T01-2016 Steps for Upgrading to BIOVIA Direct 9 to 2016 for Use with BIOVIA ELN 2016
Workbook
BIOVIA Direct 2016 is supported for use with BIOVIA Workbook (previously Electronic Lab Notebook) 2016. As of the BIOVIA Workbook 2016 release, the upgrade of an existing Workbook database from Direct 9 to Direct 2016 was not yet documented. The following information describes a tested procedure for this upgrade. If your deployment currently uses a Direct version older than 9x, please first upgrade to a 9x version of Direct; the BIOVIA Tech Note T43-2015 contains a tested set of steps for such an upgrade.
Operating System
Operating Systems supported by Accelrys Vault Server 2016 and Direct 2016
Resolution:
Within a BIOVIA Workbook system, BIOVIA Direct uses two (2) domain indexes that exist within the Vault database, named ALLCHEMSTRUCS_CHEM andALLCHEMRXNS_CHEM. The BIOVIA Tech Note T103-2015 published in December 2015 describes two approaches for upgrading such domain indexes to Direct 2016, defined as Scenario 1 and Scenario 2. This tech note follows the Scenario 2 description of this recent BIOVIA Direct tech note.
Note that if your company has compiled a significant volume of Workbook structure and reaction data over many years of use then the below steps may require significant system down time. If this is the case then we recommend contacting BIOVIA Support to discuss options.
It is recommended that previous to implementing the below steps customers use the existing (pre-upgrade) Direct 9x installation to scan the symyxdb schema to verify that all records are chemically valid. Contact BIOVIA Support for assistance if necessary to resolve any invalid Direct data.
In the following instructions we assume that you are using Oracle 12x; if you are using Oracle 11x then, per the Direct Installation Guide, use the C:\BIOVIA\Direct2016\bin11 folder rather than the bin12 folder for the remainder of these instructions. We also assume that you choose the default install directory location for Direct 2016, C:\BIOVIA; if you choose a different location then modify the below steps with your chosen location.
Finally, the below steps refer to the symyxdb and symyxdbuser oracle schemas; these are the oracle accounts that contain index data of your ELN system. If your index-data schemas have different names and you are not sure which they are then please contact BIOVIA Support.
1. Back up the current Oracle Database.
2. Using SQLPlus log into the symyxdb schema to verify that the currently active version of BIOVIA Direct is appropriate for use of this tech note.
SQL> select mdlaux.version from dual;
If the banner does not report 9x as the currently active version then abort use of this tech note and first use BIOVIA Tech Note T43-2015 stated in the above Description section.
3. While still logged into symyxdb verify that your existing domain indexes are valid:
SQL> column index_name format a20
SQL> column ityp_owner format a15
SQL> select index_name, status, domidx_status, ityp_owner from user_indexes where index_type = 'DOMAIN';
Output should indicate the domain indexes are valid and owned by the existing version of Direct. For example:
INDEX_NAME STATUS DOMIDX_STATU ITYP_OWNER
-------------------- -------- ------------ ---------------
ALLCHEMSTRUCS_CHEM VALID VALID C$DIRECT91
ALLCHEMRXNS_CHEM VALID VALID C$DIRECT91
VAULTTEXT_TEXT VALID VALID CTXSYS
4. Download from the BIOVIA Download Center to your Workbook database server the Direct 2016 documentation and the installer that matches your operating system (Windows/Linux/Solaris).
5. Stop the Vault services on your Vault server. Consult BIOVIA Support if you need to keep your ELN environment functional during this upgrade of Direct.
6. Check for non-default options in your domain indexes
Using SQLPlus, log in as the symyxdb owner and run the following commands to capture any non-default options used when your domain indexes were created and possibly modified.
SQL> select mdlaux.indexparameters('ALLCHEMSTRUCS_CHEM') from dual;
SQL> select mdlaux.indexparameters('ALLCHEMRXNS_CHEM') from dual;
If these commands return content that differs from the below content (the x.x.x will varywith your specific version) then stop and contact BIOVIA Support before continuing with the next step in order to review possible customizations to these domain indexes, and take steps to preserve as necessary.
Molecule index ALLCHEMSTRUCS_CHEM version 9.x.x.x
PREALLOCATE=NOSTORAGECHECK
Reaction index ALLCHEMRXNS_CHEM version 9.x.x.x
PREALLOCATE=NOSTORAGECHECK
In case you have a customized Direct environment (ptables, salts, sgroup, templates), please follow steps in the BIOVIA Direct 2016 Database Migration Guide.
7. Drop your domain indexes.
SQL> Drop index ‘ALLCHEMSTRUCS_CHEM’;
SQL> Drop index ‘ALLCHEMRXNS_CHEM’;
8. On your Oracle database server, complete all of the steps in the Direct 2016 documented instructions that are necessary to upgrade from your 9x version of Direct to 2016.
9. Using SQLPlus, log in as your new Direct schema, C$DIRECT2016, and execute the below command, which should return a Direct 2016 banner. If it does not then please contact BIOVIA Support, as your new installation of Direct has issues that need to be resolved.
SQL> select mdlaux.version from dual;
10. If you are using Oracle 12c, connect to your new Direct schema with a system account and run the below command before running PreInstallCheck.bat:
SQL> grant inherit privileges on user <system> to C$DIRECT2016;
11. Using SQLPlus, log into your index User account (such as symyxdbuser) to undo the setup for the existing version of Direct and then enable and verify Direct 2016:
SQL> execute mdlaux.unsetup
SQL> execute c$direct2016.mdlauxop.setup
SQL> select mdlaux.version from dual;
This last statement should return a Direct 2016 banner.
12. Using SQLPlus, log into your index account (such as symyxdb), undo the setup for the existing version of Direct and then enable and verify Direct 2016:
SQL> execute mdlaux.unsetup
SQL> execute c$direct2016.mdlauxop.setup
SQL> select mdlaux.version from dual;
This last statement should return a Direct 2016 banner.
Note: Remain logged into your index account (such as symyxdb), for the next several steps.
13. Re-create the domain indexes. This may take a significant amount of time, depending on your volume of structure and reaction data.
SQL> create index ALLCHEMRXNS_CHEM on ALLCHEMRXNS(RXNSTRUC) indextype is C$DIRECT2016.RXIXMDL;
SQL> create index ALLCHEMSTRUCS_CHEM on ALLCHEMSTRUCS(STRUCTURE) indextype is C$DIRECT2016.MXIXMDL;
14. (Optional) Scan each of these two recreated indexes to check for problems, per the Direct Administration Guide, using the mdlaux.scanindex procedure.
Then review the two LOG tables in the symyxdb schema: ALLCHEMSTRUCS_CHEM_LOG and ALLCHEMRXNS_CHEM_LOG. Contact BIOVIA Support if there are any errors.
15. Start the Vault services on your Vault server.
16. Use your BIOVIA Workbook application to test chemical structure and reaction indexing and searching
- Create a new experiment with the Workbook client, populate it with structures/reactions, and check it in. Wait a few minutes for the experiment to get indexed.
- Submit chemical and reaction searches (exact and substructure) from Notebook Explorer and verify they return both old and the newly experiments.
- Verify that no error messages have been logged on the Vault server, with regards to this Direct upgrade, specifically in the Vault logs.
Enhancement Request # NBK-24834
How to contact BIOVIA Support
If you have any questions, please contact BIOVIA Support.