Backup of WebApollo data?

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

Backup of WebApollo data?

mbeeby
Hi all,

I am sure there is a trivial answer to this, or that it is somewhere in the docs, but for the life of me I haven't been able to find it.

Could someone tell me the location of the Web Apollo user annotations are so that I can setup a backup crontab...?

I have an installation of WebApollo 2.0.6 on Linux Mint 17.3.

many thanks!

Morgan


--
Morgan Beeby | Lecturer in Structural Biology
Department of Life Sciences
Sir Ernst Chain Building
Imperial College London
South Kensington Campus
London, SW7 2AZ, UK

t: +44 (0)20 7594 5251

http://www3.imperial.ac.uk/people/m.beeby
@BeebyLab




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: Backup of WebApollo data?

nathandunn

Morgan,

They are located in your database.   If you are using postgresql and it is configured like this:

url = "jdbc:<a href="postgresql://localhost/apollo" class="">postgresql://localhost/apollo"

pg_dump apollo > dump.sql 

Or something like that.  

If you are using mysql then you would use mysqldump or script (https://stackoverflow.com/a/3259166/1739366) for H2. 

Let me know what you end up using and I’ll update the dock to reflect his.  

Nathan

On Jun 26, 2017, at 5:40 PM, Morgan Beeby <[hidden email]> wrote:

Hi all,

I am sure there is a trivial answer to this, or that it is somewhere in the docs, but for the life of me I haven't been able to find it.

Could someone tell me the location of the Web Apollo user annotations are so that I can setup a backup crontab...?

I have an installation of WebApollo 2.0.6 on Linux Mint 17.3.

many thanks!

Morgan


--
Morgan Beeby | Lecturer in Structural Biology
Department of Life Sciences
Sir Ernst Chain Building
Imperial College London
South Kensington Campus
London, SW7 2AZ, UK

t: +44 (0)20 7594 5251

http://www3.imperial.ac.uk/people/m.beeby
@BeebyLab



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: Backup of WebApollo data?

mbeeby
Nathan,

Bingo. Thanks so much! I should have figured that...

I am also working to programmatically access WebApollo but will likely send another email in the coming days after reading the docs...

Morgan




On 26/06/2017 17:22, Nathan Dunn wrote:

Morgan,

They are located in your database.   If you are using postgresql and it is configured like this:

url = "jdbc:<a moz-do-not-send="true" href="postgresql://localhost/apollo" class="">postgresql://localhost/apollo"

pg_dump apollo > dump.sql 

Or something like that.  

If you are using mysql then you would use mysqldump or script (https://stackoverflow.com/a/3259166/1739366) for H2. 

Let me know what you end up using and I’ll update the dock to reflect his.  

Nathan

On Jun 26, 2017, at 5:40 PM, Morgan Beeby <[hidden email]> wrote:

Hi all,

I am sure there is a trivial answer to this, or that it is somewhere in the docs, but for the life of me I haven't been able to find it.

Could someone tell me the location of the Web Apollo user annotations are so that I can setup a backup crontab...?

I have an installation of WebApollo 2.0.6 on Linux Mint 17.3.

many thanks!

Morgan


--
Morgan Beeby | Lecturer in Structural Biology
Department of Life Sciences
Sir Ernst Chain Building
Imperial College London
South Kensington Campus
London, SW7 2AZ, UK

t: +44 (0)20 7594 5251

http://www3.imperial.ac.uk/people/m.beeby
@BeebyLab



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. 



--
Morgan Beeby | Lecturer in Structural Biology
Department of Life Sciences
Sir Ernst Chain Building
Imperial College London
South Kensington Campus
London, SW7 2AZ, UK

t: +44 (0)20 7594 5251

http://www3.imperial.ac.uk/people/m.beeby
@BeebyLab




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: Backup of WebApollo data?

nathandunn

Excellent.  

We provide some web services for doing this:


However, and a few sample scripts in our example and tools directory.  

