INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/hl7ch/ch-emed --branch master repo DEBUG:root:Time to deadline 35879.99806 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 35878.778493 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35877.508574 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 glob@7.2.3: Glob versions prior to v9 are no longer supported npm WARN deprecated rimraf@2.6.3: Rimraf versions prior to v4 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 -> 10.9.1 npm notice Changelog: npm notice Run `npm install -g npm@10.9.1` 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/hl7ch/ch-emed/ -out /scratch/repo DEBUG:root:Time to deadline 35872.420603 seconds FHIR IG Publisher Version 1.7.5 (Git# 2ec44e6c46a5). Built 2024-11-22T15:37:50.312Z (5 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/hl7ch/ch-emed/ -out /scratch/repo Start Clock @ Thursday, November 28, 2024, 2:36:26 PM Coordinated Universal Time (2024-11-28T14:36:26Z) Build FHIR IG from /scratch/repo (00:00.035 / 00:00.036, 89Mb) API keys loaded from /etc/fhir-settings.json (00:00.005 / 00:00.040, 89Mb) Package Cache: /var/lib/.fhir/packages (00:00.003 / 00:00.044, 89Mb) Run Sushi on /scratch/repo (00:00.008 / 00:00.053, 89Mb) Sushi: info Running SUSHI v3.12.1 (implements FHIR Shorthand specification v3.0.0) (00:00.673 / 00:00.726, 113Mb) Sushi: info Arguments: (00:00.000 / 00:00.727, 113Mb) Sushi: info --require-latest (00:00.000 / 00:00.727, 113Mb) Sushi: info --out /scratch/repo (00:00.000 / 00:00.728, 113Mb) Sushi: info /scratch/repo (00:00.000 / 00:00.728, 113Mb) Sushi: info Using configuration file: /scratch/repo/sushi-config.yaml (00:00.962 / 00:01.691, 113Mb) Sushi: info Importing FSH text... (00:00.156 / 00:01.847, 113Mb) Sushi: info Preprocessed 119 documents with 16 aliases. (00:00.497 / 00:02.345, 113Mb) Sushi: info Imported 42 definitions and 78 instances. (00:00.071 / 00:02.416, 113Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.uv.tools#current... (00:00.002 / 00:02.418, 113Mb) Sushi: info Did not find hl7.fhir.uv.tools#current in /home/fhiruser/.fhir/packages. (00:00.029 / 00:02.447, 113Mb) Sushi: info Downloading hl7.fhir.uv.tools#current... https://build.fhir.org/ig/FHIR/fhir-tools-ig/branches/master/package.tgz (00:00.140 / 00:02.588, 113Mb) Sushi: info Downloaded hl7.fhir.uv.tools#current (00:00.015 / 00:02.603, 113Mb) Sushi: info Loaded package hl7.fhir.uv.tools#current (00:00.108 / 00:02.711, 113Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.uv.extensions.r4#5.1.0... (00:00.569 / 00:03.281, 113Mb) Sushi: info Did not find hl7.fhir.uv.extensions.r4#5.1.0 in /home/fhiruser/.fhir/packages. (00:00.030 / 00:03.312, 113Mb) 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 / 00:03.312, 113Mb) Sushi: info Downloaded hl7.fhir.uv.extensions.r4#5.1.0 (00:02.207 / 00:05.519, 113Mb) Sushi: info Loaded package hl7.fhir.uv.extensions.r4#5.1.0 (00:01.114 / 00:06.633, 113Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for ch.fhir.ig.ch-core#current... (00:00.000 / 00:06.634, 113Mb) Sushi: info Did not find ch.fhir.ig.ch-core#current in /home/fhiruser/.fhir/packages. (00:00.241 / 00:06.876, 113Mb) Sushi: info Downloading ch.fhir.ig.ch-core#current... https://build.fhir.org/ig/hl7ch/ch-core/branches/master/package.tgz (00:00.142 / 00:07.019, 113Mb) Sushi: info Downloaded ch.fhir.ig.ch-core#current (00:00.053 / 00:07.072, 113Mb) Sushi: info Loaded package ch.fhir.ig.ch-core#current (00:00.479 / 00:07.552, 113Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.terminology#6.1.0... (00:00.001 / 00:07.553, 113Mb) Sushi: info Did not find hl7.terminology#6.1.0 in /home/fhiruser/.fhir/packages. (00:00.350 / 00:07.904, 113Mb) Sushi: info Downloading hl7.terminology#6.1.0... https://packages.fhir.org/hl7.terminology/6.1.0 (00:00.000 / 00:07.904, 113Mb) Sushi: info Downloaded hl7.terminology#6.1.0 (00:01.913 / 00:09.817, 113Mb) Sushi: info Loaded package hl7.terminology#6.1.0 (00:02.433 / 00:12.251, 113Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.r4.core#4.0.1... (00:00.000 / 00:12.251, 113Mb) Sushi: info Did not find hl7.fhir.r4.core#4.0.1 in /home/fhiruser/.fhir/packages. (00:00.834 / 00:13.086, 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 / 00:13.086, 113Mb) Sushi: info Downloaded hl7.fhir.r4.core#4.0.1 (00:02.849 / 00:15.936, 113Mb) Sushi: info Loaded package hl7.fhir.r4.core#4.0.1 (00:03.102 / 00:19.038, 113Mb) Sushi: info Converting FSH to FHIR resources... (00:00.064 / 00:19.102, 113Mb) Sushi: info Converted 42 FHIR StructureDefinitions. (00:09.703 / 00:28.806, 113Mb) Sushi: info Converted 78 FHIR instances. (00:09.166 / 00:37.972, 121Mb) Sushi: info Exporting FHIR resources as JSON... (00:00.001 / 00:37.973, 121Mb) Sushi: info Exported 104 FHIR resources as JSON. (00:00.498 / 00:38.472, 121Mb) Sushi: info Assembling Implementation Guide sources... (00:00.004 / 00:38.477, 121Mb) Sushi: info Generated ImplementationGuide-ch.fhir.ig.ch-emed.json (00:00.044 / 00:38.521, 121Mb) Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:00.000 / 00:38.521, 121Mb) Sushi: info The sample-ig located at https://github.com/FHIR/sample-ig contains scripts useful for downloading and running the IG Publisher. (00:00.000 / 00:38.521, 121Mb) Sushi: ========================= SUSHI RESULTS =========================== (00:00.001 / 00:38.523, 121Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:38.523, 121Mb) Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:00.000 / 00:38.523, 121Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:38.524, 121Mb) Sushi: | | 35 | 7 | 0 | 0 | | (00:00.000 / 00:38.524, 121Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:38.524, 121Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:38.524, 121Mb) Sushi: | | ValueSets | CodeSystems | Instances | | (00:00.000 / 00:38.525, 121Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:38.525, 121Mb) Sushi: | | 0 | 0 | 78 | | (00:00.000 / 00:38.525, 121Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:38.525, 121Mb) Sushi: | | (00:00.000 / 00:38.526, 121Mb) Sushi: =================================================================== (00:00.000 / 00:38.526, 121Mb) Sushi: | That was a big fish to fry! 0 Errors 0 Warnings | (00:00.000 / 00:38.526, 121Mb) Sushi: =================================================================== (00:00.000 / 00:38.526, 121Mb) Unable to load IG as an r5 IG - try R4 (property code is a class com.google.gson.JsonPrimitive looking for an object) (00:00.880 / 00:39.407, 37Mb) Load Template from ch.fhir.ig.template#current (00:00.719 / 00:40.126, 77Mb) Installing ch.fhir.ig.template#current to the package cache Fetching: Installing ch.fhir.ig.template#current done. Load Template from fhir.base.template#current (00:01.444 / 00:41.571, 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 (00:04.630 / 00:46.202, 142Mb) Terminology Cache is at /scratch/repo/input-cache/txcache. Trimming now (00:00.002 / 00:46.204, 142Mb) Core Package hl7.fhir.r4.core#4.0.1 Running Terminology Log: /tmp/ohfu-fhir-ig-1095021512275767062.log Connect to Terminology Server at http://tx.fhir.org (00:29.222 / 01:15.427, 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.fhir.uv.extensions.r4#5.1.0 Installing ch.fhir.ig.ch-term#current to the package cache Fetching: Installing ch.fhir.ig.ch-term#current done. Installing ihe.formatcode.fhir#1.3.0 to the package cache Fetching: Installing ihe.formatcode.fhir#1.3.0 done. Installing hl7.terminology.r4#5.5.0 to the package cache Fetching: Installing hl7.terminology.r4#5.5.0 done. Load Package hl7.terminology.r4#5.5.0 Load Package ihe.formatcode.fhir#1.3.0 Load Package hl7.terminology#6.1.0 Load Package ch.fhir.ig.ch-term#current Load Package ch.fhir.ig.ch-core#5.0.0 Version mismatch. This IG is version 4.0.1, while the IG 'hl7.terminology' is from version 5.0.0 (will try to run anyway) (00:10.987 / 01:26.415, 785Mb) Load Package hl7.terminology#6.1.0 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 (00:03.331 / 01:29.746, 669Mb) Load Content (00:00.000 / 01:29.747, 669Mb) Using en-US as the default narrative language. (no language information in Implementation Guide or command line) (00:00.119 / 01:29.866, 677Mb) loadPrePages from FetchedFile[/scratch/repo/input/includes] as /scratch/repo/input/includes loadPrePages from FetchedFile[/scratch/repo/fsh-generated/includes] as /scratch/repo/fsh-generated/includes loadPrePages from FetchedFile[/scratch/repo/input/data] as /scratch/repo/input/data loadPrePages from FetchedFile[/scratch/repo/input/pagecontent] as /scratch/repo/input/pagecontent Fetch http://fhir.ch/ig/ch-emed/package-list.json for version check (00:01.548 / 01:31.415, 853Mb) Processing Conformance Resources (00:00.173 / 01:31.588, 861Mb) Load Dependency Info (00:00.003 / 01:31.591, 861Mb) Load Info (00:00.001 / 01:31.593, 861Mb) Load Resources (00:00.000 / 01:31.594, 865Mb) Load Paths (00:00.724 / 01:32.319, 1Gb) Generating Snapshots (00:00.000 / 01:32.319, 1Gb) Check R4 / R4B (00:03.648 / 01:35.968, 1Gb) Assign Comparison Ids (00:00.032 / 01:36.001, 1Gb) Propagating status (00:00.000 / 01:36.001, 1Gb) Generating Narratives (00:00.000 / 01:36.001, 1Gb) Validating Conformance Resources (00:04.253 / 01:40.255, 1Gb) Check profiles & code systems (00:33.289 / 02:13.545, 1Gb) Check realm rules (00:00.015 / 02:13.560, 1Gb) Previous Version Comparison (00:00.000 / 02:13.560, 1Gb) Installing ch.fhir.ig.ch-emed#5.0.0-ballot to the package cache Fetching: Installing ch.fhir.ig.ch-emed#5.0.0-ballot done. Installing ch.fhir.ig.ch-core#5.0.0-ballot to the package cache Fetching: Installing ch.fhir.ig.ch-core#5.0.0-ballot done. Installing ch.fhir.ig.ch-term#3.0.x to the package cache Fetching: Installing ch.fhir.ig.ch-term#3.0.0 done. Installing ihe.formatcode.fhir#1.2.0 to the package cache Fetching: Installing ihe.formatcode.fhir#1.2.0 done. Installing hl7.terminology.r4#5.3.0 to the package cache Fetching: Installing hl7.terminology.r4#5.3.0 done. Installing hl7.fhir.uv.extensions.r4#1.0.0 to the package cache Fetching: Installing hl7.fhir.uv.extensions.r4#1.0.0 done. Installing hl7.terminology#5.5.0 to the package cache Fetching: Installing hl7.terminology#5.5.0 done. Validating Resources (00:20.350 / 02:33.911, 2Gb) Processing Provenance Records (00:16.178 / 02:50.090, 2Gb) Generating Outputs in /scratch/repo/output (00:00.000 / 02:50.090, 2Gb) Generate Native Outputs (00:00.244 / 02:50.335, 2Gb) Run Template (00:29.530 / 03:19.865, 5Gb) 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 21 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.extend: onGenerate: Template Done (00:03.043 / 03:22.909, 5Gb) Generate HTML Outputs (00:00.000 / 03:22.909, 5Gb) 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 (00:51.476 / 04:14.386, 1Gb) Generating Summary Outputs (00:00.000 / 04:14.386, 1Gb) DB Cumulative Time invested: 00:00:01.94 Sending Usage Stats to Server (00:12.254 / 04:26.640, 1Gb) ## Memory (MB): Use = 1909, Free = 17098, Total = 19008, Max = 19008 (00:00.010 / 04:26.651, 1Gb) Reclaiming memory... (00:00.000 / 04:26.651, 1Gb) ## Memory (MB): Use = 1404, Free = 17603, Total = 19008, Max = 19008 (00:02.048 / 04:28.700, 1Gb) Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.001 / 04:28.701, 1Gb) Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.000 / 04:28.701, 1Gb) * A failure to produce a fragment that is already logged in the output above (00:00.000 / 04:28.701, 1Gb) * A reference to a manually edited file that hasn't been provided (00:00.000 / 04:28.702, 1Gb) Jekyll: Source: /scratch/repo/temp/pages (00:00.586 / 04:29.289, 1Gb) Jekyll: Generating... (00:00.000 / 04:29.289, 1Gb) Jekyll: done in 6.868 seconds. (00:06.867 / 04:36.156, 1Gb) onCheck.extend: onCheck: Checking Output HTML (00:09.485 / 04:45.642, 3Gb) found 1760 files (00:00.009 / 04:45.651, 3Gb) ....................................... ....................................... ... 1760 html files, 0 pages invalid xhtml (0%) (01:14.646 / 06:00.298, 6Gb) ... 957830 links, 0 broken links (0%) (00:00.000 / 06:00.299, 6Gb) Generate fragment-usage-analysis.csv (00:00.000 / 06:00.299, 6Gb) Build final .zip (00:00.012 / 06:00.311, 6Gb) Final .zip built (00:08.392 / 06:08.703, 6Gb) Installing hl7.fhir.uv.extensions.r5#5.1.0 to the package cache Fetching: Installing hl7.fhir.uv.extensions.r5#5.1.0 done. Built. Times: loading: 00:01.841, generate: 04:48.384, narrative generation: 00:04.253, realm-rules: 00:00.000, previous-version: 00:20.259, jekyll: 00:07.507, validation: 00:49.183 (#105), template: 00:03.054 (#3) (00:11.655 / 06:20.359, 8Gb) Generating QA (00:00.000 / 06:20.359, 8Gb) Validation output in /scratch/repo/output/qa.html Errors: 0, Warnings: 0, Info: 4, Broken Links: 0 (00:05.555 / 06:25.914, 10Gb) Finished. Max Memory Used = 10Gb (00:00.032 / 06:25.946, 10Gb)