FHIR Chat · Jekyll error · committers

Stream: committers

Topic: Jekyll error

David Hay (Mar 04 2019 at 23:41):

Ah - that's intersting. It does run when executing from the command line - java -jar org.hl7.fhir.igpublisher.jar -ig ig.json . - but not from the GUI...

Grahame Grieve (Mar 04 2019 at 23:41):

what are we talking about?

David Hay (Mar 04 2019 at 23:45):

The IG publisher. I cloned the aussie base and tried to run the publisher (as a prelude to creatiung NZ ones - I wanted to get experience with the publisher). Running the GUI (by double clicking on the .jar file and selecting the control file) then executing leads to the jekyll error I described. However, if I execute directly from the command line then jekyll seems to run OK. Yet to confirm that all the outputs are there - but no errors...

Grahame Grieve (Mar 04 2019 at 23:51):

ok. works for me in GUI mode. what error do you get?

David Hay (Mar 04 2019 at 23:53):

pasted above..(remember I'm a mac)

Grahame Grieve (Mar 04 2019 at 23:54):

I don't see any above?

David Hay (Mar 05 2019 at 00:03):

here you go (pasted from the GUI window):

Generating Summary Outputs                                                       (00:01:02.0487sec)
Jekyll has failed - not installed (correcty?). Complete output from running Jekyll:  (00:01:03.0231sec)
Error : Cannot run program "jekyll" (in directory "/Users/davidhay/aussietest/aubase/temp"): error=2, No such file or directory
   java.base/java.lang.ProcessBuilder.start(ProcessBuilder.java:1128)

(It's not critical as I can easily work from the command line)...

David Hay (Mar 05 2019 at 00:05):

To be clear - everything seems to run in the GUI - lots of messages - it just stops after a minute or so with the message about running jekyll...

Grahame Grieve (Mar 05 2019 at 00:05):

what's your system path?

David Hay (Mar 05 2019 at 00:06):

sorta sounds like it's actually trying to execute jekyll from the temp folder...

Grahame Grieve (Mar 05 2019 at 00:19):

I'll give you a version with more debugging to see if that gives us a clue

David Hay (Mar 05 2019 at 00:21):

/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin

Grahame Grieve (Mar 05 2019 at 00:22):

that feels wrong. but we'll see

David Hay (Mar 05 2019 at 00:23):

jekyll is in /usr/local/bin

David Hay (Mar 05 2019 at 00:24):

so looks like the GUI isn't picking up the path ?

Grahame Grieve (Mar 05 2019 at 00:42):

well, it has to... but I don't know. next version will dump variables

David Hay (Mar 05 2019 at 00:47):

Anyway - at least I can generate IG's! (Or at least I will be able to once I've cleared all the issues :) )

David Hay (Mar 05 2019 at 00:50):

Not sure if it's relevant - but I am getting a warning:

Validating Resources                                                             (11.0675sec)
Generating Outputs in /Users/davidhay/Dropbox/contracting/MOH/ig/output          (11.0679sec)
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.apache.poi.util.DocumentHelper (file:/Users/davidhay/Dropbox/contracting/MOH/ig/org.hl7.fhir.igpublisher.jar) to method com.sun.org.apache.xerces.internal.util.SecurityManager.setEntityExpansionLimit(int)
WARNING: Please consider reporting this to the maintainers of org.apache.poi.util.DocumentHelper
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
Generating Summary Outputs                                                       (16.0855sec)

Grahame Grieve (Mar 05 2019 at 00:51):

I've never seen that before. POI must have a special (if user.category = kiwi) mode

Grahame Grieve (Mar 05 2019 at 01:08):

ok get the latest version, an then run it twice, once in GUI mode and one in command line. In both modes, it will dump a whole pile of variables before running jekyll. Send me the variables and I'll compare them (PM me the variables)

Grahame Grieve (Mar 05 2019 at 01:42):

jekyll is in /usr/local/bin

the system path: /usr/bin:/bin:/usr/sbin:/sbin
the command line path: /usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin

Grahame Grieve (Mar 05 2019 at 01:42):

that's the source of your probelm

David Hay (Mar 05 2019 at 01:46):

well, we are special over on this side of the ditch...

David Hay (Mar 05 2019 at 01:49):

(deleted)

David Hay (Mar 05 2019 at 01:56):

tx for finding the issue btw...

Grahame Grieve (Mar 05 2019 at 02:01):

np

Bryn Rhodes (Mar 05 2019 at 22:10):

Interestingly, I'm now getting this error on the auto-build, though the IG builds locally.

Bryn Rhodes (Mar 05 2019 at 22:11):

http://build.fhir.org/ig/cqframework/cqf-measures/build.log

Grahame Grieve (Mar 06 2019 at 01:32):

that's a different error:
Could not locate the included file 'StructureDefinition-cohort-measure-cqfm-dict.xhtml'

Bryn Rhodes (Mar 06 2019 at 01:49):

I've verified that it builds locally with the latest version of the publisher, and verified that that file is in the temp/_includes directory on my local.

Grahame Grieve (Mar 06 2019 at 02:32):

it didn't build locally for you - if you were using the latest IG Publisher. I've committed a series of fixes.

Bryn Rhodes (Mar 06 2019 at 03:49):

You're right, I accidentally refreshed from hl7.org/fhir, instead of from build.fhir.org

Last updated: Apr 12 2022 at 19:14 UTC