[BioMart Users] Updates database query with biomart

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[BioMart Users] Updates database query with biomart

Mariette
Hi everyone,

I'm trying to run some update request on our database throught a biomart
plugin.
The query objects provided within biomart handle biomart query, but
those ones don't support update request.
What would be the best way to implement it ?

I didn't find any biomart DBQuery, did I miss something ? Should I have
to add in my processor the connectDB() and all related functions,
just as it is done in the QueryPlanner class ?

thanks for your answer,
Jerome


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Re: [BioMart Users] Updates database query with biomart

Syed Haider-2
Hi Jerome,

Instead of writing results to your intended output handle, write them to
a temporary handle where you can store them. Then use this temporary
buffer to return to real output handle as and when needed.

if i understand your question correctly, there is no mechanism for
asking for results as range queries.





On 04/06/2012 10:48, Mariette wrote:

> Hi everyone,
>
> I'm trying to run some update request on our database throught a biomart
> plugin.
> The query objects provided within biomart handle biomart query, but
> those ones don't support update request.
> What would be the best way to implement it ?
>
> I didn't find any biomart DBQuery, did I miss something ? Should I have
> to add in my processor the connectDB() and all related functions,
> just as it is done in the QueryPlanner class ?
>
> thanks for your answer,
> Jerome
>
>
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
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Re: [BioMart Users] Updates database query with biomart

Mariette

Hi,

there is a missunderstood. What I want is to make a SQL update query on
the database. The plugin I'm writting is displaying a set of
favorites contigs. This favorite flag is settled within the database. We
would like to allow the web user to modify this flag by updating
it in the database.

hope I was clearer, but don't hesitate to ask if you have any questions.
Jerome







Le 04/06/2012 14:25, Syed Haider a écrit :

> Hi Jerome,
>
> Instead of writing results to your intended output handle, write them
> to a temporary handle where you can store them. Then use this
> temporary buffer to return to real output handle as and when needed.
>
> if i understand your question correctly, there is no mechanism for
> asking for results as range queries.
>
>
>
>
>
> On 04/06/2012 10:48, Mariette wrote:
>> Hi everyone,
>>
>> I'm trying to run some update request on our database throught a biomart
>> plugin.
>> The query objects provided within biomart handle biomart query, but
>> those ones don't support update request.
>> What would be the best way to implement it ?
>>
>> I didn't find any biomart DBQuery, did I miss something ? Should I have
>> to add in my processor the connectDB() and all related functions,
>> just as it is done in the QueryPlanner class ?
>>
>> thanks for your answer,
>> Jerome
>>
>>
>> _______________________________________________
>> Users mailing list
>> [hidden email]
>> https://lists.biomart.org/mailman/listinfo/users

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Re: [BioMart Users] Updates database query with biomart

Syed Haider-2
Ok, thats not possible. You would need to write the UPDATE SQL yourself
and to *make sure* that you keep the mart database structure correct. I
assume if its just a matter of changing 1 value in a particular column,
it shouldnt be a huge problem if you are not filtering on this as by
default mart filter columns are indexed.

Best,
Syed

On 04/06/2012 14:57, Mariette wrote:

>
> Hi,
>
> there is a missunderstood. What I want is to make a SQL update query on
> the database. The plugin I'm writting is displaying a set of
> favorites contigs. This favorite flag is settled within the database. We
> would like to allow the web user to modify this flag by updating
> it in the database.
>
> hope I was clearer, but don't hesitate to ask if you have any questions.
> Jerome
>
>
>
>
>
>
>
> Le 04/06/2012 14:25, Syed Haider a écrit :
>> Hi Jerome,
>>
>> Instead of writing results to your intended output handle, write them
>> to a temporary handle where you can store them. Then use this
>> temporary buffer to return to real output handle as and when needed.
>>
>> if i understand your question correctly, there is no mechanism for
>> asking for results as range queries.
>>
>>
>>
>>
>>
>> On 04/06/2012 10:48, Mariette wrote:
>>> Hi everyone,
>>>
>>> I'm trying to run some update request on our database throught a biomart
>>> plugin.
>>> The query objects provided within biomart handle biomart query, but
>>> those ones don't support update request.
>>> What would be the best way to implement it ?
>>>
>>> I didn't find any biomart DBQuery, did I miss something ? Should I have
>>> to add in my processor the connectDB() and all related functions,
>>> just as it is done in the QueryPlanner class ?
>>>
>>> thanks for your answer,
>>> Jerome
>>>
>>>
>>> _______________________________________________
>>> Users mailing list
>>> [hidden email]
>>> https://lists.biomart.org/mailman/listinfo/users
>
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Re: [BioMart Users] Updates database query with biomart

Mariette

Thanks for your answer,

could you point out the best way to do it ?
There is a class in charge to handle SQL request ? (I haven't figure  
out which one does the job)

Jerome


Syed Haider <[hidden email]> a écrit :

> Ok, thats not possible. You would need to write the UPDATE SQL  
> yourself and to *make sure* that you keep the mart database  
> structure correct. I assume if its just a matter of changing 1 value  
> in a particular column, it shouldnt be a huge problem if you are not  
> filtering on this as by default mart filter columns are indexed.
>
> Best,
> Syed
>
> On 04/06/2012 14:57, Mariette wrote:
>>
>> Hi,
>>
>> there is a missunderstood. What I want is to make a SQL update query on
>> the database. The plugin I'm writting is displaying a set of
>> favorites contigs. This favorite flag is settled within the database. We
>> would like to allow the web user to modify this flag by updating
>> it in the database.
>>
>> hope I was clearer, but don't hesitate to ask if you have any questions.
>> Jerome
>>
>>
>>
>>
>>
>>
>>
>> Le 04/06/2012 14:25, Syed Haider a écrit :
>>> Hi Jerome,
>>>
>>> Instead of writing results to your intended output handle, write them
>>> to a temporary handle where you can store them. Then use this
>>> temporary buffer to return to real output handle as and when needed.
>>>
>>> if i understand your question correctly, there is no mechanism for
>>> asking for results as range queries.
>>>
>>>
>>>
>>>
>>>
>>> On 04/06/2012 10:48, Mariette wrote:
>>>> Hi everyone,
>>>>
>>>> I'm trying to run some update request on our database throught a biomart
>>>> plugin.
>>>> The query objects provided within biomart handle biomart query, but
>>>> those ones don't support update request.
>>>> What would be the best way to implement it ?
>>>>
>>>> I didn't find any biomart DBQuery, did I miss something ? Should I have
>>>> to add in my processor the connectDB() and all related functions,
>>>> just as it is done in the QueryPlanner class ?
>>>>
>>>> thanks for your answer,
>>>> Jerome
>>>>
>>>>
>>>> _______________________________________________
>>>> Users mailing list
>>>> [hidden email]
>>>> https://lists.biomart.org/mailman/listinfo/users
>>
>

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Re: [BioMart Users] Updates database query with biomart

Syed Haider-2

Hi Jerome,

Some code on how to connect using JDBC is available in the class
mentioned below, however, it doesnt do any UPDATE queries. I assume its,
just a matter of passing the SQL parameters differently.

src/org/biomart/queryEngine/SubQuery::SubQuery(...)

HTH,
Syed


On 04/06/2012 18:42, jmariett wrote:

>
> Thanks for your answer,
>
> could you point out the best way to do it ?
> There is a class in charge to handle SQL request ? (I haven't figure out
> which one does the job)
>
> Jerome
>
>
> Syed Haider <[hidden email]> a écrit :
>
>> Ok, thats not possible. You would need to write the UPDATE SQL
>> yourself and to *make sure* that you keep the mart database structure
>> correct. I assume if its just a matter of changing 1 value in a
>> particular column, it shouldnt be a huge problem if you are not
>> filtering on this as by default mart filter columns are indexed.
>>
>> Best,
>> Syed
>>
>> On 04/06/2012 14:57, Mariette wrote:
>>>
>>> Hi,
>>>
>>> there is a missunderstood. What I want is to make a SQL update query on
>>> the database. The plugin I'm writting is displaying a set of
>>> favorites contigs. This favorite flag is settled within the database. We
>>> would like to allow the web user to modify this flag by updating
>>> it in the database.
>>>
>>> hope I was clearer, but don't hesitate to ask if you have any questions.
>>> Jerome
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> Le 04/06/2012 14:25, Syed Haider a écrit :
>>>> Hi Jerome,
>>>>
>>>> Instead of writing results to your intended output handle, write them
>>>> to a temporary handle where you can store them. Then use this
>>>> temporary buffer to return to real output handle as and when needed.
>>>>
>>>> if i understand your question correctly, there is no mechanism for
>>>> asking for results as range queries.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On 04/06/2012 10:48, Mariette wrote:
>>>>> Hi everyone,
>>>>>
>>>>> I'm trying to run some update request on our database throught a
>>>>> biomart
>>>>> plugin.
>>>>> The query objects provided within biomart handle biomart query, but
>>>>> those ones don't support update request.
>>>>> What would be the best way to implement it ?
>>>>>
>>>>> I didn't find any biomart DBQuery, did I miss something ? Should I
>>>>> have
>>>>> to add in my processor the connectDB() and all related functions,
>>>>> just as it is done in the QueryPlanner class ?
>>>>>
>>>>> thanks for your answer,
>>>>> Jerome
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Users mailing list
>>>>> [hidden email]
>>>>> https://lists.biomart.org/mailman/listinfo/users
>>>
>>
>
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