On 27/07/09 5:22 PM, "Guillaume Collange" <[email protected]> wrote:
> ups...have you an idea if we have a way to get round the problem?
>
Yes, if you want to build a single dataset from two different RDBMSs you
need to port one of them to the other, so either you port oracle to mysql or
vice versa. The alternative is to build two separate dataset: one in oracle
and on in mysql and then take advantage of the federation feature of BioMart
which will allow you to query them together. Please let us know if you are
interested in the latter and we can give you some guidance on how to do it
A.
> Best regards,
> GC
>
>
>
> Le 27 juil. 2009 à 22:33, Yong Liang <[email protected]> a écrit :
>
>> Hi Guillaume,
>>
>> Current martbuilder does not support generating a dataset that from
>> two
>> different datasources. You can use martbuilder to work on multiple
>> schemas
>> from different databases (mysql, postgresql, and oracle), but when
>> you build
>> a mart, you need to choose the datasets from the same DB type.
>>
>> Regards,
>>
>> Yong
>>
>>
>> On 27/07/09 4:09 PM, "Guillaume Collange" <[email protected]> wrote:
>>
>>> Hi Anthony,
>>>
>>> No, I mean generate a dataset that link two schema, one from a
>>> mysql DB,
>>> another by an Oracle db. It's to cross data between this schema.
>>> After I try
>>> to generate SQL, but it's generate the error from the previous @.
>>> Do you think
>>> that is possible?
>>>
>>> Best regards,
>>> Guillaume.
>>>
>>> 2009/7/27 Anthony Cros <[email protected]>
>>>> Hi Guillaume,
>>>>
>>>> I suppose you mean generate a dataset from a mysql schema and
>>>> output it into
>>>> an oracle one? It that's the case then unfortunately this is not
>>>> possible.
>>>> Both your source and target schemas must be of the same instance
>>>> of the same
>>>> RDBS. I do not think we will support this even in the new system,
>>>> apologies
>>>> for the inconvenience.
>>>>
>>>>
>>>> Regards,
>>>>
>>>> Anthony
>>>>
>>>>
>>>> Guillaume Collange wrote:
>>>>> Hi Anthony,
>>>>>
>>>>> I have a problem with the mart builder. I want to connect two
>>>>> schema source
>>>>> editor between a mysql and oracle DB. Is it impossible?
>>>>>
>>>>> This is the log trace after tried to generate the sql:
>>>>>
>>>>> */org.biomart.builder.exceptions.ConstructorException: Dataset
>>>>> uses schemas
>>>>> from multiple sources that cannot be linked to each other using
>>>>> SQL.
>>>>> at
>>>>>
>> org.biomart.builder.controller.SaveDDLMartConstructor.getConstructorRunnable>
>>>>
>> (
>>>>> SaveDDLMartConstructor.java:180)
>>>>> at
>>>>>
>> org.biomart.builder.view.gui.dialogs.SaveDDLDialog.createDDL
>> (SaveDDLDialog.j>>>
>> a
>>>>> va:470)
>>>>> at
>>>>>
>> org.biomart.builder.view.gui.dialogs.SaveDDLDialog.access$900
>> (SaveDDLDialog.>>>
>> j
>>>>> ava:75)
>>>>> at
>>>>>
>> org.biomart.builder.view.gui.dialogs.SaveDDLDialog$6.actionPerformed
>> (SaveDDL>>>
>> D
>>>>> ialog.java:402)
>>>>> at javax.swing.AbstractButton.fireActionPerformed(Unknown
>>>>> Source)
>>>>> at javax.swing.AbstractButton$Handler.actionPerformed(Unknown
>>>>> Source)
>>>>> at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown
>>>>> Source)
>>>>> at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
>>>>> at javax.swing.plaf.basic.BasicButtonListener.mouseReleased
>>>>> (Unknown
>>>>> Source)
>>>>> at java.awt.Component.processMouseEvent(Unknown Source)
>>>>> at javax.swing.JComponent.processMouseEvent(Unknown Source)
>>>>> at java.awt.Component.processEvent(Unknown Source)
>>>>> at java.awt.Container.processEvent(Unknown Source)
>>>>> at java.awt.Component.dispatchEventImpl(Unknown Source)
>>>>> at java.awt.Container.dispatchEventImpl(Unknown Source)
>>>>> at java.awt.Component.dispatchEvent(Unknown Source)
>>>>> at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown
>>>>> Source)
>>>>> at java.awt.LightweightDispatcher.processMouseEvent(Unknown
>>>>> Source)
>>>>> at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
>>>>> at java.awt.Container.dispatchEventImpl(Unknown Source)
>>>>> at java.awt.Window.dispatchEventImpl(Unknown Source)
>>>>> at java.awt.Component.dispatchEvent(Unknown Source)
>>>>> at java.awt.EventQueue.dispatchEvent(Unknown Source)
>>>>> at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown
>>>>> Source)
>>>>> at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown
>>>>> Source)
>>>>> at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown
>>>>> Source)
>>>>> at java.awt.Dialog$1.run(Unknown Source)
>>>>> at java.awt.Dialog$3.run(Unknown Source)
>>>>> at java.security.AccessController.doPrivileged(Native Method)
>>>>> at java.awt.Dialog.show(Unknown Source)
>>>>> at java.awt.Component.show(Unknown Source)
>>>>> at java.awt.Component.setVisible(Unknown Source)
>>>>> at java.awt.Window.setVisible(Unknown Source)
>>>>> at java.awt.Dialog.setVisible(Unknown Source)
>>>>> at
>>>>>
>> org.biomart.builder.view.gui.MartTabSet.requestSaveDDLDialog
>> (MartTabSet.java>>>
>> :
>>>>> 587)
>>>>> at
>>>>>
>> org.biomart.builder.view.gui.MartTabSet.requestCreateDDL
>> (MartTabSet.java:549>>>
>> )
>>>>> at
>>>>>
>> org.biomart.builder.view.gui.MartBuilder
>> $MartBuilderMenuBar.actionPerformed(>>>
>> M
>>>>> artBuilder.java:918)
>>>>> at javax.swing.AbstractButton.fireActionPerformed(Unknown
>>>>> Source)
>>>>> at javax.swing.AbstractButton$Handler.actionPerformed(Unknown
>>>>> Source)
>>>>> at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown
>>>>> Source)
>>>>> at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
>>>>> at javax.swing.AbstractButton.doClick(Unknown Source)
>>>>> at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown
>>>>> Source)
>>>>> at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased
>>>>> (Unknown
>>>>> Source)
>>>>> at java.awt.Component.processMouseEvent(Unknown Source)
>>>>> at javax.swing.JComponent.processMouseEvent(Unknown Source)
>>>>> at java.awt.Component.processEvent(Unknown Source)
>>>>> at java.awt.Container.processEvent(Unknown Source)
>>>>> at java.awt.Component.dispatchEventImpl(Unknown Source)
>>>>> at java.awt.Container.dispatchEventImpl(Unknown Source)
>>>>> at java.awt.Component.dispatchEvent(Unknown Source)
>>>>> at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown
>>>>> Source)
>>>>> at java.awt.LightweightDispatcher.processMouseEvent(Unknown
>>>>> Source)
>>>>> at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
>>>>> at java.awt.Container.dispatchEventImpl(Unknown Source)
>>>>> at java.awt.Window.dispatchEventImpl(Unknown Source)
>>>>> at java.awt.Component.dispatchEvent(Unknown Source)
>>>>> at java.awt.EventQueue.dispatchEvent(Unknown Source)
>>>>> at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown
>>>>> Source)
>>>>> at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown
>>>>> Source)
>>>>> at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown
>>>>> Source)
>>>>> at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
>>>>> at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
>>>>> at java.awt.EventDispatchThread.run(Unknown Source)/*
>>>>>
>>>>>
>>>>> Best regards,
>>>>> GC.
>>>>>
>>>>> 2009/7/22 Anthony Cros <[email protected]
>>>>> <mailto:[email protected]>>
>>>>>
>>>>>
>>>>> Hi Guillaume,
>>>>>
>>>>> We recently fixed a problem regarding the use of Oracle in
>>>>> MartBuilder, you may want to upgrade your version of BioMart
>>>>> first. If this doesn't solve the problem I will let my colleague
>>>>> Yong (CC'd here) take care of the problem since he's more
>>>>> knowledgeable on MartBuilder. Please let us know how this goes
>>>>> for
>>>>> you.
>>>>> Best regards,
>>>>>
>>>>> Anthony
>>>>>
>>>>>
>>>>> Guillaume Collange wrote:
>>>>>
>>>>> Hi Anthony,
>>>>>
>>>>> I have a problem to connect a Oracle DB with the
>>>>> martbuilder,
>>>>> I'm for all my configuration, DB, Schema, login,
>>>>> password...
>>>>> is it a driver problem?
>>>>>
>>>>> Best regards,
>>>>> GC
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> *Anthony Cros
>>>>> *Database/Application Programmer
>>>>>
>>>>> *Ontario Institute for Cancer Research
>>>>> *MaRS Centre, South Tower
>>>>> 101 College Street, Suite 600
>>>>> Toronto, Ontario, Canada M5G 0A3
>>>>> Tel: 647-260-7974
>>>>> Toll-free: 1-866-678-6427
>>>>> www.oicr.on.ca <http://www.oicr.on.ca> <http://www.oicr.on.ca>
>>>>>
>>>>>
>>>>> This message and any attachments may contain confidential and/or
>>>>> privileged information for the sole use of the intended
>>>>> recipient.
>>>>> Any review or distribution by anyone other than the person for
>>>>> whom it was originally intended is strictly prohibited. If you
>>>>> have received this message in error, please contact the sender
>>>>> and
>>>>> delete all copies. Opinions, conclusions or other information
>>>>> contained in this message may not be that of the organization.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Guillaume Collange
>>>>>
>>>>> ---
>>>>> ---
>>>>> ------------------------------------------------------------------
>>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> *Anthony Cros
>>>> *Database/Application Programmer
>>>>
>>>> *Ontario Institute for Cancer Research
>>>> *MaRS Centre, South Tower
>>>> 101 College Street, Suite 600
>>>> Toronto, Ontario, Canada M5G 0A3
>>>> Tel: 647-260-7974
>>>> Toll-free: 1-866-678-6427
>>>> www.oicr.on.ca <http://www.oicr.on.ca>
>>>>
>>>> This message and any attachments may contain confidential and/or
>>>> privileged
>>>> information for the sole use of the intended recipient. Any review
>>>> or
>>>> distribution by anyone other than the person for whom it was
>>>> originally
>>>> intended is strictly prohibited. If you have received this message
>>>> in error,
>>>> please contact the sender and delete all copies. Opinions,
>>>> conclusions or
>>>> other information contained in this message may not be that of the
>>>> organization.
>>>>
>>>
>>>
>>
>> Yong Liang
>> Database/Application Programmer
>>
>> Ontario Institute for Cancer Research
>> MaRS Centre, South Tower
>> 101 College Street, Suite 800
>> Toronto, Ontario, Canada M5G 0A3
>>
>> Tel: 647-260-7951
>> Toll-free: 1-866-678-6427
>> www.oicr.on.ca
>>
>> This message and any attachments may contain confidential and/or
>> privileged
>> information for the sole use of the intended recipient. Any review or
>> distribution by anyone other than the person for whom it was
>> originally
>> intended is strictly prohibited. If you have received this message
>> in error,
>> please contact the sender and delete all copies. Opinions,
>> conclusions or
>> other information contained in this message may not be that of the
>> organization.
>>
>>
