Stream: committers
Topic: PR Maintenance
Grahame Grieve (Aug 14 2020 at 05:52):
@Gino Canessa something has gone wrong with https://github.com/HL7/fhir/pull/897 and it now would represent a massive regression for most files (197!). Can you go back and remake the actual changes?
Grahame Grieve (Aug 14 2020 at 05:53):
@Khalid Shahin due to a significant commit on my side you now have a merge problem with your latest PR - let me know if you need any help
Grahame Grieve (Aug 14 2020 at 05:53):
@Vadim Peretokin can you ping your branch by committing a white space change to something for https://github.com/HL7/fhir/pull/922
Grahame Grieve (Aug 14 2020 at 05:54):
@tery - what are you fixing in https://github.com/HL7/fhir/pull/923?
Grahame Grieve (Aug 14 2020 at 05:55):
@Rik Smithies can you review your outstanding PRs?
Grahame Grieve (Aug 14 2020 at 05:56):
@Hugh Glover can you review the status of https://github.com/HL7/fhir/pull/733 - the build failed and there's merge conflicts now. Perhaps you can make it again?
Grahame Grieve (Aug 14 2020 at 05:57):
@Josh Mandel what is the deal with https://github.com/HL7/fhir/pull/654 - what is it?
Grahame Grieve (Aug 14 2020 at 05:57):
@Jose Costa Teixeira you have 2 open PRs on the main build...
Jose Costa Teixeira (Aug 14 2020 at 05:58):
I will check and close (or merge)
Vadim Peretokin (Aug 14 2020 at 07:31):
Mine is happy now.
Rik Smithies (Aug 14 2020 at 09:23):
mine should be ok now thanks. all were junk that I had sorted out elsewhere.
Khalid Shahin (Aug 14 2020 at 12:18):
@Grahame Grieve
Don't worry. I forgot to cancel that pull request and delete that branch. I have no outstanding changes. Thanks.
Josh Mandel (Aug 14 2020 at 14:08):
Closed mine (I'm sure I had a very good reason for creating it a year ago, but it is opaque to me today :-))
Gino Canessa (Aug 14 2020 at 15:05):
Sure. It will take a bit because I've been working on a pass of document updates for the connectathon cut, but you are (probably, hopefully?) sleeping right now, so I'll just let you know when its done.
Jose Costa Teixeira (Aug 14 2020 at 15:16):
mine isn't validating - build is failing with a
org.hl7.fhir.r5.utils.client.EFhirClientException: Error sending HTTP Post/Put Payload: Read timed out
Rik Smithies (Aug 14 2020 at 15:35):
same here for me. If my pull request fails, because the build falls over, is there way to resubmit the same change?
Jose Costa Teixeira (Aug 14 2020 at 15:40):
I'm just making a whitespace commit to see if it starts working.
Gino Canessa (Aug 14 2020 at 19:41):
Mine are still failing with the same issue
Grahame Grieve (Aug 14 2020 at 20:17):
it's failing locally, or on the ci-build?
Gino Canessa (Aug 14 2020 at 20:17):
@Grahame Grieve I'm looking at the VMs and everything looks good on the pipeline, just getting a timeout
Gino Canessa (Aug 14 2020 at 20:17):
Local builds working fine
Grahame Grieve (Aug 14 2020 at 20:17):
that's going to be a pig to investigate
Gino Canessa (Aug 14 2020 at 20:17):
[java] ...validate valuesets 33.166 2495sec 1002MB
[java] Read timed out (27029ms / 10Kb for transaction)
[java] valuesets:: valuesets: Error sending HTTP Post/Put Payload: Read timed out
[java] org.hl7.fhir.r5.utils.client.EFhirClientException: Error sending HTTP Post/Put Payload: Read timed out
Gino Canessa (Aug 14 2020 at 20:17):
All of them fail with the same message
Gino Canessa (Aug 14 2020 at 20:21):
More log, since I should've done it in the first place...
