gmod-tripal — Announcements and questions about Tripal.

[Gmod-tripal] Tripal User's Meeting Friday Sept 8th

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

Hello Tripal community,

We are ready to re-start our Tripal User's Meeting schedule! Typically 
these meetings happen the first Friday of each month. We took a break 
over the summer months, and our next meeting would normally be this 
Friday on the 1st. However, in the US there is a long holiday weekend.  
Therefore, to ensure best participation we'll have our September meeting 
on Friday Sept 8th at 15:00 UTC.

You can find the specific time in your area via this link:

https://www.timeanddate.com/worldclock/fixedtime.html?msg=Tripal+User%27s+Meeting&iso=20170908T15&ah=1

The meeting is open to anyone. Those who implement or develops a Tripal 
site are particularly invited.    A link to the meeting agenda will be 
provided as the meeting nears.  If there is any topic of interest you'd 
like to discuss please let me know and I can ensure it's on the 
agenda.   Below is the meeting connection details.

Best,
Stephen

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

Access Code:762-905-221

Joining from a video-conferencing room or system?
Dial: 67.217.95.2##762905221
Cisco devices: 762905221@67.217.95.2

Re: [Gmod-tripal] Doubt about Tripal Jobs

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

Hi Raphael,

Apologies for the slow reply.  Nice to hear from you and glad to know 
you're trying Tripal.

We are now using our Github issue queue for these types of requests. It 
makes it easier for us to track issues, and other's know when things are 
resolved.    Would you mind creating an issue and we can continue the 
conversation there?

https://github.com/tripal/tripal/issues

But to get the ball rolling (if you're still having the issue). Can you 
describe what image you're using on the Amazon cloud?

Thanks,
Stephen


On 8/20/2017 3:22 PM, Raphael L. C. dos Santos wrote:
> Hi there GMOD comunity, howdy?
>
> Im new to GMOD and Tripal and I manage to have an instance running at 
> an Amazon Cloud. Unfortunatelly any of my jobs execute. I read that I 
> need a third party software, like Cron, to hpusekeeping and run this 
> for me, but I didnt realize how to, can you help me please?
>
> I didnt make a clean installation, I used an image with "all working" 
> to setup at Amazon, in that case tutorial at 
> http://tripal.info/tutorials/v2.x/installation/tripal didnt help me.
>
> Thanks in advance and best regards,
>
> Raphael
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
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>
> _______________________________________________
> Gmod-tripal mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal

[Gmod-tripal] Doubt about Tripal Jobs

[Raphael L. C. d. S. <lig...@gm...>]

Hi there GMOD comunity, howdy?

Im new to GMOD and Tripal and I manage to have an instance running at an
Amazon Cloud. Unfortunatelly any of my jobs execute. I read that I need a
third party software, like Cron, to hpusekeeping and run this for me, but I
didnt realize how to, can you help me please?

I didnt make a clean installation, I used an image with "all working" to
setup at Amazon, in that case tutorial at
http://tripal.info/tutorials/v2.x/installation/tripal didnt help me.

Thanks in advance and best regards,

Raphael

Re: [Gmod-tripal] New to Tripal

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

Hi Blake,

Welcome to the Tripal community!  Yes, we are planning to have several 
online training sessions between now and December.   We will also plan 
to have a face-to-face Hackathon and User's Meeting at San Diego in 
January during the Plant and Animal Genome conference.  So, watch for 
notices on this mailing list for more details to come!

Stephen


On 8/2/2017 4:46 PM, Inderski, Blake - ARS wrote:
>
> Greetings,
>
> I am interested in making use of the Tripal toolkit. Are there any 
> online Tripal workshops planned for the near future?
>
> Thanks,
>
> Blake Inderski
>
>
>
>
>
> This electronic message contains information generated by the USDA 
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> penalties. If you believe you have received this message in error, 
> please notify the sender and delete the email immediately.
>
>
> ------------------------------------------------------------------------------
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>
>
> _______________________________________________
> Gmod-tripal mailing list
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[Gmod-tripal] New to Tripal

[Inderski, B. - A. <Blake.Inderski@ARS.USDA.GOV>]

Greetings,

I am interested in making use of the Tripal toolkit. Are there any online Tripal workshops planned for the near future?

Thanks,
Blake Inderski




This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

[Gmod-tripal] Tripal v3.0-rc1 released!

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

Dear Tripal Community,

We have just released Tripal version 3.0 release candidate 1 
(7.x-3.0-rc1)!  We have worked to test as much as possible and therefore 
make this a "release candidate".  This is the step just before stable 
7.x-3.0 release.  There will be no major changes to infrastructure or 
design in later releases as this release represents a completed design.  
The only exception is some additional updates to come for web 
services.   We are currently in the process of upgrading several Tripal 
sites to use Tripal v3 for production so we will have multiple Tv3 sites 
online soon!

For a summary of features within Tripal 3 read more below.   We have 
improved the User's Guide and you can find it on the Tripal.info site 
here:  http://tripal.info/tutorials/v3.x.  We will be adding more 
content within the next several weeks as well.

If you notice any issues with this release please provide bug reports to 
our GitHub Issue Queue at https://github.com/tripal/tripal/issues

I'd personally like to express my appreciation to all those who 
participated in the development of this release. It has been quite a 
challenge, a lot of work and we have a wonderfully dedicated group of 
collaborators!

Sincerely,
Stephen

Below is a summary of major features in Tripal v3

1) Tripal v3 is backwards compatible with Tripal v2.  We have switched 
content types from Drupal "nodes" to Drupal "entities" but you can 
continue to use your current Tv2 "nodes" and templates as these are 
still supported.  You can migrate your content to the new entities as 
time allows and at your own pace.

2)  All data is categorized using controlled vocabularies.  Once web 
services are completed this will allow for improved data exchange 
between Tripal sites and collation of data from different sites.

3)  Tripal is no longer dependent on Chado for organization, although 
Chado is still the primary data storage back-end.

4) Because data are now organized via controlled vocabularies, the 
organization is more intuitive.  For example, you can create a 
"germplasm" content type rather than a Chado-centric "stock" content 
type, and data from your site will be shared via Web Services as 
germplasm data and not "stock" data.

5)  Content is uniform:  what you see on a gene page (or any other 
content type) is the same data that appears in web services and is 
available in Drupal Views.  If you hide a field (i.e. piece of data) it 
is hidden everywhere else.

6)  Tripal v3 fully adopts Drupal's Entities and Fields.  This means you 
no longer need to edit PHP template files just to move or hide data on 
your pages.

7)  You can customize your page layouts if you do not like the defaults 
that Tripal provides without any programming.  No more PHP templates.  
Using Drupal extension modules such as Display Suite or Panels you can 
lay out your pages how you desire.

8)  For developers, Tripal is now more object oriented!  If you need 
custom content we have expanded our API to more easily support 
integration of new fields.  This includes fields to support brand new 
content, or new "formatters" to change the way a field looks.

9) We have added a middle-layer separating the data storage back-end 
(e.g. Chado) from the data presentation layer.  This means we can more 
easily support other storage methods such as no-SQL options, direct 
access to files (e.g. indexed BAM/VCF), etc.

[Gmod-tripal] Update on Tripal v3 release

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

For those of you who have been following our Tripal v3 development 
you've realized that our expected May deadline for release has come and 
gone.   As an update, I'd like to report we are very close to a release 
and are /_*hoping *_/to have Tripal v3-rc1 (release candidate 1) ready 
for you by Wed June 28th!  (next week).

This will be a release candidate because we anticipate there may still 
be bugs but it is far from beta and the core design is stable.   There 
are several groups actively working on migration to Tripal v3 for their 
production community database site.  So, we should have some production 
Tripal sites available using Tripal v3 sometime this summer!  This is 
great news because active production usage is how many of the bugs get 
weeded out.

We'll keep you posted....

[Gmod-tripal] Summer Meeting Schedule, Mailing lists & GitHub Issue Queue

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

Dear Tripal User's.

Typically we have a monthly call-in meeting for everyone to chat about 
Tripal core development, sharing of ideas, discussion of extension 
modules, etc.    I would like to propose that we pause these meetings 
until September.  Our next meeting would have been this Friday, June 
2nd, but those of us working on the Tripal core code are actively trying 
to get the Tripal v3 release out within the next few weeks, and we would 
like the time.   Also, we typically have a lower attendance in the 
summer due to travels and I myself will not be able to make the July 
meeting and most likely will not have the time to prepare for the August 
meeting.    If there are any objections to reconvening in September 
please let us know and perhaps we can work something out.

Also, as we discussed in previous meetings, we will be shutting down the 
*gmo...@li...* and the 
*gmo...@so...* mailing lists.   Those lists will 
not go away completely. Archives will be available, but we will stop 
advertising and using them.   We will keep the 
*gmo...@li...* mailing list (this one) to send 
announcements only.    So please stay subscribed for those!

In the past this list has served for folks to ask for help or report 
problems.  From this point on we'd like to ask that if you have 
questions or problems with Tripal that those discussion be submitted to 
the Tripal Issue queue at https://github.com/tripal/tripal/issues.   
This is better way for us to keep track of questions and issues.

Thanks much!

Stephen

Re: [Gmod-tripal] Tripal Map Viewer

[Main, D. <do...@ws...>]

Hi Eliot,
We have not released it yet, I think our target is August.
Cheers
Dorrie

Sent from my iPhone

> On May 23, 2017, at 11:45 PM, Eliot Cline <eli...@gm...> wrote:
> 
> Hi,
> 
> I remember seeing at this year's PAG a presentation on the new map viewer for Tripal. Is that available for download? I can't seem to find it anywhere :-(
> 
> Thanks in advance,
> 
> Eliot Cline
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
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[Gmod-tripal] Tripal Map Viewer

[Eliot C. <eli...@gm...>]

Hi,

I remember seeing at this year's PAG a presentation on the new map viewer
for Tripal. Is that available for download? I can't seem to find it
anywhere :-(

Thanks in advance,

Eliot Cline

[Gmod-tripal] Tripal Developer and User meeting this Friday, May 5th, 2017

[Victor U. <ll...@gm...>]

Dear Tripal Developers and Users,

I hope everyone is doing great.

We will have our monthly Tripal Developer and User meeting this Friday, May
5th.

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.

The meeting start time and connection details follow below.  The meeting
will take approximately one hour.

Below is the link to the agenda for the upcoming meeting. If you have
something you'd like to discuss please add it (and include your name):

Tripal User's Meeting May/05/2017:

https://docs.google.com/document/d/1nMdkrT9HWbXGGxMsffprUtOhLPZqWQfZNDlUU-4fep8/edit?usp=sharing


If you want to check our last meeting notes for the Tripal User's Meeting,
please visit this link:

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


Best,

Victor Unda

Pacific Time,                      PT PST (UTC -7)        Fri, May 5, 2017
8:00 am
Central European Time,    CEST (UTC +1)          Fri, May 5, 2017 4:00 pm
Eastern Time,                    ET EST (UTC -4)        Fri, May 5, 2017
11:00 am
Central Time,                     CT CST (UTC -5)        Fri, May 5, 2017
10:00 am
Regina, Canada                 CST (UTC -6)             Fri, May 5, 2017
9:00 am
China Standard Time,        CST (UTC +8)            Fri, May 5, 2017 11:00
pm

Connection Details:

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] cvtermpath table: Unique violation

[Cannon, E. K [C. S] <ekc...@ia...>]

Hi Sofia,


In simple terms, ctermpath stores the paths between terms. It's helpful for quickly traversing ontology graphs.


I've been fighting with the cvterm loader and have seen this too. I made some changes that enabled me to load the GO terms. Stephen has someone working on this and have sent my changes for consideration. I also sent my changes to Meg and will send them to you as well in a personal e-mail, for use until there is a formal fix, if the code solve your problem.


Alternatively, you could disable the Postgres procedure that fills the cvtermpath table if you aren't using it.


My changes are a bit of a hack; Stephen is taking are more careful, disciplined, and generalized approach.


Ethy

________________________________
From: Sofia Robb <so...@so...>
Sent: Friday, April 28, 2017 12:01 PM
To: gmo...@li...
Subject: [Gmod-tripal] cvtermpath table: Unique violation

Hello,

I am using tripal 2 still. Should I be posting this question on the github site?

I am trying to load an ontology. I get this message about duplicate terms in the cvtermpath. What is this table? How can I fix the data to not cause this error?

Thanks,
Sofia



Tripal Job Launcher
Running as user 'administrator'
-------------------
Calling: tripal_cv_load_obo_v1_2_id(14, 732)

NOTE: Loading of this OBO file is performed using a database transaction.
If the load fails or is terminated prematurely then the entire set of
insertions/updates is rolled back and will not be found in the database

Step 1: Preloading File //var/other_data/organisms/zebrafish/Drer/ontology/zfa.obo
Parsing Line 38498 (100.00%). Memory: 37,065,912 bytes.
Step 2: Loading type defs...
8 of 8 records. (100.00%) Memory: 37,068,976 bytes
Step 3: Loading terms...
3098 of 3098 records. (100.00%) Memory: 37,068,328 bytes
Updating cvtermpath table.  This may take a while...

Updating cvtermpath for zebrafish_anatomical_ontology...

Updating cvtermpath for zebrafish_anatomy...


Updating cvtermpath for zebrafish_stages...
WD tripal_cv: Could not fill cvtermpath table: SQLSTATE[23505]: Unique violation: 7 ERROR:  duplicate key value violates unique constraint "cvtermpath_c1"                            [error]
DETAIL:  Key (subject_id, object_id, type_id, pathdistance)=(73409, 73409, 34, 0) already exists.
CONTEXT:  SQL statement "INSERT INTO cvtermpath (object_id, subject_id, cv_id, type_id, pathdistance) VALUES(origin, child_id, cvid, typeid, depth)"
PL/pgSQL function _fill_cvtermpath4node(integer,integer,integer,integer,integer) line 15 at SQL statement
SQL statement "SELECT _fill_cvtermpath4node(rootid, rootid, cvid, ttype, 0)"
PL/pgSQL function _fill_cvtermpath4root(integer,integer) line 10 at PERFORM
SQL statement "SELECT _fill_cvtermpath4root(cterm.subject_id, cvid)"
PL/pgSQL function _fill_cvtermpath4root(integer,integer) line 12 at PERFORM
SQL statement "SELECT _fill_cvtermpath4root(cterm.subject_id, cvid)"
PL/pgSQL function _fill_cvtermpath4root(integer,integer) line 12 at PERFORM
SQL statement "SELECT _fill_cvtermpath4root(root.cvterm_id, root.cv_id)"
PL/pgSQL function fill_cvtermpath(integer) line 8 at PERFORM
SQL statement "SELECT          fill_cvtermpath(cv_id)"
PL/pgSQL function fill_cvtermpath(character varying) line 8 at SQL statement
[site http://default] [TRIPAL ERROR] [TRIPAL_CV] Could not fill cvtermpath table: SQLSTATE[23505]: Unique violation: 7 ERROR:  duplicate key value violates unique constraint "cvtermpath_c1"DETAIL:  Key (subject_id, object_id, type_id, pathdistance)=(73409, 73409, 34, 0) already exists.CONTEXT:  SQL statement "INSERT INTO cvtermpath (object_id, subject_id, cv_id, type_id, pathdistance) VALUES(origin, child_id, cvid, typeid, depth)"PL/pgSQL function _fill_cvtermpath4node(integer,integer,integer,integer,integer) line 15 at SQL statementSQL statement "SELECT _fill_cvtermpath4node(rootid, rootid, cvid, ttype, 0)"PL/pgSQL function _fill_cvtermpath4root(integer,integer) line 10 at PERFORMSQL statement "SELECT _fill_cvtermpath4root(cterm.subject_id, cvid)"PL/pgSQL function _fill_cvtermpath4root(integer,integer) line 12 at PERFORMSQL statement "SELECT _fill_cvtermpath4root(cterm.subject_id, cvid)"PL/pgSQL function _fill_cvtermpath4root(integer,integer) line 12 at PERFORMSQL statement "SELECT _fill_cvtermpath4root(root.cvterm_id, root.cv_id)"PL/pgSQL function fill_cvtermpath(integer) line 8 at PERFORMSQL statement "SELECT          fill_cvtermpath(cv_id)"PL/pgSQL function fill_cvtermpath(character varying) line 8 at SQL statement

[Gmod-tripal] cvtermpath table: Unique violation

[Sofia R. <so...@so...>]

Hello,

I am using tripal 2 still. Should I be posting this question on the github
site?

I am trying to load an ontology. I get this message about duplicate terms
in the cvtermpath. What is this table? How can I fix the data to not cause
this error?

Thanks,
Sofia



Tripal Job Launcher
Running as user 'administrator'
-------------------
Calling: tripal_cv_load_obo_v1_2_id(14, 732)

NOTE: Loading of this OBO file is performed using a database transaction.
If the load fails or is terminated prematurely then the entire set of
insertions/updates is rolled back and will not be found in the database

Step 1: Preloading File
//var/other_data/organisms/zebrafish/Drer/ontology/zfa.obo
Parsing Line 38498 (100.00%). Memory: 37,065,912 bytes.
Step 2: Loading type defs...
8 of 8 records. (100.00%) Memory: 37,068,976 bytes
Step 3: Loading terms...
3098 of 3098 records. (100.00%) Memory: 37,068,328 bytes
Updating cvtermpath table.  This may take a while...

Updating cvtermpath for zebrafish_anatomical_ontology...

Updating cvtermpath for zebrafish_anatomy...


Updating cvtermpath for zebrafish_stages...
WD tripal_cv: Could not fill cvtermpath table: SQLSTATE[23505]: Unique
violation: 7 ERROR:  duplicate key value violates unique constraint
"cvtermpath_c1"                            [error]
DETAIL:  Key (subject_id, object_id, type_id, pathdistance)=(73409, 73409,
34, 0) already exists.
CONTEXT:  SQL statement "INSERT INTO cvtermpath (object_id, subject_id,
cv_id, type_id, pathdistance) VALUES(origin, child_id, cvid, typeid, depth)"
PL/pgSQL function
_fill_cvtermpath4node(integer,integer,integer,integer,integer) line 15 at
SQL statement
SQL statement "SELECT _fill_cvtermpath4node(rootid, rootid, cvid, ttype, 0)"
PL/pgSQL function _fill_cvtermpath4root(integer,integer) line 10 at PERFORM
SQL statement "SELECT _fill_cvtermpath4root(cterm.subject_id, cvid)"
PL/pgSQL function _fill_cvtermpath4root(integer,integer) line 12 at PERFORM
SQL statement "SELECT _fill_cvtermpath4root(cterm.subject_id, cvid)"
PL/pgSQL function _fill_cvtermpath4root(integer,integer) line 12 at PERFORM
SQL statement "SELECT _fill_cvtermpath4root(root.cvterm_id, root.cv_id)"
PL/pgSQL function fill_cvtermpath(integer) line 8 at PERFORM
SQL statement "SELECT          fill_cvtermpath(cv_id)"
PL/pgSQL function fill_cvtermpath(character varying) line 8 at SQL statement
[site http://default] [TRIPAL ERROR] [TRIPAL_CV] Could not fill cvtermpath
table: SQLSTATE[23505]: Unique violation: 7 ERROR:  duplicate key value
violates unique constraint "cvtermpath_c1"DETAIL:  Key (subject_id,
object_id, type_id, pathdistance)=(73409, 73409, 34, 0) already
exists.CONTEXT:  SQL statement "INSERT INTO cvtermpath (object_id,
subject_id, cv_id, type_id, pathdistance) VALUES(origin, child_id, cvid,
typeid, depth)"PL/pgSQL function
_fill_cvtermpath4node(integer,integer,integer,integer,integer) line 15 at
SQL statementSQL statement "SELECT _fill_cvtermpath4node(rootid, rootid,
cvid, ttype, 0)"PL/pgSQL function _fill_cvtermpath4root(integer,integer)
line 10 at PERFORMSQL statement "SELECT
_fill_cvtermpath4root(cterm.subject_id, cvid)"PL/pgSQL function
_fill_cvtermpath4root(integer,integer) line 12 at PERFORMSQL statement
"SELECT _fill_cvtermpath4root(cterm.subject_id, cvid)"PL/pgSQL function
_fill_cvtermpath4root(integer,integer) line 12 at PERFORMSQL statement
"SELECT _fill_cvtermpath4root(root.cvterm_id, root.cv_id)"PL/pgSQL function
fill_cvtermpath(integer) line 8 at PERFORMSQL statement "SELECT
 fill_cvtermpath(cv_id)"PL/pgSQL function fill_cvtermpath(character
varying) line 8 at SQL statement

[Gmod-tripal] Forwarded request for Ag Data Curation Survey

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

Hi All,

Please see the message below from the Ag Data Curation folks at U. of 
Maryland. If you use agricultural data please consider filling out their 
survey or forwarding along to your user base!

Best,
Stephen


Greetings on behalf of the Agricultural Data Curation project at the 
University of Maryland College of Information Studies. We are studying 
the data practices of agricultural researchers in multiple settings. As 
part of our project, we are conducting a survey of these communities.

We will ask you about your research practice, data management, reuse, 
and data sharing practices, in addition to some questions about the 
current state of research data management. This survey is voluntary and 
will take approximately 15 minutes to complete.

The survey is located athttp://ter.ps/db6.

Thank you in advance for your time and consideration. The data we 
collect from you and others will be reported in aggregate to provide 
valuable insight into data curation practice among agricultural researchers.

If you have questions, please do not hesitate to contact us via email 
(ar...@um... <mailto:ar...@um...>).



Sincerely,
Ricky Punzalan, Assistant Professor
Morgan Daniels, Postdoctoral Fellow
Kathryn Gucer, Postdoctoral Fellow
Adam Kriesberg, Postdoctoral Fellow
University of Maryland College of Information Studies

Re: [Gmod-tripal] Online Training After Party

[Sofia R. <so...@so...>]

Thanks, I will look over the changes to see if I can work it out now. Thank
you!!

On Tue, Apr 25, 2017 at 11:49 AM, Stephen Ficklin <ste...@ws...>
wrote:

> Hi Sofia,
>
> I did update the online tutorial to match the v2.1 changes in the bulk
> loader, and it was that same tutorial that we went through.  We also
> examined a data set provided by Michael Dondrup's group and discussed the
> different options for loading that file.   But unfortunately there are no
> additional notes other than the tutorial.  If you want some one-on-one help
> just let us know and we'll see what we can organize for you.
>
> Stephen
>
> On 4/24/2017 9:17 AM, Sofia Robb wrote:
>
> Hi Stephen,
>
> I was unfortunately unable to call in for this training :(  I really
> wanted to learn all about the bulk loader. Are there any notes? I have
> tried following the info on the tripal site in the past, but could never
> figure out how to make what I wanted to do work. Any additional information
> would be extremely useful!!
>
> Thanks!
> Sofia
>
>
> On Fri, Apr 21, 2017 at 11:00 AM, Stephen Ficklin <spf...@gm...>
> wrote:
>
>> Hi All,
>>
>> Well, there's really not a party.  I just wanted to say thanks to those
>> who attended our training session on the bulk loader. Please feel free
>> to send along comments or suggestions for improvement.
>>
>> Also, there are two items we failed to cover which I should have
>> mentioned in the training:
>>
>> 1)  If you have a column in your input file and you only need a portion
>> of the text in that column, you can use regular expressions to pull out
>> only the part you need.  And you can even rewrite values that might not
>> be exactly the way you want them. This is under the advanced options
>> when creating a field.
>>
>> 2)  We should have demo'ed what happens when the loader doesn't work
>> when the person who creates a template makes a mistake.  You get some
>> error messages on the terminal.
>>
>> If you have questions about any of these please feel free to ask.
>>
>> Best,
>> Stephen
>>
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Gmod-tripal mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>
>
>
>
> --
> Stephen Ficklin, PhD
> Assistant Professor
> Bioinformatics and Systems Genetics
> Department of Horticulture
> Washington State University
> 153 Johnson Hall
> Pullman, WA 99164-6414
> Office: (509) 335-4295
>
>

Re: [Gmod-tripal] Online Training After Party

[Stephen F. <ste...@ws...>]

Hi Sofia,

I did update the online tutorial to match the v2.1 changes in the bulk 
loader, and it was that same tutorial that we went through. We also 
examined a data set provided by Michael Dondrup's group and discussed 
the different options for loading that file.   But unfortunately there 
are no additional notes other than the tutorial.  If you want some 
one-on-one help just let us know and we'll see what we can organize for you.

Stephen


On 4/24/2017 9:17 AM, Sofia Robb wrote:
> Hi Stephen,
>
> I was unfortunately unable to call in for this training :(  I really 
> wanted to learn all about the bulk loader. Are there any notes? I have 
> tried following the info on the tripal site in the past, but could 
> never figure out how to make what I wanted to do work. Any additional 
> information would be extremely useful!!
>
> Thanks!
> Sofia
>
>
> On Fri, Apr 21, 2017 at 11:00 AM, Stephen Ficklin <spf...@gm... 
> <mailto:spf...@gm...>> wrote:
>
>     Hi All,
>
>     Well, there's really not a party.  I just wanted to say thanks to
>     those
>     who attended our training session on the bulk loader. Please feel free
>     to send along comments or suggestions for improvement.
>
>     Also, there are two items we failed to cover which I should have
>     mentioned in the training:
>
>     1)  If you have a column in your input file and you only need a
>     portion
>     of the text in that column, you can use regular expressions to
>     pull out
>     only the part you need.  And you can even rewrite values that
>     might not
>     be exactly the way you want them. This is under the advanced options
>     when creating a field.
>
>     2)  We should have demo'ed what happens when the loader doesn't work
>     when the person who creates a template makes a mistake.  You get some
>     error messages on the terminal.
>
>     If you have questions about any of these please feel free to ask.
>
>     Best,
>     Stephen
>
>
>     ------------------------------------------------------------------------------
>     Check out the vibrant tech community on one of the world's most
>     engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>     _______________________________________________
>     Gmod-tripal mailing list
>     Gmo...@li...
>     <mailto:Gmo...@li...>
>     https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>     <https://lists.sourceforge.net/lists/listinfo/gmod-tripal>
>
>


-- 
Stephen Ficklin, PhD
Assistant Professor
Bioinformatics and Systems Genetics
Department of Horticulture
Washington State University
153 Johnson Hall
Pullman, WA 99164-6414
Office: (509) 335-4295

Re: [Gmod-tripal] Online Training After Party

[Sofia R. <so...@so...>]

Hi Stephen,

I was unfortunately unable to call in for this training :(  I really wanted
to learn all about the bulk loader. Are there any notes? I have tried
following the info on the tripal site in the past, but could never figure
out how to make what I wanted to do work. Any additional information would
be extremely useful!!

