jcman import fails to set cd_id using --connect

Hi,





Using JChem 3.2.2 I think I have a situation where the behavior of JChemManager and jcman differs.





I am able through the JChemManager GUI to specify that when I import compounds from a smiles file into a JChem Base table that the cd_id column be populated based on the value in FIELD_0 by making this selection from the combo box next to CD_ID.





However when I try to achieve the same thing using jcman to run the same import in batch (non gui) mode with the following command:





jcman.bat -a test_table blah.smiles --connect "CD_ID=field_0" --driver oracle.jdbc.driver.OracleDriver --dburl jdbc:oracle:thin:@//myhost:myport/mydb --login myuser --password mypassword





The import succeeds BUT the CD_ID is not set based on the value in field_0 of the smiles file. I checked to make sure this was not a case sensitivity issue by trying with both field_0 and FIELD_0 in the --connect string.





Am I specifying the --connect option correctly? Any idea why jcman is not setting the cd_id based on the field_0 value in my smiles file when JChem Manager gui DOES set the cd_id as expected?





Thanks,





James

One other question I forgot to ask in my original post. I noticed that the JChem Manager shipped with version 3.1.1 of JChem Base does not give you the option to map a smiles field (or even an SD property value) to the cd_id column of a structure table even through the GUI.





Could you tell me in which version of JChem Base the ability to map a smiles field or SD property into the cd_id field was first added?





Thanks,





James

Hi,





I will check this issue shortly.





Meanwhile could you check if you are running the same version in both cases ?





Command line:

Code:

jcman --help

GUI:

Code:

Help -> About

Best regards,





Szilard

Hi,





I just checked and they are both reporting as version 3.2.2





Thanks,





James

Hi,





The bug was specific to the "cd_id" field only, it will be fixed in the next minor release of JChem.


Thank you for reporting this.

Quote:

Could you tell me in which version of JChem Base the ability to map a smiles field or SD property into the cd_id field was first added?

It's available from version 2.1., though AFAIK it was a bit different from Marvin (field names started from field_1), this was fixed in 2.3.





Best regards,





Szilard