ncls | Nested Containment List for Python | Dataset library

by biocore-ntnu C Version: 0.0.57 License: BSD-3-Clause

X-Ray Key Features Code Snippets Community Discussions(5)Vulnerabilities Install Support

kandi X-RAY | ncls Summary

ncls is a C library typically used in Artificial Intelligence, Dataset applications. ncls has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. You can download it from GitHub.

The Nested Containment List for Python. Basically a static interval-tree that is silly fast for both construction and lookups.

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Support

ncls has a low active ecosystem.

It has 149 star(s) with 12 fork(s). There are 5 watchers for this library.

It had no major release in the last 12 months.

There are 6 open issues and 18 have been closed. On average issues are closed in 33 days. There are 1 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of ncls is 0.0.57

Quality

ncls has 0 bugs and 16 code smells.

Security

ncls has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

ncls code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

ncls is licensed under the BSD-3-Clause License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

ncls releases are available to install and integrate.

Installation instructions are not available. Examples and code snippets are available.

It has 179 lines of code, 6 functions and 9 files.

It has low code complexity. Code complexity directly impacts maintainability of the code.

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ncls Key Features

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Community Discussions

Trending Discussions on ncls

Deploy war file in Payara 5 Docker container

How do we define azure policy rules for dependent resources?

Payara server not starting

This site can’t be reached - when open Glassfish remote admin

Payara Refuses to Start: java.security.KeyStoreException: JCEKS not found

QUESTION

Deploy war file in Payara 5 Docker container

Asked 2021-Sep-10 at 15:45

I'm having trouble getting my war file to deploy on application start.

According to the docs here:

The following sample Dockerfile can be used to prepare a custom Payara Server image that deploys the myapplication.war artefact at runtime:

...

ANSWER

Answered 2021-Sep-10 at 15:45

This issue should be fixed in the next release, version 5.2021.7. There has already been an issue raised on GitHub here and an accompanying PR here

Source https://stackoverflow.com/questions/69117678

QUESTION

How do we define azure policy rules for dependent resources?

Asked 2020-Oct-20 at 17:03

Given this ARM template : https://github.com/Azure/azure-quickstart-templates/blob/master/101-redis-cache/azuredeploy.json

How do we enforce that the Redis cache is deployed with diagnostic settings enabled?

Will it be only possible only if an appropriate alias is provided by Azure team?

Current Set of aliases for Redis cache:

...

ANSWER

Answered 2020-Oct-20 at 17:03

You would need to use an auditIfNotExists or deployIfNotExists policy. The auditIfNotExists will get you started in how to detect resources without diagnostics settings, however there is much more complexity in the deployIfNotExists route that would require more about your specific application in order to address.

Source https://stackoverflow.com/questions/64435453

QUESTION

Payara server not starting

Asked 2020-Sep-16 at 11:12

I'm trying out some Java EE and I can get my code to run on Glassfish 5.0.1 no problem. I want to run it on Payara but I can only get Payara Micro to work, the full and web-profile both crash and give the following errors that I cant find any info about. The closest related problem I could find told me to try changing my path to Java 8 instead, but that had no effect. Thanks!

...

ANSWER

Answered 2020-Sep-16 at 11:12

This happens because your security provider doesn't support the JCEKS algorithm to open the Payara keystore. Try using a different distribution of Java, e.g. AdoptOpenJDK (https://adoptopenjdk.net/). It's possible that your Java doesn't support that algorithm.

The reason why Payara Server fails and GlassFish doesn't is that Payara Server attempts to find configuration values in password aliases, which are protected by the keystore. This results in an exception because it can't open the keystore. I bet that GlassFish would also fail to open the keystore if it needed it at some point later. GlassFish just doesn't have the functionality of reading the configuration from password aliases and thus doesn't attempt to open the keystore at startup.

Anyway, it's definitely a bug that this exception brings down the whole server. Payara Server should just ignore the configuration and go on. Raise this as a bug in Payara bug tracker: https://github.com/payara/Payara/issues.

