gmod-tripal-devel — Discussion of Tripal development

[Gmod-tripal-devel] Monthly Tripal Meetings

[Stephen F. <spf...@gm...>]

Hi All,

Typically we have our Monthly User's meeting on the first Tuesday of 
every month at 12pm EDT (UTC 5pm), and I am usually the one who 
coordinate these meetings.  Our next is scheduled for Sept 6th. However, 
I have a scheduling conflict for the remainder of 2016 on Tuesdays. I'm 
teaching a course during the time we would normally have our meeting.

I'd like to suggest we move our Tripal meeting to the same time but on 
the 2nd Wednesday of the month?  This will prevent us from conflicting 
with the USDA Database meeting which is held on the 1st Wednesday of the 
month.

Does this time work for others?  If not, please suggest another time 
that works and we'll see if we can get as close to a consensus as possible.

Thanks,

Stephen

[Gmod-tripal-devel] Tripal Download API

[Kucheran, L. S. <la...@ma...>]

Hi everyone,

Module Release:
I just released a Tripal Download API<https://github.com/tripal/trpdownload_api> that is meant to provide a framework for module/site developers to make downloads available to their users. Currently it provides a generic download page with an ajax progress bar and file download link (attached screenshot) that you can link to from an existing form/view. There are documented code samples on the module page showing how to use it and an example module provided in the release demonstrating feature to csv downloads.

This differs from the Views Data Export module in a number of ways:
1. Uses Tripal jobs to allow for large downloads.
2. Does not create an intermediate table that remains if the user cancels a download.
3. Provides a bookmark-able download page (screenshot attached) that could easily be extended to email the user.
4. Supports download without using views (allows for custom processing of data before export).

Input on Views Support:
Next on the docket: to provide functionality allowing the developer to specify the name of a view and it would use the view to determine the query. I would like some input on what would be the most useful/performant/flexible with respect to views integration:
A) Most flexibility: Use the API to get the views query but you handle executing it, processing results and generating the file yourself.
- Ensures that the user downloads the same results they saw but allows you full control to manipulate the views results while generating the file.
B) Most Functionality: The API programatically executes the view, iterates through the results and generates the file. All you need to do is tell it how to transform a single query row into a string to write to the file.
- Could be too restrictive depending on how much processing is needed to generate your file.
- Do you need access to more than one row at a time?
- Additional functions could be made available to customize the header and footer of your file.
C) Any other ideas?

Thanks!
~Lacey

[Gmod-tripal-devel] Recording of yesterday's Tripal Developer Meeting

[Stephen F. <spf...@gm...>]

Dear Tripal Community,

It was requested by several folks that we record yesterday's Tripal 
developer's meeting and make it available online for those who were not 
able to attend.   We typically keep a copy of meeting notes on the 
Tripal website, but for yesterday's meeting we've included the recording 
as well. If you are interested in listening/viewing the meeting you can 
find the notes and the video here:

http://tripal.info/meetings/developers/2016-07-12-160000

Stephen

Re: [Gmod-tripal-devel] Tripal Developer and User Meeting - July 12th

[Stephen F. <spf...@gm...>]

Just a fix to the subject line... The meeting is July 12th.


On 7/11/2016 3:22 PM, Stephen Ficklin wrote:
> Dear Tripal Developers and Users,
>
> We will have our monthly Tripal Developer and User meeting tomorrow,  
> July 12th.   The meeting is open for everyone.  If you have not 
> previously attended, please consider attending especially if you are 
> considering development of custom extensions.  The goal of the meeting 
> is to share news about Tripal, provide an opportunity to share ideas, 
> ask questions, provide training, and to advertise what you are doing.
>
> For tomorrows meeting we will have two major items on the agenda:  1) 
> A discussion of issues with the Chado Natural Diversity Module and a 
> work-around 2)  A brief demo of Tripal v3 and Web Services.
>
> The meeting start time and connection details follow below.
>
> See you then!
> Stephen
>
> Indian (GMT+5:30):  9:30 pm
> UTC:  4pm (16:00)
> European Central (GMT+2):  6 pm
> US Eastern (GMT-4): 12 pm
> US Central (GMT-5): 11 am
> Canada Regina (GMT-5): 10 am
> US Pacific (GMT-7): 9 am
> China (GMT+8): 12 am (Wed May 4th)
>
> *Connection Details*
> Please join my meeting from your computer, tablet or smartphone.
> https://global.gotomeeting.com/join/731137733
>
> *You can also dial in using your phone.*
> United States : +1 (872) 240-3212
>
> Access Code:**731-137-733
> *****First GoToMeeting? Try a test 
> session:***http://help.citrix.com/getready**
> *
> **
> **
> * 

Re: [Gmod-tripal-devel] Tripal Developer and User Meeting - June 7th

[Stephen F. <spf...@gm...>]

Dear Tripal Developers and Users,

We will have our monthly Tripal Developer and User meeting tomorrow,  
July 12th.   The meeting is open for everyone.  If you have not 
previously attended, please consider attending especially if you are 
considering development of custom extensions.  The goal of the meeting 
is to share news about Tripal, provide an opportunity to share ideas, 
ask questions, provide training, and to advertise what you are doing.

For tomorrows meeting we will have two major items on the agenda:  1) A 
discussion of issues with the Chado Natural Diversity Module and a 
work-around 2)  A brief demo of Tripal v3 and Web Services.

The meeting start time and connection details follow below.

See you then!
Stephen

Indian (GMT+5:30):  9:30 pm
UTC:  4pm (16:00)
European Central (GMT+2):  6 pm
US Eastern (GMT-4): 12 pm
US Central (GMT-5): 11 am
Canada Regina (GMT-5): 10 am
US Pacific (GMT-7): 9 am
China (GMT+8): 12 am (Wed May 4th)

*Connection Details***
Please join my meeting from your computer, tablet or smartphone.
https://global.gotomeeting.com/join/731137733

*You can also dial in using your phone.*
United States : +1 (872) 240-3212

Access Code:**731-137-733
*****First GoToMeeting? Try a test 
session:***http://help.citrix.com/getready**
*
**
**
*

[Gmod-tripal-devel] Tripal 2.1-beta3 now available

[Stephen F. <spf...@gm...>]

Dear Tripal User Community,

We are happy to announce the third beta release of Tripal v2.1. This is 
the last 2.1 beta release. The next will be the full v2.1 release.  This 
version should be the most stable yet for v2.1 and provides all of the 
functionality that v2.1 will offer including:

1) A Chado v1.2 to v1.3 upgrade.
2) A new phylogeny module that includes a newick file importer for 
phylogenetic trees and  an NCBI taxonomy importer for taxonomic trees.  
Much thanks to Andrew Farmer and the LegumeInfo group for their 
assistance and collaboration in development and inclusion of this new 
module!
3) Improved support for multiple Chado installations
4)  Many bug fixes.

For a more details listing please see the release page:

https://www.drupal.org/project/tripal/releases/7.x-2.1-beta3

For upgrade instructions please see these links at the Tripal User's Guide:

Upgrading from a Tripal v1.1 site:
http://tripal.info/tutorials/v2.x/upgrade_6.11_to_2.1

Upgrading from a Tripal v2.0 site:
http://tripal.info/tutorials/v2.x/upgrade_2.0_to_2.1

Stephen

[Gmod-tripal-devel] Tripal v3 + web services demo and July Tripal meeting

[Stephen F. <spf...@gm...>]

Hi All,

The result of our Doodle poll for a demo of Tripal v3 + web services did 
not reach a consensus. I'm guessing it's because of summer travel and 
unfortunately I have had a conflict arise some of the best days.   
Additionally the first week in July is a major travel week in the US, 
and some folks will be settling back in from travel to the GMOD meeting 
at U. of Indiana.   So to accomdate, we will hold the Tripal Developers 
meeting on Tuesday July 12th at the usual time.   If this is of major 
inconvenience please let me know.  And, I will plan to provide the 
Tripal v3 and web services demo at that meeting.  Most likely the 
meeting will therefore surpass one hour for the demo.

Thanks,
Stephen

[Gmod-tripal-devel] A few Tripal things...

[Stephen F. <spf...@gm...>]

Hi all,

A few items to think about:

1)  I'd like to have a demo of web services for Tripal v3.  Below is a 
link for a Doodle Poll for potential dates. If you are interested in 
this please take a look and see if any dates in the poll will work for you:

http://doodle.com/poll/fwpzrve3ytgw5qgn

2)  For those who attended the Developer's meeting this morning, please 
let us know if you like the tutorials in our monthly meetings.  Also 
please let us know if you have suggestions for improvement, or topics of 
importance you want to see addressed.

3)  Lacey and I would like to meet one-on-one with groups by 
teleconference to discuss your Tripal experience, what you like, what 
you hate, what you want to see improved.   But given time constraints we 
may not be able to meet with everyone, so we'll reach out to some of 
you. Please let us know if you want to be included in those meetings and 
we'll be sure to meet.

Thanks!

Stephen

[Gmod-tripal-devel] Tripal Developer and User Meeting - June 7th

[Stephen F. <spf...@gm...>]

Dear Tripal Developers and Users,

We will have our monthly Tripal Developer and User meeting tomorrow,  
June 7th.   The meeting is open for everyone.  If you have not 
previously attended, please consider attending especially if you are 
considering development of custom extensions.  The goal of the meeting 
is to share news about Tripal, provide an opportunity to share ideas, 
ask questions, provide training, and to advertise what you are doing.

For tomorrows meeting we will have a demonstration by Lacey of the 
Site-Wide Search API functionality that is soon to be released with 
Tripal 2.

The meeting time is as follows:

*

*Indian (GMT+5:30):  9:30 pm
UTC:  4pm (16:00)
European Central (GMT+2):  6 pm
US Eastern (GMT-4): 12 pm
US Central (GMT-5): 11 am
Canada Regina (GMT-5): 10 am
US Pacific (GMT-7): 9 am
China (GMT+8): 12 am (Wed May 4th)

Please join my meeting from your computer, tablet or smartphone.
https://global.gotomeeting.com/join/762905221


*You can also dial in using your phone.*
United States : +1 (312) 757-3121

Access Code: 762-905-221

Re: [Gmod-tripal-devel] Controlled vocabularies: Installing CVs error

[Stephen F. <spf...@gm...>]

Hi Arzin,

The message in the screenshot just indicates you should use the 
--username argument instead of --user when you try to run the jobs.  
 From your other screenshot I can see some of your jobs had errors, but 
it's not possible to tell what is going on with those.  Can you re-run 
them (using the --username argument instead of --user) and send the 
resulting output?

Thanks,

Stephen


On 6/3/2016 1:09 AM, Azrin Ahmad wrote:
> Hi,
>
> I'm Azrin Ahmad, Bioinformatician from Malaysia.
> I'm new in Tripal. I already install Drupal & Tripal on Ubuntu 14.04.1 
> LTS. everything goes well but when i'm trying to install CVs 
> (ontologies), i got the error status in web browser (but it's look 
> fine when i launch the job). can you help me solve this problem? i 
> also attach screenshots (command when launch the job and web browser 
> that show status error).
>
> Thanks in advance.
>
> Best regards,
> Azrin Ahmad
> Bioinformatician,
> Centre for Marker Development and Validation.
>
>
> ------------------------------------------------------------------------------
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>
>
> _______________________________________________
> Gmod-tripal-devel mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel

[Gmod-tripal-devel] Controlled vocabularies: Installing CVs error

[Azrin A. <azr...@gm...>]

Hi,

I'm Azrin Ahmad, Bioinformatician from Malaysia.
I'm new in Tripal. I already install Drupal & Tripal on Ubuntu 14.04.1 LTS.
everything goes well but when i'm trying to install CVs (ontologies), i got
the error status in web browser (but it's look fine when i launch the job).
can you help me solve this problem? i also attach screenshots (command when
launch the job and web browser that show status error).

Thanks in advance.

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

[Gmod-tripal-devel] GMOD 2016 Meeting early reg ends May 21; Galaxy Conference Deadlines

[Dave C. <cle...@ga...>]

Hello all,

*GMOD will be holding a community meeting on June 30th and July 1st
<http://gmod.org/wiki/Jun_2016_GMOD_Meeting> in Bloomington, Indiana,
United States.*  GMOD Meetings <http://gmod.org/wiki/Meetings> are a mix of
user and developer presentations, and are a great place to find out what is
happening in the project, what's coming up, and what others are doing.

*Early bird registration <https://gmod2016.eventbrite.com/> ends May 21,
this Saturday.*

*For those who would like to present a talk or poster, the meeting
registration form includes a section for submitting the presentation title
and abstract.*

If you have any suggestions or requests for the meeting, please
contact the GMOD
help desk <he...@gm...>.


*GCC2016*

The GMOD Meeting is immediately after the 2016 Galaxy Community Conference
(GCC2016) <https://gcc2016.iu.edu/>, also in Bloomington (and sharing
housing and venue).  If you are interested in Galaxy, *GCC2016 has a number
of deadlines this Friday, May 20*.  See below.

Galaxy is a part of the GMOD project and there are several presentations at
GCC2016 that cover the GMOD integration:

   - Moving data from the warehouse to the workbench: a bridge to Galaxy
   from the Tripal community genome database software platform,
   <http://sched.co/743X> talk presented by Margaret Staton
   - Apollo: Collaborative Manual Annotation for Genomic Sequencing Projects
   <http://sched.co/743i>, talk presented by Nathan Dunn (Apollo will have
   a poster and demo)
   - Hardwood Genomics Database (HGD): a web portal and database resource
   for hardwood tree genomic and genetic research, poster presented by Ming
   Chen and Margaret Staton (posters are not online yet)

More posters and demos are in the works.

Thanks, and hope to see you in Bloomington,

Dave C


---------- Forwarded message ----------
From: Dave Clements <cle...@ga...>
Date: Mon, May 16, 2016 at 9:09 AM
Subject: GCC2016 Deadlines this Friday & Conference schedule
To: Galaxy Announcements List <gal...@li...>,
Galaxy Dev List <gal...@li...>


Hello all,

This is just a reminder that* there are some key deadlines this Friday, May
20:*

   - Early registration ends <https://gcc2016.iu.edu/registration/index.php>.
   After Friday registration rates go up by over 40%.
   - Poster abstracts <https://gcc2016.iu.edu/abstracts/index.php> are due.

   - Demo abstracts <https://gcc2016.iu.edu/abstracts/index.php> are due.
   These are new this year and can complement a poster abstract or stand on
   their own.

If you are wondering what's happening at GCC2016, the training and
conference schedules <https://gcc16.sched.org/> are now online, featuring 21
accepted talks <https://gcc16.sched.org/overview/type/Conference> and 31
training sessions
<https://gcc16.sched.org/overview/type/Training+%E2%80%94+Any>.

And, thanks to Jetstream <http://jetstream-cloud.org/> IU's newest National
Science Foundation-funded project (and in which Galaxy is a partner), and
the National Center for Genome Analysis Support <http://ncgas.org/> at IU
are sponsoring an opening reception on Monday evening <http://sched.co/72bN>
at the IU Cyberinfrastructure Building.  The first ever GCC opening
reception will feature local wine/beer, morsels from local eateries, and
demonstrations of the 15 million+ pixel IQ-Wall, IU's Data Center, Science
on a Sphere, and other IU-centric IT.

Hope to see you there,

Dave C

-- 
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
https://wiki.galaxyproject.org/

Re: [Gmod-tripal-devel] Tripal Developer and User Meeting - May 3rd

[Kucheran, L. S. <la...@ma...>]

Well it looks like our not observing Daylight Savings has struck again… Apparently the meeting was actually at 10am Canada Regina (GMT-6) rather than 11am (GMT-5) as posted below. Sorry I missed everybody!

Valentin: I will follow up in the issue queue (https://www.drupal.org/node/2567053) on your issues with the multi-chado support.

~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-3208<tel://966-3208>
Email: lac...@sh...<mailto:lac...@sh...>
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan


On May 2, 2016 at 11:54:36 AM, Stephen Ficklin (spf...@gm...<mailto:spf...@gm...>) wrote:

Dear Tripal Developers and Users,

We will have our monthly Tripal Developer and User meeting tomorrow, May 3rd.   The meeting is open for everyone.  If you have not previously attended, please consider attending especially if you are considering development of custom extensions.  The goal of the meeting is to share news about Tripal, provide an opportunity to share ideas, ask questions, and to advertise what you are doing.  Tomorrow's meeting is our non-formal agenda.  The floor is open to anyone who wishes to raise a topic.  Please consider adding topics to the open agenda on this Google Doc:

https://docs.google.com/document/d/1gzgV1EU5CPk-IG83o_z_UG590gdueySgVkCElZYfdgU/edit?usp=sharing

The time of the meeting is as follows:

Indian (GMT+5:30):  9:30 pm
UTC:  4pm (16:00)
European Central (GMT+2):  6 pm
US Eastern (GMT-4): 12 pm
US Central (GMT-5): 11 am
Canada Regina (GMT-5): 11 am
US Pacific (GMT-7): 9 am
China (GMT+8): 12 am (Wed May 4th)

Below are connection details:

Please join my meeting from your computer, tablet or smartphone.
https://global.gotomeeting.com/join/146558085

You can also dial in using your phone.
United States +1 (669) 224-3412

Access Code: 146-558-085

As a reminder, meeting notes from previous meetings can be found here:

http://tripal.info/meetings/developers/summary

See you tomorrow!
Stephen

On 2/28/2016 6:37 PM, Stephen Ficklin wrote:
Dear Tripal Community,

We will have our monthly Tripal Developer's Meeting Tuesday Mar 1st.  As usual, anyone is invited to attend. We encourage anyone who wants to customize their site to drop in. Information to connect to the teleconference is below.   If there is anything you'd like to discuss please let me know and I'll be happy to add it to our agenda.

Below are meeting times and meeting connection details:

GMT:  5pm (17:00)
European Central (GMT+1):  6 pm (18:00)
US Eastern (GMT-5): 12 pm
US Central (GMT-6): 11 am
Canada Regina (GMT-6): 11 am
US Pacific (GMT-8): 9 am
China (GMT+8): 1 am (Wed Feb 3rd)

Connection Details:

Please join my meeting from your computer, tablet or smartphone.
https://global.gotomeeting.com/join/687716749

You can also dial in using your phone.
United States : +1 (646) 749-3131

Access Code: 687-716-749





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[Gmod-tripal-devel] Tripal Developer and User Meeting - May 3rd

[Stephen F. <spf...@gm...>]

Dear Tripal Developers and Users,

We will have our monthly Tripal Developer and User meeting tomorrow, May 
3rd.   The meeting is open for everyone.  If you have not previously 
attended, please consider attending especially if you are considering 
development of custom extensions.  The goal of the meeting is to share 
news about Tripal, provide an opportunity to share ideas, ask questions, 
and to advertise what you are doing.  Tomorrow's meeting is our 
non-formal agenda.  The floor is open to anyone who wishes to raise a 
topic.  Please consider adding topics to the open agenda on this Google Doc:

https://docs.google.com/document/d/1gzgV1EU5CPk-IG83o_z_UG590gdueySgVkCElZYfdgU/edit?usp=sharing

The time of the meeting is as follows:

Indian (GMT+5:30):  9:30 pm
UTC:  4pm (16:00)
European Central (GMT+2):  6 pm
US Eastern (GMT-4): 12 pm
US Central (GMT-5): 11 am
Canada Regina (GMT-5): 11 am
US Pacific (GMT-7): 9 am
China (GMT+8): 12 am (Wed May 4th)

Below are connection details:

Please join my meeting from your computer, tablet or smartphone.
https://global.gotomeeting.com/join/146558085

You can also dial in using your phone.
United States +1 (669) 224-3412

Access Code: 146-558-085

As a reminder, meeting notes from previous meetings can be found here:

http://tripal.info/meetings/developers/summary

See you tomorrow!
Stephen

On 2/28/2016 6:37 PM, Stephen Ficklin wrote:
> Dear Tripal Community,
>
> We will have our monthly Tripal Developer's Meeting Tuesday Mar 1st.  
> As usual, anyone is invited to attend. We encourage anyone who wants 
> to customize their site to drop in. Information to connect to the 
> teleconference is below.   If there is anything you'd like to discuss 
> please let me know and I'll be happy to add it to our agenda.
>
> Below are meeting times and meeting connection details:
>
> GMT:  5pm (17:00)
> European Central (GMT+1):  6 pm (18:00)
> US Eastern (GMT-5): 12 pm
> US Central (GMT-6): 11 am
> Canada Regina (GMT-6): 11 am
> US Pacific (GMT-8): 9 am
> China (GMT+8): 1 am (Wed Feb 3rd)
>
> *Connection Details:*
>
> Please join my meeting from your computer, tablet or smartphone.
> https://global.gotomeeting.com/join/687716749
>
> You can also dial in using your phone.
> United States : +1 (646) 749-3131
>
> Access Code: 687-716-749
>
>
>
>

Re: [Gmod-tripal-devel] Some problems related to Tripal Features, follow up on a tripal update

[Kucheran, L. S. <la...@ma...>]

Hi Michael,

If you were looking for site-wide search functionality, it’s now available in the development version of Tripal 2 with documentation available in the User Guide<http://tripal.info/node/298>. As promised, I included an example for how you could index feature properties in the tutorial on the second page (Controlling which fields get indexed; Option #3).

I’m using the database backend to store my keywords and it has approximately doubled my database size. For an example of speed when using this method, you can go to KnowPulse and use the search box in the header. A good example keyword is “Lentil” which will return results across all node types. For evaluation purposes, KnowPulse has ~1.7 million nodes and is run off a mediocre, single box setup (2.67 GHz, 6 cores, 64GB RAM, 3Gbps SAS).

Hope that Helps!
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-3208<tel://966-3208>
Email: lac...@sh...<mailto:lac...@sh...>
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan


On April 14, 2016 at 9:48:25 AM, Kucheran, Lacey Sanderson (la...@ma...<mailto:la...@ma...>) wrote:

Hi Michael,

Were you meaning the site-wide search that was available in Tripal 1.0? If so that functionality was removed from Tripal 2 due to some incompatibilities with Drupal 7 as well as an intent on improving the methodology.

It’s looking like Tripal 2.1 will have site-wide searching capabilities as I am working on that as we speak so I’ll point you to the tutorial when it’s stable. Essentially it uses the Search API to expose parts of chado to searching. When complete it would require some theme extension to make it work with the theme provided search box but it is possible and will provide you a lot more control and flexibility over what is indexed (and no duplication or taxonomy terms). By default it will index the name/uniquename/accession, as well as, follow foreign keys (i.e.: index the type, organism, dbxref for features). It won’t yet index your annotation/properties or blast results but it should be easy to make it do so with a little custom code. Maybe I’ll use your use case for the tutorial ;-)

I’ll keep you updated with the progress,
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-3208<tel://966-3208>
Email: lac...@sh...<mailto:lac...@sh...>
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan


On April 12, 2016 at 11:05:20 AM, Stephen Ficklin (spf...@gm...<mailto:spf...@gm...>) wrote:

Hi Michael,

Sorry for the delay in response. I've been away from the office.

So, you have found a bug for us in the permissions. I've applied a fix
to the 7.x-2.x development branch that hopefully will fix the problem
for you. So please try it out and if you have other problems with
permissions I'll work on those too.

As for resyncing pages it's not possible. 'Sync' is probably an
unfortunate choice of a word. Essentially what happens during a sync is
a Drupal node is created that is associated with a Chado record. So,
once that association is made that's all is needed. Tripal pulls data
directly from Chado whenver the page is displayed so there's no syncing
that goes on at that point.

But it's odd that features that existed before the upgrade are not
present in the search results. Can you confirm that those older pages
still exist?

Stephen

On 4/10/2016 8:07 AM, Michael Dondrup wrote:
> Hi and sorry for bothering,
>
> is there any news on these topics? We have now opened a lot more content including the genomic content in Licebase (see https://licebase.org if you are interested).
>
> The search problem is now most relevant, because users cannot use the site search to find features. Before, the normal site search would find
> Features (by e.g. annotation, search eg. ‘chitinase’ if chitinase was annotated in the Properties) and also Blast results, but now it does not find any features. Is there any work-around to re-sync features?
>
> Best
> Michael
>
>
>
>
>> On Apr 4, 2016, at 2:45 PM, Michael Dondrup <mic...@ii...> wrote:
>>
>> Hi,
>>
>> following an ~2 month update process to D7/Tripal 2 of LiceBase, we now have resolved all outstanding issues,
>> greatly thanks to Stephen and the Tripal community. We are now in the process of honing off the few remaining issues.
>> These three are all related to the Tripal Feature module and we are not sure if they are caused by the update. I will just list them below,
>> I can also add them to the issue tracker if you like.
>>
>> 1. Features don’t appear to respect the ‘View’ permission. We tested if an anonymous user can view Features even though the View Features permission is off in the permission table. We tested this case also using the output of Devel Node Access, and it suggests that any feature is using the default node View permission for published content from the Node permissions. The other CRUD permissions ‘Create’, ‘Update’, ‘Delete’ seem to be ok. As a result, anonymous is either able to see the site including all features or not able to use it at all. I remember this was different in Tripal 1.
>>
>> A typical Debug output of the permission set per user who has full access looks like:
>>
>> username create view update delete
>> user YES: by node (permissions) YES: {node_access} YES: by node (permissions) YES: by node (permissions)
>> with the explanation YES: hook_node_access() of the following module(s) allows this: node (permissions).
>>
>> This makes me wonder whether there is something missing for hook_node_access().
>> Please see the attached screen shots for an explanation of our Permission settings.
>>
>> 2. The site search doesn’t seem to find the updated Feature pages. I have re-indexed the site via admin/config/search/settings, but that doesn’t seem
>> to have an effect. Feature pages that have been created after the update are found by the search.
>>
>> 3. I thought re-sync’ing the features might solve the above, but I do not know how to ‘Re-Sync’ already sync’ed features, without deleting them. When we attempt to sync all ‘gene’ features for example, the tripal job says “0 feature records found.”
>>
>>
>> Best
>> Michael
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> <Screen Shot 2016-04-04 at 12.44.29 PM.png>
>>
>>
>>
>> <Screen Shot 2016-04-04 at 12.25.54 PM.png>
>>
>>
>> <Screen Shot 2016-04-04 at 09.06.17 AM.png>
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> Gmod-tripal-devel mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>
> ------------------------------------------------------------------------------
> Find and fix application performance issues faster with Applications Manager
> Applications Manager provides deep performance insights into multiple tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/
> gampad/clk?id=1444514301&iu=/ca-pub-7940484522588532
> _______________________________________________
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> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel


------------------------------------------------------------------------------
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your business applications. It resolves application problems quickly and
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[Gmod-tripal-devel] Tripal 2.0 Site-wide Search

[Kucheran, L. S. <la...@ma...>]

Hi Everyone,

I took a little bit of time over the past couple of weeks and added basic site-wide search support for Tripal 2.0. This is currently only available in the development version (not quite ready for production) but a Tripal release should be coming soon. You can find documentation in the Tripal 2.0 User Guide<http://tripal.info/node/298> which shows you both how to set it up and how to customize it.

Essentially, Tripal 2.0 now has integration with the Drupal Search API which allows both a simple database-based search as well as more advanced solutions such as Apache Solr or Elastic Search. By default, all the name fields and base foreign keys (i.e.: type, organism, dbxref) are made available for indexing. You can control which fields get indexed through the Search API Index interface by checking or unchecking checkboxes. You can make additional chado fields available to be indexed by either implementing a simple hook where you just list the fields you want made available or a slightly more complicated hook which gives you complete control —both methods are included in the tutorial.

Enjoy!
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-3208<tel://966-3208>
Email: lac...@sh...<mailto:lac...@sh...>
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

Re: [Gmod-tripal-devel] [Gmod-tripal] Tripal Phylogeny Module Discussion

[Guignon, V. (Bioversity-France) <v.g...@cg...>]

Hi there!

Just a quick question as I could not attempt to the phylogeny module meeting the other day: is there any meeting notes we can access to see what has been said?

   Val


From: Stephen Ficklin [mailto:spf...@gm...]
Sent: lundi 18 avril 2016 18:44
To: gmo...@li...; gmod tripal devel <gmo...@li...>
Subject: Re: [Gmod-tripal-devel] [Gmod-tripal] Tripal Phylogeny Module Discussion


Hi All,

Below are connection details for our meeting this Wednesday regarding the Tripal Phylogeny module. Anyone interested in using this module is welcome to attend and provide feedback.

Times are at:

UTC: 15:00 (3pm)
European Central:  17:00 (5pm)
Eastern US:  11am
Central US: 10am
Regina Canada: 9am
Pacific US: 8am
Phylogeny Module Discussion

Please join my meeting from your computer, tablet or smartphone.
https://global.gotomeeting.com/join/630740901

You can also dial in using your phone.
United States : +1 (408) 650-3123

Access Code: 630-740-901

Stephen


On 4/12/2016 10:18 AM, Stephen Ficklin wrote:
For those interested in attending the Tripal Phylogeny Module discussion, it looks as though the best time will be Wednesday April 20th at the following time:

UTC: 15:00 (3pm)
European Central:  17:00 (5pm)
Eastern US:  11am
Central US: 10am
Regina Canada: 9am
Pacific US: 8am

Please mark your calendars. I will send out connection details a day or two before the meeting.

Stephen

On 3/29/16 10:37 PM, Stephen Ficklin wrote:

Hi All,

In our Tripal Developer's Meeting this month we discussed the Tripal
Phylogeny module which has been created by Andrew Farmer's group at
NCGR.  The goal is to make this module publicly available but some
feedback is needed from the larger group to identify how to generalize
the module sufficiently so that it can be used by a broad user base.  I
promised I would send out a Doodle poll to organize a meeting for that
discussion.

If you are interested in displaying phylogenetic trees on your Tripal
site please consider joining this discussion to provide feedback.  A
Doodle poll has been setup to select an optimal time for those who would
like to participate:

http://doodle.com/poll/pugdmbhpb7cerb9h

Thanks,
Stephen

------------------------------------------------------------------------------
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Re: [Gmod-tripal-devel] [Gmod-tripal] Tripal Phylogeny Module Discussion

[Andrew F. <ad...@nc...>]

Thanks Stephen-
just following up for the benefit of anyone who may be unsure if they 
should attend tomorrow's meeting or not,
the basic agenda I have in mind for the call is:

Use case driven tour of phylogeny module. Focus on utility for finding 
possible areas for
     investigation of issues around gene annotation/assembly vs truly 
interesting biological phenomena;
     illustrate gene-family connectivity to other modules/tools 
implemented on legumeinfo.org (genome context viewer,
     multiple sequence alignment display, protein domain module)
Our current protocols for building families, MSAs, trees; protocols for 
data loading; use of standard chado
     tables + tripal materialized views; could be opportunity for some 
discussion on the differences between this
     full-phylogeny approach to gene family representation vs the 
flatter representation possible through the
     up-and-coming chado group module.
Discussion of areas of divergence between phylogeny module branches 
(legumeinfo
      implementation and proposed core implementation) and attempted 
resolution of what interested
      parties would like to have included in the core (could also 
include some discussion of ideas for where
      to go next with development of new features)
If there's time, some discussion of what it will take to make the 
phylogeny module compliant with Tripal 3.

apologies for not getting this out to you all sooner (especially those 
in much earlier time zones!), but looking
forward to receiving feedback.

Andrew



On 4/18/16 10:44 AM, Stephen Ficklin wrote:
>
> Hi All,
>
> Below are connection details for our meeting this Wednesday regarding 
> the Tripal Phylogeny module. Anyone interested in using this module is 
> welcome to attend and provide feedback.
>
> Times are at:
>
> UTC: 15:00 (3pm)
> European Central:  17:00 (5pm)
> Eastern US:  11am
> Central US: 10am
> Regina Canada: 9am
> Pacific US: 8am
>
> *
> Phylogeny Module Discussion
> *
> Please join my meeting from your computer, tablet or smartphone.
> https://global.gotomeeting.com/join/630740901
>
> *You can also dial in using your phone.*
> United States : +1 (408) 650-3123
>
> Access Code: 630-740-901
>
> Stephen
>
> On 4/12/2016 10:18 AM, Stephen Ficklin wrote:
>> For those interested in attending the Tripal Phylogeny Module 
>> discussion, it looks as though the best time will be Wednesday April 
>> 20th at the following time:
>>
>> UTC: 15:00 (3pm)
>> European Central:  17:00 (5pm)
>> Eastern US:  11am
>> Central US: 10am
>> Regina Canada: 9am
>> Pacific US: 8am
>>
>> Please mark your calendars. I will send out connection details a day 
>> or two before the meeting.
>>
>> Stephen
>>
>> On 3/29/16 10:37 PM, Stephen Ficklin wrote:
>>>> Hi All,
>>>>
>>>> In our Tripal Developer's Meeting this month we discussed the Tripal
>>>> Phylogeny module which has been created by Andrew Farmer's group at
>>>> NCGR.  The goal is to make this module publicly available but some
>>>> feedback is needed from the larger group to identify how to generalize
>>>> the module sufficiently so that it can be used by a broad user 
>>>> base.  I
>>>> promised I would send out a Doodle poll to organize a meeting for that
>>>> discussion.
>>>>
>>>> If you are interested in displaying phylogenetic trees on your Tripal
>>>> site please consider joining this discussion to provide feedback.  A
>>>> Doodle poll has been setup to select an optimal time for those who 
>>>> would
>>>> like to participate:
>>>>
>>>> http://doodle.com/poll/pugdmbhpb7cerb9h
>>>>
>>>> Thanks,
>>>> Stephen
>>>>
>>>> ------------------------------------------------------------------------------ 
>>>>
>>>> Transform Data into Opportunity.
>>>> Accelerate data analysis in your applications with
>>>> Intel Data Analytics Acceleration Library.
>>>> Click to learn more.
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140
>>>> _______________________________________________
>>>> Gmod-tripal mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>
>
>
>
> ------------------------------------------------------------------------------
> Find and fix application performance issues faster with Applications Manager
> Applications Manager provides deep performance insights into multiple tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial!
> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
>
>
> _______________________________________________
> Gmod-tripal mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal

-- 
...all concepts in which an entire process is semiotically concentrated
elude definition; only that which has no history is definable.

Friedrich Nietzsche

Re: [Gmod-tripal-devel] Tripal HTML and biological web resources indexation

[Pierre L. <pie...@ir...>]

Hi Stephen, 

indeed we are talking about this ecosystem that coming with RDFa such as schema.org and now there is a new consortium BioSchema that aims to extend and specialize  it for the bioinformatics  https://github.com/BioSchemas <https://github.com/BioSchemas>

I am not involve in the project, just attended a brain storming workshop where I mentionned the work of standardization/interoperability your are doing with gmod and tripal.  Imagine several Tripal and Gmod apps that could be indexed by google/bing/Yahoo… and linked to others resources :)

raf...@el... and mar...@el... are the guys who led the discussion. 

Hope it helps.

Cheers
Pierre
> Le 15 avr. 2016 à 19:27, Stephen Ficklin <spf...@gm...> a écrit :
> 
> Hi Valentin,
> 
> Are you referring to RDFa (https://rdfa.info/) or something similar?   It would not be difficult for Tripal v3 to do this. With the redesign of Tripal v3 based on controlled vocabularies I think this could be added and was something we were already considering but we didn't have a specific use case.   It sounds like there may be one :-)  I'd be happy to chat more with anyone interested in this.
> 
> Stephen
> 
> On 4/1/2016 3:49 AM, Guignon, Valentin (Bioversity-France) wrote:
>> Hi!
>> 
>> I got a colleague (in cc) working on semantic web who would like to know if the Tripal community could include in the HTML output of its various biological objects some tags to enable a better indexation of that data by search engines.
>> 
>> Here is his question:
>> "Bioschema ( https://github.com/BioSchemas ) plans to extend schema.org ( http://schema.org/ ) and will ease the indexing of biological web resources.
>> Do you think Tripal and JBrowse could implement and contribute to these specifications in the future ?"
>> 
>> As far as I understood it, it's just a matter of HTML tag properties to add to our HTML templates.
>> For instance, if we output data of a person, it would look like this:
>> ----------
>> <div itemscope itemtype="http://schema.org/LifeSciencePerson">
>>     <div itemprop="name">John Smith</div>
>>     <div itemprop="description">John Smith is specializes in Next Generation Sequencing at the University of Soandso. </div>
>>     <div><meta itemprop="birthDate" content="1976-04-15T">Wednesday 14 April 1976</div>
>> ...
>> </div>
>> ----------
>> I think it's not a big deal but would need time to understand the thing and find out how to map our data with those tags.
>> 
>> What's our answer(s)? What do you guys think?
>> Cheers,
>> 
>>    Val
>> 
>> 
>> ------------------------------------------------------------------------------
>> Transform Data into Opportunity.
>> Accelerate data analysis in your applications with
>> Intel Data Analytics Acceleration Library.
>> Click to learn more.
>> http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140
>> _______________________________________________
>> Gmod-tripal-devel mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
> 
> 
> 
> 
> 

Re: [Gmod-tripal-devel] [Gmod-tripal] Tripal Phylogeny Module Discussion

[Stephen F. <spf...@gm...>]

Hi All,

Below are connection details for our meeting this Wednesday regarding 
the Tripal Phylogeny module. Anyone interested in using this module is 
welcome to attend and provide feedback.

Times are at:

UTC: 15:00 (3pm)
European Central:  17:00 (5pm)
Eastern US:  11am
Central US: 10am
Regina Canada: 9am
Pacific US: 8am

*
Phylogeny Module Discussion
*
Please join my meeting from your computer, tablet or smartphone.
https://global.gotomeeting.com/join/630740901

*You can also dial in using your phone.*
United States : +1 (408) 650-3123

Access Code: 630-740-901

Stephen

On 4/12/2016 10:18 AM, Stephen Ficklin wrote:
> For those interested in attending the Tripal Phylogeny Module 
> discussion, it looks as though the best time will be Wednesday April 
> 20th at the following time:
>
> UTC: 15:00 (3pm)
> European Central:  17:00 (5pm)
> Eastern US:  11am
> Central US: 10am
> Regina Canada: 9am
> Pacific US: 8am
>
> Please mark your calendars. I will send out connection details a day 
> or two before the meeting.
>
> Stephen
>
> On 3/29/16 10:37 PM, Stephen Ficklin wrote:
>>> Hi All,
>>>
>>> In our Tripal Developer's Meeting this month we discussed the Tripal
>>> Phylogeny module which has been created by Andrew Farmer's group at
>>> NCGR.  The goal is to make this module publicly available but some
>>> feedback is needed from the larger group to identify how to generalize
>>> the module sufficiently so that it can be used by a broad user base.  I
>>> promised I would send out a Doodle poll to organize a meeting for that
>>> discussion.
>>>
>>> If you are interested in displaying phylogenetic trees on your Tripal
>>> site please consider joining this discussion to provide feedback.  A
>>> Doodle poll has been setup to select an optimal time for those who 
>>> would
>>> like to participate:
>>>
>>> http://doodle.com/poll/pugdmbhpb7cerb9h
>>>
>>> Thanks,
>>> Stephen
>>>
>>> ------------------------------------------------------------------------------ 
>>>
>>> Transform Data into Opportunity.
>>> Accelerate data analysis in your applications with
>>> Intel Data Analytics Acceleration Library.
>>> Click to learn more.
>>> http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140
>>> _______________________________________________
>>> Gmod-tripal mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>

Re: [Gmod-tripal-devel] Tripal HTML and biological web resources indexation

[Stephen F. <spf...@gm...>]

Hi Valentin,

Are you referring to RDFa (https://rdfa.info/) or something similar?   
It would not be difficult for Tripal v3 to do this. With the redesign of 
Tripal v3 based on controlled vocabularies I think this could be added 
and was something we were already considering but we didn't have a 
specific use case.   It sounds like there may be one :-)  I'd be happy 
to chat more with anyone interested in this.

Stephen

On 4/1/2016 3:49 AM, Guignon, Valentin (Bioversity-France) wrote:
> Hi!
>
> I got a colleague (in cc) working on semantic web who would like to know if the Tripal community could include in the HTML output of its various biological objects some tags to enable a better indexation of that data by search engines.
>
> Here is his question:
> "Bioschema ( https://github.com/BioSchemas ) plans to extend schema.org ( http://schema.org/ ) and will ease the indexing of biological web resources.
> Do you think Tripal and JBrowse could implement and contribute to these specifications in the future ?"
>
> As far as I understood it, it's just a matter of HTML tag properties to add to our HTML templates.
> For instance, if we output data of a person, it would look like this:
> ----------
> <div itemscope itemtype="http://schema.org/LifeSciencePerson">
>      <div itemprop="name">John Smith</div>
>      <div itemprop="description">John Smith is specializes in Next Generation Sequencing at the University of Soandso. </div>
>      <div><meta itemprop="birthDate" content="1976-04-15T">Wednesday 14 April 1976</div>
> ...
> </div>
> ----------
> I think it's not a big deal but would need time to understand the thing and find out how to map our data with those tags.
>
> What's our answer(s)? What do you guys think?
> Cheers,
>
>     Val
>
>
> ------------------------------------------------------------------------------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140
> _______________________________________________
> Gmod-tripal-devel mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel

Re: [Gmod-tripal-devel] Some problems related to Tripal Features, follow up on a tripal update

[Kucheran, L. S. <la...@ma...>]

Hi Michael,

Were you meaning the site-wide search that was available in Tripal 1.0? If so that functionality was removed from Tripal 2 due to some incompatibilities with Drupal 7 as well as an intent on improving the methodology.

It’s looking like Tripal 2.1 will have site-wide searching capabilities as I am working on that as we speak so I’ll point you to the tutorial when it’s stable. Essentially it uses the Search API to expose parts of chado to searching. When complete it would require some theme extension to make it work with the theme provided search box but it is possible and will provide you a lot more control and flexibility over what is indexed (and no duplication or taxonomy terms). By default it will index the name/uniquename/accession, as well as, follow foreign keys (i.e.: index the type, organism, dbxref for features). It won’t yet index your annotation/properties or blast results but it should be easy to make it do so with a little custom code. Maybe I’ll use your use case for the tutorial ;-)

I’ll keep you updated with the progress,
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-3208<tel://966-3208>
Email: lac...@sh...<mailto:lac...@sh...>
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan


On April 12, 2016 at 11:05:20 AM, Stephen Ficklin (spf...@gm...<mailto:spf...@gm...>) wrote:

Hi Michael,

Sorry for the delay in response. I've been away from the office.

So, you have found a bug for us in the permissions. I've applied a fix
to the 7.x-2.x development branch that hopefully will fix the problem
for you. So please try it out and if you have other problems with
permissions I'll work on those too.

As for resyncing pages it's not possible. 'Sync' is probably an
unfortunate choice of a word. Essentially what happens during a sync is
a Drupal node is created that is associated with a Chado record. So,
once that association is made that's all is needed. Tripal pulls data
directly from Chado whenver the page is displayed so there's no syncing
that goes on at that point.

But it's odd that features that existed before the upgrade are not
present in the search results. Can you confirm that those older pages
still exist?

Stephen

On 4/10/2016 8:07 AM, Michael Dondrup wrote:
> Hi and sorry for bothering,
>
> is there any news on these topics? We have now opened a lot more content including the genomic content in Licebase (see https://licebase.org if you are interested).
>
> The search problem is now most relevant, because users cannot use the site search to find features. Before, the normal site search would find
> Features (by e.g. annotation, search eg. ‘chitinase’ if chitinase was annotated in the Properties) and also Blast results, but now it does not find any features. Is there any work-around to re-sync features?
>
> Best
> Michael
>
>
>
>
>> On Apr 4, 2016, at 2:45 PM, Michael Dondrup <mic...@ii...> wrote:
>>
>> Hi,
>>
>> following an ~2 month update process to D7/Tripal 2 of LiceBase, we now have resolved all outstanding issues,
>> greatly thanks to Stephen and the Tripal community. We are now in the process of honing off the few remaining issues.
>> These three are all related to the Tripal Feature module and we are not sure if they are caused by the update. I will just list them below,
>> I can also add them to the issue tracker if you like.
>>
>> 1. Features don’t appear to respect the ‘View’ permission. We tested if an anonymous user can view Features even though the View Features permission is off in the permission table. We tested this case also using the output of Devel Node Access, and it suggests that any feature is using the default node View permission for published content from the Node permissions. The other CRUD permissions ‘Create’, ‘Update’, ‘Delete’ seem to be ok. As a result, anonymous is either able to see the site including all features or not able to use it at all. I remember this was different in Tripal 1.
>>
>> A typical Debug output of the permission set per user who has full access looks like:
>>
>> username create view update delete
>> user YES: by node (permissions) YES: {node_access} YES: by node (permissions) YES: by node (permissions)
>> with the explanation YES: hook_node_access() of the following module(s) allows this: node (permissions).
>>
>> This makes me wonder whether there is something missing for hook_node_access().
>> Please see the attached screen shots for an explanation of our Permission settings.
>>
>> 2. The site search doesn’t seem to find the updated Feature pages. I have re-indexed the site via admin/config/search/settings, but that doesn’t seem
>> to have an effect. Feature pages that have been created after the update are found by the search.
>>
>> 3. I thought re-sync’ing the features might solve the above, but I do not know how to ‘Re-Sync’ already sync’ed features, without deleting them. When we attempt to sync all ‘gene’ features for example, the tripal job says “0 feature records found.”
>>
>>
>> Best
>> Michael
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> <Screen Shot 2016-04-04 at 12.44.29 PM.png>
>>
>>
>>
>> <Screen Shot 2016-04-04 at 12.25.54 PM.png>
>>
>>
>> <Screen Shot 2016-04-04 at 09.06.17 AM.png>
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> Gmod-tripal-devel mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>
> ------------------------------------------------------------------------------
> Find and fix application performance issues faster with Applications Manager
> Applications Manager provides deep performance insights into multiple tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/
> gampad/clk?id=1444514301&iu=/ca-pub-7940484522588532
> _______________________________________________
> Gmod-tripal-devel mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel


------------------------------------------------------------------------------
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
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_______________________________________________
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Re: [Gmod-tripal-devel] Some problems related to Tripal Features, follow up on a tripal update

[Stephen F. <spf...@gm...>]

Hi Michael,

Sorry for the delay in response. I've been away from the office.

So, you have found a bug for us in the permissions.  I've applied a fix 
to the 7.x-2.x development branch that hopefully will fix the problem 
for you.  So please try it out and if you have other problems with 
permissions I'll work on those too.

As for resyncing pages it's not possible.  'Sync' is probably an 
unfortunate choice of a word.  Essentially what happens during a sync is 
a Drupal node is created that is associated with a Chado record.  So, 
once that association is made that's all is needed. Tripal pulls data 
directly from Chado whenver the page is displayed so there's no syncing 
that goes on at that point.

But it's odd that features that existed before the upgrade are not 
present in the search results.  Can you confirm that those older pages 
still exist?

Stephen

On 4/10/2016 8:07 AM, Michael Dondrup wrote:
> Hi and sorry for bothering,
>
> is there any news on these topics? We have now opened a lot more content including the genomic content in Licebase (see https://licebase.org if you are interested).
>
> The search problem is now most relevant, because users cannot use the site search to find features. Before, the normal site search would find
> Features (by e.g. annotation, search eg. ‘chitinase’ if chitinase was annotated in the Properties)  and also Blast results, but now it does not find any features. Is there any work-around to re-sync features?
>
> Best
> Michael
>
>
>
>
>> On Apr 4, 2016, at 2:45 PM, Michael Dondrup <mic...@ii...> wrote:
>>
>> Hi,
>>
>> following an ~2 month update process to D7/Tripal 2 of LiceBase, we now have resolved all outstanding issues,
>> greatly thanks to Stephen and the Tripal community. We are now in the process of honing off the few remaining issues.
>> These three are all related to the Tripal Feature module and we are not sure if they are caused by the update. I will just list them below,
>> I can also add them to the issue tracker if you like.
>>
>> 1. Features don’t appear to respect the ‘View’ permission. We tested if an anonymous user can view Features even though the View Features permission is off in the permission table. We tested this case also using the output of Devel Node Access, and it suggests that any feature is using the default node View permission for published content from the Node permissions. The other CRUD permissions ‘Create’, ‘Update’, ‘Delete’  seem to be ok. As a result, anonymous is either able to see the site including all features or not able to use it at all. I remember this was different in Tripal 1.
>>
>> A typical Debug output of the permission set per user who has full access looks like:
>>
>> username	create	view	update	delete
>> user YES: by node (permissions)	YES: {node_access}	YES: by node (permissions)	YES: by node (permissions)
>> with the explanation YES: hook_node_access() of the following module(s) allows this: node (permissions).
>>
>> This makes me wonder whether there is something missing for hook_node_access().
>> Please see the attached screen shots for an explanation of our Permission settings.
>>
>> 2. The site search doesn’t seem to find the updated Feature pages. I have re-indexed the site via admin/config/search/settings, but that doesn’t seem
>> to have an effect. Feature pages that have been created after the update are found by the search.
>>
>> 3. I thought re-sync’ing the features might solve the above, but I do not know how to ‘Re-Sync’ already sync’ed features, without deleting them.  When we attempt to sync all ‘gene’ features for example, the tripal job says “0 feature records found.”
>>
>>
>> Best
>> Michael
>>
>>
>>
>>
>>    
>>
>>
>>
>>
>>
>>
>>
>>
>> <Screen Shot 2016-04-04 at 12.44.29 PM.png>
>>
>>
>>
>> <Screen Shot 2016-04-04 at 12.25.54 PM.png>
>>
>>
>> <Screen Shot 2016-04-04 at 09.06.17 AM.png>
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> Gmod-tripal-devel mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>
> ------------------------------------------------------------------------------
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Re: [Gmod-tripal-devel] Some problems related to Tripal Features, follow up on a tripal update

[Michael D. <mic...@ii...>]

Hi and sorry for bothering,

is there any news on these topics? We have now opened a lot more content including the genomic content in Licebase (see https://licebase.org if you are interested).

The search problem is now most relevant, because users cannot use the site search to find features. Before, the normal site search would find
Features (by e.g. annotation, search eg. ‘chitinase’ if chitinase was annotated in the Properties)  and also Blast results, but now it does not find any features. Is there any work-around to re-sync features?

Best
Michael




> On Apr 4, 2016, at 2:45 PM, Michael Dondrup <mic...@ii...> wrote:
> 
> Hi,
> 
> following an ~2 month update process to D7/Tripal 2 of LiceBase, we now have resolved all outstanding issues,
> greatly thanks to Stephen and the Tripal community. We are now in the process of honing off the few remaining issues. 
> These three are all related to the Tripal Feature module and we are not sure if they are caused by the update. I will just list them below,
> I can also add them to the issue tracker if you like.
> 
> 1. Features don’t appear to respect the ‘View’ permission. We tested if an anonymous user can view Features even though the View Features permission is off in the permission table. We tested this case also using the output of Devel Node Access, and it suggests that any feature is using the default node View permission for published content from the Node permissions. The other CRUD permissions ‘Create’, ‘Update’, ‘Delete’  seem to be ok. As a result, anonymous is either able to see the site including all features or not able to use it at all. I remember this was different in Tripal 1.
> 
> A typical Debug output of the permission set per user who has full access looks like:
> 
> username	create	view	update	delete
> user YES: by node (permissions)	YES: {node_access}	YES: by node (permissions)	YES: by node (permissions)
> with the explanation YES: hook_node_access() of the following module(s) allows this: node (permissions).
> 
> This makes me wonder whether there is something missing for hook_node_access().
> Please see the attached screen shots for an explanation of our Permission settings.
> 
> 2. The site search doesn’t seem to find the updated Feature pages. I have re-indexed the site via admin/config/search/settings, but that doesn’t seem 
> to have an effect. Feature pages that have been created after the update are found by the search. 
> 
> 3. I thought re-sync’ing the features might solve the above, but I do not know how to ‘Re-Sync’ already sync’ed features, without deleting them.  When we attempt to sync all ‘gene’ features for example, the tripal job says “0 feature records found.” 
> 
> 
> Best
> Michael
> 
> 
> 
> 
>   
> 
> 
> 
> 
> 
> 
> 
> 
> <Screen Shot 2016-04-04 at 12.44.29 PM.png>
> 
> 
> 
> <Screen Shot 2016-04-04 at 12.25.54 PM.png>
> 
> 
> <Screen Shot 2016-04-04 at 09.06.17 AM.png>
> ------------------------------------------------------------------------------
> _______________________________________________
> Gmod-tripal-devel mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel

Re: [Gmod-tripal-devel] [Gmod-tripal] Tripal Developer's Meeting - April 5th

[Kucheran, L. S. <la...@ma...>]

Here’s a link to the Agenda for tomorrows Meeting:
https://docs.google.com/document/d/1VvRlBNiJdfn-yd1Om5bcn_kXtC0DvgzP-X2_F_saXD0

As always, there is a round table discussion section so feel free to add any topics you are interested in.

Thanks & “See” you tomorrow!
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-3208<tel://966-3208>
Email: lac...@sh...<mailto:lac...@sh...>
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan


On April 4, 2016 at 11:14:52 AM, Stephen Ficklin (spf...@gm...<mailto:spf...@gm...>) wrote:

In case there is any confusion by the subject line of this email. I'm resending.  The date for the meeting is tomorrow: April 5th.

Apologies for any confusion.

Stephen

On 4/4/2016 10:06 AM, Stephen Ficklin wrote:
Dear Tripal Community,

We will have our monthly Tripal Developer's Meeting Tuesday April 5th.  As usual, anyone is invited to attend. We encourage anyone who wants to customize their site to drop in. Information to connect to the teleconference is below.

Below are meeting times and meeting connection details:

GMT:  4pm (16:00)
European Central (GMT+2):  6 pm (18:00)
US Eastern (GMT-4): 12 pm
US Central (GMT-5): 11 am
Canada Regina (GMT-6): 10 am
US Pacific (GMT-7): 9 am
China (GMT+8): 12 am (Wed Mar 6th)

Connection Details:

Please join my meeting from your computer, tablet or smartphone.
https://global.gotomeeting.com/join/587860997

You can also dial in using your phone.
United States : +1 (312) 757-3121

Access Code: 587-860-997



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