[Gmod-tripal-devel] Tripal Developer's Meeting / May 5th

classic Classic list List threaded Threaded
13 messages Options
Reply | Threaded
Open this post in threaded view
|

[Gmod-tripal-devel] Tripal Developer's Meeting / May 5th

Stephen Ficklin-2
Dear Tripal Community,

We will have our monthly Tripal Developer's Meeting tomorrow, Tuesday
May 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. This month's meeting is an informal agenda.
Anyone who wishes to raise a topic can do so.  Here is a listing of some
local times for the meeting:

GMT:  4pm (16:00)
European Central:  5 pm (17:00)
US Eastern: 12 pm
US Central: 11 am
Canada Saskatchewan: 10 am
US Pacific: 9 am
China:  12 am (Wed March 8th)

The current agenda is here:

https://docs.google.com/document/d/1ffdBg7j-6DP1uekctCtCcpSOk6pbPI25B4CSPVk6gmU/edit

Feel free to add a comment to that document to include an agenda item.

An archive of past meeting notes is here:

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

Hope to see you there,
Stephen


1.  Please join my meeting, Tuesday, May 05, 2015 at 12:00 PM Eastern
Daylight Time.
https://global.gotomeeting.com/join/476323925

2.  Use your microphone and speakers (VoIP) - a headset is recommended.  
Or, call in using your telephone.

Dial +1 (872) 240-3412
Access Code: 476-323-925
Audio PIN: Shown after joining the meeting

Meeting ID: 476-323-925

GoToMeeting®
Online Meetings Made Easy®

Not at your computer? Click the link to join this meeting from your
iPhone®, iPad®, Android® or Windows Phone® device via the GoToMeeting app.

------------------------------------------------------------------------------
One dashboard for servers and applications across Physical-Virtual-Cloud
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
Reply | Threaded
Open this post in threaded view
|

[Gmod-tripal-devel] Tripal Developer's Meeting / June 2nd

Stephen Ficklin-2
Dear Tripal Community,

We will have our monthly Tripal Developer's Meeting next Tuesday June
2nd.  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.  Here is a listing of some local times for the
meeting:

GMT:  4pm (16:00)
European Central:  5 pm (17:00)
US Eastern: 12 pm
US Central: 11 am
Canada Saskatchewan: 10 am
US Pacific: 9 am
China:  12 am (Wed March 8th)

The initial meeting notes document can be found here:

https://docs.google.com/document/d/1GVbwB_1zPjA9lJuEpUFHhfUW2t9XZRm_e4LpMmGZ9ik/edit

Please add comments if you have other agenda items you'd like to add.  
The document will be open for editing during the meeting.

Here is the archive of past meeting notes:

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

GoToMeeting connection details follow below.

Happy Weekend!
Stephen


1.  Please join my meeting, Tuesday, June 02, 2015 at 12:00 PM Eastern
Daylight Time.
https://global.gotomeeting.com/join/669144421

2.  Use your microphone and speakers (VoIP) - a headset is recommended.  
Or, call in using your telephone.

Dial +1 (571) 317-3131
Access Code: 669-144-421
Audio PIN: Shown after joining the meeting

Meeting ID: 669-144-421

GoToMeeting®
Online Meetings Made Easy®

Not at your computer? Click the link to join this meeting from your
iPhone®, iPad®, Android® or Windows Phone® device via the GoToMeeting app.



------------------------------------------------------------------------------
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
Reply | Threaded
Open this post in threaded view
|

Re: [Gmod-tripal-devel] Tripal Developer's Meeting / June 2nd

Stephen Ficklin-2
Hi All,

This is just a reminder about our developer's meeting today (see details
below).

Stephen

On 15-05-28 09:22 AM, Stephen Ficklin wrote:

> Dear Tripal Community,
>
> We will have our monthly Tripal Developer's Meeting next Tuesday June
> 2nd.  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.  Here is a listing of some local times
> for the meeting:
>
> GMT:  4pm (16:00)
> European Central:  5 pm (17:00)
> US Eastern: 12 pm
> US Central: 11 am
> Canada Saskatchewan: 10 am
> US Pacific: 9 am
> China:  12 am (Wed March 8th)
>
> The initial meeting notes document can be found here:
>
> https://docs.google.com/document/d/1GVbwB_1zPjA9lJuEpUFHhfUW2t9XZRm_e4LpMmGZ9ik/edit 
>
>
> Please add comments if you have other agenda items you'd like to add.  
> The document will be open for editing during the meeting.
>
> Here is the archive of past meeting notes:
>
> http://tripal.info/meetings/developers/summary
>
> GoToMeeting connection details follow below.
>
> Happy Weekend!
> Stephen
>
>
> 1.  Please join my meeting, Tuesday, June 02, 2015 at 12:00 PM Eastern
> Daylight Time.
> https://global.gotomeeting.com/join/669144421
>
> 2.  Use your microphone and speakers (VoIP) - a headset is
> recommended.  Or, call in using your telephone.
>
> Dial +1 (571) 317-3131
> Access Code: 669-144-421
> Audio PIN: Shown after joining the meeting
>
> Meeting ID: 669-144-421
>
> GoToMeeting®
> Online Meetings Made Easy®
>
> Not at your computer? Click the link to join this meeting from your
> iPhone®, iPad®, Android® or Windows Phone® device via the GoToMeeting
> app.
>
>


------------------------------------------------------------------------------
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
Reply | Threaded
Open this post in threaded view
|

Re: [Gmod-tripal-devel] Tripal Developer's Meeting / July 7th

Stephen Ficklin-2
In reply to this post by Stephen Ficklin-2
Dear Tripal Community,

We will have our monthly Tripal Developer's Meeting next Tuesday July 7th.  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.  This is our informal meeting agenda so anyone who wants to raise a topic can do so.  An editable agenda can be found at the following link. Please feel free to add items:

https://docs.google.com/document/d/1krHiWiyzwS6TnqyTMj_tBdoRLOk0NG2OUF3iXPlxVxQ/edit#

Here is a listing of some local times for the meeting:

GMT:  4pm (16:00)
European Central:  5 pm (17:00)
US Eastern: 12 pm
US Central: 11 am
Canada Saskatchewan: 10 am
US Pacific: 9 am
China:  12 am (Wed July 8th)

GoToMeeting connection details are:

Please join my meeting from your computer, tablet or smartphone.
https://global.gotomeeting.com/join/681737397

You can also dial in using your phone.
United States +1 (646) 749-3122

Access Code: 681-737-397

If interested, here is the archive of past meeting notes:

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

Talk with you soon!
Stephen



------------------------------------------------------------------------------
Don't Limit Your Business. Reach for the Cloud.
GigeNET's Cloud Solutions provide you with the tools and support that
you need to offload your IT needs and focus on growing your business.
Configured For All Businesses. Start Your Cloud Today.
https://www.gigenetcloud.com/
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
Reply | Threaded
Open this post in threaded view
|

[Gmod-tripal-devel] Tripal Developer's Meeting / August 4th

Stephen Ficklin-2
Dear Tripal Community,

We will have our monthly Tripal Developer's Meeting Tuesday August  4th.  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.  An editable agenda can be found at the following link. Please feel free to add items:

https://docs.google.com/document/d/1_boRkgbNgvfegQTbjVOlF6vgdO6JJuTHbPK1OLZlTQo/edit?usp=sharing

Here is a listing of some local times for the meeting:

GMT:  4pm (16:00)
European Central:  5 pm (17:00)
US Eastern: 12 pm
US Central: 11 am
Canada Saskatchewan: 10 am
US Pacific: 9 am
China:  12 am (Wed Aug 5th)
GoToMeeting connection details are:

https://global.gotomeeting.com/join/120312301

You can also dial in using your phone.
United States +1 (646) 749-3122

Access Code: 120-312-301

See you then!
Stephen

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

_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
Reply | Threaded
Open this post in threaded view
|

[Gmod-tripal-devel] Tripal Developer's Meeting / Sept 1st

Stephen Ficklin-2
Dear Tripal Community,

We will have our monthly Tripal Developer's Meeting tomorrow, Tuesday
September 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.  An editable agenda can be found
at the following link. Please feel free to add items:

https://docs.google.com/document/d/1OKL4CW5k8F43kELTMAb2erOyIayHlY5HiTaRWpDMeYc/edit?usp=sharing

GMT:  4pm (16:00)
European Central:  5 pm (17:00)
US Eastern: 12 pm
US Central: 11 am
Canada Saskatchewan: 10 am
US Pacific: 9 am
China:  12 am (Wed Aug 5th)

Connection Details:

Please join this meeting from your computer, tablet or smartphone.
https://global.gotomeeting.com/join/746779245

You can also dial in using your phone.
United States +1 (571) 317-3122

Access Code: 746-779-245


------------------------------------------------------------------------------
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
Reply | Threaded
Open this post in threaded view
|

[Gmod-tripal-devel] Tripal Site Indexing for search - module proposal

Guignon, Valentin (Bioversity-France)
Hi!

Yesterday, we had our monthly meeting and here is what I wanted to say about how
an indexing module should be. First, I recommand we should stick to Drupal Search
API (https://www.drupal.org/project/search_api) which is a kind of standard and
offers many features (several indexing engines support such as Solr or Elastic
Search, support for facets search, autocomplete,...). It will also have a Drupal
8 release.

How it works? We almost just need to develop a module that implements
hook_entity_property_info_alter(). For now, Tripal works with nodes, so we will
just have to add properties to chado nodes. When Tripal 3 will be out, we will
add properties to entities the same way.

Let's start with a simple example: I have accessions (Chado stock) nodes that
have a property (stockprop) "accession number". In order to have this property
indexed by my favorite engine (either Solr or ES), I will have to implement the
hook and the getter function:
<?php
/************/
/**
 * Implements hook_entity_property_info_alter().
 *
 * See http://www.drupalcontrib.org/api/drupal/contributions!entity!entity.api.php/function/hook_entity_property_info/7
 * for $info structure details.
 */
function MYMODULE_entity_property_info_alter(&$info) {
  // single accession number
  $info['node']['properties']['accession_number'] = array(
    'label' => t('Accession number'),
    'description' => t('Local collection single accession number (chado_stock)'),
    'type' => 'text',
    'getter callback' => 'MYMODULE_accession_number_getter_callback',
  );
}


/**
 * Getter callback for accession number property.
 */
function MYMODULE_accession_number_getter_callback($node, $options, $name, $type, $info) {
  // note:
  //       $node is a node object
  //       $options is an array of options like 'language', 'absolute',...
  //       $name == 'accession_number'
  //       $type == 'node'
  //       $info is an array describing the property to index

  $accession_number = NULL;
  if (('chado_stock' == $node->type) && (1 == $node->status)) {
    $properties = chado_get_property(
        array(
          'table' => 'stock',
          'id' => $node->stock->stock_id,
        ),
        array(
          'type_name' => 'accession number',
          'cv_name' => 'multicrop passport ontology',
        )
    );
    if (!empty($properties)) {
      if (is_array($properties)) {
        $first_value = array_shift($properties);
        $accession_number = $first_value->value;
      }
      else {
        $accession_number = $properties->value;
      }
    }
  }
  return $accession_number;
}

/************/
?>

Starting from that, we could just write hook that grabs all the available
properties and cvterms related to each chado content type but that would not be
very efficient and flexible. So I would better see an admin interface that
allows us to select a view that would be used to index a chado content type.

Let's take another example. I have a gene stored in feature table which is
composed by any number of exons (feature_relationship), is located on a specific
chromosome (featureloc), is "owned" by a gene curator (featureprop) and is
tagged with several cvterms (feature_cvterm). I would create a view on chado
feature content that takes as argument a feature_id. This view will have
several relationships (feature_relationship, featureloc,...) and will return
the values I need to index, for instance the number of exons, the chromosome
name (or uniquename), the curator name, a list of aggregated cvterms,...

On the admin interface I think of, I would have a line for each chado content
type. On the line for chado feature, I would have a dropdown that displays a
list of views on chado feature content type that take as argument a feature_id.
So I could select my view and have the indexing system use it for indexation (
note: when a new view is selected on that interface, the cache for entity
properties should be refreshed I guess...).

The implementation of the hook would get the list of views associated to chado
contents. Then it would extract from the views the name of each field to index
and generate the appropriate $info sub-structure with a same generic callback
function for all properties. The generic callback function will check the node
type and the name of the field requested and will execute the appropriate view
(using the views API) to extract the value of the field. Here, there might be
some cache system to think of in order to be efficient and not call several
time the same view with the same argument...

So far, the view returns string and not integers, dates or arrays. We will have
to find a way to specify the return type into the view or only index text...

Cheers,

   Val


------------------------------------------------------------------------------
Monitor Your Dynamic Infrastructure at Any Scale With Datadog!
Get real-time metrics from all of your servers, apps and tools
in one place.
SourceForge users - Click here to start your Free Trial of Datadog now!
http://pubads.g.doubleclick.net/gampad/clk?id=241902991&iu=/4140
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
Reply | Threaded
Open this post in threaded view
|

[Gmod-tripal-devel] Tripal Developer's Meeting / October 6th

Stephen Ficklin-2
In reply to this post by Stephen Ficklin-2
Dear Tripal Community,

We will have our monthly Tripal Developer's Meeting Tuesday October 6th.  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.  I will send an editable agenda early next week which you can add items for discussion.

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 Oct 7th)


Please join my meeting from your computer, tablet or smartphone.
https://global.gotomeeting.com/join/671368485

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

Access Code: 671-368-485

Chat with you soon!
Stephen


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

_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
Reply | Threaded
Open this post in threaded view
|

Re: [Gmod-tripal-devel] Tripal Developer's Meeting / October 6th

Stephen Ficklin-2
Hi All,

Here is the link to the tentative agenda for tomorrow's meeting. Please feel free to add items (or details) you may want to discuss.

https://docs.google.com/document/d/1nqjH6j_x-qq2k9uwaBw87OJCYJdYV-ILYHUXJLVTc14/edit#

Stephen

On 15-10-02 11:31 AM, Stephen Ficklin wrote:
Dear Tripal Community,

We will have our monthly Tripal Developer's Meeting Tuesday October 6th.  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.  I will send an editable agenda early next week which you can add items for discussion.

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 Oct 7th)


Please join my meeting from your computer, tablet or smartphone.
https://global.gotomeeting.com/join/671368485

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

Access Code: 671-368-485

Chat with you soon!
Stephen



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

_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
Reply | Threaded
Open this post in threaded view
|

[Gmod-tripal-devel] Tripal Developer's Meeting / Nov 3rd

Stephen Ficklin-2
In reply to this post by Stephen Ficklin-2
Dear Tripal Community,

We will have our monthly Tripal Developer's Meeting Tuesday November 3rd.  As usual, anyone is invited to attend. We encourage anyone who wants to customize their site to drop in. This is an open agenda meeting.  Therefore I have not specifically set the agenda to allow folks to add topics of interest.  Please feel free to add topics to the agenda:

https://docs.google.com/document/d/1BsZAy4joEODzGJi64amtKgGMLdKo1MwveR90-O4cYWA/edit?usp=sharing

Information to connect to the teleconference is below. 

Below are meeting times and meeting connection details:

GMT:  5pm (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): 11 am
US Pacific (GMT-7): 9 am
China (GMT+8): 1 am (Wed Nov 4th)

Please join my meeting from your computer, tablet or smartphone.
https://global.gotomeeting.com/join/441151933

Use your microphone and speakers (VoIP) for audio. You'll sound best with a headset.

Stephen

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

_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
Reply | Threaded
Open this post in threaded view
|

[Gmod-tripal-devel] Meet for Help with a New Tripal Site: Dec 1st / Jan 5th (instead of developer's call)

Stephen Ficklin-2
Dear Tripal Community,

In lieu of our regular Monthly Tripal Developer's Meeting in December and January,  I thought it would be good to open the meeting specifically for those folks who are trying to setup a new Tripal site and who would like to ask questions of developers.    If you are a new site developer (or even one who's been around awhile) and would like to ask questions directly of developers please join us tomorrow December 1st and again January 5th for a teleconference at the time listed below.

For developers who typically attend our monthly calls, perhaps if there's a question we can use the developer's mailing list? With the end of the year being extremely busy with folks preparing for end-of-year deadlines, also with the Plant and Animal Genome Conference in early January, and since our outstanding agenda items (e.g. site-wide indexing, stress testing) have not seen much progress I'd like to propose we reconvene our meetings with official agendas for the first Tuesday of February.  

For tomorrow (Dec 1st) meeting:

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 Nov 4th)

Please join my meeting from your computer, tablet or smartphone.
https://global.gotomeeting.com/join/766437149

Access Code: 766-437-149

Best,
Stephen


------------------------------------------------------------------------------
Go from Idea to Many App Stores Faster with Intel(R) XDK
Give your users amazing mobile app experiences with Intel(R) XDK.
Use one codebase in this all-in-one HTML5 development environment.
Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
Reply | Threaded
Open this post in threaded view
|

Re: [Gmod-tripal-devel] Tripal Developer's Meeting / Feb 2nd

Stephen Ficklin-2
In reply to this post by Stephen Ficklin-2
Dear Tripal Community,

We will have our monthly Tripal Developer's Meeting tomorrow Tuesday February 2nd.  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:  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)


Please join my meeting from your computer, tablet or smartphone.
https://global.gotomeeting.com/join/657536205

You can also dial in using your phone.
United States : +1 (224) 501-3412

Access Code: 657-536-205


------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
Reply | Threaded
Open this post in threaded view
|

Re: [Gmod-tripal-devel] Tripal Developer's Meeting / Feb 2nd

Stephen Ficklin-2
Hello, here is the link to the agenda for our meeting.  Please feel free to add to it:

https://docs.google.com/document/d/1zXncVcn755tJHJr1ESlaeIYCmSuH19QuN_sRhaetNos/edit?usp=sharing

Stephen

On 2/1/2016 11:26 AM, Stephen Ficklin wrote:
Dear Tripal Community,

We will have our monthly Tripal Developer's Meeting tomorrow Tuesday February 2nd.  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:  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)


Please join my meeting from your computer, tablet or smartphone.
https://global.gotomeeting.com/join/657536205

You can also dial in using your phone.
United States : +1 (224) 501-3412

Access Code: 657-536-205



------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel