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:whale: Apollo 2.X Docker Image
License: GNU General Public License v3.0
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galaxy-genome-annotation abretaud fikipollo epaule alliance-genome wezen zerocry tamu-cpt michaelp896 jay0307p robsyme jorisvansteenbruggedocker-apollo's Issues
Build issues
FYI, just documenting in case these aren't the same build issues you see...
:clean-grails[ant:exec] Execute failed: java.io.IOException: Cannot run program "grails": error=2, No such file or directory
and
bower ESUDO Cannot be run with sudo
Increasing max memory inside container?
Hi,
I have been running the WA docker container successfully for some time. Now I wanted to implement a backup routine for the curation track of a vertebrate genome (> 20.000 models). I get a an out of memory error when doing this from outside the container using the groovy get_gff3.groovy script that is bundled with WA.
The machine has plenty RAM, but I think the tomcat server inside the docker container is configured with too little.
Since I have little experience with Docker - can I somwhow increase the max memory available to Tomcat inside the container?
Cheers,
Marc
increase default docker memory and tomcat memory
- increase tomcat memory to be 2 GB max, 512MB min
- instructions for default docker memory, etc.
Notes:
https://stackoverflow.com/questions/29923531/how-to-set-java-heap-size-xms-xmx-inside-docker-container https://stackoverflow.com/questions/29923531/how-to-set-java-heap-size-xms-xmx-inside-docker-container
Upload is really slow.
Tracks view give "Object Response" Error
Hi,
I have a working docker image from the GitHub but I get object Response error when I add tracks as shown below.
The error in itself is not helpful to track the problems.
Other GitHub issue shows similar error and was fixed by adding permission in the httpd file. GMOD/jbrowse#1242
But I am not sure where can I add this in Docker.
createUser REST exceptions
creating 100 users with a rest call using the below script creates:
ERROR errors.GrailsExceptionResolver - StaleObjectStateException occurred when processing request: [POST] /user/createUser
Row was updated or deleted by another transaction (or unsaved-value mapping was incorrect) : [org.bbop.apollo.User#117]. Stacktrace follows:
org.hibernate.StaleObjectStateException: Row was updated or deleted by another transaction (or unsaved-value mapping was incorrect) : [org.bbop.apollo.User#117]
at grails.plugin.cache.web.filter.PageFragmentCachingFilter.doFilter(PageFragmentCachingFilter.java:198)
at grails.plugin.cache.web.filter.AbstractFilter.doFilter(AbstractFilter.java:63)
at org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:449)
at org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:365)
at org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90)
at org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83)
at org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:383)
at org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:362)
at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
errors, whereas it doesn't with the groovy script add_users.groovy (with a CSV file).
#!/usr/bin/env ruby
require 'net/http'
require 'uri'
require 'json'
# contains hardcoded crud
def rest_call(url,params)
uri = URI.parse('http://localhost:8888/'+url)
header = {'Content-Type': 'application/json'}
params.merge!({'username' => '[email protected]','password' => 'password'})
http = Net::HTTP.new(uri.host,uri.port)
request = Net::HTTP::Post.new(uri.request_uri,header)
request.body = params.to_json
response = http.request(request)
puts response.message if response.code != '200'
end
# creates users, organisms and sets the permisstion to rw
1.upto(100){|n|
user = "student#{n}"
username = user+'@test.tst'
params = {
'email' => username,
'firstName'=> user,
'lastName' => 'test',
'newPassword' => 'password',
'role' => 'user'
}
rest_call('user/createUser',params)
}Docker build error
When i was building the container using the Dockerfile getting this issue.
Grails not found using grailsw
Gradle not found using gradlew
Node Version: 8
Npm Version: 5
javac 1.8.0_141 found
javac installed
JDK 1.8 found: javac 1.8.0_141
OpenJDK 64-Bit Server VM warning: ignoring option PermSize=32m; support was removed in 8.0
OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=256m; support was removed in 8.0
Downloading https://github.com/grails/grails-core/releases/download/v2.5.5/grails-2.5.5.zip to /apollo/.grails/wrapper/grails-2.5.5-download.zip
Exception in thread "main" java.net.ConnectException: Connection timed out (Connection timed out)
at java.net.PlainSocketImpl.socketConnect(Native Method)
at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:589)
at sun.security.ssl.SSLSocketImpl.connect(SSLSocketImpl.java:673)
at sun.security.ssl.BaseSSLSocketImpl.connect(BaseSSLSocketImpl.java:173)
at sun.net.NetworkClient.doConnect(NetworkClient.java:180)
at sun.net.www.http.HttpClient.openServer(HttpClient.java:463)
at sun.net.www.http.HttpClient.openServer(HttpClient.java:558)
at sun.net.www.protocol.https.HttpsClient.(HttpsClient.java:264)
at sun.net.www.protocol.https.HttpsClient.New(HttpsClient.java:367)
at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(AbstractDelegateHttpsURLConnection.java:191)
at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1138)
at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:1032)
at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(AbstractDelegateHttpsURLConnection.java:177)
