Hi Syed, Thanks for the web service doc. I was able to implement it without any issues.
I just have a small question. The response generated (in the form of html) from the web service doesn't have the <html><body><table>. Is there any reason why this was not included in the HTML file which is being genearted. - Bala ________________________________________ From: Syed Haider [[email protected]] Sent: Friday, May 21, 2010 2:53 PM To: Selvaraj, Balamuruganand Cc: [email protected] Subject: Re: [mart-dev] Problem with Java API - Dataset 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 >>> >> >
