Fwd: [webapollo server setup]: jbrowse not showing data - permissions?

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Fwd: [webapollo server setup]: jbrowse not showing data - permissions?

Bert Brutzel-2
Hi,
I am trying to set up a server for cooperative annotation of some yeast
strains.
After some trial and error I am to get my data to be selectable at the
webapollo entry page. Selecting a track results in an jbrowse error that
there is not config: TypeError: config is undefined. If I manually
inspect the data/tracks.json and similar I can see all my data.

I belive it has something to do with permissions, what permission/users
should own/access the different folders? e.g. who needs access to data,
/var/lib/tomcat7/webapps/WebApollo/jbrowse, etc.....
Could I have a problem with the psql database rights?
The tomcat catalina.out log shows no errors Any other logs I should check?
I would be grateful for any pointers...

Thanks, Bert


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Re: Fwd: [webapollo server setup]: jbrowse not showing data - permissions?

ronnie.dejonge
Dear Bert,

From my experience working with/installing webapollo it is indeed essential to have all the permissions set correctly.

For me that means in : /var/lib/tomcat7/webapps/GENOME a ./tmp/ directory is set to tomcat7:tomcat7  (and this location is configured in blat_config.xml ; fasta_config.xml and gff3_config.xml).

At .../GENOME/webapollo/ I've got an ./annotations/ folder which is owned by tomcat7:tomcat7. This is were the updates from the user annotation track go (and it is found on line 8 of the config.xml in 'apps'/config/ directory).

For me it doesn't matter what permissions are set for the common files in the webapps folder (including the jbrowse/data subfolder). They are set to root:root for me...

Obviously this is assuming you have correctly added all scaffold_ids via the extract_seqids, add_tracks and set_track_permissions to the postgres database?

Hope this helps.

Regards,
Ronnie



2014-07-09 8:39 GMT+02:00 Bert Brutzel <[hidden email]>:
Hi,
I am trying to set up a server for cooperative annotation of some yeast strains.
After some trial and error I am to get my data to be selectable at the webapollo entry page. Selecting a track results in an jbrowse error that there is not config: TypeError: config is undefined. If I manually inspect the data/tracks.json and similar I can see all my data.

I belive it has something to do with permissions, what permission/users should own/access the different folders? e.g. who needs access to data, /var/lib/tomcat7/webapps/WebApollo/jbrowse, etc.....
Could I have a problem with the psql database rights?
The tomcat catalina.out log shows no errors Any other logs I should check?
I would be grateful for any pointers...

Thanks, Bert



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Re: Fwd: [webapollo server setup]: jbrowse not showing data - permissions?

Bert Brutzel-2
Dear Ronnie,

thanks for the quick response. I have my permissions set just like you, I am gratefull fot the pointer, but believe this is downstream of my current problem.
My instance is running now, created a new webapps/WebApollo/ instance by extracting the .war file. And pointed my config to the coressponding data folder...now it works. maybe I played around to much with the settings...

Thanky,
Johannes

Am 09.07.2014 09:03, schrieb Ronnie de Jonge:
Dear Bert,

From my experience working with/installing webapollo it is indeed essential to have all the permissions set correctly.

For me that means in : /var/lib/tomcat7/webapps/GENOME a ./tmp/ directory is set to tomcat7:tomcat7  (and this location is configured in blat_config.xml ; fasta_config.xml and gff3_config.xml).

At .../GENOME/webapollo/ I've got an ./annotations/ folder which is owned by tomcat7:tomcat7. This is were the updates from the user annotation track go (and it is found on line 8 of the config.xml in 'apps'/config/ directory).

For me it doesn't matter what permissions are set for the common files in the webapps folder (including the jbrowse/data subfolder). They are set to root:root for me...

Obviously this is assuming you have correctly added all scaffold_ids via the extract_seqids, add_tracks and set_track_permissions to the postgres database?

Hope this helps.

Regards,
Ronnie



2014-07-09 8:39 GMT+02:00 Bert Brutzel <[hidden email]>:
Hi,
I am trying to set up a server for cooperative annotation of some yeast strains.
After some trial and error I am to get my data to be selectable at the webapollo entry page. Selecting a track results in an jbrowse error that there is not config: TypeError: config is undefined. If I manually inspect the data/tracks.json and similar I can see all my data.

I belive it has something to do with permissions, what permission/users should own/access the different folders? e.g. who needs access to data, /var/lib/tomcat7/webapps/WebApollo/jbrowse, etc.....
Could I have a problem with the psql database rights?
The tomcat catalina.out log shows no errors Any other logs I should check?
I would be grateful for any pointers...

Thanks, Bert




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Create new Annotation

Bert Brutzel-2
In reply to this post by ronnie.dejonge
Dear All,

I got my instance somewhat up and running, but now I am unable to
selecte "create new annotaion" it is simply greyed out. How I proceed, I
loaded augustus predictions as a gff and now would like to annotate them
with a function.

Thanks for the help,
Bert
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Re: Create new Annotation

Colin
The "Create new annotation" right-click menu will normally be greyed out when you are not logged in. Are you able to login? If so, can you actually that you're logged in, and see the user created annotation track and everything? If you don't see any login type features inside the browser,  then you may need to run "bin/add-webapollo-plugin.pl" and this will add the webapollo plugin to jbrowse


-Colin




---------- Forwarded message ----------
From: Bert Brutzel <[hidden email]>
Date: Fri, Jul 11, 2014 at 4:17 AM
Subject: [apollo] Create new Annotation
To: [hidden email]


Dear All,

I got my instance somewhat up and running, but now I am unable to selecte "create new annotaion" it is simply greyed out. How I proceed, I loaded augustus predictions as a gff and now would like to annotate them with a function.

Thanks for the help,
Bert

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Re: Create new Annotation

Bert Brutzel-2
Hi Colin,

thanks for the quick reply. I issued:

$sudo bin/add-webapollo-plugin.pl -i data/trackList.json

parsed tracklist from file: data/trackList.json
output modified trackList to file: data/trackList.json

again and received no error messsage.

 I nevertheless, even after restarting tomcat7,:

sudo service tomcat7 restart
 * Stopping Tomcat servlet engine tomcat7                                                                                                                              [ OK ]
 * Starting Tomcat servlet engine tomcat7                                                                                                                              [ OK ]

can login into WebApollo, and select my chromosom, but in the newly opened jbrowse my user is not shown, loging in with the smae crendentials into jbrowse does not change this and I still have a grey outed "Create new annotation" .

My permissions are set as follows:
/home/data/Genomes/webapollo tomcat7:tomcat7 <--- contains my genome data
/var/lib/tomcat7/webapps/GENOME/jbrowse/data root:root <--- symling to genome data directory
/var/lib/tomcat7/webapps/GENOME/ root:root
/var/lib/tomcat7/webapps/GENOME/tmp tomcat7:tomcat7

My tomcat7 log shows a, i think, unrelated warning, but I am no the expert:

$tail /var/log/tomcat7/catalina.out

Jul 14, 2014 8:52:57 AM org.apache.catalina.startup.ContextConfig validateSecurityRoles
INFO: WARNING: Security role name NobodyHasThisRole used in an <auth-constraint> without being defined in a <security-role>
Jul 14, 2014 8:52:57 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/GENOME
Jul 14, 2014 8:52:57 AM org.apache.catalina.startup.ContextConfig validateSecurityRoles
INFO: WARNING: Security role name NobodyHasThisRole used in an <auth-constraint> without being defined in a <security-role>
Jul 14, 2014 8:52:57 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Jul 14, 2014 8:52:58 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 3306 ms

Thanks for the support,
Johannes

Am 11.07.2014 20:36, schrieb Colin:
The "Create new annotation" right-click menu will normally be greyed out when you are not logged in. Are you able to login? If so, can you actually that you're logged in, and see the user created annotation track and everything? If you don't see any login type features inside the browser,  then you may need to run "bin/add-webapollo-plugin.pl" and this will add the webapollo plugin to jbrowse


-Colin




---------- Forwarded message ----------
From: Bert Brutzel <[hidden email]>
Date: Fri, Jul 11, 2014 at 4:17 AM
Subject: [apollo] Create new Annotation
To: [hidden email]


Dear All,

I got my instance somewhat up and running, but now I am unable to selecte "create new annotaion" it is simply greyed out. How I proceed, I loaded augustus predictions as a gff and now would like to annotate them with a function.

Thanks for the help,
Bert


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Re: Create new Annotation

Colin
Hi Bert,
Thanks for the detailed response. I'm not sure if the file permissions would be a problem, but assuming it's not, I would like to suggest a few other things.

 Would you be able to look at your javascript console when you are in the genome browser (jbrowse) and post any contents that might be there? If, for example, you see "AnnotationEditorService status: 400" with a description that says "error: You do not have read permissions" then this might indicate some problem with the permissions setup.

I actually just faced a similar problem (not showing that i was logged in when inside the jbrowse) and  I discovered the cause of my problem was that my tracks that I loaded using extract_seqids_from_fasta.pl did not include the prefix "-p Annotations-" flag. Although, in my case, i couldn't see any chromosome names on selectTracks.jsp due to this prefix problem, so it may not be the same as your same problem, but the javascript error console may provide some insight for your situation.

