FW: cPath Question from over seas.
Gary Bader
FYI
-----Original Message-----
From: iain.d...@gsk.com
[mailto:iain.d...@gsk.com]
Sent: Monday, August 16, 2004 4:29
AM
To: ba...@cbio.mskcc.org
Subject: RE: cPath Question from
over seas.
Hi Gary,
Superb
news, that will make my life a lot easier. I've currently got a windows
system but was planning a linux setup in the next week or so. So I should
be covered. I had seen admin.pl, but not investigated it.
I'll
give it a go later this week.
Thanks
for the help.
Iain
Keddie
|
"Gary Bader" <ba...@cbio.mskcc.org> 13-Aug-2004 15:30 |
|
Hi Iain,
Cool. Yes, we have a command line
admin tool. It is cpath/bin/admin.pl and should work for you on Linux,
but may need some modification if you’re running it from Windows.
It seems we need to update our install documentation to mention this, so
thanks for asking the question.
Basically, admin.pl runs a java program that
does all the work, which is org.mskcc.pathdb.tools.Admin Here are the
steps to run the admin tool:
1.
Build cpath using ant (this compiles the
Java files of the admin tool)
2.
Set CPATH_HOME to be the absolute path of
the cpath directory (that was contained in the distribution file, not where the
actual data sits)
3.
Go to the bin directory and run admin.pl.
If all is working, you should get the following usage message:
bader@cbio:~/sander/cpath/bin$
../admin.pl
cPath
Admin. cPath Version: 0.3 (Beta)
Copyright
(c) 2004 Memorial Sloan-Kettering Cancer Center.
Administration
Program for the cPath Database
Usage:
admin.pl [OPTIONS] command
-u, -u=name Database User Name
-p, -p=name Database Password
-f, -f=filename Name of File / Directory
-d, Shows all Debug/Log Messages
-x Skips Validation of External
References
Where
command is a one of:
import Imports Specified File.
Used to Import PSI-MI
Files or External Reference Files.
index Indexes All Items in cPath
precompute Precomputes all queries in specified config file
You
should be able to give this script a directory containing all of your PSI
formatted files and it will load them all in. Let me know if you have any
problems.
-Gary
-----Original
Message-----
From: iain.d...@gsk.com [mailto:iain.d...@gsk.com]
Sent: Friday, August 13, 2004 5:04 AM
To: Bad...@mskcc.org
Cc: john.t.a...@gsk.com
Subject: cPath Question from over seas.
Gary,
My name is Iain Keddie, I am carrying out some pathways work for John Armstrong
who gave me your address. While researching tools and systems I
discovered cPath, it stood out because you appear to use similar development
practices and technologies to ourselves, and the project seems quit polished.
I have downloaded, built and installed a recent version (2nd August) of cPath
and have introduced some PSI-MI formatted data. However I have over 8,000
documents in the PSI-MI format and I wish to load them into the system. I
have scanned the web services api, the Architectural Overview the Install guide
and the directories of the project, but I cannot find a bulk loading program.
Do you have any tools to load a large number of documents into cPath? If not
can you recommend the simplest route to achieve this?
Many thanks
Iain Keddie