Release of Tripal v2.0a

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Release of Tripal v2.0a

Stephen Ficklin-3
Dear Tripal and Chado users,

The Tripal Development Team is pleased to announce an alpha release of
Tripal 2.0 for Drupal 7.

This release is expected to have bugs and there is some functionality
still under development.  However, this release is made to help early
adopters of Tripal for Drupal 7.   Reports of bugs or other issues are
highly welcomed.   Below are available resources for Tripal 2.0a

* Download Instructions:
http://tripal.info/documentation/download_tripal_v2.0a
* Installation and Tutorial: http://www.gmod.org/wiki/Tripal_Tutorial_v2.0
* Tripal 2.0 API site: http://api.tripal.info/api/tripal/2.x
* Tripal Mailing List:
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
* Tripal Developer's Mailing List:
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel

The Installation tutorial is still under development but should have
enough information for complete installation of Tripal v2.0a as well as
loading of organisms and features.   The tutorial will be completed
before the stable release of Tripal 2.0.

Regards,
Stephen



------------------------------------------------------------------------------
Flow-based real-time traffic analytics software. Cisco certified tool.
Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
Customize your own dashboards, set traffic alerts and generate reports.
Network behavioral analysis & security monitoring. All-in-one tool.
http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
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Re: Release of Tripal v2.0a

Mara Kim-3
Hi Stephen,

I am currently in the process of installing Tripal 2a.  One thing of note I've run across so far is that CKeditor no longer provides include/exclude options (https://drupal.org/node/1018920).  Do you have alternative instructions?


On Mon, Feb 24, 2014 at 4:29 PM, Stephen Ficklin <[hidden email]> wrote:
Dear Tripal and Chado users,

The Tripal Development Team is pleased to announce an alpha release of
Tripal 2.0 for Drupal 7.

This release is expected to have bugs and there is some functionality
still under development.  However, this release is made to help early
adopters of Tripal for Drupal 7.   Reports of bugs or other issues are
highly welcomed.   Below are available resources for Tripal 2.0a

* Download Instructions:
http://tripal.info/documentation/download_tripal_v2.0a
* Installation and Tutorial: http://www.gmod.org/wiki/Tripal_Tutorial_v2.0
* Tripal 2.0 API site: http://api.tripal.info/api/tripal/2.x
* Tripal Mailing List:
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
* Tripal Developer's Mailing List:
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel

The Installation tutorial is still under development but should have
enough information for complete installation of Tripal v2.0a as well as
loading of organisms and features.   The tutorial will be completed
before the stable release of Tripal 2.0.

Regards,
Stephen



------------------------------------------------------------------------------
Flow-based real-time traffic analytics software. Cisco certified tool.
Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
Customize your own dashboards, set traffic alerts and generate reports.
Network behavioral analysis & security monitoring. All-in-one tool.
http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema



--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN

------------------------------------------------------------------------------
Subversion Kills Productivity. Get off Subversion & Make the Move to Perforce.
With Perforce, you get hassle-free workflows. Merge that actually works.
Faster operations. Version large binaries.  Built-in WAN optimization and the
freedom to use Git, Perforce or both. Make the move to Perforce.
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Re: Release of Tripal v2.0a

Mara Kim-3
More updates:

The repository http://git.drupal.org/sandbox/spficklin/1578234.git
does not have the tag 7.x-2.0a-tripal_v2.0a

Here is the specific error:

(My fancy git aware bash prompt)
kimmm@rokasgate:/var/www/html/sites/all/modules/tripal_kegg_analysis (0)
d12b127c2cbf59b5e380cffb37cc5ac79a411a5f
## 6.x-1.x
$ git checkout 7.x-2.0a-tripal_v2.0a

BEGIN EXECUTION TRACE
error: pathspec '7.x-2.0a-tripal_v2.0a' did not match any file(s) known to git.
END EXECUTION TRACE

On Tue, Mar 4, 2014 at 4:29 PM, Mara Kim <[hidden email]> wrote:

> Hi Stephen,
>
> I am currently in the process of installing Tripal 2a.  One thing of note
> I've run across so far is that CKeditor no longer provides include/exclude
> options (https://drupal.org/node/1018920).  Do you have alternative
> instructions?
>
>
> On Mon, Feb 24, 2014 at 4:29 PM, Stephen Ficklin <[hidden email]>
> wrote:
>>
>> Dear Tripal and Chado users,
>>
>> The Tripal Development Team is pleased to announce an alpha release of
>> Tripal 2.0 for Drupal 7.
>>
>> This release is expected to have bugs and there is some functionality
>> still under development.  However, this release is made to help early
>> adopters of Tripal for Drupal 7.   Reports of bugs or other issues are
>> highly welcomed.   Below are available resources for Tripal 2.0a
>>
>> * Download Instructions:
>> http://tripal.info/documentation/download_tripal_v2.0a
>> * Installation and Tutorial: http://www.gmod.org/wiki/Tripal_Tutorial_v2.0
>> * Tripal 2.0 API site: http://api.tripal.info/api/tripal/2.x
>> * Tripal Mailing List:
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>> * Tripal Developer's Mailing List:
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>
>> The Installation tutorial is still under development but should have
>> enough information for complete installation of Tripal v2.0a as well as
>> loading of organisms and features.   The tutorial will be completed
>> before the stable release of Tripal 2.0.
>>
>> Regards,
>> Stephen
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Flow-based real-time traffic analytics software. Cisco certified tool.
>> Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
>> Customize your own dashboards, set traffic alerts and generate reports.
>> Network behavioral analysis & security monitoring. All-in-one tool.
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>
>
>
> --
> Mara Kim
>
> Ph.D. Candidate
> Computational Biology
> Vanderbilt University
> Nashville, TN



--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN

------------------------------------------------------------------------------
Subversion Kills Productivity. Get off Subversion & Make the Move to Perforce.
With Perforce, you get hassle-free workflows. Merge that actually works.
Faster operations. Version large binaries.  Built-in WAN optimization and the
freedom to use Git, Perforce or both. Make the move to Perforce.
http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk
_______________________________________________
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Re: Release of Tripal v2.0a

Mara Kim-3
Hmm, it seems that all the repositories (except the main Tripal
repository and the tripal_blast_analysis repository) lack the
appropriate tags as I get similar errors.  This is in reference to
these instructions:
http://www.gmod.org/wiki/Tripal_Tutorial_v2.0#Tripal_Installation

On Tue, Mar 4, 2014 at 4:35 PM, Mara Kim <[hidden email]> wrote:

> More updates:
>
> The repository http://git.drupal.org/sandbox/spficklin/1578234.git
> does not have the tag 7.x-2.0a-tripal_v2.0a
>
> Here is the specific error:
>
> (My fancy git aware bash prompt)
> kimmm@rokasgate:/var/www/html/sites/all/modules/tripal_kegg_analysis (0)
> d12b127c2cbf59b5e380cffb37cc5ac79a411a5f
> ## 6.x-1.x
> $ git checkout 7.x-2.0a-tripal_v2.0a
>
> BEGIN EXECUTION TRACE
> error: pathspec '7.x-2.0a-tripal_v2.0a' did not match any file(s) known to git.
> END EXECUTION TRACE
>
> On Tue, Mar 4, 2014 at 4:29 PM, Mara Kim <[hidden email]> wrote:
>> Hi Stephen,
>>
>> I am currently in the process of installing Tripal 2a.  One thing of note
>> I've run across so far is that CKeditor no longer provides include/exclude
>> options (https://drupal.org/node/1018920).  Do you have alternative
>> instructions?
>>
>>
>> On Mon, Feb 24, 2014 at 4:29 PM, Stephen Ficklin <[hidden email]>
>> wrote:
>>>
>>> Dear Tripal and Chado users,
>>>
>>> The Tripal Development Team is pleased to announce an alpha release of
>>> Tripal 2.0 for Drupal 7.
>>>
>>> This release is expected to have bugs and there is some functionality
>>> still under development.  However, this release is made to help early
>>> adopters of Tripal for Drupal 7.   Reports of bugs or other issues are
>>> highly welcomed.   Below are available resources for Tripal 2.0a
>>>
>>> * Download Instructions:
>>> http://tripal.info/documentation/download_tripal_v2.0a
>>> * Installation and Tutorial: http://www.gmod.org/wiki/Tripal_Tutorial_v2.0
>>> * Tripal 2.0 API site: http://api.tripal.info/api/tripal/2.x
>>> * Tripal Mailing List:
>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>> * Tripal Developer's Mailing List:
>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>>
>>> The Installation tutorial is still under development but should have
>>> enough information for complete installation of Tripal v2.0a as well as
>>> loading of organisms and features.   The tutorial will be completed
>>> before the stable release of Tripal 2.0.
>>>
>>> Regards,
>>> Stephen
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Flow-based real-time traffic analytics software. Cisco certified tool.
>>> Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
>>> Customize your own dashboards, set traffic alerts and generate reports.
>>> Network behavioral analysis & security monitoring. All-in-one tool.
>>>
>>> http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
>>> _______________________________________________
>>> Gmod-schema mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>>
>>
>>
>> --
>> Mara Kim
>>
>> Ph.D. Candidate
>> Computational Biology
>> Vanderbilt University
>> Nashville, TN
>
>
>
> --
> Mara Kim
>
> Ph.D. Candidate
> Computational Biology
> Vanderbilt University
> Nashville, TN



--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN

------------------------------------------------------------------------------
Subversion Kills Productivity. Get off Subversion & Make the Move to Perforce.
With Perforce, you get hassle-free workflows. Merge that actually works.
Faster operations. Version large binaries.  Built-in WAN optimization and the
freedom to use Git, Perforce or both. Make the move to Perforce.
http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk
_______________________________________________
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Re: [Gmod-tripal] Release of Tripal v2.0a

Lacey-Anne Sanderson-2
Hi Mara,

That is unfortunately as it should be at this point. Work is ongoing on porting the other extension modules (including the ones in my sandbox :) ) to Drupal 7 and so hopefully these will be available soon! We will keep you posted!

~Lacey

On Mar 4, 2014, at 4:37 PM, Mara Kim <[hidden email]> wrote:

Hmm, it seems that all the repositories (except the main Tripal
repository and the tripal_blast_analysis repository) lack the
appropriate tags as I get similar errors.  This is in reference to
these instructions:
http://www.gmod.org/wiki/Tripal_Tutorial_v2.0#Tripal_Installation

On Tue, Mar 4, 2014 at 4:35 PM, Mara Kim <[hidden email]> wrote:
More updates:

The repository http://git.drupal.org/sandbox/spficklin/1578234.git
does not have the tag 7.x-2.0a-tripal_v2.0a

Here is the specific error:

(My fancy git aware bash prompt)
kimmm@rokasgate:/var/www/html/sites/all/modules/tripal_kegg_analysis (0)
d12b127c2cbf59b5e380cffb37cc5ac79a411a5f
## 6.x-1.x
$ git checkout 7.x-2.0a-tripal_v2.0a

BEGIN EXECUTION TRACE
error: pathspec '7.x-2.0a-tripal_v2.0a' did not match any file(s) known to git.
END EXECUTION TRACE

On Tue, Mar 4, 2014 at 4:29 PM, Mara Kim <[hidden email]> wrote:
Hi Stephen,

I am currently in the process of installing Tripal 2a.  One thing of note
I've run across so far is that CKeditor no longer provides include/exclude
options (https://drupal.org/node/1018920).  Do you have alternative
instructions?


On Mon, Feb 24, 2014 at 4:29 PM, Stephen Ficklin <[hidden email]>
wrote:

Dear Tripal and Chado users,

The Tripal Development Team is pleased to announce an alpha release of
Tripal 2.0 for Drupal 7.

This release is expected to have bugs and there is some functionality
still under development.  However, this release is made to help early
adopters of Tripal for Drupal 7.   Reports of bugs or other issues are
highly welcomed.   Below are available resources for Tripal 2.0a

* Download Instructions:
http://tripal.info/documentation/download_tripal_v2.0a
* Installation and Tutorial: http://www.gmod.org/wiki/Tripal_Tutorial_v2.0
* Tripal 2.0 API site: http://api.tripal.info/api/tripal/2.x
* Tripal Mailing List:
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
* Tripal Developer's Mailing List:
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel

The Installation tutorial is still under development but should have
enough information for complete installation of Tripal v2.0a as well as
loading of organisms and features.   The tutorial will be completed
before the stable release of Tripal 2.0.

Regards,
Stephen




------------------------------------------------------------------------------
Flow-based real-time traffic analytics software. Cisco certified tool.
Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
Customize your own dashboards, set traffic alerts and generate reports.
Network behavioral analysis & security monitoring. All-in-one tool.

http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema




--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN



--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN



-- 
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN

------------------------------------------------------------------------------
Subversion Kills Productivity. Get off Subversion & Make the Move to Perforce.
With Perforce, you get hassle-free workflows. Merge that actually works. 
Faster operations. Version large binaries.  Built-in WAN optimization and the
freedom to use Git, Perforce or both. Make the move to Perforce.
http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal


------------------------------------------------------------------------------
Subversion Kills Productivity. Get off Subversion & Make the Move to Perforce.
With Perforce, you get hassle-free workflows. Merge that actually works.
Faster operations. Version large binaries.  Built-in WAN optimization and the
freedom to use Git, Perforce or both. Make the move to Perforce.
http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk
_______________________________________________
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Re: [Gmod-tripal] Release of Tripal v2.0a

Mara Kim-2
Hi guys,

I was wondering how you guys store BLAST results in Chado for Tripal.
I have my own way of doing it, but obviously it would be much better
if I followed your convention.  Specifically, what cvterms do you use
to name BLAST hits and hsps, and what rows does Tripal expect in what
tables?

Sorry if you are getting this twice.  My first message bounced from
the mailing list because I used the wrong address.

On Tue, Mar 4, 2014 at 7:03 PM, Lacey-Anne Sanderson
<[hidden email]> wrote:

> Hi Mara,
>
> That is unfortunately as it should be at this point. Work is ongoing on
> porting the other extension modules (including the ones in my sandbox :) )
> to Drupal 7 and so hopefully these will be available soon! We will keep you
> posted!
>
> ~Lacey
>
> On Mar 4, 2014, at 4:37 PM, Mara Kim <[hidden email]> wrote:
>
> Hmm, it seems that all the repositories (except the main Tripal
> repository and the tripal_blast_analysis repository) lack the
> appropriate tags as I get similar errors.  This is in reference to
> these instructions:
> http://www.gmod.org/wiki/Tripal_Tutorial_v2.0#Tripal_Installation
>
> On Tue, Mar 4, 2014 at 4:35 PM, Mara Kim <[hidden email]> wrote:
>
> More updates:
>
> The repository http://git.drupal.org/sandbox/spficklin/1578234.git
> does not have the tag 7.x-2.0a-tripal_v2.0a
>
> Here is the specific error:
>
> (My fancy git aware bash prompt)
> kimmm@rokasgate:/var/www/html/sites/all/modules/tripal_kegg_analysis (0)
> d12b127c2cbf59b5e380cffb37cc5ac79a411a5f
> ## 6.x-1.x
> $ git checkout 7.x-2.0a-tripal_v2.0a
>
> BEGIN EXECUTION TRACE
> error: pathspec '7.x-2.0a-tripal_v2.0a' did not match any file(s) known to
> git.
> END EXECUTION TRACE
>
> On Tue, Mar 4, 2014 at 4:29 PM, Mara Kim <[hidden email]> wrote:
>
> Hi Stephen,
>
> I am currently in the process of installing Tripal 2a.  One thing of note
> I've run across so far is that CKeditor no longer provides include/exclude
> options (https://drupal.org/node/1018920).  Do you have alternative
> instructions?
>
>
> On Mon, Feb 24, 2014 at 4:29 PM, Stephen Ficklin <[hidden email]>
> wrote:
>
>
> Dear Tripal and Chado users,
>
> The Tripal Development Team is pleased to announce an alpha release of
> Tripal 2.0 for Drupal 7.
>
> This release is expected to have bugs and there is some functionality
> still under development.  However, this release is made to help early
> adopters of Tripal for Drupal 7.   Reports of bugs or other issues are
> highly welcomed.   Below are available resources for Tripal 2.0a
>
> * Download Instructions:
> http://tripal.info/documentation/download_tripal_v2.0a
> * Installation and Tutorial: http://www.gmod.org/wiki/Tripal_Tutorial_v2.0
> * Tripal 2.0 API site: http://api.tripal.info/api/tripal/2.x
> * Tripal Mailing List:
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
> * Tripal Developer's Mailing List:
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>
> The Installation tutorial is still under development but should have
> enough information for complete installation of Tripal v2.0a as well as
> loading of organisms and features.   The tutorial will be completed
> before the stable release of Tripal 2.0.
>
> Regards,
> Stephen
>
>
>
>
> ------------------------------------------------------------------------------
> Flow-based real-time traffic analytics software. Cisco certified tool.
> Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
> Customize your own dashboards, set traffic alerts and generate reports.
> Network behavioral analysis & security monitoring. All-in-one tool.
>
> http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>
>
>
>
> --
> Mara Kim
>
> Ph.D. Candidate
> Computational Biology
> Vanderbilt University
> Nashville, TN
>
>
>
>
> --
> Mara Kim
>
> Ph.D. Candidate
> Computational Biology
> Vanderbilt University
> Nashville, TN
>
>
>
>
> --
> Mara Kim
>
> Ph.D. Candidate
> Computational Biology
> Vanderbilt University
> Nashville, TN
>
> ------------------------------------------------------------------------------
> Subversion Kills Productivity. Get off Subversion & Make the Move to
> Perforce.
> With Perforce, you get hassle-free workflows. Merge that actually works.
> Faster operations. Version large binaries.  Built-in WAN optimization and
> the
> freedom to use Git, Perforce or both. Make the move to Perforce.
> http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk
> _______________________________________________
> Gmod-tripal mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>
>



--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN


------------------------------------------------------------------------------
Subversion Kills Productivity. Get off Subversion & Make the Move to Perforce.
With Perforce, you get hassle-free workflows. Merge that actually works.
Faster operations. Version large binaries.  Built-in WAN optimization and the
freedom to use Git, Perforce or both. Make the move to Perforce.
http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
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Re: [Gmod-tripal] Release of Tripal v2.0a

Stephen Ficklin-3
Hi Mara,

Tripal stores blast results in the analysisfeatureprop table.  A blast
analysis is first added to the analysis table, and the Tripal Blast
Analysis extension module parses the blast XML file, identifies a
matching feature in the 'feature' table, and adds the link in the
featureanalysis table between the analysis and the feature.  Then
details of the blast match are added to the analysisfeatureprop table.  
But, what gets stored is the actual XML from the blast output detailing
all of the matches for that query.    When the Tripal Blast module
displays blast results, it retrieves the XML, parses it, passes it into
an array and then passes that array into the
tripal_feature_blast_restults.tpl.php template for display, thus
allowing anyone to customize the way blast results are presented.

Originally, we wanted to store all of the details about a match directly
in the analysisfeatureprop table such that the different details about a
match were entered as separate records.  The goal was to allow us to
then search matches by things like match name, accession, e-value, etc.  
But, there is not an easy way to distinguish between values that belong
to one  match and a different match using the analysisfeatureprop table.
   So, to compromise, the module stores the XML directly into the
analysisfeatureprop table and maintains a custom table named
'blast_hit_data' to allow for searching of blast results.   That
blast_hit_data table is integrated with Drupal Views (just like any
other Chado table) so you can create Drupal Views that can be used for
searching the results.  This is how blast results are searching on sites
like CottonGen and GDR.

Stephen

On 3/6/2014 2:57 PM, Mara Kim wrote:

> Hi guys,
>
> I was wondering how you guys store BLAST results in Chado for Tripal.
> I have my own way of doing it, but obviously it would be much better
> if I followed your convention.  Specifically, what cvterms do you use
> to name BLAST hits and hsps, and what rows does Tripal expect in what
> tables?
>
> Sorry if you are getting this twice.  My first message bounced from
> the mailing list because I used the wrong address.
>
> On Tue, Mar 4, 2014 at 7:03 PM, Lacey-Anne Sanderson
> <[hidden email]> wrote:
>> Hi Mara,
>>
>> That is unfortunately as it should be at this point. Work is ongoing on
>> porting the other extension modules (including the ones in my sandbox :) )
>> to Drupal 7 and so hopefully these will be available soon! We will keep you
>> posted!
>>
>> ~Lacey
>>
>> On Mar 4, 2014, at 4:37 PM, Mara Kim <[hidden email]> wrote:
>>
>> Hmm, it seems that all the repositories (except the main Tripal
>> repository and the tripal_blast_analysis repository) lack the
>> appropriate tags as I get similar errors.  This is in reference to
>> these instructions:
>> http://www.gmod.org/wiki/Tripal_Tutorial_v2.0#Tripal_Installation
>>
>> On Tue, Mar 4, 2014 at 4:35 PM, Mara Kim <[hidden email]> wrote:
>>
>> More updates:
>>
>> The repository http://git.drupal.org/sandbox/spficklin/1578234.git
>> does not have the tag 7.x-2.0a-tripal_v2.0a
>>
>> Here is the specific error:
>>
>> (My fancy git aware bash prompt)
>> kimmm@rokasgate:/var/www/html/sites/all/modules/tripal_kegg_analysis (0)
>> d12b127c2cbf59b5e380cffb37cc5ac79a411a5f
>> ## 6.x-1.x
>> $ git checkout 7.x-2.0a-tripal_v2.0a
>>
>> BEGIN EXECUTION TRACE
>> error: pathspec '7.x-2.0a-tripal_v2.0a' did not match any file(s) known to
>> git.
>> END EXECUTION TRACE
>>
>> On Tue, Mar 4, 2014 at 4:29 PM, Mara Kim <[hidden email]> wrote:
>>
>> Hi Stephen,
>>
>> I am currently in the process of installing Tripal 2a.  One thing of note
>> I've run across so far is that CKeditor no longer provides include/exclude
>> options (https://drupal.org/node/1018920).  Do you have alternative
>> instructions?
>>
>>
>> On Mon, Feb 24, 2014 at 4:29 PM, Stephen Ficklin <[hidden email]>
>> wrote:
>>
>>
>> Dear Tripal and Chado users,
>>
>> The Tripal Development Team is pleased to announce an alpha release of
>> Tripal 2.0 for Drupal 7.
>>
>> This release is expected to have bugs and there is some functionality
>> still under development.  However, this release is made to help early
>> adopters of Tripal for Drupal 7.   Reports of bugs or other issues are
>> highly welcomed.   Below are available resources for Tripal 2.0a
>>
>> * Download Instructions:
>> http://tripal.info/documentation/download_tripal_v2.0a
>> * Installation and Tutorial: http://www.gmod.org/wiki/Tripal_Tutorial_v2.0
>> * Tripal 2.0 API site: http://api.tripal.info/api/tripal/2.x
>> * Tripal Mailing List:
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>> * Tripal Developer's Mailing List:
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>
>> The Installation tutorial is still under development but should have
>> enough information for complete installation of Tripal v2.0a as well as
>> loading of organisms and features.   The tutorial will be completed
>> before the stable release of Tripal 2.0.
>>
>> Regards,
>> Stephen
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Flow-based real-time traffic analytics software. Cisco certified tool.
>> Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
>> Customize your own dashboards, set traffic alerts and generate reports.
>> Network behavioral analysis & security monitoring. All-in-one tool.
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>>
>>
>>
>>
>> --
>> Mara Kim
>>
>> Ph.D. Candidate
>> Computational Biology
>> Vanderbilt University
>> Nashville, TN
>>
>>
>>
>>
>> --
>> Mara Kim
>>
>> Ph.D. Candidate
>> Computational Biology
>> Vanderbilt University
>> Nashville, TN
>>
>>
>>
>>
>> --
>> Mara Kim
>>
>> Ph.D. Candidate
>> Computational Biology
>> Vanderbilt University
>> Nashville, TN
>>
>> ------------------------------------------------------------------------------
>> Subversion Kills Productivity. Get off Subversion & Make the Move to
>> Perforce.
>> With Perforce, you get hassle-free workflows. Merge that actually works.
>> Faster operations. Version large binaries.  Built-in WAN optimization and
>> the
>> freedom to use Git, Perforce or both. Make the move to Perforce.
>> http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk
>> _______________________________________________
>> Gmod-tripal mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>
>>
>
>


------------------------------------------------------------------------------
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With Perforce, you get hassle-free workflows. Merge that actually works.
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freedom to use Git, Perforce or both. Make the move to Perforce.
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Re: [Gmod-tripal] Release of Tripal v2.0a

Mara Kim-2
Hi guys,

I am having trouble getting Tripal 2.0a to recognize the Chado schema
that has been migrated in using the method described here:
http://tripal.info/documentation/migrate_chado

I realize these instructions are for Tripal 1.0, but seeing as how I
needed to import this data anyways, I figured I'd give it a shot.  I
run into issues when I try to enable the Tripal modules.  For example:

BEGIN EXECUTION TRACE
$ drush pm-enable tripal_views
Module tripal_views doesn't meet the requirements to be enabled.
                                                              [error]
 (Currently using tripal_views ERROR: Chado must be installed before
this module can be enabled)
[error]
END EXECUTION TRACE

It seems that Tripal isn't recognizing the migrated chado database.
Any suggestions on how to fix this?


On Thu, Mar 6, 2014 at 2:21 PM, Stephen Ficklin <[hidden email]> wrote:

> Hi Mara,
>
> Tripal stores blast results in the analysisfeatureprop table.  A blast
> analysis is first added to the analysis table, and the Tripal Blast Analysis
> extension module parses the blast XML file, identifies a matching feature in
> the 'feature' table, and adds the link in the featureanalysis table between
> the analysis and the feature.  Then details of the blast match are added to
> the analysisfeatureprop table.   But, what gets stored is the actual XML
> from the blast output detailing all of the matches for that query.    When
> the Tripal Blast module displays blast results, it retrieves the XML, parses
> it, passes it into an array and then passes that array into the
> tripal_feature_blast_restults.tpl.php template for display, thus allowing
> anyone to customize the way blast results are presented.
>
> Originally, we wanted to store all of the details about a match directly in
> the analysisfeatureprop table such that the different details about a match
> were entered as separate records.  The goal was to allow us to then search
> matches by things like match name, accession, e-value, etc.  But, there is
> not an easy way to distinguish between values that belong to one  match and
> a different match using the analysisfeatureprop table.   So, to compromise,
> the module stores the XML directly into the analysisfeatureprop table and
> maintains a custom table named 'blast_hit_data' to allow for searching of
> blast results.   That blast_hit_data table is integrated with Drupal Views
> (just like any other Chado table) so you can create Drupal Views that can be
> used for searching the results.  This is how blast results are searching on
> sites like CottonGen and GDR.
>
> Stephen
>
>
> On 3/6/2014 2:57 PM, Mara Kim wrote:
>>
>> Hi guys,
>>
>> I was wondering how you guys store BLAST results in Chado for Tripal.
>> I have my own way of doing it, but obviously it would be much better
>> if I followed your convention.  Specifically, what cvterms do you use
>> to name BLAST hits and hsps, and what rows does Tripal expect in what
>> tables?
>>
>> Sorry if you are getting this twice.  My first message bounced from
>> the mailing list because I used the wrong address.
>>
>> On Tue, Mar 4, 2014 at 7:03 PM, Lacey-Anne Sanderson
>> <[hidden email]> wrote:
>>>
>>> Hi Mara,
>>>
>>> That is unfortunately as it should be at this point. Work is ongoing on
>>> porting the other extension modules (including the ones in my sandbox :)
>>> )
>>> to Drupal 7 and so hopefully these will be available soon! We will keep
>>> you
>>> posted!
>>>
>>> ~Lacey
>>>
>>> On Mar 4, 2014, at 4:37 PM, Mara Kim <[hidden email]> wrote:
>>>
>>> Hmm, it seems that all the repositories (except the main Tripal
>>> repository and the tripal_blast_analysis repository) lack the
>>> appropriate tags as I get similar errors.  This is in reference to
>>> these instructions:
>>> http://www.gmod.org/wiki/Tripal_Tutorial_v2.0#Tripal_Installation
>>>
>>> On Tue, Mar 4, 2014 at 4:35 PM, Mara Kim <[hidden email]> wrote:
>>>
>>> More updates:
>>>
>>> The repository http://git.drupal.org/sandbox/spficklin/1578234.git
>>> does not have the tag 7.x-2.0a-tripal_v2.0a
>>>
>>> Here is the specific error:
>>>
>>> (My fancy git aware bash prompt)
>>> kimmm@rokasgate:/var/www/html/sites/all/modules/tripal_kegg_analysis (0)
>>> d12b127c2cbf59b5e380cffb37cc5ac79a411a5f
>>> ## 6.x-1.x
>>> $ git checkout 7.x-2.0a-tripal_v2.0a
>>>
>>> BEGIN EXECUTION TRACE
>>> error: pathspec '7.x-2.0a-tripal_v2.0a' did not match any file(s) known
>>> to
>>> git.
>>> END EXECUTION TRACE
>>>
>>> On Tue, Mar 4, 2014 at 4:29 PM, Mara Kim <[hidden email]> wrote:
>>>
>>> Hi Stephen,
>>>
>>> I am currently in the process of installing Tripal 2a.  One thing of note
>>> I've run across so far is that CKeditor no longer provides
>>> include/exclude
>>> options (https://drupal.org/node/1018920).  Do you have alternative
>>> instructions?
>>>
>>>
>>> On Mon, Feb 24, 2014 at 4:29 PM, Stephen Ficklin <[hidden email]>
>>> wrote:
>>>
>>>
>>> Dear Tripal and Chado users,
>>>
>>> The Tripal Development Team is pleased to announce an alpha release of
>>> Tripal 2.0 for Drupal 7.
>>>
>>> This release is expected to have bugs and there is some functionality
>>> still under development.  However, this release is made to help early
>>> adopters of Tripal for Drupal 7.   Reports of bugs or other issues are
>>> highly welcomed.   Below are available resources for Tripal 2.0a
>>>
>>> * Download Instructions:
>>> http://tripal.info/documentation/download_tripal_v2.0a
>>> * Installation and Tutorial:
>>> http://www.gmod.org/wiki/Tripal_Tutorial_v2.0
>>> * Tripal 2.0 API site: http://api.tripal.info/api/tripal/2.x
>>> * Tripal Mailing List:
>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>> * Tripal Developer's Mailing List:
>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>>
>>> The Installation tutorial is still under development but should have
>>> enough information for complete installation of Tripal v2.0a as well as
>>> loading of organisms and features.   The tutorial will be completed
>>> before the stable release of Tripal 2.0.
>>>
>>> Regards,
>>> Stephen
>>>
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Flow-based real-time traffic analytics software. Cisco certified tool.
>>> Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
>>> Customize your own dashboards, set traffic alerts and generate reports.
>>> Network behavioral analysis & security monitoring. All-in-one tool.
>>>
>>>
>>> http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
>>> _______________________________________________
>>> Gmod-schema mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>
>>>
>>>
>>>
>>>
>>> --
>>> Mara Kim
>>>
>>> Ph.D. Candidate
>>> Computational Biology
>>> Vanderbilt University
>>> Nashville, TN
>>>
>>>
>>>
>>>
>>> --
>>> Mara Kim
>>>
>>> Ph.D. Candidate
>>> Computational Biology
>>> Vanderbilt University
>>> Nashville, TN
>>>
>>>
>>>
>>>
>>> --
>>> Mara Kim
>>>
>>> Ph.D. Candidate
>>> Computational Biology
>>> Vanderbilt University
>>> Nashville, TN
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Subversion Kills Productivity. Get off Subversion & Make the Move to
>>> Perforce.
>>> With Perforce, you get hassle-free workflows. Merge that actually works.
>>> Faster operations. Version large binaries.  Built-in WAN optimization and
>>> the
>>> freedom to use Git, Perforce or both. Make the move to Perforce.
>>>
>>> http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk
>>> _______________________________________________
>>> Gmod-tripal mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>
>>>
>>
>>
>
>



--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN


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Re: [Gmod-tripal] Release of Tripal v2.0a

Stephen Ficklin-3
Hi Mara,

Yes, that document should still work for Tripal v2.0a

Could it be a permissions problem?  Does the PostgreSQL user account
used by Drupal have access to the 'chado' schema that you copied your
data into?

Stephen

On 4/1/2014 11:43 AM, Mara Kim wrote:

> Hi guys,
>
> I am having trouble getting Tripal 2.0a to recognize the Chado schema
> that has been migrated in using the method described here:
> http://tripal.info/documentation/migrate_chado
>
> I realize these instructions are for Tripal 1.0, but seeing as how I
> needed to import this data anyways, I figured I'd give it a shot.  I
> run into issues when I try to enable the Tripal modules.  For example:
>
> BEGIN EXECUTION TRACE
> $ drush pm-enable tripal_views
> Module tripal_views doesn't meet the requirements to be enabled.
>                                                                [error]
>   (Currently using tripal_views ERROR: Chado must be installed before
> this module can be enabled)
> [error]
> END EXECUTION TRACE
>
> It seems that Tripal isn't recognizing the migrated chado database.
> Any suggestions on how to fix this?
>
>
> On Thu, Mar 6, 2014 at 2:21 PM, Stephen Ficklin <[hidden email]> wrote:
>> Hi Mara,
>>
>> Tripal stores blast results in the analysisfeatureprop table.  A blast
>> analysis is first added to the analysis table, and the Tripal Blast Analysis
>> extension module parses the blast XML file, identifies a matching feature in
>> the 'feature' table, and adds the link in the featureanalysis table between
>> the analysis and the feature.  Then details of the blast match are added to
>> the analysisfeatureprop table.   But, what gets stored is the actual XML
>> from the blast output detailing all of the matches for that query.    When
>> the Tripal Blast module displays blast results, it retrieves the XML, parses
>> it, passes it into an array and then passes that array into the
>> tripal_feature_blast_restults.tpl.php template for display, thus allowing
>> anyone to customize the way blast results are presented.
>>
>> Originally, we wanted to store all of the details about a match directly in
>> the analysisfeatureprop table such that the different details about a match
>> were entered as separate records.  The goal was to allow us to then search
>> matches by things like match name, accession, e-value, etc.  But, there is
>> not an easy way to distinguish between values that belong to one  match and
>> a different match using the analysisfeatureprop table.   So, to compromise,
>> the module stores the XML directly into the analysisfeatureprop table and
>> maintains a custom table named 'blast_hit_data' to allow for searching of
>> blast results.   That blast_hit_data table is integrated with Drupal Views
>> (just like any other Chado table) so you can create Drupal Views that can be
>> used for searching the results.  This is how blast results are searching on
>> sites like CottonGen and GDR.
>>
>> Stephen
>>
>>
>> On 3/6/2014 2:57 PM, Mara Kim wrote:
>>> Hi guys,
>>>
>>> I was wondering how you guys store BLAST results in Chado for Tripal.
>>> I have my own way of doing it, but obviously it would be much better
>>> if I followed your convention.  Specifically, what cvterms do you use
>>> to name BLAST hits and hsps, and what rows does Tripal expect in what
>>> tables?
>>>
>>> Sorry if you are getting this twice.  My first message bounced from
>>> the mailing list because I used the wrong address.
>>>
>>> On Tue, Mar 4, 2014 at 7:03 PM, Lacey-Anne Sanderson
>>> <[hidden email]> wrote:
>>>> Hi Mara,
>>>>
>>>> That is unfortunately as it should be at this point. Work is ongoing on
>>>> porting the other extension modules (including the ones in my sandbox :)
>>>> )
>>>> to Drupal 7 and so hopefully these will be available soon! We will keep
>>>> you
>>>> posted!
>>>>
>>>> ~Lacey
>>>>
>>>> On Mar 4, 2014, at 4:37 PM, Mara Kim <[hidden email]> wrote:
>>>>
>>>> Hmm, it seems that all the repositories (except the main Tripal
>>>> repository and the tripal_blast_analysis repository) lack the
>>>> appropriate tags as I get similar errors.  This is in reference to
>>>> these instructions:
>>>> http://www.gmod.org/wiki/Tripal_Tutorial_v2.0#Tripal_Installation
>>>>
>>>> On Tue, Mar 4, 2014 at 4:35 PM, Mara Kim <[hidden email]> wrote:
>>>>
>>>> More updates:
>>>>
>>>> The repository http://git.drupal.org/sandbox/spficklin/1578234.git
>>>> does not have the tag 7.x-2.0a-tripal_v2.0a
>>>>
>>>> Here is the specific error:
>>>>
>>>> (My fancy git aware bash prompt)
>>>> kimmm@rokasgate:/var/www/html/sites/all/modules/tripal_kegg_analysis (0)
>>>> d12b127c2cbf59b5e380cffb37cc5ac79a411a5f
>>>> ## 6.x-1.x
>>>> $ git checkout 7.x-2.0a-tripal_v2.0a
>>>>
>>>> BEGIN EXECUTION TRACE
>>>> error: pathspec '7.x-2.0a-tripal_v2.0a' did not match any file(s) known
>>>> to
>>>> git.
>>>> END EXECUTION TRACE
>>>>
>>>> On Tue, Mar 4, 2014 at 4:29 PM, Mara Kim <[hidden email]> wrote:
>>>>
>>>> Hi Stephen,
>>>>
>>>> I am currently in the process of installing Tripal 2a.  One thing of note
>>>> I've run across so far is that CKeditor no longer provides
>>>> include/exclude
>>>> options (https://drupal.org/node/1018920).  Do you have alternative
>>>> instructions?
>>>>
>>>>
>>>> On Mon, Feb 24, 2014 at 4:29 PM, Stephen Ficklin <[hidden email]>
>>>> wrote:
>>>>
>>>>
>>>> Dear Tripal and Chado users,
>>>>
>>>> The Tripal Development Team is pleased to announce an alpha release of
>>>> Tripal 2.0 for Drupal 7.
>>>>
>>>> This release is expected to have bugs and there is some functionality
>>>> still under development.  However, this release is made to help early
>>>> adopters of Tripal for Drupal 7.   Reports of bugs or other issues are
>>>> highly welcomed.   Below are available resources for Tripal 2.0a
>>>>
>>>> * Download Instructions:
>>>> http://tripal.info/documentation/download_tripal_v2.0a
>>>> * Installation and Tutorial:
>>>> http://www.gmod.org/wiki/Tripal_Tutorial_v2.0
>>>> * Tripal 2.0 API site: http://api.tripal.info/api/tripal/2.x
>>>> * Tripal Mailing List:
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>> * Tripal Developer's Mailing List:
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>>>
>>>> The Installation tutorial is still under development but should have
>>>> enough information for complete installation of Tripal v2.0a as well as
>>>> loading of organisms and features.   The tutorial will be completed
>>>> before the stable release of Tripal 2.0.
>>>>
>>>> Regards,
>>>> Stephen
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Flow-based real-time traffic analytics software. Cisco certified tool.
>>>> Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
>>>> Customize your own dashboards, set traffic alerts and generate reports.
>>>> Network behavioral analysis & security monitoring. All-in-one tool.
>>>>
>>>>
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
>>>> _______________________________________________
>>>> Gmod-schema mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Mara Kim
>>>>
>>>> Ph.D. Candidate
>>>> Computational Biology
>>>> Vanderbilt University
>>>> Nashville, TN
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Mara Kim
>>>>
>>>> Ph.D. Candidate
>>>> Computational Biology
>>>> Vanderbilt University
>>>> Nashville, TN
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Mara Kim
>>>>
>>>> Ph.D. Candidate
>>>> Computational Biology
>>>> Vanderbilt University
>>>> Nashville, TN
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Subversion Kills Productivity. Get off Subversion & Make the Move to
>>>> Perforce.
>>>> With Perforce, you get hassle-free workflows. Merge that actually works.
>>>> Faster operations. Version large binaries.  Built-in WAN optimization and
>>>> the
>>>> freedom to use Git, Perforce or both. Make the move to Perforce.
>>>>
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk
>>>> _______________________________________________
>>>> Gmod-tripal mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>
>>>>
>>>
>>
>
>


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Fwd: [Gmod-tripal] Release of Tripal v2.0a

Mara Kim-2
In reply to this post by Mara Kim-2
Realized that I've been forgetting to add the listserve

---------- Forwarded message ----------
From: Mara Kim <[hidden email]>
Date: Mon, Apr 7, 2014 at 2:27 PM
Subject: Re: [Gmod-tripal] [Gmod-schema] Release of Tripal v2.0a
To: Stephen Ficklin <[hidden email]>


Hi Stephen,

I went ahead and added a 'null' db with db_id=0.  The rest of the fix
proceeded without errors, and I no longer see that SQL error.

I have now attempted to sync the organisms in the database with
Tripal.  I synced them via the Add Organism page (btw, you guys should
probably put the message that says "Leave them unchecked to sync all
organisms" at the top of the list rather than the bottom.  We had a
good laugh when I found the message after about 2 minutes of checking
>200 boxes XD )

The job seemed to complete successfully, but when I tried to access
the pages via the "find content" link, the pages generated the
following error:

PDOException: SQLSTATE[42P01]: Undefined table: 7 ERROR: relation
"chado.organism_feature_count" does not exist LINE 1:
..._features,OFC.feature_type,CVT.definition FROM chado.orga... ^:
SELECT OFC.num_features,OFC.feature_type,CVT.definition FROM
chado.organism_feature_count OFC INNER JOIN chado.cvterm CVT on
OFC.cvterm_id = CVT.cvterm_id WHERE organism_id = :organism_id ORDER
BY num_features desc ; Array ( [:organism_id] => 202 ) in
chado_query() (line 1332
of/var/www/html/sites/all/modules/tripal/tripal_core/api/tripal_core.chado_query.api.inc).

On Sat, Apr 5, 2014 at 1:34 PM, Mara Kim <[hidden email]> wrote:

