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Pathway Tools Installation Guide -- Upgrading from Oracle 8 to Oracle 10

Pathway Tools Installation Guide -- Upgrading from Oracle 8 to Oracle 10

Pathway Tools Solaris versions from 6.0 to 9.0 have worked with Oracle 8. The current version, Pathway Tools 9.5, does not, so if you've been using Pathway Tools with Oracle 8, you need to upgrade to Oracle 10. (We haven't tried Oracle 9.) An experienced Oracle database administrator should upgrade your data from Oracle 8 to Oracle 10. Here are the other requirements when upgrading:
  • We suggest you backup the Perk database before upgrading in case something goes wrong during upgrading.
  • The default database name has changed from perk to biocyc.
  • The default username and password have changed from ecocyc to biocyc.
  • The following new column definitions are required:
        ALTER TABLE txntable
        ADD (
          txn_comment VARCHAR(500),
          app_version VARCHAR(100)
  • Leading and trailing quotation marks need to be removed from one of the columns by running the following SQL statement after all data has been imported to Oracle 10:
    update char_slot_values set slotvalue = substr(slotvalue, 2, length(slotvalue) -2) where slotvalue like '"%"';
  • All users should be logged off during the upgrade.
Further information about setting up Oracle 10 is here.