Source https://stackoverflow.com/questions/63888915

QUESTION

This site can’t be reached - when open Glassfish remote admin

Asked 2020-Jul-09 at 18:56

After starting Glassfish, the remote Glassfish site is unreachable. An address I use is 123.123.12.12:14848 (ip number changed)

root@debian:/opt/glassfish5/glassfish/bin# ./asadmin start-domain Waiting for domain1 to start ........... Successfully started the domain : domain1 domain Location: /opt/glassfish5/glassfish/domains/domain1 Log File: /opt/glassfish5/glassfish/domains/domain1/logs/server.log Admin Port: 14848 Command start-domain executed successfully.

Here you are a log:

[2020-07-09T10:21:18.154-0400] [] [INFO] [NCLS-GFLAUNCHER-00005] [javax.enterprise.launcher] [tid: _ThreadID=1 _ThreadName=main] [timeMillis: 1594304478154] [levelValue: 800] [[ JVM invocation command line: /usr/lib/jvm/jdk1.8.0_151/bin/java -cp /opt/glassfish5/glassfish/modules/glassfish.jar -XX:+UnlockDiagnosticVMOptions -XX:NewRatio=2 -XX:MaxPermSize=192m -Xmx512m -javaagent:/opt/glassfish5/glassfish/lib/monitor/flashlight-agent.jar -client -Djavax.xml.accessExternalSchema=all -Djavax.net.ssl.trustStore=/opt/glassfish5/glassfish/domains/domain1/config/cacerts.jks -Djdk.tls.rejectClientInitiatedRenegotiation=true -Djdk.corba.allowOutputStreamSubclass=true -Dfelix.fileinstall.dir=/opt/glassfish5/glassfish/modules/autostart/ -Dorg.glassfish.additionalOSGiBundlesToStart=org.apache.felix.shell,org.apache.felix.gogo.runtime,org.apache.felix.gogo.shell,org.apache.felix.gogo.command,org.apache.felix.shell.remote,org.apache.felix.fileinstall -Dcom.sun.aas.installRoot=/opt/glassfish5/glassfish -Dfelix.fileinstall.poll=5000 -Djava.endorsed.dirs=/opt/glassfish5/glassfish/modules/endorsed:/opt/glassfish5/glassfish/lib/endorsed -Djava.security.policy=/opt/glassfish5/glassfish/domains/domain1/config/server.policy -Dosgi.shell.telnet.maxconn=1 -Dfelix.fileinstall.bundles.startTransient=true -Dcom.sun.enterprise.config.config_environment_factory_class=com.sun.enterprise.config.serverbeans.AppserverConfigEnvironmentFactory -Dfelix.fileinstall.log.level=2 -Djavax.net.ssl.keyStore=/opt/glassfish5/glassfish/domains/domain1/config/keystore.jks -Djava.security.auth.login.config=/opt/glassfish5/glassfish/domains/domain1/config/login.conf -Dfelix.fileinstall.disableConfigSave=false -Dfelix.fileinstall.bundles.new.start=true -Dcom.sun.aas.instanceRoot=/opt/glassfish5/glassfish/domains/domain1 -Dosgi.shell.telnet.port=6666 -Dgosh.args=--nointeractive -Dcom.sun.enterprise.security.httpsOutboundKeyAlias=s1as -Dosgi.shell.telnet.ip=127.0.0.1 -DANTLR_USE_DIRECT_CLASS_LOADING=true -Djava.awt.headless=true -Dcom.ctc.wstx.returnNullForDefaultNamespace=true -Djava.ext.dirs=/usr/lib/jvm/jdk1.8.0_151/lib/ext:/usr/lib/jvm/jdk1.8.0_151/jre/lib/ext:/opt/glassfish5/glassfish/domains/domain1/lib/ext -Djdbc.drivers=org.apache.derby.jdbc.ClientDriver -Djava.library.path=/opt/glassfish5/glassfish/lib:/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib com.sun.enterprise.glassfish.bootstrap.ASMain -upgrade false -domaindir /opt/glassfish5/glassfish/domains/domain1 -read-stdin true -asadmin-args --host,,,localhost,,,--port,,,4848,,,--secure=false,,,--terse=false,,,--echo=false,,,--interactive=true,,,start-domain,,,--verbose=false,,,--watchdog=false,,,--debug=false,,,--domaindir,,,/opt/glassfish5/glassfish/domains,,,domain1 -domainname domain1 -instancename server -type DAS -verbose false -asadmin-classpath /opt/glassfish5/glassfish/lib/client/appserver-cli.jar -debug false -asadmin-classname com.sun.enterprise.admin.cli.AdminMain]]

[2020-07-09T10:21:28.959-0400] [glassfish 5.0] [INFO] [NCLS-LOGGING-00009] [javax.enterprise.logging] [tid: _ThreadID=18 _ThreadName=RunLevelControllerThread-1594304488303] [timeMillis: 1594304488959] [levelValue: 800] [[ Running GlassFish Version: GlassFish Server Open Source Edition 5.0.1 (build 5)]]

[2020-07-09T10:21:28.962-0400] [glassfish 5.0] [INFO] [NCLS-LOGGING-00010] [javax.enterprise.logging] [tid: _ThreadID=18 _ThreadName=RunLevelControllerThread-1594304488303] [timeMillis: 1594304488962] [levelValue: 800] [[ Server log file is using Formatter class: com.sun.enterprise.server.logging.ODLLogFormatter]]

[2020-07-09T10:21:29.417-0400] [glassfish 5.0] [INFO] [NCLS-SECURITY-01115] [javax.enterprise.system.core.security] [tid: _ThreadID=17 _ThreadName=RunLevelControllerThread-1594304488295] [timeMillis: 1594304489417] [levelValue: 800] [[ Realm [admin-realm] of classtype [com.sun.enterprise.security.auth.realm.file.FileRealm] successfully created.]]

[2020-07-09T10:21:29.422-0400] [glassfish 5.0] [INFO] [NCLS-SECURITY-01115] [javax.enterprise.system.core.security] [tid: _ThreadID=17 _ThreadName=RunLevelControllerThread-1594304488295] [timeMillis: 1594304489422] [levelValue: 800] [[ Realm [file] of classtype [com.sun.enterprise.security.auth.realm.file.FileRealm] successfully created.]]

[2020-07-09T10:21:29.428-0400] [glassfish 5.0] [INFO] [NCLS-SECURITY-01115] [javax.enterprise.system.core.security] [tid: _ThreadID=17 _ThreadName=RunLevelControllerThread-1594304488295] [timeMillis: 1594304489428] [levelValue: 800] [[ Realm [certificate] of classtype [com.sun.enterprise.security.auth.realm.certificate.CertificateRealm] successfully created.]]

[2020-07-09T10:21:30.365-0400] [glassfish 5.0] [INFO] [] [org.glassfish.ha.store.spi.BackingStoreFactoryRegistry] [tid: _ThreadID=20 _ThreadName=RunLevelControllerThread-1594304488343] [timeMillis: 1594304490365] [levelValue: 800] [[ Registered org.glassfish.ha.store.adapter.cache.ShoalBackingStoreProxy for persistence-type = replicated in BackingStoreFactoryRegistry]]

[2020-07-09T10:21:30.466-0400] [glassfish 5.0] [INFO] [SEC-SVCS-00100] [javax.enterprise.security.services] [tid: _ThreadID=18 _ThreadName=RunLevelControllerThread-1594304488303] [timeMillis: 1594304490466] [levelValue: 800] [[ Authorization Service has successfully initialized.]]

