INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/medizininformatik-initiative/kerndatensatzmodul-molekulares-tumorboard --branch dev repo DEBUG:root:Time to deadline 35879.997868 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 35879.025772 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35877.956107 seconds 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. npm WARN deprecated rimraf@2.6.3: Rimraf versions prior to v4 are no longer supported added 140 packages in 6s 15 packages are looking for funding run `npm fund` for details npm notice npm notice New major version of npm available! 9.8.1 -> 11.5.2 npm notice Changelog: npm notice Run `npm install -g npm@11.5.2` 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/medizininformatik-initiative/kerndatensatzmodul-molekulares-tumorboard/ -out /scratch/repo DEBUG:root:Time to deadline 35871.210082 seconds FHIR IG Publisher Version 2.0.12 (Git# 1e7f5af908a3). Built 2025-07-27T20:11:20.240Z (3 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/medizininformatik-initiative/kerndatensatzmodul-molekulares-tumorboard/ -out /scratch/repo Character encoding = UTF-8 / UTF-8 Start Clock @ Thursday, July 31, 2025, 7:42:17 PM Coordinated Universal Time (2025-07-31T19:42:17Z) Build FHIR IG from /scratch/repo (00:00.025 / 00:00.026, 97Mb) API keys loaded from /etc/fhir-settings.json (00:00.002 / 00:00.028, 97Mb) Package Cache: /var/lib/.fhir/packages (00:00.003 / 00:00.032, 97Mb) Found dependency on de.basisprofil.r4#1.5.3 in Sushi config. Pre-installing (00:00.005 / 00:00.037, 97Mb) Installing de.basisprofil.r4#1.5.3 to the package cache  Fetching:  Installing de.basisprofil.r4#1.5.3  done. Found dependency on de.medizininformatikinitiative.kerndatensatz.biobank#2025.0.x in Sushi config. Pre-installing (00:02.643 / 00:02.680, 79Mb) Installing de.medizininformatikinitiative.kerndatensatz.biobank#2025.0.x to the package cache  Fetching:  Installing de.medizininformatikinitiative.kerndatensatz.biobank#2025.0.4  done. Found dependency on de.medizininformatikinitiative.kerndatensatz.consent#2025.0.x in Sushi config. Pre-installing (00:00.910 / 00:03.590, 87Mb) Installing de.medizininformatikinitiative.kerndatensatz.consent#2025.0.x to the package cache  Fetching:  Installing de.medizininformatikinitiative.kerndatensatz.consent#2025.0.4  done. Found dependency on de.medizininformatikinitiative.kerndatensatz.diagnose#2025.0.x in Sushi config. Pre-installing (00:00.334 / 00:03.925, 95Mb) Installing de.medizininformatikinitiative.kerndatensatz.diagnose#2025.0.x to the package cache  Fetching:  Installing de.medizininformatikinitiative.kerndatensatz.diagnose#2025.0.0  done. Found dependency on de.medizininformatikinitiative.kerndatensatz.fall#2025.0.x in Sushi config. Pre-installing (00:00.477 / 00:04.402, 100Mb) Installing de.medizininformatikinitiative.kerndatensatz.fall#2025.0.x to the package cache  Fetching:  Installing de.medizininformatikinitiative.kerndatensatz.fall#2025.0.0  done. Found dependency on de.medizininformatikinitiative.kerndatensatz.medikation#2025.0.x in Sushi config. Pre-installing (00:00.385 / 00:04.788, 103Mb) Installing de.medizininformatikinitiative.kerndatensatz.medikation#2025.0.x to the package cache  Fetching:  Installing de.medizininformatikinitiative.kerndatensatz.medikation#2025.0.0  done. Found dependency on de.medizininformatikinitiative.kerndatensatz.meta#2025.0.x in Sushi config. Pre-installing (00:00.626 / 00:05.415, 111Mb) Installing de.medizininformatikinitiative.kerndatensatz.meta#2025.0.x to the package cache  Fetching:  Installing de.medizininformatikinitiative.kerndatensatz.meta#2025.0.0  done. Found dependency on de.medizininformatikinitiative.kerndatensatz.molgen#2026.0.0-alpha.1 in Sushi config. Pre-installing (00:01.578 / 00:06.993, 135Mb) Installing de.medizininformatikinitiative.kerndatensatz.molgen#2026.0.0-alpha.1 to the package cache  Fetching:  Installing de.medizininformatikinitiative.kerndatensatz.molgen#2026.0.0-alpha.1  done. Found dependency on de.medizininformatikinitiative.kerndatensatz.onkologie#2025.1.0-beta in Sushi config. Pre-installing (00:01.203 / 00:08.196, 143Mb) Installing de.medizininformatikinitiative.kerndatensatz.onkologie#2025.1.0-beta to the package cache  Fetching:  Installing de.medizininformatikinitiative.kerndatensatz.onkologie#2025.1.0-beta  done. Found dependency on de.medizininformatikinitiative.kerndatensatz.patho#2025.0.x in Sushi config. Pre-installing (00:02.143 / 00:10.340, 183Mb) Installing de.medizininformatikinitiative.kerndatensatz.patho#2025.0.x to the package cache  Fetching:  Installing de.medizininformatikinitiative.kerndatensatz.patho#2025.0.2  done. Found dependency on de.medizininformatikinitiative.kerndatensatz.person#2025.0.x in Sushi config. Pre-installing (00:00.791 / 00:11.132, 191Mb) Installing de.medizininformatikinitiative.kerndatensatz.person#2025.0.x to the package cache  Fetching:  Installing de.medizininformatikinitiative.kerndatensatz.person#2025.0.0  done. Found dependency on de.medizininformatikinitiative.kerndatensatz.prozedur#2025.0.x in Sushi config. Pre-installing (00:00.446 / 00:11.578, 199Mb) Installing de.medizininformatikinitiative.kerndatensatz.prozedur#2025.0.x to the package cache  Fetching:  Installing de.medizininformatikinitiative.kerndatensatz.prozedur#2025.0.0  done. Found dependency on de.medizininformatikinitiative.kerndatensatz.studie#2025.0.x in Sushi config. Pre-installing (00:00.538 / 00:12.116, 199Mb) Installing de.medizininformatikinitiative.kerndatensatz.studie#2025.0.x to the package cache  Fetching:  Installing de.medizininformatikinitiative.kerndatensatz.studie#2025.0.0  done. Found dependency on hl7.fhir.uv.genomics-reporting#3.0.0 in Sushi config. Pre-installing (00:00.556 / 00:12.672, 212Mb) Installing hl7.fhir.uv.genomics-reporting#3.0.0 to the package cache  Fetching:  Installing hl7.fhir.uv.genomics-reporting#3.0.0  done. Run Sushi on /scratch/repo (00:01.809 / 00:14.481, 231Mb) Sushi: info Running SUSHI v3.16.3 (implements FHIR Shorthand specification v3.0.0) (00:00.761 / 00:15.243, 231Mb) Sushi: info Arguments: (00:00.000 / 00:15.243, 231Mb) Sushi: info --require-latest (00:00.000 / 00:15.243, 231Mb) Sushi: info --out /scratch/repo (00:00.000 / 00:15.244, 231Mb) Sushi: info /scratch/repo (00:00.000 / 00:15.244, 231Mb) Sushi: info Using configuration file: /scratch/repo/sushi-config.yaml (00:01.059 / 00:16.304, 231Mb) Sushi: info Importing FSH text... (00:00.165 / 00:16.469, 231Mb) Sushi: info Preprocessed 192 documents with 118 aliases. (00:00.916 / 00:17.385, 231Mb) Sushi: info Imported 106 definitions and 196 instances. (00:01.155 / 00:18.541, 231Mb) Sushi: info Loaded virtual package sushi-r5forR4#1.0.0 with 7 resources (00:00.169 / 00:18.710, 231Mb) Sushi: info Resolved hl7.fhir.uv.tools.r4#latest to concrete version 0.7.1 (00:00.627 / 00:19.338, 231Mb) Sushi: info Attempting to download hl7.fhir.uv.tools.r4#0.7.1 from https://packages.fhir.org/hl7.fhir.uv.tools.r4/0.7.1 (00:00.001 / 00:19.339, 231Mb) Sushi: info Downloaded hl7.fhir.uv.tools.r4#0.7.1 (00:00.762 / 00:20.101, 231Mb) Sushi: info Cached hl7.fhir.uv.tools.r4#0.7.1 to /home/fhiruser/.fhir/packages/hl7.fhir.uv.tools.r4#0.7.1 (00:00.002 / 00:20.104, 231Mb) Sushi: info Loaded hl7.fhir.uv.tools.r4#0.7.1 with 105 resources (00:00.081 / 00:20.186, 231Mb) Sushi: info Resolved hl7.terminology.r4#latest to concrete version 6.5.0 (00:00.448 / 00:20.635, 231Mb) Sushi: info Attempting to download hl7.terminology.r4#6.5.0 from https://packages.fhir.org/hl7.terminology.r4/6.5.0 (00:00.000 / 00:20.635, 231Mb) Sushi: info Downloaded hl7.terminology.r4#6.5.0 (00:02.634 / 00:23.270, 231Mb) Sushi: info Cached hl7.terminology.r4#6.5.0 to /home/fhiruser/.fhir/packages/hl7.terminology.r4#6.5.0 (00:00.001 / 00:23.272, 231Mb) Sushi: info Loaded hl7.terminology.r4#6.5.0 with 4392 resources (00:01.928 / 00:25.200, 231Mb) Sushi: info Resolved hl7.fhir.uv.extensions.r4#latest to concrete version 5.2.0 (00:00.440 / 00:25.640, 231Mb) Sushi: info Attempting to download hl7.fhir.uv.extensions.r4#5.2.0 from https://packages.fhir.org/hl7.fhir.uv.extensions.r4/5.2.0 (00:00.000 / 00:25.641, 231Mb) Sushi: info Downloaded hl7.fhir.uv.extensions.r4#5.2.0 (00:01.314 / 00:26.955, 231Mb) Sushi: info Cached hl7.fhir.uv.extensions.r4#5.2.0 to /home/fhiruser/.fhir/packages/hl7.fhir.uv.extensions.r4#5.2.0 (00:00.001 / 00:26.957, 231Mb) Sushi: info Loaded hl7.fhir.uv.extensions.r4#5.2.0 with 759 resources (00:00.339 / 00:27.297, 231Mb) Sushi: info Loaded de.basisprofil.r4#1.5.3 with 166 resources (00:00.058 / 00:27.355, 231Mb) Sushi: info Resolved de.medizininformatikinitiative.kerndatensatz.biobank#2025.0.x to concrete version 2025.0.4 (00:00.447 / 00:27.803, 231Mb) Sushi: info Loaded de.medizininformatikinitiative.kerndatensatz.biobank#2025.0.4 with 24 resources (00:00.018 / 00:27.821, 231Mb) Sushi: info Resolved de.medizininformatikinitiative.kerndatensatz.consent#2025.0.x to concrete version 2025.0.4 (00:00.426 / 00:28.247, 231Mb) Sushi: info Loaded de.medizininformatikinitiative.kerndatensatz.consent#2025.0.4 with 15 resources (00:00.006 / 00:28.254, 231Mb) Sushi: info Resolved de.medizininformatikinitiative.kerndatensatz.diagnose#2025.0.x to concrete version 2025.0.0 (00:00.437 / 00:28.691, 231Mb) Sushi: info Loaded de.medizininformatikinitiative.kerndatensatz.diagnose#2025.0.0 with 8 resources (00:00.008 / 00:28.700, 231Mb) Sushi: info Resolved de.medizininformatikinitiative.kerndatensatz.fall#2025.0.x to concrete version 2025.0.0 (00:00.538 / 00:29.238, 231Mb) Sushi: info Loaded de.medizininformatikinitiative.kerndatensatz.fall#2025.0.0 with 11 resources (00:00.009 / 00:29.248, 231Mb) Sushi: info Resolved de.medizininformatikinitiative.kerndatensatz.medikation#2025.0.x to concrete version 2025.0.0 (00:00.430 / 00:29.678, 231Mb) Sushi: info Loaded de.medizininformatikinitiative.kerndatensatz.medikation#2025.0.0 with 13 resources (00:00.029 / 00:29.708, 231Mb) Sushi: info Resolved de.medizininformatikinitiative.kerndatensatz.meta#2025.0.x to concrete version 2025.0.0 (00:00.432 / 00:30.140, 231Mb) Sushi: info Loaded de.medizininformatikinitiative.kerndatensatz.meta#2025.0.0 with 110 resources (00:00.038 / 00:30.179, 231Mb) Sushi: info Loaded de.medizininformatikinitiative.kerndatensatz.molgen#2026.0.0-alpha.1 with 34 resources (00:00.042 / 00:30.222, 231Mb) Sushi: info Loaded de.medizininformatikinitiative.kerndatensatz.onkologie#2025.1.0-beta with 184 resources (00:00.146 / 00:30.368, 231Mb) Sushi: info Resolved de.medizininformatikinitiative.kerndatensatz.patho#2025.0.x to concrete version 2025.0.2 (00:00.440 / 00:30.809, 231Mb) Sushi: info Loaded de.medizininformatikinitiative.kerndatensatz.patho#2025.0.2 with 28 resources (00:00.037 / 00:30.846, 231Mb) Sushi: info Resolved de.medizininformatikinitiative.kerndatensatz.person#2025.0.x to concrete version 2025.0.0 (00:00.453 / 00:31.300, 231Mb) Sushi: info Loaded de.medizininformatikinitiative.kerndatensatz.person#2025.0.0 with 10 resources (00:00.016 / 00:31.317, 231Mb) Sushi: info Resolved de.medizininformatikinitiative.kerndatensatz.prozedur#2025.0.x to concrete version 2025.0.0 (00:00.438 / 00:31.755, 231Mb) Sushi: info Loaded de.medizininformatikinitiative.kerndatensatz.prozedur#2025.0.0 with 8 resources (00:00.006 / 00:31.761, 231Mb) Sushi: info Resolved de.medizininformatikinitiative.kerndatensatz.studie#2025.0.x to concrete version 2025.0.0 (00:00.425 / 00:32.187, 231Mb) Sushi: info Loaded de.medizininformatikinitiative.kerndatensatz.studie#2025.0.0 with 40 resources (00:00.017 / 00:32.204, 231Mb) Sushi: info Loaded hl7.fhir.uv.genomics-reporting#3.0.0 with 93 resources (00:00.076 / 00:32.281, 231Mb) Sushi: info Attempting to download hl7.fhir.r4.core#4.0.1 from https://packages.fhir.org/hl7.fhir.r4.core/4.0.1 (00:00.000 / 00:32.281, 231Mb) Sushi: info Downloaded hl7.fhir.r4.core#4.0.1 (00:02.999 / 00:35.280, 231Mb) Sushi: info Cached hl7.fhir.r4.core#4.0.1 to /home/fhiruser/.fhir/packages/hl7.fhir.r4.core#4.0.1 (00:00.001 / 00:35.282, 231Mb) Sushi: info Loaded hl7.fhir.r4.core#4.0.1 with 4581 resources (00:01.800 / 00:37.083, 231Mb) Sushi: info Loaded virtual package sushi-local#LOCAL with 0 resources (00:00.012 / 00:37.095, 231Mb) Sushi: info Converting FSH to FHIR resources... (00:00.026 / 00:37.122, 231Mb) Sushi: error Structure Definition https://www.medizininformatik-initiative.de/fhir/modul-studie/StructureDefinition/mii-pr-studie-studie is missing a snapshot. Snapshot is required for import. (00:03.274 / 00:40.397, 231Mb) Sushi: File: /scratch/repo/input/fsh/profiles/Beschluss-Therapieplan/mii-pr-mtb-studie.fsh (00:00.000 / 00:40.397, 231Mb) Sushi: Line: 2 - 26 (00:00.000 / 00:40.397, 231Mb) Sushi: info Converted 61 FHIR StructureDefinitions. (00:12.118 / 00:52.516, 231Mb) Sushi: info Converted 18 FHIR CodeSystems. (00:01.176 / 00:53.692, 231Mb) Sushi: info Converted 27 FHIR ValueSets. (00:02.029 / 00:55.722, 231Mb) Sushi: error InstanceOf MII_PR_MTB_Studie not found for mii-exa-mtb-study-cldn6 (00:17.246 / 01:12.968, 231Mb) Sushi: File: /scratch/repo/input/fsh/examples/bundle/mii-exa-mtb-kim-musterperson-bundle.fsh (00:00.000 / 01:12.968, 231Mb) Sushi: Line: 8 - 173 (00:00.000 / 01:12.969, 231Mb) Sushi: error InstanceOf MII_PR_MTB_Studie not found for mii-exa-mtb-study-cldn6 (00:02.390 / 01:15.359, 231Mb) Sushi: File: /scratch/repo/input/fsh/examples/bundle/mii-exa-mtb-technical-test-bundle.fsh (00:00.000 / 01:15.359, 231Mb) Sushi: Line: 1 - 271 (00:00.000 / 01:15.359, 231Mb) Sushi: error InstanceOf MII_PR_MTB_Studie not found for mii-exa-mtb-study-cldn6 (00:00.307 / 01:15.667, 231Mb) Sushi: File: /scratch/repo/input/fsh/examples/mii-exa-mtb-kim-musterperson-studienempfehlungen.fsh (00:00.000 / 01:15.667, 231Mb) Sushi: Line: 18 - 71 (00:00.000 / 01:15.667, 231Mb) Sushi: error Structure Definition https://www.medizininformatik-initiative.de/fhir/modul-studie/StructureDefinition/mii-pr-studie-beteiligte-person is missing a snapshot. Snapshot is required for import. (00:00.470 / 01:16.138, 231Mb) Sushi: File: /scratch/repo/input/fsh/examples/mii-exa-mtb-kim-musterperson-studienempfehlungen.fsh (00:00.000 / 01:16.139, 231Mb) Sushi: Line: 160 - 165 (00:00.000 / 01:16.139, 231Mb) Sushi: error InstanceOf MII_PR_MTB_Studie not found for mii-exa-mtb-study-tedova (00:00.416 / 01:16.555, 231Mb) Sushi: File: /scratch/repo/input/fsh/examples/mii-exa-mtb-kim-musterperson-studienempfehlungen.fsh (00:00.000 / 01:16.556, 236Mb) Sushi: Line: 316 - 323 (00:00.000 / 01:16.556, 236Mb) Sushi: error InstanceOf MII_PR_MTB_Studie not found for mii-exa-mtb-study-ccne1 (00:00.081 / 01:16.637, 236Mb) Sushi: File: /scratch/repo/input/fsh/examples/mii-exa-mtb-kim-musterperson-studienempfehlungen.fsh (00:00.000 / 01:16.637, 236Mb) Sushi: Line: 337 - 342 (00:00.000 / 01:16.637, 236Mb) Sushi: info Converted 196 FHIR instances. (00:08.063 / 01:24.701, 236Mb) Sushi: info Exporting FHIR resources as JSON... (00:00.006 / 01:24.707, 236Mb) Sushi: info Exported 295 FHIR resources as JSON. (00:00.992 / 01:25.700, 236Mb) Sushi: info Assembling Implementation Guide sources... (00:00.017 / 01:25.717, 236Mb) Sushi: info Generated ImplementationGuide-mii-kerndatensatzmodul-molekulares-tumorboard.json (00:00.063 / 01:25.781, 236Mb) Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:00.000 / 01:25.781, 236Mb) Sushi: ========================= SUSHI RESULTS =========================== (00:00.001 / 01:25.783, 236Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:25.784, 236Mb) Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:00.000 / 01:25.784, 236Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 01:25.784, 236Mb) Sushi: | | 48 | 11 | 1 | 0 | | (00:00.000 / 01:25.784, 236Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:25.784, 236Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:25.784, 236Mb) Sushi: | | ValueSets | CodeSystems | Instances | | (00:00.000 / 01:25.784, 236Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 01:25.785, 236Mb) Sushi: | | 27 | 18 | 190 | | (00:00.000 / 01:25.785, 236Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:25.785, 236Mb) Sushi: | | (00:00.000 / 01:25.785, 236Mb) Sushi: =================================================================== (00:00.000 / 01:25.785, 236Mb) Sushi: | Is that squall you got? 7 Errors 0 Warnings | (00:00.000 / 01:25.785, 236Mb) Sushi: =================================================================== (00:00.000 / 01:25.785, 236Mb) Sushi couldn't be run. Complete output from running Sushi : (00:00.045 / 01:25.831, 236Mb) Note: Check that Sushi is installed correctly ("npm install -g fsh-sushi". On windows, get npm from https://www.npmjs.com/get-npm) (00:00.000 / 01:25.831, 236Mb) Exception: Process exited with an error: 7 (Exit value: 7) (00:00.000 / 01:25.831, 236Mb) Publishing Content Failed: Process exited with an error: 7 (Exit value: 7) (00:00.000 / 01:25.832, 236Mb) (00:00.000 / 01:25.832, 236Mb) Use -? to get command line help (00:00.000 / 01:25.832, 236Mb) (00:00.000 / 01:25.832, 236Mb) Stack Dump (for debugging): (00:00.000 / 01:25.832, 236Mb) org.apache.commons.exec.ExecuteException: Process exited with an error: 7 (Exit value: 7) at org.apache.commons.exec.DefaultExecutor.executeInternal(DefaultExecutor.java:404) at org.apache.commons.exec.DefaultExecutor.execute(DefaultExecutor.java:166) at org.apache.commons.exec.DefaultExecutor.execute(DefaultExecutor.java:153) at org.hl7.fhir.igtools.publisher.FSHRunner.runFsh(FSHRunner.java:89) at org.hl7.fhir.igtools.publisher.Publisher.initialize(Publisher.java:2747) at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:1017) at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:15805)