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update_repo #432

Merged
merged 1 commit into from
Feb 9, 2024
Merged

update_repo #432

merged 1 commit into from
Feb 9, 2024

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joeflack4
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@joeflack4 joeflack4 commented Feb 6, 2024 •
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Overview

This hasn't been run in a while. There are several changes that update_repo makes that are simply the result of ODK having changed since this was last run, and none of them appear to be the result of changes made within mondo-ingest. Therefore, I decided to run this first independently ahead of #433, so ideally this PR (#432) should be merged first.

Pre-merge checklist

  • Docs

    • docs/ have been added/updated OR
    • No updates to the docs necessary after careful consideration.

  • QC

    • sh run.sh make build-mondo-ingest has been run on this branch (after `docker pull obolibrary/odkfull:dev), and no errors occurred OR
    • No functional (code-related) changes to the pipeline are suggested, so no re-run is necessary.

  • Reviewed

    • Has been sufficiently reviewed by at least one review from a different team member of the Mondo Technical team.

CC @souzadevinicius

This was referenced Feb 6, 2024
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@joeflack4 joeflack4 self-assigned this Feb 6, 2024
This was referenced Feb 6, 2024
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matentzn
matentzn approved these changes Feb 7, 2024
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src/ontology/Makefile
@@ -1,7 +1,7 @@
# ----------------------------------------
# Makefile for mondo-ingest
# Generated using ontology-development-kit
# ODK Version: v1.5
# ODK Version: v1.5-dev
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Note that we are using an unstable development snapshot of ODK here - I am cool with this, indeed, I have been testing this very same pipeline locally (with the updates in this PR), but we need to remember that it is.

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@joeflack4 joeflack4 Feb 7, 2024 •
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Sorry, I actually forgot you'd already told me to do this.

Questions / issues

  1. This will be tricky for me to remember the next time I do it months from now. Is there any way to automate this so that I don't have to remember it?

  2. Is there a specific reason why we're you're asking for ODK_TAG=v1.4.3 instead of latest?

  3. If I don't specify an ODK_TAG, why isn't it defaulting to latest?
    I would figure that's what would happen, since in run.sh it has: ODK_TAG=${ODK_TAG:-latest}

  4. I'm getting the same results if I run ODK_TAG=v1.4.3 sh run.sh make update_repo or sh run.sh make ODK_TAG=v1.4.3 update_repo as when I run sh run.sh make update_repo. Why?
    The changes are exactly the same; there is no diff. I started on a fresh branch and compared the results. Even the Makefile still says # ODK Version: v1.5-dev.
    Also, I recollect you saying something a few months ago about how now "dev would run by default". Do you remember that? Is this simply a result of some configuration you did regarding that? Given (3), I would expect -latest to run, but it appears that is not so.

