KnowledgeBase Content Details

July 08, 2019

Question:

How do you Import data to Columbus using the Command Line Interface.

Answer:


Image data can be imported to Columbus using an Acapella script. Please download the required resources from here

Two versions of the Script are available.

Standard Columbus systems should use import.script

ColumbusPlus systems should use the updated import-cluster.script

The above download also includes "ArrayScan TIF" image data if required.

The image data to be imported must be available to the server's file system. Essentially you can either copy the file/s to the server or you could mount a share to the server with the files residing on it. Perhaps one of the more common shares would be a Windows share to the Linux system, in which case please review this RedHat Technical Note.

Move the script to the server using a suitable application such as WinSCP. Connect to the server's Command Line Interface then change to the path containing the script file.

Input parameters to the script are specified by the -s option.

The full list of script parameters is as follows:

ScreenId: ID of the screen to upload data to

ImportType: Name of the dataset type (take name from Columbus UI "import Type" option list on import page)

DatasetFolder: Folder containing the dataset to

Host: Columbus host name or IP

User: Columbus user account name

Password: Columbus user account password

An additional parameter is available in the import-cluster.script

ForwardPath: directory where columbus intermediately stores imported images before transferring them to the cluster; typically "/OMERO/OMERO4_4/s3-upload"

The image import is executed by command line as follows substituting * with the actual value:

$ acapella -s User=* -s Password=* -s Host=* -s ImportType=* -s DatasetFolder=* -s ScreenName=* -s ForwardPath=* import-cluster.script

For instance in the following example an "ArrayScan TIF", in the path "/home/columbus/ImportTest", will be imported to Screen named "Test" using the "columbus" user. Image data being fowarded to the typcial ForwardPath.

$ acapella -s User="columbus" -s Password="columbus" -s Host="localhost" -s ImportType="ArrayScan TIF" -s DatasetFolder=/home/columbus/ImportTest -s ScreenName="Test" -s ForwardPath=/OMERO/OMERO4_4/s3-upload import-cluster.script

In the case of import.script the parameter ForwardPath should be omitted.

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