User 5d01fe091c
29-06-2011 13:51:17
Hi,
We're upgrading a different database this time, one which contains all our central IJC databases. We were running upgrade-evol.sh. We're getting two types of failures:
1) Index rebuilding:
[main/10]: Jun 28, 2011 2:05:58 PM chemaxon.jchem.cartridge.install.IndexRebuilder next
FINE: idxSchema=PROJECT, idxName=IDX_PATENT, idxPartName=null
[main/10]: Jun 28, 2011 2:05:58 PM chemaxon.jchem.cartridge.util.JCartLoggerJdkAdapter warning
WARNING: jcptName=null for PROJECT.IDX_PATENT.null (PROJECT.PATENT)
[main/10]: Jun 28, 2011 2:05:58 PM chemaxon.jchem.cartridge.install.IndexRebuilder next
SEVERE: Error while processing index: PROJECT.IDX_PATENT
java.lang.RuntimeException: domidx_status is IDXTYP_INVLD for PROJECT.IDX_PATENT
at chemaxon.jchem.cartridge.structs.JCartIndexDescriptor.checkIdxStatus(JCartIndexDescriptor.java:243)
at chemaxon.jchem.cartridge.structs.JCartIndexDescriptor.init0(JCartIndexDescriptor.java:167)
at chemaxon.jchem.cartridge.structs.JCartIndexDescriptor.<init>(JCartIndexDescriptor.java:112)
at chemaxon.jchem.cartridge.structs.JCartIndexDescriptor.get(JCartIndexDescriptor.java:624)
at chemaxon.jchem.cartridge.structs.JCartIndexDescriptor.get(JCartIndexDescriptor.java:604)
at chemaxon.jchem.cartridge.install.IndexRebuilder.next(IndexRebuilder.java:74)
at chemaxon.jchem.cartridge.install.UpgradeCmdLine.rebuildIndices(UpgradeCmdLine.java:485)
at chemaxon.jchem.cartridge.install.UpgradeCmdLine.upgrade(UpgradeCmdLine.java:338)
at chemaxon.jchem.cartridge.install.UpgradeCmdLine.interactiveUpgrade(UpgradeCmdLine.java:98)
at chemaxon.jchem.cartridge.install.UpgradeCmdLine.upgrade(UpgradeCmdLine.java:52)
at chemaxon.jchem.cartridge.install.UpgradeCmdLine.main(UpgradeCmdLine.java:689)
2) Looking for licenses for calculated terms
[main/10]: Jun 28, 2011 2:26:26 PM chemaxon.jchem.cartridge.install.IndexRebuilder next
FINE: idxSchema=TEST, idxName=IDX_EVOTEC_T12, idxPartName=null
[Thread-42/14]: Jun 28, 2011 2:29:46 PM chemaxon.jchem.db.UpdateHandler calcChemTermColValues
SEVERE: Error for column LOGP with structure cd_id=1150: Error while evaluating expression:
logP()
No license file found.
Product name: Partitioning Plugin Group
License path:
Please contact sales _at_ chemaxon.com to obtain the corresponding license.
Students and academic researchers are entitled of free use
through our Academic Package, for more information
please visit: http://www.chemaxon.com/acpack_conditions.html style="font-family: courier new,courier;">, expression: logP()
[Thread-42/14]: Jun 28, 2011 2:29:46 PM chemaxon.jchem.db.UpdateHandler calcChemTermColValues
SEVERE: Error for column LOGD with structure cd_id=1150: Error while evaluating expression:
logd('7.4')
No license file found.
Product name: Partitioning Plugin Group
License path:
Please contact sales _at_ chemaxon.com to obtain the corresponding license.
Students and academic researchers are entitled of free use
through our Academic Package, for more information
please visit: http://www.chemaxon.com/acpack_conditions.html style="font-family: courier new,courier;">, expression: logd('7.4')
[Thread-42/14]: Jun 28, 2011 2:29:46 PM chemaxon.jchem.db.UpdateHandler calcChemTermColValues
SEVERE: Error for column LOGP with structure cd_id=1151: Error while evaluating expression:
logP()
No license file found.
Product name: Partitioning Plugin Group
License path:
Please contact sales _at_ chemaxon.com to obtain the corresponding license.
