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Permission denied error on update_repo #1098

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jseager7 opened this issue Aug 29, 2024 · 1 comment
Open

Permission denied error on update_repo #1098

jseager7 opened this issue Aug 29, 2024 · 1 comment

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@jseager7
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I recently tried to run sh run.sh make update_repo but got a permission denied error when the script tried to remove files on the second run (see console output below).

I'm not sure if the script has completed successfully so I don't want to merge these changes until I know that's the case. If all I need to do is delete these files manually, then that's fine.

Note that I'm running Docker in rootless mode, which might be part of the problem.

I ran the update_repo command twice following the instructions given here:

Now run the update command TWICE (the first time it may fail, as the update command needs to update itself).

Here's the output from the first run:

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/phipo/CONTRIBUTING.md.jinja2
INFO:root:  Copying: /tools/templates/README.md.jinja2 -> target/phipo/README.md.jinja2
INFO:root:  Copying: /tools/templates/_dynamic_files.jinja2 -> target/phipo/_dynamic_files.jinja2
INFO:root:  Copying: /tools/templates/CODE_OF_CONDUCT.md -> target/phipo/CODE_OF_CONDUCT.md
INFO:root:  Copying: /tools/templates/.gitignore.jinja2 -> target/phipo/.gitignore.jinja2
INFO:root:  Copying: /tools/templates/issue_template.md.jinja2 -> target/phipo/issue_template.md.jinja2
INFO:root:Applying templates
INFO:root:  Compiling: /tools/templates/CONTRIBUTING.md.jinja2 -> target/phipo/CONTRIBUTING.md
INFO:root:  Compiling: /tools/templates/README.md.jinja2 -> target/phipo/README.md
INFO:root:  Unpacking: target/phipo/_dynamic_files
INFO:root:  Unpacking into: target/phipo/src/ontology/phipo-edit.owl
INFO:root:  Unpacking into: target/phipo/src/ontology/phipo-idranges.owl
INFO:root:  Unpacking into: target/phipo/src/ontology/phipo.Makefile
INFO:root:  Unpacking into: target/phipo/src/ontology/imports/ido_import.owl
INFO:root:  Unpacking into: target/phipo/src/ontology/imports/go_import.owl
INFO:root:  Unpacking into: target/phipo/src/ontology/imports/ro_import.owl
INFO:root:  Unpacking into: target/phipo/src/ontology/imports/chebi_import.owl
INFO:root:  Unpacking into: target/phipo/src/ontology/imports/pato_import.owl
INFO:root:  Unpacking into: target/phipo/src/ontology/imports/so_import.owl
INFO:root:  Unpacking into: target/phipo/src/ontology/imports/cl_import.owl
INFO:root:  Unpacking into: target/phipo/src/ontology/imports/ido_terms.txt
INFO:root:  Unpacking into: target/phipo/src/ontology/imports/go_terms.txt
INFO:root:  Unpacking into: target/phipo/src/ontology/imports/ro_terms.txt
INFO:root:  Unpacking into: target/phipo/src/ontology/imports/chebi_terms.txt
INFO:root:  Unpacking into: target/phipo/src/ontology/imports/pato_terms.txt
INFO:root:  Unpacking into: target/phipo/src/ontology/imports/so_terms.txt
INFO:root:  Unpacking into: target/phipo/src/ontology/imports/cl_terms.txt
INFO:root:  Unpacking into: target/phipo/src/metadata/README.md
INFO:root:  Unpacking into: target/phipo/src/metadata/phipo.md
INFO:root:  Unpacking into: target/phipo/src/metadata/phipo.yml
INFO:root:  Unpacking into: target/phipo/src/patterns/definitions.owl
INFO:root:  Unpacking into: target/phipo/src/patterns/pattern.owl
INFO:root:  Unpacking into: target/phipo/src/patterns/README.md
INFO:root:  Unpacking into: target/phipo/src/patterns/data/default/example.tsv
INFO:root:  Unpacking into: target/phipo/src/patterns/dosdp-patterns/example.yaml
INFO:root:  Unpacking into: target/phipo/src/patterns/dosdp-patterns/external.txt
INFO:root:  Unpacking into: target/phipo/src/patterns/data/default/README.md
INFO:root:  Unpacking into: target/phipo/src/sparql/phipo_terms.sparql
INFO:root:  Unpacking into: target/phipo/src/sparql/owldef-self-reference-violation.sparql
INFO:root:  Unpacking into: target/phipo/src/sparql/iri-range-violation.sparql
INFO:root:  Unpacking into: target/phipo/src/sparql/label-with-iri-violation.sparql
INFO:root:  Unpacking into: target/phipo/src/sparql/multiple-replaced_by-violation.sparql
INFO:root:  Unpacking into: target/phipo/src/sparql/dc-properties-violation.sparql
INFO:root:  Unpacking into: target/phipo/.github/workflows/qc.yml
INFO:root:  Compiling: /tools/templates/.gitignore.jinja2 -> target/phipo/.gitignore
INFO:root:  Compiling: /tools/templates/issue_template.md.jinja2 -> target/phipo/issue_template.md
INFO:root:Applying templates
INFO:root:  Copying: /tools/templates/src/scripts/update_repo.sh.jinja2 -> target/phipo/src/scripts/update_repo.sh.jinja2
INFO:root:  Copying: /tools/templates/src/scripts/run-command.sh -> target/phipo/src/scripts/run-command.sh
INFO:root:  Copying: /tools/templates/src/scripts/validate_id_ranges.sc -> target/phipo/src/scripts/validate_id_ranges.sc
INFO:root:Applying templates
INFO:root:  Compiling: /tools/templates/src/scripts/update_repo.sh.jinja2 -> target/phipo/src/scripts/update_repo.sh
INFO:root:  Copying: /tools/templates/src/sparql/labels.sparql -> target/phipo/src/sparql/labels.sparql
INFO:root:  Copying: /tools/templates/src/sparql/README.md.jinja2 -> target/phipo/src/sparql/README.md.jinja2
INFO:root:  Copying: /tools/templates/src/sparql/class-count-by-prefix.sparql -> target/phipo/src/sparql/class-count-by-prefix.sparql
INFO:root:  Copying: /tools/templates/src/sparql/inject-synonymtype-declaration.ru.jinja2 -> target/phipo/src/sparql/inject-synonymtype-declaration.ru.jinja2
INFO:root:  Copying: /tools/templates/src/sparql/preprocess-module.ru -> target/phipo/src/sparql/preprocess-module.ru
INFO:root:  Copying: /tools/templates/src/sparql/basic-report.sparql -> target/phipo/src/sparql/basic-report.sparql
INFO:root:  Copying: /tools/templates/src/sparql/obsoletes.sparql -> target/phipo/src/sparql/obsoletes.sparql
INFO:root:  Copying: /tools/templates/src/sparql/terms.sparql -> target/phipo/src/sparql/terms.sparql
INFO:root:  Copying: /tools/templates/src/sparql/synonyms.sparql -> target/phipo/src/sparql/synonyms.sparql
INFO:root:  Copying: /tools/templates/src/sparql/edges.sparql -> target/phipo/src/sparql/edges.sparql
INFO:root:  Copying: /tools/templates/src/sparql/simple-seed.sparql -> target/phipo/src/sparql/simple-seed.sparql
INFO:root:  Copying: /tools/templates/src/sparql/postprocess-module.ru -> target/phipo/src/sparql/postprocess-module.ru
INFO:root:  Copying: /tools/templates/src/sparql/xrefs.sparql -> target/phipo/src/sparql/xrefs.sparql
INFO:root:  Copying: /tools/templates/src/sparql/inject-subset-declaration.ru.jinja2 -> target/phipo/src/sparql/inject-subset-declaration.ru.jinja2
INFO:root:  Copying: /tools/templates/src/sparql/subsets-labeled.sparql -> target/phipo/src/sparql/subsets-labeled.sparql
INFO:root:Applying templates
INFO:root:  Compiling: /tools/templates/src/sparql/README.md.jinja2 -> target/phipo/src/sparql/README.md
INFO:root:  Compiling: /tools/templates/src/sparql/inject-synonymtype-declaration.ru.jinja2 -> target/phipo/src/sparql/inject-synonymtype-declaration.ru
INFO:root:  Compiling: /tools/templates/src/sparql/inject-subset-declaration.ru.jinja2 -> target/phipo/src/sparql/inject-subset-declaration.ru
INFO:root:  Copying: /tools/templates/src/ontology/catalog-v001.xml.jinja2 -> target/phipo/src/ontology/catalog-v001.xml.jinja2
INFO:root:  Copying: /tools/templates/src/ontology/run.bat.jinja2 -> target/phipo/src/ontology/run.bat.jinja2
INFO:root:  Copying: /tools/templates/src/ontology/run.sh.jinja2 -> target/phipo/src/ontology/run.sh.jinja2
INFO:root:  Copying: /tools/templates/src/ontology/Makefile.jinja2 -> target/phipo/src/ontology/Makefile.jinja2
INFO:root:  Copying: /tools/templates/src/ontology/README-editors.md.jinja2 -> target/phipo/src/ontology/README-editors.md.jinja2
INFO:root:Applying templates
INFO:root:  Compiling: /tools/templates/src/ontology/catalog-v001.xml.jinja2 -> target/phipo/src/ontology/catalog-v001.xml
INFO:root:  Compiling: /tools/templates/src/ontology/run.bat.jinja2 -> target/phipo/src/ontology/run.bat
INFO:root:  Compiling: /tools/templates/src/ontology/run.sh.jinja2 -> target/phipo/src/ontology/run.sh
INFO:root:  Compiling: /tools/templates/src/ontology/Makefile.jinja2 -> target/phipo/src/ontology/Makefile
INFO:root:  Compiling: /tools/templates/src/ontology/README-editors.md.jinja2 -> target/phipo/src/ontology/README-editors.md
INFO:root:  Copying: /tools/templates/src/ontology/tmp/.gitkeep -> target/phipo/src/ontology/tmp/.gitkeep
INFO:root:Applying templates
INFO:root:Created files:
INFO:root:  File: target/phipo/CODE_OF_CONDUCT.md
INFO:root:  File: target/phipo/CONTRIBUTING.md
INFO:root:  File: target/phipo/README.md
INFO:root:  File: target/phipo/src/ontology/phipo-edit.owl
INFO:root:  File: target/phipo/src/ontology/phipo-idranges.owl
INFO:root:  File: target/phipo/src/ontology/phipo.Makefile
INFO:root:  File: target/phipo/src/ontology/imports/ido_import.owl
INFO:root:  File: target/phipo/src/ontology/imports/go_import.owl
INFO:root:  File: target/phipo/src/ontology/imports/ro_import.owl
INFO:root:  File: target/phipo/src/ontology/imports/chebi_import.owl
INFO:root:  File: target/phipo/src/ontology/imports/pato_import.owl
INFO:root:  File: target/phipo/src/ontology/imports/so_import.owl
INFO:root:  File: target/phipo/src/ontology/imports/cl_import.owl
INFO:root:  File: target/phipo/src/ontology/imports/ido_terms.txt
INFO:root:  File: target/phipo/src/ontology/imports/go_terms.txt
INFO:root:  File: target/phipo/src/ontology/imports/ro_terms.txt
INFO:root:  File: target/phipo/src/ontology/imports/chebi_terms.txt
INFO:root:  File: target/phipo/src/ontology/imports/pato_terms.txt
INFO:root:  File: target/phipo/src/ontology/imports/so_terms.txt
INFO:root:  File: target/phipo/src/ontology/imports/cl_terms.txt
INFO:root:  File: target/phipo/src/metadata/README.md
