Closed mictadlo closed 7 years ago
hexylena
commented
8 years ago As you can see, it fails to connect to a postgres database. We recommend using the docker-compose.yml file provided as part of this repository.
This will take care of the database for you, and allow you to make use of the new Chado export functionality in apollo if you are a Chado user. https://github.com/GMOD/docker-apollo/blob/master/docker-compose.yml
mictadlo
commented
8 years ago Thank you I could start it, but after login I get only Loading ... massage.
hexylena
commented
8 years ago At this point I'm afraid I need to turn it over to apollo people like @nathandunn, this will be out of my area.
mictadlo
commented
8 years ago P.S. the data folder is still empty ~/dockers/docker-apollo $ ls data/
hexylena
commented
8 years ago @mictadlo did you place a jbrowse data directory within the folder you're sharing with the container?
nathandunn
commented
8 years ago @mictadlo Were you able to connect to the tomcat backend and see anything in the logs?
You should connect to the docker container running tomcat (catalina.sh) and look in /var/logs/tomcat/catalina.out (or something like that).
nathandunn
commented
8 years ago I'm going to update the gmod/apollo:latest . . . it should be a bit more stable as well. @mictadlo You can also try using the latest release (2.0.2) and see if this works better:
nathandunn
commented
8 years ago @mictadlo I also update the gmod/apollo:latest to be more stable. Maybe start there and if it still fails use 2.0.2.
Is this to be loaded up via ansible (we have a few scripts for that as well).
nathandunn
commented
8 years ago @mictadlo I just got it running, but like @erasche said, you should use:
docker-compose up or
docker-compose up -dI issued some updates grabbing a newer version of apollo as well. You may need to remove the gmod/apollo:latest image to force it to refresh.
nathandunn
commented
8 years ago I was able to connect this way: http://192.168.99.100:8080/apollo/annotator/index
To add data (I'm using a mac), I copied data into the docker-compose/data/ directory and then added them to the organism tab as /data/yeast/
mictadlo
commented
8 years ago Thank you, it works. You were right and I had to do docker rmi $(docker images -q) to force to update all docker images.
I created the data folder in ~/dockers/docker-apollo-2.0.2/data/ where did you get the yeast data from?
nathandunn
commented
8 years ago If you download JBrowse: http://jbrowse.org/jbrowse-1-12-1/ http://jbrowse.org/jbrowse-1-12-1/
it should come with some sample data, also including volvox. When I install Apollo de-novo, it should install data in the jbrowse-download/sample_data directory
On Jul 21, 2016, at 4:52 PM, Michał T. Lorenc notifications@github.com wrote:
Thank you, it works. You were right and I had to do docker rmi $(docker images -q) to force to update all docker images.
I created the data folder in ~/dockers/docker-apollo-2.0.2/data/ where did you get the yeast data from?
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hexylena
commented
8 years ago @mictadlo, seconding @nathandunn, when I use the apollo image, I often supply path like /apollo/jbrowse-download/sample_data/json/yeast/, so I do not even need to mount a volume, already data in container ready to go
mictadlo
commented
8 years ago Loading /apollo/jbrowse-download/sample_data/json/yeast/ I got this error:
RequestError: Unable to load http://localhost:8080/apollo/1587307876556361724920773645/jbrowse/data/trackList.json status: 500.What did I do wrong?
nathandunn
commented
8 years ago A 500 error is usually on the server.
Can you find the tomcat logs?
In docker (if you are using a daemon), you should be able to do:
docker logs
or
docker-compose logs
(and retry the request).
If you are not running the daemon you should be able to see it directly in the console you used to start it.
Nathan
On Jul 25, 2016, at 7:14 PM, Michał T. Lorenc notifications@github.com wrote:
Loading /apollo/jbrowse-download/sample_data/json/yeast/ I got this error:
RequestError: Unable to load http://localhost:8080/apollo/1587307876556361724920773645/jbrowse/data/trackList.json status: 500. What did I do wrong?
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mictadlo
commented
8 years ago Please find below the logs /apollo/jbrowse-download/sample_data/json/volvox/
apollo_1 | 2016-07-26 03:44:14,790 [localhost-startStop-1] WARN apollo.UserService - User exists admin@local.host and can not be added again.
apollo_1 | Jul 26, 2016 3:44:15 AM org.apache.catalina.startup.HostConfig deployWAR
apollo_1 | INFO: Deployment of web application archive /usr/local/tomcat/webapps/apollo.war has finished in 126,146 ms
apollo_1 | Jul 26, 2016 3:44:15 AM org.apache.coyote.AbstractProtocol start
apollo_1 | INFO: Starting ProtocolHandler ["http-apr-8080"]
apollo_1 | Jul 26, 2016 3:44:15 AM org.apache.coyote.AbstractProtocol start
apollo_1 | INFO: Starting ProtocolHandler ["ajp-apr-8009"]
apollo_1 | Jul 26, 2016 3:44:15 AM org.apache.catalina.startup.Catalina start
apollo_1 | INFO: Server startup in 126587 ms
apollo_1 | 2016-07-26 03:44:17,806 [http-apr-8080-exec-1] ERROR apollo.AnnotatorController - User does not have permissions for the site
apollo_1 | 2016-07-26 03:44:17,823 [http-apr-8080-exec-4] ERROR apollo.AnnotatorController - User does not have permissions for the site
apollo_1 | 2016-07-26 03:44:20,404 [http-apr-8080-exec-7] ERROR apollo.PermissionService - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.
apollo_1 | 2016-07-26 03:44:20,416 [http-apr-8080-exec-8] ERROR apollo.PermissionService - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.
apollo_1 | 2016-07-26 03:44:20,425 [http-apr-8080-exec-8] ERROR apollo.GroupController - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'}
apollo_1 | 2016-07-26 03:44:20,429 [http-apr-8080-exec-7] ERROR apollo.UserController - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'}
apollo_1 | class name usernamePasswordAuthenticatorService
apollo_1 | 2016-07-26 03:44:20,962 [http-apr-8080-exec-1] ERROR authenticator.UsernamePasswordAuthenticatorService - Not implemented without a token
apollo_1 | 2016-07-26 03:44:20,963 [http-apr-8080-exec-1] WARN apollo.PermissionService - Failed to authenticate user
apollo_1 | 2016-07-26 03:44:20,963 [http-apr-8080-exec-1] ERROR apollo.UserController - Failed to authenticate
apollo_1 | class name usernamePasswordAuthenticatorService
apollo_1 | 2016-07-26 03:45:04,787 [http-apr-8080-exec-1] ERROR errors.GrailsExceptionResolver - MissingPropertyException occurred when processing request: [GET] /apollo/1587307876556361724920773645/jbrowse/data/trackList.json
apollo_1 | No such property: name for class: java.lang.String. Stacktrace follows:
apollo_1 | groovy.lang.MissingPropertyException: No such property: name for class: java.lang.String
apollo_1 | at org.bbop.apollo.JbrowseController.trackList(JbrowseController.groovy:375)
apollo_1 | at grails.plugin.cache.web.filter.PageFragmentCachingFilter.doFilter(PageFragmentCachingFilter.java:198)
apollo_1 | at grails.plugin.cache.web.filter.AbstractFilter.doFilter(AbstractFilter.java:63)
apollo_1 | at org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:449)
apollo_1 | at org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:365)
apollo_1 | at org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90)
apollo_1 | at org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83)
apollo_1 | at org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:383)
apollo_1 | at org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:362)
apollo_1 | at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125)
apollo_1 | at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
apollo_1 | at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
apollo_1 | at java.lang.Thread.run(Thread.java:745)
apollo_1 | 2016-07-26 03:45:05,095 [http-apr-8080-exec-4] WARN apollo.JbrowseController - File not found: /jbrowse/sample_data/json/volvox/successfully_runI tried to use /apollo/jbrowse-download/sample_data/json/yeast/, but I get the same error.
nathandunn
commented
8 years ago I'll take a look. What version are you running?
Nathan
On Jul 25, 2016, at 8:52 PM, Michał T. Lorenc notifications@github.com wrote:
Please find below the logs: /apollo/jbrowse-download/sample_data/json/volvox/
apollo_1 | 2016-07-26 03:44:14,790 [localhost-startStop-1] WARN apollo.UserService - User exists admin@local.host and can not be added again. apollo_1 | Jul 26, 2016 3:44:15 AM org.apache.catalina.startup.HostConfig deployWAR apollo_1 | INFO: Deployment of web application archive /usr/local/tomcat/webapps/apollo.war has finished in 126,146 ms apollo_1 | Jul 26, 2016 3:44:15 AM org.apache.coyote.AbstractProtocol start apollo_1 | INFO: Starting ProtocolHandler ["http-apr-8080"] apollo_1 | Jul 26, 2016 3:44:15 AM org.apache.coyote.AbstractProtocol start apollo_1 | INFO: Starting ProtocolHandler ["ajp-apr-8009"] apollo_1 | Jul 26, 2016 3:44:15 AM org.apache.catalina.startup.Catalina start apollo_1 | INFO: Server startup in 126587 ms apollo_1 | 2016-07-26 03:44:17,806 [http-apr-8080-exec-1] ERROR apollo.AnnotatorController - User does not have permissions for the site apollo_1 | 2016-07-26 03:44:17,823 [http-apr-8080-exec-4] ERROR apollo.AnnotatorController - User does not have permissions for the site apollo_1 | 2016-07-26 03:44:20,404 [http-apr-8080-exec-7] ERROR apollo.PermissionService - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm. apollo_1 | 2016-07-26 03:44:20,416 [http-apr-8080-exec-8] ERROR apollo.PermissionService - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm. apollo_1 | 2016-07-26 03:44:20,425 [http-apr-8080-exec-8] ERROR apollo.GroupController - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'} apollo_1 | 2016-07-26 03:44:20,429 [http-apr-8080-exec-7] ERROR apollo.UserController - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'} apollo_1 | class name usernamePasswordAuthenticatorService apollo_1 | 2016-07-26 03:44:20,962 [http-apr-8080-exec-1] ERROR authenticator.UsernamePasswordAuthenticatorService - Not implemented without a token apollo_1 | 2016-07-26 03:44:20,963 [http-apr-8080-exec-1] WARN apollo.PermissionService - Failed to authenticate user apollo_1 | 2016-07-26 03:44:20,963 [http-apr-8080-exec-1] ERROR apollo.UserController - Failed to authenticate apollo_1 | class name usernamePasswordAuthenticatorService apollo_1 | 2016-07-26 03:45:04,787 [http-apr-8080-exec-1] ERROR errors.GrailsExceptionResolver - MissingPropertyException occurred when processing request: [GET] /apollo/1587307876556361724920773645/jbrowse/data/trackList.json apollo_1 | No such property: name for class: java.lang.String. Stacktrace follows: apollo_1 | groovy.lang.MissingPropertyException: No such property: name for class: java.lang.String apollo_1 | at org.bbop.apollo.JbrowseController.trackList(JbrowseController.groovy:375) apollo_1 | at grails.plugin.cache.web.filter.PageFragmentCachingFilter.doFilter(PageFragmentCachingFilter.java:198) apollo_1 | at grails.plugin.cache.web.filter.AbstractFilter.doFilter(AbstractFilter.java:63) apollo_1 | at org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:449) apollo_1 | at org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:365) apollo_1 | at org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90) apollo_1 | at org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83) apollo_1 | at org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:383) apollo_1 | at org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:362) apollo_1 | at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125) apollo_1 | at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) apollo_1 | at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) apollo_1 | at java.lang.Thread.run(Thread.java:745) apollo_1 | 2016-07-26 03:45:05,095 [http-apr-8080-exec-4] WARN apollo.JbrowseController - File not found: /jbrowse/sample_data/json/volvox/successfully_run I tried to use /apollo/jbrowse-download/sample_data/json/yeast/, but I get the same error.
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mictadlo
commented
8 years ago 2.0.2 https://github.com/GMOD/docker-apollo/archive/2.0.2.zip or do you have a newer version?
nathandunn
commented
8 years ago You could try cloning master (which is newer), which is the 2.0.4 Release Candidate 2:
https://github.com/GMOD/docker-apollo/
I’ll create a “release” version, when we release 2.0.4.
I’m not sure if it will fix it, but I can definitely patch it on master pretty quickly if there is a problem. Just provide that error log, and I’ll see if I can’t patch it.
Also, if you list the directory you point to (should be absolute), and the top-level contents that would help, as well.
Thanks,
Nathan
On Jul 25, 2016, at 8:54 PM, Michał T. Lorenc notifications@github.com wrote:
2.0.2 https://github.com/GMOD/docker-apollo/archive/2.0.2.zip https://github.com/GMOD/docker-apollo/archive/2.0.2.zip or do you have a newer version?
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/GMOD/docker-apollo/issues/6#issuecomment-235156007, or mute the thread https://github.com/notifications/unsubscribe-auth/AAt2qg5-v9mxl5KIa6pIHjEDIB3iUxdrks5qZYUOgaJpZM4JRt8a.
nathandunn
commented
8 years ago I tested it against master and am getting this error now:
https://github.com/GMOD/Apollo/issues/1186 https://github.com/GMOD/Apollo/issues/1186
I’ll try to fix it tomorrow, and then we can hopefully resolve this as well when I update the docker build hash.
Nathan
On Jul 25, 2016, at 8:54 PM, Michał T. Lorenc notifications@github.com wrote:
2.0.2 https://github.com/GMOD/docker-apollo/archive/2.0.2.zip https://github.com/GMOD/docker-apollo/archive/2.0.2.zip or do you have a newer version?
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/GMOD/docker-apollo/issues/6#issuecomment-235156007, or mute the thread https://github.com/notifications/unsubscribe-auth/AAt2qg5-v9mxl5KIa6pIHjEDIB3iUxdrks5qZYUOgaJpZM4JRt8a.
nathandunn
commented
8 years ago @mictadlo What I would do:
Clone the newest version from here: https://github.com/GMOD/docker-apollo/
docker-compose kill
docker-compose rm
docker rmi $(docker images -q)
cp -r my_jbrowse_data /path-to-docker-apollo-clone/data/
docker-compose up I have some problems mounting the data directory on the mac (if that is what you are using) where it hangs.
nathandunn
commented
8 years ago @erasche To that end, the volume mount we have is:
volumes:
- "./data:/data"here.
Should this be:
volumes_from:
- "./data:/data:ro"Answered my own question (no).
mictadlo
commented
8 years ago Hi,
In both cases we followed your above instructions and still got the below error by loading /apollo/jbrowse-download/sample_data/json/volvox/ on both OS platforms.
apollo_1 | 2016-07-26 23:20:45,294 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table chadoprop add constraint FK_8twb5n8vjmldyy3eeyq7sppc3 foreign key (cvterm_id) references cvterm
apollo_1 | 2016-07-26 23:20:45,294 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate - ERROR: column "cvterm_id" referenced in foreign key constraint does not exist
apollo_1 | Jul 26, 2016 11:21:07 PM org.apache.catalina.startup.HostConfig deployWAR
apollo_1 | INFO: Deployment of web application archive /usr/local/tomcat/webapps/apollo.war has finished in 81,339 ms
apollo_1 | Jul 26, 2016 11:21:07 PM org.apache.coyote.AbstractProtocol start
apollo_1 | INFO: Starting ProtocolHandler ["http-apr-8080"]
apollo_1 | Jul 26, 2016 11:21:07 PM org.apache.coyote.AbstractProtocol start
apollo_1 | INFO: Starting ProtocolHandler ["ajp-apr-8009"]
apollo_1 | Jul 26, 2016 11:21:07 PM org.apache.catalina.startup.Catalina start
apollo_1 | INFO: Server startup in 81612 ms
apollo_1 | 2016-07-26 23:21:07,607 [http-apr-8080-exec-1] ERROR apollo.AnnotatorController - User does not have permissions for the site
apollo_1 | 2016-07-26 23:21:36,333 [http-apr-8080-exec-3] ERROR apollo.AnnotatorController - User does not have permissions for the site
apollo_1 | class name usernamePasswordAuthenticatorService
apollo_1 | 2016-07-26 23:22:17,379 [http-apr-8080-exec-5] ERROR authenticator.UsernamePasswordAuthenticatorService - Not implemented without a token
apollo_1 | 2016-07-26 23:22:17,383 [http-apr-8080-exec-5] WARN apollo.PermissionService - Failed to authenticate user
apollo_1 | 2016-07-26 23:22:17,383 [http-apr-8080-exec-5] ERROR apollo.UserController - Failed to authenticate
apollo_1 | 2016-07-26 23:22:17,429 [http-apr-8080-exec-3] ERROR apollo.PermissionService - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.
apollo_1 | 2016-07-26 23:22:17,439 [http-apr-8080-exec-2] ERROR apollo.PermissionService - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.
apollo_1 | 2016-07-26 23:22:17,443 [http-apr-8080-exec-2] ERROR apollo.GroupController - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'}
apollo_1 | 2016-07-26 23:22:17,442 [http-apr-8080-exec-3] ERROR apollo.UserController - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'}
apollo_1 | class name usernamePasswordAuthenticatorService
apollo_1 | 2016-07-26 23:22:40,803 [http-apr-8080-exec-3] ERROR apollo.GroupController - {error=User does not have permission for any organisms.}
apollo_1 | 2016-07-26 23:22:40,814 [http-apr-8080-exec-9] ERROR apollo.UserController - org.bbop.apollo.PermissionException: User does not have permission for any organisms.
apollo_1 | 2016-07-26 23:22:41,238 [http-apr-8080-exec-8] ERROR apollo.AnnotatorService - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.
apollo_1 | 2016-07-26 23:23:14,188 [http-apr-8080-exec-10] ERROR errors.GrailsExceptionResolver - MissingPropertyException occurred when processing request: [GET] /apollo/71046834018752989881839155493/jbrowse/data/trackList.json
apollo_1 | No such property: name for class: java.lang.String. Stacktrace follows:
apollo_1 | groovy.lang.MissingPropertyException: No such property: name for class: java.lang.String
apollo_1 | at org.bbop.apollo.JbrowseController.trackList(JbrowseController.groovy:375)
apollo_1 | at grails.plugin.cache.web.filter.PageFragmentCachingFilter.doFilter(PageFragmentCachingFilter.java:198)
apollo_1 | at grails.plugin.cache.web.filter.AbstractFilter.doFilter(AbstractFilter.java:63)
apollo_1 | at org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:449)
apollo_1 | at org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:365)
apollo_1 | at org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90)
apollo_1 | at org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83)
apollo_1 | at org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:383)
apollo_1 | at org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:362)
apollo_1 | at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125)
apollo_1 | at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
apollo_1 | at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
apollo_1 | at java.lang.Thread.run(Thread.java:745)
apollo_1 | 2016-07-26 23:23:14,246 [http-apr-8080-exec-2] WARN apollo.JbrowseController - File not found: /jbrowse/sample_data/json/volvox/successfully_runWhat happens if you try yeast?
jbrowse-download/sample_data/json/yeast/
The format of plugins (at the bottom of trackList.json) should be of this form:
"plugins": [ { "location": "./plugins/WebApollo", "name": "WebApollo" } ],
Instead of:
"plugins”:[“WebApollo”]
I create another bug so that it works with both, but for now modifying the trackList.json for pluginEntries to use a JSON should work (unless they don’t also work for JBrowse).
Nathan
On Jul 26, 2016, at 4:35 PM, Michał T. Lorenc notifications@github.com wrote:
Hi,
- We tried it on Windows as host OS and Linux Mint 18 runs in VirtualBox.
- We tried it on Mac as host OS and Linux Mint 18 runs in VirtualBox.
In both cases we followed your above instructions and still got the below error by loading /apollo/jbrowse-download/sample_data/json/volvox/ on both OS platforms.
apollo_1 | 2016-07-26 23:20:45,294 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table chadoprop add constraint FK_8twb5n8vjmldyy3eeyq7sppc3 foreign key (cvterm_id) references cvterm apollo_1 | 2016-07-26 23:20:45,294 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate - ERROR: column "cvterm_id" referenced in foreign key constraint does not exist apollo_1 | Jul 26, 2016 11:21:07 PM org.apache.catalina.startup.HostConfig deployWAR apollo_1 | INFO: Deployment of web application archive /usr/local/tomcat/webapps/apollo.war has finished in 81,339 ms apollo_1 | Jul 26, 2016 11:21:07 PM org.apache.coyote.AbstractProtocol start apollo_1 | INFO: Starting ProtocolHandler ["http-apr-8080"] apollo_1 | Jul 26, 2016 11:21:07 PM org.apache.coyote.AbstractProtocol start apollo_1 | INFO: Starting ProtocolHandler ["ajp-apr-8009"] apollo_1 | Jul 26, 2016 11:21:07 PM org.apache.catalina.startup.Catalina start apollo_1 | INFO: Server startup in 81612 ms apollo_1 | 2016-07-26 23:21:07,607 [http-apr-8080-exec-1] ERROR apollo.AnnotatorController - User does not have permissions for the site apollo_1 | 2016-07-26 23:21:36,333 [http-apr-8080-exec-3] ERROR apollo.AnnotatorController - User does not have permissions for the site apollo_1 | class name usernamePasswordAuthenticatorService apollo_1 | 2016-07-26 23:22:17,379 [http-apr-8080-exec-5] ERROR authenticator.UsernamePasswordAuthenticatorService - Not implemented without a token apollo_1 | 2016-07-26 23:22:17,383 [http-apr-8080-exec-5] WARN apollo.PermissionService - Failed to authenticate user apollo_1 | 2016-07-26 23:22:17,383 [http-apr-8080-exec-5] ERROR apollo.UserController - Failed to authenticate apollo_1 | 2016-07-26 23:22:17,429 [http-apr-8080-exec-3] ERROR apollo.PermissionService - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm. apollo_1 | 2016-07-26 23:22:17,439 [http-apr-8080-exec-2] ERROR apollo.PermissionService - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm. apollo_1 | 2016-07-26 23:22:17,443 [http-apr-8080-exec-2] ERROR apollo.GroupController - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'} apollo_1 | 2016-07-26 23:22:17,442 [http-apr-8080-exec-3] ERROR apollo.UserController - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'} apollo_1 | class name usernamePasswordAuthenticatorService apollo_1 | 2016-07-26 23:22:40,803 [http-apr-8080-exec-3] ERROR apollo.GroupController - {error=User does not have permission for any organisms.} apollo_1 | 2016-07-26 23:22:40,814 [http-apr-8080-exec-9] ERROR apollo.UserController - org.bbop.apollo.PermissionException: User does not have permission for any organisms. apollo_1 | 2016-07-26 23:22:41,238 [http-apr-8080-exec-8] ERROR apollo.AnnotatorService - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms. apollo_1 | 2016-07-26 23:23:14,188 [http-apr-8080-exec-10] ERROR errors.GrailsExceptionResolver - MissingPropertyException occurred when processing request: [GET] /apollo/71046834018752989881839155493/jbrowse/data/trackList.json apollo_1 | No such property: name for class: java.lang.String. Stacktrace follows: apollo_1 | groovy.lang.MissingPropertyException: No such property: name for class: java.lang.String apollo_1 | at org.bbop.apollo.JbrowseController.trackList(JbrowseController.groovy:375) apollo_1 | at grails.plugin.cache.web.filter.PageFragmentCachingFilter.doFilter(PageFragmentCachingFilter.java:198) apollo_1 | at grails.plugin.cache.web.filter.AbstractFilter.doFilter(AbstractFilter.java:63) apollo_1 | at org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:449) apollo_1 | at org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:365) apollo_1 | at org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90) apollo_1 | at org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83) apollo_1 | at org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:383) apollo_1 | at org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:362) apollo_1 | at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125) apollo_1 | at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) apollo_1 | at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) apollo_1 | at java.lang.Thread.run(Thread.java:745) apollo_1 | 2016-07-26 23:23:14,246 [http-apr-8080-exec-2] WARN apollo.JbrowseController - File not found: /jbrowse/sample_data/json/volvox/successfully_run
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mictadlo
commented
8 years ago I tried /apollo/jbrowse-download/sample_data/json/yeast, but now I got these errors:
apollo_1 | 2016-07-27 02:33:31,963 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table chadoprop add constraint FK_8twb5n8vjmldyy3eeyq7sppc3 foreign key (cvterm_id) references cvterm
apollo_1 | 2016-07-27 02:33:31,965 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate - ERROR: column "cvterm_id" referenced in foreign key constraint does not exist
apollo_1 | 2016-07-27 02:33:54,074 [localhost-startStop-1] WARN apollo.UserService - User exists admin@local.host and can not be added again.
apollo_1 | Jul 27, 2016 2:33:54 AM org.apache.catalina.startup.HostConfig deployWAR
apollo_1 | INFO: Deployment of web application archive /usr/local/tomcat/webapps/apollo.war has finished in 90,146 ms
apollo_1 | Jul 27, 2016 2:33:54 AM org.apache.coyote.AbstractProtocol start
apollo_1 | INFO: Starting ProtocolHandler ["http-apr-8080"]
apollo_1 | Jul 27, 2016 2:33:54 AM org.apache.coyote.AbstractProtocol start
apollo_1 | INFO: Starting ProtocolHandler ["ajp-apr-8009"]
apollo_1 | Jul 27, 2016 2:33:54 AM org.apache.catalina.startup.Catalina start
apollo_1 | INFO: Server startup in 90420 ms
apollo_1 | 2016-07-27 02:34:20,185 [http-apr-8080-exec-7] ERROR apollo.UserController - org.bbop.apollo.PermissionException: User does not have permission for any organisms.
apollo_1 | 2016-07-27 02:34:20,398 [http-apr-8080-exec-4] ERROR apollo.GroupController - {error=User does not have permission for any organisms.}
apollo_1 | 2016-07-27 02:34:21,042 [http-apr-8080-exec-9] ERROR apollo.AnnotatorService - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.
apollo_1 | class name usernamePasswordAuthenticatorService
apollo_1 | 2016-07-27 02:34:41,678 [http-apr-8080-exec-1] ERROR authenticator.UsernamePasswordAuthenticatorService - Not implemented without a token
apollo_1 | 2016-07-27 02:34:41,695 [http-apr-8080-exec-8] ERROR apollo.PermissionService - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.
apollo_1 | 2016-07-27 02:34:41,694 [http-apr-8080-exec-7] ERROR apollo.PermissionService - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm.
apollo_1 | 2016-07-27 02:34:41,699 [http-apr-8080-exec-1] WARN apollo.PermissionService - Failed to authenticate user
apollo_1 | 2016-07-27 02:34:41,699 [http-apr-8080-exec-7] ERROR apollo.GroupController - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'}
apollo_1 | 2016-07-27 02:34:41,700 [http-apr-8080-exec-1] ERROR apollo.UserController - Failed to authenticate
apollo_1 | 2016-07-27 02:34:41,698 [http-apr-8080-exec-8] ERROR apollo.UserController - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'}
apollo_1 | 2016-07-27 02:35:20,917 [http-apr-8080-exec-6] ERROR apollo.AnnotatorController - User does not have permissions for the site
apollo_1 | class name usernamePasswordAuthenticatorService
apollo_1 | 2016-07-27 02:35:25,331 [http-apr-8080-exec-3] ERROR apollo.GroupController - {error=User does not have permission for any organisms.}
apollo_1 | 2016-07-27 02:35:25,332 [http-apr-8080-exec-6] ERROR apollo.UserController - org.bbop.apollo.PermissionException: User does not have permission for any organisms.
apollo_1 | 2016-07-27 02:35:26,005 [http-apr-8080-exec-5] ERROR apollo.AnnotatorService - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.
apollo_1 | 2016-07-27 02:35:34,813 [http-apr-8080-exec-8] ERROR apollo.GroupController - {error=User does not have permission for any organisms.}
apollo_1 | 2016-07-27 02:36:20,913 [http-apr-8080-exec-9] ERROR apollo.AnnotatorController - User does not have permissions for the site
apollo_1 | 2016-07-27 02:37:20,914 [http-apr-8080-exec-3] ERROR apollo.AnnotatorController - User does not have permissions for the site
apollo_1 | 2016-07-27 02:37:26,273 [http-apr-8080-exec-7] WARN apollo.SecurityFilters - Authentication failed
apollo_1 | 2016-07-27 02:38:20,920 [http-apr-8080-exec-8] ERROR apollo.AnnotatorController - User does not have permissions for the site
apollo_1 | 2016-07-27 02:38:32,872 [http-apr-8080-exec-10] WARN apollo.AnnotatorController - Permission exception: User does not have permission for any organisms.
apollo_1 | 2016-07-27 02:38:43,015 [http-apr-8080-exec-6] ERROR apollo.GroupController - {error=User does not have permission for any organisms.}
apollo_1 | 2016-07-27 02:39:20,911 [http-apr-8080-exec-7] ERROR apollo.AnnotatorController - User does not have permissions for the site
apollo_1 | 2016-07-27 02:40:20,912 [http-apr-8080-exec-1] ERROR apollo.AnnotatorController - User does not have permissions for the site
apollo_1 | 2016-07-27 02:41:20,918 [http-apr-8080-exec-4] ERROR apollo.AnnotatorController - User does not have permissions for the siteUsing /jbrowse-download/sample_data/json/yeast I got the following error:
problem saving organism: java.lang.Exception: Invalid directory specified: /jbrowse-download/sample_data/json/yeastWhere can I find trackList.json and how can I access it?
nathandunn
commented
8 years ago It should be in that directory if you were using straight Apollo.
/jbrowse-download/sample_data/json/yeast
However with docker compose you can see in the yaml file that it is internally mounting the data file in the directory to /data.
Steps I would try: 1 -copy /jbrowse-download/sample_data/json/yeast
To docker-apollo/data.
2 - remove the plugins section of trackList.json
3 - docker-compose kill docker-compose rm docker-compose up
4 - add the directory /data/yeast to the organism tab
Let me know how that works.
We also had issues with older versions of docker and using a Mac. I got it to work on the Mac though I had to bounce it occasionally.
