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

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

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

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

Mara Kim-2
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 <[hidden email]> 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
> [hidden email]
> 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
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel




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

Stephen Ficklin-2
Hi Mara,

What about finding features via the Sequence Features search page?   It appears under the 'Search Data' menu, or at <a class="moz-txt-link-freetext" href="http://[your">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 <[hidden email]> 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
> [hidden email]
> 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
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel




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

Mara Kim-2
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 <[hidden email]> 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 <[hidden email]> 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
> [hidden email]
> 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
[hidden email]
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

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

Stephen Ficklin-2
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 <[hidden email]> 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 <[hidden email]> 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
> [hidden email]
> 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
[hidden email]
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


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

Mara Kim-2
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
TitleFeatures
PathThis display has no path.
Query build time16.01 ms
Query execute time46355.22 ms
View render time129.96 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
> [hidden email]
> 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
[hidden email]
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

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

Stephen Ficklin-2
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
> [hidden email]
> 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
[hidden email]
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


------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
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Re: [Gmod-tripal-devel] BUG: Tripal 7.x-2.x (a68b9af2f768d244ddbc7607dd94d31de55673b2) Drupal Search fails to index new Tripal pages

Mara Kim-2

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" <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
> [hidden email]
> 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
[hidden email]
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


------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
Reply | Threaded
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|

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

Stephen Ficklin-2
Well, there are two ways we have handled search forms when we didn't want to use the defaults that come with Tripal:

1) Create a materialized views (Mview) that contains the information you want to use for searching.  Then use Drupal Views to create a custom search page using the Mview
2) Write our own module to handle the searching.

On our sites, we usually go with option #1 and use option #2 when the queries become too complex for Drupal views.  The first option will increase the size of your database and require that you update the MView each time new data is added.  The second requires custom code, but probably won't grow the database any.

Stephen

On 7/8/2014 2:10 PM, Mara Kim wrote:

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" <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
> [hidden email]
> 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
[hidden email]
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



------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
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|

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

Mara Kim-2
From the ancient depths of the listserve, I have finally solved this issue.

It appears that the drupal cron search indexing job wasn't able to keep up with the number of pages we were generating.  The solution was to go to  `Home » Administration » Configuration » Search and metadata`, and increase the Indexing Throttle to maximum (500 for us).  Then, using the count of items left to index reported on that page, I calculated how many times cron would need to run to index everything.  Then run the following command in the drupal directory, where `$n` is the number of times cron needs to run:

    for i in $(seq 1 $n); do drush cron; done

Obviously this should be done in a GNU screen if performed via SSH.  Once the command finishes, all pages will be indexed!

On Tue, Jul 8, 2014 at 1:27 PM, Stephen Ficklin <[hidden email]> wrote:
Well, there are two ways we have handled search forms when we didn't want to use the defaults that come with Tripal:

1) Create a materialized views (Mview) that contains the information you want to use for searching.  Then use Drupal Views to create a custom search page using the Mview
2) Write our own module to handle the searching.

On our sites, we usually go with option #1 and use option #2 when the queries become too complex for Drupal views.  The first option will increase the size of your database and require that you update the MView each time new data is added.  The second requires custom code, but probably won't grow the database any.

Stephen

On 7/8/2014 2:10 PM, Mara Kim wrote:

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" <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
> [hidden email]
> 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
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--
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





--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN

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