Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

update_repo #432

Merged
merged 1 commit into from
Feb 9, 2024
Merged

update_repo #432

merged 1 commit into from
Feb 9, 2024

Conversation

joeflack4
Copy link
Contributor

@joeflack4 joeflack4 commented Feb 6, 2024 •
edited
Loading

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
Merged
Merged
@joeflack4 joeflack4 self-assigned this Feb 6, 2024
This was referenced Feb 6, 2024
Open
Merged
matentzn
matentzn approved these changes Feb 7, 2024
View reviewed changes
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
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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.

Copy link
Contributor Author

@joeflack4 joeflack4 Feb 7, 2024 •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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/.

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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.

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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
Merged
9 tasks
@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
Open
Open
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@matentzn matentzn matentzn approved these changes

@twhetzel twhetzel Awaiting requested review from twhetzel

Assignees

@joeflack4 joeflack4

Labels
ease:high
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@joeflack4 @matentzn