importFileFromUrl: importFileFromUrl

In cytoscape/RCy3: Functions to Access and Control Cytoscape

importFileFromUrl

Description

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 'destFile' 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 Dropbox: Use the standard Dropbox 'Get Link' feature to create the 'sourceUrl' 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 'sourceUrl' 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 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 sandboxUrlTo() and related sandbox functions.

Usage

importFileFromUrl(
  sourceURL,
  destFile,
  overwrite = TRUE,
  base.url = .defaultBaseUrl
)

Arguments

sourceURL	URL addressing cloud file to download
destFile	Name of file in the R workflow's file system ... if None, use file name in source_file
overwrite	Name of sandbox containing file. None means "the current sandbox".
base.url	Ignore unless you need to specify a custom domain, port or version to connect to the CyREST API. Default is http://127.0.0.1:1234 and the latest version of the CyREST API supported by this version of RCy3.

Value

dict: 'filePath': <new file's absolute path in Cytoscape workstation>, 'fileByteCount': number of bytes read

Examples

importFileFromUrl()

cytoscape/RCy3 documentation built on April 7, 2024, 2:17 p.m.