at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1546)
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1474)
at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:254)
at org.grails.wrapper.RemoteFileHelper.retrieve(RemoteFileHelper.java:49)
at org.grails.wrapper.GrailsWrapper.configureGrailsInstallation(GrailsWrapper.java:137)
at org.grails.wrapper.GrailsWrapper.main(GrailsWrapper.java:57)
Downloading https://services.gradle.org/distributions/gradle-2.11-all.zip
Exception in thread "main" java.net.ConnectException: Connection timed out (Connection timed out)
at java.net.PlainSocketImpl.socketConnect(Native Method)
at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:589)
at sun.security.ssl.SSLSocketImpl.connect(SSLSocketImpl.java:673)
at sun.security.ssl.BaseSSLSocketImpl.connect(BaseSSLSocketImpl.java:173)
at sun.net.NetworkClient.doConnect(NetworkClient.java:180)
at sun.net.www.http.HttpClient.openServer(HttpClient.java:463)
at sun.net.www.http.HttpClient.openServer(HttpClient.java:558)
at sun.net.www.protocol.https.HttpsClient.(HttpsClient.java:264)
at sun.net.www.protocol.https.HttpsClient.New(HttpsClient.java:367)
at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(AbstractDelegateHttpsURLConnection.java:191)
at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1138)
at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:1032)
at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(AbstractDelegateHttpsURLConnection.java:177)
at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1546)
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1474)
at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:254)
at org.gradle.wrapper.Download.downloadInternal(Download.java:58)
at org.gradle.wrapper.Download.download(Download.java:44)
at org.gradle.wrapper.Install$1.call(Install.java:61)
at org.gradle.wrapper.Install$1.call(Install.java:48)
at org.gradle.wrapper.ExclusiveFileAccessManager.access(ExclusiveFileAccessManager.java:65)
at org.gradle.wrapper.Install.createDist(Install.java:48)
at org.gradle.wrapper.WrapperExecutor.execute(WrapperExecutor.java:128)
at org.gradle.wrapper.GradleWrapperMain.main(GradleWrapperMain.java:61)
mv: cannot stat '/tmp/apollo.war': No such file or directory
The command '/bin/sh -c bash /bin/build.sh' returned a non-zero code: 1
Docker version
docker info
Containers: 25
Running: 0
Paused: 0
Stopped: 25
Images: 34
Server Version: 17.09.0-ce
Storage Driver: overlay
Backing Filesystem: xfs
Supports d_type: true
Logging Driver: json-file
Cgroup Driver: cgroupfs
Plugins:
Volume: local
Network: bridge host macvlan null overlay
Log: awslogs fluentd gcplogs gelf journald json-file logentries splunk syslog
Swarm: inactive
Runtimes: runc
Default Runtime: runc
Init Binary: docker-init
containerd version: 06b9cb35161009dcb7123345749fef02f7cea8e0
runc version: 3f2f8b84a77f73d38244dd690525642a72156c64
init version: 949e6fa
Security Options:
seccomp
Profile: default
Kernel Version: 3.10.0-693.5.2.el7.x86_64
Operating System: CentOS Linux 7 (Core)
OSType: linux
Architecture: x86_64
CPUs: 1
Total Memory: 1.629GiB
Name: leela.prasad
ID: 6BFO:YKKZ:QE4Y:5462:E4WE:3R3M:JOPF:HJV6:VWTY:NSJR:F4DQ:ETMR
Docker Root Dir: /var/lib/docker
Debug Mode (client): false
Debug Mode (server): false
Username: apoc
Registry: https://index.docker.io/v1/
Experimental: false
Insecure Registries:
127.0.0.0/8
Live Restore Enabled: false
User created annotations
Hi,
I have an Ubuntu VM with Docker-CE. I start the Apollo 2.0.6 container as shown in the Readme. All seems fine, but there are no user created annotations unlike the demo site (http://apollo.berkeleybop.io/Apollo2/annotator/index). I also get this error repeatedly in the logs...
ERROR apollo.AnnotatorController - User does not have permissions for the site
Any suggestions?
Thanks,
Tom
Exceptions and Errors
Hi,
I set up docker-apollo inside a docker-compose.yml file:
apollo:
image: quay.io/gmod/docker-apollo:latest
restart: always
ports:
- "8888:8080"
volumes:
- ./data//jbrowse:/data
- ./data/postgres-data:/var/lib/postgresql
While starting up I got the following Errors and Exceptions:
...
apollo_1 | WARNING: enabling "trust" authentication for local connections
apollo_1 | You can change this by editing pg_hba.conf or using the option -A, or
apollo_1 | --auth-local and --auth-host, the next time you run initdb.
apollo_1 | Starting PostgreSQL 9.6 database server: main.
apollo_1 | WEBAPOLLO_HOST_FLAG:
apollo_1 | CHADO_HOST_FLAG:
apollo_1 | Waiting for DB
apollo_1 | /var/run/postgresql:5432 - accepting connections
apollo_1 | Postgres is up, configuring database
apollo_1 | psql: FATAL: Peer authentication failed for user "apollo-lqt"
apollo_1 | Apollo database not found, creating...
apollo_1 | CREATE ROLE
apollo_1 | GRANT
apollo_1 | Configuring Chado
apollo_1 | psql: FATAL: Peer authentication failed for user "apollo"
apollo_1 | Chado database not found, creating...
apollo_1 | ERROR: role "apollo" already exists
apollo_1 | GRANT
apollo_1 | Loading Chado
...
apollo_1 | CREATE EXTENSION
apollo_1 | psql:/chado.sql:49: ERROR: must be owner of extension plpgsql
apollo_1 | SET
...
apollo_1 | ALTER TABLE
apollo_1 | SET
apollo_1 | psql:/chado.sql:2637928: ERROR: function create_point(integer, bigint) does not exist
apollo_1 | LINE 1: SELECT box (create_point(0, $1), create_point($2,500000000))
apollo_1 | ^
apollo_1 | HINT: No function matches the given name and argument types. You might need to add explicit type casts.
apollo_1 | QUERY: SELECT box (create_point(0, $1), create_point($2,500000000))
apollo_1 | CONTEXT: SQL function "boxrange" during inlining
apollo_1 | CREATE INDEX
...
apollo_1 | Loaded Chado
apollo_1 | Restarting tomcat with /usr/local/tomcat/
apollo_1 | Jul 04, 2018 10:25:47 AM org.apache.catalina.startup.Catalina stopServer
apollo_1 | SEVERE: Could not contact [localhost:[8005]]. Tomcat may not be running.
apollo_1 | Jul 04, 2018 10:25:47 AM org.apache.catalina.startup.Catalina stopServer
apollo_1 | SEVERE: Catalina.stop:
apollo_1 | java.net.ConnectException: Connection refused (Connection refused)
apollo_1 | at java.net.PlainSocketImpl.socketConnect(Native Method)
apollo_1 | at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
apollo_1 | at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
apollo_1 | at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
apollo_1 | at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
apollo_1 | at java.net.Socket.connect(Socket.java:589)
apollo_1 | at java.net.Socket.connect(Socket.java:538)
apollo_1 | at java.net.Socket.<init>(Socket.java:434)
apollo_1 | at java.net.Socket.<init>(Socket.java:211)
apollo_1 | at org.apache.catalina.startup.Catalina.stopServer(Catalina.java:497)
apollo_1 | at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
apollo_1 | at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
apollo_1 | at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
apollo_1 | at java.lang.reflect.Method.invoke(Method.java:498)
apollo_1 | at org.apache.catalina.startup.Bootstrap.stopServer(Bootstrap.java:406)
apollo_1 | at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:495)
apollo_1 |
apollo_1 | Tomcat started.
...
apollo_1 | Shiro Configured
apollo_1 | 2018-07-04 10:26:36,175 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table allele add constraint FK_ssx0gv6xbtu3tbwt6ekkmn4iw foreign key (variant_id) references feature
apollo_1 | 2018-07-04 10:26:36,179 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate - ERROR: constraint "fk_ssx0gv6xbtu3tbwt6ekkmn4iw" for relation "allele" already exists
apollo_1 | 2018-07-04 10:26:43,169 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table chadoprop add column cvterm_id int8 not null
apollo_1 | 2018-07-04 10:26:43,169 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate - ERROR: column "cvterm_id" contains null values
apollo_1 | 2018-07-04 10:26:49,561 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table chadoprop add constraint FK_8twb5n8vjmldyy3eeyq7sppc3 foreign key (cvterm_id) references cvterm
apollo_1 | 2018-07-04 10:26:49,561 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate - ERROR: column "cvterm_id" referenced in foreign key constraint does not exist
apollo_1 | Starting Quartz Scheduler in QuartzFactoryBean
apollo_1
...
apollo_1 | 2018-07-04 10:27:47,437 [http-nio-8080-exec-6] WARN apollo.PreferenceService - No user present, so using the client token
apollo_1 | 2018-07-04 10:27:47,486 [http-nio-8080-exec-3] ERROR apollo.PermissionService - Username not supplied so can not authenticate.
apollo_1 | 2018-07-04 10:27:47,495 [http-nio-8080-exec-3] ERROR apollo.PermissionService - User null does not exist in the database.
apollo_1 | 2018-07-04 10:27:47,549 [http-nio-8080-exec-10] ERROR authenticator.UsernamePasswordAuthenticatorService - Problem authenticating: java.lang.IllegalArgumentException: Method argumet (authentication token) cannot be null.
apollo_1 | 2018-07-04 10:27:47,550 [http-nio-8080-exec-10] WARN apollo.PermissionService - Failed to authenticate user
apollo_1 | 2018-07-04 10:27:47,550 [http-nio-8080-exec-10] ERROR apollo.UserController - Failed to authenticate
What did I miss?
Thank you in advance.
Michal
docker-compose down removes Organism
Hi @erasche and @nathandunn,
How is it possible to avoid that docker-compose down deletes Organism?
Thank you in advance,
Mic
Preparing files for Apollo
Hi,
How is it possible to prepare files for Apollo when using Apollo inside a docker container?
Thank you in advance,
Michal
GFF3 track not working
Hello,
I am trying to add a new repeat track using the GFF3 track (attached) and it got successfully loaded. However, I can't see the data as it only shows the loading sign without actual data!
Cheers,
Browser hangs on "Loading..." with latest apollo docker container
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/postgresql
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:
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.
[FAIL] Starting Tomcat servlet engine: tomcat8 failed!
Hi, guys!
I downloaded the Apollo (2.2.0 and latest) docker image and the container don't started. The tomcat fail:
.
.
.
ALTER TABLE
ALTER TABLE
Loaded Chado
Restarting tomcat with /var/lib/tomcat8
**[FAIL] Starting Tomcat servlet engine: tomcat8 failed!**
08-Feb-2019 22:15:00.361 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/usr/share/tomcat8
08-Feb-2019 22:15:00.361 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/tmp/tomcat8-tomcat8-tmp
08-Feb-2019 22:15:00.361 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/packages/lib/amd64:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib
08-Feb-2019 22:15:00.467 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
08-Feb-2019 22:15:00.488 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
08-Feb-2019 22:15:00.490 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 580 ms
08-Feb-2019 22:15:00.535 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service Catalina
08-Feb-2019 22:15:00.535 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet Engine: Apache Tomcat/8.5.14 (Debian)
08-Feb-2019 22:15:00.548 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-8080"]
08-Feb-2019 22:15:00.599 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 108 ms
08-Feb-2019 22:15:10.587 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployWAR Deploying web application archive /var/lib/tomcat8/webapps/ROOT.war
08-Feb-2019 22:15:20.216 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Configuring Shiro ...