[2020-07-09T10:21:31.035-0400] [glassfish 5.0] [INFO] [NCLS-CORE-00087] [javax.enterprise.system.core] [tid: _ThreadID=25 _ThreadName=RunLevelControllerThread-1594304489551] [timeMillis: 1594304491035] [levelValue: 800] [[ Grizzly Framework 2.4.3 started in: 52ms - bound to [/0.0.0.0:8080]]]

[2020-07-09T10:21:31.079-0400] [glassfish 5.0] [INFO] [NCLS-CORE-00087] [javax.enterprise.system.core] [tid: _ThreadID=25 _ThreadName=RunLevelControllerThread-1594304489551] [timeMillis: 1594304491079] [levelValue: 800] [[ Grizzly Framework 2.4.3 started in: 2ms - bound to [/0.0.0.0:8181]]]

[2020-07-09T10:21:31.111-0400] [glassfish 5.0] [WARNING] [] [org.glassfish.grizzly.config.GenericGrizzlyListener] [tid: _ThreadID=25 _ThreadName=RunLevelControllerThread-1594304489551] [timeMillis: 1594304491111] [levelValue: 900] [[ HTTP/2 (enabled by default) is unsupported with port unification and will be disabled for network listener admin-listener.]]

[2020-07-09T10:21:31.166-0400] [glassfish 5.0] [INFO] [NCLS-CORE-00087] [javax.enterprise.system.core] [tid: _ThreadID=25 _ThreadName=RunLevelControllerThread-1594304489551] [timeMillis: 1594304491166] [levelValue: 800] [[ Grizzly Framework 2.4.3 started in: 3ms - bound to [/0.0.0.0:14848]]]

[2020-07-09T10:21:31.396-0400] [glassfish 5.0] [INFO] [NCLS-CORE-00087] [javax.enterprise.system.core] [tid: _ThreadID=25 _ThreadName=RunLevelControllerThread-1594304489551] [timeMillis: 1594304491396] [levelValue: 800] [[ Grizzly Framework 2.4.3 started in: 80ms - bound to [/0.0.0.0:3700]]]

[2020-07-09T10:21:31.398-0400] [glassfish 5.0] [INFO] [NCLS-CORE-00017] [javax.enterprise.system.core] [tid: _ThreadID=1 _ThreadName=main] [timeMillis: 1594304491398] [levelValue: 800] [[ GlassFish Server Open Source Edition 5.0.1 (5) startup time : Felix (9,339ms), startup services(3,118ms), total(12,457ms)]]

[2020-07-09T10:21:32.439-0400] [glassfish 5.0] [INFO] [jts.startup_msg] [javax.enterprise.system.core.transaction.com.sun.jts.CosTransactions] [tid: _ThreadID=19 _ThreadName=RunLevelControllerThread-1594304488341] [timeMillis: 1594304492439] [levelValue: 800] [[ JTS5014: Recoverable JTS instance, serverId = [100]]]

[2020-07-09T10:21:32.677-0400] [glassfish 5.0] [INFO] [NCLS-BOOTSTRAP-00027] [javax.enterprise.bootstrap] [tid: _ThreadID=1 _ThreadName=main] [timeMillis: 1594304492677] [levelValue: 800] [[ Registered com.sun.enterprise.glassfish.bootstrap.osgi.EmbeddedOSGiGlassFishImpl@4aeaadc1 as OSGi service registration: org.apache.felix.framework.ServiceRegistrationImpl@263558c9.]]

[2020-07-09T10:21:33.236-0400] [glassfish 5.0] [INFO] [] [org.jvnet.hk2.osgiadapter] [tid: _ThreadID=15 _ThreadName=FelixStartLevel] [timeMillis: 1594304493236] [levelValue: 800] [[ Skipping registration of inhabitant for service reference [org.osgi.service.cm.ManagedService] as the service object could not be obtained.]]

[2020-07-09T10:21:33.248-0400] [glassfish 5.0] [INFO] [] [org.jvnet.hk2.osgiadapter] [tid: _ThreadID=15 _ThreadName=FelixStartLevel] [timeMillis: 1594304493248] [levelValue: 800] [[ Skipping registration of inhabitant for service reference [org.osgi.service.metatype.MetaTypeProvider] as the service object could not be obtained.]]

