Quantcast

Edition restricted to the annotations owned by the annotator

classic Classic list List threaded Threaded
9 messages Options
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Edition restricted to the annotations owned by the annotator

Loraine Guéguen
Hi,

I think this is not possible, but to be sure, I ask the question:
Is it possible to let annotators modifying only the annotations that
they owned, and not the annotations created by someonelse ?

Thanks

Loraine Guéguen


--
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Edition restricted to the annotations owned by the annotator

nathandunn

We have talked about having “locks” that would do just that in the past, but I don’t think its been a priority.

There is a lot of code stubbed out in the client (AnnotTrack.js) and the server (RequestHandlingService.groovy) to do just that, so it *might* be pretty easy to hack in if you have the time and we could integrate into the code as a PR.  

Either way, adding a GH issue for this (and how you want it to work), would probably be a good idea.  

Nathan

> On Jan 18, 2017, at 6:26 AM, Loraine Guéguen <[hidden email]> wrote:
>
> Hi,
>
> I think this is not possible, but to be sure, I ask the question:
> Is it possible to let annotators modifying only the annotations that they owned, and not the annotations created by someonelse ?
>
> Thanks
>
> Loraine Guéguen
>
>
> --
> Loraine Guéguen
>
> Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
> Service Informatique et Bioinformatique
> Station Biologique de Roscoff
> FR 2424 CNRS UPMC
> Place Georges Teissier
> CS 90074
> 29688 Roscoff cedex
> tel: ++33 (0)2 98 29 56 46 (interne : 415)
> http://abims.sb-roscoff.fr/
> http://www.sb-roscoff.fr/
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Edition restricted to the annotations owned by the annotator

Suzanna Lewis-3
This has not been a priority because our perspective has always been that this is a tool for collaboration, that every modification is signed (so you know who made every change), that any change can be undone, and that every annotation has to make sense in light of the evidence supporting it (i.e. there is some ascertainable biological 'reality').

In practice people have informally segregated because they only work on the genes of relevance to them, that they know best. 

In short it's not a high priority, unless a good case can be made for it.

We have spoken of different levels of access to whole genomes (i.e. view, comment, edit), but nothing finer grained.


On Wed, Jan 18, 2017 at 8:47 AM, Nathan Dunn <[hidden email]> wrote:

We have talked about having “locks” that would do just that in the past, but I don’t think its been a priority.

There is a lot of code stubbed out in the client (AnnotTrack.js) and the server (RequestHandlingService.groovy) to do just that, so it *might* be pretty easy to hack in if you have the time and we could integrate into the code as a PR.

Either way, adding a GH issue for this (and how you want it to work), would probably be a good idea.

Nathan

> On Jan 18, 2017, at 6:26 AM, Loraine Guéguen <[hidden email]> wrote:
>
> Hi,
>
> I think this is not possible, but to be sure, I ask the question:
> Is it possible to let annotators modifying only the annotations that they owned, and not the annotations created by someonelse ?
>
> Thanks
>
> Loraine Guéguen
>
>
> --
> Loraine Guéguen
>
> Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
> Service Informatique et Bioinformatique
> Station Biologique de Roscoff
> FR 2424 CNRS UPMC
> Place Georges Teissier
> CS 90074
> 29688 Roscoff cedex
> tel: <a href="tel:%2B%2B33%20%280%292%2098%2029%2056%2046" value="+33298295646">++33 (0)2 98 29 56 46 (interne : 415)
> http://abims.sb-roscoff.fr/
> http://www.sb-roscoff.fr/
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Edition restricted to the annotations owned by the annotator

Loraine Guéguen
Thanks for your answers.
I have created an issue : https://github.com/GMOD/Apollo/issues/1447

"every modification is signed (so you know who made every change), that any change can be undone"

I agree for the structural changes, but what about the functional information in the Information Editor panel ? If I am not mistaken, the history of changes is not conserved in this case, isn't it ? (I could not find it in the database)

Loraine Guéguen


Le 18/01/2017 22:25, Suzanna Lewis a écrit :
This has not been a priority because our perspective has always been that this is a tool for collaboration, that every modification is signed (so you know who made every change), that any change can be undone, and that every annotation has to make sense in light of the evidence supporting it (i.e. there is some ascertainable biological 'reality').

In practice people have informally segregated because they only work on the genes of relevance to them, that they know best. 

In short it's not a high priority, unless a good case can be made for it.

We have spoken of different levels of access to whole genomes (i.e. view, comment, edit), but nothing finer grained.


On Wed, Jan 18, 2017 at 8:47 AM, Nathan Dunn <[hidden email]> wrote:

We have talked about having “locks” that would do just that in the past, but I don’t think its been a priority.

There is a lot of code stubbed out in the client (AnnotTrack.js) and the server (RequestHandlingService.groovy) to do just that, so it *might* be pretty easy to hack in if you have the time and we could integrate into the code as a PR.

Either way, adding a GH issue for this (and how you want it to work), would probably be a good idea.

Nathan

> On Jan 18, 2017, at 6:26 AM, Loraine Guéguen <[hidden email]> wrote:
>
> Hi,
>
> I think this is not possible, but to be sure, I ask the question:
> Is it possible to let annotators modifying only the annotations that they owned, and not the annotations created by someonelse ?
>
> Thanks
>
> Loraine Guéguen
>
>
> --
> Loraine Guéguen
>
> Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
> Service Informatique et Bioinformatique
> Station Biologique de Roscoff
> FR 2424 CNRS UPMC
> Place Georges Teissier
> CS 90074
> 29688 Roscoff cedex
> tel: <a moz-do-not-send="true" href="tel:%2B%2B33%20%280%292%2098%2029%2056%2046" value="+33298295646">++33 (0)2 98 29 56 46 (interne : 415)
> http://abims.sb-roscoff.fr/
> http://www.sb-roscoff.fr/
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 


-- 
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Edition restricted to the annotations owned by the annotator

Chris Childers
If tampering with an existing annotation is a real concern, it is also good to note that when a model is deleted, the entire history is deleted and cannot be recovered.

This has had me concerned from a user error perspective (whoops, I deleted my model and changed my mind), but there is also the possibility for one user deleting the work of another for whatever reason, and we currently have no way to undo these actions, or even register if it occurs.



On Thu, Jan 19, 2017 at 8:42 AM, Loraine Guéguen <[hidden email]> wrote:
Thanks for your answers.
I have created an issue : https://github.com/GMOD/Apollo/issues/1447

"every modification is signed (so you know who made every change), that any change can be undone"

I agree for the structural changes, but what about the functional information in the Information Editor panel ? If I am not mistaken, the history of changes is not conserved in this case, isn't it ? (I could not find it in the database)

Loraine Guéguen



Le 18/01/2017 22:25, Suzanna Lewis a écrit :
This has not been a priority because our perspective has always been that this is a tool for collaboration, that every modification is signed (so you know who made every change), that any change can be undone, and that every annotation has to make sense in light of the evidence supporting it (i.e. there is some ascertainable biological 'reality').

In practice people have informally segregated because they only work on the genes of relevance to them, that they know best. 

In short it's not a high priority, unless a good case can be made for it.

We have spoken of different levels of access to whole genomes (i.e. view, comment, edit), but nothing finer grained.


On Wed, Jan 18, 2017 at 8:47 AM, Nathan Dunn <[hidden email]> wrote:

We have talked about having “locks” that would do just that in the past, but I don’t think its been a priority.

There is a lot of code stubbed out in the client (AnnotTrack.js) and the server (RequestHandlingService.groovy) to do just that, so it *might* be pretty easy to hack in if you have the time and we could integrate into the code as a PR.

Either way, adding a GH issue for this (and how you want it to work), would probably be a good idea.

Nathan

> On Jan 18, 2017, at 6:26 AM, Loraine Guéguen <[hidden email][hidden email]> wrote:
>
> Hi,
>
> I think this is not possible, but to be sure, I ask the question:
> Is it possible to let annotators modifying only the annotations that they owned, and not the annotations created by someonelse ?
>
> Thanks
>
> Loraine Guéguen
>
>
> --
> Loraine Guéguen
>
> Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
> Service Informatique et Bioinformatique
> Station Biologique de Roscoff
> FR 2424 CNRS UPMC
> Place Georges Teissier
> CS 90074
> 29688 Roscoff cedex
> tel: <a href="tel:%2B%2B33%20%280%292%2098%2029%2056%2046" value="+33298295646" target="_blank">++33 (0)2 98 29 56 46 (interne : 415)
> http://abims.sb-roscoff.fr/
> http://www.sb-roscoff.fr/
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 


-- 
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: <a href="tel:+33%202%2098%2029%2056%2046" value="+33298295646" target="_blank">++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Edition restricted to the annotations owned by the annotator

Loraine Guéguen
good point

Le 19/01/2017 15:10, Chris Childers a écrit :
If tampering with an existing annotation is a real concern, it is also good to note that when a model is deleted, the entire history is deleted and cannot be recovered.

This has had me concerned from a user error perspective (whoops, I deleted my model and changed my mind), but there is also the possibility for one user deleting the work of another for whatever reason, and we currently have no way to undo these actions, or even register if it occurs.



On Thu, Jan 19, 2017 at 8:42 AM, Loraine Guéguen <[hidden email]> wrote:
Thanks for your answers.
I have created an issue : https://github.com/GMOD/Apollo/issues/1447

"every modification is signed (so you know who made every change), that any change can be undone"

I agree for the structural changes, but what about the functional information in the Information Editor panel ? If I am not mistaken, the history of changes is not conserved in this case, isn't it ? (I could not find it in the database)

Loraine Guéguen



Le 18/01/2017 22:25, Suzanna Lewis a écrit :
This has not been a priority because our perspective has always been that this is a tool for collaboration, that every modification is signed (so you know who made every change), that any change can be undone, and that every annotation has to make sense in light of the evidence supporting it (i.e. there is some ascertainable biological 'reality').

In practice people have informally segregated because they only work on the genes of relevance to them, that they know best. 

In short it's not a high priority, unless a good case can be made for it.

We have spoken of different levels of access to whole genomes (i.e. view, comment, edit), but nothing finer grained.


On Wed, Jan 18, 2017 at 8:47 AM, Nathan Dunn <[hidden email]> wrote:

We have talked about having “locks” that would do just that in the past, but I don’t think its been a priority.

There is a lot of code stubbed out in the client (AnnotTrack.js) and the server (RequestHandlingService.groovy) to do just that, so it *might* be pretty easy to hack in if you have the time and we could integrate into the code as a PR.

Either way, adding a GH issue for this (and how you want it to work), would probably be a good idea.

Nathan

> On Jan 18, 2017, at 6:26 AM, Loraine Guéguen <[hidden email]> wrote:
>
> Hi,
>
> I think this is not possible, but to be sure, I ask the question:
> Is it possible to let annotators modifying only the annotations that they owned, and not the annotations created by someonelse ?
>
> Thanks
>
> Loraine Guéguen
>
>
> --
> Loraine Guéguen
>
> Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
> Service Informatique et Bioinformatique
> Station Biologique de Roscoff
> FR 2424 CNRS UPMC
> Place Georges Teissier
> CS 90074
> 29688 Roscoff cedex
> tel: <a moz-do-not-send="true" href="tel:%2B%2B33%20%280%292%2098%2029%2056%2046" value="+33298295646" target="_blank">++33 (0)2 98 29 56 46 (interne : 415)
> http://abims.sb-roscoff.fr/
> http://www.sb-roscoff.fr/
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 


-- 
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: <a moz-do-not-send="true" href="tel:+33%202%2098%2029%2056%2046" value="+33298295646" target="_blank">++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 


-- 
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Edition restricted to the annotations owned by the annotator

Suzanna Lewis-3
Both excellent points. We'll discuss keeping a complete history at our next project meeting because this is indeed crucial.



On Thu, Jan 19, 2017 at 6:17 AM, Loraine Guéguen <[hidden email]> wrote:
good point


Le 19/01/2017 15:10, Chris Childers a écrit :
If tampering with an existing annotation is a real concern, it is also good to note that when a model is deleted, the entire history is deleted and cannot be recovered.

This has had me concerned from a user error perspective (whoops, I deleted my model and changed my mind), but there is also the possibility for one user deleting the work of another for whatever reason, and we currently have no way to undo these actions, or even register if it occurs.



On Thu, Jan 19, 2017 at 8:42 AM, Loraine Guéguen <[hidden email]> wrote:
Thanks for your answers.
I have created an issue : https://github.com/GMOD/Apollo/issues/1447

"every modification is signed (so you know who made every change), that any change can be undone"

I agree for the structural changes, but what about the functional information in the Information Editor panel ? If I am not mistaken, the history of changes is not conserved in this case, isn't it ? (I could not find it in the database)

Loraine Guéguen



Le 18/01/2017 22:25, Suzanna Lewis a écrit :
This has not been a priority because our perspective has always been that this is a tool for collaboration, that every modification is signed (so you know who made every change), that any change can be undone, and that every annotation has to make sense in light of the evidence supporting it (i.e. there is some ascertainable biological 'reality').

In practice people have informally segregated because they only work on the genes of relevance to them, that they know best. 

In short it's not a high priority, unless a good case can be made for it.

We have spoken of different levels of access to whole genomes (i.e. view, comment, edit), but nothing finer grained.


On Wed, Jan 18, 2017 at 8:47 AM, Nathan Dunn <[hidden email][hidden email]> wrote:

We have talked about having “locks” that would do just that in the past, but I don’t think its been a priority.

There is a lot of code stubbed out in the client (AnnotTrack.js) and the server (RequestHandlingService.groovy) to do just that, so it *might* be pretty easy to hack in if you have the time and we could integrate into the code as a PR.

Either way, adding a GH issue for this (and how you want it to work), would probably be a good idea.

Nathan

> On Jan 18, 2017, at 6:26 AM, Loraine Guéguen <[hidden email]> wrote:
>
> Hi,
>
> I think this is not possible, but to be sure, I ask the question:
> Is it possible to let annotators modifying only the annotations that they owned, and not the annotations created by someonelse ?
>
> Thanks
>
> Loraine Guéguen
>
>
> --
> Loraine Guéguen
>
> Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
> Service Informatique et Bioinformatique
> Station Biologique de Roscoff
> FR 2424 CNRS UPMC
> Place Georges Teissier
> CS 90074
> 29688 Roscoff cedex
> tel: <a href="tel:%2B%2B33%20%280%292%2098%2029%2056%2046" value="+33298295646" target="_blank">++33 (0)2 98 29 56 46 (interne : 415)
> http://abims.sb-roscoff.fr/
> http://www.sb-roscoff.fr/
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email][hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 


-- 
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: <a href="tel:+33%202%2098%2029%2056%2046" value="+33298295646" target="_blank">++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 


-- 
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: <a href="tel:+33%202%2098%2029%2056%2046" value="+33298295646" target="_blank">++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Edition restricted to the annotations owned by the annotator

nathandunn
In reply to this post by Loraine Guéguen

Loraine,

Thanks for reporting this.  

I merged this issue with https://github.com/GMOD/Apollo/issues/1257 

WRT to metadata, we actually track that as well, but only between structural changes.   

We definitely need a better way of doing this.  The older model (Apollo 1.X) is that the metadata is separate from structural data, which I think is a bad model.   

I think a better model might be simply capturing those changes internally in the same way we do now and in the UI, indicating the type of change (and possibly the metadata change).  The issue discussing it is here as well:


Nathan

On Jan 19, 2017, at 5:42 AM, Loraine Guéguen <[hidden email]> wrote:

Thanks for your answers.
I have created an issue : https://github.com/GMOD/Apollo/issues/1447

"every modification is signed (so you know who made every change), that any change can be undone"

I agree for the structural changes, but what about the functional information in the Information Editor panel ? If I am not mistaken, the history of changes is not conserved in this case, isn't it ? (I could not find it in the database)

Loraine Guéguen


Le 18/01/2017 22:25, Suzanna Lewis a écrit :
This has not been a priority because our perspective has always been that this is a tool for collaboration, that every modification is signed (so you know who made every change), that any change can be undone, and that every annotation has to make sense in light of the evidence supporting it (i.e. there is some ascertainable biological 'reality').

In practice people have informally segregated because they only work on the genes of relevance to them, that they know best. 

In short it's not a high priority, unless a good case can be made for it.

We have spoken of different levels of access to whole genomes (i.e. view, comment, edit), but nothing finer grained.


On Wed, Jan 18, 2017 at 8:47 AM, Nathan Dunn <[hidden email]> wrote:

We have talked about having “locks” that would do just that in the past, but I don’t think its been a priority.

There is a lot of code stubbed out in the client (AnnotTrack.js) and the server (RequestHandlingService.groovy) to do just that, so it *might* be pretty easy to hack in if you have the time and we could integrate into the code as a PR.

Either way, adding a GH issue for this (and how you want it to work), would probably be a good idea.

