[Gmod-tripal-devel] Can't get through the updated Tripal Tutorial

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[Gmod-tripal-devel] Can't get through the updated Tripal Tutorial

Abraham Darius Llave IRRI
Hi folks! Here I am seeking your help again.

I just can't make the steps in http://www.gmod.org/wiki/Tripal_Tutorial_(v1.0)#Loading_KEGG_Analysis_Results work.

I get these errors :

Inline image 1

Inline image 2

and there isn't any Assigned KEGG Pathway.

Inline image 3

I'm quite sure I have faithfully followed every step on the way but I really stuck on this part since last week. Any tips? I did trace how the first of these warnings came to be - it looks like the code looks for an entry in the 'analysisfeatureprop' table with 'analysisfeature_id' = 164 and 'type_id' = '41505', which it cannot find. However, I found out that after drush finished, an entry is now present in that table with values matching those ( but still, the Assigned KEGG Pathways aren't there ).

 Thank you for help.


--

Abraham Darius S. Llave

Associate - BioInformatics Support | C4 Rice Project

International Rice Research Institute

Los Baños, Laguna 4027

Republic of the Philippines

[hidden email]
+63-49-536-2701 extension 2643



The International Rice Research Institute is a member of the CGIAR consortium
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Re: [Gmod-tripal-devel] Can't get through the updated Tripal Tutorial

Stephen Ficklin-2
Hi Abraham,

Sorry for the problem.  I've not seen these errors before with the KEGG module.  I'll test it and see if I can duplicate what you are seeing, and get back to you.

Stephen



On 3/20/2013 5:09 AM, Abraham Darius Llave (IRRI) wrote:
Hi folks! Here I am seeking your help again.

I just can't make the steps in http://www.gmod.org/wiki/Tripal_Tutorial_(v1.0)#Loading_KEGG_Analysis_Results work.

I get these errors :

Inline
          image 1

Inline
          image 2

and there isn't any Assigned KEGG Pathway.

Inline
          image 3

I'm quite sure I have faithfully followed every step on the way but I really stuck on this part since last week. Any tips? I did trace how the first of these warnings came to be - it looks like the code looks for an entry in the 'analysisfeatureprop' table with 'analysisfeature_id' = 164 and 'type_id' = '41505', which it cannot find. However, I found out that after drush finished, an entry is now present in that table with values matching those ( but still, the Assigned KEGG Pathways aren't there ).

 Thank you for help.


--

Abraham Darius S. Llave

Associate - BioInformatics Support | C4 Rice Project

International Rice Research Institute

Los Baños, Laguna 4027

Republic of the Philippines

[hidden email]
+63-49-536-2701 extension 2643



The International Rice Research Institute is a member of the CGIAR consortium

------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar


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Download AppDynamics Lite for free today:
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Re: [Gmod-tripal-devel] Can't get through the updated Tripal Tutorial

Stephen Ficklin-2
In reply to this post by Abraham Darius Llave IRRI
Hi Abraham,

Turns out we had some bugs in the KEGG module which you were the lucky one to first discover.   I have cleared that up and committed the code to the repository.  If you would like to retrieve those fixes follow these instructions to update

1) Update Tripal.  In the Tripal directory issue this command:
git checkout 6.x-1.x
git pull

2)  Update the KEGG analysis module.  There is a slight database correction that needs to be made so after you checkout the most recent code you'll need to run the update:
git checkout 6.x-1.x
git pull
drush updatedb
(You will notice an error about an argument must be an array, which you can safely ignore.)

Then try to reload your KEGG file.

Let me know if this helps.
Stephen

On 3/20/2013 5:09 AM, Abraham Darius Llave (IRRI) wrote:
Hi folks! Here I am seeking your help again.

I just can't make the steps in http://www.gmod.org/wiki/Tripal_Tutorial_(v1.0)#Loading_KEGG_Analysis_Results work.

I get these errors :

Inline
          image 1

Inline
          image 2

and there isn't any Assigned KEGG Pathway.

Inline
          image 3

I'm quite sure I have faithfully followed every step on the way but I really stuck on this part since last week. Any tips? I did trace how the first of these warnings came to be - it looks like the code looks for an entry in the 'analysisfeatureprop' table with 'analysisfeature_id' = 164 and 'type_id' = '41505', which it cannot find. However, I found out that after drush finished, an entry is now present in that table with values matching those ( but still, the Assigned KEGG Pathways aren't there ).

 Thank you for help.


--

Abraham Darius S. Llave

Associate - BioInformatics Support | C4 Rice Project

International Rice Research Institute

Los Baños, Laguna 4027

Republic of the Philippines

[hidden email]
+63-49-536-2701 extension 2643



The International Rice Research Institute is a member of the CGIAR consortium

------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar


_______________________________________________
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[hidden email]
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Download AppDynamics Lite for free today:
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Re: [Gmod-tripal-devel] Can't get through the updated Tripal Tutorial

Abraham Darius Llave IRRI
Alright. I will try these and attempt to get back to you in a few hours. Thanks.

On Fri, Mar 22, 2013 at 9:58 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Abraham,

Turns out we had some bugs in the KEGG module which you were the lucky one to first discover.   I have cleared that up and committed the code to the repository.  If you would like to retrieve those fixes follow these instructions to update

1) Update Tripal.  In the Tripal directory issue this command:
git checkout 6.x-1.x
git pull

2)  Update the KEGG analysis module.  There is a slight database correction that needs to be made so after you checkout the most recent code you'll need to run the update:
git checkout 6.x-1.x
git pull
drush updatedb
(You will notice an error about an argument must be an array, which you can safely ignore.)

Then try to reload your KEGG file.

Let me know if this helps.

Stephen

On 3/20/2013 5:09 AM, Abraham Darius Llave (IRRI) wrote:
Hi folks! Here I am seeking your help again.

I just can't make the steps in http://www.gmod.org/wiki/Tripal_Tutorial_(v1.0)#Loading_KEGG_Analysis_Results work.

I get these errors :

Inline
          image 1

Inline
          image 2

and there isn't any Assigned KEGG Pathway.

Inline
          image 3

I'm quite sure I have faithfully followed every step on the way but I really stuck on this part since last week. Any tips? I did trace how the first of these warnings came to be - it looks like the code looks for an entry in the 'analysisfeatureprop' table with 'analysisfeature_id' = 164 and 'type_id' = '41505', which it cannot find. However, I found out that after drush finished, an entry is now present in that table with values matching those ( but still, the Assigned KEGG Pathways aren't there ).

 Thank you for help.


--

Abraham Darius S. Llave

Associate - BioInformatics Support | C4 Rice Project

International Rice Research Institute

Los Baños, Laguna 4027

Republic of the Philippines

[hidden email]
+63-49-536-2701 extension 2643



The International Rice Research Institute is a member of the CGIAR consortium

------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar


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




-


The International Rice Research Institute is a member of the CGIAR consortium
------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar
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Re: [Gmod-tripal-devel] Can't get through the updated Tripal Tutorial

Abraham Darius Llave IRRI
Hi Sir Stephen. The issue has been fixed. All is well now. Thank you. 



On Fri, Mar 22, 2013 at 10:03 AM, Abraham Darius Llave (IRRI) <[hidden email]> wrote:
Alright. I will try these and attempt to get back to you in a few hours. Thanks.


On Fri, Mar 22, 2013 at 9:58 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Abraham,

Turns out we had some bugs in the KEGG module which you were the lucky one to first discover.   I have cleared that up and committed the code to the repository.  If you would like to retrieve those fixes follow these instructions to update

1) Update Tripal.  In the Tripal directory issue this command:
git checkout 6.x-1.x
git pull

2)  Update the KEGG analysis module.  There is a slight database correction that needs to be made so after you checkout the most recent code you'll need to run the update:
git checkout 6.x-1.x
git pull
drush updatedb
(You will notice an error about an argument must be an array, which you can safely ignore.)

Then try to reload your KEGG file.

Let me know if this helps.

Stephen

On 3/20/2013 5:09 AM, Abraham Darius Llave (IRRI) wrote:
Hi folks! Here I am seeking your help again.

I just can't make the steps in http://www.gmod.org/wiki/Tripal_Tutorial_(v1.0)#Loading_KEGG_Analysis_Results work.

I get these errors :

Inline
          image 1

Inline
          image 2

and there isn't any Assigned KEGG Pathway.

Inline
          image 3

I'm quite sure I have faithfully followed every step on the way but I really stuck on this part since last week. Any tips? I did trace how the first of these warnings came to be - it looks like the code looks for an entry in the 'analysisfeatureprop' table with 'analysisfeature_id' = 164 and 'type_id' = '41505', which it cannot find. However, I found out that after drush finished, an entry is now present in that table with values matching those ( but still, the Assigned KEGG Pathways aren't there ).

 Thank you for help.


--

Abraham Darius S. Llave

Associate - BioInformatics Support | C4 Rice Project

International Rice Research Institute

Los Baños, Laguna 4027

Republic of the Philippines

[hidden email]
+63-49-536-2701 extension 2643



The International Rice Research Institute is a member of the CGIAR consortium

------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar


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




-




--

Abraham Darius S. Llave

Associate - BioInformatics Support | C4 Rice Project

International Rice Research Institute

Los Baños, Laguna 4027

Republic of the Philippines

[hidden email]
+63-49-536-2701 extension 2643

 

This email and any attachments to it may be confidential and are intended solely for the use of the individual to whom it is addressed. Any views or opinions expressed are solely those of the author.

 

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The International Rice Research Institute is a member of the CGIAR consortium
------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar
_______________________________________________
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