Testing issues about cermine

[dtkaczyk]

Hi @ydu-sci thanks for reporting this.

About README and using the project: I've rewritten the README, hopefully it is more clear now. Try to use it again and if anything is still unclear, please explain in more detail which part is confusing. I will gladly clarify.

About Javadoc errors: I corrected the errors and warnings, it shouldn't happen again.

About test errors: Which Java and Maven versions do you use?

About building the project in general: In short, you don't need to build the project yourself to use it (more on this in the current README), unless you wish to make some changes in CERMINE code. Is that the case?

[ydu-sci]

Hi @dtkaczyk , Sorry for my late reply.

java -version

java version "1.8.0_111"
Java(TM) SE Runtime Environment (build 1.8.0_111-b14)
Java HotSpot(TM) 64-Bit Server VM (build 25.111-b14, mixed mode)

mvn -version

Apache Maven 3.3.9 (bb52d8502b132ec0a5a3f4c09453c07478323dc5; 2015-11-11T00:41:47+08:00)
Maven home: /home/software/apache-maven-3.3.9
Java version: 1.8.0_111, vendor: Oracle Corporation
Java home: /home/software/jdk1.8.0_111/jre
Default locale: en_US, platform encoding: ANSI_X3.4-1968
OS name: "linux", version: "2.6.32-358.el6.x86_64", arch: "amd64", family: "unix"

Hope your project will be better with the extensive test from the world.

Yu

[dtkaczyk]

@ydu-sci In general, the code was written and tested using Java 7. It seems that indeed there was some ambiguity in the output produced by CERMINE, which caused problems with the tests in Java 8 (the affiliations in the resulting JATS file could be in any order). I corrected this, and it seems to work with both Java 7 and Java 8 now (I tested it using a simple "mvn clean install" command). You can try to test the newest code again and we will see if it works.

What about other issues? As I mentioned, if you wish to use CERMINE as a standalone application, you shouldn't have to compile the code and build the project yourself, it should be enough to use the JAR file downloaded from the repository (more details in the README). Please let me know if you still have problems with this approach.

[ydu-sci]

Unzip the newest CERMINE and run mvn clean install in the folder, I get the same test failure as before:

Results :

Failed tests: metadataExtractionTest(pl.edu.icm.cermine.AltPdfNLMMetadataExtractorTest)
metadataExtractionTest(pl.edu.icm.cermine.bibref.KMeansBibReferenceExtractorTest): expected:<...98, 186:528-33.(..)
testAddFeatures(pl.edu.icm.cermine.metadata.affiliation.features.AffiliationDictionaryFeatureTest): Token: 18 W expected:<1> but was:<0>
getBxDocumentTest(pl.edu.icm.cermine.ContentExtractorTest)
getBxDocumentWithGeneralLabelsTest(pl.edu.icm.cermine.ContentExtractorTest)
getBxDocumentWithSpecificLabelsTest(pl.edu.icm.cermine.ContentExtractorTest)
textRawFullTextTest(pl.edu.icm.cermine.ContentExtractorTest): expected:<...nnerhagen(..)
getFullTextWithLabelsTest(pl.edu.icm.cermine.ContentExtractorTest)
getNLMBodyTest(pl.edu.icm.cermine.ContentExtractorTest)
getNLMReferencesTest(pl.edu.icm.cermine.ContentExtractorTest)
getNLMContentTest(pl.edu.icm.cermine.ContentExtractorTest)

Tests run: 118, Failures: 11, Errors: 0, Skipped: 0

[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] CERMINE Content Extractor and Miner ................ SUCCESS [ 5.290 s]
[INFO] CERMINE Engine Implementation - 1.12-SNAPSHOT ...... FAILURE [01:56 min]
[INFO] CERMINE Tools - 1.12-SNAPSHOT ...................... SKIPPED
[INFO] CERMINE Web Interface - 1.12-SNAPSHOT .............. SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 02:01 min
[INFO] Finished at: 2016-12-26T09:47:13+08:00
[INFO] Final Memory: 39M/339M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.12.4:test (default-test) on project cermine-impl: There are test failures.
[ERROR]
[ERROR] Please refer to /home/src/CERMINE-master/cermine-impl/target/surefire-reports for the individual test results.
[ERROR] -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR] mvn -rf :cermine-impl

[dtkaczyk]

@ydu-sci unfortunately, so far I wasn't able to reproduce these problems. I prepared a separate branch, where I added code for keeping the test data in a bunch of files for later debugging. It would be great if you could execute it in your environment and share the results.

More specifically, could you download the code from the new branch, try to build it again and send back the contents of two directories: cermine-impl/target/surefire-reports and cermine-impl/testdump? If you zip them, you should be able to attach them here. I hope this will give me more information on what might be the problem.

[ydu-sci]

Thanks for your reply.
I downloaded the new test branch, mvn clean install and test failed like before.
The wanted zip files will be uploaded later on, because currently Github can't accept my zip files.

[ydu-sci]

What is your email address?
The means Github gives to workaround is hard for me. I hope to send the wanted file to your email.

[ydu-sci]

Thanks for the persistent work of @dtkaczyk
I got your email yesterday and finally the successful test is done.

[INFO] Reactor Summary:
[INFO]
[INFO] CERMINE Content Extractor and Miner ................ SUCCESS [ 1.162 s]
[INFO] CERMINE Engine Implementation - 1.12-SNAPSHOT ...... SUCCESS [02:23 min]
[INFO] CERMINE Tools - 1.12-SNAPSHOT ...................... SUCCESS [ 4.485 s]
[INFO] CERMINE Web Interface - 1.12-SNAPSHOT .............. SUCCESS [01:43 min]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 04:12 min
[INFO] Finished at: 2017-01-10T10:14:08+08:00
[INFO] Final Memory: 61M/364M
[INFO] ------------------------------------------------------------------------

Thought there is a minor error about host name, which I think could be improved.

10:12:27,687 |-ERROR in ch.qos.logback.core.util.ContextUtil@7cbd213e - Failed to get local hostname java.net.UnknownHostException: t5400: t5400: Name or service not known
at java.net.UnknownHostException: t5400: t5400: Name or service not known
at at java.net.InetAddress.getLocalHost(InetAddress.java:1505)
at at ch.qos.logback.core.util.ContextUtil.getLocalHostName(ContextUtil.java:32)
at at ch.qos.logback.core.util.ContextUtil.addHostNameAsProperty(ContextUtil.java:41)
at at ch.qos.logback.classic.joran.action.ConfigurationAction.begin(ConfigurationAction.java:56)
at at ch.qos.logback.core.joran.spi.Interpreter.callBeginAction(Interpreter.java:276)
at at ch.qos.logback.core.joran.spi.Interpreter.startElement(Interpreter.java:148)
at at ch.qos.logback.core.joran.spi.Interpreter.startElement(Interpreter.java:130)
at at ch.qos.logback.core.joran.spi.EventPlayer.play(EventPlayer.java:50)
at at ch.qos.logback.core.joran.GenericConfigurator.doConfigure(GenericConfigurator.java:147)
at at ch.qos.logback.core.joran.GenericConfigurator.doConfigure(GenericConfigurator.java:133)
at at ch.qos.logback.core.joran.GenericConfigurator.doConfigure(GenericConfigurator.java:96)
at at ch.qos.logback.core.joran.GenericConfigurator.doConfigure(GenericConfigurator.java:55)
at at ch.qos.logback.classic.util.ContextInitializer.configureByResource(ContextInitializer.java:75)
at at ch.qos.logback.classic.util.ContextInitializer.autoConfig(ContextInitializer.java:148)
at at org.slf4j.impl.StaticLoggerBinder.init(StaticLoggerBinder.java:84)
at at org.slf4j.impl.StaticLoggerBinder.(StaticLoggerBinder.java:54)
at at org.slf4j.LoggerFactory.bind(LoggerFactory.java:128)
at at org.slf4j.LoggerFactory.performInitialization(LoggerFactory.java:108)
at at org.slf4j.LoggerFactory.getILoggerFactory(LoggerFactory.java:279)
at at org.slf4j.LoggerFactory.getLogger(LoggerFactory.java:252)
at at org.slf4j.LoggerFactory.getLogger(LoggerFactory.java:265)
at at pl.edu.icm.cermine.service.ArticleMeta.(ArticleMeta.java:36)
at at pl.edu.icm.cermine.service.ArticleMetaTest.testExtractNLM(ArticleMetaTest.java:61)
at at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at at java.lang.reflect.Method.invoke(Method.java:498)
at at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:44)
at at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:15)
at at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:41)
at at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:20)
at at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:28)
at at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:31)
at at org.junit.runners.BlockJUnit4ClassRunner.runNotIgnored(BlockJUnit4ClassRunner.java:79)
at at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:71)
at at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:49)
at at org.junit.runners.ParentRunner$3.run(ParentRunner.java:193)
at at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:52)
at at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:191)
at at org.junit.runners.ParentRunner.access$000(ParentRunner.java:42)
at at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:184)
at at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:28)
at at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:31)
at at org.junit.runners.ParentRunner.run(ParentRunner.java:236)
at at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:252)
at at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:141)
at at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:112)
at at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at at java.lang.reflect.Method.invoke(Method.java:498)
at at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:189)
at at org.apache.maven.surefire.booter.ProviderFactory$ProviderProxy.invoke(ProviderFactory.java:165)
at at org.apache.maven.surefire.booter.ProviderFactory.invokeProvider(ProviderFactory.java:85)
at at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:115)
at at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:75)
Caused by: java.net.UnknownHostException: t5400: Name or service not known
at at java.net.Inet6AddressImpl.lookupAllHostAddr(Native Method)
at at java.net.InetAddress$2.lookupAllHostAddr(InetAddress.java:928)
at at java.net.InetAddress.getAddressesFromNameService(InetAddress.java:1323)
at at java.net.InetAddress.getLocalHost(InetAddress.java:1500)
at ... 55 common frames omitted

[acz-icm]

Hi @ydu-sci,
your problem seems to be similar to one described here:
http://stackoverflow.com/questions/1881546/inetaddress-getlocalhost-throws-unknownhostexception
Probably your /etc/hosts file does not contain the hostname `t5400'. Try to add it as described on stackoverflow.

[dtkaczyk]

@ydu-sci did you manage to solve this problem?

[dtkaczyk]

I am assuming this is fixed, please reopen this issue/open a new one if you still experience any problems.