INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/Nyangoto2/starter-fhir-ig --branch kenya-training repo DEBUG:root:Time to deadline 35879.997096 seconds Cloning into 'repo'... DEBUG:root:running: wget -q https://github.com/HL7/fhir-ig-publisher/releases/latest/download/publisher.jar -O publisher.jar DEBUG:root:Time to deadline 35879.68006 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35878.410147 seconds npm WARN deprecated inflight@1.0.6: This module is not supported, and leaks memory. Do not use it. Check out lru-cache if you want a good and tested way to coalesce async requests by a key value, which is much more comprehensive and powerful. npm WARN deprecated rimraf@2.6.3: Rimraf versions prior to v4 are no longer supported npm WARN deprecated glob@7.2.3: Glob versions prior to v9 are no longer supported added 120 packages in 5s 8 packages are looking for funding run `npm fund` for details npm notice npm notice New major version of npm available! 9.8.1 -> 10.8.3 npm notice Changelog: npm notice Run `npm install -g npm@10.8.3` to update! npm notice DEBUG:root:running: java -Xms19000m -Xmx19000m -jar ../publisher.jar -ig ig.json -api-key-file /etc/ig.builder.keyfile.ini -fhir-settings /etc/fhir-settings.json -auto-ig-build -tx http://tx.fhir.org -target https://build.fhir.org/ig/Nyangoto2/starter-fhir-ig/ -out /scratch/repo DEBUG:root:Time to deadline 35873.422704 seconds FHIR IG Publisher Version 1.6.27 (Git# d4b1190dcc36). Built 2024-09-25T22:48:07.670Z (13 hours old) Detected Java version: 21-ea from /usr/local/openjdk-21 on Linux/amd64 (64bit). 19008MB available dir = /scratch/repo, path = /usr/local/openjdk-21/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin Parameters: -ig ig.json -api-key-file /etc/ig.builder.keyfile.ini -fhir-settings /etc/fhir-settings.json -auto-ig-build -tx http://tx.fhir.org -target https://build.fhir.org/ig/Nyangoto2/starter-fhir-ig/ -out /scratch/repo Start Clock @ Thursday, September 26, 2024, 12:25:50 PM Coordinated Universal Time (2024-09-26T12:25:50Z) Build FHIR IG from /scratch/repo (00:00.031 / 00:00.032, 89Mb) API keys loaded from /etc/fhir-settings.json (00:00.004 / 00:00.036, 89Mb) Package Cache: /var/lib/.fhir/packages (00:00.003 / 00:00.039, 89Mb) Run Sushi on /scratch/repo (00:00.006 / 00:00.046, 89Mb) Sushi: info Running SUSHI v3.11.1 (implements FHIR Shorthand specification v3.0.0-ballot) (00:00.682 / 00:00.728, 97Mb) Sushi: info Arguments: (00:00.000 / 00:00.729, 97Mb) Sushi: info --require-latest (00:00.000 / 00:00.729, 97Mb) Sushi: info --out /scratch/repo (00:00.000 / 00:00.729, 97Mb) Sushi: info /scratch/repo (00:00.000 / 00:00.730, 97Mb) Sushi: info Using configuration file: /scratch/repo/sushi-config.yaml (00:00.695 / 00:01.426, 97Mb) Sushi: info Importing FSH text... (00:00.171 / 00:01.597, 97Mb) Sushi: info Preprocessed 6 documents with 1 aliases. (00:00.119 / 00:01.717, 97Mb) Sushi: info Imported 4 definitions and 1 instances. (00:00.012 / 00:01.729, 97Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.uv.tools#current... (00:00.001 / 00:01.730, 97Mb) Sushi: info Did not find hl7.fhir.uv.tools#current in /home/fhiruser/.fhir/packages. (00:00.031 / 00:01.762, 97Mb) Sushi: info Downloading hl7.fhir.uv.tools#current... https://build.fhir.org/ig/FHIR/fhir-tools-ig/branches/master/package.tgz (00:00.126 / 00:01.889, 97Mb) Sushi: info Downloaded hl7.fhir.uv.tools#current (00:00.014 / 00:01.903, 97Mb) Sushi: info Loaded package hl7.fhir.uv.tools#current (00:00.104 / 00:02.007, 97Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.terminology.r4#6.0.2... (00:00.430 / 00:02.438, 97Mb) Sushi: info Did not find hl7.terminology.r4#6.0.2 in /home/fhiruser/.fhir/packages. (00:00.033 / 00:02.471, 97Mb) Sushi: info Downloading hl7.terminology.r4#6.0.2... https://packages.fhir.org/hl7.terminology.r4/6.0.2 (00:00.000 / 00:02.472, 97Mb) Sushi: info Downloaded hl7.terminology.r4#6.0.2 (00:01.733 / 00:04.206, 97Mb) Sushi: info Loaded package hl7.terminology.r4#6.0.2 (00:02.184 / 00:06.390, 97Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.uv.extensions.r4#5.1.0... (00:00.431 / 00:06.821, 97Mb) Sushi: info Did not find hl7.fhir.uv.extensions.r4#5.1.0 in /home/fhiruser/.fhir/packages. (00:00.522 / 00:07.343, 97Mb) Sushi: info Downloading hl7.fhir.uv.extensions.r4#5.1.0... https://packages.fhir.org/hl7.fhir.uv.extensions.r4/5.1.0 (00:00.000 / 00:07.344, 97Mb) Sushi: info Downloaded hl7.fhir.uv.extensions.r4#5.1.0 (00:01.844 / 00:09.189, 97Mb) Sushi: info Loaded package hl7.fhir.uv.extensions.r4#5.1.0 (00:01.427 / 00:10.616, 97Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.r4.core#4.0.1... (00:00.000 / 00:10.617, 97Mb) Sushi: info Did not find hl7.fhir.r4.core#4.0.1 in /home/fhiruser/.fhir/packages. (00:00.741 / 00:11.358, 97Mb) Sushi: info Downloading hl7.fhir.r4.core#4.0.1... https://packages.fhir.org/hl7.fhir.r4.core/4.0.1 (00:00.000 / 00:11.358, 97Mb) Sushi: info Downloaded hl7.fhir.r4.core#4.0.1 (00:02.809 / 00:14.168, 97Mb) Sushi: info Loaded package hl7.fhir.r4.core#4.0.1 (00:02.869 / 00:17.037, 97Mb) Sushi: info Found 6 files in input/* resource folders that were neither XML nor JSON. These files were not processed as resources by SUSHI. To see the unprocessed files in the logs, run SUSHI with the "--log-level debug" flag. (00:00.070 / 00:17.107, 97Mb) Sushi: info Converting FSH to FHIR resources... (00:00.003 / 00:17.110, 97Mb) Sushi: error Parent PatientUvIps not found for KenyaPatient (00:00.007 / 00:17.118, 97Mb) Sushi: File: /scratch/repo/input/fsh/profiles.fsh (00:00.000 / 00:17.118, 97Mb) Sushi: Line: 1 - 31 (00:00.000 / 00:17.119, 97Mb) Sushi: info Converted 2 FHIR StructureDefinitions. (00:00.076 / 00:17.195, 97Mb) Sushi: info Converted 1 FHIR CodeSystems. (00:00.026 / 00:17.221, 97Mb) Sushi: info Converted 1 FHIR ValueSets. (00:00.036 / 00:17.258, 97Mb) Sushi: error InstanceOf KenyaPatient not found for KenyaPatientExample (00:00.000 / 00:17.259, 97Mb) Sushi: File: /scratch/repo/input/fsh/examples.fsh (00:00.000 / 00:17.259, 97Mb) Sushi: Line: 1 - 27 (00:00.000 / 00:17.260, 97Mb) Sushi: info Converted 1 FHIR instances. (00:00.000 / 00:17.260, 97Mb) Sushi: info Exporting FHIR resources as JSON... (00:00.000 / 00:17.260, 97Mb) Sushi: info Exported 3 FHIR resources as JSON. (00:00.008 / 00:17.269, 97Mb) Sushi: info Assembling Implementation Guide sources... (00:00.001 / 00:17.271, 97Mb) Sushi: info Generated ImplementationGuide-kenya-training-kwamboka.json (00:00.011 / 00:17.283, 97Mb) Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:00.000 / 00:17.283, 97Mb) Sushi: ========================= SUSHI RESULTS =========================== (00:00.001 / 00:17.285, 97Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:17.285, 97Mb) Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:00.000 / 00:17.285, 97Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:17.285, 97Mb) Sushi: | | 0 | 1 | 0 | 0 | | (00:00.000 / 00:17.286, 97Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:17.286, 97Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:17.286, 97Mb) Sushi: | | ValueSets | CodeSystems | Instances | | (00:00.000 / 00:17.286, 97Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:17.287, 97Mb) Sushi: | | 1 | 1 | 0 | | (00:00.000 / 00:17.287, 97Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:17.287, 97Mb) Sushi: | | (00:00.000 / 00:17.287, 97Mb) Sushi: =================================================================== (00:00.000 / 00:17.288, 97Mb) Sushi: | You're in deep water now. 2 Errors 0 Warnings | (00:00.000 / 00:17.288, 97Mb) Sushi: =================================================================== (00:00.000 / 00:17.288, 97Mb) Sushi couldn't be run. Complete output from running Sushi : (00:00.036 / 00:17.325, 97Mb) Note: Check that Sushi is installed correctly ("npm install -g fsh-sushi". On windows, get npm from https://www.npmjs.com/get-npm) (00:00.000 / 00:17.325, 97Mb) Exception: Process exited with an error: 2 (Exit value: 2) (00:00.000 / 00:17.325, 97Mb) Publishing Content Failed: Process exited with an error: 2 (Exit value: 2) (00:00.000 / 00:17.325, 97Mb) (00:00.000 / 00:17.326, 97Mb) Use -? to get command line help (00:00.000 / 00:17.326, 97Mb) (00:00.000 / 00:17.326, 97Mb) Stack Dump (for debugging): (00:00.000 / 00:17.326, 97Mb) org.apache.commons.exec.ExecuteException: Process exited with an error: 2 (Exit value: 2) 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.FSHRunner.runFsh(FSHRunner.java:89) at org.hl7.fhir.igtools.publisher.Publisher.initialize(Publisher.java:2600) at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:1039) at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:13301)