Increase CONSECUTIVE ERRORS count settings during import

Hi,


I tried to import the Biometa DB and set duplicate filtering and Standardizers on. The problem is that after too many errors it stopped.


I have multiple other options to do that, but would it be possible to control


or ignore the error count? Because I want to use Instant-JChem as a DB cleaner, without starting JCHem or Standardizer or any other tool.


Thanks


Tobias

Code:

TOO MANY CONSECUTIVE ERRORS, TERMINATING IMPORT Import completed in 139s. 947 entries successfully imported. 217 Errors. 206 were not imported as they were duplicates

Instant JChem Version: 2.1 (build: 071002) JChem Version: 3.2.11 Marvin Version: 4.1.13 (build date: 2007-9-20) Java: 1.5.0_11; Java HotSpot(TM) Client VM 1.5.0_11-b03 System: Windows XP version 5.1 running on x86; Cp1252; en_US (instantjchem)


....


"APP.NEW_JCHEMBASE_TABLE"; uncategorized SQLException for SQL []; SQL state [null]; error code [0]; Inserting a query or Markush structure is not allowed for table: "APP.NEW_JCHEMBASE_TABLE"; nested exception is java.sql.SQLException: Inserting a query or Markush structure is not allowed for table: "APP.NEW_JCHEMBASE_TABLE"


Error:





TOO MANY CONSECUTIVE ERRORS, TERMINATING IMPORT








Import completed in 139s.


947 entries successfully imported.


217 Errors.


206 were not imported as they were duplicates

Code:

The consecutive errors catch is in there to prevent continuous errors happening - each error is caught and IJC moves on to the next record. This is to allow a rare error to happen without it causing the whole import to fault.





Somethimes there is a fundmental error (e.g. failure in the database connection) which will result in all records failing. To prevent having to wait for each record in the whole file to fail before the process finished we put a limit on the number of consecutive errors.





We can make this a configurable option so that it can be increased, but usually it's better to fix the underlying problem.





In your example it looks like you are trying to insert query structures into a JChem table whose contents are set to "Molecules" table which will cause an error. To solve this change the JChem table contents to "Any Structures" and query structures will be inserted fine.





Tim

tdudgeon wrote:

In your example it looks like you are trying to insert query structures into a JChem table whose contents are set to "Molecules" table which will cause an error. To solve this change the JChem table contents to "Any Structures" and query structures will be inserted fine. Tim

Thanks,


because I was thinking to just I-JChem alone,


but how would you filter out Markush structures?


As smiles file I can search for "*" but I don't know


to do that with Markush structures in Instant JCHEM.





Tobias