[Gmod-tripal-devel] Deleting orphaned analysisfeatures

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[Gmod-tripal-devel] Deleting orphaned analysisfeatures

Michael Dondrup-3
Hi,

during some testing attempts, I have created a lot of Blast-analyses. These imports have generated a lot of
analysis features. I have deleted the redundant Analyses, but the analysisfeature entries seem to have stayed.
Is there a safe way to delete them, or did I overlook the option? (could think of some "DELETE FROM analysisfeature WHERE …")
Otherwise, it might make sense to add a cleanup option to the Analysis configuration pages, in case it is not already there.

Best
Michael





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Re: [Gmod-tripal-devel] Deleting orphaned analysisfeatures

Michael Dondrup-3
I have to correct my first question. When I delete the Blast-analysis, analysisfeatures are correctly removed from the database.
However the blast_hit_data seem to remain. I have now deleted all blast analyses but still have 199 entries in
the blast_hit_data table, can I simply delete them?


On Sep 18, 2013, at 11:42 AM, Michael Dondrup wrote:

> Hi,
>
> during some testing attempts, I have created a lot of Blast-analyses. These imports have generated a lot of
> analysis features. I have deleted the redundant Analyses, but the analysisfeature entries seem to have stayed.
> Is there a safe way to delete them, or did I overlook the option? (could think of some "DELETE FROM analysisfeature WHERE …")
> Otherwise, it might make sense to add a cleanup option to the Analysis configuration pages, in case it is not already there.
>
> Best
> Michael
>
>
>
>

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Re: [Gmod-tripal-devel] Deleting orphaned analysisfeatures

Stephen Ficklin-2
Hi Michael,

Oh, good point those data should be removed from the blast_hit_data database.  I have added an issue to the project to fix that:  https://drupal.org/node/2092067

Yes, you can delete them.

Stephen

On 9/18/2013 7:47 AM, Michael Dondrup wrote:
I have to correct my first question. When I delete the Blast-analysis, analysisfeatures are correctly removed from the database.
However the blast_hit_data seem to remain. I have now deleted all blast analyses but still have 199 entries in 
the blast_hit_data table, can I simply delete them?


On Sep 18, 2013, at 11:42 AM, Michael Dondrup wrote:

Hi,

during some testing attempts, I have created a lot of Blast-analyses. These imports have generated a lot of 
analysis features. I have deleted the redundant Analyses, but the analysisfeature entries seem to have stayed.
Is there a safe way to delete them, or did I overlook the option? (could think of some "DELETE FROM analysisfeature WHERE …")
Otherwise, it might make sense to add a cleanup option to the Analysis configuration pages, in case it is not already there.

Best
Michael





      

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Re: [Gmod-tripal-devel] Deleting orphaned analysisfeatures

Michael Dondrup-3
Hi,
ok, I have looked at it a bit more together with a colleague who knows much more psql, and we found that blast_hit_data is not in the core chado schema, correct?
Looking at the table definition and comparing it
to analysisfeature, we recommend that  blast_hit_data could use two foreign key constraints, same as analysisfeature, so we first deleted all blast_hit_data,
for a clean start.

delete from blast_hit_data;
And then:
ALTER TABLE blast_hit_data ADD CONSTRAINT "blast_hit_data_analysis_id_fkey" FOREIGN KEY (analysis_id)  REFERENCES analysis(analysis_id)
ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED;
ALTER TABLE blast_hit_data ADD CONSTRAINT "blast_hit_data_feature_id_fkey" FOREIGN KEY (feature_id)  REFERENCES feature(feature_id)
ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED;

Hopefully, this helps keep the blast hits consistent.

Best

Michael Dondrup
Postdoctoral fellow
Sea Lice Research Centre/Department of Informatics
University of Bergen
Thormøhlensgate 55, N-5008 Bergen,
Norway

On Sep 18, 2013, at 2:52 PM, Stephen Ficklin wrote:

> Hi Michael,
>
> Oh, good point those data should be removed from the blast_hit_data database.  I have added an issue to the project to fix that:  https://drupal.org/node/2092067
>
> Yes, you can delete them.
>
> Stephen
>
> On 9/18/2013 7:47 AM, Michael Dondrup wrote:
>> I have to correct my first question. When I delete the Blast-analysis, analysisfeatures are correctly removed from the database.
>> However the blast_hit_data seem to remain. I have now deleted all blast analyses but still have 199 entries in
>> the blast_hit_data table, can I simply delete them?
>>
>>
>> On Sep 18, 2013, at 11:42 AM, Michael Dondrup wrote:
>>
>>
>>> Hi,
>>>
>>> during some testing attempts, I have created a lot of Blast-analyses. These imports have generated a lot of
>>> analysis features. I have deleted the redundant Analyses, but the analysisfeature entries seem to have stayed.
>>> Is there a safe way to delete them, or did I overlook the option? (could think of some "DELETE FROM analysisfeature WHERE …")
>>> Otherwise, it might make sense to add a cleanup option to the Analysis configuration pages, in case it is not already there.
>>>
>>> Best
>>> Michael
>>>
>>>
>>>
>>>
>>>
>>
>>
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>> Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13.
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>>
>> _______________________________________________
>> Gmod-tripal-devel mailing list
>>
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>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>
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