INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/fhir-fi/finnish-smart --branch master repo DEBUG:root:Time to deadline 35879.997598 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 35879.57969 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35878.308973 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-smart/ -out /scratch/repo DEBUG:root:Time to deadline 35873.568664 seconds FHIR IG Publisher Version 1.6.20 (Git# 7bbd1ce5defe). Built 2024-08-13T18:33:37.376Z (66 hours 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-smart/ -out /scratch/repo Start Clock @ Friday, August 16, 2024, 1:07:14 PM Coordinated Universal Time (2024-08-16T13:07:14Z) Build FHIR IG from /scratch/repo (00:00.026 / 00:00.027, 89Mb) API keys loaded from /etc/fhir-settings.json (00:00.004 / 00:00.031, 89Mb) Package Cache: /var/lib/.fhir/packages (00:00.003 / 00:00.034, 89Mb) Run Sushi on /scratch/repo (00:00.005 / 00:00.040, 89Mb) Sushi: info Running SUSHI v3.11.0 (implements FHIR Shorthand specification v3.0.0-ballot) (00:00.559 / 00:00.599, 97Mb) Sushi: info Arguments: (00:00.000 / 00:00.600, 97Mb) Sushi: info --require-latest (00:00.000 / 00:00.600, 97Mb) Sushi: info --out /scratch/repo (00:00.000 / 00:00.601, 97Mb) Sushi: info /scratch/repo (00:00.000 / 00:00.601, 97Mb) Sushi: info Using configuration file: /scratch/repo/sushi-config.yaml (00:00.852 / 00:01.454, 97Mb) Sushi: info Importing FSH text... (00:00.125 / 00:01.580, 97Mb) Sushi: info Preprocessed 3 documents with 0 aliases. (00:00.112 / 00:01.692, 97Mb) Sushi: info Imported 1 definitions and 2 instances. (00:00.008 / 00:01.700, 97Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.uv.tools#current... (00:00.001 / 00:01.702, 97Mb) Sushi: info Did not find hl7.fhir.uv.tools#current in /home/fhiruser/.fhir/packages. (00:00.023 / 00:01.726, 97Mb) Sushi: info Downloading hl7.fhir.uv.tools#current... https://build.fhir.org/ig/FHIR/fhir-tools-ig/branches/master/package.tgz (00:00.116 / 00:01.842, 97Mb) Sushi: info Downloaded hl7.fhir.uv.tools#current (00:00.014 / 00:01.856, 97Mb) Sushi: info Loaded package hl7.fhir.uv.tools#current (00:00.085 / 00:01.942, 97Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.terminology.r4#6.0.2... (00:00.481 / 00:02.424, 97Mb) Sushi: info Did not find hl7.terminology.r4#6.0.2 in /home/fhiruser/.fhir/packages. (00:00.024 / 00:02.448, 97Mb) Sushi: info Downloading hl7.terminology.r4#6.0.2... https://packages.fhir.org/hl7.terminology.r4/6.0.2 (00:00.000 / 00:02.448, 97Mb) Sushi: info Downloaded hl7.terminology.r4#6.0.2 (00:01.967 / 00:04.416, 97Mb) Sushi: info Loaded package hl7.terminology.r4#6.0.2 (00:01.881 / 00:06.298, 97Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.uv.extensions.r4#5.1.0... (00:00.496 / 00:06.794, 97Mb) Sushi: info Did not find hl7.fhir.uv.extensions.r4#5.1.0 in /home/fhiruser/.fhir/packages. (00:00.369 / 00:07.164, 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 / 00:07.164, 97Mb) Sushi: info Downloaded hl7.fhir.uv.extensions.r4#5.1.0 (00:01.996 / 00:09.160, 97Mb) Sushi: info Loaded package hl7.fhir.uv.extensions.r4#5.1.0 (00:01.110 / 00:10.270, 97Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.uv.ipa#1.0.0... (00:00.000 / 00:10.271, 97Mb) Sushi: info Did not find hl7.fhir.uv.ipa#1.0.0 in /home/fhiruser/.fhir/packages. (00:00.551 / 00:10.823, 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 / 00:10.823, 97Mb) Sushi: info Downloaded hl7.fhir.uv.ipa#1.0.0 (00:01.070 / 00:11.894, 97Mb) Sushi: info Loaded package hl7.fhir.uv.ipa#1.0.0 (00:00.542 / 00:12.437, 97Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.uv.smart-app-launch#2.1.0... (00:00.000 / 00:12.437, 97Mb) Sushi: info Did not find hl7.fhir.uv.smart-app-launch#2.1.0 in /home/fhiruser/.fhir/packages. (00:00.554 / 00:12.992, 97Mb) Sushi: info Downloading hl7.fhir.uv.smart-app-launch#2.1.0... https://packages.fhir.org/hl7.fhir.uv.smart-app-launch/2.1.0 (00:00.000 / 00:12.992, 97Mb) Sushi: info Downloaded hl7.fhir.uv.smart-app-launch#2.1.0 (00:00.729 / 00:13.722, 97Mb) Sushi: info Loaded package hl7.fhir.uv.smart-app-launch#2.1.0 (00:00.549 / 00:14.271, 97Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.r4.core#4.0.1... (00:00.000 / 00:14.271, 97Mb) Sushi: info Did not find hl7.fhir.r4.core#4.0.1 in /home/fhiruser/.fhir/packages. (00:00.536 / 00:14.808, 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 / 00:14.808, 97Mb) Sushi: info Downloaded hl7.fhir.r4.core#4.0.1 (00:02.917 / 00:17.726, 97Mb) Sushi: info Loaded package hl7.fhir.r4.core#4.0.1 (00:02.375 / 00:20.102, 97Mb) Sushi: info Converting FSH to FHIR resources... (00:00.048 / 00:20.150, 97Mb) Sushi: info Converted 1 FHIR StructureDefinitions. (00:00.123 / 00:20.273, 97Mb) Sushi: info Converted 2 FHIR instances. (00:00.195 / 00:20.469, 97Mb) Sushi: info Exporting FHIR resources as JSON... (00:00.000 / 00:20.469, 97Mb) Sushi: info Exported 3 FHIR resources as JSON. (00:00.018 / 00:20.488, 97Mb) Sushi: info Assembling Implementation Guide sources... (00:00.001 / 00:20.489, 97Mb) Sushi: info Generated ImplementationGuide-hl7.fhir.fi.smart.json (00:00.034 / 00:20.523, 97Mb) Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:00.000 / 00:20.524, 97Mb) Sushi: ========================= SUSHI RESULTS =========================== (00:00.001 / 00:20.525, 97Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:20.526, 97Mb) Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:00.000 / 00:20.526, 97Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:20.526, 97Mb) Sushi: | | 1 | 0 | 0 | 0 | | (00:00.000 / 00:20.526, 97Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:20.527, 97Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:20.527, 97Mb) Sushi: | | ValueSets | CodeSystems | Instances | | (00:00.000 / 00:20.527, 97Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:20.527, 97Mb) Sushi: | | 0 | 0 | 2 | | (00:00.000 / 00:20.528, 97Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:20.528, 97Mb) Sushi: | | (00:00.000 / 00:20.528, 97Mb) Sushi: =================================================================== (00:00.000 / 00:20.528, 97Mb) Sushi: | Ex-clam-ation point! 0 Errors 0 Warnings | (00:00.000 / 00:20.528, 97Mb) Sushi: =================================================================== (00:00.000 / 00:20.528, 97Mb) Unable to load IG as an r5 IG - try R4 (property code is a class com.google.gson.JsonPrimitive looking for an object) (00:00.635 / 00:21.164, 37Mb) Load Template from https://github.com/fhir-fi/ig-template-fhir-fi (00:00.498 / 00:21.662, 70Mb) Load Template from fhir.base.template#current (00:00.820 / 00:22.482, 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 (00:03.848 / 00:26.331, 119Mb) Terminology Cache is at /scratch/repo/input-cache/txcache. Trimming now (00:00.003 / 00:26.334, 119Mb) Core Package hl7.fhir.r4.core#4.0.1 Running Terminology Log: /tmp/ohfu-fhir-ig-14077161544795561963.log Connect to Terminology Server at http://tx.fhir.org (00:40.400 / 01:06.734, 555Mb) 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 Load Package hl7.fhir.uv.smart-app-launch#2.1.0 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) (00:40.579 / 01:47.313, 550Mb) 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 (00:03.704 / 01:51.017, 1Gb) Load Content (00:00.000 / 01:51.018, 1Gb) Using fi_FI as the default narrative language. (inferred from ImplementationGuide.jurisdiction=FI) (00:00.052 / 01:51.070, 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-smart/package-list.json for version check (00:00.257 / 01:51.327, 1Gb) Fetch http://hl7.org/fhir/uv/ipa/package-list.json for version check (00:00.632 / 01:51.960, 1Gb) Processing Conformance Resources (00:00.122 / 01:52.083, 1Gb) Load Dependency Info (00:00.000 / 01:52.083, 1Gb) Load Info (00:00.000 / 01:52.084, 1Gb) Load Resources (00:00.000 / 01:52.085, 1Gb) Load Paths (00:00.145 / 01:52.230, 1Gb) Generating Snapshots (00:00.000 / 01:52.231, 1Gb) Check R4 / R4B (00:00.272 / 01:52.503, 328Mb) Assign Comparison Ids (00:00.015 / 01:52.519, 332Mb) Propagating status (00:00.000 / 01:52.519, 334Mb) Generating Narratives (00:00.000 / 01:52.519, 334Mb) Validating Conformance Resources (00:00.498 / 01:53.018, 488Mb) Error from http://tx.fhir.org/r4: The code System "urn:ietf:bcp:13" has a grammar, and cannot be enumerated directly [x-request-id: 152-1406558] Check profiles & code systems (00:04.121 / 01:57.139, 472Mb) Check realm rules (00:00.003 / 01:57.143, 472Mb) Previous Version Comparison (00:00.001 / 01:57.144, 472Mb) Installing hl7.fhir.fi.smart#1.0.0 to the package cache Fetching: Installing hl7.fhir.fi.smart#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 (00:11.235 / 02:08.379, 992Mb) Processing Provenance Records (00:00.016 / 02:08.396, 992Mb) Generating Outputs in /scratch/repo/output (00:00.000 / 02:08.396, 992Mb) Generate Native Outputs (00:00.255 / 02:08.652, 1000Mb) Run Template (00:01.455 / 02:10.107, 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.extend: onGenerate: Template Done (00:01.050 / 02:11.158, 1Gb) Generate HTML Outputs (00:00.000 / 02:11.158, 1Gb) 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 (00:03.442 / 02:14.600, 1Gb) Generating Summary Outputs (00:00.000 / 02:14.601, 1Gb) DB Cumulative Time invested: 00:00:00.272 Sending Usage Stats to Server (00:07.276 / 02:21.878, 1Gb) ## Memory (MB): Use = 1394, Free = 17613, Total = 19008, Max = 19008 (00:00.006 / 02:21.884, 1Gb) Reclaiming memory... (00:00.000 / 02:21.884, 1Gb) ## Memory (MB): Use = 829, Free = 18178, Total = 19008, Max = 19008 (00:00.639 / 02:22.527, 837Mb) Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.004 / 02:22.529, 841Mb) Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.000 / 02:22.529, 841Mb) * A failure to produce a fragment that is already logged in the output above (00:00.000 / 02:22.529, 841Mb) * A reference to a manually edited file that hasn't been provided (00:00.000 / 02:22.529, 841Mb) Jekyll: Source: /scratch/repo/temp/pages (00:00.450 / 02:22.980, 845Mb) Jekyll: Generating... (00:00.000 / 02:22.980, 845Mb) Jekyll: done in 0.974 seconds. (00:00.973 / 02:23.953, 845Mb) Checking Output HTML (00:01.126 / 02:25.080, 1Gb) found 581 files (00:00.004 / 02:25.084, 1Gb) ......................................... ......................................... ... 581 html files, 0 pages invalid xhtml (0%) (00:02.125 / 02:27.210, 2Gb) ... 30579 links, 0 broken links (0%) (00:00.000 / 02:27.211, 2Gb) Generate fragment-usage-analysis.csv (00:00.000 / 02:27.211, 2Gb) Build final .zip (00:00.009 / 02:27.220, 2Gb) Final .zip built (00:01.554 / 02:28.774, 2Gb) Built. Times: loading: 00:01.064, generate: 00:39.140, narrative generation: 00:00.498, realm-rules: 00:00.001, previous-version: 00:11.220, jekyll: 00:01.442, validation: 00:04.136 (#5), template: 00:01.050 (#3) (00:02.469 / 02:31.244, 2Gb) Generating QA (00:00.000 / 02:31.244, 2Gb) Validation output in /scratch/repo/output/qa.html Errors: 2, Warnings: 3, Info: 1, Broken Links: 0 (00:00.304 / 02:31.549, 2Gb) Finished. Max Memory Used = 2Gb (00:00.003 / 02:31.552, 2Gb)