Shiro Configured
.
.
.
And the page not open:
In other image that I downloded last week it isn't happend. My server has a tomcat version 8.5.37 installed, is it a problem? What could have happened?
Thanks! :)
database does not keep all files
Hi @erasche and @nathandunn ,
I uploaded yeast example to Apollo by using create organism. Next, I deleted the yeast folder from data folder and I got the following error:
Could not load the reference sequence definitions. RequestError: Unable to load data/refSeqs.json status: 404.
Is there a way to store all data inside the database in order to save space?
Thank you in advance,
Mic
Using webapollo docker with postgresql docker
Hi there!
First, thanks for this dockerized version of webapollo! It's really useful!
I've forked this repository in order to customize a little bit the code. I found that the current version of the docker uses an internal postgresql service which does not allow to easily store the databases in a volume for data persistence. Alternatively, I'm using a external postgres server running in a official postgres docker.
I'm pretty sure that this is something that you were planning to incorporate to your docker image so I hope you appreciate my contribution ;)
I've changed 2 files: apollo-config.groovy and launch.sh
apollo-config.groovy
I've added a new enviroment WEBAPOLLO_DB_HOST that can be used to set the IP address or the name for the postgres server. This variable replaces the one called WEBAPOLLO_DB_URI because mine can be used for both the apollo and the chado databases. Now the URL for database is dinamically obtained.
production {
dataSource {
dbCreate = "update"
username = System.getenv("WEBAPOLLO_DB_USERNAME") ?: "apollo"
password = System.getenv("WEBAPOLLO_DB_PASSWORD") ?: "apollo"
driverClassName = "org.postgresql.Driver"
dialect = "org.hibernate.dialect.PostgresPlusDialect"
url = "jdbc:postgresql://" + (System.getenv("WEBAPOLLO_DB_HOST") ?: "127.0.0.1").replaceAll(~/\\/$/, "") + "/apollo"
....
dataSource_chado {
dbCreate = "update"
username = "apollo"
password = "apollo"
driverClassName = "org.postgresql.Driver"
dialect = "org.hibernate.dialect.PostgresPlusDialect"
url = "jdbc:postgresql://" + (System.getenv("WEBAPOLLO_DB_HOST") ?: "127.0.0.1").replaceAll(~/\\/$/, "") + "/chado"
...launch.sh
Many changes in this file. First of all I check if the variable WEBAPOLLO_DB_HOST has been set. If so, we assume that we want to use an external postgres so we don't need to start our internal postgres service. If the variable exists, we will need to use the "-h HOST" flag in all the postgres calls.
Then, I check if the apollo database already exists in the postgres server. If not, we create the new database, create the apollo user and set the privileges. After that, we do the same for the chado database. Using this approach we avoid running the chado.sql script every time that the docker starts (user.sql is not necessary anymore).
Finally, we restart tomcat but using the shutdown.sh/startup.sh binaries instead of the "service tomcat start" which sometimes is a little buggy. In a normal situation the script will continue showing the content of catalina.out until the container is stopped, however I found that sometimes this file does not exist (first time launch?) so, to avoid possible errors, I force the creation of the file using "touch" (actually no I realize that the if-then clause is not necessary).
#!/bin/bash
if [[ "${WEBAPOLLO_DB_HOST}" == "" ]]; then
echo "Using internal postgresql service..."
service postgresql start
WEBAPOLLO_DB_HOST=127.0.0.1
else
echo "Using external postgresql service (${WEBAPOLLO_DB_HOST})..."
HOST_FLAG="-h ${WEBAPOLLO_DB_HOST}"
fi
until pg_isready $HOST_FLAG; do
echo -n "."
sleep 1;
done
echo "Postgres is up..."
su postgres -c "psql -lqt | cut -d \| -f 1 | grep -qw apollo"
if [[ "$?" == "1" ]]; then
echo "Apollo database not found, creating..."
su postgres -c "createdb $HOST_FLAG apollo"
su postgres -c "psql $HOST_FLAG -c \"CREATE USER apollo WITH PASSWORD 'apollo';\""
su postgres -c "psql $HOST_FLAG -c 'GRANT ALL PRIVILEGES ON DATABASE \"apollo\" to apollo;'"
fi
su postgres -c "psql -lqt | cut -d \| -f 1 | grep -qw chado"
if [[ "$?" == "1" ]]; then
echo "Chado database not found, creating..."
su postgres -c "createdb $HOST_FLAG chado"
su postgres -c "psql $HOST_FLAG -c 'GRANT ALL PRIVILEGES ON DATABASE \"chado\" to apollo;'"
su postgres -c "PGPASSWORD=apollo psql -U apollo -h ${WEBAPOLLO_DB_HOST} chado -f /chado.sql"
fi
# https://tomcat.apache.org/tomcat-8.0-doc/config/context.html#Naming
FIXED_CTX=$(echo "${CONTEXT_PATH}" | sed 's|/|#|g')
WAR_FILE=${CATALINA_HOME}/webapps/${FIXED_CTX}.war
cp ${CATALINA_HOME}/apollo.war ${WAR_FILE}
${CATALINA_HOME}/bin/shutdown.sh
${CATALINA_HOME}/bin/startup.sh
if [[ ! -f "${CATALINA_HOME}/logs/catalina.out" ]]; then
touch ${CATALINA_HOME}/logs/catalina.out
fi
tail -f ${CATALINA_HOME}/logs/catalina.out
And finally I've also created a docker-compose.yml file that launches webapollo + postgres, and that accepts different environment variables for customizing the instance (it looks like only WEBAPOLLO_DB_HOST is working at this moment).