> Hi Stephen,
>
> With a bit of digging, I figured out that the problem is that there is
> no entry in chado.db where name='null'.  Should I add such an entry?
> There are a few others that look like they may have a similar purpose:
>
> db_id |       name        |
> description                                    | urlprefix | url
> -------+-------------------+----------------------------------------------------------------------------------+-----------+-----
>      1 | OBO_REL           |
>                                        |           |
>      2 | _global           |
>                                        |           |
>      3 | internal          |
>                                        |           |
> plus many others...
>
> On Sat, Apr 5, 2014 at 11:18 AM, Mara Kim <[hidden email]> wrote:
>> Hi Stephen,
>>
>> I made a few modifications to the code so that I could run it directly
>> on my drupal database.  Here is my updated version:
>>
>> BEGIN;
>> insert into chado.cv (name,definition) values
>> ('chado_properties','Terms that are used in the chadoprop table to
>> describe the state of the database');
>> insert into chado.dbxref (db_id,accession) values ((select db_id from
>> chado.db where name='null'), 'chado_properties:version');
>> insert into chado.cvterm (name,definition,cv_id,dbxref_id) values
>> ('version','Chado schema version',(select cv_id from chado.cv where
>> name = 'chado_properties'),(select dbxref_id from chado.dbxref where
>> accession='chado_properties:version'));
>> INSERT INTO chado.chadoprop (type_id, value) VALUES (
>>        (SELECT cvterm_id
>>         FROM chado.cvterm CVT
>>           INNER JOIN chado.cv CV on CVT.cv_id = CV.cv_id
>>          WHERE CV.name = 'chado_properties' AND CVT.name = 'version'),
>>        '1.23');
>> COMMIT;
>>
>> Summary of changes:
>> -Transactionalize
>> -Qualify table names with chado.* schema
>> -Remove curly braces around table names in final insert statement
>> -Version number 1.2 -> 1.23 (note that there is no dot between the 2 &
>> 3--is this alright?)
>>
>> However, I am still getting some errors related to dbxref_id, which
>> I'm not entirely sure how to fix:
>>
>> BEGIN
>> INSERT 0 1
>> psql:makeprepdb:3: ERROR:  null value in column "db_id" violates
>> not-null constraint
>> psql:makeprepdb:4: ERROR:  current transaction is aborted, commands
>> ignored until end of transaction block
>> psql:makeprepdb:10: ERROR:  current transaction is aborted, commands
>> ignored until end of transaction block
>> ROLLBACK
>>
>> On Fri, Apr 4, 2014 at 11:42 PM, Stephen Ficklin <[hidden email]> wrote:
>>> Hi Mara,
>>>
>>> I believe the 'make prepdb' command adds a record to the chadoprop table
>>> inserting the version number of Chado.  Somehow during install of Chado that
>>> record is added.  This is the way that Tripal is able to tell what version
>>> of Chado you are using so it can deal with the tables correctly.   The 'make
>>> prepdb' also adds a vocabulary to the cv table called 'chado_properties'
>>> which has the term 'version' and it is that term that is used in the
>>> chadoprop table.   So, since the chadoprop table is missing the version
>>> record, Tripal is giving that error message.  It should be a bit more
>>> tolerant of that so we'll see what we can do to fix that, but really Tripal
>>> has to know what version of Chado you are using.  So you'll need to have
>>> that record in the chadoprop table.  Here's some SQL code for a quick fix:
>>>
>>> insert into cv (name,definition) values ('chado_properties','Terms that are
>>> used in the chadoprop table to describe the state of the database');
>>> insert into dbxref (db_id,accession) values ((select db_id from db where
>>> name='null'), 'chado_properties:version');
>>> insert into cvterm (name,definition,cv_id,dbxref_id) values
>>> ('version','Chado schema version',(select cv_id from cv where name =
>>> 'chado_properties'),(select dbxref_id from dbxref where
>>> accession='chado_properties:version'));
>>> INSERT INTO {chadoprop} (type_id, value) VALUES (
>>>        (SELECT cvterm_id
>>>         FROM {cvterm} CVT
>>>           INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
>>>          WHERE CV.name = 'chado_properties' AND CVT.name = 'version'),
>>>        '1.2')
>>>
>>> The '1.2' in the SQL statement above should be changed to the version you
>>> are using.   You can just leave 1.2 if the version is 1.2.x as the third
>>> number just signifies changes to perl code and not to the database schema.
>>>
>>> Stephen
>>>
>>>
>>> On 4/5/2014 12:23 AM, Mara Kim wrote:
>>>>
>>>> There is nothing in the chadoprop table.
>>>>
>>>> I assume you are asking about installing Chado before the migration.
>>>> I used the included makefile, which I think calls the perl scripts.
>>>> However, I don't think I ran the `make prepdb` command.
>>>>
>>>> On Fri, Apr 4, 2014 at 4:05 PM, Stephen Ficklin <[hidden email]>
>>>> wrote:
>>>>>
>>>>> That's an interesting message.   Is there anything in the 'chadoprop'
>>>>> table?
>>>>> When installing Chado did you use the Perl scripts?  If so, did you run
>>>>> the
>>>>> 'make prepdb' command?
>>>>>
>>>>> Stephen
>>>>>
>>>>>
>>>>> On 4/4/2014 4:11 PM, Mara Kim wrote:
>>>>>>
>>>>>> Hi Stephen,
>>>>>>
>>>>>> I changed the permissions, and that solved the problem with enabling
>>>>>> the views.  However, I now get this error on the web page:
>>>>>>
>>>>>> Notice: Trying to get property of non-object in chado_get_version()
>>>>>> (line 217
>>>>>>
>>>>>> of/var/www/html/sites/all/modules/tripal/tripal_core/api/tripal_core.chado_schema.api.inc).
>>>>>> Notice: Trying to get property of non-object in chado_get_version()
>>>>>> (line 217
>>>>>>
>>>>>> of/var/www/html/sites/all/modules/tripal/tripal_core/api/tripal_core.chado_schema.api.inc).
>>>>>>
>>>>>> On Wed, Apr 2, 2014 at 10:10 PM, Stephen Ficklin <[hidden email]>
>>>>>> wrote:
>>>>>>>
>>>>>>> Hey Mara,
>>>>>>>
>>>>>>> Just curious if you got this issue resolved?
>>>>>>>
>>>>>>> Stephen
>>>>>>>
>>>>>>>
>>>>>>> On 4/1/2014 11:43 AM, Mara Kim wrote:
>>>>>>>>
>>>>>>>> Hi guys,
>>>>>>>>
>>>>>>>> I am having trouble getting Tripal 2.0a to recognize the Chado schema
>>>>>>>> that has been migrated in using the method described here:
>>>>>>>> http://tripal.info/documentation/migrate_chado
>>>>>>>>
>>>>>>>> I realize these instructions are for Tripal 1.0, but seeing as how I
>>>>>>>> needed to import this data anyways, I figured I'd give it a shot.  I
>>>>>>>> run into issues when I try to enable the Tripal modules.  For example:
>>>>>>>>
>>>>>>>> BEGIN EXECUTION TRACE
>>>>>>>> $ drush pm-enable tripal_views
>>>>>>>> Module tripal_views doesn't meet the requirements to be enabled.
>>>>>>>>
>>>>>>>> [error]
>>>>>>>>     (Currently using tripal_views ERROR: Chado must be installed
>>>>>>>> before
>>>>>>>> this module can be enabled)
>>>>>>>> [error]
>>>>>>>> END EXECUTION TRACE
>>>>>>>>
>>>>>>>> It seems that Tripal isn't recognizing the migrated chado database.
>>>>>>>> Any suggestions on how to fix this?
>>>>>>>>
>>>>>>>>
>>>>>>>> On Thu, Mar 6, 2014 at 2:21 PM, Stephen Ficklin <[hidden email]>
>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>> Hi Mara,
>>>>>>>>>
>>>>>>>>> Tripal stores blast results in the analysisfeatureprop table.  A
>>>>>>>>> blast
>>>>>>>>> analysis is first added to the analysis table, and the Tripal Blast
>>>>>>>>> Analysis
>>>>>>>>> extension module parses the blast XML file, identifies a matching
>>>>>>>>> feature
>>>>>>>>> in
>>>>>>>>> the 'feature' table, and adds the link in the featureanalysis table
>>>>>>>>> between
>>>>>>>>> the analysis and the feature.  Then details of the blast match are
>>>>>>>>> added
>>>>>>>>> to
>>>>>>>>> the analysisfeatureprop table.   But, what gets stored is the actual
>>>>>>>>> XML
>>>>>>>>> from the blast output detailing all of the matches for that query.
>>>>>>>>> When
>>>>>>>>> the Tripal Blast module displays blast results, it retrieves the XML,
>>>>>>>>> parses
>>>>>>>>> it, passes it into an array and then passes that array into the
>>>>>>>>> tripal_feature_blast_restults.tpl.php template for display, thus
>>>>>>>>> allowing
>>>>>>>>> anyone to customize the way blast results are presented.
>>>>>>>>>
>>>>>>>>> Originally, we wanted to store all of the details about a match
>>>>>>>>> directly
>>>>>>>>> in
>>>>>>>>> the analysisfeatureprop table such that the different details about a
>>>>>>>>> match
>>>>>>>>> were entered as separate records.  The goal was to allow us to then
>>>>>>>>> search
>>>>>>>>> matches by things like match name, accession, e-value, etc.  But,
>>>>>>>>> there
>>>>>>>>> is
>>>>>>>>> not an easy way to distinguish between values that belong to one
>>>>>>>>> match
>>>>>>>>> and
>>>>>>>>> a different match using the analysisfeatureprop table.   So, to
>>>>>>>>> compromise,
>>>>>>>>> the module stores the XML directly into the analysisfeatureprop table
>>>>>>>>> and
>>>>>>>>> maintains a custom table named 'blast_hit_data' to allow for
>>>>>>>>> searching
>>>>>>>>> of
>>>>>>>>> blast results.   That blast_hit_data table is integrated with Drupal
>>>>>>>>> Views
>>>>>>>>> (just like any other Chado table) so you can create Drupal Views that
>>>>>>>>> can
>>>>>>>>> be
>>>>>>>>> used for searching the results.  This is how blast results are
>>>>>>>>> searching
>>>>>>>>> on
>>>>>>>>> sites like CottonGen and GDR.
>>>>>>>>>
>>>>>>>>> Stephen
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 3/6/2014 2:57 PM, Mara Kim wrote:
>>>>>>>>>>
>>>>>>>>>> Hi guys,
>>>>>>>>>>
>>>>>>>>>> I was wondering how you guys store BLAST results in Chado for
>>>>>>>>>> Tripal.
>>>>>>>>>> I have my own way of doing it, but obviously it would be much better
>>>>>>>>>> if I followed your convention.  Specifically, what cvterms do you
>>>>>>>>>> use
>>>>>>>>>> to name BLAST hits and hsps, and what rows does Tripal expect in
>>>>>>>>>> what
>>>>>>>>>> tables?
>>>>>>>>>>
>>>>>>>>>> Sorry if you are getting this twice.  My first message bounced from
>>>>>>>>>> the mailing list because I used the wrong address.
>>>>>>>>>>
>>>>>>>>>> On Tue, Mar 4, 2014 at 7:03 PM, Lacey-Anne Sanderson
>>>>>>>>>> <[hidden email]> wrote:
>>>>>>>>>>>
>>>>>>>>>>> Hi Mara,
>>>>>>>>>>>
>>>>>>>>>>> That is unfortunately as it should be at this point. Work is
>>>>>>>>>>> ongoing
>>>>>>>>>>> on
>>>>>>>>>>> porting the other extension modules (including the ones in my
>>>>>>>>>>> sandbox
>>>>>>>>>>> :)
>>>>>>>>>>> )
>>>>>>>>>>> to Drupal 7 and so hopefully these will be available soon! We will
>>>>>>>>>>> keep
>>>>>>>>>>> you
>>>>>>>>>>> posted!
>>>>>>>>>>>
>>>>>>>>>>> ~Lacey
>>>>>>>>>>>
>>>>>>>>>>> On Mar 4, 2014, at 4:37 PM, Mara Kim <[hidden email]> wrote:
>>>>>>>>>>>
>>>>>>>>>>> Hmm, it seems that all the repositories (except the main Tripal
>>>>>>>>>>> repository and the tripal_blast_analysis repository) lack the
>>>>>>>>>>> appropriate tags as I get similar errors.  This is in reference to
>>>>>>>>>>> these instructions:
>>>>>>>>>>> http://www.gmod.org/wiki/Tripal_Tutorial_v2.0#Tripal_Installation
>>>>>>>>>>>
>>>>>>>>>>> On Tue, Mar 4, 2014 at 4:35 PM, Mara Kim <[hidden email]>
>>>>>>>>>>> wrote:
>>>>>>>>>>>
>>>>>>>>>>> More updates:
>>>>>>>>>>>
>>>>>>>>>>> The repository http://git.drupal.org/sandbox/spficklin/1578234.git
>>>>>>>>>>> does not have the tag 7.x-2.0a-tripal_v2.0a
>>>>>>>>>>>
>>>>>>>>>>> Here is the specific error:
>>>>>>>>>>>
>>>>>>>>>>> (My fancy git aware bash prompt)
>>>>>>>>>>>
>>>>>>>>>>> kimmm@rokasgate:/var/www/html/sites/all/modules/tripal_kegg_analysis
>>>>>>>>>>> (0)
>>>>>>>>>>> d12b127c2cbf59b5e380cffb37cc5ac79a411a5f
>>>>>>>>>>> ## 6.x-1.x
>>>>>>>>>>> $ git checkout 7.x-2.0a-tripal_v2.0a
>>>>>>>>>>>
>>>>>>>>>>> BEGIN EXECUTION TRACE
>>>>>>>>>>> error: pathspec '7.x-2.0a-tripal_v2.0a' did not match any file(s)
>>>>>>>>>>> known
>>>>>>>>>>> to
>>>>>>>>>>> git.
>>>>>>>>>>> END EXECUTION TRACE
>>>>>>>>>>>
>>>>>>>>>>> On Tue, Mar 4, 2014 at 4:29 PM, Mara Kim <[hidden email]>
>>>>>>>>>>> wrote:
>>>>>>>>>>>
>>>>>>>>>>> Hi Stephen,
>>>>>>>>>>>
>>>>>>>>>>> I am currently in the process of installing Tripal 2a.  One thing
>>>>>>>>>>> of
>>>>>>>>>>> note
>>>>>>>>>>> I've run across so far is that CKeditor no longer provides
>>>>>>>>>>> include/exclude
>>>>>>>>>>> options (https://drupal.org/node/1018920).  Do you have alternative
>>>>>>>>>>> instructions?
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Mon, Feb 24, 2014 at 4:29 PM, Stephen Ficklin
>>>>>>>>>>> <[hidden email]>
>>>>>>>>>>> wrote:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Dear Tripal and Chado users,
>>>>>>>>>>>
>>>>>>>>>>> The Tripal Development Team is pleased to announce an alpha release
>>>>>>>>>>> of
>>>>>>>>>>> Tripal 2.0 for Drupal 7.
>>>>>>>>>>>
>>>>>>>>>>> This release is expected to have bugs and there is some
>>>>>>>>>>> functionality
>>>>>>>>>>> still under development.  However, this release is made to help
>>>>>>>>>>> early
>>>>>>>>>>> adopters of Tripal for Drupal 7.   Reports of bugs or other issues
>>>>>>>>>>> are
>>>>>>>>>>> highly welcomed.   Below are available resources for Tripal 2.0a
>>>>>>>>>>>
>>>>>>>>>>> * Download Instructions:
>>>>>>>>>>> http://tripal.info/documentation/download_tripal_v2.0a
>>>>>>>>>>> * Installation and Tutorial:
>>>>>>>>>>> http://www.gmod.org/wiki/Tripal_Tutorial_v2.0
>>>>>>>>>>> * Tripal 2.0 API site: http://api.tripal.info/api/tripal/2.x
>>>>>>>>>>> * Tripal Mailing List:
>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>>>>>>> * Tripal Developer's Mailing List:
>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>>>>>>>>>>
>>>>>>>>>>> The Installation tutorial is still under development but should
>>>>>>>>>>> have
>>>>>>>>>>> enough information for complete installation of Tripal v2.0a as
>>>>>>>>>>> well
>>>>>>>>>>> as
>>>>>>>>>>> loading of organisms and features.   The tutorial will be completed
>>>>>>>>>>> before the stable release of Tripal 2.0.
>>>>>>>>>>>
>>>>>>>>>>> Regards,
>>>>>>>>>>> Stephen
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>>> Flow-based real-time traffic analytics software. Cisco certified
>>>>>>>>>>> tool.
>>>>>>>>>>> Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow
>>>>>>>>>>> Analyzer
>>>>>>>>>>> Customize your own dashboards, set traffic alerts and generate
>>>>>>>>>>> reports.
>>>>>>>>>>> Network behavioral analysis & security monitoring. All-in-one tool.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Gmod-schema mailing list
>>>>>>>>>>> [hidden email]
>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> Mara Kim
>>>>>>>>>>>
>>>>>>>>>>> Ph.D. Candidate
>>>>>>>>>>> Computational Biology
>>>>>>>>>>> Vanderbilt University
>>>>>>>>>>> Nashville, TN
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> Mara Kim
>>>>>>>>>>>
>>>>>>>>>>> Ph.D. Candidate
>>>>>>>>>>> Computational Biology
>>>>>>>>>>> Vanderbilt University
>>>>>>>>>>> Nashville, TN
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> Mara Kim
>>>>>>>>>>>
>>>>>>>>>>> Ph.D. Candidate
>>>>>>>>>>> Computational Biology
>>>>>>>>>>> Vanderbilt University
>>>>>>>>>>> Nashville, TN
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>>> Subversion Kills Productivity. Get off Subversion & Make the Move
>>>>>>>>>>> to
>>>>>>>>>>> Perforce.
>>>>>>>>>>> With Perforce, you get hassle-free workflows. Merge that actually
>>>>>>>>>>> works.
>>>>>>>>>>> Faster operations. Version large binaries.  Built-in WAN
>>>>>>>>>>> optimization
>>>>>>>>>>> and
>>>>>>>>>>> the
>>>>>>>>>>> freedom to use Git, Perforce or both. Make the move to Perforce.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Gmod-tripal mailing list
>>>>>>>>>>> [hidden email]
>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>>
>> --
>> Mara Kim
>>
>> Ph.D. Candidate
>> Computational Biology
>> Vanderbilt University
>> Nashville, TN
>
>
>
> --
> Mara Kim
>
> Ph.D. Candidate
> Computational Biology
> Vanderbilt University
> Nashville, TN



--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN


--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN


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Re: Fwd: [Gmod-tripal] Release of Tripal v2.0a

Stephen Ficklin-3
Hi Mara,

When the tripal feature module is enabled it automatically creates the
organism_feature_count materialized view.  The error message you are
seeing indicates that the mview was not created.   When you enabled that
module did you encounter any errors or warnings?    If you disable,
uninstall and the enable the tripal_feature module it should either give
you warning/error messages or create the missing mview for you.

Stephen

On 4/7/2014 4:56 PM, Mara Kim wrote:

> Realized that I've been forgetting to add the listserve
>
> ---------- Forwarded message ----------
> From: Mara Kim <[hidden email]>
> Date: Mon, Apr 7, 2014 at 2:27 PM
> Subject: Re: [Gmod-tripal] [Gmod-schema] Release of Tripal v2.0a
> To: Stephen Ficklin <[hidden email]>
>
>
> Hi Stephen,
>
> I went ahead and added a 'null' db with db_id=0.  The rest of the fix
> proceeded without errors, and I no longer see that SQL error.
>
> I have now attempted to sync the organisms in the database with
> Tripal.  I synced them via the Add Organism page (btw, you guys should
> probably put the message that says "Leave them unchecked to sync all
> organisms" at the top of the list rather than the bottom.  We had a
> good laugh when I found the message after about 2 minutes of checking
>> 200 boxes XD )
> The job seemed to complete successfully, but when I tried to access
> the pages via the "find content" link, the pages generated the
> following error:
>
> PDOException: SQLSTATE[42P01]: Undefined table: 7 ERROR: relation
> "chado.organism_feature_count" does not exist LINE 1:
> ..._features,OFC.feature_type,CVT.definition FROM chado.orga... ^:
> SELECT OFC.num_features,OFC.feature_type,CVT.definition FROM
> chado.organism_feature_count OFC INNER JOIN chado.cvterm CVT on
> OFC.cvterm_id = CVT.cvterm_id WHERE organism_id = :organism_id ORDER
> BY num_features desc ; Array ( [:organism_id] => 202 ) in
> chado_query() (line 1332
> of/var/www/html/sites/all/modules/tripal/tripal_core/api/tripal_core.chado_query.api.inc).
>
> On Sat, Apr 5, 2014 at 1:34 PM, Mara Kim <[hidden email]> wrote:
>> Hi Stephen,
>>
>> With a bit of digging, I figured out that the problem is that there is
>> no entry in chado.db where name='null'.  Should I add such an entry?
>> There are a few others that look like they may have a similar purpose:
>>
>> db_id |       name        |
>> description                                    | urlprefix | url
>> -------+-------------------+----------------------------------------------------------------------------------+-----------+-----
>>       1 | OBO_REL           |
>>                                         |           |
>>       2 | _global           |
>>                                         |           |
>>       3 | internal          |
>>                                         |           |
>> plus many others...
>>
>> On Sat, Apr 5, 2014 at 11:18 AM, Mara Kim <[hidden email]> wrote:
>>> Hi Stephen,
>>>
>>> I made a few modifications to the code so that I could run it directly
>>> on my drupal database.  Here is my updated version:
>>>
>>> BEGIN;
>>> insert into chado.cv (name,definition) values
>>> ('chado_properties','Terms that are used in the chadoprop table to
>>> describe the state of the database');
>>> insert into chado.dbxref (db_id,accession) values ((select db_id from
>>> chado.db where name='null'), 'chado_properties:version');
>>> insert into chado.cvterm (name,definition,cv_id,dbxref_id) values
>>> ('version','Chado schema version',(select cv_id from chado.cv where
>>> name = 'chado_properties'),(select dbxref_id from chado.dbxref where
>>> accession='chado_properties:version'));
>>> INSERT INTO chado.chadoprop (type_id, value) VALUES (
>>>         (SELECT cvterm_id
>>>          FROM chado.cvterm CVT
>>>            INNER JOIN chado.cv CV on CVT.cv_id = CV.cv_id
>>>           WHERE CV.name = 'chado_properties' AND CVT.name = 'version'),
>>>         '1.23');
>>> COMMIT;
>>>
>>> Summary of changes:
>>> -Transactionalize
>>> -Qualify table names with chado.* schema
>>> -Remove curly braces around table names in final insert statement
>>> -Version number 1.2 -> 1.23 (note that there is no dot between the 2 &
>>> 3--is this alright?)
>>>
>>> However, I am still getting some errors related to dbxref_id, which
>>> I'm not entirely sure how to fix:
>>>
>>> BEGIN
>>> INSERT 0 1
>>> psql:makeprepdb:3: ERROR:  null value in column "db_id" violates
>>> not-null constraint
>>> psql:makeprepdb:4: ERROR:  current transaction is aborted, commands
>>> ignored until end of transaction block
>>> psql:makeprepdb:10: ERROR:  current transaction is aborted, commands
>>> ignored until end of transaction block
>>> ROLLBACK
>>>
>>> On Fri, Apr 4, 2014 at 11:42 PM, Stephen Ficklin <[hidden email]> wrote:
>>>> Hi Mara,
>>>>
>>>> I believe the 'make prepdb' command adds a record to the chadoprop table
>>>> inserting the version number of Chado.  Somehow during install of Chado that
>>>> record is added.  This is the way that Tripal is able to tell what version
>>>> of Chado you are using so it can deal with the tables correctly.   The 'make
>>>> prepdb' also adds a vocabulary to the cv table called 'chado_properties'
>>>> which has the term 'version' and it is that term that is used in the
>>>> chadoprop table.   So, since the chadoprop table is missing the version
>>>> record, Tripal is giving that error message.  It should be a bit more
>>>> tolerant of that so we'll see what we can do to fix that, but really Tripal
>>>> has to know what version of Chado you are using.  So you'll need to have
>>>> that record in the chadoprop table.  Here's some SQL code for a quick fix:
>>>>
>>>> insert into cv (name,definition) values ('chado_properties','Terms that are
>>>> used in the chadoprop table to describe the state of the database');
>>>> insert into dbxref (db_id,accession) values ((select db_id from db where
>>>> name='null'), 'chado_properties:version');
>>>> insert into cvterm (name,definition,cv_id,dbxref_id) values
>>>> ('version','Chado schema version',(select cv_id from cv where name =
>>>> 'chado_properties'),(select dbxref_id from dbxref where
>>>> accession='chado_properties:version'));
>>>> INSERT INTO {chadoprop} (type_id, value) VALUES (
>>>>         (SELECT cvterm_id
>>>>          FROM {cvterm} CVT
>>>>            INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
>>>>           WHERE CV.name = 'chado_properties' AND CVT.name = 'version'),
>>>>         '1.2')
>>>>
>>>> The '1.2' in the SQL statement above should be changed to the version you
>>>> are using.   You can just leave 1.2 if the version is 1.2.x as the third
>>>> number just signifies changes to perl code and not to the database schema.
>>>>
>>>> Stephen
>>>>
>>>>
>>>> On 4/5/2014 12:23 AM, Mara Kim wrote:
>>>>> There is nothing in the chadoprop table.
>>>>>
>>>>> I assume you are asking about installing Chado before the migration.
>>>>> I used the included makefile, which I think calls the perl scripts.
>>>>> However, I don't think I ran the `make prepdb` command.
>>>>>
>>>>> On Fri, Apr 4, 2014 at 4:05 PM, Stephen Ficklin <[hidden email]>
>>>>> wrote:
>>>>>> That's an interesting message.   Is there anything in the 'chadoprop'
>>>>>> table?
>>>>>> When installing Chado did you use the Perl scripts?  If so, did you run
>>>>>> the
>>>>>> 'make prepdb' command?
>>>>>>
>>>>>> Stephen
>>>>>>
>>>>>>
>>>>>> On 4/4/2014 4:11 PM, Mara Kim wrote:
>>>>>>> Hi Stephen,
>>>>>>>
>>>>>>> I changed the permissions, and that solved the problem with enabling
>>>>>>> the views.  However, I now get this error on the web page:
>>>>>>>
>>>>>>> Notice: Trying to get property of non-object in chado_get_version()
>>>>>>> (line 217
>>>>>>>
>>>>>>> of/var/www/html/sites/all/modules/tripal/tripal_core/api/tripal_core.chado_schema.api.inc).
>>>>>>> Notice: Trying to get property of non-object in chado_get_version()
>>>>>>> (line 217
>>>>>>>
>>>>>>> of/var/www/html/sites/all/modules/tripal/tripal_core/api/tripal_core.chado_schema.api.inc).
>>>>>>>
>>>>>>> On Wed, Apr 2, 2014 at 10:10 PM, Stephen Ficklin <[hidden email]>
>>>>>>> wrote:
>>>>>>>> Hey Mara,
>>>>>>>>
>>>>>>>> Just curious if you got this issue resolved?
>>>>>>>>
>>>>>>>> Stephen
>>>>>>>>
>>>>>>>>
>>>>>>>> On 4/1/2014 11:43 AM, Mara Kim wrote:
>>>>>>>>> Hi guys,
>>>>>>>>>
>>>>>>>>> I am having trouble getting Tripal 2.0a to recognize the Chado schema
>>>>>>>>> that has been migrated in using the method described here:
>>>>>>>>> http://tripal.info/documentation/migrate_chado
>>>>>>>>>
>>>>>>>>> I realize these instructions are for Tripal 1.0, but seeing as how I
>>>>>>>>> needed to import this data anyways, I figured I'd give it a shot.  I
>>>>>>>>> run into issues when I try to enable the Tripal modules.  For example:
>>>>>>>>>
>>>>>>>>> BEGIN EXECUTION TRACE
>>>>>>>>> $ drush pm-enable tripal_views
>>>>>>>>> Module tripal_views doesn't meet the requirements to be enabled.
>>>>>>>>>
>>>>>>>>> [error]
>>>>>>>>>      (Currently using tripal_views ERROR: Chado must be installed
>>>>>>>>> before
>>>>>>>>> this module can be enabled)
>>>>>>>>> [error]
>>>>>>>>> END EXECUTION TRACE
>>>>>>>>>
>>>>>>>>> It seems that Tripal isn't recognizing the migrated chado database.
>>>>>>>>> Any suggestions on how to fix this?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Thu, Mar 6, 2014 at 2:21 PM, Stephen Ficklin <[hidden email]>
>>>>>>>>> wrote:
>>>>>>>>>> Hi Mara,
>>>>>>>>>>
>>>>>>>>>> Tripal stores blast results in the analysisfeatureprop table.  A
>>>>>>>>>> blast
>>>>>>>>>> analysis is first added to the analysis table, and the Tripal Blast
>>>>>>>>>> Analysis
>>>>>>>>>> extension module parses the blast XML file, identifies a matching
>>>>>>>>>> feature
>>>>>>>>>> in
>>>>>>>>>> the 'feature' table, and adds the link in the featureanalysis table
>>>>>>>>>> between
>>>>>>>>>> the analysis and the feature.  Then details of the blast match are
>>>>>>>>>> added
>>>>>>>>>> to
>>>>>>>>>> the analysisfeatureprop table.   But, what gets stored is the actual
>>>>>>>>>> XML
>>>>>>>>>> from the blast output detailing all of the matches for that query.
>>>>>>>>>> When
>>>>>>>>>> the Tripal Blast module displays blast results, it retrieves the XML,
>>>>>>>>>> parses
>>>>>>>>>> it, passes it into an array and then passes that array into the
>>>>>>>>>> tripal_feature_blast_restults.tpl.php template for display, thus
>>>>>>>>>> allowing
>>>>>>>>>> anyone to customize the way blast results are presented.
>>>>>>>>>>
>>>>>>>>>> Originally, we wanted to store all of the details about a match
>>>>>>>>>> directly
>>>>>>>>>> in
>>>>>>>>>> the analysisfeatureprop table such that the different details about a
>>>>>>>>>> match
>>>>>>>>>> were entered as separate records.  The goal was to allow us to then
>>>>>>>>>> search
>>>>>>>>>> matches by things like match name, accession, e-value, etc.  But,
>>>>>>>>>> there
>>>>>>>>>> is
>>>>>>>>>> not an easy way to distinguish between values that belong to one
>>>>>>>>>> match
>>>>>>>>>> and
>>>>>>>>>> a different match using the analysisfeatureprop table.   So, to
>>>>>>>>>> compromise,
>>>>>>>>>> the module stores the XML directly into the analysisfeatureprop table
>>>>>>>>>> and
>>>>>>>>>> maintains a custom table named 'blast_hit_data' to allow for
>>>>>>>>>> searching
>>>>>>>>>> of
>>>>>>>>>> blast results.   That blast_hit_data table is integrated with Drupal
>>>>>>>>>> Views
>>>>>>>>>> (just like any other Chado table) so you can create Drupal Views that
>>>>>>>>>> can
>>>>>>>>>> be
>>>>>>>>>> used for searching the results.  This is how blast results are
>>>>>>>>>> searching
>>>>>>>>>> on
>>>>>>>>>> sites like CottonGen and GDR.
>>>>>>>>>>
>>>>>>>>>> Stephen
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On 3/6/2014 2:57 PM, Mara Kim wrote:
>>>>>>>>>>> Hi guys,
>>>>>>>>>>>
>>>>>>>>>>> I was wondering how you guys store BLAST results in Chado for
>>>>>>>>>>> Tripal.
>>>>>>>>>>> I have my own way of doing it, but obviously it would be much better
>>>>>>>>>>> if I followed your convention.  Specifically, what cvterms do you
>>>>>>>>>>> use
>>>>>>>>>>> to name BLAST hits and hsps, and what rows does Tripal expect in
>>>>>>>>>>> what
>>>>>>>>>>> tables?
>>>>>>>>>>>
>>>>>>>>>>> Sorry if you are getting this twice.  My first message bounced from
>>>>>>>>>>> the mailing list because I used the wrong address.
>>>>>>>>>>>
>>>>>>>>>>> On Tue, Mar 4, 2014 at 7:03 PM, Lacey-Anne Sanderson
>>>>>>>>>>> <[hidden email]> wrote:
>>>>>>>>>>>> Hi Mara,
>>>>>>>>>>>>
>>>>>>>>>>>> That is unfortunately as it should be at this point. Work is
>>>>>>>>>>>> ongoing
>>>>>>>>>>>> on
>>>>>>>>>>>> porting the other extension modules (including the ones in my
>>>>>>>>>>>> sandbox
>>>>>>>>>>>> :)
>>>>>>>>>>>> )
>>>>>>>>>>>> to Drupal 7 and so hopefully these will be available soon! We will
>>>>>>>>>>>> keep
>>>>>>>>>>>> you
>>>>>>>>>>>> posted!
>>>>>>>>>>>>
>>>>>>>>>>>> ~Lacey
>>>>>>>>>>>>
>>>>>>>>>>>> On Mar 4, 2014, at 4:37 PM, Mara Kim <[hidden email]> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>> Hmm, it seems that all the repositories (except the main Tripal
>>>>>>>>>>>> repository and the tripal_blast_analysis repository) lack the
>>>>>>>>>>>> appropriate tags as I get similar errors.  This is in reference to
>>>>>>>>>>>> these instructions:
>>>>>>>>>>>> http://www.gmod.org/wiki/Tripal_Tutorial_v2.0#Tripal_Installation
>>>>>>>>>>>>
>>>>>>>>>>>> On Tue, Mar 4, 2014 at 4:35 PM, Mara Kim <[hidden email]>
>>>>>>>>>>>> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>> More updates:
>>>>>>>>>>>>
>>>>>>>>>>>> The repository http://git.drupal.org/sandbox/spficklin/1578234.git
>>>>>>>>>>>> does not have the tag 7.x-2.0a-tripal_v2.0a
>>>>>>>>>>>>
>>>>>>>>>>>> Here is the specific error:
>>>>>>>>>>>>
>>>>>>>>>>>> (My fancy git aware bash prompt)
>>>>>>>>>>>>
>>>>>>>>>>>> kimmm@rokasgate:/var/www/html/sites/all/modules/tripal_kegg_analysis
>>>>>>>>>>>> (0)
>>>>>>>>>>>> d12b127c2cbf59b5e380cffb37cc5ac79a411a5f
>>>>>>>>>>>> ## 6.x-1.x
>>>>>>>>>>>> $ git checkout 7.x-2.0a-tripal_v2.0a
>>>>>>>>>>>>
>>>>>>>>>>>> BEGIN EXECUTION TRACE
>>>>>>>>>>>> error: pathspec '7.x-2.0a-tripal_v2.0a' did not match any file(s)
>>>>>>>>>>>> known
>>>>>>>>>>>> to
>>>>>>>>>>>> git.
>>>>>>>>>>>> END EXECUTION TRACE
>>>>>>>>>>>>
>>>>>>>>>>>> On Tue, Mar 4, 2014 at 4:29 PM, Mara Kim <[hidden email]>
>>>>>>>>>>>> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>> Hi Stephen,
>>>>>>>>>>>>
>>>>>>>>>>>> I am currently in the process of installing Tripal 2a.  One thing
>>>>>>>>>>>> of
>>>>>>>>>>>> note
>>>>>>>>>>>> I've run across so far is that CKeditor no longer provides
>>>>>>>>>>>> include/exclude
>>>>>>>>>>>> options (https://drupal.org/node/1018920).  Do you have alternative
>>>>>>>>>>>> instructions?
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On Mon, Feb 24, 2014 at 4:29 PM, Stephen Ficklin
>>>>>>>>>>>> <[hidden email]>
>>>>>>>>>>>> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Dear Tripal and Chado users,
>>>>>>>>>>>>
>>>>>>>>>>>> The Tripal Development Team is pleased to announce an alpha release
>>>>>>>>>>>> of
>>>>>>>>>>>> Tripal 2.0 for Drupal 7.
>>>>>>>>>>>>
>>>>>>>>>>>> This release is expected to have bugs and there is some
>>>>>>>>>>>> functionality
>>>>>>>>>>>> still under development.  However, this release is made to help
>>>>>>>>>>>> early
>>>>>>>>>>>> adopters of Tripal for Drupal 7.   Reports of bugs or other issues
>>>>>>>>>>>> are
>>>>>>>>>>>> highly welcomed.   Below are available resources for Tripal 2.0a
>>>>>>>>>>>>
>>>>>>>>>>>> * Download Instructions:
>>>>>>>>>>>> http://tripal.info/documentation/download_tripal_v2.0a
>>>>>>>>>>>> * Installation and Tutorial:
>>>>>>>>>>>> http://www.gmod.org/wiki/Tripal_Tutorial_v2.0
>>>>>>>>>>>> * Tripal 2.0 API site: http://api.tripal.info/api/tripal/2.x
>>>>>>>>>>>> * Tripal Mailing List:
>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>>>>>>>> * Tripal Developer's Mailing List:
>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>>>>>>>>>>>
>>>>>>>>>>>> The Installation tutorial is still under development but should
>>>>>>>>>>>> have
>>>>>>>>>>>> enough information for complete installation of Tripal v2.0a as
>>>>>>>>>>>> well
>>>>>>>>>>>> as
>>>>>>>>>>>> loading of organisms and features.   The tutorial will be completed
>>>>>>>>>>>> before the stable release of Tripal 2.0.
>>>>>>>>>>>>
>>>>>>>>>>>> Regards,
>>>>>>>>>>>> Stephen
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>>>> Flow-based real-time traffic analytics software. Cisco certified
>>>>>>>>>>>> tool.
>>>>>>>>>>>> Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow
>>>>>>>>>>>> Analyzer
>>>>>>>>>>>> Customize your own dashboards, set traffic alerts and generate
>>>>>>>>>>>> reports.
>>>>>>>>>>>> Network behavioral analysis & security monitoring. All-in-one tool.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> Gmod-schema mailing list
>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>> Mara Kim
>>>>>>>>>>>>
>>>>>>>>>>>> Ph.D. Candidate
>>>>>>>>>>>> Computational Biology
>>>>>>>>>>>> Vanderbilt University
>>>>>>>>>>>> Nashville, TN
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>> Mara Kim
>>>>>>>>>>>>
>>>>>>>>>>>> Ph.D. Candidate
>>>>>>>>>>>> Computational Biology
>>>>>>>>>>>> Vanderbilt University
>>>>>>>>>>>> Nashville, TN
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>> Mara Kim
>>>>>>>>>>>>
>>>>>>>>>>>> Ph.D. Candidate
>>>>>>>>>>>> Computational Biology
>>>>>>>>>>>> Vanderbilt University
>>>>>>>>>>>> Nashville, TN
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>>>> Subversion Kills Productivity. Get off Subversion & Make the Move
>>>>>>>>>>>> to
>>>>>>>>>>>> Perforce.
>>>>>>>>>>>> With Perforce, you get hassle-free workflows. Merge that actually
>>>>>>>>>>>> works.
>>>>>>>>>>>> Faster operations. Version large binaries.  Built-in WAN
>>>>>>>>>>>> optimization
>>>>>>>>>>>> and
>>>>>>>>>>>> the
>>>>>>>>>>>> freedom to use Git, Perforce or both. Make the move to Perforce.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> Gmod-tripal mailing list
>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>
>>>>
>>>
>>>
>>> --
>>> Mara Kim
>>>
>>> Ph.D. Candidate
>>> Computational Biology
>>> Vanderbilt University
>>> Nashville, TN
>>
>>
>> --
>> Mara Kim
>>
>> Ph.D. Candidate
>> Computational Biology
>> Vanderbilt University
>> Nashville, TN
>
>
> --
> Mara Kim
>
> Ph.D. Candidate
> Computational Biology
> Vanderbilt University
> Nashville, TN
>
>


