import export failure in IJC 2.5.3

User bb4245cb34

10-11-2009 10:51:42


I am working

Instant JChem Version: 2.5.3 (build: 090819)
JChem Version: 5.2.4
JChem Table Version: 5020100
Marvin Version: 5.2.4 (build date: 2009-08-15)
Java: 1.6.0_13; Java HotSpot(TM) Client VM 11.3-b02
System: Windows XP version 5.1 running on x86; Cp1252; de_AT (instantjchem)


I made the next data base


data tree

synthesis (root, with structure, relation: one to many batch)

            batch (child of synthesis, without structure, relation: one to many sample)

                        sample (child of batch, without structure, relation: many to one batch)

the db has 3 records (CDID1, CDID2, CDID3), each batch has 2 records and each sample also 2 records.


I exported the db into sd and also into rd file


The exports are not correct, the exported files had 6 records (CDID1 to CDID6, controlled by text editor)


I made a new db with the same data tree (synthesis, batch, sample)


first experiment:

I tried to import sd and also rd files into the new db

without success

I got 6 entries

it is not possible to map the structures

I got everything (batch and also sample) into the root (first level)

records are doubled


second experiment

I tried to import syth to synth, batch to batch and sample to sample (levels to each other)

I got the field but the fileds were empty (data were not imported)


correct export import is possible only into the first level


if I can not export import all levels, it is not possible to make back up

without back up is every db useless

If I can not map structures, I will always get doubled records

what ist he solution

Thanks for the efforts


TU Vienna

ChemAxon fa971619eb

10-11-2009 11:08:14

The export capabilities in IJC are primarily designed for exporting a single table of data. There is some limited ability to export data from related tables, but not all combinations of tables are supported, and you will loose teh relational nature of the data (nor do SDF or RDF support all possibilites).

If your concern in just about backing up your database then this is best done at the database level. If you are using MySQL or Oracle then use these database's normal backup procedures. If you are using a local Derby database then these are just files on disk so you can make a copy or archive of these to generate a database backup. To do this locate where you saved the project on your disk, and inside that directory you will find a directory name ".config" (note the dot at the front which will cause it to be hiden by default on some sytems) and inside this will be the directory that contains your local database files. This directory will probably be named localdb. Just create a copy, or a zip archive of this directory for your backup.

If you do need your data to be exported as files then your best bet is to export each table as a separate file. e.g. export the structure table as a SD file and the non-structure tables as CSV files.

I hope this solves your problem.



User bb4245cb34

10-11-2009 12:36:30

thank you for the really quick answer

It is a great pity that the db does not support an essential export import.
An up date can still be organized, but without an import function can fill no db with data.
In many areas of chemistry can be not dispensed to the first and even to the second sublayer, because the further use of the substances requires a predefined Documentation.
If the db does not support this documentation, the software can not be used in the areas of prep. org. Chemistry, pharmaceutical chemistry and in many different but important areas of the chemistry.

I am also using ISIS Base/Isentris and can compare the softwares. IJC is much better and easier to use, but the limited import function prevent the use of IJC very much..

An elimination of this restriction would  certainly spread the use of this software.

Nevertheless, thanks for the tips.


ChemAxon fa971619eb

11-11-2009 17:01:48

We do plan to add the ability to export an entire database in the future, but this will be aimed more at transferring data from one database to another (e.g. migrate data from a local database to an oracle or mysql database).

Without this capability you are limited to:

1. backing up/exporting a database using the database's own features, in which case the same database can be re-created at a later stage from the backup.

2. exporting each table as a file, in which case each table can be individually re-created in a different database.



User da00f5c453

13-11-2009 00:27:11

Hi Laszlo,


You can import multilevel RDF files from ISIS using templates in IJC, it is not possible however to export multilevel RDF. See the attached file template I used to import hierarhical RDF for Wombat DB into IJC, it creates all required entities you just need to create the forms.



User bb4245cb34

30-11-2009 17:41:22

olegursu wrote:

Hello Oleg!
Thank you for your effort.
I tried to import multilevel rdf files from Isis, I got the fields, but lost the  data.
Would you like to explain how did you do that!
Unfortunately I can not open the attached files. Which file was it?  I can not see wheder .rdf  txt  or ...??
It would be important for me to import data (not structure) to multi level tables. I can creat multi level db and add single data to every level, but import works only on the first level.


Hi Laszlo,You can import multilevel RDF files from ISIS using templates in IJC, it is not possible however to export multilevel RDF. See the attached file template I used to import hierarhical RDF for Wombat DB into IJC, it creates all required entities you just need to create the forms.Oleg.


User da00f5c453

30-11-2009 18:11:27

Hi Laszlo,

The attached file is a text to see it on windows simply
change the extension from .propreties to .txt and double click it to open it in
your text editor, however when you want to use it in your import you will have
to change the extension back. The file was created
specifically for WOMBAT database it will not work without customization with
your database, but it can be used as template and modified to accommodate your
database structure (hierarchy). To successfully import your ISIS
database from RDf file you need to know exactly the hierarchy and fields in your
database. For example for WOMBAT there is one structure table and 2 data tables
these entities are created in IJC using the statements:

ROOT ussualy where the structures are located, lines with # at the begining are comments

# entity definition for ROOT
entity#ROOT#name=Wombat structures
# contents must be one of: MOLECULES, REACTIONS or ANY_STRUCTURES

these statements will create a table for molecular structure with no additional fields, to add fields use the statement


the field type ID is INTEGER you can have integers, float, varchar(for text), etc. you need to declare all fields from your RDF or ISIS.

the following statement will create a data table for keywords


it is a standard table meaning there is no chemical structure in it, and you can add a field to it using statements:



the same needs to be done for all tables in your ISIS db respecting your hierarchical order. Finaly your can link the tables to ROOT structure and create the datatree using:




# DataTree definitions



you will still need to create your database forms. The probable cause for your data loss is because the template file removes (drops) all entities which are going to be created during the import.

# drop artifacts
# will not fail if artifacts do not exist
# entity and table name must match the definition provided for entity creation


I hope this will help, there also IJC manual where I found this information.




ChemAxon fa971619eb

02-12-2009 09:29:49


Thanks to Oleg for his comments on importing RDF files.

I can confirm that IJC can import RDF as Oleg describes, but this support is relatively primative. The problem is that the RDF file format is very poorly defined and the meaning of the data within the file is very arbitary. For complex, or strange RDF files you may have problems getting the import to work as you wish, and in these cases you may need to resort to a  more programatic approach.