problems loading OBO Relationship Ontology into Chado using Tripal

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problems loading OBO Relationship Ontology into Chado using Tripal

Moore, Gary

I’m a first time tripal installer. Everything has gone swimmingly until I try to load an ontology at which time the job errors out with the message:

 

feof() expects parameter 1 to be resource, boolean given in /var/www/drupal-6.26/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php on line 68.

 

A similar situation is described in this thread:  http://sourceforge.net/mailarchive/forum.php?thread_name=CAGXAW%3DAQT1cOKixqwKgiyAVmHJ96%3DM6LL%3DyU9P8Vxg6vfh0uvw%40mail.gmail.com&forum_name=gmod-tripal

 

But I could not glean a solution from the responses.  I am on CentOS 5.6, Drupal 6.26, Postgresql 8.4 and php 5.3.12.  The php-process package is installed and I am not experiencing the “posix_kill()” issue also mentioned in the above thread.

 

I’m kind of under a time constraint for getting this done so any ideas/workarounds would be greatly appreciated.  Hopefully it’s something simple I’ve missed.

-Gary

 

Gary Moore, Technical Lead

LCA Digital Commons Project

National Agriculture Library/USDA/ARS

Beltsville MD

 





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Re: problems loading OBO Relationship Ontology into Chado using Tripal

Stephen Ficklin-2
Hi Gary,

It looks as though the problem is that Tripal is not able to download the remote OBO file.   I will update the code so that it gives a more meaningful error message when this occurs.  Do you have a tight firewall?  In that email thread you refer to one of the problems was that the person was using a proxy server.  Do you use a proxy?  If so, is the server that runs Apache/Tripal setup to pass all internet requests through the proxy? 

One solution is to manually download the OBO files and place them in a location on your server.   You can then specify the location of the file and load it manually using the same administrative page in Tripal.  It's a bit more work, but it should work.

Stephen

On 5/8/2012 8:31 PM, Moore, Gary wrote:

I’m a first time tripal installer. Everything has gone swimmingly until I try to load an ontology at which time the job errors out with the message:

 

feof() expects parameter 1 to be resource, boolean given in /var/www/drupal-6.26/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php on line 68.

 

A similar situation is described in this thread:  http://sourceforge.net/mailarchive/forum.php?thread_name=CAGXAW%3DAQT1cOKixqwKgiyAVmHJ96%3DM6LL%3DyU9P8Vxg6vfh0uvw%40mail.gmail.com&forum_name=gmod-tripal

 

But I could not glean a solution from the responses.  I am on CentOS 5.6, Drupal 6.26, Postgresql 8.4 and php 5.3.12.  The php-process package is installed and I am not experiencing the “posix_kill()” issue also mentioned in the above thread.

 

I’m kind of under a time constraint for getting this done so any ideas/workarounds would be greatly appreciated.  Hopefully it’s something simple I’ve missed.

-Gary

 

Gary Moore, Technical Lead

LCA Digital Commons Project

National Agriculture Library/USDA/ARS

Beltsville MD

 





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