landingzones 1.1.1

Automated data transfer system using rsync and cron

Landing Zones

Automated data transfer system using rsync with cron job generation.

Quick Start

# Install
pip install -e .

# Generate cron files, transfer scripts, and validation wrappers
landingzones --help
landingzones --config config/config.yaml build
landingzones build

# Check deployment readiness
landingzones validate deployment

# Run a hop-local validation
landingzones validate hop <flow_group> preflight
landingzones validate hop <flow_group>

# Run toy data through the configured flows
landingzones validate integration

Project Structure

landingzones/
├── src/landingzones/           # Main package
│   ├── cli.py                  # Top-level operator CLI
│   ├── generate_cron_files.py  # Cron generation tool
│   ├── check_deployment_readiness.py
│   ├── plot_transfer_status.py
│   └── config/transfers.tsv    # Default config
├── input/                      # Default input directory
├── output/                     # Default output directory
│   ├── crontab.d/              # Generated cron files
│   ├── scripts/                # Generated transfer scripts
│   └── validation_scripts/     # Generated validation wrappers
├── log/                        # Default log directory
├── tests/                      # Test suite
├── pyproject.toml              # Package config
└── README.md

Configuration

The system is configured via a tab-separated transfers.tsv file:

Column	Description	Example
identifiers	Unique transfer ID used for generated shell script names	transfer_001, gridion_to_calc
runtime_id	Required deploy/artifact identity used for cron grouping and filtering	calc_prod.f041664
system	Configured system key used for managed paths and flock settings	server1, localhost
users	Optional user/account context for review and generated headers	user1, local
source	Source directory path	/srv/data/src/
source_port	SSH port for remote sources (optional)	2222
destination	Destination (local or remote)	user@host:/dest/
destination_port	SSH port (optional)	225
rsync_options	Additional rsync flags	--chown=:group
io_nice	Optional ionice settings for rsync	-c2 -n7
log_file	Log file name resolved under the system log folder	transfers.log
flock_file	Lock file name resolved under the system flock folder	transfer.lock

Example

identifiers	runtime_id	system	users	source	source_port	destination	destination_port	rsync_options	io_nice	log_file	flock_file
local_copy	localhost_test.testuser	localhost	testuser	input/*		output/				transfers.log	landingzones.lock

CLI Commands

# Generate cron files with defaults
landingzones build

# Generate only selected runtime IDs from a shared transfers.tsv
landingzones build --runtime-id calc_prod.f041664 --runtime-id calc_prod.F041668

# Check deployment readiness
landingzones validate deployment

# Run a hop-local validation wrapper through the CLI
landingzones validate hop <flow_group>

# Seed toy data and run the real scripts/logs/locks
landingzones validate integration

# Generate an HTML health dashboard from a shared transfer TSV log
landingzones report transfers output/log/Landing_Zone_calc.transfers.tsv

Generated Cron Format

*/15 * * * * /bin/sh output/scripts/local_copy.sh

Installation

# Development mode
pip install -e ".[report]"

# With test dependencies
pip install -e ".[test]"

# Production
pip install .

Lab Sequencer Bundle

For lab machines where a managed Python environment is awkward, build a relocatable bundle using a python-build-standalone runtime. Build it on a machine that matches the lab sequencer OS, architecture, and libc family.

Download or provide a python-build-standalone install_only archive, then run:

cd app
python scripts/build_python_standalone_bundle.py --python-archive /path/to/cpython-*-install_only.tar.*

If you already extracted the runtime, point at its Python executable instead:

python scripts/build_python_standalone_bundle.py --python-bin /path/to/python/install/bin/python3

With Pixi, the app includes a packaging task that downloads a matching python-build-standalone runtime using getpybs:

cd app
pixi run build-standalone

Build the lab Linux artifact on Linux. A bundle built on macOS contains a macOS Python runtime and will fail on the sequencer with cannot execute binary file. Before copying a tarball to the lab host, verify the bundled runtime:

file packaging/dist/landingzones-standalone/python/bin/python3
packaging/dist/landingzones-standalone/python/bin/python3 -c "import platform; print(platform.system(), platform.machine())"

Expected for the current lab machines is Linux/x86_64.

The standalone bundle installs the core operator CLI without pandas, so it is intended for build, validate, and deploy on locked-down lab machines. landingzones report transfers remains a reporting extra and should run from an environment with landingzones[report] installed.

The same bundle can be produced by the GitHub Actions workflow Build Standalone Bundle. Run it manually from Actions, or push a v* tag. It uploads landingzones-standalone-linux-x86_64 containing:

landingzones-standalone-linux-x86_64.tar.gz

For v* tags, the workflow also creates or updates the matching GitHub Release and uploads landingzones-standalone-linux-x86_64.tar.gz as a release asset.

The bundle is written to:

app/packaging/dist/landingzones-standalone/
app/packaging/dist/landingzones-standalone.tar.gz

Copy the tarball to the lab machine, extract it, and run it like the normal CLI:

./landingzones --config config/config.yaml build
./landingzones --config config/config.yaml validate deployment

For offline builds, pass --wheelhouse /path/to/wheels so dependencies are installed from local wheels. The legacy shell wrapper still works:

./scripts/build_python_standalone_bundle.sh --python-archive /path/to/cpython-*-install_only.tar.*

The bundle carries Python and Python packages only; the target machine still needs system tools such as rsync, ssh, flock, curl, and cron.

Testing

# Run all tests
pytest

# Verbose
pytest -v

# With coverage
pytest --cov=landingzones --cov-report=html

# Specific test
pytest tests/test_generate_cron_files.py::TestClassName::test_method

Validation Modes

The operator-facing validation surface has three modes:

• landingzones validate deployment
• landingzones validate hop <flow_group> [preflight|run]
• landingzones validate integration

landingzones validate integration is the heavier integration-style test mode. It copies toy data into the configured starting locations, generates the real shell scripts, and runs the transfers using the normal log and flock paths. Use landingzones validate integration --slow when you want the harness to print the result of each completed step and wait for Enter before running the next one.

Generated Validation Wrappers

Each flow_group with exactly one is_entry_point=TRUE row gets a generated wrapper in the configured validation-scripts directory:

output/validation_scripts/lz_run_validation_<flow_group>.sh

Use landingzones validate hop <flow_group> as the main interface. The generated wrapper remains available directly and bakes in:

• the entry directory for that flow
• the immediate next hop for preflight checks
• the default fixture directory under test_data
• the flow_group and producer labels used in the LZTEST_... folder name

Typical usage:

# Regenerate scripts after changing config/transfers
landingzones --config config/config.yaml build

# Check only the current hop structure and immediate next-hop access
landingzones validate hop local_labnet_to_calc_seqdata preflight

# Inject a validation run with the baked-in defaults
landingzones validate hop local_labnet_to_calc_seqdata

# Inject a validation run with an explicit token suffix
landingzones validate hop local_labnet_to_calc_seqdata --token ABCD

# Direct wrapper execution still works if needed
./output/validation_scripts/lz_run_validation_local_labnet_to_calc_seqdata.sh

Wrapper/CLI behavior:

• no action defaults to run
• preflight checks only the current hop plus its immediate next hop
• options-only invocation such as --token ABCD also defaults to run

Use landingzones validate hop for lightweight producer-side validation. Use landingzones validate integration when you want the heavier integration test that seeds toy data and executes the full generated transfer chain.

Required config in your deployment config.yaml:

transfers_file: input/transfers.tsv
test_data: tests/toy_data/
validation_scripts_dir: output/validation_scripts/
rit_managed_locations:
  test_local: tests/test_local
flock_paths:
  test_local: /opt/homebrew/bin/flock
rit_managed_folder_structure:
  log: output/log/
  flock: output/flock/
  sh_output: output/scripts/
  crontabs: output/crontab.d/

Typical local fixture layout:

deploy/local/
├── config/config.yaml
├── input/transfers.tsv
├── tests/toy_data/
└── tests/test_local/

How to run it:

# Run from the deployment root that owns config/, input/, and tests/
cd deploy/local

# Generate deployment artifacts
landingzones build --config config/config.yaml

# Run the heavier integration test
landingzones --config config/config.yaml validate integration

What it does:

• Filters transfers.tsv to the current system and user
• Seeds each initial source root from test_data
• Generates scripts into the configured sh_output directory
• Uses the configured log and flock directories
• Executes the scripts in transfer order
• Validates that the seeded top-level directories reached the terminal destinations

After a successful run it asks whether you want cleanup. Answer y to remove the propagated test directories plus generated log and lock artifacts so the next run starts from the initial state. Answer n to inspect the final tree and logs.

Deployment

1. Configure transfers.tsv with your routes
2. Generate cron files: landingzones build
3. Deploy:

   cp output/crontab.d/*.cron ~/crontab.d/
   cat ~/crontab.d/*.cron | crontab -
   

Or use automated deployment:

landingzones validate deployment

Development

# Make changes in src/landingzones/
# Run tests
pytest

# Test CLI
landingzones --help

Requirements

• Python >= 3.8
• PyYAML >= 5.0.0
• pandas >= 1.0.0 only for landingzones report transfers / landingzones[report]
• System: rsync, ssh, flock