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Re: [Gmod-tripal-devel] EST_match for unigenes

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Stephen Ficklin-2

Re: [Gmod-tripal-devel] EST_match for unigenes

Hi Tony,

If you get the most recent version of the tripal_theme 6.x-1.x branch
from the development git repository it now contains an update that
resolves the issue with the EST_match that you are having. Let me know
if it works for you.

http://drupal.org/node/1342972/git-instructions/6.x-1.x

Stephen

On 7/10/2012 9:26 AM, Stephen Ficklin wrote:

> Hi Tony,
>
> Good morning. I'm CC'ing the list as your question about the
> EST_match may be helpful for others. The behavior you describe is
> correct for the way the alignments are stored. ESTs are aligned to
> contigs via an 'EST_match' feature in your GFF file. This is because
> an EST does not always overlap completely with the contig depending on
> the software used to do the assembly--only portions of ESTs may
> align. Therefore we use an EST_match feature for the alignment. See
> here for an example: http://gmod.org/wiki/GFF#Alignments
>
> EST --> EST_match <-- Contig
>
> In reality you don't want the site visitors to see the EST_match
> features. But by default Tripal treats all features the same. It
> doesn't know the difference between a gene, mRNA, contig, EST,
> EST_match, etc. So that is why you have links to EST_matches on your
> contig alignments page rather than links to ESTs. So, to get links
> to your ESTs on your contig page and to bypass the EST_match feature
> you need to edit the
> sites/all/themes/tripal_theme/tripal_feature/tripal_feature_featurelocs_as_parent.tpl.php
> to handle that special case. I believe however that I can make that
> adjustment in the template for you in the development code. When it's
> ready I'll let you know.
>
> Stephen
>
>
> On 7/10/2012 5:45 AM, Tony Power wrote:
>> Hi again Stephen,
>>
>> I noticed some strange behavior on the site.
>>
>> For instance:
>> 1-Select the first contig and then select "Alignments".
>> 2-Now select the first EST_match.
>> 3-Now "EST_match Sequence" -> No sequence is shown;
>>
>> 4-Now select "Alignments" (of that EST_match).
>> 5-From the alignments select the EST_match that it aligns to.
>> 6-Select "EST_match Sequence" -> The sequence is shown.
>>
>> What might be the problem?
>>
>> Obrigado,
>>
>>
>

------------------------------------------------------------------------------
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threat landscape has changed and how IT managers can respond. Discussions
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_______________________________________________
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Tony Power

Re: [Gmod-tripal-devel] EST_match for unigenes

Hi Stephen,

Just updated to the new Tripal Theme.
Something is not working properly. To understand what I mean, please,
click on one of the contigs.

Do I also need to update the Tripal module? I just updated the Theme.

Thanks ;)

Tony

On Sat, Jul 14, 2012 at 3:04 AM, Stephen Ficklin <[hidden email]> wrote:

> Hi Tony,
>
> If you get the most recent version of the tripal_theme 6.x-1.x branch from
> the development git repository it now contains an update that resolves the
> issue with the EST_match that you are having. Let me know if it works for
> you.
>
> http://drupal.org/node/1342972/git-instructions/6.x-1.x
>
>
> Stephen
>
>
> On 7/10/2012 9:26 AM, Stephen Ficklin wrote:
>>
>> Hi Tony,
>>
>> Good morning. I'm CC'ing the list as your question about the EST_match
>> may be helpful for others. The behavior you describe is correct for the way
>> the alignments are stored. ESTs are aligned to contigs via an 'EST_match'
>> feature in your GFF file. This is because an EST does not always overlap
>> completely with the contig depending on the software used to do the
>> assembly--only portions of ESTs may align. Therefore we use an EST_match
>> feature for the alignment. See here for an example:
>> http://gmod.org/wiki/GFF#Alignments
>>
>> EST --> EST_match <-- Contig
>>
>> In reality you don't want the site visitors to see the EST_match features.
>> But by default Tripal treats all features the same. It doesn't know the
>> difference between a gene, mRNA, contig, EST, EST_match, etc. So that is
>> why you have links to EST_matches on your contig alignments page rather than
>> links to ESTs. So, to get links to your ESTs on your contig page and to
>> bypass the EST_match feature you need to edit the
>> sites/all/themes/tripal_theme/tripal_feature/tripal_feature_featurelocs_as_parent.tpl.php
>> to handle that special case. I believe however that I can make that
>> adjustment in the template for you in the development code. When it's ready
>> I'll let you know.
>>
>> Stephen
>>
>>
>> On 7/10/2012 5:45 AM, Tony Power wrote:
>>>
>>> Hi again Stephen,
>>>
>>> I noticed some strange behavior on the site.
>>>
>>> For instance:
>>> 1-Select the first contig and then select "Alignments".
>>> 2-Now select the first EST_match.
>>> 3-Now "EST_match Sequence" -> No sequence is shown;
>>>
>>> 4-Now select "Alignments" (of that EST_match).
>>> 5-From the alignments select the EST_match that it aligns to.
>>> 6-Select "EST_match Sequence" -> The sequence is shown.
>>>
>>> What might be the problem?
>>>
>>> Obrigado,
>>>
>>>
>>
>
>

Lacey-Anne Sanderson

Re: [Gmod-tripal-devel] [Gmod-tripal] EST_match for unigenes

Hi Tony,

Yes, the theme and the module are quite closely linked (developed together) so I would suggest always updating the module at the same time as the theme.

~Lacey

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

Lacey-Anne Sanderson

Bioinformaticist

Pulse Crop Breeding and Genetics

Phone: (306) 966-4975

Email: [hidden email]

Room 3C06 Agriculture

Department of Plant Sciences

University of Saskatchewan

On 2012-07-16, at 6:58 AM, Tony Power wrote:

Hi Stephen,

Just updated to the new Tripal Theme.
Something is not working properly. To understand what I mean, please,
click on one of the contigs.

Do I also need to update the Tripal module? I just updated the Theme.

Thanks ;)

Tony

On Sat, Jul 14, 2012 at 3:04 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Tony,

If you get the most recent version of the tripal_theme 6.x-1.x branch from
the development git repository it now contains an update that resolves the
issue with the EST_match that you are having. Let me know if it works for
you.

http://drupal.org/node/1342972/git-instructions/6.x-1.x

Stephen

On 7/10/2012 9:26 AM, Stephen Ficklin wrote:

Hi Tony,

Good morning. I'm CC'ing the list as your question about the EST_match
may be helpful for others. The behavior you describe is correct for the way
the alignments are stored.   ESTs are aligned to contigs via an 'EST_match'
feature in your GFF file.   This is because an EST does not always overlap
completely with the contig depending on the software used to do the
assembly--only portions of ESTs may align. Therefore we use an EST_match
feature for the alignment.   See here for an example:
http://gmod.org/wiki/GFF#Alignments

EST --> EST_match <-- Contig

In reality you don't want the site visitors to see the EST_match features.
But by default Tripal treats all features the same. It doesn't know the
difference between a gene, mRNA, contig, EST, EST_match, etc. So that is
why you have links to EST_matches on your contig alignments page rather than
links to ESTs.   So, to get links to your ESTs on your contig page and to
bypass the EST_match feature you need to edit the
sites/all/themes/tripal_theme/tripal_feature/tripal_feature_featurelocs_as_parent.tpl.php
to handle that special case.   I believe however that I can make that
adjustment in the template for you in the development code. When it's ready
I'll let you know.

Stephen

On 7/10/2012 5:45 AM, Tony Power wrote:

Hi again Stephen,

I noticed some strange behavior on the site.

For instance:
1-Select the first contig and then select "Alignments".
2-Now select the first EST_match.
3-Now "EST_match Sequence" -> No sequence is shown;

4-Now select "Alignments" (of that EST_match).
5-From the alignments select the EST_match that it aligns to.
6-Select "EST_match Sequence" -> The sequence is shown.

What might be the problem?

Obrigado,

------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal

Tony Power

Re: [Gmod-tripal-devel] EST_match for unigenes

In reply to this post by Tony Power

Hi Stephen and Lacey-Anne,

After testing I immediately reset it to 30 secs again. But the result
is the same. 30 or 300 the errors are the same, it just takes longer
to display the (unformatted) webpage.

After trying to Lacey-Anne's suggestion I get the same result.
I have the latest dev branch for the Tripal module (I guess):
# git status
# On branch 6.x-0.4-dev
nothing to commit (working directory clean)

The new Theme version you provided me in a previous email is not
development (could it be this?)
git status
# On branch 6.x-1.x
nothing to commit (working directory clean)

If there is another module version, can I just delete the whole tripal
(module) and replace it by the new?
Where are all the tripal site related configurations saved?

Thanks,
Tony

On Mon, Jul 16, 2012 at 8:30 PM, Stephen Ficklin <[hidden email]> wrote:

> Hi Tony,
>
> I'm having a bit of trouble debugging this one because I'm not having the
> same problem. I was unable to load this feature on your site without it
> taking longer than 30 seconds: http://morse-ccmar.ualg.pt/edge/ID327210.
> Would you mind sending me the snippet of the GFF file that contains that
> contig and EST alignments?
>
> Thanks,
> Stephen
>
>
> On 7/16/2012 12:18 PM, Tony Power wrote:
>>
>> Well, it shouldn't have anything to do with the common.inc error,
>> since even if I restore the old theme I still get that error and the
>> features show well again. So, something should be happening with the
>> new version of your theme (or not) :P.
>>
>> In any case it's a weird error since I don't do any updates for a long
>> time.
>>
>> On Mon, Jul 16, 2012 at 5:10 PM, Tony Power <[hidden email]> wrote:
>>>
>>> Hi Stephen,
>>>
>>> I changed it to 300 and it just stands there waiting.
>>> Nevertheless I can see that it fired many of these errors:
>>> [Mon Jul 16 17:04:26 2012] [error] [client 10.10.228.132] PHP Parse
>>> error: syntax error, unexpected 's' (T_STRING) in
>>> /usr/share/drupal6/includes/common.inc(1731) : eval()'d code on line
>>> 1, referer: http://morse-ccmar.ualg.pt/edge/
>>>
>>> On line 1731 there is the following: print eval('?>'. $code);
>>>
>>> Does that $code variable have anything to do with your theme?
>>>
>>> After the 300 secs, I get:
>>> [Mon Jul 16 17:09:26 2012] [error] [client 10.10.228.132] PHP Fatal
>>> error: Maximum execution time of 300 seconds exceeded in
>>> /usr/share/drupal6/includes/database.inc on line 225, referer:
>>> http://morse-ccmar.ualg.pt/edge/
>>>
>>> Thanks,
>>>
>>> Tony
>>>
>>> On Mon, Jul 16, 2012 at 3:08 PM, Stephen Ficklin <[hidden email]>
>>> wrote:
>>>>
>>>> Hi Tony,
>>>>
>>>> Yes, the problem is the timeout issue. If you go into your php.ini file
>>>> (/etc/php5/apache2/php.ini on my box) and change the max_execution_time
>>>> to
>>>> something larger. However, this page should not take more than 30
>>>> seconds
>>>> to load so we can try to figure out what's going on once the page
>>>> displays.
>>>>
>>>> Stephen
>>>>
>>>>
>>>> On 7/16/2012 9:54 AM, Tony Power wrote:
>>>>>
>>>>> Hi Stephen,
>>>>>
>>>>> In the logs there is nothing about the theme loading. Everything seems
>>>>> to work well.
>>>>> You still have that admin account that allows you to access the logs,
>>>>> just in case you wish to have a look. But you wont find anything :P
>>>>> From the apache log I get:
>>>>> [Mon Jul 16 14:45:52 2012] [error] [client 10.10.228.135] PHP Parse
>>>>> error: syntax error, unexpected 's' (T_STRING) in
>>>>> /usr/share/drupal6/includes/common.inc(1731) : eval()'d code on line
>>>>> 1, referer: http://morse-ccmar.ualg.pt/edge/
>>>>> [Mon Jul 16 14:46:27 2012] [error] [client 10.10.228.135] PHP Fatal
>>>>> error: Maximum execution time of 30 seconds exceeded in
>>>>> /usr/share/drupal6/includes/database.inc on line 225, referer:
>>>>> http://morse-ccmar.ualg.pt/edge/
>>>>>
>>>>> I guess it should be related to the second error?
>>>>>
>>>>> Thanks,
>>>>> Tony
>>>>>
>>>>>
>>>>>
>>>>> On Mon, Jul 16, 2012 at 2:23 PM, Stephen Ficklin <[hidden email]>
>>>>> wrote:
>>>>>>
>>>>>> Hi Tony,
>>>>>>
>>>>>> Can you send me the server logs after you load that page and look in
>>>>>> the
>>>>>> Drupal logs and let me know if you see anything there that might
>>>>>> apply.
>>>>>>
>>>>>> You get a page that looks like that when an error occurs in building
>>>>>> the
>>>>>> template. It worked fine at my end so something is different about
>>>>>> your
>>>>>> setup that is making it do that.
>>>>>>
>>>>>> Yes, you are correct, you just needed to update the theme.
>>>>>>
>>>>>> Stephen
>>>>>>
>>>>>>
>>>>>> On 7/16/2012 8:58 AM, Tony Power wrote:
>>>>>>>
>>>>>>> Hi Stephen,
>>>>>>>
>>>>>>> Just updated to the new Tripal Theme.
>>>>>>> Something is not working properly. To understand what I mean, please,
>>>>>>> click on one of the contigs.
>>>>>>>
>>>>>>> Do I also need to update the Tripal module? I just updated the Theme.
>>>>>>>
>>>>>>> Thanks ;)
>>>>>>>
>>>>>>> Tony
>>>>>>>
>>>>>>>
>>>>>>> On Sat, Jul 14, 2012 at 3:04 AM, Stephen Ficklin
>>>>>>> <[hidden email]>
>>>>>>> wrote:
>>>>>>>>
>>>>>>>> Hi Tony,
>>>>>>>>
>>>>>>>> If you get the most recent version of the tripal_theme 6.x-1.x
>>>>>>>> branch
>>>>>>>> from
>>>>>>>> the development git repository it now contains an update that
>>>>>>>> resolves
>>>>>>>> the
>>>>>>>> issue with the EST_match that you are having. Let me know if it
>>>>>>>> works
>>>>>>>> for
>>>>>>>> you.
>>>>>>>>
>>>>>>>> http://drupal.org/node/1342972/git-instructions/6.x-1.x
>>>>>>>>
>>>>>>>>
>>>>>>>> Stephen
>>>>>>>>
>>>>>>>>
>>>>>>>> On 7/10/2012 9:26 AM, Stephen Ficklin wrote:
>>>>>>>>>
>>>>>>>>> Hi Tony,
>>>>>>>>>
>>>>>>>>> Good morning. I'm CC'ing the list as your question about the
>>>>>>>>> EST_match
>>>>>>>>> may be helpful for others. The behavior you describe is correct
>>>>>>>>> for
>>>>>>>>> the
>>>>>>>>> way
>>>>>>>>> the alignments are stored. ESTs are aligned to contigs via an
>>>>>>>>> 'EST_match'
>>>>>>>>> feature in your GFF file. This is because an EST does not always
>>>>>>>>> overlap
>>>>>>>>> completely with the contig depending on the software used to do the
>>>>>>>>> assembly--only portions of ESTs may align. Therefore we use an
>>>>>>>>> EST_match
>>>>>>>>> feature for the alignment. See here for an example:
>>>>>>>>> http://gmod.org/wiki/GFF#Alignments
>>>>>>>>>
>>>>>>>>> EST --> EST_match <-- Contig
>>>>>>>>>
>>>>>>>>> In reality you don't want the site visitors to see the EST_match
>>>>>>>>> features.
>>>>>>>>> But by default Tripal treats all features the same. It doesn't know
>>>>>>>>> the
>>>>>>>>> difference between a gene, mRNA, contig, EST, EST_match, etc. So
>>>>>>>>> that
>>>>>>>>> is
>>>>>>>>> why you have links to EST_matches on your contig alignments page
>>>>>>>>> rather
>>>>>>>>> than
>>>>>>>>> links to ESTs. So, to get links to your ESTs on your contig page
>>>>>>>>> and
>>>>>>>>> to
>>>>>>>>> bypass the EST_match feature you need to edit the
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> sites/all/themes/tripal_theme/tripal_feature/tripal_feature_featurelocs_as_parent.tpl.php
>>>>>>>>> to handle that special case. I believe however that I can make
>>>>>>>>> that
>>>>>>>>> adjustment in the template for you in the development code. When
>>>>>>>>> it's
>>>>>>>>> ready
>>>>>>>>> I'll let you know.
>>>>>>>>>
>>>>>>>>> Stephen
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 7/10/2012 5:45 AM, Tony Power wrote:
>>>>>>>>>>
>>>>>>>>>> Hi again Stephen,
>>>>>>>>>>
>>>>>>>>>> I noticed some strange behavior on the site.
>>>>>>>>>>
>>>>>>>>>> For instance:
>>>>>>>>>> 1-Select the first contig and then select "Alignments".
>>>>>>>>>> 2-Now select the first EST_match.
>>>>>>>>>> 3-Now "EST_match Sequence" -> No sequence is shown;
>>>>>>>>>>
>>>>>>>>>> 4-Now select "Alignments" (of that EST_match).
>>>>>>>>>> 5-From the alignments select the EST_match that it aligns to.
>>>>>>>>>> 6-Select "EST_match Sequence" -> The sequence is shown.
>>>>>>>>>>
>>>>>>>>>> What might be the problem?
>>>>>>>>>>
>>>>>>>>>> Obrigado,
>>>>>>>>>>
>>>>>>>>>>
>>>>
>
>

Lacey-Anne Sanderson

Re: [Gmod-tripal-devel] EST_match for unigenes

Hi Tony,

The newest dev version is on a different branch (we needed to make the change to adhere to drupal standards). You need to checkout the master branch (git checkout master) and then pull from the drupal.org repository (git pull origin master) and then checkout the new branch (git checkout 6.x-1.x). From here on in you simply need to pull from the drupal.org repository to get the latest development snapshot (git pull origin 6.x-1.x).

You can just replace the entire module directory with a new version of tripal though it is recommended to first disable all your tripal modules (configuration and sync'd features will remain and be available once you re-enable the module -you only lose data if you uninstall the modules).

Sorry for the extra steps,

~Lacey

PS. I am also not experiencing any errors on my contig pages...

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

Lacey-Anne Sanderson

Bioinformaticist

Pulse Crop Breeding and Genetics

Phone: (306) 966-4975

Email: [hidden email]

Room 3C06 Agriculture

Department of Plant Sciences

University of Saskatchewan

On 2012-07-16, at 3:05 PM, Tony Power wrote:

Hi Stephen and Lacey-Anne,

After testing I immediately reset it to 30 secs again. But the result
is the same. 30 or 300 the errors are the same, it just takes longer
to display the (unformatted) webpage.

After trying to Lacey-Anne's suggestion I get the same result.
I have the latest dev branch for the Tripal module (I guess):
# git status
# On branch 6.x-0.4-dev
nothing to commit (working directory clean)

The new Theme version you provided me in a previous email is not
development (could it be this?)
git status
# On branch 6.x-1.x
nothing to commit (working directory clean)

If there is another module version, can I just delete the whole tripal
(module) and replace it by the new?
Where are all the tripal site related configurations saved?

Thanks,
Tony

On Mon, Jul 16, 2012 at 8:30 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Tony,

I'm having a bit of trouble debugging this one because I'm not having the
same problem. I was unable to load this feature on your site without it
taking longer than 30 seconds: http://morse-ccmar.ualg.pt/edge/ID327210.
Would you mind sending me the snippet of the GFF file that contains that
contig and EST alignments?

Thanks,
Stephen

On 7/16/2012 12:18 PM, Tony Power wrote:

Well, it shouldn't have anything to do with the common.inc error,
since even if I restore the old theme I still get that error and the
features show well again. So, something should be happening with the
new version of your theme (or not) :P.

In any case it's a weird error since I don't do any updates for a long
time.

On Mon, Jul 16, 2012 at 5:10 PM, Tony Power <[hidden email]> wrote:

Hi Stephen,

I changed it to 300 and it just stands there waiting.
Nevertheless I can see that it fired many of these errors:
[Mon Jul 16 17:04:26 2012] [error] [client 10.10.228.132] PHP Parse
error: syntax error, unexpected 's' (T_STRING) in
/usr/share/drupal6/includes/common.inc(1731) : eval()'d code on line
1, referer: http://morse-ccmar.ualg.pt/edge/

On line 1731 there is the following: print eval('?>'. $code);

Does that $code variable have anything to do with your theme?

After the 300 secs, I get:
[Mon Jul 16 17:09:26 2012] [error] [client 10.10.228.132] PHP Fatal
error: Maximum execution time of 300 seconds exceeded in
/usr/share/drupal6/includes/database.inc on line 225, referer:
http://morse-ccmar.ualg.pt/edge/

Thanks,

Tony

On Mon, Jul 16, 2012 at 3:08 PM, Stephen Ficklin <[hidden email]>
wrote:

Hi Tony,

Yes, the problem is the timeout issue. If you go into your php.ini file
(/etc/php5/apache2/php.ini on my box) and change the max_execution_time
to
something larger. However, this page should not take more than 30
seconds
to load so we can try to figure out what's going on once the page
displays.

Stephen

On 7/16/2012 9:54 AM, Tony Power wrote:

Hi Stephen,

In the logs there is nothing about the theme loading. Everything seems
to work well.
You still have that admin account that allows you to access the logs,
just in case you wish to have a look. But you wont find anything :P
From the apache log I get:
[Mon Jul 16 14:45:52 2012] [error] [client 10.10.228.135] PHP Parse
error: syntax error, unexpected 's' (T_STRING) in
/usr/share/drupal6/includes/common.inc(1731) : eval()'d code on line
1, referer: http://morse-ccmar.ualg.pt/edge/
[Mon Jul 16 14:46:27 2012] [error] [client 10.10.228.135] PHP Fatal
error: Maximum execution time of 30 seconds exceeded in
/usr/share/drupal6/includes/database.inc on line 225, referer:
http://morse-ccmar.ualg.pt/edge/

I guess it should be related to the second error?

Thanks,
Tony

On Mon, Jul 16, 2012 at 2:23 PM, Stephen Ficklin <[hidden email]>
wrote:

Hi Tony,

Can you send me the server logs after you load that page and look in
the
Drupal logs and let me know if you see anything there that might
apply.

You get a page that looks like that when an error occurs in building
the
template. It worked fine at my end so something is different about
your
setup that is making it do that.

Yes, you are correct, you just needed to update the theme.

Stephen

On 7/16/2012 8:58 AM, Tony Power wrote:

Hi Stephen,

Just updated to the new Tripal Theme.
Something is not working properly. To understand what I mean, please,
click on one of the contigs.

Do I also need to update the Tripal module? I just updated the Theme.

Thanks ;)

Tony

On Sat, Jul 14, 2012 at 3:04 AM, Stephen Ficklin
<[hidden email]>
wrote:

Hi Tony,

If you get the most recent version of the tripal_theme 6.x-1.x
branch
from
the development git repository it now contains an update that
resolves
the
issue with the EST_match that you are having. Let me know if it
works
for
you.

http://drupal.org/node/1342972/git-instructions/6.x-1.x

Stephen

On 7/10/2012 9:26 AM, Stephen Ficklin wrote:

Hi Tony,

Good morning. I'm CC'ing the list as your question about the
EST_match
may be helpful for others. The behavior you describe is correct
for
the
way
the alignments are stored.   ESTs are aligned to contigs via an
'EST_match'
feature in your GFF file.   This is because an EST does not always
overlap
completely with the contig depending on the software used to do the
assembly--only portions of ESTs may align. Therefore we use an
EST_match
feature for the alignment.   See here for an example:
http://gmod.org/wiki/GFF#Alignments

EST --> EST_match <-- Contig

In reality you don't want the site visitors to see the EST_match
features.
But by default Tripal treats all features the same. It doesn't know
the
difference between a gene, mRNA, contig, EST, EST_match, etc. So
that
is
why you have links to EST_matches on your contig alignments page
rather
than
links to ESTs.   So, to get links to your ESTs on your contig page
and
to
bypass the EST_match feature you need to edit the

sites/all/themes/tripal_theme/tripal_feature/tripal_feature_featurelocs_as_parent.tpl.php
to handle that special case.   I believe however that I can make
that
adjustment in the template for you in the development code. When
it's
ready
I'll let you know.

Stephen

On 7/10/2012 5:45 AM, Tony Power wrote:

Hi again Stephen,

I noticed some strange behavior on the site.

For instance:
1-Select the first contig and then select "Alignments".
2-Now select the first EST_match.
3-Now "EST_match Sequence" -> No sequence is shown;

4-Now select "Alignments" (of that EST_match).
5-From the alignments select the EST_match that it aligns to.
6-Select "EST_match Sequence" -> The sequence is shown.

What might be the problem?

Obrigado,

Tony Power

Re: [Gmod-tripal-devel] EST_match for unigenes

Ho Lacey-Anne,

Here is what I get:
root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# git checkout master
Branch master set up to track remote branch master from origin.
Switched to a new branch 'master'
root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# git pull origin master
fatal: Couldn't find remote ref master
root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# Unexpected
end of command stream

Did I do anything wrong?

Thanks,
Tony

On Mon, Jul 16, 2012 at 10:15 PM, Lacey-Anne Sanderson
<[hidden email]> wrote:

> Hi Tony,
>
> The newest dev version is on a different branch (we needed to make the
> change to adhere to drupal standards). You need to checkout the master
> branch (git checkout master) and then pull from the drupal.org repository
> (git pull origin master) and then checkout the new branch (git checkout
> 6.x-1.x). From here on in you simply need to pull from the drupal.org
> repository to get the latest development snapshot (git pull origin 6.x-1.x).
>
> You can just replace the entire module directory with a new version of
> tripal though it is recommended to first disable all your tripal modules
> (configuration and sync'd features will remain and be available once you
> re-enable the module -you only lose data if you uninstall the modules).
>
> Sorry for the extra steps,
> ~Lacey
>
> PS. I am also not experiencing any errors on my contig pages...
>
> ------------------------------------------------------
> Lacey-Anne Sanderson
> Bioinformaticist
> Pulse Crop Breeding and Genetics
> Phone: (306) 966-4975
> Email: [hidden email]
> Room 3C06 Agriculture
> Department of Plant Sciences
> University of Saskatchewan
>
> On 2012-07-16, at 3:05 PM, Tony Power wrote:
>
> Hi Stephen and Lacey-Anne,
>
> After testing I immediately reset it to 30 secs again. But the result
> is the same. 30 or 300 the errors are the same, it just takes longer
> to display the (unformatted) webpage.
>
> After trying to Lacey-Anne's suggestion I get the same result.
> I have the latest dev branch for the Tripal module (I guess):
> # git status
> # On branch 6.x-0.4-dev
> nothing to commit (working directory clean)
>
> The new Theme version you provided me in a previous email is not
> development (could it be this?)
> git status
> # On branch 6.x-1.x
> nothing to commit (working directory clean)
>
> If there is another module version, can I just delete the whole tripal
> (module) and replace it by the new?
> Where are all the tripal site related configurations saved?
>
> Thanks,
> Tony
>
> On Mon, Jul 16, 2012 at 8:30 PM, Stephen Ficklin <[hidden email]>
> wrote:
>
> Hi Tony,
>
>
> I'm having a bit of trouble debugging this one because I'm not having the
>
> same problem. I was unable to load this feature on your site without it
>
> taking longer than 30 seconds: http://morse-ccmar.ualg.pt/edge/ID327210.
>
> Would you mind sending me the snippet of the GFF file that contains that
>
> contig and EST alignments?
>
>
> Thanks,
>
> Stephen
>
>
>
> On 7/16/2012 12:18 PM, Tony Power wrote:
>
>
> Well, it shouldn't have anything to do with the common.inc error,
>
> since even if I restore the old theme I still get that error and the
>
> features show well again. So, something should be happening with the
>
> new version of your theme (or not) :P.
>
>
> In any case it's a weird error since I don't do any updates for a long
>
> time.
>
>
> On Mon, Jul 16, 2012 at 5:10 PM, Tony Power <[hidden email]> wrote:
>
>
> Hi Stephen,
>
>
> I changed it to 300 and it just stands there waiting.
>
> Nevertheless I can see that it fired many of these errors:
>
> [Mon Jul 16 17:04:26 2012] [error] [client 10.10.228.132] PHP Parse
>
> error: syntax error, unexpected 's' (T_STRING) in
>
> /usr/share/drupal6/includes/common.inc(1731) : eval()'d code on line
>
> 1, referer: http://morse-ccmar.ualg.pt/edge/
>
>
> On line 1731 there is the following: print eval('?>'. $code);
>
>
> Does that $code variable have anything to do with your theme?
>
>
> After the 300 secs, I get:
>
> [Mon Jul 16 17:09:26 2012] [error] [client 10.10.228.132] PHP Fatal
>
> error: Maximum execution time of 300 seconds exceeded in
>
> /usr/share/drupal6/includes/database.inc on line 225, referer:
>
> http://morse-ccmar.ualg.pt/edge/
>
>
> Thanks,
>
>
> Tony
>
>
> On Mon, Jul 16, 2012 at 3:08 PM, Stephen Ficklin <[hidden email]>
>
> wrote:
>
>
> Hi Tony,
>
>
> Yes, the problem is the timeout issue. If you go into your php.ini file
>
> (/etc/php5/apache2/php.ini on my box) and change the max_execution_time
>
> to
>
> something larger. However, this page should not take more than 30
>
> seconds
>
> to load so we can try to figure out what's going on once the page
>
> displays.
>
>
> Stephen
>
>
>
> On 7/16/2012 9:54 AM, Tony Power wrote:
>
>
> Hi Stephen,
>
>
> In the logs there is nothing about the theme loading. Everything seems
>
> to work well.
>
> You still have that admin account that allows you to access the logs,
>
> just in case you wish to have a look. But you wont find anything :P
>
> From the apache log I get:
>
> [Mon Jul 16 14:45:52 2012] [error] [client 10.10.228.135] PHP Parse
>
> error: syntax error, unexpected 's' (T_STRING) in
>
> /usr/share/drupal6/includes/common.inc(1731) : eval()'d code on line
>
> 1, referer: http://morse-ccmar.ualg.pt/edge/
>
> [Mon Jul 16 14:46:27 2012] [error] [client 10.10.228.135] PHP Fatal
>
> error: Maximum execution time of 30 seconds exceeded in
>
> /usr/share/drupal6/includes/database.inc on line 225, referer:
>
> http://morse-ccmar.ualg.pt/edge/
>
>
> I guess it should be related to the second error?
>
>
> Thanks,
>
> Tony
>
>
>
>
> On Mon, Jul 16, 2012 at 2:23 PM, Stephen Ficklin <[hidden email]>
>
> wrote:
>
>
> Hi Tony,
>
>
> Can you send me the server logs after you load that page and look in
>
> the
>
> Drupal logs and let me know if you see anything there that might
>
> apply.
>
>
> You get a page that looks like that when an error occurs in building
>
> the
>
> template. It worked fine at my end so something is different about
>
> your
>
> setup that is making it do that.
>
>
> Yes, you are correct, you just needed to update the theme.
>
>
> Stephen
>
>
>
> On 7/16/2012 8:58 AM, Tony Power wrote:
>
>
> Hi Stephen,
>
>
> Just updated to the new Tripal Theme.
>
> Something is not working properly. To understand what I mean, please,
>
> click on one of the contigs.
>
>
> Do I also need to update the Tripal module? I just updated the Theme.
>
>
> Thanks ;)
>
>
> Tony
>
>
>
> On Sat, Jul 14, 2012 at 3:04 AM, Stephen Ficklin
>
> <[hidden email]>
>
> wrote:
>
>
> Hi Tony,
>
>
> If you get the most recent version of the tripal_theme 6.x-1.x
>
> branch
>
> from
>
> the development git repository it now contains an update that
>
> resolves
>
> the
>
> issue with the EST_match that you are having. Let me know if it
>
> works
>
> for
>
> you.
>
>
> http://drupal.org/node/1342972/git-instructions/6.x-1.x
>
>
>
> Stephen
>
>
>
> On 7/10/2012 9:26 AM, Stephen Ficklin wrote:
>
>
> Hi Tony,
>
>
> Good morning. I'm CC'ing the list as your question about the
>
> EST_match
>
> may be helpful for others. The behavior you describe is correct
>
> for
>
> the
>
> way
>
> the alignments are stored. ESTs are aligned to contigs via an
>
> 'EST_match'
>
> feature in your GFF file. This is because an EST does not always
>
> overlap
>
> completely with the contig depending on the software used to do the
>
> assembly--only portions of ESTs may align. Therefore we use an
>
> EST_match
>
> feature for the alignment. See here for an example:
>
> http://gmod.org/wiki/GFF#Alignments
>
>
> EST --> EST_match <-- Contig
>
>
> In reality you don't want the site visitors to see the EST_match
>
> features.
>
> But by default Tripal treats all features the same. It doesn't know
>
> the
>
> difference between a gene, mRNA, contig, EST, EST_match, etc. So
>
> that
>
> is
>
> why you have links to EST_matches on your contig alignments page
>
> rather
>
> than
>
> links to ESTs. So, to get links to your ESTs on your contig page
>
> and
>
> to
>
> bypass the EST_match feature you need to edit the
>
>
>
>
> sites/all/themes/tripal_theme/tripal_feature/tripal_feature_featurelocs_as_parent.tpl.php
>
> to handle that special case. I believe however that I can make
>
> that
>
> adjustment in the template for you in the development code. When
>
> it's
>
> ready
>
> I'll let you know.
>
>
> Stephen
>
>
>
> On 7/10/2012 5:45 AM, Tony Power wrote:
>
>
> Hi again Stephen,
>
>
> I noticed some strange behavior on the site.
>
>
> For instance:
>
> 1-Select the first contig and then select "Alignments".
>
> 2-Now select the first EST_match.
>
> 3-Now "EST_match Sequence" -> No sequence is shown;
>
>
> 4-Now select "Alignments" (of that EST_match).
>
> 5-From the alignments select the EST_match that it aligns to.
>
> 6-Select "EST_match Sequence" -> The sequence is shown.
>
>
> What might be the problem?
>
>
> Obrigado,
>
>
>
>
>
>
>

Stephen Ficklin-2

Re: [Gmod-tripal-devel] EST_match for unigenes

Hi Tony,

You should be able to just switch right over to the 6.x-1.x branch:

git checkout 6.x-1.x

If you still get problems then you can wipe it clean (after disabling
the Tripal modules) and just start over with the 6.x-1.x branch as you
suggest.

Stephen

On 7/23/2012 2:34 PM, Tony Power wrote:

> Ho Lacey-Anne,
>
> Here is what I get:
> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# git checkout master
> Branch master set up to track remote branch master from origin.
> Switched to a new branch 'master'
> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# git pull origin master
> fatal: Couldn't find remote ref master
> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# Unexpected
> end of command stream
>
> Did I do anything wrong?
>
> Thanks,
> Tony
>
> On Mon, Jul 16, 2012 at 10:15 PM, Lacey-Anne Sanderson
> <[hidden email]> wrote:
>> Hi Tony,
>>
>> The newest dev version is on a different branch (we needed to make the
>> change to adhere to drupal standards). You need to checkout the master
>> branch (git checkout master) and then pull from the drupal.org repository
>> (git pull origin master) and then checkout the new branch (git checkout
>> 6.x-1.x). From here on in you simply need to pull from the drupal.org
>> repository to get the latest development snapshot (git pull origin 6.x-1.x).
>>
>> You can just replace the entire module directory with a new version of
>> tripal though it is recommended to first disable all your tripal modules
>> (configuration and sync'd features will remain and be available once you
>> re-enable the module -you only lose data if you uninstall the modules).
>>
>> Sorry for the extra steps,
>> ~Lacey
>>
>> PS. I am also not experiencing any errors on my contig pages...
>>
>> ------------------------------------------------------
>> Lacey-Anne Sanderson
>> Bioinformaticist
>> Pulse Crop Breeding and Genetics
>> Phone: (306) 966-4975
>> Email: [hidden email]
>> Room 3C06 Agriculture
>> Department of Plant Sciences
>> University of Saskatchewan
>>
>> On 2012-07-16, at 3:05 PM, Tony Power wrote:
>>
>> Hi Stephen and Lacey-Anne,
>>
>> After testing I immediately reset it to 30 secs again. But the result
>> is the same. 30 or 300 the errors are the same, it just takes longer
>> to display the (unformatted) webpage.
>>
>> After trying to Lacey-Anne's suggestion I get the same result.
>> I have the latest dev branch for the Tripal module (I guess):
>> # git status
>> # On branch 6.x-0.4-dev
>> nothing to commit (working directory clean)
>>
>> The new Theme version you provided me in a previous email is not
>> development (could it be this?)
>> git status
>> # On branch 6.x-1.x
>> nothing to commit (working directory clean)
>>
>> If there is another module version, can I just delete the whole tripal
>> (module) and replace it by the new?
>> Where are all the tripal site related configurations saved?
>>
>> Thanks,
>> Tony
>>
>> On Mon, Jul 16, 2012 at 8:30 PM, Stephen Ficklin <[hidden email]>
>> wrote:
>>
>> Hi Tony,
>>
>>
>> I'm having a bit of trouble debugging this one because I'm not having the
>>
>> same problem. I was unable to load this feature on your site without it
>>
>> taking longer than 30 seconds: http://morse-ccmar.ualg.pt/edge/ID327210.
>>
>> Would you mind sending me the snippet of the GFF file that contains that
>>
>> contig and EST alignments?
>>
>>
>> Thanks,
>>
>> Stephen
>>
>>
>>
>> On 7/16/2012 12:18 PM, Tony Power wrote:
>>
>>
>> Well, it shouldn't have anything to do with the common.inc error,
>>
>> since even if I restore the old theme I still get that error and the
>>
>> features show well again. So, something should be happening with the
>>
>> new version of your theme (or not) :P.
>>
>>
>> In any case it's a weird error since I don't do any updates for a long
>>
>> time.
>>
>>
>> On Mon, Jul 16, 2012 at 5:10 PM, Tony Power <[hidden email]> wrote:
>>
>>
>> Hi Stephen,
>>
>>
>> I changed it to 300 and it just stands there waiting.
>>
>> Nevertheless I can see that it fired many of these errors:
>>
>> [Mon Jul 16 17:04:26 2012] [error] [client 10.10.228.132] PHP Parse
>>
>> error: syntax error, unexpected 's' (T_STRING) in
>>
>> /usr/share/drupal6/includes/common.inc(1731) : eval()'d code on line
>>
>> 1, referer: http://morse-ccmar.ualg.pt/edge/
>>
>>
>> On line 1731 there is the following: print eval('?>'. $code);
>>
>>
>> Does that $code variable have anything to do with your theme?
>>
>>
>> After the 300 secs, I get:
>>
>> [Mon Jul 16 17:09:26 2012] [error] [client 10.10.228.132] PHP Fatal
>>
>> error: Maximum execution time of 300 seconds exceeded in
>>
>> /usr/share/drupal6/includes/database.inc on line 225, referer:
>>
>> http://morse-ccmar.ualg.pt/edge/
>>
>>
>> Thanks,
>>
>>
>> Tony
>>
>>
>> On Mon, Jul 16, 2012 at 3:08 PM, Stephen Ficklin <[hidden email]>
>>
>> wrote:
>>
>>
>> Hi Tony,
>>
>>
>> Yes, the problem is the timeout issue. If you go into your php.ini file
>>
>> (/etc/php5/apache2/php.ini on my box) and change the max_execution_time
>>
>> to
>>
>> something larger. However, this page should not take more than 30
>>
>> seconds
>>
>> to load so we can try to figure out what's going on once the page
>>
>> displays.
>>
>>
>> Stephen
>>
>>
>>
>> On 7/16/2012 9:54 AM, Tony Power wrote:
>>
>>
>> Hi Stephen,
>>
>>
>> In the logs there is nothing about the theme loading. Everything seems
>>
>> to work well.
>>
>> You still have that admin account that allows you to access the logs,
>>
>> just in case you wish to have a look. But you wont find anything :P
>>
>> From the apache log I get:
>>
>> [Mon Jul 16 14:45:52 2012] [error] [client 10.10.228.135] PHP Parse
>>
>> error: syntax error, unexpected 's' (T_STRING) in
>>
>> /usr/share/drupal6/includes/common.inc(1731) : eval()'d code on line
>>
>> 1, referer: http://morse-ccmar.ualg.pt/edge/
>>
>> [Mon Jul 16 14:46:27 2012] [error] [client 10.10.228.135] PHP Fatal
>>
>> error: Maximum execution time of 30 seconds exceeded in
>>
>> /usr/share/drupal6/includes/database.inc on line 225, referer:
>>
>> http://morse-ccmar.ualg.pt/edge/
>>
>>
>> I guess it should be related to the second error?
>>
>>
>> Thanks,
>>
>> Tony
>>
>>
>>
>>
>> On Mon, Jul 16, 2012 at 2:23 PM, Stephen Ficklin <[hidden email]>
>>
>> wrote:
>>
>>
>> Hi Tony,
>>
>>
>> Can you send me the server logs after you load that page and look in
>>
>> the
>>
>> Drupal logs and let me know if you see anything there that might
>>
>> apply.
>>
>>
>> You get a page that looks like that when an error occurs in building
>>
>> the
>>
>> template. It worked fine at my end so something is different about
>>
>> your
>>
>> setup that is making it do that.
>>
>>
>> Yes, you are correct, you just needed to update the theme.
>>
>>
>> Stephen
>>
>>
>>
>> On 7/16/2012 8:58 AM, Tony Power wrote:
>>
>>
>> Hi Stephen,
>>
>>
>> Just updated to the new Tripal Theme.
>>
>> Something is not working properly. To understand what I mean, please,
>>
>> click on one of the contigs.
>>
>>
>> Do I also need to update the Tripal module? I just updated the Theme.
>>
>>
>> Thanks ;)
>>
>>
>> Tony
>>
>>
>>
>> On Sat, Jul 14, 2012 at 3:04 AM, Stephen Ficklin
>>
>> <[hidden email]>
>>
>> wrote:
>>
>>
>> Hi Tony,
>>
>>
>> If you get the most recent version of the tripal_theme 6.x-1.x
>>
>> branch
>>
>> from
>>
>> the development git repository it now contains an update that
>>
>> resolves
>>
>> the
>>
>> issue with the EST_match that you are having. Let me know if it
>>
>> works
>>
>> for
>>
>> you.
>>
>>
>> http://drupal.org/node/1342972/git-instructions/6.x-1.x
>>
>>
>>
>> Stephen
>>
>>
>>
>> On 7/10/2012 9:26 AM, Stephen Ficklin wrote:
>>
>>
>> Hi Tony,
>>
>>
>> Good morning. I'm CC'ing the list as your question about the
>>
>> EST_match
>>
>> may be helpful for others. The behavior you describe is correct
>>
>> for
>>
>> the
>>
>> way
>>
>> the alignments are stored. ESTs are aligned to contigs via an
>>
>> 'EST_match'
>>
>> feature in your GFF file. This is because an EST does not always
>>
>> overlap
>>
>> completely with the contig depending on the software used to do the
>>
>> assembly--only portions of ESTs may align. Therefore we use an
>>
>> EST_match
>>
>> feature for the alignment. See here for an example:
>>
>> http://gmod.org/wiki/GFF#Alignments
>>
>>
>> EST --> EST_match <-- Contig
>>
>>
>> In reality you don't want the site visitors to see the EST_match
>>
>> features.
>>
>> But by default Tripal treats all features the same. It doesn't know
>>
>> the
>>
>> difference between a gene, mRNA, contig, EST, EST_match, etc. So
>>
>> that
>>
>> is
>>
>> why you have links to EST_matches on your contig alignments page
>>
>> rather
>>
>> than
>>
>> links to ESTs. So, to get links to your ESTs on your contig page
>>
>> and
>>
>> to
>>
>> bypass the EST_match feature you need to edit the
>>
>>
>>
>>
>> sites/all/themes/tripal_theme/tripal_feature/tripal_feature_featurelocs_as_parent.tpl.php
>>
>> to handle that special case. I believe however that I can make
>>
>> that
>>
>> adjustment in the template for you in the development code. When
>>
>> it's
>>
>> ready
>>
>> I'll let you know.
>>
>>
>> Stephen
>>
>>
>>
>> On 7/10/2012 5:45 AM, Tony Power wrote:
>>
>>
>> Hi again Stephen,
>>
>>
>> I noticed some strange behavior on the site.
>>
>>
>> For instance:
>>
>> 1-Select the first contig and then select "Alignments".
>>
>> 2-Now select the first EST_match.
>>
>> 3-Now "EST_match Sequence" -> No sequence is shown;
>>
>>
>> 4-Now select "Alignments" (of that EST_match).
>>
>> 5-From the alignments select the EST_match that it aligns to.
>>
>> 6-Select "EST_match Sequence" -> The sequence is shown.
>>
>>
>> What might be the problem?
>>
>>
>> Obrigado,
>>
>>
>>
>>
>>
>>
>>

Tony Power

Re: [Gmod-tripal-devel] EST_match for unigenes

Hi Stephen,

Did that.
In any case, it didn't fix that problem of presenting an unformatted
feature webpage. But I guess you've already identified the problem.
I'll just wait for the fix.

Thanks,
Tony

On Mon, Jul 23, 2012 at 7:48 PM, Stephen Ficklin <[hidden email]> wrote:

> Hi Tony,
>
> You should be able to just switch right over to the 6.x-1.x branch:
>
> git checkout 6.x-1.x
>
> If you still get problems then you can wipe it clean (after disabling the
> Tripal modules) and just start over with the 6.x-1.x branch as you suggest.
>
> Stephen
>
>
>
> On 7/23/2012 2:34 PM, Tony Power wrote:
>>
>> Ho Lacey-Anne,
>>
>> Here is what I get:
>> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# git checkout
>> master
>> Branch master set up to track remote branch master from origin.
>> Switched to a new branch 'master'
>> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# git pull origin
>> master
>> fatal: Couldn't find remote ref master
>> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# Unexpected
>> end of command stream
>>
>> Did I do anything wrong?
>>
>> Thanks,
>> Tony
>>
>> On Mon, Jul 16, 2012 at 10:15 PM, Lacey-Anne Sanderson
>> <[hidden email]> wrote:
>>>
>>> Hi Tony,
>>>
>>> The newest dev version is on a different branch (we needed to make the
>>> change to adhere to drupal standards). You need to checkout the master
>>> branch (git checkout master) and then pull from the drupal.org repository
>>> (git pull origin master) and then checkout the new branch (git checkout
>>> 6.x-1.x). From here on in you simply need to pull from the drupal.org
>>> repository to get the latest development snapshot (git pull origin
>>> 6.x-1.x).
>>>
>>> You can just replace the entire module directory with a new version of
>>> tripal though it is recommended to first disable all your tripal modules
>>> (configuration and sync'd features will remain and be available once you
>>> re-enable the module -you only lose data if you uninstall the modules).
>>>
>>> Sorry for the extra steps,
>>> ~Lacey
>>>
>>> PS. I am also not experiencing any errors on my contig pages...
>>>
>>> ------------------------------------------------------
>>> Lacey-Anne Sanderson
>>> Bioinformaticist
>>> Pulse Crop Breeding and Genetics
>>> Phone: (306) 966-4975
>>> Email: [hidden email]
>>> Room 3C06 Agriculture
>>> Department of Plant Sciences
>>> University of Saskatchewan
>>>
>>> On 2012-07-16, at 3:05 PM, Tony Power wrote:
>>>
>>> Hi Stephen and Lacey-Anne,
>>>
>>> After testing I immediately reset it to 30 secs again. But the result
>>> is the same. 30 or 300 the errors are the same, it just takes longer
>>> to display the (unformatted) webpage.
>>>
>>> After trying to Lacey-Anne's suggestion I get the same result.
>>> I have the latest dev branch for the Tripal module (I guess):
>>> # git status
>>> # On branch 6.x-0.4-dev
>>> nothing to commit (working directory clean)
>>>
>>> The new Theme version you provided me in a previous email is not
>>> development (could it be this?)
>>> git status
>>> # On branch 6.x-1.x
>>> nothing to commit (working directory clean)
>>>
>>> If there is another module version, can I just delete the whole tripal
>>> (module) and replace it by the new?
>>> Where are all the tripal site related configurations saved?
>>>
>>> Thanks,
>>> Tony
>>>
>>> On Mon, Jul 16, 2012 at 8:30 PM, Stephen Ficklin <[hidden email]>
>>> wrote:
>>>
>>> Hi Tony,
>>>
>>>
>>> I'm having a bit of trouble debugging this one because I'm not having the
>>>
>>> same problem. I was unable to load this feature on your site without it
>>>
>>> taking longer than 30 seconds: http://morse-ccmar.ualg.pt/edge/ID327210.
>>>
>>> Would you mind sending me the snippet of the GFF file that contains that
>>>
>>> contig and EST alignments?
>>>
>>>
>>> Thanks,
>>>
>>> Stephen
>>>
>>>
>>>
>>> On 7/16/2012 12:18 PM, Tony Power wrote:
>>>
>>>
>>> Well, it shouldn't have anything to do with the common.inc error,
>>>
>>> since even if I restore the old theme I still get that error and the
>>>
>>> features show well again. So, something should be happening with the
>>>
>>> new version of your theme (or not) :P.
>>>
>>>
>>> In any case it's a weird error since I don't do any updates for a long
>>>
>>> time.
>>>
>>>
>>> On Mon, Jul 16, 2012 at 5:10 PM, Tony Power <[hidden email]> wrote:
>>>
>>>
>>> Hi Stephen,
>>>
>>>
>>> I changed it to 300 and it just stands there waiting.
>>>
>>> Nevertheless I can see that it fired many of these errors:
>>>
>>> [Mon Jul 16 17:04:26 2012] [error] [client 10.10.228.132] PHP Parse
>>>
>>> error: syntax error, unexpected 's' (T_STRING) in
>>>
>>> /usr/share/drupal6/includes/common.inc(1731) : eval()'d code on line
>>>
>>> 1, referer: http://morse-ccmar.ualg.pt/edge/
>>>
>>>
>>> On line 1731 there is the following: print eval('?>'. $code);
>>>
>>>
>>> Does that $code variable have anything to do with your theme?
>>>
>>>
>>> After the 300 secs, I get:
>>>
>>> [Mon Jul 16 17:09:26 2012] [error] [client 10.10.228.132] PHP Fatal
>>>
>>> error: Maximum execution time of 300 seconds exceeded in
>>>
>>> /usr/share/drupal6/includes/database.inc on line 225, referer:
>>>
>>> http://morse-ccmar.ualg.pt/edge/
>>>
>>>
>>> Thanks,
>>>
>>>
>>> Tony
>>>
>>>
>>> On Mon, Jul 16, 2012 at 3:08 PM, Stephen Ficklin <[hidden email]>
>>>
>>> wrote:
>>>
>>>
>>> Hi Tony,
>>>
>>>
>>> Yes, the problem is the timeout issue. If you go into your php.ini file
>>>
>>> (/etc/php5/apache2/php.ini on my box) and change the max_execution_time
>>>
>>> to
>>>
>>> something larger. However, this page should not take more than 30
>>>
>>> seconds
>>>
>>> to load so we can try to figure out what's going on once the page
>>>
>>> displays.
>>>
>>>
>>> Stephen
>>>
>>>
>>>
>>> On 7/16/2012 9:54 AM, Tony Power wrote:
>>>
>>>
>>> Hi Stephen,
>>>
>>>
>>> In the logs there is nothing about the theme loading. Everything seems
>>>
>>> to work well.
>>>
>>> You still have that admin account that allows you to access the logs,
>>>
>>> just in case you wish to have a look. But you wont find anything :P
>>>
>>> From the apache log I get:
>>>
>>> [Mon Jul 16 14:45:52 2012] [error] [client 10.10.228.135] PHP Parse
>>>
>>> error: syntax error, unexpected 's' (T_STRING) in
>>>
>>> /usr/share/drupal6/includes/common.inc(1731) : eval()'d code on line
>>>
>>> 1, referer: http://morse-ccmar.ualg.pt/edge/
>>>
>>> [Mon Jul 16 14:46:27 2012] [error] [client 10.10.228.135] PHP Fatal
>>>
>>> error: Maximum execution time of 30 seconds exceeded in
>>>
>>> /usr/share/drupal6/includes/database.inc on line 225, referer:
>>>
>>> http://morse-ccmar.ualg.pt/edge/
>>>
>>>
>>> I guess it should be related to the second error?
>>>
>>>
>>> Thanks,
>>>
>>> Tony
>>>
>>>
>>>
>>>
>>> On Mon, Jul 16, 2012 at 2:23 PM, Stephen Ficklin <[hidden email]>
>>>
>>> wrote:
>>>
>>>
>>> Hi Tony,
>>>
>>>
>>> Can you send me the server logs after you load that page and look in
>>>
>>> the
>>>
>>> Drupal logs and let me know if you see anything there that might
>>>
>>> apply.
>>>
>>>
>>> You get a page that looks like that when an error occurs in building
>>>
>>> the
>>>
>>> template. It worked fine at my end so something is different about
>>>
>>> your
>>>
>>> setup that is making it do that.
>>>
>>>
>>> Yes, you are correct, you just needed to update the theme.
>>>
>>>
>>> Stephen
>>>
>>>
>>>
>>> On 7/16/2012 8:58 AM, Tony Power wrote:
>>>
>>>
>>> Hi Stephen,
>>>
>>>
>>> Just updated to the new Tripal Theme.
>>>
>>> Something is not working properly. To understand what I mean, please,
>>>
>>> click on one of the contigs.
>>>
>>>
>>> Do I also need to update the Tripal module? I just updated the Theme.
>>>
>>>
>>> Thanks ;)
>>>
>>>
>>> Tony
>>>
>>>
>>>
>>> On Sat, Jul 14, 2012 at 3:04 AM, Stephen Ficklin
>>>
>>> <[hidden email]>
>>>
>>> wrote:
>>>
>>>
>>> Hi Tony,
>>>
>>>
>>> If you get the most recent version of the tripal_theme 6.x-1.x
>>>
>>> branch
>>>
>>> from
>>>
>>> the development git repository it now contains an update that
>>>
>>> resolves
>>>
>>> the
>>>
>>> issue with the EST_match that you are having. Let me know if it
>>>
>>> works
>>>
>>> for
>>>
>>> you.
>>>
>>>
>>> http://drupal.org/node/1342972/git-instructions/6.x-1.x
>>>
>>>
>>>
>>> Stephen
>>>
>>>
>>>
>>> On 7/10/2012 9:26 AM, Stephen Ficklin wrote:
>>>
>>>
>>> Hi Tony,
>>>
>>>
>>> Good morning. I'm CC'ing the list as your question about the
>>>
>>> EST_match
>>>
>>> may be helpful for others. The behavior you describe is correct
>>>
>>> for
>>>
>>> the
>>>
>>> way
>>>
>>> the alignments are stored. ESTs are aligned to contigs via an
>>>
>>> 'EST_match'
>>>
>>> feature in your GFF file. This is because an EST does not always
>>>
>>> overlap
>>>
>>> completely with the contig depending on the software used to do the
>>>
>>> assembly--only portions of ESTs may align. Therefore we use an
>>>
>>> EST_match
>>>
>>> feature for the alignment. See here for an example:
>>>
>>> http://gmod.org/wiki/GFF#Alignments
>>>
>>>
>>> EST --> EST_match <-- Contig
>>>
>>>
>>> In reality you don't want the site visitors to see the EST_match
>>>
>>> features.
>>>
>>> But by default Tripal treats all features the same. It doesn't know
>>>
>>> the
>>>
>>> difference between a gene, mRNA, contig, EST, EST_match, etc. So
>>>
>>> that
>>>
>>> is
>>>
>>> why you have links to EST_matches on your contig alignments page
>>>
>>> rather
>>>
>>> than
>>>
>>> links to ESTs. So, to get links to your ESTs on your contig page
>>>
>>> and
>>>
>>> to
>>>
>>> bypass the EST_match feature you need to edit the
>>>
>>>
>>>
>>>
>>>
>>> sites/all/themes/tripal_theme/tripal_feature/tripal_feature_featurelocs_as_parent.tpl.php
>>>
>>> to handle that special case. I believe however that I can make
>>>
>>> that
>>>
>>> adjustment in the template for you in the development code. When
>>>
>>> it's
>>>
>>> ready
>>>
>>> I'll let you know.
>>>
>>>
>>> Stephen
>>>
>>>
>>>
>>> On 7/10/2012 5:45 AM, Tony Power wrote:
>>>
>>>
>>> Hi again Stephen,
>>>
>>>
>>> I noticed some strange behavior on the site.
>>>
>>>
>>> For instance:
>>>
>>> 1-Select the first contig and then select "Alignments".
>>>
>>> 2-Now select the first EST_match.
>>>
>>> 3-Now "EST_match Sequence" -> No sequence is shown;
>>>
>>>
>>> 4-Now select "Alignments" (of that EST_match).
>>>
>>> 5-From the alignments select the EST_match that it aligns to.
>>>
>>> 6-Select "EST_match Sequence" -> The sequence is shown.
>>>
>>>
>>> What might be the problem?
>>>
>>>
>>> Obrigado,
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>

Stephen Ficklin-2

Re: [Gmod-tripal-devel] EST_match for unigenes

Hi Tony,

I provided a fix on Friday for the problem in the 6.x-1.x branch. You
have to update both Tripal and the Tripal theme to version 6.x-1.x.
Have you done both and still have the bad page?

Stephen

On 7/23/2012 3:27 PM, Tony Power wrote:

> Hi Stephen,
>
> Did that.
> In any case, it didn't fix that problem of presenting an unformatted
> feature webpage. But I guess you've already identified the problem.
> I'll just wait for the fix.
>
> Thanks,
> Tony
>
> On Mon, Jul 23, 2012 at 7:48 PM, Stephen Ficklin <[hidden email]> wrote:
>> Hi Tony,
>>
>> You should be able to just switch right over to the 6.x-1.x branch:
>>
>> git checkout 6.x-1.x
>>
>> If you still get problems then you can wipe it clean (after disabling the
>> Tripal modules) and just start over with the 6.x-1.x branch as you suggest.
>>
>> Stephen
>>
>>
>>
>> On 7/23/2012 2:34 PM, Tony Power wrote:
>>> Ho Lacey-Anne,
>>>
>>> Here is what I get:
>>> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# git checkout
>>> master
>>> Branch master set up to track remote branch master from origin.
>>> Switched to a new branch 'master'
>>> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# git pull origin
>>> master
>>> fatal: Couldn't find remote ref master
>>> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# Unexpected
>>> end of command stream
>>>
>>> Did I do anything wrong?
>>>
>>> Thanks,
>>> Tony
>>>
>>> On Mon, Jul 16, 2012 at 10:15 PM, Lacey-Anne Sanderson
>>> <[hidden email]> wrote:
>>>> Hi Tony,
>>>>
>>>> The newest dev version is on a different branch (we needed to make the
>>>> change to adhere to drupal standards). You need to checkout the master
>>>> branch (git checkout master) and then pull from the drupal.org repository
>>>> (git pull origin master) and then checkout the new branch (git checkout
>>>> 6.x-1.x). From here on in you simply need to pull from the drupal.org
>>>> repository to get the latest development snapshot (git pull origin
>>>> 6.x-1.x).
>>>>
>>>> You can just replace the entire module directory with a new version of
>>>> tripal though it is recommended to first disable all your tripal modules
>>>> (configuration and sync'd features will remain and be available once you
>>>> re-enable the module -you only lose data if you uninstall the modules).
>>>>
>>>> Sorry for the extra steps,
>>>> ~Lacey
>>>>
>>>> PS. I am also not experiencing any errors on my contig pages...
>>>>
>>>> ------------------------------------------------------
>>>> Lacey-Anne Sanderson
>>>> Bioinformaticist
>>>> Pulse Crop Breeding and Genetics
>>>> Phone: (306) 966-4975
>>>> Email: [hidden email]
>>>> Room 3C06 Agriculture
>>>> Department of Plant Sciences
>>>> University of Saskatchewan
>>>>
>>>> On 2012-07-16, at 3:05 PM, Tony Power wrote:
>>>>
>>>> Hi Stephen and Lacey-Anne,
>>>>
>>>> After testing I immediately reset it to 30 secs again. But the result
>>>> is the same. 30 or 300 the errors are the same, it just takes longer
>>>> to display the (unformatted) webpage.
>>>>
>>>> After trying to Lacey-Anne's suggestion I get the same result.
>>>> I have the latest dev branch for the Tripal module (I guess):
>>>> # git status
>>>> # On branch 6.x-0.4-dev
>>>> nothing to commit (working directory clean)
>>>>
>>>> The new Theme version you provided me in a previous email is not
>>>> development (could it be this?)
>>>> git status
>>>> # On branch 6.x-1.x
>>>> nothing to commit (working directory clean)
>>>>
>>>> If there is another module version, can I just delete the whole tripal
>>>> (module) and replace it by the new?
>>>> Where are all the tripal site related configurations saved?
>>>>
>>>> Thanks,
>>>> Tony
>>>>
>>>> On Mon, Jul 16, 2012 at 8:30 PM, Stephen Ficklin <[hidden email]>
>>>> wrote:
>>>>
>>>> Hi Tony,
>>>>
>>>>
>>>> I'm having a bit of trouble debugging this one because I'm not having the
>>>>
>>>> same problem. I was unable to load this feature on your site without it
>>>>
>>>> taking longer than 30 seconds: http://morse-ccmar.ualg.pt/edge/ID327210.
>>>>
>>>> Would you mind sending me the snippet of the GFF file that contains that
>>>>
>>>> contig and EST alignments?
>>>>
>>>>
>>>> Thanks,
>>>>
>>>> Stephen
>>>>
>>>>
>>>>
>>>> On 7/16/2012 12:18 PM, Tony Power wrote:
>>>>
>>>>
>>>> Well, it shouldn't have anything to do with the common.inc error,
>>>>
>>>> since even if I restore the old theme I still get that error and the
>>>>
>>>> features show well again. So, something should be happening with the
>>>>
>>>> new version of your theme (or not) :P.
>>>>
>>>>
>>>> In any case it's a weird error since I don't do any updates for a long
>>>>
>>>> time.
>>>>
>>>>
>>>> On Mon, Jul 16, 2012 at 5:10 PM, Tony Power <[hidden email]> wrote:
>>>>
>>>>
>>>> Hi Stephen,
>>>>
>>>>
>>>> I changed it to 300 and it just stands there waiting.
>>>>
>>>> Nevertheless I can see that it fired many of these errors:
>>>>
>>>> [Mon Jul 16 17:04:26 2012] [error] [client 10.10.228.132] PHP Parse
>>>>
>>>> error: syntax error, unexpected 's' (T_STRING) in
>>>>
>>>> /usr/share/drupal6/includes/common.inc(1731) : eval()'d code on line
>>>>
>>>> 1, referer: http://morse-ccmar.ualg.pt/edge/
>>>>
>>>>
>>>> On line 1731 there is the following: print eval('?>'. $code);
>>>>
>>>>
>>>> Does that $code variable have anything to do with your theme?
>>>>
>>>>
>>>> After the 300 secs, I get:
>>>>
>>>> [Mon Jul 16 17:09:26 2012] [error] [client 10.10.228.132] PHP Fatal
>>>>
>>>> error: Maximum execution time of 300 seconds exceeded in
>>>>
>>>> /usr/share/drupal6/includes/database.inc on line 225, referer:
>>>>
>>>> http://morse-ccmar.ualg.pt/edge/
>>>>
>>>>
>>>> Thanks,
>>>>
>>>>
>>>> Tony
>>>>
>>>>
>>>> On Mon, Jul 16, 2012 at 3:08 PM, Stephen Ficklin <[hidden email]>
>>>>
>>>> wrote:
>>>>
>>>>
>>>> Hi Tony,
>>>>
>>>>
>>>> Yes, the problem is the timeout issue. If you go into your php.ini file
>>>>
>>>> (/etc/php5/apache2/php.ini on my box) and change the max_execution_time
>>>>
>>>> to
>>>>
>>>> something larger. However, this page should not take more than 30
>>>>
>>>> seconds
>>>>
>>>> to load so we can try to figure out what's going on once the page
>>>>
>>>> displays.
>>>>
>>>>
>>>> Stephen
>>>>
>>>>
>>>>
>>>> On 7/16/2012 9:54 AM, Tony Power wrote:
>>>>
>>>>
>>>> Hi Stephen,
>>>>
>>>>
>>>> In the logs there is nothing about the theme loading. Everything seems
>>>>
>>>> to work well.
>>>>
>>>> You still have that admin account that allows you to access the logs,
>>>>
>>>> just in case you wish to have a look. But you wont find anything :P
>>>>
>>>> From the apache log I get:
>>>>
>>>> [Mon Jul 16 14:45:52 2012] [error] [client 10.10.228.135] PHP Parse
>>>>
>>>> error: syntax error, unexpected 's' (T_STRING) in
>>>>
>>>> /usr/share/drupal6/includes/common.inc(1731) : eval()'d code on line
>>>>
>>>> 1, referer: http://morse-ccmar.ualg.pt/edge/
>>>>
>>>> [Mon Jul 16 14:46:27 2012] [error] [client 10.10.228.135] PHP Fatal
>>>>
>>>> error: Maximum execution time of 30 seconds exceeded in
>>>>
>>>> /usr/share/drupal6/includes/database.inc on line 225, referer:
>>>>
>>>> http://morse-ccmar.ualg.pt/edge/
>>>>
>>>>
>>>> I guess it should be related to the second error?
>>>>
>>>>
>>>> Thanks,
>>>>
>>>> Tony
>>>>
>>>>
>>>>
>>>>
>>>> On Mon, Jul 16, 2012 at 2:23 PM, Stephen Ficklin <[hidden email]>
>>>>
>>>> wrote:
>>>>
>>>>
>>>> Hi Tony,
>>>>
>>>>
>>>> Can you send me the server logs after you load that page and look in
>>>>
>>>> the
>>>>
>>>> Drupal logs and let me know if you see anything there that might
>>>>
>>>> apply.
>>>>
>>>>
>>>> You get a page that looks like that when an error occurs in building
>>>>
>>>> the
>>>>
>>>> template. It worked fine at my end so something is different about
>>>>
>>>> your
>>>>
>>>> setup that is making it do that.
>>>>
>>>>
>>>> Yes, you are correct, you just needed to update the theme.
>>>>
>>>>
>>>> Stephen
>>>>
>>>>
>>>>
>>>> On 7/16/2012 8:58 AM, Tony Power wrote:
>>>>
>>>>
>>>> Hi Stephen,
>>>>
>>>>
>>>> Just updated to the new Tripal Theme.
>>>>
>>>> Something is not working properly. To understand what I mean, please,
>>>>
>>>> click on one of the contigs.
>>>>
>>>>
>>>> Do I also need to update the Tripal module? I just updated the Theme.
>>>>
>>>>
>>>> Thanks ;)
>>>>
>>>>
>>>> Tony
>>>>
>>>>
>>>>
>>>> On Sat, Jul 14, 2012 at 3:04 AM, Stephen Ficklin
>>>>
>>>> <[hidden email]>
>>>>
>>>> wrote:
>>>>
>>>>
>>>> Hi Tony,
>>>>
>>>>
>>>> If you get the most recent version of the tripal_theme 6.x-1.x
>>>>
>>>> branch
>>>>
>>>> from
>>>>
>>>> the development git repository it now contains an update that
>>>>
>>>> resolves
>>>>
>>>> the
>>>>
>>>> issue with the EST_match that you are having. Let me know if it
>>>>
>>>> works
>>>>
>>>> for
>>>>
>>>> you.
>>>>
>>>>
>>>> http://drupal.org/node/1342972/git-instructions/6.x-1.x
>>>>
>>>>
>>>>
>>>> Stephen
>>>>
>>>>
>>>>
>>>> On 7/10/2012 9:26 AM, Stephen Ficklin wrote:
>>>>
>>>>
>>>> Hi Tony,
>>>>
>>>>
>>>> Good morning. I'm CC'ing the list as your question about the
>>>>
>>>> EST_match
>>>>
>>>> may be helpful for others. The behavior you describe is correct
>>>>
>>>> for
>>>>
>>>> the
>>>>
>>>> way
>>>>
>>>> the alignments are stored. ESTs are aligned to contigs via an
>>>>
>>>> 'EST_match'
>>>>
>>>> feature in your GFF file. This is because an EST does not always
>>>>
>>>> overlap
>>>>
>>>> completely with the contig depending on the software used to do the
>>>>
>>>> assembly--only portions of ESTs may align. Therefore we use an
>>>>
>>>> EST_match
>>>>
>>>> feature for the alignment. See here for an example:
>>>>
>>>> http://gmod.org/wiki/GFF#Alignments
>>>>
>>>>
>>>> EST --> EST_match <-- Contig
>>>>
>>>>
>>>> In reality you don't want the site visitors to see the EST_match
>>>>
>>>> features.
>>>>
>>>> But by default Tripal treats all features the same. It doesn't know
>>>>
>>>> the
>>>>
>>>> difference between a gene, mRNA, contig, EST, EST_match, etc. So
>>>>
>>>> that
>>>>
>>>> is
>>>>
>>>> why you have links to EST_matches on your contig alignments page
>>>>
>>>> rather
>>>>
>>>> than
>>>>
>>>> links to ESTs. So, to get links to your ESTs on your contig page
>>>>
>>>> and
>>>>
>>>> to
>>>>
>>>> bypass the EST_match feature you need to edit the
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> sites/all/themes/tripal_theme/tripal_feature/tripal_feature_featurelocs_as_parent.tpl.php
>>>>
>>>> to handle that special case. I believe however that I can make
>>>>
>>>> that
>>>>
>>>> adjustment in the template for you in the development code. When
>>>>
>>>> it's
>>>>
>>>> ready
>>>>
>>>> I'll let you know.
>>>>
>>>>
>>>> Stephen
>>>>
>>>>
>>>>
>>>> On 7/10/2012 5:45 AM, Tony Power wrote:
>>>>
>>>>
>>>> Hi again Stephen,
>>>>
>>>>
>>>> I noticed some strange behavior on the site.
>>>>
>>>>
>>>> For instance:
>>>>
>>>> 1-Select the first contig and then select "Alignments".
>>>>
>>>> 2-Now select the first EST_match.
>>>>
>>>> 3-Now "EST_match Sequence" -> No sequence is shown;
>>>>
>>>>
>>>> 4-Now select "Alignments" (of that EST_match).
>>>>
>>>> 5-From the alignments select the EST_match that it aligns to.
>>>>
>>>> 6-Select "EST_match Sequence" -> The sequence is shown.
>>>>
>>>>
>>>> What might be the problem?
>>>>
>>>>
>>>> Obrigado,
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>

Tony Power

Re: [Gmod-tripal-devel] EST_match for unigenes

Hi Stephen,

Thanks for the prompt reply.
I am sorry but I didn't the theme had been updated.
Now it looks like that we have something. Nevertheless:

warning: include(./sites/all/modules/tripal/tripal_feature/tripal_feature_alignments.tpl.php):
failed to open stream: No such file or directory in
/usr/share/drupal6/includes/theme.inc on line 1079.
warning: include(): Failed opening
'./sites/all/modules/tripal/tripal_feature/tripal_feature_alignments.tpl.php'
for inclusion (include_path='.:/usr/share/php:/usr/share/pear') in
/usr/share/drupal6/includes/theme.inc on line 1079.

shows up on the top of the formatted feature page.

This is what I have in the tripal_feature dir:
root@morse-ccmar:/var/www/edge/sites/all/modules/tripal/tripal_feature# ls
fasta_loader.php tripal_feature.info
gff_loader.php tripal_feature.install
indexFeatures.php tripal_feature.module
syncFeatures.php tripal_feature-properties.inc
tripal_feature.admin.inc tripal_feature-relationships.inc
tripal_feature.api.inc tripal_feature-secondary_tables.inc
tripal_feature.coder_ignores.txt tripal_feature.views.inc
tripal_feature-db_references.inc views_handlers
tripal_feature-delete.inc

Thanks,
Tony

On Mon, Jul 23, 2012 at 8:41 PM, Stephen Ficklin <[hidden email]> wrote:

> Hi Tony,
>
> I provided a fix on Friday for the problem in the 6.x-1.x branch. You have
> to update both Tripal and the Tripal theme to version 6.x-1.x. Have you
> done both and still have the bad page?
>
> Stephen
>
>
> On 7/23/2012 3:27 PM, Tony Power wrote:
>>
>> Hi Stephen,
>>
>> Did that.
>> In any case, it didn't fix that problem of presenting an unformatted
>> feature webpage. But I guess you've already identified the problem.
>> I'll just wait for the fix.
>>
>> Thanks,
>> Tony
>>
>> On Mon, Jul 23, 2012 at 7:48 PM, Stephen Ficklin <[hidden email]>
>> wrote:
>>>
>>> Hi Tony,
>>>
>>> You should be able to just switch right over to the 6.x-1.x branch:
>>>
>>> git checkout 6.x-1.x
>>>
>>> If you still get problems then you can wipe it clean (after disabling the
>>> Tripal modules) and just start over with the 6.x-1.x branch as you
>>> suggest.
>>>
>>> Stephen
>>>
>>>
>>>
>>> On 7/23/2012 2:34 PM, Tony Power wrote:
>>>>
>>>> Ho Lacey-Anne,
>>>>
>>>> Here is what I get:
>>>> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# git checkout
>>>> master
>>>> Branch master set up to track remote branch master from origin.
>>>> Switched to a new branch 'master'
>>>> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# git pull origin
>>>> master
>>>> fatal: Couldn't find remote ref master
>>>> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# Unexpected
>>>> end of command stream
>>>>
>>>> Did I do anything wrong?
>>>>
>>>> Thanks,
>>>> Tony
>>>>
>>>> On Mon, Jul 16, 2012 at 10:15 PM, Lacey-Anne Sanderson
>>>> <[hidden email]> wrote:
>>>>>
>>>>> Hi Tony,
>>>>>
>>>>> The newest dev version is on a different branch (we needed to make the
>>>>> change to adhere to drupal standards). You need to checkout the master
>>>>> branch (git checkout master) and then pull from the drupal.org
>>>>> repository
>>>>> (git pull origin master) and then checkout the new branch (git checkout
>>>>> 6.x-1.x). From here on in you simply need to pull from the drupal.org
>>>>> repository to get the latest development snapshot (git pull origin
>>>>> 6.x-1.x).
>>>>>
>>>>> You can just replace the entire module directory with a new version of
>>>>> tripal though it is recommended to first disable all your tripal
>>>>> modules
>>>>> (configuration and sync'd features will remain and be available once
>>>>> you
>>>>> re-enable the module -you only lose data if you uninstall the modules).
>>>>>
>>>>> Sorry for the extra steps,
>>>>> ~Lacey
>>>>>
>>>>> PS. I am also not experiencing any errors on my contig pages...
>>>>>
>>>>> ------------------------------------------------------
>>>>> Lacey-Anne Sanderson
>>>>> Bioinformaticist
>>>>> Pulse Crop Breeding and Genetics
>>>>> Phone: (306) 966-4975
>>>>> Email: [hidden email]
>>>>> Room 3C06 Agriculture
>>>>> Department of Plant Sciences
>>>>> University of Saskatchewan
>>>>>
>>>>> On 2012-07-16, at 3:05 PM, Tony Power wrote:
>>>>>
>>>>> Hi Stephen and Lacey-Anne,
>>>>>
>>>>> After testing I immediately reset it to 30 secs again. But the result
>>>>> is the same. 30 or 300 the errors are the same, it just takes longer
>>>>> to display the (unformatted) webpage.
>>>>>
>>>>> After trying to Lacey-Anne's suggestion I get the same result.
>>>>> I have the latest dev branch for the Tripal module (I guess):
>>>>> # git status
>>>>> # On branch 6.x-0.4-dev
>>>>> nothing to commit (working directory clean)
>>>>>
>>>>> The new Theme version you provided me in a previous email is not
>>>>> development (could it be this?)
>>>>> git status
>>>>> # On branch 6.x-1.x
>>>>> nothing to commit (working directory clean)
>>>>>
>>>>> If there is another module version, can I just delete the whole tripal
>>>>> (module) and replace it by the new?
>>>>> Where are all the tripal site related configurations saved?
>>>>>
>>>>> Thanks,
>>>>> Tony
>>>>>
>>>>> On Mon, Jul 16, 2012 at 8:30 PM, Stephen Ficklin <[hidden email]>
>>>>> wrote:
>>>>>
>>>>> Hi Tony,
>>>>>
>>>>>
>>>>> I'm having a bit of trouble debugging this one because I'm not having
>>>>> the
>>>>>
>>>>> same problem. I was unable to load this feature on your site without
>>>>> it
>>>>>
>>>>> taking longer than 30 seconds:
>>>>> http://morse-ccmar.ualg.pt/edge/ID327210.
>>>>>
>>>>> Would you mind sending me the snippet of the GFF file that contains
>>>>> that
>>>>>
>>>>> contig and EST alignments?
>>>>>
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Stephen
>>>>>
>>>>>
>>>>>
>>>>> On 7/16/2012 12:18 PM, Tony Power wrote:
>>>>>
>>>>>
>>>>> Well, it shouldn't have anything to do with the common.inc error,
>>>>>
>>>>> since even if I restore the old theme I still get that error and the
>>>>>
>>>>> features show well again. So, something should be happening with the
>>>>>
>>>>> new version of your theme (or not) :P.
>>>>>
>>>>>
>>>>> In any case it's a weird error since I don't do any updates for a long
>>>>>
>>>>> time.
>>>>>
>>>>>
>>>>> On Mon, Jul 16, 2012 at 5:10 PM, Tony Power <[hidden email]> wrote:
>>>>>
>>>>>
>>>>> Hi Stephen,
>>>>>
>>>>>
>>>>> I changed it to 300 and it just stands there waiting.
>>>>>
>>>>> Nevertheless I can see that it fired many of these errors:
>>>>>
>>>>> [Mon Jul 16 17:04:26 2012] [error] [client 10.10.228.132] PHP Parse
>>>>>
>>>>> error: syntax error, unexpected 's' (T_STRING) in
>>>>>
>>>>> /usr/share/drupal6/includes/common.inc(1731) : eval()'d code on line
>>>>>
>>>>> 1, referer: http://morse-ccmar.ualg.pt/edge/
>>>>>
>>>>>
>>>>> On line 1731 there is the following: print eval('?>'. $code);
>>>>>
>>>>>
>>>>> Does that $code variable have anything to do with your theme?
>>>>>
>>>>>
>>>>> After the 300 secs, I get:
>>>>>
>>>>> [Mon Jul 16 17:09:26 2012] [error] [client 10.10.228.132] PHP Fatal
>>>>>
>>>>> error: Maximum execution time of 300 seconds exceeded in
>>>>>
>>>>> /usr/share/drupal6/includes/database.inc on line 225, referer:
>>>>>
>>>>> http://morse-ccmar.ualg.pt/edge/
>>>>>
>>>>>
>>>>> Thanks,
>>>>>
>>>>>
>>>>> Tony
>>>>>
>>>>>
>>>>> On Mon, Jul 16, 2012 at 3:08 PM, Stephen Ficklin <[hidden email]>
>>>>>
>>>>> wrote:
>>>>>
>>>>>
>>>>> Hi Tony,
>>>>>
>>>>>
>>>>> Yes, the problem is the timeout issue. If you go into your php.ini
>>>>> file
>>>>>
>>>>> (/etc/php5/apache2/php.ini on my box) and change the max_execution_time
>>>>>
>>>>> to
>>>>>
>>>>> something larger. However, this page should not take more than 30
>>>>>
>>>>> seconds
>>>>>
>>>>> to load so we can try to figure out what's going on once the page
>>>>>
>>>>> displays.
>>>>>
>>>>>
>>>>> Stephen
>>>>>
>>>>>
>>>>>
>>>>> On 7/16/2012 9:54 AM, Tony Power wrote:
>>>>>
>>>>>
>>>>> Hi Stephen,
>>>>>
>>>>>
>>>>> In the logs there is nothing about the theme loading. Everything seems
>>>>>
>>>>> to work well.
>>>>>
>>>>> You still have that admin account that allows you to access the logs,
>>>>>
>>>>> just in case you wish to have a look. But you wont find anything :P
>>>>>
>>>>> From the apache log I get:
>>>>>
>>>>> [Mon Jul 16 14:45:52 2012] [error] [client 10.10.228.135] PHP Parse
>>>>>
>>>>> error: syntax error, unexpected 's' (T_STRING) in
>>>>>
>>>>> /usr/share/drupal6/includes/common.inc(1731) : eval()'d code on line
>>>>>
>>>>> 1, referer: http://morse-ccmar.ualg.pt/edge/
>>>>>
>>>>> [Mon Jul 16 14:46:27 2012] [error] [client 10.10.228.135] PHP Fatal
>>>>>
>>>>> error: Maximum execution time of 30 seconds exceeded in
>>>>>
>>>>> /usr/share/drupal6/includes/database.inc on line 225, referer:
>>>>>
>>>>> http://morse-ccmar.ualg.pt/edge/
>>>>>
>>>>>
>>>>> I guess it should be related to the second error?
>>>>>
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Tony
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Mon, Jul 16, 2012 at 2:23 PM, Stephen Ficklin <[hidden email]>
>>>>>
>>>>> wrote:
>>>>>
>>>>>
>>>>> Hi Tony,
>>>>>
>>>>>
>>>>> Can you send me the server logs after you load that page and look in
>>>>>
>>>>> the
>>>>>
>>>>> Drupal logs and let me know if you see anything there that might
>>>>>
>>>>> apply.
>>>>>
>>>>>
>>>>> You get a page that looks like that when an error occurs in building
>>>>>
>>>>> the
>>>>>
>>>>> template. It worked fine at my end so something is different about
>>>>>
>>>>> your
>>>>>
>>>>> setup that is making it do that.
>>>>>
>>>>>
>>>>> Yes, you are correct, you just needed to update the theme.
>>>>>
>>>>>
>>>>> Stephen
>>>>>
>>>>>
>>>>>
>>>>> On 7/16/2012 8:58 AM, Tony Power wrote:
>>>>>
>>>>>
>>>>> Hi Stephen,
>>>>>
>>>>>
>>>>> Just updated to the new Tripal Theme.
>>>>>
>>>>> Something is not working properly. To understand what I mean, please,
>>>>>
>>>>> click on one of the contigs.
>>>>>
>>>>>
>>>>> Do I also need to update the Tripal module? I just updated the Theme.
>>>>>
>>>>>
>>>>> Thanks ;)
>>>>>
>>>>>
>>>>> Tony
>>>>>
>>>>>
>>>>>
>>>>> On Sat, Jul 14, 2012 at 3:04 AM, Stephen Ficklin
>>>>>
>>>>> <[hidden email]>
>>>>>
>>>>> wrote:
>>>>>
>>>>>
>>>>> Hi Tony,
>>>>>
>>>>>
>>>>> If you get the most recent version of the tripal_theme 6.x-1.x
>>>>>
>>>>> branch
>>>>>
>>>>> from
>>>>>
>>>>> the development git repository it now contains an update that
>>>>>
>>>>> resolves
>>>>>
>>>>> the
>>>>>
>>>>> issue with the EST_match that you are having. Let me know if it
>>>>>
>>>>> works
>>>>>
>>>>> for
>>>>>
>>>>> you.
>>>>>
>>>>>
>>>>> http://drupal.org/node/1342972/git-instructions/6.x-1.x
>>>>>
>>>>>
>>>>>
>>>>> Stephen
>>>>>
>>>>>
>>>>>
>>>>> On 7/10/2012 9:26 AM, Stephen Ficklin wrote:
>>>>>
>>>>>
>>>>> Hi Tony,
>>>>>
>>>>>
>>>>> Good morning. I'm CC'ing the list as your question about the
>>>>>
>>>>> EST_match
>>>>>
>>>>> may be helpful for others. The behavior you describe is correct
>>>>>
>>>>> for
>>>>>
>>>>> the
>>>>>
>>>>> way
>>>>>
>>>>> the alignments are stored. ESTs are aligned to contigs via an
>>>>>
>>>>> 'EST_match'
>>>>>
>>>>> feature in your GFF file. This is because an EST does not always
>>>>>
>>>>> overlap
>>>>>
>>>>> completely with the contig depending on the software used to do the
>>>>>
>>>>> assembly--only portions of ESTs may align. Therefore we use an
>>>>>
>>>>> EST_match
>>>>>
>>>>> feature for the alignment. See here for an example:
>>>>>
>>>>> http://gmod.org/wiki/GFF#Alignments
>>>>>
>>>>>
>>>>> EST --> EST_match <-- Contig
>>>>>
>>>>>
>>>>> In reality you don't want the site visitors to see the EST_match
>>>>>
>>>>> features.
>>>>>
>>>>> But by default Tripal treats all features the same. It doesn't know
>>>>>
>>>>> the
>>>>>
>>>>> difference between a gene, mRNA, contig, EST, EST_match, etc. So
>>>>>
>>>>> that
>>>>>
>>>>> is
>>>>>
>>>>> why you have links to EST_matches on your contig alignments page
>>>>>
>>>>> rather
>>>>>
>>>>> than
>>>>>
>>>>> links to ESTs. So, to get links to your ESTs on your contig page
>>>>>
>>>>> and
>>>>>
>>>>> to
>>>>>
>>>>> bypass the EST_match feature you need to edit the
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> sites/all/themes/tripal_theme/tripal_feature/tripal_feature_featurelocs_as_parent.tpl.php
>>>>>
>>>>> to handle that special case. I believe however that I can make
>>>>>
>>>>> that
>>>>>
>>>>> adjustment in the template for you in the development code. When
>>>>>
>>>>> it's
>>>>>
>>>>> ready
>>>>>
>>>>> I'll let you know.
>>>>>
>>>>>
>>>>> Stephen
>>>>>
>>>>>
>>>>>
>>>>> On 7/10/2012 5:45 AM, Tony Power wrote:
>>>>>
>>>>>
>>>>> Hi again Stephen,
>>>>>
>>>>>
>>>>> I noticed some strange behavior on the site.
>>>>>
>>>>>
>>>>> For instance:
>>>>>
>>>>> 1-Select the first contig and then select "Alignments".
>>>>>
>>>>> 2-Now select the first EST_match.
>>>>>
>>>>> 3-Now "EST_match Sequence" -> No sequence is shown;
>>>>>
>>>>>
>>>>> 4-Now select "Alignments" (of that EST_match).
>>>>>
>>>>> 5-From the alignments select the EST_match that it aligns to.
>>>>>
>>>>> 6-Select "EST_match Sequence" -> The sequence is shown.
>>>>>
>>>>>
>>>>> What might be the problem?
>>>>>
>>>>>
>>>>> Obrigado,
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>

Stephen Ficklin-2

Re: [Gmod-tripal-devel] EST_match for unigenes

Hi Tony,

There should be a file named 'tripal_feature_alignments.tpl.php' in the
tripal_theme/tripal_feature directory. Is it missing? It looks like
your site is trying to find it in the module rather than the theme
directory which is typical if the file is missing from the theme. I
just checked the repository for the 6.x-1.x branch of the Triapl theme
and the file is there.

Stephen

On 7/23/2012 4:06 PM, Tony Power wrote:

> Hi Stephen,
>
> Thanks for the prompt reply.
> I am sorry but I didn't the theme had been updated.
> Now it looks like that we have something. Nevertheless:
>
> warning: include(./sites/all/modules/tripal/tripal_feature/tripal_feature_alignments.tpl.php):
> failed to open stream: No such file or directory in
> /usr/share/drupal6/includes/theme.inc on line 1079.
> warning: include(): Failed opening
> './sites/all/modules/tripal/tripal_feature/tripal_feature_alignments.tpl.php'
> for inclusion (include_path='.:/usr/share/php:/usr/share/pear') in
> /usr/share/drupal6/includes/theme.inc on line 1079.
>
> shows up on the top of the formatted feature page.
>
> This is what I have in the tripal_feature dir:
> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal/tripal_feature# ls
> fasta_loader.php tripal_feature.info
> gff_loader.php tripal_feature.install
> indexFeatures.php tripal_feature.module
> syncFeatures.php tripal_feature-properties.inc
> tripal_feature.admin.inc tripal_feature-relationships.inc
> tripal_feature.api.inc tripal_feature-secondary_tables.inc
> tripal_feature.coder_ignores.txt tripal_feature.views.inc
> tripal_feature-db_references.inc views_handlers
> tripal_feature-delete.inc
>
>
>
> Thanks,
> Tony
>
>
> On Mon, Jul 23, 2012 at 8:41 PM, Stephen Ficklin <[hidden email]> wrote:
>> Hi Tony,
>>
>> I provided a fix on Friday for the problem in the 6.x-1.x branch. You have
>> to update both Tripal and the Tripal theme to version 6.x-1.x. Have you
>> done both and still have the bad page?
>>
>> Stephen
>>
>>
>> On 7/23/2012 3:27 PM, Tony Power wrote:
>>> Hi Stephen,
>>>
>>> Did that.
>>> In any case, it didn't fix that problem of presenting an unformatted
>>> feature webpage. But I guess you've already identified the problem.
>>> I'll just wait for the fix.
>>>
>>> Thanks,
>>> Tony
>>>
>>> On Mon, Jul 23, 2012 at 7:48 PM, Stephen Ficklin <[hidden email]>
>>> wrote:
>>>> Hi Tony,
>>>>
>>>> You should be able to just switch right over to the 6.x-1.x branch:
>>>>
>>>> git checkout 6.x-1.x
>>>>
>>>> If you still get problems then you can wipe it clean (after disabling the
>>>> Tripal modules) and just start over with the 6.x-1.x branch as you
>>>> suggest.
>>>>
>>>> Stephen
>>>>
>>>>
>>>>
>>>> On 7/23/2012 2:34 PM, Tony Power wrote:
>>>>> Ho Lacey-Anne,
>>>>>
>>>>> Here is what I get:
>>>>> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# git checkout
>>>>> master
>>>>> Branch master set up to track remote branch master from origin.
>>>>> Switched to a new branch 'master'
>>>>> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# git pull origin
>>>>> master
>>>>> fatal: Couldn't find remote ref master
>>>>> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# Unexpected
>>>>> end of command stream
>>>>>
>>>>> Did I do anything wrong?
>>>>>
>>>>> Thanks,
>>>>> Tony
>>>>>
>>>>> On Mon, Jul 16, 2012 at 10:15 PM, Lacey-Anne Sanderson
>>>>> <[hidden email]> wrote:
>>>>>> Hi Tony,
>>>>>>
>>>>>> The newest dev version is on a different branch (we needed to make the
>>>>>> change to adhere to drupal standards). You need to checkout the master
>>>>>> branch (git checkout master) and then pull from the drupal.org
>>>>>> repository
>>>>>> (git pull origin master) and then checkout the new branch (git checkout
>>>>>> 6.x-1.x). From here on in you simply need to pull from the drupal.org
>>>>>> repository to get the latest development snapshot (git pull origin
>>>>>> 6.x-1.x).
>>>>>>
>>>>>> You can just replace the entire module directory with a new version of
>>>>>> tripal though it is recommended to first disable all your tripal
>>>>>> modules
>>>>>> (configuration and sync'd features will remain and be available once
>>>>>> you
>>>>>> re-enable the module -you only lose data if you uninstall the modules).
>>>>>>
>>>>>> Sorry for the extra steps,
>>>>>> ~Lacey
>>>>>>
>>>>>> PS. I am also not experiencing any errors on my contig pages...
>>>>>>
>>>>>> ------------------------------------------------------
>>>>>> Lacey-Anne Sanderson
>>>>>> Bioinformaticist
>>>>>> Pulse Crop Breeding and Genetics
>>>>>> Phone: (306) 966-4975
>>>>>> Email: [hidden email]
>>>>>> Room 3C06 Agriculture
>>>>>> Department of Plant Sciences
>>>>>> University of Saskatchewan
>>>>>>
>>>>>> On 2012-07-16, at 3:05 PM, Tony Power wrote:
>>>>>>
>>>>>> Hi Stephen and Lacey-Anne,
>>>>>>
>>>>>> After testing I immediately reset it to 30 secs again. But the result
>>>>>> is the same. 30 or 300 the errors are the same, it just takes longer
>>>>>> to display the (unformatted) webpage.
>>>>>>
>>>>>> After trying to Lacey-Anne's suggestion I get the same result.
>>>>>> I have the latest dev branch for the Tripal module (I guess):
>>>>>> # git status
>>>>>> # On branch 6.x-0.4-dev
>>>>>> nothing to commit (working directory clean)
>>>>>>
>>>>>> The new Theme version you provided me in a previous email is not
>>>>>> development (could it be this?)
>>>>>> git status
>>>>>> # On branch 6.x-1.x
>>>>>> nothing to commit (working directory clean)
>>>>>>
>>>>>> If there is another module version, can I just delete the whole tripal
>>>>>> (module) and replace it by the new?
>>>>>> Where are all the tripal site related configurations saved?
>>>>>>
>>>>>> Thanks,
>>>>>> Tony
>>>>>>
>>>>>> On Mon, Jul 16, 2012 at 8:30 PM, Stephen Ficklin <[hidden email]>
>>>>>> wrote:
>>>>>>
>>>>>> Hi Tony,
>>>>>>
>>>>>>
>>>>>> I'm having a bit of trouble debugging this one because I'm not having
>>>>>> the
>>>>>>
>>>>>> same problem. I was unable to load this feature on your site without
>>>>>> it
>>>>>>
>>>>>> taking longer than 30 seconds:
>>>>>> http://morse-ccmar.ualg.pt/edge/ID327210.
>>>>>>
>>>>>> Would you mind sending me the snippet of the GFF file that contains
>>>>>> that
>>>>>>
>>>>>> contig and EST alignments?
>>>>>>
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Stephen
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 7/16/2012 12:18 PM, Tony Power wrote:
>>>>>>
>>>>>>
>>>>>> Well, it shouldn't have anything to do with the common.inc error,
>>>>>>
>>>>>> since even if I restore the old theme I still get that error and the
>>>>>>
>>>>>> features show well again. So, something should be happening with the
>>>>>>
>>>>>> new version of your theme (or not) :P.
>>>>>>
>>>>>>
>>>>>> In any case it's a weird error since I don't do any updates for a long
>>>>>>
>>>>>> time.
>>>>>>
>>>>>>
>>>>>> On Mon, Jul 16, 2012 at 5:10 PM, Tony Power <[hidden email]> wrote:
>>>>>>
>>>>>>
>>>>>> Hi Stephen,
>>>>>>
>>>>>>
>>>>>> I changed it to 300 and it just stands there waiting.
>>>>>>
>>>>>> Nevertheless I can see that it fired many of these errors:
>>>>>>
>>>>>> [Mon Jul 16 17:04:26 2012] [error] [client 10.10.228.132] PHP Parse
>>>>>>
>>>>>> error: syntax error, unexpected 's' (T_STRING) in
>>>>>>
>>>>>> /usr/share/drupal6/includes/common.inc(1731) : eval()'d code on line
>>>>>>
>>>>>> 1, referer: http://morse-ccmar.ualg.pt/edge/
>>>>>>
>>>>>>
>>>>>> On line 1731 there is the following: print eval('?>'. $code);
>>>>>>
>>>>>>
>>>>>> Does that $code variable have anything to do with your theme?
>>>>>>
>>>>>>
>>>>>> After the 300 secs, I get:
>>>>>>
>>>>>> [Mon Jul 16 17:09:26 2012] [error] [client 10.10.228.132] PHP Fatal
>>>>>>
>>>>>> error: Maximum execution time of 300 seconds exceeded in
>>>>>>
>>>>>> /usr/share/drupal6/includes/database.inc on line 225, referer:
>>>>>>
>>>>>> http://morse-ccmar.ualg.pt/edge/
>>>>>>
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>>
>>>>>> Tony
>>>>>>
>>>>>>
>>>>>> On Mon, Jul 16, 2012 at 3:08 PM, Stephen Ficklin <[hidden email]>
>>>>>>
>>>>>> wrote:
>>>>>>
>>>>>>
>>>>>> Hi Tony,
>>>>>>
>>>>>>
>>>>>> Yes, the problem is the timeout issue. If you go into your php.ini
>>>>>> file
>>>>>>
>>>>>> (/etc/php5/apache2/php.ini on my box) and change the max_execution_time
>>>>>>
>>>>>> to
>>>>>>
>>>>>> something larger. However, this page should not take more than 30
>>>>>>
>>>>>> seconds
>>>>>>
>>>>>> to load so we can try to figure out what's going on once the page
>>>>>>
>>>>>> displays.
>>>>>>
>>>>>>
>>>>>> Stephen
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 7/16/2012 9:54 AM, Tony Power wrote:
>>>>>>
>>>>>>
>>>>>> Hi Stephen,
>>>>>>
>>>>>>
>>>>>> In the logs there is nothing about the theme loading. Everything seems
>>>>>>
>>>>>> to work well.
>>>>>>
>>>>>> You still have that admin account that allows you to access the logs,
>>>>>>
>>>>>> just in case you wish to have a look. But you wont find anything :P
>>>>>>
>>>>>> From the apache log I get:
>>>>>>
>>>>>> [Mon Jul 16 14:45:52 2012] [error] [client 10.10.228.135] PHP Parse
>>>>>>
>>>>>> error: syntax error, unexpected 's' (T_STRING) in
>>>>>>
>>>>>> /usr/share/drupal6/includes/common.inc(1731) : eval()'d code on line
>>>>>>
>>>>>> 1, referer: http://morse-ccmar.ualg.pt/edge/
>>>>>>
>>>>>> [Mon Jul 16 14:46:27 2012] [error] [client 10.10.228.135] PHP Fatal
>>>>>>
>>>>>> error: Maximum execution time of 30 seconds exceeded in
>>>>>>
>>>>>> /usr/share/drupal6/includes/database.inc on line 225, referer:
>>>>>>
>>>>>> http://morse-ccmar.ualg.pt/edge/
>>>>>>
>>>>>>
>>>>>> I guess it should be related to the second error?
>>>>>>
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Tony
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Mon, Jul 16, 2012 at 2:23 PM, Stephen Ficklin <[hidden email]>
>>>>>>
>>>>>> wrote:
>>>>>>
>>>>>>
>>>>>> Hi Tony,
>>>>>>
>>>>>>
>>>>>> Can you send me the server logs after you load that page and look in
>>>>>>
>>>>>> the
>>>>>>
>>>>>> Drupal logs and let me know if you see anything there that might
>>>>>>
>>>>>> apply.
>>>>>>
>>>>>>
>>>>>> You get a page that looks like that when an error occurs in building
>>>>>>
>>>>>> the
>>>>>>
>>>>>> template. It worked fine at my end so something is different about
>>>>>>
>>>>>> your
>>>>>>
>>>>>> setup that is making it do that.
>>>>>>
>>>>>>
>>>>>> Yes, you are correct, you just needed to update the theme.
>>>>>>
>>>>>>
>>>>>> Stephen
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 7/16/2012 8:58 AM, Tony Power wrote:
>>>>>>
>>>>>>
>>>>>> Hi Stephen,
>>>>>>
>>>>>>
>>>>>> Just updated to the new Tripal Theme.
>>>>>>
>>>>>> Something is not working properly. To understand what I mean, please,
>>>>>>
>>>>>> click on one of the contigs.
>>>>>>
>>>>>>
>>>>>> Do I also need to update the Tripal module? I just updated the Theme.
>>>>>>
>>>>>>
>>>>>> Thanks ;)
>>>>>>
>>>>>>
>>>>>> Tony
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Sat, Jul 14, 2012 at 3:04 AM, Stephen Ficklin
>>>>>>
>>>>>> <[hidden email]>
>>>>>>
>>>>>> wrote:
>>>>>>
>>>>>>
>>>>>> Hi Tony,
>>>>>>
>>>>>>
>>>>>> If you get the most recent version of the tripal_theme 6.x-1.x
>>>>>>
>>>>>> branch
>>>>>>
>>>>>> from
>>>>>>
>>>>>> the development git repository it now contains an update that
>>>>>>
>>>>>> resolves
>>>>>>
>>>>>> the
>>>>>>
>>>>>> issue with the EST_match that you are having. Let me know if it
>>>>>>
>>>>>> works
>>>>>>
>>>>>> for
>>>>>>
>>>>>> you.
>>>>>>
>>>>>>
>>>>>> http://drupal.org/node/1342972/git-instructions/6.x-1.x
>>>>>>
>>>>>>
>>>>>>
>>>>>> Stephen
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 7/10/2012 9:26 AM, Stephen Ficklin wrote:
>>>>>>
>>>>>>
>>>>>> Hi Tony,
>>>>>>
>>>>>>
>>>>>> Good morning. I'm CC'ing the list as your question about the
>>>>>>
>>>>>> EST_match
>>>>>>
>>>>>> may be helpful for others. The behavior you describe is correct
>>>>>>
>>>>>> for
>>>>>>
>>>>>> the
>>>>>>
>>>>>> way
>>>>>>
>>>>>> the alignments are stored. ESTs are aligned to contigs via an
>>>>>>
>>>>>> 'EST_match'
>>>>>>
>>>>>> feature in your GFF file. This is because an EST does not always
>>>>>>
>>>>>> overlap
>>>>>>
>>>>>> completely with the contig depending on the software used to do the
>>>>>>
>>>>>> assembly--only portions of ESTs may align. Therefore we use an
>>>>>>
>>>>>> EST_match
>>>>>>
>>>>>> feature for the alignment. See here for an example:
>>>>>>
>>>>>> http://gmod.org/wiki/GFF#Alignments
>>>>>>
>>>>>>
>>>>>> EST --> EST_match <-- Contig
>>>>>>
>>>>>>
>>>>>> In reality you don't want the site visitors to see the EST_match
>>>>>>
>>>>>> features.
>>>>>>
>>>>>> But by default Tripal treats all features the same. It doesn't know
>>>>>>
>>>>>> the
>>>>>>
>>>>>> difference between a gene, mRNA, contig, EST, EST_match, etc. So
>>>>>>
>>>>>> that
>>>>>>
>>>>>> is
>>>>>>
>>>>>> why you have links to EST_matches on your contig alignments page
>>>>>>
>>>>>> rather
>>>>>>
>>>>>> than
>>>>>>
>>>>>> links to ESTs. So, to get links to your ESTs on your contig page
>>>>>>
>>>>>> and
>>>>>>
>>>>>> to
>>>>>>
>>>>>> bypass the EST_match feature you need to edit the
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> sites/all/themes/tripal_theme/tripal_feature/tripal_feature_featurelocs_as_parent.tpl.php
>>>>>>
>>>>>> to handle that special case. I believe however that I can make
>>>>>>
>>>>>> that
>>>>>>
>>>>>> adjustment in the template for you in the development code. When
>>>>>>
>>>>>> it's
>>>>>>
>>>>>> ready
>>>>>>
>>>>>> I'll let you know.
>>>>>>
>>>>>>
>>>>>> Stephen
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 7/10/2012 5:45 AM, Tony Power wrote:
>>>>>>
>>>>>>
>>>>>> Hi again Stephen,
>>>>>>
>>>>>>
>>>>>> I noticed some strange behavior on the site.
>>>>>>
>>>>>>
>>>>>> For instance:
>>>>>>
>>>>>> 1-Select the first contig and then select "Alignments".
>>>>>>
>>>>>> 2-Now select the first EST_match.
>>>>>>
>>>>>> 3-Now "EST_match Sequence" -> No sequence is shown;
>>>>>>
>>>>>>
>>>>>> 4-Now select "Alignments" (of that EST_match).
>>>>>>
>>>>>> 5-From the alignments select the EST_match that it aligns to.
>>>>>>
>>>>>> 6-Select "EST_match Sequence" -> The sequence is shown.
>>>>>>
>>>>>>
>>>>>> What might be the problem?
>>>>>>
>>>>>>
>>>>>> Obrigado,
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>

Tony Power

Re: [Gmod-tripal-devel] EST_match for unigenes

Hi Stephen,

This is what I have:
root@morse-ccmar:/var/www/edge/sites/all/themes/tripal_theme# git branch
* 6.x-1.x
root@morse-ccmar:/var/www/edge/sites/all/themes/tripal_theme# git pull
Already up-to-date.

root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# git branch
6.x-0.4-dev
* 6.x-1.x
master
root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# git pull
Already up-to-date.

But, for instance, if I go to: http://morse-ccmar.ualg.pt/edge/ID327210
then I get:
warning: include(./sites/all/modules/tripal/tripal_feature/tripal_feature_alignments.tpl.php):
failed to open stream: No such file or directory in
/usr/share/drupal6/includes/theme.inc on line 1079.
warning: include(): Failed opening
'./sites/all/modules/tripal/tripal_feature/tripal_feature_alignments.tpl.php'
for inclusion (include_path='.:/usr/share/php:/usr/share/pear') in
/usr/share/drupal6/includes/theme.inc on line 1079.

As you can see:
root@morse-ccmar:/var/www/edge/sites/all/modules/tripal/tripal_feature# ls
fasta_loader.php tripal_feature.info
gff_loader.php tripal_feature.install
indexFeatures.php tripal_feature.module
syncFeatures.php tripal_feature-properties.inc
tripal_feature.admin.inc tripal_feature-relationships.inc
tripal_feature.api.inc tripal_feature-secondary_tables.inc
tripal_feature.coder_ignores.txt tripal_feature.views.inc
tripal_feature-db_references.inc views_handlers
tripal_feature-delete.inc

What could be the explanation for the missing file?

Thanks,
Tony

On Mon, Jul 23, 2012 at 9:13 PM, Stephen Ficklin <[hidden email]> wrote:

> Hi Tony,
>
> There should be a file named 'tripal_feature_alignments.tpl.php' in the
> tripal_theme/tripal_feature directory. Is it missing? It looks like your
> site is trying to find it in the module rather than the theme directory
> which is typical if the file is missing from the theme. I just checked the
> repository for the 6.x-1.x branch of the Triapl theme and the file is there.
>
> Stephen
>
>
> On 7/23/2012 4:06 PM, Tony Power wrote:
>>
>> Hi Stephen,
>>
>> Thanks for the prompt reply.
>> I am sorry but I didn't the theme had been updated.
>> Now it looks like that we have something. Nevertheless:
>>
>> warning:
>> include(./sites/all/modules/tripal/tripal_feature/tripal_feature_alignments.tpl.php):
>> failed to open stream: No such file or directory in
>> /usr/share/drupal6/includes/theme.inc on line 1079.
>> warning: include(): Failed opening
>>
>> './sites/all/modules/tripal/tripal_feature/tripal_feature_alignments.tpl.php'
>> for inclusion (include_path='.:/usr/share/php:/usr/share/pear') in
>> /usr/share/drupal6/includes/theme.inc on line 1079.
>>
>> shows up on the top of the formatted feature page.
>>
>> This is what I have in the tripal_feature dir:
>> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal/tripal_feature# ls
>> fasta_loader.php tripal_feature.info
>> gff_loader.php tripal_feature.install
>> indexFeatures.php tripal_feature.module
>> syncFeatures.php tripal_feature-properties.inc
>> tripal_feature.admin.inc tripal_feature-relationships.inc
>> tripal_feature.api.inc tripal_feature-secondary_tables.inc
>> tripal_feature.coder_ignores.txt tripal_feature.views.inc
>> tripal_feature-db_references.inc views_handlers
>> tripal_feature-delete.inc
>>
>>
>>
>> Thanks,
>> Tony
>>
>>
>> On Mon, Jul 23, 2012 at 8:41 PM, Stephen Ficklin <[hidden email]>
>> wrote:
>>>
>>> Hi Tony,
>>>
>>> I provided a fix on Friday for the problem in the 6.x-1.x branch. You
>>> have
>>> to update both Tripal and the Tripal theme to version 6.x-1.x. Have you
>>> done both and still have the bad page?
>>>
>>> Stephen
>>>
>>>
>>> On 7/23/2012 3:27 PM, Tony Power wrote:
>>>>
>>>> Hi Stephen,
>>>>
>>>> Did that.
>>>> In any case, it didn't fix that problem of presenting an unformatted
>>>> feature webpage. But I guess you've already identified the problem.
>>>> I'll just wait for the fix.
>>>>
>>>> Thanks,
>>>> Tony
>>>>
>>>> On Mon, Jul 23, 2012 at 7:48 PM, Stephen Ficklin <[hidden email]>
>>>> wrote:
>>>>>
>>>>> Hi Tony,
>>>>>
>>>>> You should be able to just switch right over to the 6.x-1.x branch:
>>>>>
>>>>> git checkout 6.x-1.x
>>>>>
>>>>> If you still get problems then you can wipe it clean (after disabling
>>>>> the
>>>>> Tripal modules) and just start over with the 6.x-1.x branch as you
>>>>> suggest.
>>>>>
>>>>> Stephen
>>>>>
>>>>>
>>>>>
>>>>> On 7/23/2012 2:34 PM, Tony Power wrote:
>>>>>>
>>>>>> Ho Lacey-Anne,
>>>>>>
>>>>>> Here is what I get:
>>>>>> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# git checkout
>>>>>> master
>>>>>> Branch master set up to track remote branch master from origin.
>>>>>> Switched to a new branch 'master'
>>>>>> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# git pull
>>>>>> origin
>>>>>> master
>>>>>> fatal: Couldn't find remote ref master
>>>>>> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# Unexpected
>>>>>> end of command stream
>>>>>>
>>>>>> Did I do anything wrong?
>>>>>>
>>>>>> Thanks,
>>>>>> Tony
>>>>>>
>>>>>> On Mon, Jul 16, 2012 at 10:15 PM, Lacey-Anne Sanderson
>>>>>> <[hidden email]> wrote:
>>>>>>>
>>>>>>> Hi Tony,
>>>>>>>
>>>>>>> The newest dev version is on a different branch (we needed to make
>>>>>>> the
>>>>>>> change to adhere to drupal standards). You need to checkout the
>>>>>>> master
>>>>>>> branch (git checkout master) and then pull from the drupal.org
>>>>>>> repository
>>>>>>> (git pull origin master) and then checkout the new branch (git
>>>>>>> checkout
>>>>>>> 6.x-1.x). From here on in you simply need to pull from the drupal.org
>>>>>>> repository to get the latest development snapshot (git pull origin
>>>>>>> 6.x-1.x).
>>>>>>>
>>>>>>> You can just replace the entire module directory with a new version
>>>>>>> of
>>>>>>> tripal though it is recommended to first disable all your tripal
>>>>>>> modules
>>>>>>> (configuration and sync'd features will remain and be available once
>>>>>>> you
>>>>>>> re-enable the module -you only lose data if you uninstall the
>>>>>>> modules).
>>>>>>>
>>>>>>> Sorry for the extra steps,
>>>>>>> ~Lacey
>>>>>>>
>>>>>>> PS. I am also not experiencing any errors on my contig pages...
>>>>>>>
>>>>>>> ------------------------------------------------------
>>>>>>> Lacey-Anne Sanderson
>>>>>>> Bioinformaticist
>>>>>>> Pulse Crop Breeding and Genetics
>>>>>>> Phone: (306) 966-4975
>>>>>>> Email: [hidden email]
>>>>>>> Room 3C06 Agriculture
>>>>>>> Department of Plant Sciences
>>>>>>> University of Saskatchewan
>>>>>>>
>>>>>>> On 2012-07-16, at 3:05 PM, Tony Power wrote:
>>>>>>>
>>>>>>> Hi Stephen and Lacey-Anne,
>>>>>>>
>>>>>>> After testing I immediately reset it to 30 secs again. But the result
>>>>>>> is the same. 30 or 300 the errors are the same, it just takes longer
>>>>>>> to display the (unformatted) webpage.
>>>>>>>
>>>>>>> After trying to Lacey-Anne's suggestion I get the same result.
>>>>>>> I have the latest dev branch for the Tripal module (I guess):
>>>>>>> # git status
>>>>>>> # On branch 6.x-0.4-dev
>>>>>>> nothing to commit (working directory clean)
>>>>>>>
>>>>>>> The new Theme version you provided me in a previous email is not
>>>>>>> development (could it be this?)
>>>>>>> git status
>>>>>>> # On branch 6.x-1.x
>>>>>>> nothing to commit (working directory clean)
>>>>>>>
>>>>>>> If there is another module version, can I just delete the whole
>>>>>>> tripal
>>>>>>> (module) and replace it by the new?
>>>>>>> Where are all the tripal site related configurations saved?
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Tony
>>>>>>>
>>>>>>> On Mon, Jul 16, 2012 at 8:30 PM, Stephen Ficklin
>>>>>>> <[hidden email]>
>>>>>>> wrote:
>>>>>>>
>>>>>>> Hi Tony,
>>>>>>>
>>>>>>>
>>>>>>> I'm having a bit of trouble debugging this one because I'm not having
>>>>>>> the
>>>>>>>
>>>>>>> same problem. I was unable to load this feature on your site without
>>>>>>> it
>>>>>>>
>>>>>>> taking longer than 30 seconds:
>>>>>>> http://morse-ccmar.ualg.pt/edge/ID327210.
>>>>>>>
>>>>>>> Would you mind sending me the snippet of the GFF file that contains
>>>>>>> that
>>>>>>>
>>>>>>> contig and EST alignments?
>>>>>>>
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Stephen
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 7/16/2012 12:18 PM, Tony Power wrote:
>>>>>>>
>>>>>>>
>>>>>>> Well, it shouldn't have anything to do with the common.inc error,
>>>>>>>
>>>>>>> since even if I restore the old theme I still get that error and the
>>>>>>>
>>>>>>> features show well again. So, something should be happening with the
>>>>>>>
>>>>>>> new version of your theme (or not) :P.
>>>>>>>
>>>>>>>
>>>>>>> In any case it's a weird error since I don't do any updates for a
>>>>>>> long
>>>>>>>
>>>>>>> time.
>>>>>>>
>>>>>>>
>>>>>>> On Mon, Jul 16, 2012 at 5:10 PM, Tony Power <[hidden email]>
>>>>>>> wrote:
>>>>>>>
>>>>>>>
>>>>>>> Hi Stephen,
>>>>>>>
>>>>>>>
>>>>>>> I changed it to 300 and it just stands there waiting.
>>>>>>>
>>>>>>> Nevertheless I can see that it fired many of these errors:
>>>>>>>
>>>>>>> [Mon Jul 16 17:04:26 2012] [error] [client 10.10.228.132] PHP Parse
>>>>>>>
>>>>>>> error: syntax error, unexpected 's' (T_STRING) in
>>>>>>>
>>>>>>> /usr/share/drupal6/includes/common.inc(1731) : eval()'d code on line
>>>>>>>
>>>>>>> 1, referer: http://morse-ccmar.ualg.pt/edge/
>>>>>>>
>>>>>>>
>>>>>>> On line 1731 there is the following: print eval('?>'. $code);
>>>>>>>
>>>>>>>
>>>>>>> Does that $code variable have anything to do with your theme?
>>>>>>>
>>>>>>>
>>>>>>> After the 300 secs, I get:
>>>>>>>
>>>>>>> [Mon Jul 16 17:09:26 2012] [error] [client 10.10.228.132] PHP Fatal
>>>>>>>
>>>>>>> error: Maximum execution time of 300 seconds exceeded in
>>>>>>>
>>>>>>> /usr/share/drupal6/includes/database.inc on line 225, referer:
>>>>>>>
>>>>>>> http://morse-ccmar.ualg.pt/edge/
>>>>>>>
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>>
>>>>>>> Tony
>>>>>>>
>>>>>>>
>>>>>>> On Mon, Jul 16, 2012 at 3:08 PM, Stephen Ficklin
>>>>>>> <[hidden email]>
>>>>>>>
>>>>>>> wrote:
>>>>>>>
>>>>>>>
>>>>>>> Hi Tony,
>>>>>>>
>>>>>>>
>>>>>>> Yes, the problem is the timeout issue. If you go into your php.ini
>>>>>>> file
>>>>>>>
>>>>>>> (/etc/php5/apache2/php.ini on my box) and change the
>>>>>>> max_execution_time
>>>>>>>
>>>>>>> to
>>>>>>>
>>>>>>> something larger. However, this page should not take more than 30
>>>>>>>
>>>>>>> seconds
>>>>>>>
>>>>>>> to load so we can try to figure out what's going on once the page
>>>>>>>
>>>>>>> displays.
>>>>>>>
>>>>>>>
>>>>>>> Stephen
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 7/16/2012 9:54 AM, Tony Power wrote:
>>>>>>>
>>>>>>>
>>>>>>> Hi Stephen,
>>>>>>>
>>>>>>>
>>>>>>> In the logs there is nothing about the theme loading. Everything
>>>>>>> seems
>>>>>>>
>>>>>>> to work well.
>>>>>>>
>>>>>>> You still have that admin account that allows you to access the logs,
>>>>>>>
>>>>>>> just in case you wish to have a look. But you wont find anything :P
>>>>>>>
>>>>>>> From the apache log I get:
>>>>>>>
>>>>>>> [Mon Jul 16 14:45:52 2012] [error] [client 10.10.228.135] PHP Parse
>>>>>>>
>>>>>>> error: syntax error, unexpected 's' (T_STRING) in
>>>>>>>
>>>>>>> /usr/share/drupal6/includes/common.inc(1731) : eval()'d code on line
>>>>>>>
>>>>>>> 1, referer: http://morse-ccmar.ualg.pt/edge/
>>>>>>>
>>>>>>> [Mon Jul 16 14:46:27 2012] [error] [client 10.10.228.135] PHP Fatal
>>>>>>>
>>>>>>> error: Maximum execution time of 30 seconds exceeded in
>>>>>>>
>>>>>>> /usr/share/drupal6/includes/database.inc on line 225, referer:
>>>>>>>
>>>>>>> http://morse-ccmar.ualg.pt/edge/
>>>>>>>
>>>>>>>
>>>>>>> I guess it should be related to the second error?
>>>>>>>
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Tony
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Mon, Jul 16, 2012 at 2:23 PM, Stephen Ficklin
>>>>>>> <[hidden email]>
>>>>>>>
>>>>>>> wrote:
>>>>>>>
>>>>>>>
>>>>>>> Hi Tony,
>>>>>>>
>>>>>>>
>>>>>>> Can you send me the server logs after you load that page and look in
>>>>>>>
>>>>>>> the
>>>>>>>
>>>>>>> Drupal logs and let me know if you see anything there that might
>>>>>>>
>>>>>>> apply.
>>>>>>>
>>>>>>>
>>>>>>> You get a page that looks like that when an error occurs in building
>>>>>>>
>>>>>>> the
>>>>>>>
>>>>>>> template. It worked fine at my end so something is different about
>>>>>>>
>>>>>>> your
>>>>>>>
>>>>>>> setup that is making it do that.
>>>>>>>
>>>>>>>
>>>>>>> Yes, you are correct, you just needed to update the theme.
>>>>>>>
>>>>>>>
>>>>>>> Stephen
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 7/16/2012 8:58 AM, Tony Power wrote:
>>>>>>>
>>>>>>>
>>>>>>> Hi Stephen,
>>>>>>>
>>>>>>>
>>>>>>> Just updated to the new Tripal Theme.
>>>>>>>
>>>>>>> Something is not working properly. To understand what I mean, please,
>>>>>>>
>>>>>>> click on one of the contigs.
>>>>>>>
>>>>>>>
>>>>>>> Do I also need to update the Tripal module? I just updated the Theme.
>>>>>>>
>>>>>>>
>>>>>>> Thanks ;)
>>>>>>>
>>>>>>>
>>>>>>> Tony
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Sat, Jul 14, 2012 at 3:04 AM, Stephen Ficklin
>>>>>>>
>>>>>>> <[hidden email]>
>>>>>>>
>>>>>>> wrote:
>>>>>>>
>>>>>>>
>>>>>>> Hi Tony,
>>>>>>>
>>>>>>>
>>>>>>> If you get the most recent version of the tripal_theme 6.x-1.x
>>>>>>>
>>>>>>> branch
>>>>>>>
>>>>>>> from
>>>>>>>
>>>>>>> the development git repository it now contains an update that
>>>>>>>
>>>>>>> resolves
>>>>>>>
>>>>>>> the
>>>>>>>
>>>>>>> issue with the EST_match that you are having. Let me know if it
>>>>>>>
>>>>>>> works
>>>>>>>
>>>>>>> for
>>>>>>>
>>>>>>> you.
>>>>>>>
>>>>>>>
>>>>>>> http://drupal.org/node/1342972/git-instructions/6.x-1.x
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Stephen
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 7/10/2012 9:26 AM, Stephen Ficklin wrote:
>>>>>>>
>>>>>>>
>>>>>>> Hi Tony,
>>>>>>>
>>>>>>>
>>>>>>> Good morning. I'm CC'ing the list as your question about the
>>>>>>>
>>>>>>> EST_match
>>>>>>>
>>>>>>> may be helpful for others. The behavior you describe is correct
>>>>>>>
>>>>>>> for
>>>>>>>
>>>>>>> the
>>>>>>>
>>>>>>> way
>>>>>>>
>>>>>>> the alignments are stored. ESTs are aligned to contigs via an
>>>>>>>
>>>>>>> 'EST_match'
>>>>>>>
>>>>>>> feature in your GFF file. This is because an EST does not always
>>>>>>>
>>>>>>> overlap
>>>>>>>
>>>>>>> completely with the contig depending on the software used to do the
>>>>>>>
>>>>>>> assembly--only portions of ESTs may align. Therefore we use an
>>>>>>>
>>>>>>> EST_match
>>>>>>>
>>>>>>> feature for the alignment. See here for an example:
>>>>>>>
>>>>>>> http://gmod.org/wiki/GFF#Alignments
>>>>>>>
>>>>>>>
>>>>>>> EST --> EST_match <-- Contig
>>>>>>>
>>>>>>>
>>>>>>> In reality you don't want the site visitors to see the EST_match
>>>>>>>
>>>>>>> features.
>>>>>>>
>>>>>>> But by default Tripal treats all features the same. It doesn't know
>>>>>>>
>>>>>>> the
>>>>>>>
>>>>>>> difference between a gene, mRNA, contig, EST, EST_match, etc. So
>>>>>>>
>>>>>>> that
>>>>>>>
>>>>>>> is
>>>>>>>
>>>>>>> why you have links to EST_matches on your contig alignments page
>>>>>>>
>>>>>>> rather
>>>>>>>
>>>>>>> than
>>>>>>>
>>>>>>> links to ESTs. So, to get links to your ESTs on your contig page
>>>>>>>
>>>>>>> and
>>>>>>>
>>>>>>> to
>>>>>>>
>>>>>>> bypass the EST_match feature you need to edit the
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> sites/all/themes/tripal_theme/tripal_feature/tripal_feature_featurelocs_as_parent.tpl.php
>>>>>>>
>>>>>>> to handle that special case. I believe however that I can make
>>>>>>>
>>>>>>> that
>>>>>>>
>>>>>>> adjustment in the template for you in the development code. When
>>>>>>>
>>>>>>> it's
>>>>>>>
>>>>>>> ready
>>>>>>>
>>>>>>> I'll let you know.
>>>>>>>
>>>>>>>
>>>>>>> Stephen
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 7/10/2012 5:45 AM, Tony Power wrote:
>>>>>>>
>>>>>>>
>>>>>>> Hi again Stephen,
>>>>>>>
>>>>>>>
>>>>>>> I noticed some strange behavior on the site.
>>>>>>>
>>>>>>>
>>>>>>> For instance:
>>>>>>>
>>>>>>> 1-Select the first contig and then select "Alignments".
>>>>>>>
>>>>>>> 2-Now select the first EST_match.
>>>>>>>
>>>>>>> 3-Now "EST_match Sequence" -> No sequence is shown;
>>>>>>>
>>>>>>>
>>>>>>> 4-Now select "Alignments" (of that EST_match).
>>>>>>>
>>>>>>> 5-From the alignments select the EST_match that it aligns to.
>>>>>>>
>>>>>>> 6-Select "EST_match Sequence" -> The sequence is shown.
>>>>>>>
>>>>>>>
>>>>>>> What might be the problem?
>>>>>>>
>>>>>>>
>>>>>>> Obrigado,
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>

Stephen Ficklin-2

Re: [Gmod-tripal-devel] EST_match for unigenes

Hi Tony,

if you have version 6.x-1.x for both the theme and the modules then try
clearing you cache. If you have drush you can run 'drush cc all'
anywhere in your Drupal directory. Or go to 'Administer' -> 'Site
Configuration' -> 'Performance' and click 'Clear cached data'.

The missing file should be here:
/var/www/edge/sites/all/themes/tripal_theme/tripal_feature/tripal_feature_alignments.tpl.php.

Stephen

On 7/24/2012 5:07 AM, Tony Power wrote:

> Hi Stephen,
>
> This is what I have:
> root@morse-ccmar:/var/www/edge/sites/all/themes/tripal_theme# git branch
> * 6.x-1.x
> root@morse-ccmar:/var/www/edge/sites/all/themes/tripal_theme# git pull
> Already up-to-date.
>
> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# git branch
> 6.x-0.4-dev
> * 6.x-1.x
> master
> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# git pull
> Already up-to-date.
>
> But, for instance, if I go to: http://morse-ccmar.ualg.pt/edge/ID327210
> then I get:
> warning: include(./sites/all/modules/tripal/tripal_feature/tripal_feature_alignments.tpl.php):
> failed to open stream: No such file or directory in
> /usr/share/drupal6/includes/theme.inc on line 1079.
> warning: include(): Failed opening
> './sites/all/modules/tripal/tripal_feature/tripal_feature_alignments.tpl.php'
> for inclusion (include_path='.:/usr/share/php:/usr/share/pear') in
> /usr/share/drupal6/includes/theme.inc on line 1079.
>
> As you can see:
> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal/tripal_feature# ls
> fasta_loader.php tripal_feature.info
> gff_loader.php tripal_feature.install
> indexFeatures.php tripal_feature.module
> syncFeatures.php tripal_feature-properties.inc
> tripal_feature.admin.inc tripal_feature-relationships.inc
> tripal_feature.api.inc tripal_feature-secondary_tables.inc
> tripal_feature.coder_ignores.txt tripal_feature.views.inc
> tripal_feature-db_references.inc views_handlers
> tripal_feature-delete.inc
>
> What could be the explanation for the missing file?
>
> Thanks,
> Tony
>
>
> On Mon, Jul 23, 2012 at 9:13 PM, Stephen Ficklin <[hidden email]> wrote:
>> Hi Tony,
>>
>> There should be a file named 'tripal_feature_alignments.tpl.php' in the
>> tripal_theme/tripal_feature directory. Is it missing? It looks like your
>> site is trying to find it in the module rather than the theme directory
>> which is typical if the file is missing from the theme. I just checked the
>> repository for the 6.x-1.x branch of the Triapl theme and the file is there.
>>
>> Stephen
>>
>>
>> On 7/23/2012 4:06 PM, Tony Power wrote:
>>> Hi Stephen,
>>>
>>> Thanks for the prompt reply.
>>> I am sorry but I didn't the theme had been updated.
>>> Now it looks like that we have something. Nevertheless:
>>>
>>> warning:
>>> include(./sites/all/modules/tripal/tripal_feature/tripal_feature_alignments.tpl.php):
>>> failed to open stream: No such file or directory in
>>> /usr/share/drupal6/includes/theme.inc on line 1079.
>>> warning: include(): Failed opening
>>>
>>> './sites/all/modules/tripal/tripal_feature/tripal_feature_alignments.tpl.php'
>>> for inclusion (include_path='.:/usr/share/php:/usr/share/pear') in
>>> /usr/share/drupal6/includes/theme.inc on line 1079.
>>>
>>> shows up on the top of the formatted feature page.
>>>
>>> This is what I have in the tripal_feature dir:
>>> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal/tripal_feature# ls
>>> fasta_loader.php tripal_feature.info
>>> gff_loader.php tripal_feature.install
>>> indexFeatures.php tripal_feature.module
>>> syncFeatures.php tripal_feature-properties.inc
>>> tripal_feature.admin.inc tripal_feature-relationships.inc
>>> tripal_feature.api.inc tripal_feature-secondary_tables.inc
>>> tripal_feature.coder_ignores.txt tripal_feature.views.inc
>>> tripal_feature-db_references.inc views_handlers
>>> tripal_feature-delete.inc
>>>
>>>
>>>
>>> Thanks,
>>> Tony
>>>
>>>
>>> On Mon, Jul 23, 2012 at 8:41 PM, Stephen Ficklin <[hidden email]>
>>> wrote:
>>>> Hi Tony,
>>>>
>>>> I provided a fix on Friday for the problem in the 6.x-1.x branch. You
>>>> have
>>>> to update both Tripal and the Tripal theme to version 6.x-1.x. Have you
>>>> done both and still have the bad page?
>>>>
>>>> Stephen
>>>>
>>>>
>>>> On 7/23/2012 3:27 PM, Tony Power wrote:
>>>>> Hi Stephen,
>>>>>
>>>>> Did that.
>>>>> In any case, it didn't fix that problem of presenting an unformatted
>>>>> feature webpage. But I guess you've already identified the problem.
>>>>> I'll just wait for the fix.
>>>>>
>>>>> Thanks,
>>>>> Tony
>>>>>
>>>>> On Mon, Jul 23, 2012 at 7:48 PM, Stephen Ficklin <[hidden email]>
>>>>> wrote:
>>>>>> Hi Tony,
>>>>>>
>>>>>> You should be able to just switch right over to the 6.x-1.x branch:
>>>>>>
>>>>>> git checkout 6.x-1.x
>>>>>>
>>>>>> If you still get problems then you can wipe it clean (after disabling
>>>>>> the
>>>>>> Tripal modules) and just start over with the 6.x-1.x branch as you
>>>>>> suggest.
>>>>>>
>>>>>> Stephen
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 7/23/2012 2:34 PM, Tony Power wrote:
>>>>>>> Ho Lacey-Anne,
>>>>>>>
>>>>>>> Here is what I get:
>>>>>>> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# git checkout
>>>>>>> master
>>>>>>> Branch master set up to track remote branch master from origin.
>>>>>>> Switched to a new branch 'master'
>>>>>>> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# git pull
>>>>>>> origin
>>>>>>> master
>>>>>>> fatal: Couldn't find remote ref master
>>>>>>> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# Unexpected
>>>>>>> end of command stream
>>>>>>>
>>>>>>> Did I do anything wrong?
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Tony
>>>>>>>
>>>>>>> On Mon, Jul 16, 2012 at 10:15 PM, Lacey-Anne Sanderson
>>>>>>> <[hidden email]> wrote:
>>>>>>>> Hi Tony,
>>>>>>>>
>>>>>>>> The newest dev version is on a different branch (we needed to make
>>>>>>>> the
>>>>>>>> change to adhere to drupal standards). You need to checkout the
>>>>>>>> master
>>>>>>>> branch (git checkout master) and then pull from the drupal.org
>>>>>>>> repository
>>>>>>>> (git pull origin master) and then checkout the new branch (git
>>>>>>>> checkout
>>>>>>>> 6.x-1.x). From here on in you simply need to pull from the drupal.org
>>>>>>>> repository to get the latest development snapshot (git pull origin
>>>>>>>> 6.x-1.x).
>>>>>>>>
>>>>>>>> You can just replace the entire module directory with a new version
>>>>>>>> of
>>>>>>>> tripal though it is recommended to first disable all your tripal
>>>>>>>> modules
>>>>>>>> (configuration and sync'd features will remain and be available once
>>>>>>>> you
>>>>>>>> re-enable the module -you only lose data if you uninstall the
>>>>>>>> modules).
>>>>>>>>
>>>>>>>> Sorry for the extra steps,
>>>>>>>> ~Lacey
>>>>>>>>
>>>>>>>> PS. I am also not experiencing any errors on my contig pages...
>>>>>>>>
>>>>>>>> ------------------------------------------------------
>>>>>>>> Lacey-Anne Sanderson
>>>>>>>> Bioinformaticist
>>>>>>>> Pulse Crop Breeding and Genetics
>>>>>>>> Phone: (306) 966-4975
>>>>>>>> Email: [hidden email]
>>>>>>>> Room 3C06 Agriculture
>>>>>>>> Department of Plant Sciences
>>>>>>>> University of Saskatchewan
>>>>>>>>
>>>>>>>> On 2012-07-16, at 3:05 PM, Tony Power wrote:
>>>>>>>>
>>>>>>>> Hi Stephen and Lacey-Anne,
>>>>>>>>
>>>>>>>> After testing I immediately reset it to 30 secs again. But the result
>>>>>>>> is the same. 30 or 300 the errors are the same, it just takes longer
>>>>>>>> to display the (unformatted) webpage.
>>>>>>>>
>>>>>>>> After trying to Lacey-Anne's suggestion I get the same result.
>>>>>>>> I have the latest dev branch for the Tripal module (I guess):
>>>>>>>> # git status
>>>>>>>> # On branch 6.x-0.4-dev
>>>>>>>> nothing to commit (working directory clean)
>>>>>>>>
>>>>>>>> The new Theme version you provided me in a previous email is not
>>>>>>>> development (could it be this?)
>>>>>>>> git status
>>>>>>>> # On branch 6.x-1.x
>>>>>>>> nothing to commit (working directory clean)
>>>>>>>>
>>>>>>>> If there is another module version, can I just delete the whole
>>>>>>>> tripal
>>>>>>>> (module) and replace it by the new?
>>>>>>>> Where are all the tripal site related configurations saved?
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Tony
>>>>>>>>
>>>>>>>> On Mon, Jul 16, 2012 at 8:30 PM, Stephen Ficklin
>>>>>>>> <[hidden email]>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>> Hi Tony,
>>>>>>>>
>>>>>>>>
>>>>>>>> I'm having a bit of trouble debugging this one because I'm not having
>>>>>>>> the
>>>>>>>>
>>>>>>>> same problem. I was unable to load this feature on your site without
>>>>>>>> it
>>>>>>>>
>>>>>>>> taking longer than 30 seconds:
>>>>>>>> http://morse-ccmar.ualg.pt/edge/ID327210.
>>>>>>>>
>>>>>>>> Would you mind sending me the snippet of the GFF file that contains
>>>>>>>> that
>>>>>>>>
>>>>>>>> contig and EST alignments?
>>>>>>>>
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Stephen
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On 7/16/2012 12:18 PM, Tony Power wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>> Well, it shouldn't have anything to do with the common.inc error,
>>>>>>>>
>>>>>>>> since even if I restore the old theme I still get that error and the
>>>>>>>>
>>>>>>>> features show well again. So, something should be happening with the
>>>>>>>>
>>>>>>>> new version of your theme (or not) :P.
>>>>>>>>
>>>>>>>>
>>>>>>>> In any case it's a weird error since I don't do any updates for a
>>>>>>>> long
>>>>>>>>
>>>>>>>> time.
>>>>>>>>
>>>>>>>>
>>>>>>>> On Mon, Jul 16, 2012 at 5:10 PM, Tony Power <[hidden email]>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>> Hi Stephen,
>>>>>>>>
>>>>>>>>
>>>>>>>> I changed it to 300 and it just stands there waiting.
>>>>>>>>
>>>>>>>> Nevertheless I can see that it fired many of these errors:
>>>>>>>>
>>>>>>>> [Mon Jul 16 17:04:26 2012] [error] [client 10.10.228.132] PHP Parse
>>>>>>>>
>>>>>>>> error: syntax error, unexpected 's' (T_STRING) in
>>>>>>>>
>>>>>>>> /usr/share/drupal6/includes/common.inc(1731) : eval()'d code on line
>>>>>>>>
>>>>>>>> 1, referer: http://morse-ccmar.ualg.pt/edge/
>>>>>>>>
>>>>>>>>
>>>>>>>> On line 1731 there is the following: print eval('?>'. $code);
>>>>>>>>
>>>>>>>>
>>>>>>>> Does that $code variable have anything to do with your theme?
>>>>>>>>
>>>>>>>>
>>>>>>>> After the 300 secs, I get:
>>>>>>>>
>>>>>>>> [Mon Jul 16 17:09:26 2012] [error] [client 10.10.228.132] PHP Fatal
>>>>>>>>
>>>>>>>> error: Maximum execution time of 300 seconds exceeded in
>>>>>>>>
>>>>>>>> /usr/share/drupal6/includes/database.inc on line 225, referer:
>>>>>>>>
>>>>>>>> http://morse-ccmar.ualg.pt/edge/
>>>>>>>>
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>>
>>>>>>>> Tony
>>>>>>>>
>>>>>>>>
>>>>>>>> On Mon, Jul 16, 2012 at 3:08 PM, Stephen Ficklin
>>>>>>>> <[hidden email]>
>>>>>>>>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>> Hi Tony,
>>>>>>>>
>>>>>>>>
>>>>>>>> Yes, the problem is the timeout issue. If you go into your php.ini
>>>>>>>> file
>>>>>>>>
>>>>>>>> (/etc/php5/apache2/php.ini on my box) and change the
>>>>>>>> max_execution_time
>>>>>>>>
>>>>>>>> to
>>>>>>>>
>>>>>>>> something larger. However, this page should not take more than 30
>>>>>>>>
>>>>>>>> seconds
>>>>>>>>
>>>>>>>> to load so we can try to figure out what's going on once the page
>>>>>>>>
>>>>>>>> displays.
>>>>>>>>
>>>>>>>>
>>>>>>>> Stephen
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On 7/16/2012 9:54 AM, Tony Power wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>> Hi Stephen,
>>>>>>>>
>>>>>>>>
>>>>>>>> In the logs there is nothing about the theme loading. Everything
>>>>>>>> seems
>>>>>>>>
>>>>>>>> to work well.
>>>>>>>>
>>>>>>>> You still have that admin account that allows you to access the logs,
>>>>>>>>
>>>>>>>> just in case you wish to have a look. But you wont find anything :P
>>>>>>>>
>>>>>>>> From the apache log I get:
>>>>>>>>
>>>>>>>> [Mon Jul 16 14:45:52 2012] [error] [client 10.10.228.135] PHP Parse
>>>>>>>>
>>>>>>>> error: syntax error, unexpected 's' (T_STRING) in
>>>>>>>>
>>>>>>>> /usr/share/drupal6/includes/common.inc(1731) : eval()'d code on line
>>>>>>>>
>>>>>>>> 1, referer: http://morse-ccmar.ualg.pt/edge/
>>>>>>>>
>>>>>>>> [Mon Jul 16 14:46:27 2012] [error] [client 10.10.228.135] PHP Fatal
>>>>>>>>
>>>>>>>> error: Maximum execution time of 30 seconds exceeded in
>>>>>>>>
>>>>>>>> /usr/share/drupal6/includes/database.inc on line 225, referer:
>>>>>>>>
>>>>>>>> http://morse-ccmar.ualg.pt/edge/
>>>>>>>>
>>>>>>>>
>>>>>>>> I guess it should be related to the second error?
>>>>>>>>
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Tony
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Mon, Jul 16, 2012 at 2:23 PM, Stephen Ficklin
>>>>>>>> <[hidden email]>
>>>>>>>>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>> Hi Tony,
>>>>>>>>
>>>>>>>>
>>>>>>>> Can you send me the server logs after you load that page and look in
>>>>>>>>
>>>>>>>> the
>>>>>>>>
>>>>>>>> Drupal logs and let me know if you see anything there that might
>>>>>>>>
>>>>>>>> apply.
>>>>>>>>
>>>>>>>>
>>>>>>>> You get a page that looks like that when an error occurs in building
>>>>>>>>
>>>>>>>> the
>>>>>>>>
>>>>>>>> template. It worked fine at my end so something is different about
>>>>>>>>
>>>>>>>> your
>>>>>>>>
>>>>>>>> setup that is making it do that.
>>>>>>>>
>>>>>>>>
>>>>>>>> Yes, you are correct, you just needed to update the theme.
>>>>>>>>
>>>>>>>>
>>>>>>>> Stephen
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On 7/16/2012 8:58 AM, Tony Power wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>> Hi Stephen,
>>>>>>>>
>>>>>>>>
>>>>>>>> Just updated to the new Tripal Theme.
>>>>>>>>
>>>>>>>> Something is not working properly. To understand what I mean, please,
>>>>>>>>
>>>>>>>> click on one of the contigs.
>>>>>>>>
>>>>>>>>
>>>>>>>> Do I also need to update the Tripal module? I just updated the Theme.
>>>>>>>>
>>>>>>>>
>>>>>>>> Thanks ;)
>>>>>>>>
>>>>>>>>
>>>>>>>> Tony
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Sat, Jul 14, 2012 at 3:04 AM, Stephen Ficklin
>>>>>>>>
>>>>>>>> <[hidden email]>
>>>>>>>>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>> Hi Tony,
>>>>>>>>
>>>>>>>>
>>>>>>>> If you get the most recent version of the tripal_theme 6.x-1.x
>>>>>>>>
>>>>>>>> branch
>>>>>>>>
>>>>>>>> from
>>>>>>>>
>>>>>>>> the development git repository it now contains an update that
>>>>>>>>
>>>>>>>> resolves
>>>>>>>>
>>>>>>>> the
>>>>>>>>
>>>>>>>> issue with the EST_match that you are having. Let me know if it
>>>>>>>>
>>>>>>>> works
>>>>>>>>
>>>>>>>> for
>>>>>>>>
>>>>>>>> you.
>>>>>>>>
>>>>>>>>
>>>>>>>> http://drupal.org/node/1342972/git-instructions/6.x-1.x
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Stephen
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On 7/10/2012 9:26 AM, Stephen Ficklin wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>> Hi Tony,
>>>>>>>>
>>>>>>>>
>>>>>>>> Good morning. I'm CC'ing the list as your question about the
>>>>>>>>
>>>>>>>> EST_match
>>>>>>>>
>>>>>>>> may be helpful for others. The behavior you describe is correct
>>>>>>>>
>>>>>>>> for
>>>>>>>>
>>>>>>>> the
>>>>>>>>
>>>>>>>> way
>>>>>>>>
>>>>>>>> the alignments are stored. ESTs are aligned to contigs via an
>>>>>>>>
>>>>>>>> 'EST_match'
>>>>>>>>
>>>>>>>> feature in your GFF file. This is because an EST does not always
>>>>>>>>
>>>>>>>> overlap
>>>>>>>>
>>>>>>>> completely with the contig depending on the software used to do the
>>>>>>>>
>>>>>>>> assembly--only portions of ESTs may align. Therefore we use an
>>>>>>>>
>>>>>>>> EST_match
>>>>>>>>
>>>>>>>> feature for the alignment. See here for an example:
>>>>>>>>
>>>>>>>> http://gmod.org/wiki/GFF#Alignments
>>>>>>>>
>>>>>>>>
>>>>>>>> EST --> EST_match <-- Contig
>>>>>>>>
>>>>>>>>
>>>>>>>> In reality you don't want the site visitors to see the EST_match
>>>>>>>>
>>>>>>>> features.
>>>>>>>>
>>>>>>>> But by default Tripal treats all features the same. It doesn't know
>>>>>>>>
>>>>>>>> the
>>>>>>>>
>>>>>>>> difference between a gene, mRNA, contig, EST, EST_match, etc. So
>>>>>>>>
>>>>>>>> that
>>>>>>>>
>>>>>>>> is
>>>>>>>>
>>>>>>>> why you have links to EST_matches on your contig alignments page
>>>>>>>>
>>>>>>>> rather
>>>>>>>>
>>>>>>>> than
>>>>>>>>
>>>>>>>> links to ESTs. So, to get links to your ESTs on your contig page
>>>>>>>>
>>>>>>>> and
>>>>>>>>
>>>>>>>> to
>>>>>>>>
>>>>>>>> bypass the EST_match feature you need to edit the
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> sites/all/themes/tripal_theme/tripal_feature/tripal_feature_featurelocs_as_parent.tpl.php
>>>>>>>>
>>>>>>>> to handle that special case. I believe however that I can make
>>>>>>>>
>>>>>>>> that
>>>>>>>>
>>>>>>>> adjustment in the template for you in the development code. When
>>>>>>>>
>>>>>>>> it's
>>>>>>>>
>>>>>>>> ready
>>>>>>>>
>>>>>>>> I'll let you know.
>>>>>>>>
>>>>>>>>
>>>>>>>> Stephen
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On 7/10/2012 5:45 AM, Tony Power wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>> Hi again Stephen,
>>>>>>>>
>>>>>>>>
>>>>>>>> I noticed some strange behavior on the site.
>>>>>>>>
>>>>>>>>
>>>>>>>> For instance:
>>>>>>>>
>>>>>>>> 1-Select the first contig and then select "Alignments".
>>>>>>>>
>>>>>>>> 2-Now select the first EST_match.
>>>>>>>>
>>>>>>>> 3-Now "EST_match Sequence" -> No sequence is shown;
>>>>>>>>
>>>>>>>>
>>>>>>>> 4-Now select "Alignments" (of that EST_match).
>>>>>>>>
>>>>>>>> 5-From the alignments select the EST_match that it aligns to.
>>>>>>>>
>>>>>>>> 6-Select "EST_match Sequence" -> The sequence is shown.
>>>>>>>>
>>>>>>>>
>>>>>>>> What might be the problem?
>>>>>>>>
>>>>>>>>
>>>>>>>> Obrigado,
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>

Tony Power

Re: [Gmod-tripal-devel] EST_match for unigenes

Man, that worked perfectly :D
And, now I don't see EST_matches, only ESTs.
Thanks a million ;)
Tony

On Tue, Jul 24, 2012 at 1:38 PM, Stephen Ficklin <[hidden email]> wrote:

> Hi Tony,
>
> if you have version 6.x-1.x for both the theme and the modules then try
> clearing you cache. If you have drush you can run 'drush cc all' anywhere
> in your Drupal directory. Or go to 'Administer' -> 'Site Configuration' ->
> 'Performance' and click 'Clear cached data'.
>
> The missing file should be here:
> /var/www/edge/sites/all/themes/tripal_theme/tripal_feature/tripal_feature_alignments.tpl.php.
>
> Stephen
>
>
> On 7/24/2012 5:07 AM, Tony Power wrote:
>>
>> Hi Stephen,
>>
>> This is what I have:
>> root@morse-ccmar:/var/www/edge/sites/all/themes/tripal_theme# git branch
>> * 6.x-1.x
>> root@morse-ccmar:/var/www/edge/sites/all/themes/tripal_theme# git pull
>> Already up-to-date.
>>
>> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# git branch
>> 6.x-0.4-dev
>> * 6.x-1.x
>> master
>> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# git pull
>> Already up-to-date.
>>
>> But, for instance, if I go to: http://morse-ccmar.ualg.pt/edge/ID327210
>> then I get:
>> warning:
>> include(./sites/all/modules/tripal/tripal_feature/tripal_feature_alignments.tpl.php):
>> failed to open stream: No such file or directory in
>> /usr/share/drupal6/includes/theme.inc on line 1079.
>> warning: include(): Failed opening
>>
>> './sites/all/modules/tripal/tripal_feature/tripal_feature_alignments.tpl.php'
>> for inclusion (include_path='.:/usr/share/php:/usr/share/pear') in
>> /usr/share/drupal6/includes/theme.inc on line 1079.
>>
>> As you can see:
>> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal/tripal_feature# ls
>> fasta_loader.php tripal_feature.info
>> gff_loader.php tripal_feature.install
>> indexFeatures.php tripal_feature.module
>> syncFeatures.php tripal_feature-properties.inc
>> tripal_feature.admin.inc tripal_feature-relationships.inc
>> tripal_feature.api.inc tripal_feature-secondary_tables.inc
>> tripal_feature.coder_ignores.txt tripal_feature.views.inc
>> tripal_feature-db_references.inc views_handlers
>> tripal_feature-delete.inc
>>
>> What could be the explanation for the missing file?
>>
>> Thanks,
>> Tony
>>
>>
>> On Mon, Jul 23, 2012 at 9:13 PM, Stephen Ficklin <[hidden email]>
>> wrote:
>>>
>>> Hi Tony,
>>>
>>> There should be a file named 'tripal_feature_alignments.tpl.php' in the
>>> tripal_theme/tripal_feature directory. Is it missing? It looks like your
>>> site is trying to find it in the module rather than the theme directory
>>> which is typical if the file is missing from the theme. I just checked
>>> the
>>> repository for the 6.x-1.x branch of the Triapl theme and the file is
>>> there.
>>>
>>> Stephen
>>>
>>>
>>> On 7/23/2012 4:06 PM, Tony Power wrote:
>>>>
>>>> Hi Stephen,
>>>>
>>>> Thanks for the prompt reply.
>>>> I am sorry but I didn't the theme had been updated.
>>>> Now it looks like that we have something. Nevertheless:
>>>>
>>>> warning:
>>>>
>>>> include(./sites/all/modules/tripal/tripal_feature/tripal_feature_alignments.tpl.php):
>>>> failed to open stream: No such file or directory in
>>>> /usr/share/drupal6/includes/theme.inc on line 1079.
>>>> warning: include(): Failed opening
>>>>
>>>>
>>>> './sites/all/modules/tripal/tripal_feature/tripal_feature_alignments.tpl.php'
>>>> for inclusion (include_path='.:/usr/share/php:/usr/share/pear') in
>>>> /usr/share/drupal6/includes/theme.inc on line 1079.
>>>>
>>>> shows up on the top of the formatted feature page.
>>>>
>>>> This is what I have in the tripal_feature dir:
>>>> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal/tripal_feature#
>>>> ls
>>>> fasta_loader.php tripal_feature.info
>>>> gff_loader.php tripal_feature.install
>>>> indexFeatures.php tripal_feature.module
>>>> syncFeatures.php tripal_feature-properties.inc
>>>> tripal_feature.admin.inc tripal_feature-relationships.inc
>>>> tripal_feature.api.inc tripal_feature-secondary_tables.inc
>>>> tripal_feature.coder_ignores.txt tripal_feature.views.inc
>>>> tripal_feature-db_references.inc views_handlers
>>>> tripal_feature-delete.inc
>>>>
>>>>
>>>>
>>>> Thanks,
>>>> Tony
>>>>
>>>>
>>>> On Mon, Jul 23, 2012 at 8:41 PM, Stephen Ficklin <[hidden email]>
>>>> wrote:
>>>>>
>>>>> Hi Tony,
>>>>>
>>>>> I provided a fix on Friday for the problem in the 6.x-1.x branch. You
>>>>> have
>>>>> to update both Tripal and the Tripal theme to version 6.x-1.x. Have
>>>>> you
>>>>> done both and still have the bad page?
>>>>>
>>>>> Stephen
>>>>>
>>>>>
>>>>> On 7/23/2012 3:27 PM, Tony Power wrote:
>>>>>>
>>>>>> Hi Stephen,
>>>>>>
>>>>>> Did that.
>>>>>> In any case, it didn't fix that problem of presenting an unformatted
>>>>>> feature webpage. But I guess you've already identified the problem.
>>>>>> I'll just wait for the fix.
>>>>>>
>>>>>> Thanks,
>>>>>> Tony
>>>>>>
>>>>>> On Mon, Jul 23, 2012 at 7:48 PM, Stephen Ficklin <[hidden email]>
>>>>>> wrote:
>>>>>>>
>>>>>>> Hi Tony,
>>>>>>>
>>>>>>> You should be able to just switch right over to the 6.x-1.x branch:
>>>>>>>
>>>>>>> git checkout 6.x-1.x
>>>>>>>
>>>>>>> If you still get problems then you can wipe it clean (after disabling
>>>>>>> the
>>>>>>> Tripal modules) and just start over with the 6.x-1.x branch as you
>>>>>>> suggest.
>>>>>>>
>>>>>>> Stephen
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 7/23/2012 2:34 PM, Tony Power wrote:
>>>>>>>>
>>>>>>>> Ho Lacey-Anne,
>>>>>>>>
>>>>>>>> Here is what I get:
>>>>>>>> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# git
>>>>>>>> checkout
>>>>>>>> master
>>>>>>>> Branch master set up to track remote branch master from origin.
>>>>>>>> Switched to a new branch 'master'
>>>>>>>> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# git pull
>>>>>>>> origin
>>>>>>>> master
>>>>>>>> fatal: Couldn't find remote ref master
>>>>>>>> root@morse-ccmar:/var/www/edge/sites/all/modules/tripal# Unexpected
>>>>>>>> end of command stream
>>>>>>>>
>>>>>>>> Did I do anything wrong?
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Tony
>>>>>>>>
>>>>>>>> On Mon, Jul 16, 2012 at 10:15 PM, Lacey-Anne Sanderson
>>>>>>>> <[hidden email]> wrote:
>>>>>>>>>
>>>>>>>>> Hi Tony,
>>>>>>>>>
>>>>>>>>> The newest dev version is on a different branch (we needed to make
>>>>>>>>> the
>>>>>>>>> change to adhere to drupal standards). You need to checkout the
>>>>>>>>> master
>>>>>>>>> branch (git checkout master) and then pull from the drupal.org
>>>>>>>>> repository
>>>>>>>>> (git pull origin master) and then checkout the new branch (git
>>>>>>>>> checkout
>>>>>>>>> 6.x-1.x). From here on in you simply need to pull from the
>>>>>>>>> drupal.org
>>>>>>>>> repository to get the latest development snapshot (git pull origin
>>>>>>>>> 6.x-1.x).
>>>>>>>>>
>>>>>>>>> You can just replace the entire module directory with a new version
>>>>>>>>> of
>>>>>>>>> tripal though it is recommended to first disable all your tripal
>>>>>>>>> modules
>>>>>>>>> (configuration and sync'd features will remain and be available
>>>>>>>>> once
>>>>>>>>> you
>>>>>>>>> re-enable the module -you only lose data if you uninstall the
>>>>>>>>> modules).
>>>>>>>>>
>>>>>>>>> Sorry for the extra steps,
>>>>>>>>> ~Lacey
>>>>>>>>>
>>>>>>>>> PS. I am also not experiencing any errors on my contig pages...
>>>>>>>>>
>>>>>>>>> ------------------------------------------------------
>>>>>>>>> Lacey-Anne Sanderson
>>>>>>>>> Bioinformaticist
>>>>>>>>> Pulse Crop Breeding and Genetics
>>>>>>>>> Phone: (306) 966-4975
>>>>>>>>> Email: [hidden email]
>>>>>>>>> Room 3C06 Agriculture
>>>>>>>>> Department of Plant Sciences
>>>>>>>>> University of Saskatchewan
>>>>>>>>>
>>>>>>>>> On 2012-07-16, at 3:05 PM, Tony Power wrote:
>>>>>>>>>
>>>>>>>>> Hi Stephen and Lacey-Anne,
>>>>>>>>>
>>>>>>>>> After testing I immediately reset it to 30 secs again. But the
>>>>>>>>> result
>>>>>>>>> is the same. 30 or 300 the errors are the same, it just takes
>>>>>>>>> longer
>>>>>>>>> to display the (unformatted) webpage.
>>>>>>>>>
>>>>>>>>> After trying to Lacey-Anne's suggestion I get the same result.
>>>>>>>>> I have the latest dev branch for the Tripal module (I guess):
>>>>>>>>> # git status
>>>>>>>>> # On branch 6.x-0.4-dev
>>>>>>>>> nothing to commit (working directory clean)
>>>>>>>>>
>>>>>>>>> The new Theme version you provided me in a previous email is not
>>>>>>>>> development (could it be this?)
>>>>>>>>> git status
>>>>>>>>> # On branch 6.x-1.x
>>>>>>>>> nothing to commit (working directory clean)
>>>>>>>>>
>>>>>>>>> If there is another module version, can I just delete the whole
>>>>>>>>> tripal
>>>>>>>>> (module) and replace it by the new?
>>>>>>>>> Where are all the tripal site related configurations saved?
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>> Tony
>>>>>>>>>
>>>>>>>>> On Mon, Jul 16, 2012 at 8:30 PM, Stephen Ficklin
>>>>>>>>> <[hidden email]>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>> Hi Tony,
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> I'm having a bit of trouble debugging this one because I'm not
>>>>>>>>> having
>>>>>>>>> the
>>>>>>>>>
>>>>>>>>> same problem. I was unable to load this feature on your site
>>>>>>>>> without
>>>>>>>>> it
>>>>>>>>>
>>>>>>>>> taking longer than 30 seconds:
>>>>>>>>> http://morse-ccmar.ualg.pt/edge/ID327210.
>>>>>>>>>
>>>>>>>>> Would you mind sending me the snippet of the GFF file that contains
>>>>>>>>> that
>>>>>>>>>
>>>>>>>>> contig and EST alignments?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>>
>>>>>>>>> Stephen
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 7/16/2012 12:18 PM, Tony Power wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Well, it shouldn't have anything to do with the common.inc error,
>>>>>>>>>
>>>>>>>>> since even if I restore the old theme I still get that error and
>>>>>>>>> the
>>>>>>>>>
>>>>>>>>> features show well again. So, something should be happening with
>>>>>>>>> the
>>>>>>>>>
>>>>>>>>> new version of your theme (or not) :P.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> In any case it's a weird error since I don't do any updates for a
>>>>>>>>> long
>>>>>>>>>
>>>>>>>>> time.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Mon, Jul 16, 2012 at 5:10 PM, Tony Power <[hidden email]>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Hi Stephen,
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> I changed it to 300 and it just stands there waiting.
>>>>>>>>>
>>>>>>>>> Nevertheless I can see that it fired many of these errors:
>>>>>>>>>
>>>>>>>>> [Mon Jul 16 17:04:26 2012] [error] [client 10.10.228.132] PHP Parse
>>>>>>>>>
>>>>>>>>> error: syntax error, unexpected 's' (T_STRING) in
>>>>>>>>>
>>>>>>>>> /usr/share/drupal6/includes/common.inc(1731) : eval()'d code on
>>>>>>>>> line
>>>>>>>>>
>>>>>>>>> 1, referer: http://morse-ccmar.ualg.pt/edge/
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On line 1731 there is the following: print eval('?>'. $code);
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Does that $code variable have anything to do with your theme?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> After the 300 secs, I get:
>>>>>>>>>
>>>>>>>>> [Mon Jul 16 17:09:26 2012] [error] [client 10.10.228.132] PHP Fatal
>>>>>>>>>
>>>>>>>>> error: Maximum execution time of 300 seconds exceeded in
>>>>>>>>>
>>>>>>>>> /usr/share/drupal6/includes/database.inc on line 225, referer:
>>>>>>>>>
>>>>>>>>> http://morse-ccmar.ualg.pt/edge/
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Tony
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Mon, Jul 16, 2012 at 3:08 PM, Stephen Ficklin
>>>>>>>>> <[hidden email]>
>>>>>>>>>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Hi Tony,
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Yes, the problem is the timeout issue. If you go into your php.ini
>>>>>>>>> file
>>>>>>>>>
>>>>>>>>> (/etc/php5/apache2/php.ini on my box) and change the
>>>>>>>>> max_execution_time
>>>>>>>>>
>>>>>>>>> to
>>>>>>>>>
>>>>>>>>> something larger. However, this page should not take more than 30
>>>>>>>>>
>>>>>>>>> seconds
>>>>>>>>>
>>>>>>>>> to load so we can try to figure out what's going on once the page
>>>>>>>>>
>>>>>>>>> displays.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Stephen
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 7/16/2012 9:54 AM, Tony Power wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Hi Stephen,
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> In the logs there is nothing about the theme loading. Everything
>>>>>>>>> seems
>>>>>>>>>
>>>>>>>>> to work well.
>>>>>>>>>
>>>>>>>>> You still have that admin account that allows you to access the
>>>>>>>>> logs,
>>>>>>>>>
>>>>>>>>> just in case you wish to have a look. But you wont find anything :P
>>>>>>>>>
>>>>>>>>> From the apache log I get:
>>>>>>>>>
>>>>>>>>> [Mon Jul 16 14:45:52 2012] [error] [client 10.10.228.135] PHP Parse
>>>>>>>>>
>>>>>>>>> error: syntax error, unexpected 's' (T_STRING) in
>>>>>>>>>
>>>>>>>>> /usr/share/drupal6/includes/common.inc(1731) : eval()'d code on
>>>>>>>>> line
>>>>>>>>>
>>>>>>>>> 1, referer: http://morse-ccmar.ualg.pt/edge/
>>>>>>>>>
>>>>>>>>> [Mon Jul 16 14:46:27 2012] [error] [client 10.10.228.135] PHP Fatal
>>>>>>>>>
>>>>>>>>> error: Maximum execution time of 30 seconds exceeded in
>>>>>>>>>
>>>>>>>>> /usr/share/drupal6/includes/database.inc on line 225, referer:
>>>>>>>>>
>>>>>>>>> http://morse-ccmar.ualg.pt/edge/
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> I guess it should be related to the second error?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>>
>>>>>>>>> Tony
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Mon, Jul 16, 2012 at 2:23 PM, Stephen Ficklin
>>>>>>>>> <[hidden email]>
>>>>>>>>>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Hi Tony,
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Can you send me the server logs after you load that page and look
>>>>>>>>> in
>>>>>>>>>
>>>>>>>>> the
>>>>>>>>>
>>>>>>>>> Drupal logs and let me know if you see anything there that might
>>>>>>>>>
>>>>>>>>> apply.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> You get a page that looks like that when an error occurs in
>>>>>>>>> building
>>>>>>>>>
>>>>>>>>> the
>>>>>>>>>
>>>>>>>>> template. It worked fine at my end so something is different about
>>>>>>>>>
>>>>>>>>> your
>>>>>>>>>
>>>>>>>>> setup that is making it do that.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Yes, you are correct, you just needed to update the theme.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Stephen
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 7/16/2012 8:58 AM, Tony Power wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Hi Stephen,
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Just updated to the new Tripal Theme.
>>>>>>>>>
>>>>>>>>> Something is not working properly. To understand what I mean,
>>>>>>>>> please,
>>>>>>>>>
>>>>>>>>> click on one of the contigs.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Do I also need to update the Tripal module? I just updated the
>>>>>>>>> Theme.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Thanks ;)
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Tony
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Sat, Jul 14, 2012 at 3:04 AM, Stephen Ficklin
>>>>>>>>>
>>>>>>>>> <[hidden email]>
>>>>>>>>>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Hi Tony,
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> If you get the most recent version of the tripal_theme 6.x-1.x
>>>>>>>>>
>>>>>>>>> branch
>>>>>>>>>
>>>>>>>>> from
>>>>>>>>>
>>>>>>>>> the development git repository it now contains an update that
>>>>>>>>>
>>>>>>>>> resolves
>>>>>>>>>
>>>>>>>>> the
>>>>>>>>>
>>>>>>>>> issue with the EST_match that you are having. Let me know if it
>>>>>>>>>
>>>>>>>>> works
>>>>>>>>>
>>>>>>>>> for
>>>>>>>>>
>>>>>>>>> you.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> http://drupal.org/node/1342972/git-instructions/6.x-1.x
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Stephen
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 7/10/2012 9:26 AM, Stephen Ficklin wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Hi Tony,
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Good morning. I'm CC'ing the list as your question about the
>>>>>>>>>
>>>>>>>>> EST_match
>>>>>>>>>
>>>>>>>>> may be helpful for others. The behavior you describe is correct
>>>>>>>>>
>>>>>>>>> for
>>>>>>>>>
>>>>>>>>> the
>>>>>>>>>
>>>>>>>>> way
>>>>>>>>>
>>>>>>>>> the alignments are stored. ESTs are aligned to contigs via an
>>>>>>>>>
>>>>>>>>> 'EST_match'
>>>>>>>>>
>>>>>>>>> feature in your GFF file. This is because an EST does not always
>>>>>>>>>
>>>>>>>>> overlap
>>>>>>>>>
>>>>>>>>> completely with the contig depending on the software used to do the
>>>>>>>>>
>>>>>>>>> assembly--only portions of ESTs may align. Therefore we use an
>>>>>>>>>
>>>>>>>>> EST_match
>>>>>>>>>
>>>>>>>>> feature for the alignment. See here for an example:
>>>>>>>>>
>>>>>>>>> http://gmod.org/wiki/GFF#Alignments
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> EST --> EST_match <-- Contig
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> In reality you don't want the site visitors to see the EST_match
>>>>>>>>>
>>>>>>>>> features.
>>>>>>>>>
>>>>>>>>> But by default Tripal treats all features the same. It doesn't know
>>>>>>>>>
>>>>>>>>> the
>>>>>>>>>
>>>>>>>>> difference between a gene, mRNA, contig, EST, EST_match, etc. So
>>>>>>>>>
>>>>>>>>> that
>>>>>>>>>
>>>>>>>>> is
>>>>>>>>>
>>>>>>>>> why you have links to EST_matches on your contig alignments page
>>>>>>>>>
>>>>>>>>> rather
>>>>>>>>>
>>>>>>>>> than
>>>>>>>>>
>>>>>>>>> links to ESTs. So, to get links to your ESTs on your contig page
>>>>>>>>>
>>>>>>>>> and
>>>>>>>>>
>>>>>>>>> to
>>>>>>>>>
>>>>>>>>> bypass the EST_match feature you need to edit the
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> sites/all/themes/tripal_theme/tripal_feature/tripal_feature_featurelocs_as_parent.tpl.php
>>>>>>>>>
>>>>>>>>> to handle that special case. I believe however that I can make
>>>>>>>>>
>>>>>>>>> that
>>>>>>>>>
>>>>>>>>> adjustment in the template for you in the development code. When
>>>>>>>>>
>>>>>>>>> it's
>>>>>>>>>
>>>>>>>>> ready
>>>>>>>>>
>>>>>>>>> I'll let you know.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Stephen
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 7/10/2012 5:45 AM, Tony Power wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Hi again Stephen,
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> I noticed some strange behavior on the site.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> For instance:
>>>>>>>>>
>>>>>>>>> 1-Select the first contig and then select "Alignments".
>>>>>>>>>
>>>>>>>>> 2-Now select the first EST_match.
>>>>>>>>>
>>>>>>>>> 3-Now "EST_match Sequence" -> No sequence is shown;
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> 4-Now select "Alignments" (of that EST_match).
>>>>>>>>>
>>>>>>>>> 5-From the alignments select the EST_match that it aligns to.
>>>>>>>>>
>>>>>>>>> 6-Select "EST_match Sequence" -> The sequence is shown.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> What might be the problem?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Obrigado,
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>