Stream: IG creation
Topic: FHIR Publisher Hanging
Kurt Allen (Mar 02 2021 at 17:38):
I am having some problems getting the fhir publisher to complete.
I just returned from my Covid vacation and had to reload my computer; I reinstalled ruby, jekyll, IG Publisher etc.
I tried to run publisher on a project that worked previously and it hangs on
Jekyll: Generating.
I do get an error that publisher can't find a JIRA file.
[get] Error opening connection java.io.FileNotFoundException: https://github.com/HL7/JIRA-Spec-Artifacts/raw/master/xml/FHIR-us-breast-radiology.xml
Would that cause jekyll to hang?
Any ideas?
[From log file]
onGenerate.jira.setup:
....
[get] Error opening connection java.io.FileNotFoundException: https://github.com/HL7/JIRA-Spec-Artifacts/raw/master/xml/FHIR-us-breast-radiology.xml
[get] Error opening connection java.io.FileNotFoundException: https://github.com/HL7/JIRA-Spec-Artifacts/raw/master/xml/FHIR-us-breast-radiology.xml
[get] Error opening connection java.io.FileNotFoundException: https://github.com/HL7/JIRA-Spec-Artifacts/raw/master/xml/FHIR-us-breast-radiology.xml
[get] Can't get https://github.com/HL7/JIRA-Spec-Artifacts/raw/master/xml/FHIR-us-breast-radiology.xml to C:\Development\HL7\BreastRadiologyProfilesV3\Projects\build\input-cache\jiraspec.xml
onGenerate.jira.generate:
onGenerate.jira.check:
onGenerate.jira.skip-offline:
onGenerate.jira.skip-missing:
onGenerate.jira:
onGenerate.extend:
onGenerate:
Generating Summary Outputs (02:53.0372)
Sending Usage Stats to Server (02:59.0050)
Memory (MB): Use = 4804, Free = 1771, Total = 6576, Max =7259
Reclaiming memory...
Memory (MB): Use = 3252, Free = 2997, Total = 6250, Max =7259
Jekyll: Source: C:/Development/HL7/BreastRadiologyProfilesV3/Projects/build/temp/pages (03:09.0775)
Jekyll: Generating... (03:09.0776)
[ Hangs here indefinately ]
David Pyke (Mar 02 2021 at 17:50):
That file doesn't exist in that repo. You'll need to update your code to point to the correct file. likely https://github.com/HL7/JIRA-Spec-Artifacts/blob/master/xml/FHIR-us-breastcancerradiology.xml
Kurt Allen (Mar 02 2021 at 18:19):
Thx @David Pyke
I had previously (October, 2019) pushed FHIR-us-breast-radiology.xml to JIRA-Spec-Artifacts\xml, but it appears to have gone AWOL. I guess I will have to track down what happened there...
I was also surprised at the error message, as it references a directory in GitHub that doesn't exist (JIRA-Spec-Artifacts/raw/master/xml) - hopefully that is only the error message.
Jean Duteau (Mar 02 2021 at 18:33):
@Kurt Allen before you go and try and fix it, please reach out to @Melva Peters and @Lloyd McKenzie . We had to do a lot of cleanup to your project as you had multiple JIRA artifact files and multiple JIRA project names.
Melva Peters (Mar 02 2021 at 18:50):
@Kurt Allen please contact me before you do anything so we can help you get the correct content in place
Lloyd McKenzie (Mar 02 2021 at 18:57):
Note that, while addressing the Jira file issue is important, it's unlikely related to the hanging. Jekyll doesn't use the Jira file at all, so there's something else going on there...
Kurt Allen (Mar 02 2021 at 19:14):
@Lloyd McKenzie Any suggestions on debugging this?
@Melva Peters I will contact you offline.
Lloyd McKenzie (Mar 02 2021 at 19:32):
Jekyll is a third-party process. @Grahame Grieve has a bit of experience debugging with it. How long have you left it to run? What's your memory and processor doing? It might be you're memory bound and it's just really slow?
Lloyd McKenzie (Mar 02 2021 at 19:33):
You could monitor the output folder and see what files exist and what the last file successfully created is
Grahame Grieve (Mar 02 2021 at 19:45):
yes. my immediate take is that Jekyll can't start, and for some reason, the system process that launched it is showing an error you can't see and not terminating. So debugging this is around getting the start conditions for ruby and jekyll all sorted.
Grahame Grieve (Mar 02 2021 at 19:45):
at the point it is humg, you can run jekyll yourself from the command line on the temp folder
Kurt Allen (Mar 02 2021 at 22:50):
@Lloyd McKenzie I let it run for an hour, and in the past it only took 5-10 minutes.
When it gets to the 'Jekyll: Generating ...' system cpu goes to 0, memory at 6694.3 mb (48%).
Windows task monitor shows ruby started as a sub process of the command shell, but no Jekyll.
I don't think it is a memory issue
When I look at the build/output directory, it is empty. There is a folder called .jekyll-cache under temp that is only a couple kb long, so I agree that Jekyll is probably not starting.
I can run jekyll -v and get a valid response so I know that Jekyll is installed.
When go into the temp dir and try running 'jekyll -s pages build" I get
fatal: 'jekyll build' could not be found ...
@Grahame Grieve What is the command line to run Jekyll? Is it jekyll -s pages build' or 'jekyll -s pages compose'?
I just reinstalled everything after a clean os reinstall, so I am wondering if there is a problem with the newest versions of ruby/jekyll et all?
These are the versions:
ruby 2.7.2
jekyll 4.2
Many thanks for your time!
Grahame Grieve (Mar 02 2021 at 23:02):
When running Jekyll, the working directory is the temp dir, and the command is
jekyll build --destination {{output}}
where output is the folder the generated content is going into.
on windows, the command is prefixed with cmd /C
Grahame Grieve (Mar 02 2021 at 23:03):
'jekyll build' could not be found ...
That's what I would expect from what you described. Jekyll isn't getting started. System path issue?
Kurt Allen (Mar 03 2021 at 02:13):
I had to use the modified command line:
jekyll build --source pages --destination c:\temp\xxyyz
This gave me the error
jekyll-4.2.0/lib/jekyll/tags/include.rb:219:in `locate_include_file': Could not locate the included file 'menu.xml' in any of ["C:/Development/HL7/BreastRadiologyProfilesV3/Projects/build/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)
This looks like a FSH integration issue. I upgraded to the latest version of FSH and it changed the output directory structure. I will need to track down what I did wrong.
Is there a reason that publisher can not output an error message like this from Jekyll?
Many thanks for the pointers.
Grahame Grieve (Mar 03 2021 at 03:24):
Is there a reason that publisher can not output an error message like this from Jekyll?
I certainly expect that it would; this is a normal kind of error to be displayed. The publisher part is simple: output anything unexpected to the log, and wait for the process to finish.
Keith Boone (Jun 09 2021 at 15:04):
I've seen something like this before. The best I could figure out then is that the Jekyll process never finishes because it's waiting for some include or other file to be generated. I wish there was a way to figure out what file it's looking for because I'm having the same problem right now.
Janaka Peiris (Jun 25 2021 at 05:53):
I too had this Jekyll hanging issue, but did not see any errors in output. The only way to figure out was by debugging through the IG Generator Java project. More info on that in this thread
Last updated: Apr 12 2022 at 19:14 UTC
