INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/HL7/ihe-sdc-ecc-on-fhir --branch master repo DEBUG:root:Time to deadline 35879.997754 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 35878.627869 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35873.696248 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 -> 10.9.2 npm notice Changelog: npm notice Run `npm install -g npm@10.9.2` 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/HL7/ihe-sdc-ecc-on-fhir/ -out /scratch/repo DEBUG:root:Time to deadline 35868.457652 seconds FHIR IG Publisher Version 1.7.5 (Git# 2ec44e6c46a5). Built 2024-11-22T15:37:50.312Z (13 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/HL7/ihe-sdc-ecc-on-fhir/ -out /scratch/repo Start Clock @ Friday, December 6, 2024, 12:25:47 AM Coordinated Universal Time (2024-12-06T00:25:47Z) Build FHIR IG from /scratch/repo (00:00.024 / 00:00.025, 89Mb) API keys loaded from /etc/fhir-settings.json (00:00.003 / 00:00.028, 89Mb) Package Cache: /var/lib/.fhir/packages (00:00.003 / 00:00.031, 89Mb) Run Sushi on /scratch/repo (00:00.004 / 00:00.036, 89Mb) Sushi: info Running SUSHI v3.12.1 (implements FHIR Shorthand specification v3.0.0) (00:00.516 / 00:00.552, 113Mb) Sushi: info Arguments: (00:00.000 / 00:00.553, 113Mb) Sushi: info --require-latest (00:00.000 / 00:00.553, 113Mb) Sushi: info --out /scratch/repo (00:00.000 / 00:00.553, 113Mb) Sushi: info /scratch/repo (00:00.000 / 00:00.554, 113Mb) Sushi: info Using configuration file: /scratch/repo/sushi-config.yaml (00:00.856 / 00:01.411, 113Mb) Sushi: info Importing FSH text... (00:00.122 / 00:01.533, 113Mb) Sushi: info Preprocessed 13 documents with 12 aliases. (00:00.157 / 00:01.690, 113Mb) Sushi: info Imported 3 definitions and 9 instances. (00:00.010 / 00:01.701, 113Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.uv.tools#current... (00:00.001 / 00:01.703, 113Mb) Sushi: info Did not find hl7.fhir.uv.tools#current in /home/fhiruser/.fhir/packages. (00:00.021 / 00:01.724, 113Mb) Sushi: info Downloading hl7.fhir.uv.tools#current... https://build.fhir.org/ig/FHIR/fhir-tools-ig/branches/master/package.tgz (00:00.121 / 00:01.846, 113Mb) Sushi: info Downloaded hl7.fhir.uv.tools#current (00:00.014 / 00:01.861, 113Mb) Sushi: info Loaded package hl7.fhir.uv.tools#current (00:00.084 / 00:01.946, 113Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.terminology.r4#6.1.0... (00:00.528 / 00:02.474, 113Mb) Sushi: info Did not find hl7.terminology.r4#6.1.0 in /home/fhiruser/.fhir/packages. (00:00.022 / 00:02.497, 113Mb) Sushi: info Downloading hl7.terminology.r4#6.1.0... https://packages.fhir.org/hl7.terminology.r4/6.1.0 (00:00.000 / 00:02.497, 113Mb) Sushi: info Downloaded hl7.terminology.r4#6.1.0 (00:02.086 / 00:04.583, 113Mb) Sushi: info Loaded package hl7.terminology.r4#6.1.0 (00:01.823 / 00:06.406, 113Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.uv.extensions#current... (00:00.000 / 00:06.407, 113Mb) Sushi: info Did not find hl7.fhir.uv.extensions#current in /home/fhiruser/.fhir/packages. (00:00.336 / 00:06.743, 113Mb) Sushi: info Downloading hl7.fhir.uv.extensions#current... https://build.fhir.org/ig/HL7/fhir-extensions/branches/master/package.tgz (00:00.058 / 00:06.802, 113Mb) Sushi: info Downloaded hl7.fhir.uv.extensions#current (00:00.123 / 00:06.925, 113Mb) Sushi: info Loaded package hl7.fhir.uv.extensions#current (00:00.830 / 00:07.756, 113Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.r4.core#4.0.1... (00:00.000 / 00:07.756, 113Mb) Sushi: info Did not