[apollo] 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/

[Nathan Dunn]

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

Hi,
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/

[Suzanna Lewis]

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.

Post by Nathan Dunn
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 <
Hi,
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/

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[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

Post by Suzanna Lewis
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.
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
Hi,
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

<tel:%2B%2B33%20%280%292%2098%2029%2056%2046> (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

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--
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/

[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 <

Post by 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
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.

Post by Nathan Dunn
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 <
Hi,
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
unsubscribe apollo | 3. Leave the message body blank.
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| 2. In the subject line of your email type: unsubscribe apollo | 3. Leave
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--
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 <+33%202%2098%2029%2056%2046> (interne : 415)http://abims.sb-roscoff.fr/http://www.sb-roscoff.fr/
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[Loraine Guéguen]

good point

Post by 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
Thanks for your answers.
https://github.com/GMOD/Apollo/issues/1447
<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

Post by Suzanna Lewis
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.
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
Hi,
I think this is not possible, but to be sure, I ask the
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

<tel:%2B%2B33%20%280%292%2098%2029%2056%2046> (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
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| 3. Leave the message body blank.
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--
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 <tel:+33%202%2098%2029%2056%2046> (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/
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--
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/

[Suzanna Lewis]

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 <

Post by Loraine Guéguen
good point
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 <

Post by 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
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.

Post by Nathan Dunn
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 <
Hi,
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 <%2B%2B33%20%280%292%2098%2029%2056%2046>

(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/>http://genomearchitect.org/

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--
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 <+33%202%2098%2029%2056%2046> (interne : 415)http://abims.sb-roscoff.fr/http://www.sb-roscoff.fr/
This list is for the Apollo Annotation Editing Tool. Info at
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--
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
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[Nathan Dunn]

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

https://github.com/GMOD/Apollo/issues/1257 <https://github.com/GMOD/Apollo/issues/1257>

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.

https://github.com/GMOD/Apollo/issues/1260 <https://github.com/GMOD/Apollo/issues/1260>

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

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

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.
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

Hi,
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 <tel:%2B%2B33%20%280%292%2098%2029%2056%2046> (interne : 415)
http://abims.sb-roscoff.fr/ <http://abims.sb-roscoff.fr/>
http://www.sb-roscoff.fr/ <http://www.sb-roscoff.fr/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>

This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>

--
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 <tel:+33%202%2098%2029%2056%2046> (interne : 415)
http://abims.sb-roscoff.fr/ <http://abims.sb-roscoff.fr/>
http://www.sb-roscoff.fr/ <http://www.sb-roscoff.fr/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/

[Nathan Dunn]

Loraine,

Thanks for reporting this.

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

https://github.com/GMOD/Apollo/issues/541 <https://github.com/GMOD/Apollo/issues/541>

Nathan

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

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.
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

Hi,
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 <tel:%2B%2B33%20%280%292%2098%2029%2056%2046> (interne : 415)
http://abims.sb-roscoff.fr/ <http://abims.sb-roscoff.fr/>
http://www.sb-roscoff.fr/ <http://www.sb-roscoff.fr/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>

This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>

--
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://abims.sb-roscoff.fr/>
http://www.sb-roscoff.fr/ <http://www.sb-roscoff.fr/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/