Re: [Gmod-tripal-devel] BUG: Tripal 7.x-2.x (a68b9af2f768d244ddbc7607dd94d31de55673b2) Drupal Search fails to index new Tripal pages

[Mara K. <mar...@va...>]

Sorry to say that we haven't made any progress on this. Any ideas where to
start?
On Jul 8, 2014 2:08 PM, "Stephen Ficklin" <spf...@gm...> wrote:

>  Hi Mara,
>
> Just curious if you were able to fix this issue?
>
> Stephen
>
> On 6/18/2014 7:09 PM, Mara Kim wrote:
>
> Hmm, that helped a bit, but it is still slow.
>
>  This is especially surprising because an EXPLAIN ANALYZE of the
> underlying query is very fast:
> drupal=# EXPLAIN ANALYZE SELECT feature.uniquename AS feature_uniquename,
> feature.name AS feature_name, feature.seqlen AS feature_seqlen,
> feature.is_obsolete AS feature_is_obsolete
> FROM chado.feature feature ORDER BY feature_name ASC LIMIT 25 OFFSET 0;
>                                                                     QUERY
> PLAN
>
> ---------------------------------------------------------------------------------------------------------------------------------------------------
>  Limit  (cost=0.00..11.54 rows=25 width=42) (actual time=0.099..0.248
> rows=25 loops=1)
>    ->  Index Scan using feature_name_ind1 on feature
>  (cost=0.00..125462958.86 rows=271696608 width=42) (actual
> time=0.097..0.242 rows=25 loops=1)
>  Total runtime: 0.312 ms
> (3 rows)
>
>
>
>  Whereas Drupal takes substantially longer with the same query:
>   *Query*
>
> SELECT feature.uniquename AS feature_uniquename, feature.name AS feature_name, feature.seqlen AS feature_seqlen, feature.is_obsolete AS feature_is_obsolete
> FROM
> {chado.feature} feature
> ORDER BY feature_name ASC
> LIMIT 25 OFFSET 0
>
>   *Title* Features  *Path* This display has no path.  *Query build time* 16.01
> ms  *Query execute time* 46355.22 ms  *View render time* 129.96 ms
>
>  It seems that the Drupal query is using a different query plan...it may
> not even be using the index...
>
>
>
>  On Wed, Jun 18, 2014 at 2:00 PM, Stephen Ficklin <spf...@gm...>
> wrote:
>
>>  Oh, right. I remember you had this problem previously.  The problem is
>> that the view which provides the search page, by default, wants to provide
>> a feature type drop down with all  of the feature types that you have
>> available.  So, it spends a lot of time going through all of your features
>> to find all of the types which slows the view down.  Most likely you don't
>> want to search by all your feature types anyway, so I think you can speed
>> it up by the following:
>>
>> 1) Click the little wheel that appears in the top-left corner of the form
>> when you mouse over it and click 'Edit view'.  This will take you to the
>> View Edit page.
>> 2) Under the filter criteria section click the 'Chado Feature: Type Id
>> (exposed)' link.
>> 3) make the following changes:   Select the radio button 'Grouped
>> filters', then scroll a bit and in the table add in the feature types you
>> want to allow the user to search by and select the proper value in the drop
>> down.  Click the apply button and the overlay will close.
>> 4) Finally, click the 'Save' button on the top right hand corner.
>>
>> This should take you back to the search page which hopefully will load
>> faster.
>>
>> Stephen
>>
>>
>> On 6/18/2014 2:43 PM, Mara Kim wrote:
>>
>> Hmm, so the Sequence Features search does find the genes.  However, it
>> loads *extremely* slowly.  Is there a way to optimize the load time of this
>> page?
>>
>>
>>  On Tue, Jun 17, 2014 at 1:41 PM, Stephen Ficklin <spf...@gm...>
>> wrote:
>>
>>>  Hi Mara,
>>>
>>> What about finding features via the Sequence Features search page?   It
>>> appears under the 'Search Data' menu, or at http://[your
>>> site]/chado/feature
>>>
>>> Stephen
>>>
>>>
>>> On 6/17/2014 2:25 PM, Mara Kim wrote:
>>>
>>> It would be preferable for this to be fixed as soon as possible since
>>> finding features using the Feature Browser is a bit unwieldy.  However,
>>> this could be alleviated in the interim by adding alphabetical links in the
>>> feature browser so that it is easier to find specific features.
>>>
>>>
>>> On Tue, Jun 17, 2014 at 8:06 AM, Stephen Ficklin <spf...@gm...>
>>> wrote:
>>>
>>>> Hi Mara,
>>>>
>>>> Thanks for cluing us in. I have added this bug to the Tripal "Issues"
>>>> tracker on the Drupal website.  You can subscribe to the page to see any
>>>> updates when this bug is addressed: https://drupal.org/node/2287615.
>>>>  If
>>>> it's a critical issue to you let me know and we can try to get to it
>>>> quicker.
>>>>
>>>> Stephen
>>>>
>>>> On 6/11/2014 1:16 PM, Mara Kim wrote:
>>>> > Hello,
>>>> >
>>>> > I believe there is another bug on the 7.x-2.x branch, commit
>>>> > a68b9af2f768d244ddbc7607dd94d31de55673b2.
>>>> >
>>>> > The drupal cron job that adds new pages to the search index no longer
>>>> adds
>>>> > additional nodes.  This definitely used to work in an older commit,
>>>> > since I can find pages that Tripal created in the past via the drupal
>>>> > search tool.  Running cron.php manually via
>>>> > Administration->Configuration->System->Cron completes successfully,
>>>> > but does not add the pages to the search index.
>>>> >
>>>> > Examination of the reflog indicates that this bug was introduced
>>>> > sometime after commit 0aa9fbf9f197f92363b3adc887e36325e6930a9d
>>>> >
>>>> > Thanks,
>>>> > Mara Kim
>>>> >
>>>> > Ph.D. Candidate
>>>> > Computational Biology
>>>> > Vanderbilt University
>>>> > Nashville, TN
>>>> >
>>>> >
>>>>  >
>>>> ------------------------------------------------------------------------------
>>>> > HPCC Systems Open Source Big Data Platform from LexisNexis Risk
>>>> Solutions
>>>> > Find What Matters Most in Your Big Data with HPCC Systems
>>>> > Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
>>>> > Leverages Graph Analysis for Fast Processing & Easy Data Exploration
>>>> > http://p.sf.net/sfu/hpccsystems
>>>> > _______________________________________________
>>>> > Gmod-tripal-devel mailing list
>>>> > Gmo...@li...
>>>> > https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> HPCC Systems Open Source Big Data Platform from LexisNexis Risk
>>>> Solutions
>>>> Find What Matters Most in Your Big Data with HPCC Systems
>>>> Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
>>>> Leverages Graph Analysis for Fast Processing & Easy Data Exploration
>>>> http://p.sf.net/sfu/hpccsystems
>>>> _______________________________________________
>>>> Gmod-tripal-devel mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>>>
>>>>
>>>
>>>
>>>  --
>>>   Mara Kim
>>>
>>>  Ph.D. Candidate
>>>  Computational Biology
>>>  Vanderbilt University
>>> Nashville, TN
>>>
>>>
>>>
>>
>>
>>  --
>>   Mara Kim
>>
>>  Ph.D. Candidate
>>  Computational Biology
>>  Vanderbilt University
>> Nashville, TN
>>
>>
>>
>
>
>  --
>   Mara Kim
>
>  Ph.D. Candidate
>  Computational Biology
>  Vanderbilt University
> Nashville, TN
>
>
>