[Gmod-tripal-devel] Inquiry about bug in "Go Assignments" again

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[Gmod-tripal-devel] Inquiry about bug in "Go Assignments" again

Abraham Darius Llave IRRI
Good day fellows! Here I am again.

So I sent you an inquiry regarding the missing "Go Assignments" link in the Resources sidebar section, after "Loading InterProScan Results" in the Tripal 1.0 Tutorial. Sir Stephen eventually responded and said that there was a bug and suggested a fix which then worked and enabled me to finish following what's on the tutorial. For more on the correspondence, please go to https://sourceforge.net/mailarchive/message.php?msg_id=30759045 .

So after that, we now concluded that we can now put Tripal on our production server. A senior colleague followed the tutorial last week (downloaded Drupal, checked out source code as instructed) up until setting permissions post-loading of controlled vocabularies before handing over control to me. And now, I am thumped because this bug appeared again. Since I have made it this far, I decided to try the first suggested fix:

(excerpt from the previous correspondence about the bug fix, from Sir Stephen Ficklin)

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

Hi Abraham,


Thank you for posting the SQL dump of your tutorial database, that was very helpful.  I have found the problem.  It was a bug in one of our Chado API calls for preparing SQL statements.  I have made a fix for it on our current development branch.  If you update your Tripal code you'll retrieve the fix.   To update execute this command in your Tripal directory


git fetch

git checkout 6.x-1.x


You'll want to do this for the Tripal theme as well and extension modules.


Let me know if this fixes your problem.

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

It did fix the problem - the "Go Assignments" link is now on the Resources sidebar and its contents are there. However, the InterPro report is now messed up. (Please see picture).

Inline image 1

So that leaves us the option of restarting from scratch again ( as we were not able to have a backup before checking out Tripal modules ) and then checking out the Tripal (development) code at branch 6.x-1.x . This was what fixed my problem when I was testing half-a-month ago, but since it is development code, I do have reservations on us using it on the production server.

Which now leads me to the ..
1) Assumption: The bug fix seems to haven't made it to the main branch yet as of the time my senior colleague checked out the source, have it?
2) Question: Assuming (1) is true, as a developer too, I can relate that it might need some time so you can make sure if including the bug fix on the main branch won't cause repercussions. Knowing that, would you recommend that we just go back and check out the code at branch 6.x-1.x instead of what's outlined in the current version of the tutorial page, so we can solve the problem about the GO Assignments link and continue setting up Tripal? I do think information about GO Assignments is a vital part of this application so I prefer to be resolving issues about it before moving on.


Have a nice day!
--

Abraham Darius S. Llaveinspite of my reservations 

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(s) to whom it is addressed. Any views or opinions expressed are solely those of the author, unless categorically stated.

 

If you are not the intended recipient of this email, you must neither take any action based upon its contents, nor copy or show it to anyone - except as permitted by the author/sender and/or applicable regulations/laws of your company/organization/sovereign state.


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Re: [Gmod-tripal-devel] Inquiry about bug in "Go Assignments" again

Stephen Ficklin-2
Hi Abraham,

You are correct, the bug fixes have not yet made it to the main branch.  We will be releasing v1.1 here soon which will have all of the recent bug fixes.  So, I would recommend you use the 6.x-1.x branch to pick up the most recent fixes.  We are currently using the 6.x-1.x branch on some of our sites as well, so you should be find with it.   Also, to fix the themeing problems with the GO terms can you try the most recent 6.x-1.x branch of the tripal_theme as well?

Stephen

On 5/21/2013 5:55 AM, Abraham Darius Llave (IRRI) wrote:
Good day fellows! Here I am again.

So I sent you an inquiry regarding the missing "Go Assignments" link in the Resources sidebar section, after "Loading InterProScan Results" in the Tripal 1.0 Tutorial. Sir Stephen eventually responded and said that there was a bug and suggested a fix which then worked and enabled me to finish following what's on the tutorial. For more on the correspondence, please go to https://sourceforge.net/mailarchive/message.php?msg_id=30759045 .

So after that, we now concluded that we can now put Tripal on our production server. A senior colleague followed the tutorial last week (downloaded Drupal, checked out source code as instructed) up until setting permissions post-loading of controlled vocabularies before handing over control to me. And now, I am thumped because this bug appeared again. Since I have made it this far, I decided to try the first suggested fix:

(excerpt from the previous correspondence about the bug fix, from Sir Stephen Ficklin)

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

Hi Abraham,


Thank you for posting the SQL dump of your tutorial database, that was very helpful.  I have found the problem.  It was a bug in one of our Chado API calls for preparing SQL statements.  I have made a fix for it on our current development branch.  If you update your Tripal code you'll retrieve the fix.   To update execute this command in your Tripal directory


git fetch

git checkout 6.x-1.x


You'll want to do this for the Tripal theme as well and extension modules.


Let me know if this fixes your problem.

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

It did fix the problem - the "Go Assignments" link is now on the Resources sidebar and its contents are there. However, the InterPro report is now messed up. (Please see picture).

Inline
                image 1

So that leaves us the option of restarting from scratch again ( as we were not able to have a backup before checking out Tripal modules ) and then checking out the Tripal (development) code at branch 6.x-1.x . This was what fixed my problem when I was testing half-a-month ago, but since it is development code, I do have reservations on us using it on the production server.

Which now leads me to the ..
1) Assumption: The bug fix seems to haven't made it to the main branch yet as of the time my senior colleague checked out the source, have it?
2) Question: Assuming (1) is true, as a developer too, I can relate that it might need some time so you can make sure if including the bug fix on the main branch won't cause repercussions. Knowing that, would you recommend that we just go back and check out the code at branch 6.x-1.x instead of what's outlined in the current version of the tutorial page, so we can solve the problem about the GO Assignments link and continue setting up Tripal? I do think information about GO Assignments is a vital part of this application so I prefer to be resolving issues about it before moving on.


Have a nice day!
--

Abraham Darius S. Llaveinspite of my reservations 

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(s) to whom it is addressed. Any views or opinions expressed are solely those of the author, unless categorically stated.

 

If you are not the intended recipient of this email, you must neither take any action based upon its contents, nor copy or show it to anyone - except as permitted by the author/sender and/or applicable regulations/laws of your company/organization/sovereign state.


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


------------------------------------------------------------------------------
Try New Relic Now & We'll Send You this Cool Shirt
New Relic is the only SaaS-based application performance monitoring service
that delivers powerful full stack analytics. Optimize and monitor your
browser, app, & servers with just a few lines of code. Try New Relic
and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_may
_______________________________________________
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