🐞 Discovery service breaks on CKAN with large number of tags

[Markus92]

🔄 Duplicate Check

• [X] I have searched both open and closed issues and found no similar reports.

🔍 What Happened?

When deploying the new version (v1.2.3) of the discovery service to acceptance, it breaks the search API. It works on test. The dataset retrieve API still works.

👣 Steps to Reproduce

1. Point discovery service to https://ckan-acc.healthdata.nl
2. Query search API (e.g. POST http://localhost:8080/api/v1/datasets/search)
3. Notice you get a 500 server error
4. Notice you don't get the error at smaller CKAN instances like https://ckan-test.healthdata.nl

📸 Screenshots

See log files below.

📋 Logs

Following log indicates one very big request, probably too big for CKAN or whatever reverse proxy is in front of it:

2024-09-10 10:16:57,839 INFO  [io.qua.oid.dep.dev.OidcDevUIProcessor] (build-28) OIDC Dev Console: discovering the provider metadata at https://id.portal.dev.gdi.lu/realms/gdi/.well-known/openid-configuration
__  ____  __  _____   ___  __ ____  ______
 --/ __ \/ / / / _ | / _ \/ //_/ / / / __/
 -/ /_/ / /_/ / __ |/ , _/ ,< / /_/ /\ \
--\___\_\____/_/ |_/_/|_/_/|_|\____/___/
2024-09-10 10:16:58,320 INFO  [io.quarkus] (Quarkus Main Thread) gdi-userportal-dataset-discovery-service 0.0.0 on JVM (powered by Quarkus 3.14.1) started in 0.543s. Listening on: http://localhost:8080
2024-09-10 10:16:58,321 INFO  [io.quarkus] (Quarkus Main Thread) Profile dev activated. Live Coding activated.
2024-09-10 10:16:58,321 INFO  [io.quarkus] (Quarkus Main Thread) Installed features: [cache, cdi, hibernate-validator, oidc, qute, rest, rest-client, rest-client-jackson, rest-jackson, security, smallrye-context-propagation, smallrye-health, smallrye-openapi, swagger-ui, vertx, wiremock]
2024-09-10 10:16:58,322 INFO  [io.qua.dep.dev.RuntimeUpdatesProcessor] (vert.x-worker-thread-6) Live reload total time: 0.559s
2024-09-10 10:16:58,422 DEBUG [org.jbo.res.rea.cli.log.DefaultClientLogger] (vert.x-eventloop-thread-2) Request: GET https://ckan-acc.healthdata.nl/api/3/action/enhanced_package_search?q=&fq=&rows=1000&start=0 Headers[Accept=application/json User-Agent=Quarkus REST Client], Empty body
2024-09-10 10:16:58,768 DEBUG [org.jbo.res.rea.cli.log.DefaultClientLogger] (vert.x-eventloop-thread-2) Response: GET https://ckan-acc.healthdata.nl/api/3/action/enhanced_package_search?q=&fq=&rows=1000&start=0, Status[200 OK], Headers[Content-Length=669248 Content-Type=application/json; charset=utf-8 Date=Tue, 10 Sep 2024 08:16:58 GMT Cache-Control=public, must-revalidate, max-age=0 Set-Cookie=ckan=553a71b020d6fa6d166c6fa18057f9097aef34efgAJ9cQAoWAcAAABfZG9tYWlucQFOWAUAAABfcGF0aHECWAEAAAAvcQNYAwAAAF9pZHEEWCAAAAA4NDQ1MWU5N2M3YTM0OGI2OTk0MTQ2MjI4OWFhZjA5N3EFWAYAAABfZnJlc2hxBolYDgAAAF9jcmVhdGlvbl90aW1lcQdHQdm4AB6sc5xYDgAAAF9hY2Nlc3NlZF90aW1lcQhHQdm4AB6sc6B1Lg==; expires=Tue, 19-Jan-2038 03:14:07 GMT; HttpOnly; Path=/; SameSite=Lax Set-Cookie=ARRAffinity=751018869d3cb0b734d2d16f41072ab9f924211bbcdc76a670e2c22ceb0cc472;Path=/;HttpOnly;Secure;Domain=ckan-acc.healthdata.nl Set-Cookie=ARRAffinitySameSite=751018869d3cb0b734d2d16f41072ab9f924211bbcdc76a670e2c22ceb0cc472;Path=/;HttpOnly;SameSite=None;Secure;Domain=ckan-acc.healthdata.nl], Body:
{"help": "https://ckan-acc.healthdata.nl/api/3/action/help_show?name=enhanced_package_search", "success": true, "result": {"count": 166, "facets": {}, "results": [{"conforms_to": [{"name": "https://fdp.radboudumc.nl/profile/2f08228e-1789-40f8-84cd-28e3288c3604", "display_name": "https://fdp.radboudumc.nl/profile/2f08228e-1789-40f8-84cd-28e3288c3604", "count": null}], "creator_user_id": "22c4e55f-7782-42d1-af29-90906651772f", "id": "162fd339-6cbd-4e47-8cfe-b375a465c763", "identifier": "https://fdp.radboudumc.nl/dataset/37d6ad17-aa35-425c-946e-855838d3f9cc", "isopen": false, "issued": "2024-07-01", "language": [{"name": "http://id.loc.gov/vocabulary/iso639-1/en", "display_name": "English", "count": null}], "license_id": "", "license_title": "", "metadata_created": "2024-08-02T14:26:50.477561", "metadata_modified": "2024-09-09T22:45:10.243387", "modified": "2024-07-01", "name": "prisma-questionnaire-data", "notes": "The extensive questionnaire covers a number of potential breast cancer risk predictors such as demographics, personal characteristics, reproductive characteristics, medication, lifestyle, health status, family history, psychosocial characteristics.", "num_resources": 0, "num_tags": 0, "organization": {"id": "0626fbbc-49d5-4b61-80dc-d5a4533cdd12", "name": "radboudumc-prisma", "title": "Radboudumc(Prisma)", "type": "organization", "description": "", "image_url": "", "created": "2024-07-02T12:12:00.908716", "is_organization": true, "approval_status": "approved", "state": "active"}, "owner_org": "0626fbbc-49d5-4b61-80dc-d5a4533cdd12", "private": false, "publisher_name": "Radboudumc", "state": "active", "theme": [{"name": "http://publications.europa.eu/resource/authority/data-theme/HEAL", "display_name": "Health", "count": null}], "title": "PRISMA Questionnaire data", "type": "dataset", "contact_point": [{"contact_email": "", "contact_name": "", "contact_uri": "mailto:Mireille.Broeders@radboudumc.nl"}], "creator": [{"creator_identifier": "M.J.M. Broeders", "creator_name": "M.J.M. Broeders"}], "extras": [{"key": "uri", "value": "https://fdp.radboudumc.nl/dataset/37d6ad17-aa35-425c-946e-855838d3f9cc"}, {"key": "harvest_object_id", "value": "109259ae-b601-43e7-a76a-e366f5d95ba6"}, {"key": "harvest_source_id", "value": "f49e40e5-2a95-4bac-8980-e5fa2e80fddd"}, {"key": "harvest_source_title", "value": "Radboudumc FDP"}], "resources": [], "tags": [], "groups": [], "relationships_as_subject": [], "relationships_as_object": [], "access_rights": null, "has_version": null, "spatial_uri": null}, {"conforms_to": [{"name": "https://fdp-acc.healthdata.nl/profile/2f08228e-1789-40f8-84cd-28e3288c3604", "display_name": "https://fdp-acc.healthdata.nl/profile/2f08228e-1789-40f8-84cd-28e3288c3604", "count": null}], "creator_user_id": "22c4e55f-7782-42d1-af29-90906651772f", "id": "56b258d5-70ef-4936-849f-4273a57fbbf0", "identifier": "https://repo.metadatacenter.org/template-instances/534930c2-020c-4da3-bbcc-3939806a9b28", "isopen": false, "issued": "2021-09-06", "language": [{"name": "http://id.loc.gov/vocabulary/iso639-1/en", "display_name": "English", "count": null}], "license_id": "", "license_title": "", "metadata_created": "2024-05-24T09:35:42.262080", "metadata_modified": "2024-08-29T18:06:26.010825", "modified": "2021-09-09", "name": "kritische-materialen-in-een-crisis1", "notes": "Kritische materialen in een crisis; Material Supply Strategies in a Crisis", "num_resources": 0, "num_tags": 9, "organization": {"id": "1d578b43-f7b7-4e13-ac9f-487bb24ce99b", "name": "health-ri", "title": "Health-RI", "type": "organization", "description": "", "image_url": "", "created": "2024-04-25T11:29:47.932851", "is_organization": true, "approval_status": "approved", "state": "active"}, "owner_org": "1d578b43-f7b7-4e13-ac9f-487bb24ce99b", "private": false, "publisher_name": "Qian Zhang", "state": "active", "temporal_end": "2021-12-31", "temporal_start": "2020-09-16", "theme": [{"name": "http://purl.org/zonmw/covid19/10008", "display_name": "international", "count": null}, {"name": "http://purl.org/zonmw/covid19/10010", "display_name": "home care", "count": null}, {"name": "http://purl.org/zonmw/covid19/10013", "display_name": "nursing home care", "count": null}, {"name": "http://purl.org/zonmw/covid19/10014", "display_name": "hospital care", "count": null}, {"name": "http://purl.org/zonmw/covid19/10018", "display_name": "health care phase", "count": null}, {"name": "http://purl.org/zonmw/covid19/10033", "display_name": "COVID-19 phase", "count": null}, {"name": "http://purl.org/zonmw/generic/10006", "display_name": "other", "count": null}], "title": "Kritische materialen in een crisis", "type": "dataset", "url": "https://covid19initiatives.health-ri.nl/p/Project/27866022694497956", "contact_point": [{"contact_email": "", "contact_name": "Jan Telgen", "contact_uri": "https://orcid.org/0000-0001-7403-8800"}], "creator": [{"creator_identifier": "https://orcid.org/0000-0003-4591-7755", "creator_name": "Qian Zhang"}], "extras": [{"key": "uri", "value": "https://fdp-acc.healthdata.nl/dataset/9192eac4-44c4-4939-a2a8-ddd36d970cf5"}, {"key": "harvest_object_id", "value": "190c1c31-cad3-4217-a239-22e0f54fd1b5"}, {"key": "harvest_source_id", "value": "13f45b54-a68b-4914-a8f3-68e613c63332"}, {"key": "harvest_source_title", "value": "FDP health-ri"}], "tags": [{"display_name": "COVID-19 phase", "id": "e60ff377-b20e-444a-b7a7-769c3a01eede", "name": "COVID-19 phase", "state": "active", "vocabulary_id": null}, {"display_name": "Mentally disabled care", "id": "129b3c10-c4f6-4751-bb9d-242704cf97f5", "name": "Mentally disabled care", "state": "active", "vocabulary_id": null}, {"display_name": "People with procurement expertise involved in buying medical equipments during Covid-19", "id": "0e93900c-818d-43d2-9173-e8ea98840f3a", "name": "People with procurement expertise involved in buying medical equipments during Covid-19", "state": "active", "vocabulary_id": null}, {"display_name": "health care phase", "id": "d76ba39d-d41c-452f-a00d-b4467597670f", "name": "health care phase", "state": "active", "vocabulary_id": null}, {"display_name": "home care", "id": "25ddfe97-9b11-401c-970e-04e10a20aa90", "name": "home care", "state": "active", "vocabulary_id": null}, {"display_name": "hospital care", "id": "7872a90d-c619-4ae3-a3da-44f0a4ce4c90", "name": "hospital care", "state": "active", "vocabulary_id": null}, {"display_name": "international", "id": "ab43d0cb-aead-46b1-b072-e0658ea20797", "name": "international", "state": "active", "vocabulary_id": null}, {"display_name": "nursing home care", "id": "fbde97b6-6bd3-4849-a810-13b17ff0fab7", "name": "nursing home