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| # Description | ||
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| Please include a summary of the changes and the related issue. Please also | ||
| include relevant motivation and context. Please list issues fixed or closed by | ||
| This PR. | ||
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| - Fixes #000: How this PR fixes the issue | ||
| - `path/file.py`: Description of the change | ||
| - `path/file.py`: Description of the change | ||
| - Fixes #000: How this PR fixes the issue | ||
| - `path/file.py`: Description of the change | ||
| - `path/file.py`: Description of the change | ||
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| # Checklist: | ||
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| - [ ] This PR should be accompanied by a release: (yes/no/unsure) | ||
| - [ ] (If release) I have updated the `CITATION.cff` | ||
| - [ ] I have updated the `CHANGELOG.md` | ||
| - [ ] I have added/edited docs/notebooks to reflect the changes |
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| default_stages: [commit, push] | ||
| exclude: (^.github/|^docs/site/|^images/) | ||
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| repos: | ||
| - repo: https://github.com/executablebooks/mdformat | ||
| # Do this before other tools "fixing" the line endings | ||
| rev: 0.7.16 | ||
| hooks: | ||
| - id: mdformat | ||
| name: Format Markdown | ||
| entry: mdformat # Executable to run, with fixed options | ||
| language: python | ||
| types: [markdown] | ||
| args: [--wrap, "80", --number] | ||
| additional_dependencies: | ||
| - mdformat-toc | ||
| - mdformat-beautysh | ||
| - mdformat-config | ||
| - mdformat-black | ||
| - mdformat-web | ||
| - mdformat-gfm | ||
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| - repo: https://github.com/pre-commit/pre-commit-hooks | ||
| rev: v4.4.0 | ||
| hooks: | ||
| - id: check-json | ||
| - id: check-toml | ||
| - id: check-yaml | ||
| args: [--unsafe] | ||
| - id: requirements-txt-fixer | ||
| - id: end-of-file-fixer | ||
| - id: mixed-line-ending | ||
| args: ["--fix=lf"] | ||
| description: Forces to replace line ending by the UNIX 'lf' character. | ||
| - id: trailing-whitespace | ||
| - id: debug-statements | ||
| - id: check-added-large-files # prevent giant files from being committed | ||
| - id: check-builtin-literals | ||
| - id: check-merge-conflict | ||
| - id: check-executables-have-shebangs | ||
| - id: check-shebang-scripts-are-executable | ||
| - id: check-docstring-first | ||
| - id: check-case-conflict | ||
| - id: fix-byte-order-marker | ||
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| - repo: https://github.com/adrienverge/yamllint.git | ||
| rev: v1.29.0 | ||
| hooks: | ||
| - id: yamllint | ||
| args: | ||
| - --no-warnings | ||
| - -d | ||
| - "{extends: relaxed, rules: {line-length: {max: 90}}}" | ||
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| - repo: https://github.com/charliermarsh/ruff-pre-commit | ||
| rev: v0.0.254 | ||
| hooks: | ||
| - id: ruff | ||
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| - repo: https://github.com/PyCQA/autoflake | ||
| rev: v2.0.1 | ||
| hooks: | ||
| - id: autoflake | ||
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| - repo: https://github.com/codespell-project/codespell | ||
| rev: v2.2.2 | ||
| hooks: | ||
| - id: codespell | ||
| args: [--toml, pyproject.toml] | ||
| additional_dependencies: | ||
| - tomli |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,32 +1,12 @@ | ||
| #!/usr/bin/env python | ||
| import os | ||
| import sys | ||
| import tempfile | ||
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| # shared_modules = [ | ||
| # "common\_%", | ||
| # "spikesorting\_%", | ||
| # "decoding\_%", | ||
| # "position\_%", | ||
| # "lfp\_%", | ||
| # ] | ||
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| def add_collab_user(user_name): | ||
| # create a tempoary file for the command | ||
| file = tempfile.NamedTemporaryFile(mode="w") | ||
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| file.write( | ||
| f"GRANT ALL PRIVILEGES ON `{user_name}\_%`.* TO `{user_name}`@'%' IDENTIFIED BY 'temppass';\n" | ||
| ) | ||
| # for module in shared_modules: | ||
| # file.write(f"GRANT ALL PRIVILEGES ON `{module}`.* TO `{user_name}`@'%';\n") | ||
| file.write(f"GRANT SELECT ON `%`.* TO `{user_name}`@'%';\n") | ||
| file.flush() | ||
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| # run those commands in sql | ||
| os.system(f"mysql -p -h lmf-db.cin.ucsf.edu < {file.name}") | ||
| from warnings import warn | ||
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| from spyglass.utils.database_settings import DatabaseSettings | ||
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| if __name__ == "__main__": | ||
| add_collab_user(sys.argv[1]) | ||
| warn( | ||
| "This script is deprecated. " | ||
| + "Use spyglass.utils.database_settings.DatabaseSettings instead." | ||
| ) | ||
| DatabaseSettings(user_name=sys.argv[1]).add_collab_user() |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,29 +1,12 @@ | ||
| #!/usr/bin/env python | ||
| import os | ||
| import sys | ||
| import tempfile | ||
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| shared_modules = [ | ||
| "common\_%", | ||
| "spikesorting\_%", | ||
| "decoding\_%", | ||
| "position\_%", | ||
| "lfp\_%", | ||
| ] | ||
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| def add_user(user_name): | ||
| # create a tempoary file for the command | ||
| file = tempfile.NamedTemporaryFile(mode="w") | ||
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| file.write( | ||
| f"GRANT SELECT ON `%`.* TO `{user_name}`@'%' IDENTIFIED BY 'Data_$haring';\n" | ||
| ) | ||
| file.flush() | ||
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| # run that commands in sql | ||
| os.system(f"mysql -p -h lmf-db.cin.ucsf.edu < {file.name}") | ||
| from warnings import warn | ||
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| from spyglass.utils.database_settings import DatabaseSettings | ||
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| if __name__ == "__main__": | ||
| add_user(sys.argv[1]) | ||
| warn( | ||
| "This script is deprecated. " | ||
| + "Use spyglass.utils.database_settings.DatabaseSettings instead." | ||
| ) | ||
| DatabaseSettings(user_name=sys.argv[1]).add_dj_guest() |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,34 +1,12 @@ | ||
| #!/usr/bin/env python | ||
| import grp | ||
| import os | ||
| import sys | ||
| import tempfile | ||
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| target_group = "kachery-users" | ||
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| def add_module(module_name): | ||
| print(f"Granting everyone permissions to module {module_name}") | ||
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| # create a tempoary file for the command | ||
| file = tempfile.NamedTemporaryFile(mode="w") | ||
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| # find the kachery-users group | ||
| groups = grp.getgrall() | ||
| for group in groups: | ||
| if group.gr_name == target_group: | ||
| break | ||
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| # get a list of usernames | ||
| for user in group.gr_mem: | ||
| file.write( | ||
| f"GRANT ALL PRIVILEGES ON `{module_name}\_%`.* TO `{user}`@'%';\n" | ||
| ) | ||
| file.flush() | ||
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| # run those commands in sql | ||
| os.system(f"mysql -p -h lmf-db.cin.ucsf.edu < {file.name}") | ||
| from warnings import warn | ||
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| from spyglass.utils.database_settings import DatabaseSettings | ||
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| if __name__ == "__main__": | ||
| add_module(sys.argv[1]) | ||
| warn( | ||
| "This script is deprecated. " | ||
| + "Use spyglass.utils.database_settings.DatabaseSettings instead." | ||
| ) | ||
| DatabaseSettings().add_module(sys.argv[1]) |
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