tutorial 3.01b issues with custom pane

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tutorial 3.01b issues with custom pane

Moore, Gary

I’m trying to follow the instructions in the tutorial for creating a new features page via the custom panel layout.   The attached (if this list serve allows attachments) screenshot shows what I get when viewing the node.    I hope this is something easy which I’m overlooking.

-Gary

 

Gary Moore, Technical Lead

LCA Digital Commons Project

National Agriculture Library/USDA/ARS

Beltsville MD

 





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Re: tutorial 3.01b issues with custom pane

Stephen Ficklin-2
Hi Gary,

I don't believe I've ever seen fields that look like that before.   Can you tell me which panel modules you have enabled and which blocks you have on the page?

Stephen


On 5/14/2012 6:22 PM, Moore, Gary wrote:

I’m trying to follow the instructions in the tutorial for creating a new features page via the custom panel layout.   The attached (if this list serve allows attachments) screenshot shows what I get when viewing the node.    I hope this is something easy which I’m overlooking.

-Gary

 

Gary Moore, Technical Lead

LCA Digital Commons Project

National Agriculture Library/USDA/ARS

Beltsville MD

 





This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.



This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

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threat landscape has changed and how IT managers can respond. Discussions 
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Re: tutorial 3.01b issues with custom pane

Moore, Gary

Hi Stephen,

Panels enabled are: Mini panels; panel nodes; panels; and panels in-Place editor.   In terms of blocks on the page,  I am trying to use the ones from the tutorial.   I think this may be where I’m going off track.  In the “Left above” layout, I click the + - add content.  From the “add content to Left above” popup I select “Miscellaneous ->Tripal Feature References” ,etc. (see attached).  Is this how you put blocks into the layout?

Thanks for your patience.

Gary

From: Stephen Ficklin [mailto:[hidden email]]
Sent: Tuesday, May 15, 2012 9:46 AM
To: [hidden email]
Subject: Re: [Gmod-tripal] tutorial 3.01b issues with custom pane

 

Hi Gary,

I don't believe I've ever seen fields that look like that before.   Can you tell me which panel modules you have enabled and which blocks you have on the page?

Stephen


On 5/14/2012 6:22 PM, Moore, Gary wrote:

I’m trying to follow the instructions in the tutorial for creating a new features page via the custom panel layout.   The attached (if this list serve allows attachments) screenshot shows what I get when viewing the node.    I hope this is something easy which I’m overlooking.

-Gary

 

Gary Moore, Technical Lead

LCA Digital Commons Project

National Agriculture Library/USDA/ARS

Beltsville MD

 





This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.



This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.


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threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/




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Re: tutorial 3.01b issues with custom pane

Moore, Gary
In reply to this post by Stephen Ficklin-2

Stephen,

There is a “Renderer” option in the General section of the node template which was checked “In-Place Editor”.  If I uncheck this option, then the fields display goes away.

 

In the tutorial, you state:

Using the layout interface, the following will be demonstrated (but not shown here in this tutorial). But first, open to the feature page 'CG40042' so we can watch the changes as we proceed:

  • How to remove default content from the panel regions
  • How to add content to each panel region
  • Adding of blocks in this order:
    • Feature Details in the Left Above section
    • Feature Synonyms in the Left Above section, just below the feature details.
    • Feature References in the Right Above section
    • Feature Relationships as Object in the Middle section
    • Add any other blocks desired to the Middle or lower sections

 

If you could  provide a couple of clues as to how the blocks are added to the panel regions, I should be in business.

Thanks

Gary

From: Stephen Ficklin [mailto:[hidden email]]
Sent: Tuesday, May 15, 2012 9:46 AM
To: [hidden email]
Subject: Re: [Gmod-tripal] tutorial 3.01b issues with custom pane

 

Hi Gary,

I don't believe I've ever seen fields that look like that before.   Can you tell me which panel modules you have enabled and which blocks you have on the page?

Stephen


On 5/14/2012 6:22 PM, Moore, Gary wrote:

I’m trying to follow the instructions in the tutorial for creating a new features page via the custom panel layout.   The attached (if this list serve allows attachments) screenshot shows what I get when viewing the node.    I hope this is something easy which I’m overlooking.

-Gary

 

Gary Moore, Technical Lead

LCA Digital Commons Project

National Agriculture Library/USDA/ARS

Beltsville MD

 





This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.



This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.


