FileTransfer

File system proxy for remote Jupyter Notebooks
Categories: python, utility
*__Download this app if__ you are creating an automated Cytoscape workflow using Python and [py4cytoscape](https://py4cytoscape.readthedocs.io/en/latest/) in a Jupyter Notebook running on a remote server (e.g., [Google Colab](https://colab.research.google.com/) or [GenePattern Notebook](https://notebook.genepattern.org/)).* The FileTransfer app supports Cytoscape workflow execution in a Jupyter Notebook executing on a remote server. Such Notebooks can be written in Python (via [py4cytoscape](https://github.com/cytoscape/py4cytoscape)) or other languages when/if such support becomes available for them. To execute a workflow, a remote Notebook must have bi-directional communication with a workstation-based Cytoscape instance, which is automatically provided by the [Jupyter-Bridge](https://github.com/cytoscape/jupyter-bridge). Given this link, the FileTransfer app enables a workflow author to send files (e.g., .cys and .csv) to a Cytoscape workstation, and then fetch Cytoscape files (e.g., png and .pdf) for further analysis. This app is not necessary for workflows executing directly on the Cytoscape workstation where the Python code shares a file system with Cytoscape, but it is crucial for workflows executing on remote servers. To understand how to execute Cytoscape workflows in a Jupyter Notebook running on a remote server, see [this article](https://py4cytoscape.readthedocs.io/en/latest/concepts.html#jupyter-notebook). This app has no user interface, and is intended to be called by Jupyter Notebooks via CyREST over Jupyter-Bridge. For more information on this app, see the [functional documentation in GitHub](https://github.com/cytoscape/file-transfer-app) or in the Swagger "filetransfer" section accessible from Cytoscape via the **Help | Automation | CyREST Command API** menu. To understand the sandbox features supported by this app, see [this article](https://py4cytoscape.readthedocs.io/en/latest/concepts.html#sandboxing).

1.0

Works with Cytoscape 3.8

Release Notes

Provides sandbox functionality, including: - setSandbox - removeSandbox - getFileInfo - removeFile - toSandbox - fromSandbox

CYTOSCAPE 3

Version 1.0

License Click here

Released 5 Oct 2020

Works with Cytoscape 3.8

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