Thanks!
Sofia


On Fri, Apr 21, 2017 at 11:00 AM, Stephen Ficklin <spf...@gm...>
wrote:

> Hi All,
>
> Well, there's really not a party.  I just wanted to say thanks to those
> who attended our training session on the bulk loader. Please feel free
> to send along comments or suggestions for improvement.
>
> Also, there are two items we failed to cover which I should have
> mentioned in the training:
>
> 1)  If you have a column in your input file and you only need a portion
> of the text in that column, you can use regular expressions to pull out
> only the part you need.  And you can even rewrite values that might not
> be exactly the way you want them. This is under the advanced options
> when creating a field.
>
> 2)  We should have demo'ed what happens when the loader doesn't work
> when the person who creates a template makes a mistake.  You get some
> error messages on the terminal.
>
> If you have questions about any of these please feel free to ask.
>
> Best,
> Stephen
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-tripal mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>

[Gmod-tripal] Online Training After Party

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

Hi All,

Well, there's really not a party.  I just wanted to say thanks to those 
who attended our training session on the bulk loader. Please feel free 
to send along comments or suggestions for improvement.

Also, there are two items we failed to cover which I should have 
mentioned in the training:

1)  If you have a column in your input file and you only need a portion 
of the text in that column, you can use regular expressions to pull out 
only the part you need.  And you can even rewrite values that might not 
be exactly the way you want them. This is under the advanced options 
when creating a field.

2)  We should have demo'ed what happens when the loader doesn't work 
when the person who creates a template makes a mistake.  You get some 
error messages on the terminal.

If you have questions about any of these please feel free to ask.

Best,
Stephen

[Gmod-tripal] Contributor logo's

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

Dear Tripal folks,

Currently on our tripal.info site we have logos for WSU and U. 
Saskatchewan as the core Tripal developers are in these locations. 
However, we want to recognize all of the contribution that our community 
members make.   If you contribute bug fixes/pull requests or develop 
extension modules that you are currently sharing to the rest of the 
Tripal community and if you'd like us to recognize your contribution via 
a logo on our website can you please send me (off the list) an official 
logo image for your institution and a URL that you'd like that logo to 
link to?

Thank you!

Stephen

Re: [Gmod-tripal] Using Tripal to load data headlessly

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

Hi Mara,

We've had discussions in the past about making Tripal functionality more 
accessible via Drush.  It would be easy enough to make the OBO and other 
loaders available via drush.  We're currently working on a brand-new 
loader class from Tripal v3 that will make this easy enough to do.

I've added an issue to our queue to do this for our Tripal v3 
development: https://github.com/tripal/tripal/issues/96

Stephen


On 4/20/2017 12:48 PM, Mara Kim wrote:
> Hi everyone,
>
> We have been using Tripal for data loading, especially loading OBO 
> files.  However, we are moving away from using the Tripal web 
> components.  Is there a way to use the Tripal functions to load OBO 
> files via the command line, without running the HTTP component?
>
> Thank you,
> Mara
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
> _______________________________________________
> Gmod-tripal mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal

[Gmod-tripal] Using Tripal to load data headlessly

[Mara K. <mar...@va...>]

Hi everyone,

We have been using Tripal for data loading, especially loading OBO files.
However, we are moving away from using the Tripal web components.  Is there
a way to use the Tripal functions to load OBO files via the command line,
without running the HTTP component?

Thank you,
Mara

[Gmod-tripal] Details for Tomorrow's Online Training Workshop

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

Greetings!  Tomorrow we will have our online training workshop. The 
training topic is use of the Chado bulk loader for importing data stored 
in tab-delimited text files.   All are welcome to attend.

Below you can find connection details for our online training meeting.  
The meeting begins at 8am Pacific Daylight Time  and the same time in 
these time zones:

Beijing, China       Fri, Apr 21, 2017 at 11:00 pm CST
Oslo, Norway         Fri, Apr 21, 2017 at 5:00 pm CEST
Paris, France        Fri, Apr 21, 2017 at 5:00 pm CEST
New York, USA        Fri, Apr 21, 2017 at 11:00 am EDT
Des Moines, USA      Fri, Apr 21, 2017 at 10:00 am CDT
Saskatoon, Canada    Fri, Apr 21, 2017 at 9:00 am CST
Seattle, USA         Fri, Apr 21, 2017 at 8:00 am PDT



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

First GoToMeeting? Try a test session:http://help.citrix.com/getready

[Gmod-tripal] Training move to April 21st?

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

Hi All,

Are there any objections if we move the training session on the bulk 
loader to Friday April 21st at 8am Pacific time?  This would be to 
accommodate a group that would like to attend.

Thanks!

Stephen

[Gmod-tripal] Parsing Blast XML: Getting gnl|BL_ORD_ID IDs.

[Sofia R. <so...@so...>]

I see in this post:
  https://www.drupal.org/node/2319493

that having ids like this:
gnl|BL_ORD_ID|468795

should be resolved by defaulting to using the def instead.

I just parsed some blast xml and am seeing this in the id column of the
homology pane.
I have the parser set to use "Genbank style parser". Should I do something
different?



Thanks,
Sofia

Re: [Gmod-tripal] Tripal as Protein database

[Eric R. <es...@ta...>]

Hi Michael,

I saw that you already filed one issue, but if you have any questions
about our docker image <https://github.com/erasche/docker-tripal/>,
please feel to email or just file more issues. Either Anthony or I can
surely help. That tripal image is currently working with our dockerized
GMOD stack
<https://github.com/galaxy-genome-annotation/dockerized-gmod-deployment>if
you wish to add any of those resources to your planned deployment.

Meg: I had not known about the other docker image! That's exciting to see.

Cheers,
Eric

On 04/07/2017 05:12 PM, Michael Dondrup wrote:
> Hi Meg,
>
> Thank you very much! 
> The image is working out of the box for me.
>
> Michael
>
>
>> On Apr 7, 2017, at 5:58 PM, Meg Staton <me...@gm...> wrote:
>>
>> Hi, Michael,
>> Here is link to Ming's Docker image on tripal repo:
>> https://github.com/tripal/docker-tripal-centos
>>
>> The README has some instructions to get it started. Let us know how it goes!
>>
>> Meg
>>
>>
>> On Wed, Mar 22, 2017 at 4:41 AM, Michael Dondrup <mic...@ii...> wrote:
>> Hi Stephen,
>>
>> thank you for your confirmation. The time-frame for starting the implementation
>> is ’now’ ;) but to have a deployable version ready we have time until the end 2017.
>> So we could help with testing a bit. We will try to join the next user/developer meeting.
>>
>> With respect to the type of VM, I think I like either Docker or Virtualbox best. In the
>> end, we might test and deploy on a local cloud instance running open stack.
>>
>> I forgot about the bulk importer completely, but if it can import tab-delimited files
>> than it will most likely satisfy our needs.
>>
>> Michael
>>
>>
>>> On Mar 21, 2017, at 5:44 PM, Stephen Ficklin <spf...@gm...> wrote:
>>>
>>> Hi Michael,
>>>
>>> I agree that Tripal should be suitable :-)  When is your time frame for
>>> beginning the project?  Tripal v3 is in beta and we are finding bugs
>>> still so if you decide to go with Tv3 then you may encounter some of
>>> these.  But the benefit is you won't have to upgrade from Tv2 to Tv3
>>> later on.    We don't have a VM for Tripal v3 yet... what would be your
>>> preference?  VMWare, Virtualbox or a container such as Docker?  There is
>>> a Tv2 Docker image which you can find off of the Tripal website.
>>>
>>> Do you have an exact format for the data?  If in CSV (or specifically
>>> tab delimited) you could use the bulk loader?   I've been wanting to
>>> have a training meeting before the end of March (next week).  But that
>>> may get pushed to the second week of April. Perhaps a training session
>>> with the bulk loader would be helpful? And as an example we could look
>>> at your data files?
>>>
>>> Stephen
>>>
>>> On 3/21/2017 3:44 AM, Michael Dondrup wrote:
>>>> Hi,
>>>>
>>>> we have a student who is developing a ‘special interest’ protein database drawing from various resources. Her task is to
>>>> build a database of annotated proteins of this class and enrich the annotation with
>>>> additional information, e.g. pairwise sequence similarity, and protein interaction data, cross references, etc.
>>>> I proposed that Tripal would be suitable for this. My questions:
>>>>
>>>> - Protein data will mostly come from Uniprot and Genbank. Are there importers for supported formats used by
>>>> these databases, e.g. genbank or even csv?
>>>> - We should possibly start with Tripal 3 right away? Is there possibly a pre-configured vm for developers, so to avoid
>>>> any setup pain?
>>>>
>>>> Thank you
>>>> Michael
>>>>
>>>>
>>>>
>>>> Michael Dondrup
>>>> Researcher
>>>> Sea Lice Research Centre
>>>> Department of Informatics
>>>> University of Bergen
>>>> Thormøhlensgate 55, N-5008 Bergen,
>>>> Norway
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>> _______________________________________________
>>>> Gmod-tripal mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>
>>> ------------------------------------------------------------------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> Gmod-tripal mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Gmod-tripal mailing list
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>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>
>>
>>
>>
>> -- 
>> Margaret Staton
>> Assistant Professor
>> Department of Entomology and Plant Pathology
>> 370 PBB, 2505 EJ Chapman Drive
>> Knoxville, TN 37996-4560
>>
>> 864-506-4515 Mobile
>> mst...@ut... 
>>
>>
>>
>>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
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