Nathan
On Jul 26, 2016, at 7:49 PM, Michał T. Lorenc notifications@github.com wrote:
I tried /apollo/jbrowse-download/sample_data/json/yeast, but now I got these errors:
apollo_1 | 2016-07-27 02:33:31,963 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table chadoprop add constraint FK_8twb5n8vjmldyy3eeyq7sppc3 foreign key (cvterm_id) references cvterm apollo_1 | 2016-07-27 02:33:31,965 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate - ERROR: column "cvterm_id" referenced in foreign key constraint does not exist apollo_1 | 2016-07-27 02:33:54,074 [localhost-startStop-1] WARN apollo.UserService - User exists admin@local.host and can not be added again. apollo_1 | Jul 27, 2016 2:33:54 AM org.apache.catalina.startup.HostConfig deployWAR apollo_1 | INFO: Deployment of web application archive /usr/local/tomcat/webapps/apollo.war has finished in 90,146 ms apollo_1 | Jul 27, 2016 2:33:54 AM org.apache.coyote.AbstractProtocol start apollo_1 | INFO: Starting ProtocolHandler ["http-apr-8080"] apollo_1 | Jul 27, 2016 2:33:54 AM org.apache.coyote.AbstractProtocol start apollo_1 | INFO: Starting ProtocolHandler ["ajp-apr-8009"] apollo_1 | Jul 27, 2016 2:33:54 AM org.apache.catalina.startup.Catalina start apollo_1 | INFO: Server startup in 90420 ms apollo_1 | 2016-07-27 02:34:20,185 [http-apr-8080-exec-7] ERROR apollo.UserController - org.bbop.apollo.PermissionException: User does not have permission for any organisms. apollo_1 | 2016-07-27 02:34:20,398 [http-apr-8080-exec-4] ERROR apollo.GroupController - {error=User does not have permission for any organisms.} apollo_1 | 2016-07-27 02:34:21,042 [http-apr-8080-exec-9] ERROR apollo.AnnotatorService - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms. apollo_1 | class name usernamePasswordAuthenticatorService apollo_1 | 2016-07-27 02:34:41,678 [http-apr-8080-exec-1] ERROR authenticator.UsernamePasswordAuthenticatorService - Not implemented without a token apollo_1 | 2016-07-27 02:34:41,695 [http-apr-8080-exec-8] ERROR apollo.PermissionService - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm. apollo_1 | 2016-07-27 02:34:41,694 [http-apr-8080-exec-7] ERROR apollo.PermissionService - Problem authenticating: org.apache.shiro.authc.AccountException: Null usernames are not allowed by this realm. apollo_1 | 2016-07-27 02:34:41,699 [http-apr-8080-exec-1] WARN apollo.PermissionService - Failed to authenticate user apollo_1 | 2016-07-27 02:34:41,699 [http-apr-8080-exec-7] ERROR apollo.GroupController - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'} apollo_1 | 2016-07-27 02:34:41,700 [http-apr-8080-exec-1] ERROR apollo.UserController - Failed to authenticate apollo_1 | 2016-07-27 02:34:41,698 [http-apr-8080-exec-8] ERROR apollo.UserController - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'} apollo_1 | 2016-07-27 02:35:20,917 [http-apr-8080-exec-6] ERROR apollo.AnnotatorController - User does not have permissions for the site apollo_1 | class name usernamePasswordAuthenticatorService apollo_1 | 2016-07-27 02:35:25,331 [http-apr-8080-exec-3] ERROR apollo.GroupController - {error=User does not have permission for any organisms.} apollo_1 | 2016-07-27 02:35:25,332 [http-apr-8080-exec-6] ERROR apollo.UserController - org.bbop.apollo.PermissionException: User does not have permission for any organisms. apollo_1 | 2016-07-27 02:35:26,005 [http-apr-8080-exec-5] ERROR apollo.AnnotatorService - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms. apollo_1 | 2016-07-27 02:35:34,813 [http-apr-8080-exec-8] ERROR apollo.GroupController - {error=User does not have permission for any organisms.} apollo_1 | 2016-07-27 02:36:20,913 [http-apr-8080-exec-9] ERROR apollo.AnnotatorController - User does not have permissions for the site apollo_1 | 2016-07-27 02:37:20,914 [http-apr-8080-exec-3] ERROR apollo.AnnotatorController - User does not have permissions for the site apollo_1 | 2016-07-27 02:37:26,273 [http-apr-8080-exec-7] WARN apollo.SecurityFilters - Authentication failed apollo_1 | 2016-07-27 02:38:20,920 [http-apr-8080-exec-8] ERROR apollo.AnnotatorController - User does not have permissions for the site apollo_1 | 2016-07-27 02:38:32,872 [http-apr-8080-exec-10] WARN apollo.AnnotatorController - Permission exception: User does not have permission for any organisms. apollo_1 | 2016-07-27 02:38:43,015 [http-apr-8080-exec-6] ERROR apollo.GroupController - {error=User does not have permission for any organisms.} apollo_1 | 2016-07-27 02:39:20,911 [http-apr-8080-exec-7] ERROR apollo.AnnotatorController - User does not have permissions for the site apollo_1 | 2016-07-27 02:40:20,912 [http-apr-8080-exec-1] ERROR apollo.AnnotatorController - User does not have permissions for the site apollo_1 | 2016-07-27 02:41:20,918 [http-apr-8080-exec-4] ERROR apollo.AnnotatorController - User does not have permissions for the site Using /jbrowse-download/sample_data/json/yeast I got the following error:
problem saving organism: java.lang.Exception: Invalid directory specified: /jbrowse-download/sample_data/json/yeast Where can I find trackList.json and how can I access it?
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mictadlo
commented
8 years ago I did the following steps
$ docker run -it -v /home/apollo/dockers/docker-apollo/data/:/data gmod/apollo:latest /bin/bash
$ cp -r /apollo/jbrowse-download/sample_data/json /data
$ Removed the below plugin section `~/dockers/docker-apollo/data/json/yeast/trackList.json`
"plugins" : [
"NeatHTMLFeatures",
"NeatCanvasFeatures",
"HideTrackLabels"
],Than I was following your 3 and 4 step.
JBrowse loads now in Apollo, how it show nothing except User-created Annotations.
Do I still miss anything?
nathandunn
commented
8 years ago That is perfect. If you go to the tracks tab you should see a couple of tracks that you can select.
If for some reason it is not showing up, then click onto another tab and then back. If it is still a problem then report any javascript console errors here and I'll take a look.
nathandunn
commented
8 years ago mictadlo
commented
7 years ago Hi all,
I try my real data and I getting only Processing ... with the following trackList.json file:
{
"tracks" : [
{
"chunkSize" : 20000,
"storeClass" : "JBrowse/Store/Sequence/StaticChunked",
"urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
"category" : "Reference sequence",
"type" : "SequenceTrack",
"label" : "DNA",
"key" : "Reference sequence"
},
{
"style" : {
"className" : "feature"
},
"key" : "Scaffolds",
"storeClass" : "JBrowse/Store/SeqFeature/NCList",
"trackType" : null,
"urlTemplate" : "tracks/Scaffolds/{refseq}/trackData.json",
"compress" : 0,
"type" : "FeatureTrack",
"label" : "Scaffolds"
},
{
"style" : {
"className" : "feature"
},
"key" : "Transcript v5",
"storeClass" : "JBrowse/Store/SeqFeature/NCList",
"trackType" : "CanvasFeatures",
"urlTemplate" : "tracks/Transcript v5/{refseq}/trackData.json",
"compress" : 0,
"type" : "CanvasFeatures",
"label" : "Transcript v5"
},
{
"style" : {
"className" : "feature"
},
"key" : "Alternative Transcripts v5",
"storeClass" : "JBrowse/Store/SeqFeature/NCList",
"trackType" : "CanvasFeatures",
"urlTemplate" : "tracks/Alternative Transcripts v5/{refseq}/trackData.json",
"compress" : 0,
"type" : "CanvasFeatures",
"label" : "Alternative Transcripts v5"
},
{
"track" : "16C line Primary + Alt",
"style" : {
"className" : "feature"
},
"key" : "16C line Primary + Alt",
"feature" : [
"Nbdbv05_16C"
],
"storeClass" : "JBrowse/Store/SeqFeature/NCList",
"urlTemplate" : "tracks/16C line Primary + Alt/{refseq}/trackData.jsonz",
"compress" : 1,
"type" : "FeatureTrack",
"category" : "All Wild type transcripts",
"label" : "16C line Primary + Alt"
},
{
"style" : {
"className" : "feature"
},
"key" : "16C line Primary",
"storeClass" : "JBrowse/Store/SeqFeature/NCList",
"trackType" : "CanvasFeatures",
"urlTemplate" : "tracks/16C line Primary/{refseq}/trackData.jsonz",
"compress" : 1,
"category" : "All Wild type transcripts",
"label" : "16C line Primary",
"type" : "FeatureTrack"
},
{
"style" : {
"className" : "feature"
},
"key" : "NT line Primary + Alt",
"storeClass" : "JBrowse/Store/SeqFeature/NCList",
"trackType" : "CanvasFeatures",
"urlTemplate" : "tracks/NT line Primary + Alt/{refseq}/trackData.jsonz",
"compress" : 1,
"category" : "All Wild type transcripts",
"label" : "NT line Primary + Alt",
"type" : "FeatureTrack"
},
{
"style" : {
"className" : "feature"
},
"key" : "NT line Primary",
"storeClass" : "JBrowse/Store/SeqFeature/NCList",
"trackType" : "CanvasFeatures",
"urlTemplate" : "tracks/NT line Primary/{refseq}/trackData.jsonz",
"compress" : 1,
"category" : "All Wild type transcripts",
"label" : "NT line Primary",
"type" : "FeatureTrack"
},
{
"style" : {
"className" : "feature"
},
"key" : "NWA line Primary",
"storeClass" : "JBrowse/Store/SeqFeature/NCList",
"trackType" : "CanvasFeatures",
"urlTemplate" : "tracks/NWA line Primary/{refseq}/trackData.jsonz",
"compress" : 1,
"category" : "All Wild type transcripts",
"label" : "NWA line Primary",
"type" : "FeatureTrack"
},
{
"style" : {
"className" : "feature"
},
"key" : "WA line Primary",
"storeClass" : "JBrowse/Store/SeqFeature/NCList",
"trackType" : "CanvasFeatures",
"urlTemplate" : "tracks/WA line Primary/{refseq}/trackData.jsonz",
"compress" : 1,
"category" : "All Wild type transcripts",
"label" : "WA line Primary",
"type" : "FeatureTrack"
},
{
"style" : {
"className" : "feature"
},
"key" : "SA line Primary",
"storeClass" : "JBrowse/Store/SeqFeature/NCList",
"trackType" : "CanvasFeatures",
"urlTemplate" : "tracks/SA line Primary/{refseq}/trackData.jsonz",
"compress" : 1,
"category" : "All Wild type transcripts",
"label" : "SA line Primary",
"type" : "FeatureTrack"
},
{
"style" : {
"className" : "feature"
},
"key" : "QLD line Primary",
"storeClass" : "JBrowse/Store/SeqFeature/NCList",
"trackType" : "CanvasFeatures",
"urlTemplate" : "tracks/QLD line Primary/{refseq}/trackData.jsonz",
"compress" : 1,
"category" : "All Wild type transcripts",
"label" : "QLD line Primary",
"type" : "FeatureTrack"
},
{
"style" : {
"className" : "feature"
},
"key" : "QLD line Primary + Alt",
"storeClass" : "JBrowse/Store/SeqFeature/NCList",
"trackType" : "CanvasFeatures",
"urlTemplate" : "tracks/QLD line Primary + Alt/{refseq}/trackData.jsonz",
"compress" : 1,
"category" : "All Wild type transcripts",
"label" : "QLD line Primary + Alt",
"type" : "FeatureTrack"
},
{
"style" : {
"className" : "feature"
},
"key" : "SA line Primary + Alt",
"storeClass" : "JBrowse/Store/SeqFeature/NCList",
"trackType" : "CanvasFeatures",
"urlTemplate" : "tracks/SA line Primary + Alt/{refseq}/trackData.jsonz",
"compress" : 1,
"category" : "All Wild type transcripts",
"label" : "SA line Primary + Alt",
"type" : "FeatureTrack"
},
{
"style" : {
"className" : "feature"
},
"key" : "WA line Primary + Alt",
"storeClass" : "JBrowse/Store/SeqFeature/NCList",
"trackType" : "CanvasFeatures",
"urlTemplate" : "tracks/WA line Primary + Alt/{refseq}/trackData.jsonz",
"compress" : 1,
"category" : "All Wild type transcripts",
"label" : "WA line Primary + Alt",
"type" : "FeatureTrack"
},
{
"style" : {
"className" : "feature"
},
"key" : "NWA line Primary + Alt",
"storeClass" : "JBrowse/Store/SeqFeature/NCList",
"trackType" : "CanvasFeatures",
"urlTemplate" : "tracks/NWA line Primary + Alt/{refseq}/trackData.jsonz",
"compress" : 1,
"category" : "All Wild type transcripts",
"label" : "NWA line Primary + Alt",
"type" : "FeatureTrack"
},
{
"track" : "16Calt",
"style" : {
"className" : "feature",
"linkTemplate" : "tracks/16C line Primary + Alt/{refseq}/trackData.jsonz"
},
"key" : "16C line Primary + Alt",
"feature" : [
"Nbdbv05_16C"
],
"storeClass" : "JBrowse/Store/SeqFeature/NCList",
"compress" : 1,
"label" : "16Calt",
"type" : "FeatureTrack",
"category" : "Test - transcripts"
},
{
"track" : "Nbdbv05_16C_main",
"style" : {
"className" : "feature"
},
"key" : "16C line Primary",
"feature" : [
"Nbdbv05_16C_main"
],
"storeClass" : "JBrowse/Store/SeqFeature/NCList",
"urlTemplate" : "tracks/16C line Primary/{refseq}/trackData.jsonz",
"compress" : 1,
"type" : "CanvasFeatures",
"label" : "Nbdbv05_16C_main",
"category" : "Test - transcripts"
}
],
"names" : {
"url" : "names/",
"type" : "Hash"
},
"formatVersion" : 1
}Did I anything wrong?
nathandunn
commented
7 years ago I'll be back in a week to look (on vacation now). Short answer is that you need the tomcat logs to diagnose. I would also confirm that the mounted directory is showing up internally on the docker side.
You can also just install Apollo from source. @erasche has a working version or two as well with Galaxy where data is mounted and brought in internally so you won't have the mounting of local disk problems.
Nathan
On Aug 2, 2016, at 2:33 AM, Michał T. Lorenc notifications@github.com wrote:
Hi all, I try my real data and I getting only Processing ... with the following trackList.json file:
{ "tracks" : [ { "chunkSize" : 20000, "storeClass" : "JBrowse/Store/Sequence/StaticChunked", "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-", "category" : "Reference sequence", "type" : "SequenceTrack", "label" : "DNA", "key" : "Reference sequence" }, { "style" : { "className" : "feature" }, "key" : "Scaffolds", "storeClass" : "JBrowse/Store/SeqFeature/NCList", "trackType" : null, "urlTemplate" : "tracks/Scaffolds/{refseq}/trackData.json", "compress" : 0, "type" : "FeatureTrack", "label" : "Scaffolds" }, { "style" : { "className" : "feature" }, "key" : "Transcript v5", "storeClass" : "JBrowse/Store/SeqFeature/NCList", "trackType" : "CanvasFeatures", "urlTemplate" : "tracks/Transcript v5/{refseq}/trackData.json", "compress" : 0, "type" : "CanvasFeatures", "label" : "Transcript v5" }, { "style" : { "className" : "feature" }, "key" : "Alternative Transcripts v5", "storeClass" : "JBrowse/Store/SeqFeature/NCList", "trackType" : "CanvasFeatures", "urlTemplate" : "tracks/Alternative Transcripts v5/{refseq}/trackData.json", "compress" : 0, "type" : "CanvasFeatures", "label" : "Alternative Transcripts v5" }, { "track" : "16C line Primary + Alt", "style" : { "className" : "feature" }, "key" : "16C line Primary + Alt", "feature" : [ "Nbdbv05_16C" ], "storeClass" : "JBrowse/Store/SeqFeature/NCList", "urlTemplate" : "tracks/16C line Primary + Alt/{refseq}/trackData.jsonz", "compress" : 1, "type" : "FeatureTrack", "category" : "All Wild type transcripts", "label" : "16C line Primary + Alt" }, { "style" : { "className" : "feature" }, "key" : "16C line Primary", "storeClass" : "JBrowse/Store/SeqFeature/NCList", "trackType" : "CanvasFeatures", "urlTemplate" : "tracks/16C line Primary/{refseq}/trackData.jsonz", "compress" : 1, "category" : "All Wild type transcripts", "label" : "16C line Primary", "type" : "FeatureTrack" }, { "style" : { "className" : "feature" }, "key" : "NT line Primary + Alt", "storeClass" : "JBrowse/Store/SeqFeature/NCList", "trackType" : "CanvasFeatures", "urlTemplate" : "tracks/NT line Primary + Alt/{refseq}/trackData.jsonz", "compress" : 1, "category" : "All Wild type transcripts", "label" : "NT line Primary + Alt", "type" : "FeatureTrack" }, { "style" : { "className" : "feature" }, "key" : "NT line Primary", "storeClass" : "JBrowse/Store/SeqFeature/NCList", "trackType" : "CanvasFeatures", "urlTemplate" : "tracks/NT line Primary/{refseq}/trackData.jsonz", "compress" : 1, "category" : "All Wild type transcripts", "label" : "NT line Primary", "type" : "FeatureTrack" }, { "style" : { "className" : "feature" }, "key" : "NWA line Primary", "storeClass" : "JBrowse/Store/SeqFeature/NCList", "trackType" : "CanvasFeatures", "urlTemplate" : "tracks/NWA line Primary/{refseq}/trackData.jsonz", "compress" : 1, "category" : "All Wild type transcripts", "label" : "NWA line Primary", "type" : "FeatureTrack" }, { "style" : { "className" : "feature" }, "key" : "WA line Primary", "storeClass" : "JBrowse/Store/SeqFeature/NCList", "trackType" : "CanvasFeatures", "urlTemplate" : "tracks/WA line Primary/{refseq}/trackData.jsonz", "compress" : 1, "category" : "All Wild type transcripts", "label" : "WA line Primary", "type" : "FeatureTrack" }, { "style" : { "className" : "feature" }, "key" : "SA line Primary", "storeClass" : "JBrowse/Store/SeqFeature/NCList", "trackType" : "CanvasFeatures", "urlTemplate" : "tracks/SA line Primary/{refseq}/trackData.jsonz", "compress" : 1, "category" : "All Wild type transcripts", "label" : "SA line Primary", "type" : "FeatureTrack" }, { "style" : { "className" : "feature" }, "key" : "QLD line Primary", "storeClass" : "JBrowse/Store/SeqFeature/NCList", "trackType" : "CanvasFeatures", "urlTemplate" : "tracks/QLD line Primary/{refseq}/trackData.jsonz", "compress" : 1, "category" : "All Wild type transcripts", "label" : "QLD line Primary", "type" : "FeatureTrack" }, { "style" : { "className" : "feature" }, "key" : "QLD line Primary + Alt", "storeClass" : "JBrowse/Store/SeqFeature/NCList", "trackType" : "CanvasFeatures", "urlTemplate" : "tracks/QLD line Primary + Alt/{refseq}/trackData.jsonz", "compress" : 1, "category" : "All Wild type transcripts", "label" : "QLD line Primary + Alt", "type" : "FeatureTrack" }, { "style" : { "className" : "feature" }, "key" : "SA line Primary + Alt", "storeClass" : "JBrowse/Store/SeqFeature/NCList", "trackType" : "CanvasFeatures", "urlTemplate" : "tracks/SA line Primary + Alt/{refseq}/trackData.jsonz", "compress" : 1, "category" : "All Wild type transcripts", "label" : "SA line Primary + Alt", "type" : "FeatureTrack" }, { "style" : { "className" : "feature" }, "key" : "WA line Primary + Alt", "storeClass" : "JBrowse/Store/SeqFeature/NCList", "trackType" : "CanvasFeatures", "urlTemplate" : "tracks/WA line Primary + Alt/{refseq}/trackData.jsonz", "compress" : 1, "category" : "All Wild type transcripts", "label" : "WA line Primary + Alt", "type" : "FeatureTrack" }, { "style" : { "className" : "feature" }, "key" : "NWA line Primary + Alt", "storeClass" : "JBrowse/Store/SeqFeature/NCList", "trackType" : "CanvasFeatures", "urlTemplate" : "tracks/NWA line Primary + Alt/{refseq}/trackData.jsonz", "compress" : 1, "category" : "All Wild type transcripts", "label" : "NWA line Primary + Alt", "type" : "FeatureTrack" }, { "track" : "16Calt", "style" : { "className" : "feature", "linkTemplate" : "tracks/16C line Primary + Alt/{refseq}/trackData.jsonz" }, "key" : "16C line Primary + Alt", "feature" : [ "Nbdbv05_16C" ], "storeClass" : "JBrowse/Store/SeqFeature/NCList", "compress" : 1, "label" : "16Calt", "type" : "FeatureTrack", "category" : "Test - transcripts" }, { "track" : "Nbdbv05_16C_main", "style" : { "className" : "feature" }, "key" : "16C line Primary", "feature" : [ "Nbdbv05_16C_main" ], "storeClass" : "JBrowse/Store/SeqFeature/NCList", "urlTemplate" : "tracks/16C line Primary/{refseq}/trackData.jsonz", "compress" : 1, "type" : "CanvasFeatures", "label" : "Nbdbv05_16C_main", "category" : "Test - transcripts" } ], "names" : { "url" : "names/", "type" : "Hash" }, "formatVersion" : 1 } Did I anything wrong?
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mictadlo
commented
7 years ago It has actually finished processing, and in Organisms tab it shows the number of Ref_sequences, but the Annotation number is 0.
This is the log from gmod/apollo:latest
docker logs a032195d3685 (gmod/apollo:latest)
Shiro Configured
2016-08-02 00:51:09,617 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table chadoprop add column cvterm_id int8 not null
2016-08-02 00:51:09,713 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate - ERROR: column "cvterm_id" contains null values
2016-08-02 00:51:14,982 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table chadoprop add constraint FK_8twb5n8vjmldyy3eeyq7sppc3 foreign key (cvterm_id) references cvterm
2016-08-02 00:51:14,990 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate - ERROR: column "cvterm_id" referenced in foreign key constraint does not exist
Aug 02, 2016 12:54:28 AM org.apache.catalina.util.SessionIdGeneratorBase createSecureRandom
INFO: Creation of SecureRandom instance for session ID generation using [SHA1PRNG] took [118] milliseconds.
Aug 02, 2016 12:54:30 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /usr/local/tomcat/webapps/apollo.war has finished in 832,032 ms
Aug 02, 2016 12:54:30 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-apr-8080"]
Aug 02, 2016 12:54:30 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-apr-8009"]
Aug 02, 2016 12:54:30 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 833548 ms
class name usernamePasswordAuthenticatorService
2016-08-02 00:54:39,551 [http-apr-8080-exec-4] ERROR authenticator.UsernamePasswordAuthenticatorService - Not implemented without a token
2016-08-02 00:54:39,601 [http-apr-8080-exec-4] WARN apollo.PermissionService - Failed to authenticate user
2016-08-02 00:54:39,602 [http-apr-8080-exec-4] ERROR apollo.UserController - Failed to authenticate
2016-08-02 00:54:39,935 [http-apr-8080-exec-2] ERROR apollo.UserController - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'}
2016-08-02 00:54:39,935 [http-apr-8080-exec-10] ERROR apollo.GroupController - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'}
class name usernamePasswordAuthenticatorService
2016-08-02 01:02:37,633 [http-apr-8080-exec-5] ERROR authenticator.UsernamePasswordAuthenticatorService - Not implemented without a token
2016-08-02 01:02:37,649 [http-apr-8080-exec-6] ERROR apollo.UserController - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'}
2016-08-02 01:02:37,670 [http-apr-8080-exec-5] WARN apollo.PermissionService - Failed to authenticate user
2016-08-02 01:02:37,674 [http-apr-8080-exec-5] ERROR apollo.UserController - Failed to authenticate
2016-08-02 01:02:37,684 [http-apr-8080-exec-9] ERROR apollo.GroupController - {error=Cannot cast object 'false' with class 'java.lang.Boolean' to class 'org.codehaus.groovy.grails.web.json.JSONObject'}
class name usernamePasswordAuthenticatorService
2016-08-02 01:03:38,779 [http-apr-8080-exec-8] ERROR apollo.UserController - org.bbop.apollo.PermissionException: User does not have permission for any organisms.
2016-08-02 01:03:38,855 [http-apr-8080-exec-2] ERROR apollo.GroupController - {error=User does not have permission for any organisms.}
2016-08-02 01:03:39,938 [http-apr-8080-exec-9] ERROR apollo.AnnotatorService - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.
2016-08-02 01:52:25,771 [http-apr-8080-exec-2] ERROR apollo.AnnotatorService - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.
2016-08-02 01:52:25,820 [http-apr-8080-exec-8] WARN apollo.AnnotatorController - Permission exception: User does not have permission for any organisms.
2016-08-02 22:49:55,565 [http-apr-8080-exec-9] INFO apollo.UserController - updateTrackListPreference
2016-08-02 22:49:56,283 [http-apr-8080-exec-9] INFO apollo.UserController - Added userOrganismPreference trueand this is logs from postgres
$ docker logs cfd8d7e60c9d (postgres)
The files belonging to this database system will be owned by user "postgres".
This user must also own the server process.
The database cluster will be initialized with locale "en_US.utf8".
The default database encoding has accordingly been set to "UTF8".
The default text search configuration will be set to "english".
Data page checksums are disabled.
fixing permissions on existing directory /var/lib/postgresql/data ... ok
creating subdirectories ... ok
selecting default max_connections ... 100
selecting default shared_buffers ... 128MB
selecting dynamic shared memory implementation ... posix
creating configuration files ... ok
creating template1 database in /var/lib/postgresql/data/base/1 ... ok
initializing pg_authid ... ok
initializing dependencies ... ok
creating system views ... ok
loading system objects' descriptions ... ok
creating collations ... ok
creating conversions ... ok
creating dictionaries ... ok
setting privileges on built-in objects ... ok
creating information schema ... ok
loading PL/pgSQL server-side language ... ok
vacuuming database template1 ... ok
copying template1 to template0 ... ok
copying template1 to postgres ... ok
WARNING: enabling "trust" authentication for local connections
You can change this by editing pg_hba.conf or using the option -A, or
--auth-local and --auth-host, the next time you run initdb.
syncing data to disk ... ok
Success. You can now start the database server using:
pg_ctl -D /var/lib/postgresql/data -l logfile start
waiting for server to start....LOG: database system was shut down at 2016-08-02 00:40:34 UTC
LOG: MultiXact member wraparound protections are now enabled
LOG: autovacuum launcher started
LOG: database system is ready to accept connections
done
server started
ALTER ROLE
/docker-entrypoint.sh: ignoring /docker-entrypoint-initdb.d/*
LOG: received fast shutdown request
waiting for server to shut down...LOG: aborting any active transactions
LOG: autovacuum launcher shutting down
.LOG: shutting down
LOG: database system is shut down
done
server stopped
PostgreSQL init process complete; ready for start up.
LOG: database system was shut down at 2016-08-02 00:40:43 UTC
LOG: MultiXact member wraparound protections are now enabled
LOG: database system is ready to accept connections
LOG: autovacuum launcher started
ERROR: constraint "uk_3mkho1p232es23vtaqp0obydb" of relation "db" does not exist
STATEMENT: alter table db drop constraint UK_3mkho1p232es23vtaqp0obydb
ERROR: constraint "uk_rdmcxcj6i53kfjmb9j811ta1m" of relation "grails_user" does not exist
STATEMENT: alter table grails_user drop constraint UK_rdmcxcj6i53kfjmb9j811ta1m
ERROR: constraint "uk_8sewwnpamngi6b1dwaa88askk" of relation "role" does not exist
STATEMENT: alter table role drop constraint UK_8sewwnpamngi6b1dwaa88askkP.S. enjoy your holidays Mic
mictadlo
commented
7 years ago It is almost working now after I added the CATALINA_OPTS to docker-compose.yml file.
image: gmod/apollo:latest
links:
- db
- chado
ports:
- "8080:8080"
environment:
...
CATALINA_OPTS: "-Xmx12288m -Xms8192m \
-XX:PermSize=256m \
-XX:MaxPermSize=1024m \
-XX:ReservedCodeCacheSize=64m \
-XX:+UseG1GC \
-XX:+CMSClassUnloadingEnabled \
-XX:+PrintHeapAtGC \
-XX:+PrintGCDetails \
-XX:+PrintGCTimeStamps"When Apollo crashed and restart docker-apollo the organism is not available anymore. How it possible to keep the organism permanently.
Thank you in advance.
Mic
nathandunn
commented
7 years ago My guess is it wiped your image (not the database) as I'm not seeing your issue either. Maybe you ran out of docker volume space?
What happens if you use the docker-compose.yml file provided and do: docker-compose up ?
You may want to update as well, as I just updated the latest tag as well, but I doubt it will make any difference.
mictadlo
commented
7 years ago I think might I used accidentally docker-compose rm. Do you think this Memory setting are properly set:
image: gmod/apollo:latest
links:
- db
- chado
ports:
- "8080:8080"
environment:
...
CATALINA_OPTS: "-Xmx12288m -Xms8192m \
-XX:PermSize=256m \
-XX:MaxPermSize=1024m \
-XX:ReservedCodeCacheSize=64m \
-XX:+UseG1GC \
-XX:+CMSClassUnloadingEnabled \
-XX:+PrintHeapAtGC \
-XX:+PrintGCDetails \
-XX:+PrintGCTimeStamps"?
nathandunn
commented
7 years ago @mictadlo Unless you have about 200 very active users I would change probably use less memory, e.g. -Xmx4096m -Xms1024m but using what you have up there won't hurt anything either.
mictadlo
commented
7 years ago Thank you.
mictadlo
commented
7 years ago Hi all, apparently the double quotes has to be removed in CATALINA_OPTS (https://github.com/docker-library/tomcat/issues/8#issuecomment-242283842)
Hi, I did
sudo docker run -itP -v data:/container/data gmod/apollo:latestunder ubuntu 16.04 and Docker version 1.11.2 , but received the following errors:What did I do wrong?
Thank you in advance.
Mic