FHIR Chat · Ig publisher error · IG creation

Stream: IG creation

Topic: Ig publisher error

Sean McIlvenna (Mar 22 2018 at 17:58):

getting the following exception after "Generating Summary Outputs"

org.hl7.fhir.exceptions.FHIRException: Property build not found
at org.hl7.fhir.igtools.publisher.SpecMapManager.str(SpecMapManager.java:115)
at org.hl7.fhir.igtools.publisher.SpecMapManager.getBuild(SpecMapManager.java:91)
at org.hl7.fhir.igtools.publisher.Publisher.generateDataFile(Publisher.java:3109)
at org.hl7.fhir.igtools.publisher.Publisher.generateSummaryOutputs(Publisher.java:2764)
at org.hl7.fhir.igtools.publisher.Publisher.generate(Publisher.java:2287)
at org.hl7.fhir.igtools.publisher.Publisher.createIg(Publisher.java:396)
at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:355)
at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:4186)
Exception in thread "main" java.lang.NullPointerException
at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:4196)

Sean McIlvenna (Mar 22 2018 at 17:58):

Anyone have any idea what this is about?

Grahame Grieve (Mar 22 2018 at 19:13):

I've just fixed this. I do not know why it all works for me - I checked a build cascade before I went to sleep.... there's some special if (asleep) thing....

Sarah Gaunt (Mar 22 2018 at 19:16):

You mean, everything breaks while you are sleeping???

Sean McIlvenna (Mar 22 2018 at 19:16):

lol

Sean McIlvenna (Mar 22 2018 at 19:16):

yah, I get that

Sarah Gaunt (Mar 22 2018 at 19:17):

Only one solution to that problem! Sleep is for the weak...

Grahame Grieve (Mar 22 2018 at 19:18):

also, tx.fhir.org is back up

Sean McIlvenna (Mar 22 2018 at 20:04):

Nice @Grahame Grieve , thanks. It builds all the way now
AND am down from 640 errors in the IG, to 130

Sean McIlvenna (Mar 22 2018 at 20:04):

nice fixes

Sean McIlvenna (Mar 22 2018 at 20:05):

I'm gonna get the ig publisher debugging in my environment so I don't have to ask so many questions...

Grahame Grieve (Mar 22 2018 at 20:06):

you typically aren't asking easy questions...

Sean McIlvenna (Mar 22 2018 at 20:06):

well, that's good (I think)

Sean McIlvenna (Mar 22 2018 at 20:07):

unfortunately, I have another question

Sean McIlvenna (Mar 22 2018 at 20:08):

the only ERROR messages remaining appear to be related to link resolution

Sean McIlvenna (Mar 22 2018 at 20:08):

ex:

Sean McIlvenna (Mar 22 2018 at 20:08):