Log 

ODK_TAG=v1.4.3 sh run.sh make update_repo

Running  with -Xmx20G of memory for ROBOT and Java-based pipeline steps.
mondo-ingest.Makefile:65: warning: overriding recipe for target 'components/omim.owl'
Makefile:447: warning: ignoring old recipe for target 'components/omim.owl'
mondo-ingest.Makefile:80: warning: overriding recipe for target 'components/ordo.owl'
Makefile:458: warning: ignoring old recipe for target 'components/ordo.owl'
mondo-ingest.Makefile:99: warning: overriding recipe for target 'components/ncit.owl'
Makefile:436: warning: ignoring old recipe for target 'components/ncit.owl'
mondo-ingest.Makefile:110: warning: overriding recipe for target 'components/doid.owl'
Makefile:392: warning: ignoring old recipe for target 'components/doid.owl'
mondo-ingest.Makefile:132: warning: overriding recipe for target 'component-download-icd10cm.owl'
Makefile:410: warning: ignoring old recipe for target 'component-download-icd10cm.owl'
mondo-ingest.Makefile:138: warning: overriding recipe for target 'components/icd10cm.owl'
Makefile:414: warning: ignoring old recipe for target 'components/icd10cm.owl'
mondo-ingest.Makefile:153: warning: overriding recipe for target 'components/icd10who.owl'
Makefile:425: warning: ignoring old recipe for target 'components/icd10who.owl'
mondo-ingest.Makefile:168: warning: overriding recipe for target 'component-download-gard.owl'
Makefile:399: warning: ignoring old recipe for target 'component-download-gard.owl'
mondo-ingest.Makefile:172: warning: overriding recipe for target 'components/gard.owl'
Makefile:403: warning: ignoring old recipe for target 'components/gard.owl'
mondo-ingest.Makefile:177: warning: overriding recipe for target 'mondo-ingest-full.owl'
Makefile:588: warning: ignoring old recipe for target 'mondo-ingest-full.owl'
mondo-ingest.Makefile:584: warning: overriding recipe for target 'help'
Makefile:659: warning: ignoring old recipe for target 'help'
sh ../scripts/update_repo.sh
This (experimental) update script will create a new repo according to your config file. It will:
(1) overwrite your repositories Makefile, ODK sparql queries (your custom queries wont be touched) and docker wrapper (run.sh).
(2) and add missing files, if any.
INFO:root:  Copying: /tools/templates/CONTRIBUTING.md.jinja2 -> target/mondo-ingest/CONTRIBUTING.md.jinja2
INFO:root:  Copying: /tools/templates/.gitignore.jinja2 -> target/mondo-ingest/.gitignore.jinja2
INFO:root:  Copying: /tools/templates/README.md.jinja2 -> target/mondo-ingest/README.md.jinja2
INFO:root:  Copying: /tools/templates/issue_template.md.jinja2 -> target/mondo-ingest/issue_template.md.jinja2
INFO:root:  Copying: /tools/templates/_dynamic_files.jinja2 -> target/mondo-ingest/_dynamic_files.jinja2
INFO:root:  Copying: /tools/templates/CODE_OF_CONDUCT.md -> target/mondo-ingest/CODE_OF_CONDUCT.md
INFO:root:Applying templates
INFO:root:  Compiling: /tools/templates/CONTRIBUTING.md.jinja2 -> target/mondo-ingest/CONTRIBUTING.md
INFO:root:  Compiling: /tools/templates/.gitignore.jinja2 -> target/mondo-ingest/.gitignore
INFO:root:  Compiling: /tools/templates/README.md.jinja2 -> target/mondo-ingest/README.md
INFO:root:  Compiling: /tools/templates/issue_template.md.jinja2 -> target/mondo-ingest/issue_template.md
INFO:root:  Unpacking: target/mondo-ingest/_dynamic_files
INFO:root:  Unpacking into: target/mondo-ingest/src/ontology/mondo-ingest-edit.owl
INFO:root:  Unpacking into: target/mondo-ingest/src/ontology/mondo-ingest-idranges.owl
INFO:root:  Unpacking into: target/mondo-ingest/src/ontology/mondo-ingest.Makefile
INFO:root:  Unpacking into: target/mondo-ingest/src/ontology/imports/ro_import.owl
INFO:root:  Unpacking into: target/mondo-ingest/src/ontology/imports/omo_import.owl
INFO:root:  Unpacking into: target/mondo-ingest/src/ontology/imports/ro_terms.txt
INFO:root:  Unpacking into: target/mondo-ingest/src/ontology/imports/omo_terms.txt
INFO:root:  Unpacking into: target/mondo-ingest/src/sparql/mondo-ingest_terms.sparql
INFO:root:  Unpacking into: target/mondo-ingest/src/ontology/components/doid.owl
INFO:root:  Unpacking into: target/mondo-ingest/src/ontology/components/gard.owl
INFO:root:  Unpacking into: target/mondo-ingest/src/ontology/components/icd10cm.owl
INFO:root:  Unpacking into: target/mondo-ingest/src/ontology/components/icd10who.owl
INFO:root:  Unpacking into: target/mondo-ingest/src/ontology/components/ncit.owl
INFO:root:  Unpacking into: target/mondo-ingest/src/ontology/components/omim.owl
INFO:root:  Unpacking into: target/mondo-ingest/src/ontology/components/ordo.owl
INFO:root:  Unpacking into: target/mondo-ingest/src/ontology/profile.txt
INFO:root:  Unpacking into: target/mondo-ingest/.github/workflows/qc.yml
INFO:root:  Unpacking into: target/mondo-ingest/docs/index.md
INFO:root:  Unpacking into: target/mondo-ingest/docs/cite.md
INFO:root:  Unpacking into: target/mondo-ingest/docs/contributing.md
INFO:root:  Unpacking into: target/mondo-ingest/docs/odk-workflows/index.md
INFO:root:  Unpacking into: target/mondo-ingest/docs/odk-workflows/ContinuousIntegration.md
