INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/fhir-fi/finnish-base-profiles --branch master repo DEBUG:root:Time to deadline 35879.997571 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 35879.278868 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35877.9578 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 119 packages in 4s 8 packages are looking for funding run `npm fund` for details npm notice npm notice New major version of npm available! 9.8.1 -> 10.8.2 npm notice Changelog: npm notice Run `npm install -g npm@10.8.2` 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/fhir-fi/finnish-base-profiles/ -out /scratch/repo DEBUG:root:Time to deadline 35873.56414 seconds FHIR IG Publisher Version 1.6.20 (Git# 7bbd1ce5defe). Built 2024-08-13T18:33:37.376Z (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/fhir-fi/finnish-base-profiles/ -out /scratch/repo Start Clock @ Monday, August 19, 2024, 5:27:00 PM Coordinated Universal Time (2024-08-19T17:27:00Z) Build FHIR IG from /scratch/repo (00:00.020 / 00:00.021, 89Mb) API keys loaded from /etc/fhir-settings.json (00:00.004 / 00:00.025, 89Mb) Package Cache: /var/lib/.fhir/packages (00:00.003 / 00:00.028, 89Mb) Run Sushi on /scratch/repo (00:00.008 / 00:00.037, 89Mb) Sushi: info Running SUSHI v3.11.0 (implements FHIR Shorthand specification v3.0.0-ballot) (00:00.539 / 00:00.577, 97Mb) Sushi: info Arguments: (00:00.000 / 00:00.577, 97Mb) Sushi: info --require-latest (00:00.000 / 00:00.577, 97Mb) Sushi: info --out /scratch/repo (00:00.000 / 00:00.578, 97Mb) Sushi: info /scratch/repo (00:00.000 / 00:00.578, 97Mb) Sushi: info Using configuration file: /scratch/repo/sushi-config.yaml (00:00.601 / 00:01.180, 97Mb) Sushi: info Importing FSH text... (00:00.143 / 00:01.323, 97Mb) Sushi: info Preprocessed 52 documents with 1 aliases. (00:00.314 / 00:01.637, 97Mb) Sushi: info Imported 43 definitions and 34 instances. (00:00.027 / 00:01.664, 97Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.uv.tools#current... (00:00.002 / 00:01.666, 97Mb) Sushi: info Did not find hl7.fhir.uv.tools#current in /home/fhiruser/.fhir/packages. (00:00.022 / 00:01.688, 97Mb) Sushi: info Downloading hl7.fhir.uv.tools#current... https://build.fhir.org/ig/FHIR/fhir-tools-ig/branches/master/package.tgz (00:00.134 / 00:01.823, 97Mb) Sushi: info Downloaded hl7.fhir.uv.tools#current (00:00.017 / 00:01.841, 97Mb) Sushi: info Loaded package hl7.fhir.uv.tools#current (00:00.092 / 00:01.934, 97Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.terminology.r4#6.0.2... (00:00.524 / 00:02.458, 97Mb) Sushi: info Did not find hl7.terminology.r4#6.0.2 in /home/fhiruser/.fhir/packages. (00:00.022 / 00:02.480, 97Mb) Sushi: info Downloading hl7.terminology.r4#6.0.2... https://packages.fhir.org/hl7.terminology.r4/6.0.2 (00:00.000 / 00:02.480, 97Mb) Sushi: info Downloaded hl7.terminology.r4#6.0.2 (00:02.201 / 00:04.682, 97Mb) Sushi: info Loaded package hl7.terminology.r4#6.0.2 (00:01.846 / 00:06.528, 97Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.uv.extensions.r4#5.1.0... (00:00.455 / 00:06.984, 97Mb) Sushi: info Did not find hl7.fhir.uv.extensions.r4#5.1.0 in /home/fhiruser/.fhir/packages. (00:00.368 / 00:07.352, 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 / 00:07.352, 97Mb) Sushi: info Downloaded hl7.fhir.uv.extensions.r4#5.1.0 (00:01.866 / 00:09.219, 97Mb) Sushi: info Loaded package hl7.fhir.uv.extensions.r4#5.1.0 (00:01.154 / 00:10.373, 97Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.uv.ipa#1.0.0... (00:00.000 / 00:10.373, 97Mb) Sushi: info Did not find hl7.fhir.uv.ipa#1.0.0 in /home/fhiruser/.fhir/packages. (00:00.516 / 00:10.890, 97Mb) Sushi: info Downloading hl7.fhir.uv.ipa#1.0.0... https://packages.fhir.org/hl7.fhir.uv.ipa/1.0.0 (00:00.000 / 00:10.890, 97Mb) Sushi: info Downloaded hl7.fhir.uv.ipa#1.0.0 (00:00.922 / 00:11.813, 97Mb) Sushi: info Loaded package hl7.fhir.uv.ipa#1.0.0 (00:00.556 / 