The link 'StructureDefinition-hai-report-questionnaire-response.html#QuestionnaireResponse.item.item.answer.valueReference' cannot be resolved (valid targets: [QuestionnaireResponse.item.text, tbl-snap-inner, QuestionnaireResponse.item.item.answer.extension, tx, tabs-examples, tbl-all, QuestionnaireResponse.modifierExtension, all-tbl-diff, QuestionnaireResponse.text, tabs-summ, QuestionnaireResponse.basedOn, xml, hl7-status, tbl-summ, stripe, QuestionnaireResponse.contained, segment-footer, logo, QuestionnaireResponse.item.item.answer, QuestionnaireResponse.authored, QuestionnaireResponse.item.item.answer.id, QuestionnaireResponse.item.item, D.4.1, all-tbl-snap-inner, QuestionnaireResponse.context, tabs-xml, all-xml-inner, segment-header, QuestionnaireResponse.implicitRules, QuestionnaireResponse.item.item.modifierExtension, hl7-logo, profile, tabs-diff, tbl-diff, QuestionnaireResponse.meta, QuestionnaireResponse.item.item.answer.modifierExtension, all-json-inner, QuestionnaireResponse.item.item.subject, QuestionnaireResponse.id, QuestionnaireResponse.language, QuestionnaireResponse.item.answer.id, QuestionnaireResponse.item.item.linkId, QuestionnaireResponse.item.item.answer.item, tabs-json, QuestionnaireResponse.item.answer.value_x_, tabs-all, QuestionnaireResponse.item.answer.item, tbl-diff-inner, segment-navbar, QuestionnaireResponse.item.extension, QuestionnaireResponse.item.item.item, QuestionnaireResponse.item.definition, QuestionnaireResponse.item.id, QuestionnaireResponse.item, QuestionnaireResponse.partOf, tabs, segment-post-footer, D.4.1.3, tbl-all-inner, json-inner, QuestionnaireResponse.item.item.text, all-tbl-snap, QuestionnaireResponse.extension, QuestionnaireResponse.subject, json, QuestionnaireResponse.identifier, segment-content, QuestionnaireResponse.item.subject, QuestionnaireResponse.item.item.extension, tabs-snap, QuestionnaireResponse.item.answer.modifierExtension, introduction, tbl-snap, summary, QuestionnaireResponse.author, QuestionnaireResponse.status, QuestionnaireResponse.item.linkId, QuestionnaireResponse, QuestionnaireResponse.item.item.definition, QuestionnaireResponse.item.answer.extension, QuestionnaireResponse.item.modifierExtension, hl7-nav, QuestionnaireResponse.questionnaire, QuestionnaireResponse.item.item.id, xml-inner, all-tbl-diff-inner, all-xml, QuestionnaireResponse.item.item.answer.value_x_, segment-breadcrumb, QuestionnaireResponse.source, QuestionnaireResponse.item.answer, all-json])

Sean McIlvenna (Mar 22 2018 at 20:08):

Also not sure how ig publisher is generating this link

Sean McIlvenna (Mar 22 2018 at 20:09):

It looks like an automatically-generated link, though... (not something based on ImplementationGuide or .json config)

Grahame Grieve (Mar 22 2018 at 20:09):

I told you about this - this is your isssue. You've told the publisher that the formal definitions for a structure definition are in the page for the structure definition, but you haven't put them there. So the link can't be resolved

Sean McIlvenna (Mar 22 2018 at 20:09):

where did I tell it that?

Grahame Grieve (Mar 22 2018 at 20:09):

in the config file

Sean McIlvenna (Mar 22 2018 at 20:09):

(sorry, missed the correllation)

Sean McIlvenna (Mar 22 2018 at 20:09):

ok, I'll take a stab

Sean McIlvenna (Mar 22 2018 at 20:09):

thx

Sean McIlvenna (Mar 22 2018 at 20:12):

ok... closer!

Sean McIlvenna (Mar 22 2018 at 20:12):

the error messages are a little easier to read now, at least

Sean McIlvenna (Mar 22 2018 at 20:12):

Removed those "resource" entries from the JSON config and getting this:

Sean McIlvenna (Mar 22 2018 at 20:12):

The link 'StructureDefinition/hai-report-questionnaire.html#Questionnaire.id' cannot be resolved

Sean McIlvenna (Mar 22 2018 at 20:12):

I might be able to work that one out, though

Grahame Grieve (Mar 22 2018 at 20:15):

no you probably won't. I'll have to look at that

Sean McIlvenna (Mar 22 2018 at 20:24):

ah bummer

Sean McIlvenna (Mar 22 2018 at 20:24):

ok

Sean McIlvenna (Mar 23 2018 at 19:44):

@Grahame Grieve any update on this?

Grahame Grieve (Mar 23 2018 at 19:48):

can I reproduce this?

Sean McIlvenna (Mar 23 2018 at 20:21):

yes

Sean McIlvenna (Mar 23 2018 at 20:21):

just pushed my changes to
http://www.github.com/hl7/hai

Grahame Grieve (Mar 23 2018 at 20:25):

so I still get the same 160 errors...

