[Gmod-tripal-devel] Organism page, order by name is slow

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[Gmod-tripal-devel] Organism page, order by name is slow

Mara Kim-2
Hello,

I have noticed that the organism pages are loading extremely slowly, and I believe this is due to the use of order by `name`, as opposed to `uniquename`, which is indexed by default in Chado.  Could this behavior be changed?

--
Mara Kim

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

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Re: [Gmod-tripal-devel] Organism page, order by name is slow

Stephen Ficklin-2
Hi Mara,

Can you tell me the name of the template where you see the order by name that is causing slowness?

Thanks,
Stephen

On 1/26/2015 2:38 PM, Mara Kim wrote:
Hello,

I have noticed that the organism pages are loading extremely slowly, and I believe this is due to the use of order by `name`, as opposed to `uniquename`, which is indexed by default in Chado.  Could this behavior be changed?

--
Mara Kim

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


------------------------------------------------------------------------------
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sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/


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Re: [Gmod-tripal-devel] Organism page, order by name is slow

Mara Kim-2
Not exactly sure which template it is, but when I attempt to look at an organism page (eg. Homo sapiens), it loads very slowly.  pg_stat_activity reports the query as:

SELECT feature_id FROM chado.feature WHERE organism_id = '25' AND type_id IN ('789', '320')  ORDER BY name ASC LIMIT 25 OFFSET 0

On Mon, Jan 26, 2015 at 2:02 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Mara,

Can you tell me the name of the template where you see the order by name that is causing slowness?

Thanks,
Stephen


On 1/26/2015 2:38 PM, Mara Kim wrote:
Hello,

I have noticed that the organism pages are loading extremely slowly, and I believe this is due to the use of order by `name`, as opposed to `uniquename`, which is indexed by default in Chado.  Could this behavior be changed?

--
Mara Kim

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


------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/


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--
Mara Kim

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

------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
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Re: [Gmod-tripal-devel] Organism page, order by name is slow

Stephen Ficklin-2
I see.  Do you have the feature browser turned on?

On 1/26/2015 3:06 PM, Mara Kim wrote:
Not exactly sure which template it is, but when I attempt to look at an organism page (eg. Homo sapiens), it loads very slowly.  pg_stat_activity reports the query as:

SELECT feature_id FROM chado.feature WHERE organism_id = '25' AND type_id IN ('789', '320')  ORDER BY name ASC LIMIT 25 OFFSET 0

On Mon, Jan 26, 2015 at 2:02 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Mara,

Can you tell me the name of the template where you see the order by name that is causing slowness?

Thanks,
Stephen


On 1/26/2015 2:38 PM, Mara Kim wrote:
Hello,

I have noticed that the organism pages are loading extremely slowly, and I believe this is due to the use of order by `name`, as opposed to `uniquename`, which is indexed by default in Chado.  Could this behavior be changed?

--
Mara Kim

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


------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/


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--
Mara Kim

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


------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
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look and join the conversation now. http://goparallel.sourceforge.net/
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Re: [Gmod-tripal-devel] Organism page, order by name is slow

Mara Kim-2
I believe so.  I'm guessing that must be the problem?  Is there a way to disable it?

On Mon, Jan 26, 2015 at 2:09 PM, Stephen Ficklin <[hidden email]> wrote:
I see.  Do you have the feature browser turned on?


On 1/26/2015 3:06 PM, Mara Kim wrote:
Not exactly sure which template it is, but when I attempt to look at an organism page (eg. Homo sapiens), it loads very slowly.  pg_stat_activity reports the query as:

SELECT feature_id FROM chado.feature WHERE organism_id = '25' AND type_id IN ('789', '320')  ORDER BY name ASC LIMIT 25 OFFSET 0

On Mon, Jan 26, 2015 at 2:02 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Mara,

Can you tell me the name of the template where you see the order by name that is causing slowness?

Thanks,
Stephen


On 1/26/2015 2:38 PM, Mara Kim wrote:
Hello,

I have noticed that the organism pages are loading extremely slowly, and I believe this is due to the use of order by `name`, as opposed to `uniquename`, which is indexed by default in Chado.  Could this behavior be changed?

--
Mara Kim

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


------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/


_______________________________________________
Gmod-tripal-devel mailing list
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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

------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
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Re: [Gmod-tripal-devel] Organism page, order by name is slow

Stephen Ficklin-2
Yes, you can turn it off. If you are using v1.1 you can turn it off by navigating to Administer -> Tripal Management -> Features -> Feature Configuration.  Then on the page that appears you'll see a section titled 'Feature Browser'.  In that section you can turn off the feature browser on the organism page.

Tripal v2.0-rc1 is a bit more flexible with the links available on a page.   If you want to turn it off for all organisms you go to, Tripal -> Chado Modules -> Organisms and on the admin page in the upper right corner you'll see a tab titled 'TOC'  (meaning Table of Contents).  Here you will be presented with a form that allows your to re-order, rename or hide the elements in the TOC on the organism page.   You can check the button to hide the feature browser.

Let me know if turning that off helps your problem.

Stephen

On 1/26/2015 3:15 PM, Mara Kim wrote:
I believe so.  I'm guessing that must be the problem?  Is there a way to disable it?

On Mon, Jan 26, 2015 at 2:09 PM, Stephen Ficklin <[hidden email]> wrote:
I see.  Do you have the feature browser turned on?


On 1/26/2015 3:06 PM, Mara Kim wrote:
Not exactly sure which template it is, but when I attempt to look at an organism page (eg. Homo sapiens), it loads very slowly.  pg_stat_activity reports the query as:

SELECT feature_id FROM chado.feature WHERE organism_id = '25' AND type_id IN ('789', '320')  ORDER BY name ASC LIMIT 25 OFFSET 0

On Mon, Jan 26, 2015 at 2:02 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Mara,

Can you tell me the name of the template where you see the order by name that is causing slowness?

Thanks,
Stephen


On 1/26/2015 2:38 PM, Mara Kim wrote:
Hello,

I have noticed that the organism pages are loading extremely slowly, and I believe this is due to the use of order by `name`, as opposed to `uniquename`, which is indexed by default in Chado.  Could this behavior be changed?

--
Mara Kim

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


------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/


_______________________________________________
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


------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
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Re: [Gmod-tripal-devel] Organism page, order by name is slow

Mara Kim-2
Hmmm, so I hid both the Feature Browser and Feature Summary, but it appears the template is still sending the same queries to the database.  I guess hiding the sections doesn't actually disable query generation?

On Mon, Jan 26, 2015 at 3:06 PM, Stephen Ficklin <[hidden email]> wrote:
Yes, you can turn it off. If you are using v1.1 you can turn it off by navigating to Administer -> Tripal Management -> Features -> Feature Configuration.  Then on the page that appears you'll see a section titled 'Feature Browser'.  In that section you can turn off the feature browser on the organism page.

Tripal v2.0-rc1 is a bit more flexible with the links available on a page.   If you want to turn it off for all organisms you go to, Tripal -> Chado Modules -> Organisms and on the admin page in the upper right corner you'll see a tab titled 'TOC'  (meaning Table of Contents).  Here you will be presented with a form that allows your to re-order, rename or hide the elements in the TOC on the organism page.   You can check the button to hide the feature browser.

Let me know if turning that off helps your problem.

Stephen


On 1/26/2015 3:15 PM, Mara Kim wrote:
I believe so.  I'm guessing that must be the problem?  Is there a way to disable it?

On Mon, Jan 26, 2015 at 2:09 PM, Stephen Ficklin <[hidden email]> wrote:
I see.  Do you have the feature browser turned on?


On 1/26/2015 3:06 PM, Mara Kim wrote:
Not exactly sure which template it is, but when I attempt to look at an organism page (eg. Homo sapiens), it loads very slowly.  pg_stat_activity reports the query as:

SELECT feature_id FROM chado.feature WHERE organism_id = '25' AND type_id IN ('789', '320')  ORDER BY name ASC LIMIT 25 OFFSET 0

On Mon, Jan 26, 2015 at 2:02 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Mara,

Can you tell me the name of the template where you see the order by name that is causing slowness?

Thanks,
Stephen


On 1/26/2015 2:38 PM, Mara Kim wrote:
Hello,

I have noticed that the organism pages are loading extremely slowly, and I believe this is due to the use of order by `name`, as opposed to `uniquename`, which is indexed by default in Chado.  Could this behavior be changed?

--
Mara Kim

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


------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/


_______________________________________________
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

------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
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Re: [Gmod-tripal-devel] Organism page, order by name is slow

Stephen Ficklin-2
Okay, I'll dig into and let you know what I find.

Stephen

On 1/26/2015 4:19 PM, Mara Kim wrote:
Hmmm, so I hid both the Feature Browser and Feature Summary, but it appears the template is still sending the same queries to the database.  I guess hiding the sections doesn't actually disable query generation?

On Mon, Jan 26, 2015 at 3:06 PM, Stephen Ficklin <[hidden email]> wrote:
Yes, you can turn it off. If you are using v1.1 you can turn it off by navigating to Administer -> Tripal Management -> Features -> Feature Configuration.  Then on the page that appears you'll see a section titled 'Feature Browser'.  In that section you can turn off the feature browser on the organism page.

Tripal v2.0-rc1 is a bit more flexible with the links available on a page.   If you want to turn it off for all organisms you go to, Tripal -> Chado Modules -> Organisms and on the admin page in the upper right corner you'll see a tab titled 'TOC'  (meaning Table of Contents).  Here you will be presented with a form that allows your to re-order, rename or hide the elements in the TOC on the organism page.   You can check the button to hide the feature browser.

Let me know if turning that off helps your problem.

Stephen


On 1/26/2015 3:15 PM, Mara Kim wrote:
I believe so.  I'm guessing that must be the problem?  Is there a way to disable it?

On Mon, Jan 26, 2015 at 2:09 PM, Stephen Ficklin <[hidden email]> wrote:
I see.  Do you have the feature browser turned on?


On 1/26/2015 3:06 PM, Mara Kim wrote:
Not exactly sure which template it is, but when I attempt to look at an organism page (eg. Homo sapiens), it loads very slowly.  pg_stat_activity reports the query as:

SELECT feature_id FROM chado.feature WHERE organism_id = '25' AND type_id IN ('789', '320')  ORDER BY name ASC LIMIT 25 OFFSET 0

On Mon, Jan 26, 2015 at 2:02 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Mara,

Can you tell me the name of the template where you see the order by name that is causing slowness?

Thanks,
Stephen


On 1/26/2015 2:38 PM, Mara Kim wrote:
Hello,

I have noticed that the organism pages are loading extremely slowly, and I believe this is due to the use of order by `name`, as opposed to `uniquename`, which is indexed by default in Chado.  Could this behavior be changed?

--
Mara Kim

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


------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/


_______________________________________________
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


------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
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Re: [Gmod-tripal-devel] Organism page, order by name is slow

Mara Kim-2
In reply to this post by Mara Kim-2
Forgot to mention, I am running v2.0-rc1

On Mon, Jan 26, 2015 at 3:19 PM, Mara Kim <[hidden email]> wrote:
Hmmm, so I hid both the Feature Browser and Feature Summary, but it appears the template is still sending the same queries to the database.  I guess hiding the sections doesn't actually disable query generation?

On Mon, Jan 26, 2015 at 3:06 PM, Stephen Ficklin <[hidden email]> wrote:
Yes, you can turn it off. If you are using v1.1 you can turn it off by navigating to Administer -> Tripal Management -> Features -> Feature Configuration.  Then on the page that appears you'll see a section titled 'Feature Browser'.  In that section you can turn off the feature browser on the organism page.

Tripal v2.0-rc1 is a bit more flexible with the links available on a page.   If you want to turn it off for all organisms you go to, Tripal -> Chado Modules -> Organisms and on the admin page in the upper right corner you'll see a tab titled 'TOC'  (meaning Table of Contents).  Here you will be presented with a form that allows your to re-order, rename or hide the elements in the TOC on the organism page.   You can check the button to hide the feature browser.

Let me know if turning that off helps your problem.

Stephen


On 1/26/2015 3:15 PM, Mara Kim wrote:
I believe so.  I'm guessing that must be the problem?  Is there a way to disable it?

On Mon, Jan 26, 2015 at 2:09 PM, Stephen Ficklin <[hidden email]> wrote:
I see.  Do you have the feature browser turned on?


On 1/26/2015 3:06 PM, Mara Kim wrote:
Not exactly sure which template it is, but when I attempt to look at an organism page (eg. Homo sapiens), it loads very slowly.  pg_stat_activity reports the query as:

SELECT feature_id FROM chado.feature WHERE organism_id = '25' AND type_id IN ('789', '320')  ORDER BY name ASC LIMIT 25 OFFSET 0

On Mon, Jan 26, 2015 at 2:02 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Mara,

Can you tell me the name of the template where you see the order by name that is causing slowness?

Thanks,
Stephen


On 1/26/2015 2:38 PM, Mara Kim wrote:
Hello,

I have noticed that the organism pages are loading extremely slowly, and I believe this is due to the use of order by `name`, as opposed to `uniquename`, which is indexed by default in Chado.  Could this behavior be changed?

--
Mara Kim

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


------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/


_______________________________________________
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



--
Mara Kim

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

------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
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Re: [Gmod-tripal-devel] Organism page, order by name is slow

Stephen Ficklin-2
Hi Mara,

I think this is a bug that has already been fixed in the development branch.  Can you try updating your code to the most-recent version?   Change to the directory where you have the Tripal module installed, and If you are using the git repository then try this:

git checkout 7.x-2.x
git pull

If you are using the Drupal module installed via drush then try this:

drush pm-download tripal 7.x-2.x-dev

Stephen

On 1/26/2015 4:27 PM, Mara Kim wrote:
Forgot to mention, I am running v2.0-rc1

On Mon, Jan 26, 2015 at 3:19 PM, Mara Kim <[hidden email]> wrote:
Hmmm, so I hid both the Feature Browser and Feature Summary, but it appears the template is still sending the same queries to the database.  I guess hiding the sections doesn't actually disable query generation?

On Mon, Jan 26, 2015 at 3:06 PM, Stephen Ficklin <[hidden email]> wrote:
Yes, you can turn it off. If you are using v1.1 you can turn it off by navigating to Administer -> Tripal Management -> Features -> Feature Configuration.  Then on the page that appears you'll see a section titled 'Feature Browser'.  In that section you can turn off the feature browser on the organism page.

Tripal v2.0-rc1 is a bit more flexible with the links available on a page.   If you want to turn it off for all organisms you go to, Tripal -> Chado Modules -> Organisms and on the admin page in the upper right corner you'll see a tab titled 'TOC'  (meaning Table of Contents).  Here you will be presented with a form that allows your to re-order, rename or hide the elements in the TOC on the organism page.   You can check the button to hide the feature browser.

Let me know if turning that off helps your problem.

Stephen


On 1/26/2015 3:15 PM, Mara Kim wrote:
I believe so.  I'm guessing that must be the problem?  Is there a way to disable it?

On Mon, Jan 26, 2015 at 2:09 PM, Stephen Ficklin <[hidden email]> wrote:
I see.  Do you have the feature browser turned on?


On 1/26/2015 3:06 PM, Mara Kim wrote:
Not exactly sure which template it is, but when I attempt to look at an organism page (eg. Homo sapiens), it loads very slowly.  pg_stat_activity reports the query as:

SELECT feature_id FROM chado.feature WHERE organism_id = '25' AND type_id IN ('789', '320')  ORDER BY name ASC LIMIT 25 OFFSET 0

On Mon, Jan 26, 2015 at 2:02 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Mara,

Can you tell me the name of the template where you see the order by name that is causing slowness?

Thanks,
Stephen


On 1/26/2015 2:38 PM, Mara Kim wrote:
Hello,

I have noticed that the organism pages are loading extremely slowly, and I believe this is due to the use of order by `name`, as opposed to `uniquename`, which is indexed by default in Chado.  Could this behavior be changed?

--
Mara Kim

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


------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/


_______________________________________________
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



--
Mara Kim

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


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Re: [Gmod-tripal-devel] Organism page, order by name is slow

Mara Kim-2
I'm having trouble getting drush to update the module:

$ drush pm-download tripal 7.x-2.x-dev
Install location sites/all/modules/tripal already exists. Do you want to overwrite it? (y/n): y
Project tripal (7.x-2.0-rc1) downloaded to sites/all/modules/tripal.                                                                 [success]
Project tripal contains 18 modules: tripal_cv, tripal_pub, tripal_feature, tripal_core, tripal_project, tripal_analysis, tripal_natural_diversity, tripal_phenotype, tripal_genetic, tripal_library, tripal_example, tripal_bulk_loader, tripal_stock, tripal_featuremap, tripal_views, tripal_db, tripal_contact, tripal_organism.
No release history was found for the requested project (7.x).                                                                        [warning]
Could not download requested project(s).                                                                                             [error]



On Mon, Jan 26, 2015 at 3:55 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Mara,

I think this is a bug that has already been fixed in the development branch.  Can you try updating your code to the most-recent version?   Change to the directory where you have the Tripal module installed, and If you are using the git repository then try this:

git checkout 7.x-2.x
git pull

If you are using the Drupal module installed via drush then try this:

drush pm-download tripal 7.x-2.x-dev

Stephen


On 1/26/2015 4:27 PM, Mara Kim wrote:
Forgot to mention, I am running v2.0-rc1

On Mon, Jan 26, 2015 at 3:19 PM, Mara Kim <[hidden email]> wrote:
Hmmm, so I hid both the Feature Browser and Feature Summary, but it appears the template is still sending the same queries to the database.  I guess hiding the sections doesn't actually disable query generation?

On Mon, Jan 26, 2015 at 3:06 PM, Stephen Ficklin <[hidden email]> wrote:
Yes, you can turn it off. If you are using v1.1 you can turn it off by navigating to Administer -> Tripal Management -> Features -> Feature Configuration.  Then on the page that appears you'll see a section titled 'Feature Browser'.  In that section you can turn off the feature browser on the organism page.

Tripal v2.0-rc1 is a bit more flexible with the links available on a page.   If you want to turn it off for all organisms you go to, Tripal -> Chado Modules -> Organisms and on the admin page in the upper right corner you'll see a tab titled 'TOC'  (meaning Table of Contents).  Here you will be presented with a form that allows your to re-order, rename or hide the elements in the TOC on the organism page.   You can check the button to hide the feature browser.

Let me know if turning that off helps your problem.

Stephen


On 1/26/2015 3:15 PM, Mara Kim wrote:
I believe so.  I'm guessing that must be the problem?  Is there a way to disable it?

On Mon, Jan 26, 2015 at 2:09 PM, Stephen Ficklin <[hidden email]> wrote:
I see.  Do you have the feature browser turned on?


On 1/26/2015 3:06 PM, Mara Kim wrote:
Not exactly sure which template it is, but when I attempt to look at an organism page (eg. Homo sapiens), it loads very slowly.  pg_stat_activity reports the query as:

SELECT feature_id FROM chado.feature WHERE organism_id = '25' AND type_id IN ('789', '320')  ORDER BY name ASC LIMIT 25 OFFSET 0

On Mon, Jan 26, 2015 at 2:02 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Mara,

Can you tell me the name of the template where you see the order by name that is causing slowness?

Thanks,
Stephen


On 1/26/2015 2:38 PM, Mara Kim wrote:
Hello,

I have noticed that the organism pages are loading extremely slowly, and I believe this is due to the use of order by `name`, as opposed to `uniquename`, which is indexed by default in Chado.  Could this behavior be changed?

--
Mara Kim

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


------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/


_______________________________________________
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



--
Mara Kim

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




--
Mara Kim

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

------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
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Re: [Gmod-tripal-devel] Organism page, order by name is slow

Stephen Ficklin-2
Hi Mara,

I'm sorry. I gave you an incorrect command.  Try this instead:

drush pm-download tripal --dev

Stephen

On 1/26/2015 5:46 PM, Mara Kim wrote:
I'm having trouble getting drush to update the module:

$ drush pm-download tripal 7.x-2.x-dev
Install location sites/all/modules/tripal already exists. Do you want to overwrite it? (y/n): y
Project tripal (7.x-2.0-rc1) downloaded to sites/all/modules/tripal.                                                                 [success]
Project tripal contains 18 modules: tripal_cv, tripal_pub, tripal_feature, tripal_core, tripal_project, tripal_analysis, tripal_natural_diversity, tripal_phenotype, tripal_genetic, tripal_library, tripal_example, tripal_bulk_loader, tripal_stock, tripal_featuremap, tripal_views, tripal_db, tripal_contact, tripal_organism.
No release history was found for the requested project (7.x).                                                                        [warning]
Could not download requested project(s).                                                                                             [error]



On Mon, Jan 26, 2015 at 3:55 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Mara,

I think this is a bug that has already been fixed in the development branch.  Can you try updating your code to the most-recent version?   Change to the directory where you have the Tripal module installed, and If you are using the git repository then try this:

git checkout 7.x-2.x
git pull

If you are using the Drupal module installed via drush then try this:

drush pm-download tripal 7.x-2.x-dev

Stephen


On 1/26/2015 4:27 PM, Mara Kim wrote:
Forgot to mention, I am running v2.0-rc1

On Mon, Jan 26, 2015 at 3:19 PM, Mara Kim <[hidden email]> wrote:
Hmmm, so I hid both the Feature Browser and Feature Summary, but it appears the template is still sending the same queries to the database.  I guess hiding the sections doesn't actually disable query generation?

On Mon, Jan 26, 2015 at 3:06 PM, Stephen Ficklin <[hidden email]> wrote:
Yes, you can turn it off. If you are using v1.1 you can turn it off by navigating to Administer -> Tripal Management -> Features -> Feature Configuration.  Then on the page that appears you'll see a section titled 'Feature Browser'.  In that section you can turn off the feature browser on the organism page.

Tripal v2.0-rc1 is a bit more flexible with the links available on a page.   If you want to turn it off for all organisms you go to, Tripal -> Chado Modules -> Organisms and on the admin page in the upper right corner you'll see a tab titled 'TOC'  (meaning Table of Contents).  Here you will be presented with a form that allows your to re-order, rename or hide the elements in the TOC on the organism page.   You can check the button to hide the feature browser.

Let me know if turning that off helps your problem.

Stephen


On 1/26/2015 3:15 PM, Mara Kim wrote:
I believe so.  I'm guessing that must be the problem?  Is there a way to disable it?

On Mon, Jan 26, 2015 at 2:09 PM, Stephen Ficklin <[hidden email]> wrote:
I see.  Do you have the feature browser turned on?


On 1/26/2015 3:06 PM, Mara Kim wrote:
Not exactly sure which template it is, but when I attempt to look at an organism page (eg. Homo sapiens), it loads very slowly.  pg_stat_activity reports the query as:

SELECT feature_id FROM chado.feature WHERE organism_id = '25' AND type_id IN ('789', '320')  ORDER BY name ASC LIMIT 25 OFFSET 0

On Mon, Jan 26, 2015 at 2:02 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Mara,

Can you tell me the name of the template where you see the order by name that is causing slowness?

Thanks,
Stephen


On 1/26/2015 2:38 PM, Mara Kim wrote:
Hello,

I have noticed that the organism pages are loading extremely slowly, and I believe this is due to the use of order by `name`, as opposed to `uniquename`, which is indexed by default in Chado.  Could this behavior be changed?

--
Mara Kim

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


------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/


_______________________________________________
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



--
Mara Kim

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




--
Mara Kim

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


------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
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Re: [Gmod-tripal-devel] Organism page, order by name is slow

Mara Kim-2

That has fixed it. Thank you.

Are there plans to improve the performance of the feature browser?

On Jan 27, 2015 8:39 AM, "Stephen Ficklin" <[hidden email]> wrote:
Hi Mara,

I'm sorry. I gave you an incorrect command.  Try this instead:

drush pm-download tripal --dev

Stephen

On 1/26/2015 5:46 PM, Mara Kim wrote:
I'm having trouble getting drush to update the module:

$ drush pm-download tripal 7.x-2.x-dev
Install location sites/all/modules/tripal already exists. Do you want to overwrite it? (y/n): y
Project tripal (7.x-2.0-rc1) downloaded to sites/all/modules/tripal.                                                                 [success]
Project tripal contains 18 modules: tripal_cv, tripal_pub, tripal_feature, tripal_core, tripal_project, tripal_analysis, tripal_natural_diversity, tripal_phenotype, tripal_genetic, tripal_library, tripal_example, tripal_bulk_loader, tripal_stock, tripal_featuremap, tripal_views, tripal_db, tripal_contact, tripal_organism.
No release history was found for the requested project (7.x).                                                                        [warning]
Could not download requested project(s).                                                                                             [error]



On Mon, Jan 26, 2015 at 3:55 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Mara,

I think this is a bug that has already been fixed in the development branch.  Can you try updating your code to the most-recent version?   Change to the directory where you have the Tripal module installed, and If you are using the git repository then try this:

git checkout 7.x-2.x
git pull

If you are using the Drupal module installed via drush then try this:

drush pm-download tripal 7.x-2.x-dev

Stephen


On 1/26/2015 4:27 PM, Mara Kim wrote:
Forgot to mention, I am running v2.0-rc1

On Mon, Jan 26, 2015 at 3:19 PM, Mara Kim <[hidden email]> wrote:
Hmmm, so I hid both the Feature Browser and Feature Summary, but it appears the template is still sending the same queries to the database.  I guess hiding the sections doesn't actually disable query generation?

On Mon, Jan 26, 2015 at 3:06 PM, Stephen Ficklin <[hidden email]> wrote:
Yes, you can turn it off. If you are using v1.1 you can turn it off by navigating to Administer -> Tripal Management -> Features -> Feature Configuration.  Then on the page that appears you'll see a section titled 'Feature Browser'.  In that section you can turn off the feature browser on the organism page.

Tripal v2.0-rc1 is a bit more flexible with the links available on a page.   If you want to turn it off for all organisms you go to, Tripal -> Chado Modules -> Organisms and on the admin page in the upper right corner you'll see a tab titled 'TOC'  (meaning Table of Contents).  Here you will be presented with a form that allows your to re-order, rename or hide the elements in the TOC on the organism page.   You can check the button to hide the feature browser.

Let me know if turning that off helps your problem.

Stephen


On 1/26/2015 3:15 PM, Mara Kim wrote:
I believe so.  I'm guessing that must be the problem?  Is there a way to disable it?

On Mon, Jan 26, 2015 at 2:09 PM, Stephen Ficklin <[hidden email]> wrote:
I see.  Do you have the feature browser turned on?


On 1/26/2015 3:06 PM, Mara Kim wrote:
Not exactly sure which template it is, but when I attempt to look at an organism page (eg. Homo sapiens), it loads very slowly.  pg_stat_activity reports the query as:

SELECT feature_id FROM chado.feature WHERE organism_id = '25' AND type_id IN ('789', '320')  ORDER BY name ASC LIMIT 25 OFFSET 0

On Mon, Jan 26, 2015 at 2:02 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Mara,

Can you tell me the name of the template where you see the order by name that is causing slowness?

Thanks,
Stephen


On 1/26/2015 2:38 PM, Mara Kim wrote:
Hello,

I have noticed that the organism pages are loading extremely slowly, and I believe this is due to the use of order by `name`, as opposed to `uniquename`, which is indexed by default in Chado.  Could this behavior be changed?

--
Mara Kim

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


------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/


_______________________________________________
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



--
Mara Kim

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




--
Mara Kim

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


------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
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Re: [Gmod-tripal-devel] Organism page, order by name is slow

Stephen Ficklin-2
I'm glad that fixed it.  

We had originally created it back when Tripal was first created so that folks who land on the organism page can find features quickly.   It was basically intended to help folks find things and get a feel for what the site offered.   With the newer feature search forms and the ability to create more complex search forms I'm not sure the feature browser is really relevant anymore.   Do you find the feature browser useful for your site?

Stephen

On 1/27/2015 1:56 PM, Mara Kim wrote:

That has fixed it. Thank you.

Are there plans to improve the performance of the feature browser?

On Jan 27, 2015 8:39 AM, "Stephen Ficklin" <[hidden email]> wrote:
Hi Mara,

I'm sorry. I gave you an incorrect command.  Try this instead:

drush pm-download tripal --dev

Stephen

On 1/26/2015 5:46 PM, Mara Kim wrote:
I'm having trouble getting drush to update the module:

$ drush pm-download tripal 7.x-2.x-dev
Install location sites/all/modules/tripal already exists. Do you want to overwrite it? (y/n): y
Project tripal (7.x-2.0-rc1) downloaded to sites/all/modules/tripal.                                                                 [success]
Project tripal contains 18 modules: tripal_cv, tripal_pub, tripal_feature, tripal_core, tripal_project, tripal_analysis, tripal_natural_diversity, tripal_phenotype, tripal_genetic, tripal_library, tripal_example, tripal_bulk_loader, tripal_stock, tripal_featuremap, tripal_views, tripal_db, tripal_contact, tripal_organism.
No release history was found for the requested project (7.x).                                                                        [warning]
Could not download requested project(s).                                                                                             [error]



On Mon, Jan 26, 2015 at 3:55 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Mara,

I think this is a bug that has already been fixed in the development branch.  Can you try updating your code to the most-recent version?   Change to the directory where you have the Tripal module installed, and If you are using the git repository then try this:

git checkout 7.x-2.x
git pull

If you are using the Drupal module installed via drush then try this:

drush pm-download tripal 7.x-2.x-dev

Stephen


On 1/26/2015 4:27 PM, Mara Kim wrote:
Forgot to mention, I am running v2.0-rc1

On Mon, Jan 26, 2015 at 3:19 PM, Mara Kim <[hidden email]> wrote:
Hmmm, so I hid both the Feature Browser and Feature Summary, but it appears the template is still sending the same queries to the database.  I guess hiding the sections doesn't actually disable query generation?

On Mon, Jan 26, 2015 at 3:06 PM, Stephen Ficklin <[hidden email]> wrote:
Yes, you can turn it off. If you are using v1.1 you can turn it off by navigating to Administer -> Tripal Management -> Features -> Feature Configuration.  Then on the page that appears you'll see a section titled 'Feature Browser'.  In that section you can turn off the feature browser on the organism page.

Tripal v2.0-rc1 is a bit more flexible with the links available on a page.   If you want to turn it off for all organisms you go to, Tripal -> Chado Modules -> Organisms and on the admin page in the upper right corner you'll see a tab titled 'TOC'  (meaning Table of Contents).  Here you will be presented with a form that allows your to re-order, rename or hide the elements in the TOC on the organism page.   You can check the button to hide the feature browser.

Let me know if turning that off helps your problem.

Stephen


On 1/26/2015 3:15 PM, Mara Kim wrote:
I believe so.  I'm guessing that must be the problem?  Is there a way to disable it?

On Mon, Jan 26, 2015 at 2:09 PM, Stephen Ficklin <[hidden email]> wrote:
I see.  Do you have the feature browser turned on?


On 1/26/2015 3:06 PM, Mara Kim wrote:
Not exactly sure which template it is, but when I attempt to look at an organism page (eg. Homo sapiens), it loads very slowly.  pg_stat_activity reports the query as:

SELECT feature_id FROM chado.feature WHERE organism_id = '25' AND type_id IN ('789', '320')  ORDER BY name ASC LIMIT 25 OFFSET 0

On Mon, Jan 26, 2015 at 2:02 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Mara,

Can you tell me the name of the template where you see the order by name that is causing slowness?

Thanks,
Stephen


On 1/26/2015 2:38 PM, Mara Kim wrote:
Hello,

I have noticed that the organism pages are loading extremely slowly, and I believe this is due to the use of order by `name`, as opposed to `uniquename`, which is indexed by default in Chado.  Could this behavior be changed?

--
Mara Kim

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


------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/


_______________________________________________
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



--
Mara Kim

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




--
Mara Kim

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



------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
_______________________________________________
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] Organism page, order by name is slow

Mara Kim-2

To be honest, it is pretty difficult to use. It was nice when the search function wasn't working though.

Speaking of the search function, is it possible to expand the text that is indexed for searching? It would be nice to include gene summaries, synonyms, orthologs etc.

On Jan 27, 2015 1:12 PM, "Stephen Ficklin" <[hidden email]> wrote:
I'm glad that fixed it.  

We had originally created it back when Tripal was first created so that folks who land on the organism page can find features quickly.   It was basically intended to help folks find things and get a feel for what the site offered.   With the newer feature search forms and the ability to create more complex search forms I'm not sure the feature browser is really relevant anymore.   Do you find the feature browser useful for your site?

Stephen

On 1/27/2015 1:56 PM, Mara Kim wrote:

That has fixed it. Thank you.

Are there plans to improve the performance of the feature browser?

On Jan 27, 2015 8:39 AM, "Stephen Ficklin" <[hidden email]> wrote:
Hi Mara,

I'm sorry. I gave you an incorrect command.  Try this instead:

drush pm-download tripal --dev

Stephen

On 1/26/2015 5:46 PM, Mara Kim wrote:
I'm having trouble getting drush to update the module:

$ drush pm-download tripal 7.x-2.x-dev
Install location sites/all/modules/tripal already exists. Do you want to overwrite it? (y/n): y
Project tripal (7.x-2.0-rc1) downloaded to sites/all/modules/tripal.                                                                 [success]
Project tripal contains 18 modules: tripal_cv, tripal_pub, tripal_feature, tripal_core, tripal_project, tripal_analysis, tripal_natural_diversity, tripal_phenotype, tripal_genetic, tripal_library, tripal_example, tripal_bulk_loader, tripal_stock, tripal_featuremap, tripal_views, tripal_db, tripal_contact, tripal_organism.
No release history was found for the requested project (7.x).                                                                        [warning]
Could not download requested project(s).                                                                                             [error]



On Mon, Jan 26, 2015 at 3:55 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Mara,

I think this is a bug that has already been fixed in the development branch.  Can you try updating your code to the most-recent version?   Change to the directory where you have the Tripal module installed, and If you are using the git repository then try this:

git checkout 7.x-2.x
git pull

If you are using the Drupal module installed via drush then try this:

drush pm-download tripal 7.x-2.x-dev

Stephen


On 1/26/2015 4:27 PM, Mara Kim wrote:
Forgot to mention, I am running v2.0-rc1

On Mon, Jan 26, 2015 at 3:19 PM, Mara Kim <[hidden email]> wrote:
Hmmm, so I hid both the Feature Browser and Feature Summary, but it appears the template is still sending the same queries to the database.  I guess hiding the sections doesn't actually disable query generation?

On Mon, Jan 26, 2015 at 3:06 PM, Stephen Ficklin <[hidden email]> wrote:
Yes, you can turn it off. If you are using v1.1 you can turn it off by navigating to Administer -> Tripal Management -> Features -> Feature Configuration.  Then on the page that appears you'll see a section titled 'Feature Browser'.  In that section you can turn off the feature browser on the organism page.

Tripal v2.0-rc1 is a bit more flexible with the links available on a page.   If you want to turn it off for all organisms you go to, Tripal -> Chado Modules -> Organisms and on the admin page in the upper right corner you'll see a tab titled 'TOC'  (meaning Table of Contents).  Here you will be presented with a form that allows your to re-order, rename or hide the elements in the TOC on the organism page.   You can check the button to hide the feature browser.

Let me know if turning that off helps your problem.

Stephen


On 1/26/2015 3:15 PM, Mara Kim wrote:
I believe so.  I'm guessing that must be the problem?  Is there a way to disable it?

On Mon, Jan 26, 2015 at 2:09 PM, Stephen Ficklin <[hidden email]> wrote:
I see.  Do you have the feature browser turned on?


On 1/26/2015 3:06 PM, Mara Kim wrote:
Not exactly sure which template it is, but when I attempt to look at an organism page (eg. Homo sapiens), it loads very slowly.  pg_stat_activity reports the query as:

SELECT feature_id FROM chado.feature WHERE organism_id = '25' AND type_id IN ('789', '320')  ORDER BY name ASC LIMIT 25 OFFSET 0

On Mon, Jan 26, 2015 at 2:02 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Mara,

Can you tell me the name of the template where you see the order by name that is causing slowness?

Thanks,
Stephen


On 1/26/2015 2:38 PM, Mara Kim wrote:
Hello,

I have noticed that the organism pages are loading extremely slowly, and I believe this is due to the use of order by `name`, as opposed to `uniquename`, which is indexed by default in Chado.  Could this behavior be changed?

--
Mara Kim

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


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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




--
Mara Kim

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



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sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
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Re: [Gmod-tripal-devel] Organism page, order by name is slow

Stephen Ficklin-2
Yes, it is possible there are multiple ways to create a custom search:

1)  You can use the Drupal Views interface to customize the existing searches by removing or adding fields.   This is great because it doesn't require any programming.  It takes some getting used to Drupal Views but once you are accustomed to it, it's great.  It does have limitations though because Drupal Views has a hard time when you have to jump across multiple tables to get information (such as feature -> feature_synonym-> synonym).

2)  To overcome the problem of complex joins not supported by Views, you can create a materialized view that contains all of the information you want to allow a user to search on.   If you create this MView using the Tripal interface then it will automatically be available to Drupal Views.  You can then create a new search page using this new MView as the base table.     The only programming required is the creation of an SQL statement that will populate the MView, and if you don't like the default layout of the form you can change it by creating a PHP template file.  This is the approach we take for the sites that we work on.

3)  You can write a custom module that uses the Drupal and Tripal APIs and that creates the form and performs the search.  You may or may not need a materialized view depending on how you code it up.  The publication search that comes with Tripal is actually written in this way because of the complexity of the information and because of the design of the pub table. 

If you want to create a custom search feel free to let us know and we can provide some pointers.

Stephen

On 1/27/2015 3:32 PM, Mara Kim wrote:

To be honest, it is pretty difficult to use. It was nice when the search function wasn't working though.

Speaking of the search function, is it possible to expand the text that is indexed for searching? It would be nice to include gene summaries, synonyms, orthologs etc.

On Jan 27, 2015 1:12 PM, "Stephen Ficklin" <[hidden email]> wrote:
I'm glad that fixed it.  

We had originally created it back when Tripal was first created so that folks who land on the organism page can find features quickly.   It was basically intended to help folks find things and get a feel for what the site offered.   With the newer feature search forms and the ability to create more complex search forms I'm not sure the feature browser is really relevant anymore.   Do you find the feature browser useful for your site?

Stephen

On 1/27/2015 1:56 PM, Mara Kim wrote:

That has fixed it. Thank you.

Are there plans to improve the performance of the feature browser?

On Jan 27, 2015 8:39 AM, "Stephen Ficklin" <[hidden email]> wrote:
Hi Mara,

I'm sorry. I gave you an incorrect command.  Try this instead:

drush pm-download tripal --dev

Stephen

On 1/26/2015 5:46 PM, Mara Kim wrote:
I'm having trouble getting drush to update the module:

$ drush pm-download tripal 7.x-2.x-dev
Install location sites/all/modules/tripal already exists. Do you want to overwrite it? (y/n): y
Project tripal (7.x-2.0-rc1) downloaded to sites/all/modules/tripal.                                                                 [success]
Project tripal contains 18 modules: tripal_cv, tripal_pub, tripal_feature, tripal_core, tripal_project, tripal_analysis, tripal_natural_diversity, tripal_phenotype, tripal_genetic, tripal_library, tripal_example, tripal_bulk_loader, tripal_stock, tripal_featuremap, tripal_views, tripal_db, tripal_contact, tripal_organism.
No release history was found for the requested project (7.x).                                                                        [warning]
Could not download requested project(s).                                                                                             [error]



On Mon, Jan 26, 2015 at 3:55 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Mara,

I think this is a bug that has already been fixed in the development branch.  Can you try updating your code to the most-recent version?   Change to the directory where you have the Tripal module installed, and If you are using the git repository then try this:

git checkout 7.x-2.x
git pull

If you are using the Drupal module installed via drush then try this:

drush pm-download tripal 7.x-2.x-dev

Stephen


On 1/26/2015 4:27 PM, Mara Kim wrote:
Forgot to mention, I am running v2.0-rc1

On Mon, Jan 26, 2015 at 3:19 PM, Mara Kim <[hidden email]> wrote:
Hmmm, so I hid both the Feature Browser and Feature Summary, but it appears the template is still sending the same queries to the database.  I guess hiding the sections doesn't actually disable query generation?

On Mon, Jan 26, 2015 at 3:06 PM, Stephen Ficklin <[hidden email]> wrote:
Yes, you can turn it off. If you are using v1.1 you can turn it off by navigating to Administer -> Tripal Management -> Features -> Feature Configuration.  Then on the page that appears you'll see a section titled 'Feature Browser'.  In that section you can turn off the feature browser on the organism page.

Tripal v2.0-rc1 is a bit more flexible with the links available on a page.   If you want to turn it off for all organisms you go to, Tripal -> Chado Modules -> Organisms and on the admin page in the upper right corner you'll see a tab titled 'TOC'  (meaning Table of Contents).  Here you will be presented with a form that allows your to re-order, rename or hide the elements in the TOC on the organism page.   You can check the button to hide the feature browser.

Let me know if turning that off helps your problem.

Stephen


On 1/26/2015 3:15 PM, Mara Kim wrote:
I believe so.  I'm guessing that must be the problem?  Is there a way to disable it?

On Mon, Jan 26, 2015 at 2:09 PM, Stephen Ficklin <[hidden email]> wrote:
I see.  Do you have the feature browser turned on?


On 1/26/2015 3:06 PM, Mara Kim wrote:
Not exactly sure which template it is, but when I attempt to look at an organism page (eg. Homo sapiens), it loads very slowly.  pg_stat_activity reports the query as:

SELECT feature_id FROM chado.feature WHERE organism_id = '25' AND type_id IN ('789', '320')  ORDER BY name ASC LIMIT 25 OFFSET 0

On Mon, Jan 26, 2015 at 2:02 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Mara,

Can you tell me the name of the template where you see the order by name that is causing slowness?

Thanks,
Stephen


On 1/26/2015 2:38 PM, Mara Kim wrote:
Hello,

I have noticed that the organism pages are loading extremely slowly, and I believe this is due to the use of order by `name`, as opposed to `uniquename`, which is indexed by default in Chado.  Could this behavior be changed?

--
Mara Kim

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


------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/


_______________________________________________
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



--
Mara Kim

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




--
Mara Kim

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




------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel