[Gmod-tripal-devel] Tripal v1.1 Released

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[Gmod-tripal-devel] Tripal v1.1 Released

Stephen Ficklin-2
Dear Tripal Users,

Tripal v1.1 has been released and contains a set of bug fixes for the
v1.0 release as well as a new publication module.   Here are some
pertinent links:

* Download or Upgrade Instructions:
http://tripal.info/documentation/download_tripal_v1.1
* New Functionality:
http://tripal.info/documentation/tripal_v1.1_functionality
* Installation Instructions and Tutorial:
http://www.gmod.org/wiki/Tripal_Tutorial_v1.1

Additionally, conversion of Tripal for support of Drupal 7 is currently
underway.  We hope to release Tripal 2.0 with full compatibility with
Drupal 7 by the Fall of 2013.

We put forth our best efforts, given the small size of our development
group, to make these releases bug free, but if you happen to come across
an issue please feel free to let us know.

Thanks to those who have provided input, and who use Tripal!
Stephen

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Re: [Gmod-tripal-devel] Tripal v1.1 Released

Michael Dondrup-3
Hi Stephen and all developers,

than you for bringing us the new version. According to my experiences, there should be an additional
documentation for updating. That should contain or at least that is what I am going to do:

- Set Drupal to maintenance mode
- Make a backup of the database
- Disable Tripal modules in reverse order as to what described in
http://www.gmod.org/wiki/Tripal_Tutorial_(v1.0)
using
> drush pm-disable ...

download the new modules following:
> http://tripal.info/documentation/download_tripal_v1.1
enable all tripal modules in order as in
> http://www.gmod.org/wiki/Tripal_Tutorial_v1.1

using drush pm-enable
- Set Drupal to on-line mode

I am not totally sure about the drush pm-disable step, but I had the impression that it was required. Is it correct?


Michael


On Jun 25, 2013, at 6:56 AM, Stephen Ficklin wrote:

> Dear Tripal Users,
>
> Tripal v1.1 has been released and contains a set of bug fixes for the
> v1.0 release as well as a new publication module.   Here are some
> pertinent links:
>
> * Download or Upgrade Instructions:
> http://tripal.info/documentation/download_tripal_v1.1
> * New Functionality:
> http://tripal.info/documentation/tripal_v1.1_functionality
> * Installation Instructions and Tutorial:
> http://www.gmod.org/wiki/Tripal_Tutorial_v1.1
>
> Additionally, conversion of Tripal for support of Drupal 7 is currently
> underway.  We hope to release Tripal 2.0 with full compatibility with
> Drupal 7 by the Fall of 2013.
>
> We put forth our best efforts, given the small size of our development
> group, to make these releases bug free, but if you happen to come across
> an issue please feel free to let us know.
>
> Thanks to those who have provided input, and who use Tripal!
> Stephen
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Windows:
>
> Build for Windows Store.
>
> http://p.sf.net/sfu/windows-dev2dev
> _______________________________________________
> Gmod-tripal-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel


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Re: [Gmod-tripal-devel] Tripal v1.1 Released

Stephen Ficklin-2
In reply to this post by Stephen Ficklin-2
Hi Michael,

Because this update does not contain a lot of changes you don't need to
disable all the Tripal modules and then re-enable them again.  You
should be able to just update the code using 'git' and then run the
'updatedb'.  We've successfully done this on many of our sites.   But
you are correct, it is best practice to make sure you have a backup
before making any major changes and switching to maintenance mode so
I'll add that to the upgrade documentation.

Thanks for your comments!
Stephen

On 6/25/2013 4:29 AM, Michael Dondrup wrote:

> Hi Stephen and all developers,
>
> than you for bringing us the new version. According to my experiences, there should be an additional
> documentation for updating. That should contain or at least that is what I am going to do:
>
> - Set Drupal to maintenance mode
> - Make a backup of the database
> - Disable Tripal modules in reverse order as to what described in
> http://www.gmod.org/wiki/Tripal_Tutorial_(v1.0)
> using
>> drush pm-disable ...
> download the new modules following:
>> http://tripal.info/documentation/download_tripal_v1.1
> enable all tripal modules in order as in
>> http://www.gmod.org/wiki/Tripal_Tutorial_v1.1
> using drush pm-enable
> - Set Drupal to on-line mode
>
> I am not totally sure about the drush pm-disable step, but I had the impression that it was required. Is it correct?
>
>
> Michael
>
>
> On Jun 25, 2013, at 6:56 AM, Stephen Ficklin wrote:
>
>> Dear Tripal Users,
>>
>> Tripal v1.1 has been released and contains a set of bug fixes for the
>> v1.0 release as well as a new publication module.   Here are some
>> pertinent links:
>>
>> * Download or Upgrade Instructions:
>> http://tripal.info/documentation/download_tripal_v1.1
>> * New Functionality:
>> http://tripal.info/documentation/tripal_v1.1_functionality
>> * Installation Instructions and Tutorial:
>> http://www.gmod.org/wiki/Tripal_Tutorial_v1.1
>>
>> Additionally, conversion of Tripal for support of Drupal 7 is currently
>> underway.  We hope to release Tripal 2.0 with full compatibility with
>> Drupal 7 by the Fall of 2013.
>>
>> We put forth our best efforts, given the small size of our development
>> group, to make these releases bug free, but if you happen to come across
>> an issue please feel free to let us know.
>>
>> Thanks to those who have provided input, and who use Tripal!
>> Stephen
>>
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by Windows:
>>
>> Build for Windows Store.
>>
>> http://p.sf.net/sfu/windows-dev2dev
>> _______________________________________________
>> Gmod-tripal-devel mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel


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Re: [Gmod-tripal-devel] Tripal v1.1 Released

Stephen Ficklin-2
In reply to this post by Stephen Ficklin-2
Hi Michael,

I just realized the link for the upgrade documentation was not in the
email I first sent.  It is here:
http://tripal.info/documentation/upgrade_1.0_to_1.1

It is also available by clicking 'Download & Upgrade' under 'Quick
Links' on the Tripal site.  Your suggestions to backup and put in
maintenance mode were missing from that document so I just added them.  
Thank you.

Stephen


On 6/25/2013 4:29 AM, Michael Dondrup wrote:

> Hi Stephen and all developers,
>
> than you for bringing us the new version. According to my experiences, there should be an additional
> documentation for updating. That should contain or at least that is what I am going to do:
>
> - Set Drupal to maintenance mode
> - Make a backup of the database
> - Disable Tripal modules in reverse order as to what described in
> http://www.gmod.org/wiki/Tripal_Tutorial_(v1.0)
> using
>> drush pm-disable ...
> download the new modules following:
>> http://tripal.info/documentation/download_tripal_v1.1
> enable all tripal modules in order as in
>> http://www.gmod.org/wiki/Tripal_Tutorial_v1.1
> using drush pm-enable
> - Set Drupal to on-line mode
>
> I am not totally sure about the drush pm-disable step, but I had the impression that it was required. Is it correct?
>
>
> Michael
>
>
> On Jun 25, 2013, at 6:56 AM, Stephen Ficklin wrote:
>
>> Dear Tripal Users,
>>
>> Tripal v1.1 has been released and contains a set of bug fixes for the
>> v1.0 release as well as a new publication module.   Here are some
>> pertinent links:
>>
>> * Download or Upgrade Instructions:
>> http://tripal.info/documentation/download_tripal_v1.1
>> * New Functionality:
>> http://tripal.info/documentation/tripal_v1.1_functionality
>> * Installation Instructions and Tutorial:
>> http://www.gmod.org/wiki/Tripal_Tutorial_v1.1
>>
>> Additionally, conversion of Tripal for support of Drupal 7 is currently
>> underway.  We hope to release Tripal 2.0 with full compatibility with
>> Drupal 7 by the Fall of 2013.
>>
>> We put forth our best efforts, given the small size of our development
>> group, to make these releases bug free, but if you happen to come across
>> an issue please feel free to let us know.
>>
>> Thanks to those who have provided input, and who use Tripal!
>> Stephen
>>
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by Windows:
>>
>> Build for Windows Store.
>>
>> http://p.sf.net/sfu/windows-dev2dev
>> _______________________________________________
>> Gmod-tripal-devel mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel


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Re: [Gmod-tripal-devel] Tripal v1.1 Released

Michael Dondrup-3
In reply to this post by Stephen Ficklin-2
Hi, again, thank you for your response.
I have another little observation:
After doing the update (did the diable/enable), I noticed I had to run the updatedb script, ran it directly from the web-ui.
This generates a job to load the contact cv, but running this yields:

ripal Job Launcher
Running as user ' . admin . '
-------------------
Calling: tripal_update_mview(2, 36)
Calling: tripal_cv_load_obo_v1_2_id(10, 37)
ERROR: counld not find OBO file: '/export/home/licebase/drupal/sites/all/modules/tripal/tripal_contact/tcontact.obo'
Calling: tripal_update_mview(9, 38)
however this file is in
./sites/all/modules/tripal/tripal_contact/files/tcontact.obo
The job also is not in Error state.

I have copied the file to the location the job was looking for it, and re-run the job
Load OBO Tripal Contacts
which gives the following output

-------------------
Calling: tripal_cv_load_obo_v1_2_id(10, 39)

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 /export/home/licebase/drupal/sites/all/modules/tripal/tripal_contact/tcontact.obo
Parsing Line 160 (100.00%). Memory: 37,210,312 bytes.
Step 2: Loading type defs...
2 of 2 records. (100.00%) Memory: 37,226,232 bytes
Step 3: Loading terms...
28 of 28 records. (100.00%) Memory: 37,244,368 bytes
Done

Updating cvtermpath table.  This may take a while...

Updating cvtermpath for tripal_contact...

I believe that everyone who installed tripal_contact  should do this.




Best
Michael



On Jun 25, 2013, at 2:59 PM, Stephen Ficklin wrote:

> Hi Michael,
>
> Because this update does not contain a lot of changes you don't need to
> disable all the Tripal modules and then re-enable them again.  You
> should be able to just update the code using 'git' and then run the
> 'updatedb'.  We've successfully done this on many of our sites.   But
> you are correct, it is best practice to make sure you have a backup
> before making any major changes and switching to maintenance mode so
> I'll add that to the upgrade documentation.
>
> Thanks for your comments!
> Stephen
>
> On 6/25/2013 4:29 AM, Michael Dondrup wrote:
>> Hi Stephen and all developers,
>>
>> than you for bringing us the new version. According to my experiences, there should be an additional
>> documentation for updating. That should contain or at least that is what I am going to do:
>>
>> - Set Drupal to maintenance mode
>> - Make a backup of the database
>> - Disable Tripal modules in reverse order as to what described in
>> http://www.gmod.org/wiki/Tripal_Tutorial_(v1.0)
>> using
>>> drush pm-disable ...
>> download the new modules following:
>>> http://tripal.info/documentation/download_tripal_v1.1
>> enable all tripal modules in order as in
>>> http://www.gmod.org/wiki/Tripal_Tutorial_v1.1
>> using drush pm-enable
>> - Set Drupal to on-line mode
>>
>> I am not totally sure about the drush pm-disable step, but I had the impression that it was required. Is it correct?
>>
>>
>> Michael
>>
>>
>> On Jun 25, 2013, at 6:56 AM, Stephen Ficklin wrote:
>>
>>> Dear Tripal Users,
>>>
>>> Tripal v1.1 has been released and contains a set of bug fixes for the
>>> v1.0 release as well as a new publication module.   Here are some
>>> pertinent links:
>>>
>>> * Download or Upgrade Instructions:
>>> http://tripal.info/documentation/download_tripal_v1.1
>>> * New Functionality:
>>> http://tripal.info/documentation/tripal_v1.1_functionality
>>> * Installation Instructions and Tutorial:
>>> http://www.gmod.org/wiki/Tripal_Tutorial_v1.1
>>>
>>> Additionally, conversion of Tripal for support of Drupal 7 is currently
>>> underway.  We hope to release Tripal 2.0 with full compatibility with
>>> Drupal 7 by the Fall of 2013.
>>>
>>> We put forth our best efforts, given the small size of our development
>>> group, to make these releases bug free, but if you happen to come across
>>> an issue please feel free to let us know.
>>>
>>> Thanks to those who have provided input, and who use Tripal!
>>> Stephen
>>>
>>> ------------------------------------------------------------------------------
>>> This SF.net email is sponsored by Windows:
>>>
>>> Build for Windows Store.
>>>
>>> http://p.sf.net/sfu/windows-dev2dev
>>> _______________________________________________
>>> Gmod-tripal-devel mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Windows:
>
> Build for Windows Store.
>
> http://p.sf.net/sfu/windows-dev2dev
> _______________________________________________
> Gmod-tripal-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel


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Re: [Gmod-tripal-devel] Tripal v1.1 Released

Stephen Ficklin-2
Hi Michael,

Were you using the development version prior to v1.1?  If so, there was
a point in the development branch that the tcontact.obo was in the
'tripal_contact/tcontact.obo' directory, but it was moved to
'tripal_contact/files/tcontact.obo', which is why you are getting this
error.  The same is true for the tpub.obo from the publication module.  
For folks who were not using the development version this problem should
not occur.

But, I'll add this to the upgrade documentation for folks who were using
the development version.

Thanks for pointing it out!
Stephen

On 6/25/2013 9:09 AM, Michael Dondrup wrote:

> Hi, again, thank you for your response.
> I have another little observation:
> After doing the update (did the diable/enable), I noticed I had to run the updatedb script, ran it directly from the web-ui.
> This generates a job to load the contact cv, but running this yields:
>
> ripal Job Launcher
> Running as user ' . admin . '
> -------------------
> Calling: tripal_update_mview(2, 36)
> Calling: tripal_cv_load_obo_v1_2_id(10, 37)
> ERROR: counld not find OBO file: '/export/home/licebase/drupal/sites/all/modules/tripal/tripal_contact/tcontact.obo'
> Calling: tripal_update_mview(9, 38)
> however this file is in
> ./sites/all/modules/tripal/tripal_contact/files/tcontact.obo
> The job also is not in Error state.
>
> I have copied the file to the location the job was looking for it, and re-run the job
> Load OBO Tripal Contacts
> which gives the following output
>
> -------------------
> Calling: tripal_cv_load_obo_v1_2_id(10, 39)
>
> 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 /export/home/licebase/drupal/sites/all/modules/tripal/tripal_contact/tcontact.obo
> Parsing Line 160 (100.00%). Memory: 37,210,312 bytes.
> Step 2: Loading type defs...
> 2 of 2 records. (100.00%) Memory: 37,226,232 bytes
> Step 3: Loading terms...
> 28 of 28 records. (100.00%) Memory: 37,244,368 bytes
> Done
>
> Updating cvtermpath table.  This may take a while...
>
> Updating cvtermpath for tripal_contact...
>
> I believe that everyone who installed tripal_contact  should do this.
>
>
>
>
> Best
> Michael
>
>
>
> On Jun 25, 2013, at 2:59 PM, Stephen Ficklin wrote:
>
>> Hi Michael,
>>
>> Because this update does not contain a lot of changes you don't need to
>> disable all the Tripal modules and then re-enable them again.  You
>> should be able to just update the code using 'git' and then run the
>> 'updatedb'.  We've successfully done this on many of our sites.   But
>> you are correct, it is best practice to make sure you have a backup
>> before making any major changes and switching to maintenance mode so
>> I'll add that to the upgrade documentation.
>>
>> Thanks for your comments!
>> Stephen
>>
>> On 6/25/2013 4:29 AM, Michael Dondrup wrote:
>>> Hi Stephen and all developers,
>>>
>>> than you for bringing us the new version. According to my experiences, there should be an additional
>>> documentation for updating. That should contain or at least that is what I am going to do:
>>>
>>> - Set Drupal to maintenance mode
>>> - Make a backup of the database
>>> - Disable Tripal modules in reverse order as to what described in
>>> http://www.gmod.org/wiki/Tripal_Tutorial_(v1.0)
>>> using
>>>> drush pm-disable ...
>>> download the new modules following:
>>>> http://tripal.info/documentation/download_tripal_v1.1
>>> enable all tripal modules in order as in
>>>> http://www.gmod.org/wiki/Tripal_Tutorial_v1.1
>>> using drush pm-enable
>>> - Set Drupal to on-line mode
>>>
>>> I am not totally sure about the drush pm-disable step, but I had the impression that it was required. Is it correct?
>>>
>>>
>>> Michael
>>>
>>>
>>> On Jun 25, 2013, at 6:56 AM, Stephen Ficklin wrote:
>>>
>>>> Dear Tripal Users,
>>>>
>>>> Tripal v1.1 has been released and contains a set of bug fixes for the
>>>> v1.0 release as well as a new publication module.   Here are some
>>>> pertinent links:
>>>>
>>>> * Download or Upgrade Instructions:
>>>> http://tripal.info/documentation/download_tripal_v1.1
>>>> * New Functionality:
>>>> http://tripal.info/documentation/tripal_v1.1_functionality
>>>> * Installation Instructions and Tutorial:
>>>> http://www.gmod.org/wiki/Tripal_Tutorial_v1.1
>>>>
>>>> Additionally, conversion of Tripal for support of Drupal 7 is currently
>>>> underway.  We hope to release Tripal 2.0 with full compatibility with
>>>> Drupal 7 by the Fall of 2013.
>>>>
>>>> We put forth our best efforts, given the small size of our development
>>>> group, to make these releases bug free, but if you happen to come across
>>>> an issue please feel free to let us know.
>>>>
>>>> Thanks to those who have provided input, and who use Tripal!
>>>> Stephen
>>>>
>>>> ------------------------------------------------------------------------------
>>>> This SF.net email is sponsored by Windows:
>>>>
>>>> Build for Windows Store.
>>>>
>>>> http://p.sf.net/sfu/windows-dev2dev
>>>> _______________________________________________
>>>> Gmod-tripal-devel mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by Windows:
>>
>> Build for Windows Store.
>>
>> http://p.sf.net/sfu/windows-dev2dev
>> _______________________________________________
>> Gmod-tripal-devel mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel


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Re: [Gmod-tripal-devel] Tripal v1.1 Released

Michael Dondrup-3


On Jun 25, 2013, at 3:18 PM, Stephen Ficklin wrote:

> Hi Michael,
>
> Were you using the development version prior to v1.1?  

Yes, that is correct. However, I have moved all directories aside (at least I think so)
and stated from scratch. I am unfortunately still a noob when it comes to git.

> If so, there was
> a point in the development branch that the tcontact.obo was in the
> 'tripal_contact/tcontact.obo' directory, but it was moved to
> 'tripal_contact/files/tcontact.obo', which is why you are getting this
> error.  The same is true for the tpub.obo from the publication module.  
> For folks who were not using the development version this problem should
> not occur.
>
> But, I'll add this to the upgrade documentation for folks who were using
> the development version.
>
> Thanks for pointing it out!
> Stephen
>
> On 6/25/2013 9:09 AM, Michael Dondrup wrote:
>> Hi, again, thank you for your response.
>> I have another little observation:
>> After doing the update (did the diable/enable), I noticed I had to run the updatedb script, ran it directly from the web-ui.
>> This generates a job to load the contact cv, but running this yields:
>>
>> ripal Job Launcher
>> Running as user ' . admin . '
>> -------------------
>> Calling: tripal_update_mview(2, 36)
>> Calling: tripal_cv_load_obo_v1_2_id(10, 37)
>> ERROR: counld not find OBO file: '/export/home/licebase/drupal/sites/all/modules/tripal/tripal_contact/tcontact.obo'
>> Calling: tripal_update_mview(9, 38)
>> however this file is in
>> ./sites/all/modules/tripal/tripal_contact/files/tcontact.obo
>> The job also is not in Error state.
>>
>> I have copied the file to the location the job was looking for it, and re-run the job
>> Load OBO Tripal Contacts
>> which gives the following output
>>
>> -------------------
>> Calling: tripal_cv_load_obo_v1_2_id(10, 39)
>>
>> 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 /export/home/licebase/drupal/sites/all/modules/tripal/tripal_contact/tcontact.obo
>> Parsing Line 160 (100.00%). Memory: 37,210,312 bytes.
>> Step 2: Loading type defs...
>> 2 of 2 records. (100.00%) Memory: 37,226,232 bytes
>> Step 3: Loading terms...
>> 28 of 28 records. (100.00%) Memory: 37,244,368 bytes
>> Done
>>
>> Updating cvtermpath table.  This may take a while...
>>
>> Updating cvtermpath for tripal_contact...
>>
>> I believe that everyone who installed tripal_contact  should do this.
>>
>>
>>
>>
>> Best
>> Michael
>>
>>
>>
>> On Jun 25, 2013, at 2:59 PM, Stephen Ficklin wrote:
>>
>>> Hi Michael,
>>>
>>> Because this update does not contain a lot of changes you don't need to
>>> disable all the Tripal modules and then re-enable them again.  You
>>> should be able to just update the code using 'git' and then run the
>>> 'updatedb'.  We've successfully done this on many of our sites.   But
>>> you are correct, it is best practice to make sure you have a backup
>>> before making any major changes and switching to maintenance mode so
>>> I'll add that to the upgrade documentation.
>>>
>>> Thanks for your comments!
>>> Stephen
>>>
>>> On 6/25/2013 4:29 AM, Michael Dondrup wrote:
>>>> Hi Stephen and all developers,
>>>>
>>>> than you for bringing us the new version. According to my experiences, there should be an additional
>>>> documentation for updating. That should contain or at least that is what I am going to do:
>>>>
>>>> - Set Drupal to maintenance mode
>>>> - Make a backup of the database
>>>> - Disable Tripal modules in reverse order as to what described in
>>>> http://www.gmod.org/wiki/Tripal_Tutorial_(v1.0)
>>>> using
>>>>> drush pm-disable ...
>>>> download the new modules following:
>>>>> http://tripal.info/documentation/download_tripal_v1.1
>>>> enable all tripal modules in order as in
>>>>> http://www.gmod.org/wiki/Tripal_Tutorial_v1.1
>>>> using drush pm-enable
>>>> - Set Drupal to on-line mode
>>>>
>>>> I am not totally sure about the drush pm-disable step, but I had the impression that it was required. Is it correct?
>>>>
>>>>
>>>> Michael
>>>>
>>>>
>>>> On Jun 25, 2013, at 6:56 AM, Stephen Ficklin wrote:
>>>>
>>>>> Dear Tripal Users,
>>>>>
>>>>> Tripal v1.1 has been released and contains a set of bug fixes for the
>>>>> v1.0 release as well as a new publication module.   Here are some
>>>>> pertinent links:
>>>>>
>>>>> * Download or Upgrade Instructions:
>>>>> http://tripal.info/documentation/download_tripal_v1.1
>>>>> * New Functionality:
>>>>> http://tripal.info/documentation/tripal_v1.1_functionality
>>>>> * Installation Instructions and Tutorial:
>>>>> http://www.gmod.org/wiki/Tripal_Tutorial_v1.1
>>>>>
>>>>> Additionally, conversion of Tripal for support of Drupal 7 is currently
>>>>> underway.  We hope to release Tripal 2.0 with full compatibility with
>>>>> Drupal 7 by the Fall of 2013.
>>>>>
>>>>> We put forth our best efforts, given the small size of our development
>>>>> group, to make these releases bug free, but if you happen to come across
>>>>> an issue please feel free to let us know.
>>>>>
>>>>> Thanks to those who have provided input, and who use Tripal!
>>>>> Stephen
>>>>>
>>>>> ------------------------------------------------------------------------------
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Re: [Gmod-tripal-devel] Tripal v1.1 Released

Stephen Ficklin-2
In reply to this post by Michael Dondrup-3
HI Michael,

Rather than copy the tcontact.obo you should make a symbolic link to
it.  This way, for future updates, Tripal can see new updates to the
ontology file.  Instructions for creating this link are found on the
upgrade page at the bottom:
http://tripal.info/documentation/upgrade_1.0_to_1.1

Stephen

On 6/25/2013 9:09 AM, Michael Dondrup wrote:

> Hi, again, thank you for your response.
> I have another little observation:
> After doing the update (did the diable/enable), I noticed I had to run the updatedb script, ran it directly from the web-ui.
> This generates a job to load the contact cv, but running this yields:
>
> ripal Job Launcher
> Running as user ' . admin . '
> -------------------
> Calling: tripal_update_mview(2, 36)
> Calling: tripal_cv_load_obo_v1_2_id(10, 37)
> ERROR: counld not find OBO file: '/export/home/licebase/drupal/sites/all/modules/tripal/tripal_contact/tcontact.obo'
> Calling: tripal_update_mview(9, 38)
> however this file is in
> ./sites/all/modules/tripal/tripal_contact/files/tcontact.obo
> The job also is not in Error state.
>
> I have copied the file to the location the job was looking for it, and re-run the job
> Load OBO Tripal Contacts
> which gives the following output
>
> -------------------
> Calling: tripal_cv_load_obo_v1_2_id(10, 39)
>
> 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 /export/home/licebase/drupal/sites/all/modules/tripal/tripal_contact/tcontact.obo
> Parsing Line 160 (100.00%). Memory: 37,210,312 bytes.
> Step 2: Loading type defs...
> 2 of 2 records. (100.00%) Memory: 37,226,232 bytes
> Step 3: Loading terms...
> 28 of 28 records. (100.00%) Memory: 37,244,368 bytes
> Done
>
> Updating cvtermpath table.  This may take a while...
>
> Updating cvtermpath for tripal_contact...
>
> I believe that everyone who installed tripal_contact  should do this.
>
>
>
>
> Best
> Michael
>
>
>
> On Jun 25, 2013, at 2:59 PM, Stephen Ficklin wrote:
>
>> Hi Michael,
>>
>> Because this update does not contain a lot of changes you don't need to
>> disable all the Tripal modules and then re-enable them again.  You
>> should be able to just update the code using 'git' and then run the
>> 'updatedb'.  We've successfully done this on many of our sites.   But
>> you are correct, it is best practice to make sure you have a backup
>> before making any major changes and switching to maintenance mode so
>> I'll add that to the upgrade documentation.
>>
>> Thanks for your comments!
>> Stephen
>>
>> On 6/25/2013 4:29 AM, Michael Dondrup wrote:
>>> Hi Stephen and all developers,
>>>
>>> than you for bringing us the new version. According to my experiences, there should be an additional
>>> documentation for updating. That should contain or at least that is what I am going to do:
>>>
>>> - Set Drupal to maintenance mode
>>> - Make a backup of the database
>>> - Disable Tripal modules in reverse order as to what described in
>>> http://www.gmod.org/wiki/Tripal_Tutorial_(v1.0)
>>> using
>>>> drush pm-disable ...
>>> download the new modules following:
>>>> http://tripal.info/documentation/download_tripal_v1.1
>>> enable all tripal modules in order as in
>>>> http://www.gmod.org/wiki/Tripal_Tutorial_v1.1
>>> using drush pm-enable
>>> - Set Drupal to on-line mode
>>>
>>> I am not totally sure about the drush pm-disable step, but I had the impression that it was required. Is it correct?
>>>
>>>
>>> Michael
>>>
>>>
>>> On Jun 25, 2013, at 6:56 AM, Stephen Ficklin wrote:
>>>
>>>> Dear Tripal Users,
>>>>
>>>> Tripal v1.1 has been released and contains a set of bug fixes for the
>>>> v1.0 release as well as a new publication module.   Here are some
>>>> pertinent links:
>>>>
>>>> * Download or Upgrade Instructions:
>>>> http://tripal.info/documentation/download_tripal_v1.1
>>>> * New Functionality:
>>>> http://tripal.info/documentation/tripal_v1.1_functionality
>>>> * Installation Instructions and Tutorial:
>>>> http://www.gmod.org/wiki/Tripal_Tutorial_v1.1
>>>>
>>>> Additionally, conversion of Tripal for support of Drupal 7 is currently
>>>> underway.  We hope to release Tripal 2.0 with full compatibility with
>>>> Drupal 7 by the Fall of 2013.
>>>>
>>>> We put forth our best efforts, given the small size of our development
>>>> group, to make these releases bug free, but if you happen to come across
>>>> an issue please feel free to let us know.
>>>>
>>>> Thanks to those who have provided input, and who use Tripal!
>>>> Stephen
>>>>
>>>> ------------------------------------------------------------------------------
>>>> This SF.net email is sponsored by Windows:
>>>>
>>>> Build for Windows Store.
>>>>
>>>> http://p.sf.net/sfu/windows-dev2dev
>>>> _______________________________________________
>>>> Gmod-tripal-devel mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>
>> ------------------------------------------------------------------------------
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>>
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>>
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Re: [Gmod-tripal-devel] Tripal v1.1 Released

Stephen Ficklin-2
In reply to this post by Michael Dondrup-3
Hi Michael,

The path for the ontology files are saved in the public.tripal_cv_obo
table.   This got set when you first installed the Contact module using
an earlier version of the development branch.  We moved the file to make
the directory structure a bit cleaner and unfortunately caused this
problem for you.  But, the path doesn't get reset even when you update
the code.  If you want to permanently fix it (without having to use a
symbolic link) you can edit the entry in the tripal_cv_obo table for
Tripal Contacts ontology.

Sorry for the problem...  And thanks for pointing out issues.

Stephen

On 6/25/2013 9:22 AM, Michael Dondrup wrote:

>
> On Jun 25, 2013, at 3:18 PM, Stephen Ficklin wrote:
>
>> Hi Michael,
>>
>> Were you using the development version prior to v1.1?
> Yes, that is correct. However, I have moved all directories aside (at least I think so)
> and stated from scratch. I am unfortunately still a noob when it comes to git.
>
>> If so, there was
>> a point in the development branch that the tcontact.obo was in the
>> 'tripal_contact/tcontact.obo' directory, but it was moved to
>> 'tripal_contact/files/tcontact.obo', which is why you are getting this
>> error.  The same is true for the tpub.obo from the publication module.
>> For folks who were not using the development version this problem should
>> not occur.
>>
>> But, I'll add this to the upgrade documentation for folks who were using
>> the development version.
>>
>> Thanks for pointing it out!
>> Stephen
>>
>> On 6/25/2013 9:09 AM, Michael Dondrup wrote:
>>> Hi, again, thank you for your response.
>>> I have another little observation:
>>> After doing the update (did the diable/enable), I noticed I had to run the updatedb script, ran it directly from the web-ui.
>>> This generates a job to load the contact cv, but running this yields:
>>>
>>> ripal Job Launcher
>>> Running as user ' . admin . '
>>> -------------------
>>> Calling: tripal_update_mview(2, 36)
>>> Calling: tripal_cv_load_obo_v1_2_id(10, 37)
>>> ERROR: counld not find OBO file: '/export/home/licebase/drupal/sites/all/modules/tripal/tripal_contact/tcontact.obo'
>>> Calling: tripal_update_mview(9, 38)
>>> however this file is in
>>> ./sites/all/modules/tripal/tripal_contact/files/tcontact.obo
>>> The job also is not in Error state.
>>>
>>> I have copied the file to the location the job was looking for it, and re-run the job
>>> Load OBO Tripal Contacts
>>> which gives the following output
>>>
>>> -------------------
>>> Calling: tripal_cv_load_obo_v1_2_id(10, 39)
>>>
>>> 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 /export/home/licebase/drupal/sites/all/modules/tripal/tripal_contact/tcontact.obo
>>> Parsing Line 160 (100.00%). Memory: 37,210,312 bytes.
>>> Step 2: Loading type defs...
>>> 2 of 2 records. (100.00%) Memory: 37,226,232 bytes
>>> Step 3: Loading terms...
>>> 28 of 28 records. (100.00%) Memory: 37,244,368 bytes
>>> Done
>>>
>>> Updating cvtermpath table.  This may take a while...
>>>
>>> Updating cvtermpath for tripal_contact...
>>>
>>> I believe that everyone who installed tripal_contact  should do this.
>>>
>>>
>>>
>>>
>>> Best
>>> Michael
>>>
>>>
>>>
>>> On Jun 25, 2013, at 2:59 PM, Stephen Ficklin wrote:
>>>
>>>> Hi Michael,
>>>>
>>>> Because this update does not contain a lot of changes you don't need to
>>>> disable all the Tripal modules and then re-enable them again.  You
>>>> should be able to just update the code using 'git' and then run the
>>>> 'updatedb'.  We've successfully done this on many of our sites.   But
>>>> you are correct, it is best practice to make sure you have a backup
>>>> before making any major changes and switching to maintenance mode so
>>>> I'll add that to the upgrade documentation.
>>>>
>>>> Thanks for your comments!
>>>> Stephen
>>>>
>>>> On 6/25/2013 4:29 AM, Michael Dondrup wrote:
>>>>> Hi Stephen and all developers,
>>>>>
>>>>> than you for bringing us the new version. According to my experiences, there should be an additional
>>>>> documentation for updating. That should contain or at least that is what I am going to do:
>>>>>
>>>>> - Set Drupal to maintenance mode
>>>>> - Make a backup of the database
>>>>> - Disable Tripal modules in reverse order as to what described in
>>>>> http://www.gmod.org/wiki/Tripal_Tutorial_(v1.0)
>>>>> using
>>>>>> drush pm-disable ...
>>>>> download the new modules following:
>>>>>> http://tripal.info/documentation/download_tripal_v1.1
>>>>> enable all tripal modules in order as in
>>>>>> http://www.gmod.org/wiki/Tripal_Tutorial_v1.1
>>>>> using drush pm-enable
>>>>> - Set Drupal to on-line mode
>>>>>
>>>>> I am not totally sure about the drush pm-disable step, but I had the impression that it was required. Is it correct?
>>>>>
>>>>>
>>>>> Michael
>>>>>
>>>>>
>>>>> On Jun 25, 2013, at 6:56 AM, Stephen Ficklin wrote:
>>>>>
>>>>>> Dear Tripal Users,
>>>>>>
>>>>>> Tripal v1.1 has been released and contains a set of bug fixes for the
>>>>>> v1.0 release as well as a new publication module.   Here are some
>>>>>> pertinent links:
>>>>>>
>>>>>> * Download or Upgrade Instructions:
>>>>>> http://tripal.info/documentation/download_tripal_v1.1
>>>>>> * New Functionality:
>>>>>> http://tripal.info/documentation/tripal_v1.1_functionality
>>>>>> * Installation Instructions and Tutorial:
>>>>>> http://www.gmod.org/wiki/Tripal_Tutorial_v1.1
>>>>>>
>>>>>> Additionally, conversion of Tripal for support of Drupal 7 is currently
>>>>>> underway.  We hope to release Tripal 2.0 with full compatibility with
>>>>>> Drupal 7 by the Fall of 2013.
>>>>>>
>>>>>> We put forth our best efforts, given the small size of our development
>>>>>> group, to make these releases bug free, but if you happen to come across
>>>>>> an issue please feel free to let us know.
>>>>>>
>>>>>> Thanks to those who have provided input, and who use Tripal!
>>>>>> Stephen
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> This SF.net email is sponsored by Windows:
>>>>>>
>>>>>> Build for Windows Store.
>>>>>>
>>>>>> http://p.sf.net/sfu/windows-dev2dev
>>>>>> _______________________________________________
>>>>>> Gmod-tripal-devel mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>>> ------------------------------------------------------------------------------
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>>>>
>>>> Build for Windows Store.
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>>
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