[jira] [Work logged] (BEAM-9468) Add Google Cloud Healthcare API IO Connectors

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https://issues.apache.org/jira/browse/BEAM-9468?focusedWorklogId=435787=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#worklog-435787
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Author: ASF GitHub Bot
Created on: 21/May/20 00:28
Start Date: 21/May/20 00:28
Worklog Time Spent: 10m 
  Work Description: pabloem merged pull request #11339:
URL: https://github.com/apache/beam/pull/11339


   



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Issue Time Tracking
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Worklog Id: (was: 435787)
Time Spent: 53.5h  (was: 53h 20m)

> Add Google Cloud Healthcare API IO Connectors
> -
>
> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: P3
>  Time Spent: 53.5h
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
> Healthcare API|https://cloud.google.com/healthcare/docs/]
> HL7v2IO
> FHIRIO
> DICOM 



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Author: ASF GitHub Bot
Created on: 21/May/20 00:19
Start Date: 21/May/20 00:19
Worklog Time Spent: 10m 
  Work Description: jaketf commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-631805319


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> Add Google Cloud Healthcare API IO Connectors
> -
>
> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: P3
>  Time Spent: 53h 20m
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
> Healthcare API|https://cloud.google.com/healthcare/docs/]
> HL7v2IO
> FHIRIO
> DICOM 



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[jira] [Work logged] (BEAM-9468) Add Google Cloud Healthcare API IO Connectors

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Author: ASF GitHub Bot
Created on: 20/May/20 23:15
Start Date: 20/May/20 23:15
Worklog Time Spent: 10m 
  Work Description: pabloem commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-631786516


   Run Java PreCommit



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> Add Google Cloud Healthcare API IO Connectors
> -
>
> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: P3
>  Time Spent: 53h 10m
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
> Healthcare API|https://cloud.google.com/healthcare/docs/]
> HL7v2IO
> FHIRIO
> DICOM 



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Author: ASF GitHub Bot
Created on: 20/May/20 23:04
Start Date: 20/May/20 23:04
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  Work Description: pabloem commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-631782829


   Run Java PreCommit



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> Add Google Cloud Healthcare API IO Connectors
> -
>
> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: P3
>  Time Spent: 53h
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
> Healthcare API|https://cloud.google.com/healthcare/docs/]
> HL7v2IO
> FHIRIO
> DICOM 



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[jira] [Work logged] (BEAM-9468) Add Google Cloud Healthcare API IO Connectors

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 ]

ASF GitHub Bot logged work on BEAM-9468:


Author: ASF GitHub Bot
Created on: 20/May/20 22:57
Start Date: 20/May/20 22:57
Worklog Time Spent: 10m 
  Work Description: pabloem commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-631778141


   Run Java PostCommit



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Issue Time Tracking
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Worklog Id: (was: 435750)
Time Spent: 52h 50m  (was: 52h 40m)

> Add Google Cloud Healthcare API IO Connectors
> -
>
> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: P3
>  Time Spent: 52h 50m
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
> Healthcare API|https://cloud.google.com/healthcare/docs/]
> HL7v2IO
> FHIRIO
> DICOM 



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[jira] [Work logged] (BEAM-9468) Add Google Cloud Healthcare API IO Connectors

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 ]

ASF GitHub Bot logged work on BEAM-9468:


Author: ASF GitHub Bot
Created on: 20/May/20 22:56
Start Date: 20/May/20 22:56
Worklog Time Spent: 10m 
  Work Description: jaketf commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-631777614


   are we able to run post commit?
   



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Time Spent: 52h 40m  (was: 52.5h)

> Add Google Cloud Healthcare API IO Connectors
> -
>
> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: P3
>  Time Spent: 52h 40m
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
> Healthcare API|https://cloud.google.com/healthcare/docs/]
> HL7v2IO
> FHIRIO
> DICOM 



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[jira] [Work logged] (BEAM-9468) Add Google Cloud Healthcare API IO Connectors

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 ]

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Author: ASF GitHub Bot
Created on: 20/May/20 22:52
Start Date: 20/May/20 22:52
Worklog Time Spent: 10m 
  Work Description: TheNeuralBit commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-631773038


   That definitely seems like a flake to me



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Issue Time Tracking
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Worklog Id: (was: 435747)
Time Spent: 52.5h  (was: 52h 20m)

> Add Google Cloud Healthcare API IO Connectors
> -
>
> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: P3
>  Time Spent: 52.5h
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
> Healthcare API|https://cloud.google.com/healthcare/docs/]
> HL7v2IO
> FHIRIO
> DICOM 



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 ]

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Author: ASF GitHub Bot
Created on: 20/May/20 22:46
Start Date: 20/May/20 22:46
Worklog Time Spent: 10m 
  Work Description: jaketf commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-631768508


   Seems pre-commit is stuck reporting back to github.
   There's one unrelated test that failed
   
https://builds.apache.org/job/beam_PreCommit_Java_Commit/11508/testReport/org.apache.beam.sdk.extensions.ml/VideoIntelligenceIT/annotateVideoFromURINoContext/



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Time Spent: 52h 20m  (was: 52h 10m)

> Add Google Cloud Healthcare API IO Connectors
> -
>
> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: P3
>  Time Spent: 52h 20m
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
> Healthcare API|https://cloud.google.com/healthcare/docs/]
> HL7v2IO
> FHIRIO
> DICOM 



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ASF GitHub Bot logged work on BEAM-9468:


Author: ASF GitHub Bot
Created on: 20/May/20 21:03
Start Date: 20/May/20 21:03
Worklog Time Spent: 10m 
  Work Description: pabloem commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-631725726


   retest this please



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> Add Google Cloud Healthcare API IO Connectors
> -
>
> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: P3
>  Time Spent: 52h 10m
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
> Healthcare API|https://cloud.google.com/healthcare/docs/]
> HL7v2IO
> FHIRIO
> DICOM 



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Author: ASF GitHub Bot
Created on: 20/May/20 20:22
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  Work Description: pabloem commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-631704878


   retest this please



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> Add Google Cloud Healthcare API IO Connectors
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> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: P3
>  Time Spent: 52h
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
> Healthcare API|https://cloud.google.com/healthcare/docs/]
> HL7v2IO
> FHIRIO
> DICOM 



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Author: ASF GitHub Bot
Created on: 20/May/20 20:10
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  Work Description: pabloem commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-631699571


   retest this please



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> Add Google Cloud Healthcare API IO Connectors
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> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: P3
>  Time Spent: 51h 50m
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
> Healthcare API|https://cloud.google.com/healthcare/docs/]
> HL7v2IO
> FHIRIO
> DICOM 



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Author: ASF GitHub Bot
Created on: 20/May/20 20:06
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  Work Description: pabloem commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-631697338


   I found these examples:
   
https://softwareengineering.stackexchange.com/questions/212639/should-i-store-test-files-in-source-control
   
https://softwareengineering.stackexchange.com/questions/257881/should-test-data-be-checked-into-version-control
   
https://stackoverflow.com/questions/3060764/tfs-testing-and-placement-of-test-files-where
   
https://stackoverflow.com/questions/28253556/what-is-a-right-way-to-deal-with-tests-temporary-files-and-version-control



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Time Spent: 51h 40m  (was: 51.5h)

> Add Google Cloud Healthcare API IO Connectors
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> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: P3
>  Time Spent: 51h 40m
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
> Healthcare API|https://cloud.google.com/healthcare/docs/]
> HL7v2IO
> FHIRIO
> DICOM 



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Author: ASF GitHub Bot
Created on: 20/May/20 20:00
Start Date: 20/May/20 20:00
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  Work Description: TheNeuralBit commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-631694434


   > after looking around, it seems like it's a fairly common pattern to have 
test files committed to source control as resources. These aren't huge, so I'll 
merge them.
   
   Ok, as long as there's precedent for it. And you're right these files aren't 
that big as far as test data goes, it just looks a little scary to see a 300k 
line diff since they're human readable



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> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: P3
>  Time Spent: 51.5h
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
> Healthcare API|https://cloud.google.com/healthcare/docs/]
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> FHIRIO
> DICOM 



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Author: ASF GitHub Bot
Created on: 20/May/20 19:55
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  Work Description: pabloem commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-631692197


   retest this please



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> Key: BEAM-9468
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> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: P3
>  Time Spent: 51h 20m
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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> DICOM 



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  Work Description: TheNeuralBit commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-631691154


   retest this please



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>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
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> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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> Project: Beam
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>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
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>  Time Spent: 51h
>  Remaining Estimate: 0h
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> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
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>  Time Spent: 50h 50m
>  Remaining Estimate: 0h
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> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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> Project: Beam
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>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
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>  Time Spent: 50h 40m
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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Author: ASF GitHub Bot
Created on: 20/May/20 18:25
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  Work Description: pabloem commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-631645585


   heh no worries. I'll discuss with @jaketf to see what we do...



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> Project: Beam
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>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
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>  Time Spent: 50.5h
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>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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Author: ASF GitHub Bot
Created on: 20/May/20 18:22
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  Work Description: TheNeuralBit commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-631643889


   @pabloem I'm fine with adding the test data in this PR if you are. Sorry to 
jump in with a random comment.



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> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: P3
>  Time Spent: 50h 20m
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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> FHIRIO
> DICOM 



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Author: ASF GitHub Bot
Created on: 20/May/20 17:15
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  Work Description: jaketf commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-631609714


   We could stage these / pull these in from GCS.
   This will mean devs would need access to this bucket to run the tests.



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> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: P3
>  Time Spent: 50h 10m
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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Author: ASF GitHub Bot
Created on: 20/May/20 16:42
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  Work Description: TheNeuralBit commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-631591988


   This PR is almost 300k lines, it seems to mostly be due to committing a lot 
of JSON test data, which isn't ideal. Is there any way to store that test data 
elsewhere?



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> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: P3
>  Time Spent: 50h
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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Author: ASF GitHub Bot
Created on: 20/May/20 16:30
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  Work Description: pabloem commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-631585253


   Run Java Postcommit



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> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: P3
>  Time Spent: 49h 50m
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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   retest this please



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> Project: Beam
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>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: P3
>  Time Spent: 49h 40m
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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   retest this please



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> Project: Beam
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>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
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>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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>Assignee: Jacob Ferriero
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> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
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>  Time Spent: 48h 50m
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>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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  Work Description: pabloem commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-631521592


   Run Java PostCommit



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> Add Google Cloud Healthcare API IO Connectors
> -
>
> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: P3
>  Time Spent: 48h 40m
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
> Healthcare API|https://cloud.google.com/healthcare/docs/]
> HL7v2IO
> FHIRIO
> DICOM 



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Author: ASF GitHub Bot
Created on: 20/May/20 14:47
Start Date: 20/May/20 14:47
Worklog Time Spent: 10m 
  Work Description: pabloem commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-631521398


   Retest this please



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> Add Google Cloud Healthcare API IO Connectors
> -
>
> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: P3
>  Time Spent: 48.5h
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
> Healthcare API|https://cloud.google.com/healthcare/docs/]
> HL7v2IO
> FHIRIO
> DICOM 



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Author: ASF GitHub Bot
Created on: 20/May/20 06:31
Start Date: 20/May/20 06:31
Worklog Time Spent: 10m 
  Work Description: jaketf edited a comment on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-631265943


   I think that something about `TestPubsubSignal` does not play well with the 
way this integration test suite runs on Dataflow.
   
   Following in suit with `PubsubReadIT` (which also uses `TestPububSignal`) 
`BigQueryIOReadIT` and `BigQueryIOStorageReadTableRowIT` I've added this to the 
exclude of this project's build file.
   
   This test can still be run (and passes) using DirectRunner and the evidence 
in the [above 
comment](https://github.com/apache/beam/pull/11339#issuecomment-631203002) 
points to this being a red herring of an issue with test pubsub signal and 
dataflow runner. 
   
   Potentially related issue: 
[BEAM-6804](https://issues.apache.org/jira/browse/BEAM-6804?jql=text%20~%20%22TestPubsubSignal%22)
   
   I've filed an issue for this instance 
[BEAM-10040](https://issues.apache.org/jira/browse/BEAM-10040).
   
   @pabloem please let me know if this is acceptable.



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Issue Time Tracking
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Time Spent: 48h 20m  (was: 48h 10m)

> Add Google Cloud Healthcare API IO Connectors
> -
>
> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: P3
>  Time Spent: 48h 20m
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
> Healthcare API|https://cloud.google.com/healthcare/docs/]
> HL7v2IO
> FHIRIO
> DICOM 



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 ]

ASF GitHub Bot logged work on BEAM-9468:


Author: ASF GitHub Bot
Created on: 20/May/20 06:30
Start Date: 20/May/20 06:30
Worklog Time Spent: 10m 
  Work Description: jaketf commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-631265943


   I think that something about `TestPubsubSignal` does not play well with the 
way this integration test suite runs on Dataflow.
   
   Following in suit with `PubsubReadIT` (which also uses `TestPububSignal`) 
`BigQueryIOReadIT` and `BigQueryIOStorageReadTableRowIT` I've added this to the 
exclude of this project's build file.
   
   This test can still be run (and passes) using DirectRunner and the evidence 
in the [above 
comment](https://github.com/apache/beam/pull/11339#issuecomment-631203002) 
points to this being a red herring of an issue with test pubsub signal and 
dataflow runner. 
   
   Potentially related issue: 
[BEAM-6804](https://issues.apache.org/jira/browse/BEAM-6804?jql=text%20~%20%22TestPubsubSignal%22)
   
   I've filed an issue for this instance.
   
   @pabloem please let me know if this is acceptable.



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Issue Time Tracking
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Time Spent: 48h 10m  (was: 48h)

> Add Google Cloud Healthcare API IO Connectors
> -
>
> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: P3
>  Time Spent: 48h 10m
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
> Healthcare API|https://cloud.google.com/healthcare/docs/]
> HL7v2IO
> FHIRIO
> DICOM 



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 ]

ASF GitHub Bot logged work on BEAM-9468:


Author: ASF GitHub Bot
Created on: 20/May/20 06:17
Start Date: 20/May/20 06:17
Worklog Time Spent: 10m 
  Work Description: jaketf edited a comment on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-631203002


   The issue with FhirIOReadIT seems to be some misuse of 
[TestPubsubSignal](https://beam.apache.org/releases/javadoc/2.20.0/org/apache/beam/sdk/io/gcp/pubsub/TestPubsubSignal.html)
   [Example 
Job](https://pantheon.corp.google.com/dataflow/jobs/us-central1/2020-05-19_19_05_19-1057064265214622054?project=apache-beam-testing)
 clearly has the expected >2000 elements added to the "waitForAnyMessage" task
   but the success signal never gets published to the results topic.
   
   Notably there are job level warnings about metric descriptors and [warnings 
in shuffle 
logs](https://pantheon.corp.google.com/logs/viewer?dateRangeEnd=2020-05-20T02:18:25.642Z=2020-05-20T02:05:21.347Z=false=CUSTOM=apache-beam-testing=dataflow_step%2Fjob_id%2F2020-05-19_19_05_19-1057064265214622054=2020-05-20T02:57:46.18700Z=projects%2Fapache-beam-testing%2Flogs%2Fdataflow.googleapis.com%252Fshuffler=0==true=2020-05-20T02:15:27.999165390Z)
 which warns:
   ```
   "Update range task returned 'invalid argument'. Assuming lost lease for work 
with id 5061980071068333770 (expiration time: 1589940982000, now: 
1589940923590, full status: INVALID_ARGUMENT: Http(400) Bad Request). For more 
information, see https://cloud.google.com/dataflow/docs/guides/common-errors.; 
   ```
   the 
[docs](https://cloud.google.com/dataflow/docs/guides/common-errors#bad-request-shuffler-logs)
 say this can be ignored but smells suspicious here.
   
   
   This is orthogonal to the behavior being tested. Investigating other means 
of performing this test.



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Issue Time Tracking
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Worklog Id: (was: 435359)
Time Spent: 48h  (was: 47h 50m)

> Add Google Cloud Healthcare API IO Connectors
> -
>
> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: P3
>  Time Spent: 48h
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
> Healthcare API|https://cloud.google.com/healthcare/docs/]
> HL7v2IO
> FHIRIO
> DICOM 



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 ]

ASF GitHub Bot logged work on BEAM-9468:


Author: ASF GitHub Bot
Created on: 20/May/20 03:27
Start Date: 20/May/20 03:27
Worklog Time Spent: 10m 
  Work Description: jaketf edited a comment on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-631203002


   The issue with FhirIOReadIT seems to be some misuse of 
[TestPubsubSignal](https://beam.apache.org/releases/javadoc/2.20.0/org/apache/beam/sdk/io/gcp/pubsub/TestPubsubSignal.html)
   [Example 
Job](https://pantheon.corp.google.com/dataflow/jobs/us-central1/2020-05-19_19_05_19-1057064265214622054?project=apache-beam-testing)
 clearly has elements added to the "waitForAnyMessage" task
   but the success signal never gets published to the results topic.
   
   Notably there are job level warnings about metric descriptors and [warnings 
in shuffle 
logs](https://pantheon.corp.google.com/logs/viewer?dateRangeEnd=2020-05-20T02:18:25.642Z=2020-05-20T02:05:21.347Z=false=CUSTOM=apache-beam-testing=dataflow_step%2Fjob_id%2F2020-05-19_19_05_19-1057064265214622054=2020-05-20T02:57:46.18700Z=projects%2Fapache-beam-testing%2Flogs%2Fdataflow.googleapis.com%252Fshuffler=0==true=2020-05-20T02:15:27.999165390Z)
 which warns:
   ```
   "Update range task returned 'invalid argument'. Assuming lost lease for work 
with id 5061980071068333770 (expiration time: 1589940982000, now: 
1589940923590, full status: INVALID_ARGUMENT: Http(400) Bad Request). For more 
information, see https://cloud.google.com/dataflow/docs/guides/common-errors.; 
   ```
   the 
[docs](https://cloud.google.com/dataflow/docs/guides/common-errors#bad-request-shuffler-logs)
 say this can be ignored but smells suspicious here.
   
   
   This is orthogonal to the behavior being tested. Investigating other means 
of performing this test.



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Issue Time Tracking
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Worklog Id: (was: 435325)
Time Spent: 47h 50m  (was: 47h 40m)

> Add Google Cloud Healthcare API IO Connectors
> -
>
> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: P3
>  Time Spent: 47h 50m
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
> Healthcare API|https://cloud.google.com/healthcare/docs/]
> HL7v2IO
> FHIRIO
> DICOM 



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 ]

ASF GitHub Bot logged work on BEAM-9468:


Author: ASF GitHub Bot
Created on: 20/May/20 03:02
Start Date: 20/May/20 03:02
Worklog Time Spent: 10m 
  Work Description: jaketf edited a comment on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-631203002


   The issue with FhirIOReadIT seems to be some misuse of 
[TestPubsubSignal](https://beam.apache.org/releases/javadoc/2.20.0/org/apache/beam/sdk/io/gcp/pubsub/TestPubsubSignal.html)
   [Example 
Job](https://pantheon.corp.google.com/dataflow/jobs/us-central1/2020-05-19_19_05_19-1057064265214622054?project=apache-beam-testing)
 clearly has elements added to the "waitForAnyMessage" task
   but the success signal never gets published to the results topic.
   
   Notably there are [warnings in shuffle 
logs](https://pantheon.corp.google.com/logs/viewer?dateRangeEnd=2020-05-20T02:18:25.642Z=2020-05-20T02:05:21.347Z=false=CUSTOM=apache-beam-testing=dataflow_step%2Fjob_id%2F2020-05-19_19_05_19-1057064265214622054=2020-05-20T02:57:46.18700Z=projects%2Fapache-beam-testing%2Flogs%2Fdataflow.googleapis.com%252Fshuffler=0==true=2020-05-20T02:15:27.999165390Z)
 which warns:
   ```
   "Update range task returned 'invalid argument'. Assuming lost lease for work 
with id 5061980071068333770 (expiration time: 1589940982000, now: 
1589940923590, full status: INVALID_ARGUMENT: Http(400) Bad Request). For more 
information, see https://cloud.google.com/dataflow/docs/guides/common-errors.; 
   ```
   the 
[docs](https://cloud.google.com/dataflow/docs/guides/common-errors#bad-request-shuffler-logs)
 say this can be ignored but smells suspicious here.
   
   
   This is orthogonal to the behavior being tested. Investigating other means 
of performing this test.



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Issue Time Tracking
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Worklog Id: (was: 435323)
Time Spent: 47h 40m  (was: 47.5h)

> Add Google Cloud Healthcare API IO Connectors
> -
>
> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: P3
>  Time Spent: 47h 40m
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
> Healthcare API|https://cloud.google.com/healthcare/docs/]
> HL7v2IO
> FHIRIO
> DICOM 



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 ]

ASF GitHub Bot logged work on BEAM-9468:


Author: ASF GitHub Bot
Created on: 20/May/20 02:50
Start Date: 20/May/20 02:50
Worklog Time Spent: 10m 
  Work Description: jaketf commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-631203002


   The issue with FhirIOReadIT seems to be some misuse of 
[TestPubsubSignal](https://beam.apache.org/releases/javadoc/2.20.0/org/apache/beam/sdk/io/gcp/pubsub/TestPubsubSignal.html)
   [Example 
Job](https://pantheon.corp.google.com/dataflow/jobs/us-central1/2020-05-19_19_05_19-1057064265214622054?project=apache-beam-testing)
 clearly has elements added to the "waitForAnyMessage" task
   but the success signal never gets published to the results topic.
   
   This is tangential to the behavior being tested. Investigating other means 
of performing this test.



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Issue Time Tracking
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Worklog Id: (was: 435316)
Time Spent: 47h 20m  (was: 47h 10m)

> Add Google Cloud Healthcare API IO Connectors
> -
>
> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: P3
>  Time Spent: 47h 20m
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
> Healthcare API|https://cloud.google.com/healthcare/docs/]
> HL7v2IO
> FHIRIO
> DICOM 



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 [ 
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 ]

ASF GitHub Bot logged work on BEAM-9468:


Author: ASF GitHub Bot
Created on: 20/May/20 02:50
Start Date: 20/May/20 02:50
Worklog Time Spent: 10m 
  Work Description: jaketf edited a comment on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-631203002


   The issue with FhirIOReadIT seems to be some misuse of 
[TestPubsubSignal](https://beam.apache.org/releases/javadoc/2.20.0/org/apache/beam/sdk/io/gcp/pubsub/TestPubsubSignal.html)
   [Example 
Job](https://pantheon.corp.google.com/dataflow/jobs/us-central1/2020-05-19_19_05_19-1057064265214622054?project=apache-beam-testing)
 clearly has elements added to the "waitForAnyMessage" task
   but the success signal never gets published to the results topic.
   
   This is orthogonal to the behavior being tested. Investigating other means 
of performing this test.



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Issue Time Tracking
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Worklog Id: (was: 435317)
Time Spent: 47.5h  (was: 47h 20m)

> Add Google Cloud Healthcare API IO Connectors
> -
>
> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: P3
>  Time Spent: 47.5h
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
> Healthcare API|https://cloud.google.com/healthcare/docs/]
> HL7v2IO
> FHIRIO
> DICOM 



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 ]

ASF GitHub Bot logged work on BEAM-9468:


Author: ASF GitHub Bot
Created on: 19/May/20 21:05
Start Date: 19/May/20 21:05
Worklog Time Spent: 10m 
  Work Description: pabloem commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-631081683


   Run Java PreCommit



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Issue Time Tracking
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Worklog Id: (was: 435195)
Time Spent: 47h 10m  (was: 47h)

> Add Google Cloud Healthcare API IO Connectors
> -
>
> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: P3
>  Time Spent: 47h 10m
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
> Healthcare API|https://cloud.google.com/healthcare/docs/]
> HL7v2IO
> FHIRIO
> DICOM 



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 ]

ASF GitHub Bot logged work on BEAM-9468:


Author: ASF GitHub Bot
Created on: 19/May/20 20:17
Start Date: 19/May/20 20:17
Worklog Time Spent: 10m 
  Work Description: pabloem commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-631058742


   Run Java_Examples_Dataflow PreCommit



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> Add Google Cloud Healthcare API IO Connectors
> -
>
> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
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>  Time Spent: 47h
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> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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   retest this please



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> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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   retest this please



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   retest this please



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  Work Description: pabloem commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-629426161


   retest this please



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Author: ASF GitHub Bot
Created on: 15/May/20 17:11
Start Date: 15/May/20 17:11
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  Work Description: jaketf commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-629376974


   @pabloem 843104d was a pretty simple fix for api surface test
   ```
   git rev-parse HEAD && ./gradlew 
:sdks:java:io:google-cloud-platform:cleanTest 
:sdks:java:io:google-cloud-platform:test --tests 
"org.apache.beam.sdk.io.gcp.GcpApiSurfaceTest"
   843104dacaa9a7064247d6870032c9d69d51afe8
   Configuration on demand is an incubating feature.
   
   > Task :sdks:java:io:google-cloud-platform:compileTestJava
   Note: Some input files use or override a deprecated API.
   Note: Recompile with -Xlint:deprecation for details.
   Note: Some input files use unchecked or unsafe operations.
   Note: Recompile with -Xlint:unchecked for details.
   
   Deprecated Gradle features were used in this build, making it incompatible 
with Gradle 6.0.
   Use '--warning-mode all' to show the individual deprecation warnings.
   See 
https://docs.gradle.org/5.2.1/userguide/command_line_interface.html#sec:command_line_warnings
   
   BUILD SUCCESSFUL in 13s
   68 actionable tasks: 2 executed, 66 up-to-date
   ```



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> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
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>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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Author: ASF GitHub Bot
Created on: 15/May/20 16:51
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  Work Description: jaketf commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-629367380


   @pabloem re: api surface.
   So the history here is that the client library executeBundle method is 
broken so we were forced to use out own http client (and our own exceptions).
   
   I think I can make the constructor / factory that include apache http deps 
private as they wouldn't be constructed by user. I'll take a look.