I hope that helps!
Thanks and best regards!!
missing data folder
Hello, I cloned the docker-apollo project, but I can not do Copy JBrowse folders into ./data, because I do not know which JBrowse folder and ./data is meant in QuickStart.
git clone https://github.com/GMOD/docker-apollo
ls docker-apollo/
Dockerfile LICENSE README.md apollo-config.groovy build.sh docker-compose.yml img
Thank you in advance.
Mic
pg user / password is not passed to psql
in docker-apollo/launch.sh on master
you probably want:
a.) PGPASSWORD=$WEBAPOLLO_DB_PASSWORD passed along
b.) a -U $WEBAPOLLO_DB_PASSWORD passed into the options
2.2.0 seems to hide introns
Ran this with both honeybee and volvox data and it hides introns in both cases.
Either the feature, feature-render, annot-render or plus-annot has somehow lost its internal bits (I think).
PSQL Password auth fails for user "apollo" when different DB_USERNAME is supplied
Starting the docker-apollo container using the environment flags WEBAPOLLO_DB_USERNAME and CHADO_DB_USERNAME set to 'postgres' instead of the default results in positive messages and connections to the databases at the beginning of the launch script but after Shiro is configured I get the following error, and several similar ones after.
SEVERE [localhost-startStop-2] org.apache.tomcat.jdbc.pool.ConnectionPool.init Unable to create initial connections of pool.
org.postgresql.util.PSQLException: FATAL: password authentication failed for user "apollo"
I also get a "Starting Tomcat servlet engine: tomcat8 failed!" message and some catalina INFO messages before Shiro.
Here are the environment variables being passed to the container via Dockerfile through Rancher.
"environment": {
"CONTEXT_PATH": "/apollo-testing",
"WEBAPOLLO_DB_HOST": "db.apollo-testing.rancher.internal",
"WEBAPOLLO_DB_NAME": "postgres",
"WEBAPOLLO_DB_USERNAME": "postgres",
"WEBAPOLLO_DB_PASSWORD": REMOVED,
"CHADO_DB_HOST": "chado.apollo-testing.rancher.internal",
"CHADO_DB_NAME": "postgres",
"CHADO_DB_USERNAME": "postgres",
"CHADO_DB_PASSWORD": REMOVED,
"WEBAPOLLO_COMMON_DATA_DIRECTORY": "/opt/apollo/data/galaxy",
"WEBAPOLLO_TRANSLATION_TABLE": "11",
},
This is a dump of the errors from startup to the end, if left alive the container just repeats the errors from the one quoted above. I removed much of the stacktrace for easier reading but I can provide it if needed.
docker-apollo-startup-logs-short.txt
pool.ConnectionPool errors
Hi, I did sudo docker run -itP -v data:/container/data gmod/apollo:latest under ubuntu 16.04 and Docker version 1.11.2 , but received the following errors:
Configuring Shiro ...
Shiro Configured
2016-07-21 11:45:25,717 [localhost-startStop-1] ERROR pool.ConnectionPool - Unable to create initial connections of pool.
java.sql.SQLException: Driver:org.postgresql.Driver@38e8fd54 returned null for URL:jdbc:h2:mem:grailsDB;MVCC=TRUE;LOCK_TIMEOUT=10000
at org.apache.tomcat.jdbc.pool.PooledConnection.connectUsingDriver(PooledConnection.java:296)
at org.apache.tomcat.jdbc.pool.PooledConnection.connect(PooledConnection.java:182)
at org.apache.tomcat.jdbc.pool.ConnectionPool.createConnection(ConnectionPool.java:701)
at org.apache.tomcat.jdbc.pool.ConnectionPool.borrowConnection(ConnectionPool.java:635)
at org.apache.tomcat.jdbc.pool.ConnectionPool.init(ConnectionPool.java:486)
at org.apache.tomcat.jdbc.pool.ConnectionPool.<init>(ConnectionPool.java:144)
at org.apache.tomcat.jdbc.pool.DataSourceProxy.pCreatePool(DataSourceProxy.java:116)
at org.apache.tomcat.jdbc.pool.DataSourceProxy.createPool(DataSourceProxy.java:103)
at org.apache.tomcat.jdbc.pool.DataSourceProxy.getConnection(DataSourceProxy.java:127)
at org.springframework.jdbc.datasource.LazyConnectionDataSourceProxy.afterPropertiesSet(LazyConnectionDataSourceProxy.java:162)
at org.springframework.jdbc.datasource.LazyConnectionDataSourceProxy.<init>(LazyConnectionDataSourceProxy.java:106)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:147)
at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:122)
at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:267)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1137)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1040)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:504)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:194)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:351)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:108)
at org.springframework.beans.factory.support.ConstructorResolver.resolveConstructorArguments(ConstructorResolver.java:648)
at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:140)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1137)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1040)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:504)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:194)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:351)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:108)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1475)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1220)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:537)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:194)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:351)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:108)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1475)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1220)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:537)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:194)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:351)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:108)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveManagedList(BeanDefinitionValueResolver.java:382)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:157)
at org.springframework.beans.factory.support.ConstructorResolver.resolveConstructorArguments(ConstructorResolver.java:634)
at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:140)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1137)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1040)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:504)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199)
at org.codehaus.groovy.grails.orm.support.TransactionManagerPostProcessor.initialize(TransactionManagerPostProcessor.java:74)
at org.codehaus.groovy.grails.orm.support.TransactionManagerPostProcessor.setBeanFactory(TransactionManagerPostProcessor.java:52)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeAwareMethods(AbstractAutowireCapableBeanFactory.java:1591)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1559)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:539)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199)
at org.springframework.context.support.PostProcessorRegistrationDelegate.registerBeanPostProcessors(PostProcessorRegistrationDelegate.java:199)