INFO:root:  Unpacking into: target/mondo-ingest/docs/odk-workflows/EditorsWorkflow.md
INFO:root:  Unpacking into: target/mondo-ingest/docs/odk-workflows/ReleaseWorkflow.md
INFO:root:  Unpacking into: target/mondo-ingest/docs/odk-workflows/RepoManagement.md
INFO:root:  Unpacking into: target/mondo-ingest/docs/odk-workflows/RepositoryFileStructure.md
INFO:root:  Unpacking into: target/mondo-ingest/docs/odk-workflows/SettingUpDockerForODK.md
INFO:root:  Unpacking into: target/mondo-ingest/docs/odk-workflows/UpdateImports.md
INFO:root:  Unpacking into: target/mondo-ingest/docs/odk-workflows/components.md
INFO:root:  Unpacking into: target/mondo-ingest/docs/odk-workflows/ManageDocumentation.md
INFO:root:  Unpacking into: target/mondo-ingest/mkdocs.yaml
INFO:root:  Unpacking into: target/mondo-ingest/.github/workflows/docs.yml
INFO:root:Applying templates
INFO:root:  Copying: /tools/templates/src/sparql/xrefs.sparql -> target/mondo-ingest/src/sparql/xrefs.sparql
INFO:root:  Copying: /tools/templates/src/sparql/labels.sparql -> target/mondo-ingest/src/sparql/labels.sparql
INFO:root:  Copying: /tools/templates/src/sparql/subsets-labeled.sparql -> target/mondo-ingest/src/sparql/subsets-labeled.sparql
INFO:root:  Copying: /tools/templates/src/sparql/edges.sparql -> target/mondo-ingest/src/sparql/edges.sparql
INFO:root:  Copying: /tools/templates/src/sparql/inject-synonymtype-declaration.ru.jinja2 -> target/mondo-ingest/src/sparql/inject-synonymtype-declaration.ru.jinja2
INFO:root:  Copying: /tools/templates/src/sparql/obsoletes.sparql -> target/mondo-ingest/src/sparql/obsoletes.sparql
INFO:root:  Copying: /tools/templates/src/sparql/README.md.jinja2 -> target/mondo-ingest/src/sparql/README.md.jinja2
INFO:root:  Copying: /tools/templates/src/sparql/preprocess-module.ru -> target/mondo-ingest/src/sparql/preprocess-module.ru
INFO:root:  Copying: /tools/templates/src/sparql/terms.sparql -> target/mondo-ingest/src/sparql/terms.sparql
INFO:root:  Copying: /tools/templates/src/sparql/inject-subset-declaration.ru.jinja2 -> target/mondo-ingest/src/sparql/inject-subset-declaration.ru.jinja2
INFO:root:  Copying: /tools/templates/src/sparql/basic-report.sparql -> target/mondo-ingest/src/sparql/basic-report.sparql
INFO:root:  Copying: /tools/templates/src/sparql/simple-seed.sparql -> target/mondo-ingest/src/sparql/simple-seed.sparql
INFO:root:  Copying: /tools/templates/src/sparql/synonyms.sparql -> target/mondo-ingest/src/sparql/synonyms.sparql
INFO:root:  Copying: /tools/templates/src/sparql/postprocess-module.ru -> target/mondo-ingest/src/sparql/postprocess-module.ru
INFO:root:Applying templates
INFO:root:  Compiling: /tools/templates/src/sparql/inject-synonymtype-declaration.ru.jinja2 -> target/mondo-ingest/src/sparql/inject-synonymtype-declaration.ru
INFO:root:  Compiling: /tools/templates/src/sparql/README.md.jinja2 -> target/mondo-ingest/src/sparql/README.md
INFO:root:  Compiling: /tools/templates/src/sparql/inject-subset-declaration.ru.jinja2 -> target/mondo-ingest/src/sparql/inject-subset-declaration.ru
INFO:root:  Copying: /tools/templates/src/scripts/update_repo.sh.jinja2 -> target/mondo-ingest/src/scripts/update_repo.sh.jinja2
INFO:root:  Copying: /tools/templates/src/scripts/validate_id_ranges.sc -> target/mondo-ingest/src/scripts/validate_id_ranges.sc
INFO:root:  Copying: /tools/templates/src/scripts/run-command.sh -> target/mondo-ingest/src/scripts/run-command.sh
INFO:root:Applying templates
INFO:root:  Compiling: /tools/templates/src/scripts/update_repo.sh.jinja2 -> target/mondo-ingest/src/scripts/update_repo.sh
INFO:root:  Copying: /tools/templates/src/ontology/run.sh.jinja2 -> target/mondo-ingest/src/ontology/run.sh.jinja2
INFO:root:  Copying: /tools/templates/src/ontology/README-editors.md.jinja2 -> target/mondo-ingest/src/ontology/README-editors.md.jinja2
INFO:root:  Copying: /tools/templates/src/ontology/run.bat.jinja2 -> target/mondo-ingest/src/ontology/run.bat.jinja2
INFO:root:  Copying: /tools/templates/src/ontology/catalog-v001.xml.jinja2 -> target/mondo-ingest/src/ontology/catalog-v001.xml.jinja2
INFO:root:  Copying: /tools/templates/src/ontology/Makefile.jinja2 -> target/mondo-ingest/src/ontology/Makefile.jinja2
INFO:root:Applying templates
INFO:root:  Compiling: /tools/templates/src/ontology/run.sh.jinja2 -> target/mondo-ingest/src/ontology/run.sh
INFO:root:  Compiling: /tools/templates/src/ontology/README-editors.md.jinja2 -> target/mondo-ingest/src/ontology/README-editors.md
INFO:root:  Compiling: /tools/templates/src/ontology/run.bat.jinja2 -> target/mondo-ingest/src/ontology/run.bat
INFO:root:  Compiling: /tools/templates/src/ontology/catalog-v001.xml.jinja2 -> target/mondo-ingest/src/ontology/catalog-v001.xml
INFO:root:  Compiling: /tools/templates/src/ontology/Makefile.jinja2 -> target/mondo-ingest/src/ontology/Makefile
INFO:root:Created files:
INFO:root:  File: target/mondo-ingest/CODE_OF_CONDUCT.md
INFO:root:  File: target/mondo-ingest/CONTRIBUTING.md
INFO:root:  File: target/mondo-ingest/.gitignore
INFO:root:  File: target/mondo-ingest/README.md
