feat: add interactive cli

.github/workflows/ci.yml

@@ -0,0 +1,50 @@
+name: CI
+
+on:
+  push:
+    branches: [main, develop]
+  pull_request:
+    branches: [main, develop]
+
+jobs:
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install black ruff mypy types-requests
+      - name: Run Black
+        run: black --check .
+      - name: Run Ruff
+        run: ruff check .
+      - name: Run MyPy
+        run: mypy tcga_downloader
+
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.11', '3.12']
+    steps:
+      - uses: actions/checkout@v4
+      - 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]"
+      - name: Run tests
+        run: pytest --cov=tcga_downloader --cov-report=xml --cov-report=term
+      - name: Upload coverage
+        uses: codecov/codecov-action@v4
+        if: matrix.python-version == '3.11'
+        with:
+          files: ./coverage.xml

.gitignore

@@ -2,3 +2,61 @@
 __pycache__
 *.egg-info
 .pytest_cache/
+
+# Python
+*.py[cod]
+*$py.class
+*.so
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg
+MANIFEST
+
+# Virtual environments
+venv/
+ENV/
+env/
+.venv
+
+# IDEs
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+
+# Testing
+.pytest_cache/
+.coverage
+htmlcov/
+.tox/
+.nox/
+
+# Type checking
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Distribution / packaging
+*.whl
+
+# Logs
+*.log
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Pre-commit
+.pre-commit-config.yaml.bak

.pre-commit-config.yaml

@@ -0,0 +1,27 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+
+  - repo: https://github.com/psf/black
+    rev: 24.4.2
+    hooks:
+      - id: black
+        language_version: python3.11
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.5
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.10.0
+    hooks:
+      - id: mypy
+        additional_dependencies: [types-requests]
+        args: [--ignore-missing-imports]

CHANGELOG.md

@@ -0,0 +1,47 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+### Added
+- Logging system with configurable verbosity and file output
+- Enhanced error handling with automatic retry logic for API queries
+- Data statistics feature showing file count, total size, and data type breakdown
+- Additional query filters: sample type and platform
+- Verbose mode (`--verbose`) for detailed logging
+- Log file output option (`--log-file`)
+- Pre-commit hooks configuration for code quality
+- CI/CD pipeline with GitHub Actions
+- Code formatting with Black
+- Linting with Ruff
+- Type checking with MyPy
+- Code coverage with pytest-cov
+- Comprehensive documentation (README, CONTRIBUTING, CHANGELOG)
+- Extended test suite with coverage for new features
+
+### Changed
+- Improved error messages with actionable guidance
+- Enhanced download error handling with detailed diagnostics
+- Better logging throughout all modules
+
+### Fixed
+- Corrected TSV manifest size parsing (convert to int)
+- Improved error handling for missing gdc-client
+
+## [0.1.0] - 2024-01-XX
+
+### Added
+- Initial release
+- Query TCGA files by project and data type
+- Generate manifests in TSV or JSON format
+- Download files via gdc-client
+- CLI with `query`, `download`, and `run` commands
+- Basic test suite
+- Project structure and documentation
+
+[Unreleased]: https://github.com/yourusername/tcga-downloader/compare/v0.1.0...HEAD
+[0.1.0]: https://github.com/yourusername/tcga-downloader/releases/tag/v0.1.0

CONTRIBUTING.md

@@ -0,0 +1,243 @@
+# Contributing to TCGA Downloader
+
+Thank you for your interest in contributing! This document provides guidelines and instructions for contributing to the project.
+
+## Getting Started
+
+### Prerequisites
+
+- Python 3.11 or higher
+- pip or uv
+- gdc-client (for testing downloads)
+- Git
+
+### Setting Up Development Environment
+
+1. Fork the repository
+2. Clone your fork:
+
+```bash
+git clone <your-fork-url>
+cd tcga-downloader
+```
+
+3. Install the package in development mode:
+
+```bash
+pip install -e ".[dev]"
+```
+
+4. Install and setup pre-commit hooks:
+
+```bash
+pip install pre-commit
+pre-commit install
+```
+
+## Development Workflow
+
+### Branch Strategy
+
+- `main`: Production-ready code
+- Create feature branches from `main`: `feature/your-feature-name`
+- Use descriptive branch names
+
+### Making Changes
+
+1. Create a new branch for your feature:
+
+```bash
+git checkout -b feature/your-feature-name
+```
+
+2. Make your changes following the coding standards (see below)
+
+3. Run tests and linting:
+
+```bash
+pytest
+black .
+ruff check --fix .
+mypy tcga_downloader
+```
+
+4. Commit your changes with descriptive messages:
+
+```bash
+git add .
+git commit -m "feat: add new filtering option for sample type"
+```
+
+5. Push to your fork:
+
+```bash
+git push origin feature/your-feature-name
+```
+
+6. Create a Pull Request
+
+## Coding Standards
+
+### Code Style
+
+This project uses:
+- **Black**: Code formatting (line length: 100)
+- **Ruff**: Linting
+- **mypy**: Type checking
+
+Before committing, run:
+
+```bash
+black .
+ruff check --fix .
+mypy tcga_downloader
+```
+
+Or use pre-commit hooks which run automatically:
+
+```bash
+pre-commit run --all-files
+```
+
+### Type Hints
+
+All public functions should include type hints. Use standard library types:
+
+```python
+from typing import List, Optional
+
+def query_files(
+    project: str,
+    data_type: str,
+    fields: Optional[List[str]] = None,
+) -> List[dict]:
+    ...
+```
+
+### Logging
+
+Use the logging module instead of print statements:
+
+```python
+from tcga_downloader.logger import get_logger
+
+logger = get_logger("module_name")
+logger.info("Processing file: %s", filename)
+logger.debug("Detailed debug information")
+```
+
+### Error Handling
+
+Use descriptive error messages and appropriate exception types:
+
+```python
+if not manifest_path.exists():
+    raise FileNotFoundError(f"Manifest file not found: {manifest_path}")
+```
+
+## Testing
+
+### Running Tests
+
+```bash
+pytest
+```
+
+With coverage:
+
+```bash
+pytest --cov=tcga_downloader --cov-report=html --cov-report=term
+```
+
+### Writing Tests
+
+- Place tests in the `tests/` directory
+- Name test files: `test_<module>.py`
+- Name test functions: `test_<function>_<scenario>`
+
+Example:
+
+```python
+def test_manifest_roundtrip_tsv(tmp_path):
+    records = [ManifestRecord(...)]
+    path = tmp_path / "m.tsv"
+    write_manifest(records, path, fmt="tsv")
+    loaded = load_manifest(path)
+    assert loaded == records
+```
+
+### Test Coverage
+
+Aim for high test coverage. New features should include tests.
+
+## Documentation
+
+### Code Documentation
+
+Use docstrings for public APIs:
+
+```python
+def build_filters(project: str, data_type: str) -> dict:
+    """Build GDC API filters for querying files.
+
+    Args:
+        project: TCGA project ID (e.g., "TCGA-BRCA")
+        data_type: Data type to filter (e.g., "Gene Expression")
+
+    Returns:
+        Filter dictionary for GDC API query
+    """
+    ...
+```
+
+### Documentation Updates
+
+When adding new features:
+1. Update README.md with usage examples
+2. Add type hints
+3. Update relevant sections in documentation
+
+## Pull Request Process
+
+### PR Checklist
+
+Before submitting a PR, ensure:
+
+- [ ] Code follows project style guidelines
+- [ ] All tests pass
+- [ ] New features include tests
+- [ ] Documentation is updated
+- [ ] Commit messages are clear and descriptive
+- [ ] Pre-commit hooks pass
+
+### PR Template
+
+```markdown
+## Description
+Brief description of changes
+
+## Type of Change
+- [ ] Bug fix
+- [ ] New feature
+- [ ] Breaking change
+- [ ] Documentation update
+
+## Testing
+Describe tests added/updated
+
+## Checklist
+- [ ] Tests pass
+- [ ] Code style checks pass
+- [ ] Documentation updated
+```
+
+## Code Review
+
+- Be constructive and respectful
+- Focus on code quality and correctness
+- Address review comments promptly
+- Request changes when necessary
+
+## Questions or Issues?
+
+Feel free to open an issue or ask in discussions for any questions!

README.md

@@ -1,17 +1,225 @@
 # TCGA Downloader
 
-Python package + CLI to query public TCGA files and download via gdc-client.
+Python package + CLI to query public TCGA (The Cancer Genome Atlas) files and download via gdc-client with retry logic, checksum verification, and progress logging.
 
-## Install
+## Features
+
+- Query TCGA files by project, data type, sample type, and platform
+- Generate reproducible manifests (TSV/JSON) for downloads
+- Reliable downloads with automatic retries and checksum verification
+- Data statistics (file count, total size, data types breakdown)
+- Comprehensive logging with verbose mode support
+- Resumable and concurrent downloads via gdc-client
+
+## Requirements
+
+- Python 3.11+
+- gdc-client (external tool, see [Installation](#installation))
+- pip or uv for package installation
+
+## Installation
+
+### 1. Install gdc-client
+
+Download and install the GDC Data Transfer Tool from [https://gdc.cancer.gov/access-data/gdc-data-transfer-tool](https://gdc.cancer.gov/access-data/gdc-data-transfer-tool)
+
+Make sure `gdc-client` is in your PATH:
 
 ```bash
+gdc-client version
+```
+
+### 2. Install this package
+
+```bash
+git clone <repository-url>
+cd tcga-downloader
 pip install -e .
 ```
 
-## Example
+For development:
 
 ```bash
-tcga-downloader query --project TCGA-BRCA --data-type "Gene Expression" --out manifest.tsv
+pip install -e ".[dev]"
-
-tcga-downloader download --manifest manifest.tsv --out-dir ./data
 ```
+
+This installs additional development tools:
+- pytest (testing)
+- pytest-cov (coverage)
+- black (code formatting)
+- ruff (linting)
+- mypy (type checking)
+
+## Usage
+
+### Basic Query
+
+Query TCGA files by project and data type:
+
+```bash
+tcga-downloader query \
+  --project TCGA-BRCA \
+  --data-type "Gene Expression" \
+  --out manifest.tsv
+```
+
+### Advanced Query with Filters
+
+Filter by sample type and platform:
+
+```bash
+tcga-downloader query \
+  --project TCGA-BRCA \
+  --data-type "Gene Expression" \
+  --sample-type "Primary Tumor" \
+  --platform "Illumina HiSeq" \
+  --out manifest.tsv
+```
+
+### Download Files
+
+Download files using a manifest:
+
+```bash
+tcga-downloader download \
+  --manifest manifest.tsv \
+  --out-dir ./data
+```
+
+### One-Step Query and Download
+
+Query and download in a single command:
+
+```bash
+tcga-downloader run \
+  --project TCGA-BRCA \
+  --data-type "Gene Expression" \
+  --out manifest.tsv \
+  --out-dir ./data
+```
+
+### Verbose Mode
+
+Enable detailed logging:
+
+```bash
+tcga-downloader query \
+  --project TCGA-BRCA \
+  --data-type "Gene Expression" \
+  --out manifest.tsv \
+  --verbose
+```
+
+### Log to File
+
+Save logs to a file:
+
+```bash
+tcga-downloader query \
+  --project TCGA-BRCA \
+  --data-type "Gene Expression" \
+  --out manifest.tsv \
+  --log-file download.log
+```
+
+### Custom Download Options
+
+Adjust concurrency and retry settings:
+
+```bash
+tcga-downloader download \
+  --manifest manifest.tsv \
+  --out-dir ./data \
+  --processes 8 \
+  --retries 5
+```
+
+### Downloading Controlled-Access Data
+
+Some TCGA data types (e.g., Clinical Supplement) require controlled access. To download these files, you need:
+
+1. **Obtain an authentication token** from GDC Data Portal:
+   - Log in to https://portal.gdc.cancer.gov/
+   - Click on your username → "Download Token"
+   - Save the token file to a secure location
+
+2. **Use the `--token` parameter** when downloading:
+
+```bash
+tcga-downloader download \
+  --manifest manifest.tsv \
+  --out-dir ./data \
+  --token /path/to/gdc-user-token.txt
+```
+
+Or add `token` to your config file:
+
+```json
+{
+  "download": {
+    "out_dir": "./data",
+    "processes": 4,
+    "retries": 3,
+    "token": "/path/to/gdc-user-token.txt"
+  }
+}
+```
+
+**Note**: Open-access data does not require a token. Only controlled-access files (marked in GDC Data Portal) need authentication.
+
+## Common TCGA Projects
+
+- TCGA-BRCA: Breast invasive carcinoma
+- TCGA-LUAD: Lung adenocarcinoma
+- TCGA-COAD: Colon adenocarcinoma
+- TCGA-PRAD: Prostate adenocarcinoma
+- TCGA-SKCM: Skin cutaneous melanoma
+
+## Common Data Types
+
+- Gene Expression
+- Copy Number Variation
+- DNA Methylation
+- miRNA Expression
+- Protein Expression
+- Somatic Mutation
+
+## Development
+
+### Setup pre-commit hooks
+
+```bash
+pip install pre-commit
+pre-commit install
+```
+
+### Run tests
+
+```bash
+pytest
+```
+
+With coverage:
+
+```bash
+pytest --cov=tcga_downloader --cov-report=html
+```
+
+### Code formatting
+
+```bash
+black .
+ruff check --fix .
+mypy tcga_downloader
+```
+
+### CI/CD
+
+The project uses GitHub Actions for CI:
+- Linting with black, ruff, mypy
+- Testing with pytest
+- Coverage reporting
+
+## License
+
+MIT License

examples/README.md

@@ -0,0 +1,135 @@
+# Examples
+
+This directory contains example scripts demonstrating various use cases of TCGA Downloader.
+
+## Examples
+
+### 1. Basic Query and Download
+
+**File:** `basic_query_download.py`
+
+Demonstrates:
+- Querying a single TCGA project
+- Creating a manifest file
+- Downloading files using the manifest
+
+```bash
+python examples/basic_query_download.py
+```
+
+### 2. Batch Query Multiple Projects
+
+**File:** `batch_query.py`
+
+Demonstrates:
+- Querying multiple TCGA projects in one command
+- Combining results from multiple queries
+- Statistics for combined results
+
+```bash
+python examples/batch_query.py
+```
+
+### 3. Advanced Filtering
+
+**File:** `advanced_filtering.py`
+
+Demonstrates:
+- Querying with sample type filter
+- Querying with platform filter
+- Multiple filter criteria at once
+
+```bash
+python examples/advanced_filtering.py
+```
+
+### 4. Using Configuration Files
+
+**File:** `using_config.py`
+
+Demonstrates:
+- Creating a default configuration file
+- Using configuration for other commands
+
+```bash
+python examples/using_config.py
+tcga-downloader query --file config.json
+```
+
+### 5. Validate Downloads
+
+**File:** `validate_downloads.py`
+
+Demonstrates:
+- Loading a manifest file
+- Validating manifest structure
+- Checking downloaded files against manifest
+- Verifying MD5 checksums
+
+```bash
+python examples/validate_downloads.py
+```
+
+## Running Examples
+
+Make sure you have TCGA Downloader installed:
+
+```bash
+pip install -e .
+```
+
+Then run any example:
+
+```bash
+cd examples
+python <example_name>.py
+```
+
+## Common TCGA Projects
+
+- TCGA-BRCA: Breast invasive carcinoma
+- TCGA-LUAD: Lung adenocarcinoma
+- TCGA-COAD: Colon adenocarcinoma
+- TCGA-PRAD: Prostate adenocarcinoma
+- TCGA-SKCM: Skin cutaneous melanoma
+- TCGA-KIRC: Kidney renal clear cell carcinoma
+- TCGA-GBM: Glioblastoma multiforme
+
+## Common Data Types
+
+- Gene Expression
+- Copy Number Variation
+- DNA Methylation
+- miRNA Expression
+- Protein Expression
+- Somatic Mutation
+
+## Interactive Mode
+
+**File:** `interactive_example.py`
+
+Demonstrates:
+- Dynamic project selection from API
+- Dynamic data type selection based on selected project
+- Interactive menu-driven workflow
+
+Usage:
+```bash
+tcga-downloader interactive --out manifest.tsv --out-dir ./data
+```
+
+The interactive mode provides a user-friendly menu-driven workflow:
+
+1. **Dynamic Project List**: Fetches available TCGA projects from GDC API
+2. **Project Selection**: Interactive menu to select a project
+3. **Dynamic Data Types**: Fetches available data types for selected project
+4. **Data Type Selection**: Interactive menu to select data type
+5. **Manifest Generation**: Creates manifest based on selections
+6. **Download**: Downloads files using gdc-client
+
+Usage:
+```bash
+tcga-downloader interactive --out manifest.tsv --out-dir ./data
+```
+
+This mode requires `questionary` library, which is included in the main package dependencies.

examples/advanced_filtering.py

@@ -0,0 +1,62 @@
+#!/usr/bin/env python3
+
+"""
+Example: Advanced filtering with sample type and platform.
+"""
+
+from pathlib import Path
+
+from tcga_downloader.manifest import (
+    ManifestRecord,
+    format_manifest_stats,
+    get_manifest_stats,
+    write_manifest,
+)
+from tcga_downloader.query import query_files
+
+
+def main():
+    project = "TCGA-BRCA"
+    data_type = "Gene Expression"
+    sample_type = "Primary Tumor"
+    platform = "Illumina HiSeq"
+    manifest_path = Path("filtered_manifest.tsv")
+
+    print("Advanced Query Parameters:")
+    print(f"  Project: {project}")
+    print(f"  Data Type: {data_type}")
+    print(f"  Sample Type: {sample_type}")
+    print(f"  Platform: {platform}")
+
+    hits = query_files(
+        project=project,
+        data_type=data_type,
+        sample_type=sample_type,
+        platform=platform,
+    )
+
+    records = [
+        ManifestRecord(
+            file_id=h["file_id"],
+            file_name=h["file_name"],
+            data_type=h["data_type"],
+            data_format=h["data_format"],
+            size=int(h["file_size"]),
+            md5=h["md5sum"],
+        )
+        for h in hits
+    ]
+
+    write_manifest(records, manifest_path, fmt="tsv")
+
+    stats = get_manifest_stats(records)
+    print("\nManifest Statistics:")
+    print(format_manifest_stats(stats))
+
+    print(f"\nManifest written to: {manifest_path}")
+    print("You can now download with:")
+    print(f"  tcga-downloader download --manifest {manifest_path} --out-dir ./data")
+
+
+if __name__ == "__main__":
+    main()

examples/basic_query_download.py

@@ -0,0 +1,48 @@
+#!/usr/bin/env python3
+
+"""
+Basic example: Query TCGA data and download files.
+"""
+
+from pathlib import Path
+
+from tcga_downloader.download import run_gdc_download
+from tcga_downloader.manifest import ManifestRecord, write_manifest
+from tcga_downloader.query import query_files
+
+
+def main():
+    query_project = "TCGA-BRCA"
+    data_type = "Gene Expression"
+    manifest_path = Path("manifest.tsv")
+    data_dir = Path("data")
+
+    print(f"Querying {query_project} for {data_type}...")
+    hits = query_files(query_project, data_type)
+
+    print(f"Found {len(hits)} files")
+    print(f"Writing manifest to {manifest_path}...")
+
+    records = [
+        ManifestRecord(
+            file_id=h["file_id"],
+            file_name=h["file_name"],
+            data_type=h["data_type"],
+            data_format=h["data_format"],
+            size=int(h["file_size"]),
+            md5=h["md5sum"],
+        )
+        for h in hits
+    ]
+
+    write_manifest(records, manifest_path, fmt="tsv")
+
+    print(f"Downloading files to {data_dir}...")
+    data_dir.mkdir(exist_ok=True)
+    run_gdc_download(manifest_path, data_dir, processes=4, retries=3)
+
+    print("Download complete!")
+
+
+if __name__ == "__main__":
+    main()

examples/batch_query.py

@@ -0,0 +1,48 @@
+#!/usr/bin/env python3
+
+"""
+Example: Query multiple TCGA projects at once.
+"""
+
+from pathlib import Path
+
+from tcga_downloader.manifest import (
+    ManifestRecord,
+    format_manifest_stats,
+    get_manifest_stats,
+    write_manifest,
+)
+from tcga_downloader.query import query_multiple_projects
+
+
+def main():
+    projects = ["TCGA-BRCA", "TCGA-LUAD", "TCGA-COAD"]
+    data_type = "Gene Expression"
+    manifest_path = Path("multi_project_manifest.tsv")
+
+    print(f"Querying {len(projects)} projects: {', '.join(projects)}...")
+    print(f"Data type: {data_type}")
+
+    hits = query_multiple_projects(projects, data_type)
+
+    records = [
+        ManifestRecord(
+            file_id=h["file_id"],
+            file_name=h["file_name"],
+            data_type=h["data_type"],
+            data_format=h["data_format"],
+            size=int(h["file_size"]),
+            md5=h["md5sum"],
+        )
+        for h in hits
+    ]
+
+    write_manifest(records, manifest_path, fmt="tsv")
+
+    stats = get_manifest_stats(records)
+    print("\nManifest Statistics:")
+    print(format_manifest_stats(stats))
+
+
+if __name__ == "__main__":
+    main()

examples/interactive_example.py

@@ -0,0 +1,33 @@
+#!/usr/bin/env python3
+
+"""
+Example: Interactive mode for TCGA Downloader.
+
+This script demonstrates how to use the interactive CLI to:
+1. Select a TCGA project from a dynamic list
+2. Select a data type for that project
+3. Download the selected data
+
+Usage:
+    tcga-downloader interactive --out manifest.tsv --out-dir ./data
+"""
+
+from pathlib import Path
+
+from tcga_downloader.interactive import interactive_select
+
+
+def main():
+    print("Starting TCGA Downloader in interactive mode...")
+    print("This will guide you through:")
+    print("  1. Selecting a TCGA project")
+    print("  2. Selecting a data type")
+    print("  3. Generating manifest")
+    print("  4. Downloading files")
+    print()
+
+    interactive_select()
+
+
+if __name__ == "__main__":
+    main()

examples/using_config.py

@@ -0,0 +1,31 @@
+#!/usr/bin/env python3
+
+"""
+Example: Use configuration file for downloads.
+"""
+
+from pathlib import Path
+
+from tcga_downloader.cli import main
+from tcga_downloader.config import save_default_config
+
+
+def main():
+    config_path = Path("config.json")
+
+    print("Creating default configuration file...")
+    save_default_config(config_path)
+    print(f"Config file created at: {config_path}")
+
+    print("\nEdit the config file to customize:")
+    print("  - project: TCGA project ID")
+    print("  - data_type: Type of data to query")
+    print("  - out_dir: Directory for downloads")
+
+    print("\nYou can use the config file with:")
+    print("  tcga-downloader query --file config.json")
+    print("  tcga-downloader run --file config.json")
+
+
+if __name__ == "__main__":
+    main()

examples/validate_downloads.py

@@ -0,0 +1,62 @@
+#!/usr/bin/env python3
+
+"""
+Example: Validate manifest and downloaded files.
+"""
+
+from pathlib import Path
+
+from tcga_downloader.manifest import (
+    load_manifest,
+    validate_files_against_manifest,
+    validate_manifest,
+)
+
+
+def main():
+    manifest_path = Path("manifest.tsv")
+    data_dir = Path("data")
+
+    print("Loading manifest...")
+    records = load_manifest(manifest_path)
+
+    print(f"Loaded {len(records)} records from manifest")
+
+    print("\nValidating manifest structure...")
+    errors = validate_manifest(records)
+
+    if errors:
+        print("Manifest validation errors found:")
+        for error in errors:
+            print(f"  - {error}")
+    else:
+        print("Manifest structure is valid!")
+
+    if data_dir.exists():
+        print("\nValidating downloaded files against manifest...")
+        missing, checksum_errors = validate_files_against_manifest(records, data_dir)
+
+        if missing:
+            print(f"\nMissing files ({len(missing)}):")
+            for filename in missing[:10]:
+                print(f"  - {filename}")
+            if len(missing) > 10:
+                print(f"  ... and {len(missing) - 10} more")
+
+        if checksum_errors:
+            print(f"\nChecksum errors ({len(checksum_errors)}):")
+            for error in checksum_errors[:10]:
+                print(f"  - {error}")
+            if len(checksum_errors) > 10:
+                print(f"  ... and {len(checksum_errors) - 10} more")
+
+        if not missing and not checksum_errors:
+            print("\nAll files are present and checksums match!")
+        else:
+            print("\nValidation failed. Please re-download missing files.")
+    else:
+        print(f"\nData directory {data_dir} does not exist. Skipping file validation.")
+
+
+if __name__ == "__main__":
+    main()

pyproject.toml

@@ -3,10 +3,108 @@ name = "tcga-downloader"
 version = "0.1.0"
 description = "TCGA public data downloader"
 requires-python = ">=3.11"
-dependencies = ["requests>=2.31"]
+dependencies = ["requests>=2.31", "questionary>=2.0.0"]
 
 [project.optional-dependencies]
-dev = ["pytest>=7.4"]
+dev = [
+    "pytest>=7.4",
+    "pytest-cov>=5.0",
+    "black>=24.0",
+    "ruff>=0.1.0",
+    "mypy>=1.8.0",
+    "types-requests",
+    "questionary>=2.0.0",
+    "tqdm>=4.66.0",
+]
+yaml = ["pyyaml>=6.0"]
 
 [project.scripts]
 tcga-downloader = "tcga_downloader.cli:main"
+
+[tool.black]
+line-length = 100
+target-version = ['py311', 'py312']
+include = '\.pyi?$'
+extend-exclude = '''
+/(
+  # directories
+  \.eggs
+  | \.git
+  | \.hg
+  | \.mypy_cache
+  | \.tox
+  | \.venv
+  | build
+  | dist
+)/
+'''
+
+[tool.ruff]
+target-version = "py311"
+line-length = 100
+lint.select = [
+    "E",   # pycodestyle errors
+    "W",   # pycodestyle warnings
+    "F",   # pyflakes
+    "I",   # isort
+    "B",   # flake8-bugbear
+    "C4",  # flake8-comprehensions
+    "UP",  # pyupgrade
+    "ARG", # flake8-unused-arguments
+    "SIM", # flake8-simplify
+]
+lint.ignore = [
+    "E501",  # line too long (handled by black)
+    "B008",  # do not perform function calls in argument defaults
+    "C901",  # too complex
+]
+
+[tool.ruff.lint.isort]
+known-first-party = ["tcga_downloader"]
+
+[tool.mypy]
+python_version = "3.11"
+warn_return_any = true
+warn_unused_configs = true
+disallow_untyped_defs = false
+disallow_incomplete_defs = false
+check_untyped_defs = true
+no_implicit_optional = true
+warn_redundant_casts = true
+warn_unused_ignores = true
+warn_no_return = true
+strict_equality = true
+
+[[tool.mypy.overrides]]
+module = "tests.*"
+disallow_untyped_defs = false
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+python_files = ["test_*.py"]
+python_classes = ["Test*"]
+python_functions = ["test_*"]
+addopts = "-v --tb=short --strict-markers"
+markers = [
+    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
+    "integration: marks tests as integration tests",
+]
+
+[tool.coverage.run]
+source = ["tcga_downloader"]
+omit = [
+    "*/tests/*",
+    "*/__pycache__/*",
+    "*/site-packages/*",
+]
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "def __repr__",
+    "raise AssertionError",
+    "raise NotImplementedError",
+    "if __name__ == .__main__.:",
+    "if TYPE_CHECKING:",
+    "if typing.TYPE_CHECKING:",
+]

tcga_downloader/__init__.py

@@ -1 +1,5 @@
 __version__ = "0.1.0"
+
+from .cli import main
+
+from .cli import main

tcga_downloader/cli.py

@@ -3,18 +3,36 @@ from __future__ import annotations
 import argparse
 from pathlib import Path
 
+from tcga_downloader.config import load_config
 from tcga_downloader.download import run_gdc_download
-from tcga_downloader.manifest import ManifestRecord, write_manifest
+from tcga_downloader.interactive import interactive_select
-from tcga_downloader.query import query_files
+from tcga_downloader.logger import get_logger, setup_logging
+from tcga_downloader.manifest import (
+    ManifestRecord,
+    format_manifest_stats,
+    get_manifest_stats,
+    load_manifest,
+    validate_files_against_manifest,
+    validate_manifest,
+    write_manifest,
+)
+from tcga_downloader.query import query_files, query_multiple_projects
+
+logger = get_logger("cli")
 
 
 def build_parser() -> argparse.ArgumentParser:
     parser = argparse.ArgumentParser(prog="tcga-downloader")
+    parser.add_argument("--verbose", "-v", action="store_true", help="Enable verbose logging")
+    parser.add_argument("--log-file", type=str, help="Log file path")
     sub = parser.add_subparsers(dest="command", required=True)
 
     q = sub.add_parser("query")
-    q.add_argument("--project", required=True)
+    q.add_argument("--project", help="TCGA project ID (e.g., TCGA-BRCA)")
+    q.add_argument("--projects", nargs="+", help="Multiple TCGA project IDs")
     q.add_argument("--data-type", required=True)
+    q.add_argument("--sample-type", help="Filter by sample type (e.g., 'Primary Tumor')")
+    q.add_argument("--platform", help="Filter by platform (e.g., 'Illumina HiSeq')")
     q.add_argument("--out", required=True)
     q.add_argument("--format", choices=["tsv", "json"], default="tsv")
 
@@ -23,15 +41,34 @@ def build_parser() -> argparse.ArgumentParser:
     d.add_argument("--out-dir", required=True)
     d.add_argument("--processes", type=int, default=4)
     d.add_argument("--retries", type=int, default=3)
+    d.add_argument("--token", help="Authentication token for controlled-access data")
 
     r = sub.add_parser("run")
-    r.add_argument("--project", required=True)
+    r.add_argument("--project", help="TCGA project ID (e.g., TCGA-BRCA)")
+    r.add_argument("--projects", nargs="+", help="Multiple TCGA project IDs")
     r.add_argument("--data-type", required=True)
+    r.add_argument("--sample-type", help="Filter by sample type (e.g., 'Primary Tumor')")
+    r.add_argument("--platform", help="Filter by platform (e.g., 'Illumina HiSeq')")
     r.add_argument("--out", required=True)
     r.add_argument("--format", choices=["tsv", "json"], default="tsv")
     r.add_argument("--out-dir", required=True)
     r.add_argument("--processes", type=int, default=4)
     r.add_argument("--retries", type=int, default=3)
+    r.add_argument("--token", help="Authentication token for controlled-access data")
+
+    c = sub.add_parser("config")
+    c.add_argument("--init", type=str, help="Generate default config file at path")
+    c.add_argument("--file", type=str, help="Use config file for other commands")
+
+    v = sub.add_parser("validate")
+    v.add_argument("--manifest", required=True, help="Manifest file to validate")
+    v.add_argument("--data-dir", help="Validate downloaded files against manifest")
+
+    i = sub.add_parser("interactive")
+    i.add_argument("--out", required=True, help="Output manifest file path")
+    i.add_argument("--format", choices=["tsv", "json"], default="tsv")
+    i.add_argument("--out-dir", required=True, help="Download directory")
+    i.add_argument("--token", help="Authentication token for controlled-access data")
 
     return parser
 
@@ -56,11 +93,117 @@ def main() -> None:
     parser = build_parser()
     args = parser.parse_args()
 
+    config = None
+    if args.command == "config":
+        if getattr(args, "init", None):
+            from tcga_downloader.config import save_default_config
+
+            save_default_config(Path(args.init))
+            return
+        else:
+            parser.print_help()
+            return
+
+    if args.command == "validate":
+        setup_logging(verbose=args.verbose, log_file=args.log_file)
+        records = load_manifest(Path(args.manifest))
+
+        errors = validate_manifest(records)
+        if errors:
+            logger.error("Manifest validation errors:")
+            for error in errors:
+                logger.error("  - %s", error)
+            return
+
+        logger.info("Manifest is valid (%d records)", len(records))
+
+        if hasattr(args, "data_dir") and args.data_dir:
+            data_dir = Path(args.data_dir)
+            missing, checksum_errors = validate_files_against_manifest(records, data_dir)
+
+            if missing:
+                logger.warning("Missing files (%d):", len(missing))
+                for filename in missing:
+                    logger.warning("  - %s", filename)
+
+            if checksum_errors:
+                logger.error("Checksum errors (%d):", len(checksum_errors))
+                for error in checksum_errors:
+                    logger.error("  - %s", error)
+
+            if not missing and not checksum_errors:
+                logger.info("All files validated successfully!")
+
+        return
+
+    if args.command != "config" and hasattr(args, "file") and args.file:
+        try:
+            config = load_config(Path(args.file))
+        except Exception as e:
+            logger.error("Failed to load config: %s", e)
+            return
+
+        setup_logging(
+            verbose=config.verbose or args.verbose, log_file=config.log_file or args.log_file
+        )
+    else:
+        setup_logging(verbose=args.verbose, log_file=args.log_file)
+
     if args.command in {"query", "run"}:
-        hits = query_files(args.project, args.data_type)
+        project = args.project
+        projects = getattr(args, "projects", None)
+        data_type = args.data_type
+        sample_type = getattr(args, "sample_type", None)
+        platform = getattr(args, "platform", None)
+        out = args.out
+        fmt = getattr(args, "format", "tsv")
+
+        if config and args.command == "query":
+            project = project or config.query.project
+            data_type = data_type or config.query.data_type
+            sample_type = sample_type or config.query.sample_type
+            platform = platform or config.query.platform
+
+        if projects:
+            hits = query_multiple_projects(
+                projects, data_type, sample_type=sample_type, platform=platform
+            )
+        else:
+            hits = query_files(project, data_type, sample_type=sample_type, platform=platform)
+
+        records = _records_from_hits(hits)
+        write_manifest(records, Path(out), fmt=fmt)
+        stats = get_manifest_stats(records)
+        logger.info("Manifest statistics:\n%s", format_manifest_stats(stats))
+
+    if args.command == "interactive":
+        setup_logging(verbose=args.verbose, log_file=args.log_file)
+
+        project_id, data_type = interactive_select()
+
+        hits = query_files(project_id, data_type)
         records = _records_from_hits(hits)
         write_manifest(records, Path(args.out), fmt=args.format)
+        stats = get_manifest_stats(records)
+        logger.info("Manifest statistics:\n%s", format_manifest_stats(stats))
+
+        run_gdc_download(Path(args.out), Path(args.out_dir), token=getattr(args, "token", None))
 
     if args.command in {"download", "run"}:
-        manifest_path = Path(args.manifest if args.command == "download" else args.out)
+        manifest = getattr(args, "manifest", None)
-        run_gdc_download(manifest_path, Path(args.out_dir), args.processes, args.retries)
+        out_dir = args.out_dir
+        processes = args.processes
+        retries = args.retries
+        token = getattr(args, "token", None)
+
+        if config:
+            if args.command == "download":
+                out_dir = out_dir or config.download.out_dir
+            else:
+                out_dir = config.download.out_dir
+            processes = processes or config.download.processes
+            retries = retries or config.download.retries
+            token = token or config.download.token
+
+        manifest_path = Path(manifest if args.command == "download" else args.out)
+        run_gdc_download(manifest_path, Path(out_dir), processes, retries, token)

tcga_downloader/config.py

@@ -0,0 +1,136 @@
+from __future__ import annotations
+
+import json
+from dataclasses import dataclass
+from pathlib import Path
+
+from tcga_downloader.logger import get_logger
+
+logger = get_logger("config")
+
+
+@dataclass
+class QueryConfig:
+    project: str
+    data_type: str
+    sample_type: str | None = None
+    platform: str | None = None
+    max_files: int = 1000
+
+
+@dataclass
+class DownloadConfig:
+    out_dir: str
+    processes: int = 4
+    retries: int = 3
+    token: str | None = None
+
+
+@dataclass
+class Config:
+    query: QueryConfig
+    download: DownloadConfig
+    log_file: str | None = None
+    verbose: bool = False
+
+
+def load_config(path: Path) -> Config:
+    """Load configuration from JSON or YAML file."""
+    if not path.exists():
+        raise FileNotFoundError(f"Config file not found: {path}")
+
+    suffix = path.suffix.lower()
+
+    if suffix == ".json":
+        with path.open() as f:
+            data = json.load(f)
+    elif suffix in {".yaml", ".yml"}:
+        try:
+            import yaml
+
+            with path.open() as f:
+                data = yaml.safe_load(f)
+        except ImportError as e:
+            raise ImportError(
+                "PyYAML is required for YAML config files. Install with: pip install pyyaml"
+            ) from e
+    else:
+        raise ValueError(f"Unsupported config format: {suffix}")
+
+    return _parse_config(data)
+
+
+def _parse_config(data: dict) -> Config:
+    query_data = data.get("query", {})
+    download_data = data.get("download", {})
+
+    query = QueryConfig(
+        project=query_data.get("project"),
+        data_type=query_data.get("data_type"),
+        sample_type=query_data.get("sample_type"),
+        platform=query_data.get("platform"),
+        max_files=query_data.get("max_files", 1000),
+    )
+
+    download = DownloadConfig(
+        out_dir=download_data.get("out_dir", "./data"),
+        processes=download_data.get("processes", 4),
+        retries=download_data.get("retries", 3),
+        token=download_data.get("token"),
+    )
+
+    return Config(
+        query=query,
+        download=download,
+        log_file=data.get("log_file"),
+        verbose=data.get("verbose", False),
+    )
+
+
+def save_default_config(path: Path) -> None:
+    """Save a default configuration template to file."""
+    config = Config(
+        query=QueryConfig(project="TCGA-BRCA", data_type="Gene Expression"),
+        download=DownloadConfig(out_dir="./data"),
+    )
+
+    suffix = path.suffix.lower()
+
+    if suffix == ".json":
+        with path.open("w") as f:
+            json.dump(_config_to_dict(config), f, indent=2)
+    elif suffix in {".yaml", ".yml"}:
+        try:
+            import yaml
+
+            with path.open("w") as f:
+                yaml.dump(_config_to_dict(config), f, default_flow_style=False)
+        except ImportError as e:
+            raise ImportError(
+                "PyYAML is required for YAML config files. Install with: pip install pyyaml"
+            ) from e
+    else:
+        raise ValueError(f"Unsupported config format: {suffix}")
+
+    logger.info("Default config saved to %s", path)
+
+
+def _config_to_dict(config: Config) -> dict:
+    """Convert Config dataclass to dictionary."""
+    return {
+        "query": {
+            "project": config.query.project,
+            "data_type": config.query.data_type,
+            "sample_type": config.query.sample_type,
+            "platform": config.query.platform,
+            "max_files": config.query.max_files,
+        },
+        "download": {
+            "out_dir": config.download.out_dir,
+            "processes": config.download.processes,
+            "retries": config.download.retries,
+            "token": config.download.token,
+        },
+        "log_file": config.log_file,
+        "verbose": config.verbose,
+    }

tcga_downloader/download.py

@@ -4,9 +4,15 @@ import shutil
 import subprocess
 from pathlib import Path
 
+from tcga_downloader.logger import get_logger
 
-def build_gdc_command(manifest_path: Path, out_dir: Path, processes: int, retries: int) -> list[str]:
+logger = get_logger("download")
-    return [
+
+
+def build_gdc_command(
+    manifest_path: Path, out_dir: Path, processes: int, retries: int, token: str | None = None
+) -> list[str]:
+    cmd = [
         "gdc-client",
         "download",
         "-m",
@@ -15,14 +21,43 @@ def build_gdc_command(manifest_path: Path, out_dir: Path, processes: int, retrie
         str(out_dir),
         "--n-processes",
         str(processes),
-        "--retry-count",
+        "--retry-amount",
         str(retries),
-        "--checksum",
     ]
+    if token:
+        cmd.extend(["--token", token])
+    return cmd
 
 
-def run_gdc_download(manifest_path: Path, out_dir: Path, processes: int = 4, retries: int = 3) -> None:
+def run_gdc_download(
+    manifest_path: Path,
+    out_dir: Path,
+    processes: int = 4,
+    retries: int = 3,
+    token: str | None = None,
+) -> None:
+    if not manifest_path.exists():
+        raise FileNotFoundError(f"Manifest file not found: {manifest_path}")
+
     if not shutil.which("gdc-client"):
-        raise RuntimeError("gdc-client not found in PATH")
+        raise RuntimeError(
-    cmd = build_gdc_command(manifest_path, out_dir, processes, retries)
+            "gdc-client not found in PATH. Install from https://gdc.cancer.gov/access-data/gdc-data-transfer-tool"
-    subprocess.run(cmd, check=True)
+        )
+
+    cmd = build_gdc_command(manifest_path, out_dir, processes, retries, token)
+    logger.info("Starting download: manifest=%s, out_dir=%s", manifest_path, out_dir)
+    logger.debug("Running command: %s", " ".join(cmd))
+
+    try:
+        result = subprocess.run(cmd, check=True, capture_output=True, text=True)
+        if result.stdout:
+            logger.debug("gdc-client output: %s", result.stdout)
+    except subprocess.CalledProcessError as e:
+        logger.error("Download failed with exit code %d", e.returncode)
+        if e.stdout:
+            logger.info("gdc-client output:\n%s", e.stdout)
+        if e.stderr:
+            logger.error("gdc-client error:\n%s", e.stderr)
+        raise RuntimeError(f"gdc-client download failed with exit code {e.returncode}") from e
+
+    logger.info("Download completed successfully")

tcga_downloader/interactive.py

@@ -0,0 +1,165 @@
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+import questionary
+import requests
+
+if TYPE_CHECKING:
+    pass
+
+from tcga_downloader.logger import get_logger
+
+logger = get_logger("interactive")
+
+GDC_PROJECTS_URL = "https://api.gdc.cancer.gov/projects"
+GDC_FILES_URL = "https://api.gdc.cancer.gov/files"
+
+
+def fetch_projects(size: int = 1000) -> list[dict]:
+    """
+    Fetch all available TCGA projects from GDC API.
+
+    Args:
+        size: Number of projects to return
+
+    Returns:
+        List of project dictionaries containing project_id, name, etc.
+    """
+    logger.info("Fetching TCGA projects...")
+    params = {"size": size}
+    try:
+        resp = requests.get(GDC_PROJECTS_URL, params=params, timeout=30)
+        resp.raise_for_status()
+        data = resp.json()
+
+        projects = data.get("data", {}).get("hits", [])
+        logger.info("Fetched %d projects", len(projects))
+        return projects
+    except requests.exceptions.RequestException as e:
+        logger.error("Failed to fetch TCGA projects: %s", e)
+        raise
+
+
+def fetch_data_types(project_id: str, size: int = 1000) -> list[str]:
+    """
+    Fetch available data types for a specific project using GDC Files API facets.
+
+    Args:
+        project_id: TCGA project ID (e.g., TCGA-BRCA)
+        size: Maximum number of data types to return
+
+    Returns:
+        List of unique data type names
+    """
+    logger.info("Fetching data types for project %s...", project_id)
+    payload = {
+        "filters": {
+            "op": "and",
+            "content": [
+                {
+                    "op": "in",
+                    "content": {"field": "cases.project.project_id", "value": [project_id]},
+                }
+            ],
+        },
+        "size": 0,
+        "facets": "data_type",
+        "format": "JSON",
+    }
+    try:
+        resp = requests.post(GDC_FILES_URL, json=payload, timeout=30)
+        resp.raise_for_status()
+        data = resp.json()
+
+        aggregations = data.get("data", {}).get("aggregations", {})
+        data_types = aggregations.get("data_type", {}).get("buckets", [])
+        unique_types = [bucket.get("key") for bucket in data_types if bucket.get("key")]
+        logger.info("Found %d data types", len(unique_types))
+        return unique_types[:size]
+    except requests.exceptions.RequestException as e:
+        logger.error("Failed to fetch data types for project %s: %s", project_id, e)
+        raise
+
+
+def select_project(projects: list[dict]) -> dict:
+    """
+    Interactive selection of project from list.
+
+    Args:
+        projects: List of available projects
+
+    Returns:
+        Selected project dictionary
+    """
+    choices = [f"{p['project_id']} - {p.get('name', 'Unknown')}" for p in projects]
+    answer = questionary.select(
+        message="Select a TCGA project:",
+        choices=choices,
+    ).ask()
+
+    if answer is None:
+        logger.info("No project selected")
+        raise SystemExit(0)
+
+    selected = None
+    for p in projects:
+        if answer.startswith(p["project_id"]):
+            selected = p
+            break
+
+    if not selected:
+        logger.warning("Could not parse selection: %s", answer)
+        raise SystemExit(1)
+
+    return selected
+
+
+def select_data_type(data_types: list[str]) -> str:
+    """
+    Interactive selection of data type from list.
+
+    Args:
+        data_types: List of available data types
+
+    Returns:
+        Selected data type
+    """
+    if not data_types:
+        logger.warning("No data types available")
+        raise SystemExit(1)
+
+    answer = questionary.select(
+        message="Select a data type:",
+        choices=data_types,
+    ).ask()
+
+    if answer is None:
+        logger.info("No data type selected")
+        raise SystemExit(0)
+
+    return answer
+
+
+def interactive_select() -> tuple[str, str]:
+    """
+    Run interactive selection workflow: project -> data type.
+
+    Returns:
+        Tuple of (project_id, data_type)
+    """
+    print("\n" + "=" * 60)
+    print("TCGA Downloader - Interactive Mode")
+    print("=" * 60 + "\n")
+
+    projects = fetch_projects()
+    selected_project = select_project(projects)
+
+    project_id = selected_project["project_id"]
+    data_types = fetch_data_types(project_id)
+    selected_data_type = select_data_type(data_types)
+
+    print(f"\nSelected project: {selected_project.get('name', project_id)}")
+    print(f"Selected data type: {selected_data_type}\n")
+
+    return project_id, selected_data_type

tcga_downloader/logger.py

@@ -0,0 +1,24 @@
+import logging
+import sys
+from logging import Handler, StreamHandler
+
+
+def setup_logging(verbose: bool = False, log_file: str | None = None) -> logging.Logger:
+    log_level = logging.DEBUG if verbose else logging.INFO
+
+    handlers: list[Handler] = [StreamHandler(sys.stderr)]
+
+    if log_file:
+        handlers.append(logging.FileHandler(log_file))
+
+    logging.basicConfig(
+        level=log_level,
+        format="%(asctime)s - %(name)s - %(levelname)s - %(message)s",
+        handlers=handlers,
+    )
+
+    return logging.getLogger("tcga_downloader")
+
+
+def get_logger(name: str) -> logging.Logger:
+    return logging.getLogger(f"tcga_downloader.{name}")

tcga_downloader/manifest.py

@@ -2,9 +2,13 @@ from __future__ import annotations
 
 import csv
 import json
+from collections.abc import Iterable
 from dataclasses import dataclass
 from pathlib import Path
-from typing import Iterable, List
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    pass
 
 REQUIRED_FIELDS = ["file_id", "file_name", "data_type", "data_format", "size", "md5"]
 
@@ -39,14 +43,22 @@ def write_manifest(records: Iterable[ManifestRecord], path: Path, fmt: str = "ts
         path.write_text(json.dumps(data, indent=2))
         return
 
+    gdc_fields = ["id", "filename", "md5", "size", "state"]
     with path.open("w", newline="") as f:
-        writer = csv.DictWriter(f, fieldnames=REQUIRED_FIELDS, delimiter="\t")
+        writer = csv.DictWriter(f, fieldnames=gdc_fields, delimiter="\t")
         writer.writeheader()
         for rec in records:
-            writer.writerow(rec.__dict__)
+            row = {
+                "id": rec.file_id,
+                "filename": rec.file_name,
+                "md5": rec.md5,
+                "size": rec.size,
+                "state": "live",  # Default state for gdc-client manifest
+            }
+            writer.writerow(row)
 
 
-def load_manifest(path: Path) -> List[ManifestRecord]:
+def load_manifest(path: Path) -> list[ManifestRecord]:
     path = Path(path)
     if path.suffix.lower() == ".json":
         data = json.loads(path.read_text())
@@ -54,8 +66,127 @@ def load_manifest(path: Path) -> List[ManifestRecord]:
 
     with path.open("r", newline="") as f:
         reader = csv.DictReader(f, delimiter="\t")
-        records: List[ManifestRecord] = []
+        records: list[ManifestRecord] = []
+
         for row in reader:
-            row["size"] = int(row["size"])
+            # Detect manifest format: gdc-client format uses 'id'/'filename', old format uses 'file_id'/'file_name'
-            records.append(ManifestRecord(**row))
+            if "id" in row and "filename" in row:
+                file_id = row["id"]
+                file_name = row["filename"]
+            elif "file_id" in row and "file_name" in row:
+                file_id = row["file_id"]
+                file_name = row["file_name"]
+            else:
+                raise ValueError("Invalid manifest: missing required columns")
+
+            records.append(
+                ManifestRecord(
+                    file_id=file_id,
+                    file_name=file_name,
+                    data_type=row.get("data_type", "Unknown"),
+                    data_format=row.get("data_format", "Unknown"),
+                    size=int(row["size"]),
+                    md5=row["md5"],
+                )
+            )
         return records
+
+
+def get_manifest_stats(
+    records: Iterable[ManifestRecord],
+) -> dict[str, int | float | dict[str, int]]:
+    records = list(records)
+    total_size = sum(rec.size for rec in records)
+    data_types: dict[str, int] = {}
+    data_formats: dict[str, int] = {}
+
+    for rec in records:
+        data_types[rec.data_type] = data_types.get(rec.data_type, 0) + 1
+        data_formats[rec.data_format] = data_formats.get(rec.data_format, 0) + 1
+
+    return {
+        "file_count": len(records),
+        "total_size_bytes": total_size,
+        "total_size_mb": total_size / (1024 * 1024),
+        "total_size_gb": total_size / (1024 * 1024 * 1024),
+        "data_types": data_types,
+        "data_formats": data_formats,
+    }
+
+
+def format_manifest_stats(stats: dict[str, int | float | dict[str, int]]) -> str:
+    lines = [
+        f"File count: {stats['file_count']}",
+        f"Total size: {stats['total_size_gb']:.2f} GB ({stats['total_size_mb']:.2f} MB)",
+    ]
+
+    data_types = stats.get("data_types")
+    if data_types and isinstance(data_types, dict):
+        lines.append("\nData types:")
+        for data_type, count in sorted(data_types.items()):
+            lines.append(f"  - {data_type}: {count}")
+
+    data_formats = stats.get("data_formats")
+    if data_formats and isinstance(data_formats, dict):
+        lines.append("\nData formats:")
+        for data_format, count in sorted(data_formats.items()):
+            lines.append(f"  - {data_format}: {count}")
+
+    return "\n".join(lines)
+
+
+def validate_manifest(records: list[ManifestRecord]) -> list[str]:
+    """Validate manifest records and return list of error messages."""
+    errors = []
+
+    for i, rec in enumerate(records, 1):
+        if not rec.file_id:
+            errors.append(f"Record {i}: Missing file_id")
+        if not rec.file_name:
+            errors.append(f"Record {i}: Missing file_name")
+        if not rec.data_type:
+            errors.append(f"Record {i}: Missing data_type")
+        if not rec.data_format:
+            errors.append(f"Record {i}: Missing data_format")
+        if rec.size < 0:
+            errors.append(f"Record {i}: Invalid size (must be non-negative)")
+        if not rec.md5 or len(rec.md5) != 32:
+            errors.append(f"Record {i}: Invalid MD5 checksum (must be 32 characters)")
+
+    return errors
+
+
+def validate_files_against_manifest(
+    records: list[ManifestRecord], data_dir: Path
+) -> tuple[list[str], list[str]]:
+    """Validate that downloaded files match manifest records.
+
+    Returns:
+        Tuple of (missing_files, checksum_errors)
+    """
+    missing_files = []
+    checksum_errors = []
+
+    for rec in records:
+        file_path = data_dir / rec.file_name
+
+        if not file_path.exists():
+            missing_files.append(rec.file_name)
+            continue
+
+        if rec.md5:
+            actual_md5 = _calculate_md5(file_path)
+            if actual_md5 != rec.md5:
+                checksum_errors.append(f"{rec.file_name}: Expected {rec.md5}, got {actual_md5}")
+
+    return missing_files, checksum_errors
+
+
+def _calculate_md5(file_path: Path) -> str:
+    import hashlib
+
+    hash_md5 = hashlib.md5()
+    with file_path.open("rb") as f:
+        for chunk in iter(lambda: f.read(4096), b""):
+            hash_md5.update(chunk)
+    return hash_md5.hexdigest()

tcga_downloader/query.py

@@ -1,42 +1,146 @@
 from __future__ import annotations
 
+import time
+
 import requests
+from requests.exceptions import HTTPError, RequestException, Timeout
+
+from tcga_downloader.logger import get_logger
 
 GDC_FILES_URL = "https://api.gdc.cancer.gov/files"
+logger = get_logger("query")
 
 
-def build_filters(project: str, data_type: str) -> dict:
+def build_filters(
+    project: str,
+    data_type: str,
+    sample_type: str | None = None,
+    platform: str | None = None,
+) -> dict:
+    filters = [
+        {
+            "op": "in",
+            "content": {
+                "field": "cases.project.project_id",
+                "value": [project],
+            },
+        },
+        {
+            "op": "in",
+            "content": {
+                "field": "data_type",
+                "value": [data_type],
+            },
+        },
+    ]
+
+    if sample_type:
+        filters.append(
+            {
+                "op": "in",
+                "content": {
+                    "field": "samples.sample_type",
+                    "value": [sample_type],
+                },
+            }
+        )
+
+    if platform:
+        filters.append(
+            {
+                "op": "in",
+                "content": {
+                    "field": "platform",
+                    "value": [platform],
+                },
+            }
+        )
+
     return {
         "op": "and",
-        "content": [
+        "content": filters,
-            {
-                "op": "in",
-                "content": {
-                    "field": "cases.project.project_id",
-                    "value": [project],
-                },
-            },
-            {
-                "op": "in",
-                "content": {
-                    "field": "data_type",
-                    "value": [data_type],
-                },
-            },
-        ],
     }
 
 
-def query_files(project: str, data_type: str, fields: list[str] | None = None, size: int = 1000) -> list[dict]:
+def query_files(
+    project: str,
+    data_type: str,
+    fields: list[str] | None = None,
+    size: int = 1000,
+    max_retries: int = 3,
+    retry_delay: float = 1.0,
+    sample_type: str | None = None,
+    platform: str | None = None,
+) -> list[dict]:
     if fields is None:
         fields = ["file_id", "file_name", "data_type", "data_format", "file_size", "md5sum"]
     payload = {
-        "filters": build_filters(project, data_type),
+        "filters": build_filters(project, data_type, sample_type, platform),
         "fields": ",".join(fields),
         "format": "JSON",
         "size": size,
     }
-    resp = requests.post(GDC_FILES_URL, json=payload, timeout=30)
+    logger.info(
-    resp.raise_for_status()
+        "Querying GDC: project=%s, data_type=%s, sample_type=%s, platform=%s",
-    data = resp.json()
+        project,
-    return data.get("data", {}).get("hits", [])
+        data_type,
+        sample_type,
+        platform,
+    )
+
+    last_error: RequestException | None = None
+    for attempt in range(max_retries):
+        try:
+            resp = requests.post(GDC_FILES_URL, json=payload, timeout=30)
+            resp.raise_for_status()
+            data: dict = resp.json()
+            hits = data.get("data", {}).get("hits", [])
+            assert isinstance(hits, list)
+            logger.info("Found %d files", len(hits))
+            return hits
+        except Timeout as e:
+            last_error = e
+            logger.warning("Timeout on attempt %d/%d", attempt + 1, max_retries)
+        except HTTPError as e:
+            last_error = e
+            logger.warning("HTTP error on attempt %d/%d: %s", attempt + 1, max_retries, e)
+        except RequestException as e:
+            last_error = e
+            logger.warning("Request error on attempt %d/%d: %s", attempt + 1, max_retries, e)
+
+        if attempt < max_retries - 1:
+            sleep_time = retry_delay * (2**attempt)
+            logger.debug("Retrying in %.1f seconds...", sleep_time)
+            time.sleep(sleep_time)
+
+    raise RuntimeError(f"Failed to query GDC after {max_retries} attempts: {last_error}")
+
+
+def query_multiple_projects(
+    projects: list[str],
+    data_type: str,
+    fields: list[str] | None = None,
+    size: int = 1000,
+    max_retries: int = 3,
+    retry_delay: float = 1.0,
+    sample_type: str | None = None,
+    platform: str | None = None,
+) -> list[dict]:
+    """Query multiple TCGA projects and return combined results."""
+    all_hits = []
+    for i, project in enumerate(projects):
+        logger.info("Processing project %d/%d: %s", i + 1, len(projects), project)
+        hits = query_files(
+            project,
+            data_type,
+            fields,
+            size,
+            max_retries,
+            retry_delay,
+            sample_type,
+            platform,
+        )
+        all_hits.extend(hits)
+
+    logger.info("Total files found across %d projects: %d", len(projects), len(all_hits))
+    return all_hits

test_simple.py

@@ -0,0 +1,30 @@
+#!/usr/bin/env python3
+
+import unittest.mock
+
+from tcga_downloader.interactive import fetch_projects
+
+
+def main():
+    with unittest.mock.patch("tcga_downloader.interactive.requests.get") as mock_get:
+        mock_response = mock_get.return_value
+        mock_response.status_code = 200
+        mock_response.json.return_value = {
+            "data": {
+                "hits": [
+                    {
+                        "project_id": "TCGA-BRCA",
+                        "name": "Breast Invasive Carcinoma",
+                    },
+                ]
+            }
+        }
+
+        projects = fetch_projects()
+        print(f"Projects fetched: {len(projects)}")
+        assert len(projects) == 1
+        print("Test passed!")
+
+
+if __name__ == "__main__":
+    main()

tests/test_cli.py

@@ -1,4 +1,6 @@
-from tcga_downloader.cli import build_parser
+from unittest.mock import patch
+
+from tcga_downloader.cli import build_parser, main
 
 
 def test_cli_has_subcommands():
@@ -6,10 +8,6 @@ def test_cli_has_subcommands():
     subparsers = parser._subparsers
     assert subparsers is not None
 
-from unittest.mock import patch
-
-from tcga_downloader.cli import main
-
 
 def test_cli_query_writes_manifest(tmp_path, monkeypatch):
     args = [

tests/test_config.py

@@ -0,0 +1,122 @@
+import pytest
+
+from tcga_downloader.config import (
+    Config,
+    DownloadConfig,
+    QueryConfig,
+    _config_to_dict,
+    load_config,
+    save_default_config,
+)
+
+
+@pytest.mark.skipif("yaml" not in dir(__builtins__), reason="yaml module not available")
+def test_save_default_yaml_config(tmp_path):
+    config = QueryConfig(
+        project="TCGA-BRCA", data_type="Gene Expression", sample_type="Primary Tumor"
+    )
+    assert config.project == "TCGA-BRCA"
+    assert config.data_type == "Gene Expression"
+    assert config.sample_type == "Primary Tumor"
+    assert config.max_files == 1000
+
+
+def test_download_config():
+    config = DownloadConfig(out_dir="./data", processes=8, retries=5)
+    assert config.out_dir == "./data"
+    assert config.processes == 8
+    assert config.retries == 5
+
+
+def test_config_dataclass():
+    query = QueryConfig(project="TCGA-BRCA", data_type="Gene Expression")
+    download = DownloadConfig(out_dir="./data")
+    config = Config(query=query, download=download, verbose=True)
+
+    assert config.query.project == "TCGA-BRCA"
+    assert config.download.out_dir == "./data"
+    assert config.verbose is True
+
+
+def test_load_json_config(tmp_path):
+    config_data = {
+        "query": {
+            "project": "TCGA-BRCA",
+            "data_type": "Gene Expression",
+            "sample_type": "Primary Tumor",
+            "platform": "Illumina HiSeq",
+        },
+        "download": {"out_dir": "./data", "processes": 8, "retries": 5},
+        "verbose": True,
+        "log_file": "test.log",
+    }
+    config_file = tmp_path / "config.json"
+    import json
+
+    config_file.write_text(json.dumps(config_data))
+
+    config = load_config(config_file)
+    assert config.query.project == "TCGA-BRCA"
+    assert config.query.data_type == "Gene Expression"
+    assert config.query.sample_type == "Primary Tumor"
+    assert config.query.platform == "Illumina HiSeq"
+    assert config.download.out_dir == "./data"
+    assert config.download.processes == 8
+    assert config.download.retries == 5
+    assert config.verbose is True
+    assert config.log_file == "test.log"
+
+
+def test_save_default_json_config(tmp_path):
+    config_file = tmp_path / "config.json"
+    save_default_config(config_file)
+
+    assert config_file.exists()
+    import json
+
+    data = json.loads(config_file.read_text())
+    assert "query" in data
+    assert "download" in data
+    assert data["query"]["project"] == "TCGA-BRCA"
+    assert data["query"]["data_type"] == "Gene Expression"
+    assert data["download"]["out_dir"] == "./data"
+
+
+def test_save_default_yaml_config(tmp_path):
+    try:
+        import yaml
+
+        config_file = tmp_path / "config.yaml"
+        save_default_config(config_file)
+
+        assert config_file.exists()
+    except ImportError:
+        pytest.skip("PyYAML not installed")
+
+
+def test_config_to_dict():
+    query = QueryConfig(project="TCGA-BRCA", data_type="Gene Expression", max_files=500)
+    download = DownloadConfig(out_dir="./data", processes=2)
+    config = Config(query=query, download=download, verbose=False, log_file="app.log")
+
+    result = _config_to_dict(config)
+    assert result["query"]["project"] == "TCGA-BRCA"
+    assert result["query"]["data_type"] == "Gene Expression"
+    assert result["query"]["max_files"] == 500
+    assert result["download"]["out_dir"] == "./data"
+    assert result["download"]["processes"] == 2
+    assert result["verbose"] is False
+    assert result["log_file"] == "app.log"
+
+
+def test_load_nonexistent_config(tmp_path):
+    with pytest.raises(FileNotFoundError):
+        load_config(tmp_path / "nonexistent.json")
+
+
+def test_load_unsupported_format(tmp_path):
+    config_file = tmp_path / "config.txt"
+    config_file.write_text("invalid")
+
+    with pytest.raises(ValueError, match="Unsupported config format"):
+        load_config(config_file)

tests/test_download.py

@@ -5,5 +5,15 @@ from tcga_downloader.download import build_gdc_command
 
 def test_build_gdc_command():
     cmd = build_gdc_command(Path("/tmp/m.tsv"), Path("/data"), processes=4, retries=3)
-    assert "gdc-client" in cmd[0]
+    assert cmd == [
-    assert "-m" in cmd
+        "gdc-client",
+        "download",
+        "-m",
+        "/tmp/m.tsv",
+        "-d",
+        "/data",
+        "--n-processes",
+        "4",
+        "--retry-amount",
+        "3",
+    ]

tests/test_integration.py

@@ -0,0 +1,93 @@
+from unittest.mock import patch
+
+from tcga_downloader.cli import main
+
+
+@patch(
+    "sys.argv",
+    [
+        "tcga-downloader",
+        "query",
+        "--project",
+        "TCGA-BRCA",
+        "--data-type",
+        "Gene Expression",
+        "--out",
+        "/tmp/m.tsv",
+    ],
+)
+@patch("tcga_downloader.cli.query_files")
+def test_cli_integration_query_full(mock_query, tmp_path, monkeypatch):
+    mock_query.return_value = [
+        {
+            "file_id": "f1",
+            "file_name": "file1.tsv",
+            "data_type": "Gene Expression",
+            "data_format": "TSV",
+            "file_size": 1000,
+            "md5sum": "a" * 32,
+        }
+    ]
+
+    out_path = tmp_path / "m.tsv"
+    monkeypatch.setattr(
+        "sys.argv",
+        [
+            "tcga-downloader",
+            "query",
+            "--project",
+            "TCGA-BRCA",
+            "--data-type",
+            "Gene Expression",
+            "--out",
+            str(out_path),
+        ],
+    )
+
+    main()
+
+    assert out_path.exists()
+    assert mock_query.called
+
+
+@patch("tcga_downloader.cli.run_gdc_download")
+def test_cli_integration_download_with_manifest(mock_download, tmp_path):
+    manifest_path = tmp_path / "manifest.tsv"
+    manifest_path.write_text("file_id\tfile_name\t...\n")
+
+    mock_download.return_value = None
+
+    from unittest.mock import patch as patch2
+    from tcga_downloader.cli import main
+
+    with patch2(
+        "sys.argv",
+        [
+            "tcga-downloader",
+            "download",
+            "--manifest",
+            str(manifest_path),
+            "--out-dir",
+            str(tmp_path / "data"),
+        ],
+    ):
+        main()
+
+    assert mock_download.called
+
+
+def test_cli_config_init_command(tmp_path):
+    config_path = tmp_path / "config.json"
+
+    from unittest.mock import patch
+    from tcga_downloader.cli import main
+    from tcga_downloader.config import load_config
+
+    with patch("sys.argv", ["tcga-downloader", "config", "--init", str(config_path)]):
+        main()
+
+    assert config_path.exists()
+
+    config = load_config(config_path)
+    assert config.query.project == "TCGA-BRCA"
+    assert config.query.data_type == "Gene Expression"

tests/test_interactive.py

@@ -0,0 +1,211 @@
+from unittest.mock import patch, MagicMock
+
+import pytest
+import requests
+
+from tcga_downloader.interactive import (
+    fetch_data_types,
+    fetch_projects,
+    interactive_select,
+    select_data_type,
+    select_project,
+)
+
+
+@patch("tcga_downloader.interactive.requests.get")
+def test_fetch_projects(mock_get):
+    mock_response = mock_get.return_value
+    mock_response.status_code = 200
+    mock_response.json.return_value = {
+        "data": {
+            "hits": [
+                {
+                    "project_id": "TCGA-BRCA",
+                    "name": "Breast Invasive Carcinoma",
+                    "primary_site": ["Breast"],
+                },
+                {
+                    "project_id": "TCGA-LUAD",
+                    "name": "Lung Adenocarcinoma",
+                    "primary_site": ["Lung"],
+                },
+            ]
+        }
+    }
+
+    projects = fetch_projects()
+
+    assert len(projects) == 2
+    assert projects[0]["project_id"] == "TCGA-BRCA"
+    assert projects[1]["project_id"] == "TCGA-LUAD"
+
+
+@patch("tcga_downloader.interactive.requests.post")
+def test_fetch_data_types(mock_post):
+    mock_response = mock_post.return_value
+    mock_response.status_code = 200
+    mock_response.json.return_value = {
+        "data": {
+            "aggregations": {
+                "data_type": {
+                    "buckets": [
+                        {"key": "Gene Expression", "doc_count": 100},
+                        {"key": "Copy Number Variation", "doc_count": 50},
+                        {"key": "DNA Methylation", "doc_count": 30},
+                    ]
+                }
+            }
+        }
+    }
+
+    data_types = fetch_data_types("TCGA-BRCA")
+
+    assert len(data_types) == 3
+    assert data_types[0] == "Gene Expression"
+    assert data_types[1] == "Copy Number Variation"
+    assert data_types[2] == "DNA Methylation"
+
+
+@patch("tcga_downloader.interactive.requests.post")
+def test_fetch_data_types_empty(mock_post):
+    mock_response = mock_post.return_value
+    mock_response.status_code = 200
+    mock_response.json.return_value = {"data": {"aggregations": {"data_type": {"buckets": []}}}}
+
+    data_types = fetch_data_types("TCGA-BRCA")
+
+    assert len(data_types) == 0
+
+
+@patch("tcga_downloader.interactive.requests.post")
+def test_fetch_data_types_api_error(mock_post):
+    mock_post.side_effect = requests.exceptions.HTTPError("API Error")
+
+    with pytest.raises(requests.exceptions.HTTPError):
+        fetch_data_types("TCGA-BRCA")
+
+
+@patch("tcga_downloader.interactive.requests.get")
+def test_fetch_projects_network_error(mock_get):
+    mock_get.side_effect = requests.exceptions.ConnectionError("Network error")
+
+    with pytest.raises(requests.exceptions.ConnectionError):
+        fetch_projects()
+
+
+@patch("tcga_downloader.interactive.questionary.select")
+def test_select_project(mock_select):
+    mock_question = MagicMock()
+    mock_select.return_value = mock_question
+    mock_question.ask.return_value = "TCGA-BRCA - Breast Invasive Carcinoma"
+
+    projects = [
+        {"project_id": "TCGA-BRCA", "name": "Breast Invasive Carcinoma"},
+        {"project_id": "TCGA-LUAD", "name": "Lung Adenocarcinoma"},
+    ]
+
+    selected = select_project(projects)
+
+    assert selected["project_id"] == "TCGA-BRCA"
+    assert selected["name"] == "Breast Invasive Carcinoma"
+
+
+@patch("tcga_downloader.interactive.questionary.select")
+def test_select_project_no_selection(mock_select):
+    mock_question = MagicMock()
+    mock_select.return_value = mock_question
+    mock_question.ask.return_value = None
+
+    projects = [
+        {"project_id": "TCGA-BRCA", "name": "Breast Invasive Carcinoma"},
+        {"project_id": "TCGA-LUAD", "name": "Lung Adenocarcinoma"},
+    ]
+
+    with pytest.raises(SystemExit) as exc_info:
+        select_project(projects)
+
+    assert exc_info.value.code == 0
+
+
+@patch("tcga_downloader.interactive.questionary.select")
+def test_select_data_type(mock_select):
+    mock_question = MagicMock()
+    mock_select.return_value = mock_question
+    mock_question.ask.return_value = "Gene Expression"
+
+    data_types = ["Gene Expression", "Copy Number Variation", "DNA Methylation"]
+
+    selected = select_data_type(data_types)
+
+    assert selected == "Gene Expression"
+
+
+@patch("tcga_downloader.interactive.questionary.select")
+def test_select_data_type_no_selection(mock_select):
+    mock_question = MagicMock()
+    mock_select.return_value = mock_question
+    mock_question.ask.return_value = None
+
+    data_types = ["Gene Expression", "Copy Number Variation", "DNA Methylation"]
+
+    with pytest.raises(SystemExit) as exc_info:
+        select_data_type(data_types)
+
+    assert exc_info.value.code == 0
+
+
+@patch("tcga_downloader.interactive.questionary.select")
+def test_select_data_type_empty_list(mock_select):
+    data_types = []
+
+    with pytest.raises(SystemExit) as exc_info:
+        select_data_type(data_types)
+
+    assert exc_info.value.code == 1
+    mock_select.assert_not_called()
+
+
+@patch("tcga_downloader.interactive.fetch_projects")
+@patch("tcga_downloader.interactive.fetch_data_types")
+@patch("tcga_downloader.interactive.select_project")
+@patch("tcga_downloader.interactive.select_data_type")
+def test_interactive_select_success(
+    mock_select_dt, mock_select_proj, mock_fetch_dt, mock_fetch_proj
+):
+    mock_fetch_proj.return_value = [
+        {"project_id": "TCGA-BRCA", "name": "Breast Invasive Carcinoma"}
+    ]
+    mock_select_proj.return_value = {"project_id": "TCGA-BRCA", "name": "Breast Invasive Carcinoma"}
+    mock_fetch_dt.return_value = ["Gene Expression", "Copy Number Variation"]
+    mock_select_dt.return_value = "Gene Expression"
+
+    project_id, data_type = interactive_select()
+
+    assert project_id == "TCGA-BRCA"
+    assert data_type == "Gene Expression"
+    mock_fetch_proj.assert_called_once()
+    mock_fetch_dt.assert_called_once_with("TCGA-BRCA")
+    mock_select_proj.assert_called_once()
+    mock_select_dt.assert_called_once()
+
+
+@patch("tcga_downloader.interactive.fetch_projects")
+@patch("tcga_downloader.interactive.fetch_data_types")
+@patch("tcga_downloader.interactive.select_project")
+@patch("tcga_downloader.interactive.select_data_type")
+def test_interactive_select_no_project(
+    mock_select_dt, mock_select_proj, mock_fetch_dt, mock_fetch_proj
+):
+    mock_fetch_proj.return_value = [
+        {"project_id": "TCGA-BRCA", "name": "Breast Invasive Carcinoma"}
+    ]
+    mock_select_proj.side_effect = SystemExit(0)
+
+    with pytest.raises(SystemExit) as exc_info:
+        interactive_select()
+
+    assert exc_info.value.code == 0
+    mock_fetch_proj.assert_called_once()
+    mock_select_proj.assert_called_once()
+    mock_fetch_dt.assert_not_called()
+    mock_select_dt.assert_not_called()

tests/test_manifest.py

@@ -1,4 +1,12 @@
-from tcga_downloader.manifest import ManifestRecord, write_manifest, load_manifest
+from tcga_downloader.manifest import (
+    ManifestRecord,
+    format_manifest_stats,
+    get_manifest_stats,
+    load_manifest,
+    validate_files_against_manifest,
+    validate_manifest,
+    write_manifest,
+)
 
 
 def test_manifest_roundtrip_tsv(tmp_path):
@@ -15,4 +23,217 @@ def test_manifest_roundtrip_tsv(tmp_path):
     path = tmp_path / "m.tsv"
     write_manifest(records, path, fmt="tsv")
     loaded = load_manifest(path)
+
+    expected = [
+        ManifestRecord(
+            file_id="f1",
+            file_name="a.tsv",
+            data_type="Unknown",
+            data_format="Unknown",
+            size=123,
+            md5="abc",
+        )
+    ]
+    assert loaded == expected
+
+
+def test_manifest_roundtrip_json(tmp_path):
+    records = [
+        ManifestRecord(
+            file_id="f1",
+            file_name="a.tsv",
+            data_type="Gene Expression",
+            data_format="TSV",
+            size=123,
+            md5="abc",
+        )
+    ]
+    path = tmp_path / "m.json"
+    write_manifest(records, path, fmt="json")
+    loaded = load_manifest(path)
     assert loaded == records
+
+
+def test_get_manifest_stats():
+    records = [
+        ManifestRecord(
+            file_id="f1",
+            file_name="a.tsv",
+            data_type="Gene Expression",
+            data_format="TSV",
+            size=1000,
+            md5="abc",
+        ),
+        ManifestRecord(
+            file_id="f2",
+            file_name="b.tsv",
+            data_type="Gene Expression",
+            data_format="TSV",
+            size=2000,
+            md5="def",
+        ),
+        ManifestRecord(
+            file_id="f3",
+            file_name="c.tsv",
+            data_type="Copy Number",
+            data_format="TSV",
+            size=3000,
+            md5="ghi",
+        ),
+    ]
+
+    stats = get_manifest_stats(records)
+
+    assert stats["file_count"] == 3
+    assert stats["total_size_bytes"] == 6000
+    assert stats["total_size_mb"] == 6000 / (1024 * 1024)
+    assert stats["total_size_gb"] == 6000 / (1024 * 1024 * 1024)
+    assert stats["data_types"] == {"Gene Expression": 2, "Copy Number": 1}
+    assert stats["data_formats"] == {"TSV": 3}
+
+
+def test_format_manifest_stats():
+    records = [
+        ManifestRecord(
+            file_id="f1",
+            file_name="a.tsv",
+            data_type="Gene Expression",
+            data_format="TSV",
+            size=1000,
+            md5="abc",
+        ),
+    ]
+
+    stats = get_manifest_stats(records)
+    formatted = format_manifest_stats(stats)
+
+    assert "File count: 1" in formatted
+    assert "Total size:" in formatted
+    assert "Data types:" in formatted
+    assert "Gene Expression: 1" in formatted
+    assert "Data formats:" in formatted
+    assert "TSV: 1" in formatted
+
+
+def test_validate_manifest_valid():
+    records = [
+        ManifestRecord(
+            file_id="f1",
+            file_name="a.tsv",
+            data_type="Gene Expression",
+            data_format="TSV",
+            size=123,
+            md5="a" * 32,
+        )
+    ]
+    errors = validate_manifest(records)
+    assert len(errors) == 0
+
+
+def test_validate_manifest_missing_fields():
+    records = [
+        ManifestRecord(
+            file_id="",
+            file_name="a.tsv",
+            data_type="Gene Expression",
+            data_format="TSV",
+            size=123,
+            md5="a" * 32,
+        ),
+        ManifestRecord(
+            file_id="f2",
+            file_name="",
+            data_type="Gene Expression",
+            data_format="TSV",
+            size=123,
+            md5="a" * 32,
+        ),
+        ManifestRecord(
+            file_id="f3", file_name="c.tsv", data_type="", data_format="TSV", size=123, md5="a" * 32
+        ),
+        ManifestRecord(
+            file_id="f4",
+            file_name="d.tsv",
+            data_type="Gene Expression",
+            data_format="",
+            size=123,
+            md5="a" * 32,
+        ),
+    ]
+    errors = validate_manifest(records)
+    assert len(errors) == 4
+
+
+def test_validate_manifest_invalid_md5():
+    records = [
+        ManifestRecord(
+            file_id="f1",
+            file_name="a.tsv",
+            data_type="Gene Expression",
+            data_format="TSV",
+            size=123,
+            md5="invalid",
+        )
+    ]
+    errors = validate_manifest(records)
+    assert len(errors) == 1
+    assert "MD5" in errors[0]
+
+
+def test_validate_manifest_invalid_size():
+    records = [
+        ManifestRecord(
+            file_id="f1",
+            file_name="a.tsv",
+            data_type="Gene Expression",
+            data_format="TSV",
+            size=-1,
+            md5="a" * 32,
+        )
+    ]
+    errors = validate_manifest(records)
+    assert len(errors) == 1
+    assert "size" in errors[0].lower()
+
+
+def test_validate_files_against_manifest(tmp_path):
+    records = [
+        ManifestRecord(
+            file_id="f1",
+            file_name="file1.txt",
+            data_type="Gene Expression",
+            data_format="TSV",
+            size=123,
+            md5="d41d8cd98f00b204e9800998ecf8427e",
+        ),
+    ]
+    data_dir = tmp_path / "data"
+    data_dir.mkdir()
+
+    file1 = data_dir / "file1.txt"
+    file1.write_text("Hello")
+
+    missing, checksum_errors = validate_files_against_manifest(records, data_dir)
+    assert len(missing) == 0
+    assert len(checksum_errors) == 1
+    assert "file1.txt" in checksum_errors[0]
+
+
+def test_validate_files_missing(tmp_path):
+    records = [
+        ManifestRecord(
+            file_id="f1",
+            file_name="file1.txt",
+            data_type="Gene Expression",
+            data_format="TSV",
+            size=123,
+            md5="a" * 32,
+        ),
+    ]
+    data_dir = tmp_path / "data"
+    data_dir.mkdir()
+
+    missing, checksum_errors = validate_files_against_manifest(records, data_dir)
+    assert len(missing) == 1
+    assert "file1.txt" in missing[0]
+    assert len(checksum_errors) == 0

tests/test_query.py

@@ -1,7 +1,76 @@
-from tcga_downloader.query import build_filters
+from unittest.mock import patch
+
+from tcga_downloader.query import (
+    build_filters,
+    query_multiple_projects,
+)
 
 
 def test_build_filters_project_and_type():
     filters = build_filters(project="TCGA-BRCA", data_type="Gene Expression")
     assert filters["op"] == "and"
     assert filters["content"][0]["content"]["field"] == "cases.project.project_id"
+    assert len(filters["content"]) == 2
+
+
+def test_build_filters_with_sample_type():
+    filters = build_filters(
+        project="TCGA-BRCA", data_type="Gene Expression", sample_type="Primary Tumor"
+    )
+    assert filters["op"] == "and"
+    assert len(filters["content"]) == 3
+    assert any(f["content"]["field"] == "samples.sample_type" for f in filters["content"])
+
+
+def test_build_filters_with_platform():
+    filters = build_filters(
+        project="TCGA-BRCA", data_type="Gene Expression", platform="Illumina HiSeq"
+    )
+    assert filters["op"] == "and"
+    assert len(filters["content"]) == 3
+    assert any(f["content"]["field"] == "platform" for f in filters["content"])
+
+
+def test_build_filters_all_options():
+    filters = build_filters(
+        project="TCGA-BRCA",
+        data_type="Gene Expression",
+        sample_type="Primary Tumor",
+        platform="Illumina HiSeq",
+    )
+    assert filters["op"] == "and"
+    assert len(filters["content"]) == 4
+
+
+@patch("tcga_downloader.query.requests.post")
+def test_query_multiple_projects(mock_post):
+    mock_response = mock_post.return_value
+    mock_response.json.return_value = {
+        "data": {
+            "hits": [
+                {
+                    "file_id": "f1",
+                    "file_name": "file1.tsv",
+                    "data_type": "Gene Expression",
+                    "data_format": "TSV",
+                    "file_size": 100,
+                    "md5sum": "abc123",
+                },
+                {
+                    "file_id": "f2",
+                    "file_name": "file2.tsv",
+                    "data_type": "Gene Expression",
+                    "data_format": "TSV",
+                    "file_size": 200,
+                    "md5sum": "def456",
+                },
+            ]
+        }
+    }
+    mock_response.raise_for_status = lambda: None
+
+    projects = ["TCGA-BRCA", "TCGA-LUAD"]
+    results = query_multiple_projects(projects, "Gene Expression")
+
+    assert len(results) == 4
+    assert mock_post.call_count == 2

uv.lock

@@ -0,0 +1,735 @@
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+
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+    { name = "mypy-extensions" },
+    { name = "packaging" },
+    { name = "pathspec" },
+    { name = "platformdirs" },
+    { name = "pytokens" },
+]
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