Stream: implementers
Topic: IG Publisher Tool throws error on window
Satyaki Bhargava (Apr 04 2018 at 12:50):
IG publisher tool is throwing error when ran on window:
Load Configuration from C:\Users\320008152\Downloads\igpack\ig-template\test-ig.json (00.0000sec)
Root directory: C:\Users\320008152\Downloads\igpack\ig-template (00.0060sec)
Terminology Cache is at C:\Users\320008152\fhircache. 1 files in cache (00.0085sec)
Load Validation Pack (internal) (00.0085sec)
Definitions 3.0.1-11917 (12.0494sec)
Connect to Terminology Server at http://tx.fhir.org/r3 (12.0495sec)
Error : Error sending Http Request: Connection to http://tx.fhir.org refused
org.hl7.fhir.dstu3.utils.client.ClientUtils.sendRequest(ClientUtils.java:256)
org.hl7.fhir.dstu3.utils.client.ClientUtils.issueResourceRequest(ClientUtils.java:177)
org.hl7.fhir.dstu3.utils.client.ClientUtils.issueResourceRequest(ClientUtils.java:161)
org.hl7.fhir.dstu3.utils.client.ClientUtils.issueResourceRequest(ClientUtils.java:152)
org.hl7.fhir.dstu3.utils.client.ClientUtils.issueGetResourceRequest(ClientUtils.java:99)
org.hl7.fhir.dstu3.utils.client.FHIRToolingClient.getCapabilitiesStatementQuick(FHIRToolingClient.java:169)
org.hl7.fhir.dstu3.context.SimpleWorkerContext.connectToTSServer(SimpleWorkerContext.java:161)
org.hl7.fhir.igtools.publisher.Publisher.initialize(Publisher.java:754)
org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:299)
org.hl7.fhir.igtools.ui.IGPublisherFrame$BackgroundPublisherTask.doInBackground(IGPublisherFrame.java:250)
org.hl7.fhir.igtools.ui.IGPublisherFrame$BackgroundPublisherTask.doInBackground(IGPublisherFrame.java:1)
java.desktop/javax.swing.SwingWorker$1.call(Unknown Source)
java.base/java.util.concurrent.FutureTask.run(Unknown Source)
java.desktop/javax.swing.SwingWorker.run(Unknown Source)
java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
java.base/java.lang.Thread.run(Unknown Source)
Can anyone please let me know, how to fix this error?
Grahame Grieve (Apr 04 2018 at 13:09):
try again - the terminology server is down
Grahame Grieve (Apr 04 2018 at 13:09):
back up now
Satyaki Bhargava (Apr 04 2018 at 15:31):
@Grahame Grieve : Thank for your reply, I tried again, but get the same error. When I tried through command prompt I get different error:
C:\Users\320008152\Downloads\igpub>java -jar org.hl7.fhir.igpublisher.jar -ig ig.json -tx n/a
FHIR Implementation Guide Publisher (3.0.1-11916) @ Wednesday, April 4, 2018, 7:31:20 PM
Detected Java version: 9.0.4 from C:\Program Files\Java\jre-9.0.4 on amd64 (64bit). 2020MB available
Load Configuration from C:\Users\320008152\Downloads\igpub\ig.json (00.0000sec)
File log: C:\Users\320008~1\AppData\Local\Temp\fhir-ig-publisher-tmp.log
Root directory: C:\Users\320008152\Downloads\igpub (00.0066sec)
Terminology Cache is at C:\Users\320008152\fhircache. 1 files in cache (00.0088sec)
Load Validation Pack (internal) (00.0092sec)
Definitions 3.0.1-11917 (12.0594sec)
Connect to Terminology Server at n/a (12.0599sec)
WARNING: Running without terminology server - terminology content will likely not publish correctly (12.0608sec)
Initialization complete (13.0437sec)
Load Content (13.0445sec)
Processing Conformance Resources (13.0899sec)
Generating Narratives (13.0928sec)
Validating Resources (14.0063sec)
Generating Outputs in C:\Users\320008152\Downloads\igpub\output (14.0337sec)
Generating Summary Outputs (14.0470sec)
Jekyll: 'jekyll' is not recognized as an internal or external command, (14.0711sec)
Jekyll: operable program or batch file. (14.0714sec)
Complete output from Jekyll: operable program or batch file.
