No user annotations after upgrade from 2.0.5 to 2.6.1

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No user annotations after upgrade from 2.0.5 to 2.6.1

Surya Saha
Hi Nathan et al,

I have upgraded an installation from v2.0.5 to v2.6.1 and moved the postgresql db to a different server. No issues building the .WAR file. I have downloaded https://github.com/GMOD/Apollo/archive/2.6.1.tar.gz and followed
My current config is
Apollo Version: 2.6.1
Grails version: 2.5.5
Groovy version: 2.4.4
JVM version: 1.8.0_272
Servlet Container Version: Apache Tomcat/8.5.54 (Debian)
JBrowse config: 1.16.9-release

I can add a new organism and tracks but cannot create new user annotations.
I see an access error in the tomcat log even though the directory is owned by tomcat8. I also see 403 errors in the console so maybe it's a permission issue in apache2/tomcat8? Apollo can connect to postgresql as I see all the old users, user annotations and organisms. The messages are in this gist
Any suggestions? I am happy to provide a test login if that helps.

Belated Happy Thanksgiving to all!

Cheers,
Surya

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Re: No user annotations after upgrade from 2.0.5 to 2.6.1

nathandunn


Oh, thanks for the logs.  

> spring-websocket.js:1213 WebSocket connection to 'wss://apollo.sgn.cornell.edu/apollo-2.6.1/stomp/733/yuxp71f5/websocketfailed: Error during WebSocket handshake: Unexpected response code: 403
> SockJS.websocket @ spring-websocket.js:1213
> /apollo-2.6.1/stomp/733/nva3rn3i/xhr_streaming:1 Failed to load resource: the server responded with a status of 403 ()
> /apollo-2.6.1/stomp/733/om6nby3l/xhr:1 Failed to load resource: the server responded with a status of 403 ()


I think its a problem with the web socket proxy.  If you are accessing Apollo through a proxy, the proxy changed slightly between 2.0 and 2.6.   More info can be found here.

https://genomearchitect.readthedocs.io/en/latest/Configure.html?highlight=nginx#apache-nginx-configuration

If you connect directly to tomcat it **should** work as desired and then you can update directly.

Nathan


> On Nov 27, 2020, at 4:26 AM, Surya Saha <[hidden email]> wrote:
>
> Hi Nathan et al,
>
> I have upgraded an installation from v2.0.5 to v2.6.1 and moved the postgresql db to a different server. No issues building the .WAR file. I have downloaded https://github.com/GMOD/Apollo/archive/2.6.1.tar.gz and followed
> standard instructions https://genomearchitect.readthedocs.io/en/latest/Setup.html
> My current config is
> Apollo Version: 2.6.1
> Grails version: 2.5.5
> Groovy version: 2.4.4
> JVM version: 1.8.0_272
> Servlet Container Version: Apache Tomcat/8.5.54 (Debian)
> JBrowse config: 1.16.9-release
>
> I can add a new organism and tracks but cannot create new user annotations.
> I see an access error in the tomcat log even though the directory is owned by tomcat8. I also see 403 errors in the console so maybe it's a permission issue in apache2/tomcat8? Apollo can connect to postgresql as I see all the old users, user annotations and organisms. The messages are in this gist
> https://gist.github.com/suryasaha/238d0522a274c5d90dc160e663c208f9
> Any suggestions? I am happy to provide a test login if that helps.
>
> Belated Happy Thanksgiving to all!
>
> Cheers,
> Surya
>
> --
>
> Surya Saha
> Sol Genomics Network
> Boyce Thompson Institute, Ithaca, NY, USA
> https://citrusgreening.org/
> https://orcid.org/0000-0002-1160-1413
> http://www.linkedin.com/in/suryasaha
> https://twitter.com/SahaSurya

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Re: No user annotations after upgrade from 2.0.5 to 2.6.1

Surya Saha
Hi Nathan,

Thank you for taking time during the break!

We tried both apache2 and nginx as described in the instructions but the websocket handshaking problem between the proxy and tomcat is still there. We also tried tomcat9. I can file an issue if that will be useful.

So it's on plain HTTP for the moment which is not great but a working solution. There is an issue with the JBrowse. The old Apollo 2.0.5 was working with a mix of Jbrowse 1.12 and 1.11 data files.

Now I see this error for a bunch of the genomes
"TypeError: Cannot read property 'name' of undefined at Object.renderDatasetSelect (http://apollo.sgn.cornell.edu/apollo/6175841221635210385384582466/jbrowse/dist/1.bundle.js:1:31154)

If I create a new Jbrowse installation with the 1.16.9 files in Apollo 2.6.1, it works fine. Any ideas? Many thanks!

Cheers,
Surya




On Fri, Nov 27, 2020 at 1:03 PM Nathan Dunn <[hidden email]> wrote:


Oh, thanks for the logs. 

> spring-websocket.js:1213 WebSocket connection to 'wss://apollo.sgn.cornell.edu/apollo-2.6.1/stomp/733/yuxp71f5/websocketfailed: Error during WebSocket handshake: Unexpected response code: 403
> SockJS.websocket @ spring-websocket.js:1213
> /apollo-2.6.1/stomp/733/nva3rn3i/xhr_streaming:1 Failed to load resource: the server responded with a status of 403 ()
> /apollo-2.6.1/stomp/733/om6nby3l/xhr:1 Failed to load resource: the server responded with a status of 403 ()


I think its a problem with the web socket proxy.  If you are accessing Apollo through a proxy, the proxy changed slightly between 2.0 and 2.6.   More info can be found here.

https://genomearchitect.readthedocs.io/en/latest/Configure.html?highlight=nginx#apache-nginx-configuration

If you connect directly to tomcat it **should** work as desired and then you can update directly.

Nathan


> On Nov 27, 2020, at 4:26 AM, Surya Saha <[hidden email]> wrote:
>
> Hi Nathan et al,
>
> I have upgraded an installation from v2.0.5 to v2.6.1 and moved the postgresql db to a different server. No issues building the .WAR file. I have downloaded https://github.com/GMOD/Apollo/archive/2.6.1.tar.gz and followed
> standard instructions https://genomearchitect.readthedocs.io/en/latest/Setup.html
> My current config is
> Apollo Version: 2.6.1
> Grails version: 2.5.5
> Groovy version: 2.4.4
> JVM version: 1.8.0_272
> Servlet Container Version: Apache Tomcat/8.5.54 (Debian)
> JBrowse config: 1.16.9-release
>
> I can add a new organism and tracks but cannot create new user annotations.
> I see an access error in the tomcat log even though the directory is owned by tomcat8. I also see 403 errors in the console so maybe it's a permission issue in apache2/tomcat8? Apollo can connect to postgresql as I see all the old users, user annotations and organisms. The messages are in this gist
> https://gist.github.com/suryasaha/238d0522a274c5d90dc160e663c208f9
> Any suggestions? I am happy to provide a test login if that helps.
>
> Belated Happy Thanksgiving to all!
>
> Cheers,
> Surya
>
> --
>
> Surya Saha
> Sol Genomics Network
> Boyce Thompson Institute, Ithaca, NY, USA
> https://citrusgreening.org/
> https://orcid.org/0000-0002-1160-1413
> http://www.linkedin.com/in/suryasaha
> https://twitter.com/SahaSurya

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Re: No user annotations after upgrade from 2.0.5 to 2.6.1

nathandunn

Oh, this makes sense. 

If I create a new Jbrowse installation with the 1.16.9 files in Apollo 2.6.1, it works fine. Any ideas? Many thanks!

Apollo 2.5+ needs a requires version of JBrowse.   I think 1.15+. 

My suggestion, use Apollo 2.6.X with JBrowse 1.16.X.  By default it should be using 1.16 internally, so not sure how the data format would be changing. 

Other than potential CSS differences, there shouldn’t be any actual differences in data files. 

I would upgrade all of your JBrowses to 1.16.X if possible anyway as there have been numerous bug fixes and enhancements.

Good luck,

Nathan


On Nov 30, 2020, at 9:16 AM, Surya Saha <[hidden email]> wrote:

Hi Nathan,

Thank you for taking time during the break!

We tried both apache2 and nginx as described in the instructions but the websocket handshaking problem between the proxy and tomcat is still there. We also tried tomcat9. I can file an issue if that will be useful.

So it's on plain HTTP for the moment which is not great but a working solution. There is an issue with the JBrowse. The old Apollo 2.0.5 was working with a mix of Jbrowse 1.12 and 1.11 data files.

Now I see this error for a bunch of the genomes
"TypeError: Cannot read property 'name' of undefined at Object.renderDatasetSelect (http://apollo.sgn.cornell.edu/apollo/6175841221635210385384582466/jbrowse/dist/1.bundle.js:1:31154)

If I create a new Jbrowse installation with the 1.16.9 files in Apollo 2.6.1, it works fine. Any ideas? Many thanks!

Cheers,
Surya




On Fri, Nov 27, 2020 at 1:03 PM Nathan Dunn <[hidden email]> wrote:


Oh, thanks for the logs. 

> spring-websocket.js:1213 WebSocket connection to 'wss://apollo.sgn.cornell.edu/apollo-2.6.1/stomp/733/yuxp71f5/websocketfailed: Error during WebSocket handshake: Unexpected response code: 403
> SockJS.websocket @ spring-websocket.js:1213
> /apollo-2.6.1/stomp/733/nva3rn3i/xhr_streaming:1 Failed to load resource: the server responded with a status of 403 ()
> /apollo-2.6.1/stomp/733/om6nby3l/xhr:1 Failed to load resource: the server responded with a status of 403 ()


I think its a problem with the web socket proxy.  If you are accessing Apollo through a proxy, the proxy changed slightly between 2.0 and 2.6.   More info can be found here.

https://genomearchitect.readthedocs.io/en/latest/Configure.html?highlight=nginx#apache-nginx-configuration

If you connect directly to tomcat it **should** work as desired and then you can update directly.

Nathan


> On Nov 27, 2020, at 4:26 AM, Surya Saha <[hidden email]> wrote:
>
> Hi Nathan et al,
>
> I have upgraded an installation from v2.0.5 to v2.6.1 and moved the postgresql db to a different server. No issues building the .WAR file. I have downloaded https://github.com/GMOD/Apollo/archive/2.6.1.tar.gz and followed
> standard instructions https://genomearchitect.readthedocs.io/en/latest/Setup.html
> My current config is
> Apollo Version: 2.6.1
> Grails version: 2.5.5
> Groovy version: 2.4.4
> JVM version: 1.8.0_272
> Servlet Container Version: Apache Tomcat/8.5.54 (Debian)
> JBrowse config: 1.16.9-release
>
> I can add a new organism and tracks but cannot create new user annotations.
> I see an access error in the tomcat log even though the directory is owned by tomcat8. I also see 403 errors in the console so maybe it's a permission issue in apache2/tomcat8? Apollo can connect to postgresql as I see all the old users, user annotations and organisms. The messages are in this gist
> https://gist.github.com/suryasaha/238d0522a274c5d90dc160e663c208f9
> Any suggestions? I am happy to provide a test login if that helps.
>
> Belated Happy Thanksgiving to all!
>
> Cheers,
> Surya
>
> --
>
> Surya Saha
> Sol Genomics Network
> Boyce Thompson Institute, Ithaca, NY, USA
> https://citrusgreening.org/
> https://orcid.org/0000-0002-1160-1413
> http://www.linkedin.com/in/suryasaha
> https://twitter.com/SahaSurya

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To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].



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