Students and academic researchers are entitled of free use
through our Academic Package, for more information
please visit: http://www.chemaxon.com/acpack_conditions.html style="font-family: courier new,courier;">, expression: logP()
Our full license file is on the server in the licenses directory for the cartridge (or should it be elsewhere too?)
Many thanks for your help
ian
User 5d01fe091c
29-06-2011 14:26:57
Ok I think that we have fixed the second one (by putting the license in the jchem profile directory)
But now we have this error:
====> Recalculating JChem structure tables...
java.sql.SQLException: ORA-00904: "STRONGEST_ACIDIC_PKA": invalid identifier
at oracle.jdbc.driver.SQLStateMapping.newSQLException(SQLStateMapping.java:74)
at oracle.jdbc.driver.DatabaseError.newSQLException(DatabaseError.java:131)
at oracle.jdbc.driver.DatabaseError.throwSqlException(DatabaseError.java:204)
at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:455)
at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:413)
at oracle.jdbc.driver.T4C8Oall.receive(T4C8Oall.java:1034)
at oracle.jdbc.driver.T4CStatement.doOall8(T4CStatement.java:183)
at oracle.jdbc.driver.T4CStatement.executeForDescribe(T4CStatement.java:780)
at oracle.jdbc.driver.T4CStatement.executeMaybeDescribe(T4CStatement.java:855)
at oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(OracleStatement.java:1186)
at oracle.jdbc.driver.OracleStatement.executeQuery(OracleStatement.java:1377)
at oracle.jdbc.driver.OracleStatementWrapper.executeQuery(OracleStatementWrapper.java:387)
at chemaxon.jchem.db.CTColumnRegenerator.getCTFieldTypes(CTColumnRegenerator.java:387)
at chemaxon.jchem.db.CTColumnRegenerator.run(CTColumnRegenerator.java:313)
at chemaxon.jchem.db.UpdateHandler.recalculateCTColumns(UpdateHandler.java:3158)
at chemaxon.jchem.db.UpdateHandler.recalculateCTColumns(UpdateHandler.java:3132)
at chemaxon.jchem.db.Updater.regenerateCTColumns(Updater.java:1170)
at chemaxon.jchem.db.Updater.performCurrentUpdate(Updater.java:219)
at chemaxon.jchem.db.Updater.performCurrentUpdate(Updater.java:198)
at chemaxon.jchem.cartridge.install.UpgradeCmdLine.regenerateTable(UpgradeCmdLine.java:677)
at chemaxon.jchem.cartridge.install.UpgradeCmdLine.regenerateJChemTables(UpgradeCmdLine.java:629)
at chemaxon.jchem.cartridge.install.UpgradeCmdLine.rebuildIndices(UpgradeCmdLine.java:524)
at chemaxon.jchem.cartridge.install.UpgradeCmdLine.upgrade(UpgradeCmdLine.java:338)
at chemaxon.jchem.cartridge.install.UpgradeCmdLine.interactiveUpgrade(UpgradeCmdLine.java:98)
at chemaxon.jchem.cartridge.install.UpgradeCmdLine.upgrade(UpgradeCmdLine.java:52)
at chemaxon.jchem.cartridge.install.UpgradeCmdLine.main(UpgradeCmdLine.java:689)
chemaxon.jchem.db.UpdateHandlerException: java.sql.SQLException: ORA-00904: "STRONGEST_ACIDIC_PKA": invalid identifier
Caused by:
ORA-00904: "STRONGEST_ACIDIC_PKA": invalid identifier
at chemaxon.jchem.db.UpdateHandler.recalculateCTColumns(UpdateHandler.java:3162)
at chemaxon.jchem.db.UpdateHandler.recalculateCTColumns(UpdateHandler.java:3132)
at chemaxon.jchem.db.Updater.regenerateCTColumns(Updater.java:1170)
at chemaxon.jchem.db.Updater.performCurrentUpdate(Updater.java:219)
at chemaxon.jchem.db.Updater.performCurrentUpdate(Updater.java:198)
at chemaxon.jchem.cartridge.install.UpgradeCmdLine.regenerateTable(UpgradeCmdLine.java:677)
at chemaxon.jchem.cartridge.install.UpgradeCmdLine.regenerateJChemTables(UpgradeCmdLine.java:629)
at chemaxon.jchem.cartridge.install.UpgradeCmdLine.rebuildIndices(UpgradeCmdLine.java:524)
at chemaxon.jchem.cartridge.install.UpgradeCmdLine.upgrade(UpgradeCmdLine.java:338)
at chemaxon.jchem.cartridge.install.UpgradeCmdLine.interactiveUpgrade(UpgradeCmdLine.java:98)
at chemaxon.jchem.cartridge.install.UpgradeCmdLine.upgrade(UpgradeCmdLine.java:52)
at chemaxon.jchem.cartridge.install.UpgradeCmdLine.main(UpgradeCmdLine.java:689)
Caused by: java.sql.SQLException: ORA-00904: "STRONGEST_ACIDIC_PKA": invalid identifier
at oracle.jdbc.driver.SQLStateMapping.newSQLException(SQLStateMapping.java:74)
at oracle.jdbc.driver.DatabaseError.newSQLException(DatabaseError.java:131)
at oracle.jdbc.driver.DatabaseError.throwSqlException(DatabaseError.java:204)
at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:455)
at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:413)
at oracle.jdbc.driver.T4C8Oall.receive(T4C8Oall.java:1034)
at oracle.jdbc.driver.T4CStatement.doOall8(T4CStatement.java:183)
at oracle.jdbc.driver.T4CStatement.executeForDescribe(T4CStatement.java:780)
at oracle.jdbc.driver.T4CStatement.executeMaybeDescribe(T4CStatement.java:855)
at oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(OracleStatement.java:1186)
at oracle.jdbc.driver.OracleStatement.executeQuery(OracleStatement.java:1377)
at oracle.jdbc.driver.OracleStatementWrapper.executeQuery(OracleStatementWrapper.java:387)
at chemaxon.jchem.db.CTColumnRegenerator.getCTFieldTypes(CTColumnRegenerator.java:387)
at chemaxon.jchem.db.CTColumnRegenerator.run(CTColumnRegenerator.java:313)
at chemaxon.jchem.db.UpdateHandler.recalculateCTColumns(UpdateHandler.java:3158)
... 11 more
ChemAxon aa7c50abf8
29-06-2011 16:42:35
Hi Ian,
SEVERE: Error while processing index: PROJECT.IDX_PATENT
java.lang.RuntimeException: domidx_status is IDXTYP_INVLD for PROJECT.IDX_PATENT
The index type of the index has become invalid. Try dropping the index and recreating it after upgrade.
java.sql.SQLException: ORA-00904: "STRONGEST_ACIDIC_PKA": invalid identifier
We will get back on this tomorrow.
Peter
User 8cbba88c0e
04-07-2011 14:43:53
pkovacs wrote: |
java.sql.SQLException: ORA-00904: "STRONGEST_ACIDIC_PKA": invalid identifier
We will get back on this tomorrow.
Peter
|
Hi Peter,
Any suggestions? This crashes the upgrade process completely...
cheers
Ian
ChemAxon 4a2fc68cd1
05-07-2011 21:43:35
Hi Ian,
According to the error message we presume that the information stored in the JChemProperties table is incompatible with the actual structure of the considered table. In particular, a column named "STRONGEST_ACIDIC_PKA" is registered for this table in JChemProperties, but such a column may not exist currently in the considered table.
Could you check this? Could you send us all records from the JChemProperties table which are related to the problematic table as well as the actual structure of the table (list of columns and column types)?
Regards,
Peter
ChemAxon aa7c50abf8
23-07-2011 17:18:12
For the record:
During off-line communications, we found that our assumption in the previous post was correct: the Chemical Terms acidic pKa was associated with a non-existent column. It is unclear exactly what user actions lead to this inconsistent state -- determining this is a separate issue.
Actions to take:
1. Establish the desired state of acidic pKa autocalculation.
1/a If autocalculation is required, remove the Chemical Terms association from the jchemproperties table manually.
1/b If autocalculation is not required, remove the Chemical Terms association from the jchemproperties table manually and re-create this auto-calculation item using the appropriate tools (JCB or IJC).
Peter
ChemAxon aa7c50abf8
16-09-2011 10:44:39
Hi Ian,
JChem version 5.6.0.0 has been released with the fix for the license problem during upgrade.
Peter