Tripal v3.0-beta1 released!

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Tripal v3.0-beta1 released!

Stephen Ficklin-2

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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Re: Tripal v3.0-beta1 released!

Daniel Sobral
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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engaging tech sites, SlashDot.org! http://sdm.link/slashdot


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Head of Bioinformatics Unit
Instituto Gulbenkian de Ciência
+351214407965

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Re: Tripal v3.0-beta1 released!

Kucheran, Lacey Sanderson
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) <a href="tel://966-3208">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On February 15, 2017 at 9:32:49 AM, Daniel Sobral ([hidden email]) 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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engaging tech sites, SlashDot.org! http://sdm.link/slashdot


_______________________________________________
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--  
Daniel Sobral, PhD
Head of Bioinformatics Unit
Instituto Gulbenkian de Ciência
+351214407965
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Re: Tripal v3.0-beta1 released!

Stephen Ficklin-2
In reply to this post by Daniel Sobral

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.


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


_______________________________________________
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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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