INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/winnie-abuor/FHIR --branch master repo DEBUG:root:Time to deadline 35879.998044 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 35879.580252 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35878.510523 seconds 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 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. added 140 packages in 6s 14 packages are looking for funding run `npm fund` for details npm notice npm notice New major version of npm available! 9.8.1 -> 11.6.1 npm notice Changelog: npm notice Run `npm install -g npm@11.6.1` 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/winnie-abuor/FHIR/ -out /scratch/repo DEBUG:root:Time to deadline 35872.154504 seconds FHIR IG Publisher Version 2.0.17 (Git# 98facbadd305). Built 2025-09-09T06:53:45.198Z (17 days 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/winnie-abuor/FHIR/ -out /scratch/repo Character encoding = UTF-8 / UTF-8 Start Clock @ Friday, September 26, 2025, 9:51:45 AM Coordinated Universal Time (2025-09-26T09:51:45Z) Build FHIR IG from /scratch/repo (00:00.029 / 00:00.030, 97Mb) API keys loaded from /etc/fhir-settings.json (00:00.003 / 00:00.033, 97Mb) Package Cache: /var/lib/.fhir/packages (00:00.003 / 00:00.036, 97Mb) Run Sushi on /scratch/repo (00:00.006 / 00:00.043, 97Mb) Sushi: info Running SUSHI v3.16.5 (implements FHIR Shorthand specification v3.0.0) (00:00.737 / 00:00.780, 113Mb) Sushi: info Arguments: (00:00.000 / 00:00.781, 113Mb) Sushi: info --require-latest (00:00.000 / 00:00.781, 113Mb) Sushi: info --out /scratch/repo (00:00.000 / 00:00.781, 113Mb) Sushi: info /scratch/repo (00:00.000 / 00:00.782, 113Mb) Sushi: info Using configuration file: /scratch/repo/sushi-config.yaml (00:00.679 / 00:01.462, 113Mb) Sushi: warn Configuration property dependencies has a value with an unexpected type. (00:00.161 / 00:01.623, 113Mb) Sushi: info Importing FSH text... (00:00.000 / 00:01.623, 113Mb) Sushi: info Preprocessed 10 documents with 6 aliases. (00:00.254 / 00:01.877, 113Mb) Sushi: info Imported 16 definitions and 6 instances. (00:00.019 / 00:01.897, 113Mb) Sushi: info Resolved hl7.fhir.uv.tools.r5#latest to concrete version 0.8.0 (00:00.792 / 00:02.689, 113Mb) Sushi: info Attempting to download hl7.fhir.uv.tools.r5#0.8.0 from https://packages.fhir.org/hl7.fhir.uv.tools.r5/0.8.0 (00:00.001 / 00:02.691, 113Mb) Sushi: info Downloaded hl7.fhir.uv.tools.r5#0.8.0 (00:00.935 / 00:03.626, 113Mb) Sushi: info Cached hl7.fhir.uv.tools.r5#0.8.0 to /home/fhiruser/.fhir/packages/hl7.fhir.uv.tools.r5#0.8.0 (00:00.003 / 00:03.629, 113Mb) Sushi: info Loaded hl7.fhir.uv.tools.r5#0.8.0 with 107 resources (00:00.102 / 00:03.732, 113Mb) Sushi: info Resolved hl7.terminology.r5#latest to concrete version 6.5.0 (00:00.479 / 00:04.212, 113Mb) Sushi: info Attempting to download hl7.terminology.r5#6.5.0 from https://packages.fhir.org/hl7.terminology.r5/6.5.0 (00:00.000 / 00:04.213, 113Mb) Sushi: info Downloaded hl7.terminology.r5#6.5.0 (00:02.927 / 00:07.140, 113Mb) Sushi: info Cached hl7.terminology.r5#6.5.0 to /home/fhiruser/.fhir/packages/hl7.terminology.r5#6.5.0 (00:00.002 / 00:07.142, 113Mb) Sushi: info Loaded hl7.terminology.r5#6.5.0 with 4392 resources (00:01.777 / 00:08.920, 113Mb) Sushi: info Resolved hl7.fhir.uv.extensions.r5#latest to concrete version 5.2.0 (00:00.472 / 00:09.392, 113Mb) Sushi: info Attempting to download hl7.fhir.uv.extensions.r5#5.2.0 from https://packages.fhir.org/hl7.fhir.uv.extensions.r5/5.2.0 (00:00.000 / 00:09.392, 113Mb) Sushi: info Downloaded hl7.fhir.uv.extensions.r5#5.2.0 (00:01.476 / 00:10.868, 113Mb) Sushi: info Cached hl7.fhir.uv.extensions.r5#5.2.0 to /home/fhiruser/.fhir/packages/hl7.fhir.uv.extensions.r5#5.2.0 (00:00.001 / 00:10.870, 113Mb) Sushi: info Loaded hl7.fhir.uv.extensions.r5#5.2.0 with 759 resources (00:00.333 / 00:11.203, 113Mb) Sushi: info Attempting to download