lmckenzi
commented
1 year ago Can you please point to a Git repository that reproduces this? (A single FSH file isn't enough to allow us to reproduce.)
Open VictorShiller opened 1 year ago
lmckenzi
commented
1 year ago Can you please point to a Git repository that reproduces this? (A single FSH file isn't enough to allow us to reproduce.)
VictorShiller
commented
1 year ago @lmckenzi a repo that reproduces this error: https://github.com/VictorShiller/IG-Sample2
grahamegrieve
commented
1 year ago FHIR IG Publisher Version 1.3.1-SNAPSHOT (Git# 3b2c78368cc6). Built 2023-03-23T04:32:19.872+11:00 (63 days old)
Detected Java version: 17.0.2 from /Users/grahamegrieve/.p2/pool/plugins/org.eclipse.justj.openjdk.hotspot.jre.full.macosx.aarch64_17.0.2.v20220201-1208/jre on Mac OS X/aarch64 (64bit). 16384MB available
dir = /Users/grahamegrieve/work/ig-pub/org.hl7.fhir.publisher.core, path = /usr/bin:/bin:/usr/sbin:/sbin
Parameters: -ig /Users/grahamegrieve/temp/igs/VictorShiller-IG-Sample2#master
Start Clock @ Thursday, 25 May 2023 at 6:57:05 am Australian Eastern Standard Time (2023-05-25T06:57:05+10:00)
Build FHIR IG from /Users/grahamegrieve/temp/igs/VictorShiller-IG-Sample2#master (00:00.013)
API keys loaded from /Users/grahamegrieve/.fhir/fhir-settings.json (00:00.014)
Package Cache: /Users/grahamegrieve/.fhir/packages (00:00.018)
Run Sushi on /Users/grahamegrieve/temp/igs/VictorShiller-IG-Sample2#master (00:00.022)
Unable to load IG as an r5 IG - try R4 (/Users/grahamegrieve/temp/igs/VictorShiller-IG-Sample2#master/fsh-generated/resources/ImplementationGuide-sample.fhir.json (No such file or directory)) (00:00.499)
Publishing Content Failed: Error Parsing File /Users/grahamegrieve/temp/igs/VictorShiller-IG-Sample2#master/fsh-generated/resources/ImplementationGuide-sample.fhir.json: /Users/grahamegrieve/temp/igs/VictorShiller-IG-Sample2#master/fsh-generated/resources/ImplementationGuide-sample.fhir.json (No such file or directory) (00:00.526)
(00:00.526)
Use -? to get command line help (00:00.527)
(00:00.527)
Stack Dump (for debugging): (00:00.527)
java.lang.Exception: Error Parsing File /Users/grahamegrieve/temp/igs/VictorShiller-IG-Sample2#master/fsh-generated/resources/ImplementationGuide-sample.fhir.json: /Users/grahamegrieve/temp/igs/VictorShiller-IG-Sample2#master/fsh-generated/resources/ImplementationGuide-sample.fhir.json (No such file or directory)
at org.hl7.fhir.igtools.publisher.Publisher.initializeFromIg(Publisher.java:2407)
at org.hl7.fhir.igtools.publisher.Publisher.initialize(Publisher.java:2287)
at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:923)
at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:11384)
Caused by: java.io.FileNotFoundException: /Users/grahamegrieve/temp/igs/VictorShiller-IG-Sample2#master/fsh-generated/resources/ImplementationGuide-sample.fhir.json (No such file or directory)
at java.base/java.io.FileInputStream.open0(Native Method)
at java.base/java.io.FileInputStream.open(FileInputStream.java:216)
at java.base/java.io.FileInputStream.<init>(FileInputStream.java:157)
at org.hl7.fhir.utilities.TextFile.fileToBytes(TextFile.java:208)
at org.hl7.fhir.r4.formats.FormatUtilities.loadFile(FormatUtilities.java:168)
at org.hl7.fhir.igtools.publisher.Publisher.initializeFromIg(Publisher.java:2404)
... 3 more
@cmoesel sushi failed somehow?
VictorShiller
commented
1 year ago Output when I run _genonce.sh
Online
Picked up JAVA_TOOL_OPTIONS: -Dfile.encoding=UTF-8
FHIR IG Publisher Version 1.3.2 (Git# 60cb067f5635). Built 2023-03-25T13:13:01.551Z (60 days old)
Detected Java version: 17.0.5 from C:\Program Files\Java\jdk-17.0.5 on Windows 10/amd64 (64bit). 16352MB available
dir = C:\Users\shillev\source\repos\github.com\IG-Sample, path = C:\Users\shillev\bin;C:\Program Files\Git\mingw64\bin;C:\Program Files\Git\usr\local\bin;C:\Program Files\Git\usr\bin;C:\Program Files\Git\usr\bin;C:\Program Files\Git\mingw64\bin;C:\Program Files\Git\usr\bin;C:\Users\shillev\bin;C:\Program Files\Java\jdk-17.0.5\bin;C:\windows\system32;C:\windows;C:\windows\System32\Wbem;C:\windows\System32\WindowsPowerShell\v1.0;C:\windows\System32\OpenSSH;C:\Program Files\WindowsPowerShell\Scripts\HP.ClientScriptLibrary;C:\Program Files\Microsoft SQL Server\130\Tools\Binn;C:\Users\shillev\AppData\Roaming\nvm;C:\Program Files\nodejs;C:\Program Files\nodejs;C:\Program Files (x86)\Webex\Plugins;C:\Program Files (x86)\Microsoft SQL Server\150\DTS\Binn;C:\Program Files\Azure Data Studio\bin;C:\Program Files\1E\Client\Extensibility\NomadBranch;C:\Program Files\Microsoft SQL Server\Client SDK\ODBC\170\Tools\Binn;C:\Program Files\dotnet;C:\Program Files\Microsoft SQL Server\150\Tools\Binn;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0;C:\WINDOWS\System32\OpenSSH;C:\Program Files\Docker\Docker\resources\bin;C:\ProgramData\DockerDesktop\version-bin;C:\Program Files\Git\cmd;C:\Program Files\Amazon\AWSCLIV2;C:\Program Files\Java\jdk-17.0.5\bin;C:\Users\shillev\AppData\Local\Programs\Python\Python37\Scripts;C:\Users\shillev\AppData\Local\Programs\Python\Python37;C:\Ruby27-x64\bin;C:\Users\shillev\AppData\Local\Microsoft\WindowsApps;C:\Users\shillev\AppData\Local\Programs\Microsoft VS Code\bin;C:\Program Files\Git\cmd;C:\Users\shillev\AppData\Roaming\nvm;C:\Program Files\nodejs;C:\Users\shillev\AppData\Roaming\npm;C:\Program Files\Azure Data Studio\bin;C:\Users\shillev\.dotnet\tools;C:\Users\shillev\AppData\Local\Programs\Fiddler;C:\Users\shillev\.dotnet\tools;C:\Users\shillev\AppData\Local\Microsoft\WindowsApps;C:\Program Files\Git\usr\bin\vendor_perl;C:\Program Files\Git\usr\bin\core_perl
Parameters: -ig .
Start Clock @ Wednesday, May 24, 2023 at 4:04:23 PM Central Daylight Time (2023-05-24T16:04:23-05:00)
Build FHIR IG from C:\Users\shillev\source\repos\github.com\IG-Sample\. (00:00.160)
API keys loaded from C:\Users\shillev\fhir-api-keys.ini (00:00.318)
Package Cache: C:\Users\shillev\.fhir\packages (00:00.323)
Run Sushi on C:\Users\shillev\source\repos\github.com\IG-Sample (00:00.471)
Sushi: info Running SUSHI v2.10.2 (implements FHIR Shorthand specification v2.0.0) (00:24.679)
Sushi: info Arguments: (00:24.680)
Sushi: info --out C:\Users\shillev\source\repos\github.com\IG-Sample (00:24.681)
Sushi: info C:\Users\shillev\source\repos\github.com\IG-Sample (00:24.683)
Sushi: info Using configuration file: C:\Users\shillev\source\repos\github.com\IG-Sample\sushi-config.yaml (00:28.144)
Sushi: info Importing FSH text... (00:28.154)
Sushi: info Preprocessed 1 documents with 0 aliases. (00:28.204)
Sushi: info Imported 3 definitions and 0 instances. (00:28.211)
Sushi: info Checking local cache for hl7.fhir.uv.tools#current... (00:28.212)
Sushi: info Found hl7.fhir.uv.tools#current in local cache. (00:28.237)
Sushi: (node:31296) Warning: Accessing non-existent property 'INVALID_ALT_NUMBER' of module exports inside circular dependency (00:28.271)
Sushi: (Use `node --trace-warnings ...` to show where the warning was created) (00:28.273)
Sushi: (node:31296) Warning: Accessing non-existent property 'INVALID_ALT_NUMBER' of module exports inside circular dependency (00:28.274)
Sushi: info Loaded package hl7.fhir.uv.tools#current (00:29.163)
Sushi: info Checking local cache for hl7.terminology.r4#5.0.0... (00:30.658)
Sushi: info Found hl7.terminology.r4#5.0.0 in local cache. (00:31.963)
Sushi: info Loaded package hl7.terminology.r4#5.0.0 (00:31.964)
Sushi: info Checking local cache for hl7.fhir.r4.core#4.0.1... (00:31.965)
Sushi: info Found hl7.fhir.r4.core#4.0.1 in local cache. (00:33.523)
Sushi: info Loaded package hl7.fhir.r4.core#4.0.1 (00:33.524)
Sushi: info Converting FSH to FHIR resources... (00:33.603)
Sushi: info Converted 3 FHIR StructureDefinitions. (00:33.839)
Sushi: info Exporting FHIR resources as JSON... (00:33.840)
Sushi: info Exported 3 FHIR resources as JSON. (00:33.865)
Sushi: info Assembling Implementation Guide sources... (00:33.866)
Sushi: info Generated ImplementationGuide-sample.fhir.json (00:33.874)
Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:33.876)
Sushi: (00:33.877)
Sushi: ========================= SUSHI RESULTS =========================== (00:33.878)
Sushi: | ------------------------------------------------------------- | (00:33.879)
Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:33.880)
Sushi: | |-------------------------------------------------------------| | (00:33.881)
Sushi: | | 2 | 1 | 0 | 0 | | (00:33.882)
Sushi: | ------------------------------------------------------------- | (00:33.883)
Sushi: | ------------------------------------------------------------- | (00:33.885)
Sushi: | | ValueSets | CodeSystems | Instances | | (00:33.886)
Sushi: | |-------------------------------------------------------------| | (00:33.886)
Sushi: | | 0 | 0 | 0 | | (00:33.887)
Sushi: | ------------------------------------------------------------- | (00:33.888)
Sushi: | | (00:33.890)
Sushi: =================================================================== (00:33.891)
Sushi: | You're piranha roll now! 0 Errors 0 Warnings | (00:33.892)
Sushi: =================================================================== (00:33.893)
Sushi: (00:33.895)
Unable to load IG as an r5 IG - try R4 (property code is a class com.google.gson.JsonPrimitive looking for an object) (00:45.267)
Load Template from fhir.base.template#current (00:45.768)
onLoad.findSpreadsheets:
onLoad.updateIg:
[xslt] Processing C:\Users\shillev\source\repos\github.com\IG-Sample\template\onLoad-ig-working.xml to C:\Users\shillev\source\repos\github.com\IG-Sample\template\onLoad-ig-updated.xml
[xslt] Loading stylesheet C:\Users\shillev\source\repos\github.com\IG-Sample\template\scripts\onLoad.xslt
onLoad.extend:
onLoad:
Root directory: C:\Users\shillev\source\repos\github.com\IG-Sample (00:50.517)
Core Package hl7.fhir.r4.core#4.0.1
.:Terminology Cache is at C:\Users\shillev\source\repos\github.com\IG-Sample\input-cache\txcache. 21 files in cache (00:56.354)
Connect to Terminology Server at http://tx.fhir.org (00:56.357)
Load Package hl7.fhir.pubpack#0.1.4
Load Package hl7.fhir.xver-extensions#0.0.12
Load Package hl7.terminology.r4#5.0.0
Version mismatch. This IG is version 4.0.1, while the IG 'igtools' is from version 5.0.0 (will try to run anyway) (00:59.034)
Load Package hl7.fhir.uv.tools#0.1.0
Load R5 Extensions - 157 resources (01:07.705)
Initialization complete (01:08.716)
Fetch http://test.com/fhir/sample/package-list.json for version check (01:08.718)
Load Content (01:23.887)
loadPrePages from FetchedFile[C:\Users\shillev\source\repos\github.com\IG-Sample\fsh-generated\includes] as C:\Users\shillev\source\repos\github.com\IG-Sample\fsh-generated\includes
loadPrePages from FetchedFile[C:\Users\shillev\source\repos\github.com\IG-Sample\input\pagecontent] as C:\Users\shillev\source\repos\github.com\IG-Sample\input\pagecontent
Processing Conformance Resources (01:24.287)
Generating Snapshots (01:24.390)
Exception in thread "main" java.lang.StackOverflowError
at org.hl7.fhir.r5.model.ElementDefinition$ElementDefinitionSlicingDiscriminatorComponent.copyValues(ElementDefinition.java:1640)
at org.hl7.fhir.r5.model.ElementDefinition$ElementDefinitionSlicingDiscriminatorComponent.copy(ElementDefinition.java:1635)
at org.hl7.fhir.r5.model.ElementDefinition$ElementDefinitionSlicingComponent.copyValues(ElementDefinition.java:1382)
at org.hl7.fhir.r5.model.ElementDefinition$ElementDefinitionSlicingComponent.copy(ElementDefinition.java:1373)
at org.hl7.fhir.r5.model.ElementDefinition.copyValues(ElementDefinition.java:12581)
at org.hl7.fhir.r5.model.ElementDefinition.copy(ElementDefinition.java:12561)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBaseDefault(ProfilePathProcessor.java:884)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBase(ProfilePathProcessor.java:864)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPaths(ProfilePathProcessor.java:179)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBaseDefault(ProfilePathProcessor.java:1067)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBase(ProfilePathProcessor.java:864)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPaths(ProfilePathProcessor.java:179)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBaseDefault(ProfilePathProcessor.java:1067)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBase(ProfilePathProcessor.java:864)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPaths(ProfilePathProcessor.java:179)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBaseDefault(ProfilePathProcessor.java:1067)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBase(ProfilePathProcessor.java:864)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPaths(ProfilePathProcessor.java:179)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBaseDefault(ProfilePathProcessor.java:1067)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBase(ProfilePathProcessor.java:864)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPaths(ProfilePathProcessor.java:179)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBaseDefault(ProfilePathProcessor.java:1067)
....................... (same recurring set of errors)```
cmoesel
commented
1 year ago @grahamegrieve - Why are you running IG Publisher 1.3.1-SNAPSHOT (built March 23)? I've just tried it with IG Publisher 1.3.12 (built May 24) and it worked fine for me.
@VictorShiller - I'm not getting any errors when I run _genonce. I'm on Mac with Java 11, but I wouldn't think that would make a difference.
I also noticed you have a fsh.ini file with sushi-version=latest. I guess that's valid, but I don't think it's common. You may want to consider removing that (~and don't worry, the IG Publisher will bark at you if your installed SUSHI is out of date~ edit: IG Publisher only barks in publication or auto-build mode, neither of which are used during normal development).
grahamegrieve
commented
1 year ago @cmoesel - it's the latest running under the java debugger. the version is just wrong in that case. Sushi bombed with no error message because it wasn't current - not sure what happened there
@VictorShiller it builds fine for me too. FHIR IG Publisher Version 1.3.2 is extremely old - update to the current version
cmoesel
commented
1 year ago @grahamegrieve - Ah... ok. That is weird that you didn't get any out-of-date errors from SUSHI. I ran with the -publish flag (to force the --require-latest flag on SUSHI) and I got the error in my output:
error Current SUSHI version (2.10.0) is not the latest version. Upgrade to the latest version (2.10.2) or run SUSHI again without the --require-latest flag. (00:01.188)updated IG Publisher to latest and the error slightly changed. I also noticed when I comment out section[section1].section[section2].extension[abc].valueCanonical = Canonical(CompositionOutput) line 34 in composition.fsh it builds.
It seems that something about setting the valueCononical of my extension on the Composition profile is causing it to fail, I am on windows behind a corporate proxy, though that should not affect this error.
Checking internet connection...
Online
Picked up JAVA_TOOL_OPTIONS: -Dfile.encoding=UTF-8
FHIR IG Publisher Version 1.3.12 (Git# d881c69d4461). Built 2023-05-24T15:44:32.700Z (22 hours old)
Detected Java version: 17.0.5 from C:\Program Files\Java\jdk-17.0.5 on Windows 10/amd64 (64bit). 16352MB available
dir = C:\Users\shillev\source\repos\github.com\IG-Sample, path = C:\Users\shillev\bin;C:\Program Files\Git\mingw64\bin;C:\Program Files\Git\usr\local\bin;C:\Program Files\Git\usr\bin;C:\Program Files\Git\usr\bin;C:\Program Files\Git\mingw64\bin;C:\Program Files\Git\usr\bin;C:\Users\shillev\bin;C:\Program Files\Java\jdk-17.0.5\bin;C:\windows\system32;C:\windows;C:\windows\System32\Wbem;C:\windows\System32\WindowsPowerShell\v1.0;C:\windows\System32\OpenSSH;C:\Program Files\WindowsPowerShell\Scripts\HP.ClientScriptLibrary;C:\Program Files\Microsoft SQL Server\130\Tools\Binn;C:\Users\shillev\AppData\Roaming\nvm;C:\Program Files\nodejs;C:\Program Files\nodejs;C:\Program Files (x86)\Webex\Plugins;C:\Program Files (x86)\Microsoft SQL Server\150\DTS\Binn;C:\Program Files\Azure Data Studio\bin;C:\Program Files\1E\Client\Extensibility\NomadBranch;C:\Program Files\Microsoft SQL Server\Client SDK\ODBC\170\Tools\Binn;C:\Program Files\dotnet;C:\Program Files\Microsoft SQL Server\150\Tools\Binn;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0;C:\WINDOWS\System32\OpenSSH;C:\Program Files\Docker\Docker\resources\bin;C:\ProgramData\DockerDesktop\version-bin;C:\Program Files\Git\cmd;C:\Program Files\Amazon\AWSCLIV2;C:\Program Files\Java\jdk-17.0.5\bin;C:\Users\shillev\AppData\Local\Programs\Python\Python37\Scripts;C:\Users\shillev\AppData\Local\Programs\Python\Python37;C:\Ruby27-x64\bin;C:\Users\shillev\AppData\Local\Microsoft\WindowsApps;C:\Users\shillev\AppData\Local\Programs\Microsoft VS Code\bin;C:\Program Files\Git\cmd;C:\Users\shillev\AppData\Roaming\nvm;C:\Program Files\nodejs;C:\Users\shillev\AppData\Roaming\npm;C:\Program Files\Azure Data Studio\bin;C:\Users\shillev\.dotnet\tools;C:\Users\shillev\AppData\Local\Programs\Fiddler;C:\Users\shillev\.dotnet\tools;C:\Users\shillev\AppData\Local\Microsoft\WindowsApps;C:\Program Files\Git\usr\bin\vendor_perl;C:\Program Files\Git\usr\bin\core_perl
Parameters: -ig .
Start Clock @ Thursday, May 25, 2023 at 9:26:22 AM Central Daylight Time (2023-05-25T09:26:22-05:00)
Build FHIR IG from C:\Users\shillev\source\repos\github.com\IG-Sample\. (00:00.184)
API keys loaded from C:\Users\shillev\.fhir\fhir-settings.json (00:00.186)
Package Cache: C:\Users\shillev\.fhir\packages (00:00.190)
Run Sushi on C:\Users\shillev\source\repos\github.com\IG-Sample (00:00.365)
Sushi: info Running SUSHI v2.10.2 (implements FHIR Shorthand specification v2.0.0) (00:23.031)
Sushi: info Arguments: (00:23.032)
Sushi: info --out C:\Users\shillev\source\repos\github.com\IG-Sample (00:23.033)
Sushi: info C:\Users\shillev\source\repos\github.com\IG-Sample (00:23.034)
Sushi: info Using configuration file: C:\Users\shillev\source\repos\github.com\IG-Sample\sushi-config.yaml (00:26.579)
Sushi: info Importing FSH text... (00:26.593)
Sushi: info Preprocessed 1 documents with 0 aliases. (00:26.649)
Sushi: info Imported 3 definitions and 0 instances. (00:26.653)
Sushi: info Checking local cache for hl7.fhir.uv.tools#current... (00:26.655)
Sushi: info Found hl7.fhir.uv.tools#current in local cache. (00:26.681)
Sushi: (node:6448) Warning: Accessing non-existent property 'INVALID_ALT_NUMBER' of module exports inside circular dependency (00:26.712)
Sushi: (Use `node --trace-warnings ...` to show where the warning was created) (00:26.714)
Sushi: (node:6448) Warning: Accessing non-existent property 'INVALID_ALT_NUMBER' of module exports inside circular dependency (00:26.715)
Sushi: info Loaded package hl7.fhir.uv.tools#current (00:27.575)
Sushi: info Checking local cache for hl7.terminology.r4#5.0.0... (00:28.326)
Sushi: info Found hl7.terminology.r4#5.0.0 in local cache. (00:29.632)
Sushi: info Loaded package hl7.terminology.r4#5.0.0 (00:29.633)
Sushi: info Checking local cache for hl7.fhir.r4.core#4.0.1... (00:29.634)
Sushi: info Found hl7.fhir.r4.core#4.0.1 in local cache. (00:31.069)
Sushi: info Loaded package hl7.fhir.r4.core#4.0.1 (00:31.070)
Sushi: info Converting FSH to FHIR resources... (00:31.125)
Sushi: info Converted 3 FHIR StructureDefinitions. (00:31.322)
Sushi: info Exporting FHIR resources as JSON... (00:31.324)
Sushi: info Exported 3 FHIR resources as JSON. (00:31.347)
Sushi: info Assembling Implementation Guide sources... (00:31.348)
Sushi: info Generated ImplementationGuide-sample.fhir.json (00:31.358)
Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:31.359)
Sushi: (00:31.360)
Sushi: ========================= SUSHI RESULTS =========================== (00:31.361)
Sushi: | ------------------------------------------------------------- | (00:31.362)
Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:31.364)
Sushi: | |-------------------------------------------------------------| | (00:31.365)
Sushi: | | 2 | 1 | 0 | 0 | | (00:31.366)
Sushi: | ------------------------------------------------------------- | (00:31.367)
Sushi: | ------------------------------------------------------------- | (00:31.368)
Sushi: | | ValueSets | CodeSystems | Instances | | (00:31.369)
Sushi: | |-------------------------------------------------------------| | (00:31.370)
Sushi: | | 0 | 0 | 0 | | (00:31.371)
Sushi: | ------------------------------------------------------------- | (00:31.372)
Sushi: | | (00:31.373)
Sushi: =================================================================== (00:31.373)
Sushi: | Fin-tastic job! 0 Errors 0 Warnings | (00:31.374)
Sushi: =================================================================== (00:31.375)
Sushi: (00:31.376)
