INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/nmdp-ig/matchsync-ig --branch TestPublishBranch repo DEBUG:root:Time to deadline 35879.997754 seconds Cloning into 'repo'... 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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 35845.452974 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35844.332446 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 6s 8 packages are looking for funding run `npm fund` for details npm notice npm notice New major version of npm available! 9.8.1 -> 10.9.0 npm notice Changelog: npm notice Run `npm install -g npm@10.9.0` 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/nmdp-ig/matchsync-ig/ -out /scratch/repo DEBUG:root:Time to deadline 35838.188564 seconds FHIR IG Publisher Version 1.7.4 (Git# 9a619c4c6ceb). Built 2024-11-21T19:00:07.193Z (96 mins 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/nmdp-ig/matchsync-ig/ -out /scratch/repo Start Clock @ Thursday, November 21, 2024, 8:36:49 PM Coordinated Universal Time (2024-11-21T20:36:49Z) Build FHIR IG from /scratch/repo (00:00.038 / 00:00.039, 89Mb) API keys loaded from /etc/fhir-settings.json (00:00.005 / 00:00.044, 89Mb) Package Cache: /var/lib/.fhir/packages (00:00.004 / 00:00.048, 89Mb) Unable to load IG as an r5 IG - try R4 (property code is a class com.google.gson.JsonPrimitive looking for an object) (00:00.854 / 00:00.903, 37Mb) Load Template from fhir.base.template#current (00:00.853 / 00:01.756, 78Mb) 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 (00:06.281 / 00:08.037, 152Mb) Terminology Cache is at /scratch/repo/input-cache/txcache. Trimming now (00:00.040 / 00:08.077, 152Mb) Core Package hl7.fhir.r4.core#4.0.1 Installing hl7.fhir.r4.core#4.0.1 to the package cache Fetching: Installing hl7.fhir.r4.core#4.0.1 done. Running Terminology Log: /tmp/ohfu-fhir-ig-8158670765875665806.log Connect to Terminology Server at http://tx.fhir.org (00:44.862 / 00:52.940, 731Mb) 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 Installing hl7.fhir.uv.extensions.r4#5.1.0 to the package cache Fetching: Installing hl7.fhir.uv.extensions.r4#5.1.0 done. 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.us.core#4.0.0 to the package cache Fetching: Installing hl7.fhir.us.core#4.0.0 done. Installing hl7.fhir.uv.bulkdata#1.0.1 to the package cache Fetching: Installing hl7.fhir.uv.bulkdata#1.0.1 done. Load Package hl7.fhir.uv.bulkdata#1.0.1 Installing us.nlm.vsac#0.3.0 to the package cache Fetching: Installing us.nlm.vsac#0.3.0 done. Load Package us.nlm.vsac#0.3.0 Load Package hl7.fhir.us.core#4.0.0 Installing hl7.fhir.us.mcode#2.0.0 to the package cache Fetching: Installing hl7.fhir.us.mcode#2.0.0 done. Load Package hl7.fhir.us.mcode#2.0.0 Installing hl7.fhir.uv.genomics-reporting#2.0.0 to the package cache Fetching: Installing hl7.fhir.uv.genomics-reporting#2.0.0 done. Load Package hl7.fhir.uv.genomics-reporting#2.0.0 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 (01:41.817 / 02:34.757, 790Mb) Load Content (00:00.000 / 02:34.758, 790Mb) Using en-US as the default narrative language. (no language information in Implementation Guide or command line) (00:00.195 / 02:34.954, 814Mb) Publishing Content Failed: Unable to find the source file for StructureDefinition/hla-genotype: not specified, so tried StructureDefinition-hla-genotype.xml, hla-genotype.StructureDefinition.xml, StructureDefinition-hla-genotype.json, StructureDefinition/hla-genotype.xml, StructureDefinition/hla-genotype.json, hla-genotype.xml, and hla-genotype.json (and lowercase resource name variants) in dirs [/scratch/repo/fsh-generated/resources, /scratch/repo/fsh-generated/resources] (00:00.114 / 02:35.069, 830Mb) (00:00.000 / 02:35.069, 830Mb) Use -? to get command line help (00:00.000 / 02:35.069, 830Mb) (00:00.000 / 02:35.069, 830Mb) Stack Dump (for debugging): (00:00.000 / 02:35.069, 830Mb) java.lang.Exception: Unable to find the source file for StructureDefinition/hla-genotype: not specified, so tried StructureDefinition-hla-genotype.xml, hla-genotype.StructureDefinition.xml, StructureDefinition-hla-genotype.json, StructureDefinition/hla-genotype.xml, StructureDefinition/hla-genotype.json, hla-genotype.xml, and hla-genotype.json (and lowercase resource name variants) in dirs [/scratch/repo/fsh-generated/resources, /scratch/repo/fsh-generated/resources] at org.hl7.fhir.igtools.publisher.SimpleFetcher.fetch(SimpleFetcher.java:246) at org.hl7.fhir.igtools.publisher.Publisher.load(Publisher.java:4576) at org.hl7.fhir.igtools.publisher.Publisher.createIg(Publisher.java:1228) at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:1072) at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:14122)