api and cli refactoring

.dockerignore

@@ -5,4 +5,4 @@
 Dockerfile
 LICENSE
 README.md
-setup.cfg
+tests/

.github/workflows/dogfood.yml

@@ -0,0 +1,52 @@
+# This workflow tests the workbench-agent by scanning its own repository.
+## This workflow runs manually on whatever branch its pointed at.
+name: Scan a Branch!
+on: workflow_dispatch
+
+jobs:
+  fossid_scan:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+# Zipping the code uploads a single file for Workbench to extract.
+      - name: ZIP up the code
+        run: |
+          zip -r $GITHUB_WORKSPACE/code.zip . -x \
+          '*.tmp' '*.temp' '*.bak' \
+          '*.cache' '*.db' '*.idx' \
+          '*.log' '*.txt' '*.event' \
+          '*.sample' '*.demo' '*.example' \
+          '*.sql' '*.hprof' '*.dmp' \
+          '.gitignore' '.dockerignore' \
+          '.git/*' '.github/*'
+
+# Since we're running with Python, install the dependencies.
+# This is not needed when running the container image.
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+
+      - name: Install Workbench Agent Dependencies
+        run: pip install -e .
+
+# We omit License Extraction to speed up the scan process.
+# Built-In Env Vars map Branches to Scans in Workbench for this repo's Project.
+# Additionally, Delta Scan reduces scan time by only scanning new files.
+      - name: Scan the ZIP
+        run: |
+          python workbench-agent.py \
+            --api_url ${{ secrets.WORKBENCH_URL }} \
+            --api_user ${{ secrets.WORKBENCH_USER }} \
+            --api_token ${{ secrets.WORKBENCH_TOKEN }} \
+            --project_code $GITHUB_REPOSITORY \
+            --scan_code $GITHUB_REPOSITORY/$GITHUB_REF_NAME \
+            --path $GITHUB_WORKSPACE/code.zip \
+            --reuse_identifications \
+            --chunked_upload \
+            --identification_reuse_type specific_project \
+            --specific_code $GITHUB_REPOSITORY \
+            --run_dependency_analysis \
+            --delta_only 

.github/workflows/linters.yml

@@ -5,11 +5,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v1
-      - name: Code linters
+      - name: Code formatting check
         run: |
-          pip install -r requirements.txt
-          pycodestyle workbench-agent.py
-          pylint --errors-only --rcfile .pylintrc workbench-agent.py
+          pip install -e .[dev]
+          black --check workbench-agent.py api/
 
 
 

.github/workflows/tests.yml

@@ -0,0 +1,44 @@
+# .github/workflows/tests.yml
+name: Run Tests
+
+# Run on pushes and pull requests
+on:
+  push:
+    paths-ignore:
+      - '*.md'
+      - '.gitignore'
+  pull_request:
+    paths-ignore:
+      - '*.md'
+      - '.gitignore'
+
+jobs:
+  unit_tests:
+    name: Unit Tests (Python ${{ matrix.python-version }})
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.9', '3.10', '3.11', '3.12']
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e .[dev,test]
+
+      - name: Run unit tests
+        run: |
+          pytest tests/unit/ -v --tb=short
+
+      - name: Run tests with coverage (Python 3.11 only)
+        if: matrix.python-version == '3.11'
+        run: |
+          pip install coverage pytest-cov
+          pytest tests/unit/ --cov=api --cov-report=xml --cov-report=term-missing

.gitignore

@@ -12,4 +12,10 @@
 Thumbs.db
 
 # Log file
-log-agent.txt
+log-agent.txt
+
+# Sample Code
+inspiration/
+test-commands.txt
+original-wb-agent.py
+workbench-agent-log.txt

Dockerfile

@@ -1,7 +1,7 @@
 FROM cgr.dev/chainguard/python:latest-dev as builder
 WORKDIR /app
-COPY requirements.txt .
-RUN pip install -r requirements.txt --user
+COPY pyproject.toml .
+RUN pip install -e . --user
 
 FROM cgr.dev/chainguard/python:latest
 WORKDIR /app

README.md

@@ -235,4 +235,4 @@ Linting
 Run pylint in order reveal possible issues:
 ```bash
     pylint workbench-agent.py
-```
+```

pyproject.toml

@@ -0,0 +1,113 @@
+[build-system]
+requires = ["setuptools>=45", "wheel", "setuptools_scm[toml]>=6.2"]
+
+[project]
+name = "workbench-agent"
+version = "0.8.0"
+description = "FossID Workbench Agent - Modular API client for automated scanning"
+requires-python = ">=3.9"
+dependencies = [
+    "requests",
+    "python-dotenv",
+]
+
+[project.optional-dependencies]
+dev = [
+    "black",
+]
+test = [
+    "pytest>=7.0.0",
+    "pytest-mock>=3.6.1",
+    "requests>=2.25.1",
+]
+
+[tool.black]
+line-length = 100
+target-version = ['py39']
+include = '\.pyi?$'
+exclude = '''
+/(
+    \.eggs
+  | \.git
+  | \.hg
+  | \.mypy_cache
+  | \.tox
+  | \.venv
+  | _build
+  | buck-out
+  | build
+  | dist
+  | inspiration
+)/
+'''
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.isort]
+profile = "black"
+line_length = 100
+multi_line_output = 3
+include_trailing_comma = true
+force_grid_wrap = 0
+use_parentheses = true
+ensure_newline_before_comments = true
+skip = ["inspiration"]
+
+[tool.mypy]
+python_version = "3.9"
+warn_return_any = true
+warn_unused_configs = true
+disallow_untyped_defs = false
+disallow_incomplete_defs = false
+check_untyped_defs = true
+disallow_untyped_decorators = false
+no_implicit_optional = true
+warn_redundant_casts = true
+warn_unused_ignores = true
+warn_no_return = true
+warn_unreachable = true
+strict_equality = true
+exclude = [
+    "inspiration/",
+    "build/",
+    "dist/"
+]
+
+[tool.coverage.run]
+source = ["api"]
+omit = [
+    "*/tests/*",
+    "*/inspiration/*",
+    "*/__pycache__/*"
+]
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "def __repr__",
+    "if self.debug:",
+    "if settings.DEBUG",
+    "raise AssertionError",
+    "raise NotImplementedError",
+    "if 0:",
+    "if __name__ == .__main__.:"
+]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+python_files = ["test_*.py"]
+python_classes = ["Test*"]
+python_functions = ["test_*"]
+addopts = [
+    "-v",
+    "--tb=short",
+    "--strict-markers"
+]
+markers = [
+    "unit: Unit tests",
+    "integration: Integration tests", 
+    "slow: Slow-running tests"
+]
+
+

src/workbench_agent.egg-info/PKG-INFO

@@ -0,0 +1,15 @@
+Metadata-Version: 2.4
+Name: workbench-agent
+Version: 0.7.1
+Summary: FossID Workbench Agent - Modular API client for automated scanning
+Requires-Python: >=3.9
+License-File: LICENSE
+Requires-Dist: requests
+Requires-Dist: python-dotenv
+Provides-Extra: dev
+Requires-Dist: black; extra == "dev"
+Provides-Extra: test
+Requires-Dist: pytest>=7.0.0; extra == "test"
+Requires-Dist: pytest-mock>=3.6.1; extra == "test"
+Requires-Dist: requests>=2.25.1; extra == "test"
+Dynamic: license-file

src/workbench_agent.egg-info/SOURCES.txt

@@ -0,0 +1,50 @@
+.dockerignore
+.gitignore
+.pylintrc
+Dockerfile
+LICENSE
+README.md
+pyproject.toml
+workbench-agent.py
+.github/workflows/build-image.yml
+.github/workflows/dogfood.yml
+.github/workflows/linters.yml
+.github/workflows/tests.yml
+api/__init__.py
+api/projects_api.py
+api/scans_api.py
+api/upload_api.py
+api/workbench_api.py
+api/helpers/__init__.py
+api/helpers/api_base.py
+api/helpers/exceptions.py
+api/helpers/process_waiters.py
+api/helpers/project_scan_checks.py
+api/helpers/status_checkers.py
+api/helpers/upload_helpers.py
+src/workbench_agent/__init__.py
+src/workbench_agent.egg-info/PKG-INFO
+src/workbench_agent.egg-info/SOURCES.txt
+src/workbench_agent.egg-info/dependency_links.txt
+src/workbench_agent.egg-info/requires.txt
+src/workbench_agent.egg-info/top_level.txt
+src/workbench_agent/api/__init__.py
+src/workbench_agent/api/projects_api.py
+src/workbench_agent/api/scans_api.py
+src/workbench_agent/api/upload_api.py
+src/workbench_agent/api/workbench_api.py
+src/workbench_agent/api/helpers/__init__.py
+src/workbench_agent/api/helpers/api_base.py
+src/workbench_agent/api/helpers/process_waiters.py
+src/workbench_agent/api/helpers/project_scan_checks.py
+src/workbench_agent/api/helpers/status_checkers.py
+src/workbench_agent/api/helpers/upload_helpers.py
+src/workbench_agent/utilities/__init__.py
+src/workbench_agent/utilities/error_handling.py
+src/workbench_agent/utilities/exceptions.py
+tests/__init__.py
+tests/unit/__init__.py
+tests/unit/api/__init__.py
+tests/unit/api/test_projects_api.py
+tests/unit/api/test_scans_api.py
+tests/unit/api/test_workbench_api.py

src/workbench_agent.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

src/workbench_agent.egg-info/requires.txt

@@ -0,0 +1,10 @@
+requests
+python-dotenv
+
+[dev]
+black
+
+[test]
+pytest>=7.0.0
+pytest-mock>=3.6.1
+requests>=2.25.1

src/workbench_agent.egg-info/top_level.txt

@@ -0,0 +1 @@
+workbench_agent

src/workbench_agent/__init__.py

@@ -0,0 +1,11 @@
+"""
+FossID Workbench Agent - Modular API client for automated scanning
+"""
+
+__version__ = "0.8.0"
+
+# Import main API class
+from .api import WorkbenchAPI
+
+# Keep backward compatibility by creating an alias
+Workbench = WorkbenchAPI 

src/workbench_agent/api/__init__.py

@@ -0,0 +1,10 @@
+"""
+API modules for FossID Workbench Agent
+"""
+
+from .projects_api import ProjectsAPI
+from .scans_api import ScansAPI  
+from .upload_api import UploadAPI
+from .workbench_api import WorkbenchAPI
+
+__all__ = ["ProjectsAPI", "ScansAPI", "UploadAPI", "WorkbenchAPI"]