at org.springframework.context.support.AbstractApplicationContext.registerBeanPostProcessors(AbstractApplicationContext.java:616)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:465)
at org.codehaus.groovy.grails.commons.spring.DefaultRuntimeSpringConfiguration.getApplicationContext(DefaultRuntimeSpringConfiguration.java:156)
at org.codehaus.groovy.grails.commons.spring.GrailsRuntimeConfigurator.initializeContext(GrailsRuntimeConfigurator.java:188)
at org.codehaus.groovy.grails.commons.spring.GrailsRuntimeConfigurator.configure(GrailsRuntimeConfigurator.java:168)
at org.codehaus.groovy.grails.commons.spring.GrailsRuntimeConfigurator.configure(GrailsRuntimeConfigurator.java:127)
at org.codehaus.groovy.grails.web.context.GrailsConfigUtils.configureWebApplicationContext(GrailsConfigUtils.java:126)
at org.codehaus.groovy.grails.web.context.GrailsContextLoaderListener.initWebApplicationContext(GrailsContextLoaderListener.java:109)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:106)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5068)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5584)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:147)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1092)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1984)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
2016-07-21 11:45:25,768 [localhost-startStop-1] ERROR pool.ConnectionPool - Unable to create initial connections of pool.
java.sql.SQLException: Driver:org.postgresql.Driver@1f7855c9 returned null for URL:jdbc:h2:mem:grailsDB;MVCC=TRUE;LOCK_TIMEOUT=10000
at org.apache.tomcat.jdbc.pool.PooledConnection.connectUsingDriver(PooledConnection.java:296)
at org.apache.tomcat.jdbc.pool.PooledConnection.connect(PooledConnection.java:182)
at org.apache.tomcat.jdbc.pool.ConnectionPool.createConnection(ConnectionPool.java:701)
at org.apache.tomcat.jdbc.pool.ConnectionPool.borrowConnection(ConnectionPool.java:635)
at org.apache.tomcat.jdbc.pool.ConnectionPool.init(ConnectionPool.java:486)
at org.apache.tomcat.jdbc.pool.ConnectionPool.<init>(ConnectionPool.java:144)
at org.apache.tomcat.jdbc.pool.DataSourceProxy.pCreatePool(DataSourceProxy.java:116)
at org.apache.tomcat.jdbc.pool.DataSourceProxy.createPool(DataSourceProxy.java:103)
at org.apache.tomcat.jdbc.pool.DataSourceProxy.getConnection(DataSourceProxy.java:127)
at org.springframework.jdbc.datasource.LazyConnectionDataSourceProxy.afterPropertiesSet(LazyConnectionDataSourceProxy.java:162)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1631)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1568)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:539)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:194)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:351)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:108)
at org.springframework.beans.factory.support.ConstructorResolver.resolveConstructorArguments(ConstructorResolver.java:648)
at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:140)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1137)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1040)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:504)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:194)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:351)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:108)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1475)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1220)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:537)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:194)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:351)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:108)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1475)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1220)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:537)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:194)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:351)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:108)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveManagedList(BeanDefinitionValueResolver.java:382)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:157)
at org.springframework.beans.factory.support.ConstructorResolver.resolveConstructorArguments(ConstructorResolver.java:634)
at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:140)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1137)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1040)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:504)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199)
at org.codehaus.groovy.grails.orm.support.TransactionManagerPostProcessor.initialize(TransactionManagerPostProcessor.java:74)
at org.codehaus.groovy.grails.orm.support.TransactionManagerPostProcessor.setBeanFactory(TransactionManagerPostProcessor.java:52)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeAwareMethods(AbstractAutowireCapableBeanFactory.java:1591)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1559)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:539)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199)
at org.springframework.context.support.PostProcessorRegistrationDelegate.registerBeanPostProcessors(PostProcessorRegistrationDelegate.java:199)
at org.springframework.context.support.AbstractApplicationContext.registerBeanPostProcessors(AbstractApplicationContext.java:616)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:465)
at org.codehaus.groovy.grails.commons.spring.DefaultRuntimeSpringConfiguration.getApplicationContext(DefaultRuntimeSpringConfiguration.java:156)
at org.codehaus.groovy.grails.commons.spring.GrailsRuntimeConfigurator.initializeContext(GrailsRuntimeConfigurator.java:188)
at org.codehaus.groovy.grails.commons.spring.GrailsRuntimeConfigurator.configure(GrailsRuntimeConfigurator.java:168)
at org.codehaus.groovy.grails.commons.spring.GrailsRuntimeConfigurator.configure(GrailsRuntimeConfigurator.java:127)
at org.codehaus.groovy.grails.web.context.GrailsConfigUtils.configureWebApplicationContext(GrailsConfigUtils.java:126)
at org.codehaus.groovy.grails.web.context.GrailsContextLoaderListener.initWebApplicationContext(GrailsContextLoaderListener.java:109)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:106)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5068)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5584)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:147)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1092)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1984)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
2016-07-21 11:45:27,052 [localhost-startStop-1] ERROR pool.ConnectionPool - Unable to create initial connections of pool.
