py4cytoscape.tools.import_file_from_url

import_file_from_url(source_url, dest_file, overwrite=True, base_url='http://127.0.0.1:1234/v1')[source]

Transfer a cloud-based file to the current Cytoscape directory.

The source URL identifies a file to be transferred from a cloud resource to either the to the current Cytoscape directory (if executing on the Cytoscape workstation) or sandbox (if executing on a remote server or a sandbox was explicitly created). If the destination file already exists, it is overwritten. The dest_file can be an absolute path if the workflow is executing on the local Cytoscape workstation.

Supported URLs include:

Raw URL: URL directly references the file to download (e.g., http://tpsoft.com/museum_images/IBM%20PC.JPG

Dropbox: Use the standard Dropbox Get Link feature to create the source_url link in the clipboard (e.g., https://www.dropbox.com/s/r15azh0xb53smu1/GDS112_full.soft?dl=0)

GDrive: Use the standard Google Drive Get Link feature to create the source_url link in the clipboard (e.g., https://drive.google.com/file/d/12sJaKQQbesF10xsrbgiNtUcqCQYY1YI3/view?usp=sharing)

OneDrive: Use the OneDrive web site to right click on the file, choose the Embed menu option, then copy the URL in the iframe’s src parameter into the clipboard (e.g., https://onedrive.live.com/embed?cid=C357475E90DD89C4&resid=C357475E90DD89C4%217207&authkey=ACEU5LrVtI_jWTU)

GitHub: Use the GitHub web site to show the file or a link to it, and capture the URL in the clipboard (e.g., https://github.com/cytoscape/file-transfer-app/blob/master/test_data/GDS112_full.soft)

Note that GitHub enforces a limit on the size of a file that can be stored there. We advise that you take this into account when choosing a cloud service for your files.

When you capture a URL in the clipboard, you should copy it into your program for use with this function.

This function is most useful for Notebooks running on the local Cytoscape workstation. For Notebooks that could run on a remote server, consider using sandbox_url_to() and related sandbox functions.

Parameters

source_url (str) – URL addressing cloud file to download
dest_file (str) – Name of file to write (as Cytoscape-relative path, absolute file system path or sandbox-relative path)
overwrite (bool) – False causes error if dest_file already exists; True replaces it if it exists
base_url (str) – Ignore unless you need to specify a custom domain, port or version to connect to the CyREST API. Default is http://localhost:1234 and the latest version of the CyREST API supported by this version of py4cytoscape.

Returns

{‘filePath’: <new file’s absolute path in Cytoscape workstation>, ‘fileByteCount’: number of bytes read}

Return type

dict

Raises

CyError – if file name or URL is invalid
requests.exceptions.HTTPError – if can’t connect to Cytoscape, Cytoscape returns an error, or sandbox is invalid

Examples

>>> import_file_from_url('https://www.dropbox.com/s/r15azh0xb53smu1/GDS112_full.soft?dl=0', 'test file')
{'filePath': 'C:\Users\CyDeveloper\CytoscapeConfiguration\filetransfer\default_sandbox\test file', 'fileByteCount': 5536880}
>>> import_file_from_url('https://www.dropbox.com/s/r15azh0xb53smu1/GDS112_full.soft?dl=0', 'test file', overwrite=True)
{'filePath': 'C:\Users\CyDeveloper\CytoscapeConfiguration\filetransfer\default_sandbox\test file', 'fileByteCount': 5536880}