[Gmod-tripal-devel] Some problems related to Tripal Features, follow up on a tripal update

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[Gmod-tripal-devel] Some problems related to Tripal Features, follow up on a tripal update

Michael Dondrup-3
Hi,

following an ~2 month update process to D7/Tripal 2 of LiceBase, we now have resolved all outstanding issues,
greatly thanks to Stephen and the Tripal community. We are now in the process of honing off the few remaining issues. 
These three are all related to the Tripal Feature module and we are not sure if they are caused by the update. I will just list them below,
I can also add them to the issue tracker if you like.

1. Features don’t appear to respect the ‘View’ permission. We tested if an anonymous user can view Features even though the View Features permission is off in the permission table. We tested this case also using the output of Devel Node Access, and it suggests that any feature is using the default node View permission for published content from the Node permissions. The other CRUD permissions ‘Create’, ‘Update’, ‘Delete’  seem to be ok. As a result, anonymous is either able to see the site including all features or not able to use it at all. I remember this was different in Tripal 1.

A typical Debug output of the permission set per user who has full access looks like:

username create view update delete
user YES: by node (permissions) YES: {node_access} YES: by node (permissions) YES: by node (permissions)
with the explanation YES: hook_node_access() of the following module(s) allows this: node (permissions).

This makes me wonder whether there is something missing for hook_node_access().
Please see the attached screen shots for an explanation of our Permission settings.

2. The site search doesn’t seem to find the updated Feature pages. I have re-indexed the site via admin/config/search/settings, but that doesn’t seem 
to have an effect. Feature pages that have been created after the update are found by the search. 

3. I thought re-sync’ing the features might solve the above, but I do not know how to ‘Re-Sync’ already sync’ed features, without deleting them.  When we attempt to sync all ‘gene’ features for example, the tripal job says “0 feature records found.” 


Best
Michael




  














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Re: [Gmod-tripal-devel] Some problems related to Tripal Features, follow up on a tripal update

Michael Dondrup-3
Hi and sorry for bothering,

is there any news on these topics? We have now opened a lot more content including the genomic content in Licebase (see https://licebase.org if you are interested).

The search problem is now most relevant, because users cannot use the site search to find features. Before, the normal site search would find
Features (by e.g. annotation, search eg. ‘chitinase’ if chitinase was annotated in the Properties)  and also Blast results, but now it does not find any features. Is there any work-around to re-sync features?

Best
Michael




> On Apr 4, 2016, at 2:45 PM, Michael Dondrup <[hidden email]> wrote:
>
> Hi,
>
> following an ~2 month update process to D7/Tripal 2 of LiceBase, we now have resolved all outstanding issues,
> greatly thanks to Stephen and the Tripal community. We are now in the process of honing off the few remaining issues.
> These three are all related to the Tripal Feature module and we are not sure if they are caused by the update. I will just list them below,
> I can also add them to the issue tracker if you like.
>
> 1. Features don’t appear to respect the ‘View’ permission. We tested if an anonymous user can view Features even though the View Features permission is off in the permission table. We tested this case also using the output of Devel Node Access, and it suggests that any feature is using the default node View permission for published content from the Node permissions. The other CRUD permissions ‘Create’, ‘Update’, ‘Delete’  seem to be ok. As a result, anonymous is either able to see the site including all features or not able to use it at all. I remember this was different in Tripal 1.
>
> A typical Debug output of the permission set per user who has full access looks like:
>
> username create view update delete
> user YES: by node (permissions) YES: {node_access} YES: by node (permissions) YES: by node (permissions)
> with the explanation YES: hook_node_access() of the following module(s) allows this: node (permissions).
>
> This makes me wonder whether there is something missing for hook_node_access().
> Please see the attached screen shots for an explanation of our Permission settings.
>
> 2. The site search doesn’t seem to find the updated Feature pages. I have re-indexed the site via admin/config/search/settings, but that doesn’t seem
> to have an effect. Feature pages that have been created after the update are found by the search.
>
> 3. I thought re-sync’ing the features might solve the above, but I do not know how to ‘Re-Sync’ already sync’ed features, without deleting them.  When we attempt to sync all ‘gene’ features for example, the tripal job says “0 feature records found.”
>
>
> Best
> Michael
>
>
>
>
>  
>
>
>
>
>
>
>
>
> <Screen Shot 2016-04-04 at 12.44.29 PM.png>
>
>
>
> <Screen Shot 2016-04-04 at 12.25.54 PM.png>
>
>
> <Screen Shot 2016-04-04 at 09.06.17 AM.png>
> ------------------------------------------------------------------------------
> _______________________________________________
> Gmod-tripal-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel


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Re: [Gmod-tripal-devel] Some problems related to Tripal Features, follow up on a tripal update

Stephen Ficklin-2
Hi Michael,

Sorry for the delay in response. I've been away from the office.

So, you have found a bug for us in the permissions.  I've applied a fix
to the 7.x-2.x development branch that hopefully will fix the problem
for you.  So please try it out and if you have other problems with
permissions I'll work on those too.

As for resyncing pages it's not possible.  'Sync' is probably an
unfortunate choice of a word.  Essentially what happens during a sync is
a Drupal node is created that is associated with a Chado record.  So,
once that association is made that's all is needed. Tripal pulls data
directly from Chado whenver the page is displayed so there's no syncing
that goes on at that point.

But it's odd that features that existed before the upgrade are not
present in the search results.  Can you confirm that those older pages
still exist?

Stephen

On 4/10/2016 8:07 AM, Michael Dondrup wrote:

> Hi and sorry for bothering,
>
> is there any news on these topics? We have now opened a lot more content including the genomic content in Licebase (see https://licebase.org if you are interested).
>
> The search problem is now most relevant, because users cannot use the site search to find features. Before, the normal site search would find
> Features (by e.g. annotation, search eg. ‘chitinase’ if chitinase was annotated in the Properties)  and also Blast results, but now it does not find any features. Is there any work-around to re-sync features?
>
> Best
> Michael
>
>
>
>
>> On Apr 4, 2016, at 2:45 PM, Michael Dondrup <[hidden email]> wrote:
>>
>> Hi,
>>
>> following an ~2 month update process to D7/Tripal 2 of LiceBase, we now have resolved all outstanding issues,
>> greatly thanks to Stephen and the Tripal community. We are now in the process of honing off the few remaining issues.
>> These three are all related to the Tripal Feature module and we are not sure if they are caused by the update. I will just list them below,
>> I can also add them to the issue tracker if you like.
>>
>> 1. Features don’t appear to respect the ‘View’ permission. We tested if an anonymous user can view Features even though the View Features permission is off in the permission table. We tested this case also using the output of Devel Node Access, and it suggests that any feature is using the default node View permission for published content from the Node permissions. The other CRUD permissions ‘Create’, ‘Update’, ‘Delete’  seem to be ok. As a result, anonymous is either able to see the site including all features or not able to use it at all. I remember this was different in Tripal 1.
>>
>> A typical Debug output of the permission set per user who has full access looks like:
>>
>> username create view update delete
>> user YES: by node (permissions) YES: {node_access} YES: by node (permissions) YES: by node (permissions)
>> with the explanation YES: hook_node_access() of the following module(s) allows this: node (permissions).
>>
>> This makes me wonder whether there is something missing for hook_node_access().
>> Please see the attached screen shots for an explanation of our Permission settings.
>>
>> 2. The site search doesn’t seem to find the updated Feature pages. I have re-indexed the site via admin/config/search/settings, but that doesn’t seem
>> to have an effect. Feature pages that have been created after the update are found by the search.
>>
>> 3. I thought re-sync’ing the features might solve the above, but I do not know how to ‘Re-Sync’ already sync’ed features, without deleting them.  When we attempt to sync all ‘gene’ features for example, the tripal job says “0 feature records found.”
>>
>>
>> Best
>> Michael
>>
>>
>>
>>
>>    
>>
>>
>>
>>
>>
>>
>>
>>
>> <Screen Shot 2016-04-04 at 12.44.29 PM.png>
>>
>>
>>
>> <Screen Shot 2016-04-04 at 12.25.54 PM.png>
>>
>>
>> <Screen Shot 2016-04-04 at 09.06.17 AM.png>
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> Gmod-tripal-devel mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>
> ------------------------------------------------------------------------------
> Find and fix application performance issues faster with Applications Manager
> Applications Manager provides deep performance insights into multiple tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/
> gampad/clk?id=1444514301&iu=/ca-pub-7940484522588532
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> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel


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Re: [Gmod-tripal-devel] Some problems related to Tripal Features, follow up on a tripal update

Kucheran, Lacey Sanderson
Hi Michael,

Were you meaning the site-wide search that was available in Tripal 1.0? If so that functionality was removed from Tripal 2 due to some incompatibilities with Drupal 7 as well as an intent on improving the methodology. 

It’s looking like Tripal 2.1 will have site-wide searching capabilities as I am working on that as we speak so I’ll point you to the tutorial when it’s stable. Essentially it uses the Search API to expose parts of chado to searching. When complete it would require some theme extension to make it work with the theme provided search box but it is possible and will provide you a lot more control and flexibility over what is indexed (and no duplication or taxonomy terms). By default it will index the name/uniquename/accession, as well as, follow foreign keys (i.e.: index the type, organism, dbxref for features). It won’t yet index your annotation/properties or blast results but it should be easy to make it do so with a little custom code. Maybe I’ll use your use case for the tutorial ;-)

I’ll keep you updated with the progress,
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On April 12, 2016 at 11:05:20 AM, Stephen Ficklin ([hidden email]) wrote:

Hi Michael,

Sorry for the delay in response. I've been away from the office.

So, you have found a bug for us in the permissions. I've applied a fix
to the 7.x-2.x development branch that hopefully will fix the problem
for you. So please try it out and if you have other problems with
permissions I'll work on those too.

As for resyncing pages it's not possible. 'Sync' is probably an
unfortunate choice of a word. Essentially what happens during a sync is
a Drupal node is created that is associated with a Chado record. So,
once that association is made that's all is needed. Tripal pulls data
directly from Chado whenver the page is displayed so there's no syncing
that goes on at that point.

But it's odd that features that existed before the upgrade are not
present in the search results. Can you confirm that those older pages
still exist?

Stephen

On 4/10/2016 8:07 AM, Michael Dondrup wrote:
> Hi and sorry for bothering,
>
> is there any news on these topics? We have now opened a lot more content including the genomic content in Licebase (see https://licebase.org if you are interested).
>
> The search problem is now most relevant, because users cannot use the site search to find features. Before, the normal site search would find
> Features (by e.g. annotation, search eg. ‘chitinase’ if chitinase was annotated in the Properties) and also Blast results, but now it does not find any features. Is there any work-around to re-sync features?
>
> Best
> Michael
>
>
>
>
>> On Apr 4, 2016, at 2:45 PM, Michael Dondrup <[hidden email]> wrote:
>>
>> Hi,
>>
>> following an ~2 month update process to D7/Tripal 2 of LiceBase, we now have resolved all outstanding issues,
>> greatly thanks to Stephen and the Tripal community. We are now in the process of honing off the few remaining issues.
>> These three are all related to the Tripal Feature module and we are not sure if they are caused by the update. I will just list them below,
>> I can also add them to the issue tracker if you like.
>>
>> 1. Features don’t appear to respect the ‘View’ permission. We tested if an anonymous user can view Features even though the View Features permission is off in the permission table. We tested this case also using the output of Devel Node Access, and it suggests that any feature is using the default node View permission for published content from the Node permissions. The other CRUD permissions ‘Create’, ‘Update’, ‘Delete’ seem to be ok. As a result, anonymous is either able to see the site including all features or not able to use it at all. I remember this was different in Tripal 1.
>>
>> A typical Debug output of the permission set per user who has full access looks like:
>>
>> username create view update delete
>> user YES: by node (permissions) YES: {node_access} YES: by node (permissions) YES: by node (permissions)
>> with the explanation YES: hook_node_access() of the following module(s) allows this: node (permissions).
>>
>> This makes me wonder whether there is something missing for hook_node_access().
>> Please see the attached screen shots for an explanation of our Permission settings.
>>
>> 2. The site search doesn’t seem to find the updated Feature pages. I have re-indexed the site via admin/config/search/settings, but that doesn’t seem
>> to have an effect. Feature pages that have been created after the update are found by the search.
>>
>> 3. I thought re-sync’ing the features might solve the above, but I do not know how to ‘Re-Sync’ already sync’ed features, without deleting them. When we attempt to sync all ‘gene’ features for example, the tripal job says “0 feature records found.”
>>
>>
>> Best
>> Michael
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> <Screen Shot 2016-04-04 at 12.44.29 PM.png>
>>
>>
>>
>> <Screen Shot 2016-04-04 at 12.25.54 PM.png>
>>
>>
>> <Screen Shot 2016-04-04 at 09.06.17 AM.png>
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> Gmod-tripal-devel mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>
> ------------------------------------------------------------------------------
> Find and fix application performance issues faster with Applications Manager
> Applications Manager provides deep performance insights into multiple tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/
> gampad/clk?id=1444514301&iu=/ca-pub-7940484522588532
> _______________________________________________
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> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel


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Re: [Gmod-tripal-devel] Some problems related to Tripal Features, follow up on a tripal update

Kucheran, Lacey Sanderson
Hi Michael,

If you were looking for site-wide search functionality, it’s now available in the development version of Tripal 2 with documentation available in the User Guide. As promised, I included an example for how you could index feature properties in the tutorial on the second page (Controlling which fields get indexed; Option #3).

I’m using the database backend to store my keywords and it has approximately doubled my database size. For an example of speed when using this method, you can go to KnowPulse and use the search box in the header. A good example keyword is “Lentil” which will return results across all node types. For evaluation purposes, KnowPulse has ~1.7 million nodes and is run off a mediocre, single box setup (2.67 GHz, 6 cores, 64GB RAM, 3Gbps SAS).

Hope that Helps!
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On April 14, 2016 at 9:48:25 AM, Kucheran, Lacey Sanderson ([hidden email]) wrote:

Hi Michael,

Were you meaning the site-wide search that was available in Tripal 1.0? If so that functionality was removed from Tripal 2 due to some incompatibilities with Drupal 7 as well as an intent on improving the methodology. 

It’s looking like Tripal 2.1 will have site-wide searching capabilities as I am working on that as we speak so I’ll point you to the tutorial when it’s stable. Essentially it uses the Search API to expose parts of chado to searching. When complete it would require some theme extension to make it work with the theme provided search box but it is possible and will provide you a lot more control and flexibility over what is indexed (and no duplication or taxonomy terms). By default it will index the name/uniquename/accession, as well as, follow foreign keys (i.e.: index the type, organism, dbxref for features). It won’t yet index your annotation/properties or blast results but it should be easy to make it do so with a little custom code. Maybe I’ll use your use case for the tutorial ;-)

I’ll keep you updated with the progress,
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On April 12, 2016 at 11:05:20 AM, Stephen Ficklin ([hidden email]) wrote:

Hi Michael,

Sorry for the delay in response. I've been away from the office.

So, you have found a bug for us in the permissions. I've applied a fix
to the 7.x-2.x development branch that hopefully will fix the problem
for you. So please try it out and if you have other problems with
permissions I'll work on those too.

As for resyncing pages it's not possible. 'Sync' is probably an
unfortunate choice of a word. Essentially what happens during a sync is
a Drupal node is created that is associated with a Chado record. So,
once that association is made that's all is needed. Tripal pulls data
directly from Chado whenver the page is displayed so there's no syncing
that goes on at that point.

But it's odd that features that existed before the upgrade are not
present in the search results. Can you confirm that those older pages
still exist?

Stephen

On 4/10/2016 8:07 AM, Michael Dondrup wrote:
> Hi and sorry for bothering,
>
> is there any news on these topics? We have now opened a lot more content including the genomic content in Licebase (see https://licebase.org if you are interested).
>
> The search problem is now most relevant, because users cannot use the site search to find features. Before, the normal site search would find
> Features (by e.g. annotation, search eg. ‘chitinase’ if chitinase was annotated in the Properties) and also Blast results, but now it does not find any features. Is there any work-around to re-sync features?
>
> Best
> Michael
>
>
>
>
>> On Apr 4, 2016, at 2:45 PM, Michael Dondrup <[hidden email]> wrote:
>>
>> Hi,
>>
>> following an ~2 month update process to D7/Tripal 2 of LiceBase, we now have resolved all outstanding issues,
>> greatly thanks to Stephen and the Tripal community. We are now in the process of honing off the few remaining issues.
>> These three are all related to the Tripal Feature module and we are not sure if they are caused by the update. I will just list them below,
>> I can also add them to the issue tracker if you like.
>>
>> 1. Features don’t appear to respect the ‘View’ permission. We tested if an anonymous user can view Features even though the View Features permission is off in the permission table. We tested this case also using the output of Devel Node Access, and it suggests that any feature is using the default node View permission for published content from the Node permissions. The other CRUD permissions ‘Create’, ‘Update’, ‘Delete’ seem to be ok. As a result, anonymous is either able to see the site including all features or not able to use it at all. I remember this was different in Tripal 1.
>>
>> A typical Debug output of the permission set per user who has full access looks like:
>>
>> username create view update delete
>> user YES: by node (permissions) YES: {node_access} YES: by node (permissions) YES: by node (permissions)
>> with the explanation YES: hook_node_access() of the following module(s) allows this: node (permissions).
>>
>> This makes me wonder whether there is something missing for hook_node_access().
>> Please see the attached screen shots for an explanation of our Permission settings.
>>
>> 2. The site search doesn’t seem to find the updated Feature pages. I have re-indexed the site via admin/config/search/settings, but that doesn’t seem
>> to have an effect. Feature pages that have been created after the update are found by the search.
>>
>> 3. I thought re-sync’ing the features might solve the above, but I do not know how to ‘Re-Sync’ already sync’ed features, without deleting them. When we attempt to sync all ‘gene’ features for example, the tripal job says “0 feature records found.”
>>
>>
>> Best
>> Michael
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> <Screen Shot 2016-04-04 at 12.44.29 PM.png>
>>
>>
>>
>> <Screen Shot 2016-04-04 at 12.25.54 PM.png>
>>
>>
>> <Screen Shot 2016-04-04 at 09.06.17 AM.png>
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> Gmod-tripal-devel mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>
> ------------------------------------------------------------------------------
> Find and fix application performance issues faster with Applications Manager
> Applications Manager provides deep performance insights into multiple tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/
> gampad/clk?id=1444514301&iu=/ca-pub-7940484522588532
> _______________________________________________
> Gmod-tripal-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel


------------------------------------------------------------------------------
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your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
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your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
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