diff --git a/.deprecated_files b/.deprecated_files index ca3684e..af2a4cf 100644 --- a/.deprecated_files +++ b/.deprecated_files @@ -21,3 +21,4 @@ setup.cfg .pylintrc .flake8 +.editorconfig diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 90ee325..89ff58f 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -10,37 +10,15 @@ "vscode": { // Set *default* container specific settings.json values on container create. "settings": { + "files.eol": "\n", "terminal.integrated.profiles.linux": { "bash": { "path": "/bin/bash" } }, - "sqltools.connections": [ - { - "name": "Container database", - "driver": "PostgreSQL", - "previewLimit": 50, - "server": "localhost", - "port": 5432, - "database": "postgres", - "username": "postgres", - "password": "postgres" - } - ], "python.pythonPath": "/usr/local/bin/python", "python.languageServer": "Pylance", - "python.linting.enabled": true, - "python.linting.pylintEnabled": true, - "python.formatting.autopep8Path": "/usr/local/py-utils/bin/autopep8", - "python.formatting.blackPath": "/usr/local/py-utils/bin/black", - "python.formatting.yapfPath": "/usr/local/py-utils/bin/yapf", - "python.formatting.provider": "black", "python.analysis.typeCheckingMode": "basic", - "python.linting.banditPath": "/usr/local/py-utils/bin/bandit", - "python.linting.mypyPath": "/usr/local/py-utils/bin/mypy", - "python.linting.pycodestylePath": "/usr/local/py-utils/bin/pycodestyle", - "python.linting.pydocstylePath": "/usr/local/py-utils/bin/pydocstyle", - "python.linting.pylintPath": "/usr/local/py-utils/bin/pylint", "python.testing.pytestPath": "/usr/local/py-utils/bin/pytest", "python.testing.pytestArgs": [ "--profile" @@ -52,6 +30,7 @@ "editor.rulers": [ 88 ], + "editor.defaultFormatter": "ms-python.black-formatter", "licenser.license": "Custom", "licenser.customHeaderFile": "/workspace/.devcontainer/license_header.txt" }, @@ -60,7 +39,6 @@ "mikestead.dotenv", "ms-azuretools.vscode-docker", "ms-python.python", - "ms-python.isort", "ms-python.vscode-pylance", "ms-toolsai.jupyter", "njpwerner.autodocstring", @@ -73,7 +51,9 @@ "yzhang.markdown-all-in-one", "visualstudioexptteam.vscodeintellicode", "ymotongpoo.licenser", - "editorconfig.editorconfig" + "charliermarsh.ruff", + "ms-python.black-formatter", + "ms-python.mypy-type-checker" ] } }, diff --git a/.editorconfig b/.editorconfig deleted file mode 100644 index 3fa06b5..0000000 --- a/.editorconfig +++ /dev/null @@ -1,14 +0,0 @@ -# Top-most EditorConfig file. -root = true - -# For all files ... -[*] - -# Unix-style LF newlines. -end_of_line = lf - -# Force a newline at the end of the file. -insert_final_newline = true - -# Use UTF-8. -charset = utf-8 diff --git a/.gitignore b/.gitignore index a71cfd2..d9ba614 100644 --- a/.gitignore +++ b/.gitignore @@ -133,6 +133,12 @@ dmypy.json # ignore VS Code settings: .vscode/ +# key stores +*.key +*.rnd +.keystore +.ssl/ + # desktop settings and thumbnails .DS_Store desktop.ini diff --git a/.mandatory_files b/.mandatory_files index 20b6c56..ba9f6c3 100644 --- a/.mandatory_files +++ b/.mandatory_files @@ -7,7 +7,6 @@ .devcontainer/dev_launcher .devcontainer/docker-compose.yml -.devcontainer/Dockerfile tests/__init__.py tests/fixtures/__init__.py diff --git a/.static_files b/.static_files index 6983902..5f035a9 100644 --- a/.static_files +++ b/.static_files @@ -40,7 +40,6 @@ scripts/README.md example_data/README.md .coveragerc -.editorconfig .gitattributes .gitignore .mypy.ini diff --git a/pyproject.toml b/pyproject.toml index 7120a5b..899be0c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta" [project] name = "ghga_event_schemas" -version = "1.0.0" +version = "2.0.0" description = "GHGA Event Schemas: A package that collects schemas used for events exchanged between GHGA service." readme = "README.md" authors = [ diff --git a/scripts/license_checker.py b/scripts/license_checker.py index 0ddc786..5d8be06 100755 --- a/scripts/license_checker.py +++ b/scripts/license_checker.py @@ -88,6 +88,9 @@ "xml", "yaml", "yml", + "tsv", + "fastq", + "gz", ] # exclude any files with names that match any of the following regex: diff --git a/src/ghga_event_schemas/pydantic_.py b/src/ghga_event_schemas/pydantic_.py index cd4a18e..344b441 100644 --- a/src/ghga_event_schemas/pydantic_.py +++ b/src/ghga_event_schemas/pydantic_.py @@ -159,7 +159,7 @@ class FileUploadReceived(UploadDateModel): s3_endpoint_alias: str = Field( ..., description="Alias for the object storage location where the given object is stored." - + "This can be uniquely mapped to an endpoint URL in the service configuration.", + + "This can be uniquely mapped to an endpoint configuration in the service.", ) submitter_public_key: str = Field( ..., @@ -194,7 +194,7 @@ class FileUploadValidationSuccess(UploadDateModel): s3_endpoint_alias: str = Field( ..., description="Alias for the object storage location where the given object is stored." - + "This can be uniquely mapped to an endpoint URL in the service configuration.", + + "This can be uniquely mapped to an endpoint configuration in the service.", ) decrypted_size: int = Field( ..., @@ -260,7 +260,7 @@ class FileUploadValidationFailure(UploadDateModel): s3_endpoint_alias: str = Field( ..., description="Alias for the object storage location where the given object is stored." - + "This can be uniquely mapped to an endpoint URL in the service configuration.", + + "This can be uniquely mapped to an endpoint configuration in the service.", ) reason: str = Field( ..., @@ -314,7 +314,7 @@ class NonStagedFileRequested(BaseModel): s3_endpoint_alias: str = Field( ..., description="Alias for the object storage location where the given object is stored." - + "This can be uniquely mapped to an endpoint URL in the service configuration.", + + "This can be uniquely mapped to an endpoint configuration in the service.", ) decrypted_sha256: str = Field( ..., @@ -380,6 +380,11 @@ class FileDeletionRequested(BaseModel): file_id: str = Field( ..., description="The public ID of the file as present in the metadata catalog." ) + s3_endpoint_alias: str = Field( + ..., + description="Alias for the object storage location where the given object is stored." + + "This can be uniquely mapped to an endpoint configuration in the service.", + ) model_config = ConfigDict(title="file_deletion_requested")