gmod-tripal — Announcements and questions about Tripal.

Re: [Gmod-tripal] Tripal as Protein database

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

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
> Gmo...@li...
> 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... 
> 
> 
> 
> 

Re: [Gmod-tripal] Tripal as Protein database

[Meg S. <me...@gm...>]

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
> Gmo...@li...
> 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...

[Gmod-tripal] obo vs owl

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

Hi,

In Tripal 2, the controlled vocabulary loader asks for obo files. Can it
also take owl formatted files?

Thanks,
Sofia

[Gmod-tripal] Tripal v2.1 released!

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

Dear Tripal Community,

Tripal v2.1 is now available!  This release provides major bug fixes as 
well as support for Chado v1.3.   Here are links to upgrade instructions:

  * Upgrade from Tripal v2.0 to v2.1:
    http://tripal.info/tutorials/v2.x/upgrade_2.0_to_2.1
  * Upgrade from Tripal v1.1 to v2.1:
    http://tripal.info/tutorials/v2.x/upgrade_6.11_to_2.1

Please remember to back up your sites before upgrading and it's always 
best to try your upgrade on a developmental copy first.

Additionally, we have made new releases of the Tripal Analysis Blast, 
GO, InterPro and KEGG modules.   Please consider upgrading those as well 
if you use them. Instructions for updating those are also provided in 
the links above.   Some new visualizations have been provided for some 
of these modules thanks to contributions by some of you!

The Drupal issue queue will no longer be used to track bugs or feature 
requests.  If you notice any problems with this release please help us 
by reporting them to our GitHub issue queue: 
https://github.com/tripal/tripal/issues

We have added a new 'Powered by Tripal' block in this new version.  
Please consider adding this block to the footer section of your site.  
If you prefer to use something other than the block I've attached 
several images to this email for your to consider placing on your sites.

Thank you to those who provided bug fixes and pull requests!

[Gmod-tripal] Plant Biology 2017 -- Tripal Meeting -- Last call

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

Hi All,

Will anyone be attending the Plant Biology meeting in Hawaii this summer 
(http://plantbiology.aspb.org/)?  If we have enough interest I'd like to 
put together a hackathon or training meeting.     Please let me know if 
you would be interested and could attend.

Thanks,
Stephen

[Gmod-tripal] Tripal Training Meeting 4/14

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

Hi All,

I was hoping to arrange a training meeting this month for our Tripal 
community but it was not possible.   So, I'd like to organize one for 
Friday the 14th of April.   Some topics include

* How to use of the bulk loader to load tab delimited files.
* How to develop  your own extensions for Tripal v3.

If you have any other topic suggestions or prefer one of these over the 
other please let me know.

I'm suggesting we hold the training meeting a week after our normal 
Tripal User's meeting (will be on 4/7) but at the same time at 8am PDT 
(or click this link to see the time of the meeting in your time zone: 
https://www.timeanddate.com/worldclock/fixedtime.html?msg=Tripal+Training+Meeting&iso=20170414T08&p1=234&ah=2)

Also, if this time is not conducive we can be flexible based on 
responses received.

Thanks,
Stephen

Re: [Gmod-tripal] Tripal as Protein database

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

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

Re: [Gmod-tripal] Tripal as Protein database

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

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

[Gmod-tripal] Tripal as Protein database

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

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

Re: [Gmod-tripal] New release of MGIS website - URL

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

Oups, I forgot the URL: https://www.crop-diversity.org/mgis/
:-p

   Val


From: Guignon, Valentin (Bioversity-France) [mailto:v.g...@cg...]
Sent: mardi 14 mars 2017 10:59
To: gmo...@li...
Subject: [Gmod-tripal] New release of MGIS website

Hi!

We are pleased to announce that the new version of Musa Germplasm Information System, built on Tripal, has been released!
This release includes both new germplasm collection data and software features.

Have a look and if you're interested by any feature we got for your website, feel free to ask me directly how to do it.
Cheers,

   Val & the MGIS team

[Gmod-tripal] New release of MGIS website

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

Hi!

We are pleased to announce that the new version of Musa Germplasm Information System, built on Tripal, has been released!
This release includes both new germplasm collection data and software features.

Have a look and if you're interested by any feature we got for your website, feel free to ask me directly how to do it.
Cheers,

   Val & the MGIS team

Re: [Gmod-tripal] How to delete an old Blast analysis.

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

Okay, we'll add to our testing for Tripal 2.1 to check the analysis 
delete functionality.   It sounds like the other two methods work as 
advertised except on your production server. Tripal doesn't restrict 
operations to User 0 specifically. It allows you to set who can do what, 
but is possible there could be a permission problem.  We'll look into it.

Stephen


On 3/3/2017 9:03 AM, Michael Dondrup wrote:
> Hi,
> There seem to be 3 different ways to delete the analysis out of which 
> only 1.,2. seems to work:
>
> The first approach is from admin/tripal/chado/tripal_analysis -> 
> Search. In the right column there are links to ‘edit’ and ‘delete’ 
> (node/123/delete&destination=admin/tripal/chado/tripal_analysis/analysis%3Fname%3D%26program%3D%26sourcename%3D)
> These links are only shown for analyses that are synced.
>
> The second is to go via content directly: 
> node/123/delete&destination=admin/content . This seems to work now on 
> our test server, on our
> production server, this had only removed the drupal node, maybe 
> because I was not logged in as User 0 or because my other attempts had 
> created a mess. I should say, that I was trying to replace an old 
> Blast analysis with a newer one which were using the same data base (NR).
>
> The third approach would be via the Analysis -> Delete tab 
> (admin/tripal/chado/tripal_analysis/delete). This generates a tripal 
> job. When trying to run this job, the error messages below are generated.
>
>
>
>
> Tripal Job Launcher
> Running as user 'lb_admin'
> -------------------
> Calling: tripal_analysis_delete_analyses(Array, 382)
>
> NOTE: Deleting analyses is performed using a database transaction.
> If the load fails or is terminated prematurely then the entire set of
> deletions is rolled back and will not be found in the database
>
> Deleting 1 analyses
> strcmp() expects parameter 1 to be string, array given 
> tripal_core.chado_query.api.inc:882       [warning]
> Removing orphaned analysis pages
> Missing argument 3 for chado_cleanup_orphaned_nodes(), called in       
>                         [warning]
> /home/licebase/d7/sites/all/modules/tripal/tripal_analysis/includes/tripal_analysis.delete.inc 
> on
> line 108 and defined tripal_core.chado_nodes.api.inc:988
> Missing argument 4 for chado_cleanup_orphaned_nodes(), called in       
>                         [warning]
> /home/licebase/d7/sites/all/modules/tripal/tripal_analysis/includes/tripal_analysis.delete.inc 
> on
> line 108 and defined tripal_core.chado_nodes.api.inc:988
>
> FAILED: Rolling back database changes...
> WD tripal_analysis: PDOException: SQLSTATE[42601]: Syntax error: 7 
> ERROR:  syntax error at end of[error]
> input
> LINE 1: SELECT COUNT(*) FROM
>                              ^: SELECT COUNT(*) FROM ; Array
> (
> )
>  in chado_cleanup_orphaned_nodes() (line 1000 of
> /home/licebase/d7/sites/all/modules/tripal/tripal_core/api/tripal_core.chado_nodes.api.inc). 
>
>
>
>> On Mar 2, 2017, at 6:56 PM, Stephen Ficklin <spf...@gm... 
>> <mailto:spf...@gm...>> wrote:
>>
>> Hi Michael,
>>
>> I think I see where the problem lies.  But one question.  When you 
>> tried to delete the node it should have cascade deleted the analysis 
>> in Chado.  Did you receive any error messages during either of your 
>> two delete attempts?
>>
>> Thanks,
>> Stephen
>>
>> On 3/1/2017 4:22 AM, Michael Dondrup wrote:
>>> Hi,
>>> I was trying to delete an old Blast analysis, however, I have been 
>>> unable to
>>> figure out the proper way of doing that. The aim is to have the old 
>>> blast results
>>> no longer appear  under the homology tab for each feature. I have 
>>> tried several
>>> things:
>>> 1. delete via tripal/chado/tripal_analysis/delete , run drush, the 
>>> Analysis is still there
>>> 2. Delete drupal node for the analysis and clean up orphans, node is 
>>> gone but the analysis is still listed
>>> in chado.
>>>
>>> Please let me know to fix this.
>>>
>>> Michael
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, SlashDot.org <http://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://slashdot.org>! 
>> http://sdm.link/slashdot_______________________________________________
>> Gmod-tripal mailing list
>> Gmo...@li... 
>> <mailto:Gmo...@li...>
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal

Re: [Gmod-tripal] How to delete an old Blast analysis.

