diff --git a/.cruft.json b/.cruft.json
new file mode 100644
index 0000000..d30a3ab
--- /dev/null
+++ b/.cruft.json
@@ -0,0 +1,21 @@
+{
+ "template": "https://github.com/elixir-cloud-aai/cookiecutter-python",
+ "commit": "ea72128ea94f0693d2a940f3f1657554178b6b66",
+ "checkout": null,
+ "context": {
+ "cookiecutter": {
+ "author_name": "ELIXIR Cloud AAI",
+ "author_email": "cloud-service@elixir-europe.org",
+ "development_status": "1 - Planning",
+ "short_description": "File handler utilizing TUS and MinIO with DRS-Filer integration.",
+ "project_name": "tus-storagehandler",
+ "project_slug": "tus_storagehandler",
+ "github_username": "elixir-cloud-aai",
+ "python_version": "3.11",
+ "add_script": "n",
+ "year": "2024",
+ "_template": "https://github.com/elixir-cloud-aai/cookiecutter-python"
+ }
+ },
+ "directory": null
+}
diff --git a/.github/ISSUE_TEMPLATE/general-purpose.md b/.github/ISSUE_TEMPLATE/general-purpose.md
new file mode 100644
index 0000000..9130566
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/general-purpose.md
@@ -0,0 +1,45 @@
+Your issue may already be reported! Please search on the
+[issue tracker][issue-tracker] before creating one.
+
+## Expected Behavior
+
+
+
+
+
+## Current Behavior
+
+
+
+
+
+## Possible Solution
+
+
+
+
+
+## Steps to Reproduce (for bugs)
+
+
+
+
+
+1.
+
+## Context
+
+
+
+
+
+## Your Environment
+
+
+
+- Version used:
+- Browser Name and version:
+- Operating System and version (desktop or mobile):
+- Link to your project:
+
+[issue-tracker]: https://github.com/elixir-cloud-aai/tus-storagehandler/issues
diff --git a/.github/actions/setup/poetry/action.yaml b/.github/actions/setup/poetry/action.yaml
new file mode 100644
index 0000000..92154b2
--- /dev/null
+++ b/.github/actions/setup/poetry/action.yaml
@@ -0,0 +1,92 @@
+---
+name: Setup Python and Poetry Action
+description: Configure system, Python, Poetry and deps and cache management.
+
+inputs:
+ os:
+ default: ubuntu-latest
+ description: The operating system to use
+ python-version:
+ default: '3.11'
+ description: The version of Python to use
+ poetry-version:
+ default: '1.8.2'
+ description: The version of Poetry to install
+ poetry-install-options:
+ default: ''
+ description: Additional options to pass to poetry install
+ poetry-export-options:
+ default: ''
+ description: Options to pass to poetry export for hash generation for cache
+ invalidation
+
+runs:
+ using: composite
+ steps:
+ - uses: 'actions/setup-python@v5'
+ id: setup-python
+ with:
+ python-version: '${{ inputs.python-version }}'
+
+ - name: Setup pipx environment Variables
+ id: pipx-env-setup
+ # pipx default home and bin dir are not writable by the cache action
+ # so override them here and add the bin dir to PATH for later steps.
+ # This also ensures the pipx cache only contains poetry
+ run: |
+ SEP="${{ !startsWith(runner.os, 'windows') && '/' || '\\' }}"
+ PIPX_CACHE="${{ github.workspace }}${SEP}pipx_cache"
+ echo "pipx-cache-path=${PIPX_CACHE}" >> $GITHUB_OUTPUT
+ echo "pipx-version=$(pipx --version)" >> $GITHUB_OUTPUT
+ echo "PIPX_HOME=${PIPX_CACHE}${SEP}home" >> $GITHUB_ENV
+ echo "PIPX_BIN_DIR=${PIPX_CACHE}${SEP}bin" >> $GITHUB_ENV
+ echo "PIPX_MAN_DIR=${PIPX_CACHE}${SEP}man" >> $GITHUB_ENV
+ echo "${PIPX_CACHE}${SEP}bin" >> $GITHUB_PATH
+ shell: bash
+
+ - name: Pipx cache
+ id: pipx-cache
+ uses: actions/cache@v4
+ with:
+ path: ${{ steps.pipx-env-setup.outputs.pipx-cache-path }}
+ key: ${{ runner.os }}-python-
+ ${{ steps.setup-python.outputs.python-version }}-
+ pipx-${{ steps.pipx-env-setup.outputs.pipx-version }}-
+ poetry-${{ inputs.poetry-version }}
+
+ - name: Install poetry
+ if: steps.pipx-cache.outputs.cache-hit != 'true'
+ id: install-poetry
+ shell: bash
+ run: |
+ pipx install poetry \
+ --python "${{ steps.setup-python.outputs.python-path }}"
+
+ - name: Read poetry cache location
+ id: poetry-cache-location
+ shell: bash
+ run: |
+ echo "poetry-venv-location=$(poetry config virtualenvs.path)" \
+ >> $GITHUB_OUTPUT
+
+ - name: Generate hash only for required deps
+ run: |
+ poetry export ${{ inputs.poetry-export-options }} \
+ --format=requirements.txt --output=requirements.txt
+ echo "DEP_HASH=$(sha256sum requirements.txt | cut -d ' ' -f 1)" \
+ >> $GITHUB_ENV
+ shell: bash
+
+ - uses: actions/cache@v4
+ name: Poetry cache
+ with:
+ path: ${{ steps.poetry-cache-location.outputs.poetry-venv-location }}
+ key: ${{ runner.os }}-[python-
+ ${{ steps.setup-python.outputs.python-version }}]-[
+ ${{ env.DEP_HASH }}]-[${{ inputs.poetry-install-options }}]
+
+ - name: 'Poetry install'
+ if: steps.poetry-cache.outputs.cache-hit != 'true'
+ shell: bash
+ run: poetry install ${{ inputs.poetry-install-options }} --no-interaction
+...
diff --git a/.github/workflows/code_quality.yaml b/.github/workflows/code_quality.yaml
new file mode 100644
index 0000000..8b64d3b
--- /dev/null
+++ b/.github/workflows/code_quality.yaml
@@ -0,0 +1,84 @@
+---
+name: Code Quality
+
+on:
+ push:
+ branches:
+ - main
+ pull_request:
+ branches:
+ - main
+
+jobs:
+ format:
+ name: Format
+ runs-on: ubuntu-latest
+ steps:
+ - name: Check out repository
+ uses: actions/checkout@v4
+
+ - name: Set up environment
+ uses: ./.github/actions/setup/poetry
+ with:
+ os: ${{ job.os }}
+ python-version: '3.11'
+ poetry-install-options: "--only=code_quality --no-root"
+ poetry-export-options: "--only=code_quality"
+
+ - name: Check code style
+ run: poetry run ruff format --check
+
+ lint:
+ name: Lint
+ runs-on: ubuntu-latest
+ steps:
+ - name: Check out repository
+ uses: actions/checkout@v4
+
+ - name: Set up environment
+ uses: ./.github/actions/setup/poetry
+ with:
+ os: ${{ job.os }}
+ python-version: '3.11'
+ poetry-install-options: "--only=code_quality --no-root"
+ poetry-export-options: "--only=code_quality"
+
+ - name: Check code quality
+ run: poetry run ruff check .
+
+ spell-check:
+ name: Spell Check
+ runs-on: ubuntu-latest
+ steps:
+ - name: Check out repository
+ uses: actions/checkout@v4
+
+ - name: Set up environment
+ uses: ./.github/actions/setup/poetry
+ with:
+ os: ${{ job.os }}
+ python-version: '3.11'
+ poetry-install-options: "--only=code_quality --no-root"
+ poetry-export-options: "--only=code_quality"
+
+ - name: Check spellings
+ run: poetry run typos .
+
+ type-check:
+ name: Type Check
+ runs-on: ubuntu-latest
+ steps:
+ - name: Check out repository
+ uses: actions/checkout@v4
+
+ - name: Set up environment
+ uses: ./.github/actions/setup/poetry
+ with:
+ os: ${{ job.os }}
+ python-version: '3.11'
+ poetry-install-options: "--with=code_quality --with=types --no-root"
+ poetry-export-options: "--with=code_quality --with=types"
+
+ - name: Check types
+ run: poetry run mypy tus_storagehandler/
+...
diff --git a/.github/workflows/code_test.yaml b/.github/workflows/code_test.yaml
new file mode 100644
index 0000000..07b9309
--- /dev/null
+++ b/.github/workflows/code_test.yaml
@@ -0,0 +1,74 @@
+---
+name: Code Test
+
+on:
+ push:
+ branches:
+ - main
+ pull_request:
+ branches:
+ - main
+
+jobs:
+ integration-test:
+ name: Integration Test
+ runs-on: ubuntu-latest
+ steps:
+ - name: Check out repository
+ uses: actions/checkout@v4
+
+ - name: Set up environment
+ uses: ./.github/actions/setup/poetry
+ with:
+ os: ${{ job.os }}
+ python-version: '3.11'
+ poetry-install-options: "--with=test"
+ poetry-export-options: "--with=test"
+
+ - name: Run tests and generate coverage as test_integration.xml
+ run: |
+ poetry run pytest \
+ --cov-report term \
+ --cov-report xml:test_integration.xml \
+ --cov=tests/test_integration
+
+ - name: Upload coverage to Codecov
+ uses: codecov/codecov-action@v4
+ with:
+ token: ${{ secrets.CODECOV_TOKEN }}
+ flags: test_integration
+ files: ./test_integration.xml
+ fail_ci_if_error: true
+ verbose: true
+
+ unit-test:
+ name: Unit Test
+ runs-on: ubuntu-latest
+ steps:
+ - name: Check out repository
+ uses: actions/checkout@v4
+
+ - name: Set up environment
+ uses: ./.github/actions/setup/poetry
+ with:
+ os: ${{ job.os }}
+ python-version: '3.11'
+ poetry-install-options: "--with=test"
+ poetry-export-options: "--with=test"
+
+ - name: Run tests and generate coverage as test_unit.xml
+ run: |
+ poetry run pytest \
+ --cov-report term \
+ --cov-report xml:test_unit.xml \
+ --cov=tests/test_unit
+
+ - name: Upload coverage to Codecov
+ uses: codecov/codecov-action@v4
+ with:
+ token: ${{ secrets.CODECOV_TOKEN }}
+ flags: test_unit
+ files: ./test_unit.xml
+ fail_ci_if_error: true
+ verbose: true
+...
diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml
new file mode 100644
index 0000000..a0f28a1
--- /dev/null
+++ b/.github/workflows/docs.yaml
@@ -0,0 +1,46 @@
+---
+name: Documentation Check
+
+on:
+ push:
+ branches:
+ - main
+ pull_request:
+ branches:
+ - main
+
+jobs:
+ check-api-docs:
+ runs-on: ubuntu-latest
+
+ steps:
+ - name: Check out repository
+ uses: actions/checkout@v4
+
+ - name: Set up environment
+ uses: ./.github/actions/setup/poetry
+ with:
+ os: ${{ job.os }}
+ python-version: '3.11'
+ poetry-install-options: "--with=docs --with=types --no-root"
+ poetry-export-options: "--with=docs --with=types"
+
+ - name: Generate API docs
+ run: |
+ poetry run sphinx-apidoc -o /tmp/docs/source/pages tus_storagehandler/
+
+ - name: Compare docs with main branch
+ id: check_docs_diff
+ run: |
+ shasum /tmp/docs/source/pages/* > /tmp/docs.sha
+ shasum docs/source/pages/* > docs/project_doc.sha
+ awk '{print $1}' /tmp/docs.sha > /tmp/docs_hashes.sha
+ awk '{print $1}' docs/project_doc.sha > docs/project_doc_hashes.sha
+ diff=$(diff /tmp/docs_hashes.sha docs/project_doc_hashes.sha) || true
+ if [[ -n "$diff" ]]; then
+ echo "::error::API documentation is out of date."
+ exit 1
+ else
+ echo "API documentation is up to date."
+ fi
+...
diff --git a/.github/workflows/pr_validation.yaml b/.github/workflows/pr_validation.yaml
new file mode 100644
index 0000000..4e43caa
--- /dev/null
+++ b/.github/workflows/pr_validation.yaml
@@ -0,0 +1,67 @@
+---
+name: PR Evaluation
+
+on:
+ pull_request:
+ types: [opened, synchronize, reopened, ready_for_review, edited]
+ branches: ['main']
+
+jobs:
+ detect-unresolved-conflicts:
+ name: Detect unresolved merge conflicts
+ runs-on: ubuntu-latest
+ needs: semantic_pr
+ steps:
+ - uses: actions/checkout@v3
+ - name: List files with merge conflict markers
+ run: git --no-pager grep "<<<<<<<" ":(exclude).github/" || true
+ - name: Fail or succeed job if any files with merge conflict markers
+ run: exit $(git grep "<<<<<<<" ":(exclude).github/" | wc --lines)
+
+ pre-commit:
+ name: Pre-commit checks
+ runs-on: ubuntu-latest
+ steps:
+ - name: Check out repository
+ uses: actions/checkout@v4
+
+ - name: Set up environment
+ uses: ./.github/actions/setup/poetry
+ with:
+ os: ${{ job.os }}
+ python-version: '3.11'
+ poetry-install-options: "--only=misc --no-root"
+ poetry-export-options: "--only=misc"
+
+ - name: Check all the pre-commit hooks passed
+ run: pre-commit run --all-files
+
+ semantic-pr:
+ name: Semantic PR title
+ runs-on: ubuntu-latest
+ if: ${{ github.event.action != 'edited' ||
+ github.event.changes.title != null }}
+ steps:
+ - uses: amannn/action-semantic-pull-request@v5
+ env:
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+ with:
+ types: |
+ fix
+ feat
+ docs
+ style
+ refactor
+ perf
+ test
+ build
+ ci
+ chore
+ revert
+ subjectPattern: ^(?![A-Z])(?=.{1,50}$).+$
+ subjectPatternError: |
+ The subject "{subject}" found in the pull request title "{title}"
+ didn't match the configured pattern. Please ensure that the subject
+ doesn't start with an uppercase character & not have more than 50
+ characters.
+...
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
new file mode 100644
index 0000000..e03080f
--- /dev/null
+++ b/.github/workflows/release.yaml
@@ -0,0 +1,26 @@
+---
+name: Release package
+
+on:
+ release:
+ types: [released]
+
+jobs:
+ pypi:
+ name: Publish to PyPI
+ runs-on: ubuntu-latest
+ steps:
+ - name: Checkout code
+ uses: actions/checkout@v4
+
+ - name: Set up environment
+ uses: ./.github/actions/setup/poetry
+ with:
+ os: ${{ job.os }}
+ python-version: '3.11'
+ poetry-install-options: "--only=main"
+ poetry-export-options: "--only=main"
+
+ - name: Publish package to PyPI
+ run: poetry publish --build -u __token__ -p ${{ secrets.PYPI_TOKEN }}
+...
diff --git a/.github/workflows/update.yaml b/.github/workflows/update.yaml
new file mode 100644
index 0000000..10030bb
--- /dev/null
+++ b/.github/workflows/update.yaml
@@ -0,0 +1,55 @@
+---
+name: Update project structure
+
+on:
+ schedule:
+ - cron: "0 2 * * 1" # Every Monday at 2am
+
+jobs:
+ update-template:
+ runs-on: ubuntu-latest
+ steps:
+ - name: Check out repository
+ uses: actions/checkout@v4
+
+ - name: Set up environment
+ uses: ./.github/actions/setup/poetry
+ with:
+ os: ${{ job.os }}
+ python-version: '3.11'
+ poetry-install-options: "--only=misc --no-root"
+ poetry-export-options: "--only=misc"
+
+ - name: Update project structure
+ run: |
+ cruft update -y
+
+ - name: Check if there are changes
+ id: changes
+ uses: UnicornGlobal/has-changes-action@v1.0.11
+
+ - name: Apply additional changes and fixes
+ if: steps.changes.outputs.changed == 1
+ run: |
+ poetry lock --no-update
+ poetry install
+ pre-commit run --all-files
+
+ - name: Get new template version
+ if: steps.changes.outputs.changed == 1
+ run: |
+ COMMIT_HASH=$(cat .cruft.json | jello -r "_['commit'][:8]")
+ echo "TEMPLATE_COMMIT=${COMMIT_HASH}" >> $GITHUB_ENV
+
+ - name: Create Pull Request
+ if: steps.changes.outputs.changed == 1
+ uses: peter-evans/create-pull-request@v6
+ with:
+ token: ${{ secrets.AUTO_UPDATE_GITHUB_TOKEN }}
+ commit-message: >-
+ chore: update project structure to ${{ env.TEMPLATE_COMMIT }}
+ title: "chore: auto-sync cookiecutter template"
+ body: ""
+ branch: chore/cookiecutter-pypackage
+ delete-branch: true
+...
diff --git a/.github/workflows/vulnerability.yaml b/.github/workflows/vulnerability.yaml
new file mode 100644
index 0000000..270104c
--- /dev/null
+++ b/.github/workflows/vulnerability.yaml
@@ -0,0 +1,48 @@
+---
+name: Vulnerability Test
+
+on:
+ push:
+ branches:
+ - main
+ pull_request:
+ branches:
+ - main
+
+jobs:
+ code-vulnerabilities:
+ name: Code
+ runs-on: ubuntu-latest
+ steps:
+ - name: Check out repository
+ uses: actions/checkout@v4
+
+ - name: Set up environment
+ uses: ./.github/actions/setup/poetry
+ with:
+ os: ${{ job.os }}
+ python-version: '3.11'
+ poetry-install-options: "--only=vulnerability --no-root"
+ poetry-export-options: "--only=vulnerability"
+
+ - name: Check code vulnerabilities with bandit
+ run: poetry run bandit -c pyproject.toml -r tus_storagehandler/
+
+ dependency-vulnerabilities:
+ name: Dependencies
+ runs-on: ubuntu-latest
+ steps:
+ - name: Check out repository
+ uses: actions/checkout@v4
+
+ - name: Set up environment
+ uses: ./.github/actions/setup/poetry
+ with:
+ os: ${{ job.os }}
+ python-version: '3.11'
+ poetry-install-options: "--only=vulnerability --no-root"
+ poetry-export-options: "--only=vulnerability"
+
+ - name: Check dependency vulnerabilities with safety
+ run: poetry run safety check --full-report
+...
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..14505df
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,183 @@
+######## This section contains auto-generated .gitignore patterns for #########
+######## Python projects. Write project level gitignore below this #########
+######## section. #########
+
+# Created by https://www.toptal.com/developers/gitignore/api/python
+# Edit at https://www.toptal.com/developers/gitignore?templates=python
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+# Usually these files are written by a python script from a template
+# before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+# For a library or package, you might want to ignore these files since the code is
+# intended to run in multiple environments; otherwise, check them in:
+.python-version
+
+# pipenv
+# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+# However, in case of collaboration, if having platform-specific dependencies or dependencies
+# having no cross-platform support, pipenv may install dependencies that don't work, or not
+# install all needed dependencies.
+Pipfile.lock
+
+# pdm
+# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+# in version control.
+# https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+# JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+# and can be added to the global gitignore or merged into this file. For a more nuclear
+# option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/
+
+### Python Patch ###
+# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration
+poetry.toml
+
+# ruff
+.ruff_cache/
+
+# LSP config files
+pyrightconfig.json
+
+# End of https://www.toptal.com/developers/gitignore/api/python
+SquareX Safe File Viewer
+✕
+
+######### End of auto generated .gitignore file for Python projects. #########
+
+######### Project level .gitignore. #########
+
+# Keep pre-commit hooks and .yamllint file
+!.pre-commit-config.yaml
+!.yamllint.yaml
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..1e8f56f
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,39 @@
+---
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+# Common commands:
+# pre-commit install
+# pre-commit autoupdate
+# pre-commit run --all-files --hook-stage commit
+repos:
+ - repo: https://github.com/pre-commit/pre-commit-hooks
+ rev: v4.6.0
+ hooks:
+ - id: check-added-large-files
+ - id: destroyed-symlinks
+ - id: detect-private-key
+ - id: end-of-file-fixer
+ - id: mixed-line-ending
+ args: [--fix=auto]
+ - id: trailing-whitespace
+ - repo: https://github.com/executablebooks/mdformat
+ rev: 0.7.17
+ hooks:
+ - id: mdformat
+ additional_dependencies:
+ - mdformat-config
+ - mdformat-black
+ - mdformat-frontmatter
+ args: [--wrap=80]
+ - repo: https://github.com/adrienverge/yamllint.git
+ rev: v1.35.1
+ hooks:
+ - id: yamllint
+ exclude: ^deployment/charts
+ - repo: https://github.com/pappasam/toml-sort
+ rev: v0.23.1
+ hooks:
+ - id: toml-sort-fix
+ args: [--in-place, --all, --trailing-comma-inline-array]
+ exclude: poetry\.lock
+...
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
new file mode 100644
index 0000000..ec7defb
--- /dev/null
+++ b/.readthedocs.yaml
@@ -0,0 +1,16 @@
+---
+version: 2
+
+build:
+ os: ubuntu-22.04
+ tools:
+ python: '3.11'
+ jobs:
+ post_create_environment:
+ - python -m pip install poetry
+ post_install:
+ - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs
+
+sphinx:
+ configuration: docs/source/conf.py
+...
diff --git a/.safety-policy.yml b/.safety-policy.yml
new file mode 100644
index 0000000..7089764
--- /dev/null
+++ b/.safety-policy.yml
@@ -0,0 +1,43 @@
+---
+version: '3.0'
+
+scanning-settings:
+ max-depth: 6
+ exclude: []
+ include-files: []
+ system:
+ targets: []
+
+security:
+ ignore-vulnerabilities:
+ 70612:
+ reason: "Won't use untrusted templates without sandboxing."
+ expires: '2025-5-27'
+
+report:
+ dependency-vulnerabilities:
+ enabled: true
+ auto-ignore-in-report:
+ python:
+ environment-results: true
+ unpinned-requirements: true
+ cvss-severity: []
+
+fail-scan-with-exit-code:
+ dependency-vulnerabilities:
+ enabled: true
+ fail-on-any-of:
+ cvss-severity:
+ - critical
+ - high
+ - medium
+ exploitability:
+ - critical
+ - high
+ - medium
+
+security-updates:
+ dependency-vulnerabilities:
+ auto-security-updates-limit:
+ - patch
+...
diff --git a/.yamllint.yaml b/.yamllint.yaml
new file mode 100644
index 0000000..ad3171a
--- /dev/null
+++ b/.yamllint.yaml
@@ -0,0 +1,13 @@
+---
+# https://yamllint.readthedocs.io/en/stable/configuration.html#default-configuration
+extends: default
+
+rules:
+ truthy:
+ ignore:
+ .github/**/*.yaml
+ document-start:
+ level: error
+ document-end:
+ level: error
+...
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..35c9d67
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,201 @@
+ Apache License
+ Version 2.0, January 2004
+ http://www.apache.org/licenses/
+
+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+ 1. Definitions.
+
+ "License" shall mean the terms and conditions for use, reproduction,
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+ "Licensor" shall mean the copyright owner or entity authorized by
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+ "You" (or "Your") shall mean an individual or Legal Entity
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+ "Derivative Works" shall mean any work, whether in Source or Object
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+ "Contribution" shall mean any work of authorship, including
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+ "Contributor" shall mean Licensor and any individual or Legal Entity
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+ (except as stated in this section) patent license to make, have made,
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+ meet the following conditions:
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+ (a) You must give any other recipients of the Work or
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+ (b) You must cause any modified files to carry prominent notices
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+ (c) You must retain, in the Source form of any Derivative Works
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+ of the following places: within a NOTICE text file distributed
+ as part of the Derivative Works; within the Source form or
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+ within a display generated by the Derivative Works, if and
+ wherever such third-party notices normally appear. The contents
+ of the NOTICE file are for informational purposes only and
+ do not modify the License. You may add Your own attribution
+ notices within Derivative Works that You distribute, alongside
+ or as an addendum to the NOTICE text from the Work, provided
+ that such additional attribution notices cannot be construed
+ as modifying the License.
+
+ You may add Your own copyright statement to Your modifications and
+ may provide additional or different license terms and conditions
+ for use, reproduction, or distribution of Your modifications, or
+ for any such Derivative Works as a whole, provided Your use,
+ reproduction, and distribution of the Work otherwise complies with
+ the conditions stated in this License.
+
+ 5. Submission of Contributions. Unless You explicitly state otherwise,
+ any Contribution intentionally submitted for inclusion in the Work
+ by You to the Licensor shall be under the terms and conditions of
+ this License, without any additional terms or conditions.
+ Notwithstanding the above, nothing herein shall supersede or modify
+ the terms of any separate license agreement you may have executed
+ with Licensor regarding such Contributions.
+
+ 6. Trademarks. This License does not grant permission to use the trade
+ names, trademarks, service marks, or product names of the Licensor,
+ except as required for reasonable and customary use in describing the
+ origin of the Work and reproducing the content of the NOTICE file.
+
+ 7. Disclaimer of Warranty. Unless required by applicable law or
+ agreed to in writing, Licensor provides the Work (and each
+ Contributor provides its Contributions) on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+ implied, including, without limitation, any warranties or conditions
+ of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+ PARTICULAR PURPOSE. You are solely responsible for determining the
+ appropriateness of using or redistributing the Work and assume any
+ risks associated with Your exercise of permissions under this License.
+
+ 8. Limitation of Liability. In no event and under no legal theory,
+ whether in tort (including negligence), contract, or otherwise,
+ unless required by applicable law (such as deliberate and grossly
+ negligent acts) or agreed to in writing, shall any Contributor be
+ liable to You for damages, including any direct, indirect, special,
+ incidental, or consequential damages of any character arising as a
+ result of this License or out of the use or inability to use the
+ Work (including but not limited to damages for loss of goodwill,
+ work stoppage, computer failure or malfunction, or any and all
+ other commercial damages or losses), even if such Contributor
+ has been advised of the possibility of such damages.
+
+ 9. Accepting Warranty or Additional Liability. While redistributing
+ the Work or Derivative Works thereof, You may choose to offer,
+ and charge a fee for, acceptance of support, warranty, indemnity,
+ or other liability obligations and/or rights consistent with this
+ License. However, in accepting such obligations, You may act only
+ on Your own behalf and on Your sole responsibility, not on behalf
+ of any other Contributor, and only if You agree to indemnify,
+ defend, and hold each Contributor harmless for any liability
+ incurred by, or claims asserted against, such Contributor by reason
+ of your accepting any such warranty or additional liability.
+
+ END OF TERMS AND CONDITIONS
+
+ APPENDIX: How to apply the Apache License to your work.
+
+ To apply the Apache License to your work, attach the following
+ boilerplate notice, with the fields enclosed by brackets "[]"
+ replaced with your own identifying information. (Don't include
+ the brackets!) The text should be enclosed in the appropriate
+ comment syntax for the file format. We also recommend that a
+ file or class name and description of purpose be included on the
+ same "printed page" as the copyright notice for easier
+ identification within third-party archives.
+
+ Copyright 2024 ELIXIR Cloud AAI
+
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..428044c
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,137 @@
+# NOTE: This Makefile assumes that dependencies are installed and, if a virtual
+# environment is used, it is activated.
+
+## Variables ##################################################################
+# NOTE: Define any variables here if needed in the future
+
+## Documentation ##############################################################
+# NOTE: Keep all the targets in alphabetical order for better readability.
+
+default: help
+
+.PHONY: help
+help:
+ @echo "\nUsage: make [target] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n"
+ @echo "Available targets:\n"
+
+ @echo "Code Quality ------------------------------------------------------------------"
+ @echo " \033[1m\033[35mformat-lint\033[0m \033[37m(fl)\033[0m: \033[36mRun linter, formatter, spellcheck.\033[0m"
+ @echo " \033[1m\033[35mprecommit-check\033[0m \033[37m(pc)\033[0m: \033[36mRun all pre-commit checks.\033[0m"
+ @echo " \033[1m\033[35msecurity\033[0m \033[37m(s)\033[0m: \033[36mRun security scans.\033[0m"
+ @echo " \033[1m\033[35mtype-check\033[0m \033[37m(tc)\033[0m: \033[36mPerform type checking.\033[0m\n"
+
+ @echo "Documentation -----------------------------------------------------------------"
+ @echo " \033[1m\033[35mdocs\033[0m \033[37m(d)\033[0m: \033[36mGenerate project documentation.\033[0m\n"
+
+ @echo "Environment Management --------------------------------------------------------"
+ @echo " \033[1m\033[35mclean-venv\033[0m \033[37m(cv)\033[0m: \033[36mRemove virtual environment.\033[0m"
+ @echo " \033[1m\033[35minstall\033[0m \033[37m(i)\033[0m: \033[36mInstall dependencies and tus_storagehandler.\033[0m"
+ @echo " \033[1m\033[35mvenv\033[0m \033[37m(v)\033[0m: \033[36mCreate virtual environment.\033[0m\n"
+
+ @echo "Miscellaneous -----------------------------------------------------------------"
+ @echo " \033[1m\033[35mupdate\033[0m \033[37m(u)\033[0m: \033[36mUpdate the template.\033[0m\n"
+
+ @echo "Testing -----------------------------------------------------------------------"
+ @echo " \033[1m\033[35mtest\033[0m \033[37m(t)\033[0m: \033[36mRun all tests.\033[0m\n"
+
+## Autogenerated Targets ######################################################
+# NOTE: Keep all the targets in alphabetical order for better readability.
+# NOTE: Do not modify the autogenerated targets, unless necessary, write custom
+# targets in the custom section below..
+
+.PHONY: clean-venv
+clean-venv:
+ @echo "\nRemoving the virtual environment ++++++++++++++++++++++++++++++++++++++++++++++\n"
+ @rm -rf .venv
+
+.PHONY: cv
+cv: clean-venv
+
+.PHONY: docs
+docs:
+ @echo "\nGenerating project documentation ++++++++++++++++++++++++++++++++++++++++++++++\n"
+ @poetry run sphinx-apidoc -f -o docs/source/pages tus_storagehandler
+ @cd docs && make html
+ @echo "\nSummary ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n"
+ @echo "Documentation generated successfully."
+ @echo "Open docs/build/html/index.html in your browser."
+ @echo "Or serve it locally using:"
+ @echo "python -m http.server -d docs/build/html/"
+
+.PHONY: d
+d: docs
+
+.PHONY: format-lint
+format-lint:
+ @echo "\nRunning linter and formatter using ruff and typos +++++++++++++++++++++++++++++\n"
+ @poetry run ruff format && poetry run ruff check --fix
+ @typos .
+
+.PHONY: fl
+fl: format-lint
+
+.PHONY: install
+install:
+ @echo "\nInstalling dependencies and with this package +++++++++++++++++++++++++++++++++\n"
+ @poetry install --with=code_quality,docs,misc,test,types,vulnerability
+
+.PHONY: i
+i: install
+
+.PHONY: precommit-check
+precommit-check:
+ @echo "\nRunning pre-commit checks +++++++++++++++++++++++++++++++++++++++++++++++++++++\n"
+ @poetry run pre-commit run --all-files
+
+.PHONY: pc
+pc: precommit-check
+
+.PHONY: security
+security:
+ @echo "\nRunning security scans using bandit and safety ++++++++++++++++++++++++++++++++\n"
+ @poetry run safety check --full-report
+ @poetry run bandit -c pyproject.toml -r tus_storagehandler
+
+.PHONY: s
+s: security
+
+.PHONY: test
+test:
+ @echo "\nRunning tests using pytest ++++++++++++++++++++++++++++++++++++++++++++++++++++\n"
+ @poetry run pytest tests/
+
+.PHONY: t
+t: test
+
+.PHONY: type-check
+type-check:
+ @echo "\nPerforming type checking with mypy ++++++++++++++++++++++++++++++++++++++++++++\n"
+ @poetry run mypy tus_storagehandler
+
+.PHONY: tc
+tc: type-check
+
+.PHONY: update
+update:
+ @echo "\nUpdating the template +++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n"
+ @echo "Using latest version from remote: https://github.com/elixir-cloud-aai/cookiecutter-python."
+ @poetry run cruff update -y
+
+.PHONY: u
+u: update
+
+.PHONY: venv
+venv:
+ @echo "\nCreating a virtual environment ++++++++++++++++++++++++++++++++++++++++++++++++\n"
+ @python -m venv .venv
+ @echo "\nSummary +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n"
+ @echo "Virtual environment created successfully."
+ @echo "To activate the environment for this shell session, run:"
+ @echo "source .venv/bin/activate"
+
+.PHONY: v
+v: venv
+
+## Custom Targets #############################################################
+# NOTE: Keep all the targets in alphabetical order for better readability.
+# NOTE: Add any custom targets here if needed in the future.
diff --git a/PULL_REQUEST_TEMPLATE.md b/PULL_REQUEST_TEMPLATE.md
new file mode 100644
index 0000000..fb6b561
--- /dev/null
+++ b/PULL_REQUEST_TEMPLATE.md
@@ -0,0 +1,63 @@
+#### Description
+
+
+
+- Fixes #(issue number)
+
+#### Checklist
+
+
+
+- \[ \] My code follows the [contributing guidelines][contributing-guidelines]
+ of this project, including, in particular, with regard to any style guidelines
+- \[ \] The title of my PR complies with the
+ [Conventional Commits specification][conv-commits]; in particular, it clearly
+ indicates that a change is a breaking change
+- \[ \] I acknowledge that all my commits will be squashed into a single commit,
+ using the PR title as the commit message
+- \[ \] I have performed a self-review of my own code
+- \[ \] I have commented my code in hard-to-understand areas
+- \[ \] I have updated the user-facing documentation to describe any new or
+ changed behavior
+- \[ \] I have added type annotations for all function/class/method interfaces
+ or updated existing ones (only for Python, TypeScript, etc.)
+- \[ \] I have provided appropriate documentation
+ ([Google-style Python docstrings][py-doc-google]) for all
+ packages/modules/functions/classes/methods or updated existing ones
+- \[ \] My changes generate no new warnings
+- \[ \] I have added tests that prove my fix is effective or that my feature
+ works
+- \[ \] New and existing unit tests pass locally with my changes
+- \[ \] I have not reduced the existing code coverage
+
+#### Comments
+
+
+
+[contributing-guidelines]: https://elixir-cloud-aai.github.io/guides/guide-contributor/workflow/
+[conv-commits]: https://www.conventionalcommits.org/en
+[py-doc-google]: https://google.github.io/styleguide/pyguide.html
diff --git a/README.md b/README.md
index 9ce6277..937e18f 100644
--- a/README.md
+++ b/README.md
@@ -1,24 +1,177 @@
-# TUS Storage Handler
-
-## Synopsis
-This Flask application provides endpoints for uploading, downloading, and listing files in a MinIO bucket, with TUS protocol support for uploads, and CORS enabled for cross-origin requests.
-
-## Installation
-
-### Prerequisites
-This flask application requires a running instance of [minio](https://min.io/download)
-
-Run the minio instance by executing the following command in the location where minio is installed
-
-`minio server /data --console-address ":9001"`
-
-Download the required dependencies
-
-1. Navigate to the folder `TusStorageHandler`
-2. Create a virtual environment and activate it (optional)
-3. `pip install -r requirements.txt`
-
-### Running the application
-
-`flask run`
-The application will be running on `http://127.0.0.1:5000` by default.
+[![Bandit](https://img.shields.io/badge/security-bandit-yellow.svg)](https://bandit.readthedocs.io/en/latest/)
+[![codecov](https://codecov.io/gh/elixir-cloud-aai/tus-storagehandler/branch/main/graph/badge.svg)](https://codecov.io/gh/elixir-cloud-aai/tus-storagehandler)
+[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](code_of_conduct.md)
+[![Documentation Status](https://readthedocs.org/projects/tus_storagehandler/badge/?version=latest)](https://tus_storagehandler.readthedocs.io/en/latest/?badge=latest)
+[![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](./LICENSE)
+[![Python 3.11](https://img.shields.io/badge/python-3.11-blue.svg)](https://www.python.org/)
+[![GitHub contributors](https://img.shields.io/github/contributors/elixir-cloud-aai/tus-storagehandler)](https://github.com/elixir-cloud-aai/tus-storagehandler/graphs/contributors)
+[![Ruff](https://img.shields.io/badge/linter%20&%20formatter-ruff-000000.svg)](https://docs.astral.sh/ruff/)
+[![Safety](https://img.shields.io/badge/security-safety-orange.svg)](https://safetycli.com/product/safety-cli)
+
+# tus-storagehandler
+
+File handler utilizing TUS and MinIO with DRS-Filer integration.
+
+## Table of Contents
+
+- [Basic Usage](#basic-usage)
+- [Installation](#installation)
+- [Development](#development)
+- [Contributing](#contributing)
+- [Code of Conduct](#code-of-conduct)
+- [Versioning](#versioning)
+- [License](#license)
+- [Contact](#contact)
+
+## Basic Usage
+
+## Installation
+
+## Development
+
+For ease, certain scripts have been abbreviated in `Makefile`, make sure that
+you have installed the dependencies before running the commands.
+
+> **Note**: `make` commands are only available for Unix-based systems.
+
+To view the commands available, run:
+
+```sh
+make
+```
+
+Here are certain commands that you might find useful:
+
+- Making a virtual environment
+
+```sh
+make v
+```
+
+- Installing all dependencies including optional dependencies
+
+```sh
+make i
+```
+
+> **Note**: This project uses optional dependency groups such as `types`,
+> `code_quality`, `docs`, `vulnerability`, `test`, and `misc`. To install stubs
+> or types for the dependencies, you **must** use the following command:
+>
+> ```sh
+> poetry add types-foo --group types
+> ```
+>
+> Replace `types-foo` with the name of the package for the types. All runtime
+> dependencies should be added to the `default` group. For example, to install
+> `requests` and its type stubs, run:
+>
+> ```sh
+> poetry add requests
+> poetry add types-requests --group types
+> ```
+>
+> This ensures that the type checker functions correctly.
+
+> **Note**: Since the dependencies are segregated into groups, if you add a new
+> group make sure to add it in `make install` command in [Makefile](Makefile).
+
+- Running tests
+
+```sh
+make t
+```
+
+- Running linter, formatter and spell checker
+
+```sh
+make fl
+```
+
+- Building the documentation
+
+```sh
+make d
+```
+
+> **Note**: If you make changes to the code, make sure to generate and push the
+> documentation using above command, else the documentation check CI will fail.
+
+- Running type checker
+
+```sh
+make tc
+```
+
+- Running all pre-commit checks
+
+```sh
+make pc
+```
+
+- Update the cookiecutter template
+
+```sh
+make u
+```
+
+> **Note**: This is not the complete list of commands, run `make` to find out if
+> more have been added.
+
+## Contributing
+
+This project is a community effort and lives off _your_ contributions, be it in
+the form of bug reports, feature requests, discussions, fixes or any other form
+of contribution!
+
+Please refer to the guidelines available at [`CONTRIBUTING.md`][contributing] if
+you are interested in contributing.
+
+## Code of Conduct
+
+We kindly request all contributors to abide by our
+[organization's Code of Conduct][code-of-conduct]. Please also refer to this
+document if you want to report an incident with respect to conduct in our
+community. Thank you for your cooperation.
+
+## Versioning
+
+The project adopts the [semantic versioning][semver] scheme for versioning.
+Currently the software is in a pre-release stage, so changes to the API,
+including breaking changes, may occur at any time without further notice.
+
+## License
+
+This project is distributed under the [Apache License 2.0][badge-license-url], a
+copy of which is also available in [`LICENSE`][license].
+
+## Contact
+
+The project is maintained by [ELIXIR Cloud & AAI][elixir-cloud-aai], a Driver
+Project of the [Global Alliance for Genomics and Health (GA4GH)][ga4gh], under
+the umbrella of the [ELIXIR] [Compute Platform][elixir-compute].
+
+To get in touch with us, please use one of the following routes:
+
+- For filing bug reports, feature requests or other code-related issues, please
+ make use of the project's [issue tracker][issue-tracker].
+- For private/personal issues, more involved communication, or if you would like
+ to join our team as a regular contributor, you can either join our
+ [chat board][badge-chat-url] or [email] the community leaders.
+
+[![logo-elixir]][elixir] [![logo-elixir-cloud-aai]][elixir-cloud-aai]
+
+[badge-chat-url]: https://join.slack.com/t/elixir-cloud/shared_invite/enQtNzA3NTQ5Mzg2NjQ3LTZjZGI1OGQ5ZTRiOTRkY2ExMGUxNmQyODAxMDdjM2EyZDQ1YWM0ZGFjOTJhNzg5NjE0YmJiZTZhZDVhOWE4MWM
+[badge-license-url]: http://www.apache.org/licenses/LICENSE-2.0
+[code-of-conduct]: https://elixir-cloud-aai.github.io/about/code-of-conduct/
+[contributing]: https://elixir-cloud-aai.github.io/guides/guide-contributor/
+[elixir]: https://elixir-europe.org/
+[elixir-cloud-aai]: https://elixir-cloud.dcc.sib.swiss/
+[elixir-compute]: https://elixir-europe.org/platforms/compute
+[email]: mailto:cloud-service@elixir-europe.org
+[ga4gh]: https://ga4gh.org/
+[issue-tracker]: https://github.com/elixir-cloud-aai/tus-storagehandler/issues
+[license]: LICENSE
+[logo-elixir]: images/logo-elixir.svg
+[logo-elixir-cloud-aai]: images/logo-elixir-cloud-aai.svg
+[semver]: https://semver.org/
diff --git a/docs/Makefile b/docs/Makefile
new file mode 100644
index 0000000..d0c3cbf
--- /dev/null
+++ b/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS ?=
+SPHINXBUILD ?= sphinx-build
+SOURCEDIR = source
+BUILDDIR = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+ @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+ @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/make.bat b/docs/make.bat
new file mode 100644
index 0000000..747ffb7
--- /dev/null
+++ b/docs/make.bat
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+ set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+ echo.
+ echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+ echo.installed, then set the SPHINXBUILD environment variable to point
+ echo.to the full path of the 'sphinx-build' executable. Alternatively you
+ echo.may add the Sphinx directory to PATH.
+ echo.
+ echo.If you don't have Sphinx installed, grab it from
+ echo.https://www.sphinx-doc.org/
+ exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
diff --git a/docs/source/conf.py b/docs/source/conf.py
new file mode 100644
index 0000000..8bb724a
--- /dev/null
+++ b/docs/source/conf.py
@@ -0,0 +1,102 @@
+"""Configuration file for the Sphinx documentation builder."""
+
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+import datetime
+import os
+import sys
+from pathlib import Path
+
+import tomli
+
+sys.path.insert(0, os.path.abspath("../.."))
+
+
+# -- Project information -----------------------------------------------------
+def _get_project_meta():
+ _pyproject_path = Path(__file__).parents[2] / "pyproject.toml"
+ with open(_pyproject_path, mode="rb") as pyproject:
+ return tomli.load(pyproject)["tool"]["poetry"]
+
+
+pkg_meta = _get_project_meta()
+current_year = datetime.datetime.now().year
+project = str(pkg_meta["name"])
+project_copyright = f"{current_year}, {str(pkg_meta['authors'][0])}"
+author = str(pkg_meta["authors"][0])
+
+version = str(pkg_meta["version"])
+release = version
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+ "sphinx.ext.autodoc",
+ "sphinx.ext.doctest",
+ "sphinx.ext.todo",
+ "sphinx.ext.coverage",
+ "sphinx.ext.viewcode",
+ "sphinx.ext.autosummary",
+ # Used to write beautiful docstrings:
+ "sphinx.ext.napoleon",
+ # Used to include .md files:
+ "m2r2",
+ # Used to insert typehints into the final docs:
+ "sphinx_autodoc_typehints",
+ # Used to embed values from the source code into the docs:
+ "added_value",
+]
+# Set `typing.TYPE_CHECKING` to `True`:
+# https://pypi.org/project/sphinx-autodoc-typehints/
+set_type_checking_flag = False
+always_document_param_types = False
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+
+source_suffix = [".rst", ".md"]
+
+# The master toctree document.
+master_doc = "index"
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = "en"
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path .
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+# The theme to use for HTML and HTML Help pages. See the documentation for
+# a list of builtin themes.
+html_theme = "furo"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static"]
+
+# -- Extension configuration -------------------------------------------------
+napoleon_numpy_docstring = False
+
+# -- Options for todo extension ----------------------------------------------
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True
diff --git a/docs/source/index.rst b/docs/source/index.rst
new file mode 100644
index 0000000..f51987b
--- /dev/null
+++ b/docs/source/index.rst
@@ -0,0 +1,15 @@
+Welcome to tus_storagehandler's documentation!
+===========================================================
+
+.. toctree::
+ :maxdepth: 2
+ :caption: Contents:
+
+ pages/modules
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/docs/source/pages/modules.rst b/docs/source/pages/modules.rst
new file mode 100644
index 0000000..66ab2b8
--- /dev/null
+++ b/docs/source/pages/modules.rst
@@ -0,0 +1,7 @@
+tus_storagehandler
+==================
+
+.. toctree::
+ :maxdepth: 4
+
+ tus_storagehandler
diff --git a/docs/source/pages/tus_storagehandler.rst b/docs/source/pages/tus_storagehandler.rst
new file mode 100644
index 0000000..50d75ff
--- /dev/null
+++ b/docs/source/pages/tus_storagehandler.rst
@@ -0,0 +1,21 @@
+tus\_storagehandler package
+===========================
+
+Submodules
+----------
+
+tus\_storagehandler.main module
+-------------------------------
+
+.. automodule:: tus_storagehandler.main
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tus_storagehandler
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/images/logo-elixir-cloud-aai.svg b/images/logo-elixir-cloud-aai.svg
new file mode 100644
index 0000000..18ecf21
--- /dev/null
+++ b/images/logo-elixir-cloud-aai.svg
@@ -0,0 +1,112 @@
+
+
diff --git a/images/logo-elixir.svg b/images/logo-elixir.svg
new file mode 100644
index 0000000..af9d4b9
--- /dev/null
+++ b/images/logo-elixir.svg
@@ -0,0 +1,82 @@
+
+
+
+
diff --git a/poetry.lock b/poetry.lock
new file mode 100644
index 0000000..7084211
--- /dev/null
+++ b/poetry.lock
@@ -0,0 +1,1892 @@
+# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand.
+
+[[package]]
+name = "added-value"
+version = "0.24.0"
+description = "Sphinx extension for embedding values extracted from Python modules"
+optional = false
+python-versions = "*"
+files = [
+ {file = "added-value-0.24.0.tar.gz", hash = "sha256:4c71f756db1589b596a0f2a35c8a35ddd86dd70b9335504c9ee29e2b95d40440"},
+ {file = "added_value-0.24.0-py2.py3-none-any.whl", hash = "sha256:637464409e84759cfae1d3809a944ac000d0655bffd46bed958ffb5b8569c1f8"},
+]
+
+[package.dependencies]
+docutils = "*"
+les-iterables = ">=0.6.0"
+more-itertools = "*"
+natsort = "*"
+six = "*"
+sphinx = "*"
+
+[package.extras]
+dev = ["build", "bumpversion", "twine", "wheel"]
+doc = ["better-apidoc", "sphinx", "sphinx-rtd-theme"]
+test = ["beautifulsoup4", "hypothesis", "pytest"]
+
+[[package]]
+name = "alabaster"
+version = "0.7.16"
+description = "A light, configurable Sphinx theme"
+optional = false
+python-versions = ">=3.9"
+files = [
+ {file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"},
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+]
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+[[package]]
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+version = "0.7.0"
+description = "Reusable constraint types to use with typing.Annotated"
+optional = false
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+files = [
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+[[package]]
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+version = "1.3.0"
+description = "Better dates & times for Python"
+optional = false
+python-versions = ">=3.8"
+files = [
+ {file = "arrow-1.3.0-py3-none-any.whl", hash = "sha256:c728b120ebc00eb84e01882a6f5e7927a53960aa990ce7dd2b10f39005a67f80"},
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+[package.dependencies]
+python-dateutil = ">=2.7.0"
+types-python-dateutil = ">=2.8.10"
+
+[package.extras]
+doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"]
+test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (==3.*)"]
+
+[[package]]
+name = "authlib"
+version = "1.3.1"
+description = "The ultimate Python library in building OAuth and OpenID Connect servers and clients."
+optional = false
+python-versions = ">=3.8"
+files = [
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+[package.dependencies]
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+
+[[package]]
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+optional = false
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+[package.extras]
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+
+[[package]]
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+optional = false
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+files = [
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+PyYAML = ">=5.3.1"
+rich = "*"
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+
+[package.extras]
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+[[package]]
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+name = "typos"
+version = "1.23.1"
+description = "Source Code Spelling Correction"
+optional = false
+python-versions = ">=3.7"
+files = [
+ {file = "typos-1.23.1-py3-none-macosx_10_12_x86_64.whl", hash = "sha256:c6ac98510ac54b7ea9ab73806ba22935c960f8d09678e358dd336e2a9dd7018b"},
+ {file = "typos-1.23.1-py3-none-macosx_11_0_arm64.whl", hash = "sha256:31e1200e28c78a7ac5b4bc7673f9299c85682e838b8e05e413146c8fe6be980a"},
+ {file = "typos-1.23.1-py3-none-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:89cf023373f3581cd38e41d43bddb5902e55a0ec93b1899699dec3fe95e2f9be"},
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+ {file = "typos-1.23.1-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:7dddb05fc60ccf979761e4a10a3a280fa701fe55b1835b94d435c34dc06cf05d"},
+ {file = "typos-1.23.1-py3-none-musllinux_1_2_aarch64.whl", hash = "sha256:86b23fbdfc192851e9dada7db9d7269c15267c2e0b422906e7c36226f5100f4e"},
+ {file = "typos-1.23.1-py3-none-musllinux_1_2_x86_64.whl", hash = "sha256:34d2f693111fedffeec7fe5cf096ec8cff9c0b01f2c13e4ddee34bd063aa2c6f"},
+ {file = "typos-1.23.1-py3-none-win32.whl", hash = "sha256:822ea2ba610f91a7f1c037d91c9f5d12cf8d92e3f6470747dd76e85711558dc3"},
+ {file = "typos-1.23.1-py3-none-win_amd64.whl", hash = "sha256:d7fedee1b0c9aa2a796bffa5d30285cc7a32eb4850336b91c84ef672852ddd7f"},
+ {file = "typos-1.23.1.tar.gz", hash = "sha256:390b071b2081d61d3c1718b1c05b92756692ed066907f04caf7297c9a25c7eee"},
+]
+
+[[package]]
+name = "urllib3"
+version = "2.2.2"
+description = "HTTP library with thread-safe connection pooling, file post, and more."
+optional = false
+python-versions = ">=3.8"
+files = [
+ {file = "urllib3-2.2.2-py3-none-any.whl", hash = "sha256:a448b2f64d686155468037e1ace9f2d2199776e17f0a46610480d311f73e3472"},
+ {file = "urllib3-2.2.2.tar.gz", hash = "sha256:dd505485549a7a552833da5e6063639d0d177c04f23bc3864e41e5dc5f612168"},
+]
+
+[package.extras]
+brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
+h2 = ["h2 (>=4,<5)"]
+socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
+zstd = ["zstandard (>=0.18.0)"]
+
+[[package]]
+name = "virtualenv"
+version = "20.26.3"
+description = "Virtual Python Environment builder"
+optional = false
+python-versions = ">=3.7"
+files = [
+ {file = "virtualenv-20.26.3-py3-none-any.whl", hash = "sha256:8cc4a31139e796e9a7de2cd5cf2489de1217193116a8fd42328f1bd65f434589"},
+ {file = "virtualenv-20.26.3.tar.gz", hash = "sha256:4c43a2a236279d9ea36a0d76f98d84bd6ca94ac4e0f4a3b9d46d05e10fea542a"},
+]
+
+[package.dependencies]
+distlib = ">=0.3.7,<1"
+filelock = ">=3.12.2,<4"
+platformdirs = ">=3.9.1,<5"
+
+[package.extras]
+docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2,!=7.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
+test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"]
+
+[metadata]
+lock-version = "2.0"
+python-versions = ">=3.11"
+content-hash = "c1a49802343cc8f576d75f0627d84a909ef801801e9017419646a7d288b87a34"
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..f85f11e
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,100 @@
+[build-system]
+build-backend = "poetry.core.masonry.api"
+requires = ["poetry-core"]
+
+[tool.mypy]
+warn_return_any = true
+warn_unused_configs = true
+
+[tool.poetry]
+authors = ["ELIXIR Cloud AAI "]
+classifiers = [
+ "Development Status :: 1 - Planning",
+ "License :: OSI Approved :: Apache Software License",
+ "Programming Language :: Python :: 3",
+ "Programming Language :: Python :: 3.11",
+]
+description = "File handler utilizing TUS and MinIO with DRS-Filer integration."
+license = "Apache-2.0"
+maintainers = ["ELIXIR Cloud AAI "]
+name = "tus_storagehandler"
+readme = "README.md"
+repository = "https://github.com/elixir-cloud-aai/tus-storagehandler"
+version = "0.1.0"
+
+[tool.poetry.dependencies]
+python = ">=3.11"
+
+[tool.poetry.group.code_quality]
+optional = true
+
+[tool.poetry.group.code_quality.dependencies]
+mypy = ">=1.10.0,<2.0.0"
+ruff = ">=0.4.10,<1.0.0"
+typos = ">=1.22.8,<2.0.0"
+
+[tool.poetry.group.docs]
+optional = true
+
+[tool.poetry.group.docs.dependencies]
+added-value = ">=0.24.0,<1.0.0"
+docutils = "0.20.1"
+furo = ">=2024.5.6,<2025.0.0"
+m2r2 = "^0.3.3.post2"
+sphinx = "^7.3.7"
+sphinx-autodoc-typehints = "^2.1.0"
+tomli = ">=2.0.1,<3.0.0"
+
+[tool.poetry.group.misc]
+optional = true
+
+[tool.poetry.group.misc.dependencies]
+cruft = ">=2.15.0,<3.0.0"
+jello = ">=1.6.0,<2.0.0"
+pre-commit = ">=3.7.1,<4.0.0"
+
+[tool.poetry.group.test]
+optional = true
+
+[tool.poetry.group.test.dependencies]
+pytest = ">=8.2.2,<9.0.0"
+pytest-cov = ">=5.0.0,<=6.0.0"
+
+[tool.poetry.group.types]
+optional = true
+
+[tool.poetry.group.types.dependencies]
+
+[tool.poetry.group.vulnerability]
+optional = true
+
+[tool.poetry.group.vulnerability.dependencies]
+bandit = ">=1.7.8,<2.0.0"
+safety = ">=3.2.0,<4.0.0"
+
+[tool.poetry.scripts]
+tus_storagehandler = "tus_storagehandler.main:main"
+
+[tool.ruff]
+indent-width = 4
+
+[tool.ruff.format]
+docstring-code-format = true
+indent-style = "space"
+line-ending = "lf"
+quote-style = "double"
+
+[tool.ruff.lint]
+select = [
+ "B", # flake8-bugbear
+ "D", # pydocstyle
+ "E", # pycodestyle
+ "F", # Pyflakes
+ "I", # isort
+ "PL", # pylint
+ "SIM", # flake8-simplify
+ "UP", # pyupgrade
+]
+
+[tool.ruff.lint.pydocstyle]
+convention = "google"
diff --git a/tests/__init__.py b/tests/__init__.py
new file mode 100644
index 0000000..f1365f8
--- /dev/null
+++ b/tests/__init__.py
@@ -0,0 +1 @@
+"""This package contains tests."""
diff --git a/tests/test_integration/__init__.py b/tests/test_integration/__init__.py
new file mode 100644
index 0000000..9a74cfd
--- /dev/null
+++ b/tests/test_integration/__init__.py
@@ -0,0 +1 @@
+"""This package contains integration tests."""
diff --git a/tests/test_integration/test_dummy.py b/tests/test_integration/test_dummy.py
new file mode 100644
index 0000000..6b28c1b
--- /dev/null
+++ b/tests/test_integration/test_dummy.py
@@ -0,0 +1,10 @@
+"""Dummy test file to avoid the error."""
+
+
+# TODO: Remove this file when adding real tests.
+# This test is a placeholder for the integration tests. It is a workaround
+# to avoid the error "Module has no tests" when running the tests with pytest.
+# Cf. https://github.com/pytest-dev/pytest/issues/2393
+def test_placeholder():
+ """Dummy test to avoid the error."""
+ pass
diff --git a/tests/test_unit/__init__.py b/tests/test_unit/__init__.py
new file mode 100644
index 0000000..2f312a6
--- /dev/null
+++ b/tests/test_unit/__init__.py
@@ -0,0 +1 @@
+"""This package contains unit tests."""
diff --git a/tests/test_unit/test_dummy.py b/tests/test_unit/test_dummy.py
new file mode 100644
index 0000000..b69c7ca
--- /dev/null
+++ b/tests/test_unit/test_dummy.py
@@ -0,0 +1,10 @@
+"""Dummy test file to avoid the error."""
+
+
+# TODO: Remove this file when adding real tests.
+# This test is a placeholder for the unit tests. It is a workaround
+# to avoid the error "Module has no tests" when running the tests with pytest.
+# Cf. https://github.com/pytest-dev/pytest/issues/2393
+def test_placeholder():
+ """Dummy test to avoid the error."""
+ pass
diff --git a/tus_storagehandler/__init__.py b/tus_storagehandler/__init__.py
new file mode 100644
index 0000000..9f8346a
--- /dev/null
+++ b/tus_storagehandler/__init__.py
@@ -0,0 +1 @@
+"""This package contains module for the tus_storagehandler."""
diff --git a/tus_storagehandler/main.py b/tus_storagehandler/main.py
new file mode 100644
index 0000000..24de557
--- /dev/null
+++ b/tus_storagehandler/main.py
@@ -0,0 +1,10 @@
+"""Entry point for python_cookiecutter."""
+
+
+def main():
+ """Main entry point for tus_storagehandler."""
+ print("Hello from tus_storagehandler!")
+
+
+if __name__ == "__main__":
+ main()