find hl7.fhir.r4.core#4.0.1 in /home/fhiruser/.fhir/packages. (00:00.509 / 00:08.266, 113Mb) Sushi: info Downloading hl7.fhir.r4.core#4.0.1... https://packages.fhir.org/hl7.fhir.r4.core/4.0.1 (00:00.000 / 00:08.266, 113Mb) Sushi: info Downloaded hl7.fhir.r4.core#4.0.1 (00:03.262 / 00:11.529, 113Mb) Sushi: info Loaded package hl7.fhir.r4.core#4.0.1 (00:02.318 / 00:13.848, 113Mb) Sushi: info Converting FSH to FHIR resources... (00:00.041 / 00:13.889, 113Mb) Sushi: info Converted 3 FHIR StructureDefinitions. (00:00.259 / 00:14.149, 113Mb) Sushi: info Converted 9 FHIR instances. (00:00.428 / 00:14.577, 113Mb) Sushi: info Exporting FHIR resources as JSON... (00:00.000 / 00:14.577, 113Mb) Sushi: info Exported 12 FHIR resources as JSON. (00:00.013 / 00:14.591, 113Mb) Sushi: info Assembling Implementation Guide sources... (00:00.001 / 00:14.592, 113Mb) Sushi: info Generated ImplementationGuide-hl7.fhir.uv.ihe-sdc-ecc.json (00:00.023 / 00:14.615, 113Mb) Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:00.000 / 00:14.616, 113Mb) Sushi: ========================= SUSHI RESULTS =========================== (00:00.000 / 00:14.617, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:14.617, 113Mb) Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:00.000 / 00:14.617, 113Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:14.617, 113Mb) Sushi: | | 3 | 0 | 0 | 0 | | (00:00.000 / 00:14.617, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:14.618, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:14.618, 113Mb) Sushi: | | ValueSets | CodeSystems | Instances | | (00:00.000 / 00:14.618, 113Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:14.618, 113Mb) Sushi: | | 0 | 0 | 9 | | (00:00.000 / 00:14.618, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:14.619, 113Mb) Sushi: | | (00:00.000 / 00:14.619, 113Mb) Sushi: =================================================================== (00:00.000 / 00:14.619, 113Mb) Sushi: | You're in the swim of things now! 0 Errors 0 Warnings | (00:00.000 / 00:14.619, 113Mb) Sushi: =================================================================== (00:00.000 / 00:14.619, 113Mb) Unable to load IG as an r5 IG - try R4 (property code is a class com.google.gson.JsonPrimitive looking for an object) (00:00.627 / 00:15.247, 37Mb) Load Template from hl7.fhir.template#current (00:00.472 / 00:15.719, 69Mb) Installing hl7.fhir.template#current to the package cache Fetching: Installing hl7.fhir.template#current done. Load Template from hl7.base.template#current (00:01.158 / 00:16.877, 133Mb) Installing hl7.base.template#current to the package cache Fetching: Installing hl7.base.template#current done. Load Template from fhir.base.template#current (00:00.217 / 00:17.095, 133Mb) Installing fhir.base.template#current to the package cache Fetching: Installing fhir.base.template#current done. onLoad.findSpreadsheets: onLoad.updateIg: [xslt] Processing /scratch/repo/template/onLoad-ig-working.xml to /scratch/repo/template/onLoad-ig-updated.xml [xslt] Loading stylesheet /scratch/repo/template/scripts/onLoad.xslt onLoad.extend: onLoad: Root directory: /scratch/repo (00:03.201 / 00:20.297, 127Mb) Terminology Cache is at /scratch/repo/input-cache/txcache. Trimming now (00:00.001 / 00:20.299, 127Mb) Core Package hl7.fhir.r4.core#4.0.1 Running Terminology Log: /tmp/ohfu-fhir-ig-9597502697145155060.log Connect to Terminology Server at http://tx.fhir.org (00:34.571 / 00:54.870, 586Mb) Installing hl7.fhir.pubpack#0.1.9 to the package cache Fetching: Installing hl7.fhir.pubpack#0.1.9 done. Load Package hl7.fhir.pubpack#0.1.9 Installing hl7.fhir.xver-extensions#0.1.0 to the package cache Fetching: Installing hl7.fhir.xver-extensions#0.1.0 done. Load Package hl7.fhir.xver-extensions#0.1.0 Load Package hl7.terminology.r4#6.1.0 Version mismatch. This IG is version 4.0.1, while the IG 'hl7.fhir.uv.extensions' is from version 5.0.0 (will try to run anyway) (00:04.098 / 00:58.968, 882Mb) Installing hl7.terminology.r5#6.1.0 to the package cache Fetching: Installing hl7.terminology.r5#6.1.0 done. Ignore Dependency on Core FHIR hl7.fhir.r5.core#5.0.0, from package 'hl7.terminology.r5#6.1.0' (00:01.802 / 01:00.771, 226Mb) Load Package hl7.terminology.r5#6.1.0 Load Package hl7.fhir.uv.extensions#5.2.0-ballot Installing hl7.fhir.uv.tools.r4#0.3.0 to the package cache Fetching: Installing hl7.fhir.uv.tools.r4#0.3.0 done. Load Package hl7.fhir.uv.tools.r4#0.3.0 Load R5 Specials Installing hl7.fhir.r5.core#5.0.0 to the package cache Fetching: Installing hl7.fhir.r5.core#5.0.0 done. Initialization complete (00:04.773 / 01:05.544, 949Mb) Load Content (00:00.000 / 01:05.545, 949Mb) Using en-US as the default narrative language. (no language information in Implementation Guide or command line) (00:00.062 / 01:05.607, 949Mb) loadPrePages from FetchedFile[/scratch/repo/fsh-generated/includes] as /scratch/repo/fsh-generated/includes loadPrePages from FetchedFile[/scratch/repo/input/pagecontent] as /scratch/repo/input/pagecontent Fetch http://hl7.org/fhir/uv/ihe-sdc-ecc/package-list.json for version check (00:00.410 / 01:06.017, 965Mb) Processing Conformance Resources (00:00.178 / 01:06.196, 965Mb) Load Dependency Info (00:00.000 / 01:06.196, 965Mb) Load Info (00:00.000 / 01:06.197, 965Mb) Load Resources (00:00.000 / 01:06.198, 969Mb) Load Paths (00:00.054 / 01:06.252, 981Mb) Generating Snapshots (00:00.000 / 01:06.252, 981Mb) Check R4 / R4B (00:00.229 / 01:06.482, 1Gb) Assign Comparison Ids (00:00.007 / 01:06.489, 1Gb) Propagating status (00:00.000 / 01:06.489, 1Gb) Generating Narratives (00:00.000 / 01:06.490, 1Gb) Validating Conformance Resources (00:01.149 / 01:07.639, 535Mb) Check profiles & code systems (00:02.612 / 01:10.251, 943Mb) Check realm rules (00:00.001 / 01:10.252, 943Mb) Previous Version Comparison (00:00.000 / 01:10.253, 943Mb) Validating Resources (00:00.015 / 01:10.268, 943Mb) Processing Provenance Records (00:00.596 / 01:10.865, 991Mb) Generating Outputs in /scratch/repo/output (00:00.000 / 01:10.865, 991Mb) Generate Native Outputs (00:00.221 / 01:11.087, 999Mb) Run Template (00:01.466 / 01:12.553, 1Gb) onGenerate.checkVersions: [xslt] Processing /scratch/repo/template/onGenerate-ig-working.xml to /scratch/repo/template/versions.txt [xslt] Loading stylesheet /scratch/repo/template/scripts/onGenerate.getVersions.xslt [mkdir] Created dir: /scratch/repo/input-cache/schemas onGenerate.r5-schemas: [mkdir] Created dir: /scratch/repo/input-cache/schemas/R5 [get] Getting: http://build.fhir.org/fhir-single.xsd [get] To: /scratch/repo/input-cache/schemas/R5/fhir-single.xsd [get] Getting: http://build.fhir.org/fhir-xhtml.xsd [get] To: /scratch/repo/input-cache/schemas/R5/fhir-xhtml.xsd [get] Getting: http://build.fhir.org/xml.xsd [get] To: /scratch/repo/input-cache/schemas/R5/xml.xsd [get] Getting: http://build.fhir.org/xmldsig-core-schema.xsd [get] To: /scratch/repo/input-cache/schemas/R5/xmldsig-core-schema.xsd onGenerate.r4-schemas: [mkdir] Created dir: /scratch/repo/input-cache/schemas/R4 [get] Getting: http://hl7.org/fhir/R4/fhir-single.xsd [get] To: /scratch/repo/input-cache/schemas/R4/fhir-single.xsd [get] Getting: http://hl7.org/fhir/R4/fhir-xhtml.xsd [get] To: /scratch/repo/input-cache/schemas/R4/fhir-xhtml.xsd [get] Getting: http://hl7.org/fhir/R4/xml.xsd [get] To: /scratch/repo/input-cache/schemas/R4/xml.xsd [get] Getting: http://hl7.org/fhir/R4/xmldsig-core-schema.xsd [get] To: /scratch/repo/input-cache/schemas/R4/xmldsig-core-schema.xsd onGenerate.r3-schemas: onGenerate.r2b-schemas: onGenerate.r2-schemas: onGenerate.schemas: onGenerate.data: [xslt] Processing /scratch/repo/template/onGenerate-ig-working.xml to /scratch/repo/temp/pages/_data/artifacts.json [xslt] Loading stylesheet /scratch/repo/template/scripts/onGenerate.data.xslt onGenerate.setup: onGenerate.infoFile: [xslt] Processing /scratch/repo/template/onGenerate-ig-working.xml to /scratch/repo/temp/pages/_data/info.json [xslt] Loading stylesheet /scratch/repo/template/scripts/onGenerate.genJson.xslt onGenerate.processIncludes: [copy] Copying 19 files to /scratch/repo/temp/pages/_includes onGenerate.processIg: [xslt] Processing /scratch/repo/template/onGenerate-ig-working.xml to /scratch/repo/template/onGenerate-ig-working.1.xml [xslt] Loading stylesheet /scratch/repo/template/scripts/onGenerate.group.xslt [xslt] Processing /scratch/repo/template/onGenerate-ig-working.1.xml to /scratch/repo/template/onGenerate-ig-working.2.xml [xslt] Loading stylesheet /scratch/repo/template/scripts/onGenerate.groupSort.xslt [xslt] Processing /scratch/repo/template/onGenerate-ig-working.2.xml to /scratch/repo/template/onGenerate-ig-updated.xml [xslt] Loading stylesheet /scratch/repo/template/scripts/onGenerate.final.xslt onGenerate.igQa: [xslt] Processing /scratch/repo/template/onGenerate-ig-updated.xml to /scratch/repo/template/ongenerate-validation-igqa.json [xslt] Loading stylesheet /scratch/repo/template/scripts/onGenerate.qa.xslt onGenerate.artifactList: [xslt] Processing /scratch/repo/template/onGenerate-ig-updated.xml to /scratch/repo/temp/pages/_includes/artifacts.xml [xslt] Loading stylesheet /scratch/repo/template/scripts/createArtifactSummary.xslt check-plantumlfiles: onGenerate.plantUml.ig: onGenerate.plantUml.template: onGenerate.plantUml: onGenerate.copyDataFiles: onGenerate.jira.setup: [xslt] Processing /scratch/repo/template/onGenerate-ig-updated.xml to /scratch/repo/template/properties.txt [xslt] Loading stylesheet /scratch/repo/template/scripts/onGenerate.genProperties.xslt [get] Getting: https://github.com/HL7/JIRA-Spec-Artifacts/raw/master/xml/_workgroups.xml [get] To: /scratch/repo/input-cache/workgroups.xml [get] https://github.com/HL7/JIRA-Spec-Artifacts/raw/master/xml/_workgroups.xml moved to https://raw.githubusercontent.com/HL7/JIRA-Spec-Artifacts/master/xml/_workgroups.xml [get] Getting: https://github.com/HL7/JIRA-Spec-Artifacts/raw/master/xml/FHIR-ihe-sdc-ecc.xml [get] To: /scratch/repo/input-cache/jiraspec.xml [get] https://github.com/HL7/JIRA-Spec-Artifacts/raw/master/xml/FHIR-ihe-sdc-ecc.xml moved to https://raw.githubusercontent.com/HL7/JIRA-Spec-Artifacts/master/xml/FHIR-ihe-sdc-ecc.xml onGenerate.jira.packagelistcopy: onGenerate.jira.packagelistget: [get] Getting: http://hl7.org/fhir/uv/ihe-sdc-ecc/package-list.json [get] To: /scratch/repo/template/onGenerate.jira.workingpackage-list.json onGenerate.jira.packagelistProcess: [xslt] Processing /scratch/repo/template/onGenerate.jira.package-list.tmp.xml to /scratch/repo/template/onGenerate.jira.package-list.xml [xslt] Loading stylesheet /scratch/repo/template/scripts/onGenerate.package-list.xslt onGenerate.jira.packagelistSkip: onGenerate.jira.pubrequestProcess: [xslt] Processing /scratch/repo/template/onGenerate.jira.pubrequest.tmp.xml to /scratch/repo/template/onGenerate.jira.pubrequest.xml [xslt] Loading stylesheet /scratch/repo/template/scripts/onGenerate.pubrequest.xslt onGenerate.jira.pubrequestSkip: onGenerate.jira.generate: [xslt] Processing /scratch/repo/template/onGenerate.jira.tmp.xml to /scratch/repo/template/onGenerate.jira.tmp2.xml [xslt] Loading stylesheet /scratch/repo/template/scripts/onGenerate.process-pkg-list.xslt [xslt] Processing /scratch/repo/template/onGenerate.jira.tmp2.xml to /scratch/repo/template/onGenerate.jira.xml [xslt] Loading stylesheet /scratch/repo/template/scripts/onGenerate.jira.xslt [xslt] Processing /scratch/repo/template/onGenerate.jira.xml to /scratch/repo/template/jira-new.xml [xslt] Loading stylesheet /scratch/repo/template/scripts/onGenerate.normalize.xslt [xslt] Processing /scratch/repo/input-cache/jiraspec.xml to /scratch/repo/template/jira-current.xml [xslt] Loading stylesheet /scratch/repo/template/scripts/onGenerate.normalize.xslt [copy] Copying 1 file to /scratch/repo onGenerate.jira.check: onGenerate.jira.skip-offline: onGenerate.jira.skip-missing: onGenerate.jira: onGenerate.extend: onGenerate: Template Done (00:02.167 / 01:14.721, 413Mb) Generate HTML Outputs (00:00.000 / 01:14.721, 413Mb) ERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using SimpleLogger to log to the console... Generate Summaries (00:04.338 / 01:19.059, 496Mb) Generating Summary Outputs (00:00.000 / 01:19.060, 496Mb) DB Cumulative Time invested: 00:00:00.323 Sending Usage Stats to Server (00:03.026 / 01:22.086, 993Mb) ## Memory (MB): Use = 993, Free = 18014, Total = 19008, Max = 19008 (00:00.010 / 01:22.097, 996Mb) Reclaiming memory... (00:00.000 / 01:22.097, 996Mb) ## Memory (MB): Use = 333, Free = 18673, Total = 19008, Max = 19008 (00:00.318 / 01:22.415, 342Mb) Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.001 / 01:22.417, 342Mb) Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.000 / 01:22.417, 342Mb) * A failure to produce a fragment that is already logged in the output above (00:00.000 / 01:22.417, 342Mb) * A reference to a manually edited file that hasn't been provided (00:00.000 / 01:22.417, 342Mb) Jekyll: Source: /scratch/repo/temp/pages (00:00.448 / 01:22.865, 350Mb) Jekyll: Generating... (00:00.000 / 01:22.865, 350Mb) Jekyll: done in 0.741 seconds. (00:00.740 / 01:23.606, 350Mb) onCheck.extend: onCheck: Checking Output HTML (00:00.997 / 01:24.603, 589Mb) found 663 files (00:00.003 / 01:24.607, 589Mb) ......................................... ......................................... ... 663 html files, 0 pages invalid xhtml (0%) (00:02.357 / 01:26.964, 1Gb) ... 30715 links, 0 broken links (0%) (00:00.000 / 01:26.965, 1Gb) Generate fragment-usage-analysis.csv (00:00.000 / 01:26.965, 1Gb) Build final .zip (00:00.009 / 01:26.975, 1Gb) Final .zip built (00:00.595 / 01:27.570, 1Gb) Built. Times: loading: 00:00.650, generate: 00:22.761, narrative generation: 00:01.149, realm-rules: 00:00.000, previous-version: 00:00.000, jekyll: 00:01.205, validation: 00:03.207 (#13), template: 00:02.179 (#3) (00:01.400 / 01:28.971, 2Gb) Generating QA (00:00.000 / 01:28.971, 2Gb) Validation output in /scratch/repo/output/qa.html Errors: 0, Warnings: 12, Info: 2, Broken Links: 0 (00:00.404 / 01:29.375, 2Gb) Finished. Max Memory Used = 2Gb (00:00.005 / 01:29.381, 2Gb)