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Quay.io Swagger not right for pull_robot field

See original GitHub issue

Describe the bug Swagger defines pull_robot field as a string; in at least one case, it’s an object.

This causes refreshing Quay tools that have pull_robot set to a non-null value to fail.

To Reproduce curl -H "accept: application/json" https://quay.io/api/v1/repository/ucsc_cgl%2Fkallisto/build/?limit=1 > jq '.'

Notice pull_robot portion of response:

...
      "pull_robot": {
        "kind": "user",
        "name": "ucsc_cgl+robot",
        "is_robot": true
      },
...

But it is defined here as a string. When Swagger tries to deserialize the response, it gets an error:

ERROR [2020-06-09 00:55:16,153] io.dropwizard.jersey.errors.LoggingExceptionMapper: Error handling a request: f60cd43fa97ff34b
! com.fasterxml.jackson.databind.exc.MismatchedInputException: Cannot deserialize instance of `java.lang.String` out of START_OBJECT token
!  at [Source: (org.glassfish.jersey.message.internal.ReaderInterceptorExecutor$UnCloseableInputStream); line: 1, column: 249] (through reference chain: io.swagger.quay.client.model.InlineResponse2001["builds"]->java.util.ArrayList[0]->io.swagger.quay.client.model.QuayBuild["pull_robot"])
! at com.fasterxml.jackson.databind.exc.MismatchedInputException.from(MismatchedInputException.java:59)

Expected behavior Should deserialize correctly.

Additional context

Webservice version: develop branch

I believe this hasn’t come up before because most other responses I see have the value set to null.

┆Issue is synchronized with this Jira Story ┆Fix Versions: Dockstore 1.9 ┆Issue Number: DOCK-1401 ┆Sprint: Sprint 40 Octopus ┆Issue Type: Story

Issue Analytics

State:
Created 3 years ago
Comments:6 (5 by maintainers)

Top GitHub Comments

1reaction

coverbeckcommented, Jul 9, 2020

Getting an error when refreshing that tool in dev. See this in logs:

! at [Source: (org.glassfish.jersey.message.internal.ReaderInterceptorExecutor$UnCloseableInputStream); line: 1, column: 249] (through reference chain: io.swagger.quay.client.model.InlineResponse2001["builds"]->java.util.ArrayList[0]->io.swagger.quay.client.model.QuayBuild["pull_robot"])
! at com.fasterxml.jackson.databind.exc.MismatchedInputException.from(MismatchedInputException.java:59)
! at com.fasterxml.jackson.databind.DeserializationContext.reportInputMismatch(DeserializationContext.java:1442)
! at com.fasterxml.jackson.databind.DeserializationContext.handleUnexpectedToken(DeserializationContext.java:1216)
! at com.fasterxml.jackson.databind.DeserializationContext.handleUnexpectedToken(DeserializationContext.java:1126)
! at com.fasterxml.jackson.databind.deser.std.StringDeserializer.deserialize(StringDeserializer.java:63)
! at com.fasterxml.jackson.databind.deser.std.StringDeserializer.deserialize(StringDeserializer.java:10)
! at com.fasterxml.jackson.databind.deser.impl.MethodProperty.deserializeAndSet(MethodProperty.java:129)
! at com.fasterxml.jackson.databind.deser.BeanDeserializer.vanillaDeserialize(BeanDeserializer.java:288)
! at com.fasterxml.jackson.databind.deser.BeanDeserializer.deserialize(BeanDeserializer.java:151)
! at com.fasterxml.jackson.databind.deser.std.CollectionDeserializer.deserialize(CollectionDeserializer.java:286)
! at com.fasterxml.jackson.databind.deser.std.CollectionDeserializer.deserialize(CollectionDeserializer.java:245)
! at com.fasterxml.jackson.databind.deser.std.CollectionDeserializer.deserialize(CollectionDeserializer.java:27)
! at com.fasterxml.jackson.databind.deser.impl.MethodProperty.deserializeAndSet(MethodProperty.java:129)
! at com.fasterxml.jackson.databind.deser.BeanDeserializer.vanillaDeserialize(BeanDeserializer.java:288)
! at com.fasterxml.jackson.databind.deser.BeanDeserializer.deserialize(BeanDeserializer.java:151)
! at com.fasterxml.jackson.databind.ObjectReader._bind(ObjectReader.java:1682)
! at com.fasterxml.jackson.databind.ObjectReader.readValue(ObjectReader.java:977)
! at com.fasterxml.jackson.jaxrs.base.ProviderBase.readFrom(ProviderBase.java:814)
! at org.glassfish.jersey.message.internal.ReaderInterceptorExecutor$TerminalReaderInterceptor.invokeReadFrom(ReaderInterceptorExecutor.java:256)
! at org.glassfish.jersey.message.internal.ReaderInterceptorExecutor$TerminalReaderInterceptor.aroundReadFrom(ReaderInterceptorExecutor.java:235)
! at org.glassfish.jersey.message.internal.ReaderInterceptorExecutor.proceed(ReaderInterceptorExecutor.java:155)
! at org.glassfish.jersey.message.internal.MessageBodyFactory.readFrom(MessageBodyFactory.java:1085)
! at org.glassfish.jersey.message.internal.InboundMessageContext.readEntity(InboundMessageContext.java:874)
! ... 83 common frames omitted
! Causing: javax.ws.rs.ProcessingException: Error reading entity from input stream.
! at org.glassfish.jersey.message.internal.InboundMessageContext.readEntity(InboundMessageContext.java:889)
! at org.glassfish.jersey.message.internal.InboundMessageContext.readEntity(InboundMessageContext.java:834)
! at org.glassfish.jersey.client.ClientResponse.readEntity(ClientResponse.java:368)
! at org.glassfish.jersey.client.InboundJaxrsResponse$2.call(InboundJaxrsResponse.java:126)
! at org.glassfish.jersey.internal.Errors.process(Errors.java:315)
! at org.glassfish.jersey.internal.Errors.process(Errors.java:297)
! at org.glassfish.jersey.internal.Errors.process(Errors.java:228)
! at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:419)
! at org.glassfish.jersey.client.InboundJaxrsResponse.runInScopeIfPossible(InboundJaxrsResponse.java:267)
! at org.glassfish.jersey.client.InboundJaxrsResponse.readEntity(InboundJaxrsResponse.java:123)
! at io.swagger.quay.client.ApiClient.deserialize(ApiClient.java:568)
! at io.swagger.quay.client.ApiClient.invokeAPI(ApiClient.java:703)
! at io.swagger.quay.client.api.BuildApi.getRepoBuildsWithHttpInfo(BuildApi.java:337)
! at io.swagger.quay.client.api.BuildApi.getRepoBuilds(BuildApi.java:290)
! at io.dockstore.webservice.helpers.QuayImageRegistry.updateAPIToolsWithBuildInformation(QuayImageRegistry.java:286)
! at io.dockstore.webservice.helpers.AbstractImageRegistry.refreshTool(AbstractImageRegistry.java:301)
! at io.dockstore.webservice.resources.DockerRepoResource.refreshContainer(DockerRepoResource.java:310)
! at io.dockstore.webservice.resources.DockerRepoResource.refresh(DockerRepoResource.java:264)

0reactions

NatalieEOcommented, Aug 13, 2020

Wa able to refresh the tool mentioned in the ticket on develop API - 1.10.0-alpha.0-SNAPSHOT UI - 2.6.1-26-gb76540bb

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