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

Hi,
There seem to be 3 different ways to delete the analysis out of which only 1.,2. seems to work:

The first approach is from admin/tripal/chado/tripal_analysis -> Search. In the right column there are links to ‘edit’ and ‘delete’ (node/123/delete&destination=admin/tripal/chado/tripal_analysis/analysis%3Fname%3D%26program%3D%26sourcename%3D)
These links are only shown for analyses that are synced.

The second is to go via content directly: node/123/delete&destination=admin/content . This seems to work now on our test server, on our
production server, this had only removed the drupal node, maybe because I was not logged in as User 0 or because my other attempts had created a mess. I should say, that I was trying to replace an old Blast analysis with a newer one which were using the same data base (NR).

The third approach would be via the Analysis -> Delete tab (admin/tripal/chado/tripal_analysis/delete). This generates a tripal job. When trying to run this job, the error messages below are generated.




Tripal Job Launcher
Running as user 'lb_admin'
-------------------
Calling: tripal_analysis_delete_analyses(Array, 382)

NOTE: Deleting analyses is performed using a database transaction.
If the load fails or is terminated prematurely then the entire set of
deletions is rolled back and will not be found in the database

Deleting 1 analyses
strcmp() expects parameter 1 to be string, array given tripal_core.chado_query.api.inc:882       [warning]
Removing orphaned analysis pages
Missing argument 3 for chado_cleanup_orphaned_nodes(), called in                                 [warning]
/home/licebase/d7/sites/all/modules/tripal/tripal_analysis/includes/tripal_analysis.delete.inc on
line 108 and defined tripal_core.chado_nodes.api.inc:988
Missing argument 4 for chado_cleanup_orphaned_nodes(), called in                                 [warning]
/home/licebase/d7/sites/all/modules/tripal/tripal_analysis/includes/tripal_analysis.delete.inc on
line 108 and defined tripal_core.chado_nodes.api.inc:988

FAILED: Rolling back database changes...
WD tripal_analysis: PDOException: SQLSTATE[42601]: Syntax error: 7 ERROR:  syntax error at end of[error]
input
LINE 1: SELECT COUNT(*) FROM
                             ^: SELECT COUNT(*) FROM ; Array
(
)
 in chado_cleanup_orphaned_nodes() (line 1000 of
/home/licebase/d7/sites/all/modules/tripal/tripal_core/api/tripal_core.chado_nodes.api.inc).


> On Mar 2, 2017, at 6:56 PM, Stephen Ficklin <spf...@gm...> wrote:
> 
> Hi Michael,
> 
> I think I see where the problem lies.  But one question.  When you tried to delete the node it should have cascade deleted the analysis in Chado.  Did you receive any error messages during either of your two delete attempts?
> 
> Thanks,
> Stephen
> 
> On 3/1/2017 4:22 AM, Michael Dondrup wrote:
>> Hi,
>> I was trying to delete an old Blast analysis, however, I have been unable to
>> figure out the proper way of doing that. The aim is to have the old blast results
>> no longer appear  under the homology tab for each feature. I have tried several
>> things:
>> 1. delete via tripal/chado/tripal_analysis/delete , run drush, the Analysis is still there
>> 2. Delete drupal node for the analysis and clean up orphans, node is gone but the analysis is still listed
>> in chado.
>> 
>> Please let me know to fix this.
>> 
>> Michael
>> 
>> 
>> 
>> ------------------------------------------------------------------------------
>> 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
> 
> ------------------------------------------------------------------------------
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> engaging tech sites, SlashDot.org! http://sdm.link/slashdot_______________________________________________
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[Gmod-tripal] Our meeting in 1 hour

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

Hi All,

It seems the email regarding our Tripal User's Meeting may not have 
reached everyone.   If you are interested in attending please join us if 
you can.  This is our open agenda meeting so we have a limited formal 
agenda to give folks an opportunity to raise their own 
questions/discussions.  The meeting starts in approximately 50 minutes 
at 8am US Pacific Time.  Here is the connection details:

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


Here is the link to the agenda

https://docs.google.com/document/d/1TzKXs11S10TXXqfxK3GKP1Bkm5VZ2Gui5exRlrvw-3k/edit?usp=sharing

Best,
Stephen

Re: [Gmod-tripal] How to delete an old Blast analysis.

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

Hi Michael,

I think I see where the problem lies.  But one question.  When you tried 
to delete the node it should have cascade deleted the analysis in 
Chado.  Did you receive any error messages during either of your two 
delete attempts?

Thanks,
Stephen


On 3/1/2017 4:22 AM, Michael Dondrup wrote:
> Hi,
> I was trying to delete an old Blast analysis, however, I have been unable to
> figure out the proper way of doing that. The aim is to have the old blast results
> no longer appear  under the homology tab for each feature. I have tried several
> things:
> 1. delete via tripal/chado/tripal_analysis/delete , run drush, the Analysis is still there
> 2. Delete drupal node for the analysis and clean up orphans, node is gone but the analysis is still listed
> in chado.
>
> Please let me know to fix this.
>
> Michael
>
>
> ------------------------------------------------------------------------------
> 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] Editing a feature deletes all its relationships

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

Hi,
Unfortunately I have discovered another problem. Editing a feature,
and then saving it apparently removes all the features relationships,
without the ability to restore them manually.
Has this been reported?

Michael



Michael Dondrup
Researcher
Sea Lice Research Centre
Department of Informatics
University of Bergen
Thormøhlensgate 55, N-5008 Bergen,
Norway

[Gmod-tripal] How to delete an old Blast analysis.

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

Hi,
I was trying to delete an old Blast analysis, however, I have been unable to
figure out the proper way of doing that. The aim is to have the old blast results
no longer appear  under the homology tab for each feature. I have tried several
things:
1. delete via tripal/chado/tripal_analysis/delete , run drush, the Analysis is still there
2. Delete drupal node for the analysis and clean up orphans, node is gone but the analysis is still listed
in chado.

Please let me know to fix this.

Michael

Re: [Gmod-tripal] Tripal 2 nagging warning on missing tripal theme

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

Hi Daniel,

That one is fixed in the dev version of Tripal 2 thanks to a user contribution: https://github.com/tripal/tripal/pull/4

Thus the fix will be in the next release of Tripal 2 (sorry I don’t know when that will be) or you could make the small changes shown here (https://github.com/tripal/tripal/pull/4/files) to make the error go away on your current site.

Regardless, it’s nothing to be concerned about and can be safely ignored!

~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Department of Plant Sciences
University of Saskatchewan


On February 17, 2017 at 3:43:15 AM, Daniel Sobral (ds...@ig...<mailto:ds...@ig...>) wrote:

While I'm still testing Tripal V3 (the Organism bug was sorted, thanks!) I'm also testing V2 from the Installation Guide.
It all went well, but my website keeps nagging that there's a missing tripal theme.

User warning: The following theme is missing from the file system: tripal. For information about how to fix this, see the documentation page<https://www.drupal.org/node/2487215>. in _drupal_trigger_error_with_delayed_logging() (line 1138 of /var/www/html/includes/bootstrap.inc).

It's not clear what one needs to do.

Daniel

--
Daniel Sobral, PhD
Head of Bioinformatics Unit
Instituto Gulbenkian de Ciência
+351214407965

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Re: [Gmod-tripal] Modifying title in feature page

[Abdullah A. <alm...@gm...>]

Hello Sudhansu,

Using some javascript would solve your issue. If you have jQuery installed, this code snippet will work if placed in the tripal_feature_expression.tpl.php template file. You can place it anywhere since it will execute after the page has loaded.

<script>
 $(function() {
   $('.figure-tripal-data-pane-title.tripal-data-pane-title').html('Expression <?php echo $feature->name?>')
 })
</script>

I hope that helps! Please let us know if we can assist you any further.

Thanks,
Abdullah Almsaeed
Staton Lab - UTK

> On Feb 16, 2017, at 5:13 PM, Sudhansu Dash <sd...@nc...> wrote:
> 
> Hello,
> In our gene feature page I have a panel called 'Expression' coming from the tripal_analysis_expression module.  
> This comes from the '#tripal_toc_title' => 'Expression' defined in $node->contents array  in the hook_node_view. The effect of this is that it appears as the panel label as well as the page title.
> 
> I want to have the page title for this panel modified to 'Expression ($feature->name)' while keeping the panel label unaltered.
> How do I accomplish that?  Is there another markup element like '#tripal_toc_title' that specifies the page title that I can define here? 
> Even suppressing the page title while not affecting the panel label would serve my purpose.
> (I have already tried putting '($feature->name)' below the page title: It works but not what I ideally want to do.)
> 
> Thanks.
> 
> Sudhansu Dash
> 
> ------------------------------------------------------------------------------
> 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] Tripal 2 nagging warning on missing tripal theme

[Daniel S. <ds...@ig...>]

While I'm still testing Tripal V3 (the Organism bug was sorted, thanks!) 
I'm also testing V2 from the Installation Guide.
It all went well, but my website keeps nagging that there's a missing 
tripal theme.

/User warning/: The following theme is missing from the file system: 
/tripal/. For information about how to fix this, see the documentation 
page <https://www.drupal.org/node/2487215>. in 
/_drupal_trigger_error_with_delayed_logging()/ (line /1138/ of 
//var/www/html/includes/bootstrap.inc/).

It's not clear what one needs to do.

Daniel

-- 
Daniel Sobral, PhD
Head of Bioinformatics Unit
Instituto Gulbenkian de Ciência
+351214407965

[Gmod-tripal] Modifying title in feature page

[Sudhansu D. <sd...@nc...>]

Hello,
In our gene feature page I have a panel called 'Expression' coming from 
the tripal_analysis_expression module.
This comes from the '#tripal_toc_title' => 'Expression' defined in 
$node->contents array  in the hook_node_view. The effect of this is that 
it appears as the panel label _as well as_ the page title.

I want to have the page title for this panel modified to 'Expression 
($feature->name)' while keeping the panel label unaltered.
How do I accomplish that?  Is there another markup element like 
'#tripal_toc_title' that specifies the page title that I can define here?
Even suppressing the page title while not affecting the panel label 
would serve my purpose.
(I have already tried putting '($feature->name)' below the page title: 
It works but not what I ideally want to do.)

Thanks.

Sudhansu Dash

[Gmod-tripal] Tripal 2.3?

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

While I recognize the Tripal effort is focused on 3.0, is there an ETA on the next stable release of Tripal 2, or has it already happened? We would like to bring our Tripal code up to date. Also, does/will the new stable version upgrade to Chado 1.3? (I should know the answer to both questions ... but don't.)


Ethy

[Gmod-tripal] Frequent Beta releases

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

Dear Tripal Community,

As bugs are reported we are fixing them and making minor releases.  We 
are already up to beta3 release.   From this point on we'll make minor 
announcements for releases on our Twitter account:  
https://twitter.com/TripalProject.  If interested, please subscribe for 
up-to-the-minute updates.  To reduce emails we won't post beta releases 
to the mailing list unless they are of important significance.   The 
stable release, which we expect in May will be announced on our mailing 
lists.

Thanks,
Stephen

Re: [Gmod-tripal] Tripal v3.0-beta1 released!

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

Hi Daniel,

Thanks for reporting your experience. This helps!

The error about not being able to create the pub.minref can be safely 
ignored.   Tripal 3 tries to create "Fields" for every column of every 
table in Chado.  The pub table has a column named "miniref" which we 
just haven't handled yet.   We will have this resolved in a future beta 
release.  For now we put a note in the User's Guide to let folks know 
they can ignore this message.

As per the organism issue.  That was indeed a bug as Lacey mentioned, 
that slipped through our testing.  We have committed a fix for it.  This 
fix is in a new beta3 release that we just made.   It's just some minor 
fixes so we're not making a major announcement, but the Tutorial has 
been updated to refer to the beta3 release now and we've made a few 
other corrections to the tutorial as well.  You can upgrade Tripal with 
this command:

drush pm-download tripal-7.x-3.0-beta3

One thing you may hit on is that we incorrectly put in the tutorial for 
the tripal_ds module to be installed after the Chado preparation step.  
This was a mistake and will cause your pages to not have the default 
layouts.     If you have this problem the solution would be 1) to start 
over with a fresh install of Drupal/Tripal or 2) install the beta3 
release and go to Administration -> Structure -> Tripal Content Types 
and click the "Manage Display" link for each content type.  There will 
be a new 'Apply Tripal Layout' link which will let you apply the default 
layouts.  Afterwards they will look like they are shown in the User's Guide.

Sorry for the troubles and please keep us in the loop on other issues 
you might find.

Also, we have opened up the Issue queue on our Tripal GitHub page 
(https://github.com/tripal/tripal/issues). It's much nicer than the 
Drupal Issue queue so please feel free to submit issues there as well.

Best,
Stephen


On 2/15/2017 7:13 AM, Daniel Sobral wrote:
> Hello,
>
> This sounds very exciting! I'm now redoing from scratch a tripal site 
> and I'm trying to follow the installation guide.
> I'm using Ubuntu 16.04 server (not desktop).
>
> All went reasonably well, except a small glitch when making the drupal 
> and tripal connection (loading the ontologies), I've got some errors 
> which I guess can be ignored for now:
>
> WD tripal: Cannot create field for "pub.miniref". Missing an 
> appropriate vocabulary term [error]
> [site http://default] [TRIPAL ERROR] [TRIPAL] Cannot create field for 
> "pub.miniref". Missing an appropriate vocabulary term
> Cannot create field for "pub.miniref". Missing an appropriate 
> vocabulary term [error]
>
> I carried on with the tutorial.
> But when I try to insert an Organism, it fails:
>
>   * /Notice/: Undefined offset: 0 in
>     /tripal_chado_field_storage_write_table()/ (line /154/ of
>     //var/www/html/sites/all/modules/tripal/tripal_chado/includes/tripal_chado.field_storage.inc/).
>   * /Notice/: Trying to get property of non-object in
>     /tripal_chado_field_storage_write_table()/ (line /154/ of
>     //var/www/html/sites/all/modules/tripal/tripal_chado/includes/tripal_chado.field_storage.inc/).
>   * Could not save the entity: SQLSTATE[42P01]: Undefined table: 7
>     ERROR: relation "field_data_data__image" does not exist LINE 1:
>     INSERT INTO field_data_data__image (entity_type, entity_id, ... ^
>   * Cannot save entity
>
>
>  Did I do something wrong?
>
> Best,
> Daniel
>
>
>
>
>
> On 11-02-2017 07:16, Stephen Ficklin wrote:
>>
>> Dear Tripal Community,
>>
>> We are happy to announce the release of Tripal v3.0-beta1! Here are 
>> some quick links:
>>
>> Tripal v3.x User's Guide: http://tripal.info/tutorials/v3.x
>> Tripal v3.x Download Page at Drupal.org: 
>> https://www.drupal.org/project/tripal/releases/7.x-3.0-beta1
>> The Tripal Issue Queue: https://www.drupal.org/project/issues/tripal
>>
>> This release represents a major improvement over the 7.x-3.0-alpha1 
>> release. This represents a stable design for Tripal v3, although 
>> perhaps a still buggy implementation. We expect future v3 beta 
>> releases to be primarily bug fixes and addition of some outstanding 
>> features that need completion.
>>
>> _Remember, this is a beta release version!_ We expect you will find 
>> bugs. We recommend testing Tripal v3.0-beta1 on a development server. 
>> Future updates to the beta version will provide Drupal based updates. 
>> These will ensure that periodic updates can easily transition your 
>> Tripal v3.0-beta site to a full stable Tripal v3.0 site once the 
>> stable version is finally released (expected in May 2017). Please 
>> help us speed our stable release by reporting any bugs you may find 
>> with instructions for how to reproduce them to our issue Queue above 
>> or ask questions on our mailing lists.
>>
>> This release provides the following:
>>
>>  1. All Tripal content types are now implemented using Entities
>>     rather than Nodes.
>>  2. Tripal content types no longer follow the Chado schema structure.
>>     Content types are now more intuitive and based on controlled
>>     vocabulary terms. For example, previously feature pages would
>>     provide content for genes, SNPs, mRNA, genetic markers, etc. Now
>>     each of those types can be their own Tripal Content Typel
>>  3. Site admins can create as many content types as they have data in
>>     their site. There is no limit to the type and number of content
>>     types.
>>  4. A new Storage API layer has been added to separate Tripal from
>>     Chado. Chado still serves as the primary storage location for
>>     data, but the new layer will allow for integration of data from
>>     other data sources. This beta version does not yet support any
>>     other data storage other than Chado. The full stable v3.0 release
>>     will.
>>  5. Ancillary data about Tripal Content Types are now "attached" as
>>     fields to Entities. This allows the site admin to full customize
>>     the layout of the site without writing PHP templates. Templates
>>     can still be used if desired, but now it's possible to create a
>>     much more custom layout than previously.
>>  6. This version now provides the first introduction of RESTful web
>>     services to Tripal. Remote programmers can now access data from a
>>     Tripal site using any scripting language they desire to retrieve
>>     data formatted in JSON-LD using the W3C Hydra vocabulary. Web
>>     services still require implementation of access controls, and a
>>     much richer querying structure. The full stable v3.0 release will
>>     have a mature RESTFul web services.
>>  7. To assist with layout of new content types with lots of attached
>>     fields a new tripal_ds module is provided that automatically
>>     creates new layouts for each content type using Display Suites.
>>     The layout is designed to resemble the Tripal v2 template based
>>     layout for consistency. But site admins are free to change these
>>     layouts using the Tripal Content Type graphical interface.
>>  8. Tripal v3 provides a migration tool to help ease the burden of
>>     converting your Tripal v2 nodes over to Tripal v3. It especially
>>     allows for use of your custom Tripal v2 templates even with
>>     Tripal v3 Entities. This will allow for faster upgrade to v3
>>     while still affording a gradual transition from v2 templates to
>>     v3 layouts.
>>
>> Some current limitations:
>>
>>  1. The User's Guide is still not complete, although it will walk you
>>     through installation and setup of a very simple example genomics
>>     website.
>>  2. The Developer's Handbook and API documentation are not yet
>>     available.
>>  3. The RESTful web services currently lack access controls and a
>>     more complicated query interface is needed.  These updates will
>>     be made in a later beta release and the stable version.
>>  4. Integration of non Chado data stores is not yet ready. This
>>     should be ready in a future beta release and in the final stable
>>     version.
>>  5. Bugs!  Please let us know what you find.
>>
>>
>>
>> ------------------------------------------------------------------------------
>> 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
>
>
> -- 
> Daniel Sobral, PhD
> Head of Bioinformatics Unit
> Instituto Gulbenkian de Ciência
> +351214407965
>
>
> ------------------------------------------------------------------------------
> 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

Re: [Gmod-tripal] Tripal v3.0-beta1 released!

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

Hi,

I’m glad to hear you’re trying out the beta! These errors somehow squeaked through our testing process —Sorry! We’ve got a fix we’re testing right now so hopefully there will be a new beta release out today :-)

Thanks for reporting the errors!
~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 February 15, 2017 at 9:32:49 AM, Daniel Sobral (ds...@ig...<mailto:ds...@ig...>) wrote:

Hello,

This sounds very exciting! I'm now redoing from scratch a tripal site and I'm trying to follow the installation guide.
I'm using Ubuntu 16.04 server (not desktop).

All went reasonably well, except a small glitch when making the drupal and tripal connection (loading the ontologies), I've got some errors which I guess can be ignored for now:

WD tripal: Cannot create field for "pub.miniref". Missing an appropriate vocabulary term                                [error]
[site http://default] [TRIPAL ERROR] [TRIPAL] Cannot create field for "pub.miniref". Missing an appropriate vocabulary term
Cannot create field for "pub.miniref". Missing an appropriate vocabulary term                                           [error]

I carried on with the tutorial.
But when I try to insert an Organism, it fails:


  *   Notice: Undefined offset: 0 in tripal_chado_field_storage_write_table() (line 154 of /var/www/html/sites/all/modules/tripal/tripal_chado/includes/tripal_chado.field_storage.inc).
  *   Notice: Trying to get property of non-object in tripal_chado_field_storage_write_table() (line 154 of /var/www/html/sites/all/modules/tripal/tripal_chado/includes/tripal_chado.field_storage.inc).
  *   Could not save the entity: SQLSTATE[42P01]: Undefined table: 7 ERROR: relation "field_data_data__image" does not exist LINE 1: INSERT INTO field_data_data__image (entity_type, entity_id, ... ^
  *   Cannot save entity


 Did I do something wrong?

