just updated and cannot add or delete annotations
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just updated and cannot add or delete annotations
 
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Hello All,
I just did a git pull from the master branch. I tried to add an annotation as a test, and I got an error. I logged out and back in, and I see my test annotations. I tried to delete it and I get another error. When I was creating a new war file with my updates, I said Y to these two questions:
Packaging Grails application > You currently already have a version of the plugin installed [spring-websocket-1.2.0]. Do you want to upgrade to [spring-websocket-1.3.1]? [y,n] y | Installed plugin spring-websocket-1.3.1..... > You currently already have a version of the plugin installed [tomcat-7.0.55.2]. Do you want to upgrade to [tomcat-8.0.33]? [y,n] y | Compiling 225 source files
but when I go to my_server:8080 I see the tomcat/7.0.54 page.
I stopped and started tomcat, but I do not see tomcat-8 running. Could my error have something to do with the tomcat version? Thank you, Sofia Add Error" Error Performing Operation {"features":[{"owner":"[hidden email]","parent_name":" Delete Error: Error Performing Operation {"features":[{"owner":"[hidden email]","parent_name":" This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. |
Re: just updated and cannot add or delete annotations
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So, the do get added, and they do get deleted. I just need to close the error window and reload the page, and everything is as it should be, but this happens for every new annotation and deletion event. On Thu, Nov 16, 2017 at 2:35 PM, Sofia Robb <[hidden email]> wrote:
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. |
Re: just updated and cannot add or delete annotations
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In reply to this post by Sofia Robb
Is there anything in the catalina.out? The build part looks fine.
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. |
Re: just updated and cannot add or delete annotations
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In reply to this post by Sofia Robb
Have you purged the cache / used an anonymous different browser? Is there anything weird in the console at startup? Mostly wondering if there is a library collision with the web sockets. Nathan
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. |
Re: just updated and cannot add or delete annotations
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In reply to this post by nathandunn
There is some SEVERE stuff but it is all before I stopped tomcat and started up the new war. I highlighed in yellow where I restarted and launched the new war file. Nov 16, 2017 1:58:24 PM org.apache.coyote.AbstractProtocol pause INFO: Pausing ProtocolHandler ["http-bio-8080"] Nov 16, 2017 1:58:24 PM org.apache.catalina.core.StandardServer await INFO: A valid shutdown command was received via the shutdown port. Stopping the Server instance. Nov 16, 2017 1:58:24 PM org.apache.coyote.AbstractProtocol pause INFO: Pausing ProtocolHandler ["ajp-bio-8009"] Nov 16, 2017 1:58:24 PM org.apache.catalina.core.StandardService stopInternal INFO: Stopping service Catalina Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader 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. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 1] but has failed to stop it. This is very likely to create a memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 2] but has failed to stop it. This is very likely to create a memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 3] but has failed to stop it. This is very likely to create a memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 4] but has failed to stop it. This is very likely to create a memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads SEVERE: The web application [/apollo] appears to have started a thread named [Actor Thread 5] but has failed to stop it. This is very likely to create a memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@37e2f15b]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@687a09db]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.apache.shiro.util.ThreadContext.InheritableThreadLocalMap] (value [org.apache.shiro.util.ThreadContext$InheritableThreadLocalMap@7a6d01a]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@3f2a35e4]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.apache.shiro.util.ThreadContext.InheritableThreadLocalMap] (value [org.apache.shiro.util.ThreadContext$InheritableThreadLocalMap@7a6d01a]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@65efc8d2]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@638725a1]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@decb920]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@16de5917]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@44d3c564]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@1e235a72]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@76eed52f]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@121c2c04]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@48be23c6]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@4cca0069]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@4c8de372]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@3f829aeb]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@61b2ece]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@1aceaf2c]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@397b4974]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@1205d972]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@4db7e8a2]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@226f89f7]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@41bc4427]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.ThreadLocalRandom$1] (value [com.codahale.metrics.ThreadLocalRandom$1@663ca34f]) and a value of type [com.codahale.metrics.ThreadLocalRandom] (value [com.codahale.metrics.ThreadLocalRandom@7d4ecb2b]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@fceced8]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [com.codahale.metrics.Striped64.ThreadHashCode] (value [com.codahale.metrics.Striped64$ThreadHashCode@6b5ff924]) and a value of type [com.codahale.metrics.Striped64.HashCode] (value [com.codahale.metrics.Striped64$HashCode@5130dee7]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@186864bf]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks SEVERE: The web application [/apollo] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@529009e9]) and a value of type [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.CounterHashCode] (value [com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8$CounterHashCode@720e259a]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. Nov 16, 2017 1:58:27 PM org.apache.coyote.AbstractProtocol stop INFO: Stopping ProtocolHandler ["http-bio-8080"] Nov 16, 2017 1:58:27 PM org.apache.coyote.AbstractProtocol stop INFO: Stopping ProtocolHandler ["ajp-bio-8009"] Nov 16, 2017 1:58:27 PM org.apache.coyote.AbstractProtocol destroy INFO: Destroying ProtocolHandler ["http-bio-8080"] Nov 16, 2017 1:58:27 PM org.apache.coyote.AbstractProtocol destroy INFO: Destroying ProtocolHandler ["ajp-bio-8009"] Nov 16, 2017 1:59:07 PM org.apache.catalina.core.AprLifecycleListener init INFO: 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/lib64:/lib64:/lib:/usr/lib Nov 16, 2017 1:59:07 PM org.apache.coyote.AbstractProtocol init INFO: Initializing ProtocolHandler ["http-bio-8080"] Nov 16, 2017 1:59:07 PM org.apache.coyote.AbstractProtocol init INFO: Initializing ProtocolHandler ["ajp-bio-8009"] Nov 16, 2017 1:59:07 PM org.apache.catalina.startup.Catalina load INFO: Initialization processed in 347 ms Nov 16, 2017 1:59:07 PM org.apache.catalina.core.StandardService startInternal INFO: Starting service Catalina Nov 16, 2017 1:59:07 PM org.apache.catalina.core.StandardEngine startInternal INFO: Starting Servlet Engine: Apache Tomcat/7.0.54 Nov 16, 2017 1:59:07 PM org.apache.catalina.startup.HostConfig deployWAR INFO: Deploying web application archive /var/lib/tomcat/webapps/apollo.war Nov 16, 2017 1:59:17 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined Nov 16, 2017 1:59:17 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined Nov 16, 2017 2:00:01 PM org.apache.catalina.util.SessionIdGenerator createSecureRandom INFO: Creation of SecureRandom instance for session ID generation using [SHA1PRNG] took [9,099] milliseconds. Nov 16, 2017 2:00:01 PM org.apache.catalina.startup.HostConfig deployWAR INFO: Deployment of web application archive /var/lib/tomcat/webapps/apollo.war has finished in 53,582 ms Nov 16, 2017 2:00:01 PM org.apache.catalina.startup.HostConfig deployDirectory INFO: Deploying web application directory /var/lib/tomcat/webapps/ROOT Nov 16, 2017 2:00:01 PM org.apache.catalina.startup.HostConfig deployDirectory INFO: Deployment of web application directory /var/lib/tomcat/webapps/ROOT has finished in 214 ms Nov 16, 2017 2:00:01 PM org.apache.catalina.startup.HostConfig deployDirectory INFO: Deploying web application directory /var/lib/tomcat/webapps/examples Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://java.sun.com/jstl/core_rt is already defined Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://java.sun.com/jstl/core is already defined Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/core is already defined Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt_rt is already defined Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt is already defined Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/fmt is already defined Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/functions is already defined Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/standard/permittedTaglibs is already defined Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/standard/scriptfree is already defined Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://java.sun.com/jstl/sql_rt is already defined Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://java.sun.com/jstl/sql is already defined Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/sql is already defined Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://java.sun.com/jstl/xml_rt is already defined Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://java.sun.com/jstl/xml is already defined Nov 16, 2017 2:00:02 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/xml is already defined Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory INFO: Deployment of web application directory /var/lib/tomcat/webapps/examples has finished in 1,285 ms Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory INFO: Deploying web application directory /var/lib/tomcat/webapps/sample Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory INFO: Deployment of web application directory /var/lib/tomcat/webapps/sample has finished in 332 ms Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory INFO: Deploying web application directory /var/lib/tomcat/webapps/docs Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory INFO: Deployment of web application directory /var/lib/tomcat/webapps/docs has finished in 314 ms Nov 16, 2017 2:00:03 PM org.apache.catalina.startup.HostConfig deployDirectory INFO: Deploying web application directory /var/lib/tomcat/webapps/host-manager Nov 16, 2017 2:00:04 PM org.apache.catalina.startup.HostConfig deployDirectory INFO: Deployment of web application directory /var/lib/tomcat/webapps/host-manager has finished in 499 ms Nov 16, 2017 2:00:04 PM org.apache.catalina.startup.HostConfig deployDirectory INFO: Deploying web application directory /var/lib/tomcat/webapps/manager Nov 16, 2017 2:00:04 PM org.apache.catalina.startup.HostConfig deployDirectory INFO: Deployment of web application directory /var/lib/tomcat/webapps/manager has finished in 253 ms Nov 16, 2017 2:00:04 PM org.apache.coyote.AbstractProtocol start INFO: Starting ProtocolHandler ["http-bio-8080"] Nov 16, 2017 2:00:04 PM org.apache.coyote.AbstractProtocol start INFO: Starting ProtocolHandler ["ajp-bio-8009"] Nov 16, 2017 2:00:04 PM org.apache.catalina.startup.Catalina start INFO: Server startup in 56841 ms Nov 16, 2017 2:03:50 PM org.apache.catalina.core.StandardServer await INFO: A valid shutdown command was received via the shutdown port. Stopping the Server instance. Nov 16, 2017 2:03:50 PM org.apache.coyote.AbstractProtocol pause INFO: Pausing ProtocolHandler ["http-bio-8080"] Nov 16, 2017 2:04:39 PM org.apache.catalina.core.AprLifecycleListener init INFO: 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/lib64:/lib64:/lib:/usr/lib Nov 