nathandunn
commented
5 years ago So, I'm not sure where its producing those errors from, but I would probably update to use the latest (versus 2.3.1) quay image instead of building it locally.
I added a common directory to the configuration that needs to be specified. Typically on startup it will query you or you can set it in the config (having some network trouble, but it is in here https://genomearchitect.readthedocs.io/en/latest/ https://genomearchitect.readthedocs.io/en/latest/).
Worst-case, you can set it in the database manually either someplace mounted or internal, but I’m really hoping that’s not necessary.
This is my system version:
select * from application_preference
apollo-none-# ;
id | version | name | value
-------+---------+-----------------------+-----------------------
16511 | 0 | common_data_directory | /opt/temporary/apollo
I’ve been running it locally like this without issue:
docker run -it -v /opt/apollo/:/data -v postgres-data:/var/lib/postgresql -p 8888:8080 quay.io/gmod/docker-apollo:latest
Let me know if that helps or I can see if I can’t build it from your instructions.
Nathan
On Apr 3, 2019, at 10:57 PM, quokkamole notifications@github.com wrote:
I have built the latest docker-apollo using the supplied Dockerfile and associated files and a Docker-compose file:
version: '3' services: webapollo-docker:
image: quay.io/gmod/docker-apollo:2.3.1
build: ports: - "8888:8080" volumes: - ./jbrowse-root:/data - ./postgres-data:/var/lib/postgresqlThe container seems to build correctly and starts up. The first problem I encounter in my browser when navigating to the web-apollo installation is that it complains about /temporary/apollo_data not being present. So I have gone into the container and created it. The folder is then visible in my mounted folder on the host (jbrowse-root). After solving that problem the browser then hangs on "Loading.." after logging in. The docker container logs show:
webapollo-docker_1 | 2019-04-03 21:25:00,599 [http-nio-8080-exec-15] WARN apollo.PermissionService - No user provided, please log in webapollo-docker_1 | 2019-04-03 21:25:00,650 [http-nio-8080-exec-12] WARN apollo.PreferenceService - No user present, so using the client token webapollo-docker_1 | 2019-04-03 21:25:00,747 [http-nio-8080-exec-13] WARN apollo.PermissionService - Failed to authenticate user webapollo-docker_1 | 2019-04-03 21:25:20,808 [http-nio-8080-exec-15] WARN apollo.AnnotatorService - Unable to write to the database directory, so checking the config file webapollo-docker_1 | 2019-04-03 21:25:21,239 [http-nio-8080-exec-14] INFO apollo.UserController - updateTrackListPreference webapollo-docker_1 | 2019-04-03 21:25:21,279 [http-nio-8080-exec-14] INFO apollo.UserController - Added userOrganismPreference false webapollo-docker_1 | 2019-04-03 21:25:21,516 [http-nio-8080-exec-11] ERROR errors.GrailsExceptionResolver - NullPointerException occurred when processing request: [GET] /annotator/getAppState webapollo-docker_1 | Cannot get property 'value' on null object. Stacktrace follows: webapollo-docker_1 | java.lang.NullPointerException: Cannot get property 'value' on null object webapollo-docker_1 | at org.bbop.apollo.AnnotatorService.getCommonDataDirectory(AnnotatorService.groovy:101) webapollo-docker_1 | at org.bbop.apollo.AnnotatorService.$tt__getAppState(AnnotatorService.groovy:85) webapollo-docker_1 | at org.bbop.apollo.AnnotatorController.$tt__getAppState(AnnotatorController.groovy:580) webapollo-docker_1 | at grails.plugin.cache.web.filter.PageFragmentCachingFilter.doFilter(PageFragmentCachingFilter.java:198) webapollo-docker_1 | at grails.plugin.cache.web.filter.AbstractFilter.doFilter(AbstractFilter.java:63) webapollo-docker_1 | at org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:449) webapollo-docker_1 | at org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:365) webapollo-docker_1 | at org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90) webapollo-docker_1 | at org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83) webapollo-docker_1 | at org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:383) webapollo-docker_1 | at org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:362) webapollo-docker_1 | at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125) webapollo-docker_1 | at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) webapollo-docker_1 | at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) webapollo-docker_1 | at java.lang.Thread.run(Thread.java:748)
Perhaps you can give some suggestions on what is going wrong here (permission issue with the host folders? What permissions are needed?).
Thanks.
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I have built the latest docker-apollo using the supplied Dockerfile and associated files and a Docker-compose file:
The container seems to build correctly and starts up. The first problem I encounter in my browser when navigating to the web-apollo installation is that it complains about /temporary/apollo_data not being present. So I have gone into the container and created it. The folder is then visible in my mounted folder on the host (jbrowse-root). After solving that problem the browser then hangs on "Loading.." after logging in. The docker container logs show:
Perhaps you can give some suggestions on what is going wrong here (permission issue with the host folders? What permissions are needed?).
Thanks.