Hi Bala,
i guess the URL API that you are using is not what you are after. This
will return you the whole HTML page, its used for bookmarking and
providing URL links to BioMart installation. For web-service based
access, please have a look at the first section (RESTful Access) on this
page:
http://www.biomart.org/martservice.html
you can learn more about the section 'a' of the said page using
MartView's XML button.
Best,
Syed
On 21/05/2010 19:29, Selvaraj, Balamuruganand wrote:
Well. I guess I need to modify my question.
For the webservice, the documentation says I need to provide attribute in the
following format
ATTRIBUTES=<datasetInternalName>.<Interface>.<AttributePageIntern
alName>.<AtrributeInternalName>
while I am able to figure out the rest of the values, I am not able to find
what value I should use for the
datasetInternalName. Should it be the one I have mentioned in registry.xml ? or
kindly let me know where would this unique value be present
-Bala
________________________________________
From: Syed Haider [[email protected]]
Sent: Friday, May 21, 2010 2:34 PM
To: Selvaraj, Balamuruganand
Cc: [email protected]
Subject: Re: [mart-dev] Problem with Java API - Dataset
Its the unique name of the dataset that is used for querying the meta
data as well as resultset from the dataset.
hope that helps,
Best
Syed
On 21/05/2010 19:11, Selvaraj, Balamuruganand wrote:
Syed,
Can you tell me what is actually meant by datasetInternalName. Where do I find
this this value ?
-Bala
________________________________________
From: Syed Haider [[email protected]]
Sent: Friday, May 21, 2010 1:17 PM
To: Selvaraj, Balamuruganand
Cc: [email protected]
Subject: Re: [mart-dev] Problem with Java API - Dataset
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
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