INFO:root:  File: target/mondo-ingest/issue_template.md
INFO:root:  File: target/mondo-ingest/src/ontology/mondo-ingest-edit.owl
INFO:root:  File: target/mondo-ingest/src/ontology/mondo-ingest-idranges.owl
INFO:root:  File: target/mondo-ingest/src/ontology/mondo-ingest.Makefile
INFO:root:  File: target/mondo-ingest/src/ontology/imports/ro_import.owl
INFO:root:  File: target/mondo-ingest/src/ontology/imports/omo_import.owl
INFO:root:  File: target/mondo-ingest/src/ontology/imports/ro_terms.txt
INFO:root:  File: target/mondo-ingest/src/ontology/imports/omo_terms.txt
INFO:root:  File: target/mondo-ingest/src/sparql/mondo-ingest_terms.sparql
INFO:root:  File: target/mondo-ingest/src/ontology/components/doid.owl
INFO:root:  File: target/mondo-ingest/src/ontology/components/gard.owl
INFO:root:  File: target/mondo-ingest/src/ontology/components/icd10cm.owl
INFO:root:  File: target/mondo-ingest/src/ontology/components/icd10who.owl
INFO:root:  File: target/mondo-ingest/src/ontology/components/ncit.owl
INFO:root:  File: target/mondo-ingest/src/ontology/components/omim.owl
INFO:root:  File: target/mondo-ingest/src/ontology/components/ordo.owl
INFO:root:  File: target/mondo-ingest/src/ontology/profile.txt
INFO:root:  File: target/mondo-ingest/.github/workflows/qc.yml
INFO:root:  File: target/mondo-ingest/docs/index.md
INFO:root:  File: target/mondo-ingest/docs/cite.md
INFO:root:  File: target/mondo-ingest/docs/contributing.md
INFO:root:  File: target/mondo-ingest/docs/odk-workflows/index.md
INFO:root:  File: target/mondo-ingest/docs/odk-workflows/ContinuousIntegration.md
INFO:root:  File: target/mondo-ingest/docs/odk-workflows/EditorsWorkflow.md
INFO:root:  File: target/mondo-ingest/docs/odk-workflows/ReleaseWorkflow.md
INFO:root:  File: target/mondo-ingest/docs/odk-workflows/RepoManagement.md
INFO:root:  File: target/mondo-ingest/docs/odk-workflows/RepositoryFileStructure.md
INFO:root:  File: target/mondo-ingest/docs/odk-workflows/SettingUpDockerForODK.md
INFO:root:  File: target/mondo-ingest/docs/odk-workflows/UpdateImports.md
INFO:root:  File: target/mondo-ingest/docs/odk-workflows/components.md
INFO:root:  File: target/mondo-ingest/docs/odk-workflows/ManageDocumentation.md
INFO:root:  File: target/mondo-ingest/mkdocs.yaml
INFO:root:  File: target/mondo-ingest/.github/workflows/docs.yml
INFO:root:  File: target/mondo-ingest/src/sparql/xrefs.sparql
INFO:root:  File: target/mondo-ingest/src/sparql/labels.sparql
INFO:root:  File: target/mondo-ingest/src/sparql/subsets-labeled.sparql
INFO:root:  File: target/mondo-ingest/src/sparql/edges.sparql
INFO:root:  File: target/mondo-ingest/src/sparql/obsoletes.sparql
INFO:root:  File: target/mondo-ingest/src/sparql/preprocess-module.ru
INFO:root:  File: target/mondo-ingest/src/sparql/terms.sparql
INFO:root:  File: target/mondo-ingest/src/sparql/basic-report.sparql
INFO:root:  File: target/mondo-ingest/src/sparql/simple-seed.sparql
INFO:root:  File: target/mondo-ingest/src/sparql/synonyms.sparql
INFO:root:  File: target/mondo-ingest/src/sparql/postprocess-module.ru
INFO:root:  File: target/mondo-ingest/src/sparql/inject-synonymtype-declaration.ru
INFO:root:  File: target/mondo-ingest/src/sparql/README.md
INFO:root:  File: target/mondo-ingest/src/sparql/inject-subset-declaration.ru
INFO:root:  File: target/mondo-ingest/src/scripts/validate_id_ranges.sc
INFO:root:  File: target/mondo-ingest/src/scripts/run-command.sh
INFO:root:  File: target/mondo-ingest/src/scripts/update_repo.sh
INFO:root:  File: target/mondo-ingest/src/ontology/run.sh
INFO:root:  File: target/mondo-ingest/src/ontology/README-editors.md
INFO:root:  File: target/mondo-ingest/src/ontology/run.bat
INFO:root:  File: target/mondo-ingest/src/ontology/catalog-v001.xml
INFO:root:  File: target/mondo-ingest/src/ontology/Makefile
INFO:root:  File: target/mondo-ingest/src/ontology/mondo-ingest-odk.yaml
Repository files have been successfully copied, but no git commands have been run.
total 0
drwxr-xr-x 14 odkuser dialout 448 Feb  7 19:37 ontology
drwxr-xr-x  5 odkuser dialout 160 Feb  7 19:37 scripts
drwxr-xr-x 17 odkuser dialout 544 Feb  7 19:37 sparql
total 0
drwxr-xr-x  3 odkuser dialout   96 Oct 14 21:32 analysis
drwxr-xr-x 14 odkuser dialout  448 Feb  6 22:31 mappings
drwxr-xr-x 28 root    root     896 Feb  7 19:37 ontology
drwxr-xr-x 24 odkuser dialout  768 Feb  7 19:37 scripts
drwxr-xr-x 72 odkuser dialout 2304 Feb  6 22:31 sparql
WARNING: These files should be manually migrated: mkdocs.yaml, .gitignore, src/ontology/catalog.xml (if you added a new import or component)
WARNING: Your QC workflows have not been updated automatically. Please update the ODK version number(s) in .github/workflows/qc.yml.
../scripts/update_repo.sh: 39: Syntax error: Unterminated quoted string
make: *** [Makefile:642: update_repo] Error 2
Command exited with non-zero status 2
### DEBUG STATS ###
Elapsed time: 0:00.33
Peak memory: 33172 kb
run.sh: line 100: DEBUG: command not found
run.sh: line 101: syntax error near unexpected token `fi'
run.sh: line 101: `fi'
ODK_TAG=v1.4.3 sh run.sh make update_repo