hl7.fhir.r5.core#5.0.0 from https://packages.fhir.org/hl7.fhir.r5.core/5.0.0 (00:00.000 / 00:11.204, 113Mb) Sushi: info Downloaded hl7.fhir.r5.core#5.0.0 (00:04.144 / 00:15.349, 113Mb) Sushi: info Cached hl7.fhir.r5.core#5.0.0 to /home/fhiruser/.fhir/packages/hl7.fhir.r5.core#5.0.0 (00:00.001 / 00:15.350, 113Mb) Sushi: info Loaded hl7.fhir.r5.core#5.0.0 with 2968 resources (00:01.434 / 00:16.785, 113Mb) Sushi: info Found 1 non-JSON / non-XML file(s) in directory: /scratch/repo/input/examples. Only resource files with JSON or XML extensions are supported. To see the skipped files in the logs, use debug logging. (00:00.013 / 00:16.798, 113Mb) Sushi: info Found 1 non-JSON / non-XML file(s) in directory: /scratch/repo/input/extensions. Only resource files with JSON or XML extensions are supported. To see the skipped files in the logs, use debug logging. (00:00.000 / 00:16.799, 113Mb) Sushi: info Found 1 non-JSON / non-XML file(s) in directory: /scratch/repo/input/models. Only resource files with JSON or XML extensions are supported. To see the skipped files in the logs, use debug logging. (00:00.000 / 00:16.799, 113Mb) Sushi: info Found 1 non-JSON / non-XML file(s) in directory: /scratch/repo/input/profiles. Only resource files with JSON or XML extensions are supported. To see the skipped files in the logs, use debug logging. (00:00.000 / 00:16.799, 113Mb) Sushi: info Found 1 non-JSON / non-XML file(s) in directory: /scratch/repo/input/resources. Only resource files with JSON or XML extensions are supported. To see the skipped files in the logs, use debug logging. (00:00.000 / 00:16.800, 113Mb) Sushi: info Found 1 non-JSON / non-XML file(s) in directory: /scratch/repo/input/vocabulary. Only resource files with JSON or XML extensions are supported. To see the skipped files in the logs, use debug logging. (00:00.000 / 00:16.800, 113Mb) Sushi: info Loaded virtual package sushi-local#LOCAL with 0 resources (00:00.000 / 00:16.801, 113Mb) Sushi: info Converting FSH to FHIR resources... (00:00.024 / 00:16.825, 113Mb) Sushi: warn The name "My-Communication" may not be suitable for machine processing applications such as code generation. Valid names start with an upper-case ASCII letter ('A'..'Z') followed by any combination of upper- or lower-case ASCII letters ('A'..'Z', and 'a'..'z'), numerals ('0'..'9') and '_', with a length limit of 255 characters. (00:00.036 / 00:16.862, 113Mb) Sushi: File: /scratch/repo/input/fsh/communication.fsh (00:00.000 / 00:16.862, 113Mb) Sushi: Line: 1 - 21 (00:00.000 / 00:16.863, 113Mb) Sushi: error Resolved value "ConditionSuspectedDiagnosisVS" is not a valid URI. (00:00.197 / 00:17.060, 113Mb) Sushi: File: /scratch/repo/input/fsh/condition.fsh (00:00.000 / 00:17.060, 113Mb) Sushi: Line: 10 (00:00.000 / 00:17.061, 113Mb) Sushi: error Resolved value "ConditionSeverityVS" is not a valid URI. (00:00.006 / 00:17.067, 113Mb) Sushi: File: /scratch/repo/input/fsh/condition.fsh (00:00.000 / 00:17.067, 113Mb) Sushi: Line: 16 (00:00.000 / 00:17.068, 113Mb) Sushi: warn The name "organization-profile" may not be suitable for machine processing applications such as code generation. Valid names start with an upper-case ASCII letter ('A'..'Z') followed by any combination of upper- or lower-case ASCII letters ('A'..'Z', and 'a'..'z'), numerals ('0'..'9') and '_', with a length limit of 255 characters. (00:00.099 / 00:17.167, 113Mb) Sushi: File: /scratch/repo/input/fsh/organization.fsh (00:00.000 / 00:17.168, 113Mb) Sushi: Line: 1 - 7 (00:00.000 / 00:17.168, 113Mb) Sushi: warn The name "sample-patient" may not be suitable for machine processing applications such as code generation. Valid names start with an upper-case ASCII letter ('A'..'Z') followed by any combination of upper- or lower-case ASCII letters ('A'..'Z', and 'a'..'z'), numerals ('0'..'9') and '_', with a length limit of 255 characters. (00:00.021 / 00:17.190, 113Mb) Sushi: File: /scratch/repo/input/fsh/profiles.fsh (00:00.000 / 00:17.190, 113Mb) Sushi: Line: 1 - 49 (00:00.000 / 00:17.191, 113Mb) Sushi: warn The name "patient-referral" may not be suitable for machine processing applications such as code generation. Valid names start with an upper-case ASCII letter ('A'..'Z') followed by any combination of upper- or lower-case ASCII letters ('A'..'Z', and 'a'..'z'), numerals ('0'..'9') and '_', with a length limit of 255 characters. (00:00.372 / 00:17.563, 113Mb) Sushi: File: /scratch/repo/input/fsh/referral.fsh (00:00.000 / 00:17.564, 113Mb) Sushi: Line: 1 - 13 (00:00.000 / 00:17.564, 113Mb) Sushi: info Converted 7 FHIR StructureDefinitions. (00:00.011 / 00:17.576, 113Mb) Sushi: info Converted 4 FHIR CodeSystems. (00:00.105 / 00:17.681, 113Mb) Sushi: info Converted 5 FHIR ValueSets. (00:00.166 / 00:17.847, 113Mb) Sushi: warn Cannot find the entity referenced at EncounterExample. The provided reference value will be used, but this reference does not conform to the FHIR Reference format. (00:00.384 / 00:18.232, 113Mb) Sushi: File: /scratch/repo/input/fsh/observation.fsh (00:00.000 / 00:18.232, 113Mb) Sushi: Line: 28 (00:00.000 / 00:18.233, 113Mb) Sushi: warn Cannot find the entity referenced at PractitionerExample. The provided reference value will be used, but this reference does not conform to the FHIR Reference format. (00:00.000 / 00:18.233, 113Mb) Sushi: File: /scratch/repo/input/fsh/observation.fsh (00:00.000 / 00:18.234, 113Mb) Sushi: Line: 30 (00:00.000 / 00:18.234, 113Mb) Sushi: info Converted 6 FHIR instances. (00:00.210 / 00:18.444, 113Mb) Sushi: info Exporting FHIR resources as JSON... (00:00.000 / 00:18.445, 113Mb) Sushi: info Exported 22 FHIR resources as JSON. (00:00.041 / 00:18.486, 113Mb) Sushi: info Assembling Implementation Guide sources... (00:00.002 / 00:18.488, 113Mb) Sushi: info Generated ImplementationGuide-fhir.starter.ig.json (00:00.010 / 00:18.499, 113Mb) Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:00.000 / 00:18.499, 113Mb) Sushi: ========================= SUSHI RESULTS =========================== (00:00.001 / 00:18.501, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:18.502, 113Mb) Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:00.000 / 00:18.502, 113Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:18.502, 113Mb) Sushi: | | 6 | 1 | 0 | 0 | | (00:00.000 / 00:18.502, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:18.502, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:18.503, 113Mb) Sushi: | | ValueSets | CodeSystems | Instances | | (00:00.000 / 00:18.503, 113Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:18.503, 113Mb) Sushi: | | 5 | 4 | 6 | | (00:00.000 / 00:18.503, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:18.504, 113Mb) Sushi: | | (00:00.000 / 00:18.504, 113Mb) Sushi: =================================================================== (00:00.000 / 00:18.504, 113Mb) Sushi: | Documentation may be kelp-ful. 2 Errors 7 Warnings | (00:00.000 / 00:18.504, 113Mb) Sushi: =================================================================== (00:00.000 / 00:18.505, 113Mb) Sushi couldn't be run. Complete output from running Sushi : (00:00.032 / 00:18.537, 113Mb) 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 / 00:18.538, 113Mb) Exception: Process exited with an error: 2 (Exit value: 2) (00:00.000 / 00:18.538, 113Mb) Publishing Content Failed: Process exited with an error: 2 (Exit value: 2) (00:00.000 / 00:18.538, 113Mb) (00:00.000 / 00:18.539, 113Mb) Use -? to get command line help (00:00.000 / 00:18.539, 113Mb) (00:00.000 / 00:18.539, 113Mb) Stack Dump (for debugging): (00:00.000 / 00:18.539, 113Mb) 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.PublisherIGLoader.initialize(PublisherIGLoader.java:130) at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:208) at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:1482)