[2020-07-09T10:21:34.772-0400] [glassfish 5.0] [INFO] [NCLS-JMX-00024] [javax.enterprise.system.jmx] [tid: _ThreadID=55 _ThreadName=Thread-15] [timeMillis: 1594304494772] [levelValue: 800] [[ Creating a SecureRMIServerSocketFactory @ 0.0.0.0 with ssl config = GlassFishConfigBean.org.glassfish.grizzly.config.dom.Ssl]]

[2020-07-09T10:21:34.781-0400] [glassfish 5.0] [INFO] [] [] [tid: _ThreadID=55 _ThreadName=Thread-8] [timeMillis: 1594304494781] [levelValue: 800] [[ SSLParams =org.glassfish.admin.mbeanserver.ssl.SSLParams@415d224e]]

[2020-07-09T10:21:34.803-0400] [glassfish 5.0] [WARNING] [NCLS-JMX-00020] [javax.enterprise.system.jmx] [tid: _ThreadID=55 _ThreadName=Thread-15] [timeMillis: 1594304494803] [levelValue: 900] [[ All SSL cipher suites disabled for network-listener(s). Using SSL implementation specific defaults]]

[2020-07-09T10:21:34.812-0400] [glassfish 5.0] [WARNING] [NCLS-JMX-00020] [javax.enterprise.system.jmx] [tid: _ThreadID=55 _ThreadName=Thread-15] [timeMillis: 1594304494812] [levelValue: 900] [[ All SSL cipher suites disabled for network-listener(s). Using SSL implementation specific defaults]]

[2020-07-09T10:21:34.810-0400] [glassfish 5.0] [INFO] [] [] [tid: _ThreadID=55 _ThreadName=Thread-8] [timeMillis: 1594304494810] [levelValue: 800] [[ SSLParams =org.glassfish.admin.mbeanserver.ssl.SSLParams@415d224e]]

[2020-07-09T10:21:35.187-0400] [glassfish 5.0] [INFO] [NCLS-JMX-00025] [javax.enterprise.system.jmx] [tid: _ThreadID=55 _ThreadName=Thread-15] [timeMillis: 1594304495187] [levelValue: 800] [[ SSLServerSocket /0.0.0.0:8686 and [SSL: ServerSocket[addr=/0.0.0.0,localport=8686]] created]]

[2020-07-09T10:21:35.318-0400] [glassfish 5.0] [WARNING] [NCLS-JMX-00007] [javax.enterprise.system.jmx] [tid: _ThreadID=55 _ThreadName=Thread-15] [timeMillis: 1594304495318] [levelValue: 900] [[ Cannot start JMX connector JmxConnector config: { name = system, Protocol = rmi_jrmp, Address = 0.0.0.0, Port = 8686, AcceptAll = false, AuthRealmName = admin-realm, SecurityEnabled = true} due to exception java.lang.NoClassDefFoundError: sun/security/ssl/HandshakeStateManager]]

[2020-07-09T10:21:35.318-0400] [glassfish 5.0] [WARNING] [] [sun.rmi.transport.tcp] [tid: _ThreadID=80 _ThreadName=RMI TCP Accept-8686] [timeMillis: 1594304495318] [levelValue: 900] [[ RMI TCP Accept-8686: accept loop for [SSL: ServerSocket[addr=/0.0.0.0,localport=8686]] throws java.lang.NoClassDefFoundError: sun/security/ssl/HandshakeStateManager at sun.security.ssl.Handshaker.init(Handshaker.java:306) at sun.security.ssl.Handshaker.(Handshaker.java:266) at sun.security.ssl.ServerHandshaker.(ServerHandshaker.java:183) at sun.security.ssl.SSLSocketImpl.initHandshaker(SSLSocketImpl.java:1332) at sun.security.ssl.SSLSocketImpl.doneConnect(SSLSocketImpl.java:700) at sun.security.ssl.SSLServerSocketImpl.accept(SSLServerSocketImpl.java:349) at sun.rmi.transport.tcp.TCPTransport$AcceptLoop.executeAcceptLoop(TCPTransport.java:400) at sun.rmi.transport.tcp.TCPTransport$AcceptLoop.run(TCPTransport.java:372) at java.lang.Thread.run(Thread.java:748) ]]