java.sql.SQLException: Driver:org.postgresql.Driver@4facf567 returned null for URL:jdbc:h2:mem:grailsDB;MVCC=TRUE;LOCK_TIMEOUT=10000
at org.apache.tomcat.jdbc.pool.PooledConnection.connectUsingDriver(PooledConnection.java:296)
at org.apache.tomcat.jdbc.pool.PooledConnection.connect(PooledConnection.java:182)
at org.apache.tomcat.jdbc.pool.ConnectionPool.createConnection(ConnectionPool.java:701)
at org.apache.tomcat.jdbc.pool.ConnectionPool.borrowConnection(ConnectionPool.java:635)
at org.apache.tomcat.jdbc.pool.ConnectionPool.init(ConnectionPool.java:486)
at org.apache.tomcat.jdbc.pool.ConnectionPool.<init>(ConnectionPool.java:144)
at org.apache.tomcat.jdbc.pool.DataSourceProxy.pCreatePool(DataSourceProxy.java:116)
at org.apache.tomcat.jdbc.pool.DataSourceProxy.createPool(DataSourceProxy.java:103)
at org.apache.tomcat.jdbc.pool.DataSourceProxy.getConnection(DataSourceProxy.java:127)
at org.springframework.jdbc.datasource.LazyConnectionDataSourceProxy$LazyConnectionInvocationHandler.getTargetConnection(LazyConnectionDataSourceProxy.java:403)
at org.springframework.jdbc.datasource.LazyConnectionDataSourceProxy$LazyConnectionInvocationHandler.invoke(LazyConnectionDataSourceProxy.java:376)
at com.sun.proxy.$Proxy40.getMetaData(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.springframework.jdbc.datasource.TransactionAwareDataSourceProxy$TransactionAwareInvocationHandler.invoke(TransactionAwareDataSourceProxy.java:240)
at com.sun.proxy.$Proxy40.getMetaData(Unknown Source)
at org.hibernate.engine.jdbc.internal.JdbcServicesImpl.configure(JdbcServicesImpl.java:126)
at org.hibernate.boot.registry.internal.StandardServiceRegistryImpl.configureService(StandardServiceRegistryImpl.java:111)
at org.hibernate.service.internal.AbstractServiceRegistryImpl.initializeService(AbstractServiceRegistryImpl.java:234)
at org.hibernate.service.internal.AbstractServiceRegistryImpl.getService(AbstractServiceRegistryImpl.java:206)
at org.hibernate.cfg.Configuration.buildTypeRegistrations(Configuration.java:1887)
at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1845)
at org.codehaus.groovy.grails.orm.hibernate.cfg.GrailsAnnotationConfiguration.buildSessionFactory(GrailsAnnotationConfiguration.java:372)
at org.codehaus.groovy.grails.orm.hibernate.ConfigurableLocalSessionFactoryBean.doBuildSessionFactory(ConfigurableLocalSessionFactoryBean.java:479)
at org.codehaus.groovy.grails.orm.hibernate.ConfigurableLocalSessionFactoryBean.buildSessionFactory(ConfigurableLocalSessionFactoryBean.java:473)
at org.codehaus.groovy.grails.orm.hibernate.ConfigurableLocalSessionFactoryBean.afterPropertiesSet(ConfigurableLocalSessionFactoryBean.java:387)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1631)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1568)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:539)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:194)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:351)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:108)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1475)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1220)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:537)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:194)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:351)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:108)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveManagedList(BeanDefinitionValueResolver.java:382)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:157)
at org.springframework.beans.factory.support.ConstructorResolver.resolveConstructorArguments(ConstructorResolver.java:634)
at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:140)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1137)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1040)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:504)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199)
at org.codehaus.groovy.grails.orm.support.TransactionManagerPostProcessor.initialize(TransactionManagerPostProcessor.java:74)
at org.codehaus.groovy.grails.orm.support.TransactionManagerPostProcessor.setBeanFactory(TransactionManagerPostProcessor.java:52)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeAwareMethods(AbstractAutowireCapableBeanFactory.java:1591)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1559)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:539)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199)
at org.springframework.context.support.PostProcessorRegistrationDelegate.registerBeanPostProcessors(PostProcessorRegistrationDelegate.java:199)
at org.springframework.context.support.AbstractApplicationContext.registerBeanPostProcessors(AbstractApplicationContext.java:616)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:465)
at org.codehaus.groovy.grails.commons.spring.DefaultRuntimeSpringConfiguration.getApplicationContext(DefaultRuntimeSpringConfiguration.java:156)
at org.codehaus.groovy.grails.commons.spring.GrailsRuntimeConfigurator.initializeContext(GrailsRuntimeConfigurator.java:188)
at org.codehaus.groovy.grails.commons.spring.GrailsRuntimeConfigurator.configure(GrailsRuntimeConfigurator.java:168)
at org.codehaus.groovy.grails.commons.spring.GrailsRuntimeConfigurator.configure(GrailsRuntimeConfigurator.java:127)
at org.codehaus.groovy.grails.web.context.GrailsConfigUtils.configureWebApplicationContext(GrailsConfigUtils.java:126)
at org.codehaus.groovy.grails.web.context.GrailsContextLoaderListener.initWebApplicationContext(GrailsContextLoaderListener.java:109)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:106)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5068)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5584)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:147)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1092)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1984)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
2016-07-21 11:45:27,237 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener - Error initializing the application: Error creating bean with name 'transactionManagerPostProcessor': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean '$primaryTransactionManager' while setting constructor argument with key [0]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '$primaryTransactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is java.lang.NullPointerException
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManagerPostProcessor': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean '$primaryTransactionManager' while setting constructor argument with key [0]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '$primaryTransactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is java.lang.NullPointerException
