Hi Bala,
Java API is not supported anymore, anything that works there would be a
bonus. I would suggest to refrain from using it. It will be replaced in
couple of months time wiht brand new Java API. If you want to use Java
as your preferred language at this time, please use the web services as
a medium of data exchange.
Best
Syed
On 21/05/2010 17:52, Selvaraj, Balamuruganand wrote:
Hi Biomart-Dev Team,
I am trying to use the Java API provided by the Biomart. However, I am shown a
error with the java implementation as shown in the reference doc.
The registry gets loaded properly. However, the following code is creating
error.
DatasetConfig config = adaptor.getDatasetConfigByDatasetInternalName("Fly",
"default");
Fly --> is the name of the MartDB present in registry.xml file as
<MartDBLocation
name = "Fly"
displayName = "Fly"
databaseType = "mysql"
host = "localhost"
port = "3306"
database = "Fly_mart"
schema = "Fly_Mart"
user = "gmod"
password = "gmod"
visible = "1"
default = ""
includeDatasets = ""
martUser = ""
/>
when I run the above Java code after loading the registry file, I get an error
message saying
Caused by: java.sql.SQLException: You have an error in your SQL syntax; check
the manual that corresponds to your MySQL server version for the right syntax
to use near 'Fly_Mart.meta_conf__xml__dm mx WHERE
md.dataset_id_key=mi.dataset_id_key A' at line 1
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2975)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1695)
at com.mysql.jdbc.Connection.execSQL(Connection.java:3026)
at
com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1137)
at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:1231)
at
org.ewin.java.sql.ExceptionPreparedStatement.executeQuery(ExceptionPreparedStatement.java:206)
at
org.ensembl.mart.lib.config.DatabaseDatasetConfigUtils.initMartConfigForUser(DatabaseDatasetConfigUtils.java:3385)
I am not sure if the DataSetInternal name that I have provided is correct.
Could you tell me where I could be wrong or
is there any other detail I need to be add for the dataSetInternalName.
Thanks,
Bala