Sean McIlvenna (Mar 23 2018 at 23:34):

yes, but when I mentioned this error:
The link 'StructureDefinition/hai-report-questionnaire.html#Questionnaire.id' cannot be resolved
you said that is something you would have to look into...

Grahame Grieve (Mar 23 2018 at 23:35):

so I don't get that specific error. I get 160 others related to the definitions

Sean McIlvenna (Mar 26 2018 at 23:17):

ok, downloaded the latest build code. re-built, ran the igpublisher with ONLY wants in the HAI repository.
currently getting 348 errors. Almost all are related to "The link XXX cannot be resolved".
For example: "The link 'StructureDefinition/hai-report-questionnaire.html#Questionnaire.id' cannot be resolved"

Sean McIlvenna (Mar 26 2018 at 23:17):

... it's almost as though anchors aren't being created for ElementDefinitions

Grahame Grieve (Mar 27 2018 at 00:48):

well, you're not adding them

Sean McIlvenna (Mar 27 2018 at 20:39):

do I just add an anchor tag in the description of the element definition, or something?

Grahame Grieve (Mar 27 2018 at 20:42):

if you look at a typical IG, you'll see something like this page:

Grahame Grieve (Mar 27 2018 at 20:43):

http://hl7.org/fhir/us/core/StructureDefinition-us-core-allergyintolerance-definitions.html#AllergyIntolerance.criticality

Grahame Grieve (Mar 27 2018 at 20:43):

all the links in this page: http://hl7.org/fhir/us/core/StructureDefinition-us-core-allergyintolerance.html - they point to the first page.

Grahame Grieve (Mar 27 2018 at 20:44):

your IG is configured that the content in the first page is in the same page, not another page. but you don't actually put that content in the page

Grahame Grieve (Mar 27 2018 at 20:44):

so you have 100s of broken links. The IG publisher cannot resolve them for you

Eric Haas (Mar 27 2018 at 21:26):

that happened to me too a while back and I think I fixed by making the ig.json explicitly list every file like you can see in the US-Core repo.

Grahame Grieve (Mar 27 2018 at 21:44):

no it doesn't need to do that. @Sean McIlvenna let's start with a simple question: where do you want the formal definitions to go?

Sarah Gaunt (Mar 28 2018 at 06:59):

Ok, so stolen sd-definitions.html from US Core and added it as the StructureDefinition template-defns file. I've also done as @Eric Haas suggested and specified the particular name of the defns file:
"StructureDefinition/hai-report-questionnaire": { "base": "StructureDefinition-hai-report-questionnaire.html", "defns": "StructureDefinition-hai-report-questionnaire-definitions.html" }

Sarah Gaunt (Mar 28 2018 at 07:01):

Still getting all the broken links though - they are pointing to eg. 'StructureDefinition/hai-report-questionnaire-response.html#QuestionnaireResponse.id' cannot be resolved. Looks like the same file (i.e. pointing to itself) but with a badly formed name "StructureDefinition/" instead of StructureDefinition-hai-report-questionnaire-response.html.

It should be pointing to StructureDefinition-hai-report-questionnaire-response-definitions.html.

Where are these links created and how can I fix?

Sarah Gaunt (Mar 28 2018 at 07:16):

And... I fixed my own problem - didn't wrap the specific resources in resource:{}

I think @Eric Haas is correct and this doesn't seem to work without specifying each specific resource to have it's own defns file...

Sarah Gaunt (Mar 28 2018 at 07:27):

Only getting these errors now (156 of pretty much the same error -everywhere there is a choice):

The link 'StructureDefinition-hai-report-questionnaire-response.html#QuestionnaireResponse.item.answer.valueBoolean' cannot be resolved (valid targets: [QuestionnaireResponse.item.text, tbl-snap-inner, QuestionnaireResponse.item.item.answer.extension, tx, tabs-examples, tbl-all, QuestionnaireResponse.modifierExtension, all-tbl-diff, QuestionnaireResponse.text, tabs-summ, QuestionnaireResponse.basedOn, xml, hl7-status, tbl-summ, stripe, QuestionnaireResponse.contained, segment-footer, logo, QuestionnaireResponse.item.item.answer, QuestionnaireResponse.authored, QuestionnaireResponse.item.item.answer.id, QuestionnaireResponse.item.item, D.4.1, all-tbl-snap-inner, QuestionnaireResponse.context, tabs-xml, all-xml-inner, segment-header, QuestionnaireResponse.implicitRules, QuestionnaireResponse.item.item.modifierExtension, hl7-logo, profile, tabs-diff, tbl-diff, QuestionnaireResponse.meta, QuestionnaireResponse.item.item.answer.modifierExtension, all-json-inner, QuestionnaireResponse.item.item.subject, QuestionnaireResponse.id, QuestionnaireResponse.language, QuestionnaireResponse.item.answer.id, QuestionnaireResponse.item.item.linkId, QuestionnaireResponse.item.item.answer.item, tabs-json, QuestionnaireResponse.item.answer.value_x_, tabs-all, QuestionnaireResponse.item.answer.item, tbl-diff-inner, segment-navbar, QuestionnaireResponse.item.extension, QuestionnaireResponse.item.item.item, QuestionnaireResponse.item.definition, QuestionnaireResponse.item.id, QuestionnaireResponse.item, QuestionnaireResponse.partOf, tabs, segment-post-footer, D.4.1.3, tbl-all-inner, json-inner, QuestionnaireResponse.item.item.text, all-tbl-snap, QuestionnaireResponse.extension, QuestionnaireResponse.subject, json, QuestionnaireResponse.identifier, segment-content, QuestionnaireResponse.item.subject, QuestionnaireResponse.item.item.extension, tabs-snap, QuestionnaireResponse.item.answer.modifierExtension, introduction, tbl-snap, summary, QuestionnaireResponse.author, QuestionnaireResponse.status, QuestionnaireResponse.item.linkId, QuestionnaireResponse, QuestionnaireResponse.item.item.definition, QuestionnaireResponse.item.answer.extension, QuestionnaireResponse.item.modifierExtension, hl7-nav, QuestionnaireResponse.questionnaire, QuestionnaireResponse.item.item.id, xml-inner, all-tbl-diff-inner, all-xml, QuestionnaireResponse.item.item.answer.value_x_, segment-breadcrumb, QuestionnaireResponse.source, QuestionnaireResponse.item.answer, all-json])

Sarah Gaunt (Mar 28 2018 at 07:27):

Seems to be trying to put a link in for each possible value of item.answer...

Sarah Gaunt (Mar 28 2018 at 08:08):

Well, fixed that issue too - again copied US Core - removed the XML and JSON templates from the StructureDefinition page... 0 Errors and 1 Warning! :)

Rob Hausam (Mar 29 2018 at 19:50):

@Sarah Gaunt What exactly did you do to fix this? I think I'm getting a lot of similar link errors (they may or may not be exactly the same issue). But IPS doesn't reference US Core, so I can't do anything with that.

Sarah Gaunt (Mar 29 2018 at 19:52):

For the first bunch of bad links I had to specifically add each resource type to the json control file and point them to the specific templates like:

"StructureDefinition/hai-report-questionnaire": {
      "base": "StructureDefinition-hai-report-questionnaire.html",
      "defns": "StructureDefinition-hai-report-questionnaire-definitions.html"
    },
    "StructureDefinition/hai-report-questionnaire-response": {
      "base": "StructureDefinition-hai-report-questionnaire-response.html",
      "defns": "StructureDefinition-hai-report-questionnaire-response-definitions.html"
    }

Sarah Gaunt (Mar 29 2018 at 19:53):

The second lot was totally my error - I didn't have that stuff above wrapped in the "resources": {}

Sarah Gaunt (Mar 29 2018 at 19:54):

I just had them sitting out on their own.

Sarah Gaunt (Mar 29 2018 at 19:57):

Then there was another issue that I fixed by removing the XML and JSON tabs from the sd-template-base template file:

<ul>
                  <li>
                    <a href="#tabs-summ">Text Summary</a>
                  </li>
                  <li>
                    <a href="#tabs-diff">Differential Table</a>
                  </li>
                  <li>
                    <a href="#tabs-snap">Snapshot Table</a>
                  </li>
                  <!--<li>
                    <a href="#tabs-xml">XML Template</a>
                  </li>
                  <li>
                    <a href="#tabs-json">JSON Template</a>
                  </li>-->
                  {% if examples %}
                  <li>
                    <a href="#tabs-examples">Examples</a>
                  </li>
                  {% endif %}
                  <li>
                    <a href="#tabs-all">All</a>
                  </li>
                </ul>

You can see above where I've commented them out. I just couldn't get them working properly and I noticed that US Core didn't have them either... Not sure if any of the other IGs do or not.

Rob Hausam (Mar 29 2018 at 20:03):

Thanks, @Sarah Gaunt. We're already doing the first part (but not complete yet, hence likely many of the errors). I'm not sure that we have anything like the second, but I'll look.

Mounika (Aug 21 2018 at 10:36):

Hi all,
I am getting the error while publishing our IG using STU3 IG publisher jar file. Can anyone know how fix it?
Capture25.PNG

Grahame Grieve (Aug 21 2018 at 11:09):

change the serer to /r4 not /r3

Mounika (Aug 21 2018 at 11:37):

@Grahame Grieve But I want to use R3 server for publishing.

Grahame Grieve (Aug 21 2018 at 12:30):

... because?

Mounika (Aug 21 2018 at 12:49):

because I created profiles prevoiusly using Forge STU3.

Lloyd McKenzie (Aug 23 2018 at 15:41):

You should always use the current IG Publisher which uses the current terminology server. That's independent of what version of artifacts are used as inputs and produced as output. I.e. you can point to the current terminology server and still consume STU3 profiles and produce an STU3 IG.

Halina Labikova (Nov 14 2019 at 19:53):

I can't figure out why I'm getting this error, any pointers? (All my local files have FHIRVersion set to 4.0.0)

Stack Dump (for debugging):                                                      (13.0997sec)
org.hl7.fhir.r5.utils.client.EFhirClientException: Error parsing response message: Unknown FHIRVersion code '4.0.1'
        at org.hl7.fhir.r5.utils.client.ClientUtils.unmarshalReference(ClientUtils.java:357)
        at org.hl7.fhir.r5.utils.client.ClientUtils.issueResourceRequest(ClientUtils.java:252)
        at org.hl7.fhir.r5.utils.client.ClientUtils.issueResourceRequest(ClientUtils.java:234)
        at org.hl7.fhir.r5.utils.client.ClientUtils.issueResourceRequest(ClientUtils.java:225)
        at org.hl7.fhir.r5.utils.client.ClientUtils.issueGetResourceRequest(ClientUtils.java:161)
        at org.hl7.fhir.r5.utils.client.FHIRToolingClient.getCapabilitiesStatementQuick(FHIRToolingClient.java:202)
        at org.hl7.fhir.r5.terminologies.TerminologyClientR5.getCapabilitiesStatementQuick(TerminologyClientR5.java:80)
        at org.hl7.fhir.r5.context.SimpleWorkerContext.connectToTSServer(SimpleWorkerContext.java:224)
        at org.hl7.fhir.igtools.publisher.Publisher.initializeFromJson(Publisher.java:1162)
        at org.hl7.fhir.igtools.publisher.Publisher.initialize(Publisher.java:984)
        at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:555)
        at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:5172)
Caused by: java.lang.IllegalArgumentException: Unknown FHIRVersion code '4.0.1'
        at org.hl7.fhir.r5.model.Enumerations$FHIRVersionEnumFactory.fromCode(Enumerations.java:10234)
        at org.hl7.fhir.r5.model.Enumerations$FHIRVersionEnumFactory.fromCode(Enumerations.java:1)
        at org.hl7.fhir.r5.formats.XmlParser.parseEnumeration(XmlParser.java:105)
        at org.hl7.fhir.r5.formats.XmlParser.parseCapabilityStatementContent(XmlParser.java:3414)
        at org.hl7.fhir.r5.formats.XmlParser.parseCapabilityStatement(XmlParser.java:3365)
        at org.hl7.fhir.r5.formats.XmlParser.parseResource(XmlParser.java:23733)
        at org.hl7.fhir.r5.formats.XmlParserBase.parse(XmlParserBase.java:126)
        at org.hl7.fhir.r5.formats.XmlParserBase.parse(XmlParserBase.java:110)

