Stream: IG creation
Topic: 1.1.71 Broken?
Sarah Gaunt (May 14 2021 at 20:39):
Looks like IG Publisher 1.1.71 isn't working? Crashing for all IGs since it was released. @Mark Iantorno
Lloyd McKenzie (May 14 2021 at 20:48):
Common failure is:
Exception in thread "main" java.lang.Error: This needs to be checked for profile path
at org.hl7.fhir.igtools.publisher.Publisher.fixSearchForm(Publisher.java:5190)
at org.hl7.fhir.igtools.publisher.Publisher.generate(Publisher.java:5059)
at org.hl7.fhir.igtools.publisher.Publisher.createIg(Publisher.java:901)
at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:745)
at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:8577)
Lloyd McKenzie (May 14 2021 at 20:48):
Also @Grahame Grieve
Rick Geimer (May 14 2021 at 20:55):
And verified that 1.1.68 works against the same IG that Sarah is having problems with.
Grahame Grieve (May 14 2021 at 21:01):
yes it's a piece of debugging that slipped in. I failed to commit it before @Mark Iantorno released. Doing another release now
Sarah Gaunt (May 14 2021 at 21:08):
Thanks!
John Moehrke (May 16 2021 at 12:38):
There seems to be a problem yet...
C:\Users\johnm\Git\us-odh>_updatePublisher
Checking internet connection...
Reply from 104.196.166.17: bytes=32 time=57ms TTL=118
We're online
IG Publisher FOUND in input-cache
Overwrite "C:\Users\johnm\Git\us-odh\input-cache\publisher.jar"? (Y/N) y
Downloading most recent publisher to Input Cache - it's ~100 MB, so this may take a bit
At line:1 char:1
+ if ('System.Net.WebClient' -as [type]) {(new-object System.Net.WebCli ...
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This script contains malicious content and has been blocked by your antivirus software.
+ CategoryInfo : ParserError: (:) [], ParentContainsErrorRecordException
+ FullyQualifiedErrorId : ScriptContainedMaliciousContent
Jose Costa Teixeira (May 16 2021 at 13:22):
I don't know how a new publisher version would trigger this. This is your antivirus complaining that it doesn't want to download the publisher
Jose Costa Teixeira (May 16 2021 at 13:23):
was there any change to your system @John Moehrke ?
John Moehrke (May 16 2021 at 13:28):
not that I know of, but it is as you point out antivirus... which likely updates constantly.
John Moehrke (May 16 2021 at 13:29):
my other machine is not complaining
John Moehrke (May 16 2021 at 13:30):
I can do the copy manually. just wanted to record this in case there was something odd going on
John Moehrke (May 16 2021 at 13:31):
note that both machines are windows 10 and both using microsoft defender. So, no idea why one machine is happy and the other is not.
John Moehrke (May 16 2021 at 13:32):
im doing a deep Defender scan on the machine that was not unhappy
John Moehrke (May 16 2021 at 13:39):
as far as I can tell it doesn't like our use of powershell for this purpose. It directs me to this article
https://www.microsoft.com/en-us/wdsi/threats/malware-encyclopedia-description?name=Trojan%3aPowerShell%2fMountsi.A!ml&threatid=2147726489
John Moehrke (May 16 2021 at 13:40):
I think the difference is that this machine that is unhappy has "App & Browsing Controls" turned on, but when I turn them off it still is not happy.
John Moehrke (May 16 2021 at 13:48):
note that the _updatePublisher.bat use of powershell to replace the .sh and .bat files works. just fails on the jar
John Moehrke (May 16 2021 at 15:06):
I find the QA.html output of a build, that indicates your build is old, and provides the download link; works well enough in a pinch.
Jose Costa Teixeira (May 16 2021 at 16:18):
Yes, it's the AV that doesn't like scripts downloading other executables.