-Colin


On Mon, Jul 14, 2014 at 2:05 AM, Bert Brutzel <[hidden email]> wrote:
Hi Colin,

thanks for the quick reply. I issued:

$sudo bin/add-webapollo-plugin.pl -i data/trackList.json

parsed tracklist from file: data/trackList.json
output modified trackList to file: data/trackList.json

again and received no error messsage.

 I nevertheless, even after restarting tomcat7,:

sudo service tomcat7 restart
 * Stopping Tomcat servlet engine tomcat7                                                                                                                              [ OK ]
 * Starting Tomcat servlet engine tomcat7                                                                                                                              [ OK ]

can login into WebApollo, and select my chromosom, but in the newly opened jbrowse my user is not shown, loging in with the smae crendentials into jbrowse does not change this and I still have a grey outed "Create new annotation" .

My permissions are set as follows:
/home/data/Genomes/webapollo tomcat7:tomcat7 <--- contains my genome data
/var/lib/tomcat7/webapps/GENOME/jbrowse/data root:root <--- symling to genome data directory
/var/lib/tomcat7/webapps/GENOME/ root:root
/var/lib/tomcat7/webapps/GENOME/tmp tomcat7:tomcat7

My tomcat7 log shows a, i think, unrelated warning, but I am no the expert:

$tail /var/log/tomcat7/catalina.out

Jul 14, 2014 8:52:57 AM org.apache.catalina.startup.ContextConfig validateSecurityRoles
INFO: WARNING: Security role name NobodyHasThisRole used in an <auth-constraint> without being defined in a <security-role>
Jul 14, 2014 8:52:57 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/GENOME
Jul 14, 2014 8:52:57 AM org.apache.catalina.startup.ContextConfig validateSecurityRoles
INFO: WARNING: Security role name NobodyHasThisRole used in an <auth-constraint> without being defined in a <security-role>
Jul 14, 2014 8:52:57 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Jul 14, 2014 8:52:58 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 3306 ms

Thanks for the support,
Johannes

Am 11.07.2014 20:36, schrieb Colin:
The "Create new annotation" right-click menu will normally be greyed out when you are not logged in. Are you able to login? If so, can you actually that you're logged in, and see the user created annotation track and everything? If you don't see any login type features inside the browser,  then you may need to run "bin/add-webapollo-plugin.pl" and this will add the webapollo plugin to jbrowse


-Colin




---------- Forwarded message ----------
From: Bert Brutzel <[hidden email]>
Date: Fri, Jul 11, 2014 at 4:17 AM
Subject: [apollo] Create new Annotation
To: [hidden email]


Dear All,

I got my instance somewhat up and running, but now I am unable to selecte "create new annotaion" it is simply greyed out. How I proceed, I loaded augustus predictions as a gff and now would like to annotate them with a function.

Thanks for the help,
Bert



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Re: Create new Annotation

Bert Brutzel-2
Hi Colin,


I looked through my bash_history and I did add the "-p Annotation-" flag while getting the seqids.
Thus below is my JavaScript Console output.
Thanks again for the help,
Bert


Object { message: "Unable to load data/names/root.json status: 404", stack: "[hidden email]
[hidden email]
[hidden email]
", response: Object, status: 404, responseText: "<html><head><title>Apache Tomcat/7.0.26 - Error report</title><style><!--H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;} BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color : black;}A.name {color : black;}HR {color : #525D76;}--></style> </head><body><h1>HTTP Status 404 - /Yarrowia/jbrowse/data/names/root.json</h1><HR size="1" noshade="noshade"><p><b>type</b> Status report</p><p><b>message</b> <u>/Yarrowia/jbrowse/data/names/root.json</u></p><p><b>description</b> <u>The requested resource (/Yarrowia/jbrowse/data/names/root.json) is not available.</u></p><HR size="1" noshade="noshade"><h3>Apache Tomcat/7.0.26</h3></body></html>", xhr: XMLHttpRequest } xhr.js:440
"loaded WebApollo plugin" main.js:38
"In JBrowse configuration, datasets specified, but dataset_id not set.  Dataset selector will not be shown." Browser.js:583
Object { message: "Unable to load ../AnnotationEditorService status: 500", stack: "[hidden email]
[hidden email]
[hidden email]
[hidden email]
[hidden email]
[hidden email]
AnnotTrack<.getPermission@http://undecan:8080/Yarrowia/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:4147:1
AnnotTrack<.setViewInfo@http://undecan:8080/Yarrowia/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:246:1
.renderTrack/makeTrack<@http://undecan:8080/Yarrowia/jbrowse/src/JBrowse/GenomeView.js:2221:1
lang.hitch/<@http://undecan:8080/Yarrowia/jbrowse/src/dojo/_base/lang.js:375:41
.renderTrack/<@http://undecan:8080/Yarrowia/jbrowse/src/JBrowse/GenomeView.js:2245:17
.getStore/<@http://undecan:8080/Yarrowia/jbrowse/src/JBrowse/Browser.js:1203:18
lang.hitch/<@http://undecan:8080/Yarrowia/jbrowse/src/dojo/_base/lang.js:375:41
[hidden email]
[hidden email]
checkComplete/<@http://undecan:8080/Yarrowia/jbrowse/src/dojo/dojo.js:1258:6
[hidden email]
[hidden email]
[hidden email]
[hidden email]
", response: Object, status: 500, responseText: "<html><head><title>Apache Tomcat/7.0.26 - Error report</title><style><!--H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;} BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color : black;}A.name {color : black;}HR {color : #525D76;}--></style> </head><body><h1>HTTP Status 500 - </h1><HR size="1" noshade="noshade"><p><b>type</b> Exception report</p><p><b>message</b> <u></u></p><p><b>description</b> <u>The server encountered an internal error () that prevented it from fulfilling this request.</u></p><p><b>exception</b> <pre>javax.servlet.ServletException: java.lang.ArrayIndexOutOfBoundsException: 1
    org.bbop.apollo.web.AnnotationEditorService.init(AnnotationEditorService.java:235)
    org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
    java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    java.lang.Thread.run(Thread.java:701)
</pre></p><p><b>root cause</b> <pre>java.lang.ArrayIndexOutOfBoundsException: 1
    org.bbop.apollo.web.AnnotationEditorService.init(AnnotationEditorService.java:159)
    org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
    java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    java.lang.Thread.run(Thread.java:701)
</pre></p><p><b>note</b> <u>The full stack trace of the root cause is available in the Apache Tomcat/7.0.26 logs.</u></p><HR size="1" noshade="noshade"><h3>Apache Tomcat/7.0.26</h3></body></html>", xhr: XMLHttpRequest } xhr.js:440
Object { message: "Unable to load ../AnnotationEditorService status: 500", stack: "[hidden email]
[hidden email]
[hidden email]
[hidden email]
[hidden email]
[hidden email]
AnnotTrack<.initSaveMenu@http://undecan:8080/Yarrowia/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:4069:1
AnnotTrack<.setViewInfo@http://undecan:8080/Yarrowia/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:265:9
.renderTrack/makeTrack<@http://undecan:8080/Yarrowia/jbrowse/src/JBrowse/GenomeView.js:2221:1
lang.hitch/<@http://undecan:8080/Yarrowia/jbrowse/src/dojo/_base/lang.js:375:41
.renderTrack/<@http://undecan:8080/Yarrowia/jbrowse/src/JBrowse/GenomeView.js:2245:17
.getStore/<@http://undecan:8080/Yarrowia/jbrowse/src/JBrowse/Browser.js:1203:18
lang.hitch/<@http://undecan:8080/Yarrowia/jbrowse/src/dojo/_base/lang.js:375:41
[hidden email]
[hidden email]
checkComplete/<@http://undecan:8080/Yarrowia/jbrowse/src/dojo/dojo.js:1258:6
[hidden email]
[hidden email]
[hidden email]
[hidden email]
", response: Object, status: 500, responseText: "<html><head><title>Apache Tomcat/7.0.26 - Error report</title><style><!--H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;} BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color : black;}A.name {color : black;}HR {color : #525D76;}--></style> </head><body><h1>HTTP Status 500 - </h1><HR size="1" noshade="noshade"><p><b>type</b> Exception report</p><p><b>message</b> <u></u></p><p><b>description</b> <u>The server encountered an internal error () that prevented it from fulfilling this request.</u></p><p><b>exception</b> <pre>javax.servlet.ServletException: java.lang.ArrayIndexOutOfBoundsException: 1
    org.bbop.apollo.web.AnnotationEditorService.init(AnnotationEditorService.java:235)
    org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
    java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    java.lang.Thread.run(Thread.java:701)
</pre></p><p><b>root cause</b> <pre>java.lang.ArrayIndexOutOfBoundsException: 1
    org.bbop.apollo.web.AnnotationEditorService.init(AnnotationEditorService.java:159)
    org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
    java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    java.lang.Thread.run(Thread.java:701)
</pre></p><p><b>note</b> <u>The full stack trace of the root cause is available in the Apache Tomcat/7.0.26 logs.</u></p><HR size="1" noshade="noshade"><h3>Apache Tomcat/7.0.26</h3></body></html>", xhr: XMLHttpRequest } xhr.js:440
Object { message: "Unable to load ../AnnotationEditorService status: 500", stack: "[hidden email]
[hidden email]
[hidden email]
", response: Object, status: 500, responseText: "<html><head><title>Apache Tomcat/7.0.26 - Error report</title><style><!--H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;} BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color : black;}A.name {color : black;}HR {color : #525D76;}--></style> </head><body><h1>HTTP Status 500 - </h1><HR size="1" noshade="noshade"><p><b>type</b> Exception report</p><p><b>message</b> <u></u></p><p><b>description</b> <u>The server encountered an internal error () that prevented it from fulfilling this request.</u></p><p><b>exception</b> <pre>javax.servlet.ServletException: java.lang.ArrayIndexOutOfBoundsException: 1
    org.bbop.apollo.web.AnnotationEditorService.init(AnnotationEditorService.java:235)
    org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
    java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    java.lang.Thread.run(Thread.java:701)
</pre></p><p><b>root cause</b> <pre>java.lang.ArrayIndexOutOfBoundsException: 1
    org.bbop.apollo.web.AnnotationEditorService.init(AnnotationEditorService.java:159)
    org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
    java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    java.lang.Thread.run(Thread.java:701)
</pre></p><p><b>note</b> <u>The full stack trace of the root cause is available in the Apache Tomcat/7.0.26 logs.</u></p><HR size="1" noshade="noshade"><h3>Apache Tomcat/7.0.26</h3></body></html>", xhr: XMLHttpRequest }

