Errors when Installing Chado schema

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Errors when Installing Chado schema

gtoth

When I run “drush trpjob-run administrator” I get the following errors:

 

·         warning: pg_query(): Query failed: ERROR: relation "chado.cv" does not exist LINE 1: SELECT * FROM chado.cv WHERE name = 'tripal' ^ in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 138.

·         user warning: query: SELECT * FROM chado.cv WHERE name = 'tripal' in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 159.

·         warning: pg_query(): Query failed: ERROR: relation "chado.cv" does not exist LINE 1: INSERT INTO chado.cv (name,definition) VALUES ('tripal', 'Te... ^ in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 138.

·         user warning: query: INSERT INTO chado.cv (name,definition) VALUES ('tripal', 'Terms used by Tripal for modules to manage data such as that stored in property tables like featureprop, analysisprop, etc') in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 159.

 

A 2011 posting shows the problem to be fixed?

cid:image001.png@01CED72A.2C225990

 

Any thoughts?

 

Thanks,

Greg Toth


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Re: Errors when Installing Chado schema

Stephen Ficklin-2
Hi Greg,

I believe you get this kind of error if you have not yet installed Chado but you have other Tripal modules enabled besides the Tripal Core module (e.g. Tripal CV module, Tripal DB module, etc.).   Is this the case for you?   If so, then you can disable all but the Tripal core modules and this should make the error go away.  Then, install Chado using the Chado installer.  Once Chado is installed you can enable the other modules. 

Stephen



On 11/1/2013 8:56 PM, Toth, Greg wrote:

When I run “drush trpjob-run administrator” I get the following errors:

 

·         warning: pg_query(): Query failed: ERROR: relation "chado.cv" does not exist LINE 1: SELECT * FROM chado.cv WHERE name = 'tripal' ^ in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 138.

·         user warning: query: SELECT * FROM chado.cv WHERE name = 'tripal' in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 159.

·         warning: pg_query(): Query failed: ERROR: relation "chado.cv" does not exist LINE 1: INSERT INTO chado.cv (name,definition) VALUES ('tripal', 'Te... ^ in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 138.

·         user warning: query: INSERT INTO chado.cv (name,definition) VALUES ('tripal', 'Terms used by Tripal for modules to manage data such as that stored in property tables like featureprop, analysisprop, etc') in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 159.

 

A 2011 posting shows the problem to be fixed?

imap://spficklin%40gmail%2Ecom@imap.googlemail.com:993/fetch%3EUID%3E/INBOX%3E194738?header=quotebody&part=1.1.2&filename=image001.png

 

Any thoughts?

 

Thanks,

Greg Toth



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Re: Errors when Installing Chado schema

gtoth

Stephen,

 

Thanks for the response.  No, other Tripal modules were not enabled.  FYI, the installation is on Bluehost where I’ve got another separate site/folder running Drupal 7 for work bibliographic needs.

 

BTW, I am now subscribed to the Gmod-tripal mailing list.

 

Greg

 

 

Greg Toth, Ph.D., Deputy Director Ecological Exposure Research Division (MD591)

National Exposure Research Laboratory, USEPA, Cincinnati, OH 45268

513-569-7242

 

 

 

From: Stephen Ficklin [mailto:[hidden email]]
Sent: Monday, November 04, 2013 8:32 AM
To: Toth, Greg; [hidden email]
Subject: Re: [Gmod-tripal] Errors when Installing Chado schema

 

Hi Greg,

I believe you get this kind of error if you have not yet installed Chado but you have other Tripal modules enabled besides the Tripal Core module (e.g. Tripal CV module, Tripal DB module, etc.).   Is this the case for you?   If so, then you can disable all but the Tripal core modules and this should make the error go away.  Then, install Chado using the Chado installer.  Once Chado is installed you can enable the other modules. 

Stephen



On 11/1/2013 8:56 PM, Toth, Greg wrote:

When I run “drush trpjob-run administrator” I get the following errors:

 

·         warning: pg_query(): Query failed: ERROR: relation "chado.cv" does not exist LINE 1: SELECT * FROM chado.cv WHERE name = 'tripal' ^ in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 138.

·         user warning: query: SELECT * FROM chado.cv WHERE name = 'tripal' in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 159.

·         warning: pg_query(): Query failed: ERROR: relation "chado.cv" does not exist LINE 1: INSERT INTO chado.cv (name,definition) VALUES ('tripal', 'Te... ^ in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 138.

·         user warning: query: INSERT INTO chado.cv (name,definition) VALUES ('tripal', 'Terms used by Tripal for modules to manage data such as that stored in property tables like featureprop, analysisprop, etc') in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 159.

 

A 2011 posting shows the problem to be fixed?

imap://spficklin%40gmail%2Ecom@imap.googlemail.com:993/fetch%3EUID%3E/INBOX%3E194738?header=quotebody&part=1.1.2&filename=image001.png

 

Any thoughts?

 

Thanks,

Greg Toth




------------------------------------------------------------------------------
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developers love is also attractive to malware creators. Download this white
paper to learn more about secure code signing practices that can help keep
Android apps secure.
http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk




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Re: Errors when Installing Chado schema

Stephen Ficklin-2
Hi Greg,

What job were you trying to execute when you ran the 'drush trpjob-run administrator' command?  Did you already install Chado via the Tripal interface?

Stephen

On 11/5/2013 8:57 AM, Toth, Greg wrote:

Stephen,

 

Thanks for the response.  No, other Tripal modules were not enabled.  FYI, the installation is on Bluehost where I’ve got another separate site/folder running Drupal 7 for work bibliographic needs.

 

BTW, I am now subscribed to the Gmod-tripal mailing list.

 

Greg

 

 

Greg Toth, Ph.D., Deputy Director Ecological Exposure Research Division (MD591)

National Exposure Research Laboratory, USEPA, Cincinnati, OH 45268

513-569-7242

 

 

 

From: Stephen Ficklin [[hidden email]]
Sent: Monday, November 04, 2013 8:32 AM
To: Toth, Greg; [hidden email]
Subject: Re: [Gmod-tripal] Errors when Installing Chado schema

 

Hi Greg,

I believe you get this kind of error if you have not yet installed Chado but you have other Tripal modules enabled besides the Tripal Core module (e.g. Tripal CV module, Tripal DB module, etc.).   Is this the case for you?   If so, then you can disable all but the Tripal core modules and this should make the error go away.  Then, install Chado using the Chado installer.  Once Chado is installed you can enable the other modules. 

Stephen



On 11/1/2013 8:56 PM, Toth, Greg wrote:

When I run “drush trpjob-run administrator” I get the following errors:

 

·         warning: pg_query(): Query failed: ERROR: relation "chado.cv" does not exist LINE 1: SELECT * FROM chado.cv WHERE name = 'tripal' ^ in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 138.

·         user warning: query: SELECT * FROM chado.cv WHERE name = 'tripal' in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 159.

·         warning: pg_query(): Query failed: ERROR: relation "chado.cv" does not exist LINE 1: INSERT INTO chado.cv (name,definition) VALUES ('tripal', 'Te... ^ in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 138.

·         user warning: query: INSERT INTO chado.cv (name,definition) VALUES ('tripal', 'Terms used by Tripal for modules to manage data such as that stored in property tables like featureprop, analysisprop, etc') in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 159.

 

A 2011 posting shows the problem to be fixed?

imap://spficklin%40gmail%2Ecom@imap.googlemail.com:993/fetch%3EUID%3E/INBOX%3E194738?header=quotebody&part=1.1.2&filename=image001.png

 

Any thoughts?

 

Thanks,

Greg Toth




------------------------------------------------------------------------------
Android is increasing in popularity, but the open development platform that
developers love is also attractive to malware creators. Download this white
paper to learn more about secure code signing practices that can help keep
Android apps secure.
http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk




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Re: Errors when Installing Chado schema

Stephen Ficklin-2
Hi Greg,

Do you have a 'chado' entry in the $db_url of your sites/default/settings.php file?  Tripal does support Chado when it is in a database external from the Drupal database, and if you do have Chado in a separate databaes then you can have a 'chado' entry in the $db_url of the settings.php file.  If you do have a 'chado' entry then Tripal thinks Chado is already installed and tries to do some queries which could be the cause of the error you are seeing.  

If you do have a 'chado' entry in the $db_url variable then you should remove it if you want to install Chado using the Tripal installer.   If not, let me know and we'll keep digging.

Stephen


On 11/5/2013 9:10 AM, Toth, Greg wrote:

Stephen,

 

On the “Install Chado Schema” page I had checked off “New install of Chado V1.2” which then showed up on the “Jobs” page.  At that point I ran the ‘drush trpjob-run administrator’ command’ (I was unable to run the sudo crontab –e) – the tutorial said “So, we will run the jobs manually. Tripal supports Drush and therefore has it's own commands. We can use drush to manually launch the job:”

 

Greg

 

From: Stephen Ficklin [[hidden email]]
Sent: Tuesday, November 05, 2013 9:01 AM
To: Toth, Greg; [hidden email]
Subject: Re: [Gmod-tripal] Errors when Installing Chado schema

 

Hi Greg,

What job were you trying to execute when you ran the 'drush trpjob-run administrator' command?  Did you already install Chado via the Tripal interface?

Stephen

On 11/5/2013 8:57 AM, Toth, Greg wrote:

Stephen,

 

Thanks for the response.  No, other Tripal modules were not enabled.  FYI, the installation is on Bluehost where I’ve got another separate site/folder running Drupal 7 for work bibliographic needs.

 

BTW, I am now subscribed to the Gmod-tripal mailing list.

 

Greg

 

 

Greg Toth, Ph.D., Deputy Director Ecological Exposure Research Division (MD591)

National Exposure Research Laboratory, USEPA, Cincinnati, OH 45268

513-569-7242

 

 

 

From: Stephen Ficklin [[hidden email]]
Sent: Monday, November 04, 2013 8:32 AM
To: Toth, Greg; [hidden email]
Subject: Re: [Gmod-tripal] Errors when Installing Chado schema

 

Hi Greg,

I believe you get this kind of error if you have not yet installed Chado but you have other Tripal modules enabled besides the Tripal Core module (e.g. Tripal CV module, Tripal DB module, etc.).   Is this the case for you?   If so, then you can disable all but the Tripal core modules and this should make the error go away.  Then, install Chado using the Chado installer.  Once Chado is installed you can enable the other modules. 

Stephen



On 11/1/2013 8:56 PM, Toth, Greg wrote:

When I run “drush trpjob-run administrator” I get the following errors:

 

·         warning: pg_query(): Query failed: ERROR: relation "chado.cv" does not exist LINE 1: SELECT * FROM chado.cv WHERE name = 'tripal' ^ in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 138.

·         user warning: query: SELECT * FROM chado.cv WHERE name = 'tripal' in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 159.

·         warning: pg_query(): Query failed: ERROR: relation "chado.cv" does not exist LINE 1: INSERT INTO chado.cv (name,definition) VALUES ('tripal', 'Te... ^ in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 138.

·         user warning: query: INSERT INTO chado.cv (name,definition) VALUES ('tripal', 'Terms used by Tripal for modules to manage data such as that stored in property tables like featureprop, analysisprop, etc') in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 159.

 

A 2011 posting shows the problem to be fixed?

imap://spficklin%40gmail%2Ecom@imap.googlemail.com:993/fetch%3EUID%3E/INBOX%3E194738?header=quotebody&part=1.1.2&filename=image001.png

 

Any thoughts?

 

Thanks,

Greg Toth





------------------------------------------------------------------------------
Android is increasing in popularity, but the open development platform that
developers love is also attractive to malware creators. Download this white
paper to learn more about secure code signing practices that can help keep
Android apps secure.
http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk





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Re: Errors when Installing Chado schema

gtoth

Stephen,

 

Chado is not in the $db_url variable in the settings.php file (it’s attached).

 

Greg

 

From: Stephen Ficklin [mailto:[hidden email]]
Sent: Tuesday, November 05, 2013 9:47 AM
To: Toth, Greg; gmod-tripal
Subject: Re: [Gmod-tripal] Errors when Installing Chado schema

 

Hi Greg,

Do you have a 'chado' entry in the $db_url of your sites/default/settings.php file?  Tripal does support Chado when it is in a database external from the Drupal database, and if you do have Chado in a separate databaes then you can have a 'chado' entry in the $db_url of the settings.php file.  If you do have a 'chado' entry then Tripal thinks Chado is already installed and tries to do some queries which could be the cause of the error you are seeing.  

If you do have a 'chado' entry in the $db_url variable then you should remove it if you want to install Chado using the Tripal installer.   If not, let me know and we'll keep digging.

Stephen


On 11/5/2013 9:10 AM, Toth, Greg wrote:

Stephen,

 

On the “Install Chado Schema” page I had checked off “New install of Chado V1.2” which then showed up on the “Jobs” page.  At that point I ran the ‘drush trpjob-run administrator’ command’ (I was unable to run the sudo crontab –e) – the tutorial said “So, we will run the jobs manually. Tripal supports Drush and therefore has it's own commands. We can use drush to manually launch the job:”

 

Greg

 

From: Stephen Ficklin [[hidden email]]
Sent: Tuesday, November 05, 2013 9:01 AM
To: Toth, Greg; [hidden email]
Subject: Re: [Gmod-tripal] Errors when Installing Chado schema

 

Hi Greg,

What job were you trying to execute when you ran the 'drush trpjob-run administrator' command?  Did you already install Chado via the Tripal interface?

Stephen

On 11/5/2013 8:57 AM, Toth, Greg wrote:

Stephen,

 

Thanks for the response.  No, other Tripal modules were not enabled.  FYI, the installation is on Bluehost where I’ve got another separate site/folder running Drupal 7 for work bibliographic needs.

 

BTW, I am now subscribed to the Gmod-tripal mailing list.

 

Greg

 

 

Greg Toth, Ph.D., Deputy Director Ecological Exposure Research Division (MD591)

National Exposure Research Laboratory, USEPA, Cincinnati, OH 45268

513-569-7242

 

 

 

From: Stephen Ficklin [[hidden email]]
Sent: Monday, November 04, 2013 8:32 AM
To: Toth, Greg; [hidden email]
Subject: Re: [Gmod-tripal] Errors when Installing Chado schema

 

Hi Greg,

I believe you get this kind of error if you have not yet installed Chado but you have other Tripal modules enabled besides the Tripal Core module (e.g. Tripal CV module, Tripal DB module, etc.).   Is this the case for you?   If so, then you can disable all but the Tripal core modules and this should make the error go away.  Then, install Chado using the Chado installer.  Once Chado is installed you can enable the other modules. 

Stephen



On 11/1/2013 8:56 PM, Toth, Greg wrote:

When I run “drush trpjob-run administrator” I get the following errors:

 

·         warning: pg_query(): Query failed: ERROR: relation "chado.cv" does not exist LINE 1: SELECT * FROM chado.cv WHERE name = 'tripal' ^ in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 138.

·         user warning: query: SELECT * FROM chado.cv WHERE name = 'tripal' in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 159.

·         warning: pg_query(): Query failed: ERROR: relation "chado.cv" does not exist LINE 1: INSERT INTO chado.cv (name,definition) VALUES ('tripal', 'Te... ^ in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 138.

·         user warning: query: INSERT INTO chado.cv (name,definition) VALUES ('tripal', 'Terms used by Tripal for modules to manage data such as that stored in property tables like featureprop, analysisprop, etc') in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 159.

 

A 2011 posting shows the problem to be fixed?

imap://spficklin%40gmail%2Ecom@imap.googlemail.com:993/fetch%3EUID%3E/INBOX%3E194738?header=quotebody&part=1.1.2&filename=image001.png

 

Any thoughts?

 

Thanks,

Greg Toth






------------------------------------------------------------------------------
Android is increasing in popularity, but the open development platform that
developers love is also attractive to malware creators. Download this white
paper to learn more about secure code signing practices that can help keep
Android apps secure.
http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk






_______________________________________________
Gmod-tripal mailing list
[hidden email]
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techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
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Re: Errors when Installing Chado schema

Stephen Ficklin-2
Hi Greg,

Tripal is trying insert a record into the chado cv table because it thinks that the Chado tables are already installed.  It checks to see if Chado is installed by looking at the $db_url in the settings.php file or by querying the postgres database to look for a 'chado' schema.  Do you have a 'chado' schema in your 'thegtoth_drupal' database?  Does it have any tables in it?  If so, does it have the 'cv' table? 

If it does exist and you remove it (as well as the so, frange, and genetic_code schemas) then perhaps that will solve the problem for you.

Stephen

On 11/5/2013 11:06 AM, Toth, Greg wrote:

Stephen,

 

Chado is not in the $db_url variable in the settings.php file (it’s attached).

 

Greg

 

From: Stephen Ficklin [[hidden email]]
Sent: Tuesday, November 05, 2013 9:47 AM
To: Toth, Greg; gmod-tripal
Subject: Re: [Gmod-tripal] Errors when Installing Chado schema

 

Hi Greg,

Do you have a 'chado' entry in the $db_url of your sites/default/settings.php file?  Tripal does support Chado when it is in a database external from the Drupal database, and if you do have Chado in a separate databaes then you can have a 'chado' entry in the $db_url of the settings.php file.  If you do have a 'chado' entry then Tripal thinks Chado is already installed and tries to do some queries which could be the cause of the error you are seeing.  

If you do have a 'chado' entry in the $db_url variable then you should remove it if you want to install Chado using the Tripal installer.   If not, let me know and we'll keep digging.

Stephen


On 11/5/2013 9:10 AM, Toth, Greg wrote:

Stephen,

 

On the “Install Chado Schema” page I had checked off “New install of Chado V1.2” which then showed up on the “Jobs” page.  At that point I ran the ‘drush trpjob-run administrator’ command’ (I was unable to run the sudo crontab –e) – the tutorial said “So, we will run the jobs manually. Tripal supports Drush and therefore has it's own commands. We can use drush to manually launch the job:”

 

Greg

 

From: Stephen Ficklin [[hidden email]]
Sent: Tuesday, November 05, 2013 9:01 AM
To: Toth, Greg; [hidden email]
Subject: Re: [Gmod-tripal] Errors when Installing Chado schema

 

Hi Greg,

What job were you trying to execute when you ran the 'drush trpjob-run administrator' command?  Did you already install Chado via the Tripal interface?

Stephen

On 11/5/2013 8:57 AM, Toth, Greg wrote:

Stephen,

 

Thanks for the response.  No, other Tripal modules were not enabled.  FYI, the installation is on Bluehost where I’ve got another separate site/folder running Drupal 7 for work bibliographic needs.

 

BTW, I am now subscribed to the Gmod-tripal mailing list.

 

Greg

 

 

Greg Toth, Ph.D., Deputy Director Ecological Exposure Research Division (MD591)

National Exposure Research Laboratory, USEPA, Cincinnati, OH 45268

513-569-7242

 

 

 

From: Stephen Ficklin [[hidden email]]
Sent: Monday, November 04, 2013 8:32 AM
To: Toth, Greg; [hidden email]
Subject: Re: [Gmod-tripal] Errors when Installing Chado schema

 

Hi Greg,

I believe you get this kind of error if you have not yet installed Chado but you have other Tripal modules enabled besides the Tripal Core module (e.g. Tripal CV module, Tripal DB module, etc.).   Is this the case for you?   If so, then you can disable all but the Tripal core modules and this should make the error go away.  Then, install Chado using the Chado installer.  Once Chado is installed you can enable the other modules. 

Stephen



On 11/1/2013 8:56 PM, Toth, Greg wrote:

When I run “drush trpjob-run administrator” I get the following errors:

 

·         warning: pg_query(): Query failed: ERROR: relation "chado.cv" does not exist LINE 1: SELECT * FROM chado.cv WHERE name = 'tripal' ^ in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 138.

·         user warning: query: SELECT * FROM chado.cv WHERE name = 'tripal' in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 159.

·         warning: pg_query(): Query failed: ERROR: relation "chado.cv" does not exist LINE 1: INSERT INTO chado.cv (name,definition) VALUES ('tripal', 'Te... ^ in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 138.

·         user warning: query: INSERT INTO chado.cv (name,definition) VALUES ('tripal', 'Terms used by Tripal for modules to manage data such as that stored in property tables like featureprop, analysisprop, etc') in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 159.

 

A 2011 posting shows the problem to be fixed?

imap://spficklin%40gmail%2Ecom@imap.googlemail.com:993/fetch%3EUID%3E/INBOX%3E194738?header=quotebody&part=1.1.2&filename=image001.png

 

Any thoughts?

 

Thanks,

Greg Toth






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Re: Errors when Installing Chado schema

gtoth

Stephen,

 

Yes, there is a Chado schema, but no ‘cv’ table:

 

 

Greg

 

From: Stephen Ficklin [mailto:[hidden email]]
Sent: Tuesday, November 05, 2013 12:13 PM
To: Toth, Greg; gmod-tripal
Subject: Re: [Gmod-tripal] Errors when Installing Chado schema

 

Hi Greg,

Tripal is trying insert a record into the chado cv table because it thinks that the Chado tables are already installed.  It checks to see if Chado is installed by looking at the $db_url in the settings.php file or by querying the postgres database to look for a 'chado' schema.  Do you have a 'chado' schema in your 'thegtoth_drupal' database?  Does it have any tables in it?  If so, does it have the 'cv' table? 

If it does exist and you remove it (as well as the so, frange, and genetic_code schemas) then perhaps that will solve the problem for you.

Stephen

On 11/5/2013 11:06 AM, Toth, Greg wrote:

Stephen,

 

Chado is not in the $db_url variable in the settings.php file (it’s attached).

 

Greg

 

From: Stephen Ficklin [[hidden email]]
Sent: Tuesday, November 05, 2013 9:47 AM
To: Toth, Greg; gmod-tripal
Subject: Re: [Gmod-tripal] Errors when Installing Chado schema

 

Hi Greg,

Do you have a 'chado' entry in the $db_url of your sites/default/settings.php file?  Tripal does support Chado when it is in a database external from the Drupal database, and if you do have Chado in a separate databaes then you can have a 'chado' entry in the $db_url of the settings.php file.  If you do have a 'chado' entry then Tripal thinks Chado is already installed and tries to do some queries which could be the cause of the error you are seeing.  

If you do have a 'chado' entry in the $db_url variable then you should remove it if you want to install Chado using the Tripal installer.   If not, let me know and we'll keep digging.

Stephen


On 11/5/2013 9:10 AM, Toth, Greg wrote:

Stephen,

 

On the “Install Chado Schema” page I had checked off “New install of Chado V1.2” which then showed up on the “Jobs” page.  At that point I ran the ‘drush trpjob-run administrator’ command’ (I was unable to run the sudo crontab –e) – the tutorial said “So, we will run the jobs manually. Tripal supports Drush and therefore has it's own commands. We can use drush to manually launch the job:”

 

Greg

 

From: Stephen Ficklin [[hidden email]]
Sent: Tuesday, November 05, 2013 9:01 AM
To: Toth, Greg; [hidden email]
Subject: Re: [Gmod-tripal] Errors when Installing Chado schema

 

Hi Greg,

What job were you trying to execute when you ran the 'drush trpjob-run administrator' command?  Did you already install Chado via the Tripal interface?

Stephen

On 11/5/2013 8:57 AM, Toth, Greg wrote:

Stephen,

 

Thanks for the response.  No, other Tripal modules were not enabled.  FYI, the installation is on Bluehost where I’ve got another separate site/folder running Drupal 7 for work bibliographic needs.

 

BTW, I am now subscribed to the Gmod-tripal mailing list.

 

Greg

 

 

Greg Toth, Ph.D., Deputy Director Ecological Exposure Research Division (MD591)

National Exposure Research Laboratory, USEPA, Cincinnati, OH 45268

513-569-7242

 

 

 

From: Stephen Ficklin [[hidden email]]
Sent: Monday, November 04, 2013 8:32 AM
To: Toth, Greg; [hidden email]
Subject: Re: [Gmod-tripal] Errors when Installing Chado schema

 

Hi Greg,

I believe you get this kind of error if you have not yet installed Chado but you have other Tripal modules enabled besides the Tripal Core module (e.g. Tripal CV module, Tripal DB module, etc.).   Is this the case for you?   If so, then you can disable all but the Tripal core modules and this should make the error go away.  Then, install Chado using the Chado installer.  Once Chado is installed you can enable the other modules. 

Stephen



On 11/1/2013 8:56 PM, Toth, Greg wrote:

When I run “drush trpjob-run administrator” I get the following errors:

 

·         warning: pg_query(): Query failed: ERROR: relation "chado.cv" does not exist LINE 1: SELECT * FROM chado.cv WHERE name = 'tripal' ^ in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 138.

·         user warning: query: SELECT * FROM chado.cv WHERE name = 'tripal' in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 159.

·         warning: pg_query(): Query failed: ERROR: relation "chado.cv" does not exist LINE 1: INSERT INTO chado.cv (name,definition) VALUES ('tripal', 'Te... ^ in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 138.

·         user warning: query: INSERT INTO chado.cv (name,definition) VALUES ('tripal', 'Terms used by Tripal for modules to manage data such as that stored in property tables like featureprop, analysisprop, etc') in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 159.

 

A 2011 posting shows the problem to be fixed?

imap://spficklin%40gmail%2Ecom@imap.googlemail.com:993/fetch%3EUID%3E/INBOX%3E194738?header=quotebody&part=1.1.2&filename=image001.png

 

Any thoughts?

 

Thanks,

Greg Toth







------------------------------------------------------------------------------
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developers love is also attractive to malware creators. Download this white
paper to learn more about secure code signing practices that can help keep
Android apps secure.
http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk







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Re: Errors when Installing Chado schema

Stephen Ficklin-2
Do you know how that chado schema got there?  Was there a previous run of the Chado installer via Tripal that failed partially through?   In any event, if you delete the 'chado' schema and try to re-install Chado via Tripal I think it will work without problem for you.

Stephen

On 11/5/2013 12:21 PM, Toth, Greg wrote:

Stephen,

 

Yes, there is a Chado schema, but no ‘cv’ table:

 

 

Greg

 

From: Stephen Ficklin [[hidden email]]
Sent: Tuesday, November 05, 2013 12:13 PM
To: Toth, Greg; gmod-tripal
Subject: Re: [Gmod-tripal] Errors when Installing Chado schema

 

Hi Greg,

Tripal is trying insert a record into the chado cv table because it thinks that the Chado tables are already installed.  It checks to see if Chado is installed by looking at the $db_url in the settings.php file or by querying the postgres database to look for a 'chado' schema.  Do you have a 'chado' schema in your 'thegtoth_drupal' database?  Does it have any tables in it?  If so, does it have the 'cv' table? 

If it does exist and you remove it (as well as the so, frange, and genetic_code schemas) then perhaps that will solve the problem for you.

Stephen

On 11/5/2013 11:06 AM, Toth, Greg wrote:

Stephen,

 

Chado is not in the $db_url variable in the settings.php file (it’s attached).

 

Greg

 

From: Stephen Ficklin [[hidden email]]
Sent: Tuesday, November 05, 2013 9:47 AM
To: Toth, Greg; gmod-tripal
Subject: Re: [Gmod-tripal] Errors when Installing Chado schema

 

Hi Greg,

Do you have a 'chado' entry in the $db_url of your sites/default/settings.php file?  Tripal does support Chado when it is in a database external from the Drupal database, and if you do have Chado in a separate databaes then you can have a 'chado' entry in the $db_url of the settings.php file.  If you do have a 'chado' entry then Tripal thinks Chado is already installed and tries to do some queries which could be the cause of the error you are seeing.  

If you do have a 'chado' entry in the $db_url variable then you should remove it if you want to install Chado using the Tripal installer.   If not, let me know and we'll keep digging.

Stephen


On 11/5/2013 9:10 AM, Toth, Greg wrote:

Stephen,

 

On the “Install Chado Schema” page I had checked off “New install of Chado V1.2” which then showed up on the “Jobs” page.  At that point I ran the ‘drush trpjob-run administrator’ command’ (I was unable to run the sudo crontab –e) – the tutorial said “So, we will run the jobs manually. Tripal supports Drush and therefore has it's own commands. We can use drush to manually launch the job:”

 

Greg

 

From: Stephen Ficklin [[hidden email]]
Sent: Tuesday, November 05, 2013 9:01 AM
To: Toth, Greg; [hidden email]
Subject: Re: [Gmod-tripal] Errors when Installing Chado schema

 

Hi Greg,

What job were you trying to execute when you ran the 'drush trpjob-run administrator' command?  Did you already install Chado via the Tripal interface?

Stephen

On 11/5/2013 8:57 AM, Toth, Greg wrote:

Stephen,

 

Thanks for the response.  No, other Tripal modules were not enabled.  FYI, the installation is on Bluehost where I’ve got another separate site/folder running Drupal 7 for work bibliographic needs.

 

BTW, I am now subscribed to the Gmod-tripal mailing list.

 

Greg

 

 

Greg Toth, Ph.D., Deputy Director Ecological Exposure Research Division (MD591)

National Exposure Research Laboratory, USEPA, Cincinnati, OH 45268

513-569-7242

 

 

 

From: Stephen Ficklin [[hidden email]]
Sent: Monday, November 04, 2013 8:32 AM
To: Toth, Greg; [hidden email]
Subject: Re: [Gmod-tripal] Errors when Installing Chado schema

 

Hi Greg,

I believe you get this kind of error if you have not yet installed Chado but you have other Tripal modules enabled besides the Tripal Core module (e.g. Tripal CV module, Tripal DB module, etc.).   Is this the case for you?   If so, then you can disable all but the Tripal core modules and this should make the error go away.  Then, install Chado using the Chado installer.  Once Chado is installed you can enable the other modules. 

Stephen



On 11/1/2013 8:56 PM, Toth, Greg wrote:

When I run “drush trpjob-run administrator” I get the following errors:

 

·         warning: pg_query(): Query failed: ERROR: relation "chado.cv" does not exist LINE 1: SELECT * FROM chado.cv WHERE name = 'tripal' ^ in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 138.

·         user warning: query: SELECT * FROM chado.cv WHERE name = 'tripal' in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 159.

·         warning: pg_query(): Query failed: ERROR: relation "chado.cv" does not exist LINE 1: INSERT INTO chado.cv (name,definition) VALUES ('tripal', 'Te... ^ in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 138.

·         user warning: query: INSERT INTO chado.cv (name,definition) VALUES ('tripal', 'Terms used by Tripal for modules to manage data such as that stored in property tables like featureprop, analysisprop, etc') in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 159.

 

A 2011 posting shows the problem to be fixed?

imap://spficklin%40gmail%2Ecom@imap.googlemail.com:993/fetch%3EUID%3E/INBOX%3E194738?header=quotebody&part=1.1.2&filename=image001.png

 

Any thoughts?

 

Thanks,

Greg Toth







------------------------------------------------------------------------------
Android is increasing in popularity, but the open development platform that
developers love is also attractive to malware creators. Download this white
paper to learn more about secure code signing practices that can help keep
Android apps secure.
http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk







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

 

 

 

 



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Accelerate application performance with scalable programming models. Explore
techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
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Re: Errors when Installing Chado schema

gtoth

Stephen,

 

When I reinstalled Drupal and created a new database (thegtoth_drupal with user thegtoth_drupal), then ran drush trpjob-run administrator, I get the following response:

 

[hidden email] [~/public_html/work3373back]# drush trpjob-run administrator

Tripal Job Launcher

Running as user 'administrator'

-------------------

Calling: tripal_core_install_chado(Install Chado v1.2, 1)

Creating 'chado' schema

pg_query(): Query failed: ERROR:  must be owner of database thegtoth_drupal database.pgsql.inc:138                                        [warning]

ERROR:  must be owner of database thegtoth_drupal                                                                                         [warning]

query: create language plpgsql database.pgsql.inc:159

Loading sites/all/modules/tripal/tripal_core/chado_schema/default_schema-1.2.sql...

pg_query(): Query failed: ERROR:  language "plpgsql" does not exist                                                                       [warning]

HINT:  Use CREATE LANGUAGE to load the language into the database. database.pgsql.inc:138

ERROR:  language "plpgsql" does not exist                                                                                       [warning]

HINT:  Use CREATE LANGUAGE to load the language into the database.

query: CREATE OR REPLACE FUNCTION store_db (VARCHAR)

  RETURNS INT AS

'DECLARE

   v_name             ALIAS FOR $1;

   v_db_id            INTEGER;

BEGIN

    SELECT INTO v_db_id db_id

      FROM db

      WHERE name=v_name;

    IF NOT FOUND THEN

      INSERT INTO db

       (name)

         VALUES

       (v_name);

       RETURN currval(''db_db_id_seq'');

    END IF;

    RETURN v_db_id;

END;

' LANGUAGE 'plpgsql';

database.pgsql.inc:159

FAILED. Line  92, 0

ERROR:  language "plpgsql" does not exist

HINT:  Use CREATE LANGUAGE to load the language into the database.:

CREATE OR REPLACE FUNCTION store_db (VARCHAR)

  RETURNS INT AS

'DECLARE

   v_name             ALIAS FOR $1;

   v_db_id            INTEGER;

BEGIN

    SELECT INTO v_db_id db_id

      FROM db

      WHERE name=v_name;

    IF NOT FOUND THEN

      INSERT INTO db

       (name)

         VALUES

       (v_name);

       RETURN currval(''db_db_id_seq'');

    END IF;

    RETURN v_db_id;

END;

' LANGUAGE 'plpgsql';

 

 

Installation (Step 1 of 2) Problems!  Please check output above for errors.

Drush command terminated abnormally due to an unrecoverable error.                                                                        [error]

[hidden email] [~/public_html/work3373back]#

 

Greg

From: Stephen Ficklin [mailto:[hidden email]]
Sent: Tuesday, November 05, 2013 12:33 PM
To: Toth, Greg; gmod-tripal
Subject: Re: [Gmod-tripal] Errors when Installing Chado schema

 

Do you know how that chado schema got there?  Was there a previous run of the Chado installer via Tripal that failed partially through?   In any event, if you delete the 'chado' schema and try to re-install Chado via Tripal I think it will work without problem for you.

Stephen

On 11/5/2013 12:21 PM, Toth, Greg wrote:

Stephen,

 

Yes, there is a Chado schema, but no ‘cv’ table:

 

cid:image001.png@01CEDBF8.30676D60

 

Greg

 

From: Stephen Ficklin [[hidden email]]
Sent: Tuesday, November 05, 2013 12:13 PM
To: Toth, Greg; gmod-tripal
Subject: Re: [Gmod-tripal] Errors when Installing Chado schema

 

Hi Greg,

Tripal is trying insert a record into the chado cv table because it thinks that the Chado tables are already installed.  It checks to see if Chado is installed by looking at the $db_url in the settings.php file or by querying the postgres database to look for a 'chado' schema.  Do you have a 'chado' schema in your 'thegtoth_drupal' database?  Does it have any tables in it?  If so, does it have the 'cv' table? 

If it does exist and you remove it (as well as the so, frange, and genetic_code schemas) then perhaps that will solve the problem for you.

Stephen

On 11/5/2013 11:06 AM, Toth, Greg wrote:

Stephen,

 

Chado is not in the $db_url variable in the settings.php file (it’s attached).

 

Greg

 

From: Stephen Ficklin [[hidden email]]
Sent: Tuesday, November 05, 2013 9:47 AM
To: Toth, Greg; gmod-tripal
Subject: Re: [Gmod-tripal] Errors when Installing Chado schema

 

Hi Greg,

Do you have a 'chado' entry in the $db_url of your sites/default/settings.php file?  Tripal does support Chado when it is in a database external from the Drupal database, and if you do have Chado in a separate databaes then you can have a 'chado' entry in the $db_url of the settings.php file.  If you do have a 'chado' entry then Tripal thinks Chado is already installed and tries to do some queries which could be the cause of the error you are seeing.  

If you do have a 'chado' entry in the $db_url variable then you should remove it if you want to install Chado using the Tripal installer.   If not, let me know and we'll keep digging.

Stephen


On 11/5/2013 9:10 AM, Toth, Greg wrote:

Stephen,

 

On the “Install Chado Schema” page I had checked off “New install of Chado V1.2” which then showed up on the “Jobs” page.  At that point I ran the ‘drush trpjob-run administrator’ command’ (I was unable to run the sudo crontab –e) – the tutorial said “So, we will run the jobs manually. Tripal supports Drush and therefore has it's own commands. We can use drush to manually launch the job:”

 

Greg

 

From: Stephen Ficklin [[hidden email]]
Sent: Tuesday, November 05, 2013 9:01 AM
To: Toth, Greg; [hidden email]
Subject: Re: [Gmod-tripal] Errors when Installing Chado schema

 

Hi Greg,

What job were you trying to execute when you ran the 'drush trpjob-run administrator' command?  Did you already install Chado via the Tripal interface?

Stephen

On 11/5/2013 8:57 AM, Toth, Greg wrote:

Stephen,

 

Thanks for the response.  No, other Tripal modules were not enabled.  FYI, the installation is on Bluehost where I’ve got another separate site/folder running Drupal 7 for work bibliographic needs.

 

BTW, I am now subscribed to the Gmod-tripal mailing list.

 

Greg

 

 

Greg Toth, Ph.D., Deputy Director Ecological Exposure Research Division (MD591)

National Exposure Research Laboratory, USEPA, Cincinnati, OH 45268

513-569-7242

 

 

 

From: Stephen Ficklin [[hidden email]]
Sent: Monday, November 04, 2013 8:32 AM
To: Toth, Greg; [hidden email]
Subject: Re: [Gmod-tripal] Errors when Installing Chado schema

 

Hi Greg,

I believe you get this kind of error if you have not yet installed Chado but you have other Tripal modules enabled besides the Tripal Core module (e.g. Tripal CV module, Tripal DB module, etc.).   Is this the case for you?   If so, then you can disable all but the Tripal core modules and this should make the error go away.  Then, install Chado using the Chado installer.  Once Chado is installed you can enable the other modules. 

Stephen



On 11/1/2013 8:56 PM, Toth, Greg wrote:

When I run “drush trpjob-run administrator” I get the following errors:

 

·         warning: pg_query(): Query failed: ERROR: relation "chado.cv" does not exist LINE 1: SELECT * FROM chado.cv WHERE name = 'tripal' ^ in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 138.

·         user warning: query: SELECT * FROM chado.cv WHERE name = 'tripal' in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 159.

·         warning: pg_query(): Query failed: ERROR: relation "chado.cv" does not exist LINE 1: INSERT INTO chado.cv (name,definition) VALUES ('tripal', 'Te... ^ in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 138.

·         user warning: query: INSERT INTO chado.cv (name,definition) VALUES ('tripal', 'Terms used by Tripal for modules to manage data such as that stored in property tables like featureprop, analysisprop, etc') in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 159.

 

A 2011 posting shows the problem to be fixed?

imap://spficklin%40gmail%2Ecom@imap.googlemail.com:993/fetch%3EUID%3E/INBOX%3E194738?header=quotebody&part=1.1.2&filename=image001.png

 

Any thoughts?

 

Thanks,

Greg Toth








------------------------------------------------------------------------------
Android is increasing in popularity, but the open development platform that
developers love is also attractive to malware creators. Download this white
paper to learn more about secure code signing practices that can help keep
Android apps secure.
http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk








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

 

 

 

 

 


------------------------------------------------------------------------------
November Webinars for C, C++, Fortran Developers
Accelerate application performance with scalable programming models. Explore
techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
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Re: Errors when Installing Chado schema

Stephen Ficklin-2
Hi Greg,

Can you check the permissions on the 'thegtoth_drupal' database to make sure that the user (specified in your settings.php file) has permission to create new schemas.  I'm looking at this error message:

Creating 'chado' schema pg_query(): Query failed: ERROR:  must be owner of database thegtoth_drupal database.pgsql.inc:138                                        [warning]

Stephen

On 11/7/2013 9:20 PM, Toth, Greg wrote:

Stephen,

 

When I reinstalled Drupal and created a new database (thegtoth_drupal with user thegtoth_drupal), then ran drush trpjob-run administrator, I get the following response:

 

[hidden email] [~/public_html/work3373back]# drush trpjob-run administrator

Tripal Job Launcher

Running as user 'administrator'

-------------------

Calling: tripal_core_install_chado(Install Chado v1.2, 1)

Creating 'chado' schema

pg_query(): Query failed: ERROR:  must be owner of database thegtoth_drupal database.pgsql.inc:138                                        [warning]

ERROR:  must be owner of database thegtoth_drupal                                                                                         [warning]

query: create language plpgsql database.pgsql.inc:159

Loading sites/all/modules/tripal/tripal_core/chado_schema/default_schema-1.2.sql...

pg_query(): Query failed: ERROR:  language "plpgsql" does not exist                                                                       [warning]

HINT:  Use CREATE LANGUAGE to load the language into the database. database.pgsql.inc:138

ERROR:  language "plpgsql" does not exist                                                                                       [warning]

HINT:  Use CREATE LANGUAGE to load the language into the database.

query: CREATE OR REPLACE FUNCTION store_db (VARCHAR)

  RETURNS INT AS

'DECLARE

   v_name             ALIAS FOR $1;

   v_db_id            INTEGER;

BEGIN

    SELECT INTO v_db_id db_id

      FROM db

      WHERE name=v_name;

    IF NOT FOUND THEN

      INSERT INTO db

       (name)

         VALUES

       (v_name);

       RETURN currval(''db_db_id_seq'');

    END IF;

    RETURN v_db_id;

END;

' LANGUAGE 'plpgsql';

database.pgsql.inc:159

FAILED. Line  92, 0

ERROR:  language "plpgsql" does not exist

HINT:  Use CREATE LANGUAGE to load the language into the database.:

CREATE OR REPLACE FUNCTION store_db (VARCHAR)

  RETURNS INT AS

'DECLARE

   v_name             ALIAS FOR $1;

   v_db_id            INTEGER;

BEGIN

    SELECT INTO v_db_id db_id

      FROM db

      WHERE name=v_name;

    IF NOT FOUND THEN

      INSERT INTO db

       (name)

         VALUES

       (v_name);

       RETURN currval(''db_db_id_seq'');

    END IF;

    RETURN v_db_id;

END;

' LANGUAGE 'plpgsql';

 

 

Installation (Step 1 of 2) Problems!  Please check output above for errors.

Drush command terminated abnormally due to an unrecoverable error.                                                                        [error]

[hidden email] [~/public_html/work3373back]#

 

Greg

From: Stephen Ficklin [[hidden email]]
Sent: Tuesday, November 05, 2013 12:33 PM
To: Toth, Greg; gmod-tripal
Subject: Re: [Gmod-tripal] Errors when Installing Chado schema

 

Do you know how that chado schema got there?  Was there a previous run of the Chado installer via Tripal that failed partially through?   In any event, if you delete the 'chado' schema and try to re-install Chado via Tripal I think it will work without problem for you.

Stephen

On 11/5/2013 12:21 PM, Toth, Greg wrote:

Stephen,

 

Yes, there is a Chado schema, but no ‘cv’ table:

 

imap://spficklin%40gmail%2Ecom@imap.googlemail.com:993/fetch%3EUID%3E/INBOX%3E195967?header=quotebody&part=1.2&filename=image001.png

 

Greg

 

From: Stephen Ficklin [[hidden email]]
Sent: Tuesday, November 05, 2013 12:13 PM
To: Toth, Greg; gmod-tripal
Subject: Re: [Gmod-tripal] Errors when Installing Chado schema

 

Hi Greg,

Tripal is trying insert a record into the chado cv table because it thinks that the Chado tables are already installed.  It checks to see if Chado is installed by looking at the $db_url in the settings.php file or by querying the postgres database to look for a 'chado' schema.  Do you have a 'chado' schema in your 'thegtoth_drupal' database?  Does it have any tables in it?  If so, does it have the 'cv' table? 

If it does exist and you remove it (as well as the so, frange, and genetic_code schemas) then perhaps that will solve the problem for you.

Stephen

On 11/5/2013 11:06 AM, Toth, Greg wrote:

Stephen,

 

Chado is not in the $db_url variable in the settings.php file (it’s attached).

 

Greg

 

From: Stephen Ficklin [[hidden email]]
Sent: Tuesday, November 05, 2013 9:47 AM
To: Toth, Greg; gmod-tripal
Subject: Re: [Gmod-tripal] Errors when Installing Chado schema

 

Hi Greg,

Do you have a 'chado' entry in the $db_url of your sites/default/settings.php file?  Tripal does support Chado when it is in a database external from the Drupal database, and if you do have Chado in a separate databaes then you can have a 'chado' entry in the $db_url of the settings.php file.  If you do have a 'chado' entry then Tripal thinks Chado is already installed and tries to do some queries which could be the cause of the error you are seeing.  

If you do have a 'chado' entry in the $db_url variable then you should remove it if you want to install Chado using the Tripal installer.   If not, let me know and we'll keep digging.

Stephen


On 11/5/2013 9:10 AM, Toth, Greg wrote:

Stephen,

 

On the “Install Chado Schema” page I had checked off “New install of Chado V1.2” which then showed up on the “Jobs” page.  At that point I ran the ‘drush trpjob-run administrator’ command’ (I was unable to run the sudo crontab –e) – the tutorial said “So, we will run the jobs manually. Tripal supports Drush and therefore has it's own commands. We can use drush to manually launch the job:”

 

Greg

 

From: Stephen Ficklin [[hidden email]]
Sent: Tuesday, November 05, 2013 9:01 AM
To: Toth, Greg; [hidden email]
Subject: Re: [Gmod-tripal] Errors when Installing Chado schema

 

Hi Greg,

What job were you trying to execute when you ran the 'drush trpjob-run administrator' command?  Did you already install Chado via the Tripal interface?

Stephen

On 11/5/2013 8:57 AM, Toth, Greg wrote:

Stephen,

 

Thanks for the response.  No, other Tripal modules were not enabled.  FYI, the installation is on Bluehost where I’ve got another separate site/folder running Drupal 7 for work bibliographic needs.

 

BTW, I am now subscribed to the Gmod-tripal mailing list.

 

Greg

 

 

Greg Toth, Ph.D., Deputy Director Ecological Exposure Research Division (MD591)

National Exposure Research Laboratory, USEPA, Cincinnati, OH 45268

513-569-7242

 

 

 

From: Stephen Ficklin [[hidden email]]
Sent: Monday, November 04, 2013 8:32 AM
To: Toth, Greg; [hidden email]
Subject: Re: [Gmod-tripal] Errors when Installing Chado schema

 

Hi Greg,

I believe you get this kind of error if you have not yet installed Chado but you have other Tripal modules enabled besides the Tripal Core module (e.g. Tripal CV module, Tripal DB module, etc.).   Is this the case for you?   If so, then you can disable all but the Tripal core modules and this should make the error go away.  Then, install Chado using the Chado installer.  Once Chado is installed you can enable the other modules. 

Stephen



On 11/1/2013 8:56 PM, Toth, Greg wrote:

When I run “drush trpjob-run administrator” I get the following errors:

 

·         warning: pg_query(): Query failed: ERROR: relation "chado.cv" does not exist LINE 1: SELECT * FROM chado.cv WHERE name = 'tripal' ^ in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 138.

·         user warning: query: SELECT * FROM chado.cv WHERE name = 'tripal' in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 159.

·         warning: pg_query(): Query failed: ERROR: relation "chado.cv" does not exist LINE 1: INSERT INTO chado.cv (name,definition) VALUES ('tripal', 'Te... ^ in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 138.

·         user warning: query: INSERT INTO chado.cv (name,definition) VALUES ('tripal', 'Terms used by Tripal for modules to manage data such as that stored in property tables like featureprop, analysisprop, etc') in /home1/thegtoth/public_html/work3373back/includes/database.pgsql.inc on line 159.

 

A 2011 posting shows the problem to be fixed?

imap://spficklin%40gmail%2Ecom@imap.googlemail.com:993/fetch%3EUID%3E/INBOX%3E194738?header=quotebody&part=1.1.2&filename=image001.png

 

Any thoughts?

 

Thanks,

Greg Toth








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