limit data export for annotators

[Loraine Guéguen]

Hi,

Within a "careful" tendency again, one of my users would like to limit
export capacities of annotators (people with read and write rights).
So, is it possible to :
1- disable annotations export, both from the "User-created annotations"
track label ("Save track data") AND from the "admin" panel on the right
through tab "Ref Sequence"
2- disable export of the evidence tracks from the track label ("Save
track data")

Thanks,

Loraine

--
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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[nathandunn]

Loraine,

What is your use-case here?    

What are is your user trying to prevent and does this going to be universal to every organism / user on your server? 

On Feb 17, 2017, at 7:54 AM, Loraine Guéguen <[hidden email]> wrote:

Hi,

Within a "careful" tendency again, one of my users would like to limit export capacities of annotators (people with read and write rights).
So, is it possible to :
1- disable annotations export, both from the "User-created annotations" track label ("Save track data") AND from the "admin" panel on the right through tab "Ref Sequence”

A user will always have access to the genomic data as JSON if they can read it (though obviously not as convenient) by the necessity of displaying it on the page. 

But, to clarify, you want only “admins" to be able to do “Export” on the admin panel and the "user-created annotation" tracks? 

I’m sure that something can throw up something to be hacked in there to remove it from the interface, if so.  However, I’m not sure if that is the best approach to solve this problem. 

2- disable export of the evidence tracks from the track label ("Save track data”)

You can disable track by track from JBrowse (but it does this for ALL users AFAIK). 

http://gmod.org/wiki/JBrowse_Configuration_Guide#Export_Configuration

If you want some tracks to be private, you can always remove it and then open it directly as a link or a file name. 

We’ve had an open GitHub issue on making tracks private for awhile.  Though, it would not be difficult we have yet to find the time to do it.

https://github.com/GMOD/Apollo/issues/17 

Nathan

Thanks,

Loraine

--
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 prompt answer.
I tried to clarify the needs below.

Le 17/02/2017 19:16, Nathan Dunn a écrit :

Loraine,

What is your use-case here?  

What are is your user trying to prevent and does this going to be universal to every organism / user on your server?

Yes.
The project is about annotating 5 genomes of 5 different organisms included in a dedicated Apollo instance (only genomes of this project inside).
The annotation community will have around 20 people and, to protect data before it is published, the lead scientists would rather prevent them to download the data (User-created annotations and evidence data).
If all users need read and write rights, only the lead scientists and the admins should be able to download data "massively", that is to say data of one whole scaffold.

By discussing further with one of the lead scientists, they are now considering to ask all annotators to sign a charter before being granted access to the Apollo instance (code of conduct, data protection...). That would be the best solution I think.

On Feb 17, 2017, at 7:54 AM, Loraine Guéguen <[hidden email]> wrote:

Hi,

Within a "careful" tendency again, one of my users would like to limit export capacities of annotators (people with read and write rights).
So, is it possible to :
1- disable annotations export, both from the "User-created annotations" track label ("Save track data") AND from the "admin" panel on the right through tab "Ref Sequence”

A user will always have access to the genomic data as JSON if they can read it (though obviously not as convenient) by the necessity of displaying it on the page.

right

But, to clarify, you want only “admins" to be able to do “Export” on the admin panel and the "user-created annotation" tracks?

yes

I’m sure that something can throw up something to be hacked in there to remove it from the interface, if so.  However, I’m not sure if that is the best approach to solve this problem.

I am wondering if it is possible to limit export rights on the admin panel (tab "users", then "organisms") by deselecting "export". But I have made tests and I have seen no change in the export behaviour when selecting or deselecting "export". Is this normal ? I use release 2.0.4.

2- disable export of the evidence tracks from the track label ("Save track data”)

You can disable track by track from JBrowse (but it does this for ALL users AFAIK). 

http://gmod.org/wiki/JBrowse_Configuration_Guide#Export_Configuration

I didn't know that. Thanks. It could be part of the solution indeed.

If you want some tracks to be private, you can always remove it and then open it directly as a link or a file name.

No, they don't need this.

We’ve had an open GitHub issue on making tracks private for awhile.  Though, it would not be difficult we have yet to find the time to do it.

https://github.com/GMOD/Apollo/issues/17 

Nathan

Thanks,

Loraine

--
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.

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[nathandunn]

On Feb 20, 2017, at 2:40 AM, Loraine Guéguen <[hidden email]> wrote:

Thanks for your prompt answer.
I tried to clarify the needs below.

Le 17/02/2017 19:16, Nathan Dunn a écrit :

Loraine,

What is your use-case here?  

What are is your user trying to prevent and does this going to be universal to every organism / user on your server?

Yes.
The project is about annotating 5 genomes of 5 different organisms included in a dedicated Apollo instance (only genomes of this project inside).
The annotation community will have around 20 people and, to protect data before it is published, the lead scientists would rather prevent them to download the data (User-created annotations and evidence data).
If all users need read and write rights, only the lead scientists and the admins should be able to download data "massively", that is to say data of one whole scaffold.

By discussing further with one of the lead scientists, they are now considering to ask all annotators to sign a charter before being granted access to the Apollo instance (code of conduct, data protection...). That would be the best solution I think.

Agreed.

On Feb 17, 2017, at 7:54 AM, Loraine Guéguen <[hidden email]> wrote:

Hi,

Within a "careful" tendency again, one of my users would like to limit export capacities of annotators (people with read and write rights).
So, is it possible to :
1- disable annotations export, both from the "User-created annotations" track label ("Save track data") AND from the "admin" panel on the right through tab "Ref Sequence”

A user will always have access to the genomic data as JSON if they can read it (though obviously not as convenient) by the necessity of displaying it on the page.

right

But, to clarify, you want only “admins" to be able to do “Export” on the admin panel and the "user-created annotation" tracks?

yes

I’m sure that something can throw up something to be hacked in there to remove it from the interface, if so.  However, I’m not sure if that is the best approach to solve this problem.

I am wondering if it is possible to limit export rights on the admin panel (tab "users", then "organisms") by deselecting "export". But I have made tests and I have seen no change in the export behaviour when selecting or deselecting "export". Is this normal ? I use release 2.0.4.

I think we need to rethink this a bit to do it properly.   Currently “export” is another ranked permission, but clearly its an alternate permission.   

https://github.com/GMOD/Apollo/issues/1499

I started a pull-request to begin addressing it, but I won’t have time to fully finish it for at least a couple of months.   If you want to use it as a starting point for any sort of fix, please feel free:

https://github.com/GMOD/Apollo/pull/1500

Hopefully this helps get things started.  

Nathan

2- disable export of the evidence tracks from the track label ("Save track data”)

You can disable track by track from JBrowse (but it does this for ALL users AFAIK). 

http://gmod.org/wiki/JBrowse_Configuration_Guide#Export_Configuration

I didn't know that. Thanks. It could be part of the solution indeed.

If you want some tracks to be private, you can always remove it and then open it directly as a link or a file name.

No, they don't need this.

We’ve had an open GitHub issue on making tracks private for awhile.  Though, it would not be difficult we have yet to find the time to do it.

https://github.com/GMOD/Apollo/issues/17 

Nathan

Thanks,

Loraine

--
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.

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[Loraine Guéguen-2]

ok, thanks for your answer.

Le 21/02/2017 18:56, Nathan Dunn a écrit :

On Feb 20, 2017, at 2:40 AM, Loraine Guéguen <[hidden email]> wrote:

Thanks for your prompt answer.
I tried to clarify the needs below.

Le 17/02/2017 19:16, Nathan Dunn a écrit :

Loraine,

What is your use-case here?  

What are is your user trying to prevent and does this going to be universal to every organism / user on your server?

Yes.
The project is about annotating 5 genomes of 5 different organisms included in a dedicated Apollo instance (only genomes of this project inside).
The annotation community will have around 20 people and, to protect data before it is published, the lead scientists would rather prevent them to download the data (User-created annotations and evidence data).
If all users need read and write rights, only the lead scientists and the admins should be able to download data "massively", that is to say data of one whole scaffold.

By discussing further with one of the lead scientists, they are now considering to ask all annotators to sign a charter before being granted access to the Apollo instance (code of conduct, data protection...). That would be the best solution I think.

Agreed.

On Feb 17, 2017, at 7:54 AM, Loraine Guéguen <[hidden email]> wrote:

Hi,

Within a "careful" tendency again, one of my users would like to limit export capacities of annotators (people with read and write rights).
So, is it possible to :
1- disable annotations export, both from the "User-created annotations" track label ("Save track data") AND from the "admin" panel on the right through tab "Ref Sequence”

A user will always have access to the genomic data as JSON if they can read it (though obviously not as convenient) by the necessity of displaying it on the page.

right

But, to clarify, you want only “admins" to be able to do “Export” on the admin panel and the "user-created annotation" tracks?

yes

I’m sure that something can throw up something to be hacked in there to remove it from the interface, if so.  However, I’m not sure if that is the best approach to solve this problem.

I am wondering if it is possible to limit export rights on the admin panel (tab "users", then "organisms") by deselecting "export". But I have made tests and I have seen no change in the export behaviour when selecting or deselecting "export". Is this normal ? I use release 2.0.4.

I think we need to rethink this a bit to do it properly.   Currently “export” is another ranked permission, but clearly its an alternate permission.   

https://github.com/GMOD/Apollo/issues/1499

I started a pull-request to begin addressing it, but I won’t have time to fully finish it for at least a couple of months.   If you want to use it as a starting point for any sort of fix, please feel free:

https://github.com/GMOD/Apollo/pull/1500

Hopefully this helps get things started.  

Nathan

2- disable export of the evidence tracks from the track label ("Save track data”)

You can disable track by track from JBrowse (but it does this for ALL users AFAIK). 

http://gmod.org/wiki/JBrowse_Configuration_Guide#Export_Configuration

I didn't know that. Thanks. It could be part of the solution indeed.

If you want some tracks to be private, you can always remove it and then open it directly as a link or a file name.

No, they don't need this.

We’ve had an open GitHub issue on making tracks private for awhile.  Though, it would not be difficult we have yet to find the time to do it.

https://github.com/GMOD/Apollo/issues/17 

Nathan

Thanks,

Loraine

--
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.

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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. 

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