Upgrade to 5.5 - IJC host database

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

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

Hi Ian,

SEVERE: Error while processing index: PROJECT.IDX_PATENT
java.lang.RuntimeException: domidx_status is IDXTYP_INVLD for PROJECT.IDX_PATENT

java.sql.SQLException: ORA-00904: "STRONGEST_ACIDIC_PKA": invalid identifier

java.sql.SQLException: ORA-00904: "STRONGEST_ACIDIC_PKA": invalid identifier

Hi Peter,

Any suggestions?  This crashes the upgrade process completely...

cheers

Ian

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

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

Hi Ian,

JChem version 5.6.0.0 has been released with the fix for the license problem during upgrade.

Peter