internal or external command,
(14.0718sec)
Publishing Content Failed: Process exited with an error: 1 (Exit value: 1) (14.0723sec)
(14.0727sec)
Use -? to get command line help (14.0729sec)
(14.0736sec)
Stack Dump (for debugging): (14.0741sec)
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:2305)
at org.hl7.fhir.igtools.publisher.Publisher.runTool(Publisher.java:2229)
at org.hl7.fhir.igtools.publisher.Publisher.generate(Publisher.java:1977)
at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:316)
at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:3589)
Lloyd McKenzie (Apr 04 2018 at 15:35):
That's because you haven't installed Jekyll yet - please follow the IG Publisher instructions from the wiki: http://wiki.hl7.org/index.php?title=IG_Publisher_Documentation
Satyaki Bhargava (Apr 04 2018 at 15:44):
That's because you haven't installed Jekyll yet - please follow the IG Publisher instructions from the wiki: http://wiki.hl7.org/index.php?title=IG_Publisher_Documentation
I tried installing Jekyll on windows 10, but it never worked for me. So then I moved to docker solution. There I am able to get Jekyll installed. However now I get new error:
/usr/src/ig-publisher # java -jar /usr/src/ig-publisher/publisher.jar -ig /usr/src/input/ig.json -tx n/a -watch
FHIR Implementation Guide Publisher (3.0.1-11916) @ Wednesday, April 4, 2018 3:38:20 PM
Detected Java version: 1.8.0_151 from /usr/lib/jvm/java-1.8-openjdk/jre on amd64 (64bit). 441MB available
Load Configuration from /usr/src/input/ig.json (00.0000sec)
File log: /tmp/fhir-ig-publisher-tmp.log
Root directory: /usr/src/input (00.0036sec)
Terminology Cache is at /root/fhircache. 0 files in cache (00.0309sec)
Load Validation Pack (internal) (00.0310sec)
Definitions 3.0.1-11917 (23.0937sec)
Connect to Terminology Server at n/a (23.0938sec)
WARNING: Running without terminology server - terminology content will likely not publish correctly (23.0942sec)
Initialization complete (26.0166sec)
Load Content (26.0166sec)
Processing Conformance Resources (26.0357sec)
Generating Narratives (26.0370sec)
Validating Resources (26.0467sec)
Generating Outputs in /usr/src/input/output (26.0514sec)
Generating Summary Outputs (26.0641sec)
Jekyll: Source: /usr/src/input/temp (27.0320sec)
Jekyll: Generating... (27.0320sec)
Complete output from Jekyll: Liquid Exception: Could not locate the included file 'table-logicals.xhtml' in any of ["/usr/src/input/temp/_includes"]. Ensure it exists in one of those directories and, if it is a symlink, does not point outside your site source. in index.html (27.0881sec)
Publishing Content Failed: Process exited with an error: 1 (Exit value: 1) (27.0882sec)
(27.0884sec)
Use -? to get command line help (27.0885sec)
(27.0886sec)
Stack Dump (for debugging): (27.0887sec)
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:2307)
at org.hl7.fhir.igtools.publisher.Publisher.runTool(Publisher.java:2229)
at org.hl7.fhir.igtools.publisher.Publisher.generate(Publisher.java:1977)
at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:316)
at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:3589)
Eric Haas (Apr 04 2018 at 17:14):
this is your error:
Complete output from Jekyll: Liquid Exception: Could not locate the included file 'table-logicals.xhtml' in any of ["/usr/src/input/temp/_includes"]. Ensure it exists in one of those directories and, if it is a symlink, does not point outside your site source. in index.html (27.0881sec)
trying to include a file that does not exist. You have a page with {% include table-logicals.xhtml %} somewhere but not logical model artifacts in the IG. So this file is not generated.
Satyaki Bhargava (Apr 05 2018 at 07:02):
this is your error:
Complete output from Jekyll: Liquid Exception: Could not locate the included file 'table-logicals.xhtml' in any of ["/usr/src/input/temp/_includes"]. Ensure it exists in one of those directories and, if it is a symlink, does not point outside your site source. in index.html (27.0881sec)
trying to include a file that does not exist. You have a page with {% include table-logicals.xhtml %} somewhere but not logical model artifacts in the IG. So this file is not generated.
Hi Eric,
From where I can get file named "table-logicals.xhtml" for STU3?
Grahame Grieve (Apr 05 2018 at 07:44):
it won't be generated if your IG doesn't contain any logical models
Satyaki Bhargava (Apr 05 2018 at 09:10):
it won't be generated if your IG doesn't contain any logical models
I downloaded the whole IG Pack for STU3 from IG Publisher website. So how it is possible that it does not have any file for logical methods.
Satyaki Bhargava (Apr 05 2018 at 09:36):
it won't be generated if your IG doesn't contain any logical models
I downloaded the whole IG Pack for STU3 from IG Publisher website. So how it is possible that it does not have any file for logical methods.
I removed the entry of table-logicals.xhtml from index.html file, now output is generated but there is error on command prompt:
Jekyll: Source: /usr/src/input/temp (28.0454sec)
Jekyll: Generating... (28.0455sec)
Jekyll: done in 1.044 seconds. (29.0498sec)
Publishing Content Failed: URL Mismatch http://hl7.org/fhir/template-adhoc-ig/ImplementationGuide/ig vs http://hl7.org/fhir/ig (29.0511sec)
(29.0511sec)
Use -? to get command line help (29.0512sec)
(29.0514sec)
Stack Dump (for debugging): (29.0516sec)
java.lang.Exception: URL Mismatch http://hl7.org/fhir/template-adhoc-ig/ImplementationGuide/ig vs http://hl7.org/fhir/ig
at org.hl7.fhir.igtools.publisher.Publisher.generateZips(Publisher.java:2111)
at org.hl7.fhir.igtools.publisher.Publisher.generate(Publisher.java:1979)
at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:316)
at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:3589)
Grahame Grieve (Apr 05 2018 at 09:46):
umm. I think you should start with an empty IG that contains only an implementation guide resource, get it running on the auto-builder, and then gradually add things one at a time
Satyaki Bhargava (Apr 05 2018 at 09:48):
umm. I think you should start with an empty IG that contains only an implementation guide resource, get it running on the auto-builder, and then gradually add things one at a time
Thanks for your quick replies. Sure I will check further.
Last updated: Apr 12 2022 at 19:14 UTC
