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Setup for PGDB access on an alternate MySQL server

Setup for PGDB access on an alternate MySQL server

Starting with Pathway Tools 17.0, PGDBs stored in more than one MySQL server can be accessed simultaneously, in the same session. The access parameters for the primary MySQL server still need to be configured in the ptools-init.dat file, as described in the User Guide. In the following, setup instructions are described for accessing PGDBs that are located on alternate MySQL servers.

  • Install the PGDB's *cyc directory on the local computer running Pathway Tools. Instructions regarding how to copy such directories can be found at

  • Edit the *cyc/version/input/organism.dat file. Find the line for the STORAGE attribute and doublecheck that it is set to MYSQL. Then, add a new line for this attribute:
    WXYZ names a symbol in Common LISP, as will be defined in the next step. The symbol name can be changed, but the same name has to be used here and in the next step. It can consist of letters and dashes as characters. Be careful that the whitespace separator between the attribute and its value is exactly 1 Tab character.

  • A code snippet that defines the connection parameters for the alternate MySQL server has to be added at the bottom of the file aic-export/aic-init.lisp on the local computer running Pathway Tools. Add this text template verbatim and then customize for the exact parameters of your MySQL server (inside the double quotes):
    ;;;kr:Oct-24-2012 The new way of specifying an alternate MySQL server.
    ;;; The symbol name of this parameter has to be put in the organism.dat file of the PGDB,
    ;;; as a value for the ALT-SERVER line.
    ;;; This location for this definition was chosen, because it seems to be the earliest file loaded,
    ;;; and certainly before scanning all the kbs, which happens even before loading any user's init files !
    (defparameter ec::WXYZ
        '(:host ""
          :port 3306
          :database "ptools_database"
          :username "some_user"
          :password "some_password"))
  • After that, restart Pathway Tools, and the PGDB on the alternate MySQL server should also be selectable from the GUI.

Last modified: Thu Apr 11 19:25:31 PDT 2013