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Re: Fwd: [Gmod-tripal] Release of Tripal v2.0a

Mara Kim-2
I disabled, uninstalled, and renabled and got this message:

$ drush pm-enable tripal_feature
The following extensions will be enabled: tripal_feature
Do you really want to continue? (y/n): y
WD tripal_cv: Materialized view, organism_feature_count, already
exists. Cannot create.
[warning]
tripal_feature was enabled successfully.
                                                              [ok]
tripal_feature defines the following permissions: access chado_feature
content, create chado_feature content, delete chado_feature content,
edit chado_feature content, adminster tripal feature
Materialized view, organism_feature_count, already exists. Cannot
create.
[status]

I then renamed 'organism_feature_count' in 'tripal_mviews' to
'organism_feature_count_old'.  I was unable to find a view named
'organism_feature_count' in either the public or chado schemas.  Going
to the same process, I got the following error:

$ drush pm-enable tripal_feature
The following extensions will be enabled: tripal_feature
Do you really want to continue? (y/n): y
WD php: PDOException: SQLSTATE[23505]: Unique violation: 7 ERROR:
duplicate key value violates unique constraint
[error]
"tripal_mviews_mv_table_key": INSERT INTO tripal_mviews (name,
modulename, mv_table, mv_schema, query, comment) VALUES
(:db_insert_placeholder_0, :db_insert_placeholder_1,
:db_insert_placeholder_2, :db_insert_placeholder_3,
:db_insert_placeholder_4,
:db_insert_placeholder_5); Array
(
)
 in drupal_write_record() (line 7194 of /var/www/html/includes/common.inc).
Cannot modify header information - headers already sent by (output
started at /usr/share/pear/drush/includes/output.inc:38)
[warning]
bootstrap.inc:1217
PDOException: SQLSTATE[23505]: Unique violation: 7 ERROR:  duplicate
key value violates unique constraint "tripal_mviews_mv_table_key":
INSERT INTO tripal_mviews (name, modulename, mv_table, mv_schema,
query, comment) VALUES (:db_insert_placeholder_0,
:db_insert_placeholder_1, :db_insert_placeholder_2,
:db_insert_placeholder_3, :db_insert_placeholder_4,
:db_insert_placeholder_5); Array
(
)
 in drupal_write_record() (line 7194 of /var/www/html/includes/common.inc).
Drush command terminated abnormally due to an unrecoverable error.
                                                              [error]

On Tue, Apr 8, 2014 at 8:04 AM, Stephen Ficklin <[hidden email]> wrote:

> Hi Mara,
>
> When the tripal feature module is enabled it automatically creates the
> organism_feature_count materialized view.  The error message you are seeing
> indicates that the mview was not created.   When you enabled that module did
> you encounter any errors or warnings?    If you disable, uninstall and the
> enable the tripal_feature module it should either give you warning/error
> messages or create the missing mview for you.
>
> Stephen
>
>
> On 4/7/2014 4:56 PM, Mara Kim wrote:
>>
>> Realized that I've been forgetting to add the listserve
>>
>> ---------- Forwarded message ----------
>> From: Mara Kim <[hidden email]>
>> Date: Mon, Apr 7, 2014 at 2:27 PM
>> Subject: Re: [Gmod-tripal] [Gmod-schema] Release of Tripal v2.0a
>> To: Stephen Ficklin <[hidden email]>
>>
>>
>> Hi Stephen,
>>
>> I went ahead and added a 'null' db with db_id=0.  The rest of the fix
>> proceeded without errors, and I no longer see that SQL error.
>>
>> I have now attempted to sync the organisms in the database with
>> Tripal.  I synced them via the Add Organism page (btw, you guys should
>> probably put the message that says "Leave them unchecked to sync all
>> organisms" at the top of the list rather than the bottom.  We had a
>> good laugh when I found the message after about 2 minutes of checking
>>>
>>> 200 boxes XD )
>>
>> The job seemed to complete successfully, but when I tried to access
>> the pages via the "find content" link, the pages generated the
>> following error:
>>
>> PDOException: SQLSTATE[42P01]: Undefined table: 7 ERROR: relation
>> "chado.organism_feature_count" does not exist LINE 1:
>> ..._features,OFC.feature_type,CVT.definition FROM chado.orga... ^:
>> SELECT OFC.num_features,OFC.feature_type,CVT.definition FROM
>> chado.organism_feature_count OFC INNER JOIN chado.cvterm CVT on
>> OFC.cvterm_id = CVT.cvterm_id WHERE organism_id = :organism_id ORDER
>> BY num_features desc ; Array ( [:organism_id] => 202 ) in
>> chado_query() (line 1332
>>
>> of/var/www/html/sites/all/modules/tripal/tripal_core/api/tripal_core.chado_query.api.inc).
>>
>> On Sat, Apr 5, 2014 at 1:34 PM, Mara Kim <[hidden email]> wrote:
>>>
>>> Hi Stephen,
>>>
>>> With a bit of digging, I figured out that the problem is that there is
>>> no entry in chado.db where name='null'.  Should I add such an entry?
>>> There are a few others that look like they may have a similar purpose:
>>>
>>> db_id |       name        |
>>> description                                    | urlprefix | url
>>>
>>> -------+-------------------+----------------------------------------------------------------------------------+-----------+-----
>>>       1 | OBO_REL           |
>>>                                         |           |
>>>       2 | _global           |
>>>                                         |           |
>>>       3 | internal          |
>>>                                         |           |
>>> plus many others...
>>>
>>> On Sat, Apr 5, 2014 at 11:18 AM, Mara Kim <[hidden email]>
>>> wrote:
>>>>
>>>> Hi Stephen,
>>>>
>>>> I made a few modifications to the code so that I could run it directly
>>>> on my drupal database.  Here is my updated version:
>>>>
>>>> BEGIN;
>>>> insert into chado.cv (name,definition) values
>>>> ('chado_properties','Terms that are used in the chadoprop table to
>>>> describe the state of the database');
>>>> insert into chado.dbxref (db_id,accession) values ((select db_id from
>>>> chado.db where name='null'), 'chado_properties:version');
>>>> insert into chado.cvterm (name,definition,cv_id,dbxref_id) values
>>>> ('version','Chado schema version',(select cv_id from chado.cv where
>>>> name = 'chado_properties'),(select dbxref_id from chado.dbxref where
>>>> accession='chado_properties:version'));
>>>> INSERT INTO chado.chadoprop (type_id, value) VALUES (
>>>>         (SELECT cvterm_id
>>>>          FROM chado.cvterm CVT
>>>>            INNER JOIN chado.cv CV on CVT.cv_id = CV.cv_id
>>>>           WHERE CV.name = 'chado_properties' AND CVT.name = 'version'),
>>>>         '1.23');
>>>> COMMIT;
>>>>
>>>> Summary of changes:
>>>> -Transactionalize
>>>> -Qualify table names with chado.* schema
>>>> -Remove curly braces around table names in final insert statement
>>>> -Version number 1.2 -> 1.23 (note that there is no dot between the 2 &
>>>> 3--is this alright?)
>>>>
>>>> However, I am still getting some errors related to dbxref_id, which
>>>> I'm not entirely sure how to fix:
>>>>
>>>> BEGIN
>>>> INSERT 0 1
>>>> psql:makeprepdb:3: ERROR:  null value in column "db_id" violates
>>>> not-null constraint
>>>> psql:makeprepdb:4: ERROR:  current transaction is aborted, commands
>>>> ignored until end of transaction block
>>>> psql:makeprepdb:10: ERROR:  current transaction is aborted, commands
>>>> ignored until end of transaction block
>>>> ROLLBACK
>>>>
>>>> On Fri, Apr 4, 2014 at 11:42 PM, Stephen Ficklin <[hidden email]>
>>>> wrote:
>>>>>
>>>>> Hi Mara,
>>>>>
>>>>> I believe the 'make prepdb' command adds a record to the chadoprop
>>>>> table
>>>>> inserting the version number of Chado.  Somehow during install of Chado
>>>>> that
>>>>> record is added.  This is the way that Tripal is able to tell what
>>>>> version
>>>>> of Chado you are using so it can deal with the tables correctly.   The
>>>>> 'make
>>>>> prepdb' also adds a vocabulary to the cv table called
>>>>> 'chado_properties'
>>>>> which has the term 'version' and it is that term that is used in the
>>>>> chadoprop table.   So, since the chadoprop table is missing the version
>>>>> record, Tripal is giving that error message.  It should be a bit more
>>>>> tolerant of that so we'll see what we can do to fix that, but really
>>>>> Tripal
>>>>> has to know what version of Chado you are using.  So you'll need to
>>>>> have
>>>>> that record in the chadoprop table.  Here's some SQL code for a quick
>>>>> fix:
>>>>>
>>>>> insert into cv (name,definition) values ('chado_properties','Terms that
>>>>> are
>>>>> used in the chadoprop table to describe the state of the database');
>>>>> insert into dbxref (db_id,accession) values ((select db_id from db
>>>>> where
>>>>> name='null'), 'chado_properties:version');
>>>>> insert into cvterm (name,definition,cv_id,dbxref_id) values
>>>>> ('version','Chado schema version',(select cv_id from cv where name =
>>>>> 'chado_properties'),(select dbxref_id from dbxref where
>>>>> accession='chado_properties:version'));
>>>>> INSERT INTO {chadoprop} (type_id, value) VALUES (
>>>>>         (SELECT cvterm_id
>>>>>          FROM {cvterm} CVT
>>>>>            INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
>>>>>           WHERE CV.name = 'chado_properties' AND CVT.name = 'version'),
>>>>>         '1.2')
>>>>>
>>>>> The '1.2' in the SQL statement above should be changed to the version
>>>>> you
>>>>> are using.   You can just leave 1.2 if the version is 1.2.x as the
>>>>> third
>>>>> number just signifies changes to perl code and not to the database
>>>>> schema.
>>>>>
>>>>> Stephen
>>>>>
>>>>>
>>>>> On 4/5/2014 12:23 AM, Mara Kim wrote:
>>>>>>
>>>>>> There is nothing in the chadoprop table.
>>>>>>
>>>>>> I assume you are asking about installing Chado before the migration.
>>>>>> I used the included makefile, which I think calls the perl scripts.
>>>>>> However, I don't think I ran the `make prepdb` command.
>>>>>>
>>>>>> On Fri, Apr 4, 2014 at 4:05 PM, Stephen Ficklin <[hidden email]>
>>>>>> wrote:
>>>>>>>
>>>>>>> That's an interesting message.   Is there anything in the 'chadoprop'
>>>>>>> table?
>>>>>>> When installing Chado did you use the Perl scripts?  If so, did you
>>>>>>> run
>>>>>>> the
>>>>>>> 'make prepdb' command?
>>>>>>>
>>>>>>> Stephen
>>>>>>>
>>>>>>>
>>>>>>> On 4/4/2014 4:11 PM, Mara Kim wrote:
>>>>>>>>
>>>>>>>> Hi Stephen,
>>>>>>>>
>>>>>>>> I changed the permissions, and that solved the problem with enabling
>>>>>>>> the views.  However, I now get this error on the web page:
>>>>>>>>
>>>>>>>> Notice: Trying to get property of non-object in chado_get_version()
>>>>>>>> (line 217
>>>>>>>>
>>>>>>>>
>>>>>>>> of/var/www/html/sites/all/modules/tripal/tripal_core/api/tripal_core.chado_schema.api.inc).
>>>>>>>> Notice: Trying to get property of non-object in chado_get_version()
>>>>>>>> (line 217
>>>>>>>>
>>>>>>>>
>>>>>>>> of/var/www/html/sites/all/modules/tripal/tripal_core/api/tripal_core.chado_schema.api.inc).
>>>>>>>>
>>>>>>>> On Wed, Apr 2, 2014 at 10:10 PM, Stephen Ficklin
>>>>>>>> <[hidden email]>
>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>> Hey Mara,
>>>>>>>>>
>>>>>>>>> Just curious if you got this issue resolved?
>>>>>>>>>
>>>>>>>>> Stephen
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 4/1/2014 11:43 AM, Mara Kim wrote:
>>>>>>>>>>
>>>>>>>>>> Hi guys,
>>>>>>>>>>
>>>>>>>>>> I am having trouble getting Tripal 2.0a to recognize the Chado
>>>>>>>>>> schema
>>>>>>>>>> that has been migrated in using the method described here:
>>>>>>>>>> http://tripal.info/documentation/migrate_chado
>>>>>>>>>>
>>>>>>>>>> I realize these instructions are for Tripal 1.0, but seeing as how
>>>>>>>>>> I
>>>>>>>>>> needed to import this data anyways, I figured I'd give it a shot.
>>>>>>>>>> I
>>>>>>>>>> run into issues when I try to enable the Tripal modules.  For
>>>>>>>>>> example:
>>>>>>>>>>
>>>>>>>>>> BEGIN EXECUTION TRACE
>>>>>>>>>> $ drush pm-enable tripal_views
>>>>>>>>>> Module tripal_views doesn't meet the requirements to be enabled.
>>>>>>>>>>
>>>>>>>>>> [error]
>>>>>>>>>>      (Currently using tripal_views ERROR: Chado must be installed
>>>>>>>>>> before
>>>>>>>>>> this module can be enabled)
>>>>>>>>>> [error]
>>>>>>>>>> END EXECUTION TRACE
>>>>>>>>>>
>>>>>>>>>> It seems that Tripal isn't recognizing the migrated chado
>>>>>>>>>> database.
>>>>>>>>>> Any suggestions on how to fix this?
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Thu, Mar 6, 2014 at 2:21 PM, Stephen Ficklin
>>>>>>>>>> <[hidden email]>
>>>>>>>>>> wrote:
>>>>>>>>>>>
>>>>>>>>>>> Hi Mara,
>>>>>>>>>>>
>>>>>>>>>>> Tripal stores blast results in the analysisfeatureprop table.  A
>>>>>>>>>>> blast
>>>>>>>>>>> analysis is first added to the analysis table, and the Tripal
>>>>>>>>>>> Blast
>>>>>>>>>>> Analysis
>>>>>>>>>>> extension module parses the blast XML file, identifies a matching
>>>>>>>>>>> feature
>>>>>>>>>>> in
>>>>>>>>>>> the 'feature' table, and adds the link in the featureanalysis
>>>>>>>>>>> table
>>>>>>>>>>> between
>>>>>>>>>>> the analysis and the feature.  Then details of the blast match
>>>>>>>>>>> are
>>>>>>>>>>> added
>>>>>>>>>>> to
>>>>>>>>>>> the analysisfeatureprop table.   But, what gets stored is the
>>>>>>>>>>> actual
>>>>>>>>>>> XML
>>>>>>>>>>> from the blast output detailing all of the matches for that
>>>>>>>>>>> query.
>>>>>>>>>>> When
>>>>>>>>>>> the Tripal Blast module displays blast results, it retrieves the
>>>>>>>>>>> XML,
>>>>>>>>>>> parses
>>>>>>>>>>> it, passes it into an array and then passes that array into the
>>>>>>>>>>> tripal_feature_blast_restults.tpl.php template for display, thus
>>>>>>>>>>> allowing
>>>>>>>>>>> anyone to customize the way blast results are presented.
>>>>>>>>>>>
>>>>>>>>>>> Originally, we wanted to store all of the details about a match
>>>>>>>>>>> directly
>>>>>>>>>>> in
>>>>>>>>>>> the analysisfeatureprop table such that the different details
>>>>>>>>>>> about a
>>>>>>>>>>> match
>>>>>>>>>>> were entered as separate records.  The goal was to allow us to
>>>>>>>>>>> then
>>>>>>>>>>> search
>>>>>>>>>>> matches by things like match name, accession, e-value, etc.  But,
>>>>>>>>>>> there
>>>>>>>>>>> is
>>>>>>>>>>> not an easy way to distinguish between values that belong to one
>>>>>>>>>>> match
>>>>>>>>>>> and
>>>>>>>>>>> a different match using the analysisfeatureprop table.   So, to
>>>>>>>>>>> compromise,
>>>>>>>>>>> the module stores the XML directly into the analysisfeatureprop
>>>>>>>>>>> table
>>>>>>>>>>> and
>>>>>>>>>>> maintains a custom table named 'blast_hit_data' to allow for
>>>>>>>>>>> searching
>>>>>>>>>>> of
>>>>>>>>>>> blast results.   That blast_hit_data table is integrated with
>>>>>>>>>>> Drupal
>>>>>>>>>>> Views
>>>>>>>>>>> (just like any other Chado table) so you can create Drupal Views
>>>>>>>>>>> that
>>>>>>>>>>> can
>>>>>>>>>>> be
>>>>>>>>>>> used for searching the results.  This is how blast results are
>>>>>>>>>>> searching
>>>>>>>>>>> on
>>>>>>>>>>> sites like CottonGen and GDR.
>>>>>>>>>>>
>>>>>>>>>>> Stephen
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On 3/6/2014 2:57 PM, Mara Kim wrote:
>>>>>>>>>>>>
>>>>>>>>>>>> Hi guys,
>>>>>>>>>>>>
>>>>>>>>>>>> I was wondering how you guys store BLAST results in Chado for
>>>>>>>>>>>> Tripal.
>>>>>>>>>>>> I have my own way of doing it, but obviously it would be much
>>>>>>>>>>>> better
>>>>>>>>>>>> if I followed your convention.  Specifically, what cvterms do
>>>>>>>>>>>> you
>>>>>>>>>>>> use
>>>>>>>>>>>> to name BLAST hits and hsps, and what rows does Tripal expect in
>>>>>>>>>>>> what
>>>>>>>>>>>> tables?
>>>>>>>>>>>>
>>>>>>>>>>>> Sorry if you are getting this twice.  My first message bounced
>>>>>>>>>>>> from
>>>>>>>>>>>> the mailing list because I used the wrong address.
>>>>>>>>>>>>
>>>>>>>>>>>> On Tue, Mar 4, 2014 at 7:03 PM, Lacey-Anne Sanderson
>>>>>>>>>>>> <[hidden email]> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Mara,
>>>>>>>>>>>>>
>>>>>>>>>>>>> That is unfortunately as it should be at this point. Work is
>>>>>>>>>>>>> ongoing
>>>>>>>>>>>>> on
>>>>>>>>>>>>> porting the other extension modules (including the ones in my
>>>>>>>>>>>>> sandbox
>>>>>>>>>>>>> :)
>>>>>>>>>>>>> )
>>>>>>>>>>>>> to Drupal 7 and so hopefully these will be available soon! We
>>>>>>>>>>>>> will
>>>>>>>>>>>>> keep
>>>>>>>>>>>>> you
>>>>>>>>>>>>> posted!
>>>>>>>>>>>>>
>>>>>>>>>>>>> ~Lacey
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Mar 4, 2014, at 4:37 PM, Mara Kim <[hidden email]>
>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>> Hmm, it seems that all the repositories (except the main Tripal
>>>>>>>>>>>>> repository and the tripal_blast_analysis repository) lack the
>>>>>>>>>>>>> appropriate tags as I get similar errors.  This is in reference
>>>>>>>>>>>>> to
>>>>>>>>>>>>> these instructions:
>>>>>>>>>>>>>
>>>>>>>>>>>>> http://www.gmod.org/wiki/Tripal_Tutorial_v2.0#Tripal_Installation
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Tue, Mar 4, 2014 at 4:35 PM, Mara Kim <[hidden email]>
>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>> More updates:
>>>>>>>>>>>>>
>>>>>>>>>>>>> The repository
>>>>>>>>>>>>> http://git.drupal.org/sandbox/spficklin/1578234.git
>>>>>>>>>>>>> does not have the tag 7.x-2.0a-tripal_v2.0a
>>>>>>>>>>>>>
>>>>>>>>>>>>> Here is the specific error:
>>>>>>>>>>>>>
>>>>>>>>>>>>> (My fancy git aware bash prompt)
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> kimmm@rokasgate:/var/www/html/sites/all/modules/tripal_kegg_analysis
>>>>>>>>>>>>> (0)
>>>>>>>>>>>>> d12b127c2cbf59b5e380cffb37cc5ac79a411a5f
>>>>>>>>>>>>> ## 6.x-1.x
>>>>>>>>>>>>> $ git checkout 7.x-2.0a-tripal_v2.0a
>>>>>>>>>>>>>
>>>>>>>>>>>>> BEGIN EXECUTION TRACE
>>>>>>>>>>>>> error: pathspec '7.x-2.0a-tripal_v2.0a' did not match any
>>>>>>>>>>>>> file(s)
>>>>>>>>>>>>> known
>>>>>>>>>>>>> to
>>>>>>>>>>>>> git.
>>>>>>>>>>>>> END EXECUTION TRACE
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Tue, Mar 4, 2014 at 4:29 PM, Mara Kim <[hidden email]>
>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Stephen,
>>>>>>>>>>>>>
>>>>>>>>>>>>> I am currently in the process of installing Tripal 2a.  One
>>>>>>>>>>>>> thing
>>>>>>>>>>>>> of
>>>>>>>>>>>>> note
>>>>>>>>>>>>> I've run across so far is that CKeditor no longer provides
>>>>>>>>>>>>> include/exclude
>>>>>>>>>>>>> options (https://drupal.org/node/1018920).  Do you have
>>>>>>>>>>>>> alternative
>>>>>>>>>>>>> instructions?
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Mon, Feb 24, 2014 at 4:29 PM, Stephen Ficklin
>>>>>>>>>>>>> <[hidden email]>
>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Dear Tripal and Chado users,
>>>>>>>>>>>>>
>>>>>>>>>>>>> The Tripal Development Team is pleased to announce an alpha
>>>>>>>>>>>>> release
>>>>>>>>>>>>> of
>>>>>>>>>>>>> Tripal 2.0 for Drupal 7.
>>>>>>>>>>>>>
>>>>>>>>>>>>> This release is expected to have bugs and there is some
>>>>>>>>>>>>> functionality
>>>>>>>>>>>>> still under development.  However, this release is made to help
>>>>>>>>>>>>> early
>>>>>>>>>>>>> adopters of Tripal for Drupal 7.   Reports of bugs or other
>>>>>>>>>>>>> issues
>>>>>>>>>>>>> are
>>>>>>>>>>>>> highly welcomed.   Below are available resources for Tripal
>>>>>>>>>>>>> 2.0a
>>>>>>>>>>>>>
>>>>>>>>>>>>> * Download Instructions:
>>>>>>>>>>>>> http://tripal.info/documentation/download_tripal_v2.0a
>>>>>>>>>>>>> * Installation and Tutorial:
>>>>>>>>>>>>> http://www.gmod.org/wiki/Tripal_Tutorial_v2.0
>>>>>>>>>>>>> * Tripal 2.0 API site: http://api.tripal.info/api/tripal/2.x
>>>>>>>>>>>>> * Tripal Mailing List:
>>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>>>>>>>>> * Tripal Developer's Mailing List:
>>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>>>>>>>>>>>>
>>>>>>>>>>>>> The Installation tutorial is still under development but should
>>>>>>>>>>>>> have
>>>>>>>>>>>>> enough information for complete installation of Tripal v2.0a as
>>>>>>>>>>>>> well
>>>>>>>>>>>>> as
>>>>>>>>>>>>> loading of organisms and features.   The tutorial will be
>>>>>>>>>>>>> completed
>>>>>>>>>>>>> before the stable release of Tripal 2.0.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Regards,
>>>>>>>>>>>>> Stephen
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>>>>> Flow-based real-time traffic analytics software. Cisco
>>>>>>>>>>>>> certified
>>>>>>>>>>>>> tool.
>>>>>>>>>>>>> Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow
>>>>>>>>>>>>> Analyzer
>>>>>>>>>>>>> Customize your own dashboards, set traffic alerts and generate
>>>>>>>>>>>>> reports.
>>>>>>>>>>>>> Network behavioral analysis & security monitoring. All-in-one
>>>>>>>>>>>>> tool.
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> Gmod-schema mailing list
>>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> --
>>>>>>>>>>>>> Mara Kim
>>>>>>>>>>>>>
>>>>>>>>>>>>> Ph.D. Candidate
>>>>>>>>>>>>> Computational Biology
>>>>>>>>>>>>> Vanderbilt University
>>>>>>>>>>>>> Nashville, TN
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> --
>>>>>>>>>>>>> Mara Kim
>>>>>>>>>>>>>
>>>>>>>>>>>>> Ph.D. Candidate
>>>>>>>>>>>>> Computational Biology
>>>>>>>>>>>>> Vanderbilt University
>>>>>>>>>>>>> Nashville, TN
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> --
>>>>>>>>>>>>> Mara Kim
>>>>>>>>>>>>>
>>>>>>>>>>>>> Ph.D. Candidate
>>>>>>>>>>>>> Computational Biology
>>>>>>>>>>>>> Vanderbilt University
>>>>>>>>>>>>> Nashville, TN
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>>>>> Subversion Kills Productivity. Get off Subversion & Make the
>>>>>>>>>>>>> Move
>>>>>>>>>>>>> to
>>>>>>>>>>>>> Perforce.
>>>>>>>>>>>>> With Perforce, you get hassle-free workflows. Merge that
>>>>>>>>>>>>> actually
>>>>>>>>>>>>> works.
>>>>>>>>>>>>> Faster operations. Version large binaries.  Built-in WAN
>>>>>>>>>>>>> optimization
>>>>>>>>>>>>> and
>>>>>>>>>>>>> the
>>>>>>>>>>>>> freedom to use Git, Perforce or both. Make the move to
>>>>>>>>>>>>> Perforce.
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> Gmod-tripal mailing list
>>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Mara Kim
>>>>
>>>> Ph.D. Candidate
>>>> Computational Biology
>>>> Vanderbilt University
>>>> Nashville, TN
>>>
>>>
>>>
>>> --
>>> Mara Kim
>>>
>>> Ph.D. Candidate
>>> Computational Biology
>>> Vanderbilt University
>>> Nashville, TN
>>
>>
>>
>> --
>> Mara Kim
>>
>> Ph.D. Candidate
>> Computational Biology
>> Vanderbilt University
>> Nashville, TN
>>
>>
>
>



--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN


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Re: [Gmod-tripal] Release of Tripal v2.0a

Kucheran, Lacey Sanderson
Hi Stephen,

Something that may help debug this error. I just noticed that if I try to add a custom table (Mara: all views in Tripal are just a special case of custom table including the organism_feature_count view) through the user interface (admin/tripal/schema/custom_tables/new) I get the following error:
Could not add custom table. SQLSTATE[42P07]: Duplicate table: 7 ERROR: relation "project_organism_feature_count_project_organism_feature_count_i" already exists.

This is weird since I know for a fact that it didn't exist prior to me clicking "Add" on that form, yet afterwards, it does exist. Maybe there's a bug in the custom table code that attempts to create the table 2X?

~Lacey

PS. Also, that table I'm trying to add is project_organism_feature_count NOT project_organism_feature_count_project_organism_feature_count_i
------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-4975
Room 3C06 Agriculture
Department of Plant Sciences
University of Saskatchewan

On Apr 8, 2014, at 1:51 PM, Mara Kim <[hidden email]> wrote:

I disabled, uninstalled, and renabled and got this message:

$ drush pm-enable tripal_feature
The following extensions will be enabled: tripal_feature
Do you really want to continue? (y/n): y
WD tripal_cv: Materialized view, organism_feature_count, already
exists. Cannot create.
[warning]
tripal_feature was enabled successfully.
                                                             [ok]
tripal_feature defines the following permissions: access chado_feature
content, create chado_feature content, delete chado_feature content,
edit chado_feature content, adminster tripal feature
Materialized view, organism_feature_count, already exists. Cannot
create.
[status]

I then renamed 'organism_feature_count' in 'tripal_mviews' to
'organism_feature_count_old'.  I was unable to find a view named
'organism_feature_count' in either the public or chado schemas.  Going
to the same process, I got the following error:

$ drush pm-enable tripal_feature
The following extensions will be enabled: tripal_feature
Do you really want to continue? (y/n): y
WD php: PDOException: SQLSTATE[23505]: Unique violation: 7 ERROR:
duplicate key value violates unique constraint
[error]
"tripal_mviews_mv_table_key": INSERT INTO tripal_mviews (name,
modulename, mv_table, mv_schema, query, comment) VALUES
(:db_insert_placeholder_0, :db_insert_placeholder_1,
:db_insert_placeholder_2, :db_insert_placeholder_3,
:db_insert_placeholder_4,
:db_insert_placeholder_5); Array
(
)
in drupal_write_record() (line 7194 of /var/www/html/includes/common.inc).
Cannot modify header information - headers already sent by (output
started at /usr/share/pear/drush/includes/output.inc:38)
[warning]
bootstrap.inc:1217
PDOException: SQLSTATE[23505]: Unique violation: 7 ERROR:  duplicate
key value violates unique constraint "tripal_mviews_mv_table_key":
INSERT INTO tripal_mviews (name, modulename, mv_table, mv_schema,
query, comment) VALUES (:db_insert_placeholder_0,
:db_insert_placeholder_1, :db_insert_placeholder_2,
:db_insert_placeholder_3, :db_insert_placeholder_4,
:db_insert_placeholder_5); Array
(
)
in drupal_write_record() (line 7194 of /var/www/html/includes/common.inc).
Drush command terminated abnormally due to an unrecoverable error.
                                                             [error]

On Tue, Apr 8, 2014 at 8:04 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Mara,

When the tripal feature module is enabled it automatically creates the
organism_feature_count materialized view.  The error message you are seeing
indicates that the mview was not created.   When you enabled that module did
you encounter any errors or warnings?    If you disable, uninstall and the
enable the tripal_feature module it should either give you warning/error
messages or create the missing mview for you.

Stephen


On 4/7/2014 4:56 PM, Mara Kim wrote:

Realized that I've been forgetting to add the listserve

---------- Forwarded message ----------
From: Mara Kim <[hidden email]>
Date: Mon, Apr 7, 2014 at 2:27 PM
Subject: Re: [Gmod-tripal] [Gmod-schema] Release of Tripal v2.0a
To: Stephen Ficklin <[hidden email]>


Hi Stephen,

I went ahead and added a 'null' db with db_id=0.  The rest of the fix
proceeded without errors, and I no longer see that SQL error.

I have now attempted to sync the organisms in the database with
Tripal.  I synced them via the Add Organism page (btw, you guys should
probably put the message that says "Leave them unchecked to sync all
organisms" at the top of the list rather than the bottom.  We had a
good laugh when I found the message after about 2 minutes of checking

200 boxes XD )

The job seemed to complete successfully, but when I tried to access
the pages via the "find content" link, the pages generated the
following error:

PDOException: SQLSTATE[42P01]: Undefined table: 7 ERROR: relation
"chado.organism_feature_count" does not exist LINE 1:
..._features,OFC.feature_type,CVT.definition FROM chado.orga... ^:
SELECT OFC.num_features,OFC.feature_type,CVT.definition FROM
chado.organism_feature_count OFC INNER JOIN chado.cvterm CVT on
OFC.cvterm_id = CVT.cvterm_id WHERE organism_id = :organism_id ORDER
BY num_features desc ; Array ( [:organism_id] => 202 ) in
chado_query() (line 1332

of/var/www/html/sites/all/modules/tripal/tripal_core/api/tripal_core.chado_query.api.inc).

On Sat, Apr 5, 2014 at 1:34 PM, Mara Kim <[hidden email]> wrote:

Hi Stephen,

With a bit of digging, I figured out that the problem is that there is
no entry in chado.db where name='null'.  Should I add such an entry?
There are a few others that look like they may have a similar purpose:

db_id |       name        |
description                                    | urlprefix | url

-------+-------------------+----------------------------------------------------------------------------------+-----------+-----
     1 | OBO_REL           |
                                       |           |
     2 | _global           |
                                       |           |
     3 | internal          |
                                       |           |
plus many others...

On Sat, Apr 5, 2014 at 11:18 AM, Mara Kim <[hidden email]>
wrote:

Hi Stephen,

I made a few modifications to the code so that I could run it directly
on my drupal database.  Here is my updated version:

BEGIN;
insert into chado.cv (name,definition) values
('chado_properties','Terms that are used in the chadoprop table to
describe the state of the database');
insert into chado.dbxref (db_id,accession) values ((select db_id from
chado.db where name='null'), 'chado_properties:version');
insert into chado.cvterm (name,definition,cv_id,dbxref_id) values
('version','Chado schema version',(select cv_id from chado.cv where
name = 'chado_properties'),(select dbxref_id from chado.dbxref where
accession='chado_properties:version'));
INSERT INTO chado.chadoprop (type_id, value) VALUES (
       (SELECT cvterm_id
        FROM chado.cvterm CVT
          INNER JOIN chado.cv CV on CVT.cv_id = CV.cv_id
         WHERE CV.name = 'chado_properties' AND CVT.name = 'version'),
       '1.23');
COMMIT;

Summary of changes:
-Transactionalize
-Qualify table names with chado.* schema
-Remove curly braces around table names in final insert statement
-Version number 1.2 -> 1.23 (note that there is no dot between the 2 &
3--is this alright?)

However, I am still getting some errors related to dbxref_id, which
I'm not entirely sure how to fix:

BEGIN
INSERT 0 1
psql:makeprepdb:3: ERROR:  null value in column "db_id" violates
not-null constraint
psql:makeprepdb:4: ERROR:  current transaction is aborted, commands
ignored until end of transaction block
psql:makeprepdb:10: ERROR:  current transaction is aborted, commands
ignored until end of transaction block
ROLLBACK

On Fri, Apr 4, 2014 at 11:42 PM, Stephen Ficklin <[hidden email]>
wrote:

Hi Mara,

I believe the 'make prepdb' command adds a record to the chadoprop
table
inserting the version number of Chado.  Somehow during install of Chado
that
record is added.  This is the way that Tripal is able to tell what
version
of Chado you are using so it can deal with the tables correctly.   The
'make
prepdb' also adds a vocabulary to the cv table called
'chado_properties'
which has the term 'version' and it is that term that is used in the
chadoprop table.   So, since the chadoprop table is missing the version
record, Tripal is giving that error message.  It should be a bit more
tolerant of that so we'll see what we can do to fix that, but really
Tripal
has to know what version of Chado you are using.  So you'll need to
have
that record in the chadoprop table.  Here's some SQL code for a quick
fix:

insert into cv (name,definition) values ('chado_properties','Terms that
are
used in the chadoprop table to describe the state of the database');
insert into dbxref (db_id,accession) values ((select db_id from db
where
name='null'), 'chado_properties:version');
insert into cvterm (name,definition,cv_id,dbxref_id) values
('version','Chado schema version',(select cv_id from cv where name =
'chado_properties'),(select dbxref_id from dbxref where
accession='chado_properties:version'));
INSERT INTO {chadoprop} (type_id, value) VALUES (
       (SELECT cvterm_id
        FROM {cvterm} CVT
          INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
         WHERE CV.name = 'chado_properties' AND CVT.name = 'version'),
       '1.2')

The '1.2' in the SQL statement above should be changed to the version
you
are using.   You can just leave 1.2 if the version is 1.2.x as the
third
number just signifies changes to perl code and not to the database
schema.

Stephen


On 4/5/2014 12:23 AM, Mara Kim wrote:

There is nothing in the chadoprop table.

I assume you are asking about installing Chado before the migration.
I used the included makefile, which I think calls the perl scripts.
However, I don't think I ran the `make prepdb` command.

On Fri, Apr 4, 2014 at 4:05 PM, Stephen Ficklin <[hidden email]>
wrote:

That's an interesting message.   Is there anything in the 'chadoprop'
table?
When installing Chado did you use the Perl scripts?  If so, did you
run
the
'make prepdb' command?

Stephen


On 4/4/2014 4:11 PM, Mara Kim wrote:

Hi Stephen,

I changed the permissions, and that solved the problem with enabling
the views.  However, I now get this error on the web page:

Notice: Trying to get property of non-object in chado_get_version()
(line 217


of/var/www/html/sites/all/modules/tripal/tripal_core/api/tripal_core.chado_schema.api.inc).
Notice: Trying to get property of non-object in chado_get_version()
(line 217


of/var/www/html/sites/all/modules/tripal/tripal_core/api/tripal_core.chado_schema.api.inc).

On Wed, Apr 2, 2014 at 10:10 PM, Stephen Ficklin
<[hidden email]>
wrote:

Hey Mara,

Just curious if you got this issue resolved?

Stephen


On 4/1/2014 11:43 AM, Mara Kim wrote:

Hi guys,

I am having trouble getting Tripal 2.0a to recognize the Chado
schema
that has been migrated in using the method described here:
http://tripal.info/documentation/migrate_chado

I realize these instructions are for Tripal 1.0, but seeing as how
I
needed to import this data anyways, I figured I'd give it a shot.
I
run into issues when I try to enable the Tripal modules.  For
example:

BEGIN EXECUTION TRACE
$ drush pm-enable tripal_views
Module tripal_views doesn't meet the requirements to be enabled.

[error]
    (Currently using tripal_views ERROR: Chado must be installed
before
this module can be enabled)
[error]
END EXECUTION TRACE

It seems that Tripal isn't recognizing the migrated chado
database.
Any suggestions on how to fix this?


On Thu, Mar 6, 2014 at 2:21 PM, Stephen Ficklin
<[hidden email]>
wrote:

Hi Mara,

Tripal stores blast results in the analysisfeatureprop table.  A
blast
analysis is first added to the analysis table, and the Tripal
Blast
Analysis
extension module parses the blast XML file, identifies a matching
feature
in
the 'feature' table, and adds the link in the featureanalysis
table
between
the analysis and the feature.  Then details of the blast match
are
added
to
the analysisfeatureprop table.   But, what gets stored is the
actual
XML
from the blast output detailing all of the matches for that
query.
When
the Tripal Blast module displays blast results, it retrieves the
XML,
parses
it, passes it into an array and then passes that array into the
tripal_feature_blast_restults.tpl.php template for display, thus
allowing
anyone to customize the way blast results are presented.

Originally, we wanted to store all of the details about a match
directly
in
the analysisfeatureprop table such that the different details
about a
match
were entered as separate records.  The goal was to allow us to
then
search
matches by things like match name, accession, e-value, etc.  But,
there
is
not an easy way to distinguish between values that belong to one
match
and
a different match using the analysisfeatureprop table.   So, to
compromise,
the module stores the XML directly into the analysisfeatureprop
table
and
maintains a custom table named 'blast_hit_data' to allow for
searching
of
blast results.   That blast_hit_data table is integrated with
Drupal
Views
(just like any other Chado table) so you can create Drupal Views
that
can
be
used for searching the results.  This is how blast results are
searching
on
sites like CottonGen and GDR.

Stephen


On 3/6/2014 2:57 PM, Mara Kim wrote:

Hi guys,

I was wondering how you guys store BLAST results in Chado for
Tripal.
I have my own way of doing it, but obviously it would be much
better
if I followed your convention.  Specifically, what cvterms do
you
use
to name BLAST hits and hsps, and what rows does Tripal expect in
what
tables?

Sorry if you are getting this twice.  My first message bounced
from
the mailing list because I used the wrong address.

On Tue, Mar 4, 2014 at 7:03 PM, Lacey-Anne Sanderson
<[hidden email]> wrote:

Hi Mara,

That is unfortunately as it should be at this point. Work is
ongoing
on
porting the other extension modules (including the ones in my
sandbox
:)
)
to Drupal 7 and so hopefully these will be available soon! We
will
keep
you
posted!

~Lacey

On Mar 4, 2014, at 4:37 PM, Mara Kim <[hidden email]>
wrote:

Hmm, it seems that all the repositories (except the main Tripal
repository and the tripal_blast_analysis repository) lack the
appropriate tags as I get similar errors.  This is in reference
to
these instructions:

http://www.gmod.org/wiki/Tripal_Tutorial_v2.0#Tripal_Installation

On Tue, Mar 4, 2014 at 4:35 PM, Mara Kim <[hidden email]>
wrote:

More updates:

The repository
http://git.drupal.org/sandbox/spficklin/1578234.git
does not have the tag 7.x-2.0a-tripal_v2.0a

Here is the specific error:

(My fancy git aware bash prompt)


kimmm@rokasgate:/var/www/html/sites/all/modules/tripal_kegg_analysis
(0)
d12b127c2cbf59b5e380cffb37cc5ac79a411a5f
## 6.x-1.x
$ git checkout 7.x-2.0a-tripal_v2.0a

BEGIN EXECUTION TRACE
error: pathspec '7.x-2.0a-tripal_v2.0a' did not match any
file(s)
known
to
git.
END EXECUTION TRACE

On Tue, Mar 4, 2014 at 4:29 PM, Mara Kim <[hidden email]>
wrote:

Hi Stephen,

I am currently in the process of installing Tripal 2a.  One
thing
of
note
I've run across so far is that CKeditor no longer provides
include/exclude
options (https://drupal.org/node/1018920).  Do you have
alternative
instructions?


On Mon, Feb 24, 2014 at 4:29 PM, Stephen Ficklin
<[hidden email]>
wrote:


Dear Tripal and Chado users,

The Tripal Development Team is pleased to announce an alpha
release
of
Tripal 2.0 for Drupal 7.

This release is expected to have bugs and there is some
functionality
still under development.  However, this release is made to help
early
adopters of Tripal for Drupal 7.   Reports of bugs or other
issues
are
highly welcomed.   Below are available resources for Tripal
2.0a

* Download Instructions:
http://tripal.info/documentation/download_tripal_v2.0a
* Installation and Tutorial:
http://www.gmod.org/wiki/Tripal_Tutorial_v2.0
* Tripal 2.0 API site: http://api.tripal.info/api/tripal/2.x
* Tripal Mailing List:
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
* Tripal Developer's Mailing List:
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel

The Installation tutorial is still under development but should
have
enough information for complete installation of Tripal v2.0a as
well
as
loading of organisms and features.   The tutorial will be
completed
before the stable release of Tripal 2.0.

Regards,
Stephen









------------------------------------------------------------------------------
Flow-based real-time traffic analytics software. Cisco
certified
tool.
Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow
Analyzer
Customize your own dashboards, set traffic alerts and generate
reports.
Network behavioral analysis & security monitoring. All-in-one
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_______________________________________________
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--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN




--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN




--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN






------------------------------------------------------------------------------
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--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN



--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN



--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN







--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN



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