00:12.369, 97Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.r4.core#4.0.1... (00:00.000 / 00:12.370, 97Mb) Sushi: info Did not find hl7.fhir.r4.core#4.0.1 in /home/fhiruser/.fhir/packages. (00:00.547 / 00:12.917, 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 / 00:12.918, 97Mb) Sushi: info Downloaded hl7.fhir.r4.core#4.0.1 (00:03.242 / 00:16.161, 97Mb) Sushi: info Loaded package hl7.fhir.r4.core#4.0.1 (00:02.475 / 00:18.637, 97Mb) Sushi: info Converting FSH to FHIR resources... (00:00.090 / 00:18.727, 97Mb) Sushi: info Converted 40 FHIR StructureDefinitions. (01:26.638 / 01:45.365, 121Mb) Sushi: info Converted 1 FHIR CodeSystems. (00:00.176 / 01:45.542, 121Mb) Sushi: info Converted 2 FHIR ValueSets. (00:00.487 / 01:46.030, 121Mb) Sushi: info Converted 34 FHIR instances. (03:22.468 / 05:08.498, 145Mb) Sushi: info Exporting FHIR resources as JSON... (00:00.000 / 05:08.499, 145Mb) Sushi: info Exported 77 FHIR resources as JSON. (00:00.189 / 05:08.689, 145Mb) Sushi: info Assembling Implementation Guide sources... (00:00.002 / 05:08.692, 145Mb) Sushi: info Generated ImplementationGuide-hl7.fhir.fi.base.json (00:00.035 / 05:08.727, 145Mb) Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:00.000 / 05:08.727, 145Mb) Sushi: ========================= SUSHI RESULTS =========================== (00:00.001 / 05:08.728, 145Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 05:08.729, 145Mb) Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:00.000 / 05:08.729, 145Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 05:08.729, 145Mb) Sushi: | | 29 | 11 | 0 | 0 | | (00:00.000 / 05:08.730, 145Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 05:08.730, 145Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 05:08.730, 145Mb) Sushi: | | ValueSets | CodeSystems | Instances | | (00:00.000 / 05:08.730, 145Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 05:08.731, 145Mb) Sushi: | | 2 | 1 | 34 | | (00:00.000 / 05:08.731, 145Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 05:08.731, 145Mb) Sushi: | | (00:00.000 / 05:08.731, 145Mb) Sushi: =================================================================== (00:00.000 / 05:08.731, 145Mb) Sushi: | Valedictorian of the School of FSH! 0 Errors 0 Warnings | (00:00.000 / 05:08.731, 145Mb) Sushi: =================================================================== (00:00.000 / 05:08.732, 145Mb) Unable to load IG as an r5 IG - try R4 (property code is a class com.google.gson.JsonPrimitive looking for an object) (00:00.652 / 05:09.385, 37Mb) Load Template from https://github.com/fhir-fi/ig-template-fhir-fi (00:00.515 / 05:09.900, 77Mb) Load Template from fhir.base.template#current (00:00.701 / 05:10.601, 86Mb) 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 (00:03.838 / 05:14.440, 136Mb) Terminology Cache is at /scratch/repo/input-cache/txcache. Trimming now (00:00.002 / 05:14.442, 136Mb) Core Package hl7.fhir.r4.core#4.0.1 Running Terminology Log: /tmp/ohfu-fhir-ig-9840924708955960373.log Connect to Terminology Server at http://tx.fhir.org (00:36.680 / 05:51.123, 569Mb) Installing hl7.fhir.pubpack#0.1.8 to the package cache Fetching: Installing hl7.fhir.pubpack#0.1.8 done. Load Package hl7.fhir.pubpack#0.1.8 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#6.0.2 Load Package hl7.fhir.uv.extensions.r4#5.1.0 Installing hl7.terminology.r4#5.0.0 to the package cache Fetching: Installing hl7.terminology.r4#5.0.0 done. Load Package hl7.terminology.r4#5.0.0 Installing hl7.fhir.uv.smart-app-launch#2.0.0 to the package cache Fetching: Installing hl7.fhir.uv.smart-app-launch#2.0.0 done. Load Package hl7.fhir.uv.smart-app-launch#2.0.0 Load Package hl7.fhir.uv.ipa#1.0.0 Installing hl7.fhir.uv.tools#0.2.0 to the package cache Fetching: Installing hl7.fhir.uv.tools#0.2.0 done. Version mismatch. This IG is version 4.0.1, while the IG 'hl7.fhir.uv.tools' is from version 5.0.0 (will try to run anyway) (00:39.927 / 06:31.050, 579Mb) Load Package hl7.fhir.uv.tools#0.2.0 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 (00:03.685 / 06:34.736, 1Gb) Load Content (00:00.000 / 06:34.736, 1Gb) Using fi_FI as the default narrative language. (inferred from ImplementationGuide.jurisdiction=FI) (00:00.092 / 06:34.828, 1Gb) 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/pagecontent] as /scratch/repo/input/pagecontent Fetch https://hl7.fi/fhir/finnish-base-profiles/package-list.json for version check (00:03.473 / 06:38.302, 826Mb) Fetch http://hl7.org/fhir/uv/ipa/package-list.json for version check (00:00.724 / 06:39.027, 829Mb) Processing Conformance Resources (00:00.113 / 06:39.141, 837Mb) Load Dependency Info (00:00.003 / 06:39.144, 837Mb) Load Info (00:00.001 / 06:39.146, 837Mb) Load Resources (00:00.000 / 06:39.147, 840Mb) Load Paths (00:01.316 / 06:40.463, 965Mb) Generating Snapshots (00:00.000 / 06:40.463, 965Mb) Check R4 / R4B (00:01.746 / 06:42.210, 1Gb) Assign Comparison Ids (00:00.366 / 06:42.577, 1Gb) Propagating status (00:00.000 / 06:42.577, 1Gb) Generating Narratives (00:00.000 / 06:42.577, 1Gb) Validating Conformance Resources (00:06.123 / 06:48.701, 1Gb) Check profiles & code systems (00:10.809 / 06:59.511, 1Gb) Check realm rules (00:00.004 / 06:59.516, 1Gb) Previous Version Comparison (00:00.000 / 06:59.516, 1Gb) Installing hl7.fhir.fi.base#1.0.0 to the package cache Fetching: Installing hl7.fhir.fi.base#1.0.0 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. Validating Resources (00:13.997 / 07:13.513, 2Gb) Processing Provenance Records (00:07.264 / 07:20.778, 1Gb) Generating Outputs in /scratch/repo/output (00:00.000 / 07:20.778, 1Gb) Generate Native Outputs (00:00.289 / 07:21.068, 1Gb) Run Template (00:22.651 / 07:43.719, 3Gb) 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.extend: onGenerate: Template Done (00:01.445 / 07:45.165, 3Gb) Generate HTML Outputs (00:00.000 / 07:45.165, 3Gb) 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 (00:28.371 / 08:13.537, 6Gb) Generating Summary Outputs (00:00.000 / 08:13.537, 6Gb) DB Cumulative Time invested: 00:00:01.455 Sending Usage Stats to Server (00:12.874 / 08:26.411, 7Gb) ## Memory (MB): Use = 7475, Free = 11532, Total = 19008, Max = 19008 (00:00.007 / 08:26.419, 7Gb) Reclaiming memory... (00:00.000 / 08:26.419, 7Gb) ## Memory (MB): Use = 1498, Free = 17509, Total = 19008, Max = 19008 (00:01.362 / 08:27.782, 1Gb) Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.004 / 08:27.787, 1Gb) Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.000 / 08:27.787, 1Gb) * A failure to produce a fragment that is already logged in the output above (00:00.000 / 08:27.787, 1Gb) * A reference to a manually edited file that hasn't been provided (00:00.000 / 08:27.787, 1Gb) Jekyll: Source: /scratch/repo/temp/pages (00:00.494 / 08:28.282, 1Gb) Jekyll: Generating... (00:00.000 / 08:28.282, 1Gb) Jekyll: done in 8.462 seconds. (00:08.461 / 08:36.744, 1Gb) Checking Output HTML (00:05.004 / 08:41.748, 4Gb) found 1987 files (00:00.010 / 08:41.759, 4Gb) ........................................ ........................................ ... 1987 html files, 0 pages invalid xhtml (0%) (00:30.140 / 09:11.900, 3Gb) ... 859290 links, 8 broken links (0%) (00:00.000 / 09:11.900, 3Gb) Generate fragment-usage-analysis.csv (00:00.000 / 09:11.900, 3Gb) Build final .zip (00:00.007 / 09:11.908, 3Gb) Final .zip built (00:05.148 / 09:17.056, 3Gb) Built. Times: loading: 00:04.403, generate: 02:47.407, narrative generation: 00:06.123, realm-rules: 00:00.000, previous-version: 00:13.929, jekyll: 00:09.036, validation: 00:17.567 (#136), template: 00:01.445 (#3) (00:09.558 / 09:26.614, 4Gb) Generating QA (00:00.000 / 09:26.614, 4Gb) Validation output in /scratch/repo/output/qa.html Errors: 86, Warnings: 76, Info: 249, Broken Links: 8 (00:09.158 / 09:35.773, 9Gb) Finished. Max Memory Used = 9Gb (00:00.024 / 09:35.797, 9Gb)