I have been trying to import an sdf which has some records that have especial structure,such as "POLY(ACRYLONITRILE-CO-BUTADIENE-CO-STYRENE)"/CAS#9003-56-9/MFCD00133993.
I am using the version of IJC 3.0.4. I have created an empty local database and selected "import file".
The import generates the following message :
Warning: Failed to import row 1,017: Inserting a query or Markush structure is not allowed for table: "APP.STRUCTURES"; uncategorized SQLException for SQL ; SQL state [null]; error code ; Inserting a query or Markush structure is not allowed for table: "APP.STRUCTURES"; nested exception is java.sql.SQLException: Inserting a query or Markush structure is not allowed for table: "APP.STRUCTURES"
After about 30 "WARNING"s above are found the import terminates with the following
TOO MANY CONSECUTIVE ERRORS, TERMINATING IMPORT
Any ideas for this bug?
This probelm is related to the type of structure table that is used during import. IJC supports various structure table types, as described here: http://www.chemaxon.com/instantjchem/ijc_latest/docs/user/help/htmlfiles/editing_database/editing_entities.html#settings
When a file is imported IJC tries to work out the best setting, but it does not necessarily read the whole file. It only reads until nothing has changed for a long time. This means that it is possible for different types of structures to appear later in the file that are incompatible with the chosen table type.
To address this you have 2 options:
1. Manually change the table type setting. Use the ... button next to the 'Table settings' selector and in the resulting dialog change the 'Table contents' setting as appropriate.
2. Parse more, or all of the file so that IJC knows about all the different types of structures in the file. To do this use the 'Read more' button at the bottom of the imort dialog. You can set the number of records to read to zero to read the whole file.
Which table type to use? Well, this of course depends on your data, but if in doubt you can use 'Any structures' which will accept any type of structure.
Thank you for your prompt reply. Now the problem is solved.