ImageScanInfoLoader.pm
 

Location

Name

Description

Synopsis

Options and Arguments

Important

More

Bugs

Author

 


Location    

    /GUS/perl/lib/GUS30/GA_plugins/RA_plugins

Name    

    ImageScanInfoLoader.pm

Description   

    This is a plug-in that updates RAD3 array image scan information tables including Acquisition, AcquisitionParam, RelatedAcquisition, Quantification, QuantificationParam and RelatedQuantification.

Synopsis   

    ga  RA_plugins::ImageScanInfoLoader  --help

    ga  RA_plugins::ImageScanInfoLoader  --cfg_file <cfgFileName>   --assay_id <number>  --debug > logfile

    ga  RA_plugins::ImageScanInfoLoader  --cfg_file <cfgFileName>   --assay_id <number>  --is_related  --debug > logfile

    ga  RA_plugins::ImageScanInfoLoader  --cfg_file <cfgFileName>   --assay_id <number>  --acquisition_only!  --debug > logfile

    ga  RA_plugins::ImageScanInfoLoader  --cfg_file <cfgFileName>   --assay_id <number>  --is_related  --commit > logfile

 

Options and Arguments   

 
--debug            optional boolean, default 0 debugging output,
--help  optional boolean, default 0 get usage; same as usage
--verbose optional boolean, default 0 lots of output
--commit optional boolean, default 0 if set, the plug-in will commit the data to database
--cfg_file mandatory string, must be full-path file name This file maps the values for attributes in image scan information tables.
--assay_id mandatory number, must be one of assay_id in RAD3::Assay table set value for the Acquisition.assay_id
--is_related optional boolean, default 0 if set, will load image scan information for the associated channel.
--acquisition_only! optional boolean, default 0 if set, will only update  value for the Acquisition, AcquisitionParam, RelatedAcquisition
--user             optional string, must be one of user in Core::UserInfo table set value for row_user_id. default: (from your .gus30.cfg file)
--group             optional string, must be one of group in Core::GroupInfo table set value for row_group_id. default: (from your .gus30.cfg file)
--project optional string, must be one of project in Core::ProjectInfo table set value for row_project_id. default: (from your .gus30.cfg file)

Important   

    Before you can run this plug-in you need to create the Perl objects for the views you will be loading, should these objects not exist yet.

    The plug-in outputs a print statement to STDOUT (for possible redirection to a log file) which lists the number of data file lines read (counting empty lines, but not counting the header and the lines preceding it in the data file) and any warning statement(s) regarding data lines which have not been loaded into RAD3.

    Make sure your .gus30.cfg file contains the correct login name, which should be RAD3.

More   

cfg_file   

This configuration file tells the plug-in how to map table attributes to values. Here is a detailed description of the format:

You should save this file in the CVS repository, in the directory GUS/perl/lib/GUS30/GA_plugins/RA_plugins/cfg_files (the name of this file, stripped of its path, is stored by the ga as an algorithm parameter).

Bugs   

To be reported

Author   

Junmin Liu, junmin@pcbi.upenn.edu