However, you should also check out the “arrow” repo by Eric Rasche which is a very nice approach to doing this:


Please raise an issue if you run into any problems. 

Nathan

On Jun 27, 2017, at 8:06 PM, Morgan Beeby <[hidden email]> wrote:

Nathan,

Bingo. Thanks so much! I should have figured that...

I am also working to programmatically access WebApollo but will likely send another email in the coming days after reading the docs...

Morgan




On 26/06/2017 17:22, Nathan Dunn wrote:

Morgan,

They are located in your database.   If you are using postgresql and it is configured like this:

url = "jdbc:<a moz-do-not-send="true" href="postgresql://localhost/apollo" class="">postgresql://localhost/apollo"

pg_dump apollo > dump.sql 

Or something like that.  

If you are using mysql then you would use mysqldump or script (https://stackoverflow.com/a/3259166/1739366) for H2. 

Let me know what you end up using and I’ll update the dock to reflect his.  

Nathan

On Jun 26, 2017, at 5:40 PM, Morgan Beeby <[hidden email]> wrote:

Hi all,

I am sure there is a trivial answer to this, or that it is somewhere in the docs, but for the life of me I haven't been able to find it.

Could someone tell me the location of the Web Apollo user annotations are so that I can setup a backup crontab...?

I have an installation of WebApollo 2.0.6 on Linux Mint 17.3.

many thanks!

Morgan


--
Morgan Beeby | Lecturer in Structural Biology
Department of Life Sciences
Sir Ernst Chain Building
Imperial College London
South Kensington Campus
London, SW7 2AZ, UK

t: +44 (0)20 7594 5251

http://www3.imperial.ac.uk/people/m.beeby
@BeebyLab



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. 



--
Morgan Beeby | Lecturer in Structural Biology
Department of Life Sciences
Sir Ernst Chain Building
Imperial College London
South Kensington Campus
London, SW7 2AZ, UK

t: +44 (0)20 7594 5251

http://www3.imperial.ac.uk/people/m.beeby
@BeebyLab



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: Backup of WebApollo data?

Eric Rasche-3
Hi Morgan,

We maintain some 200 viruses in Apollo, and we developed this https://github.com/galaxy-genome-annotation/apollo-git-backup to backup our apollo instance. Especially since we have small organisms this works quite well and allows us to have historical records / logs of historical changes to feature qualifiers / comments since that isn't (currently) available in Apollo.

If you try "arrow" (which is in beta), you can use commands like

arrow io write_text $organism_common_name --export_type GFF3

to export the gff3 for an organism. Let me know if you try either of these approaches and have any questions.

Cheers,
Eric


2017-06-27 19:39 GMT+00:00 Nathan Dunn <[hidden email]>:

Excellent.  

We provide some web services for doing this:


However, and a few sample scripts in our example and tools directory.  

However, you should also check out the “arrow” repo by Eric Rasche which is a very nice approach to doing this:


Please raise an issue if you run into any problems. 

Nathan

On Jun 27, 2017, at 8:06 PM, Morgan Beeby <[hidden email]> wrote:

Nathan,

Bingo. Thanks so much! I should have figured that...

I am also working to programmatically access WebApollo but will likely send another email in the coming days after reading the docs...

Morgan




On 26/06/2017 17:22, Nathan Dunn wrote:

Morgan,

They are located in your database.   If you are using postgresql and it is configured like this:

pg_dump apollo > dump.sql 

Or something like that.  

If you are using mysql then you would use mysqldump or script (https://stackoverflow.com/a/3259166/1739366) for H2. 

Let me know what you end up using and I’ll update the dock to reflect his.  

Nathan

On Jun 26, 2017, at 5:40 PM, Morgan Beeby <[hidden email]> wrote:

Hi all,

I am sure there is a trivial answer to this, or that it is somewhere in the docs, but for the life of me I haven't been able to find it.

Could someone tell me the location of the Web Apollo user annotations are so that I can setup a backup crontab...?

I have an installation of WebApollo 2.0.6 on Linux Mint 17.3.

many thanks!

Morgan


--
Morgan Beeby | Lecturer in Structural Biology
Department of Life Sciences
Sir Ernst Chain Building
Imperial College London
South Kensington Campus
London, SW7 2AZ, UK

t: +44 (0)20 7594 5251

http://www3.imperial.ac.uk/people/m.beeby
@BeebyLab



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. 



--
Morgan Beeby | Lecturer in Structural Biology
Department of Life Sciences
Sir Ernst Chain Building
Imperial College London
South Kensington Campus
London, SW7 2AZ, UK

t: +44 (0)20 7594 5251

http://www3.imperial.ac.uk/people/m.beeby
@BeebyLab



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.





--
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
404-692-2048




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: Backup of WebApollo data?

mbeeby
Hi Eric,

Great -- your Arrow example was a big help (I'd been struggling a bit to find examples). Thanks. I'm a bit overwhelmed with various admin duties at the moment but hope to take a look at your backup script soon.

best,

Morgan



On 28/06/2017 07:54, Eric Rasche wrote:
Hi Morgan,

We maintain some 200 viruses in Apollo, and we developed this https://github.com/galaxy-genome-annotation/apollo-git-backup to backup our apollo instance. Especially since we have small organisms this works quite well and allows us to have historical records / logs of historical changes to feature qualifiers / comments since that isn't (currently) available in Apollo.

If you try "arrow" (which is in beta), you can use commands like

arrow io write_text $organism_common_name --export_type GFF3

to export the gff3 for an organism. Let me know if you try either of these approaches and have any questions.

Cheers,
Eric


2017-06-27 19:39 GMT+00:00 Nathan Dunn <[hidden email]>:

Excellent.  

We provide some web services for doing this:


However, and a few sample scripts in our example and tools directory.  

However, you should also check out the “arrow” repo by Eric Rasche which is a very nice approach to doing this:


Please raise an issue if you run into any problems. 

Nathan

On Jun 27, 2017, at 8:06 PM, Morgan Beeby <[hidden email]> wrote:

Nathan,

Bingo. Thanks so much! I should have figured that...

I am also working to programmatically access WebApollo but will likely send another email in the coming days after reading the docs...

Morgan




On 26/06/2017 17:22, Nathan Dunn wrote:

Morgan,

They are located in your database.   If you are using postgresql and it is configured like this:

pg_dump apollo > dump.sql 
Or something like that.  
If you are using mysql then you would use mysqldump or script (https://stackoverflow.com/a/3259166/1739366) for H2. 
Let me know what you end up using and I’ll update the dock to reflect his.  
Nathan
On Jun 26, 2017, at 5:40 PM, Morgan Beeby <[hidden email]> wrote:
Hi all, I am sure there is a trivial answer to this, or that it is somewhere in the docs, but for the life of me I haven't been able to find it. Could someone tell me the location of the Web Apollo user annotations are so that I can setup a backup crontab...? I have an installation of WebApollo 2.0.6 on Linux Mint 17.3. many thanks! Morgan
-- Morgan Beeby | Lecturer in Structural Biology Department of Life Sciences Sir Ernst Chain Building Imperial College London South Kensington Campus London, SW7 2AZ, UK t: +44 (0)20 7594 5251 http://www3.imperial.ac.uk/people/m.beeby @BeebyLab
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. 

-- Morgan Beeby | Lecturer in Structural Biology Department of Life Sciences Sir Ernst Chain Building Imperial College London South Kensington Campus London, SW7 2AZ, UK t: +44 (0)20 7594 5251 http://www3.imperial.ac.uk/people/m.beeby @BeebyLab
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.
--
Eric Rasche
Programmer II
Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
404-692-2048


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. 

-- Morgan Beeby | Lecturer in Structural Biology Department of Life Sciences Sir Ernst Chain Building Imperial College London South Kensington Campus London, SW7 2AZ, UK t: +44 (0)20 7594 5251 http://www3.imperial.ac.uk/people/m.beeby @BeebyLab




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: Backup of WebApollo data?

Eric Rasche-3
Hi Morgan,

Yep, great point, the documentation on arrow isn't really written yet. I'm hoping to polish that up before release but I haven't gotten around to it yet.

Please let me know if you have questions, happy to help with any of these pain points with this new tool that I've built. We use the git backup more regularly, but it's slightly less easy to configure and may not be appropriate / useful to your usecase. Hence saying "here's a single CLI command that does what you need".

Cheers,
Eric

2017-06-30 14:45 GMT+00:00 Morgan Beeby <[hidden email]>:
Hi Eric,

Great -- your Arrow example was a big help (I'd been struggling a bit to find examples). Thanks. I'm a bit overwhelmed with various admin duties at the moment but hope to take a look at your backup script soon.

best,

Morgan




On 28/06/2017 07:54, Eric Rasche wrote:
Hi Morgan,

We maintain some 200 viruses in Apollo, and we developed this https://github.com/galaxy-genome-annotation/apollo-git-backup to backup our apollo instance. Especially since we have small organisms this works quite well and allows us to have historical records / logs of historical changes to feature qualifiers / comments since that isn't (currently) available in Apollo.

If you try "arrow" (which is in beta), you can use commands like

arrow io write_text $organism_common_name --export_type GFF3

to export the gff3 for an organism. Let me know if you try either of these approaches and have any questions.

Cheers,
Eric


2017-06-27 19:39 GMT+00:00 Nathan Dunn <[hidden email]>:

Excellent.  

We provide some web services for doing this:


However, and a few sample scripts in our example and tools directory.  

However, you should also check out the “arrow” repo by Eric Rasche which is a very nice approach to doing this:


Please raise an issue if you run into any problems. 

Nathan

On Jun 27, 2017, at 8:06 PM, Morgan Beeby <[hidden email]> wrote:

Nathan,

Bingo. Thanks so much! I should have figured that...

I am also working to programmatically access WebApollo but will likely send another email in the coming days after reading the docs...

Morgan




On 26/06/2017 17:22, Nathan Dunn wrote:

Morgan,

They are located in your database.   If you are using postgresql and it is configured like this:

pg_dump apollo > dump.sql 
Or something like that.  
If you are using mysql then you would use mysqldump or script (https://stackoverflow.com/a/3259166/1739366) for H2. 
Let me know what you end up using and I’ll update the dock to reflect his.  
Nathan
On Jun 26, 2017, at 5:40 PM, Morgan Beeby <[hidden email]> wrote:
Hi all, I am sure there is a trivial answer to this, or that it is somewhere in the docs, but for the life of me I haven't been able to find it. Could someone tell me the location of the Web Apollo user annotations are so that I can setup a backup crontab...? I have an installation of WebApollo 2.0.6 on Linux Mint 17.3. many thanks! Morgan
-- Morgan Beeby | Lecturer in Structural Biology Department of Life Sciences Sir Ernst Chain Building Imperial College London South Kensington Campus London, SW7 2AZ, UK t: +44 (0)20 7594 5251 http://www3.imperial.ac.uk/people/m.beeby @BeebyLab
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. 

-- Morgan Beeby | Lecturer in Structural Biology Department of Life Sciences Sir Ernst Chain Building Imperial College London South Kensington Campus London, SW7 2AZ, UK t: +44 (0)20 7594 5251 http://www3.imperial.ac.uk/people/m.beeby @BeebyLab
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.
--
Eric Rasche
Programmer II
Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
404-692-2048

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. 

-- Morgan Beeby | Lecturer in Structural Biology Department of Life Sciences Sir Ernst Chain Building Imperial College London South Kensington Campus London, SW7 2AZ, UK t: +44 (0)20 7594 5251 http://www3.imperial.ac.uk/people/m.beeby @BeebyLab




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.





--
Eric Rasche
Software Application Developer II

Center for Phage Technology
Texas A&M University
College Station, TX 77843




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...