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Link-Out

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Sofia Robb

Link-Out

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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Kucheran, Lacey Sanderson

Re: Link-Out

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

Email: [hidden email]

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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Sofia Robb

Re: Link-Out

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

Email: [hidden email]

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

------------------------------------------------------------------------------
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal

Kucheran, Lacey Sanderson

Re: Link-Out

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

Email: [hidden email]

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

Email: [hidden email]

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

------------------------------------------------------------------------------
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal

Sofia Robb

Re: Link-Out

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

Email: [hidden email]

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

Email: [hidden email]

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

------------------------------------------------------------------------------
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal