[Gmod-tripal-devel] Tripal GFF import page

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[Gmod-tripal-devel] Tripal GFF import page

Michael Dondrup
Hi,

the tripal gff import page seems to have problems with filenames that contain capital letters, for example:

I can submit an import job for /home/licebase/importdata/lsalatl1s.fasta.gff while
/home/licebase/importdata/LSalAtl1S.fasta.gff gives an error:

Cannot find the /home/licebase/drupal/LSalAtl1S.fasta.gff on the system.
Check that the file exists or that the web server has permissions to read the file.
(I edited the error message to really see the file name, so normally it would say "Cannot find the file ..." or something),
but this file exists and is readable. Also, the Fasta importer didn't have the problem as it took LSalAtl1S.fasta just fine.

Both files are world readable and in the same directory:

-rw-rw-r-- 1 licebase licebase       0 Oct  4 16:07 /home/licebase/importdata/lsalatl1s.fasta.gff
-rw-rw-r-- 1 licebase licebase 5735466 Oct  4 14:43 /home/licebase/importdata/LSalAtl1S.fasta.gff

php is 5.3.3,
Tripal is 1.x from the git repository.


Best
Michael
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Re: [Gmod-tripal-devel] Tripal GFF import page

Stephen Ficklin-2
Hi Michael,

An unfortunate side effect of using the development branch of Tripal is
that the code changes and sometimes we inadvertently break things.  
Because we have not yet released v1.0 of Tripal the tutorial uses the
development branch.  I think though that the problem you are
encountering is for a bug that has already been fixed.   If you could
update your Tripal code (both the module and the theme) then I think the
problem should be resolved:

cd /var/www/sites/all/modules/tripal
git pull

cd /var/www/sites/all/themes/tripal_theme
git pull

If not let me know and we can look further at the problem for you.
Stephen

On 10/4/2012 10:31 AM, Michael Dondrup wrote:

> Hi,
>
> the tripal gff import page seems to have problems with filenames that contain capital letters, for example:
>
> I can submit an import job for /home/licebase/importdata/lsalatl1s.fasta.gff while
> /home/licebase/importdata/LSalAtl1S.fasta.gff gives an error:
>
> Cannot find the /home/licebase/drupal/LSalAtl1S.fasta.gff on the system.
> Check that the file exists or that the web server has permissions to read the file.
> (I edited the error message to really see the file name, so normally it would say "Cannot find the file ..." or something),
> but this file exists and is readable. Also, the Fasta importer didn't have the problem as it took LSalAtl1S.fasta just fine.
>
> Both files are world readable and in the same directory:
>
> -rw-rw-r-- 1 licebase licebase       0 Oct  4 16:07 /home/licebase/importdata/lsalatl1s.fasta.gff
> -rw-rw-r-- 1 licebase licebase 5735466 Oct  4 14:43 /home/licebase/importdata/LSalAtl1S.fasta.gff
>
> php is 5.3.3,
> Tripal is 1.x from the git repository.
>
>
> Best
> Michael
> ------------------------------------------------------------------------------
> Don't let slow site performance ruin your business. Deploy New Relic APM
> Deploy New Relic app performance management and know exactly
> what is happening inside your Ruby, Python, PHP, Java, and .NET app
> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
> http://p.sf.net/sfu/newrelic-dev2dev
> _______________________________________________
> Gmod-tripal-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel


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Re: [Gmod-tripal-devel] Tripal GFF import page

Stephen Ficklin-2
Hi Michael,

Disregard my message below. I thought I was responding to a different
question from someone else.   So, my response does not apply to your
question.   I'll respond in just a bit.

My apologies
Stephen

On 10/4/2012 11:07 AM, Stephen Ficklin wrote:

> Hi Michael,
>
> An unfortunate side effect of using the development branch of Tripal
> is that the code changes and sometimes we inadvertently break things.  
> Because we have not yet released v1.0 of Tripal the tutorial uses the
> development branch.  I think though that the problem you are
> encountering is for a bug that has already been fixed.   If you could
> update your Tripal code (both the module and the theme) then I think
> the problem should be resolved:
>
> cd /var/www/sites/all/modules/tripal
> git pull
>
> cd /var/www/sites/all/themes/tripal_theme
> git pull
>
> If not let me know and we can look further at the problem for you.
> Stephen


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Re: [Gmod-tripal-devel] Tripal GFF import page

Stephen Ficklin-2
In reply to this post by Michael Dondrup
Hi Michael,

Okay, this is an appropriate response to your question :-)

Are you getting this error message on the web form or when you run your
job?   The code for checking if the file exists seems to be the same for
both the FASTA and GFF loaders.  Could it be you may have had a space at
the end or beginning of the filename?   We seem to forget to trim white
space from values provided in forms.   I've made a slight adjustment to
the code to trim whitespace.  If that's the problem it should help.  If
not we can dig deeper.

Stephen

On 10/4/2012 10:31 AM, Michael Dondrup wrote:

> Hi,
>
> the tripal gff import page seems to have problems with filenames that contain capital letters, for example:
>
> I can submit an import job for /home/licebase/importdata/lsalatl1s.fasta.gff while
> /home/licebase/importdata/LSalAtl1S.fasta.gff gives an error:
>
> Cannot find the /home/licebase/drupal/LSalAtl1S.fasta.gff on the system.
> Check that the file exists or that the web server has permissions to read the file.
> (I edited the error message to really see the file name, so normally it would say "Cannot find the file ..." or something),
> but this file exists and is readable. Also, the Fasta importer didn't have the problem as it took LSalAtl1S.fasta just fine.
>
> Both files are world readable and in the same directory:
>
> -rw-rw-r-- 1 licebase licebase       0 Oct  4 16:07 /home/licebase/importdata/lsalatl1s.fasta.gff
> -rw-rw-r-- 1 licebase licebase 5735466 Oct  4 14:43 /home/licebase/importdata/LSalAtl1S.fasta.gff
>
> php is 5.3.3,
> Tripal is 1.x from the git repository.
>
>
> Best
> Michael
> ------------------------------------------------------------------------------
> Don't let slow site performance ruin your business. Deploy New Relic APM
> Deploy New Relic app performance management and know exactly
> what is happening inside your Ruby, Python, PHP, Java, and .NET app
> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
> http://p.sf.net/sfu/newrelic-dev2dev
> _______________________________________________
> Gmod-tripal-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel


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Re: [Gmod-tripal-devel] Tripal GFF import page

Michael Dondrup
Hi,

excellent. Yes there was a trailing space, I was referring to the web-form! I admit I was on the wrong track with capital letters. I have updated the code and it works fine with or without whitespace.

Thank you

Michael

On Oct 4, 2012, at 5:20 PM, Stephen Ficklin wrote:

> Hi Michael,
>
> Okay, this is an appropriate response to your question :-)
>
> Are you getting this error message on the web form or when you run your job?   The code for checking if the file exists seems to be the same for both the FASTA and GFF loaders.  Could it be you may have had a space at the end or beginning of the filename?   We seem to forget to trim white space from values provided in forms.   I've made a slight adjustment to the code to trim whitespace.  If that's the problem it should help.  If not we can dig deeper.
>
> Stephen
>
> On 10/4/2012 10:31 AM, Michael Dondrup wrote:
>> Hi,
>>
>> the tripal gff import page seems to have problems with filenames that contain capital letters, for example:
>>
>> I can submit an import job for /home/licebase/importdata/lsalatl1s.fasta.gff while
>> /home/licebase/importdata/LSalAtl1S.fasta.gff gives an error:
>>
>> Cannot find the /home/licebase/drupal/LSalAtl1S.fasta.gff on the system.
>> Check that the file exists or that the web server has permissions to read the file.
>> (I edited the error message to really see the file name, so normally it would say "Cannot find the file ..." or something),
>> but this file exists and is readable. Also, the Fasta importer didn't have the problem as it took LSalAtl1S.fasta just fine.
>>
>> Both files are world readable and in the same directory:
>>
>> -rw-rw-r-- 1 licebase licebase       0 Oct  4 16:07 /home/licebase/importdata/lsalatl1s.fasta.gff
>> -rw-rw-r-- 1 licebase licebase 5735466 Oct  4 14:43 /home/licebase/importdata/LSalAtl1S.fasta.gff
>>
>> php is 5.3.3,
>> Tripal is 1.x from the git repository.
>>
>>
>> Best
>> Michael
>> ------------------------------------------------------------------------------
>> Don't let slow site performance ruin your business. Deploy New Relic APM
>> Deploy New Relic app performance management and know exactly
>> what is happening inside your Ruby, Python, PHP, Java, and .NET app
>> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
>> http://p.sf.net/sfu/newrelic-dev2dev
>> _______________________________________________
>> Gmod-tripal-devel mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>


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