care", "state": "active", "vocabulary_id": null}, {"display_name": "other", "id": "f5ab4735-47aa-4ad5-a639-074796a39f92", "name": "other", "state": "active", "vocabulary_id": null}], "resources": [], "groups": [], "relationships_as_subject": [], "relationships_as_object": [], "access_rights": null, "has_version": null, "spatial_uri": null}, {"conforms_to": [{"name": "https://fdp-acc.healthdata.nl/profile/2f08228e-1789-40f8-84cd-28e3288c3604", "display_name": "https://fdp-acc.healthdata.nl/profile/2f08228e-1789-40f8-84cd-28e3288c3604", "count": null}], "creator_user_id": "22c4e55f-7782-42d1-af29-90906651772f", "id": "d7874929-1abf-40bf-8482-8557cf48c36d", "identifier": "https://repo.metadatacenter.org/template-instances/9b8367af-6502-4aa6-9d6f-8e80044e947a", "isopen": false, "issued": "2021-09-07", "language": [{"name": "http://id.loc.gov/vocabulary/iso639-1/en", "display_name": "English", "count": null}], "license_id": "", "license_title": "", "metadata_created": "2024-05-24T09:38:19.625064", "metadata_modified": "2024-08-29T18:06:23.942930", "modified": "2022-09-22", "name": "countercovid-study-oral-imatinib-for-covid-191", "notes": "CounterCOVID study - oral imatinib for COVID-19", "num_resources": 0, "num_tags": 6, "organization": {"id": "1d578b43-f7b7-4e13-ac9f-487bb24ce99b", "name": "health-ri", "title": "Health-RI", "type": "organization", "description": "", "image_url": "", "created": "2024-04-25T11:29:47.932851", "is_organization": true, "approval_status": "approved", "state": "active"}, "owner_org": "1d578b43-f7b7-4e13-ac9f-487bb24ce99b", "private": false, "publisher_name": "Erik Duijvelaar", "state": "active", "temporal_end": "2022-07-01", "temporal_start": "2020-07-01", "theme": [{"name": "http://purl.bioontology.org/ontology/ICD10CM/J12.81", "display_name": "Pneumonia due to SARS-associated coronavirus", "count": null}, {"name": "http://purl.org/zonmw/covid19/10007", "display_name": "national", "count": null}, {"name": "http://purl.org/zonmw/covid19/10014", "display_name": "hospital care", "count": null}, {"name": "http://purl.org/zonmw/covid19/10033", "display_name": "COVID-19 phase", "count": null}, {"name": "http://purl.org/zonmw/covid19/10091", "display_name": "COVID-19 patient grouping", "count": null}, {"name": "http://purl.org/zonmw/generic/10095", "display_name": "human disease", "count": null}], "title": "CounterCOVID study - oral imatinib for COVID-19", "type": "dataset", "url": "https://covid19initiatives.health-ri.nl/p/Project/27866022694497957", "contact_point": [{"contact_email": "", "contact_name": "Harm Jan Bogaard", "contact_uri": "https://orcid.org/0000-0001-5371-0346"}], "creator": [{"creator_identifier": "https://orcid.org/0000-0002-5547-5578", "creator_name": "Erik Duijvelaar"}], "extras": [{"key": "uri", "value": "https://fdp-acc.healthdata.nl/dataset/95df3d9c-97ee-4c98-aa5c-f2024-09-10 10:16:58,807 DEBUG [org.jbo.res.rea.cli.log.DefaultClientLogger] (vert.x-eventloop-thread-2) Request: GET 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10:16:58,851 DEBUG [org.jbo.res.rea.cli.log.DefaultClientLogger] (vert.x-eventloop-thread-2) Response: GET 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10:16:58,853 SEVERE [io.git.gen.dis.api.GlobalExceptionMapper] (executor-thread-1) Received: 'Internal Server Error, status code 500' when invoking: Rest Client method: 'io.github.genomicdatainfrastructure.discovery.remote.ckan.api.CkanQueryApi#packageSearch'ite=751018869d3cb0b734d2d16f41072ab9f924211bbcdc76a670e2c22ceb0cc472;Path=/;HttpOnly;SameSite=None;Secure;Domain=ckan-acc.healthdata.nl], Body:

Exception in CkanDatasetsRepository.java:72
       70                  .build());
       71
    -> 72          var response = ckanQueryApi.packageSearch(
       73                  null,
       74                  facetsQuery,

Exception in SearchDatasetsQuery.java:41
       39                  .orElse(List.of());
       40
    -> 41          var datasets = repository.search(datasetIds,
       42                  query.getSort(),
       43                  query.getRows(),

Exception in DatasetQueryApiImpl.java:24
       22      @Override
       23      public Response datasetSearch(DatasetSearchQuery datasetSearchQuery) {
    -> 24          var content = searchDatasetsQuery.execute(datasetSearchQuery, accessToken());
       25          return Response.ok(content).build();
       26      }

: org.jboss.resteasy.reactive.ClientWebApplicationException: Received: 'Internal Server Error, status code 500' when invoking: Rest Client method: 'io.github.genomicdatainfrastructure.discovery.remote.ckan.api.CkanQueryApi#packageSearch'
    at org.jboss.resteasy.reactive.client.impl.RestClientRequestContext.unwrapException(RestClientRequestContext.java:205)
    at org.jboss.resteasy.reactive.common.core.AbstractResteasyReactiveContext.handleException(AbstractResteasyReactiveContext.java:329)
    at org.jboss.resteasy.reactive.common.core.AbstractResteasyReactiveContext.run(AbstractResteasyReactiveContext.java:175)
    at org.jboss.resteasy.reactive.client.impl.RestClientRequestContext$1.lambda$execute$0(RestClientRequestContext.java:324)
    at io.vertx.core.impl.ContextInternal.dispatch(ContextInternal.java:279)
    at io.vertx.core.impl.ContextInternal.dispatch(ContextInternal.java:261)
    at io.vertx.core.impl.ContextInternal.lambda$runOnContext$0(ContextInternal.java:59)
    at io.netty.util.concurrent.AbstractEventExecutor.runTask(AbstractEventExecutor.java:173)
    at io.netty.util.concurrent.AbstractEventExecutor.safeExecute(AbstractEventExecutor.java:166)
    at io.netty.util.concurrent.SingleThreadEventExecutor.runAllTasks(SingleThreadEventExecutor.java:469)
    at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:566)
    at io.netty.util.concurrent.SingleThreadEventExecutor$4.run(SingleThreadEventExecutor.java:994)
    at io.netty.util.internal.ThreadExecutorMap$2.run(ThreadExecutorMap.java:74)
    at io.netty.util.concurrent.FastThreadLocalRunnable.run(FastThreadLocalRunnable.java:30)
    at java.base/java.lang.Thread.run(Thread.java:1583)
Caused by: jakarta.ws.rs.WebApplicationException: Internal Server Error, status code 500
    at io.github.genomicdatainfrastructure.discovery.datasets.infrastructure.ckan.persistence.CkanDatasetsRepository.search(CkanDatasetsRepository.java:72)
    at io.github.genomicdatainfrastructure.discovery.datasets.infrastructure.ckan.persistence.CkanDatasetsRepository_ClientProxy.search(Unknown Source)
    at io.github.genomicdatainfrastructure.discovery.datasets.application.usecases.SearchDatasetsQuery.execute(SearchDatasetsQuery.java:41)
    at io.github.genomicdatainfrastructure.discovery.datasets.application.usecases.SearchDatasetsQuery_ClientProxy.execute(Unknown Source)
    at io.github.genomicdatainfrastructure.discovery.api.DatasetQueryApiImpl.datasetSearch(DatasetQueryApiImpl.java:24)
    at io.github.genomicdatainfrastructure.discovery.api.DatasetQueryApi$quarkusrestinvoker$datasetSearch_c4328b800400c86a6926a6c7ee6203b4f96b871f.invoke(Unknown Source)
    at org.jboss.resteasy.reactive.server.handlers.InvocationHandler.handle(InvocationHandler.java:29)
    at io.quarkus.resteasy.reactive.server.runtime.QuarkusResteasyReactiveRequestContext.invokeHandler(QuarkusResteasyReactiveRequestContext.java:141)
    at org.jboss.resteasy.reactive.common.core.AbstractResteasyReactiveContext.run(AbstractResteasyReactiveContext.java:147)
    at io.quarkus.vertx.core.runtime.VertxCoreRecorder$14.runWith(VertxCoreRecorder.java:635)
    at org.jboss.threads.EnhancedQueueExecutor$Task.doRunWith(EnhancedQueueExecutor.java:2516)
    at org.jboss.threads.EnhancedQueueExecutor$Task.run(EnhancedQueueExecutor.java:2495)
    at org.jboss.threads.EnhancedQueueExecutor$ThreadBody.run(EnhancedQueueExecutor.java:1521)
    at org.jboss.threads.DelegatingRunnable.run(DelegatingRunnable.java:11)
    at org.jboss.threads.ThreadLocalResettingRunnable.run(ThreadLocalResettingRunnable.java:11)
    ... 2 more

🌐 Affected Browsers

No response

💻 Operating System

Windows, macOS

🤝 Want to Contribute to the Fix?

Yes, I'd like to help fix this.

ℹ️ Additional Information

I can do a bisect later to find the relevant commit, but you guys might know better.

[admy7]

Hello Markus,

Thank you for pointing it out.

How many datasets did you try to fetch from CKAN?

If it is more than ckan.search.rows_max (normally default is 1000), I would expect the endpoint to fail.

[Markus92]

We have 166 datasets in this CKAN. It even fails with the following query (1 dataset):

curl --location 'http://localhost:8080/api/v1/datasets/search' \
--header 'Content-Type: application/json' \
--header 'Cookie: ckan=4f8a2962e32592bf26b3f2830479ff617e46e500gAJ9cQAoWAcAAABfZG9tYWlucQFOWAUAAABfcGF0aHECWAEAAAAvcQNYAwAAAF9pZHEEWCAAAAA5YTA5ZGUwYTBhZjU0MDQyYjQxYTY0NWMzODY4NDJkNnEFWA4AAABfY3JlYXRpb25fdGltZXEGR0HZtrrsoyykWA4AAABfYWNjZXNzZWRfdGltZXEHR0HZt7sZuJV4WAgAAABfZXhwaXJlc3EIY2RhdGV0aW1lCmRhdGV0aW1lCnEJY19jb2RlY3MKZW5jb2RlCnEKWAsAAAAHw7YBEwMOBwAAAHELWAYAAABsYXRpbjFxDIZxDVJxDoVxD1JxEFgGAAAAX2ZyZXNocRGJdS4=' \
--data '{
    "start": 0,
    "rows": 1,
    "query": "",
    "sort": "title asc",
    "facets": []
}'

[admy7]

To search datasets, the first step is to collect dataset ids from every data source and then call package_search, passing it the identifier facet with all the ids found.

I assume that the problem comes from the URL, as package_search uses query parameters. With 166 datasets, we would have 166 identifiers in the URL, making it probably too long.

We have planned to investigate this issue during this sprint.