[java] ...validate v3-codesystems 399.259 2392sec 1078MB
[java] ...validate valuesets 32.572 2424sec 1002MB
[java] Read timed out (27003ms / 10Kb for transaction)org.hl7.fhir.r5.utils.client.EFhirClientException: Error sending HTTP Post/Put Payload: Read timed out
[java]
[java] valuesets:: valuesets: Error sending HTTP Post/Put Payload: Read timed out
[java] at org.hl7.fhir.r5.utils.client.ClientUtils.sendPayload(ClientUtils.java:316)
[java] at org.hl7.fhir.r5.utils.client.ClientUtils.postBatchRequest(ClientUtils.java:195)
[java] at org.hl7.fhir.r5.utils.client.FHIRToolingClient.transaction(FHIRToolingClient.java:517)
[java] at org.hl7.fhir.convertors.txClient.TerminologyClientR5.validateBatch(TerminologyClientR5.java:116)
[java] at org.hl7.fhir.r5.context.BaseWorkerContext.validateCodeBatch(BaseWorkerContext.java:796)
[java] at org.hl7.fhir.validation.instance.type.ValueSetValidator.validateValueSetInclude(ValueSetValidator.java:114)
[java] at org.hl7.fhir.validation.instance.type.ValueSetValidator.validateValueSetCompose(ValueSetValidator.java:65)
[java] at org.hl7.fhir.validation.instance.type.ValueSetValidator.validateValueSet(ValueSetValidator.java:55)
[java] at org.hl7.fhir.validation.instance.InstanceValidator.checkSpecials(InstanceValidator.java:3648)
[java] at org.hl7.fhir.validation.instance.InstanceValidator.startInner(InstanceValidator.java:3620)
[java] at org.hl7.fhir.validation.instance.InstanceValidator.start(InstanceValidator.java:3498)
[java] at org.hl7.fhir.validation.instance.InstanceValidator.validateResource(InstanceValidator.java:4596)
[java] at org.hl7.fhir.validation.instance.InstanceValidator.validateContains(InstanceValidator.java:3768)
[java] at org.hl7.fhir.validation.instance.InstanceValidator.checkChild(InstanceValidator.java:4039)
[java] at org.hl7.fhir.validation.instance.InstanceValidator.validateElement(InstanceValidator.java:3868)
[java] at org.hl7.fhir.validation.instance.InstanceValidator.checkChild(InstanceValidator.java:4056)
[java] at org.hl7.fhir.validation.instance.InstanceValidator.validateElement(InstanceValidator.java:3868)
[java] at org.hl7.fhir.validation.instance.InstanceValidator.startInner(InstanceValidator.java:3611)
[java] at org.hl7.fhir.validation.instance.InstanceValidator.start(InstanceValidator.java:3498)
[java] at org.hl7.fhir.validation.instance.InstanceValidator.validateResource(InstanceValidator.java:4596)
[java] at org.hl7.fhir.validation.instance.InstanceValidator.validate(InstanceValidator.java:686)
[java] at org.hl7.fhir.validation.instance.InstanceValidator.validate(InstanceValidator.java:662)
[java] at org.hl7.fhir.tools.publisher.ExampleInspector.validateLogical(ExampleInspector.java:338)
[java] at org.hl7.fhir.tools.publisher.ExampleInspector.doValidate(ExampleInspector.java:306)
[java] at org.hl7.fhir.tools.publisher.ExampleInspector.validate(ExampleInspector.java:299)
[java] at org.hl7.fhir.tools.publisher.Publisher.validationProcess(Publisher.java:5901)
[java] at org.hl7.fhir.tools.publisher.Publisher.execute(Publisher.java:636)
[java] at org.hl7.fhir.tools.publisher.Publisher.main(Publisher.java:491)
[java] Caused by: java.net.SocketTimeoutException: Read timed out
[java] at java.net.SocketInputStream.socketRead0(Native Method)
[java] at java.net.SocketInputStream.socketRead(SocketInputStream.java:116)
[java] at java.net.SocketInputStream.read(SocketInputStream.java:171)
[java] at java.net.SocketInputStream.read(SocketInputStream.java:141)
[java] at org.apache.http.impl.io.AbstractSessionInputBuffer.fillBuffer(AbstractSessionInputBuffer.java:166)
[java] at org.apache.http.impl.io.SocketInputBuffer.fillBuffer(SocketInputBuffer.java:90)
[java] at org.apache.http.impl.io.AbstractSessionInputBuffer.readLine(AbstractSessionInputBuffer.java:281)
[java] at org.apache.http.impl.conn.DefaultHttpResponseParser.parseHead(DefaultHttpResponseParser.java:92)
[java] at org.apache.http.impl.conn.DefaultHttpResponseParser.parseHead(DefaultHttpResponseParser.java:62)
[java] at org.apache.http.impl.io.AbstractMessageParser.parse(AbstractMessageParser.java:254)
[java] at org.apache.http.impl.AbstractHttpClientConnection.receiveResponseHeader(AbstractHttpClientConnection.java:289)
[java] at org.apache.http.impl.conn.DefaultClientConnection.receiveResponseHeader(DefaultClientConnection.java:252)
[java] at org.apache.http.impl.conn.ManagedClientConnectionImpl.receiveResponseHeader(ManagedClientConnectionImpl.java:191)
[java] at org.apache.http.protocol.HttpRequestExecutor.doReceiveResponse(HttpRequestExecutor.java:300)
[java] at org.apache.http.protocol.HttpRequestExecutor.execute(HttpRequestExecutor.java:127)
[java] at org.apache.http.impl.client.DefaultRequestDirector.tryExecute(DefaultRequestDirector.java:717)
[java] at org.apache.http.impl.client.DefaultRequestDirector.execute(DefaultRequestDirector.java:522)
[java] at org.apache.http.impl.client.AbstractHttpClient.execute(AbstractHttpClient.java:906)
[java] at org.apache.http.impl.client.AbstractHttpClient.execute(AbstractHttpClient.java:805)
[java] at org.apache.http.impl.client.AbstractHttpClient.execute(AbstractHttpClient.java:784)
[java] at org.hl7.fhir.r5.utils.client.ClientUtils.sendPayload(ClientUtils.java:302)
[java] ... 27 more
[java] ...validate conceptmaps 49.447 2474sec 1056MB
[java] ...validate profiles-types 0.627 2474sec 905MB
[java] ...validate profiles-resources 19.996 2494sec 933MB
[java] ...validate profiles-others 342.65 2837sec 1332MB
[java] ...validate search-parameters 88.28 2925sec 982MB
[java] ...validate extension-definitions 14.638 2940sec 948MB
[java] Summary: Errors=1, Warnings=14174, Information messages=5767
[java] ERROR @ valuesets: valuesets:: valuesets: Error sending HTTP Post/Put Payload: Read timed out (src = InstanceValidator)
[java] This was a Full Build 59.069 2999sec 1538MB
[java] org.hl7.fhir.tools.publisher.ExampleInspector$EValidationFailed: Resource Examples failed instance validation
[java] at org.hl7.fhir.tools.publisher.ExampleInspector.summarise(ExampleInspector.java:412)
[java] at org.hl7.fhir.tools.publisher.Publisher.validationProcess(Publisher.java:5915)
[java] at org.hl7.fhir.tools.publisher.Publisher.execute(Publisher.java:636)
[java] at org.hl7.fhir.tools.publisher.Publisher.main(Publisher.java:491)
[java] FHIR build failure @ Fri, Aug 14, 2020 19:10+0000 0.104 2999sec 1538MB
[java] Error: Resource Examples failed instance validation
Gino Canessa (Aug 14 2020 at 21:00):
The manually triggered job I submitted hasn't officially failed yet, but already has the same error up.
Grahame Grieve (Aug 14 2020 at 21:01):
I'm going to add some more debugging. Just testing it locally now
John Moehrke (Aug 14 2020 at 21:46):
my local build fails because it can't get to the IHE ftp site... which is a known fact that they shutdown the ftp site... I got the FormatCode vocab published now... is that the problem?
