Re: [Gmod-tripal-devel] Gmod-tripal-devel Digest, Vol 26, Issue 1

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Re: [Gmod-tripal-devel] Gmod-tripal-devel Digest, Vol 26, Issue 1

Nathan Weeks
Stephen,

We're using PHP 5.4.x, and are unable to upgrade to Tripal v1.1: the
tripal_pub module appears to use syntax that was deprecated in PHP 5.3
and removed in PHP 5.4. I've filed a bug report:

https://drupal.org/node/2027915

--
Nathan Weeks
IT Specialist
USDA-ARS Corn Insects and Crop Genetics Research Unit
http://weeks.public.iastate.edu/


On Tue, Jun 25, 2013 at 8:18 AM,
<[hidden email]> wrote:

> ------------------------------
> Message: 4
> Date: Tue, 25 Jun 2013 09:08:54 -0400
> From: Stephen Ficklin <[hidden email]>
> Subject: Re: [Gmod-tripal-devel] Tripal v1.1 Released
> To: Michael Dondrup <[hidden email]>
> Cc: gmod tripal devel <[hidden email]>,
>         gmod-tripal <[hidden email]>
> Message-ID: <[hidden email]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> 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
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 25 Jun 2013 15:09:48 +0200
> From: Michael Dondrup <[hidden email]>
> Subject: Re: [Gmod-tripal-devel] Tripal v1.1 Released
> To: Stephen Ficklin <[hidden email]>
> Cc: gmod tripal devel <[hidden email]>,
>         gmod-tripal <[hidden email]>
> Message-ID: <[hidden email]>
> Content-Type: text/plain; charset=us-ascii
>
> 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
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 25 Jun 2013 09:18:04 -0400
> From: Stephen Ficklin <[hidden email]>
> Subject: Re: [Gmod-tripal-devel] Tripal v1.1 Released
> To: Michael Dondrup <[hidden email]>
> Cc: gmod tripal devel <[hidden email]>,
>         gmod-tripal <[hidden email]>
> Message-ID: <[hidden email]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> 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
>
>
>
>
> ------------------------------
>
> ------------------------------------------------------------------------------
> 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
>
>
> End of Gmod-tripal-devel Digest, Vol 26, Issue 1
> ************************************************

------------------------------------------------------------------------------
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Re: [Gmod-tripal-devel] Gmod-tripal-devel Digest, Vol 26, Issue 1

Stephen Ficklin-2
Hi Nathan,

Thanks much for catching this.  I'll get it fixed for you.  Was this the
only module you had troubles with?  If you do not install the tripal_pub
module does all else go well for you?

Thanks,
Stephen

On 6/25/2013 2:07 PM, Nathan Weeks wrote:

> Stephen,
>
> We're using PHP 5.4.x, and are unable to upgrade to Tripal v1.1: the
> tripal_pub module appears to use syntax that was deprecated in PHP 5.3
> and removed in PHP 5.4. I've filed a bug report:
>
> https://drupal.org/node/2027915
>
> --
> Nathan Weeks
> IT Specialist
> USDA-ARS Corn Insects and Crop Genetics Research Unit
> http://weeks.public.iastate.edu/
>
>
> On Tue, Jun 25, 2013 at 8:18 AM,
> <[hidden email]> wrote:
>> ------------------------------
>> Message: 4
>> Date: Tue, 25 Jun 2013 09:08:54 -0400
>> From: Stephen Ficklin <[hidden email]>
>> Subject: Re: [Gmod-tripal-devel] Tripal v1.1 Released
>> To: Michael Dondrup <[hidden email]>
>> Cc: gmod tripal devel <[hidden email]>,
>>          gmod-tripal <[hidden email]>
>> Message-ID: <[hidden email]>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> 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
>>
>>
>>
>> ------------------------------
>>
>> Message: 5
>> Date: Tue, 25 Jun 2013 15:09:48 +0200
>> From: Michael Dondrup <[hidden email]>
>> Subject: Re: [Gmod-tripal-devel] Tripal v1.1 Released
>> To: Stephen Ficklin <[hidden email]>
>> Cc: gmod tripal devel <[hidden email]>,
>>          gmod-tripal <[hidden email]>
>> Message-ID: <[hidden email]>
>> Content-Type: text/plain; charset=us-ascii
>>
>> 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
>>
>>
>>
>> ------------------------------
>>
>> Message: 6
>> Date: Tue, 25 Jun 2013 09:18:04 -0400
>> From: Stephen Ficklin <[hidden email]>
>> Subject: Re: [Gmod-tripal-devel] Tripal v1.1 Released
>> To: Michael Dondrup <[hidden email]>
>> Cc: gmod tripal devel <[hidden email]>,
>>          gmod-tripal <[hidden email]>
>> Message-ID: <[hidden email]>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> 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
>>
>>
>>
>> ------------------------------
>>
>> ------------------------------------------------------------------------------
>> 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
>>
>>
>> End of Gmod-tripal-devel Digest, Vol 26, Issue 1
>> ************************************************


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Re: [Gmod-tripal-devel] Gmod-tripal-devel Digest, Vol 26, Issue 1

Nathan Weeks
Stephen,

If I remove the tripal_pub directory, I get the same error with
tripal_featuremap, in a call to tripal_core_create_custom_table():

=========================================
$ drush cc all
PHP Fatal error:  Call-time pass-by-reference has been removed in
/usr/local/www/drupal6/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install
on line 221

Fatal error: Call-time pass-by-reference has been removed in
/usr/local/www/drupal6/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install
on line 221
Drush command terminated abnormally due to an unrecoverable error.
                                                            [error]
Error: Call-time pass-by-reference has been removed in
/usr/local/www/drupal6/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install,
line 221
=========================================

--
Nathan Weeks
IT Specialist
USDA-ARS Corn Insects and Crop Genetics Research Unit
http://weeks.public.iastate.edu/


On Tue, Jun 25, 2013 at 1:14 PM, Stephen Ficklin <[hidden email]> wrote:

> Hi Nathan,
>
> Thanks much for catching this.  I'll get it fixed for you.  Was this the
> only module you had troubles with?  If you do not install the tripal_pub
> module does all else go well for you?
>
> Thanks,
> Stephen
>
>
> On 6/25/2013 2:07 PM, Nathan Weeks wrote:
>>
>> Stephen,
>>
>> We're using PHP 5.4.x, and are unable to upgrade to Tripal v1.1: the
>> tripal_pub module appears to use syntax that was deprecated in PHP 5.3
>> and removed in PHP 5.4. I've filed a bug report:
>>
>> https://drupal.org/node/2027915
>>
>> --
>> Nathan Weeks
>> IT Specialist
>> USDA-ARS Corn Insects and Crop Genetics Research Unit
>> http://weeks.public.iastate.edu/
>>
>>
>> On Tue, Jun 25, 2013 at 8:18 AM,
>> <[hidden email]> wrote:
>>>
>>> ------------------------------
>>> Message: 4
>>> Date: Tue, 25 Jun 2013 09:08:54 -0400
>>> From: Stephen Ficklin <[hidden email]>
>>> Subject: Re: [Gmod-tripal-devel] Tripal v1.1 Released
>>> To: Michael Dondrup <[hidden email]>
>>> Cc: gmod tripal devel <[hidden email]>,
>>>          gmod-tripal <[hidden email]>
>>> Message-ID: <[hidden email]>
>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>
>>> 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
>>>
>>>
>>>
>>>
>>> ------------------------------
>>>
>>> Message: 5
>>> Date: Tue, 25 Jun 2013 15:09:48 +0200
>>> From: Michael Dondrup <[hidden email]>
>>> Subject: Re: [Gmod-tripal-devel] Tripal v1.1 Released
>>> To: Stephen Ficklin <[hidden email]>
>>> Cc: gmod tripal devel <[hidden email]>,
>>>          gmod-tripal <[hidden email]>
>>> Message-ID: <[hidden email]>
>>> Content-Type: text/plain; charset=us-ascii
>>>
>>> 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
>>>
>>>
>>>
>>>
>>> ------------------------------
>>>
>>> Message: 6
>>> Date: Tue, 25 Jun 2013 09:18:04 -0400
>>> From: Stephen Ficklin <[hidden email]>
>>> Subject: Re: [Gmod-tripal-devel] Tripal v1.1 Released
>>> To: Michael Dondrup <[hidden email]>
>>> Cc: gmod tripal devel <[hidden email]>,
>>>          gmod-tripal <[hidden email]>
>>> Message-ID: <[hidden email]>
>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>
>>> 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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>>>
>>>
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>>>
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>>> End of Gmod-tripal-devel Digest, Vol 26, Issue 1
>>> ************************************************
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Re: [Gmod-tripal-devel] Gmod-tripal-devel Digest, Vol 26, Issue 1

Stephen Ficklin-2
Hi Nathan,

I've fixed the problem in both the featuremap and pub modules in the dev
branch.  The dev branch and v1.1 are currently identical aside from the
fix I just put.  Can you switch to the dev branch and test again?  If
this solves your problem then I'll tag it with 6.x-1.1-1

Stephen

On 6/25/2013 2:19 PM, Nathan Weeks wrote:

> Stephen,
>
> If I remove the tripal_pub directory, I get the same error with
> tripal_featuremap, in a call to tripal_core_create_custom_table():
>
> =========================================
> $ drush cc all
> PHP Fatal error:  Call-time pass-by-reference has been removed in
> /usr/local/www/drupal6/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install
> on line 221
>
> Fatal error: Call-time pass-by-reference has been removed in
> /usr/local/www/drupal6/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install
> on line 221
> Drush command terminated abnormally due to an unrecoverable error.
>                                                              [error]
> Error: Call-time pass-by-reference has been removed in
> /usr/local/www/drupal6/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install,
> line 221
> =========================================
>
> --
> Nathan Weeks
> IT Specialist
> USDA-ARS Corn Insects and Crop Genetics Research Unit
> http://weeks.public.iastate.edu/
>
>
> On Tue, Jun 25, 2013 at 1:14 PM, Stephen Ficklin <[hidden email]> wrote:
>> Hi Nathan,
>>
>> Thanks much for catching this.  I'll get it fixed for you.  Was this the
>> only module you had troubles with?  If you do not install the tripal_pub
>> module does all else go well for you?
>>
>> Thanks,
>> Stephen
>>
>>
>> On 6/25/2013 2:07 PM, Nathan Weeks wrote:
>>> Stephen,
>>>
>>> We're using PHP 5.4.x, and are unable to upgrade to Tripal v1.1: the
>>> tripal_pub module appears to use syntax that was deprecated in PHP 5.3
>>> and removed in PHP 5.4. I've filed a bug report:
>>>
>>> https://drupal.org/node/2027915
>>>
>>> --
>>> Nathan Weeks
>>> IT Specialist
>>> USDA-ARS Corn Insects and Crop Genetics Research Unit
>>> http://weeks.public.iastate.edu/
>>>
>>>
>>> On Tue, Jun 25, 2013 at 8:18 AM,
>>> <[hidden email]> wrote:
>>>> ------------------------------
>>>> Message: 4
>>>> Date: Tue, 25 Jun 2013 09:08:54 -0400
>>>> From: Stephen Ficklin <[hidden email]>
>>>> Subject: Re: [Gmod-tripal-devel] Tripal v1.1 Released
>>>> To: Michael Dondrup <[hidden email]>
>>>> Cc: gmod tripal devel <[hidden email]>,
>>>>           gmod-tripal <[hidden email]>
>>>> Message-ID: <[hidden email]>
>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>>
>>>> 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
>>>>
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 5
>>>> Date: Tue, 25 Jun 2013 15:09:48 +0200
>>>> From: Michael Dondrup <[hidden email]>
>>>> Subject: Re: [Gmod-tripal-devel] Tripal v1.1 Released
>>>> To: Stephen Ficklin <[hidden email]>
>>>> Cc: gmod tripal devel <[hidden email]>,
>>>>           gmod-tripal <[hidden email]>
>>>> Message-ID: <[hidden email]>
>>>> Content-Type: text/plain; charset=us-ascii
>>>>
>>>> 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
>>>>
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 6
>>>> Date: Tue, 25 Jun 2013 09:18:04 -0400
>>>> From: Stephen Ficklin <[hidden email]>
>>>> Subject: Re: [Gmod-tripal-devel] Tripal v1.1 Released
>>>> To: Michael Dondrup <[hidden email]>
>>>> Cc: gmod tripal devel <[hidden email]>,
>>>>           gmod-tripal <[hidden email]>
>>>> Message-ID: <[hidden email]>
>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>>
>>>> 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
>>>>
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> 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
>>>>
>>>>
>>>> End of Gmod-tripal-devel Digest, Vol 26, Issue 1
>>>> ************************************************
>>


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Re: [Gmod-tripal-devel] Gmod-tripal-devel Digest, Vol 26, Issue 1

Nathan Weeks
Hi Stephen,

Looks like one call was missed:
=====================================
$ drush cc all
PHP Fatal error:  Call-time pass-by-reference has been removed in
/usr/local/www/drupal6/sites/all/modules/tripal/tripal_pub/includes/pub_importers.inc
on line 470
Drush command terminated abnormally due to an unrecoverable error.
                                                            [error]
Error: Call-time pass-by-reference has been removed in
/usr/local/www/drupal6/sites/all/modules/tripal/tripal_pub/includes/pub_importers.inc,
line 470

Fatal error: Call-time pass-by-reference has been removed in
/usr/local/www/drupal6/sites/all/modules/tripal/tripal_pub/includes/pub_importers.inc
on line 470
=====================================

--
Nathan Weeks
IT Specialist
USDA-ARS Corn Insects and Crop Genetics Research Unit
http://weeks.public.iastate.edu/


On Tue, Jun 25, 2013 at 1:32 PM, Stephen Ficklin <[hidden email]> wrote:

> Hi Nathan,
>
> I've fixed the problem in both the featuremap and pub modules in the dev
> branch.  The dev branch and v1.1 are currently identical aside from the fix
> I just put.  Can you switch to the dev branch and test again?  If this
> solves your problem then I'll tag it with 6.x-1.1-1
>
> Stephen
>
>
> On 6/25/2013 2:19 PM, Nathan Weeks wrote:
>>
>> Stephen,
>>
>> If I remove the tripal_pub directory, I get the same error with
>> tripal_featuremap, in a call to tripal_core_create_custom_table():
>>
>> =========================================
>> $ drush cc all
>> PHP Fatal error:  Call-time pass-by-reference has been removed in
>>
>> /usr/local/www/drupal6/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install
>> on line 221
>>
>> Fatal error: Call-time pass-by-reference has been removed in
>>
>> /usr/local/www/drupal6/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install
>> on line 221
>> Drush command terminated abnormally due to an unrecoverable error.
>>                                                              [error]
>> Error: Call-time pass-by-reference has been removed in
>>
>> /usr/local/www/drupal6/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install,
>> line 221
>> =========================================
>>
>> --
>> Nathan Weeks
>> IT Specialist
>> USDA-ARS Corn Insects and Crop Genetics Research Unit
>> http://weeks.public.iastate.edu/
>>
>>
>> On Tue, Jun 25, 2013 at 1:14 PM, Stephen Ficklin <[hidden email]>
>> wrote:
>>>
>>> Hi Nathan,
>>>
>>> Thanks much for catching this.  I'll get it fixed for you.  Was this the
>>> only module you had troubles with?  If you do not install the tripal_pub
>>> module does all else go well for you?
>>>
>>> Thanks,
>>> Stephen
>>>
>>>
>>> On 6/25/2013 2:07 PM, Nathan Weeks wrote:
>>>>
>>>> Stephen,
>>>>
>>>> We're using PHP 5.4.x, and are unable to upgrade to Tripal v1.1: the
>>>> tripal_pub module appears to use syntax that was deprecated in PHP 5.3
>>>> and removed in PHP 5.4. I've filed a bug report:
>>>>
>>>> https://drupal.org/node/2027915
>>>>
>>>> --
>>>> Nathan Weeks
>>>> IT Specialist
>>>> USDA-ARS Corn Insects and Crop Genetics Research Unit
>>>> http://weeks.public.iastate.edu/
>>>>
>>>>
>>>> On Tue, Jun 25, 2013 at 8:18 AM,
>>>> <[hidden email]> wrote:
>>>>>
>>>>> ------------------------------
>>>>> Message: 4
>>>>> Date: Tue, 25 Jun 2013 09:08:54 -0400
>>>>> From: Stephen Ficklin <[hidden email]>
>>>>> Subject: Re: [Gmod-tripal-devel] Tripal v1.1 Released
>>>>> To: Michael Dondrup <[hidden email]>
>>>>> Cc: gmod tripal devel <[hidden email]>,
>>>>>           gmod-tripal <[hidden email]>
>>>>> Message-ID: <[hidden email]>
>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>>>
>>>>> 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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------
>>>>>
>>>>> Message: 5
>>>>> Date: Tue, 25 Jun 2013 15:09:48 +0200
>>>>> From: Michael Dondrup <[hidden email]>
>>>>> Subject: Re: [Gmod-tripal-devel] Tripal v1.1 Released
>>>>> To: Stephen Ficklin <[hidden email]>
>>>>> Cc: gmod tripal devel <[hidden email]>,
>>>>>           gmod-tripal <[hidden email]>
>>>>> Message-ID: <[hidden email]>
>>>>> Content-Type: text/plain; charset=us-ascii
>>>>>
>>>>> 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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------
>>>>>
>>>>> Message: 6
>>>>> Date: Tue, 25 Jun 2013 09:18:04 -0400
>>>>> From: Stephen Ficklin <[hidden email]>
>>>>> Subject: Re: [Gmod-tripal-devel] Tripal v1.1 Released
>>>>> To: Michael Dondrup <[hidden email]>
>>>>> Cc: gmod tripal devel <[hidden email]>,
>>>>>           gmod-tripal <[hidden email]>
>>>>> Message-ID: <[hidden email]>
>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>>>
>>>>> 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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> 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
>>>>>
>>>>>
>>>>> End of Gmod-tripal-devel Digest, Vol 26, Issue 1
>>>>> ************************************************
>>>
>>>
>

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Re: [Gmod-tripal-devel] Gmod-tripal-devel Digest, Vol 26, Issue 1

Stephen Ficklin-2
Whoops sorry about that.  I've fixed that one now too.

On 6/25/2013 2:41 PM, Nathan Weeks wrote:

> Hi Stephen,
>
> Looks like one call was missed:
> =====================================
> $ drush cc all
> PHP Fatal error:  Call-time pass-by-reference has been removed in
> /usr/local/www/drupal6/sites/all/modules/tripal/tripal_pub/includes/pub_importers.inc
> on line 470
> Drush command terminated abnormally due to an unrecoverable error.
>                                                              [error]
> Error: Call-time pass-by-reference has been removed in
> /usr/local/www/drupal6/sites/all/modules/tripal/tripal_pub/includes/pub_importers.inc,
> line 470
>
> Fatal error: Call-time pass-by-reference has been removed in
> /usr/local/www/drupal6/sites/all/modules/tripal/tripal_pub/includes/pub_importers.inc
> on line 470
> =====================================
>
> --
> Nathan Weeks
> IT Specialist
> USDA-ARS Corn Insects and Crop Genetics Research Unit
> http://weeks.public.iastate.edu/
>
>
> On Tue, Jun 25, 2013 at 1:32 PM, Stephen Ficklin <[hidden email]> wrote:
>> Hi Nathan,
>>
>> I've fixed the problem in both the featuremap and pub modules in the dev
>> branch.  The dev branch and v1.1 are currently identical aside from the fix
>> I just put.  Can you switch to the dev branch and test again?  If this
>> solves your problem then I'll tag it with 6.x-1.1-1
>>
>> Stephen
>>
>>
>> On 6/25/2013 2:19 PM, Nathan Weeks wrote:
>>> Stephen,
>>>
>>> If I remove the tripal_pub directory, I get the same error with
>>> tripal_featuremap, in a call to tripal_core_create_custom_table():
>>>
>>> =========================================
>>> $ drush cc all
>>> PHP Fatal error:  Call-time pass-by-reference has been removed in
>>>
>>> /usr/local/www/drupal6/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install
>>> on line 221
>>>
>>> Fatal error: Call-time pass-by-reference has been removed in
>>>
>>> /usr/local/www/drupal6/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install
>>> on line 221
>>> Drush command terminated abnormally due to an unrecoverable error.
>>>                                                               [error]
>>> Error: Call-time pass-by-reference has been removed in
>>>
>>> /usr/local/www/drupal6/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install,
>>> line 221
>>> =========================================
>>>
>>> --
>>> Nathan Weeks
>>> IT Specialist
>>> USDA-ARS Corn Insects and Crop Genetics Research Unit
>>> http://weeks.public.iastate.edu/
>>>
>>>
>>> On Tue, Jun 25, 2013 at 1:14 PM, Stephen Ficklin <[hidden email]>
>>> wrote:
>>>> Hi Nathan,
>>>>
>>>> Thanks much for catching this.  I'll get it fixed for you.  Was this the
>>>> only module you had troubles with?  If you do not install the tripal_pub
>>>> module does all else go well for you?
>>>>
>>>> Thanks,
>>>> Stephen
>>>>
>>>>
>>>> On 6/25/2013 2:07 PM, Nathan Weeks wrote:
>>>>> Stephen,
>>>>>
>>>>> We're using PHP 5.4.x, and are unable to upgrade to Tripal v1.1: the
>>>>> tripal_pub module appears to use syntax that was deprecated in PHP 5.3
>>>>> and removed in PHP 5.4. I've filed a bug report:
>>>>>
>>>>> https://drupal.org/node/2027915
>>>>>
>>>>> --
>>>>> Nathan Weeks
>>>>> IT Specialist
>>>>> USDA-ARS Corn Insects and Crop Genetics Research Unit
>>>>> http://weeks.public.iastate.edu/
>>>>>
>>>>>
>>>>> On Tue, Jun 25, 2013 at 8:18 AM,
>>>>> <[hidden email]> wrote:
>>>>>> ------------------------------
>>>>>> Message: 4
>>>>>> Date: Tue, 25 Jun 2013 09:08:54 -0400
>>>>>> From: Stephen Ficklin <[hidden email]>
>>>>>> Subject: Re: [Gmod-tripal-devel] Tripal v1.1 Released
>>>>>> To: Michael Dondrup <[hidden email]>
>>>>>> Cc: gmod tripal devel <[hidden email]>,
>>>>>>            gmod-tripal <[hidden email]>
>>>>>> Message-ID: <[hidden email]>
>>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>>>>
>>>>>> 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
>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 5
>>>>>> Date: Tue, 25 Jun 2013 15:09:48 +0200
>>>>>> From: Michael Dondrup <[hidden email]>
>>>>>> Subject: Re: [Gmod-tripal-devel] Tripal v1.1 Released
>>>>>> To: Stephen Ficklin <[hidden email]>
>>>>>> Cc: gmod tripal devel <[hidden email]>,
>>>>>>            gmod-tripal <[hidden email]>
>>>>>> Message-ID: <[hidden email]>
>>>>>> Content-Type: text/plain; charset=us-ascii
>>>>>>
>>>>>> 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
>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 6
>>>>>> Date: Tue, 25 Jun 2013 09:18:04 -0400
>>>>>> From: Stephen Ficklin <[hidden email]>
>>>>>> Subject: Re: [Gmod-tripal-devel] Tripal v1.1 Released
>>>>>> To: Michael Dondrup <[hidden email]>
>>>>>> Cc: gmod tripal devel <[hidden email]>,
>>>>>>            gmod-tripal <[hidden email]>
>>>>>> Message-ID: <[hidden email]>
>>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>>>>
>>>>>> 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
>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> 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
>>>>>>
>>>>>>
>>>>>> End of Gmod-tripal-devel Digest, Vol 26, Issue 1
>>>>>> ************************************************
>>>>


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Re: [Gmod-tripal-devel] Gmod-tripal-devel Digest, Vol 26, Issue 1

Nathan Weeks
Same thing in another spot:
=================================
$ drush pm-list
PHP Fatal error:  Call-time pass-by-reference has been removed in
/usr/local/www/drupal6/sites/all/modules/tripal/tripal_pub/includes/importers/AGL.inc
on line 332
Drush command terminated abnormally due to an unrecoverable error.
                                                            [error]
Error: Call-time pass-by-reference has been removed in
/usr/local/www/drupal6/sites/all/modules/tripal/tripal_pub/includes/importers/AGL.inc,
line 332

Fatal error: Call-time pass-by-reference has been removed in
/usr/local/www/drupal6/sites/all/modules/tripal/tripal_pub/includes/importers/AGL.inc
on line 332
=================================

--
Nathan Weeks
IT Specialist
USDA-ARS Corn Insects and Crop Genetics Research Unit
http://weeks.public.iastate.edu/


On Tue, Jun 25, 2013 at 1:50 PM, Stephen Ficklin <[hidden email]> wrote:

> Whoops sorry about that.  I've fixed that one now too.
>
>
> On 6/25/2013 2:41 PM, Nathan Weeks wrote:
>>
>> Hi Stephen,
>>
>> Looks like one call was missed:
>> =====================================
>> $ drush cc all
>> PHP Fatal error:  Call-time pass-by-reference has been removed in
>>
>> /usr/local/www/drupal6/sites/all/modules/tripal/tripal_pub/includes/pub_importers.inc
>> on line 470
>> Drush command terminated abnormally due to an unrecoverable error.
>>                                                              [error]
>> Error: Call-time pass-by-reference has been removed in
>>
>> /usr/local/www/drupal6/sites/all/modules/tripal/tripal_pub/includes/pub_importers.inc,
>> line 470
>>
>> Fatal error: Call-time pass-by-reference has been removed in
>>
>> /usr/local/www/drupal6/sites/all/modules/tripal/tripal_pub/includes/pub_importers.inc
>> on line 470
>> =====================================
>>
>> --
>> Nathan Weeks
>> IT Specialist
>> USDA-ARS Corn Insects and Crop Genetics Research Unit
>> http://weeks.public.iastate.edu/
>>
>>
>> On Tue, Jun 25, 2013 at 1:32 PM, Stephen Ficklin <[hidden email]>
>> wrote:
>>>
>>> Hi Nathan,
>>>
>>> I've fixed the problem in both the featuremap and pub modules in the dev
>>> branch.  The dev branch and v1.1 are currently identical aside from the
>>> fix
>>> I just put.  Can you switch to the dev branch and test again?  If this
>>> solves your problem then I'll tag it with 6.x-1.1-1
>>>
>>> Stephen
>>>
>>>
>>> On 6/25/2013 2:19 PM, Nathan Weeks wrote:
>>>>
>>>> Stephen,
>>>>
>>>> If I remove the tripal_pub directory, I get the same error with
>>>> tripal_featuremap, in a call to tripal_core_create_custom_table():
>>>>
>>>> =========================================
>>>> $ drush cc all
>>>> PHP Fatal error:  Call-time pass-by-reference has been removed in
>>>>
>>>>
>>>> /usr/local/www/drupal6/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install
>>>> on line 221
>>>>
>>>> Fatal error: Call-time pass-by-reference has been removed in
>>>>
>>>>
>>>> /usr/local/www/drupal6/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install
>>>> on line 221
>>>> Drush command terminated abnormally due to an unrecoverable error.
>>>>                                                               [error]
>>>> Error: Call-time pass-by-reference has been removed in
>>>>
>>>>
>>>> /usr/local/www/drupal6/sites/all/modules/tripal/tripal_featuremap/tripal_featuremap.install,
>>>> line 221
>>>> =========================================
>>>>
>>>> --
>>>> Nathan Weeks
>>>> IT Specialist
>>>> USDA-ARS Corn Insects and Crop Genetics Research Unit
>>>> http://weeks.public.iastate.edu/
>>>>
>>>>
>>>> On Tue, Jun 25, 2013 at 1:14 PM, Stephen Ficklin <[hidden email]>
>>>> wrote:
>>>>>
>>>>> Hi Nathan,
>>>>>
>>>>> Thanks much for catching this.  I'll get it fixed for you.  Was this
>>>>> the
>>>>> only module you had troubles with?  If you do not install the
>>>>> tripal_pub
>>>>> module does all else go well for you?
>>>>>
>>>>> Thanks,
>>>>> Stephen
>>>>>
>>>>>
>>>>> On 6/25/2013 2:07 PM, Nathan Weeks wrote:
>>>>>>
>>>>>> Stephen,
>>>>>>
>>>>>> We're using PHP 5.4.x, and are unable to upgrade to Tripal v1.1: the
>>>>>> tripal_pub module appears to use syntax that was deprecated in PHP 5.3
>>>>>> and removed in PHP 5.4. I've filed a bug report:
>>>>>>
>>>>>> https://drupal.org/node/2027915
>>>>>>
>>>>>> --
>>>>>> Nathan Weeks
>>>>>> IT Specialist
>>>>>> USDA-ARS Corn Insects and Crop Genetics Research Unit
>>>>>> http://weeks.public.iastate.edu/
>>>>>>
>>>>>>
>>>>>> On Tue, Jun 25, 2013 at 8:18 AM,
>>>>>> <[hidden email]> wrote:
>>>>>>>
>>>>>>> ------------------------------
>>>>>>> Message: 4
>>>>>>> Date: Tue, 25 Jun 2013 09:08:54 -0400
>>>>>>> From: Stephen Ficklin <[hidden email]>
>>>>>>> Subject: Re: [Gmod-tripal-devel] Tripal v1.1 Released
>>>>>>> To: Michael Dondrup <[hidden email]>
>>>>>>> Cc: gmod tripal devel <[hidden email]>,
>>>>>>>            gmod-tripal <[hidden email]>
>>>>>>> Message-ID: <[hidden email]>
>>>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>>>>>
>>>>>>> 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
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------
>>>>>>>
>>>>>>> Message: 5
>>>>>>> Date: Tue, 25 Jun 2013 15:09:48 +0200
>>>>>>> From: Michael Dondrup <[hidden email]>
>>>>>>> Subject: Re: [Gmod-tripal-devel] Tripal v1.1 Released
>>>>>>> To: Stephen Ficklin <[hidden email]>
>>>>>>> Cc: gmod tripal devel <[hidden email]>,
>>>>>>>            gmod-tripal <[hidden email]>
>>>>>>> Message-ID: <[hidden email]>
>>>>>>> Content-Type: text/plain; charset=us-ascii
>>>>>>>
>>>>>>> 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
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------
>>>>>>>
>>>>>>> Message: 6
>>>>>>> Date: Tue, 25 Jun 2013 09:18:04 -0400
>>>>>>> From: Stephen Ficklin <[hidden email]>
>>>>>>> Subject: Re: [Gmod-tripal-devel] Tripal v1.1 Released
>>>>>>> To: Michael Dondrup <[hidden email]>
>>>>>>> Cc: gmod tripal devel <[hidden email]>,
>>>>>>>            gmod-tripal <[hidden email]>
>>>>>>> Message-ID: <[hidden email]>
>>>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>>>>>
>>>>>>> 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
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> 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
>>>>>>>
>>>>>>>
>>>>>>> End of Gmod-tripal-devel Digest, Vol 26, Issue 1
>>>>>>> ************************************************
>>>>>
>>>>>
>

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