Jose Costa Teixeira (May 16 2021 at 16:20):
My win10 works fine even after updates
Jose Costa Teixeira (May 17 2021 at 10:52):
I got this error, not sure what is missing
java.lang.NullPointerException: key == null
at com.google.gson.internal.LinkedTreeMap.put(LinkedTreeMap.java:92)
at com.google.gson.JsonObject.add(JsonObject.java:61)
at org.hl7.fhir.igtools.publisher.Publisher.addPageDataRow(Publisher.java:6222)
at org.hl7.fhir.igtools.publisher.Publisher.addPageData(Publisher.java:6205)
at org.hl7.fhir.igtools.publisher.Publisher.addPageData(Publisher.java:6170)
at org.hl7.fhir.igtools.publisher.Publisher.addPageData(Publisher.java:6214)
at org.hl7.fhir.igtools.publisher.Publisher.addPageData(Publisher.java:6170)
at org.hl7.fhir.igtools.publisher.Publisher.addPageData(Publisher.java:6214)
at org.hl7.fhir.igtools.publisher.Publisher.addPageData(Publisher.java:6170)
at org.hl7.fhir.igtools.publisher.Publisher.generateSummaryOutputs(Publisher.java:5979)
at org.hl7.fhir.igtools.publisher.Publisher.generate(Publisher.java:5004)
at org.hl7.fhir.igtools.publisher.Publisher.createIg(Publisher.java:901)
at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:745)
at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:8577)
Press any key to continue . . .
Jose Costa Teixeira (May 17 2021 at 10:53):
Hijacking this stream for an issue with 1.1.72
John Moehrke (May 17 2021 at 12:45):
_updatePublisher worked fine today.
John Moehrke (May 17 2021 at 12:58):
correction... _updatePublisher works in some folders... so I guess I have a glitch in my folder.
Lloyd McKenzie (May 17 2021 at 17:17):
@Mark Iantorno
Lloyd McKenzie (May 17 2021 at 17:17):
@Jose Costa Teixeira - is there a place this is checked in that Mark can test with?
Mark Iantorno (May 17 2021 at 17:21):
@Jose Costa Teixeira send me what you're working with, and I'll run it in my IDE so I can debug
Jose Costa Teixeira (May 17 2021 at 17:54):
@Mark Iantorno https://github.com/openhie/hiv-ig/tree/rework-questionnaire
Jose Costa Teixeira (May 17 2021 at 17:54):
https://github.com/openhie/hiv-ig/pull/55/checks?check_run_id=2603365047
Mark Iantorno (May 17 2021 at 18:03):
what is the exact command you're running
Mark Iantorno (May 17 2021 at 18:03):
on the publisher
Mark Iantorno (May 17 2021 at 18:04):
I apologize for asking for so much detail, I just don't use the publisher as much
Jose Costa Teixeira (May 17 2021 at 18:06):
i use the batch _genonce,
Jose Costa Teixeira (May 17 2021 at 18:06):
which actually does java-jar publisher.jar .
Mark Iantorno (May 17 2021 at 18:07):
so you clone the repo rework-questionnaire
Mark Iantorno (May 17 2021 at 18:07):
then run the publisher
Mark Iantorno (May 17 2021 at 18:07):
how do you point it to the cloned repo?
Mark Iantorno (May 17 2021 at 18:07):
or do you jsut run it from within the base folder of the repo
Jose Costa Teixeira (May 17 2021 at 18:07):
i clone the branch of that repo
Jose Costa Teixeira (May 17 2021 at 18:08):
i run it from the base folder
Jose Costa Teixeira (May 17 2021 at 18:08):
the . in the command line points is the base folder
Mark Iantorno (May 17 2021 at 18:08):
yup, sounds good
Jose Costa Teixeira (May 17 2021 at 18:08):
(sorry, i should have mentioned it)
Mark Iantorno (May 17 2021 at 18:08):
np, realistically, I should know
Mark Iantorno (May 17 2021 at 18:09):
I'm going to try reproducing your bug now
Mark Iantorno (May 17 2021 at 18:16):
wait
Mark Iantorno (May 17 2021 at 18:16):
ignore me
Mark Iantorno (May 17 2021 at 18:16):
nevermind
Mark Iantorno (May 17 2021 at 18:27):
Alright I get the same error
Mark Iantorno (May 17 2021 at 18:44):
@Jose Costa Teixeira
Mark Iantorno (May 17 2021 at 18:44):
it's crashing because it's getting a null url passed in
Mark Iantorno (May 17 2021 at 18:44):
from this:
Mark Iantorno (May 17 2021 at 18:44):
Adding key url:: null,
title -> Example Scenario #1 - Description,
label -> 13.4,
breadcrumb -> <li><a href='toc.html'><b>Table of Contents</b></a></li><li><a href='artifacts.html'><b>Artifacts Summary</b></a></li><li><b>Example Scenario #1</b></li>
Mark Iantorno (May 17 2021 at 18:45):
All the other Examples have associated URLs
Mark Iantorno (May 17 2021 at 18:45):
Adding key url:: QuestionnaireResponse-exampleresponse.json.html,
title -> Example QuestionnaireResponse - JSON Representation,
label -> 13.3,
breadcrumb -> <li><a href='toc.html'><b>Table of Contents</b></a></li><li><a href='artifacts.html'><b>Artifacts Summary</b></a></li><li><b>Example QuestionnaireResponse</b></li>
Adding key url:: QuestionnaireResponse-exampleresponse.ttl.html,
title -> Example QuestionnaireResponse - TTL Representation,
label -> 13.3,
breadcrumb -> <li><a href='toc.html'><b>Table of Contents</b></a></li><li><a href='artifacts.html'><b>Artifacts Summary</b></a></li><li><b>Example QuestionnaireResponse</b></li>
Adding key url:: ExampleScenario-hiv-case-reporting-scenario.html,
title -> Example Scenario #1,
label -> 13.4,
breadcrumb -> <li><a href='toc.html'><b>Table of Contents</b></a></li><li><a href='artifacts.html'><b>Artifacts Summary</b></a></li><li><b>Example Scenario #1</b></li>
Adding key url:: ExampleScenario-hiv-case-reporting-scenario-resources.html,
title -> Example Scenario #1 - Resources,
label -> 13.4,
breadcrumb -> <li><a href='toc.html'><b>Table of Contents</b></a></li><li><a href='artifacts.html'><b>Artifacts Summary</b></a></li><li><b>Example Scenario #1</b></li>
Mark Iantorno (May 17 2021 at 18:48):
Is this something that was working on an older version, and now has stopped working?
Mark Iantorno (May 17 2021 at 18:48):
or is this something that was just added to your IG?
Mark Iantorno (May 17 2021 at 18:52):
So, @Lloyd McKenzie did make some changes to how output name is generated (which is what is used for the key in some cases), in this commit here -> https://github.com/HL7/fhir-ig-publisher/commit/cd5b67c8c34dda16bf5dfa0d095f46c1d61b66f0
Mark Iantorno (May 17 2021 at 18:53):
Those are the only recent changes I can see that might change how it's processed
Mark Iantorno (May 17 2021 at 18:54):
If this has worked before, please send me the version number of the publisher it last worked on, and I can do a diff and look into exactly what changed and determine what might have caused your issue, if this is actually an issue and not just a missing url or field in the ig
Mark Iantorno (May 17 2021 at 18:54):
ping me, I'll be around
Jose Costa Teixeira (May 17 2021 at 18:57):
this was working before. I'll check if it worked on 1.1.69
Jose Costa Teixeira (May 17 2021 at 18:58):
1.1.68 it is
Jose Costa Teixeira (May 17 2021 at 19:03):
so @Mark Iantorno this worked in 1.1.68
Jose Costa Teixeira (May 17 2021 at 19:03):
correction - I think it did
Jose Costa Teixeira (May 17 2021 at 19:03):
I'm trying to publish with 1.1.68 and now I have a jekyll error - but I presume that is because of the changes to the template
Mark Iantorno (May 17 2021 at 19:05):
So then the only changes that I think would affect this are the ones I linked above. I could be wrong... but @Lloyd McKenzie what are your thought on this?
Jose Costa Teixeira (May 17 2021 at 19:09):
Not knowing more, I'd consider those changes to be responsible
Lloyd McKenzie (May 17 2021 at 19:13):
Running a connectathon track right now - will try to look this evening.
Mark Iantorno (May 17 2021 at 19:20):
ok
Mark Iantorno (May 17 2021 at 19:20):
thanks Lloyd
Grahame Grieve (May 17 2021 at 19:50):
Lloyd made some changes to the template to generate something new. This will be a discovered issue
Lloyd McKenzie (May 18 2021 at 01:49):
Ok, I'll shortly be submitting a pull request that will improve error reporting. The new code will spit out the following error:
org.hl7.fhir.exceptions.FHIRException: Error in publisher template. Unable to find file-path property description for resource type ExampleScenario when property template-description is defined.
at org.hl7.fhir.igtools.publisher.Publisher.addPageData(Publisher.java:6205)
This is triggered by a problem with the template, which says:
"ExampleScenario": {
"template-base": "template/layouts/layout-examplescenario.html",
"template-description": "template/layouts/layout-examplescenario-description.html",
"template-resources": "template/layouts/layout-examplescenario-resources.html",
"base": "{{[type]}}-{{[id]}}.html",
"desc": "{{[type]}}-{{[id]}}-description.html",
"resources": "{{[type]}}-{{[id]}}-resources.html",
"template-format": ""
}
The "desc": should be "description":
Last updated: Apr 12 2022 at 19:14 UTC