Nathan

> On Jan 18, 2017, at 6:26 AM, Loraine Guéguen <[hidden email][hidden email]> wrote:
>
> Hi,
>
> I think this is not possible, but to be sure, I ask the question:
> Is it possible to let annotators modifying only the annotations that they owned, and not the annotations created by someonelse ?
>
> Thanks
>
> Loraine Guéguen
>
>
> --
> Loraine Guéguen
>
> Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
> Service Informatique et Bioinformatique
> Station Biologique de Roscoff
> FR 2424 CNRS UPMC
> Place Georges Teissier
> CS 90074
> 29688 Roscoff cedex
> tel: <a moz-do-not-send="true" href="tel:%2B%2B33%20%280%292%2098%2029%2056%2046" value="+33298295646" class="">++33 (0)2 98 29 56 46 (interne : 415)
> http://abims.sb-roscoff.fr/
> http://www.sb-roscoff.fr/
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 


-- 
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Edition restricted to the annotations owned by the annotator

nathandunn
In reply to this post by Chris Childers

We have created to issues covering these and this process is a priority in 2.0.7:


To note though, you should get a prompt asking you if you want to delete an annotation, so it would be a pretty willful action to do this.  

I think its still worth noting deletions however.  

WRT people modifying others, I think that is a more interesting issue, as this would be the more likely scenario for deletion.  From the notes in the case where we talk about this, it hasn’t been a problem, but maybe our user groups have gotten large enough that we need to begin tracking this information.  


Like Suzi said, we’ll talk about this next week and come up with a more comprehensive solution. 

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory
[hidden email]


On Jan 19, 2017, at 6:10 AM, Chris Childers <[hidden email]> wrote:

If tampering with an existing annotation is a real concern, it is also good to note that when a model is deleted, the entire history is deleted and cannot be recovered.

This has had me concerned from a user error perspective (whoops, I deleted my model and changed my mind), but there is also the possibility for one user deleting the work of another for whatever reason, and we currently have no way to undo these actions, or even register if it occurs.



On Thu, Jan 19, 2017 at 8:42 AM, Loraine Guéguen <[hidden email]> wrote:
Thanks for your answers.
I have created an issue : https://github.com/GMOD/Apollo/issues/1447

"every modification is signed (so you know who made every change), that any change can be undone"

I agree for the structural changes, but what about the functional information in the Information Editor panel ? If I am not mistaken, the history of changes is not conserved in this case, isn't it ? (I could not find it in the database)

Loraine Guéguen



Le 18/01/2017 22:25, Suzanna Lewis a écrit :
This has not been a priority because our perspective has always been that this is a tool for collaboration, that every modification is signed (so you know who made every change), that any change can be undone, and that every annotation has to make sense in light of the evidence supporting it (i.e. there is some ascertainable biological 'reality').

In practice people have informally segregated because they only work on the genes of relevance to them, that they know best. 

In short it's not a high priority, unless a good case can be made for it.

We have spoken of different levels of access to whole genomes (i.e. view, comment, edit), but nothing finer grained.


On Wed, Jan 18, 2017 at 8:47 AM, Nathan Dunn <[hidden email]> wrote:

We have talked about having “locks” that would do just that in the past, but I don’t think its been a priority.

There is a lot of code stubbed out in the client (AnnotTrack.js) and the server (RequestHandlingService.groovy) to do just that, so it *might* be pretty easy to hack in if you have the time and we could integrate into the code as a PR.

Either way, adding a GH issue for this (and how you want it to work), would probably be a good idea.

Nathan

> On Jan 18, 2017, at 6:26 AM, Loraine Guéguen <[hidden email][hidden email]> wrote:
>
> Hi,
>
> I think this is not possible, but to be sure, I ask the question:
> Is it possible to let annotators modifying only the annotations that they owned, and not the annotations created by someonelse ?
>
> Thanks
>
> Loraine Guéguen
>
>
> --
> Loraine Guéguen
>
> Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
> Service Informatique et Bioinformatique
> Station Biologique de Roscoff
> FR 2424 CNRS UPMC
> Place Georges Teissier
> CS 90074
> 29688 Roscoff cedex
> tel: <a href="tel:%2B%2B33%20%280%292%2098%2029%2056%2046" value="+33298295646" target="_blank" class="">++33 (0)2 98 29 56 46 (interne : 415)
> http://abims.sb-roscoff.fr/
> http://www.sb-roscoff.fr/
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 


-- 
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: <a href="tel:+33%202%2098%2029%2056%2046" value="+33298295646" target="_blank" class="">++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

Loading...