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 35879.997821 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 35879.179048 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35877.557838 seconds npm WARN deprecated rimraf@2.6.3: Rimraf versions prior to v4 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. 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/fhir-fi/finnish-base-profiles/ -out /scratch/repo DEBUG:root:Time to deadline 35871.867177 seconds FHIR IG Publisher Version 1.6.22 (Git# 33e2566af5b4). Built 2024-08-28T19:21:55.278Z (10 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 @ Sunday, September 8, 2024, 3:17:09 PM Coordinated Universal Time (2024-09-08T15:17:09Z) Build FHIR IG from /scratch/repo (00:00.033 / 00:00.034, 89Mb) API keys loaded from /etc/fhir-settings.json (00:00.004 / 00:00.037, 89Mb) Package Cache: /var/lib/.fhir/packages (00:00.003 / 00:00.041, 89Mb) Run Sushi on /scratch/repo (00:00.009 / 00:00.050, 89Mb) Sushi: info Running SUSHI v3.11.1 (implements FHIR Shorthand specification v3.0.0-ballot) (00:00.691 / 00:00.742, 113Mb) Sushi: info Arguments: (00:00.000 / 00:00.742, 113Mb) Sushi: info --require-latest (00:00.000 / 00:00.742, 113Mb) Sushi: info --out /scratch/repo (00:00.000 / 00:00.742, 113Mb) Sushi: info /scratch/repo (00:00.000 / 00:00.743, 113Mb) Sushi: info Using configuration file: /scratch/repo/sushi-config.yaml (00:00.935 / 00:01.679, 113Mb) Sushi: info Importing FSH text... (00:00.175 / 00:01.855, 113Mb) Sushi: info Preprocessed 52 documents with 1 aliases. (00:00.406 / 00:02.261, 113Mb) Sushi: info Imported 43 definitions and 34 instances. (00:00.033 / 00:02.294, 113Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.uv.tools#current... (00:00.002 / 00:02.297, 113Mb) Sushi: info Did not find hl7.fhir.uv.tools#current in /home/fhiruser/.fhir/packages. (00:00.029 / 00:02.327, 113Mb) Sushi: info Downloading hl7.fhir.uv.tools#current... https://build.fhir.org/ig/FHIR/fhir-tools-ig/branches/master/package.tgz (00:00.175 / 00:02.502, 113Mb) Sushi: info Downloaded hl7.fhir.uv.tools#current (00:00.017 / 00:02.519, 113Mb) Sushi: info Loaded package hl7.fhir.uv.tools#current (00:00.112 / 00:02.631, 113Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.terminology.r4#6.0.2... (00:00.551 / 00:03.182, 113Mb) Sushi: info Did not find hl7.terminology.r4#6.0.2 in /home/fhiruser/.fhir/packages. (00:00.028 / 00:03.211, 113Mb) Sushi: info Downloading hl7.terminology.r4#6.0.2... https://packages.fhir.org/hl7.terminology.r4/6.0.2 (00:00.000 / 00:03.211, 113Mb) Sushi: info Downloaded hl7.terminology.r4#6.0.2 (00:02.187 / 00:05.399, 113Mb) Sushi: info Loaded package hl7.terminology.r4#6.0.2 (00:02.249 / 00:07.648, 113Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.uv.extensions.r4#5.1.0... (00:00.443 / 00:08.091, 113Mb) Sushi: info Did not find hl7.fhir.uv.extensions.r4#5.1.0 in /home/fhiruser/.fhir/packages. (00:00.540 / 00:08.632, 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 / 00:08.632, 113Mb) Sushi: info Downloaded hl7.fhir.uv.extensions.r4#5.1.0 (00:01.982 / 00:10.615, 113Mb) Sushi: info Loaded package hl7.fhir.uv.extensions.r4#5.1.0 (00:01.478 / 00:12.094, 113Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.uv.ipa#1.0.0... (00:00.000 / 00:12.094, 113Mb) Sushi: info Did not find hl7.fhir.uv.ipa#1.0.0 in /home/fhiruser/.fhir/packages. (00:00.810 / 00:12.905, 113Mb) Sushi: info Downloading hl7.fhir.uv.ipa#1.0.0... https://packages.fhir.org/hl7.fhir.uv.ipa/1.0.0 (00:00.000 / 00:12.905, 113Mb) Sushi: info Downloaded hl7.fhir.uv.ipa#1.0.0 (00:01.207 / 00:14.112, 113Mb) Sushi: info Loaded package hl7.fhir.uv.ipa#1.0.0 (00:00.797 / 00:14.910, 113Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.r4.core#4.0.1... (00:00.000 / 00:14.911, 113Mb) Sushi: info Did not find hl7.fhir.r4.core#4.0.1 in /home/fhiruser/.fhir/packages. (00:00.779 / 00:15.690, 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 / 00:15.690, 113Mb) Sushi: info Downloaded hl7.fhir.r4.core#4.0.1 (00:02.809 / 00:18.499, 113Mb) Sushi: info Loaded package hl7.fhir.r4.core#4.0.1 (00:03.110 / 00:21.610, 113Mb) Sushi: info Converting FSH to FHIR resources... (00:00.121 / 00:21.731, 113Mb) Sushi: info Converted 40 FHIR StructureDefinitions. (00:03.128 / 00:24.859, 113Mb) Sushi: info Converted 1 FHIR CodeSystems. (00:00.022 / 00:24.882, 113Mb) Sushi: info Converted 2 FHIR ValueSets. (00:00.062 / 00:24.944, 113Mb) Sushi: info Converted 34 FHIR instances. (00:02.743 / 00:27.687, 113Mb) Sushi: info Exporting FHIR resources as JSON... (00:00.001 / 00:27.688, 113Mb) Sushi: info Exported 77 FHIR resources as JSON. (00:00.186 / 00:27.875, 113Mb) Sushi: info Assembling Implementation Guide sources... (00:00.004 / 00:27.879, 113Mb) Sushi: info Generated ImplementationGuide-hl7.fhir.fi.base.json (00:00.045 / 00:27.924, 113Mb) Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:00.000 / 00:27.924, 113Mb) Sushi: ========================= SUSHI RESULTS =========================== (00:00.001 / 00:27.926, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:27.927, 113Mb) Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:00.000 / 00:27.927, 113Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:27.927, 113Mb) Sushi: | | 29 | 11 | 0 | 0 | | (00:00.000 / 00:27.928, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:27.928, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:27.928, 113Mb) Sushi: | | ValueSets | CodeSystems | Instances | | (00:00.000 / 00:27.928, 113Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:27.929, 113Mb) Sushi: | | 2 | 1 | 34 | | (00:00.000 / 00:27.929, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:27.929, 113Mb) Sushi: | | (00:00.000 / 00:27.929, 113Mb) Sushi: =================================================================== (00:00.000 / 00:27.930, 113Mb) Sushi: | You're catching on now! 0 Errors 0 Warnings | (00:00.000 / 00:27.930, 113Mb) Sushi: =================================================================== (00:00.000 / 00:27.930, 113Mb) Unable to load IG as an r5 IG - try R4 (property code is a class com.google.gson.JsonPrimitive looking for an object) (00:00.856 / 00:28.787, 37Mb) Load Template from https://github.com/fhir-fi/ig-template-fhir-fi (00:00.735 / 00:29.523, 77Mb) Load Template from fhir.base.template#current (00:00.866 / 00:30.390, 102Mb) 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 (00:05.511 / 00:35.901, 143Mb) Terminology Cache is at /scratch/repo/input-cache/txcache. Trimming now (00:00.002 / 00:35.904, 143Mb) Core Package hl7.fhir.r4.core#4.0.1 Running Terminology Log: /tmp/ohfu-fhir-ig-4182711379539397592.log Connect to Terminology Server at http://tx.fhir.org (00:38.690 / 01:14.595, 578Mb) 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) (00:47.636 / 02:02.231, 534Mb) 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 (00:04.206 / 02:06.438, 1Gb) Load Content (00:00.000 / 02:06.439, 1Gb) Using fi_FI as the default narrative language. (inferred from ImplementationGuide.jurisdiction=FI) (00:00.126 / 02:06.565, 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 (00:04.107 / 02:10.672, 792Mb) Fetch http://hl7.org/fhir/uv/ipa/package-list.json for version check (00:00.762 / 02:11.435, 803Mb) Processing Conformance Resources (00:00.199 / 02:11.635, 805Mb) Load Dependency Info (00:00.003 / 02:11.638, 805Mb) Load Info (00:00.003 / 02:11.642, 805Mb) Load Resources (00:00.001 / 02:11.643, 816Mb) Load Paths (00:02.562 / 02:14.205, 1016Mb) Generating Snapshots (00:00.000 / 02:14.206, 1016Mb) Check R4 / R4B (00:02.762 / 02:16.969, 1Gb) Assign Comparison Ids (00:00.322 / 02:17.291, 1Gb) Propagating status (00:00.000 / 02:17.292, 1Gb) Generating Narratives (00:00.000 / 02:17.292, 1Gb) Validating Conformance Resources (00:10.115 / 02:27.408, 1Gb) Check profiles & code systems (00:17.332 / 02:44.740, 1Gb) Check realm rules (00:00.007 / 02:44.747, 1Gb) Previous Version Comparison (00:00.000 / 02:44.748, 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 (00:20.459 / 03:05.208, 1Gb) Processing Provenance Records (00:10.539 / 03:15.747, 1Gb) Generating Outputs in /scratch/repo/output (00:00.000 / 03:15.748, 1Gb) Generate Native Outputs (00:00.343 / 03:16.091, 1Gb) Run Template (00:24.104 / 03:40.196, 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 (00:01.885 / 03:42.081, 3Gb) Generate HTML Outputs (00:00.000 / 03:42.082, 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 (00:44.921 / 04:27.004, 6Gb) Generating Summary Outputs (00:00.000 / 04:27.004, 6Gb) DB Cumulative Time invested: 00:00:01.653 Sending Usage Stats to Server (00:12.439 / 04:39.444, 1Gb) ## Memory (MB): Use = 2034, Free = 16973, Total = 19008, Max = 19008 (00:00.010 / 04:39.455, 1Gb) Reclaiming memory... (00:00.000 / 04:39.455, 1Gb) ## Memory (MB): Use = 1499, Free = 17508, Total = 19008, Max = 19008 (00:01.868 / 04:41.324, 1Gb) Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.002 / 04:41.326, 1Gb) Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.000 / 04:41.326, 1Gb) * A failure to produce a fragment that is already logged in the output above (00:00.000 / 04:41.326, 1Gb) * A reference to a manually edited file that hasn't been provided (00:00.000 / 04:41.326, 1Gb) Jekyll: Source: /scratch/repo/temp/pages (00:00.573 / 04:41.900, 1Gb) Jekyll: Generating... (00:00.000 / 04:41.900, 1Gb) Jekyll: done in 10.983 seconds. (00:10.982 / 04:52.883, 1Gb) Checking Output HTML (00:07.889 / 05:00.772, 4Gb) found 1987 files (00:00.013 / 05:00.785, 4Gb) ........................................ ........................................ ... 1987 html files, 0 pages invalid xhtml (0%) (00:57.939 / 05:58.725, 10Gb) ... 859302 links, 8 broken links (0%) (00:00.000 / 05:58.725, 10Gb) Generate fragment-usage-analysis.csv (00:00.000 / 05:58.726, 10Gb) Build final .zip (00:00.008 / 05:58.734, 10Gb) Final .zip built (00:06.590 / 06:05.325, 10Gb) Built. Times: loading: 00:05.194, generate: 04:10.095, narrative generation: 00:10.114, realm-rules: 00:00.000, previous-version: 00:20.371, jekyll: 00:11.603, validation: 00:27.441 (#136), template: 00:01.884 (#3) (00:16.521 / 06:21.847, 11Gb) Generating QA (00:00.000 / 06:21.847, 11Gb) Validation output in /scratch/repo/output/qa.html Errors: 86, Warnings: 76, Info: 249, Broken Links: 8 (00:14.844 / 06:36.692, 5Gb) Finished. Max Memory Used = 11Gb (00:00.051 / 06:36.743, 5Gb)