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean '$primaryTransactionManager' while setting constructor argument with key [0]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '$primaryTransactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is java.lang.NullPointerException
... 5 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name '$primaryTransactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is java.lang.NullPointerException
... 5 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is java.lang.NullPointerException
... 5 more
Caused by: java.lang.NullPointerException
... 5 more
2016-07-21 11:45:27,258 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener - Error initializing Grails: Error creating bean with name 'transactionManagerPostProcessor': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean '$primaryTransactionManager' while setting constructor argument with key [0]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '$primaryTransactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is java.lang.NullPointerException
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManagerPostProcessor': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean '$primaryTransactionManager' while setting constructor argument with key [0]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '$primaryTransactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is java.lang.NullPointerException
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean '$primaryTransactionManager' while setting constructor argument with key [0]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '$primaryTransactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is java.lang.NullPointerException
... 5 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name '$primaryTransactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is java.lang.NullPointerException
... 5 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is java.lang.NullPointerException
... 5 more
Caused by: java.lang.NullPointerException
... 5 more
Jul 21, 2016 11:45:27 AM org.apache.catalina.core.StandardContext startInternal
SEVERE: One or more listeners failed to start. Full details will be found in the appropriate container log file
Jul 21, 2016 11:45:27 AM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Jul 21, 2016 11:45:27 AM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesJdbc
SEVERE: The web application [/apollo] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Jul 21, 2016 11:45:27 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /usr/local/tomcat/webapps/apollo.war has finished in 60,009 ms
Jul 21, 2016 11:45:27 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-apr-8080"]
Jul 21, 2016 11:45:27 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-apr-8009"]
Jul 21, 2016 11:45:27 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 60354 ms
What did I do wrong?
Thank you in advance.
Mic
Always re-expands WAR file, even when not needed.
apollo_1 | 10-Jan-2017 19:36:32.068 INFO [localhost-startStop-1] org.apache.catalina.startup.ExpandWar.expand An expanded directory [/usr/local/tomcat/webapps/ROOT] was found with a last modified time that did not match the associated WAR. It will be deleted.
change root URL
I have successfully installed the docker, have it working, and have my organism viewable. I have also made the docker instance accessible behind Apache using the ProxyPass and ProxyPassReverse parameters so that I can easily use HTTPS. The problem I have now is that there are a number of links that are hard coded to the root i.e. any of the admin functions, public organisms. Is there a way of setting a parameter in the docker image to change the default root?
BLAT error - Error running search: Cannot run program "/usr/local/bin/blat": error=2, No such file or directory
I set up Apollo from the container and I'm trying to get blat working.
I installed blat in /usr/local/bin:
and when I added my organism I set the path to the search directory to go to the .2bit file:
in the setup guide it mentioned something about configuring the groovy file for the search tools. Is this necessary when running production from the container? Is there anything else I need to configure?
Thanks!
commonsDirectory not created correctly via docker on ubuntu
When running:
sudo docker run -it -v jbrowse-data:/data -v postgres-data:/var/lib/postgresql -p 8888:8080 quay.io/gmod/docker-apollo:latest
It fails to ever do a mkdirs() when the directories are there or not and world-readable or not. Using this method, though, it seems to work correctly.
sudo docker run -it -v /opt/jbrowse:/data -v postgres-data:/var/lib/postgresql -p 8888:8080 quay.io/gmod/docker-apollo:latest
How to edit annot.json in the docker ?
I want to add custom tracks (like pfam domains, blast results, etc ...)
I have these data in gff format, but for example the type "domain" is not present in the annot.json
perl /home/apollo/jbrowse-master/bin/flatfile-to-json.pl \
> --gff /home/apollo/rawdata/pfam_domains.gff \
> --type domain \
> --trackLabel pfam_domains \
> --out /home/apollo/jbrowse-data
WARNING: No matching features found for domain
Is there a solution ?
Thanks
Apollo docker running... but now ?
Hi,
After many unsuccesfull try to install Apollo, I shifted to the docker version :
But, I realise that it's impossible to add data after that.
I have to generate the data (ref genome, and all gff file) inside a jbrowse-data
directory and after that run apollo-docker
Am I right ?
But in this case, where can I find the scripts described here : https://genomearchitect.readthedocs.io/en/latest/Data_loading.html#data-generation-pipeline
Thanks
Sample data
Hi @nathandunn
Just a question "out of the topic", Do you now where can I find some test data for Webapollo? All the documentation and tutorials uses the "pyu_data" but it is not available anymore at http://genomearchitect.org/webapollo/data/pyu_data.tgz
Thanks
Rafa
add docker-apollo doc for adding the temp data directory / create temporary data
Based on the volume mounted, need to add the temporary directory
e.g., chmod -R 777 temporary/
ubuntu@ip-172-30-0-60:~/apollo_data$ pwd
/home/ubuntu/apollo_data
Overriding apollo-config.groovy?
Hello,
Is there a proper way to change the content of apollo-config.groovy? I tried mounting my modified version like this:
volumes:
- ./apollo-config.groovy:/apollo/apollo-config.groovy
or like this:
volumes:
- ./apollo-config.groovy:/var/lib/tomcat8/webapps/ROOT/WEB-INF/classes/apollo-config.groovy
But first one fails probably because apollo would need to be rebuilt, and with second one the war fails to deploy.
I'm trying to do it to use the REMOTE_USER auth.
(no hurry on this, I'm leaving now)
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