "localhost:8089"
ssm         | 13:39:01.326  INFO u.a.s.i.s.s.u.PaletteGenerator:445: Created palette for domain: http://it-innovation.soton.ac.uk/ontologies/trustworthiness/domain-network
ssm         | 13:39:01.331  INFO u.a.s.i.s.s.u.PaletteGenerator:446: Location: /var/lib/tomcat/webapps/system-modeller/WEB-INF/classes/static/data//palette-domain-network.json
ssm-proxy   | 172.22.0.1 - - [31/May/2023:13:39:01 +0000] "GET /auth/admin/realms/ssm-realm/users?username=testadmin HTTP/1.1" 200 392 "-" "Apache-HttpClient/4.5.12 (Java/1.8.0_275)" "host.docker.internal:8089"
ssm-proxy   | 172.22.0.1 - - [31/May/2023:13:39:01 +0000] "GET /auth/admin/realms/ssm-realm/users/b32c55ab-43f0-41d0-b983-e4992d488015 HTTP/1.1" 200 390 "-" "Apache-HttpClient/4.5.12 (Java/1.8.0_275)" "host.docker.internal:8089"
ssm         | 13:39:01.431 DEBUG u.a.s.i.s.s.r.DomainModelController:93: Getting domain models for: testadmin
ssm         | 13:39:01.433  INFO u.a.s.i.s.s.s.ModelObjectsHelper:1436: Syncing users with Keycloak
ssm         | 13:39:01.442 DEBUG u.a.s.i.s.s.s.ModelObjectsHelper:1439: Current users [testadmin, testuser]
ssm-proxy   | 2023/05/31 13:39:01 [error] 9#9: *4 upstream timed out (110: Operation timed out) while reading response header from upstream, client: 172.22.0.1, server: , request: "POST /system-modeller/domains/upload HTTP/1.1", upstream: "http://172.22.0.4:8080/system-modeller/domains/upload", host: "localhost:8089", referrer: "http://localhost:8089/system-modeller/domain-manager"
ssm-proxy   | 172.22.0.1 - - [31/May/2023:13:39:01 +0000] "POST /system-modeller/domains/upload HTTP/1.1" 504 569 "http://localhost:8089/system-modeller/domain-manager" "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/113.0.0.0 Safari/537.36" "localhost:8089"
ssm-proxy   | 172.22.0.1 - - [31/May/2023:13:39:01 +0000] "GET /auth/admin/realms/ssm-realm/users HTTP/1.1" 200 782 "-" "Apache-HttpClient/4.5.12 (Java/1.8.0_275)" "host.docker.internal:8089"

[scp93ch]

Error messages: