Link-Out

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Link-Out

Sofia Robb
Hello,

I just set up a new machine with tripal.  I have the Database "Link-out Type" for my blast database on my old system but not on my new.

I am running 
Tripal Core  7.x-2.0+37-dev on my new machine (this one does not have the linkout type)

And 7.x-2.0+33-dev on my old machine. (this one has the link out type)

Should I enable a different dev version?

Thanks,
Sofia

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Re: Link-Out

Kucheran, Lacey Sanderson
Hello Sofia,

I’m assuming when you refer to link-out type you are talking about the setting for blast databases? If so this related to the Tripal BLAST (BLAST UI) module as compared to core Tripal. For Link-out functionality you currently need the development version of Tripal BLAST which is available via git (Instructions: https://www.drupal.org/project/tripal_blast/git-instructions). Another alternative is to just copy the Tripal blast module from yours site where link-outs are available to the one where they are not. 

~Lacey

PS. There should be a new release of Tripal BLAST within the month -there’s just one little piece I want to improve first. This will negate the need for use of a development version.

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On January 6, 2016 at 5:46:31 PM, Sofia Robb ([hidden email]) wrote:

Hello,

I just set up a new machine with tripal.  I have the Database "Link-out Type" for my blast database on my old system but not on my new.

I am running 
Tripal Core  7.x-2.0+37-dev on my new machine (this one does not have the linkout type)

And 7.x-2.0+33-dev on my old machine. (this one has the link out type)

Should I enable a different dev version?

Thanks,
Sofia
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Re: Link-Out

Sofia Robb
Hi Lacey,

Thanks. I have the dev version now and it is enabled. When I go to "Find Content" to find my already created blastDBs to add the Link out type I get this error. This error appears as soon as I click the "Find Content" link in the header of the tripal site.

PDOException: SQLSTATE[42703]: Undefined column: 7 ERROR: column "dbxref_linkout_type" does not exist LINE 3: dbxref_linkout_type ^: SELECT nid, name, path, dbtype, dbxref_id_regex, dbxref_db_id, dbxref_linkout_type FROM {blastdb} WHERE nid IN (:nids_0, :nids_1); Array ( [:nids_0] => 601884 [:nids_1] => 601885 ) in blastdb_load() (line 364 of/var/www/html/sites/all/modules/tripal_blast/includes/blast_ui.node.inc).

On Fri, Jan 22, 2016 at 8:43 AM, Kucheran, Lacey Sanderson <[hidden email]> wrote:
Hello Sofia,

I’m assuming when you refer to link-out type you are talking about the setting for blast databases? If so this related to the Tripal BLAST (BLAST UI) module as compared to core Tripal. For Link-out functionality you currently need the development version of Tripal BLAST which is available via git (Instructions: https://www.drupal.org/project/tripal_blast/git-instructions). Another alternative is to just copy the Tripal blast module from yours site where link-outs are available to the one where they are not. 

~Lacey

PS. There should be a new release of Tripal BLAST within the month -there’s just one little piece I want to improve first. This will negate the need for use of a development version.

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208" target="_blank">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On January 6, 2016 at 5:46:31 PM, Sofia Robb ([hidden email]) wrote:

Hello,

I just set up a new machine with tripal.  I have the Database "Link-out Type" for my blast database on my old system but not on my new.

I am running 
Tripal Core  7.x-2.0+37-dev on my new machine (this one does not have the linkout type)

And 7.x-2.0+33-dev on my old machine. (this one has the link out type)

Should I enable a different dev version?

Thanks,
Sofia
------------------------------------------------------------------------------
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[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal


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Re: Link-Out

Kucheran, Lacey Sanderson
Did you run the database updates? (i.e.: http://yoursite/updates.php)

~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On January 22, 2016 at 10:50:45 AM, Sofia Robb ([hidden email]) wrote:

Hi Lacey,

Thanks. I have the dev version now and it is enabled. When I go to "Find Content" to find my already created blastDBs to add the Link out type I get this error. This error appears as soon as I click the "Find Content" link in the header of the tripal site.

PDOException: SQLSTATE[42703]: Undefined column: 7 ERROR: column "dbxref_linkout_type" does not exist LINE 3: dbxref_linkout_type ^: SELECT nid, name, path, dbtype, dbxref_id_regex, dbxref_db_id, dbxref_linkout_type FROM {blastdb} WHERE nid IN (:nids_0, :nids_1); Array ( [:nids_0] => 601884 [:nids_1] => 601885 ) in blastdb_load() (line 364 of/var/www/html/sites/all/modules/tripal_blast/includes/blast_ui.node.inc).

On Fri, Jan 22, 2016 at 8:43 AM, Kucheran, Lacey Sanderson <[hidden email]> wrote:
Hello Sofia,

I’m assuming when you refer to link-out type you are talking about the setting for blast databases? If so this related to the Tripal BLAST (BLAST UI) module as compared to core Tripal. For Link-out functionality you currently need the development version of Tripal BLAST which is available via git (Instructions: https://www.drupal.org/project/tripal_blast/git-instructions). Another alternative is to just copy the Tripal blast module from yours site where link-outs are available to the one where they are not. 

~Lacey

PS. There should be a new release of Tripal BLAST within the month -there’s just one little piece I want to improve first. This will negate the need for use of a development version.

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208" target="_blank">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On January 6, 2016 at 5:46:31 PM, Sofia Robb ([hidden email]) wrote:

Hello,

I just set up a new machine with tripal.  I have the Database "Link-out Type" for my blast database on my old system but not on my new.

I am running 
Tripal Core  7.x-2.0+37-dev on my new machine (this one does not have the linkout type)

And 7.x-2.0+33-dev on my old machine. (this one has the link out type)

Should I enable a different dev version?

Thanks,
Sofia
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[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal


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Re: Link-Out

Sofia Robb
Thanks!! Yes, I forgot. 

By the way, you have a typo, it should be http://yoursite/update.php not updates.php. I freak out for a second when I tried updates.php and the page was not found :) 

Thank you very much!!
Sofia

On Fri, Jan 22, 2016 at 9:52 AM, Kucheran, Lacey Sanderson <[hidden email]> wrote:
Did you run the database updates? (i.e.: http://yoursite/updates.php)

~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208" target="_blank">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On January 22, 2016 at 10:50:45 AM, Sofia Robb ([hidden email]) wrote:

Hi Lacey,

Thanks. I have the dev version now and it is enabled. When I go to "Find Content" to find my already created blastDBs to add the Link out type I get this error. This error appears as soon as I click the "Find Content" link in the header of the tripal site.

PDOException: SQLSTATE[42703]: Undefined column: 7 ERROR: column "dbxref_linkout_type" does not exist LINE 3: dbxref_linkout_type ^: SELECT nid, name, path, dbtype, dbxref_id_regex, dbxref_db_id, dbxref_linkout_type FROM {blastdb} WHERE nid IN (:nids_0, :nids_1); Array ( [:nids_0] => 601884 [:nids_1] => 601885 ) in blastdb_load() (line 364 of/var/www/html/sites/all/modules/tripal_blast/includes/blast_ui.node.inc).

On Fri, Jan 22, 2016 at 8:43 AM, Kucheran, Lacey Sanderson <[hidden email]> wrote:
Hello Sofia,

I’m assuming when you refer to link-out type you are talking about the setting for blast databases? If so this related to the Tripal BLAST (BLAST UI) module as compared to core Tripal. For Link-out functionality you currently need the development version of Tripal BLAST which is available via git (Instructions: https://www.drupal.org/project/tripal_blast/git-instructions). Another alternative is to just copy the Tripal blast module from yours site where link-outs are available to the one where they are not. 

~Lacey

PS. There should be a new release of Tripal BLAST within the month -there’s just one little piece I want to improve first. This will negate the need for use of a development version.

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208" target="_blank">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On January 6, 2016 at 5:46:31 PM, Sofia Robb ([hidden email]) wrote:

Hello,

I just set up a new machine with tripal.  I have the Database "Link-out Type" for my blast database on my old system but not on my new.

I am running 
Tripal Core  7.x-2.0+37-dev on my new machine (this one does not have the linkout type)

And 7.x-2.0+33-dev on my old machine. (this one has the link out type)

Should I enable a different dev version?

Thanks,
Sofia
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[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal



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APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
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