Running  with -Xmx20G of memory for ROBOT and Java-based pipeline steps.
mondo-ingest.Makefile:65: warning: overriding recipe for target 'components/omim.owl'
Makefile:501: warning: ignoring old recipe for target 'components/omim.owl'
mondo-ingest.Makefile:80: warning: overriding recipe for target 'components/ordo.owl'
Makefile:515: warning: ignoring old recipe for target 'components/ordo.owl'
mondo-ingest.Makefile:99: warning: overriding recipe for target 'components/ncit.owl'
Makefile:487: warning: ignoring old recipe for target 'components/ncit.owl'
mondo-ingest.Makefile:110: warning: overriding recipe for target 'components/doid.owl'
Makefile:431: warning: ignoring old recipe for target 'components/doid.owl'
mondo-ingest.Makefile:132: warning: overriding recipe for target 'component-download-icd10cm.owl'
Makefile:455: warning: ignoring old recipe for target 'component-download-icd10cm.owl'
mondo-ingest.Makefile:138: warning: overriding recipe for target 'components/icd10cm.owl'
Makefile:459: warning: ignoring old recipe for target 'components/icd10cm.owl'
mondo-ingest.Makefile:153: warning: overriding recipe for target 'components/icd10who.owl'
Makefile:473: warning: ignoring old recipe for target 'components/icd10who.owl'
mondo-ingest.Makefile:168: warning: overriding recipe for target 'component-download-gard.owl'
Makefile:441: warning: ignoring old recipe for target 'component-download-gard.owl'
mondo-ingest.Makefile:172: warning: overriding recipe for target 'components/gard.owl'
Makefile:445: warning: ignoring old recipe for target 'components/gard.owl'
mondo-ingest.Makefile:177: warning: overriding recipe for target 'mondo-ingest-full.owl'
Makefile:651: warning: ignoring old recipe for target 'mondo-ingest-full.owl'
mondo-ingest.Makefile:584: warning: overriding recipe for target 'help'
Makefile:722: warning: ignoring old recipe for target 'help'
sh ../scripts/update_repo.sh
This (experimental) update script will create a new repo according to your config file. It will:
(1) overwrite your repositories Makefile, ODK sparql queries (your custom queries wont be touched) and docker wrapper (run.sh).
(2) and add missing files, if any.
INFO:root:  Copying: /tools/templates/CONTRIBUTING.md.jinja2 -> target/mondo-ingest/CONTRIBUTING.md.jinja2
INFO:root:  Copying: /tools/templates/.gitignore.jinja2 -> target/mondo-ingest/.gitignore.jinja2
INFO:root:  Copying: /tools/templates/README.md.jinja2 -> target/mondo-ingest/README.md.jinja2
INFO:root:  Copying: /tools/templates/issue_template.md.jinja2 -> target/mondo-ingest/issue_template.md.jinja2
INFO:root:  Copying: /tools/templates/_dynamic_files.jinja2 -> target/mondo-ingest/_dynamic_files.jinja2
INFO:root:  Copying: /tools/templates/CODE_OF_CONDUCT.md -> target/mondo-ingest/CODE_OF_CONDUCT.md
INFO:root:Applying templates
INFO:root:  Compiling: /tools/templates/CONTRIBUTING.md.jinja2 -> target/mondo-ingest/CONTRIBUTING.md
INFO:root:  Compiling: /tools/templates/.gitignore.jinja2 -> target/mondo-ingest/.gitignore
INFO:root:  Compiling: /tools/templates/README.md.jinja2 -> target/mondo-ingest/README.md
INFO:root:  Compiling: /tools/templates/issue_template.md.jinja2 -> target/mondo-ingest/issue_template.md
INFO:root:  Unpacking: target/mondo-ingest/_dynamic_files
INFO:root:  Unpacking into: target/mondo-ingest/src/ontology/mondo-ingest-edit.owl
INFO:root:  Unpacking into: target/mondo-ingest/src/ontology/mondo-ingest-idranges.owl
INFO:root:  Unpacking into: target/mondo-ingest/src/ontology/mondo-ingest.Makefile
INFO:root:  Unpacking into: target/mondo-ingest/src/ontology/imports/ro_import.owl
INFO:root:  Unpacking into: target/mondo-ingest/src/ontology/imports/omo_import.owl
INFO:root:  Unpacking into: target/mondo-ingest/src/ontology/imports/ro_terms.txt
INFO:root:  Unpacking into: target/mondo-ingest/src/ontology/imports/omo_terms.txt
INFO:root:  Unpacking into: target/mondo-ingest/src/sparql/mondo-ingest_terms.sparql
INFO:root:  Unpacking into: target/mondo-ingest/src/ontology/components/doid.owl
INFO:root:  Unpacking into: target/mondo-ingest/src/ontology/components/gard.owl
INFO:root:  Unpacking into: target/mondo-ingest/src/ontology/components/icd10cm.owl
INFO:root:  Unpacking into: target/mondo-ingest/src/ontology/components/icd10who.owl
INFO:root:  Unpacking into: target/mondo-ingest/src/ontology/components/ncit.owl
INFO:root:  Unpacking into: target/mondo-ingest/src/ontology/components/omim.owl
INFO:root:  Unpacking into: target/mondo-ingest/src/ontology/components/ordo.owl
INFO:root:  Unpacking into: target/mondo-ingest/src/ontology/profile.txt
INFO:root:  Unpacking into: target/mondo-ingest/.github/workflows/qc.yml
INFO:root:  Unpacking into: target/mondo-ingest/docs/index.md
INFO:root:  Unpacking into: target/mondo-ingest/docs/cite.md
INFO:root:  Unpacking into: target/mondo-ingest/docs/contributing.md
INFO:root:  Unpacking into: target/mondo-ingest/docs/odk-workflows/index.md
INFO:root:  Unpacking into: target/mondo-ingest/docs/odk-workflows/ContinuousIntegration.md
INFO:root:  Unpacking into: target/mondo-ingest/docs/odk-workflows/EditorsWorkflow.md
INFO:root:  Unpacking into: target/mondo-ingest/docs/odk-workflows/ReleaseWorkflow.md
INFO:root:  Unpacking into: target/mondo-ingest/docs/odk-workflows/RepoManagement.md
INFO:root:  Unpacking into: target/mondo-ingest/docs/odk-workflows/RepositoryFileStructure.md
INFO:root:  Unpacking into: target/mondo-ingest/docs/odk-workflows/SettingUpDockerForODK.md
INFO:root:  Unpacking into: target/mondo-ingest/docs/odk-workflows/UpdateImports.md
INFO:root:  Unpacking into: target/mondo-ingest/docs/odk-workflows/components.md
INFO:root:  Unpacking into: target/mondo-ingest/docs/odk-workflows/ManageDocumentation.md
INFO:root:  Unpacking into: target/mondo-ingest/mkdocs.yaml
INFO:root:  Unpacking into: target/mondo-ingest/.github/workflows/docs.yml
INFO:root:Applying templates
INFO:root:  Copying: /tools/templates/src/sparql/xrefs.sparql -> target/mondo-ingest/src/sparql/xrefs.sparql
INFO:root:  Copying: /tools/templates/src/sparql/labels.sparql -> target/mondo-ingest/src/sparql/labels.sparql
INFO:root:  Copying: /tools/templates/src/sparql/subsets-labeled.sparql -> target/mondo-ingest/src/sparql/subsets-labeled.sparql
INFO:root:  Copying: /tools/templates/src/sparql/edges.sparql -> target/mondo-ingest/src/sparql/edges.sparql
INFO:root:  Copying: /tools/templates/src/sparql/inject-synonymtype-declaration.ru.jinja2 -> target/mondo-ingest/src/sparql/inject-synonymtype-declaration.ru.jinja2
INFO:root:  Copying: /tools/templates/src/sparql/obsoletes.sparql -> target/mondo-ingest/src/sparql/obsoletes.sparql
INFO:root:  Copying: /tools/templates/src/sparql/README.md.jinja2 -> target/mondo-ingest/src/sparql/README.md.jinja2
INFO:root:  Copying: /tools/templates/src/sparql/preprocess-module.ru -> target/mondo-ingest/src/sparql/preprocess-module.ru
INFO:root:  Copying: /tools/templates/src/sparql/terms.sparql -> target/mondo-ingest/src/sparql/terms.sparql
INFO:root:  Copying: /tools/templates/src/sparql/inject-subset-declaration.ru.jinja2 -> target/mondo-ingest/src/sparql/inject-subset-declaration.ru.jinja2
INFO:root:  Copying: /tools/templates/src/sparql/basic-report.sparql -> target/mondo-ingest/src/sparql/basic-report.sparql
INFO:root:  Copying: /tools/templates/src/sparql/simple-seed.sparql -> target/mondo-ingest/src/sparql/simple-seed.sparql
INFO:root:  Copying: /tools/templates/src/sparql/synonyms.sparql -> target/mondo-ingest/src/sparql/synonyms.sparql
INFO:root:  Copying: /tools/templates/src/sparql/postprocess-module.ru -> target/mondo-ingest/src/sparql/postprocess-module.ru
INFO:root:Applying templates
INFO:root:  Compiling: /tools/templates/src/sparql/inject-synonymtype-declaration.ru.jinja2 -> target/mondo-ingest/src/sparql/inject-synonymtype-declaration.ru
INFO:root:  Compiling: /tools/templates/src/sparql/README.md.jinja2 -> target/mondo-ingest/src/sparql/README.md
INFO:root:  Compiling: /tools/templates/src/sparql/inject-subset-declaration.ru.jinja2 -> target/mondo-ingest/src/sparql/inject-subset-declaration.ru
INFO:root:  Copying: /tools/templates/src/scripts/update_repo.sh.jinja2 -> target/mondo-ingest/src/scripts/update_repo.sh.jinja2
INFO:root:  Copying: /tools/templates/src/scripts/validate_id_ranges.sc -> target/mondo-ingest/src/scripts/validate_id_ranges.sc
INFO:root:  Copying: /tools/templates/src/scripts/run-command.sh -> target/mondo-ingest/src/scripts/run-command.sh
INFO:root:Applying templates
INFO:root:  Compiling: /tools/templates/src/scripts/update_repo.sh.jinja2 -> target/mondo-ingest/src/scripts/update_repo.sh
INFO:root:  Copying: /tools/templates/src/ontology/run.sh.jinja2 -> target/mondo-ingest/src/ontology/run.sh.jinja2
INFO:root:  Copying: /tools/templates/src/ontology/README-editors.md.jinja2 -> target/mondo-ingest/src/ontology/README-editors.md.jinja2
INFO:root:  Copying: /tools/templates/src/ontology/run.bat.jinja2 -> target/mondo-ingest/src/ontology/run.bat.jinja2
INFO:root:  Copying: /tools/templates/src/ontology/catalog-v001.xml.jinja2 -> target/mondo-ingest/src/ontology/catalog-v001.xml.jinja2
INFO:root:  Copying: /tools/templates/src/ontology/Makefile.jinja2 -> target/mondo-ingest/src/ontology/Makefile.jinja2
INFO:root:Applying templates
INFO:root:  Compiling: /tools/templates/src/ontology/run.sh.jinja2 -> target/mondo-ingest/src/ontology/run.sh
INFO:root:  Compiling: /tools/templates/src/ontology/README-editors.md.jinja2 -> target/mondo-ingest/src/ontology/README-editors.md
INFO:root:  Compiling: /tools/templates/src/ontology/run.bat.jinja2 -> target/mondo-ingest/src/ontology/run.bat
INFO:root:  Compiling: /tools/templates/src/ontology/catalog-v001.xml.jinja2 -> target/mondo-ingest/src/ontology/catalog-v001.xml
INFO:root:  Compiling: /tools/templates/src/ontology/Makefile.jinja2 -> target/mondo-ingest/src/ontology/Makefile
INFO:root:Created files:
INFO:root:  File: target/mondo-ingest/CODE_OF_CONDUCT.md
INFO:root:  File: target/mondo-ingest/CONTRIBUTING.md
INFO:root:  File: target/mondo-ingest/.gitignore
INFO:root:  File: target/mondo-ingest/README.md
INFO:root:  File: target/mondo-ingest/issue_template.md
INFO:root:  File: target/mondo-ingest/src/ontology/mondo-ingest-edit.owl
INFO:root:  File: target/mondo-ingest/src/ontology/mondo-ingest-idranges.owl
INFO:root:  File: target/mondo-ingest/src/ontology/mondo-ingest.Makefile
INFO:root:  File: target/mondo-ingest/src/ontology/imports/ro_import.owl
INFO:root:  File: target/mondo-ingest/src/ontology/imports/omo_import.owl
INFO:root:  File: target/mondo-ingest/src/ontology/imports/ro_terms.txt
INFO:root:  File: target/mondo-ingest/src/ontology/imports/omo_terms.txt
INFO:root:  File: target/mondo-ingest/src/sparql/mondo-ingest_terms.sparql
INFO:root:  File: target/mondo-ingest/src/ontology/components/doid.owl
INFO:root:  File: target/mondo-ingest/src/ontology/components/gard.owl
INFO:root:  File: target/mondo-ingest/src/ontology/components/icd10cm.owl
INFO:root:  File: target/mondo-ingest/src/ontology/components/icd10who.owl
INFO:root:  File: target/mondo-ingest/src/ontology/components/ncit.owl
INFO:root:  File: target/mondo-ingest/src/ontology/components/omim.owl
INFO:root:  File: target/mondo-ingest/src/ontology/components/ordo.owl
INFO:root:  File: target/mondo-ingest/src/ontology/profile.txt
INFO:root:  File: target/mondo-ingest/.github/workflows/qc.yml
INFO:root:  File: target/mondo-ingest/docs/index.md
INFO:root:  File: target/mondo-ingest/docs/cite.md
INFO:root:  File: target/mondo-ingest/docs/contributing.md
INFO:root:  File: target/mondo-ingest/docs/odk-workflows/index.md
INFO:root:  File: target/mondo-ingest/docs/odk-workflows/ContinuousIntegration.md
INFO:root:  File: target/mondo-ingest/docs/odk-workflows/EditorsWorkflow.md
INFO:root:  File: target/mondo-ingest/docs/odk-workflows/ReleaseWorkflow.md
INFO:root:  File: target/mondo-ingest/docs/odk-workflows/RepoManagement.md
INFO:root:  File: target/mondo-ingest/docs/odk-workflows/RepositoryFileStructure.md
INFO:root:  File: target/mondo-ingest/docs/odk-workflows/SettingUpDockerForODK.md
INFO:root:  File: target/mondo-ingest/docs/odk-workflows/UpdateImports.md
INFO:root:  File: target/mondo-ingest/docs/odk-workflows/components.md
INFO:root:  File: target/mondo-ingest/docs/odk-workflows/ManageDocumentation.md
INFO:root:  File: target/mondo-ingest/mkdocs.yaml
INFO:root:  File: target/mondo-ingest/.github/workflows/docs.yml
INFO:root:  File: target/mondo-ingest/src/sparql/xrefs.sparql
INFO:root:  File: target/mondo-ingest/src/sparql/labels.sparql
INFO:root:  File: target/mondo-ingest/src/sparql/subsets-labeled.sparql
INFO:root:  File: target/mondo-ingest/src/sparql/edges.sparql
INFO:root:  File: target/mondo-ingest/src/sparql/obsoletes.sparql
INFO:root:  File: target/mondo-ingest/src/sparql/preprocess-module.ru
INFO:root:  File: target/mondo-ingest/src/sparql/terms.sparql
INFO:root:  File: target/mondo-ingest/src/sparql/basic-report.sparql
INFO:root:  File: target/mondo-ingest/src/sparql/simple-seed.sparql
INFO:root:  File: target/mondo-ingest/src/sparql/synonyms.sparql
INFO:root:  File: target/mondo-ingest/src/sparql/postprocess-module.ru
INFO:root:  File: target/mondo-ingest/src/sparql/inject-synonymtype-declaration.ru
INFO:root:  File: target/mondo-ingest/src/sparql/README.md
INFO:root:  File: target/mondo-ingest/src/sparql/inject-subset-declaration.ru
INFO:root:  File: target/mondo-ingest/src/scripts/validate_id_ranges.sc
INFO:root:  File: target/mondo-ingest/src/scripts/run-command.sh
INFO:root:  File: target/mondo-ingest/src/scripts/update_repo.sh
INFO:root:  File: target/mondo-ingest/src/ontology/run.sh
INFO:root:  File: target/mondo-ingest/src/ontology/README-editors.md
INFO:root:  File: target/mondo-ingest/src/ontology/run.bat
INFO:root:  File: target/mondo-ingest/src/ontology/catalog-v001.xml
INFO:root:  File: target/mondo-ingest/src/ontology/Makefile
INFO:root:  File: target/mondo-ingest/src/ontology/mondo-ingest-odk.yaml
Repository files have been successfully copied, but no git commands have been run.
total 0
drwxr-xr-x 14 odkuser dialout 448 Feb  7 19:37 ontology
drwxr-xr-x  5 odkuser dialout 160 Feb  7 19:37 scripts
drwxr-xr-x 17 odkuser dialout 544 Feb  7 19:37 sparql
total 0
drwxr-xr-x  3 odkuser dialout   96 Oct 14 21:32 analysis
drwxr-xr-x 14 odkuser dialout  448 Feb  6 22:31 mappings
drwxr-xr-x 28 root    root     896 Feb  7 19:37 ontology
drwxr-xr-x 25 odkuser dialout  800 Feb  7 19:37 scripts
drwxr-xr-x 72 odkuser dialout 2304 Feb  6 22:31 sparql
WARNING: These files should be manually migrated: mkdocs.yaml, .gitignore, src/ontology/catalog.xml (if you added a new import or component)
WARNING: Your QC workflows have not been updated automatically. Please update the ODK version number(s) in .github/workflows/qc.yml.
Ontology repository update successfully completed.
### DEBUG STATS ###
Elapsed time: 0:00.34
Peak memory: 33180 kb
Please remember to update your ODK image from time to time: https://oboacademy.github.io/obook/howto/odk-update/.