Unable to load IG as an r5 IG - try R4 (property code is a class com.google.gson.JsonPrimitive looking for an object) (00:42.376)
Load Template from fhir.base.template#current (00:42.900)
onLoad.findSpreadsheets:
onLoad.updateIg:
[xslt] Processing C:\Users\shillev\source\repos\github.com\IG-Sample\template\onLoad-ig-working.xml to C:\Users\shillev\source\repos\github.com\IG-Sample\template\onLoad-ig-updated.xml
[xslt] Loading stylesheet C:\Users\shillev\source\repos\github.com\IG-Sample\template\scripts\onLoad.xslt
onLoad.extend:
onLoad:
Root directory: C:\Users\shillev\source\repos\github.com\IG-Sample (00:47.538)
Core Package hl7.fhir.r4.core#4.0.1
Terminology Cache is at C:\Users\shillev\source\repos\github.com\IG-Sample\input-cache\txcache. 21 files in cache (00:53.618)
Connect to Terminology Server at http://tx.fhir.org (00:53.621)
Load Package hl7.fhir.pubpack#0.1.4
Load Package hl7.fhir.xver-extensions#0.0.12
Load Package hl7.terminology.r4#5.0.0
Load Package hl7.fhir.uv.extensions.r4#1.0.0
Version mismatch. This IG is version 4.0.1, while the IG 'igtools' is from version 5.0.0 (will try to run anyway) (00:56.879)
Load Package hl7.fhir.uv.tools#0.1.0
Load R5 SpecialsInitialization complete (01:00.864)
Fetch http://test.com/fhir/sample/package-list.json for version check (01:00.866)
Load Content (01:15.937)
loadPrePages from FetchedFile[C:\Users\shillev\source\repos\github.com\IG-Sample\fsh-generated\includes] as C:\Users\shillev\source\repos\github.com\IG-Sample\fsh-generated\includes
loadPrePages from FetchedFile[C:\Users\shillev\source\repos\github.com\IG-Sample\input\pagecontent] as C:\Users\shillev\source\repos\github.com\IG-Sample\input\pagecontent
Processing Conformance Resources (01:16.367)
Generating Snapshots (01:16.483)
Exception in thread "main" java.lang.StackOverflowError
at org.hl7.fhir.r5.context.CanonicalResourceManager.get(CanonicalResourceManager.java:491)
at org.hl7.fhir.r5.context.BaseWorkerContext.fetchResourceWithExceptionByVersion(BaseWorkerContext.java:1592)
at org.hl7.fhir.r5.context.BaseWorkerContext.fetchResourceWithException(BaseWorkerContext.java:1473)
at org.hl7.fhir.r5.context.BaseWorkerContext.fetchResource(BaseWorkerContext.java:1949)
at org.hl7.fhir.r5.context.SimpleWorkerContext.fetchResource(SimpleWorkerContext.java:681)
at org.hl7.fhir.r5.conformance.profile.ProfileUtilities.updateFromDefinition(ProfileUtilities.java:2089)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBaseDefault(ProfilePathProcessor.java:1071)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBase(ProfilePathProcessor.java:910)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPaths(ProfilePathProcessor.java:183)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBaseDefault(ProfilePathProcessor.java:1119)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBase(ProfilePathProcessor.java:910)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPaths(ProfilePathProcessor.java:183)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBaseDefault(ProfilePathProcessor.java:1119)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBase(ProfilePathProcessor.java:910)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPaths(ProfilePathProcessor.java:183)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBaseDefault(ProfilePathProcessor.java:1119)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBase(ProfilePathProcessor.java:910)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPaths(ProfilePathProcessor.java:183)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBaseDefault(ProfilePathProcessor.java:1119)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBase(ProfilePathProcessor.java:910)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPaths(ProfilePathProcessor.java:183)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBaseDefault(ProfilePathProcessor.java:1119)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBase(ProfilePathProcessor.java:910)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPaths(ProfilePathProcessor.java:183)
....well, I'm not going to look at this unless you provide a git repository that reproduces this error exactly
AymericGrassart
commented
11 months ago Hi @grahamegrieve , @cmoesel, @lmckenzi, I am able to reproduce the error with @VictorShiller's repo using the latest FHIR IG Publisher Version 1.5.5.