Grahame Grieve (Nov 14 2019 at 19:56):

is this running the IG publisher? what version are you running?

Halina Labikova (Nov 14 2019 at 20:04):

FHIR Implementation Guide Publisher (v?? (not a build IGPublisher?), gen-code v4.1.0 / 3)

Grahame Grieve (Nov 14 2019 at 20:09):

that is a very old one indeed. I'm surprised it's only broken now. Please use the current version

Halina Labikova (Nov 14 2019 at 20:23):

duh. thank you!!

Halina Labikova (Mar 20 2020 at 10:27):

Hello, any suggestions on how to fix this one?

Stack Dump (for debugging):                                                      (00:18.0888)
java.lang.Exception: Error parsing C:\Users\fpw3296\Documents\Profiling\ImplementationGuides R4\Decision-Support-Service-IG\resources\StructureDefinitions\promptResource: Not a JSON Object: "DataRequirement"
        at org.hl7.fhir.igtools.publisher.Publisher.load(Publisher.java:3670)
        at org.hl7.fhir.igtools.publisher.Publisher.loadConformance(Publisher.java:3270)
        at org.hl7.fhir.igtools.publisher.Publisher.createIg(Publisher.java:774)
        at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:661)
        at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:6738)
Caused by: java.lang.IllegalStateException: Not a JSON Object: "DataRequirement"
        at com.google.gson.JsonElement.getAsJsonObject(JsonElement.java:91)
        at org.hl7.fhir.r4.formats.JsonParser.parseStructureDefinitionProperties(JsonParser.java:23590)
        at org.hl7.fhir.r4.formats.JsonParser.parseStructureDefinition(JsonParser.java:23489)
        at org.hl7.fhir.r4.formats.JsonParser.parseResource(JsonParser.java:27669)
        at org.hl7.fhir.r4.formats.JsonParserBase.parse(JsonParserBase.java:113)
        at org.hl7.fhir.r4.formats.ParserBase.parse(ParserBase.java:79)
        at org.hl7.fhir.igtools.publisher.Publisher.parseContent(Publisher.java:3994)
        at org.hl7.fhir.igtools.publisher.Publisher.parse(Publisher.java:4045)
        at org.hl7.fhir.igtools.publisher.Publisher.load(Publisher.java:3667)
        ... 4 more

Lloyd McKenzie (Mar 20 2020 at 15:03):

Can you post promptResource?

Halina Labikova (Mar 20 2020 at 17:30):

voila @Lloyd McKenzie promptResource.json

Jose Costa Teixeira (Mar 20 2020 at 17:36):

the content of this file is not correct.

Jose Costa Teixeira (Mar 20 2020 at 17:36):

    "context": [
        "DataRequirement"
    ],

seems like something is missing

Jose Costa Teixeira (Mar 20 2020 at 17:41):

  "context" : [{
    "type" : "element",
    "expression" : "DataRequirement"
  }],

Jose Costa Teixeira (Mar 20 2020 at 17:41):

(I assume this is an extension on the DataRequirement data type)

Halina Labikova (Mar 20 2020 at 18:02):

Wohoo! That works, thank you.
Now to figure out why am I generating faulty diff files in the first place (maybe my fhirclient source is messed up?)

Jose Costa Teixeira (Mar 20 2020 at 18:09):

I don't know the tool you're using

Last updated: Apr 12 2022 at 19:14 UTC