RE: Problems with the xsd validation

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Gary Bader

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Oct 13, 2004, 3:09:45 PM10/13/04

to iain.d...@gsk.com, Ethan Cerami, cpat...@googlegroups.com

Hi Iain,

Yes, please let us know these things (!) – preferably via the cpath-dev list, so it is archived for other users. I haven’t come across this problem, so I’m passing it to Ethan to answer (although he’s out today, but will be back tomorrow).

-Gary

-----Original Message-----
From: iain.d...@gsk.com [mailto:iain.d...@gsk.com]
Sent: Wednesday, October 13, 2004 3:03 PM
To: ba...@cbio.mskcc.org
Subject: Problems with the xsd validation

Gary,

Please let me know if you don't want me to mail you problems I have come across,or whether you have another mechanism you'd like me to use.

I downloaded a cpath release on October 12th and it's having some issues validating the xml against the schema. I have a document that I have previously entered into the system using a previous build. I validated the document using xerces functionality and double checked it using xml spy. However on importing the document using the admin.pl, I get given validation errors.

Note: I have changed the xsd reference to be a local one because I cannot get through our proxy to get the remote xsd.

Thanks

Iain K

Note: I can pass you the source code for the small validator I used if you'd like, it's the least I could do. I created the validator to validate the data HPRD sent me, before I sent it to cPath; which sounds like functionality you're building in at present.

Gary Bader

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Oct 14, 2004, 11:06:59 AM10/14/04

to iain.d...@gsk.com, cpat...@googlegroups.com

Hi Iain,

Actually, I just realized that this is a logged bug that is high priority to get fixed. I think it has to do with the protein interactors in an input file that don’t contain any xrefs, only a protein name. For instance, HPRD contains a number of these interactors. cPath currently depends on xrefs to match up proteins, but they are optional in the PSI-MI XML Schema, so it shouldn’t depend on them. I have been progressively testing all databases that export to PSI-MI for cPath compatibility and working with the databases involved to fix their PSI exports as necessary as well as logging cPath bugs that will get fixed in the next short while. HPRD is the last one after IntAct, MINT and DIP.