16, 2017 2:04:39 PM org.apache.coyote.AbstractProtocol init INFO: Initializing ProtocolHandler ["http-bio-8080"] Nov 16, 2017 2:04:39 PM org.apache.coyote.AbstractProtocol init INFO: Initializing ProtocolHandler ["ajp-bio-8009"] Nov 16, 2017 2:04:39 PM org.apache.catalina.startup.Catalina load INFO: Initialization processed in 309 ms Nov 16, 2017 2:04:39 PM org.apache.catalina.core.StandardService startInternal INFO: Starting service Catalina Nov 16, 2017 2:04:39 PM org.apache.catalina.core.StandardEngine startInternal INFO: Starting Servlet Engine: Apache Tomcat/7.0.54 Nov 16, 2017 2:04:39 PM org.apache.catalina.startup.HostConfig deployWAR INFO: Deploying web application archive /var/lib/tomcat/webapps/apollo.war Nov 16, 2017 2:04:48 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined Nov 16, 2017 2:04:48 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined Nov 16, 2017 2:05:12 PM org.apache.catalina.startup.HostConfig deployWAR INFO: Deployment of web application archive /var/lib/tomcat/webapps/apollo.war has finished in 32,682 ms Nov 16, 2017 2:05:12 PM org.apache.catalina.startup.HostConfig deployDirectory INFO: Deploying web application directory /var/lib/tomcat/webapps/ROOT Nov 16, 2017 2:05:12 PM org.apache.catalina.startup.HostConfig deployDirectory INFO: Deployment of web application directory /var/lib/tomcat/webapps/ROOT has finished in 195 ms Nov 16, 2017 2:05:12 PM org.apache.catalina.startup.HostConfig deployDirectory INFO: Deploying web application directory /var/lib/tomcat/webapps/examples Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://java.sun.com/jstl/core_rt is already defined Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://java.sun.com/jstl/core is already defined Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/core is already defined Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt_rt is already defined Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://java.sun.com/jstl/fmt is already defined Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/fmt is already defined Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/functions is already defined Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/standard/permittedTaglibs is already defined Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/standard/scriptfree is already defined Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://java.sun.com/jstl/sql_rt is already defined Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://java.sun.com/jstl/sql is already defined Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/sql is already defined Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://java.sun.com/jstl/xml_rt is already defined Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://java.sun.com/jstl/xml is already defined Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.TaglibUriRule body INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/xml is already defined Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory INFO: Deployment of web application directory /var/lib/tomcat/webapps/examples has finished in 302 ms Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory INFO: Deploying web application directory /var/lib/tomcat/webapps/sample Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory INFO: Deployment of web application directory /var/lib/tomcat/webapps/sample has finished in 150 ms Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory INFO: Deploying web application directory /var/lib/tomcat/webapps/docs Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory INFO: Deployment of web application directory /var/lib/tomcat/webapps/docs has finished in 134 ms Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory INFO: Deploying web application directory /var/lib/tomcat/webapps/host-manager Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory INFO: Deployment of web application directory /var/lib/tomcat/webapps/host-manager has finished in 215 ms Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory INFO: Deploying web application directory /var/lib/tomcat/webapps/manager Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.HostConfig deployDirectory INFO: Deployment of web application directory /var/lib/tomcat/webapps/manager has finished in 140 ms Nov 16, 2017 2:05:13 PM org.apache.coyote.AbstractProtocol start INFO: Starting ProtocolHandler ["http-bio-8080"] Nov 16, 2017 2:05:13 PM org.apache.coyote.AbstractProtocol start INFO: Starting ProtocolHandler ["ajp-bio-8009"] Nov 16, 2017 2:05:13 PM org.apache.catalina.startup.Catalina start INFO: Server startup in 33883 ms On Thu, Nov 16, 2017 at 3:07 PM, Nathan Dunn <[hidden email]> wrote:
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. |
Re: just updated and cannot add or delete annotations
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Not seeing anything remarkable. If you are updating from master directly, it may have also changed the JBrowse version. I would do a clean-all in there as well. ./apollo clean-all && ./apollo deploy Hopefully that fixes it. Nathan
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. |
Re: just updated and cannot add or delete annotations
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In reply to this post by Sofia Robb
I cleaned and deployed, same messages. But I had another user try it out and he says it works just fine for him. Whats up with that? On Thu, Nov 16, 2017 at 3:32 PM, Nathan Dunn <[hidden email]> wrote:
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Re: just updated and cannot add or delete annotations
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Nathan
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. |
Re: just updated and cannot add or delete annotations
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In reply to this post by Sofia Robb
Yeah, that is what is was. I tried in safari and it worked, i opened a new chrome window and it worked. Thank you for your hand holding :) Fixed!!! On Thu, Nov 16, 2017 at 3:56 PM, Nathan Dunn <[hidden email]> wrote:
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. |
Re: just updated and cannot add or delete annotations
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NP. I’m glad I didn’t have to patch anything.
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. |
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