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View Code? Open in Web Editor NEWORR - Ontology Registry & Repository integrated system
License: Apache License 2.0
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broken link: http://sensorml.com/ont/csm/property/SENSOR_TYPE
Hello. Some of the concepts served by the NERC Vocab Server (NVS) are linked to concepts in MMI in ORR. It looks like the link to http://sensorml.com/ont/csm/property/SENSOR_TYPE is broken. Can you advise? Many thanks.
JVM not getting enough memory in the container
@brandonnodnarb thanks again for the testing and exposing this issue.
As indicated on slack, I suspect the issue is not enough memory given to the JVM, even though the container itself has plenty.
Below are some snippets from the log and some ctop screenshots.
2020-09-02 00:58:18.094 [http-nio-8080-exec-3] DEBUG org.mmisw.orr.ont.app.OntController -
createOntology:
user: AuthUser(brandon)
uri: http://synaptica.net/owl
originalUri: None
name: NASA STI Thesaurus
version: 20200902T005818
versionVisibility: Some(owner)
versionStatus: Some(unstable)
log: None
date: 2020-09-02T00:58:18
ownerName: ~brandon
ontFileWriter.format: ttl
2020-09-02 00:58:26.958 [http-nio-8080-exec-3] DEBUG org.mmisw.orr.ont.service.OntService - createOntology: md=Map(http://www.w3.org/2000/01/rdf-schema#comment -> List(Synaptica output using OWL syntax.), http://www.w3.org/2002/07/owl#versionInfo -> List(Synaptica OWL), http://www.w3.org/1999/02/22-rdf-syntax-ns#type -> List(http://www.w3.org/2002/07/owl#Ontology)) authorOpt=Some(brandon whitehead)
02-Sep-2020 01:07:05.050 WARNING [cluster-1-thread-1] com.mongodb.ServerStateNotifier.run Exception in monitor thread during notification of server description state change
java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "AsyncFileHandlerWriter-1259475182" java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "http-nio-8080-ClientPoller-0" java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "http-nio-8080-ClientPoller-1" java.lang.OutOfMemoryError: GC overhead limit exceeded
02-Sep-2020 01:10:47.569 SEVERE [http-nio-8080-exec-9] org.apache.coyote.AbstractProtocol$ConnectionHandler.process Failed to complete processing of a request
java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "http-nio-8080-exec-7" java.lang.OutOfMemoryError: GC overhead limit exceeded
02-Sep-2020 01:11:38.271 SEVERE [ContainerBackgroundProcessor[StandardEngine[Catalina]]] org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.run Unexpected death of background thread [ContainerBackgroundProcessor[StandardEngine[Catalina]]]
java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "ContainerBackgroundProcessor[StandardEngine[Catalina]]" java.lang.OutOfMemoryError: GC overhead limit exceeded
During the registration processing:
git submodule foreach "(git checkout master; git pull)" not working
Hi @carueda I'm trying to build locally for the first time in a while.
When I execute git submodule foreach "(git checkout master; git pull)"... nothing is happening.
Any ideas?
Thanks
ontologies don't contain versions
When you download an ontology, it is a particular version of the ontology. However, the version is not visible within the ontology. Exported hosted ontologies ideally could contain the ORR version in the versionIRI attribute.
License
@graybeal, @lewismc, @brandonnodnarb :
John: we haven't associated any license to the ORR related software repositories. Are you OK with using Apache2? I'll go ahead with adding Apache2 if I don't hear any objections within say a couple days from now.
faster startup
On the COR instance I noted a rather long delay for the orr service to completely be up and running:
$ docker logs -f orr
...
WARNING .. org.apache.catalina.util.SessionIdGeneratorBase.createSecureRandom
Creation of SecureRandom instance for session ID generation using [SHA1PRNG] took [144,668] milliseconds.
...
https://wiki.apache.org/tomcat/HowTo/FasterStartUp#Entropy_Source suggests:
There is a way to configure JRE to use a non-blocking entropy source by setting the following system property:
-Djava.security.egd=file:/dev/./urandom
which is mentioned in docker-library/tomcat#12
link changes from https to http
If you visit https://mmisw.org/ont/cf/parameter and search (for example), 'latitude', the links are in http but the hyperlinks are in https. This link 'https://mmisw.org/ont/cf/parameter/latitude' will throw an error (IRI not found) but not if you manually change it to http://mmisw.org/ont/cf/parameter/latitude
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