------------------------------------------------------------------------------
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Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/




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Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: tutorial 3.01b issues with custom pane

Stephen Ficklin-2
Hi Gary,

It has been a while since I looked at Panels as we are using template files for our production sites, so let me get it setup on my end and I can try and give you a better answer.

if you're interested in customizing your site by altering templates you can find documentation here: http://gmod.org/wiki/Tripal_Developer's_Handbook


Stephen

On 5/15/2012 1:21 PM, Moore, Gary wrote:

Stephen,

There is a “Renderer” option in the General section of the node template which was checked “In-Place Editor”.  If I uncheck this option, then the fields display goes away.

 

In the tutorial, you state:

Using the layout interface, the following will be demonstrated (but not shown here in this tutorial). But first, open to the feature page 'CG40042' so we can watch the changes as we proceed:

  • How to remove default content from the panel regions
  • How to add content to each panel region
  • Adding of blocks in this order:
    • Feature Details in the Left Above section
    • Feature Synonyms in the Left Above section, just below the feature details.
    • Feature References in the Right Above section
    • Feature Relationships as Object in the Middle section
    • Add any other blocks desired to the Middle or lower sections

 

If you could  provide a couple of clues as to how the blocks are added to the panel regions, I should be in business.

Thanks

Gary

From: Stephen Ficklin [[hidden email]]
Sent: Tuesday, May 15, 2012 9:46 AM
To: [hidden email]
Subject: Re: [Gmod-tripal] tutorial 3.01b issues with custom pane

 

Hi Gary,

I don't believe I've ever seen fields that look like that before.   Can you tell me which panel modules you have enabled and which blocks you have on the page?

Stephen


On 5/14/2012 6:22 PM, Moore, Gary wrote:

I’m trying to follow the instructions in the tutorial for creating a new features page via the custom panel layout.   The attached (if this list serve allows attachments) screenshot shows what I get when viewing the node.    I hope this is something easy which I’m overlooking.

-Gary

 

Gary Moore, Technical Lead

LCA Digital Commons Project

National Agriculture Library/USDA/ARS

Beltsville MD

 





This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.



This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.


------------------------------------------------------------------------------
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Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/




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threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: tutorial 3.01b issues with custom pane

Moore, Gary

Hi Stephan,

The template option sounds fine to me.  Do you have instructions/hints as to how to add the GBrowse Image to the template (the last item in the tutorial)?  I’ve created the GBrowse view but am at a bit of a loss as to how to hook it into a template.  I’m not a Drupal expert so please excuse my cluelessness.  Thanks

Gary

From: Stephen Ficklin [mailto:[hidden email]]
Sent: Tuesday, May 15, 2012 5:02 PM
To: Moore, Gary
Cc: [hidden email]
Subject: Re: [Gmod-tripal] tutorial 3.01b issues with custom pane

 

Hi Gary,

It has been a while since I looked at Panels as we are using template files for our production sites, so let me get it setup on my end and I can try and give you a better answer.

if you're interested in customizing your site by altering templates you can find documentation here: http://gmod.org/wiki/Tripal_Developer's_Handbook


Stephen

On 5/15/2012 1:21 PM, Moore, Gary wrote:

Stephen,

There is a “Renderer” option in the General section of the node template which was checked “In-Place Editor”.  If I uncheck this option, then the fields display goes away.

 

In the tutorial, you state:

Using the layout interface, the following will be demonstrated (but not shown here in this tutorial). But first, open to the feature page 'CG40042' so we can watch the changes as we proceed:

  • How to remove default content from the panel regions
  • How to add content to each panel region
  • Adding of blocks in this order:
    • Feature Details in the Left Above section
    • Feature Synonyms in the Left Above section, just below the feature details.
    • Feature References in the Right Above section
    • Feature Relationships as Object in the Middle section
    • Add any other blocks desired to the Middle or lower sections

 

If you could  provide a couple of clues as to how the blocks are added to the panel regions, I should be in business.

Thanks

Gary

From: Stephen Ficklin [[hidden email]]
Sent: Tuesday, May 15, 2012 9:46 AM
To: [hidden email]
Subject: Re: [Gmod-tripal] tutorial 3.01b issues with custom pane

 

Hi Gary,

I don't believe I've ever seen fields that look like that before.   Can you tell me which panel modules you have enabled and which blocks you have on the page?

Stephen


On 5/14/2012 6:22 PM, Moore, Gary wrote:

I’m trying to follow the instructions in the tutorial for creating a new features page via the custom panel layout.   The attached (if this list serve allows attachments) screenshot shows what I get when viewing the node.    I hope this is something easy which I’m overlooking.