[2020-07-09T10:21:35.390-0400] [glassfish 5.0] [SEVERE] [] [] [tid: _ThreadID=55 _ThreadName=Thread-9] [timeMillis: 1594304495390] [levelValue: 1000] [[ java.lang.NoClassDefFoundError: sun/security/ssl/HandshakeStateManager at sun.security.ssl.Handshaker.init(Handshaker.java:306) at sun.security.ssl.Handshaker.(Handshaker.java:266) at sun.security.ssl.ClientHandshaker.(ClientHandshaker.java:184) at sun.security.ssl.SSLSocketImpl.initHandshaker(SSLSocketImpl.java:1339) at sun.security.ssl.SSLSocketImpl.doneConnect(SSLSocketImpl.java:700) at sun.security.ssl.SSLSocketImpl.connect(SSLSocketImpl.java:679) at sun.security.ssl.SSLSocketImpl.(SSLSocketImpl.java:432) at sun.security.ssl.SSLSocketFactoryImpl.createSocket(SSLSocketFactoryImpl.java:88) at javax.rmi.ssl.SslRMIClientSocketFactory.createSocket(SslRMIClientSocketFactory.java:121) at sun.rmi.transport.tcp.TCPEndpoint.newSocket(TCPEndpoint.java:613) at sun.rmi.transport.tcp.TCPChannel.createConnection(TCPChannel.java:216) at sun.rmi.transport.tcp.TCPChannel.newConnection(TCPChannel.java:202) at sun.rmi.server.UnicastRef.newCall(UnicastRef.java:338) at sun.rmi.registry.RegistryImpl_Stub.rebind(RegistryImpl_Stub.java:147) at com.sun.jndi.rmi.registry.RegistryContext.rebind(RegistryContext.java:175) at com.sun.jndi.toolkit.url.GenericURLContext.rebind(GenericURLContext.java:251) at javax.naming.InitialContext.rebind(InitialContext.java:433) at javax.naming.InitialContext.rebind(InitialContext.java:433) at javax.management.remote.rmi.RMIConnectorServer.bind(RMIConnectorServer.java:642) at javax.management.remote.rmi.RMIConnectorServer.start(RMIConnectorServer.java:427) at org.glassfish.admin.mbeanserver.RMIConnectorStarter.start(RMIConnectorStarter.java:320) at org.glassfish.admin.mbeanserver.JMXStartupService$JMXConnectorsStarterThread.startConnector(JMXStartupService.java:314) at org.glassfish.admin.mbeanserver.JMXStartupService$JMXConnectorsStarterThread.run(JMXStartupService.java:346) ]]

How to fix it?

...

ANSWER

Answered 2020-Jul-09 at 18:56

I installed Glassfish 5.1 and Oracle jdk 8u241. Than it worked.

Source https://stackoverflow.com/questions/62817351

QUESTION

Payara Refuses to Start: java.security.KeyStoreException: JCEKS not found

Asked 2020-May-30 at 14:15

Running a Java EE 8 web Application on Payara 5.194. it has been a while since I started Payara and the application.

When I start the server: I gets messages for 6 expired certificates.

...

ANSWER

Answered 2020-May-30 at 14:15

So I found the issue. I did upgrade to JDK 9 and so my JAVA_HOME and path env variables were pointing to the JDK 9. So I changed them to point back to JDK 8 for the time being. and everything works.

Source https://stackoverflow.com/questions/62101773

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Vulnerabilities

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Install ncls

You can download it from GitHub.

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