[Gmod-tripal-devel] Analysis: Cannot save materials and method field content

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[Gmod-tripal-devel] Analysis: Cannot save materials and method field content

Michael Dondrup
Hi,
I am trying to edit an Analysis I have made, trying to add Material&Methods content.
However, it seems like that the content is not saved for me. The fields stay empty.
Can I have turned this off accidentially?

Best
Michael
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Re: [Gmod-tripal-devel] Analysis: Cannot save materials and method field content

Stephen Ficklin-2
Hi Michael,

I will take a look at both issues you've posted and get back to you
within the next 24 hours.  In the meantime, are there any error messages
in the Drupal recent logs from when you tried to post the analysis?

Thanks,
Stephen

On 2/19/2013 8:11 AM, Michael Dondrup wrote:

> Hi,
> I am trying to edit an Analysis I have made, trying to add Material&Methods content.
> However, it seems like that the content is not saved for me. The fields stay empty.
> Can I have turned this off accidentially?
>
> Best
> Michael
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> _______________________________________________
> Gmod-tripal-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel


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Re: [Gmod-tripal-devel] Analysis: Cannot save materials and method field content

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

Thanks for your patience.  So, I tested updating an existing analysis
and I tested the feature browser which you mentioned in a separate email
you were also having problems with.  In both cases, using the most
recent version of the development branch of Tripal (updated this
morning) both worked well.

Some of the analysis details, such as the 'M&M' section are not stored
in the 'analysis' table, as that table has no 'description' field.   So
those details get stored in the 'analysisprop' table of Chado.  There
was a bug, which I fixed perhaps a week ago that inserted a second
property for the M&M rather than replace the current one.  That caused
problems with the template and made it appear as though nothing was
saved. Perhaps this is the problem?   To resolve it,  you'll have to do
two things

1).  Make sure you have the most current version of the Tripal theme as
well as the Tripal modules.
2).  Clear the Drupal cache (drush cc all) to make sure Drupal picks up
any changes.
3).  Look in the database for properties belonging to your analysis.  If
the problem is how I described above you'll have to entries for the M&M
in the analysisprop table for your analysis.   You will need to delete
one of them.  You should then be able to edit your analysis

If this doesn't help let me know and I can dig deeper.  If you don't
want to look at the tables in Chado (step 3) let me know and I can write
up some queries you can run to check and fix.

As far as the feature browser on the organism page, it sounds as though
the Javascript isn't working correctly.   I'm assuming you have recently
update the Tripal theme?  Are you using IE?  IE has a problem when there
are too many different CSS and JS files it refuses to load them all.  If
the browser works in Firefox, Chrome, Safari and not in IE then this is
most likely the problem.  You can fix this by enabling JS and CSS
compression under 'Administer' -> 'Site Configuration' ->
'Performance'.  If this is not the problem then something else is
throwing off the javascript and we'll need to look deeper.

Stephen

On 2/19/2013 8:11 AM, Michael Dondrup wrote:

> Hi,
> I am trying to edit an Analysis I have made, trying to add Material&Methods content.
> However, it seems like that the content is not saved for me. The fields stay empty.
> Can I have turned this off accidentially?
>
> Best
> Michael
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> _______________________________________________
> Gmod-tripal-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel


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Re: [Gmod-tripal-devel] Analysis: Cannot save materials and method field content

Michael Dondrup
Hi Stephen,

after a complete update the problem with the M&M disappeared and I could save everything. I had forgotten to update the tripal_theme, and I had
repeated this mistake already before, so I am now using the following script to update everything and not forget anything over and over again:

#!/bin/sh
DDIR=/home/licebase/drupal
DIRS=`find $DDIR/sites/all/modules/ -maxdepth 1 -name 'tripal*'`
DIRS="$DIRS $DDIR/sites/all/themes/tripal_theme"
echo $DIRS
for  DIR in $DIRS  ; do
  cd $DIR
  git pull
done
drush cc all

Can you confirm that this is all that is needed to update the install? Sorry for repeatedly doing the same mistake.

The problem in the feature browser didn't disappear though. I am using Chrome and Safari, also cleared the browser cache.

This is the URL to open the feature selection page (unfortunately the page is not visible from the outside yet).
http://lb-test.bccs.uib.no/?q=node/450542#tripal_organism-feature_browser-box
which works.
Then the links for the pagination look like this:
http://lb-test.bccs.uib.no/?q=node/450542&page=1
There is no output in the javascript console, except
Resource interpreted as Image but transferred with MIME type application/octet-stream: "http://lb-test.bccs.uib.no/sites/default/files/garland_favicon.ico".
which is possibly unrelated.

I attach the full html code of the resulting page (have uncommented two alerts for debugging). When I load
feature URL, the alert:
correct: #tripal_organism-feature_browser-box

appears, the other alert never appears.

Hoping this is not another stupid mistakeā€¦

Best
Michael



On Feb 20, 2013, at 7:22 PM, Stephen Ficklin wrote:

> Hi Michael,
>
> Thanks for your patience.  So, I tested updating an existing analysis and I tested the feature browser which you mentioned in a separate email you were also having problems with.  In both cases, using the most recent version of the development branch of Tripal (updated this morning) both worked well.
>
> Some of the analysis details, such as the 'M&M' section are not stored in the 'analysis' table, as that table has no 'description' field.   So those details get stored in the 'analysisprop' table of Chado.  There was a bug, which I fixed perhaps a week ago that inserted a second property for the M&M rather than replace the current one.  That caused problems with the template and made it appear as though nothing was saved. Perhaps this is the problem?   To resolve it,  you'll have to do two things
>
> 1).  Make sure you have the most current version of the Tripal theme as well as the Tripal modules.
> 2).  Clear the Drupal cache (drush cc all) to make sure Drupal picks up any changes.
> 3).  Look in the database for properties belonging to your analysis.  If the problem is how I described above you'll have to entries for the M&M in the analysisprop table for your analysis.   You will need to delete one of them.  You should then be able to edit your analysis
>
> If this doesn't help let me know and I can dig deeper.  If you don't want to look at the tables in Chado (step 3) let me know and I can write up some queries you can run to check and fix.
>
> As far as the feature browser on the organism page, it sounds as though the Javascript isn't working correctly.   I'm assuming you have recently update the Tripal theme?  Are you using IE?  IE has a problem when there are too many different CSS and JS files it refuses to load them all.  If the browser works in Firefox, Chrome, Safari and not in IE then this is most likely the problem.  You can fix this by enabling JS and CSS compression under 'Administer' -> 'Site Configuration' -> 'Performance'.  If this is not the problem then something else is throwing off the javascript and we'll need to look deeper.
>
> Stephen
>
> On 2/19/2013 8:11 AM, Michael Dondrup wrote:
>> Hi,
>> I am trying to edit an Analysis I have made, trying to add Material&Methods content.
>> However, it seems like that the content is not saved for me. The fields stay empty.
>> Can I have turned this off accidentially?
>>
>> Best
>> Michael
>> ------------------------------------------------------------------------------
>> Everyone hates slow websites. So do we.
>> Make your web apps faster with AppDynamics
>> Download AppDynamics Lite for free today:
>> http://p.sf.net/sfu/appdyn_d2d_feb
>> _______________________________________________
>> Gmod-tripal-devel mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>

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