[GeneX-dev] Questions about command line interface for loading "bulk" data

[Hrishikesh D. <hde...@gm...>]

Jason,

I hope there were no problems in Madurai,coz of tsunami?

I want to give a shot at using command line interface to load "bulk" 
data. Could you please explain this part:

You use it like:
 >
 >   run-mbad-insert.pl --file /tmp/file.txt --user genex --pass XXX \
 >      --ad 1133 --exp 1195 --qt 756 --fe 752 --ro 671 --rw 679

1)What are these numbers? I understand "ad" stands for ArrayDesign but 
what are "ro" and "rw", meanwhile you are at it could you explain all, 
this i will doc them.
2)How do i get them?
3)I assume the .CEL files (they are not binary) which i have do not need 
to be renamed to .txt

Eagerly waiting for your reply.

Thanks,
Hrishi



Jason E. Stewart wrote:
> Hi Hrishi,
> 
> Sorry, I let this one slip.
> 
> hde...@gm... writes:
> 
> 
>>Can one do a "bulk" upload of data?
>>I have like 200 .CEL files for the dataset!
> 
> 
> Yes. 
> 
> You can either select 200 files in the GUI - maybe a bit tedious, or
> you can use the command line interface. To learn how to use it type:
> 
>   /usr/local/genex/bin/mbad-insert.pl --man
> 
> this spits out the documentation (you can use --help for the brief
> docs if you just want a reminder what the required options are). All
> the genex Perl scripts honor the --help flag, some of the more
> important ones now honor --man, I convert the scripts a little at a
> time to the new self-documentation system.
> 
> Anyway...
> 
>       required parameters:
>         --username=name   : the DB username to login as
>         --password=word   : the DB password to login with
>         --mba_name=name   : the MeasuredBioAssay name (list)
>         --pba_name=name   : the PhysicalBioAssay name (list)
>         --ad_pk=pk        : the ArrayDesign used
>         --exp_pk=pk       : the primary key of the Experiment
>         --qtdim_pk=pk     : the primary key of the QuantitationTypeDimension
>         --fe_sw_pk=pk     : the primary key of the FeatureExtraction SW
>         --ro_group_id=pk  : the primary key of the read-only group
>         --rw_group_id=pk  : the primary key of the read/write group
> 
> are the required params. You need to use the genex browsing interface
> to get all the pkey numbers for Experiment, ArrayDesign, QTD, FE SW,
> read and write groups. The only tricky bit is --mba_name and
> --pba_name. These need to be specified once for each input file - in
> the same order that you list the files.
> 
> To make things easier, I just wrote a helper utility,
> run-mbad-insert.pl, that reads the name and file information in from a
> tab-delimited text file.
> 
> You use it like:
> 
>   run-mbad-insert.pl --file /tmp/file.txt --user genex --pass XXX \
>      --ad 1133 --exp 1195 --qt 756 --fe 752 --ro 671 --rw 679
> 
> here is an example input file:
> 
> /usr/local/genex/uploads/genex/200-short.txt	PBA 200-short2	MBA 200-short2
> /usr/local/genex/uploads/genex/201-short.txt	PBA 201-short2	MBA 201-short2
> /usr/local/genex/uploads/genex/202-short.txt	PBA 202-short2	MBA 202-short2
> 
> spaces are allowed in the names, just not tabs. run-mbad-insert.pl is
> installed and tested on genex2 in /usr/local/genex/bin.
> 
> BTW - the svn checkout directory on genex2 is:
> 
>   /home/jasons/work/genex-server
> 
> in case you need to update something.
> 
> Cheers,
> jas.
> 
> 
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