INFO:root:  File: target/phipo/src/metadata/phipo.md
INFO:root:  File: target/phipo/src/metadata/phipo.yml
INFO:root:  File: target/phipo/src/patterns/definitions.owl
INFO:root:  File: target/phipo/src/patterns/pattern.owl
INFO:root:  File: target/phipo/src/patterns/README.md
INFO:root:  File: target/phipo/src/patterns/data/default/example.tsv
INFO:root:  File: target/phipo/src/patterns/dosdp-patterns/example.yaml
INFO:root:  File: target/phipo/src/patterns/dosdp-patterns/external.txt
INFO:root:  File: target/phipo/src/patterns/data/default/README.md
INFO:root:  File: target/phipo/src/sparql/phipo_terms.sparql
INFO:root:  File: target/phipo/src/sparql/owldef-self-reference-violation.sparql
INFO:root:  File: target/phipo/src/sparql/iri-range-violation.sparql
INFO:root:  File: target/phipo/src/sparql/label-with-iri-violation.sparql
INFO:root:  File: target/phipo/src/sparql/multiple-replaced_by-violation.sparql
INFO:root:  File: target/phipo/src/sparql/dc-properties-violation.sparql
INFO:root:  File: target/phipo/.github/workflows/qc.yml
INFO:root:  File: target/phipo/.gitignore
INFO:root:  File: target/phipo/issue_template.md
INFO:root:  File: target/phipo/src/scripts/run-command.sh
INFO:root:  File: target/phipo/src/scripts/validate_id_ranges.sc
INFO:root:  File: target/phipo/src/scripts/update_repo.sh
INFO:root:  File: target/phipo/src/sparql/labels.sparql
INFO:root:  File: target/phipo/src/sparql/class-count-by-prefix.sparql
INFO:root:  File: target/phipo/src/sparql/preprocess-module.ru
INFO:root:  File: target/phipo/src/sparql/basic-report.sparql
INFO:root:  File: target/phipo/src/sparql/obsoletes.sparql
INFO:root:  File: target/phipo/src/sparql/terms.sparql
INFO:root:  File: target/phipo/src/sparql/synonyms.sparql
INFO:root:  File: target/phipo/src/sparql/edges.sparql
INFO:root:  File: target/phipo/src/sparql/simple-seed.sparql
INFO:root:  File: target/phipo/src/sparql/postprocess-module.ru
INFO:root:  File: target/phipo/src/sparql/xrefs.sparql
INFO:root:  File: target/phipo/src/sparql/subsets-labeled.sparql
INFO:root:  File: target/phipo/src/sparql/README.md
INFO:root:  File: target/phipo/src/sparql/inject-synonymtype-declaration.ru
INFO:root:  File: target/phipo/src/sparql/inject-subset-declaration.ru
INFO:root:  File: target/phipo/src/ontology/catalog-v001.xml
INFO:root:  File: target/phipo/src/ontology/run.bat
INFO:root:  File: target/phipo/src/ontology/run.sh
INFO:root:  File: target/phipo/src/ontology/Makefile
INFO:root:  File: target/phipo/src/ontology/README-editors.md
INFO:root:  File: target/phipo/src/ontology/tmp/.gitkeep
INFO:root:  File: target/phipo/src/ontology/phipo-odk.yaml
Repository files have been successfully copied, but no git commands have been run.
total 20
drwxr-xr-x 2 root root 4096 Aug 29 09:33 metadata
drwxr-xr-x 4 root root 4096 Aug 29 09:33 ontology
drwxr-xr-x 4 root root 4096 Aug 29 09:33 patterns
drwxr-xr-x 2 root root 4096 Aug 29 09:33 scripts
drwxr-xr-x 2 root root 4096 Aug 29 09:33 sparql
total 20
drwxrwxr-x 2 root root 4096 Sep  5  2021 metadata
drwxrwxr-x 7 root root 4096 Aug 29 09:33 ontology
drwxrwxr-x 4 root root 4096 Aug 29 09:33 patterns
drwxrwxr-x 3 root root 4096 Nov 23  2022 scripts
drwxrwxr-x 2 root root 4096 Oct 12  2023 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.
run.sh: 77: Syntax error: word unexpected