Best,
Daniel





On 11-02-2017 07:16, Stephen Ficklin wrote:

Dear Tripal Community,

We are happy to announce the release of Tripal v3.0-beta1!  Here are some quick links:

Tripal v3.x User's Guide: http://tripal.info/tutorials/v3.x
Tripal v3.x Download Page at Drupal.org: https://www.drupal.org/project/tripal/releases/7.x-3.0-beta1
The Tripal Issue Queue: https://www.drupal.org/project/issues/tripal

This release represents a major improvement over the 7.x-3.0-alpha1 release. This represents a stable design for Tripal v3, although perhaps a still buggy implementation. We expect future v3 beta releases to be primarily bug fixes and addition of some outstanding features that need completion.

Remember, this is a beta release version! We expect you will find bugs. We recommend testing Tripal v3.0-beta1 on a development server. Future updates to the beta version will provide Drupal based updates. These will ensure that periodic updates can easily transition your Tripal v3.0-beta site to a full stable Tripal v3.0 site once the stable version is finally released (expected in May 2017). Please help us speed our stable release by reporting any bugs you may find with instructions for how to reproduce them to our issue Queue above or ask questions on our mailing lists.

This release provides the following:

  1.  All Tripal content types are now implemented using Entities rather than Nodes.
  2.  Tripal content types no longer follow the Chado schema structure. Content types are now more intuitive and based on controlled vocabulary terms. For example, previously feature pages would provide content for genes, SNPs, mRNA, genetic markers, etc. Now each of those types can be their own Tripal Content Typel
  3.  Site admins can create as many content types as they have data in their site. There is no limit to the type and number of content types.
  4.  A new Storage API layer has been added to separate Tripal from Chado. Chado still serves as the primary storage location for data, but the new layer will allow for integration of data from other data sources. This beta version does not yet support any other data storage other than Chado. The full stable v3.0 release will.
  5.  Ancillary data about Tripal Content Types are now "attached" as fields to Entities. This allows the site admin to full customize the layout of the site without writing PHP templates. Templates can still be used if desired, but now it's possible to create a much more custom layout than previously.
  6.  This version now provides the first introduction of RESTful web services to Tripal. Remote programmers can now access data from a Tripal site using any scripting language they desire to retrieve data formatted in JSON-LD using the W3C Hydra vocabulary. Web services still require implementation of access controls, and a much richer querying structure. The full stable v3.0 release will have a mature RESTFul web services.
  7.  To assist with layout of new content types with lots of attached fields a new tripal_ds module is provided that automatically creates new layouts for each content type using Display Suites. The layout is designed to resemble the Tripal v2 template based layout for consistency. But site admins are free to change these layouts using the Tripal Content Type graphical interface.
  8.  Tripal v3 provides a migration tool to help ease the burden of converting your Tripal v2 nodes over to Tripal v3. It especially allows for use of your custom Tripal v2 templates even with Tripal v3 Entities. This will allow for faster upgrade to v3 while still affording a gradual transition from v2 templates to v3 layouts.

Some current limitations:

  1.  The User's Guide is still not complete, although it will walk you through installation and setup of a very simple example genomics website.
  2.  The Developer's Handbook and API documentation are not yet available.
  3.  The RESTful web services currently lack access controls and a more complicated query interface is needed.  These updates will be made in a later beta release and the stable version.
  4.  Integration of non Chado data stores is not yet ready.  This should be ready in a future beta release and in the final stable version.
  5.  Bugs!  Please let us know what you find.



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--
Daniel Sobral, PhD
Head of Bioinformatics Unit
Instituto Gulbenkian de Ciência
+351214407965

------------------------------------------------------------------------------
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engaging tech sites, SlashDot.org! http://sdm.link/slashdot_______________________________________________
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