Two issues

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Two issues

Robin A. Ohm
Dear apollo team,

I've run into two separate issues:

The first issue is upgrading from version 2.0.5 to 2.0.8. The login
screen appears and allows me to log in. Everything looks fine, except
that Jbrowse doesn't load. In catalina.out I see these error messages,
indeed pointing to a problem with Jbrowse:

2018-02-06 10:46:21,046 [http-bio-8080-exec-8] ERROR
apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
2018-02-06 10:46:21,136 [http-bio-8080-exec-10] ERROR
apollo.JbrowseController  - File not found:
/jbrowse/src/dijit/themes/tundra/tundra.css
2018-02-06 10:46:21,138 [http-bio-8080-exec-4] ERROR
apollo.JbrowseController  - File not found:
/jbrowse/src/dojo/resources/dojo.css
2018-02-06 10:46:21,140 [http-bio-8080-exec-1] ERROR
apollo.JbrowseController  - File not found: /jbrowse/src/dgrid/css/dgrid.css
2018-02-06 10:46:21,157 [http-bio-8080-exec-3] ERROR
apollo.JbrowseController  - File not found:
/jbrowse/src/dojox/form/resources/UploaderFileList.css
2018-02-06 10:46:21,176 [http-bio-8080-exec-4] ERROR
apollo.JbrowseController  - File not found:
/jbrowse/src/dojox/grid/resources/tundraGrid.css
2018-02-06 10:46:21,198 [http-bio-8080-exec-2] ERROR
apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
2018-02-06 10:46:30,533 [http-bio-8080-exec-8] ERROR
apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
2018-02-06 10:46:30,601 [http-bio-8080-exec-5] ERROR
apollo.JbrowseController  - File not found: /jbrowse/src/dgrid/css/dgrid.css
2018-02-06 10:46:30,602 [http-bio-8080-exec-6] ERROR
apollo.JbrowseController  - File not found:
/jbrowse/src/dojox/grid/resources/tundraGrid.css
2018-02-06 10:46:30,603 [http-bio-8080-exec-10] ERROR
apollo.JbrowseController  - File not found:
/jbrowse/src/dojox/form/resources/UploaderFileList.css
2018-02-06 10:46:30,612 [http-bio-8080-exec-3] ERROR
apollo.JbrowseController  - File not found:
/jbrowse/src/dojo/resources/dojo.css
2018-02-06 10:46:30,614 [http-bio-8080-exec-4] ERROR
apollo.JbrowseController  - File not found:
/jbrowse/src/dijit/themes/tundra/tundra.css
2018-02-06 10:46:30,635 [http-bio-8080-exec-7] ERROR
apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js

In the 2.0.8 release text on github
(https://github.com/GMOD/Apollo/releases) I see a few remarks about
Jbrowse, but I'm not sure what you mean. In any case, I tried to deploy
with the jbrowse block (in apollo-config.groovy) commented or
uncommented, but the results were the same. I did upgrade node to
version 8.9.4. This problem doesn't happen after rolling back to 2.0.5.
I probably missed something obvious, but could you please give advice
about what I could try?

The second issue happens in 2.0.5 (but I noticed it in previous versions
too) and is a little harder to describe/reproduce. I currently have
several strains of Saccharomyces cerevisiae, and several species of
Ophiocordyceps. Initially this works well, but after switching a few
times between the various strains and species, we notice the following
problems:

- Genes in the User-created Annotations track from one strain of S.
cerevisiae appear in the portal of another strain. Same for
Ophiocordyceps species.
- Tracks from 1 strain show up in the Tracks tab of another strain.
- Bigwig tracks that have worked fine can suddenly not be found.
- If I hit reload on the web browser, I end up in a different strain.
- Oddly, these 'bleed-through' problems only happen between organisms
with a similar (but still unique) organism name. So only between strains
of Saccharomyces, and between species of Ophiocordyceps, but never
between Sac and Ophio. We have several other unique species, which don't
appear to have any problems.
- Reloading the web browser doesn't fix it and and neither does using a
private window in Firefox.
- What does seem to help is to run the following mysql command: "delete
from preference;"  This fixes the problem briefly, but after switching
between organisms a few times the problem comes back.
- These problems were reported by several users and it makes it
hard/impossible to actually use apollo for these organisms.

Hopefully you can give some advice on what I could try. These organisms
are currently not public, so I can't provide a direct link. However, if
it would be helpful for troubleshooting then I could give you a user
name and password.

Thanks for your help! Best regards,

Robin

--
Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University | Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 30 2533016 | [hidden email]





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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Re: Two issues

nathandunn

For the first issue, if you are upgrading from an existing Apollo in-place, likely the apollo clean-all , apollo deploy may be necessary.   It looks like you have the right version of node / npm.    

So:
1- confirm that the apollo-config.groovy jbrowse section looks the same as it does in the Config.groovy (except with any added plugins you might have) or simply exclude the section entirely.
2 - run, apollo clean-all, apollo deploy  and then deploy


For your second issue, I made a lot of fixes to the preferences code, so hopefully upgrading to 2.0.8 fixes those (if not, please raise an issue).

Nathan


> On Feb 6, 2018, at 3:05 AM, Robin A. Ohm <[hidden email]> wrote:
>
> Dear apollo team,
>
> I've run into two separate issues:
>
> The first issue is upgrading from version 2.0.5 to 2.0.8. The login screen appears and allows me to log in. Everything looks fine, except that Jbrowse doesn't load. In catalina.out I see these error messages, indeed pointing to a problem with Jbrowse:
>
> 2018-02-06 10:46:21,046 [http-bio-8080-exec-8] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
> 2018-02-06 10:46:21,136 [http-bio-8080-exec-10] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dijit/themes/tundra/tundra.css
> 2018-02-06 10:46:21,138 [http-bio-8080-exec-4] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/resources/dojo.css
> 2018-02-06 10:46:21,140 [http-bio-8080-exec-1] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dgrid/css/dgrid.css
> 2018-02-06 10:46:21,157 [http-bio-8080-exec-3] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojox/form/resources/UploaderFileList.css
> 2018-02-06 10:46:21,176 [http-bio-8080-exec-4] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojox/grid/resources/tundraGrid.css
> 2018-02-06 10:46:21,198 [http-bio-8080-exec-2] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
> 2018-02-06 10:46:30,533 [http-bio-8080-exec-8] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
> 2018-02-06 10:46:30,601 [http-bio-8080-exec-5] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dgrid/css/dgrid.css
> 2018-02-06 10:46:30,602 [http-bio-8080-exec-6] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojox/grid/resources/tundraGrid.css
> 2018-02-06 10:46:30,603 [http-bio-8080-exec-10] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojox/form/resources/UploaderFileList.css
> 2018-02-06 10:46:30,612 [http-bio-8080-exec-3] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/resources/dojo.css
> 2018-02-06 10:46:30,614 [http-bio-8080-exec-4] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dijit/themes/tundra/tundra.css
> 2018-02-06 10:46:30,635 [http-bio-8080-exec-7] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
>
> In the 2.0.8 release text on github (https://github.com/GMOD/Apollo/releases) I see a few remarks about Jbrowse, but I'm not sure what you mean. In any case, I tried to deploy with the jbrowse block (in apollo-config.groovy) commented or uncommented, but the results were the same. I did upgrade node to version 8.9.4. This problem doesn't happen after rolling back to 2.0.5. I probably missed something obvious, but could you please give advice about what I could try?
>
> The second issue happens in 2.0.5 (but I noticed it in previous versions too) and is a little harder to describe/reproduce. I currently have several strains of Saccharomyces cerevisiae, and several species of Ophiocordyceps. Initially this works well, but after switching a few times between the various strains and species, we notice the following problems:
>
> - Genes in the User-created Annotations track from one strain of S. cerevisiae appear in the portal of another strain. Same for Ophiocordyceps species.
> - Tracks from 1 strain show up in the Tracks tab of another strain.
> - Bigwig tracks that have worked fine can suddenly not be found.
> - If I hit reload on the web browser, I end up in a different strain.
> - Oddly, these 'bleed-through' problems only happen between organisms with a similar (but still unique) organism name. So only between strains of Saccharomyces, and between species of Ophiocordyceps, but never between Sac and Ophio. We have several other unique species, which don't appear to have any problems.
> - Reloading the web browser doesn't fix it and and neither does using a private window in Firefox.
> - What does seem to help is to run the following mysql command: "delete from preference;"  This fixes the problem briefly, but after switching between organisms a few times the problem comes back.
> - These problems were reported by several users and it makes it hard/impossible to actually use apollo for these organisms.
>
> Hopefully you can give some advice on what I could try. These organisms are currently not public, so I can't provide a direct link. However, if it would be helpful for troubleshooting then I could give you a user name and password.
>
> Thanks for your help! Best regards,
>
> Robin
>
> --
> Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University | Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 30 2533016 | [hidden email]
>
>
>
>
> 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.

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Re: Two issues

Robin A. Ohm

Hi Nathan,

I think I already tried all that, but just to make sure, here's what I did:

wget https://github.com/GMOD/Apollo/archive/2.0.8.zip
Unzip, rename the sample mysql config file to apollo-config.groovy, fill out mysql credentials and database name/locations. I keep the JBrowse section commented.
./apollo clean-all
./apollo deploy
The output can be found in apollo_deploy.txt in attachment. Judging from this it appears that JBrowse is installed. No obvious errors, but some warnings that may be significant to you?
Stop tomcat7, remove 2.0.5 WAR file and directory, copy 2.0.8 WAR file, start tomcat7
After a few minutes I can log in to apollo and the organisms are shown, but the JBrowse frame doesn't load.
See catalina.out in attachment for more details (contains logs since tomcat7 was restarted). Note the jbrowse errors, but also java errors (although those errors were also present in 2.0.5, I just noticed...)

Thanks, best regards,

Robin

Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University | Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 30 2533016 | [hidden email]
On 02/06/2018 05:41 PM, Nathan Dunn wrote:

For the first issue, if you are upgrading from an existing Apollo in-place, likely the apollo clean-all , apollo deploy may be necessary.   It looks like you have the right version of node / npm.   

So:
1- confirm that the apollo-config.groovy jbrowse section looks the same as it does in the Config.groovy (except with any added plugins you might have) or simply exclude the section entirely.
2 - run, apollo clean-all, apollo deploy  and then deploy


For your second issue, I made a lot of fixes to the preferences code, so hopefully upgrading to 2.0.8 fixes those (if not, please raise an issue).

Nathan


> On Feb 6, 2018, at 3:05 AM, Robin A. Ohm [hidden email] wrote:
>
> Dear apollo team,
>
> I've run into two separate issues:
>
> The first issue is upgrading from version 2.0.5 to 2.0.8. The login screen appears and allows me to log in. Everything looks fine, except that Jbrowse doesn't load. In catalina.out I see these error messages, indeed pointing to a problem with Jbrowse:
>
> 2018-02-06 10:46:21,046 [http-bio-8080-exec-8] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
> 2018-02-06 10:46:21,136 [http-bio-8080-exec-10] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dijit/themes/tundra/tundra.css
> 2018-02-06 10:46:21,138 [http-bio-8080-exec-4] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/resources/dojo.css
> 2018-02-06 10:46:21,140 [http-bio-8080-exec-1] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dgrid/css/dgrid.css
> 2018-02-06 10:46:21,157 [http-bio-8080-exec-3] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojox/form/resources/UploaderFileList.css
> 2018-02-06 10:46:21,176 [http-bio-8080-exec-4] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojox/grid/resources/tundraGrid.css
> 2018-02-06 10:46:21,198 [http-bio-8080-exec-2] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
> 2018-02-06 10:46:30,533 [http-bio-8080-exec-8] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
> 2018-02-06 10:46:30,601 [http-bio-8080-exec-5] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dgrid/css/dgrid.css
> 2018-02-06 10:46:30,602 [http-bio-8080-exec-6] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojox/grid/resources/tundraGrid.css
> 2018-02-06 10:46:30,603 [http-bio-8080-exec-10] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojox/form/resources/UploaderFileList.css
> 2018-02-06 10:46:30,612 [http-bio-8080-exec-3] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/resources/dojo.css
> 2018-02-06 10:46:30,614 [http-bio-8080-exec-4] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dijit/themes/tundra/tundra.css
> 2018-02-06 10:46:30,635 [http-bio-8080-exec-7] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
>
> In the 2.0.8 release text on github (https://github.com/GMOD/Apollo/releases) I see a few remarks about Jbrowse, but I'm not sure what you mean. In any case, I tried to deploy with the jbrowse block (in apollo-config.groovy) commented or uncommented, but the results were the same. I did upgrade node to version 8.9.4. This problem doesn't happen after rolling back to 2.0.5. I probably missed something obvious, but could you please give advice about what I could try?
>
> The second issue happens in 2.0.5 (but I noticed it in previous versions too) and is a little harder to describe/reproduce. I currently have several strains of Saccharomyces cerevisiae, and several species of Ophiocordyceps. Initially this works well, but after switching a few times between the various strains and species, we notice the following problems:
>
> - Genes in the User-created Annotations track from one strain of S. cerevisiae appear in the portal of another strain. Same for Ophiocordyceps species.
> - Tracks from 1 strain show up in the Tracks tab of another strain.
> - Bigwig tracks that have worked fine can suddenly not be found.
> - If I hit reload on the web browser, I end up in a different strain.
> - Oddly, these 'bleed-through' problems only happen between organisms with a similar (but still unique) organism name. So only between strains of Saccharomyces, and between species of Ophiocordyceps, but never between Sac and Ophio. We have several other unique species, which don't appear to have any problems.
> - Reloading the web browser doesn't fix it and and neither does using a private window in Firefox.
> - What does seem to help is to run the following mysql command: "delete from preference;"  This fixes the problem briefly, but after switching between organisms a few times the problem comes back.
> - These problems were reported by several users and it makes it hard/impossible to actually use apollo for these organisms.
>
> Hopefully you can give some advice on what I could try. These organisms are currently not public, so I can't provide a direct link. However, if it would be helpful for troubleshooting then I could give you a user name and password.
>
> Thanks for your help! Best regards,
>
> Robin
>
> --
> Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University | Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 30 2533016 | [hidden email]
>
>
>
>
> 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.


apollo_deploy.log (5K) Download Attachment
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Re: Two issues

nathandunn

Robin,

Just a caveat (I think you probably did this, but I wanted to make sure):

1 - turn off tomcat
2 - rm -rf /var/lib/webapps/apollo*   (remove directories and the war file file they are built from)
3 - copy new built war file into /var/lib/webapps  (you were doing the apollo clean-all and apollo deploy already)
4 - start up the tomcat server

If, in step 2, you don’t remove the directories you may run into problems if you simply copy the next one in to.   

You may also want to remove all entries from the preference table (“delete from preference”) might help if you still run into problems. 

If there are still issues, if you could look for those files within web-app/jbrowse please post as well as look in the web-apps directory. 

Thanks,

Nathan


On Feb 7, 2018, at 5:54 AM, Robin A. Ohm <[hidden email]> wrote:

Hi Nathan,

I think I already tried all that, but just to make sure, here's what I did:

wget https://github.com/GMOD/Apollo/archive/2.0.8.zip
Unzip, rename the sample mysql config file to apollo-config.groovy, fill out mysql credentials and database name/locations. I keep the JBrowse section commented.
./apollo clean-all
./apollo deploy
The output can be found in apollo_deploy.txt in attachment. Judging from this it appears that JBrowse is installed. No obvious errors, but some warnings that may be significant to you?
Stop tomcat7, remove 2.0.5 WAR file and directory, copy 2.0.8 WAR file, start tomcat7
After a few minutes I can log in to apollo and the organisms are shown, but the JBrowse frame doesn't load.
See catalina.out in attachment for more details (contains logs since tomcat7 was restarted). Note the jbrowse errors, but also java errors (although those errors were also present in 2.0.5, I just noticed...)

Thanks, best regards,

Robin

Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University | Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 30 2533016 | [hidden email]
On 02/06/2018 05:41 PM, Nathan Dunn wrote:

For the first issue, if you are upgrading from an existing Apollo in-place, likely the apollo clean-all , apollo deploy may be necessary.   It looks like you have the right version of node / npm.   

So:
1- confirm that the apollo-config.groovy jbrowse section looks the same as it does in the Config.groovy (except with any added plugins you might have) or simply exclude the section entirely.
2 - run, apollo clean-all, apollo deploy  and then deploy


For your second issue, I made a lot of fixes to the preferences code, so hopefully upgrading to 2.0.8 fixes those (if not, please raise an issue).

Nathan


> On Feb 6, 2018, at 3:05 AM, Robin A. Ohm [hidden email] wrote:
>
> Dear apollo team,
>
> I've run into two separate issues:
>
> The first issue is upgrading from version 2.0.5 to 2.0.8. The login screen appears and allows me to log in. Everything looks fine, except that Jbrowse doesn't load. In catalina.out I see these error messages, indeed pointing to a problem with Jbrowse:
>
> 2018-02-06 10:46:21,046 [http-bio-8080-exec-8] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
> 2018-02-06 10:46:21,136 [http-bio-8080-exec-10] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dijit/themes/tundra/tundra.css
> 2018-02-06 10:46:21,138 [http-bio-8080-exec-4] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/resources/dojo.css
> 2018-02-06 10:46:21,140 [http-bio-8080-exec-1] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dgrid/css/dgrid.css
> 2018-02-06 10:46:21,157 [http-bio-8080-exec-3] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojox/form/resources/UploaderFileList.css
> 2018-02-06 10:46:21,176 [http-bio-8080-exec-4] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojox/grid/resources/tundraGrid.css
> 2018-02-06 10:46:21,198 [http-bio-8080-exec-2] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
> 2018-02-06 10:46:30,533 [http-bio-8080-exec-8] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
> 2018-02-06 10:46:30,601 [http-bio-8080-exec-5] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dgrid/css/dgrid.css
> 2018-02-06 10:46:30,602 [http-bio-8080-exec-6] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojox/grid/resources/tundraGrid.css
> 2018-02-06 10:46:30,603 [http-bio-8080-exec-10] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojox/form/resources/UploaderFileList.css
> 2018-02-06 10:46:30,612 [http-bio-8080-exec-3] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/resources/dojo.css
> 2018-02-06 10:46:30,614 [http-bio-8080-exec-4] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dijit/themes/tundra/tundra.css
> 2018-02-06 10:46:30,635 [http-bio-8080-exec-7] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
>
> In the 2.0.8 release text on github (https://github.com/GMOD/Apollo/releases) I see a few remarks about Jbrowse, but I'm not sure what you mean. In any case, I tried to deploy with the jbrowse block (in apollo-config.groovy) commented or uncommented, but the results were the same. I did upgrade node to version 8.9.4. This problem doesn't happen after rolling back to 2.0.5. I probably missed something obvious, but could you please give advice about what I could try?
>
> The second issue happens in 2.0.5 (but I noticed it in previous versions too) and is a little harder to describe/reproduce. I currently have several strains of Saccharomyces cerevisiae, and several species of Ophiocordyceps. Initially this works well, but after switching a few times between the various strains and species, we notice the following problems:
>
> - Genes in the User-created Annotations track from one strain of S. cerevisiae appear in the portal of another strain. Same for Ophiocordyceps species.
> - Tracks from 1 strain show up in the Tracks tab of another strain.
> - Bigwig tracks that have worked fine can suddenly not be found.
> - If I hit reload on the web browser, I end up in a different strain.
> - Oddly, these 'bleed-through' problems only happen between organisms with a similar (but still unique) organism name. So only between strains of Saccharomyces, and between species of Ophiocordyceps, but never between Sac and Ophio. We have several other unique species, which don't appear to have any problems.
> - Reloading the web browser doesn't fix it and and neither does using a private window in Firefox.
> - What does seem to help is to run the following mysql command: "delete from preference;"  This fixes the problem briefly, but after switching between organisms a few times the problem comes back.
> - These problems were reported by several users and it makes it hard/impossible to actually use apollo for these organisms.
>
> Hopefully you can give some advice on what I could try. These organisms are currently not public, so I can't provide a direct link. However, if it would be helpful for troubleshooting then I could give you a user name and password.
>
> Thanks for your help! Best regards,
>
> Robin
>
> --
> Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University | Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 30 2533016 | [hidden email]
>
>
>
>
> 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.


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RE: Two issues

Robin A. Ohm
Hi Nathan,

That is indeed what I did to upgrade to 2.0.8 (as well as for all previous upgrades over the past years). The only small difference is that my webapps folder is here: /var/lib/tomcat7/webapps

"delete from preference" didn't help.

I assume you meant that I should look for the files that were reported as not found in catalina.out? Such as: /jbrowse/src/dojo/dojo.js

Those files indeed appear to be missing (see output below). In the 2.0.5 version those files do exist. So it looks like something went wrong during the installation of JBrowse. I'm not sure what went wrong and I hope you have advice on how I can fix this?

Thanks! Robin


root@science-vs62:/var/lib/tomcat7/webapps# ll apollo/jbrowse/
total 424
drwxr-xr-x 12 tomcat7 tomcat7   4096 Feb  7 21:05 ./
drwxr-xr-x 12 tomcat7 tomcat7   4096 Feb  7 21:05 ../
drwxr-xr-x  2 tomcat7 tomcat7   4096 Feb  7 21:05 bin/
-rw-r--r--  1 tomcat7 tomcat7    520 Feb  7 13:42 bower.json
-rw-r--r--  1 tomcat7 tomcat7     25 Feb  7 13:42 .bowerrc
drwxr-xr-x  2 tomcat7 tomcat7   4096 Feb  7 21:05 browser/
drwxr-xr-x  2 tomcat7 tomcat7   4096 Feb  7 21:05 build/
-rw-r--r--  1 tomcat7 tomcat7   2462 Feb  7 13:42 compat_121.html
drwxr-xr-x  2 tomcat7 tomcat7   4096 Feb  7 21:05 css/
drwxr-xr-x  5 tomcat7 tomcat7   4096 Feb  7 21:05 docs/
drwxr-xr-x  4 tomcat7 tomcat7   4096 Feb  7 21:05 extlib/
-rw-r--r--  1 tomcat7 tomcat7    503 Feb  7 13:42 .htaccess
drwxr-xr-x  2 tomcat7 tomcat7   4096 Feb  7 21:05 img/
-rw-r--r--  1 tomcat7 tomcat7   5226 Feb  7 13:42 index.html
-rw-r--r--  1 tomcat7 tomcat7     97 Feb  7 13:42 INSTALL
-rw-r--r--  1 tomcat7 tomcat7   2893 Feb  7 13:42 jbrowse.conf
-rw-r--r--  1 tomcat7 tomcat7    299 Feb  7 13:42 jbrowse_conf.json
-rw-r--r--  1 tomcat7 tomcat7    718 Feb  7 13:42 .jshintrc
-rw-r--r--  1 tomcat7 tomcat7  33634 Feb  7 13:42 LICENSE
-rw-r--r--  1 tomcat7 tomcat7  59942 Feb  7 13:42 Makefile
-rw-r--r--  1 tomcat7 tomcat7   2962 Feb  7 13:42 Makefile.PL
-rw-r--r--  1 tomcat7 tomcat7   2582 Feb  7 13:42 MYMETA.json
-rw-r--r--  1 tomcat7 tomcat7   1396 Feb  7 13:42 MYMETA.yml
-rw-r--r--  1 tomcat7 tomcat7   1904 Feb  7 13:42 package.json
-rw-r--r--  1 tomcat7 tomcat7  20856 Feb  7 13:42 package-lock.json
drwxr-xr-x 10 tomcat7 tomcat7   4096 Feb  7 21:05 plugins/
-rw-r--r--  1 tomcat7 tomcat7   4418 Feb  7 13:42 README.md
-rw-r--r--  1 tomcat7 tomcat7 117361 Feb  7 13:42 release-notes.txt
-rw-r--r--  1 tomcat7 tomcat7  57716 Feb  7 13:42 setup.log
-rw-r--r--  1 tomcat7 tomcat7   8337 Feb  7 13:42 setup.sh
drwxr-xr-x  5 tomcat7 tomcat7   4096 Feb  7 21:05 src/
-rw-r--r--  1 tomcat7 tomcat7    787 Feb  7 13:42 .travis.yml
drwxr-xr-x  2 tomcat7 tomcat7   4096 Feb  7 21:05 utils/

root@science-vs62:/var/lib/tomcat7/webapps# ll apollo/jbrowse/src/
total 20
drwxr-xr-x  5 tomcat7 tomcat7 4096 Feb  7 21:05 ./
drwxr-xr-x 12 tomcat7 tomcat7 4096 Feb  7 21:05 ../
drwxr-xr-x  8 tomcat7 tomcat7 4096 Feb  7 21:05 JBrowse/
drwxr-xr-x  4 tomcat7 tomcat7 4096 Feb  7 21:05 perl5/
drwxr-xr-x  3 tomcat7 tomcat7 4096 Feb  7 21:05 wig2png/


Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 (0) 30 2533016


From: [hidden email] [[hidden email]] on behalf of Nathan Dunn [[hidden email]]
Sent: Wednesday, February 07, 2018 18:39
To: Apollo List
Subject: Re: [apollo] Two issues


Robin,

Just a caveat (I think you probably did this, but I wanted to make sure):

1 - turn off tomcat
2 - rm -rf /var/lib/webapps/apollo*   (remove directories and the war file file they are built from)
3 - copy new built war file into /var/lib/webapps  (you were doing the apollo clean-all and apollo deploy already)
4 - start up the tomcat server

If, in step 2, you don’t remove the directories you may run into problems if you simply copy the next one in to.   

You may also want to remove all entries from the preference table (“delete from preference”) might help if you still run into problems. 

If there are still issues, if you could look for those files within web-app/jbrowse please post as well as look in the web-apps directory. 

Thanks,

Nathan


On Feb 7, 2018, at 5:54 AM, Robin A. Ohm <[hidden email]> wrote:

Hi Nathan,

I think I already tried all that, but just to make sure, here's what I did:

wget https://github.com/GMOD/Apollo/archive/2.0.8.zip
Unzip, rename the sample mysql config file to apollo-config.groovy, fill out mysql credentials and database name/locations. I keep the JBrowse section commented.
./apollo clean-all
./apollo deploy
The output can be found in apollo_deploy.txt in attachment. Judging from this it appears that JBrowse is installed. No obvious errors, but some warnings that may be significant to you?
Stop tomcat7, remove 2.0.5 WAR file and directory, copy 2.0.8 WAR file, start tomcat7
After a few minutes I can log in to apollo and the organisms are shown, but the JBrowse frame doesn't load.
See catalina.out in attachment for more details (contains logs since tomcat7 was restarted). Note the jbrowse errors, but also java errors (although those errors were also present in 2.0.5, I just noticed...)

Thanks, best regards,

Robin

Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University | Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 30 2533016 | [hidden email]
On 02/06/2018 05:41 PM, Nathan Dunn wrote:

For the first issue, if you are upgrading from an existing Apollo in-place, likely the apollo clean-all , apollo deploy may be necessary.   It looks like you have the right version of node / npm.   

So:
1- confirm that the apollo-config.groovy jbrowse section looks the same as it does in the Config.groovy (except with any added plugins you might have) or simply exclude the section entirely.
2 - run, apollo clean-all, apollo deploy  and then deploy


For your second issue, I made a lot of fixes to the preferences code, so hopefully upgrading to 2.0.8 fixes those (if not, please raise an issue).

Nathan


> On Feb 6, 2018, at 3:05 AM, Robin A. Ohm [hidden email] wrote:
>
> Dear apollo team,
>
> I've run into two separate issues:
>
> The first issue is upgrading from version 2.0.5 to 2.0.8. The login screen appears and allows me to log in. Everything looks fine, except that Jbrowse doesn't load. In catalina.out I see these error messages, indeed pointing to a problem with Jbrowse:
>
> 2018-02-06 10:46:21,046 [http-bio-8080-exec-8] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
> 2018-02-06 10:46:21,136 [http-bio-8080-exec-10] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dijit/themes/tundra/tundra.css
> 2018-02-06 10:46:21,138 [http-bio-8080-exec-4] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/resources/dojo.css
> 2018-02-06 10:46:21,140 [http-bio-8080-exec-1] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dgrid/css/dgrid.css
> 2018-02-06 10:46:21,157 [http-bio-8080-exec-3] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojox/form/resources/UploaderFileList.css
> 2018-02-06 10:46:21,176 [http-bio-8080-exec-4] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojox/grid/resources/tundraGrid.css
> 2018-02-06 10:46:21,198 [http-bio-8080-exec-2] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
> 2018-02-06 10:46:30,533 [http-bio-8080-exec-8] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
> 2018-02-06 10:46:30,601 [http-bio-8080-exec-5] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dgrid/css/dgrid.css
> 2018-02-06 10:46:30,602 [http-bio-8080-exec-6] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojox/grid/resources/tundraGrid.css
> 2018-02-06 10:46:30,603 [http-bio-8080-exec-10] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojox/form/resources/UploaderFileList.css
> 2018-02-06 10:46:30,612 [http-bio-8080-exec-3] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/resources/dojo.css
> 2018-02-06 10:46:30,614 [http-bio-8080-exec-4] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dijit/themes/tundra/tundra.css
> 2018-02-06 10:46:30,635 [http-bio-8080-exec-7] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
>
> In the 2.0.8 release text on github (https://github.com/GMOD/Apollo/releases) I see a few remarks about Jbrowse, but I'm not sure what you mean. In any case, I tried to deploy with the jbrowse block (in apollo-config.groovy) commented or uncommented, but the results were the same. I did upgrade node to version 8.9.4. This problem doesn't happen after rolling back to 2.0.5. I probably missed something obvious, but could you please give advice about what I could try?
>
> The second issue happens in 2.0.5 (but I noticed it in previous versions too) and is a little harder to describe/reproduce. I currently have several strains of Saccharomyces cerevisiae, and several species of Ophiocordyceps. Initially this works well, but after switching a few times between the various strains and species, we notice the following problems:
>
> - Genes in the User-created Annotations track from one strain of S. cerevisiae appear in the portal of another strain. Same for Ophiocordyceps species.
> - Tracks from 1 strain show up in the Tracks tab of another strain.
> - Bigwig tracks that have worked fine can suddenly not be found.
> - If I hit reload on the web browser, I end up in a different strain.
> - Oddly, these 'bleed-through' problems only happen between organisms with a similar (but still unique) organism name. So only between strains of Saccharomyces, and between species of Ophiocordyceps, but never between Sac and Ophio. We have several other unique species, which don't appear to have any problems.
> - Reloading the web browser doesn't fix it and and neither does using a private window in Firefox.
> - What does seem to help is to run the following mysql command: "delete from preference;"  This fixes the problem briefly, but after switching between organisms a few times the problem comes back.
> - These problems were reported by several users and it makes it hard/impossible to actually use apollo for these organisms.
>
> Hopefully you can give some advice on what I could try. These organisms are currently not public, so I can't provide a direct link. However, if it would be helpful for troubleshooting then I could give you a user name and password.
>
> Thanks for your help! Best regards,
>
> Robin
>
> --
> Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University | Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 30 2533016 | [hidden email]
>
>
>
>
> 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.


<apollo_deploy.log><catalina.out>


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.

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Re: Two issues

nathandunn

So, I have two things two try:

1 - do the apollo deploy but not as root, but just as your regular user if you can.
2 - if that doesn’t work, then try cloning master and repeat the above e exercise. 

Nathan

On Feb 7, 2018, at 12:37 PM, Ohm, R.A. (Robin) <[hidden email]> wrote:

Hi Nathan,

That is indeed what I did to upgrade to 2.0.8 (as well as for all previous upgrades over the past years). The only small difference is that my webapps folder is here: /var/lib/tomcat7/webapps

"delete from preference" didn't help.

I assume you meant that I should look for the files that were reported as not found in catalina.out? Such as: /jbrowse/src/dojo/dojo.js

Those files indeed appear to be missing (see output below). In the 2.0.5 version those files do exist. So it looks like something went wrong during the installation of JBrowse. I'm not sure what went wrong and I hope you have advice on how I can fix this?

Thanks! Robin


root@science-vs62:/var/lib/tomcat7/webapps# ll apollo/jbrowse/
total 424
drwxr-xr-x 12 tomcat7 tomcat7   4096 Feb  7 21:05 ./
drwxr-xr-x 12 tomcat7 tomcat7   4096 Feb  7 21:05 ../
drwxr-xr-x  2 tomcat7 tomcat7   4096 Feb  7 21:05 bin/
-rw-r--r--  1 tomcat7 tomcat7    520 Feb  7 13:42 bower.json
-rw-r--r--  1 tomcat7 tomcat7     25 Feb  7 13:42 .bowerrc
drwxr-xr-x  2 tomcat7 tomcat7   4096 Feb  7 21:05 browser/
drwxr-xr-x  2 tomcat7 tomcat7   4096 Feb  7 21:05 build/
-rw-r--r--  1 tomcat7 tomcat7   2462 Feb  7 13:42 compat_121.html
drwxr-xr-x  2 tomcat7 tomcat7   4096 Feb  7 21:05 css/
drwxr-xr-x  5 tomcat7 tomcat7   4096 Feb  7 21:05 docs/
drwxr-xr-x  4 tomcat7 tomcat7   4096 Feb  7 21:05 extlib/
-rw-r--r--  1 tomcat7 tomcat7    503 Feb  7 13:42 .htaccess
drwxr-xr-x  2 tomcat7 tomcat7   4096 Feb  7 21:05 img/
-rw-r--r--  1 tomcat7 tomcat7   5226 Feb  7 13:42 index.html
-rw-r--r--  1 tomcat7 tomcat7     97 Feb  7 13:42 INSTALL
-rw-r--r--  1 tomcat7 tomcat7   2893 Feb  7 13:42 jbrowse.conf
-rw-r--r--  1 tomcat7 tomcat7    299 Feb  7 13:42 jbrowse_conf.json
-rw-r--r--  1 tomcat7 tomcat7    718 Feb  7 13:42 .jshintrc
-rw-r--r--  1 tomcat7 tomcat7  33634 Feb  7 13:42 LICENSE
-rw-r--r--  1 tomcat7 tomcat7  59942 Feb  7 13:42 Makefile
-rw-r--r--  1 tomcat7 tomcat7   2962 Feb  7 13:42 Makefile.PL
-rw-r--r--  1 tomcat7 tomcat7   2582 Feb  7 13:42 MYMETA.json
-rw-r--r--  1 tomcat7 tomcat7   1396 Feb  7 13:42 MYMETA.yml
-rw-r--r--  1 tomcat7 tomcat7   1904 Feb  7 13:42 package.json
-rw-r--r--  1 tomcat7 tomcat7  20856 Feb  7 13:42 package-lock.json
drwxr-xr-x 10 tomcat7 tomcat7   4096 Feb  7 21:05 plugins/
-rw-r--r--  1 tomcat7 tomcat7   4418 Feb  7 13:42 README.md
-rw-r--r--  1 tomcat7 tomcat7 117361 Feb  7 13:42 release-notes.txt
-rw-r--r--  1 tomcat7 tomcat7  57716 Feb  7 13:42 setup.log
-rw-r--r--  1 tomcat7 tomcat7   8337 Feb  7 13:42 setup.sh
drwxr-xr-x  5 tomcat7 tomcat7   4096 Feb  7 21:05 src/
-rw-r--r--  1 tomcat7 tomcat7    787 Feb  7 13:42 .travis.yml
drwxr-xr-x  2 tomcat7 tomcat7   4096 Feb  7 21:05 utils/

root@science-vs62:/var/lib/tomcat7/webapps# ll apollo/jbrowse/src/
total 20
drwxr-xr-x  5 tomcat7 tomcat7 4096 Feb  7 21:05 ./
drwxr-xr-x 12 tomcat7 tomcat7 4096 Feb  7 21:05 ../
drwxr-xr-x  8 tomcat7 tomcat7 4096 Feb  7 21:05 JBrowse/
drwxr-xr-x  4 tomcat7 tomcat7 4096 Feb  7 21:05 perl5/
drwxr-xr-x  3 tomcat7 tomcat7 4096 Feb  7 21:05 wig2png/


Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 (0) 30 2533016


From: [hidden email] [[hidden email]] on behalf of Nathan Dunn [[hidden email]]
Sent: Wednesday, February 07, 2018 18:39
To: Apollo List
Subject: Re: [apollo] Two issues


Robin,

Just a caveat (I think you probably did this, but I wanted to make sure):

1 - turn off tomcat
2 - rm -rf /var/lib/webapps/apollo*   (remove directories and the war file file they are built from)
3 - copy new built war file into /var/lib/webapps  (you were doing the apollo clean-all and apollo deploy already)
4 - start up the tomcat server

If, in step 2, you don’t remove the directories you may run into problems if you simply copy the next one in to.   

You may also want to remove all entries from the preference table (“delete from preference”) might help if you still run into problems. 

If there are still issues, if you could look for those files within web-app/jbrowse please post as well as look in the web-apps directory. 

Thanks,

Nathan


On Feb 7, 2018, at 5:54 AM, Robin A. Ohm <[hidden email]> wrote:

Hi Nathan,
I think I already tried all that, but just to make sure, here's what I did:
wget https://github.com/GMOD/Apollo/archive/2.0.8.zip
Unzip, rename the sample mysql config file to apollo-config.groovy, fill out mysql credentials and database name/locations. I keep the JBrowse section commented.
./apollo clean-all
./apollo deploy
The output can be found in apollo_deploy.txt in attachment. Judging from this it appears that JBrowse is installed. No obvious errors, but some warnings that may be significant to you?
Stop tomcat7, remove 2.0.5 WAR file and directory, copy 2.0.8 WAR file, start tomcat7
After a few minutes I can log in to apollo and the organisms are shown, but the JBrowse frame doesn't load.
See catalina.out in attachment for more details (contains logs since tomcat7 was restarted). Note the jbrowse errors, but also java errors (although those errors were also present in 2.0.5, I just noticed...)
Thanks, best regards,
Robin
Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University | Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 30 2533016 | [hidden email]
On 02/06/2018 05:41 PM, Nathan Dunn wrote:

For the first issue, if you are upgrading from an existing Apollo in-place, likely the apollo clean-all , apollo deploy may be necessary.   It looks like you have the right version of node / npm.    

So:
1- confirm that the apollo-config.groovy jbrowse section looks the same as it does in the Config.groovy (except with any added plugins you might have) or simply exclude the section entirely.
2 - run, apollo clean-all, apollo deploy  and then deploy 


For your second issue, I made a lot of fixes to the preferences code, so hopefully upgrading to 2.0.8 fixes those (if not, please raise an issue). 

Nathan


> On Feb 6, 2018, at 3:05 AM, Robin A. Ohm [hidden email] wrote:
> 
> Dear apollo team,
> 
> I've run into two separate issues:
> 
> The first issue is upgrading from version 2.0.5 to 2.0.8. The login screen appears and allows me to log in. Everything looks fine, except that Jbrowse doesn't load. In catalina.out I see these error messages, indeed pointing to a problem with Jbrowse:
> 
> 2018-02-06 10:46:21,046 [http-bio-8080-exec-8] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
> 2018-02-06 10:46:21,136 [http-bio-8080-exec-10] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dijit/themes/tundra/tundra.css
> 2018-02-06 10:46:21,138 [http-bio-8080-exec-4] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/resources/dojo.css
> 2018-02-06 10:46:21,140 [http-bio-8080-exec-1] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dgrid/css/dgrid.css
> 2018-02-06 10:46:21,157 [http-bio-8080-exec-3] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojox/form/resources/UploaderFileList.css
> 2018-02-06 10:46:21,176 [http-bio-8080-exec-4] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojox/grid/resources/tundraGrid.css
> 2018-02-06 10:46:21,198 [http-bio-8080-exec-2] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
> 2018-02-06 10:46:30,533 [http-bio-8080-exec-8] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
> 2018-02-06 10:46:30,601 [http-bio-8080-exec-5] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dgrid/css/dgrid.css
> 2018-02-06 10:46:30,602 [http-bio-8080-exec-6] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojox/grid/resources/tundraGrid.css
> 2018-02-06 10:46:30,603 [http-bio-8080-exec-10] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojox/form/resources/UploaderFileList.css
> 2018-02-06 10:46:30,612 [http-bio-8080-exec-3] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/resources/dojo.css
> 2018-02-06 10:46:30,614 [http-bio-8080-exec-4] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dijit/themes/tundra/tundra.css
> 2018-02-06 10:46:30,635 [http-bio-8080-exec-7] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
> 
> In the 2.0.8 release text on github (https://github.com/GMOD/Apollo/releases) I see a few remarks about Jbrowse, but I'm not sure what you mean. In any case, I tried to deploy with the jbrowse block (in apollo-config.groovy) commented or uncommented, but the results were the same. I did upgrade node to version 8.9.4. This problem doesn't happen after rolling back to 2.0.5. I probably missed something obvious, but could you please give advice about what I could try?
> 
> The second issue happens in 2.0.5 (but I noticed it in previous versions too) and is a little harder to describe/reproduce. I currently have several strains of Saccharomyces cerevisiae, and several species of Ophiocordyceps. Initially this works well, but after switching a few times between the various strains and species, we notice the following problems:
> 
> - Genes in the User-created Annotations track from one strain of S. cerevisiae appear in the portal of another strain. Same for Ophiocordyceps species.
> - Tracks from 1 strain show up in the Tracks tab of another strain.
> - Bigwig tracks that have worked fine can suddenly not be found.
> - If I hit reload on the web browser, I end up in a different strain.
> - Oddly, these 'bleed-through' problems only happen between organisms with a similar (but still unique) organism name. So only between strains of Saccharomyces, and between species of Ophiocordyceps, but never between Sac and Ophio. We have several other unique species, which don't appear to have any problems.
> - Reloading the web browser doesn't fix it and and neither does using a private window in Firefox.
> - What does seem to help is to run the following mysql command: "delete from preference;"  This fixes the problem briefly, but after switching between organisms a few times the problem comes back.
> - These problems were reported by several users and it makes it hard/impossible to actually use apollo for these organisms.
> 
> Hopefully you can give some advice on what I could try. These organisms are currently not public, so I can't provide a direct link. However, if it would be helpful for troubleshooting then I could give you a user name and password.
> 
> Thanks for your help! Best regards,
> 
> Robin
> 
> -- 
> Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University | Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 30 2533016 | [hidden email]
> 
> 
> 
> 
> 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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Re: Two issues

Robin A. Ohm

Hi Nathan,

Running deploy as a regular user did indeed fix the problem! During deploy those missing files are now explicitly copied. Also nice: at first glance my second issue (bleed-through between organisms) has also gone away after the upgrade. I'll let you know if it comes back in some form.

By the way, I looked at catalina.out and the java/grails errors are still there (see previous email). Is that a problem, even if the browser appears to be working fine? It was also there in 2.0.5.

SEVERE: ClassNotFoundException while loading persisted sessions: java.lang.ClassNotFoundException: org.codehaus.groovy.grails.web.servlet.GrailsFlashScope
java.lang.ClassNotFoundException: org.codehaus.groovy.grails.web.servlet.GrailsFlashScope
[...]
SEVERE: Exception loading sessions from persistent storage
java.lang.ClassNotFoundException: org.codehaus.groovy.grails.web.servlet.GrailsFlashScope

Thanks for your help, best regards

Robin
Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University | Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 30 2533016 | [hidden email]
On 02/07/2018 11:30 PM, Nathan Dunn wrote:

So, I have two things two try:

1 - do the apollo deploy but not as root, but just as your regular user if you can.
2 - if that doesn’t work, then try cloning master and repeat the above e exercise. 

Nathan

On Feb 7, 2018, at 12:37 PM, Ohm, R.A. (Robin) <[hidden email]> wrote:

Hi Nathan,

That is indeed what I did to upgrade to 2.0.8 (as well as for all previous upgrades over the past years). The only small difference is that my webapps folder is here: /var/lib/tomcat7/webapps

"delete from preference" didn't help.

I assume you meant that I should look for the files that were reported as not found in catalina.out? Such as: /jbrowse/src/dojo/dojo.js

Those files indeed appear to be missing (see output below). In the 2.0.5 version those files do exist. So it looks like something went wrong during the installation of JBrowse. I'm not sure what went wrong and I hope you have advice on how I can fix this?

Thanks! Robin


root@science-vs62:/var/lib/tomcat7/webapps# ll apollo/jbrowse/
total 424
drwxr-xr-x 12 tomcat7 tomcat7   4096 Feb  7 21:05 ./
drwxr-xr-x 12 tomcat7 tomcat7   4096 Feb  7 21:05 ../
drwxr-xr-x  2 tomcat7 tomcat7   4096 Feb  7 21:05 bin/
-rw-r--r--  1 tomcat7 tomcat7    520 Feb  7 13:42 bower.json
-rw-r--r--  1 tomcat7 tomcat7     25 Feb  7 13:42 .bowerrc
drwxr-xr-x  2 tomcat7 tomcat7   4096 Feb  7 21:05 browser/
drwxr-xr-x  2 tomcat7 tomcat7   4096 Feb  7 21:05 build/
-rw-r--r--  1 tomcat7 tomcat7   2462 Feb  7 13:42 compat_121.html
drwxr-xr-x  2 tomcat7 tomcat7   4096 Feb  7 21:05 css/
drwxr-xr-x  5 tomcat7 tomcat7   4096 Feb  7 21:05 docs/
drwxr-xr-x  4 tomcat7 tomcat7   4096 Feb  7 21:05 extlib/
-rw-r--r--  1 tomcat7 tomcat7    503 Feb  7 13:42 .htaccess
drwxr-xr-x  2 tomcat7 tomcat7   4096 Feb  7 21:05 img/
-rw-r--r--  1 tomcat7 tomcat7   5226 Feb  7 13:42 index.html
-rw-r--r--  1 tomcat7 tomcat7     97 Feb  7 13:42 INSTALL
-rw-r--r--  1 tomcat7 tomcat7   2893 Feb  7 13:42 jbrowse.conf
-rw-r--r--  1 tomcat7 tomcat7    299 Feb  7 13:42 jbrowse_conf.json
-rw-r--r--  1 tomcat7 tomcat7    718 Feb  7 13:42 .jshintrc
-rw-r--r--  1 tomcat7 tomcat7  33634 Feb  7 13:42 LICENSE
-rw-r--r--  1 tomcat7 tomcat7  59942 Feb  7 13:42 Makefile
-rw-r--r--  1 tomcat7 tomcat7   2962 Feb  7 13:42 Makefile.PL
-rw-r--r--  1 tomcat7 tomcat7   2582 Feb  7 13:42 MYMETA.json
-rw-r--r--  1 tomcat7 tomcat7   1396 Feb  7 13:42 MYMETA.yml
-rw-r--r--  1 tomcat7 tomcat7   1904 Feb  7 13:42 package.json
-rw-r--r--  1 tomcat7 tomcat7  20856 Feb  7 13:42 package-lock.json
drwxr-xr-x 10 tomcat7 tomcat7   4096 Feb  7 21:05 plugins/
-rw-r--r--  1 tomcat7 tomcat7   4418 Feb  7 13:42 README.md
-rw-r--r--  1 tomcat7 tomcat7 117361 Feb  7 13:42 release-notes.txt
-rw-r--r--  1 tomcat7 tomcat7  57716 Feb  7 13:42 setup.log
-rw-r--r--  1 tomcat7 tomcat7   8337 Feb  7 13:42 setup.sh
drwxr-xr-x  5 tomcat7 tomcat7   4096 Feb  7 21:05 src/
-rw-r--r--  1 tomcat7 tomcat7    787 Feb  7 13:42 .travis.yml
drwxr-xr-x  2 tomcat7 tomcat7   4096 Feb  7 21:05 utils/

root@science-vs62:/var/lib/tomcat7/webapps# ll apollo/jbrowse/src/
total 20
drwxr-xr-x  5 tomcat7 tomcat7 4096 Feb  7 21:05 ./
drwxr-xr-x 12 tomcat7 tomcat7 4096 Feb  7 21:05 ../
drwxr-xr-x  8 tomcat7 tomcat7 4096 Feb  7 21:05 JBrowse/
drwxr-xr-x  4 tomcat7 tomcat7 4096 Feb  7 21:05 perl5/
drwxr-xr-x  3 tomcat7 tomcat7 4096 Feb  7 21:05 wig2png/


Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 (0) 30 2533016


From: [hidden email] [[hidden email]] on behalf of Nathan Dunn [[hidden email]]
Sent: Wednesday, February 07, 2018 18:39
To: Apollo List
Subject: Re: [apollo] Two issues


Robin,

Just a caveat (I think you probably did this, but I wanted to make sure):

1 - turn off tomcat
2 - rm -rf /var/lib/webapps/apollo*   (remove directories and the war file file they are built from)
3 - copy new built war file into /var/lib/webapps  (you were doing the apollo clean-all and apollo deploy already)
4 - start up the tomcat server

If, in step 2, you don’t remove the directories you may run into problems if you simply copy the next one in to.   

You may also want to remove all entries from the preference table (“delete from preference”) might help if you still run into problems. 

If there are still issues, if you could look for those files within web-app/jbrowse please post as well as look in the web-apps directory. 

Thanks,

Nathan


On Feb 7, 2018, at 5:54 AM, Robin A. Ohm <[hidden email]> wrote:

Hi Nathan,
I think I already tried all that, but just to make sure, here's what I did:
wget https://github.com/GMOD/Apollo/archive/2.0.8.zip
Unzip, rename the sample mysql config file to apollo-config.groovy, fill out mysql credentials and database name/locations. I keep the JBrowse section commented.
./apollo clean-all
./apollo deploy
The output can be found in apollo_deploy.txt in attachment. Judging from this it appears that JBrowse is installed. No obvious errors, but some warnings that may be significant to you?
Stop tomcat7, remove 2.0.5 WAR file and directory, copy 2.0.8 WAR file, start tomcat7
After a few minutes I can log in to apollo and the organisms are shown, but the JBrowse frame doesn't load.
See catalina.out in attachment for more details (contains logs since tomcat7 was restarted). Note the jbrowse errors, but also java errors (although those errors were also present in 2.0.5, I just noticed...)
Thanks, best regards,
Robin
Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University | Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 30 2533016 | [hidden email]
On 02/06/2018 05:41 PM, Nathan Dunn wrote:

For the first issue, if you are upgrading from an existing Apollo in-place, likely the apollo clean-all , apollo deploy may be necessary.   It looks like you have the right version of node / npm.    

So:
1- confirm that the apollo-config.groovy jbrowse section looks the same as it does in the Config.groovy (except with any added plugins you might have) or simply exclude the section entirely.
2 - run, apollo clean-all, apollo deploy  and then deploy 


For your second issue, I made a lot of fixes to the preferences code, so hopefully upgrading to 2.0.8 fixes those (if not, please raise an issue). 

Nathan


> On Feb 6, 2018, at 3:05 AM, Robin A. Ohm [hidden email] wrote:
> 
> Dear apollo team,
> 
> I've run into two separate issues:
> 
> The first issue is upgrading from version 2.0.5 to 2.0.8. The login screen appears and allows me to log in. Everything looks fine, except that Jbrowse doesn't load. In catalina.out I see these error messages, indeed pointing to a problem with Jbrowse:
> 
> 2018-02-06 10:46:21,046 [http-bio-8080-exec-8] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
> 2018-02-06 10:46:21,136 [http-bio-8080-exec-10] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dijit/themes/tundra/tundra.css
> 2018-02-06 10:46:21,138 [http-bio-8080-exec-4] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/resources/dojo.css
> 2018-02-06 10:46:21,140 [http-bio-8080-exec-1] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dgrid/css/dgrid.css
> 2018-02-06 10:46:21,157 [http-bio-8080-exec-3] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojox/form/resources/UploaderFileList.css
> 2018-02-06 10:46:21,176 [http-bio-8080-exec-4] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojox/grid/resources/tundraGrid.css
> 2018-02-06 10:46:21,198 [http-bio-8080-exec-2] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
> 2018-02-06 10:46:30,533 [http-bio-8080-exec-8] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
> 2018-02-06 10:46:30,601 [http-bio-8080-exec-5] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dgrid/css/dgrid.css
> 2018-02-06 10:46:30,602 [http-bio-8080-exec-6] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojox/grid/resources/tundraGrid.css
> 2018-02-06 10:46:30,603 [http-bio-8080-exec-10] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojox/form/resources/UploaderFileList.css
> 2018-02-06 10:46:30,612 [http-bio-8080-exec-3] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/resources/dojo.css
> 2018-02-06 10:46:30,614 [http-bio-8080-exec-4] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dijit/themes/tundra/tundra.css
> 2018-02-06 10:46:30,635 [http-bio-8080-exec-7] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
> 
> In the 2.0.8 release text on github (https://github.com/GMOD/Apollo/releases) I see a few remarks about Jbrowse, but I'm not sure what you mean. In any case, I tried to deploy with the jbrowse block (in apollo-config.groovy) commented or uncommented, but the results were the same. I did upgrade node to version 8.9.4. This problem doesn't happen after rolling back to 2.0.5. I probably missed something obvious, but could you please give advice about what I could try?
> 
> The second issue happens in 2.0.5 (but I noticed it in previous versions too) and is a little harder to describe/reproduce. I currently have several strains of Saccharomyces cerevisiae, and several species of Ophiocordyceps. Initially this works well, but after switching a few times between the various strains and species, we notice the following problems:
> 
> - Genes in the User-created Annotations track from one strain of S. cerevisiae appear in the portal of another strain. Same for Ophiocordyceps species.
> - Tracks from 1 strain show up in the Tracks tab of another strain.
> - Bigwig tracks that have worked fine can suddenly not be found.
> - If I hit reload on the web browser, I end up in a different strain.
> - Oddly, these 'bleed-through' problems only happen between organisms with a similar (but still unique) organism name. So only between strains of Saccharomyces, and between species of Ophiocordyceps, but never between Sac and Ophio. We have several other unique species, which don't appear to have any problems.
> - Reloading the web browser doesn't fix it and and neither does using a private window in Firefox.
> - What does seem to help is to run the following mysql command: "delete from preference;"  This fixes the problem briefly, but after switching between organisms a few times the problem comes back.
> - These problems were reported by several users and it makes it hard/impossible to actually use apollo for these organisms.
> 
> Hopefully you can give some advice on what I could try. These organisms are currently not public, so I can't provide a direct link. However, if it would be helpful for troubleshooting then I could give you a user name and password.
> 
> Thanks for your help! Best regards,
> 
> Robin
> 
> -- 
> Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University | Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 30 2533016 | [hidden email]
> 
> 
> 
> 
> 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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Re: Two issues

nathandunn

Glad it worked out. 

My guess is the GrailsFlashScope is an artifact of some type of funky build.  

You *could* try removing the tomcat “work” directory if one exists, but so long as its not causing you issues, I’m not too worried. 

https://stackoverflow.com/a/22473479

Nathan

On Feb 8, 2018, at 4:09 AM, Robin A. Ohm <[hidden email]> wrote:

Hi Nathan,

Running deploy as a regular user did indeed fix the problem! During deploy those missing files are now explicitly copied. Also nice: at first glance my second issue (bleed-through between organisms) has also gone away after the upgrade. I'll let you know if it comes back in some form.

By the way, I looked at catalina.out and the java/grails errors are still there (see previous email). Is that a problem, even if the browser appears to be working fine? It was also there in 2.0.5.

SEVERE: ClassNotFoundException while loading persisted sessions: java.lang.ClassNotFoundException: org.codehaus.groovy.grails.web.servlet.GrailsFlashScope
java.lang.ClassNotFoundException: org.codehaus.groovy.grails.web.servlet.GrailsFlashScope
[...]
SEVERE: Exception loading sessions from persistent storage
java.lang.ClassNotFoundException: org.codehaus.groovy.grails.web.servlet.GrailsFlashScope

Thanks for your help, best regards

Robin
Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University | Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 30 2533016 | [hidden email]
On 02/07/2018 11:30 PM, Nathan Dunn wrote:

So, I have two things two try:

1 - do the apollo deploy but not as root, but just as your regular user if you can.
2 - if that doesn’t work, then try cloning master and repeat the above e exercise. 

Nathan

On Feb 7, 2018, at 12:37 PM, Ohm, R.A. (Robin) <[hidden email]> wrote:

Hi Nathan,

That is indeed what I did to upgrade to 2.0.8 (as well as for all previous upgrades over the past years). The only small difference is that my webapps folder is here: /var/lib/tomcat7/webapps

"delete from preference" didn't help.

I assume you meant that I should look for the files that were reported as not found in catalina.out? Such as: /jbrowse/src/dojo/dojo.js

Those files indeed appear to be missing (see output below). In the 2.0.5 version those files do exist. So it looks like something went wrong during the installation of JBrowse. I'm not sure what went wrong and I hope you have advice on how I can fix this?

Thanks! Robin


root@science-vs62:/var/lib/tomcat7/webapps# ll apollo/jbrowse/
total 424
drwxr-xr-x 12 tomcat7 tomcat7   4096 Feb  7 21:05 ./
drwxr-xr-x 12 tomcat7 tomcat7   4096 Feb  7 21:05 ../
drwxr-xr-x  2 tomcat7 tomcat7   4096 Feb  7 21:05 bin/
-rw-r--r--  1 tomcat7 tomcat7    520 Feb  7 13:42 bower.json
-rw-r--r--  1 tomcat7 tomcat7     25 Feb  7 13:42 .bowerrc
drwxr-xr-x  2 tomcat7 tomcat7   4096 Feb  7 21:05 browser/
drwxr-xr-x  2 tomcat7 tomcat7   4096 Feb  7 21:05 build/
-rw-r--r--  1 tomcat7 tomcat7   2462 Feb  7 13:42 compat_121.html
drwxr-xr-x  2 tomcat7 tomcat7   4096 Feb  7 21:05 css/
drwxr-xr-x  5 tomcat7 tomcat7   4096 Feb  7 21:05 docs/
drwxr-xr-x  4 tomcat7 tomcat7   4096 Feb  7 21:05 extlib/
-rw-r--r--  1 tomcat7 tomcat7    503 Feb  7 13:42 .htaccess
drwxr-xr-x  2 tomcat7 tomcat7   4096 Feb  7 21:05 img/
-rw-r--r--  1 tomcat7 tomcat7   5226 Feb  7 13:42 index.html
-rw-r--r--  1 tomcat7 tomcat7     97 Feb  7 13:42 INSTALL
-rw-r--r--  1 tomcat7 tomcat7   2893 Feb  7 13:42 jbrowse.conf
-rw-r--r--  1 tomcat7 tomcat7    299 Feb  7 13:42 jbrowse_conf.json
-rw-r--r--  1 tomcat7 tomcat7    718 Feb  7 13:42 .jshintrc
-rw-r--r--  1 tomcat7 tomcat7  33634 Feb  7 13:42 LICENSE
-rw-r--r--  1 tomcat7 tomcat7  59942 Feb  7 13:42 Makefile
-rw-r--r--  1 tomcat7 tomcat7   2962 Feb  7 13:42 Makefile.PL
-rw-r--r--  1 tomcat7 tomcat7   2582 Feb  7 13:42 MYMETA.json
-rw-r--r--  1 tomcat7 tomcat7   1396 Feb  7 13:42 MYMETA.yml
-rw-r--r--  1 tomcat7 tomcat7   1904 Feb  7 13:42 package.json
-rw-r--r--  1 tomcat7 tomcat7  20856 Feb  7 13:42 package-lock.json
drwxr-xr-x 10 tomcat7 tomcat7   4096 Feb  7 21:05 plugins/
-rw-r--r--  1 tomcat7 tomcat7   4418 Feb  7 13:42 README.md
-rw-r--r--  1 tomcat7 tomcat7 117361 Feb  7 13:42 release-notes.txt
-rw-r--r--  1 tomcat7 tomcat7  57716 Feb  7 13:42 setup.log
-rw-r--r--  1 tomcat7 tomcat7   8337 Feb  7 13:42 setup.sh
drwxr-xr-x  5 tomcat7 tomcat7   4096 Feb  7 21:05 src/
-rw-r--r--  1 tomcat7 tomcat7    787 Feb  7 13:42 .travis.yml
drwxr-xr-x  2 tomcat7 tomcat7   4096 Feb  7 21:05 utils/

root@science-vs62:/var/lib/tomcat7/webapps# ll apollo/jbrowse/src/
total 20
drwxr-xr-x  5 tomcat7 tomcat7 4096 Feb  7 21:05 ./
drwxr-xr-x 12 tomcat7 tomcat7 4096 Feb  7 21:05 ../
drwxr-xr-x  8 tomcat7 tomcat7 4096 Feb  7 21:05 JBrowse/
drwxr-xr-x  4 tomcat7 tomcat7 4096 Feb  7 21:05 perl5/
drwxr-xr-x  3 tomcat7 tomcat7 4096 Feb  7 21:05 wig2png/


Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University
Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 (0) 30 2533016


From: [hidden email] [[hidden email]] on behalf of Nathan Dunn [[hidden email]]
Sent: Wednesday, February 07, 2018 18:39
To: Apollo List
Subject: Re: [apollo] Two issues


Robin,

Just a caveat (I think you probably did this, but I wanted to make sure):

1 - turn off tomcat
2 - rm -rf /var/lib/webapps/apollo*   (remove directories and the war file file they are built from)
3 - copy new built war file into /var/lib/webapps  (you were doing the apollo clean-all and apollo deploy already)
4 - start up the tomcat server

If, in step 2, you don’t remove the directories you may run into problems if you simply copy the next one in to.   

You may also want to remove all entries from the preference table (“delete from preference”) might help if you still run into problems. 

If there are still issues, if you could look for those files within web-app/jbrowse please post as well as look in the web-apps directory. 

Thanks,

Nathan


On Feb 7, 2018, at 5:54 AM, Robin A. Ohm <[hidden email]> wrote:

Hi Nathan,
I think I already tried all that, but just to make sure, here's what I did:
wget https://github.com/GMOD/Apollo/archive/2.0.8.zip
Unzip, rename the sample mysql config file to apollo-config.groovy, fill out mysql credentials and database name/locations. I keep the JBrowse section commented.
./apollo clean-all
./apollo deploy
The output can be found in apollo_deploy.txt in attachment. Judging from this it appears that JBrowse is installed. No obvious errors, but some warnings that may be significant to you?
Stop tomcat7, remove 2.0.5 WAR file and directory, copy 2.0.8 WAR file, start tomcat7
After a few minutes I can log in to apollo and the organisms are shown, but the JBrowse frame doesn't load.
See catalina.out in attachment for more details (contains logs since tomcat7 was restarted). Note the jbrowse errors, but also java errors (although those errors were also present in 2.0.5, I just noticed...)
Thanks, best regards,
Robin
Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University | Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 30 2533016 | [hidden email]
On 02/06/2018 05:41 PM, Nathan Dunn wrote:

For the first issue, if you are upgrading from an existing Apollo in-place, likely the apollo clean-all , apollo deploy may be necessary.   It looks like you have the right version of node / npm.    

So:
1- confirm that the apollo-config.groovy jbrowse section looks the same as it does in the Config.groovy (except with any added plugins you might have) or simply exclude the section entirely.
2 - run, apollo clean-all, apollo deploy  and then deploy 


For your second issue, I made a lot of fixes to the preferences code, so hopefully upgrading to 2.0.8 fixes those (if not, please raise an issue). 

Nathan


> On Feb 6, 2018, at 3:05 AM, Robin A. Ohm [hidden email] wrote:
> 
> Dear apollo team,
> 
> I've run into two separate issues:
> 
> The first issue is upgrading from version 2.0.5 to 2.0.8. The login screen appears and allows me to log in. Everything looks fine, except that Jbrowse doesn't load. In catalina.out I see these error messages, indeed pointing to a problem with Jbrowse:
> 
> 2018-02-06 10:46:21,046 [http-bio-8080-exec-8] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
> 2018-02-06 10:46:21,136 [http-bio-8080-exec-10] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dijit/themes/tundra/tundra.css
> 2018-02-06 10:46:21,138 [http-bio-8080-exec-4] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/resources/dojo.css
> 2018-02-06 10:46:21,140 [http-bio-8080-exec-1] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dgrid/css/dgrid.css
> 2018-02-06 10:46:21,157 [http-bio-8080-exec-3] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojox/form/resources/UploaderFileList.css
> 2018-02-06 10:46:21,176 [http-bio-8080-exec-4] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojox/grid/resources/tundraGrid.css
> 2018-02-06 10:46:21,198 [http-bio-8080-exec-2] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
> 2018-02-06 10:46:30,533 [http-bio-8080-exec-8] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
> 2018-02-06 10:46:30,601 [http-bio-8080-exec-5] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dgrid/css/dgrid.css
> 2018-02-06 10:46:30,602 [http-bio-8080-exec-6] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojox/grid/resources/tundraGrid.css
> 2018-02-06 10:46:30,603 [http-bio-8080-exec-10] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojox/form/resources/UploaderFileList.css
> 2018-02-06 10:46:30,612 [http-bio-8080-exec-3] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/resources/dojo.css
> 2018-02-06 10:46:30,614 [http-bio-8080-exec-4] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dijit/themes/tundra/tundra.css
> 2018-02-06 10:46:30,635 [http-bio-8080-exec-7] ERROR apollo.JbrowseController  - File not found: /jbrowse/src/dojo/dojo.js
> 
> In the 2.0.8 release text on github (https://github.com/GMOD/Apollo/releases) I see a few remarks about Jbrowse, but I'm not sure what you mean. In any case, I tried to deploy with the jbrowse block (in apollo-config.groovy) commented or uncommented, but the results were the same. I did upgrade node to version 8.9.4. This problem doesn't happen after rolling back to 2.0.5. I probably missed something obvious, but could you please give advice about what I could try?
> 
> The second issue happens in 2.0.5 (but I noticed it in previous versions too) and is a little harder to describe/reproduce. I currently have several strains of Saccharomyces cerevisiae, and several species of Ophiocordyceps. Initially this works well, but after switching a few times between the various strains and species, we notice the following problems:
> 
> - Genes in the User-created Annotations track from one strain of S. cerevisiae appear in the portal of another strain. Same for Ophiocordyceps species.
> - Tracks from 1 strain show up in the Tracks tab of another strain.
> - Bigwig tracks that have worked fine can suddenly not be found.
> - If I hit reload on the web browser, I end up in a different strain.
> - Oddly, these 'bleed-through' problems only happen between organisms with a similar (but still unique) organism name. So only between strains of Saccharomyces, and between species of Ophiocordyceps, but never between Sac and Ophio. We have several other unique species, which don't appear to have any problems.
> - Reloading the web browser doesn't fix it and and neither does using a private window in Firefox.
> - What does seem to help is to run the following mysql command: "delete from preference;"  This fixes the problem briefly, but after switching between organisms a few times the problem comes back.
> - These problems were reported by several users and it makes it hard/impossible to actually use apollo for these organisms.
> 
> Hopefully you can give some advice on what I could try. These organisms are currently not public, so I can't provide a direct link. However, if it would be helpful for troubleshooting then I could give you a user name and password.
> 
> Thanks for your help! Best regards,
> 
> Robin
> 
> -- 
> Robin A. Ohm, PhD | Assistant Professor | Microbiology | Utrecht University | Kruyt Building | Room W402 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 30 2533016 | [hidden email]
> 
> 
> 
> 
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<apollo_deploy.log><catalina.out>


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