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Is there a specific reason why we're you're asking for ODK_TAG=v1.4.3 instead of latest?

No, using latest and v1.4.3 would be the same. I need to use v1.4.3 because I also built the ODK locally on my machine, so my latest is not the official latest.

If I don't specify an ODK_TAG, why isn't it defaulting to latest?

see file src/ontology/run.sh.conf which specifies the default environment variables. We need dev for everything other than update_repo.

I'm getting the same results if I run ODK_TAG=v1.4.3 sh run.sh make update_repo or sh run.sh make ODK_TAG=v1.4.3 update_repo as when I run sh run.sh make update_repo. Why?

I dont know. I run ODK_TAG=v1.4.3 ./run.sh make update_repo but I cant imagine that makes a difference. run.sh.conf should determine your defaults.

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I haven't looked at run.sh.conf before, I'll take a look. If I'm still confounded after that, maybe I can show you on Monday.

docs/odk-workflows/ManageDocumentation.md Show resolved Hide resolved
@joeflack4 joeflack4 mentioned this pull request Feb 8, 2024
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@joeflack4 joeflack4 changed the title Ran update_repo update_repo Feb 8, 2024
@matentzn matentzn merged commit d43dd41 into main Feb 9, 2024
@joeflack4 joeflack4 deleted the update-repo branch February 9, 2024 19:37
This was referenced Feb 9, 2024
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@matentzn matentzn matentzn approved these changes

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