-Gary

 

Gary Moore, Technical Lead

LCA Digital Commons Project

National Agriculture Library/USDA/ARS

Beltsville MD

 





This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.



This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.



------------------------------------------------------------------------------
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Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/





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Re: tutorial 3.01b issues with custom pane

Stephen Ficklin-2
Hi Gary,

No worries.  Drupal is great the more you get used to it.  Panels are nice and allows you to customize your pages the way you want, but editing templates gives you the most power over the layout of your site.  It does require some PHP and Chado knowledge though.

For the citrus site we added a GBrowse image to our gene pages (for example: http://www.citrusgenomedb.org/PAC:19274706, click the 'Genomic Location' link on the right).

This was done by editing the template file:  theme_tripal/tripal_feature/tripal_feature_featurelocs.tpl.php.  In that file you can simply add the link to GBrowse wherever you prefer.  Example code that goes in the for loop that iterates through the featurelocs:

<?php               
  // build the link to GBrowse
   $location = $featureloc->srcfeature_id->name .":". ($featureloc->fmin + 1) . ".." . $featureloc->fmax;
   $gbrowse_link = "/gb/gbrowse/citrus_sinensis_v1.0/?name=".  $feature->name;
    print "<a href=\"$gbrowse_link\" target=\"_blank\">".$location."</a>";

  // build the GBrowse image
   $gbrowse_img = "/gb/gbrowse_img/citrus_sinensis_v1.0/?name=" . $feature->name;
   print "<img border=0 src=\"".$gbrowse_img ."&width=500\">";             
?>

If you have more than one species you can use an if statement to customize the gbrowse links. If there is only one location where this feature maps, which is the case for genes and mRNA then you should only get a single GBrowse image and link.

Hope that helps,
Stephen

On 5/16/2012 10:48 AM, Moore, Gary wrote:

Hi Stephan,

The template option sounds fine to me.  Do you have instructions/hints as to how to add the GBrowse Image to the template (the last item in the tutorial)?  I’ve created the GBrowse view but am at a bit of a loss as to how to hook it into a template.  I’m not a Drupal expert so please excuse my cluelessness.  Thanks

Gary

From: Stephen Ficklin [[hidden email]]
Sent: Tuesday, May 15, 2012 5:02 PM
To: Moore, Gary
Cc: [hidden email]
Subject: Re: [Gmod-tripal] tutorial 3.01b issues with custom pane

 

Hi Gary,

It has been a while since I looked at Panels as we are using template files for our production sites, so let me get it setup on my end and I can try and give you a better answer.

if you're interested in customizing your site by altering templates you can find documentation here: http://gmod.org/wiki/Tripal_Developer's_Handbook


Stephen

On 5/15/2012 1:21 PM, Moore, Gary wrote:

Stephen,

There is a “Renderer” option in the General section of the node template which was checked “In-Place Editor”.  If I uncheck this option, then the fields display goes away.

 

In the tutorial, you state:

Using the layout interface, the following will be demonstrated (but not shown here in this tutorial). But first, open to the feature page 'CG40042' so we can watch the changes as we proceed:

  • How to remove default content from the panel regions
  • How to add content to each panel region
  • Adding of blocks in this order:
    • Feature Details in the Left Above section
    • Feature Synonyms in the Left Above section, just below the feature details.
    • Feature References in the Right Above section
    • Feature Relationships as Object in the Middle section
    • Add any other blocks desired to the Middle or lower sections

 

If you could  provide a couple of clues as to how the blocks are added to the panel regions, I should be in business.

Thanks

Gary

From: Stephen Ficklin [[hidden email]]
Sent: Tuesday, May 15, 2012 9:46 AM
To: [hidden email]
Subject: Re: [Gmod-tripal] tutorial 3.01b issues with custom pane

 

Hi Gary,

I don't believe I've ever seen fields that look like that before.   Can you tell me which panel modules you have enabled and which blocks you have on the page?

Stephen


On 5/14/2012 6:22 PM, Moore, Gary wrote:

I’m trying to follow the instructions in the tutorial for creating a new features page via the custom panel layout.   The attached (if this list serve allows attachments) screenshot shows what I get when viewing the node.    I hope this is something easy which I’m overlooking.

-Gary

 

Gary Moore, Technical Lead

LCA Digital Commons Project

National Agriculture Library/USDA/ARS

Beltsville MD

 





This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.



This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.



------------------------------------------------------------------------------
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threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/





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threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: tutorial 3.01b issues with custom pane

Moore, Gary

Well, that was easy! ;)  Thanks for all your help, Stephen.

Gary

 

From: Stephen Ficklin [mailto:[hidden email]]
Sent: Wednesday, May 16, 2012 11:18 AM
To: Moore, Gary
Cc: [hidden email]
Subject: Re: [Gmod-tripal] tutorial 3.01b issues with custom pane

 

Hi Gary,

No worries.  Drupal is great the more you get used to it.  Panels are nice and allows you to customize your pages the way you want, but editing templates gives you the most power over the layout of your site.  It does require some PHP and Chado knowledge though.

For the citrus site we added a GBrowse image to our gene pages (for example: http://www.citrusgenomedb.org/PAC:19274706, click the 'Genomic Location' link on the right).

This was done by editing the template file:  theme_tripal/tripal_feature/tripal_feature_featurelocs.tpl.php.  In that file you can simply add the link to GBrowse wherever you prefer.  Example code that goes in the for loop that iterates through the featurelocs:

<?php               
  // build the link to GBrowse
   $location = $featureloc->srcfeature_id->name .":". ($featureloc->fmin + 1) . ".." . $featureloc->fmax;
   $gbrowse_link = "/gb/gbrowse/citrus_sinensis_v1.0/?name=".  $feature->name;
    print "<a href=\"$gbrowse_link\" target=\"_blank\">".$location."</a>";

  // build the GBrowse image
   $gbrowse_img = "/gb/gbrowse_img/citrus_sinensis_v1.0/?name=" . $feature->name;
   print "<img border=0 src=\"".$gbrowse_img ."&width=500\">";             
?>

If you have more than one species you can use an if statement to customize the gbrowse links. If there is only one location where this feature maps, which is the case for genes and mRNA then you should only get a single GBrowse image and link.

Hope that helps,
Stephen

On 5/16/2012 10:48 AM, Moore, Gary wrote:

Hi Stephan,

The template option sounds fine to me.  Do you have instructions/hints as to how to add the GBrowse Image to the template (the last item in the tutorial)?  I’ve created the GBrowse view but am at a bit of a loss as to how to hook it into a template.  I’m not a Drupal expert so please excuse my cluelessness.  Thanks

Gary

From: Stephen Ficklin [[hidden email]]
Sent: Tuesday, May 15, 2012 5:02 PM
To: Moore, Gary
Cc: [hidden email]
Subject: Re: [Gmod-tripal] tutorial 3.01b issues with custom pane

 

Hi Gary,

It has been a while since I looked at Panels as we are using template files for our production sites, so let me get it setup on my end and I can try and give you a better answer.

if you're interested in customizing your site by altering templates you can find documentation here: http://gmod.org/wiki/Tripal_Developer's_Handbook


Stephen

On 5/15/2012 1:21 PM, Moore, Gary wrote:

Stephen,

There is a “Renderer” option in the General section of the node template which was checked “In-Place Editor”.  If I uncheck this option, then the fields display goes away.

 

In the tutorial, you state:

Using the layout interface, the following will be demonstrated (but not shown here in this tutorial). But first, open to the feature page 'CG40042' so we can watch the changes as we proceed:

  • How to remove default content from the panel regions
  • How to add content to each panel region
  • Adding of blocks in this order:
    • Feature Details in the Left Above section
    • Feature Synonyms in the Left Above section, just below the feature details.
    • Feature References in the Right Above section
    • Feature Relationships as Object in the Middle section
    • Add any other blocks desired to the Middle or lower sections

 

If you could  provide a couple of clues as to how the blocks are added to the panel regions, I should be in business.

Thanks

Gary

From: Stephen Ficklin [[hidden email]]
Sent: Tuesday, May 15, 2012 9:46 AM
To: [hidden email]
Subject: Re: [Gmod-tripal] tutorial 3.01b issues with custom pane

 

Hi Gary,

I don't believe I've ever seen fields that look like that before.   Can you tell me which panel modules you have enabled and which blocks you have on the page?

Stephen


On 5/14/2012 6:22 PM, Moore, Gary wrote:

I’m trying to follow the instructions in the tutorial for creating a new features page via the custom panel layout.   The attached (if this list serve allows attachments) screenshot shows what I get when viewing the node.    I hope this is something easy which I’m overlooking.

-Gary

 

Gary Moore, Technical Lead

LCA Digital Commons Project

National Agriculture Library/USDA/ARS

Beltsville MD

 





This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.



This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.




------------------------------------------------------------------------------
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Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/






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Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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