Smart middleware for working with a variety of storage media with Scientific Computing datasets. Supports Python 2.7 and Python 3.*.
This tool was used in in this paper:
"Rapid development of cloud-native intelligent data pipelines for scientific data streams using the HASTE Toolkit"
https://www.biorxiv.org/content/10.1101/2020.09.13.274779v1
To reproduce the results from that paper, deploy and run the application according to the instructions at https://github.com/HASTE-project/k8s-deployments
pip install haste-storage-client
To send blobs to Pachyderm, python-pachyderm is required. Because of this issue, it needs to be installed manually:
git clone [email protected]:pachyderm/python-pachyderm.git
cd python-pachyderm
pip3 install -e .
Note that Pachyderm no longer supports Python 2.x
See example.py.
pip3 install -U pytest
pytest tests
Optionally, place haste_storage_client_config.json in ~/.haste/ (or windows equivalent),
instead of specifying config in constructor.
It isn't possible to connect to the database server from outside the SNIC cloud, so for local dev/testing you'll need to use port forwarding from another machine. https://help.ubuntu.com/community/SSH/OpenSSH/PortForwarding
Ben Blamey, Andreas Hellander