Re: Controlled vocabularies: Installing CVs error

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Re: Controlled vocabularies: Installing CVs error

Scott Cain
Hi Azrin,

In my last email, I said I was going to cc the Tripal mailing list, but forgot to do it.  I'm doing so now so they can weigh in.

However, it looks to me like you are still asking Tripal to fetch the RO file, which is failing.  I think you should be asking it to load the ontology file that you downloaded from git "manually".  

What are other Tripal users doing about this now?

Thanks,
Scott


On Mon, Jun 13, 2016 at 10:48 PM, Azrin Ahmad <[hidden email]> wrote:
Thanks Scott for your quick reply :)

I already download the ro.obo file in the link and load it through Tripal. And also load the GO again. Again, there is still errors. Here are attached files of the error screenshots. How to solve this errors?

Thanks Scott :) 

On Mon, Jun 13, 2016 at 10:27 PM, Scott Cain <[hidden email]> wrote:
Hi Azrin,

I'm cc'ing this message to the tripal mailing list; please keep it cc'ed in your responses.

I suspect the root of your problem is the same as reported here:


Basically, the Relationship ontology was replaced with another ontology that isn't backward compatible with Chado.  You'll probably need to download the ro.obo file I linked to in the discussion of the problem and load it through Tripal.  After you do that, try loading GO again.

Scott


On Mon, Jun 13, 2016 at 12:04 AM, Azrin Ahmad <[hidden email]> wrote:
Hi Scott Cain,

I'm Azrin Ahmad, Bioinformatician from Malaysia. 
I'm new in Tripal. I already install Drupal & Tripal on Ubuntu 14.04.1 LTS. Everything goes well but when i'm trying to install CVs (ontologies), I got the error status in web browser for Relationship Ontology & Gene Ontology (Sequence Ontology looks fine 100% completed). When I check the error in OBO file (for gene ontology's error: could not find object term GO:0048308), the object term for GO:0048308 in the OBO fileAll the OBO files (ro.obo, gene_ontology.obo and so.obo) are manually downloaded and in the /var/www/html/sites/default/files. Can you help me solve this problem? i also attach screenshots (command when launch the job and web browser that show status error). 

Thanks in advance.

Best regards,
Azrin Ahmad
Bioinformatician,
Centre for Marker Development and Validation.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
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Re: Controlled vocabularies: Installing CVs error

Cannon, Ethalinda K [COM S]

Hi Azrin,


Yes, I had this same trouble with the current RO and solved it by manually loading the older ro.obo file. I know the fix is on the to-do list for Tripal 2.1, but hasn't been implemented yet. The discussion link below pretty well covers the issue.


https://github.com/GMOD/Chado/issues/17

Ethy

From: Scott Cain <[hidden email]>
Sent: Tuesday, June 14, 2016 8:58 AM
To: Azrin Ahmad
Cc: [hidden email]
Subject: Re: [Gmod-tripal] Controlled vocabularies: Installing CVs error
 
Hi Azrin,

In my last email, I said I was going to cc the Tripal mailing list, but forgot to do it.  I'm doing so now so they can weigh in.

However, it looks to me like you are still asking Tripal to fetch the RO file, which is failing.  I think you should be asking it to load the ontology file that you downloaded from git "manually".  

What are other Tripal users doing about this now?

Thanks,
Scott


On Mon, Jun 13, 2016 at 10:48 PM, Azrin Ahmad <[hidden email]> wrote:
Thanks Scott for your quick reply :)

I already download the ro.obo file in the link and load it through Tripal. And also load the GO again. Again, there is still errors. Here are attached files of the error screenshots. How to solve this errors?

Thanks Scott :) 

On Mon, Jun 13, 2016 at 10:27 PM, Scott Cain <[hidden email]> wrote:
Hi Azrin,

I'm cc'ing this message to the tripal mailing list; please keep it cc'ed in your responses.

I suspect the root of your problem is the same as reported here:


Basically, the Relationship ontology was replaced with another ontology that isn't backward compatible with Chado.  You'll probably need to download the ro.obo file I linked to in the discussion of the problem and load it through Tripal.  After you do that, try loading GO again.

Scott


On Mon, Jun 13, 2016 at 12:04 AM, Azrin Ahmad <[hidden email]> wrote:
Hi Scott Cain,

I'm Azrin Ahmad, Bioinformatician from Malaysia. 
I'm new in Tripal. I already install Drupal & Tripal on Ubuntu 14.04.1 LTS. Everything goes well but when i'm trying to install CVs (ontologies), I got the error status in web browser for Relationship Ontology & Gene Ontology (Sequence Ontology looks fine 100% completed). When I check the error in OBO file (for gene ontology's error: could not find object term GO:0048308), the object term for GO:0048308 in the OBO fileAll the OBO files (ro.obo, gene_ontology.obo and so.obo) are manually downloaded and in the /var/www/html/sites/default/files. Can you help me solve this problem? i also attach screenshots (command when launch the job and web browser that show status error). 

Thanks in advance.

Best regards,
Azrin Ahmad
Bioinformatician,
Centre for Marker Development and Validation.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="&#43;12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
_______________________________________________
Gmod-tripal mailing list
[hidden email]
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Re: Controlled vocabularies: Installing CVs error

azrinahmad
Thanks Scott & Ethy for your responses :)

I've tried both old & gist with the old ro.obo file in the link that have been given but unfortunately the errors still same. How can I fix this?

Thanks in advance.
Azrin 

On Tue, Jun 14, 2016 at 10:07 PM, Cannon, Ethalinda K [COM S] <[hidden email]> wrote:

Hi Azrin,


Yes, I had this same trouble with the current RO and solved it by manually loading the older ro.obo file. I know the fix is on the to-do list for Tripal 2.1, but hasn't been implemented yet. The discussion link below pretty well covers the issue.


https://github.com/GMOD/Chado/issues/17

Ethy

From: Scott Cain <[hidden email]>
Sent: Tuesday, June 14, 2016 8:58 AM
To: Azrin Ahmad
Cc: [hidden email]
Subject: Re: [Gmod-tripal] Controlled vocabularies: Installing CVs error
 
Hi Azrin,

In my last email, I said I was going to cc the Tripal mailing list, but forgot to do it.  I'm doing so now so they can weigh in.

However, it looks to me like you are still asking Tripal to fetch the RO file, which is failing.  I think you should be asking it to load the ontology file that you downloaded from git "manually".  

What are other Tripal users doing about this now?

Thanks,
Scott


On Mon, Jun 13, 2016 at 10:48 PM, Azrin Ahmad <[hidden email]> wrote:
Thanks Scott for your quick reply :)

I already download the ro.obo file in the link and load it through Tripal. And also load the GO again. Again, there is still errors. Here are attached files of the error screenshots. How to solve this errors?

Thanks Scott :) 

On Mon, Jun 13, 2016 at 10:27 PM, Scott Cain <[hidden email]> wrote:
Hi Azrin,

I'm cc'ing this message to the tripal mailing list; please keep it cc'ed in your responses.

I suspect the root of your problem is the same as reported here:


Basically, the Relationship ontology was replaced with another ontology that isn't backward compatible with Chado.  You'll probably need to download the ro.obo file I linked to in the discussion of the problem and load it through Tripal.  After you do that, try loading GO again.

Scott


On Mon, Jun 13, 2016 at 12:04 AM, Azrin Ahmad <[hidden email]> wrote:
Hi Scott Cain,

I'm Azrin Ahmad, Bioinformatician from Malaysia. 
I'm new in Tripal. I already install Drupal & Tripal on Ubuntu 14.04.1 LTS. Everything goes well but when i'm trying to install CVs (ontologies), I got the error status in web browser for Relationship Ontology & Gene Ontology (Sequence Ontology looks fine 100% completed). When I check the error in OBO file (for gene ontology's error: could not find object term GO:0048308), the object term for GO:0048308 in the OBO fileAll the OBO files (ro.obo, gene_ontology.obo and so.obo) are manually downloaded and in the /var/www/html/sites/default/files. Can you help me solve this problem? i also attach screenshots (command when launch the job and web browser that show status error). 

Thanks in advance.

Best regards,
Azrin Ahmad
Bioinformatician,
Centre for Marker Development and Validation.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports. http://pubads.g.doubleclick.net/gampad/clk?id=1444514421&iu=/41014381
_______________________________________________
Gmod-tripal mailing list
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https://lists.sourceforge.net/lists/listinfo/gmod-tripal
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Re: Controlled vocabularies: Installing CVs error

Stephen Ficklin-2

Hi Arzin,

Can you provide the error message you are getting?

Thanks,

Stephen


On 6/14/2016 5:46 PM, Azrin Ahmad wrote:
Thanks Scott & Ethy for your responses :)

I've tried both old & gist with the old ro.obo file in the link that have been given but unfortunately the errors still same. How can I fix this?

Thanks in advance.
Azrin 

On Tue, Jun 14, 2016 at 10:07 PM, Cannon, Ethalinda K [COM S] <[hidden email]> wrote:

Hi Azrin,


Yes, I had this same trouble with the current RO and solved it by manually loading the older ro.obo file. I know the fix is on the to-do list for Tripal 2.1, but hasn't been implemented yet. The discussion link below pretty well covers the issue.


https://github.com/GMOD/Chado/issues/17

Ethy

From: Scott Cain <[hidden email]>
Sent: Tuesday, June 14, 2016 8:58 AM
To: Azrin Ahmad
Cc: [hidden email]
Subject: Re: [Gmod-tripal] Controlled vocabularies: Installing CVs error
 
Hi Azrin,

In my last email, I said I was going to cc the Tripal mailing list, but forgot to do it.  I'm doing so now so they can weigh in.

However, it looks to me like you are still asking Tripal to fetch the RO file, which is failing.  I think you should be asking it to load the ontology file that you downloaded from git "manually".  

What are other Tripal users doing about this now?

Thanks,
Scott


On Mon, Jun 13, 2016 at 10:48 PM, Azrin Ahmad <[hidden email]> wrote:
Thanks Scott for your quick reply :)

I already download the ro.obo file in the link and load it through Tripal. And also load the GO again. Again, there is still errors. Here are attached files of the error screenshots. How to solve this errors?

Thanks Scott :) 

On Mon, Jun 13, 2016 at 10:27 PM, Scott Cain <[hidden email]> wrote:
Hi Azrin,

I'm cc'ing this message to the tripal mailing list; please keep it cc'ed in your responses.

I suspect the root of your problem is the same as reported here:


Basically, the Relationship ontology was replaced with another ontology that isn't backward compatible with Chado.  You'll probably need to download the ro.obo file I linked to in the discussion of the problem and load it through Tripal.  After you do that, try loading GO again.

Scott


On Mon, Jun 13, 2016 at 12:04 AM, Azrin Ahmad <[hidden email]> wrote:
Hi Scott Cain,

I'm Azrin Ahmad, Bioinformatician from Malaysia. 
I'm new in Tripal. I already install Drupal & Tripal on Ubuntu 14.04.1 LTS. Everything goes well but when i'm trying to install CVs (ontologies), I got the error status in web browser for Relationship Ontology & Gene Ontology (Sequence Ontology looks fine 100% completed). When I check the error in OBO file (for gene ontology's error: could not find object term GO:0048308), the object term for GO:0048308 in the OBO fileAll the OBO files (ro.obo, gene_ontology.obo and so.obo) are manually downloaded and in the /var/www/html/sites/default/files. Can you help me solve this problem? i also attach screenshots (command when launch the job and web browser that show status error). 

Thanks in advance.

Best regards,
Azrin Ahmad
Bioinformatician,
Centre for Marker Development and Validation.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a moz-do-not-send="true" href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a moz-do-not-send="true" href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports. http://pubads.g.doubleclick.net/gampad/clk?id=1444514421&iu=/41014381


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


------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports. http://pubads.g.doubleclick.net/gampad/clk?id=1444514421&iu=/41014381
_______________________________________________
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[hidden email]
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Re: Controlled vocabularies: Installing CVs error

azrinahmad
Hi Stephen,

Thanks for your respond. Here are attached files of the error screenshots. How to solve this errors?

Thanks in advance :)
Azrin


On Wed, Jun 15, 2016 at 11:39 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Arzin,

Can you provide the error message you are getting?

Thanks,

Stephen


On 6/14/2016 5:46 PM, Azrin Ahmad wrote:
Thanks Scott & Ethy for your responses :)

I've tried both old & gist with the old ro.obo file in the link that have been given but unfortunately the errors still same. How can I fix this?

Thanks in advance.
Azrin 

On Tue, Jun 14, 2016 at 10:07 PM, Cannon, Ethalinda K [COM S] <[hidden email][hidden email]> wrote:

Hi Azrin,


Yes, I had this same trouble with the current RO and solved it by manually loading the older ro.obo file. I know the fix is on the to-do list for Tripal 2.1, but hasn't been implemented yet. The discussion link below pretty well covers the issue.


https://github.com/GMOD/Chado/issues/17

Ethy

From: Scott Cain <[hidden email]>
Sent: Tuesday, June 14, 2016 8:58 AM
To: Azrin Ahmad
Cc: [hidden email]
Subject: Re: [Gmod-tripal] Controlled vocabularies: Installing CVs error
 
Hi Azrin,

In my last email, I said I was going to cc the Tripal mailing list, but forgot to do it.  I'm doing so now so they can weigh in.

However, it looks to me like you are still asking Tripal to fetch the RO file, which is failing.  I think you should be asking it to load the ontology file that you downloaded from git "manually".  

What are other Tripal users doing about this now?

Thanks,
Scott


On Mon, Jun 13, 2016 at 10:48 PM, Azrin Ahmad <[hidden email]> wrote:
Thanks Scott for your quick reply :)

I already download the ro.obo file in the link and load it through Tripal. And also load the GO again. Again, there is still errors. Here are attached files of the error screenshots. How to solve this errors?

Thanks Scott :) 

On Mon, Jun 13, 2016 at 10:27 PM, Scott Cain <[hidden email]> wrote:
Hi Azrin,

I'm cc'ing this message to the tripal mailing list; please keep it cc'ed in your responses.

I suspect the root of your problem is the same as reported here:


Basically, the Relationship ontology was replaced with another ontology that isn't backward compatible with Chado.  You'll probably need to download the ro.obo file I linked to in the discussion of the problem and load it through Tripal.  After you do that, try loading GO again.

Scott


On Mon, Jun 13, 2016 at 12:04 AM, Azrin Ahmad <[hidden email][hidden email]> wrote:
Hi Scott Cain,

I'm Azrin Ahmad, Bioinformatician from Malaysia. 
I'm new in Tripal. I already install Drupal & Tripal on Ubuntu 14.04.1 LTS. Everything goes well but when i'm trying to install CVs (ontologies), I got the error status in web browser for Relationship Ontology & Gene Ontology (Sequence Ontology looks fine 100% completed). When I check the error in OBO file (for gene ontology's error: could not find object term GO:0048308), the object term for GO:0048308 in the OBO fileAll the OBO files (ro.obo, gene_ontology.obo and so.obo) are manually downloaded and in the /var/www/html/sites/default/files. Can you help me solve this problem? i also attach screenshots (command when launch the job and web browser that show status error). 

Thanks in advance.

Best regards,
Azrin Ahmad
Bioinformatician,
Centre for Marker Development and Validation.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports. http://pubads.g.doubleclick.net/gampad/clk?id=1444514421&iu=/41014381


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



------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports. http://pubads.g.doubleclick.net/gampad/clk?id=1444514421&iu=/41014381
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal

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Re: Controlled vocabularies: Installing CVs error

Stephen Ficklin-2

Hi Arzin,

It looks like GO now has a PURL link.  Can you try changing the URL for the Gene Ontology to this: 

http://purl.obolibrary.org/obo/go.obo

And then try to reload.

Thanks,

Stephen


On 6/15/2016 12:27 AM, Azrin Ahmad wrote:
Hi Stephen,

Thanks for your respond. Here are attached files of the error screenshots. How to solve this errors?

Thanks in advance :)
Azrin


On Wed, Jun 15, 2016 at 11:39 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Arzin,

Can you provide the error message you are getting?

Thanks,

Stephen


On 6/14/2016 5:46 PM, Azrin Ahmad wrote:
Thanks Scott & Ethy for your responses :)

I've tried both old & gist with the old ro.obo file in the link that have been given but unfortunately the errors still same. How can I fix this?

Thanks in advance.
Azrin 

On Tue, Jun 14, 2016 at 10:07 PM, Cannon, Ethalinda K [COM S] <[hidden email]> wrote:

Hi Azrin,


Yes, I had this same trouble with the current RO and solved it by manually loading the older ro.obo file. I know the fix is on the to-do list for Tripal 2.1, but hasn't been implemented yet. The discussion link below pretty well covers the issue.


https://github.com/GMOD/Chado/issues/17

Ethy

From: Scott Cain <[hidden email]>
Sent: Tuesday, June 14, 2016 8:58 AM
To: Azrin Ahmad
Cc: [hidden email]
Subject: Re: [Gmod-tripal] Controlled vocabularies: Installing CVs error
 
Hi Azrin,

In my last email, I said I was going to cc the Tripal mailing list, but forgot to do it.  I'm doing so now so they can weigh in.

However, it looks to me like you are still asking Tripal to fetch the RO file, which is failing.  I think you should be asking it to load the ontology file that you downloaded from git "manually".  

What are other Tripal users doing about this now?

Thanks,
Scott


On Mon, Jun 13, 2016 at 10:48 PM, Azrin Ahmad <[hidden email]> wrote:
Thanks Scott for your quick reply :)

I already download the ro.obo file in the link and load it through Tripal. And also load the GO again. Again, there is still errors. Here are attached files of the error screenshots. How to solve this errors?

Thanks Scott :) 

On Mon, Jun 13, 2016 at 10:27 PM, Scott Cain <[hidden email]> wrote:
Hi Azrin,

I'm cc'ing this message to the tripal mailing list; please keep it cc'ed in your responses.

I suspect the root of your problem is the same as reported here:


Basically, the Relationship ontology was replaced with another ontology that isn't backward compatible with Chado.  You'll probably need to download the ro.obo file I linked to in the discussion of the problem and load it through Tripal.  After you do that, try loading GO again.

Scott


On Mon, Jun 13, 2016 at 12:04 AM, Azrin Ahmad <[hidden email]> wrote:
Hi Scott Cain,

I'm Azrin Ahmad, Bioinformatician from Malaysia. 
I'm new in Tripal. I already install Drupal & Tripal on Ubuntu 14.04.1 LTS. Everything goes well but when i'm trying to install CVs (ontologies), I got the error status in web browser for Relationship Ontology & Gene Ontology (Sequence Ontology looks fine 100% completed). When I check the error in OBO file (for gene ontology's error: could not find object term GO:0048308), the object term for GO:0048308 in the OBO fileAll the OBO files (ro.obo, gene_ontology.obo and so.obo) are manually downloaded and in the /var/www/html/sites/default/files. Can you help me solve this problem? i also attach screenshots (command when launch the job and web browser that show status error). 

Thanks in advance.

Best regards,
Azrin Ahmad
Bioinformatician,
Centre for Marker Development and Validation.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a moz-do-not-send="true" href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a moz-do-not-send="true" href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports. http://pubads.g.doubleclick.net/gampad/clk?id=1444514421&iu=/41014381


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




------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports. http://pubads.g.doubleclick.net/gampad/clk?id=1444514421&iu=/41014381
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
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Re: Controlled vocabularies: Installing CVs error

azrinahmad
Hi Stephen,

Thank you for your respond. I already use the PURL link and stored go.obo file in /var/www/html/sites/default/files. Then, i reload it again. But, the errors still there. It looks like it's still use the same (old) URL for the Gene Ontology. Or should I change the PURL link in the tripal_cv.obo_loader.inc?? And how about for Relationship Ontology?

Thanks,
Azrin.  


On Thu, Jun 16, 2016 at 12:06 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Arzin,

It looks like GO now has a PURL link.  Can you try changing the URL for the Gene Ontology to this: 

http://purl.obolibrary.org/obo/go.obo

And then try to reload.

Thanks,

Stephen


On 6/15/2016 12:27 AM, Azrin Ahmad wrote:
Hi Stephen,

Thanks for your respond. Here are attached files of the error screenshots. How to solve this errors?

Thanks in advance :)
Azrin


On Wed, Jun 15, 2016 at 11:39 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Arzin,

Can you provide the error message you are getting?

Thanks,

Stephen


On 6/14/2016 5:46 PM, Azrin Ahmad wrote:
Thanks Scott & Ethy for your responses :)

I've tried both old & gist with the old ro.obo file in the link that have been given but unfortunately the errors still same. How can I fix this?

Thanks in advance.
Azrin 

On Tue, Jun 14, 2016 at 10:07 PM, Cannon, Ethalinda K [COM S] <[hidden email]> wrote:

Hi Azrin,


Yes, I had this same trouble with the current RO and solved it by manually loading the older ro.obo file. I know the fix is on the to-do list for Tripal 2.1, but hasn't been implemented yet. The discussion link below pretty well covers the issue.


https://github.com/GMOD/Chado/issues/17

Ethy

From: Scott Cain <[hidden email]>
Sent: Tuesday, June 14, 2016 8:58 AM
To: Azrin Ahmad
Cc: [hidden email][hidden email]
Subject: Re: [Gmod-tripal] Controlled vocabularies: Installing CVs error
 
Hi Azrin,

In my last email, I said I was going to cc the Tripal mailing list, but forgot to do it.  I'm doing so now so they can weigh in.

However, it looks to me like you are still asking Tripal to fetch the RO file, which is failing.  I think you should be asking it to load the ontology file that you downloaded from git "manually".  

What are other Tripal users doing about this now?

Thanks,
Scott


On Mon, Jun 13, 2016 at 10:48 PM, Azrin Ahmad <[hidden email][hidden email]> wrote:
Thanks Scott for your quick reply :)

I already download the ro.obo file in the link and load it through Tripal. And also load the GO again. Again, there is still errors. Here are attached files of the error screenshots. How to solve this errors?

Thanks Scott :) 

On Mon, Jun 13, 2016 at 10:27 PM, Scott Cain <[hidden email][hidden email]> wrote:
Hi Azrin,

I'm cc'ing this message to the tripal mailing list; please keep it cc'ed in your responses.

I suspect the root of your problem is the same as reported here:


Basically, the Relationship ontology was replaced with another ontology that isn't backward compatible with Chado.  You'll probably need to download the ro.obo file I linked to in the discussion of the problem and load it through Tripal.  After you do that, try loading GO again.

Scott


On Mon, Jun 13, 2016 at 12:04 AM, Azrin Ahmad <[hidden email][hidden email]> wrote:
Hi Scott Cain,

I'm Azrin Ahmad, Bioinformatician from Malaysia. 
I'm new in Tripal. I already install Drupal & Tripal on Ubuntu 14.04.1 LTS. Everything goes well but when i'm trying to install CVs (ontologies), I got the error status in web browser for Relationship Ontology & Gene Ontology (Sequence Ontology looks fine 100% completed). When I check the error in OBO file (for gene ontology's error: could not find object term GO:0048308), the object term for GO:0048308 in the OBO fileAll the OBO files (ro.obo, gene_ontology.obo and so.obo) are manually downloaded and in the /var/www/html/sites/default/files. Can you help me solve this problem? i also attach screenshots (command when launch the job and web browser that show status error). 

Thanks in advance.

Best regards,
Azrin Ahmad
Bioinformatician,
Centre for Marker Development and Validation.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports. http://pubads.g.doubleclick.net/gampad/clk?id=1444514421&iu=/41014381


_______________________________________________
Gmod-tripal mailing list
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https://lists.sourceforge.net/lists/listinfo/gmod-tripal





------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports. http://pubads.g.doubleclick.net/gampad/clk?id=1444514421&iu=/41014381
_______________________________________________
Gmod-tripal mailing list
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Re: Controlled vocabularies: Installing CVs error

Stephen Ficklin-2

Hi Arzin,

After you downloaded the OBO file to /var/www/html/sites/default/files directory did you also do the following:

1) Go to OBO setup page at Tripal -> Chado Data Loaders -> OBO File Loader

2) Select the ontology from the select box

3) Remove the Remote URL and add in the path to the Local file (e.g. /var/www/html/sites/default/files/go.obo)

4) Click 'Update Ontology Details'.  This will save the new location of the file for Tripal to use.

5) Select the ontology again from the select box and click 'Load Vocabulary'.

Stephen


On 6/15/2016 8:53 PM, Azrin Ahmad wrote:
Hi Stephen,

Thank you for your respond. I already use the PURL link and stored go.obo file in /var/www/html/sites/default/files. Then, i reload it again. But, the errors still there. It looks like it's still use the same (old) URL for the Gene Ontology. Or should I change the PURL link in the tripal_cv.obo_loader.inc?? And how about for Relationship Ontology?

Thanks,
Azrin.  


On Thu, Jun 16, 2016 at 12:06 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Arzin,

It looks like GO now has a PURL link.  Can you try changing the URL for the Gene Ontology to this: 

http://purl.obolibrary.org/obo/go.obo

And then try to reload.

Thanks,

Stephen


On 6/15/2016 12:27 AM, Azrin Ahmad wrote:
Hi Stephen,

Thanks for your respond. Here are attached files of the error screenshots. How to solve this errors?

Thanks in advance :)
Azrin


On Wed, Jun 15, 2016 at 11:39 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Arzin,

Can you provide the error message you are getting?

Thanks,

Stephen


On 6/14/2016 5:46 PM, Azrin Ahmad wrote:
Thanks Scott & Ethy for your responses :)

I've tried both old & gist with the old ro.obo file in the link that have been given but unfortunately the errors still same. How can I fix this?

Thanks in advance.
Azrin 

On Tue, Jun 14, 2016 at 10:07 PM, Cannon, Ethalinda K [COM S] <[hidden email]> wrote:

Hi Azrin,


Yes, I had this same trouble with the current RO and solved it by manually loading the older ro.obo file. I know the fix is on the to-do list for Tripal 2.1, but hasn't been implemented yet. The discussion link below pretty well covers the issue.


https://github.com/GMOD/Chado/issues/17

Ethy

From: Scott Cain <[hidden email]>
Sent: Tuesday, June 14, 2016 8:58 AM
To: Azrin Ahmad
Cc: [hidden email]
Subject: Re: [Gmod-tripal] Controlled vocabularies: Installing CVs error
 
Hi Azrin,

In my last email, I said I was going to cc the Tripal mailing list, but forgot to do it.  I'm doing so now so they can weigh in.

However, it looks to me like you are still asking Tripal to fetch the RO file, which is failing.  I think you should be asking it to load the ontology file that you downloaded from git "manually".  

What are other Tripal users doing about this now?

Thanks,
Scott


On Mon, Jun 13, 2016 at 10:48 PM, Azrin Ahmad <[hidden email]> wrote:
Thanks Scott for your quick reply :)

I already download the ro.obo file in the link and load it through Tripal. And also load the GO again. Again, there is still errors. Here are attached files of the error screenshots. How to solve this errors?

Thanks Scott :) 

On Mon, Jun 13, 2016 at 10:27 PM, Scott Cain <[hidden email]> wrote:
Hi Azrin,

I'm cc'ing this message to the tripal mailing list; please keep it cc'ed in your responses.

I suspect the root of your problem is the same as reported here:


Basically, the Relationship ontology was replaced with another ontology that isn't backward compatible with Chado.  You'll probably need to download the ro.obo file I linked to in the discussion of the problem and load it through Tripal.  After you do that, try loading GO again.

Scott


On Mon, Jun 13, 2016 at 12:04 AM, Azrin Ahmad <[hidden email]> wrote:
Hi Scott Cain,

I'm Azrin Ahmad, Bioinformatician from Malaysia. 
I'm new in Tripal. I already install Drupal & Tripal on Ubuntu 14.04.1 LTS. Everything goes well but when i'm trying to install CVs (ontologies), I got the error status in web browser for Relationship Ontology & Gene Ontology (Sequence Ontology looks fine 100% completed). When I check the error in OBO file (for gene ontology's error: could not find object term GO:0048308), the object term for GO:0048308 in the OBO fileAll the OBO files (ro.obo, gene_ontology.obo and so.obo) are manually downloaded and in the /var/www/html/sites/default/files. Can you help me solve this problem? i also attach screenshots (command when launch the job and web browser that show status error). 

Thanks in advance.

Best regards,
Azrin Ahmad
Bioinformatician,
Centre for Marker Development and Validation.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a moz-do-not-send="true" href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a moz-do-not-send="true" href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports. http://pubads.g.doubleclick.net/gampad/clk?id=1444514421&iu=/41014381


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






------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports. http://pubads.g.doubleclick.net/gampad/clk?id=1444514421&iu=/41014381
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
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Re: Controlled vocabularies: Installing CVs error

azrinahmad
Hi Stephen,

Thanks for your respond. In my web-based, there is no option 'Update Ontology Details'. It can be seen in my screenshot in attached file. How can this be missing?

Thanks.
Azrin

On Thu, Jun 16, 2016 at 2:09 PM, Stephen Ficklin <[hidden email]> wrote:

Hi Arzin,

After you downloaded the OBO file to /var/www/html/sites/default/files directory did you also do the following:

1) Go to OBO setup page at Tripal -> Chado Data Loaders -> OBO File Loader

2) Select the ontology from the select box

3) Remove the Remote URL and add in the path to the Local file (e.g. /var/www/html/sites/default/files/go.obo)

4) Click 'Update Ontology Details'.  This will save the new location of the file for Tripal to use.

5) Select the ontology again from the select box and click 'Load Vocabulary'.

Stephen


On 6/15/2016 8:53 PM, Azrin Ahmad wrote:
Hi Stephen,

Thank you for your respond. I already use the PURL link and stored go.obo file in /var/www/html/sites/default/files. Then, i reload it again. But, the errors still there. It looks like it's still use the same (old) URL for the Gene Ontology. Or should I change the PURL link in the tripal_cv.obo_loader.inc?? And how about for Relationship Ontology?

Thanks,
Azrin.  


On Thu, Jun 16, 2016 at 12:06 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Arzin,

It looks like GO now has a PURL link.  Can you try changing the URL for the Gene Ontology to this: 

http://purl.obolibrary.org/obo/go.obo

And then try to reload.

Thanks,

Stephen


On 6/15/2016 12:27 AM, Azrin Ahmad wrote:
Hi Stephen,

Thanks for your respond. Here are attached files of the error screenshots. How to solve this errors?

Thanks in advance :)
Azrin


On Wed, Jun 15, 2016 at 11:39 AM, Stephen Ficklin <[hidden email][hidden email]> wrote:

Hi Arzin,

Can you provide the error message you are getting?

Thanks,

Stephen


On 6/14/2016 5:46 PM, Azrin Ahmad wrote:
Thanks Scott & Ethy for your responses :)

I've tried both old & gist with the old ro.obo file in the link that have been given but unfortunately the errors still same. How can I fix this?

Thanks in advance.
Azrin 

On Tue, Jun 14, 2016 at 10:07 PM, Cannon, Ethalinda K [COM S] <[hidden email][hidden email]> wrote:

Hi Azrin,


Yes, I had this same trouble with the current RO and solved it by manually loading the older ro.obo file. I know the fix is on the to-do list for Tripal 2.1, but hasn't been implemented yet. The discussion link below pretty well covers the issue.


https://github.com/GMOD/Chado/issues/17

Ethy

From: Scott Cain <[hidden email][hidden email]>
Sent: Tuesday, June 14, 2016 8:58 AM
To: Azrin Ahmad
Cc: [hidden email][hidden email]
Subject: Re: [Gmod-tripal] Controlled vocabularies: Installing CVs error
 
Hi Azrin,

In my last email, I said I was going to cc the Tripal mailing list, but forgot to do it.  I'm doing so now so they can weigh in.

However, it looks to me like you are still asking Tripal to fetch the RO file, which is failing.  I think you should be asking it to load the ontology file that you downloaded from git "manually".  

What are other Tripal users doing about this now?

Thanks,
Scott


On Mon, Jun 13, 2016 at 10:48 PM, Azrin Ahmad <[hidden email][hidden email]> wrote:
Thanks Scott for your quick reply :)

I already download the ro.obo file in the link and load it through Tripal. And also load the GO again. Again, there is still errors. Here are attached files of the error screenshots. How to solve this errors?

Thanks Scott :) 

On Mon, Jun 13, 2016 at 10:27 PM, Scott Cain <[hidden email][hidden email]> wrote:
Hi Azrin,

I'm cc'ing this message to the tripal mailing list; please keep it cc'ed in your responses.

I suspect the root of your problem is the same as reported here:


Basically, the Relationship ontology was replaced with another ontology that isn't backward compatible with Chado.  You'll probably need to download the ro.obo file I linked to in the discussion of the problem and load it through Tripal.  After you do that, try loading GO again.

Scott


On Mon, Jun 13, 2016 at 12:04 AM, Azrin Ahmad <[hidden email][hidden email]> wrote:
Hi Scott Cain,

I'm Azrin Ahmad, Bioinformatician from Malaysia. 
I'm new in Tripal. I already install Drupal & Tripal on Ubuntu 14.04.1 LTS. Everything goes well but when i'm trying to install CVs (ontologies), I got the error status in web browser for Relationship Ontology & Gene Ontology (Sequence Ontology looks fine 100% completed). When I check the error in OBO file (for gene ontology's error: could not find object term GO:0048308), the object term for GO:0048308 in the OBO fileAll the OBO files (ro.obo, gene_ontology.obo and so.obo) are manually downloaded and in the /var/www/html/sites/default/files. Can you help me solve this problem? i also attach screenshots (command when launch the job and web browser that show status error). 

Thanks in advance.

Best regards,
Azrin Ahmad
Bioinformatician,
Centre for Marker Development and Validation.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports. http://pubads.g.doubleclick.net/gampad/clk?id=1444514421&iu=/41014381


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







------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports. http://pubads.g.doubleclick.net/gampad/clk?id=1444514421&iu=/41014381
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal

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Re: Controlled vocabularies: Installing CVs error

Stephen Ficklin-2

Hi Arzin,

I see. The instructions I gave were for the version in the development branch which will soon be released as version 2.1 which explains why you don't have that button.  So, in your case, select the ontology from the drop-down and the fields below should then be populated with values.  Remove the Remote URL and add the full path to the OBO file in the 'Local File' text field and click 'Submit'.  I believe that should add a job which should then try to load the OBO from the file you downloaded rather than trying to fetch it from the Internet. 

BTW... do you have a firewall that is preventing Tripal from retrieving these OBO files from the internet?  Typically, Tripal can do this on it's own.

Stephen


On 6/16/2016 12:12 AM, Azrin Ahmad wrote:
Hi Stephen,

Thanks for your respond. In my web-based, there is no option 'Update Ontology Details'. It can be seen in my screenshot in attached file. How can this be missing?

Thanks.
Azrin

On Thu, Jun 16, 2016 at 2:09 PM, Stephen Ficklin <[hidden email]> wrote:

Hi Arzin,

After you downloaded the OBO file to /var/www/html/sites/default/files directory did you also do the following:

1) Go to OBO setup page at Tripal -> Chado Data Loaders -> OBO File Loader

2) Select the ontology from the select box

3) Remove the Remote URL and add in the path to the Local file (e.g. /var/www/html/sites/default/files/go.obo)

4) Click 'Update Ontology Details'.  This will save the new location of the file for Tripal to use.

5) Select the ontology again from the select box and click 'Load Vocabulary'.

Stephen


On 6/15/2016 8:53 PM, Azrin Ahmad wrote:
Hi Stephen,

Thank you for your respond. I already use the PURL link and stored go.obo file in /var/www/html/sites/default/files. Then, i reload it again. But, the errors still there. It looks like it's still use the same (old) URL for the Gene Ontology. Or should I change the PURL link in the tripal_cv.obo_loader.inc?? And how about for Relationship Ontology?

Thanks,
Azrin.  


On Thu, Jun 16, 2016 at 12:06 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Arzin,

It looks like GO now has a PURL link.  Can you try changing the URL for the Gene Ontology to this: 

http://purl.obolibrary.org/obo/go.obo

And then try to reload.

Thanks,

Stephen


On 6/15/2016 12:27 AM, Azrin Ahmad wrote:
Hi Stephen,

Thanks for your respond. Here are attached files of the error screenshots. How to solve this errors?

Thanks in advance :)
Azrin


On Wed, Jun 15, 2016 at 11:39 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Arzin,

Can you provide the error message you are getting?

Thanks,

Stephen


On 6/14/2016 5:46 PM, Azrin Ahmad wrote:
Thanks Scott & Ethy for your responses :)

I've tried both old & gist with the old ro.obo file in the link that have been given but unfortunately the errors still same. How can I fix this?

Thanks in advance.
Azrin 

On Tue, Jun 14, 2016 at 10:07 PM, Cannon, Ethalinda K [COM S] <[hidden email]> wrote:

Hi Azrin,


Yes, I had this same trouble with the current RO and solved it by manually loading the older ro.obo file. I know the fix is on the to-do list for Tripal 2.1, but hasn't been implemented yet. The discussion link below pretty well covers the issue.


https://github.com/GMOD/Chado/issues/17

Ethy

From: Scott Cain <[hidden email]>
Sent: Tuesday, June 14, 2016 8:58 AM
To: Azrin Ahmad
Cc: [hidden email]
Subject: Re: [Gmod-tripal] Controlled vocabularies: Installing CVs error
 
Hi Azrin,

In my last email, I said I was going to cc the Tripal mailing list, but forgot to do it.  I'm doing so now so they can weigh in.

However, it looks to me like you are still asking Tripal to fetch the RO file, which is failing.  I think you should be asking it to load the ontology file that you downloaded from git "manually".  

What are other Tripal users doing about this now?

Thanks,
Scott


On Mon, Jun 13, 2016 at 10:48 PM, Azrin Ahmad <[hidden email]> wrote:
Thanks Scott for your quick reply :)

I already download the ro.obo file in the link and load it through Tripal. And also load the GO again. Again, there is still errors. Here are attached files of the error screenshots. How to solve this errors?

Thanks Scott :) 

On Mon, Jun 13, 2016 at 10:27 PM, Scott Cain <[hidden email]> wrote:
Hi Azrin,

I'm cc'ing this message to the tripal mailing list; please keep it cc'ed in your responses.

I suspect the root of your problem is the same as reported here:


Basically, the Relationship ontology was replaced with another ontology that isn't backward compatible with Chado.  You'll probably need to download the ro.obo file I linked to in the discussion of the problem and load it through Tripal.  After you do that, try loading GO again.

Scott


On Mon, Jun 13, 2016 at 12:04 AM, Azrin Ahmad <[hidden email]> wrote:
Hi Scott Cain,

I'm Azrin Ahmad, Bioinformatician from Malaysia. 
I'm new in Tripal. I already install Drupal & Tripal on Ubuntu 14.04.1 LTS. Everything goes well but when i'm trying to install CVs (ontologies), I got the error status in web browser for Relationship Ontology & Gene Ontology (Sequence Ontology looks fine 100% completed). When I check the error in OBO file (for gene ontology's error: could not find object term GO:0048308), the object term for GO:0048308 in the OBO fileAll the OBO files (ro.obo, gene_ontology.obo and so.obo) are manually downloaded and in the /var/www/html/sites/default/files. Can you help me solve this problem? i also attach screenshots (command when launch the job and web browser that show status error). 

Thanks in advance.

Best regards,
Azrin Ahmad
Bioinformatician,
Centre for Marker Development and Validation.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a moz-do-not-send="true" href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a moz-do-not-send="true" href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports. http://pubads.g.doubleclick.net/gampad/clk?id=1444514421&iu=/41014381


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








------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports. http://sdm.link/zohomanageengine
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
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Re: Controlled vocabularies: Installing CVs error

azrinahmad
Hi Stephen,

Thanks for your respond. Oh, no wonder I don't have that option. I tried to do so, but it's still fetch the OBO file from the internet (it can be seen in attached file). How to remove the remote URL? My firewall also inactive (it is also can be seen in attached file). It looks fine when I tried to retrieve other file from internet. Attached files are the screenshot of the job errors and the submit job. 

Thanks,
Azrin.

On Fri, Jun 17, 2016 at 1:32 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Arzin,

I see. The instructions I gave were for the version in the development branch which will soon be released as version 2.1 which explains why you don't have that button.  So, in your case, select the ontology from the drop-down and the fields below should then be populated with values.  Remove the Remote URL and add the full path to the OBO file in the 'Local File' text field and click 'Submit'.  I believe that should add a job which should then try to load the OBO from the file you downloaded rather than trying to fetch it from the Internet. 

BTW... do you have a firewall that is preventing Tripal from retrieving these OBO files from the internet?  Typically, Tripal can do this on it's own.

Stephen


On 6/16/2016 12:12 AM, Azrin Ahmad wrote:
Hi Stephen,

Thanks for your respond. In my web-based, there is no option 'Update Ontology Details'. It can be seen in my screenshot in attached file. How can this be missing?

Thanks.
Azrin

On Thu, Jun 16, 2016 at 2:09 PM, Stephen Ficklin <[hidden email]> wrote:

Hi Arzin,

After you downloaded the OBO file to /var/www/html/sites/default/files directory did you also do the following:

1) Go to OBO setup page at Tripal -> Chado Data Loaders -> OBO File Loader

2) Select the ontology from the select box

3) Remove the Remote URL and add in the path to the Local file (e.g. /var/www/html/sites/default/files/go.obo)

4) Click 'Update Ontology Details'.  This will save the new location of the file for Tripal to use.

5) Select the ontology again from the select box and click 'Load Vocabulary'.

Stephen


On 6/15/2016 8:53 PM, Azrin Ahmad wrote:
Hi Stephen,

Thank you for your respond. I already use the PURL link and stored go.obo file in /var/www/html/sites/default/files. Then, i reload it again. But, the errors still there. It looks like it's still use the same (old) URL for the Gene Ontology. Or should I change the PURL link in the tripal_cv.obo_loader.inc?? And how about for Relationship Ontology?

Thanks,
Azrin.  


On Thu, Jun 16, 2016 at 12:06 AM, Stephen Ficklin <[hidden email][hidden email]> wrote:

Hi Arzin,

It looks like GO now has a PURL link.  Can you try changing the URL for the Gene Ontology to this: 

http://purl.obolibrary.org/obo/go.obo

And then try to reload.

Thanks,

Stephen


On 6/15/2016 12:27 AM, Azrin Ahmad wrote:
Hi Stephen,

Thanks for your respond. Here are attached files of the error screenshots. How to solve this errors?

Thanks in advance :)
Azrin


On Wed, Jun 15, 2016 at 11:39 AM, Stephen Ficklin <[hidden email][hidden email]> wrote:

Hi Arzin,

Can you provide the error message you are getting?

Thanks,

Stephen


On 6/14/2016 5:46 PM, Azrin Ahmad wrote:
Thanks Scott & Ethy for your responses :)

I've tried both old & gist with the old ro.obo file in the link that have been given but unfortunately the errors still same. How can I fix this?

Thanks in advance.
Azrin 

On Tue, Jun 14, 2016 at 10:07 PM, Cannon, Ethalinda K [COM S] <[hidden email][hidden email]> wrote:

Hi Azrin,


Yes, I had this same trouble with the current RO and solved it by manually loading the older ro.obo file. I know the fix is on the to-do list for Tripal 2.1, but hasn't been implemented yet. The discussion link below pretty well covers the issue.


https://github.com/GMOD/Chado/issues/17

Ethy

From: Scott Cain <[hidden email][hidden email]>
Sent: Tuesday, June 14, 2016 8:58 AM
To: Azrin Ahmad
Cc: [hidden email][hidden email]
Subject: Re: [Gmod-tripal] Controlled vocabularies: Installing CVs error
 
Hi Azrin,

In my last email, I said I was going to cc the Tripal mailing list, but forgot to do it.  I'm doing so now so they can weigh in.

However, it looks to me like you are still asking Tripal to fetch the RO file, which is failing.  I think you should be asking it to load the ontology file that you downloaded from git "manually".  

What are other Tripal users doing about this now?

Thanks,
Scott


On Mon, Jun 13, 2016 at 10:48 PM, Azrin Ahmad <[hidden email][hidden email]> wrote:
Thanks Scott for your quick reply :)

I already download the ro.obo file in the link and load it through Tripal. And also load the GO again. Again, there is still errors. Here are attached files of the error screenshots. How to solve this errors?

Thanks Scott :) 

On Mon, Jun 13, 2016 at 10:27 PM, Scott Cain <[hidden email][hidden email]> wrote:
Hi Azrin,

I'm cc'ing this message to the tripal mailing list; please keep it cc'ed in your responses.

I suspect the root of your problem is the same as reported here:


Basically, the Relationship ontology was replaced with another ontology that isn't backward compatible with Chado.  You'll probably need to download the ro.obo file I linked to in the discussion of the problem and load it through Tripal.  After you do that, try loading GO again.

Scott


On Mon, Jun 13, 2016 at 12:04 AM, Azrin Ahmad <[hidden email][hidden email]> wrote:
Hi Scott Cain,

I'm Azrin Ahmad, Bioinformatician from Malaysia. 
I'm new in Tripal. I already install Drupal & Tripal on Ubuntu 14.04.1 LTS. Everything goes well but when i'm trying to install CVs (ontologies), I got the error status in web browser for Relationship Ontology & Gene Ontology (Sequence Ontology looks fine 100% completed). When I check the error in OBO file (for gene ontology's error: could not find object term GO:0048308), the object term for GO:0048308 in the OBO fileAll the OBO files (ro.obo, gene_ontology.obo and so.obo) are manually downloaded and in the /var/www/html/sites/default/files. Can you help me solve this problem? i also attach screenshots (command when launch the job and web browser that show status error). 

Thanks in advance.

Best regards,
Azrin Ahmad
Bioinformatician,
Centre for Marker Development and Validation.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



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Re: Controlled vocabularies: Installing CVs error

azrinahmad
Hi Stephen,

I would like to share with you that finally, I'm succeed load OBO file for both RO and GO file. Both of them I saved as a new vocabulary name (RO for relationship ontology and Gene_Ontology for gene ontology), as for RO, I used remote URL (URL that given by Scott Cain: https://gist.githubusercontent.com/scottcain/10e255c991a41bcf0187/raw/7faba8c6f26766f5a686eb681f5cb2f48e49b78a/ro.obo) and for GO, I used local file (http://www.geneontology.org/ontology/gene_ontology.obo that have been stored in local path: /var/www/html/sites/default/files/gene_ontology.obo). Attached files are the screenshots of jobs. 

Thanks in advance :)
Azrin.

On Fri, Jun 17, 2016 at 9:25 AM, Azrin Ahmad <[hidden email]> wrote:
Hi Stephen,

Thanks for your respond. Oh, no wonder I don't have that option. I tried to do so, but it's still fetch the OBO file from the internet (it can be seen in attached file). How to remove the remote URL? My firewall also inactive (it is also can be seen in attached file). It looks fine when I tried to retrieve other file from internet. Attached files are the screenshot of the job errors and the submit job. 

Thanks,
Azrin.

On Fri, Jun 17, 2016 at 1:32 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Arzin,

I see. The instructions I gave were for the version in the development branch which will soon be released as version 2.1 which explains why you don't have that button.  So, in your case, select the ontology from the drop-down and the fields below should then be populated with values.  Remove the Remote URL and add the full path to the OBO file in the 'Local File' text field and click 'Submit'.  I believe that should add a job which should then try to load the OBO from the file you downloaded rather than trying to fetch it from the Internet. 

BTW... do you have a firewall that is preventing Tripal from retrieving these OBO files from the internet?  Typically, Tripal can do this on it's own.

Stephen


On 6/16/2016 12:12 AM, Azrin Ahmad wrote:
Hi Stephen,

Thanks for your respond. In my web-based, there is no option 'Update Ontology Details'. It can be seen in my screenshot in attached file. How can this be missing?

Thanks.
Azrin

On Thu, Jun 16, 2016 at 2:09 PM, Stephen Ficklin <[hidden email]> wrote:

Hi Arzin,

After you downloaded the OBO file to /var/www/html/sites/default/files directory did you also do the following:

1) Go to OBO setup page at Tripal -> Chado Data Loaders -> OBO File Loader

2) Select the ontology from the select box

3) Remove the Remote URL and add in the path to the Local file (e.g. /var/www/html/sites/default/files/go.obo)

4) Click 'Update Ontology Details'.  This will save the new location of the file for Tripal to use.

5) Select the ontology again from the select box and click 'Load Vocabulary'.

Stephen


On 6/15/2016 8:53 PM, Azrin Ahmad wrote:
Hi Stephen,

Thank you for your respond. I already use the PURL link and stored go.obo file in /var/www/html/sites/default/files. Then, i reload it again. But, the errors still there. It looks like it's still use the same (old) URL for the Gene Ontology. Or should I change the PURL link in the tripal_cv.obo_loader.inc?? And how about for Relationship Ontology?

Thanks,
Azrin.  


On Thu, Jun 16, 2016 at 12:06 AM, Stephen Ficklin <[hidden email][hidden email]> wrote:

Hi Arzin,

It looks like GO now has a PURL link.  Can you try changing the URL for the Gene Ontology to this: 

http://purl.obolibrary.org/obo/go.obo

And then try to reload.

Thanks,

Stephen


On 6/15/2016 12:27 AM, Azrin Ahmad wrote:
Hi Stephen,

Thanks for your respond. Here are attached files of the error screenshots. How to solve this errors?

Thanks in advance :)
Azrin


On Wed, Jun 15, 2016 at 11:39 AM, Stephen Ficklin <[hidden email][hidden email]> wrote:

Hi Arzin,

Can you provide the error message you are getting?

Thanks,

Stephen


On 6/14/2016 5:46 PM, Azrin Ahmad wrote:
Thanks Scott & Ethy for your responses :)

I've tried both old & gist with the old ro.obo file in the link that have been given but unfortunately the errors still same. How can I fix this?

Thanks in advance.
Azrin 

On Tue, Jun 14, 2016 at 10:07 PM, Cannon, Ethalinda K [COM S] <[hidden email][hidden email]> wrote:

Hi Azrin,


Yes, I had this same trouble with the current RO and solved it by manually loading the older ro.obo file. I know the fix is on the to-do list for Tripal 2.1, but hasn't been implemented yet. The discussion link below pretty well covers the issue.


https://github.com/GMOD/Chado/issues/17

Ethy

From: Scott Cain <[hidden email][hidden email]>
Sent: Tuesday, June 14, 2016 8:58 AM
To: Azrin Ahmad
Cc: [hidden email][hidden email]
Subject: Re: [Gmod-tripal] Controlled vocabularies: Installing CVs error
 
Hi Azrin,

In my last email, I said I was going to cc the Tripal mailing list, but forgot to do it.  I'm doing so now so they can weigh in.

However, it looks to me like you are still asking Tripal to fetch the RO file, which is failing.  I think you should be asking it to load the ontology file that you downloaded from git "manually".  

What are other Tripal users doing about this now?

Thanks,
Scott


On Mon, Jun 13, 2016 at 10:48 PM, Azrin Ahmad <[hidden email][hidden email]> wrote:
Thanks Scott for your quick reply :)

I already download the ro.obo file in the link and load it through Tripal. And also load the GO again. Again, there is still errors. Here are attached files of the error screenshots. How to solve this errors?

Thanks Scott :) 

On Mon, Jun 13, 2016 at 10:27 PM, Scott Cain <[hidden email][hidden email]> wrote:
Hi Azrin,

I'm cc'ing this message to the tripal mailing list; please keep it cc'ed in your responses.

I suspect the root of your problem is the same as reported here:


Basically, the Relationship ontology was replaced with another ontology that isn't backward compatible with Chado.  You'll probably need to download the ro.obo file I linked to in the discussion of the problem and load it through Tripal.  After you do that, try loading GO again.

Scott


On Mon, Jun 13, 2016 at 12:04 AM, Azrin Ahmad <[hidden email][hidden email]> wrote:
Hi Scott Cain,

I'm Azrin Ahmad, Bioinformatician from Malaysia. 
I'm new in Tripal. I already install Drupal & Tripal on Ubuntu 14.04.1 LTS. Everything goes well but when i'm trying to install CVs (ontologies), I got the error status in web browser for Relationship Ontology & Gene Ontology (Sequence Ontology looks fine 100% completed). When I check the error in OBO file (for gene ontology's error: could not find object term GO:0048308), the object term for GO:0048308 in the OBO fileAll the OBO files (ro.obo, gene_ontology.obo and so.obo) are manually downloaded and in the /var/www/html/sites/default/files. Can you help me solve this problem? i also attach screenshots (command when launch the job and web browser that show status error). 

Thanks in advance.

Best regards,
Azrin Ahmad
Bioinformatician,
Centre for Marker Development and Validation.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports. http://pubads.g.doubleclick.net/gampad/clk?id=1444514421&iu=/41014381


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










------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports. http://sdm.link/zohomanageengine
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal

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