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> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
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>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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Author: ASF GitHub Bot
Created on: 15/May/20 16:46
Start Date: 15/May/20 16:46
Worklog Time Spent: 10m 
  Work Description: jaketf commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-629364334


   @mwalenia 
   > What exactly causes this 
error?https://builds.apache.org/job/beam_PostCommit_Java_PR/362/testReport/junit/org.apache.beam.sdk.io.gcp.healthcare/FhirIOWriteIT/testFhirIO_ExecuteBundle_R4_/
   
   potentially there was an issue staging all appropriate files
   ```
   May 14, 2020 2:05:45 AM 
org.apache.beam.runners.dataflow.options.DataflowPipelineOptions$StagingLocationFactory
 create
   INFO: No stagingLocation provided, falling back to gcpTempLocation
   May 14, 2020 2:05:45 AM org.apache.beam.runners.dataflow.DataflowRunner 
fromOptions
   INFO: PipelineOptions.filesToStage was not specified. Defaulting to files 
from the classpath: will stage 183 files. Enable logging at DEBUG level to see 
which files will be staged.
   May 14, 2020 2:05:46 AM 
org.apache.beam.runners.dataflow.options.DataflowPipelineOptions$StagingLocationFactory
 create
   INFO: No stagingLocation provided, falling back to gcpTempLocation
   May 14, 2020 2:05:46 AM org.apache.beam.runners.dataflow.DataflowRunner 
fromOptions
   INFO: PipelineOptions.filesToStage was not specified. Defaulting to files 
from the classpath: will stage 183 files. Enable logging at DEBUG level to see 
which files will be staged.
   May 14, 2020 2:05:46 AM 
org.apache.beam.runners.dataflow.options.DataflowPipelineOptions$StagingLocationFactory
 create
   INFO: No stagingLocation provided, falling back to gcpTempLocation
   May 14, 2020 2:05:46 AM org.apache.beam.runners.dataflow.DataflowRunner 
fromOptions
   INFO: PipelineOptions.filesToStage was not specified. Defaulting to files 
from the classpath: will stage 183 files. Enable logging at DEBUG level to see 
which files will be staged.
   ```



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> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
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>  Components: io-java-gcp
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Author: ASF GitHub Bot
Created on: 15/May/20 16:32
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  Work Description: pabloem commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-629357697


   this test checks that we're not increasing the dependencies that we expose 
in the API. We can add the Healthcare IO classes.
   Other classes I think we should try to figure out how to avoid exposing 
them. It seems that they mostly come from the 
`HttpHealthcareApiClient$HealthcareHttpException`



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Author: ASF GitHub Bot
Created on: 15/May/20 16:29
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  Work Description: pabloem commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-629356272


   We have a failure from a test checking out the API surface for the gcp io 
package: 
https://builds.apache.org/job/beam_PreCommit_Java_Commit/11386/testReport/junit/org.apache.beam.sdk.io.gcp/GcpApiSurfaceTest/testGcpApiSurface/



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> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
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>Reporter: Jacob Ferriero
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>  Remaining Estimate: 0h
>
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> Healthcare API|https://cloud.google.com/healthcare/docs/]
> HL7v2IO
> FHIRIO
> DICOM 



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Created on: 15/May/20 08:47
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  Work Description: mwalenia commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-629113897


   @pabloem everything should be bundled, `build.gradle` for 
`io.google-cloud-platform` contains everything that's needed. Maybe there's 
some other error?
   
   @jaketf Can you elaborate on the `java.lang.NoClassDefFoundError: Could not 
initialize class org.apache.beam.sdk.io.gcp.healthcare.FhirIOTestUtil`? What 
exactly causes this error?
   
   >Are test utility classes not bundled up and set to dataflow?
   
   what do you mean by this?



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> Add Google Cloud Healthcare API IO Connectors
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> Key: BEAM-9468
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> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
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>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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> HL7v2IO
> FHIRIO
> DICOM 



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  Work Description: pabloem commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-628933465


   retest this please



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> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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> HL7v2IO
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> DICOM 



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  Work Description: jaketf commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-628875209


   @pabloem  I'm not sure what's going on with the class loading IT issue but I 
think we could re-run the precommit



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  Work Description: jaketf commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-628872612


   - [x] Fixed javadoc checkstyle issue
   - [x] Added pubsub.close() to the @After in FhirIOReadIT (this should fix 
the pubsub not shutdown properly message)
   - [x] Added KV coders to FhirIO.Import
   
   see pre-commit output here.
   https://gist.github.com/jaketf/e7c9116daed60e7babffdb4c99ae1d54



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> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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Author: ASF GitHub Bot
Created on: 14/May/20 19:46
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  Work Description: pabloem commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-628850532


   afaik, the test classes should be bundled together (see 
https://github.com/apache/beam/blob/4c7d5460ba1d643e7fd57fa8f2f8e6a87d80bee5/sdks/java/io/google-cloud-platform/build.gradle#L118-L122)
   
   @mwalenia do you know why the testutil classes could be missing from the IT 
test?



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> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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  Work Description: jaketf edited a comment on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-628842736


   Yeah all the FhirIO read tests are  parameterized tests that are all failing 
like this:
   ```
   WARNING: No terminal state was returned within allotted timeout. State value 
RUNNING
   May 14, 2020 2:37:23 AM org.apache.beam.runners.dataflow.TestDataflowRunner 
waitForStreamingJobTermination
   INFO: Dataflow job 2020-05-13_19_27_22-9842849986096969383 took longer than 
600 seconds to complete, cancelling.
   May 14, 2020 2:37:23 AM org.apache.beam.runners.dataflow.TestDataflowRunner 
run
   WARNING: Dataflow job 2020-05-13_19_27_22-9842849986096969383 did not output 
a success or failure metric.
   May 14, 2020 2:37:24 AM 
io.grpc.internal.ManagedChannelOrphanWrapper$ManagedChannelReference cleanQueue
   SEVERE: *~*~*~ Channel ManagedChannelImpl{logId=15, 
target=pubsub.googleapis.com:443} was not shutdown properly!!! ~*~*~*
   Make sure to call shutdown()/shutdownNow() and wait until 
awaitTermination() returns true.
   java.lang.RuntimeException: ManagedChannel allocation site
   ```



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> URL: https://issues.apache.org/jira/browse/BEAM-9468
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> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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> DICOM 



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Created on: 14/May/20 19:37
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  Work Description: jaketf commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-628846183


   There is a separate crop of issues of 
   
   ```java.lang.NoClassDefFoundError: Could not initialize class 
org.apache.beam.sdk.io.gcp.healthcare.FhirIOTestUtil```
   
   In the execute bundles test. Are test utility classes not bundled up and set 
to dataflow? should I move this under main in the source tree?



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> Project: Beam
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> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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Author: ASF GitHub Bot
Created on: 14/May/20 19:35
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  Work Description: jaketf commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-628845239


   
[FhirIOReadIT](https://github.com/apache/beam/pull/11339/files#diff-7a1359c60a094e73275769adb69b35d3R57)
 borrows the 
[TestPubsubSignal](https://github.com/apache/beam/blob/44f3d3f2d52e93a34b05068bf76f6f9d2611bf77/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/pubsub/TestPubsubSignal.java)
 pattern from 
[PubsubReadIT](https://github.com/apache/beam/blob/a9e14ff7f4b1aafa9915cb95e1bb7e7d3ab6a28b/sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/pubsub/PubsubReadIT.java#L41)
   This works fine on direct runner for me. 
   It seems this is a dataflow runner / test pubsub signal thing.
   I will look into if I'm not closing some channel in my tests.

   @pabloem Have we seen anything flaky on this before?



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Author: ASF GitHub Bot
Created on: 14/May/20 19:29
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  Work Description: jaketf commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-628842736


   Yeah they are  parameterized tests that are all failing like this:
   ```
   WARNING: No terminal state was returned within allotted timeout. State value 
RUNNING
   May 14, 2020 2:37:23 AM org.apache.beam.runners.dataflow.TestDataflowRunner 
waitForStreamingJobTermination
   INFO: Dataflow job 2020-05-13_19_27_22-9842849986096969383 took longer than 
600 seconds to complete, cancelling.
   May 14, 2020 2:37:23 AM org.apache.beam.runners.dataflow.TestDataflowRunner 
run
   WARNING: Dataflow job 2020-05-13_19_27_22-9842849986096969383 did not output 
a success or failure metric.
   May 14, 2020 2:37:24 AM 
io.grpc.internal.ManagedChannelOrphanWrapper$ManagedChannelReference cleanQueue
   SEVERE: *~*~*~ Channel ManagedChannelImpl{logId=15, 
target=pubsub.googleapis.com:443} was not shutdown properly!!! ~*~*~*
   Make sure to call shutdown()/shutdownNow() and wait until 
awaitTermination() returns true.
   java.lang.RuntimeException: ManagedChannel allocation site
   ```



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> Key: BEAM-9468
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> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
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>Assignee: Jacob Ferriero
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>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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> HL7v2IO
> FHIRIO
> DICOM 



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Author: ASF GitHub Bot
Created on: 14/May/20 19:19
Start Date: 14/May/20 19:19
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  Work Description: pabloem commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-628838083


   I see at least this one (
   
https://builds.apache.org/job/beam_PostCommit_Java_PR/362/testReport/junit/org.apache.beam.sdk.io.gcp.healthcare/FhirIOReadIT/testFhirIORead_DSTU2_/)
   with a Dataflow job error. Perhaps once that's fixed, other issues will be
   fixed.
   
   On Thu, May 14, 2020 at 12:10 PM Jacob Ferriero 
   wrote:
   
   > I'm unsure if the failures are due to an issue with this PR. Feel free to
   > inspect:
   > https://scans.gradle.com/s/c4wwwmeidugrc/failure#top=0
   >
   > There's not much information in that scan. Running
   > ./gradlew checkstyleMain checkstyleTest locally there was an issue in
   > FhirIO
   >
   > > Task :sdks:java:io:google-cloud-platform:checkstyleMain FAILED
   > [ant:checkstyle] [ERROR] 
/usr/local/google/home/jferriero/VersionControl/beam/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java:846:42:
 Name 'LOG' must match pattern '^[a-z][a-zA-Z0-9]*$'. [MemberName]
   >
   > I'll clean this up.
   > However there were many failures due to FlinkState internals
   >
   > Fhir postcomits are failing:
   > https://builds.apache.org/job/beam_PostCommit_Java_PR/362/
   >
   > ACK looking into this.
   >
   > —
   > You are receiving this because you were mentioned.
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> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
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>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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> FHIRIO
> DICOM 



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Author: ASF GitHub Bot
Created on: 14/May/20 19:11
Start Date: 14/May/20 19:11
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  Work Description: jaketf edited a comment on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-628833485


   > I'm unsure if the failures are due to an issue with this PR. Feel free to 
inspect:
   > https://scans.gradle.com/s/c4wwwmeidugrc/failure#top=0
   
   There's not much information in that scan. Running
   `./gradlew checkstyleMain checkstyleTest` locally there was an issue in 
FhirIO
   ```
   > Task :sdks:java:io:google-cloud-platform:checkstyleMain FAILED
   [ant:checkstyle] [ERROR] 
/usr/local/google/home/jferriero/VersionControl/beam/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java:846:42:
 Name 'LOG' must match pattern '^[a-z][a-zA-Z0-9]*$'. [MemberName]
   ```
   I'll clean this up. 
   However there were many failures due to FlinkState internals
   [full log](https://gist.github.com/jaketf/4c784c6e9831caac1a9aaf4d25926b69)
   
   > Fhir postcomits are failing: 
https://builds.apache.org/job/beam_PostCommit_Java_PR/362/
   
   ACK looking into this.



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>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: Minor
>  Time Spent: 40.5h
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
> Healthcare API|https://cloud.google.com/healthcare/docs/]
> HL7v2IO
> FHIRIO
> DICOM 



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Author: ASF GitHub Bot
Created on: 14/May/20 19:10
Start Date: 14/May/20 19:10
Worklog Time Spent: 10m 
  Work Description: jaketf commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-628833485


   > I'm unsure if the failures are due to an issue with this PR. Feel free to 
inspect:
   > https://scans.gradle.com/s/c4wwwmeidugrc/failure#top=0
   
   There's not much information in that scan. Running
   `./gradlew checkstyleMain checkstyleTest` locally there was an issue in 
FhirIO
   ```
   > Task :sdks:java:io:google-cloud-platform:checkstyleMain FAILED
   [ant:checkstyle] [ERROR] 
/usr/local/google/home/jferriero/VersionControl/beam/sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java:846:42:
 Name 'LOG' must match pattern '^[a-z][a-zA-Z0-9]*$'. [MemberName]
   ```
   I'll clean this up. 
   However there were many failures due to FlinkState internals
   
   > Fhir postcomits are failing: 
https://builds.apache.org/job/beam_PostCommit_Java_PR/362/
   
   ACK looking into this.



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> Key: BEAM-9468
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>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
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>  Time Spent: 40h 20m
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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   Fhir postcomits are failing: 
https://builds.apache.org/job/beam_PostCommit_Java_PR/362/



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   Run Java PostCommit



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>Assignee: Jacob Ferriero
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> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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> Key: BEAM-9468
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   retest this please



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   retest this please



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   retest this pleas



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  Work Description: pabloem commented on a change in pull request #11339:
URL: https://github.com/apache/beam/pull/11339#discussion_r424715107



##
File path: 
sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java
##
@@ -0,0 +1,1144 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.gcp.healthcare;
+
+import static 
org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Preconditions.checkState;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.api.services.healthcare.v1beta1.model.HttpBody;
+import com.google.api.services.healthcare.v1beta1.model.Operation;
+import com.google.auto.value.AutoValue;
+import java.io.IOException;
+import java.nio.ByteBuffer;
+import java.nio.channels.WritableByteChannel;
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
+import java.util.UUID;
+import java.util.concurrent.ThreadLocalRandom;
+import javax.annotation.Nullable;
+import org.apache.beam.sdk.Pipeline;
+import org.apache.beam.sdk.coders.StringUtf8Coder;
+import org.apache.beam.sdk.coders.VoidCoder;
+import org.apache.beam.sdk.io.FileIO;
+import org.apache.beam.sdk.io.FileSystems;
+import org.apache.beam.sdk.io.fs.EmptyMatchTreatment;
+import org.apache.beam.sdk.io.fs.MatchResult.Metadata;
+import org.apache.beam.sdk.io.fs.MoveOptions.StandardMoveOptions;
+import org.apache.beam.sdk.io.fs.ResolveOptions.StandardResolveOptions;
+import org.apache.beam.sdk.io.fs.ResourceId;
+import 
org.apache.beam.sdk.io.gcp.healthcare.HttpHealthcareApiClient.HealthcareHttpException;
+import org.apache.beam.sdk.io.gcp.pubsub.PubsubIO;
+import org.apache.beam.sdk.metrics.Counter;
+import org.apache.beam.sdk.metrics.Metrics;
+import org.apache.beam.sdk.options.ValueProvider;
+import org.apache.beam.sdk.transforms.Create;
+import org.apache.beam.sdk.transforms.DoFn;
+import org.apache.beam.sdk.transforms.GroupIntoBatches;
+import org.apache.beam.sdk.transforms.PTransform;
+import org.apache.beam.sdk.transforms.ParDo;
+import org.apache.beam.sdk.transforms.Wait;
+import org.apache.beam.sdk.transforms.WithKeys;
+import org.apache.beam.sdk.transforms.windowing.BoundedWindow;
+import org.apache.beam.sdk.values.KV;
+import org.apache.beam.sdk.values.PCollection;
+import org.apache.beam.sdk.values.PCollection.IsBounded;
+import org.apache.beam.sdk.values.PCollectionTuple;
+import org.apache.beam.sdk.values.PInput;
+import org.apache.beam.sdk.values.POutput;
+import org.apache.beam.sdk.values.PValue;
+import org.apache.beam.sdk.values.TupleTag;
+import org.apache.beam.sdk.values.TupleTagList;
+import 
org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Throwables;
+import 
org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableList;
+import 
org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableMap;
+import org.codehaus.jackson.JsonProcessingException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * {@link FhirIO} provides an API for reading and writing resources to https://cloud.google.com/healthcare/docs/concepts/fhir;>Google Cloud 
Healthcare Fhir API.
+ * 
+ *
+ * Reading
+ *
+ * FHIR resources can be read with {@link FhirIO.Read}, which supports use 
cases where you have a
+ * ${@link PCollection} of message IDS. This is appropriate for reading the 
Fhir notifications from
+ * a Pub/Sub subscription with {@link PubsubIO#readStrings()} or in cases 
where you have a manually
+ * prepared list of messages that you need to process (e.g. in a text file 
read with {@link
+ * org.apache.beam.sdk.io.TextIO}*) .
+ *
+ * Fetch Resource contents 

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Author: ASF GitHub Bot
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URL: https://github.com/apache/beam/pull/11339#issuecomment-628225001


   retest this please



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> Add Google Cloud Healthcare API IO Connectors
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> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
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>  Time Spent: 38h 50m
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>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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Author: ASF GitHub Bot
Created on: 13/May/20 20:19
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  Work Description: pabloem commented on a change in pull request #11339:
URL: https://github.com/apache/beam/pull/11339#discussion_r424706864



##
File path: 
sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2MessageCoder.java
##
@@ -29,7 +29,15 @@
 import org.apache.beam.sdk.coders.StringUtf8Coder;
 
 public class HL7v2MessageCoder extends CustomCoder {
-  public HL7v2MessageCoder() {}
+  HL7v2MessageCoder() {}
+
+  public static HL7v2MessageCoder of() {
+return new HL7v2MessageCoder();
+  }
+
+  public static HL7v2MessageCoder of(Class clazz) {

Review comment:
   Ah you're right  : ) - cool.





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> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
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>  Time Spent: 38h 40m
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> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
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  Work Description: pabloem commented on a change in pull request #11339:
URL: https://github.com/apache/beam/pull/11339#discussion_r424706395



##
File path: 
sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java
##
@@ -0,0 +1,1107 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.gcp.healthcare;
+
+import static 
org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Preconditions.checkState;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.api.services.healthcare.v1beta1.model.HttpBody;
+import com.google.api.services.healthcare.v1beta1.model.Operation;
+import com.google.auto.value.AutoValue;
+import java.io.IOException;
+import java.nio.ByteBuffer;
+import java.nio.channels.WritableByteChannel;
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
+import java.util.UUID;
+import java.util.concurrent.ThreadLocalRandom;
+import javax.annotation.Nullable;
+import org.apache.beam.sdk.Pipeline;
+import org.apache.beam.sdk.coders.StringUtf8Coder;
+import org.apache.beam.sdk.coders.VoidCoder;
+import org.apache.beam.sdk.io.FileIO;
+import org.apache.beam.sdk.io.FileSystems;
+import org.apache.beam.sdk.io.fs.EmptyMatchTreatment;
+import org.apache.beam.sdk.io.fs.MatchResult.Metadata;
+import org.apache.beam.sdk.io.fs.MoveOptions.StandardMoveOptions;
+import org.apache.beam.sdk.io.fs.ResolveOptions.StandardResolveOptions;
+import org.apache.beam.sdk.io.fs.ResourceId;
+import 
org.apache.beam.sdk.io.gcp.healthcare.HttpHealthcareApiClient.HealthcareHttpException;
+import org.apache.beam.sdk.io.gcp.pubsub.PubsubIO;
+import org.apache.beam.sdk.metrics.Counter;
+import org.apache.beam.sdk.metrics.Metrics;
+import org.apache.beam.sdk.options.ValueProvider;
+import org.apache.beam.sdk.transforms.Create;
+import org.apache.beam.sdk.transforms.DoFn;
+import org.apache.beam.sdk.transforms.GroupIntoBatches;
+import org.apache.beam.sdk.transforms.PTransform;
+import org.apache.beam.sdk.transforms.ParDo;
+import org.apache.beam.sdk.transforms.Wait;
+import org.apache.beam.sdk.transforms.WithKeys;
+import org.apache.beam.sdk.transforms.windowing.BoundedWindow;
+import org.apache.beam.sdk.values.KV;
+import org.apache.beam.sdk.values.PCollection;
+import org.apache.beam.sdk.values.PCollection.IsBounded;
+import org.apache.beam.sdk.values.PCollectionTuple;
+import org.apache.beam.sdk.values.PInput;
+import org.apache.beam.sdk.values.POutput;
+import org.apache.beam.sdk.values.PValue;
+import org.apache.beam.sdk.values.TupleTag;
+import org.apache.beam.sdk.values.TupleTagList;
+import 
org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Throwables;
+import 
org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableList;
+import 
org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableMap;
+import org.codehaus.jackson.JsonProcessingException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * {@link FhirIO} provides an API for reading and writing resources to https://cloud.google.com/healthcare/docs/concepts/fhir;>Google Cloud 
Healthcare Fhir API.
+ * 
+ *
+ * Read
+ *
+ * FHIR resources can be read with {@link FhirIO.Read} supports use cases 
where you have a
+ * ${@link PCollection} of message IDS. This is appropriate for reading the 
Fhir notifications from
+ * a Pub/Sub subscription with {@link PubsubIO#readStrings()} or in cases 
where you have a manually
+ * prepared list of messages that you need to process (e.g. in a text file 
read with {@link
+ * org.apache.beam.sdk.io.TextIO}*) .
+ *
+ * Fetch Resource contents from Fhir 

[jira] [Work logged] (BEAM-9468) Add Google Cloud Healthcare API IO Connectors

[ASF GitHub Bot (Jira)]

 [ 
https://issues.apache.org/jira/browse/BEAM-9468?focusedWorklogId=432797=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#worklog-432797
 ]

ASF GitHub Bot logged work on BEAM-9468:


Author: ASF GitHub Bot
Created on: 13/May/20 20:18
Start Date: 13/May/20 20:18
Worklog Time Spent: 10m 
  Work Description: pabloem commented on a change in pull request #11339:
URL: https://github.com/apache/beam/pull/11339#discussion_r424706218



##
File path: 
sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java
##
@@ -0,0 +1,1107 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.gcp.healthcare;
+
+import static 
org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Preconditions.checkState;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.api.services.healthcare.v1beta1.model.HttpBody;
+import com.google.api.services.healthcare.v1beta1.model.Operation;
+import com.google.auto.value.AutoValue;
+import java.io.IOException;
+import java.nio.ByteBuffer;
+import java.nio.channels.WritableByteChannel;
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
+import java.util.UUID;
+import java.util.concurrent.ThreadLocalRandom;
+import javax.annotation.Nullable;
+import org.apache.beam.sdk.Pipeline;
+import org.apache.beam.sdk.coders.StringUtf8Coder;
+import org.apache.beam.sdk.coders.VoidCoder;
+import org.apache.beam.sdk.io.FileIO;
+import org.apache.beam.sdk.io.FileSystems;
+import org.apache.beam.sdk.io.fs.EmptyMatchTreatment;
+import org.apache.beam.sdk.io.fs.MatchResult.Metadata;
+import org.apache.beam.sdk.io.fs.MoveOptions.StandardMoveOptions;
+import org.apache.beam.sdk.io.fs.ResolveOptions.StandardResolveOptions;
+import org.apache.beam.sdk.io.fs.ResourceId;
+import 
org.apache.beam.sdk.io.gcp.healthcare.HttpHealthcareApiClient.HealthcareHttpException;
+import org.apache.beam.sdk.io.gcp.pubsub.PubsubIO;
+import org.apache.beam.sdk.metrics.Counter;
+import org.apache.beam.sdk.metrics.Metrics;
+import org.apache.beam.sdk.options.ValueProvider;
+import org.apache.beam.sdk.transforms.Create;
+import org.apache.beam.sdk.transforms.DoFn;
+import org.apache.beam.sdk.transforms.GroupIntoBatches;
+import org.apache.beam.sdk.transforms.PTransform;
+import org.apache.beam.sdk.transforms.ParDo;
+import org.apache.beam.sdk.transforms.Wait;
+import org.apache.beam.sdk.transforms.WithKeys;
+import org.apache.beam.sdk.transforms.windowing.BoundedWindow;
+import org.apache.beam.sdk.values.KV;
+import org.apache.beam.sdk.values.PCollection;
+import org.apache.beam.sdk.values.PCollection.IsBounded;
+import org.apache.beam.sdk.values.PCollectionTuple;
+import org.apache.beam.sdk.values.PInput;
+import org.apache.beam.sdk.values.POutput;
+import org.apache.beam.sdk.values.PValue;
+import org.apache.beam.sdk.values.TupleTag;
+import org.apache.beam.sdk.values.TupleTagList;
+import 
org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Throwables;
+import 
org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableList;
+import 
org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableMap;
+import org.codehaus.jackson.JsonProcessingException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * {@link FhirIO} provides an API for reading and writing resources to https://cloud.google.com/healthcare/docs/concepts/fhir;>Google Cloud 
Healthcare Fhir API.
+ * 
+ *
+ * Read
+ *
+ * FHIR resources can be read with {@link FhirIO.Read} supports use cases 
where you have a
+ * ${@link PCollection} of message IDS. This is appropriate for reading the 
Fhir notifications from
+ * a Pub/Sub subscription with {@link PubsubIO#readStrings()} or in cases 
where you have a manually
+ * prepared list of messages that you need to process (e.g. in a text file 
read with {@link
+ * org.apache.beam.sdk.io.TextIO}*) .
+ *
+ * Fetch Resource contents from Fhir 

[jira] [Work logged] (BEAM-9468) Add Google Cloud Healthcare API IO Connectors

[ASF GitHub Bot (Jira)]

 [ 
https://issues.apache.org/jira/browse/BEAM-9468?focusedWorklogId=429122=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#worklog-429122
 ]

ASF GitHub Bot logged work on BEAM-9468:


Author: ASF GitHub Bot
Created on: 30/Apr/20 16:36
Start Date: 30/Apr/20 16:36
Worklog Time Spent: 10m 
  Work Description: jaketf edited a comment on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-621525975


   @pabloem @lastomato  the refactor to remove unnecessary use of `HttpBody` 
model (and associated coder) in favor of `String` is complete, plus an adding 
of HTTP status code similar to the one recently added in #11538 



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Issue Time Tracking
---

Worklog Id: (was: 429122)
Time Spent: 38h  (was: 37h 50m)

> Add Google Cloud Healthcare API IO Connectors
> -
>
> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: Minor
>  Time Spent: 38h
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
> Healthcare API|https://cloud.google.com/healthcare/docs/]
> HL7v2IO
> FHIRIO
> DICOM 



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[jira] [Work logged] (BEAM-9468) Add Google Cloud Healthcare API IO Connectors

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 [ 
https://issues.apache.org/jira/browse/BEAM-9468?focusedWorklogId=428797=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#worklog-428797
 ]

ASF GitHub Bot logged work on BEAM-9468:


Author: ASF GitHub Bot
Created on: 29/Apr/20 23:41
Start Date: 29/Apr/20 23:41
Worklog Time Spent: 10m 
  Work Description: jaketf commented on pull request #11339:
URL: https://github.com/apache/beam/pull/11339#issuecomment-621525975


   @pabloem @lastomato  the refactor to remove unnecessary use of `HttpBody` 
model (and associated coder) in favor of `String` is complete, plus an adding 
of HTTP status code similar to the one recently added in #11531 



This is an automated message from the Apache Git Service.
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Issue Time Tracking
---

Worklog Id: (was: 428797)
Time Spent: 37h 50m  (was: 37h 40m)

> Add Google Cloud Healthcare API IO Connectors
> -
>
> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: Minor
>  Time Spent: 37h 50m
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
> Healthcare API|https://cloud.google.com/healthcare/docs/]
> HL7v2IO
> FHIRIO
> DICOM 



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 [ 
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 ]

ASF GitHub Bot logged work on BEAM-9468:


Author: ASF GitHub Bot
Created on: 28/Apr/20 22:18
Start Date: 28/Apr/20 22:18
Worklog Time Spent: 10m 
  Work Description: jaketf commented on a change in pull request #11339:
URL: https://github.com/apache/beam/pull/11339#discussion_r416957719



##
File path: 
sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java
##
@@ -0,0 +1,977 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.gcp.healthcare;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.api.services.healthcare.v1beta1.model.HttpBody;
+import com.google.api.services.healthcare.v1beta1.model.Operation;
+import com.google.auto.value.AutoValue;
+import java.io.IOException;
+import java.nio.ByteBuffer;
+import java.nio.channels.WritableByteChannel;
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
+import java.util.UUID;
+import java.util.concurrent.ThreadLocalRandom;
+import javax.annotation.Nullable;
+import org.apache.beam.sdk.Pipeline;
+import org.apache.beam.sdk.coders.StringUtf8Coder;
+import org.apache.beam.sdk.io.FileSystems;
+import org.apache.beam.sdk.io.fs.ResolveOptions.StandardResolveOptions;
+import org.apache.beam.sdk.io.fs.ResourceId;
+import org.apache.beam.sdk.io.gcp.pubsub.PubsubIO;
+import org.apache.beam.sdk.metrics.Counter;
+import org.apache.beam.sdk.metrics.Metrics;
+import org.apache.beam.sdk.options.ValueProvider;
+import org.apache.beam.sdk.transforms.DoFn;
+import org.apache.beam.sdk.transforms.GroupIntoBatches;
+import org.apache.beam.sdk.transforms.PTransform;
+import org.apache.beam.sdk.transforms.ParDo;
+import org.apache.beam.sdk.transforms.WithKeys;
+import org.apache.beam.sdk.transforms.windowing.BoundedWindow;
+import org.apache.beam.sdk.util.Sleeper;
+import org.apache.beam.sdk.values.KV;
+import org.apache.beam.sdk.values.PCollection;
+import org.apache.beam.sdk.values.PCollectionTuple;
+import org.apache.beam.sdk.values.PInput;
+import org.apache.beam.sdk.values.POutput;
+import org.apache.beam.sdk.values.PValue;
+import org.apache.beam.sdk.values.TupleTag;
+import org.apache.beam.sdk.values.TupleTagList;
+import 
org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Throwables;
+import 
org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableList;
+import 
org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableMap;
+import org.codehaus.jackson.JsonProcessingException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * {@link FhirIO} provides an API for reading and writing resources to https://cloud.google.com/healthcare/docs/concepts/fhir;>Google Cloud 
Healthcare Fhir API.
+ * 
+ *
+ * Read
+ *
+ * FHIR resources can be read with {@link FhirIO.Read} supports use cases 
where you have a
+ * ${@link PCollection} of message IDS. This is appropriate for reading the 
Fhir notifications from
+ * a Pub/Sub subscription with {@link PubsubIO#readStrings()} or in cases 
where you have a manually
+ * prepared list of messages that you need to process (e.g. in a text file 
read with {@link
+ * org.apache.beam.sdk.io.TextIO}*) .
+ *
+ * Fetch Resource contents from Fhir Store based on the {@link PCollection} 
of message ID strings
+ * {@link FhirIO.Read.Result} where one can call {@link 
Read.Result#getResources()} to retrieved a
+ * {@link PCollection} containing the successfully fetched {@link HttpBody}s 
and/or {@link
+ * FhirIO.Read.Result#getFailedReads()}* to retrieve a {@link PCollection} of 
{@link
+ * HealthcareIOError}* containing the resource ID that could not be fetched 
and the exception as a
+ * {@link HealthcareIOError}, this can be used to write to the dead letter 
storage system of your
+ * choosing. This error handling is mainly to transparently 

[jira] [Work logged] (BEAM-9468) Add Google Cloud Healthcare API IO Connectors

[ASF GitHub Bot (Jira)]

 [ 
https://issues.apache.org/jira/browse/BEAM-9468?focusedWorklogId=427896=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#worklog-427896
 ]

ASF GitHub Bot logged work on BEAM-9468:


Author: ASF GitHub Bot
Created on: 27/Apr/20 23:31
Start Date: 27/Apr/20 23:31
Worklog Time Spent: 10m 
  Work Description: jaketf commented on a change in pull request #11339:
URL: https://github.com/apache/beam/pull/11339#discussion_r416218974



##
File path: 
sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java
##
@@ -0,0 +1,977 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.gcp.healthcare;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.api.services.healthcare.v1beta1.model.HttpBody;
+import com.google.api.services.healthcare.v1beta1.model.Operation;
+import com.google.auto.value.AutoValue;
+import java.io.IOException;
+import java.nio.ByteBuffer;
+import java.nio.channels.WritableByteChannel;
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
+import java.util.UUID;
+import java.util.concurrent.ThreadLocalRandom;
+import javax.annotation.Nullable;
+import org.apache.beam.sdk.Pipeline;
+import org.apache.beam.sdk.coders.StringUtf8Coder;
+import org.apache.beam.sdk.io.FileSystems;
+import org.apache.beam.sdk.io.fs.ResolveOptions.StandardResolveOptions;
+import org.apache.beam.sdk.io.fs.ResourceId;
+import org.apache.beam.sdk.io.gcp.pubsub.PubsubIO;
+import org.apache.beam.sdk.metrics.Counter;
+import org.apache.beam.sdk.metrics.Metrics;
+import org.apache.beam.sdk.options.ValueProvider;
+import org.apache.beam.sdk.transforms.DoFn;
+import org.apache.beam.sdk.transforms.GroupIntoBatches;
+import org.apache.beam.sdk.transforms.PTransform;
+import org.apache.beam.sdk.transforms.ParDo;
+import org.apache.beam.sdk.transforms.WithKeys;
+import org.apache.beam.sdk.transforms.windowing.BoundedWindow;
+import org.apache.beam.sdk.util.Sleeper;
+import org.apache.beam.sdk.values.KV;
+import org.apache.beam.sdk.values.PCollection;
+import org.apache.beam.sdk.values.PCollectionTuple;
+import org.apache.beam.sdk.values.PInput;
+import org.apache.beam.sdk.values.POutput;
+import org.apache.beam.sdk.values.PValue;
+import org.apache.beam.sdk.values.TupleTag;
+import org.apache.beam.sdk.values.TupleTagList;
+import 
org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Throwables;
+import 
org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableList;
+import 
org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableMap;
+import org.codehaus.jackson.JsonProcessingException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * {@link FhirIO} provides an API for reading and writing resources to https://cloud.google.com/healthcare/docs/concepts/fhir;>Google Cloud 
Healthcare Fhir API.
+ * 
+ *
+ * Read
+ *
+ * FHIR resources can be read with {@link FhirIO.Read} supports use cases 
where you have a
+ * ${@link PCollection} of message IDS. This is appropriate for reading the 
Fhir notifications from
+ * a Pub/Sub subscription with {@link PubsubIO#readStrings()} or in cases 
where you have a manually
+ * prepared list of messages that you need to process (e.g. in a text file 
read with {@link
+ * org.apache.beam.sdk.io.TextIO}*) .
+ *
+ * Fetch Resource contents from Fhir Store based on the {@link PCollection} 
of message ID strings
+ * {@link FhirIO.Read.Result} where one can call {@link 
Read.Result#getResources()} to retrieved a
+ * {@link PCollection} containing the successfully fetched {@link HttpBody}s 
and/or {@link
+ * FhirIO.Read.Result#getFailedReads()}* to retrieve a {@link PCollection} of 
{@link
+ * HealthcareIOError}* containing the resource ID that could not be fetched 
and the exception as a
+ * {@link HealthcareIOError}, this can be used to write to the dead letter 
storage system of your
+ * choosing. This error handling is mainly to transparently 

[jira] [Work logged] (BEAM-9468) Add Google Cloud Healthcare API IO Connectors

[ASF GitHub Bot (Jira)]

 [ 
https://issues.apache.org/jira/browse/BEAM-9468?focusedWorklogId=427112=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#worklog-427112
 ]

ASF GitHub Bot logged work on BEAM-9468:


Author: ASF GitHub Bot
Created on: 24/Apr/20 21:56
Start Date: 24/Apr/20 21:56
Worklog Time Spent: 10m 
  Work Description: lastomato commented on a change in pull request #11339:
URL: https://github.com/apache/beam/pull/11339#discussion_r414885816



##
File path: 
sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java
##
@@ -0,0 +1,977 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.gcp.healthcare;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.api.services.healthcare.v1beta1.model.HttpBody;
+import com.google.api.services.healthcare.v1beta1.model.Operation;
+import com.google.auto.value.AutoValue;
+import java.io.IOException;
+import java.nio.ByteBuffer;
+import java.nio.channels.WritableByteChannel;
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
+import java.util.UUID;
+import java.util.concurrent.ThreadLocalRandom;
+import javax.annotation.Nullable;
+import org.apache.beam.sdk.Pipeline;
+import org.apache.beam.sdk.coders.StringUtf8Coder;
+import org.apache.beam.sdk.io.FileSystems;
+import org.apache.beam.sdk.io.fs.ResolveOptions.StandardResolveOptions;
+import org.apache.beam.sdk.io.fs.ResourceId;
+import org.apache.beam.sdk.io.gcp.pubsub.PubsubIO;
+import org.apache.beam.sdk.metrics.Counter;
+import org.apache.beam.sdk.metrics.Metrics;
+import org.apache.beam.sdk.options.ValueProvider;
+import org.apache.beam.sdk.transforms.DoFn;
+import org.apache.beam.sdk.transforms.GroupIntoBatches;
+import org.apache.beam.sdk.transforms.PTransform;
+import org.apache.beam.sdk.transforms.ParDo;
+import org.apache.beam.sdk.transforms.WithKeys;
+import org.apache.beam.sdk.transforms.windowing.BoundedWindow;
+import org.apache.beam.sdk.util.Sleeper;
+import org.apache.beam.sdk.values.KV;
+import org.apache.beam.sdk.values.PCollection;
+import org.apache.beam.sdk.values.PCollectionTuple;
+import org.apache.beam.sdk.values.PInput;
+import org.apache.beam.sdk.values.POutput;
+import org.apache.beam.sdk.values.PValue;
+import org.apache.beam.sdk.values.TupleTag;
+import org.apache.beam.sdk.values.TupleTagList;
+import 
org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Throwables;
+import 
org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableList;
+import 
org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableMap;
+import org.codehaus.jackson.JsonProcessingException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * {@link FhirIO} provides an API for reading and writing resources to https://cloud.google.com/healthcare/docs/concepts/fhir;>Google Cloud 
Healthcare Fhir API.
+ * 
+ *
+ * Read
+ *
+ * FHIR resources can be read with {@link FhirIO.Read} supports use cases 
where you have a
+ * ${@link PCollection} of message IDS. This is appropriate for reading the 
Fhir notifications from
+ * a Pub/Sub subscription with {@link PubsubIO#readStrings()} or in cases 
where you have a manually
+ * prepared list of messages that you need to process (e.g. in a text file 
read with {@link
+ * org.apache.beam.sdk.io.TextIO}*) .
+ *
+ * Fetch Resource contents from Fhir Store based on the {@link PCollection} 
of message ID strings
+ * {@link FhirIO.Read.Result} where one can call {@link 
Read.Result#getResources()} to retrieved a
+ * {@link PCollection} containing the successfully fetched {@link HttpBody}s 
and/or {@link
+ * FhirIO.Read.Result#getFailedReads()}* to retrieve a {@link PCollection} of 
{@link
+ * HealthcareIOError}* containing the resource ID that could not be fetched 
and the exception as a
+ * {@link HealthcareIOError}, this can be used to write to the dead letter 
storage system of your
+ * choosing. This error handling is mainly to transparently 

[jira] [Work logged] (BEAM-9468) Add Google Cloud Healthcare API IO Connectors

[ASF GitHub Bot (Jira)]

 [ 
https://issues.apache.org/jira/browse/BEAM-9468?focusedWorklogId=424395=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#worklog-424395
 ]

ASF GitHub Bot logged work on BEAM-9468:


Author: ASF GitHub Bot
Created on: 17/Apr/20 20:22
Start Date: 17/Apr/20 20:22
Worklog Time Spent: 10m 
  Work Description: jaketf commented on pull request #11450: [BEAM-9468] 
Hl7v2 io patches
URL: https://github.com/apache/beam/pull/11450#discussion_r410451265
 
 

 ##
 File path: 
sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2IOWriteIT.java
 ##
 @@ -46,6 +45,8 @@
   private static final String HL7V2_STORE_NAME =
   "hl7v2_store_write_it_" + System.currentTimeMillis() + "_" + (new 
SecureRandom().nextInt(32));
 
+  @Rule public transient TestPipeline pipeline = TestPipeline.create();
 
 Review comment:
   I could add 
   ```java
   pipeline.getOptions().as(DirectOptions.class).setBlockOnRun(true);
   ```
   But I think this is the same as `pipeline.run().waitUntilFinish();` for 
batch pipelines which I already use.
 

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Issue Time Tracking
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Worklog Id: (was: 424395)
Time Spent: 37h 10m  (was: 37h)

> Add Google Cloud Healthcare API IO Connectors
> -
>
> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: Minor
>  Time Spent: 37h 10m
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
> Healthcare API|https://cloud.google.com/healthcare/docs/]
> HL7v2IO
> FHIRIO
> DICOM 



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[jira] [Work logged] (BEAM-9468) Add Google Cloud Healthcare API IO Connectors

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 [ 
https://issues.apache.org/jira/browse/BEAM-9468?focusedWorklogId=424373=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#worklog-424373
 ]

ASF GitHub Bot logged work on BEAM-9468:


Author: ASF GitHub Bot
Created on: 17/Apr/20 19:25
Start Date: 17/Apr/20 19:25
Worklog Time Spent: 10m 
  Work Description: chamikaramj commented on issue #11450: [BEAM-9468] 
Hl7v2 io patches
URL: https://github.com/apache/beam/pull/11450#issuecomment-615424199
 
 
   Run Java PostCommit
 

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Issue Time Tracking
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Worklog Id: (was: 424373)
Time Spent: 37h  (was: 36h 50m)

> Add Google Cloud Healthcare API IO Connectors
> -
>
> Key: BEAM-9468
> URL: https://issues.apache.org/jira/browse/BEAM-9468
> Project: Beam
>  Issue Type: New Feature
>  Components: io-java-gcp
>Reporter: Jacob Ferriero
>Assignee: Jacob Ferriero
>Priority: Minor
>  Time Spent: 37h
>  Remaining Estimate: 0h
>
> Add IO Transforms for the HL7v2, FHIR and DICOM stores in the [Google Cloud 
> Healthcare API|https://cloud.google.com/healthcare/docs/]
> HL7v2IO
> FHIRIO
> DICOM 



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[jira] [Work logged] (BEAM-9468) Add Google Cloud Healthcare API IO Connectors

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 [ 
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 ]

ASF GitHub Bot logged work on BEAM-9468:


Author: ASF GitHub Bot
Created on: 17/Apr/20 19:21
Start Date: 17/Apr/20 19:21
Worklog Time Spent: 10m 
  Work Description: jaketf commented on pull request #11450: [BEAM-9468] 
Hl7v2 io patches
URL: https://github.com/apache/beam/pull/11450
 
 
   * Use TestPipeline in ITs
   * Drop schematized data before calling message ingest (should be output 
only) to help pipelines that read/write from/to two HL7v2 stores
   * Make HL7v2MessageCoder constructor public
   
   **Please** add a meaningful description for your change here
   
   
   
   Thank you for your contribution! Follow this checklist to help us 
incorporate your contribution quickly and easily:
   
- [ ] [**Choose 
reviewer(s)**](https://beam.apache.org/contribute/#make-your-change) and 
mention them in a comment (`R: @username`).
- [ ] Format the pull request title like `[BEAM-XXX] Fixes bug in 
ApproximateQuantiles`, where you replace `BEAM-XXX` with the appropriate JIRA 
issue, if applicable. This will automatically link the pull request to the 
issue.
- [ ] Update `CHANGES.md` with noteworthy changes.
- [ ] If this contribution is large, please file an Apache [Individual 
Contributor License Agreement](https://www.apache.org/licenses/icla.pdf).
   
   See the [Contributor Guide](https://beam.apache.org/contribute) for more 
tips on [how to make review process 
smoother](https://beam.apache.org/contribute/#make-reviewers-job-easier).
   
   Post-Commit Tests Status (on master branch)
   

   
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