Grahame Grieve (Aug 14 2020 at 23:17):
my local build fails because it can't get to the IHE ftp site
this doesn't make any sense to me. What's the exact error?
John Moehrke (Aug 15 2020 at 00:24):
[java] This was a Full Build 1.052 21sec 1003MB
[java] Error
[java] SXXP0003: Error reported by XML parser: Premature end of file.
[java] FHIR build failure @ Fri, Aug 14, 2020 09:22-0500 2.817 24sec 1003MB
[java] java.lang.Exception: Unable to retrieve ftp://ftp.ihe.net/TF_Implementation_Material/fhir/CodeSystem/IHE.formatcode.codesystem.xmlError: Unable to retrieve ftp://ftp.ihe.net/TF_Implementation_Material/fhir/CodeSystem/IHE.formatcode.codesystem.xml
[java] at org.hl7.fhir.definitions.parsers.SourceParser.ftpFetch(SourceParser.java:407)
[java]
[java] at org.hl7.fhir.definitions.parsers.SourceParser.loadExternal(SourceParser.java:366)
[java] at org.hl7.fhir.definitions.parsers.SourceParser.loadExternals(SourceParser.java:355)
[java] at org.hl7.fhir.definitions.parsers.SourceParser.parse(SourceParser.java:204)
[java] at org.hl7.fhir.tools.publisher.Publisher.execute(Publisher.java:597)
[java] at org.hl7.fhir.tools.publisher.Publisher.main(Publisher.java:491)
Press any key to continue . . .
Jose Costa Teixeira (Aug 15 2020 at 06:18):
I confirm I'm still getting the same issue as before. The log is exactly the same as Gino posted
tery (Aug 17 2020 at 07:31):
Grahame Grieve said:
tery - what are you fixing in https://github.com/HL7/fhir/pull/923?
The Commits on Jul 4, 2020 fixed some Element's name which is belong to STU3, for example:
GET [base]/MedicationAdministration?encounter:above=21
instead of "encounter" the MedicationAdministration's encounter element is "context" in R4:
GET [base]/MedicationAdministration?context:above=21
Other commits are operations on my own fork which intend to build a Chinese Edition of R5.
Grahame Grieve (Aug 18 2020 at 03:45):
@John Moehrke how can I reproduce this?
Grahame Grieve (Aug 18 2020 at 03:46):
@tery that looks ok to me as ?encounter=
tery (Aug 18 2020 at 09:56):
Grahame Grieve said:
tery that looks ok to me as ?encounter=
I notice that it's roll back as MedicationAdministration.encounter in CI build, but the R4 is MedicationAdministration.context which can not only search by encounter but also by EpisodeOfCare.
http://hl7.org/fhir/medicationadministration-definitions.html#MedicationAdministration.context
another example is :
GET [base]/Observation?_include=Observation:related-target
in section 3.1.1.5.4 of search.html should update to
GET [base]/Observation?_include=Observation:hasMember
John Moehrke (Aug 18 2020 at 13:22):
Grahame Grieve said:
John Moehrke how can I reproduce this?
I think it happened after I did a clean on my core build. It is not happening to me now.
Grahame Grieve (Aug 19 2020 at 01:51):
ok thanks. fixed
tery (Aug 19 2020 at 10:19):
34E13E33-38FC-42e2-8E3E-A1B74FEAA347.png
tery (Aug 19 2020 at 10:27):
I got the error message after the XML formated as the picture show above. if all the <B> tag in one line, it will be fine.
Error: [line: 10646, col: 1 ] Broken IRI (newline): http://hl7.org/fhir/MedicationRequest.group
[java] org.apache.jena.riot.RiotException: [line: 10646, col: 1 ] Broken IRI (newline): http://hl7.org/fhir/MedicationRequest.group
Grahame Grieve (Aug 19 2020 at 10:31):
where exactly do you get this error?
tery (Aug 20 2020 at 06:03):
if the value of <ssData> tag is not contain line feeds or carriage returns, the build possess goes well, otherwise the error will be shown, because the builder generate too many space characters so that the string is too long.
Last updated: Apr 12 2022 at 19:14 UTC
