FHIR Chat · Error with Citation resource · IG creation

Stream: IG creation

Topic: Error with Citation resource

Giorgio Cangioli (Feb 24 2021 at 13:09):

I've the following error when I try to profile the Citation resource

java.lang.Exception: Error generating snapshot for C:\Users\giorg\OneDrive\github\fhir-forfair-4b\input\profiles\StructureDefinition-Citation-uv-f4f(Citation-uv-f4f): Cannot find or generate snapshot for base definition (http://hl7.org/fhir/StructureDefinition/Citation from

FHIR version is set to "4.5.0"

I have this error even if I make a very trivial profile

Profile:  CitationF4F
Parent:   Citation
Id:       Citation-uv-f4f
Title:    "Citation (FHIR for FAIR)"
Description: "This profile defines how to use the Citation resource to convey metadata information for a FAIR dataset by using HL7 FHIR"
* identifier MS

Giorgio Cangioli (Feb 24 2021 at 18:04):

suggestions ?

Rob Hausam (Feb 24 2021 at 20:15):

Quick thought - try cleaning out your .class files and see if that helps?

Grahame Grieve (Feb 24 2021 at 20:18):

now you don't do that anymore. class files are now irrelevant. It'll be something to do with packages and versions

Rob Hausam (Feb 24 2021 at 21:40):

OK. Good to know we don't need to consider the .class files any longer - I don't recall hearing anything about that. Agree it then makes sense to look at packages and versions.

Giorgio Cangioli (Feb 25 2021 at 07:40):

Grahame Grieve said:

now you don't do that anymore. class files are now irrelevant. It'll be something to do with packages and versions

Basically what do you suggest me to do? :-)

Giorgio Cangioli (Mar 01 2021 at 16:18):

Hi @Grahame Grieve have you any suggestion for me on this point ?

Grahame Grieve (Mar 01 2021 at 21:20):

oh - I meant ot ask - how do I reproduce this?

Giorgio Cangioli (Mar 02 2021 at 20:59):

Grahame Grieve said:

oh - I meant ot ask - how do I reproduce this?

https://github.com/HL7/fhir-forfair.
Thanks a lot

Giorgio Cangioli (Mar 03 2021 at 13:24):

I don't know if it can help.. but creating a Citation instance, instead of a profile based on the Citation, the error that is returned is the following

Giorgio Cangioli (Mar 03 2021 at 13:24):

Exception in thread "main" java.lang.Error: The resource type "Citation" does not implement the property "publisher"
at org.hl7.fhir.r5.model.Citation.getPublisher(Citation.java:11392)
at org.hl7.fhir.igtools.renderers.StatusRenderer.readOwner(StatusRenderer.java:121)
at org.hl7.fhir.igtools.renderers.StatusRenderer.analyse(StatusRenderer.java:62)
at org.hl7.fhir.igtools.publisher.Publisher.genStatus(Publisher.java:7402)
at org.hl7.fhir.igtools.publisher.Publisher.saveDirectResourceOutputs(Publisher.java:7165)
at org.hl7.fhir.igtools.publisher.Publisher.generateHtmlOutputs(Publisher.java:6651)
at org.hl7.fhir.igtools.publisher.Publisher.generate(Publisher.java:4906)
at org.hl7.fhir.igtools.publisher.Publisher.createIg(Publisher.java:888)
at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:732)
at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:8417)

Grahame Grieve (Mar 03 2021 at 19:42):

so that github repo generates without error for me

Grahame Grieve (Mar 03 2021 at 19:45):

so the stack was very useful. fixed next release

Giorgio Cangioli (Mar 04 2021 at 08:14):

Thank you so much Grahame !

Giorgio Cangioli (Mar 10 2021 at 08:13):

The Citation profile now works (thanks :-) ), but if I add an example as the following..

{
  "resourceType": "Citation",
  "id": "10.1038-s41597-021-00811-3",
  "identifier": [
    {
      "system": "https://doi.org",
      "value": "10.13026/c4n5-3b04"
    }
  ],
  "name": "NInFEA",
  "title": "A non-invasive multimodal foetal ECG-doppler dataset for antenatal cardiology research",
  "status": "active"
}

Giorgio Cangioli (Mar 10 2021 at 08:15):

the following error is returned

Generating Summary Outputs                                                       (01:58.0066)
Publishing Content Failed: Cannot invoke "String.compareTo(String)" because the return value of "org.hl7.fhir.r5.model.CanonicalResource.getUrl()" is null (02:16.0464)
<..>
Stack Dump (for debugging):                                                      (02:16.0473)
java.lang.NullPointerException: Cannot invoke "String.compareTo(String)" because the return value of "org.hl7.fhir.r5.model.CanonicalResource.getUrl()" is null
        at org.hl7.fhir.r5.utils.ResourceSorters$CanonicalResourceSortByUrl.compare(ResourceSorters.java:13)
        at org.hl7.fhir.r5.utils.ResourceSorters$CanonicalResourceSortByUrl.compare(ResourceSorters.java:9)
        at java.base/java.util.TimSort.countRunAndMakeAscending(TimSort.java:355)
        at java.base/java.util.TimSort.sort(TimSort.java:220)
        at java.base/java.util.Arrays.sort(Arrays.java:1306)
        at java.base/java.util.ArrayList.sort(ArrayList.java:1721)
        at java.base/java.util.Collections.sort(Collections.java:179)
        at org.hl7.fhir.igtools.publisher.Publisher.generateCanonicalSummary(Publisher.java:5871)
        at org.hl7.fhir.igtools.publisher.Publisher.generateSummaryOutputs(Publisher.java:5657)
        at org.hl7.fhir.igtools.publisher.Publisher.generate(Publisher.java:4916)
        at org.hl7.fhir.igtools.publisher.Publisher.createIg(Publisher.java:888)
        at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:732)
        at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:8424)

Giorgio Cangioli (Mar 10 2021 at 08:16):

any suggestion on where I should look at ?

Grahame Grieve (Mar 30 2021 at 19:29):

something doesn't have a canonical URL?

Last updated: Apr 12 2022 at 19:14 UTC