Stream: IG creation
Topic: fsh projects
Preston Lee (Jun 11 2021 at 22:15):
We have been getting build errors on multiple projects, including the sample FSH project as generated by sushi --init. The errors always boil down to a jekyll error on not finding something it's looking for. We've tried with multiple versions of ruby and are using jekyll 4.2.0 (current). What's going on?
Generating Summary Outputs (00:14.0156)
Sending Usage Stats to Server (00:15.0351)
Jekyll: Source: /Users/preston/Developer/git/ExampleIG/temp/pages (00:16.0719)
Jekyll: Generating... (00:16.0719)
Jekyll has failed. Complete output from running Jekyll: Liquid Exception: Could not locate the included file 'StructureDefinition-MyPatient-summary-table.xhtml' in any of ["/Users/preston/Developer/git/ExampleIG/temp/pages/_includes"]. Ensure it exists in one of those directories and, if it is a symlink, (00:16.0823)
Note: Check that Jekyll is installed correctly (00:16.0824)
Publishing Content Failed: Process exited with an error: 1 (Exit value: 1) (00:16.0825)
(00:16.0825)
Use -? to get command line help (00:16.0825)
(00:16.0825)
Stack Dump (for debugging): (00:16.0826)
org.apache.commons.exec.ExecuteException: Process exited with an error: 1 (Exit value: 1)
at org.apache.commons.exec.DefaultExecutor.executeInternal(DefaultExecutor.java:404)
at org.apache.commons.exec.DefaultExecutor.execute(DefaultExecutor.java:166)
at org.apache.commons.exec.DefaultExecutor.execute(DefaultExecutor.java:153)
at org.hl7.fhir.igtools.publisher.Publisher.runJekyll(Publisher.java:5338)
at org.hl7.fhir.igtools.publisher.Publisher.runTool(Publisher.java:5244)
at org.hl7.fhir.igtools.publisher.Publisher.generate(Publisher.java:4711)
at org.hl7.fhir.igtools.publisher.Publisher.createIg(Publisher.java:858)
at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:707)
at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:7756)
Preston Lee (Jun 11 2021 at 22:17):
@Mark Kramer Could this be something sushi is doing? This is the template project throwing the error on the current publisher version. CC @Nathan Davis @Patrick Langford
Mark Kramer (Jun 11 2021 at 22:20):
I doesn’t look like SUSHI. Are you using the latest IG Pub?
Preston Lee (Jun 11 2021 at 22:22):
Yup .. that's the publisher output using the template files generated by sushi
Jose Costa Teixeira (Jun 11 2021 at 22:22):
can you paste the full log? is there any error above? look for mentions to xslt way before that.
Jose Costa Teixeira (Jun 11 2021 at 22:23):
in parallel, see if your MyPatient compiles well with sushi (use fshschool for that)
Preston Lee (Jun 11 2021 at 22:23):
Jose Costa Teixeira (Jun 11 2021 at 22:26):
nope, this isn't it
Preston Lee (Jun 11 2021 at 22:26):
I'm not seeing any obvious errors or warnings prior :-/
Jose Costa Teixeira (Jun 11 2021 at 22:26):
can you share your MyPatient sushi content?
Preston Lee (Jun 11 2021 at 22:26):
// This is a simple example of a FSH file.
// This file can be renamed, and additional FSH files can be added.
// SUSHI will look for definitions in any file using the .fsh ending.
Profile: MyPatient
Parent: Patient
* name 1..* MS
Jose Costa Teixeira (Jun 11 2021 at 22:29):
that's it?
Jose Costa Teixeira (Jun 11 2021 at 22:29):
Strange
Preston Lee (Jun 11 2021 at 22:30):
Yup. ;) We have real projects with a similar error, but this is the simplest possible project doing it and it is reproducable..
Jose Costa Teixeira (Jun 11 2021 at 22:37):
I can't reproduce it.
Mark Kramer (Jun 11 2021 at 22:37):
I would reinstall Jekyll or try a different template (in ig.ini)
Jose Costa Teixeira (Jun 11 2021 at 22:37):
i put a fsh file with that content in an empty ig and it is working well
Jose Costa Teixeira (Jun 11 2021 at 22:37):
update your publisher, see if jekyll / ruby is well installed
Jose Costa Teixeira (Jun 11 2021 at 22:39):
maybe it's something in the sushi-config.
Jose Costa Teixeira (Jun 11 2021 at 22:40):
you are using the base template. and that is fine. you may want to clear that package cache
Preston Lee (Jun 11 2021 at 22:41):
Yup, done reinstalls a few times already. @Mark Kramer if you create a completely fresh project with sushi --init (accepting all defaults), does it build for you? I literally haven't changed anything from the generated project.
Jose Costa Teixeira (Jun 11 2021 at 22:41):
the sushi you sent does build perfectly well:
Jose Costa Teixeira (Jun 11 2021 at 22:41):
https://costateixeira.github.io/testpreston/StructureDefinition-MyPatient.html
Preston Lee (Jun 11 2021 at 22:51):
Cleared package cache, same error. Also just tried on both macOS and a separate Ubuntu container with exactly the same error
Mark Kramer (Jun 11 2021 at 22:53):
Try clearing .fhir directory
Preston Lee (Jun 11 2021 at 23:01):
nope, same error
Grahame Grieve (Jun 14 2021 at 04:40):
on some systems, Jekyll error output is lost. that seems to be case for you.
Grahame Grieve (Jun 14 2021 at 04:41):
at the point that it fails, run Jekyll manually, and see if it reports any additional error message
Preston Lee (Jun 21 2021 at 18:19):
It appears to be the same error, not the jekyll installation:
jekyll build -s temp/pages
Configuration file: /Users/preston/Developer/git/ExampleIG/temp/pages/_config.yml
Source: /Users/preston/Developer/git/ExampleIG/temp/pages
Destination: /Users/preston/Developer/git/ExampleIG/_site
Incremental build: disabled. Enable with --incremental
Generating...
Liquid Exception: Could not locate the included file 'StructureDefinition-MyPatient-summary-table.xhtml' in any of ["/Users/preston/Developer/git/ExampleIG/temp/pages/_includes"]. Ensure it exists in one of those directories and, if it is a symlink, does not point outside your site source. in StructureDefinition-MyPatient.html
------------------------------------------------
Jekyll 4.2.0 Please append `--trace` to the `build` command
for any additional information or backtrace.
------------------------------------------------
/Users/preston/.rvm/gems/ruby-3.0.1/gems/jekyll-4.2.0/lib/jekyll/tags/include.rb:219:in `locate_include_file': Could not locate the included file 'StructureDefinition-MyPatient-summary-table.xhtml' in any of ["/Users/preston/Developer/git/ExampleIG/temp/pages/_includes"]. Ensure it exists in one of those directories and, if it is a symlink, does not point outside your site source. (IOError)
Preston Lee (Jun 21 2021 at 18:21):
Could it be that something in the "summary" file naming has changed? It's complaining about "StructureDefinition-MyPatient-summary-table.xhtml" being missing, but only a "StructureDefinition-MyPatient-summary.xhtml" exists.
Grahame Grieve (Jun 22 2021 at 06:05):
what template are you using? A file by that name will be generated unless the template tells the IG publisher not to generate it - so look in the config.json file for anything about "summary-table"
Last updated: Apr 12 2022 at 19:14 UTC
