Map server database errors when starting

[dbrnz]

This is with the latest version.

[2026-03-11 01:24:23.062] [litestar] [INFO] Starting flatmap server version 1.9.1
2026-03-11 01:24:23 [warning  ] No NPO release given: used sckan-2026-02-11 type=knowledge
2026-03-11 01:24:50 [warning  ] [rdflib.term.URIRef('http://uri.interlex.org/composer/uris/set/portal/5'), [['ilxtr:hasSomaPhenotype', 'PATO:0000366'], ['ilxtr:hasProjectionLaterality', 'PATO:0000618']]] type=knowledge
2026-03-11 01:24:50 [warning  ] [rdflib.term.URIRef('http://uri.interlex.org/tgbugs/uris/readable/sparc-nlp/kidney/153'), [['ilxtr:hasSomaPhenotype', 'PATO:0000366']]] type=knowledge
2026-03-11 01:24:50 [warning  ] [rdflib.term.URIRef('http://uri.interlex.org/tgbugs/uris/readable/sparc-nlp/kidney/154'), [['ilxtr:hasSomaPhenotype', 'PATO:0000367']]] type=knowledge
2026-03-11 01:24:50 [warning  ] [rdflib.term.URIRef('http://uri.interlex.org/composer/uris/set/portal/2'), [['ilxtr:hasSomaPhenotype', 'PATO:0000366']]] type=knowledge
2026-03-11 01:24:50 [warning  ] [rdflib.term.URIRef('http://uri.interlex.org/tgbugs/uris/readable/sparc-nlp/liver/115'), [['ilxtr:hasSomaPhenotype', 'PATO:0000367']]] type=knowledge
2026-03-11 01:24:50 [warning  ] [rdflib.term.URIRef('http://uri.interlex.org/tgbugs/uris/readable/sparc-nlp/liver/118'), [['ilxtr:hasSomaPhenotype', 'PATO:0000367']]] type=knowledge
2026-03-11 01:24:50 [warning  ] [rdflib.term.URIRef('http://uri.interlex.org/tgbugs/uris/readable/sparc-nlp/liver/117'), [['ilxtr:hasSomaPhenotype', 'PATO:0000366']]] type=knowledge
2026-03-11 01:24:51 [warning  ] [rdflib.term.URIRef('http://uri.interlex.org/tgbugs/uris/readable/sparc-nlp/liver/122'), [['ilxtr:hasSomaPhenotype', 'PATO:0000366']]] type=knowledge
2026-03-11 01:24:51 [warning  ] [rdflib.term.URIRef('http://uri.interlex.org/composer/uris/set/pain1/3'), [['ilxtr:hasAxonPhenotype', 'ILX:0796514']]] type=knowledge
2026-03-11 01:24:51 [warning  ] [rdflib.term.URIRef('http://uri.interlex.org/composer/uris/set/pain1/1'), [['ilxtr:hasAxonPhenotype', 'ILX:0796514']]] type=knowledge
2026-03-11 01:24:51 [warning  ] [rdflib.term.URIRef('http://uri.interlex.org/composer/uris/set/pain1/4'), [['ilxtr:hasAxonPhenotype', 'ILX:0796516']]] type=knowledge
2026-03-11 01:24:51 [warning  ] [rdflib.term.URIRef('http://uri.interlex.org/composer/uris/set/pain1/2'), [['ilxtr:hasAxonPhenotype', 'ILX:0796516']]] type=knowledge
2026-03-11 01:24:51 [warning  ] [rdflib.term.URIRef('http://uri.interlex.org/composer/uris/set/pain1/12'), [['ilxtr:hasAxonPhenotype', 'ILX:0796514']]] type=knowledge
2026-03-11 01:24:51 [warning  ] [rdflib.term.URIRef('http://uri.interlex.org/composer/uris/set/pain1/7'), [['ilxtr:hasAxonPhenotype', 'ILX:0796514']]] type=knowledge
2026-03-11 01:24:51 [warning  ] [rdflib.term.URIRef('http://uri.interlex.org/composer/uris/set/pain1/5'), [['ilxtr:hasAxonPhenotype', 'ILX:0796516']]] type=knowledge