Am 14.07.2014 19:12, schrieb Colin:
Hi Bert,
Thanks for the detailed response. I'm not sure if the file permissions would be a problem, but assuming it's not, I would like to suggest a few other things.

 Would you be able to look at your javascript console when you are in the genome browser (jbrowse) and post any contents that might be there? If, for example, you see "AnnotationEditorService status: 400" with a description that says "error: You do not have read permissions" then this might indicate some problem with the permissions setup.

I actually just faced a similar problem (not showing that i was logged in when inside the jbrowse) and  I discovered the cause of my problem was that my tracks that I loaded using extract_seqids_from_fasta.pl did not include the prefix "-p Annotations-" flag. Although, in my case, i couldn't see any chromosome names on selectTracks.jsp due to this prefix problem, so it may not be the same as your same problem, but the javascript error console may provide some insight for your situation.

-Colin


On Mon, Jul 14, 2014 at 2:05 AM, Bert Brutzel <[hidden email]> wrote:
Hi Colin,

thanks for the quick reply. I issued:

$sudo bin/add-webapollo-plugin.pl -i data/trackList.json

parsed tracklist from file: data/trackList.json
output modified trackList to file: data/trackList.json

again and received no error messsage.

 I nevertheless, even after restarting tomcat7,:

sudo service tomcat7 restart
 * Stopping Tomcat servlet engine tomcat7                                                                                                                              [ OK ]
 * Starting Tomcat servlet engine tomcat7                                                                                                                              [ OK ]

can login into WebApollo, and select my chromosom, but in the newly opened jbrowse my user is not shown, loging in with the smae crendentials into jbrowse does not change this and I still have a grey outed "Create new annotation" .

My permissions are set as follows:
/home/data/Genomes/webapollo tomcat7:tomcat7 <--- contains my genome data
/var/lib/tomcat7/webapps/GENOME/jbrowse/data root:root <--- symling to genome data directory
/var/lib/tomcat7/webapps/GENOME/ root:root
/var/lib/tomcat7/webapps/GENOME/tmp tomcat7:tomcat7

My tomcat7 log shows a, i think, unrelated warning, but I am no the expert:

$tail /var/log/tomcat7/catalina.out

Jul 14, 2014 8:52:57 AM org.apache.catalina.startup.ContextConfig validateSecurityRoles
INFO: WARNING: Security role name NobodyHasThisRole used in an <auth-constraint> without being defined in a <security-role>
Jul 14, 2014 8:52:57 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/GENOME
Jul 14, 2014 8:52:57 AM org.apache.catalina.startup.ContextConfig validateSecurityRoles
INFO: WARNING: Security role name NobodyHasThisRole used in an <auth-constraint> without being defined in a <security-role>
Jul 14, 2014 8:52:57 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Jul 14, 2014 8:52:58 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 3306 ms

Thanks for the support,
Johannes

Am 11.07.2014 20:36, schrieb Colin:
The "Create new annotation" right-click menu will normally be greyed out when you are not logged in. Are you able to login? If so, can you actually that you're logged in, and see the user created annotation track and everything? If you don't see any login type features inside the browser,  then you may need to run "bin/add-webapollo-plugin.pl" and this will add the webapollo plugin to jbrowse


-Colin




---------- Forwarded message ----------
From: Bert Brutzel <[hidden email]>
Date: Fri, Jul 11, 2014 at 4:17 AM
Subject: [apollo] Create new Annotation
To: [hidden email]


Dear All,

I got my instance somewhat up and running, but now I am unable to selecte "create new annotaion" it is simply greyed out. How I proceed, I loaded augustus predictions as a gff and now would like to annotate them with a function.

Thanks for the help,
Bert




Reply | Threaded
Open this post in threaded view
|

Re: Create new Annotation

Colin
Thanks again. I know at least one thing that can cause this type of problem:

In config.xml there is an item that normally appears like:

        <!-- CV term for the genomic sequences - should be in the form
        of "CV:term".  This applies to all sequences -->
        <sequence_type>sequence:chromosome</sequence_type>

But if instead you have just

        <sequence_type>chromosome</sequence_type>

Then this can cause the ArrayOutOfBoundsException. If it is something else, then perhaps emailing the catalina.out would help.
Hope that helps

-Colin


On Tue, Jul 15, 2014 at 9:37 AM, Bert Brutzel <[hidden email]> wrote:
Hi Colin,


I looked through my bash_history and I did add the "-p Annotation-" flag while getting the seqids.
Thus below is my JavaScript Console output.
Thanks again for the help,
Bert


Object { message: "Unable to load data/names/root.json status: 404", stack: "[hidden email]
[hidden email]
[hidden email]
", response: Object, status: 404, responseText: "<html><head><title>Apache Tomcat/7.0.26 - Error report</title><style><!--H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;} BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color : black;}A.name {color : black;}HR {color : #525D76;}--></style> </head><body><h1>HTTP Status 404 - /Yarrowia/jbrowse/data/names/root.json</h1><HR size="1" noshade="noshade"><p><b>type</b> Status report</p><p><b>message</b> <u>/Yarrowia/jbrowse/data/names/root.json</u></p><p><b>description</b> <u>The requested resource (/Yarrowia/jbrowse/data/names/root.json) is not available.</u></p><HR size="1" noshade="noshade"><h3>Apache Tomcat/7.0.26</h3></body></html>", xhr: XMLHttpRequest } xhr.js:440
"loaded WebApollo plugin" main.js:38
"In JBrowse configuration, datasets specified, but dataset_id not set.  Dataset selector will not be shown." Browser.js:583
Object { message: "Unable to load ../AnnotationEditorService status: 500", stack: "[hidden email]
[hidden email]
[hidden email]
[hidden email]
[hidden email]
[hidden email]
AnnotTrack<.getPermission@http://undecan:8080/Yarrowia/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:4147:1
AnnotTrack<.setViewInfo@http://undecan:8080/Yarrowia/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:246:1
.renderTrack/makeTrack<@http://undecan:8080/Yarrowia/jbrowse/src/JBrowse/GenomeView.js:2221:1
lang.hitch/<@http://undecan:8080/Yarrowia/jbrowse/src/dojo/_base/lang.js:375:41
.renderTrack/<@http://undecan:8080/Yarrowia/jbrowse/src/JBrowse/GenomeView.js:2245:17
.getStore/<@http://undecan:8080/Yarrowia/jbrowse/src/JBrowse/Browser.js:1203:18
lang.hitch/<@http://undecan:8080/Yarrowia/jbrowse/src/dojo/_base/lang.js:375:41
[hidden email]
[hidden email]
checkComplete/<@http://undecan:8080/Yarrowia/jbrowse/src/dojo/dojo.js:1258:6
[hidden email]
[hidden email]
[hidden email]
[hidden email]
", response: Object, status: 500, responseText: "<html><head><title>Apache Tomcat/7.0.26 - Error report</title><style><!--H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;} BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color : black;}A.name {color : black;}HR {color : #525D76;}--></style> </head><body><h1>HTTP Status 500 - </h1><HR size="1" noshade="noshade"><p><b>type</b> Exception report</p><p><b>message</b> <u></u></p><p><b>description</b> <u>The server encountered an internal error () that prevented it from fulfilling this request.</u></p><p><b>exception</b> <pre>javax.servlet.ServletException: java.lang.ArrayIndexOutOfBoundsException: 1
    org.bbop.apollo.web.AnnotationEditorService.init(AnnotationEditorService.java:235)
    org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
    java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    java.lang.Thread.run(Thread.java:701)
</pre></p><p><b>root cause</b> <pre>java.lang.ArrayIndexOutOfBoundsException: 1
    org.bbop.apollo.web.AnnotationEditorService.init(AnnotationEditorService.java:159)
    org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
    java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    java.lang.Thread.run(Thread.java:701)
</pre></p><p><b>note</b> <u>The full stack trace of the root cause is available in the Apache Tomcat/7.0.26 logs.</u></p><HR size="1" noshade="noshade"><h3>Apache Tomcat/7.0.26</h3></body></html>", xhr: XMLHttpRequest } xhr.js:440
Object { message: "Unable to load ../AnnotationEditorService status: 500", stack: "[hidden email]
[hidden email]
[hidden email]
[hidden email]
[hidden email]
[hidden email]
AnnotTrack<.initSaveMenu@http://undecan:8080/Yarrowia/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:4069:1
AnnotTrack<.setViewInfo@http://undecan:8080/Yarrowia/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:265:9
.renderTrack/makeTrack<@http://undecan:8080/Yarrowia/jbrowse/src/JBrowse/GenomeView.js:2221:1
lang.hitch/<@http://undecan:8080/Yarrowia/jbrowse/src/dojo/_base/lang.js:375:41
.renderTrack/<@http://undecan:8080/Yarrowia/jbrowse/src/JBrowse/GenomeView.js:2245:17
.getStore/<@http://undecan:8080/Yarrowia/jbrowse/src/JBrowse/Browser.js:1203:18
lang.hitch/<@http://undecan:8080/Yarrowia/jbrowse/src/dojo/_base/lang.js:375:41
[hidden email]
[hidden email]
checkComplete/<@http://undecan:8080/Yarrowia/jbrowse/src/dojo/dojo.js:1258:6
[hidden email]
[hidden email]
[hidden email]
[hidden email]
", response: Object, status: 500, responseText: "<html><head><title>Apache Tomcat/7.0.26 - Error report</title><style><!--H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;} BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color : black;}A.name {color : black;}HR {color : #525D76;}--></style> </head><body><h1>HTTP Status 500 - </h1><HR size="1" noshade="noshade"><p><b>type</b> Exception report</p><p><b>message</b> <u></u></p><p><b>description</b> <u>The server encountered an internal error () that prevented it from fulfilling this request.</u></p><p><b>exception</b> <pre>javax.servlet.ServletException: java.lang.ArrayIndexOutOfBoundsException: 1
    org.bbop.apollo.web.AnnotationEditorService.init(AnnotationEditorService.java:235)
    org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
    java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    java.lang.Thread.run(Thread.java:701)
</pre></p><p><b>root cause</b> <pre>java.lang.ArrayIndexOutOfBoundsException: 1
    org.bbop.apollo.web.AnnotationEditorService.init(AnnotationEditorService.java:159)
    org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
    java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    java.lang.Thread.run(Thread.java:701)
</pre></p><p><b>note</b> <u>The full stack trace of the root cause is available in the Apache Tomcat/7.0.26 logs.</u></p><HR size="1" noshade="noshade"><h3>Apache Tomcat/7.0.26</h3></body></html>", xhr: XMLHttpRequest } xhr.js:440
Object { message: "Unable to load ../AnnotationEditorService status: 500", stack: "[hidden email]
[hidden email]
[hidden email]
", response: Object, status: 500, responseText: "<html><head><title>Apache Tomcat/7.0.26 - Error report</title><style><!--H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;} BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color : black;}A.name {color : black;}HR {color : #525D76;}--></style> </head><body><h1>HTTP Status 500 - </h1><HR size="1" noshade="noshade"><p><b>type</b> Exception report</p><p><b>message</b> <u></u></p><p><b>description</b> <u>The server encountered an internal error () that prevented it from fulfilling this request.</u></p><p><b>exception</b> <pre>javax.servlet.ServletException: java.lang.ArrayIndexOutOfBoundsException: 1
    org.bbop.apollo.web.AnnotationEditorService.init(AnnotationEditorService.java:235)
    org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
    java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    java.lang.Thread.run(Thread.java:701)
</pre></p><p><b>root cause</b> <pre>java.lang.ArrayIndexOutOfBoundsException: 1
    org.bbop.apollo.web.AnnotationEditorService.init(AnnotationEditorService.java:159)
    org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
    java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    java.lang.Thread.run(Thread.java:701)
</pre></p><p><b>note</b> <u>The full stack trace of the root cause is available in the Apache Tomcat/7.0.26 logs.</u></p><HR size="1" noshade="noshade"><h3>Apache Tomcat/7.0.26</h3></body></html>", xhr: XMLHttpRequest }

Am 14.07.2014 19:12, schrieb Colin:
Hi Bert,
Thanks for the detailed response. I'm not sure if the file permissions would be a problem, but assuming it's not, I would like to suggest a few other things.

 Would you be able to look at your javascript console when you are in the genome browser (jbrowse) and post any contents that might be there? If, for example, you see "AnnotationEditorService status: 400" with a description that says "error: You do not have read permissions" then this might indicate some problem with the permissions setup.

I actually just faced a similar problem (not showing that i was logged in when inside the jbrowse) and  I discovered the cause of my problem was that my tracks that I loaded using extract_seqids_from_fasta.pl did not include the prefix "-p Annotations-" flag. Although, in my case, i couldn't see any chromosome names on selectTracks.jsp due to this prefix problem, so it may not be the same as your same problem, but the javascript error console may provide some insight for your situation.

-Colin


On Mon, Jul 14, 2014 at 2:05 AM, Bert Brutzel <[hidden email]> wrote:
Hi Colin,

thanks for the quick reply. I issued:

$sudo bin/add-webapollo-plugin.pl -i data/trackList.json

parsed tracklist from file: data/trackList.json
output modified trackList to file: data/trackList.json

again and received no error messsage.

 I nevertheless, even after restarting tomcat7,:

sudo service tomcat7 restart
 * Stopping Tomcat servlet engine tomcat7                                                                                                                              [ OK ]
 * Starting Tomcat servlet engine tomcat7                                                                                                                              [ OK ]

can login into WebApollo, and select my chromosom, but in the newly opened jbrowse my user is not shown, loging in with the smae crendentials into jbrowse does not change this and I still have a grey outed "Create new annotation" .

My permissions are set as follows:
/home/data/Genomes/webapollo tomcat7:tomcat7 <--- contains my genome data
/var/lib/tomcat7/webapps/GENOME/jbrowse/data root:root <--- symling to genome data directory
/var/lib/tomcat7/webapps/GENOME/ root:root
/var/lib/tomcat7/webapps/GENOME/tmp tomcat7:tomcat7

My tomcat7 log shows a, i think, unrelated warning, but I am no the expert:

$tail /var/log/tomcat7/catalina.out

Jul 14, 2014 8:52:57 AM org.apache.catalina.startup.ContextConfig validateSecurityRoles
INFO: WARNING: Security role name NobodyHasThisRole used in an <auth-constraint> without being defined in a <security-role>
Jul 14, 2014 8:52:57 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/GENOME
Jul 14, 2014 8:52:57 AM org.apache.catalina.startup.ContextConfig validateSecurityRoles
INFO: WARNING: Security role name NobodyHasThisRole used in an <auth-constraint> without being defined in a <security-role>
Jul 14, 2014 8:52:57 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Jul 14, 2014 8:52:58 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 3306 ms

Thanks for the support,
Johannes

Am 11.07.2014 20:36, schrieb Colin:
The "Create new annotation" right-click menu will normally be greyed out when you are not logged in. Are you able to login? If so, can you actually that you're logged in, and see the user created annotation track and everything? If you don't see any login type features inside the browser,  then you may need to run "bin/add-webapollo-plugin.pl" and this will add the webapollo plugin to jbrowse


-Colin




---------- Forwarded message ----------
From: Bert Brutzel <[hidden email]>
Date: Fri, Jul 11, 2014 at 4:17 AM
Subject: [apollo] Create new Annotation
To: [hidden email]


Dear All,

I got my instance somewhat up and running, but now I am unable to selecte "create new annotaion" it is simply greyed out. How I proceed, I loaded augustus predictions as a gff and now would like to annotate them with a function.

Thanks for the help,
Bert





Reply | Threaded
Open this post in threaded view
|

Re: Create new Annotation [SOLVED]

Bert Brutzel-2
Hi Colin,

that hit the spot. I actually forgot, during all my reinstallations, to fill out this field. Works like a charm now....

Thank you very much for helping me debug my own mistakes.
Greets,
Bert


Am 15.07.2014 18:15, schrieb Colin:
Thanks again. I know at least one thing that can cause this type of problem:

In config.xml there is an item that normally appears like:

        <!-- CV term for the genomic sequences - should be in the form
        of "CV:term".  This applies to all sequences -->
        <sequence_type>sequence:chromosome</sequence_type>

But if instead you have just

        <sequence_type>chromosome</sequence_type>

Then this can cause the ArrayOutOfBoundsException. If it is something else, then perhaps emailing the catalina.out would help.
Hope that helps

-Colin


On Tue, Jul 15, 2014 at 9:37 AM, Bert Brutzel <[hidden email]> wrote:
Hi Colin,


I looked through my bash_history and I did add the "-p Annotation-" flag while getting the seqids.
Thus below is my JavaScript Console output.
Thanks again for the help,
Bert


Object { message: "Unable to load data/names/root.json status: 404", stack: "[hidden email]
[hidden email]
[hidden email]
", response: Object, status: 404, responseText: "<html><head><title>Apache Tomcat/7.0.26 - Error report</title><style><!--H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;} BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color : black;}A.name {color : black;}HR {color : #525D76;}--></style> </head><body><h1>HTTP Status 404 - /Yarrowia/jbrowse/data/names/root.json</h1><HR size="1" noshade="noshade"><p><b>type</b> Status report</p><p><b>message</b> <u>/Yarrowia/jbrowse/data/names/root.json</u></p><p><b>description</b> <u>The requested resource (/Yarrowia/jbrowse/data/names/root.json) is not available.</u></p><HR size="1" noshade="noshade"><h3>Apache Tomcat/7.0.26</h3></body></html>", xhr: XMLHttpRequest } xhr.js:440
"loaded WebApollo plugin" main.js:38
"In JBrowse configuration, datasets specified, but dataset_id not set.  Dataset selector will not be shown." Browser.js:583
Object { message: "Unable to load ../AnnotationEditorService status: 500", stack: "[hidden email]
[hidden email]
[hidden email]
[hidden email]
[hidden email]
[hidden email]
AnnotTrack<.getPermission@http://undecan:8080/Yarrowia/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:4147:1
AnnotTrack<.setViewInfo@http://undecan:8080/Yarrowia/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:246:1
.renderTrack/makeTrack<@http://undecan:8080/Yarrowia/jbrowse/src/JBrowse/GenomeView.js:2221:1
lang.hitch/<@http://undecan:8080/Yarrowia/jbrowse/src/dojo/_base/lang.js:375:41
.renderTrack/<@http://undecan:8080/Yarrowia/jbrowse/src/JBrowse/GenomeView.js:2245:17
.getStore/<@http://undecan:8080/Yarrowia/jbrowse/src/JBrowse/Browser.js:1203:18
lang.hitch/<@http://undecan:8080/Yarrowia/jbrowse/src/dojo/_base/lang.js:375:41
[hidden email]
[hidden email]
checkComplete/<@http://undecan:8080/Yarrowia/jbrowse/src/dojo/dojo.js:1258:6
[hidden email]
[hidden email]
[hidden email]
[hidden email]
", response: Object, status: 500, responseText: "<html><head><title>Apache Tomcat/7.0.26 - Error report</title><style><!--H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;} BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color : black;}A.name {color : black;}HR {color : #525D76;}--></style> </head><body><h1>HTTP Status 500 - </h1><HR size="1" noshade="noshade"><p><b>type</b> Exception report</p><p><b>message</b> <u></u></p><p><b>description</b> <u>The server encountered an internal error () that prevented it from fulfilling this request.</u></p><p><b>exception</b> <pre>javax.servlet.ServletException: java.lang.ArrayIndexOutOfBoundsException: 1
    org.bbop.apollo.web.AnnotationEditorService.init(AnnotationEditorService.java:235)
    org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
    java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    java.lang.Thread.run(Thread.java:701)
</pre></p><p><b>root cause</b> <pre>java.lang.ArrayIndexOutOfBoundsException: 1
    org.bbop.apollo.web.AnnotationEditorService.init(AnnotationEditorService.java:159)
    org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
    java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    java.lang.Thread.run(Thread.java:701)
</pre></p><p><b>note</b> <u>The full stack trace of the root cause is available in the Apache Tomcat/7.0.26 logs.</u></p><HR size="1" noshade="noshade"><h3>Apache Tomcat/7.0.26</h3></body></html>", xhr: XMLHttpRequest } xhr.js:440
Object { message: "Unable to load ../AnnotationEditorService status: 500", stack: "[hidden email]
[hidden email]
[hidden email]
[hidden email]
[hidden email]
[hidden email]
AnnotTrack<.initSaveMenu@http://undecan:8080/Yarrowia/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:4069:1
AnnotTrack<.setViewInfo@http://undecan:8080/Yarrowia/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:265:9
.renderTrack/makeTrack<@http://undecan:8080/Yarrowia/jbrowse/src/JBrowse/GenomeView.js:2221:1
lang.hitch/<@http://undecan:8080/Yarrowia/jbrowse/src/dojo/_base/lang.js:375:41
.renderTrack/<@http://undecan:8080/Yarrowia/jbrowse/src/JBrowse/GenomeView.js:2245:17
.getStore/<@http://undecan:8080/Yarrowia/jbrowse/src/JBrowse/Browser.js:1203:18
lang.hitch/<@http://undecan:8080/Yarrowia/jbrowse/src/dojo/_base/lang.js:375:41
[hidden email]
[hidden email]
checkComplete/<@http://undecan:8080/Yarrowia/jbrowse/src/dojo/dojo.js:1258:6
[hidden email]
[hidden email]
[hidden email]
[hidden email]
", response: Object, status: 500, responseText: "<html><head><title>Apache Tomcat/7.0.26 - Error report</title><style><!--H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;} BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color : black;}A.name {color : black;}HR {color : #525D76;}--></style> </head><body><h1>HTTP Status 500 - </h1><HR size="1" noshade="noshade"><p><b>type</b> Exception report</p><p><b>message</b> <u></u></p><p><b>description</b> <u>The server encountered an internal error () that prevented it from fulfilling this request.</u></p><p><b>exception</b> <pre>javax.servlet.ServletException: java.lang.ArrayIndexOutOfBoundsException: 1
    org.bbop.apollo.web.AnnotationEditorService.init(AnnotationEditorService.java:235)
    org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
    java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    java.lang.Thread.run(Thread.java:701)
</pre></p><p><b>root cause</b> <pre>java.lang.ArrayIndexOutOfBoundsException: 1
    org.bbop.apollo.web.AnnotationEditorService.init(AnnotationEditorService.java:159)
    org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
    java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    java.lang.Thread.run(Thread.java:701)
</pre></p><p><b>note</b> <u>The full stack trace of the root cause is available in the Apache Tomcat/7.0.26 logs.</u></p><HR size="1" noshade="noshade"><h3>Apache Tomcat/7.0.26</h3></body></html>", xhr: XMLHttpRequest } xhr.js:440
Object { message: "Unable to load ../AnnotationEditorService status: 500", stack: "[hidden email]
[hidden email]
[hidden email]
", response: Object, status: 500, responseText: "<html><head><title>Apache Tomcat/7.0.26 - Error report</title><style><!--H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;} BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color : black;}A.name {color : black;}HR {color : #525D76;}--></style> </head><body><h1>HTTP Status 500 - </h1><HR size="1" noshade="noshade"><p><b>type</b> Exception report</p><p><b>message</b> <u></u></p><p><b>description</b> <u>The server encountered an internal error () that prevented it from fulfilling this request.</u></p><p><b>exception</b> <pre>javax.servlet.ServletException: java.lang.ArrayIndexOutOfBoundsException: 1
    org.bbop.apollo.web.AnnotationEditorService.init(AnnotationEditorService.java:235)
    org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
    java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    java.lang.Thread.run(Thread.java:701)
</pre></p><p><b>root cause</b> <pre>java.lang.ArrayIndexOutOfBoundsException: 1
    org.bbop.apollo.web.AnnotationEditorService.init(AnnotationEditorService.java:159)
    org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
    java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    java.lang.Thread.run(Thread.java:701)
</pre></p><p><b>note</b> <u>The full stack trace of the root cause is available in the Apache Tomcat/7.0.26 logs.</u></p><HR size="1" noshade="noshade"><h3>Apache Tomcat/7.0.26</h3></body></html>", xhr: XMLHttpRequest }

Am 14.07.2014 19:12, schrieb Colin:
Hi Bert,
Thanks for the detailed response. I'm not sure if the file permissions would be a problem, but assuming it's not, I would like to suggest a few other things.

 Would you be able to look at your javascript console when you are in the genome browser (jbrowse) and post any contents that might be there? If, for example, you see "AnnotationEditorService status: 400" with a description that says "error: You do not have read permissions" then this might indicate some problem with the permissions setup.

I actually just faced a similar problem (not showing that i was logged in when inside the jbrowse) and  I discovered the cause of my problem was that my tracks that I loaded using extract_seqids_from_fasta.pl did not include the prefix "-p Annotations-" flag. Although, in my case, i couldn't see any chromosome names on selectTracks.jsp due to this prefix problem, so it may not be the same as your same problem, but the javascript error console may provide some insight for your situation.

-Colin


On Mon, Jul 14, 2014 at 2:05 AM, Bert Brutzel <[hidden email]> wrote:
Hi Colin,

thanks for the quick reply. I issued:

$sudo bin/add-webapollo-plugin.pl -i data/trackList.json

parsed tracklist from file: data/trackList.json
output modified trackList to file: data/trackList.json

again and received no error messsage.

 I nevertheless, even after restarting tomcat7,:

sudo service tomcat7 restart
 * Stopping Tomcat servlet engine tomcat7                                                                                                                              [ OK ]
 * Starting Tomcat servlet engine tomcat7                                                                                                                              [ OK ]

can login into WebApollo, and select my chromosom, but in the newly opened jbrowse my user is not shown, loging in with the smae crendentials into jbrowse does not change this and I still have a grey outed "Create new annotation" .

My permissions are set as follows:
/home/data/Genomes/webapollo tomcat7:tomcat7 <--- contains my genome data
/var/lib/tomcat7/webapps/GENOME/jbrowse/data root:root <--- symling to genome data directory
/var/lib/tomcat7/webapps/GENOME/ root:root
/var/lib/tomcat7/webapps/GENOME/tmp tomcat7:tomcat7

My tomcat7 log shows a, i think, unrelated warning, but I am no the expert:

$tail /var/log/tomcat7/catalina.out

Jul 14, 2014 8:52:57 AM org.apache.catalina.startup.ContextConfig validateSecurityRoles
INFO: WARNING: Security role name NobodyHasThisRole used in an <auth-constraint> without being defined in a <security-role>
Jul 14, 2014 8:52:57 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/GENOME
Jul 14, 2014 8:52:57 AM org.apache.catalina.startup.ContextConfig validateSecurityRoles
INFO: WARNING: Security role name NobodyHasThisRole used in an <auth-constraint> without being defined in a <security-role>
Jul 14, 2014 8:52:57 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Jul 14, 2014 8:52:58 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 3306 ms

Thanks for the support,
Johannes

Am 11.07.2014 20:36, schrieb Colin:
The "Create new annotation" right-click menu will normally be greyed out when you are not logged in. Are you able to login? If so, can you actually that you're logged in, and see the user created annotation track and everything? If you don't see any login type features inside the browser,  then you may need to run "bin/add-webapollo-plugin.pl" and this will add the webapollo plugin to jbrowse


-Colin




---------- Forwarded message ----------
From: Bert Brutzel <[hidden email]>
Date: Fri, Jul 11, 2014 at 4:17 AM
Subject: [apollo] Create new Annotation
To: [hidden email]


Dear All,

I got my instance somewhat up and running, but now I am unable to selecte "create new annotaion" it is simply greyed out. How I proceed, I loaded augustus predictions as a gff and now would like to annotate them with a function.

Thanks for the help,
Bert






Reply | Threaded
Open this post in threaded view
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Re: Create new Annotation [SOLVED]

ronnie.dejonge
Hi Bert,
Well to comment on "your own mistakes"; I happen to have installed WebApollo a bunch of times too by now, but was never able to successfully install it in one go (I have a webapollo-install-cheatsheet for this exact purpose..). Then again, the tool works well and does its job :-).
Ronnie


2014-07-16 9:16 GMT+02:00 Bert Brutzel <[hidden email]>:
Hi Colin,

that hit the spot. I actually forgot, during all my reinstallations, to fill out this field. Works like a charm now....

Thank you very much for helping me debug my own mistakes.
Greets,
Bert


Am 15.07.2014 18:15, schrieb Colin:
Thanks again. I know at least one thing that can cause this type of problem:

In config.xml there is an item that normally appears like:

        <!-- CV term for the genomic sequences - should be in the form
        of "CV:term".  This applies to all sequences -->
        <sequence_type>sequence:chromosome</sequence_type>

But if instead you have just

        <sequence_type>chromosome</sequence_type>

Then this can cause the ArrayOutOfBoundsException. If it is something else, then perhaps emailing the catalina.out would help.
Hope that helps

-Colin


On Tue, Jul 15, 2014 at 9:37 AM, Bert Brutzel <[hidden email]> wrote:
Hi Colin,


I looked through my bash_history and I did add the "-p Annotation-" flag while getting the seqids.
Thus below is my JavaScript Console output.
Thanks again for the help,
Bert


Object { message: "Unable to load data/names/root.json status: 404", stack: "[hidden email]
[hidden email]
[hidden email]
", response: Object, status: 404, responseText: "<html><head><title>Apache Tomcat/7.0.26 - Error report</title><style><!--H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;} BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color : black;}A.name {color : black;}HR {color : #525D76;}--></style> </head><body><h1>HTTP Status 404 - /Yarrowia/jbrowse/data/names/root.json</h1><HR size="1" noshade="noshade"><p><b>type</b> Status report</p><p><b>message</b> <u>/Yarrowia/jbrowse/data/names/root.json</u></p><p><b>description</b> <u>The requested resource (/Yarrowia/jbrowse/data/names/root.json) is not available.</u></p><HR size="1" noshade="noshade"><h3>Apache Tomcat/7.0.26</h3></body></html>", xhr: XMLHttpRequest } xhr.js:440
"loaded WebApollo plugin" main.js:38
"In JBrowse configuration, datasets specified, but dataset_id not set.  Dataset selector will not be shown." Browser.js:583
Object { message: "Unable to load ../AnnotationEditorService status: 500", stack: "[hidden email]
[hidden email]
[hidden email]
[hidden email]
[hidden email]
[hidden email]
AnnotTrack<.getPermission@http://undecan:8080/Yarrowia/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:4147:1
AnnotTrack<.setViewInfo@http://undecan:8080/Yarrowia/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:246:1
.renderTrack/makeTrack<@http://undecan:8080/Yarrowia/jbrowse/src/JBrowse/GenomeView.js:2221:1
lang.hitch/<@http://undecan:8080/Yarrowia/jbrowse/src/dojo/_base/lang.js:375:41
.renderTrack/<@http://undecan:8080/Yarrowia/jbrowse/src/JBrowse/GenomeView.js:2245:17
.getStore/<@http://undecan:8080/Yarrowia/jbrowse/src/JBrowse/Browser.js:1203:18
lang.hitch/<@http://undecan:8080/Yarrowia/jbrowse/src/dojo/_base/lang.js:375:41
[hidden email]
[hidden email]
checkComplete/<@http://undecan:8080/Yarrowia/jbrowse/src/dojo/dojo.js:1258:6
[hidden email]
[hidden email]
[hidden email]
[hidden email]
", response: Object, status: 500, responseText: "<html><head><title>Apache Tomcat/7.0.26 - Error report</title><style><!--H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;} BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color : black;}A.name {color : black;}HR {color : #525D76;}--></style> </head><body><h1>HTTP Status 500 - </h1><HR size="1" noshade="noshade"><p><b>type</b> Exception report</p><p><b>message</b> <u></u></p><p><b>description</b> <u>The server encountered an internal error () that prevented it from fulfilling this request.</u></p><p><b>exception</b> <pre>javax.servlet.ServletException: java.lang.ArrayIndexOutOfBoundsException: 1
    org.bbop.apollo.web.AnnotationEditorService.init(AnnotationEditorService.java:235)
    org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
    java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    java.lang.Thread.run(Thread.java:701)
</pre></p><p><b>root cause</b> <pre>java.lang.ArrayIndexOutOfBoundsException: 1
    org.bbop.apollo.web.AnnotationEditorService.init(AnnotationEditorService.java:159)
    org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
    java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    java.lang.Thread.run(Thread.java:701)
</pre></p><p><b>note</b> <u>The full stack trace of the root cause is available in the Apache Tomcat/7.0.26 logs.</u></p><HR size="1" noshade="noshade"><h3>Apache Tomcat/7.0.26</h3></body></html>", xhr: XMLHttpRequest } xhr.js:440
Object { message: "Unable to load ../AnnotationEditorService status: 500", stack: "[hidden email]
[hidden email]
[hidden email]
[hidden email]
[hidden email]
[hidden email]
AnnotTrack<.initSaveMenu@http://undecan:8080/Yarrowia/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:4069:1
AnnotTrack<.setViewInfo@http://undecan:8080/Yarrowia/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:265:9
.renderTrack/makeTrack<@http://undecan:8080/Yarrowia/jbrowse/src/JBrowse/GenomeView.js:2221:1
lang.hitch/<@http://undecan:8080/Yarrowia/jbrowse/src/dojo/_base/lang.js:375:41
.renderTrack/<@http://undecan:8080/Yarrowia/jbrowse/src/JBrowse/GenomeView.js:2245:17
.getStore/<@http://undecan:8080/Yarrowia/jbrowse/src/JBrowse/Browser.js:1203:18
lang.hitch/<@http://undecan:8080/Yarrowia/jbrowse/src/dojo/_base/lang.js:375:41
[hidden email]
[hidden email]
checkComplete/<@http://undecan:8080/Yarrowia/jbrowse/src/dojo/dojo.js:1258:6
[hidden email]
[hidden email]
[hidden email]
[hidden email]
", response: Object, status: 500, responseText: "<html><head><title>Apache Tomcat/7.0.26 - Error report</title><style><!--H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;} BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color : black;}A.name {color : black;}HR {color : #525D76;}--></style> </head><body><h1>HTTP Status 500 - </h1><HR size="1" noshade="noshade"><p><b>type</b> Exception report</p><p><b>message</b> <u></u></p><p><b>description</b> <u>The server encountered an internal error () that prevented it from fulfilling this request.</u></p><p><b>exception</b> <pre>javax.servlet.ServletException: java.lang.ArrayIndexOutOfBoundsException: 1
    org.bbop.apollo.web.AnnotationEditorService.init(AnnotationEditorService.java:235)
    org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
    java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    java.lang.Thread.run(Thread.java:701)
</pre></p><p><b>root cause</b> <pre>java.lang.ArrayIndexOutOfBoundsException: 1
    org.bbop.apollo.web.AnnotationEditorService.init(AnnotationEditorService.java:159)
    org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
    java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    java.lang.Thread.run(Thread.java:701)
</pre></p><p><b>note</b> <u>The full stack trace of the root cause is available in the Apache Tomcat/7.0.26 logs.</u></p><HR size="1" noshade="noshade"><h3>Apache Tomcat/7.0.26</h3></body></html>", xhr: XMLHttpRequest } xhr.js:440
Object { message: "Unable to load ../AnnotationEditorService status: 500", stack: "[hidden email]
[hidden email]
[hidden email]
", response: Object, status: 500, responseText: "<html><head><title>Apache Tomcat/7.0.26 - Error report</title><style><!--H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;} BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color : black;}A.name {color : black;}HR {color : #525D76;}--></style> </head><body><h1>HTTP Status 500 - </h1><HR size="1" noshade="noshade"><p><b>type</b> Exception report</p><p><b>message</b> <u></u></p><p><b>description</b> <u>The server encountered an internal error () that prevented it from fulfilling this request.</u></p><p><b>exception</b> <pre>javax.servlet.ServletException: java.lang.ArrayIndexOutOfBoundsException: 1
    org.bbop.apollo.web.AnnotationEditorService.init(AnnotationEditorService.java:235)
    org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
    java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    java.lang.Thread.run(Thread.java:701)
</pre></p><p><b>root cause</b> <pre>java.lang.ArrayIndexOutOfBoundsException: 1
    org.bbop.apollo.web.AnnotationEditorService.init(AnnotationEditorService.java:159)
    org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
    java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    java.lang.Thread.run(Thread.java:701)
</pre></p><p><b>note</b> <u>The full stack trace of the root cause is available in the Apache Tomcat/7.0.26 logs.</u></p><HR size="1" noshade="noshade"><h3>Apache Tomcat/7.0.26</h3></body></html>", xhr: XMLHttpRequest }

Am 14.07.2014 19:12, schrieb Colin:
Hi Bert,
Thanks for the detailed response. I'm not sure if the file permissions would be a problem, but assuming it's not, I would like to suggest a few other things.

 Would you be able to look at your javascript console when you are in the genome browser (jbrowse) and post any contents that might be there? If, for example, you see "AnnotationEditorService status: 400" with a description that says "error: You do not have read permissions" then this might indicate some problem with the permissions setup.

I actually just faced a similar problem (not showing that i was logged in when inside the jbrowse) and  I discovered the cause of my problem was that my tracks that I loaded using extract_seqids_from_fasta.pl did not include the prefix "-p Annotations-" flag. Although, in my case, i couldn't see any chromosome names on selectTracks.jsp due to this prefix problem, so it may not be the same as your same problem, but the javascript error console may provide some insight for your situation.

-Colin


On Mon, Jul 14, 2014 at 2:05 AM, Bert Brutzel <[hidden email]> wrote:
Hi Colin,

thanks for the quick reply. I issued:

$sudo bin/add-webapollo-plugin.pl -i data/trackList.json

parsed tracklist from file: data/trackList.json
output modified trackList to file: data/trackList.json

again and received no error messsage.

 I nevertheless, even after restarting tomcat7,:

sudo service tomcat7 restart
 * Stopping Tomcat servlet engine tomcat7                                                                                                                              [ OK ]
 * Starting Tomcat servlet engine tomcat7                                                                                                                              [ OK ]

can login into WebApollo, and select my chromosom, but in the newly opened jbrowse my user is not shown, loging in with the smae crendentials into jbrowse does not change this and I still have a grey outed "Create new annotation" .

My permissions are set as follows:
/home/data/Genomes/webapollo tomcat7:tomcat7 <--- contains my genome data
/var/lib/tomcat7/webapps/GENOME/jbrowse/data root:root <--- symling to genome data directory
/var/lib/tomcat7/webapps/GENOME/ root:root
/var/lib/tomcat7/webapps/GENOME/tmp tomcat7:tomcat7

My tomcat7 log shows a, i think, unrelated warning, but I am no the expert:

$tail /var/log/tomcat7/catalina.out

Jul 14, 2014 8:52:57 AM org.apache.catalina.startup.ContextConfig validateSecurityRoles
INFO: WARNING: Security role name NobodyHasThisRole used in an <auth-constraint> without being defined in a <security-role>
Jul 14, 2014 8:52:57 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/GENOME
Jul 14, 2014 8:52:57 AM org.apache.catalina.startup.ContextConfig validateSecurityRoles
INFO: WARNING: Security role name NobodyHasThisRole used in an <auth-constraint> without being defined in a <security-role>
Jul 14, 2014 8:52:57 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Jul 14, 2014 8:52:58 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 3306 ms

Thanks for the support,
Johannes

Am 11.07.2014 20:36, schrieb Colin:
The "Create new annotation" right-click menu will normally be greyed out when you are not logged in. Are you able to login? If so, can you actually that you're logged in, and see the user created annotation track and everything? If you don't see any login type features inside the browser,  then you may need to run "bin/add-webapollo-plugin.pl" and this will add the webapollo plugin to jbrowse


-Colin




---------- Forwarded message ----------
From: Bert Brutzel <[hidden email]>
Date: Fri, Jul 11, 2014 at 4:17 AM
Subject: [apollo] Create new Annotation
To: [hidden email]


Dear All,

I got my instance somewhat up and running, but now I am unable to selecte "create new annotaion" it is simply greyed out. How I proceed, I loaded augustus predictions as a gff and now would like to annotate them with a function.

Thanks for the help,
Bert







Reply | Threaded
Open this post in threaded view
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Re: Create new Annotation [SOLVED]

Bert Brutzel-2
Hi Ronnie,

thanks for the encouraging words. I actually plan to make a blog entry as soon as I feel in total control of the installation, on "how i managed to get WebApollo running with my own data". I really appreciate the work the developers put into this very handy tool as well, but I am sure there is more people out there that are to impatient to fully comprehend the tutorial in an abstract manner.

Bert

Am 16.07.2014 09:27, schrieb Ronnie de Jonge:
Hi Bert,
Well to comment on "your own mistakes"; I happen to have installed WebApollo a bunch of times too by now, but was never able to successfully install it in one go (I have a webapollo-install-cheatsheet for this exact purpose..). Then again, the tool works well and does its job :-).
Ronnie


2014-07-16 9:16 GMT+02:00 Bert Brutzel <[hidden email]>:
Hi Colin,

that hit the spot. I actually forgot, during all my reinstallations, to fill out this field. Works like a charm now....

Thank you very much for helping me debug my own mistakes.
Greets,
Bert


Am 15.07.2014 18:15, schrieb Colin:
Thanks again. I know at least one thing that can cause this type of problem:

In config.xml there is an item that normally appears like:

        <!-- CV term for the genomic sequences - should be in the form
        of "CV:term".  This applies to all sequences -->
        <sequence_type>sequence:chromosome</sequence_type>

But if instead you have just

        <sequence_type>chromosome</sequence_type>

Then this can cause the ArrayOutOfBoundsException. If it is something else, then perhaps emailing the catalina.out would help.
Hope that helps

-Colin


On Tue, Jul 15, 2014 at 9:37 AM, Bert Brutzel <[hidden email]> wrote:
Hi Colin,


I looked through my bash_history and I did add the "-p Annotation-" flag while getting the seqids.
Thus below is my JavaScript Console output.
Thanks again for the help,
Bert


Object { message: "Unable to load data/names/root.json status: 404", stack: "[hidden email]
[hidden email]
[hidden email]
", response: Object, status: 404, responseText: "<html><head><title>Apache Tomcat/7.0.26 - Error report</title><style><!--H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;} BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color : black;}A.name {color : black;}HR {color : #525D76;}--></style> </head><body><h1>HTTP Status 404 - /Yarrowia/jbrowse/data/names/root.json</h1><HR size="1" noshade="noshade"><p><b>type</b> Status report</p><p><b>message</b> <u>/Yarrowia/jbrowse/data/names/root.json</u></p><p><b>description</b> <u>The requested resource (/Yarrowia/jbrowse/data/names/root.json) is not available.</u></p><HR size="1" noshade="noshade"><h3>Apache Tomcat/7.0.26</h3></body></html>", xhr: XMLHttpRequest } xhr.js:440
"loaded WebApollo plugin" main.js:38
"In JBrowse configuration, datasets specified, but dataset_id not set.  Dataset selector will not be shown." Browser.js:583
Object { message: "Unable to load ../AnnotationEditorService status: 500", stack: "[hidden email]
[hidden email]
[hidden email]
[hidden email]
[hidden email]
[hidden email]
AnnotTrack<.getPermission@http://undecan:8080/Yarrowia/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:4147:1
AnnotTrack<.setViewInfo@http://undecan:8080/Yarrowia/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:246:1
.renderTrack/makeTrack<@http://undecan:8080/Yarrowia/jbrowse/src/JBrowse/GenomeView.js:2221:1
lang.hitch/<@http://undecan:8080/Yarrowia/jbrowse/src/dojo/_base/lang.js:375:41
.renderTrack/<@http://undecan:8080/Yarrowia/jbrowse/src/JBrowse/GenomeView.js:2245:17
.getStore/<@http://undecan:8080/Yarrowia/jbrowse/src/JBrowse/Browser.js:1203:18
lang.hitch/<@http://undecan:8080/Yarrowia/jbrowse/src/dojo/_base/lang.js:375:41
[hidden email]
[hidden email]
checkComplete/<@http://undecan:8080/Yarrowia/jbrowse/src/dojo/dojo.js:1258:6
[hidden email]
[hidden email]
[hidden email]
[hidden email]
", response: Object, status: 500, responseText: "<html><head><title>Apache Tomcat/7.0.26 - Error report</title><style><!--H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;} BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color : black;}A.name {color : black;}HR {color : #525D76;}--></style> </head><body><h1>HTTP Status 500 - </h1><HR size="1" noshade="noshade"><p><b>type</b> Exception report</p><p><b>message</b> <u></u></p><p><b>description</b> <u>The server encountered an internal error () that prevented it from fulfilling this request.</u></p><p><b>exception</b> <pre>javax.servlet.ServletException: java.lang.ArrayIndexOutOfBoundsException: 1
    org.bbop.apollo.web.AnnotationEditorService.init(AnnotationEditorService.java:235)
    org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
    java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    java.lang.Thread.run(Thread.java:701)
</pre></p><p><b>root cause</b> <pre>java.lang.ArrayIndexOutOfBoundsException: 1
    org.bbop.apollo.web.AnnotationEditorService.init(AnnotationEditorService.java:159)
    org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
    java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    java.lang.Thread.run(Thread.java:701)
</pre></p><p><b>note</b> <u>The full stack trace of the root cause is available in the Apache Tomcat/7.0.26 logs.</u></p><HR size="1" noshade="noshade"><h3>Apache Tomcat/7.0.26</h3></body></html>", xhr: XMLHttpRequest } xhr.js:440
Object { message: "Unable to load ../AnnotationEditorService status: 500", stack: "[hidden email]
[hidden email]
[hidden email]
[hidden email]
[hidden email]
[hidden email]
AnnotTrack<.initSaveMenu@http://undecan:8080/Yarrowia/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:4069:1
AnnotTrack<.setViewInfo@http://undecan:8080/Yarrowia/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:265:9
.renderTrack/makeTrack<@http://undecan:8080/Yarrowia/jbrowse/src/JBrowse/GenomeView.js:2221:1
lang.hitch/<@http://undecan:8080/Yarrowia/jbrowse/src/dojo/_base/lang.js:375:41
.renderTrack/<@http://undecan:8080/Yarrowia/jbrowse/src/JBrowse/GenomeView.js:2245:17
.getStore/<@http://undecan:8080/Yarrowia/jbrowse/src/JBrowse/Browser.js:1203:18
lang.hitch/<@http://undecan:8080/Yarrowia/jbrowse/src/dojo/_base/lang.js:375:41
[hidden email]
[hidden email]
checkComplete/<@http://undecan:8080/Yarrowia/jbrowse/src/dojo/dojo.js:1258:6
[hidden email]
[hidden email]
[hidden email]
[hidden email]
", response: Object, status: 500, responseText: "<html><head><title>Apache Tomcat/7.0.26 - Error report</title><style><!--H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;} BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color : black;}A.name {color : black;}HR {color : #525D76;}--></style> </head><body><h1>HTTP Status 500 - </h1><HR size="1" noshade="noshade"><p><b>type</b> Exception report</p><p><b>message</b> <u></u></p><p><b>description</b> <u>The server encountered an internal error () that prevented it from fulfilling this request.</u></p><p><b>exception</b> <pre>javax.servlet.ServletException: java.lang.ArrayIndexOutOfBoundsException: 1
    org.bbop.apollo.web.AnnotationEditorService.init(AnnotationEditorService.java:235)
    org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
    java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    java.lang.Thread.run(Thread.java:701)
</pre></p><p><b>root cause</b> <pre>java.lang.ArrayIndexOutOfBoundsException: 1
    org.bbop.apollo.web.AnnotationEditorService.init(AnnotationEditorService.java:159)
    org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
    java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    java.lang.Thread.run(Thread.java:701)
</pre></p><p><b>note</b> <u>The full stack trace of the root cause is available in the Apache Tomcat/7.0.26 logs.</u></p><HR size="1" noshade="noshade"><h3>Apache Tomcat/7.0.26</h3></body></html>", xhr: XMLHttpRequest } xhr.js:440
Object { message: "Unable to load ../AnnotationEditorService status: 500", stack: "[hidden email]
[hidden email]
[hidden email]
", response: Object, status: 500, responseText: "<html><head><title>Apache Tomcat/7.0.26 - Error report</title><style><!--H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;} BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color : black;}A.name {color : black;}HR {color : #525D76;}--></style> </head><body><h1>HTTP Status 500 - </h1><HR size="1" noshade="noshade"><p><b>type</b> Exception report</p><p><b>message</b> <u></u></p><p><b>description</b> <u>The server encountered an internal error () that prevented it from fulfilling this request.</u></p><p><b>exception</b> <pre>javax.servlet.ServletException: java.lang.ArrayIndexOutOfBoundsException: 1
    org.bbop.apollo.web.AnnotationEditorService.init(AnnotationEditorService.java:235)
    org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
    java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    java.lang.Thread.run(Thread.java:701)
</pre></p><p><b>root cause</b> <pre>java.lang.ArrayIndexOutOfBoundsException: 1
    org.bbop.apollo.web.AnnotationEditorService.init(AnnotationEditorService.java:159)
    org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
    java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    java.lang.Thread.run(Thread.java:701)
</pre></p><p><b>note</b> <u>The full stack trace of the root cause is available in the Apache Tomcat/7.0.26 logs.</u></p><HR size="1" noshade="noshade"><h3>Apache Tomcat/7.0.26</h3></body></html>", xhr: XMLHttpRequest }

Am 14.07.2014 19:12, schrieb Colin:
Hi Bert,
Thanks for the detailed response. I'm not sure if the file permissions would be a problem, but assuming it's not, I would like to suggest a few other things.

 Would you be able to look at your javascript console when you are in the genome browser (jbrowse) and post any contents that might be there? If, for example, you see "AnnotationEditorService status: 400" with a description that says "error: You do not have read permissions" then this might indicate some problem with the permissions setup.

I actually just faced a similar problem (not showing that i was logged in when inside the jbrowse) and  I discovered the cause of my problem was that my tracks that I loaded using extract_seqids_from_fasta.pl did not include the prefix "-p Annotations-" flag. Although, in my case, i couldn't see any chromosome names on selectTracks.jsp due to this prefix problem, so it may not be the same as your same problem, but the javascript error console may provide some insight for your situation.

-Colin


On Mon, Jul 14, 2014 at 2:05 AM, Bert Brutzel <[hidden email]> wrote:
Hi Colin,

thanks for the quick reply. I issued:

$sudo bin/add-webapollo-plugin.pl -i data/trackList.json

parsed tracklist from file: data/trackList.json
output modified trackList to file: data/trackList.json

again and received no error messsage.

 I nevertheless, even after restarting tomcat7,:

sudo service tomcat7 restart
 * Stopping Tomcat servlet engine tomcat7                                                                                                                              [ OK ]
 * Starting Tomcat servlet engine tomcat7                                                                                                                              [ OK ]

can login into WebApollo, and select my chromosom, but in the newly opened jbrowse my user is not shown, loging in with the smae crendentials into jbrowse does not change this and I still have a grey outed "Create new annotation" .

My permissions are set as follows:
/home/data/Genomes/webapollo tomcat7:tomcat7 <--- contains my genome data
/var/lib/tomcat7/webapps/GENOME/jbrowse/data root:root <--- symling to genome data directory
/var/lib/tomcat7/webapps/GENOME/ root:root
/var/lib/tomcat7/webapps/GENOME/tmp tomcat7:tomcat7

My tomcat7 log shows a, i think, unrelated warning, but I am no the expert:

$tail /var/log/tomcat7/catalina.out

Jul 14, 2014 8:52:57 AM org.apache.catalina.startup.ContextConfig validateSecurityRoles
INFO: WARNING: Security role name NobodyHasThisRole used in an <auth-constraint> without being defined in a <security-role>
Jul 14, 2014 8:52:57 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat7/webapps/GENOME
Jul 14, 2014 8:52:57 AM org.apache.catalina.startup.ContextConfig validateSecurityRoles
INFO: WARNING: Security role name NobodyHasThisRole used in an <auth-constraint> without being defined in a <security-role>
Jul 14, 2014 8:52:57 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Jul 14, 2014 8:52:58 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 3306 ms

Thanks for the support,
Johannes

Am 11.07.2014 20:36, schrieb Colin:
The "Create new annotation" right-click menu will normally be greyed out when you are not logged in. Are you able to login? If so, can you actually that you're logged in, and see the user created annotation track and everything? If you don't see any login type features inside the browser,  then you may need to run "bin/add-webapollo-plugin.pl" and this will add the webapollo plugin to jbrowse


-Colin




---------- Forwarded message ----------
From: Bert Brutzel <[hidden email]>
Date: Fri, Jul 11, 2014 at 4:17 AM
Subject: [apollo] Create new Annotation
To: [hidden email]


Dear All,

I got my instance somewhat up and running, but now I am unable to selecte "create new annotaion" it is simply greyed out. How I proceed, I loaded augustus predictions as a gff and now would like to annotate them with a function.

Thanks for the help,
Bert