Just to confirm from a FHIR specification point of view, are extensions supported on recursive fields using slicing to target specific levels? My tests have shown that it works at the root and second level, yet breaks at the third level.
Here is a fsh example redacted from the repo that demonstrates the issue:
Extension: Extension1
Id: extension-1
Title: "Title"
Description: "Desc"
* value[x] 1..1 MS
* value[x] only string
Profile: CompositionProfile
Parent: Composition
Id: composition-profile
Title: "Composition"
Description: "A profile on the Composition resource"
* section.extension contains Extension1 named abc 0..1 MS
* section.extension[abc].valueString = "parent works"
* section ^slicing.discriminator.type = #pattern
* section ^slicing.discriminator.path = "$this"
* section ^slicing.rules = #open
* section contains
section1 0..1 MS
* section[section1].extension contains Extension1 named abc1 0..1 MS
* section[section1].extension[abc1].valueString = "level 1 child works"
* section[section1].section ^slicing.discriminator.type = #pattern
* section[section1].section ^slicing.discriminator.path = "$this"
* section[section1].section ^slicing.rules = #open
* section[section1].section contains
section2 0..1 MS
* section[section1].section[section2].extension contains Extension1 named abc2 0..1 MS
//Throws error
* section[section1].section[section2].extension[abc2].valueString = "level 2 child fails"stacktrace from repo:
Picked up JAVA_TOOL_OPTIONS: -Dfile.encoding=UTF-8
FHIR IG Publisher Version 1.5.5 (Git# 3db07b9b9942). Built 2023-11-24T21:11:01.665Z (13 days old)
Detected Java version: 17.0.2
...
Generating Snapshots (00:00.002 / 01:03.000, 528Mb)
Exception in thread "main" java.lang.StackOverflowError
at org.hl7.fhir.r5.conformance.profile.ProfileUtilities.checkExtensionDoco(ProfileUtilities.java:1725)
at org.hl7.fhir.r5.conformance.profile.ProfileUtilities.updateFromDefinition(ProfileUtilities.java:2358)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBaseDefault(ProfilePathProcessor.java:1151)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBase(ProfilePathProcessor.java:988)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPaths(ProfilePathProcessor.java:184)
...varying stacktraces from example fsh above:
Generating Snapshots (00:00.002 / 01:02.161, 741Mb)
Exception in thread "main" java.lang.StackOverflowError
at java.base/java.lang.String.startsWith(String.java:2297)
at org.hl7.fhir.r5.context.BaseWorkerContext.fetchResourceWithExceptionByVersion(BaseWorkerContext.java:1835)
at org.hl7.fhir.r5.context.BaseWorkerContext.fetchResourceWithException(BaseWorkerContext.java:1827)
at org.hl7.fhir.r5.context.BaseWorkerContext.fetchResource(BaseWorkerContext.java:2328)
at org.hl7.fhir.r5.context.SimpleWorkerContext.fetchResource(SimpleWorkerContext.java:708)
at org.hl7.fhir.r5.conformance.profile.ProfileUtilities.updateFromDefinition(ProfileUtilities.java:2390)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBaseDefault(ProfilePathProcessor.java:1151)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBase(ProfilePathProcessor.java:988)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPaths(ProfilePathProcessor.java:184)
...Generating Snapshots (00:00.001 / 01:02.023, 408Mb)
Exception in thread "main" java.lang.StackOverflowError
at org.hl7.fhir.r5.conformance.profile.ProfileUtilities.checkExtensionDoco(ProfileUtilities.java:1725)
at org.hl7.fhir.r5.conformance.profile.ProfileUtilities.updateFromDefinition(ProfileUtilities.java:2358)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBaseDefault(ProfilePathProcessor.java:1151)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBase(ProfilePathProcessor.java:988)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPaths(ProfilePathProcessor.java:184)
...Generating Snapshots (00:00.001 / 01:04.250, 616Mb)
Exception in thread "main" java.lang.StackOverflowError
at java.base/java.util.HashMap.getNode(HashMap.java:570)
at java.base/java.util.HashMap.containsKey(HashMap.java:594)
at org.hl7.fhir.r5.context.CanonicalResourceManager.get(CanonicalResourceManager.java:516)
at org.hl7.fhir.r5.context.CanonicalResourceManager.get(CanonicalResourceManager.java:525)
at org.hl7.fhir.r5.context.BaseWorkerContext.fetchResourceWithExceptionByVersion(BaseWorkerContext.java:1962)
at org.hl7.fhir.r5.context.BaseWorkerContext.fetchResourceWithException(BaseWorkerContext.java:1827)
at org.hl7.fhir.r5.context.BaseWorkerContext.fetchResource(BaseWorkerContext.java:2328)
at org.hl7.fhir.r5.context.SimpleWorkerContext.fetchResource(SimpleWorkerContext.java:708)
at org.hl7.fhir.r5.conformance.profile.ProfileUtilities.updateFromDefinition(ProfileUtilities.java:2390)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBaseDefault(ProfilePathProcessor.java:1151)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBase(ProfilePathProcessor.java:988)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPaths(ProfilePathProcessor.java:184)
...Generating Snapshots (00:00.003 / 01:05.602, 621Mb)
Exception in thread "main" java.lang.StackOverflowError
at org.hl7.fhir.r5.model.Base.setUserData(Base.java:164)
at org.hl7.fhir.r5.conformance.profile.ProfileUtilities.updateFromDefinition(ProfileUtilities.java:2352)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBaseDefault(ProfilePathProcessor.java:1151)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBase(ProfilePathProcessor.java:988)
at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPaths(ProfilePathProcessor.java:184)
...I can't reproduce the error with 1.5.6, though I don't think I changed anything of relevance. Can anyone provide a repository that demonstrates the problem?
gauravgso
commented
8 months ago I am getting the same error. The packages at https://simplifier.net/packages (https://packages.fhir.org/) hl7.fhir.r4.core 4.0.1 does not match with the one present at https://hl7.org/fhir/R4/downloads.html which was causing the error.
The one from package.fhir.org does not work.
When adding an extension to a subsection of a composition an error or throws by _genonce.sh when its value is set.
Generating Snapshots (01:14.645) Exception in thread "main" java.lang.StackOverflowError at org.hl7.fhir.r5.model.DataType.copyValues(DataType.java:72) at org.hl7.fhir.r5.model.BackboneType.copyValues(BackboneType.java:205) at org.hl7.fhir.r5.model.ElementDefinition.copyValues(ElementDefinition.java:12566) at org.hl7.fhir.r5.model.ElementDefinition.copy(ElementDefinition.java:12561) at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processSimplePathWithEmptyDiffMatches(ProfilePathProcessor.java:724) at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processSimplePath(ProfilePathProcessor.java:219) at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPaths(ProfilePathProcessor.java:171) at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBaseDefault(ProfilePathProcessor.java:1067) at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBase(ProfilePathProcessor.java:864) at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPaths(ProfilePathProcessor.java:179) at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBaseDefault(ProfilePathProcessor.java:1067) at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBase(ProfilePathProcessor.java:864) at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPaths(ProfilePathProcessor.java:179) at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBaseDefault(ProfilePathProcessor.java:1067) at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPathWithSlicedBase(ProfilePathProcessor.java:864) at org.hl7.fhir.r5.conformance.profile.ProfilePathProcessor.processPaths(ProfilePathProcessor.java:179)fsh: `// Extension Extension: Extension1 Id: Extension-1 Title: "Title" Description: "Desc"
//target for extensions valueCanonical Profile: CompositionOutput Parent: Composition Id: composition2
//Throws error Profile: CompositionOutput2 Parent: Composition Id: composition Title: "Composition" Description: "A profile on the Composition resource"
section ^slicing.discriminator.type = #pattern
section ^slicing.discriminator.path = "$this"
section ^slicing.rules = #open
section contains section1 0..1 MS
section[section1].section ^slicing.discriminator.type = #pattern
section[section1].section ^slicing.discriminator.path = "$this"
section[section1].section ^slicing.rules = #open
section[section1].section contains section2 0..1 MS
section[section1].section[section2].extension contains Extension1 named abc 0..1 MS
section[section1].section[section2].extension[abc].valueCanonical = Canonical(CompositionOutput) `