Then the second run, where the error happens:

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.
rm: cannot remove 'target/phipo/src/scripts/run-command.sh': Permission denied
rm: cannot remove 'target/phipo/src/scripts/update_repo.sh': Permission denied
rm: cannot remove 'target/phipo/src/scripts/validate_id_ranges.sc': Permission denied
rm: cannot remove 'target/phipo/src/sparql/labels.sparql': Permission denied
rm: cannot remove 'target/phipo/src/sparql/class-count-by-prefix.sparql': Permission denied
rm: cannot remove 'target/phipo/src/sparql/inject-subset-declaration.ru': Permission denied
rm: cannot remove 'target/phipo/src/sparql/preprocess-module.ru': Permission denied
rm: cannot remove 'target/phipo/src/sparql/basic-report.sparql': Permission denied
rm: cannot remove 'target/phipo/src/sparql/obsoletes.sparql': Permission denied
rm: cannot remove 'target/phipo/src/sparql/owldef-self-reference-violation.sparql': Permission denied
rm: cannot remove 'target/phipo/src/sparql/terms.sparql': Permission denied
rm: cannot remove 'target/phipo/src/sparql/phipo_terms.sparql': Permission denied
rm: cannot remove 'target/phipo/src/sparql/label-with-iri-violation.sparql': Permission denied
rm: cannot remove 'target/phipo/src/sparql/synonyms.sparql': Permission denied
rm: cannot remove 'target/phipo/src/sparql/dc-properties-violation.sparql': Permission denied
rm: cannot remove 'target/phipo/src/sparql/edges.sparql': Permission denied
rm: cannot remove 'target/phipo/src/sparql/simple-seed.sparql': Permission denied
rm: cannot remove 'target/phipo/src/sparql/postprocess-module.ru': Permission denied
rm: cannot remove 'target/phipo/src/sparql/inject-synonymtype-declaration.ru': Permission denied
rm: cannot remove 'target/phipo/src/sparql/multiple-replaced_by-violation.sparql': Permission denied
rm: cannot remove 'target/phipo/src/sparql/xrefs.sparql': Permission denied
rm: cannot remove 'target/phipo/src/sparql/iri-range-violation.sparql': Permission denied
rm: cannot remove 'target/phipo/src/sparql/subsets-labeled.sparql': Permission denied
rm: cannot remove 'target/phipo/src/sparql/README.md': Permission denied
rm: cannot remove 'target/phipo/src/ontology/phipo.Makefile': Permission denied
rm: cannot remove 'target/phipo/src/ontology/run.bat': Permission denied
rm: cannot remove 'target/phipo/src/ontology/Makefile': Permission denied
rm: cannot remove 'target/phipo/src/ontology/phipo-edit.owl': Permission denied
rm: cannot remove 'target/phipo/src/ontology/README-editors.md': Permission denied
rm: cannot remove 'target/phipo/src/ontology/phipo-idranges.owl': Permission denied
rm: cannot remove 'target/phipo/src/ontology/run.sh': Permission denied
rm: cannot remove 'target/phipo/src/ontology/imports/ro_import.owl': Permission denied
rm: cannot remove 'target/phipo/src/ontology/imports/cl_terms.txt': Permission denied
rm: cannot remove 'target/phipo/src/ontology/imports/ido_import.owl': Permission denied
rm: cannot remove 'target/phipo/src/ontology/imports/chebi_import.owl': Permission denied
rm: cannot remove 'target/phipo/src/ontology/imports/go_import.owl': Permission denied
rm: cannot remove 'target/phipo/src/ontology/imports/ro_terms.txt': Permission denied
rm: cannot remove 'target/phipo/src/ontology/imports/cl_import.owl': Permission denied
rm: cannot remove 'target/phipo/src/ontology/imports/pato_import.owl': Permission denied
rm: cannot remove 'target/phipo/src/ontology/imports/chebi_terms.txt': Permission denied
rm: cannot remove 'target/phipo/src/ontology/imports/so_terms.txt': Permission denied
rm: cannot remove 'target/phipo/src/ontology/imports/so_import.owl': Permission denied
rm: cannot remove 'target/phipo/src/ontology/imports/go_terms.txt': Permission denied
rm: cannot remove 'target/phipo/src/ontology/imports/ido_terms.txt': Permission denied
rm: cannot remove 'target/phipo/src/ontology/imports/pato_terms.txt': Permission denied
rm: cannot remove 'target/phipo/src/ontology/catalog-v001.xml': Permission denied
rm: cannot remove 'target/phipo/src/ontology/phipo-odk.yaml': Permission denied
rm: cannot remove 'target/phipo/src/ontology/tmp/.gitkeep': Permission denied
rm: cannot remove 'target/phipo/src/metadata/phipo.md': Permission denied
rm: cannot remove 'target/phipo/src/metadata/phipo.yml': Permission denied
rm: cannot remove 'target/phipo/src/metadata/README.md': Permission denied
rm: cannot remove 'target/phipo/src/patterns/data/default/example.tsv': Permission denied
rm: cannot remove 'target/phipo/src/patterns/data/default/README.md': Permission denied
rm: cannot remove 'target/phipo/src/patterns/definitions.owl': Permission denied
rm: cannot remove 'target/phipo/src/patterns/pattern.owl': Permission denied
rm: cannot remove 'target/phipo/src/patterns/dosdp-patterns/example.yaml': Permission denied
rm: cannot remove 'target/phipo/src/patterns/dosdp-patterns/external.txt': Permission denied
rm: cannot remove 'target/phipo/src/patterns/README.md': Permission denied
rm: cannot remove 'target/phipo/.gitignore': Permission denied
rm: cannot remove 'target/phipo/CODE_OF_CONDUCT.md': Permission denied
rm: cannot remove 'target/phipo/CONTRIBUTING.md': Permission denied
rm: cannot remove 'target/phipo/.github/workflows/qc.yml': Permission denied
rm: cannot remove 'target/phipo/README.md': Permission denied
rm: cannot remove 'target/phipo/issue_template.md': Permission denied
make: *** [Makefile:755: update_repo] Error 1
@gouttegd
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From which version were you migrating?

I'm not sure if the script has completed successfully

Most likely, yes.

To check, you can try generating a diff of all changed files in the repository. Post that diff here and we’ll be able to tell you whether everything that should have changed has indeed changed.

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@jseager7 @gouttegd