2026-03-11 01:24:51 [warning  ] [rdflib.term.URIRef('http://uri.interlex.org/composer/uris/set/pain1/6'), [['ilxtr:hasAxonPhenotype', 'ILX:0796516']]] type=knowledge
2026-03-11 01:24:51 [warning  ] [rdflib.term.URIRef('http://uri.interlex.org/composer/uris/set/pain1/8'), [['ilxtr:hasAxonPhenotype', 'ILX:0796514']]] type=knowledge
2026-03-11 01:24:51 [warning  ] [rdflib.term.URIRef('http://uri.interlex.org/composer/uris/set/pain1/9'), [['ilxtr:hasAxonPhenotype', 'ILX:0796516']]] type=knowledge
[2026-03-11 01:24:54.043] [_granian.workers] [INFO] Started worker-1
[2026-03-11 01:24:54.044] [_granian.workers] [INFO] Started worker-1 runtime-1
[2026-03-11 01:24:54.100] [litestar] [WARNING] 22475458-a29b-514b-9fcf-2c75c6436cc3 is not an anatomical map, ignored.
[2026-03-11 01:24:55.728] [litestar] [WARNING] 942aa818-4278-58a6-a7e1-0a919ecaffca/vagus_n-1 has no connectivity, path not imported.
[2026-03-11 01:25:04.065] [litestar] [ERROR] insert or update on table "path_node_mappings" violates foreign key constraint "pnm_sckan_fk"
DETAIL:  Key (sckan_id)=(sckan-2026-02-11) is not present in table "knowledge_sources".
[2026-03-11 01:25:05.237] [litestar] [WARNING] 704f4fe8-33b2-590f-b6a0-7f85cb1ba929/n_78 has no connectivity, path not imported.
[2026-03-11 01:25:05.995] [litestar] [ERROR] insert or update on table "path_node_mappings" violates foreign key constraint "pnm_sckan_fk"
DETAIL:  Key (sckan_id)=(sckan-2026-02-11) is not present in table "knowledge_sources".
[2026-03-11 01:25:07.215] [litestar] [WARNING] 1901e17d-1ac9-5f43-ab86-542761e81339/C6_ardell-1 has no connectivity, path not imported.
[2026-03-11 01:25:07.796] [litestar] [ERROR] insert or update on table "path_node_mappings" violates foreign key constraint "pnm_sckan_fk"
DETAIL:  Key (sckan_id)=(sckan-2026-02-11) is not present in table "knowledge_sources".
[2026-03-11 01:25:08.812] [litestar] [WARNING] 5755cfe5-da7a-57fb-a543-10048a1acabf/pelvic_splanchnic_n has no connectivity, path not imported.
[2026-03-11 01:25:08.932] [litestar] [ERROR] insert or update on table "path_node_mappings" violates foreign key constraint "pnm_sckan_fk"
DETAIL:  Key (sckan_id)=(sckan-2026-02-11) is not present in table "knowledge_sources".
[2026-03-11 01:25:10.071] [litestar] [WARNING] 2243176e-f347-5994-b0b1-32a02159ab13/pelvic_splanchnic_n has no connectivity, path not imported.
[2026-03-11 01:25:10.270] [litestar] [ERROR] insert or update on table "path_forward_connections" violates foreign key constraint "forward_path_constraint"
DETAIL:  Key (source_id, forward_path_id)=(2243176e-f347-5994-b0b1-32a02159ab13, ilxtr:neuron-type-keast-2) is not present in table "feature_terms".
[2026-03-11 01:25:11.273] [litestar] [WARNING] 6a9598af-53ab-5eb4-8864-0d7eac4c7eb3 is not an anatomical map, ignored.
[2026-03-11 01:25:12.276] [litestar] [WARNING] 0525bdec-ce68-5230-b10e-bdde3269e55f has no rendered connectivity (mapmaker v1.13.1), ignored.
[2026-03-11 01:25:13.279] [litestar] [WARNING] b80d90cb-d6df-5a76-b9a1-0be7b5ea6c3e has no rendered connectivity (mapmaker v1.6.6-b.1), ignored.
[2026-03-11 01:25:14.281] [litestar] [WARNING] 7cd5352c-3878-5690-b0dd-705ea0f26360 is not an anatomical map, ignored.
[2026-03-11 01:25:15.284] [litestar] [WARNING] cd989ec7-c025-5315-95d8-522ec8ec060c has no rendered connectivity (mapmaker v1.6.6-b.1), ignored.
[2026-03-11 01:25:16.287] [litestar] [WARNING] 7f003862-6dbd-5871-8e8e-9a33c7ccefc5 has no rendered connectivity (mapmaker v1.17.2), ignored.
[2026-03-11 01:25:17.475] [litestar] [WARNING] 720a179b-3460-5167-8ea7-0d8bddd19678/AADN_1 has no connectivity, path not imported.
[2026-03-11 01:25:18.075] [litestar] [ERROR] insert or update on table "path_node_mappings" violates foreign key constraint "pnm_sckan_fk"
DETAIL:  Key (sckan_id)=(sckan-2026-02-11) is not present in table "knowledge_sources".
[2026-03-11 01:25:19.081] [litestar] [WARNING] 41e1c506-4482-5354-9d4b-f76509a2b685 is not an anatomical map, ignored.
[2026-03-11 01:25:20.084] [litestar] [WARNING] 6b051f89-85eb-5755-9352-d07e2e9d75ec is not an anatomical map, ignored.
[2026-03-11 01:25:21.087] [litestar] [WARNING] 18e744ac-0234-5175-b6d0-72d781b9f0ed has no rendered connectivity (mapmaker v1.7.0), ignored.
[2026-03-11 01:25:22.299] [litestar] [WARNING] 49f4a868-5637-5bd8-beef-67db6488729f/C6_ardell-1 has no connectivity, path not imported.
[2026-03-11 01:25:22.933] [litestar] [ERROR] insert or update on table "path_node_mappings" violates foreign key constraint "pnm_sckan_fk"
DETAIL:  Key (sckan_id)=(sckan-2026-02-11) is not present in table "knowledge_sources".
[2026-03-11 01:25:23.938] [litestar] [WARNING] b9fffaa8-9b8d-5931-a146-1a6f2c919c74 is not an anatomical map, ignored.
[2026-03-11 01:25:25.125] [litestar] [WARNING] bf779791-c2df-5745-b81b-3705c93f2351/bolser_31 has no connectivity, path not imported.
[2026-03-11 01:25:25.772] [litestar] [ERROR] insert or update on table "path_node_mappings" violates foreign key constraint "pnm_sckan_fk"
DETAIL:  Key (sckan_id)=(sckan-2026-02-11) is not present in table "knowledge_sources".

[dbrnz]

Oops, I suspect this could be because the latest SCKAN hasn't been loaded into the CQ database...

[napakalas]

Yes, pretty sure it is because sckan-2026-02-11 is not yet in CQ.

[dbrnz]

Have now loaded sckan-2026-02-11 and:

1. There are still the rdflib errors.
2. There is [2026-03-11 01:41:32.005] [litestar] [ERROR] insert or update on table "path_forward_connections" violates foreign key constraint "forward_path_constraint" DETAIL: Key (source_id, forward_path_id)=(2243176e-f347-5994-b0b1-32a02159ab13, ilxtr:neuron-type-keast-2) is not present in table "feature_terms".

[dbrnz]

The second error above is likely to be something about map 2243176e-f347-5994-b0b1-32a02159ab13 and not the new SCKAN...

[napakalas]

Mmm, interesting that this map is old test-flatmap. It was generated on 22-07-2025.

[dbrnz]

In which case it can safely be deleted, which I've just done.

[napakalas]

Thanks, Dave.