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[BEAM-10871] Fix FhirLROIT tests #12902

Merged
merged 29 commits into from
Sep 22, 2020
Merged

[BEAM-10871] Fix FhirLROIT tests #12902

merged 29 commits into from
Sep 22, 2020

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trucleduc
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Please add a meaningful description for your change here

In #12721 , we delete all FHIR stores in the clean up which may interfere with other integration tests. This PR fixes this by only deleting FHIR stores generated by the test.

R: @pabloem
R: @TheNeuralBit


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LGTM, thank you! I'll merge when Java PostCommit passes

@trucleduc
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@TheNeuralBit Would you please hold on merging, I realized that there could be flakiness issue for the existing tests. I'll investigate.

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ok I'll hold off, thanks

@trucleduc
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@TheNeuralBit ok fixed. I tried to run the test 10 times and they all passed.

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@trucleduc there was a failure:

com.google.api.client.googleapis.json.GoogleJsonResponseException: 409 Conflict
{
  "code" : 409,
  "errors" : [ {
    "domain" : "global",
    "message" : "already exists",
    "reason" : "alreadyExists"
  } ],
  "message" : "already exists",
  "status" : "ALREADY_EXISTS"
}
	at com.google.api.client.googleapis.json.GoogleJsonResponseException.from(GoogleJsonResponseException.java:149)
	at com.google.api.client.googleapis.services.json.AbstractGoogleJsonClientRequest.newExceptionOnError(AbstractGoogleJsonClientRequest.java:112)
	at com.google.api.client.googleapis.services.json.AbstractGoogleJsonClientRequest.newExceptionOnError(AbstractGoogleJsonClientRequest.java:39)
	at com.google.api.client.googleapis.services.AbstractGoogleClientRequest$1.interceptResponse(AbstractGoogleClientRequest.java:443)
	at com.google.api.client.http.HttpRequest.execute(HttpRequest.java:1108)
	at com.google.api.client.googleapis.services.AbstractGoogleClientRequest.executeUnparsed(AbstractGoogleClientRequest.java:541)
	at com.google.api.client.googleapis.services.AbstractGoogleClientRequest.executeUnparsed(AbstractGoogleClientRequest.java:474)
	at com.google.api.client.googleapis.services.AbstractGoogleClientRequest.execute(AbstractGoogleClientRequest.java:591)
	at org.apache.beam.sdk.io.gcp.healthcare.HttpHealthcareApiClient.createFhirStore(HttpHealthcareApiClient.java:161)
	at org.apache.beam.sdk.io.gcp.healthcare.FhirIOLROIT.test_FhirIO_deidentify(FhirIOLROIT.java:102)

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Java PostComit passed
PreCommit failed but it looks like unrelated flake BEAM-7827

@TheNeuralBit TheNeuralBit merged commit b80117e into apache:master Sep 22, 2020
ibzib pushed a commit to ibzib/beam that referenced this pull request Sep 30, 2020
* Add export FHIR resources to GCS method for HealthcareApiClient.

* Add export FHIR resources to GCS method for HealthcareApiClient.

* Add export FHIR resources to GCS method for HealthcareApiClient.

* Add export FHIR resources to GCS IO connector.

* Add export FHIR resources to GCS IO connector.

* Add export FHIR resources to GCS IO connector.

* Add export FHIR resources to GCS IO connector.

* Add export FHIR resources to GCS IO connector.

* Add export FHIR resources to GCS IO connector.

* Add export FHIR resources to GCS IO connector.

* Add export FHIR resources to GCS IO connector.

* Add export FHIR resources to GCS IO connector.

* Add deidentify FHIR resources IO connector.

* Add deidentify FHIR resources IO connector.

* Add deidentify FHIR resources IO connector.

* Add deidentify FHIR resources IO connector.

* Add deidentify FHIR resources IO connector.

* Add deidentify FHIR resources IO connector.

* Add deidentify FHIR resources IO connector.

* Add deidentify FHIR resources IO connector.

* Add deidentify FHIR resources IO connector.

* Add deidentify FHIR resources IO connector.

* Add deidentify FHIR resources IO connector.

* Add deidentify FHIR resources IO connector.

* Add deidentify FHIR resources IO connector.

* Only delete FHIR stores that were being used in FhirIOLROIT tests. This is to follow-up [BEAM-10871] Add deidentify for FhirIO connector apache#12721

R: @pabloem

* Correct FhirLROIT test.

* Fix FhirLROIT tests

* Fix FhirLROIT tests
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