User permissions and Tripal content nodes

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User permissions and Tripal content nodes

Scott Cain
Hi Stephen,

I have what is probably a fairly dumb question, but here goes:  I've created a sample Tripal install at cloud.gmod.org, including a guest account (you can probably guess the password), but the problem is that user doesn't have permission to see actual Tripal nodes like gene and organism pages.  I've set all of the Tripal "access" permissions for authenticated users, but I still get the permission denied message for those nodes.  Any idea what I'm doing wrong?

Thanks,
Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: User permissions and Tripal content nodes

Lacey-Anne Sanderson
Hi Scott,

There is currently a bug in our permissions, in so far as they don't actually work. In order for people to get access to organism and feature pages you need to give that user "access nodes" permissions which unfortunately allows them to access all nodes. I haven't had the chance to dig further into this problem... maybe Stephen has?

~Lacey

PS. The discussion about this is in "Re: [Gmod-tripal] Missing Edit Tab (Features and Stocks)"

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-2430
Room 3D10 Agriculture
Department of Plant Sciences
University of Saskatchewan

On 2011-11-02, at 3:38 PM, Scott Cain wrote:

Hi Stephen,

I have what is probably a fairly dumb question, but here goes:  I've created a sample Tripal install at cloud.gmod.org, including a guest account (you can probably guess the password), but the problem is that user doesn't have permission to see actual Tripal nodes like gene and organism pages.  I've set all of the Tripal "access" permissions for authenticated users, but I still get the permission denied message for those nodes.  Any idea what I'm doing wrong?

Thanks,
Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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Register now
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Re: User permissions and Tripal content nodes

Scott Cain
Hi Lacey-Anne,

I gave "access content" under the Nodes module section; this is what you're referring to, right?  That doesn't seem to help.

Scott


On Wed, Nov 2, 2011 at 6:20 PM, Lacey-Anne Sanderson <[hidden email]> wrote:
Hi Scott,

There is currently a bug in our permissions, in so far as they don't actually work. In order for people to get access to organism and feature pages you need to give that user "access nodes" permissions which unfortunately allows them to access all nodes. I haven't had the chance to dig further into this problem... maybe Stephen has?

~Lacey

PS. The discussion about this is in "Re: [Gmod-tripal] Missing Edit Tab (Features and Stocks)"

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: <a href="tel:%28306%29%20966-2430" value="+13069662430" target="_blank">(306) 966-2430
Room 3D10 Agriculture
Department of Plant Sciences
University of Saskatchewan

On 2011-11-02, at 3:38 PM, Scott Cain wrote:

Hi Stephen,

I have what is probably a fairly dumb question, but here goes:  I've created a sample Tripal install at cloud.gmod.org, including a guest account (you can probably guess the password), but the problem is that user doesn't have permission to see actual Tripal nodes like gene and organism pages.  I've set all of the Tripal "access" permissions for authenticated users, but I still get the permission denied message for those nodes.  Any idea what I'm doing wrong?

Thanks,
Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research
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RSA(R) Conference 2012
Save $700 by Nov 18
Register now
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: User permissions and Tripal content nodes

Scott Cain
Ok, I'm zeroing in on the problem.  The attached picture shows the story; the nodes are not marked viewable.  I tried going to the content admin page and making it viewable for authenticated and anonymous users and it failed for feature nodes (unable to update feature), but I was able to update the organism node to make it viewable for all users.  Any ideas?

Thanks,
Scott


On Wed, Nov 2, 2011 at 6:38 PM, Scott Cain <[hidden email]> wrote:
Hi Lacey-Anne,

I gave "access content" under the Nodes module section; this is what you're referring to, right?  That doesn't seem to help.

Scott



On Wed, Nov 2, 2011 at 6:20 PM, Lacey-Anne Sanderson <[hidden email]> wrote:
Hi Scott,

There is currently a bug in our permissions, in so far as they don't actually work. In order for people to get access to organism and feature pages you need to give that user "access nodes" permissions which unfortunately allows them to access all nodes. I haven't had the chance to dig further into this problem... maybe Stephen has?

~Lacey

PS. The discussion about this is in "Re: [Gmod-tripal] Missing Edit Tab (Features and Stocks)"

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: <a href="tel:%28306%29%20966-2430" value="+13069662430" target="_blank">(306) 966-2430
Room 3D10 Agriculture
Department of Plant Sciences
University of Saskatchewan

On 2011-11-02, at 3:38 PM, Scott Cain wrote:

Hi Stephen,

I have what is probably a fairly dumb question, but here goes:  I've created a sample Tripal install at cloud.gmod.org, including a guest account (you can probably guess the password), but the problem is that user doesn't have permission to see actual Tripal nodes like gene and organism pages.  I've set all of the Tripal "access" permissions for authenticated users, but I still get the permission denied message for those nodes.  Any idea what I'm doing wrong?

Thanks,
Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research
------------------------------------------------------------------------------
RSA(R) Conference 2012
Save $700 by Nov 18
Register now
http://p.sf.net/sfu/rsa-sfdev2dev1_______________________________________________
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[hidden email]
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
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Register now
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Re: User permissions and Tripal content nodes

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

Are you using any type of permissions module such as "Privacy by Role" other than just the default Drupal access permissions?   Using the default permission management that comes with Drupal should allow you to set this up.  We use permissions on the Cacao genome site in this way to only allow view of gene pages, etc to authenticated users.  Also, I just tested it again on my development version of Tripal.  I created a guest account and enabled access for only authenticated users and it worked.

Lacey and I both had problems with permission on some of our sites. I discovered that my problem was an incompatiblity with the "Privacy by Role" module.  As soon as I disabled that module things were fine.

If you are not using any other type of permission management module I have found that every now and then Drupal gets out of whack with permissions and you have to rebuild the node permissions under 'Administer' -> 'Content Mangement' -> 'Post Settings'.  That step may take awhile if you have a lot of feature pages.

Let me know if any of that helps.  If not I'll be happy to help you debug this.

Stephen

On 11/2/2011 6:38 PM, Scott Cain wrote:
Hi Lacey-Anne,

I gave "access content" under the Nodes module section; this is what you're referring to, right?  That doesn't seem to help.

Scott


On Wed, Nov 2, 2011 at 6:20 PM, Lacey-Anne Sanderson <[hidden email]> wrote:
Hi Scott,

There is currently a bug in our permissions, in so far as they don't actually work. In order for people to get access to organism and feature pages you need to give that user "access nodes" permissions which unfortunately allows them to access all nodes. I haven't had the chance to dig further into this problem... maybe Stephen has?

~Lacey

PS. The discussion about this is in "Re: [Gmod-tripal] Missing Edit Tab (Features and Stocks)"

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: <a moz-do-not-send="true" href="tel:%28306%29%20966-2430" value="+13069662430" target="_blank">(306) 966-2430
Room 3D10 Agriculture
Department of Plant Sciences
University of Saskatchewan

On 2011-11-02, at 3:38 PM, Scott Cain wrote:

Hi Stephen,

I have what is probably a fairly dumb question, but here goes:  I've created a sample Tripal install at cloud.gmod.org, including a guest account (you can probably guess the password), but the problem is that user doesn't have permission to see actual Tripal nodes like gene and organism pages.  I've set all of the Tripal "access" permissions for authenticated users, but I still get the permission denied message for those nodes.  Any idea what I'm doing wrong?

Thanks,
Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a moz-do-not-send="true" href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research
------------------------------------------------------------------------------
RSA(R) Conference 2012
Save $700 by Nov 18
Register now
http://p.sf.net/sfu/rsa-sfdev2dev1_______________________________________________
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[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
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Save $700 by Nov 18
Register now
http://p.sf.net/sfu/rsa-sfdev2dev1
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Re: User permissions and Tripal content nodes

Scott Cain
Hi Stephen,

I think we're getting close to the source of the problem.  In this database, I had a problem with the GFF file I loaded, so I deleted the entire contents of the Chado feature table:

  DELETE FROM chado.feature;

and then reloaded the GFF file through Tripal and synced features again.  Now, when i tried to rebuild permissions, it gets to 50% done and then dies with a 500 error, though nothing apparently useful went into the error.log.  It doesn't seem like a coincidence that the number of nodes is twice the size of the number of features that should be in the Chado feature table, and the rebuild died at 50%, don't you think?  So did my deleting features via SQL do something to the Drupal side of the database?

Thanks,
Scott
 

On Thu, Nov 3, 2011 at 4:48 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Scott,

Are you using any type of permissions module such as "Privacy by Role" other than just the default Drupal access permissions?   Using the default permission management that comes with Drupal should allow you to set this up.  We use permissions on the Cacao genome site in this way to only allow view of gene pages, etc to authenticated users.  Also, I just tested it again on my development version of Tripal.  I created a guest account and enabled access for only authenticated users and it worked.

Lacey and I both had problems with permission on some of our sites. I discovered that my problem was an incompatiblity with the "Privacy by Role" module.  As soon as I disabled that module things were fine.

If you are not using any other type of permission management module I have found that every now and then Drupal gets out of whack with permissions and you have to rebuild the node permissions under 'Administer' -> 'Content Mangement' -> 'Post Settings'.  That step may take awhile if you have a lot of feature pages.

Let me know if any of that helps.  If not I'll be happy to help you debug this.

Stephen


On 11/2/2011 6:38 PM, Scott Cain wrote:
Hi Lacey-Anne,

I gave "access content" under the Nodes module section; this is what you're referring to, right?  That doesn't seem to help.

Scott


On Wed, Nov 2, 2011 at 6:20 PM, Lacey-Anne Sanderson <[hidden email]> wrote:
Hi Scott,

There is currently a bug in our permissions, in so far as they don't actually work. In order for people to get access to organism and feature pages you need to give that user "access nodes" permissions which unfortunately allows them to access all nodes. I haven't had the chance to dig further into this problem... maybe Stephen has?

~Lacey

PS. The discussion about this is in "Re: [Gmod-tripal] Missing Edit Tab (Features and Stocks)"

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: <a href="tel:%28306%29%20966-2430" value="+13069662430" target="_blank">(306) 966-2430
Room 3D10 Agriculture
Department of Plant Sciences
University of Saskatchewan

On 2011-11-02, at 3:38 PM, Scott Cain wrote:

Hi Stephen,

I have what is probably a fairly dumb question, but here goes:  I've created a sample Tripal install at cloud.gmod.org, including a guest account (you can probably guess the password), but the problem is that user doesn't have permission to see actual Tripal nodes like gene and organism pages.  I've set all of the Tripal "access" permissions for authenticated users, but I still get the permission denied message for those nodes.  Any idea what I'm doing wrong?

Thanks,
Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research
------------------------------------------------------------------------------
RSA(R) Conference 2012
Save $700 by Nov 18
Register now
http://p.sf.net/sfu/rsa-sfdev2dev1_______________________________________________
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[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
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Save $700 by Nov 18
Register now
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Re: User permissions and Tripal content nodes

Stephen Ficklin-2
Hi Scott,

If you manually delete features from Chado after you've synced with Drupal then those Drupal nodes will still be around.  And you'd need to get rid of those too.  But this is okay, as we can't expect folks to not manually do things in the database.   There is functionality at the bottom of the Tripal feature configuration page called "Clean Up".  If you click that button and run the job it will cleanup any nodes in Drupal that don't have a corresponding record in Chado.   So try that and see if it fixes the problem with resetting node permissions.  By the way, how many features do you have pages for in Drupal?  Just curious.
.
Also, we do have a feature delete page in Tripal (Administer -> Tripal management -> Features -> Delete Features which if you use that will delete both features in Chado and the Drupal content.

Stephen

On 11/3/2011 10:00 AM, Scott Cain wrote:
Hi Stephen,

I think we're getting close to the source of the problem.  In this database, I had a problem with the GFF file I loaded, so I deleted the entire contents of the Chado feature table:

  DELETE FROM chado.feature;

and then reloaded the GFF file through Tripal and synced features again.  Now, when i tried to rebuild permissions, it gets to 50% done and then dies with a 500 error, though nothing apparently useful went into the error.log.  It doesn't seem like a coincidence that the number of nodes is twice the size of the number of features that should be in the Chado feature table, and the rebuild died at 50%, don't you think?  So did my deleting features via SQL do something to the Drupal side of the database?

Thanks,
Scott
 

On Thu, Nov 3, 2011 at 4:48 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Scott,

Are you using any type of permissions module such as "Privacy by Role" other than just the default Drupal access permissions?   Using the default permission management that comes with Drupal should allow you to set this up.  We use permissions on the Cacao genome site in this way to only allow view of gene pages, etc to authenticated users.  Also, I just tested it again on my development version of Tripal.  I created a guest account and enabled access for only authenticated users and it worked.

Lacey and I both had problems with permission on some of our sites. I discovered that my problem was an incompatiblity with the "Privacy by Role" module.  As soon as I disabled that module things were fine.

If you are not using any other type of permission management module I have found that every now and then Drupal gets out of whack with permissions and you have to rebuild the node permissions under 'Administer' -> 'Content Mangement' -> 'Post Settings'.  That step may take awhile if you have a lot of feature pages.

Let me know if any of that helps.  If not I'll be happy to help you debug this.

Stephen


On 11/2/2011 6:38 PM, Scott Cain wrote:
Hi Lacey-Anne,

I gave "access content" under the Nodes module section; this is what you're referring to, right?  That doesn't seem to help.

Scott


On Wed, Nov 2, 2011 at 6:20 PM, Lacey-Anne Sanderson <[hidden email]> wrote:
Hi Scott,

There is currently a bug in our permissions, in so far as they don't actually work. In order for people to get access to organism and feature pages you need to give that user "access nodes" permissions which unfortunately allows them to access all nodes. I haven't had the chance to dig further into this problem... maybe Stephen has?

~Lacey

PS. The discussion about this is in "Re: [Gmod-tripal] Missing Edit Tab (Features and Stocks)"

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: <a moz-do-not-send="true" href="tel:%28306%29%20966-2430" value="+13069662430" target="_blank">(306) 966-2430
Room 3D10 Agriculture
Department of Plant Sciences
University of Saskatchewan

On 2011-11-02, at 3:38 PM, Scott Cain wrote:

Hi Stephen,

I have what is probably a fairly dumb question, but here goes:  I've created a sample Tripal install at cloud.gmod.org, including a guest account (you can probably guess the password), but the problem is that user doesn't have permission to see actual Tripal nodes like gene and organism pages.  I've set all of the Tripal "access" permissions for authenticated users, but I still get the permission denied message for those nodes.  Any idea what I'm doing wrong?

Thanks,
Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a moz-do-not-send="true" href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research
------------------------------------------------------------------------------
RSA(R) Conference 2012
Save $700 by Nov 18
Register now
http://p.sf.net/sfu/rsa-sfdev2dev1_______________________________________________
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[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a moz-do-not-send="true" href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
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Register now
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Re: User permissions and Tripal content nodes

Scott Cain
Hi Stephen,

Well, shoot.  I did clean up, sync features and rebuild permissions, and the rebuild still dies at 50% complete and I get permission denied for feature node pages.  There are only about 16,000 feature nodes.  Any other ideas?  If you want, you can send me a public key that I can put in the authorized_keys file on this machine and you can log in.  I can also tell you off line what the admin user password is.

About the feature delete functionality: can I just select an organism and delete all features (rather than supplying types or feature uniquenames)?

Thanks,
Scott


On Thu, Nov 3, 2011 at 10:12 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Scott,

If you manually delete features from Chado after you've synced with Drupal then those Drupal nodes will still be around.  And you'd need to get rid of those too.  But this is okay, as we can't expect folks to not manually do things in the database.   There is functionality at the bottom of the Tripal feature configuration page called "Clean Up".  If you click that button and run the job it will cleanup any nodes in Drupal that don't have a corresponding record in Chado.   So try that and see if it fixes the problem with resetting node permissions.  By the way, how many features do you have pages for in Drupal?  Just curious.
.
Also, we do have a feature delete page in Tripal (Administer -> Tripal management -> Features -> Delete Features which if you use that will delete both features in Chado and the Drupal content.

Stephen


On 11/3/2011 10:00 AM, Scott Cain wrote:
Hi Stephen,

I think we're getting close to the source of the problem.  In this database, I had a problem with the GFF file I loaded, so I deleted the entire contents of the Chado feature table:

  DELETE FROM chado.feature;

and then reloaded the GFF file through Tripal and synced features again.  Now, when i tried to rebuild permissions, it gets to 50% done and then dies with a 500 error, though nothing apparently useful went into the error.log.  It doesn't seem like a coincidence that the number of nodes is twice the size of the number of features that should be in the Chado feature table, and the rebuild died at 50%, don't you think?  So did my deleting features via SQL do something to the Drupal side of the database?

Thanks,
Scott
 

On Thu, Nov 3, 2011 at 4:48 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Scott,

Are you using any type of permissions module such as "Privacy by Role" other than just the default Drupal access permissions?   Using the default permission management that comes with Drupal should allow you to set this up.  We use permissions on the Cacao genome site in this way to only allow view of gene pages, etc to authenticated users.  Also, I just tested it again on my development version of Tripal.  I created a guest account and enabled access for only authenticated users and it worked.

Lacey and I both had problems with permission on some of our sites. I discovered that my problem was an incompatiblity with the "Privacy by Role" module.  As soon as I disabled that module things were fine.

If you are not using any other type of permission management module I have found that every now and then Drupal gets out of whack with permissions and you have to rebuild the node permissions under 'Administer' -> 'Content Mangement' -> 'Post Settings'.  That step may take awhile if you have a lot of feature pages.

Let me know if any of that helps.  If not I'll be happy to help you debug this.

Stephen


On 11/2/2011 6:38 PM, Scott Cain wrote:
Hi Lacey-Anne,

I gave "access content" under the Nodes module section; this is what you're referring to, right?  That doesn't seem to help.

Scott


On Wed, Nov 2, 2011 at 6:20 PM, Lacey-Anne Sanderson <[hidden email]> wrote:
Hi Scott,

There is currently a bug in our permissions, in so far as they don't actually work. In order for people to get access to organism and feature pages you need to give that user "access nodes" permissions which unfortunately allows them to access all nodes. I haven't had the chance to dig further into this problem... maybe Stephen has?

~Lacey

PS. The discussion about this is in "Re: [Gmod-tripal] Missing Edit Tab (Features and Stocks)"

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: <a href="tel:%28306%29%20966-2430" value="+13069662430" target="_blank">(306) 966-2430
Room 3D10 Agriculture
Department of Plant Sciences
University of Saskatchewan

On 2011-11-02, at 3:38 PM, Scott Cain wrote:

Hi Stephen,

I have what is probably a fairly dumb question, but here goes:  I've created a sample Tripal install at cloud.gmod.org, including a guest account (you can probably guess the password), but the problem is that user doesn't have permission to see actual Tripal nodes like gene and organism pages.  I've set all of the Tripal "access" permissions for authenticated users, but I still get the permission denied message for those nodes.  Any idea what I'm doing wrong?

Thanks,
Scott


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Scott Cain, Ph. D.                                   scott at scottcain dot net
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Ontario Institute for Cancer Research




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Scott Cain, Ph. D.                                   scott at scottcain dot net
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Ontario Institute for Cancer Research

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Re: User permissions and Tripal content nodes

Stephen Ficklin-2
Hi Scott,

I'll send you a public key, offline, in a bit. 

Yes, I believe you should be able to select an organism and delete all features for the organism.

Stephen

On 11/3/2011 11:16 AM, Scott Cain wrote:
Hi Stephen,

Well, shoot.  I did clean up, sync features and rebuild permissions, and the rebuild still dies at 50% complete and I get permission denied for feature node pages.  There are only about 16,000 feature nodes.  Any other ideas?  If you want, you can send me a public key that I can put in the authorized_keys file on this machine and you can log in.  I can also tell you off line what the admin user password is.

About the feature delete functionality: can I just select an organism and delete all features (rather than supplying types or feature uniquenames)?

Thanks,
Scott


On Thu, Nov 3, 2011 at 10:12 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Scott,

If you manually delete features from Chado after you've synced with Drupal then those Drupal nodes will still be around.  And you'd need to get rid of those too.  But this is okay, as we can't expect folks to not manually do things in the database.   There is functionality at the bottom of the Tripal feature configuration page called "Clean Up".  If you click that button and run the job it will cleanup any nodes in Drupal that don't have a corresponding record in Chado.   So try that and see if it fixes the problem with resetting node permissions.  By the way, how many features do you have pages for in Drupal?  Just curious.
.
Also, we do have a feature delete page in Tripal (Administer -> Tripal management -> Features -> Delete Features which if you use that will delete both features in Chado and the Drupal content.

Stephen


On 11/3/2011 10:00 AM, Scott Cain wrote:
Hi Stephen,

I think we're getting close to the source of the problem.  In this database, I had a problem with the GFF file I loaded, so I deleted the entire contents of the Chado feature table:

  DELETE FROM chado.feature;

and then reloaded the GFF file through Tripal and synced features again.  Now, when i tried to rebuild permissions, it gets to 50% done and then dies with a 500 error, though nothing apparently useful went into the error.log.  It doesn't seem like a coincidence that the number of nodes is twice the size of the number of features that should be in the Chado feature table, and the rebuild died at 50%, don't you think?  So did my deleting features via SQL do something to the Drupal side of the database?

Thanks,
Scott
 

On Thu, Nov 3, 2011 at 4:48 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Scott,

Are you using any type of permissions module such as "Privacy by Role" other than just the default Drupal access permissions?   Using the default permission management that comes with Drupal should allow you to set this up.  We use permissions on the Cacao genome site in this way to only allow view of gene pages, etc to authenticated users.  Also, I just tested it again on my development version of Tripal.  I created a guest account and enabled access for only authenticated users and it worked.

Lacey and I both had problems with permission on some of our sites. I discovered that my problem was an incompatiblity with the "Privacy by Role" module.  As soon as I disabled that module things were fine.

If you are not using any other type of permission management module I have found that every now and then Drupal gets out of whack with permissions and you have to rebuild the node permissions under 'Administer' -> 'Content Mangement' -> 'Post Settings'.  That step may take awhile if you have a lot of feature pages.

Let me know if any of that helps.  If not I'll be happy to help you debug this.

Stephen


On 11/2/2011 6:38 PM, Scott Cain wrote:
Hi Lacey-Anne,

I gave "access content" under the Nodes module section; this is what you're referring to, right?  That doesn't seem to help.

Scott


On Wed, Nov 2, 2011 at 6:20 PM, Lacey-Anne Sanderson <[hidden email]> wrote:
Hi Scott,

There is currently a bug in our permissions, in so far as they don't actually work. In order for people to get access to organism and feature pages you need to give that user "access nodes" permissions which unfortunately allows them to access all nodes. I haven't had the chance to dig further into this problem... maybe Stephen has?

~Lacey

PS. The discussion about this is in "Re: [Gmod-tripal] Missing Edit Tab (Features and Stocks)"

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: <a moz-do-not-send="true" href="tel:%28306%29%20966-2430" value="+13069662430" target="_blank">(306) 966-2430
Room 3D10 Agriculture
Department of Plant Sciences
University of Saskatchewan

On 2011-11-02, at 3:38 PM, Scott Cain wrote:

Hi Stephen,

I have what is probably a fairly dumb question, but here goes:  I've created a sample Tripal install at cloud.gmod.org, including a guest account (you can probably guess the password), but the problem is that user doesn't have permission to see actual Tripal nodes like gene and organism pages.  I've set all of the Tripal "access" permissions for authenticated users, but I still get the permission denied message for those nodes.  Any idea what I'm doing wrong?

Thanks,
Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a moz-do-not-send="true" href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research
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Save $700 by Nov 18
Register now
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a moz-do-not-send="true" href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a moz-do-not-send="true" href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


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