introducing new external db links

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iain.d...@gsk.com

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Oct 1, 2004, 11:49:40 AM10/1/04

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Hi guys,

I'm trying to introduce a couple of new external database links to my cPath install, but I'm getting a little stuck. I used the following sql to setup the tables:
INSERT INTO external_db_cv VALUES ('33', '33', 'HPRD');
INSERT INTO external_db VALUES ('42', 'HPRD', 'http://www.hprd.org/protein/%ID%', 'Human Protein Reference Database', '33', NULL, NULL,'20041001162924', '20041001162924');

However on importing my data I'm getting the error:

Normalizing PSI Document...
Normalization Complete: Document is valid
Validating all External References:
.**** Error: org.mskcc.pathdb.sql.dao.ExternalDatabaseNotFoundException: No matching database found for: HPRD[00001]
org.mskcc.pathdb.sql.transfer.ImportException: org.mskcc.pathdb.sql.dao.ExternalDatabaseNotFoundException: No matching database found for: HPRD[00001]
at org.mskcc.pathdb.sql.transfer.ImportPsiToCPath.addRecord(ImportPsiToCPath.java:190)
at org.mskcc.pathdb.tool.ImportRecords.transferRecord(ImportRecords.java:100)
at org.mskcc.pathdb.tool.ImportRecords.transferAllImportRecords(ImportRecords.java:82)
at org.mskcc.pathdb.tool.ImportRecords.transferData(ImportRecords.java:61)
at org.mskcc.pathdb.tool.Admin.importData(Admin.java:119)
at org.mskcc.pathdb.tool.Admin.main(Admin.java:82)
Caused by: org.mskcc.pathdb.sql.dao.ExternalDatabaseNotFoundException: No matching database found for: HPRD[00001]
at org.mskcc.pathdb.sql.dao.DaoExternalLink.validateExternalReferences(DaoExternalLink.java:170)
at org.mskcc.pathdb.sql.transfer.ImportPsiToCPath.validateExternalRefs(ImportPsiToCPath.java:221)
at org.mskcc.pathdb.sql.transfer.ImportPsiToCPath.addRecord(ImportPsiToCPath.java:172)

Any suggestions?

Many thanks

PS Am I right in noticing that something very similar is in your current to do list?

Iain Keddie

Gary Bader

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Oct 1, 2004, 5:33:46 PM10/1/04

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Hi Iain,

Your first insert statement needs to be:

INSERT INTO external_db_cv VALUES ('33', '42', 'HPRD');

The first value is the primary key in this table, the second value is a foreign key – the primary key in the external_db table.

Yes, this is on our TODO list. ;) Actually, I’m just doing HPRD compatibility tests right now – working with HPRD to help them make their PSI-MI output Level 1 and cPath compatible. Once I’m done, I was planning on checking in an updated files into CVS that would contain all of the database references that HPRD uses.

That should work, but let me know if doesn’t.

Best,

Gary

-----Original Message-----
From: iain.d...@gsk.com [mailto:iain.d...@gsk.com]
Sent: Friday, October 01, 2004 11:50 AM
To: cpat...@googlegroups.com
Subject: introducing new external db links

at org.mskcc.pathdb.sql.transfer.ImportPsiToCPath.addRecord(ImportPsiToCPath..java:190)

at org.mskcc.pathdb.tool.ImportRecords.transferRecord(ImportRecords.java:100)
at org.mskcc.pathdb.tool.ImportRecords.transferAllImportRecords(ImportRecords.java:82)
at org.mskcc.pathdb.tool.ImportRecords.transferData(ImportRecords.java:61)
at org.mskcc.pathdb.tool.Admin.importData(Admin.java:119)
at org.mskcc.pathdb.tool.Admin.main(Admin.java:82)
Caused by: org.mskcc.pathdb.sql.dao.ExternalDatabaseNotFoundException: No matching database found for: HPRD[00001]
at org.mskcc.pathdb.sql.dao.DaoExternalLink.validateExternalReferences(DaoExternalLink.java:170)
at org.mskcc.pathdb.sql.transfer.ImportPsiToCPath.validateExternalRefs(ImportPsiToCPath.java:221)

at org.mskcc.pathdb.sql.transfer.ImportPsiToCPath.addRecord(ImportPsiToCPath..java:172)

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