Comments (27)
Hi @asdf5252,
which command are you running? The issue you have seems a problem due to the grobid version. which version are you using locally?
from entity-fishing.
Hello @lfoppiano
I am using the third step command i.e mvn clean install of the following link
http://nerd.readthedocs.io/en/latest/build.html
I have installed GROBID from the below link
http://grobid.readthedocs.io/en/latest/Install-Grobid/
grobid is running succesfully locally at the address http://localhost:8070/
But issue occurs when i am trying to build nerd by command mvn clean install
I get this
[INFO] Scanning for projects...
[WARNING]
[WARNING] Some problems were encountered while building the effective model for com.scienceminer.nerd:nerd-service:war:0.0.2
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 47, column 21
[WARNING]
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING]
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING]
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building (N)ERD 0.0.2
[INFO] ------------------------------------------------------------------------
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-core/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: https://oss.sonatype.org/content/groups/public/org/grobid/grobid-core/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: http://download.java.net/maven/2/org/grobid/grobid-core/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: https://oss.sonatype.org/content/groups/public/org/grobid/grobid-parent/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: http://download.java.net/maven/2/org/grobid/grobid-parent/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: http://repository.springsource.com/maven/bundles/external/org/grobid/grobid-parent/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-parent/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: https://oss.sonatype.org/content/groups/public/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: http://download.java.net/maven/2/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/grobid-ner-0.4.3-SNAPSHOT.pom
Downloading: http://download.java.net/maven/2/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/grobid-ner-0.4.3-SNAPSHOT.pom
Downloading: https://oss.sonatype.org/content/groups/public/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/grobid-ner-0.4.3-SNAPSHOT.pom
[WARNING] The POM for org.grobid.ner:grobid-ner:jar:0.4.3-SNAPSHOT is missing, no dependency information available
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/trainer/grobid-trainer/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: http://download.java.net/maven/2/org/grobid/trainer/grobid-trainer/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: https://oss.sonatype.org/content/groups/public/org/grobid/trainer/grobid-trainer/0.4.3-SNAPSHOT/maven-metadata.xml
[INFO]
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ nerd-service ---
[INFO] Deleting /home/grid/Desktop/uf/nerd/target
[INFO]
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ nerd-service ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 5 resources
[INFO]
[INFO] --- maven-compiler-plugin:3.6.1:compile (default-compile) @ nerd-service ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 138 source files to /home/grid/Desktop/uf/nerd/target/classes
[INFO] /home/grid/Desktop/uf/nerd/src/main/java/com/scienceminer/nerd/disambiguation/NerdEngine.java: Some input files use or override a deprecated API.
[INFO] /home/grid/Desktop/uf/nerd/src/main/java/com/scienceminer/nerd/disambiguation/NerdEngine.java: Recompile with -Xlint:deprecation for details.
[INFO] /home/grid/Desktop/uf/nerd/src/main/java/com/scienceminer/nerd/kb/model/Redirect.java: Some input files use unchecked or unsafe operations.
[INFO] /home/grid/Desktop/uf/nerd/src/main/java/com/scienceminer/nerd/kb/model/Redirect.java: Recompile with -Xlint:unchecked for details.
[INFO]
[INFO] --- maven-jar-plugin:3.0.2:jar (make-a-jar) @ nerd-service ---
[INFO] Building jar: /home/grid/Desktop/uf/nerd/target/nerd-service-0.0.2.jar
[INFO]
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ nerd-service ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 10 resources
[INFO]
[INFO] --- maven-compiler-plugin:3.6.1:testCompile (default-testCompile) @ nerd-service ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 10 source files to /home/grid/Desktop/uf/nerd/target/test-classes
[INFO]
[INFO] --- maven-surefire-plugin:2.20:test (default-test) @ nerd-service ---
[INFO]
[INFO] -------------------------------------------------------
[INFO] T E S T S
[INFO] -------------------------------------------------------
[INFO] Running com.scienceminer.nerd.utilities.mediaWiki.TestMediaWikiParser
log4j:WARN No appenders could be found for logger (com.scienceminer.nerd.utilities.mediaWiki.MediaWikiParser).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.055 s - in com.scienceminer.nerd.utilities.mediaWiki.TestMediaWikiParser
[INFO] Running com.scienceminer.nerd.utilities.NerdPropertyTest
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.206 s - in com.scienceminer.nerd.utilities.NerdPropertyTest
[INFO] Running com.scienceminer.nerd.service.NerdQueryTest
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.094 s - in com.scienceminer.nerd.service.NerdQueryTest
[INFO] Running com.scienceminer.nerd.service.TestQueryParser
aQuery1: {"text":"bla bla","abstract_":null,"claims":null,"description":null,"shortText":null,"language":null,"entities":null,"sentences":null,"resultLanguages":null,"runtime":0,"onlyNER":false,"nbest":false,"sentence":false,"format":"JSON","customisation":"generic","processSentence":null,"termVector":null,"globalCategories":null,"tokens":null,"context":null,"filter":null,"full":false,"minSelectorScore":0.0,"minRankerScore":0.0}
/home/grid/Desktop/uf/nerd/src/test/resources/query.json
{"text":"John","abstract_":null,"claims":null,"description":null,"shortText":null,"language":null,"entities":null,"sentences":null,"resultLanguages":null,"runtime":0,"onlyNER":false,"nbest":false,"sentence":false,"format":"JSON","customisation":"generic","processSentence":null,"termVector":null,"globalCategories":null,"tokens":null,"context":null,"filter":null,"full":false,"minSelectorScore":0.0,"minRankerScore":0.0}
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.06 s - in com.scienceminer.nerd.service.TestQueryParser
[INFO] Running com.scienceminer.nerd.disambiguation.TestWeightedTerm
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in com.scienceminer.nerd.disambiguation.TestWeightedTerm
[INFO] Running com.scienceminer.nerd.disambiguation.TestProcessText
>>>>>>>> GROBID_HOME=/home/grid/Desktop/uf/grobid/grobid-home
init upper level language independent environment
building Environment for upper knowledge base
Environment built - 9155139 concepts.
init Environment for language en
building Environment for language en
isLoaded: true
Environment built - 14651883 pages.
domains en / isLoaded: true
Warning: Orthopedic surgery is not a category found in Wikipedia.
Warning: Environment is not a category found in Wikipedia.
init Environment for language de
building Environment for language de
isLoaded: true
Environment built - 3523959 pages.
init Environment for language fr
building Environment for language fr
isLoaded: true
Environment built - 3631810 pages.
Setophaga ruticilla: 1.0
Setophaga: 0.0015192830367373664
ruticilla: 0.0
bird: 9.534052637295964E-5
washing machine: 0.45897020520637166
washing: 3.942409146377737E-4
machine: 3.896923023222438E-5
[ERROR] Tests run: 6, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 15.479 s <<< FAILURE! - in com.scienceminer.nerd.disambiguation.TestProcessText
[ERROR] testProcess(com.scienceminer.nerd.disambiguation.TestProcessText) Time elapsed: 3.805 s <<< ERROR!
java.lang.NoSuchFieldError: year
at com.scienceminer.nerd.disambiguation.TestProcessText.testProcess(TestProcessText.java:50)
[INFO] Running com.scienceminer.nerd.disambiguation.SentenceTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in com.scienceminer.nerd.disambiguation.SentenceTest
[INFO]
[INFO] Results:
[INFO]
[ERROR] Errors:
[ERROR] TestProcessText.testProcess:50 » NoSuchField year
[INFO]
[ERROR] Tests run: 30, Failures: 0, Errors: 1, Skipped: 0
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 35.216 s
[INFO] Finished at: 2018-01-09T11:03:26+05:30
[INFO] Final Memory: 34M/307M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.20:test (default-test) on project nerd-service: There are test failures.
[ERROR]
[ERROR] Please refer to /home/grid/Desktop/uf/nerd/target/surefire-reports for the individual test results.
[ERROR] Please refer to dump files (if any exist) [date]-jvmRun[N].dump, [date].dumpstream and [date]-jvmRun[N].dumpstream.
[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
from entity-fishing.
@asdf5252 the issue is due to come conflict of the grobid versions. I'm trying to think what can have been gone wrong.
Which version of grobid do you have in /home/grid/Desktop/uf/grobid/
? i guess you mvn clean install
it?
As a test could you try to remove everything you have in ~/.m2/repository/org/grobid
and rebuild nerd again?
from entity-fishing.
Hello @lfoppiano
In this /home/grid/Desktop/uf/grobid/ the version is 0.5.0
As you suggest to remove everything from ~/.m2/repository/org/grobid , I have performed this still build failure occurs with the following error
mvn clean install
[INFO] Scanning for projects...
[WARNING]
[WARNING] Some problems were encountered while building the effective model for com.scienceminer.nerd:nerd-service:war:0.0.2
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 47, column 21
[WARNING]
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING]
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING]
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building (N)ERD 0.0.2
[INFO] ------------------------------------------------------------------------
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-core/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: https://oss.sonatype.org/content/groups/public/org/grobid/grobid-core/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: http://download.java.net/maven/2/org/grobid/grobid-core/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-core/0.4.3-SNAPSHOT/grobid-core-0.4.3-SNAPSHOT.pom
[WARNING] Could not validate integrity of download from file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-core/0.4.3-SNAPSHOT/grobid-core-0.4.3-SNAPSHOT.pom: Checksum validation failed, no checksums available
[WARNING] Checksum validation failed, no checksums available for file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-core/0.4.3-SNAPSHOT/grobid-core-0.4.3-SNAPSHOT.pom
Downloaded: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-core/0.4.3-SNAPSHOT/grobid-core-0.4.3-SNAPSHOT.pom (9 KB at 500.3 KB/sec)
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-parent/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: https://oss.sonatype.org/content/groups/public/org/grobid/grobid-parent/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: http://download.java.net/maven/2/org/grobid/grobid-parent/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: http://repository.springsource.com/maven/bundles/external/org/grobid/grobid-parent/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-parent/0.4.3-SNAPSHOT/grobid-parent-0.4.3-SNAPSHOT.pom
Downloading: http://download.java.net/maven/2/org/grobid/grobid-parent/0.4.3-SNAPSHOT/grobid-parent-0.4.3-SNAPSHOT.pom
Downloading: https://oss.sonatype.org/content/groups/public/org/grobid/grobid-parent/0.4.3-SNAPSHOT/grobid-parent-0.4.3-SNAPSHOT.pom
Downloading: http://repository.springsource.com/maven/bundles/external/org/grobid/grobid-parent/0.4.3-SNAPSHOT/grobid-parent-0.4.3-SNAPSHOT.pom
Downloading: https://oss.sonatype.org/content/groups/public/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: http://download.java.net/maven/2/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/grobid-ner-0.4.3-SNAPSHOT.pom
Downloading: http://download.java.net/maven/2/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/grobid-ner-0.4.3-SNAPSHOT.pom
Downloading: https://oss.sonatype.org/content/groups/public/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/grobid-ner-0.4.3-SNAPSHOT.pom
[WARNING] The POM for org.grobid.ner:grobid-ner:jar:0.4.3-SNAPSHOT is missing, no dependency information available
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/trainer/grobid-trainer/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: http://download.java.net/maven/2/org/grobid/trainer/grobid-trainer/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: https://oss.sonatype.org/content/groups/public/org/grobid/trainer/grobid-trainer/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/trainer/grobid-trainer/0.4.3-SNAPSHOT/grobid-trainer-0.4.3-SNAPSHOT.pom
[WARNING] Could not validate integrity of download from file:////home/grid/Desktop/uf/nerd/lib/org/grobid/trainer/grobid-trainer/0.4.3-SNAPSHOT/grobid-trainer-0.4.3-SNAPSHOT.pom: Checksum validation failed, no checksums available
[WARNING] Checksum validation failed, no checksums available for file:////home/grid/Desktop/uf/nerd/lib/org/grobid/trainer/grobid-trainer/0.4.3-SNAPSHOT/grobid-trainer-0.4.3-SNAPSHOT.pom
Downloaded: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/trainer/grobid-trainer/0.4.3-SNAPSHOT/grobid-trainer-0.4.3-SNAPSHOT.pom (20 KB at 3213.7 KB/sec)
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 10.757 s
[INFO] Finished at: 2018-01-09T15:03:54+05:30
[INFO] Final Memory: 15M/195M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal on project nerd-service: Could not resolve dependencies for project com.scienceminer.nerd:nerd-service:war:0.0.2: Failed to collect dependencies at org.grobid:grobid-core:jar:0.4.3-SNAPSHOT: Failed to read artifact descriptor for org.grobid:grobid-core:jar:0.4.3-SNAPSHOT: Could not find artifact org.grobid:grobid-parent:pom:0.4.3-SNAPSHOT in 3rd-party-local-repo (file:////home/grid/Desktop/uf/nerd/lib/) -> [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/DependencyResolutionException
from entity-fishing.
Ok could you now update nerd with git pull
and try again?
from entity-fishing.
After git pull , I get this
/Desktop/uf/nerd$ git pull
remote: Counting objects: 29, done.
remote: Compressing objects: 100% (11/11), done.
remote: Total 29 (delta 15), reused 29 (delta 15), pack-reused 0
Unpacking objects: 100% (29/29), done.
From https://github.com/kermitt2/nerd
1500b6b..ca88fd0 master -> origin/master
c1656f2..60c856c 0.0.3 -> origin/0.0.3
Updating 1500b6b..ca88fd0
Fast-forward
lib/org/grobid/grobid-parent/0.4.3-SNAPSHOT/grobid-parent-0.4.3-SNAPSHOT.pom | 264 ++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 264 insertions(+)
create mode 100644 lib/org/grobid/grobid-parent/0.4.3-SNAPSHOT/grobid-parent-0.4.3-SNAPSHOT.pom
BUT STILL BUILD FAILURE EXIST
With the following error
mvn clean install
[INFO] Scanning for projects...
[WARNING]
[WARNING] Some problems were encountered while building the effective model for com.scienceminer.nerd:nerd-service:war:0.0.2
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 47, column 21
[WARNING]
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING]
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING]
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building (N)ERD 0.0.2
[INFO] ------------------------------------------------------------------------
[WARNING] The POM for org.grobid.ner:grobid-ner:jar:0.4.3-SNAPSHOT is missing, no dependency information available
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 0.735 s
[INFO] Finished at: 2018-01-09T15:16:09+05:30
[INFO] Final Memory: 11M/212M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal on project nerd-service: Could not resolve dependencies for project com.scienceminer.nerd:nerd-service:war:0.0.2: Failed to collect dependencies at org.grobid:grobid-core:jar:0.4.3-SNAPSHOT: Failed to read artifact descriptor for org.grobid:grobid-core:jar:0.4.3-SNAPSHOT: Failure to find org.grobid:grobid-parent:pom:0.4.3-SNAPSHOT in file:////home/grid/Desktop/uf/nerd/lib/ was cached in the local repository, resolution will not be reattempted until the update interval of 3rd-party-local-repo has elapsed or updates are forced -> [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/DependencyResolutionException
from entity-fishing.
OK so you have to run mvn clean install -U
the flag -U
should try to fetch again all the dependencies...
Give it a try
from entity-fishing.
Still build failure with following error
mvn clean install -U
[INFO] Scanning for projects...
[WARNING]
[WARNING] Some problems were encountered while building the effective model for com.scienceminer.nerd:nerd-service:war:0.0.2
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 47, column 21
[WARNING]
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING]
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING]
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building (N)ERD 0.0.2
[INFO] ------------------------------------------------------------------------
Downloading: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-jar-plugin/maven-metadata.xml
Downloaded: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-jar-plugin/maven-metadata.xml (743 B at 0.4 KB/sec)
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-core/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: http://download.java.net/maven/2/org/grobid/grobid-core/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: https://oss.sonatype.org/content/groups/public/org/grobid/grobid-core/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-parent/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: http://download.java.net/maven/2/org/grobid/grobid-parent/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: https://oss.sonatype.org/content/groups/public/org/grobid/grobid-parent/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: http://repository.springsource.com/maven/bundles/external/org/grobid/grobid-parent/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-parent/0.4.3-SNAPSHOT/grobid-parent-0.4.3-SNAPSHOT.pom
[WARNING] Could not validate integrity of download from file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-parent/0.4.3-SNAPSHOT/grobid-parent-0.4.3-SNAPSHOT.pom: Checksum validation failed, no checksums available
[WARNING] Checksum validation failed, no checksums available for file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-parent/0.4.3-SNAPSHOT/grobid-parent-0.4.3-SNAPSHOT.pom
Downloaded: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-parent/0.4.3-SNAPSHOT/grobid-parent-0.4.3-SNAPSHOT.pom (12 KB at 2265.4 KB/sec)
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: http://download.java.net/maven/2/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: https://oss.sonatype.org/content/groups/public/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/grobid-ner-0.4.3-SNAPSHOT.pom
Downloading: http://download.java.net/maven/2/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/grobid-ner-0.4.3-SNAPSHOT.pom
Downloading: https://oss.sonatype.org/content/groups/public/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/grobid-ner-0.4.3-SNAPSHOT.pom
[WARNING] The POM for org.grobid.ner:grobid-ner:jar:0.4.3-SNAPSHOT is missing, no dependency information available
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/trainer/grobid-trainer/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: https://oss.sonatype.org/content/groups/public/org/grobid/trainer/grobid-trainer/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: http://download.java.net/maven/2/org/grobid/trainer/grobid-trainer/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-core/0.4.3-SNAPSHOT/grobid-core-0.4.3-SNAPSHOT.jar
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/grobid-ner-0.4.3-SNAPSHOT.jar
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/trainer/grobid-trainer/0.4.3-SNAPSHOT/grobid-trainer-0.4.3-SNAPSHOT.jar
[WARNING] Could not validate integrity of download from file:////home/grid/Desktop/uf/nerd/lib/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/grobid-ner-0.4.3-SNAPSHOT.jar: Checksum validation failed, no checksums available
[WARNING] Checksum validation failed, no checksums available for file:////home/grid/Desktop/uf/nerd/lib/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/grobid-ner-0.4.3-SNAPSHOT.jar
Downloaded: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/grobid-ner-0.4.3-SNAPSHOT.jar (127 KB at 1726.3 KB/sec)
[WARNING] Could not validate integrity of download from file:////home/grid/Desktop/uf/nerd/lib/org/grobid/trainer/grobid-trainer/0.4.3-SNAPSHOT/grobid-trainer-0.4.3-SNAPSHOT.jar: Checksum validation failed, no checksums available
[WARNING] Checksum validation failed, no checksums available for file:////home/grid/Desktop/uf/nerd/lib/org/grobid/trainer/grobid-trainer/0.4.3-SNAPSHOT/grobid-trainer-0.4.3-SNAPSHOT.jar
Downloaded: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/trainer/grobid-trainer/0.4.3-SNAPSHOT/grobid-trainer-0.4.3-SNAPSHOT.jar (195 KB at 2266.0 KB/sec)
[WARNING] Could not validate integrity of download from file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-core/0.4.3-SNAPSHOT/grobid-core-0.4.3-SNAPSHOT.jar: Checksum validation failed, no checksums available
[WARNING] Checksum validation failed, no checksums available for file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-core/0.4.3-SNAPSHOT/grobid-core-0.4.3-SNAPSHOT.jar
Downloaded: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-core/0.4.3-SNAPSHOT/grobid-core-0.4.3-SNAPSHOT.jar (38037 KB at 57284.4 KB/sec)
[INFO]
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ nerd-service ---
[INFO] Deleting /home/grid/Desktop/uf/nerd/target
[INFO]
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ nerd-service ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 5 resources
[INFO]
[INFO] --- maven-compiler-plugin:3.6.1:compile (default-compile) @ nerd-service ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 138 source files to /home/grid/Desktop/uf/nerd/target/classes
[INFO] /home/grid/Desktop/uf/nerd/src/main/java/com/scienceminer/nerd/disambiguation/NerdEngine.java: Some input files use or override a deprecated API.
[INFO] /home/grid/Desktop/uf/nerd/src/main/java/com/scienceminer/nerd/disambiguation/NerdEngine.java: Recompile with -Xlint:deprecation for details.
[INFO] /home/grid/Desktop/uf/nerd/src/main/java/com/scienceminer/nerd/kb/model/Redirect.java: Some input files use unchecked or unsafe operations.
[INFO] /home/grid/Desktop/uf/nerd/src/main/java/com/scienceminer/nerd/kb/model/Redirect.java: Recompile with -Xlint:unchecked for details.
[INFO]
[INFO] --- maven-jar-plugin:3.0.2:jar (make-a-jar) @ nerd-service ---
[INFO] Building jar: /home/grid/Desktop/uf/nerd/target/nerd-service-0.0.2.jar
[INFO]
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ nerd-service ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 10 resources
[INFO]
[INFO] --- maven-compiler-plugin:3.6.1:testCompile (default-testCompile) @ nerd-service ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 10 source files to /home/grid/Desktop/uf/nerd/target/test-classes
[INFO]
[INFO] --- maven-surefire-plugin:2.20:test (default-test) @ nerd-service ---
[INFO]
[INFO] -------------------------------------------------------
[INFO] T E S T S
[INFO] -------------------------------------------------------
[INFO] Running com.scienceminer.nerd.utilities.mediaWiki.TestMediaWikiParser
log4j:WARN No appenders could be found for logger (com.scienceminer.nerd.utilities.mediaWiki.MediaWikiParser).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.075 s - in com.scienceminer.nerd.utilities.mediaWiki.TestMediaWikiParser
[INFO] Running com.scienceminer.nerd.utilities.NerdPropertyTest
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.168 s - in com.scienceminer.nerd.utilities.NerdPropertyTest
[INFO] Running com.scienceminer.nerd.service.NerdQueryTest
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.094 s - in com.scienceminer.nerd.service.NerdQueryTest
[INFO] Running com.scienceminer.nerd.service.TestQueryParser
aQuery1: {"text":"bla bla","abstract_":null,"claims":null,"description":null,"shortText":null,"language":null,"entities":null,"sentences":null,"resultLanguages":null,"runtime":0,"onlyNER":false,"nbest":false,"sentence":false,"format":"JSON","customisation":"generic","processSentence":null,"termVector":null,"globalCategories":null,"tokens":null,"context":null,"filter":null,"full":false,"minSelectorScore":0.0,"minRankerScore":0.0}
/home/grid/Desktop/uf/nerd/src/test/resources/query.json
{"text":"John","abstract_":null,"claims":null,"description":null,"shortText":null,"language":null,"entities":null,"sentences":null,"resultLanguages":null,"runtime":0,"onlyNER":false,"nbest":false,"sentence":false,"format":"JSON","customisation":"generic","processSentence":null,"termVector":null,"globalCategories":null,"tokens":null,"context":null,"filter":null,"full":false,"minSelectorScore":0.0,"minRankerScore":0.0}
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.06 s - in com.scienceminer.nerd.service.TestQueryParser
[INFO] Running com.scienceminer.nerd.disambiguation.TestWeightedTerm
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in com.scienceminer.nerd.disambiguation.TestWeightedTerm
[INFO] Running com.scienceminer.nerd.disambiguation.TestProcessText
>>>>>>>> GROBID_HOME=/home/grid/Desktop/uf/grobid/grobid-home
init upper level language independent environment
building Environment for upper knowledge base
Environment built - 9155139 concepts.
init Environment for language en
building Environment for language en
isLoaded: true
Environment built - 14651883 pages.
domains en / isLoaded: true
Warning: Orthopedic surgery is not a category found in Wikipedia.
Warning: Environment is not a category found in Wikipedia.
init Environment for language de
building Environment for language de
isLoaded: true
Environment built - 3523959 pages.
init Environment for language fr
building Environment for language fr
isLoaded: true
Environment built - 3631810 pages.
Setophaga ruticilla: 1.0
Setophaga: 0.0015192830367373664
ruticilla: 0.0
bird: 9.534052637295964E-5
washing machine: 0.45897020520637166
washing: 3.942409146377737E-4
machine: 3.896923023222438E-5
[ERROR] Tests run: 6, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 14.928 s <<< FAILURE! - in com.scienceminer.nerd.disambiguation.TestProcessText
[ERROR] testProcess(com.scienceminer.nerd.disambiguation.TestProcessText) Time elapsed: 3.489 s <<< ERROR!
java.lang.NoSuchFieldError: year
at com.scienceminer.nerd.disambiguation.TestProcessText.testProcess(TestProcessText.java:50)
[INFO] Running com.scienceminer.nerd.disambiguation.SentenceTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in com.scienceminer.nerd.disambiguation.SentenceTest
[INFO]
[INFO] Results:
[INFO]
[ERROR] Errors:
[ERROR] TestProcessText.testProcess:50 » NoSuchField year
[INFO]
[ERROR] Tests run: 30, Failures: 0, Errors: 1, Skipped: 0
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 36.988 s
[INFO] Finished at: 2018-01-09T15:31:56+05:30
[INFO] Final Memory: 36M/426M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.20:test (default-test) on project nerd-service: There are test failures.
[ERROR]
[ERROR] Please refer to /home/grid/Desktop/uf/nerd/target/surefire-reports for the individual test results.
[ERROR] Please refer to dump files (if any exist) [date]-jvmRun[N].dump, [date].dumpstream and [date]-jvmRun[N].dumpstream.
[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
from entity-fishing.
@asdf5252 that's very strange, I tested nerd with a pristine installation without any maven libraries and it worked fine. I'm failing to understand what's going on.
Could you show me the content of your .m2/repository/org/grobid
using the command tree
?
from entity-fishing.
Hello @lfoppiano
Check the content
tree /home/grid/.m2/repository/org/grobid/
/home/grid/.m2/repository/org/grobid/
├── grobid-core
│ ├── 0.4.3-SNAPSHOT
│ │ ├── grobid-core-0.4.3-SNAPSHOT.jar
│ │ ├── grobid-core-0.4.3-SNAPSHOT.pom
│ │ ├── _remote.repositories
│ │ └── resolver-status.properties
│ ├── 0.5.1-SNAPSHOT
│ │ ├── grobid-core-0.5.1-SNAPSHOT.jar
│ │ ├── grobid-core-0.5.1-SNAPSHOT-onejar.jar
│ │ ├── grobid-core-0.5.1-SNAPSHOT.pom
│ │ ├── grobid-core-0.5.1-SNAPSHOT-sources.jar
│ │ └── maven-metadata-local.xml
│ └── maven-metadata-local.xml
├── grobid-home
│ ├── 0.5.1-SNAPSHOT
│ │ ├── grobid-home-0.5.1-SNAPSHOT.jar
│ │ ├── grobid-home-0.5.1-SNAPSHOT.pom
│ │ ├── grobid-home-0.5.1-SNAPSHOT-sources.jar
│ │ ├── grobid-home-0.5.1-SNAPSHOT.zip
│ │ └── maven-metadata-local.xml
│ └── maven-metadata-local.xml
├── grobid-ner
│ ├── 0.5.0-SNAPSHOT
│ │ ├── grobid-ner-0.5.0-SNAPSHOT.jar
│ │ ├── grobid-ner-0.5.0-SNAPSHOT-onejar.jar
│ │ ├── grobid-ner-0.5.0-SNAPSHOT.pom
│ │ ├── maven-metadata-local.xml
│ │ └── _remote.repositories
│ └── maven-metadata-local.xml
├── grobid-parent
│ └── 0.4.3-SNAPSHOT
│ ├── grobid-parent-0.4.3-SNAPSHOT.pom
│ ├── grobid-parent-0.4.3-SNAPSHOT.pom.lastUpdated
│ ├── _remote.repositories
│ └── resolver-status.properties
├── grobid-service
│ ├── 0.5.1-SNAPSHOT
│ │ ├── grobid-service-0.5.1-SNAPSHOT.jar
│ │ ├── grobid-service-0.5.1-SNAPSHOT.pom
│ │ ├── grobid-service-0.5.1-SNAPSHOT-sources.jar
│ │ ├── grobid-service-0.5.1-SNAPSHOT.tar
│ │ ├── grobid-service-0.5.1-SNAPSHOT.zip
│ │ └── maven-metadata-local.xml
│ └── maven-metadata-local.xml
├── grobid-trainer
│ ├── 0.5.1-SNAPSHOT
│ │ ├── grobid-trainer-0.5.1-SNAPSHOT.jar
│ │ ├── grobid-trainer-0.5.1-SNAPSHOT-onejar.jar
│ │ ├── grobid-trainer-0.5.1-SNAPSHOT.pom
│ │ ├── grobid-trainer-0.5.1-SNAPSHOT-sources.jar
│ │ └── maven-metadata-local.xml
│ └── maven-metadata-local.xml
├── ner
│ └── grobid-ner
│ └── 0.4.3-SNAPSHOT
│ ├── grobid-ner-0.4.3-SNAPSHOT.jar
│ ├── grobid-ner-0.4.3-SNAPSHOT.pom.lastUpdated
│ ├── _remote.repositories
│ └── resolver-status.properties
└── trainer
└── grobid-trainer
└── 0.4.3-SNAPSHOT
├── grobid-trainer-0.4.3-SNAPSHOT.jar
├── grobid-trainer-0.4.3-SNAPSHOT.pom
├── _remote.repositories
└── resolver-status.properties
19 directories, 47 files
from entity-fishing.
OK let's try again...
so can you wipe out org/grobid
using the command rm -rf /home/grid/.m2/repository/org/grobid/
and then re-build nerd again (do not rebuild grobid)?
from entity-fishing.
Still build failure occurs with the following error
mvn clean install
[INFO] Scanning for projects...
[WARNING]
[WARNING] Some problems were encountered while building the effective model for com.scienceminer.nerd:nerd-service:war:0.0.2
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 47, column 21
[WARNING]
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING]
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING]
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building (N)ERD 0.0.2
[INFO] ------------------------------------------------------------------------
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-core/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: https://oss.sonatype.org/content/groups/public/org/grobid/grobid-core/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: http://download.java.net/maven/2/org/grobid/grobid-core/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-core/0.4.3-SNAPSHOT/grobid-core-0.4.3-SNAPSHOT.pom
[WARNING] Could not validate integrity of download from file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-core/0.4.3-SNAPSHOT/grobid-core-0.4.3-SNAPSHOT.pom: Checksum validation failed, no checksums available
[WARNING] Checksum validation failed, no checksums available for file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-core/0.4.3-SNAPSHOT/grobid-core-0.4.3-SNAPSHOT.pom
Downloaded: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-core/0.4.3-SNAPSHOT/grobid-core-0.4.3-SNAPSHOT.pom (9 KB at 242.6 KB/sec)
Downloading: https://oss.sonatype.org/content/groups/public/org/grobid/grobid-parent/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-parent/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: http://repository.springsource.com/maven/bundles/external/org/grobid/grobid-parent/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: http://download.java.net/maven/2/org/grobid/grobid-parent/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-parent/0.4.3-SNAPSHOT/grobid-parent-0.4.3-SNAPSHOT.pom
[WARNING] Could not validate integrity of download from file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-parent/0.4.3-SNAPSHOT/grobid-parent-0.4.3-SNAPSHOT.pom: Checksum validation failed, no checksums available
[WARNING] Checksum validation failed, no checksums available for file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-parent/0.4.3-SNAPSHOT/grobid-parent-0.4.3-SNAPSHOT.pom
Downloaded: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-parent/0.4.3-SNAPSHOT/grobid-parent-0.4.3-SNAPSHOT.pom (12 KB at 707.9 KB/sec)
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: http://download.java.net/maven/2/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: https://oss.sonatype.org/content/groups/public/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/grobid-ner-0.4.3-SNAPSHOT.pom
Downloading: http://download.java.net/maven/2/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/grobid-ner-0.4.3-SNAPSHOT.pom
Downloading: https://oss.sonatype.org/content/groups/public/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/grobid-ner-0.4.3-SNAPSHOT.pom
[WARNING] The POM for org.grobid.ner:grobid-ner:jar:0.4.3-SNAPSHOT is missing, no dependency information available
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/trainer/grobid-trainer/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: https://oss.sonatype.org/content/groups/public/org/grobid/trainer/grobid-trainer/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: http://download.java.net/maven/2/org/grobid/trainer/grobid-trainer/0.4.3-SNAPSHOT/maven-metadata.xml
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/trainer/grobid-trainer/0.4.3-SNAPSHOT/grobid-trainer-0.4.3-SNAPSHOT.pom
[WARNING] Could not validate integrity of download from file:////home/grid/Desktop/uf/nerd/lib/org/grobid/trainer/grobid-trainer/0.4.3-SNAPSHOT/grobid-trainer-0.4.3-SNAPSHOT.pom: Checksum validation failed, no checksums available
[WARNING] Checksum validation failed, no checksums available for file:////home/grid/Desktop/uf/nerd/lib/org/grobid/trainer/grobid-trainer/0.4.3-SNAPSHOT/grobid-trainer-0.4.3-SNAPSHOT.pom
Downloaded: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/trainer/grobid-trainer/0.4.3-SNAPSHOT/grobid-trainer-0.4.3-SNAPSHOT.pom (20 KB at 1134.2 KB/sec)
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-core/0.4.3-SNAPSHOT/grobid-core-0.4.3-SNAPSHOT.jar
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/grobid-ner-0.4.3-SNAPSHOT.jar
Downloading: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/trainer/grobid-trainer/0.4.3-SNAPSHOT/grobid-trainer-0.4.3-SNAPSHOT.jar
[WARNING] Could not validate integrity of download from file:////home/grid/Desktop/uf/nerd/lib/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/grobid-ner-0.4.3-SNAPSHOT.jar: Checksum validation failed, no checksums available
[WARNING] Checksum validation failed, no checksums available for file:////home/grid/Desktop/uf/nerd/lib/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/grobid-ner-0.4.3-SNAPSHOT.jar
Downloaded: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/ner/grobid-ner/0.4.3-SNAPSHOT/grobid-ner-0.4.3-SNAPSHOT.jar (127 KB at 857.3 KB/sec)
[WARNING] Could not validate integrity of download from file:////home/grid/Desktop/uf/nerd/lib/org/grobid/trainer/grobid-trainer/0.4.3-SNAPSHOT/grobid-trainer-0.4.3-SNAPSHOT.jar: Checksum validation failed, no checksums available
[WARNING] Checksum validation failed, no checksums available for file:////home/grid/Desktop/uf/nerd/lib/org/grobid/trainer/grobid-trainer/0.4.3-SNAPSHOT/grobid-trainer-0.4.3-SNAPSHOT.jar
Downloaded: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/trainer/grobid-trainer/0.4.3-SNAPSHOT/grobid-trainer-0.4.3-SNAPSHOT.jar (195 KB at 1282.1 KB/sec)
[WARNING] Could not validate integrity of download from file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-core/0.4.3-SNAPSHOT/grobid-core-0.4.3-SNAPSHOT.jar: Checksum validation failed, no checksums available
[WARNING] Checksum validation failed, no checksums available for file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-core/0.4.3-SNAPSHOT/grobid-core-0.4.3-SNAPSHOT.jar
Downloaded: file:////home/grid/Desktop/uf/nerd/lib/org/grobid/grobid-core/0.4.3-SNAPSHOT/grobid-core-0.4.3-SNAPSHOT.jar (38037 KB at 56267.5 KB/sec)
[INFO]
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ nerd-service ---
[INFO] Deleting /home/grid/Desktop/uf/nerd/target
[INFO]
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ nerd-service ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 5 resources
[INFO]
[INFO] --- maven-compiler-plugin:3.6.1:compile (default-compile) @ nerd-service ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 138 source files to /home/grid/Desktop/uf/nerd/target/classes
[INFO] /home/grid/Desktop/uf/nerd/src/main/java/com/scienceminer/nerd/disambiguation/NerdEngine.java: Some input files use or override a deprecated API.
[INFO] /home/grid/Desktop/uf/nerd/src/main/java/com/scienceminer/nerd/disambiguation/NerdEngine.java: Recompile with -Xlint:deprecation for details.
[INFO] /home/grid/Desktop/uf/nerd/src/main/java/com/scienceminer/nerd/kb/model/Redirect.java: Some input files use unchecked or unsafe operations.
[INFO] /home/grid/Desktop/uf/nerd/src/main/java/com/scienceminer/nerd/kb/model/Redirect.java: Recompile with -Xlint:unchecked for details.
[INFO]
[INFO] --- maven-jar-plugin:3.0.2:jar (make-a-jar) @ nerd-service ---
[INFO] Building jar: /home/grid/Desktop/uf/nerd/target/nerd-service-0.0.2.jar
[INFO]
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ nerd-service ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 10 resources
[INFO]
[INFO] --- maven-compiler-plugin:3.6.1:testCompile (default-testCompile) @ nerd-service ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 10 source files to /home/grid/Desktop/uf/nerd/target/test-classes
[INFO]
[INFO] --- maven-surefire-plugin:2.20:test (default-test) @ nerd-service ---
[INFO]
[INFO] -------------------------------------------------------
[INFO] T E S T S
[INFO] -------------------------------------------------------
[INFO] Running com.scienceminer.nerd.utilities.mediaWiki.TestMediaWikiParser
log4j:WARN No appenders could be found for logger (com.scienceminer.nerd.utilities.mediaWiki.MediaWikiParser).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.058 s - in com.scienceminer.nerd.utilities.mediaWiki.TestMediaWikiParser
[INFO] Running com.scienceminer.nerd.utilities.NerdPropertyTest
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.25 s - in com.scienceminer.nerd.utilities.NerdPropertyTest
[INFO] Running com.scienceminer.nerd.service.NerdQueryTest
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.09 s - in com.scienceminer.nerd.service.NerdQueryTest
[INFO] Running com.scienceminer.nerd.service.TestQueryParser
aQuery1: {"text":"bla bla","abstract_":null,"claims":null,"description":null,"shortText":null,"language":null,"entities":null,"sentences":null,"resultLanguages":null,"runtime":0,"onlyNER":false,"nbest":false,"sentence":false,"format":"JSON","customisation":"generic","processSentence":null,"termVector":null,"globalCategories":null,"tokens":null,"context":null,"filter":null,"full":false,"minSelectorScore":0.0,"minRankerScore":0.0}
/home/grid/Desktop/uf/nerd/src/test/resources/query.json
{"text":"John","abstract_":null,"claims":null,"description":null,"shortText":null,"language":null,"entities":null,"sentences":null,"resultLanguages":null,"runtime":0,"onlyNER":false,"nbest":false,"sentence":false,"format":"JSON","customisation":"generic","processSentence":null,"termVector":null,"globalCategories":null,"tokens":null,"context":null,"filter":null,"full":false,"minSelectorScore":0.0,"minRankerScore":0.0}
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.067 s - in com.scienceminer.nerd.service.TestQueryParser
[INFO] Running com.scienceminer.nerd.disambiguation.TestWeightedTerm
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in com.scienceminer.nerd.disambiguation.TestWeightedTerm
[INFO] Running com.scienceminer.nerd.disambiguation.TestProcessText
>>>>>>>> GROBID_HOME=/home/grid/Desktop/uf/grobid/grobid-home
init upper level language independent environment
building Environment for upper knowledge base
Environment built - 9155139 concepts.
init Environment for language en
building Environment for language en
isLoaded: true
Environment built - 14651883 pages.
domains en / isLoaded: true
Warning: Orthopedic surgery is not a category found in Wikipedia.
Warning: Environment is not a category found in Wikipedia.
init Environment for language de
building Environment for language de
isLoaded: true
Environment built - 3523959 pages.
init Environment for language fr
building Environment for language fr
isLoaded: true
Environment built - 3631810 pages.
Setophaga ruticilla: 1.0
Setophaga: 0.0015192830367373664
ruticilla: 0.0
bird: 9.534052637295964E-5
washing machine: 0.45897020520637166
washing: 3.942409146377737E-4
machine: 3.896923023222438E-5
[ERROR] Tests run: 6, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 15.098 s <<< FAILURE! - in com.scienceminer.nerd.disambiguation.TestProcessText
[ERROR] testProcess(com.scienceminer.nerd.disambiguation.TestProcessText) Time elapsed: 3.529 s <<< ERROR!
java.lang.NoSuchFieldError: year
at com.scienceminer.nerd.disambiguation.TestProcessText.testProcess(TestProcessText.java:50)
[INFO] Running com.scienceminer.nerd.disambiguation.SentenceTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in com.scienceminer.nerd.disambiguation.SentenceTest
[INFO]
[INFO] Results:
[INFO]
[ERROR] Errors:
[ERROR] TestProcessText.testProcess:50 » NoSuchField year
[INFO]
[ERROR] Tests run: 30, Failures: 0, Errors: 1, Skipped: 0
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 37.770 s
[INFO] Finished at: 2018-01-09T17:04:35+05:30
[INFO] Final Memory: 34M/298M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.20:test (default-test) on project nerd-service: There are test failures.
[ERROR]
[ERROR] Please refer to /home/grid/Desktop/uf/nerd/target/surefire-reports for the individual test results.
[ERROR] Please refer to dump files (if any exist) [date]-jvmRun[N].dump, [date].dumpstream and [date]-jvmRun[N].dumpstream.
[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
AND IN THE /home/grid/.m2/repository/org/grobid , the following content shows
tree /home/grid/.m2/repository/org/grobid/
/home/grid/.m2/repository/org/grobid/
├── grobid-core
│ └── 0.4.3-SNAPSHOT
│ ├── grobid-core-0.4.3-SNAPSHOT.jar
│ ├── grobid-core-0.4.3-SNAPSHOT.pom
│ ├── _remote.repositories
│ └── resolver-status.properties
├── grobid-parent
│ └── 0.4.3-SNAPSHOT
│ ├── grobid-parent-0.4.3-SNAPSHOT.pom
│ ├── _remote.repositories
│ └── resolver-status.properties
├── ner
│ └── grobid-ner
│ └── 0.4.3-SNAPSHOT
│ ├── grobid-ner-0.4.3-SNAPSHOT.jar
│ ├── grobid-ner-0.4.3-SNAPSHOT.pom.lastUpdated
│ ├── _remote.repositories
│ └── resolver-status.properties
└── trainer
└── grobid-trainer
└── 0.4.3-SNAPSHOT
├── grobid-trainer-0.4.3-SNAPSHOT.jar
├── grobid-trainer-0.4.3-SNAPSHOT.pom
├── _remote.repositories
└── resolver-status.properties
10 directories, 15 files
from entity-fishing.
@asdf5252 I've checked and double checked the various libraries and the field year
should be there.
Which version of java do you have? You have to have java 8.
Could you try to build and run it by excluding the tests and try to process some text (the default english WW1 from the interface would do) using mvn clean jetty:run-war -Dmaven.test.skip=true
?
If this is not working could you please send me the output of mvn clean install -X
?
(when paste code here, please include it using the correct markup for it, I'm correcting all your comments otherwise they are not readable.
from entity-fishing.
Hello @lfoppiano
Yes , I am having java 8.
When I exclude the testProcess(com.scienceminer.nerd.disambiguation.TestProcessText) , BUILD SUCCESS occurs .
Running nerd (entity fishing) locally at the address http://localhost:8090/
When I am trying to get output , the following error occurs
the server responded with a status of 500 (Internal Server Error)
on http://localhost:8090/service/disambiguate
HTTP ERROR 405
Problem accessing /service/disambiguate. Reason:
Method Not Allowed
The output of mvn clean install -X I have attached
a.txt
from entity-fishing.
@asdf5252 while I'm checking the maven output, could you tell me if you get any result running this:
curl 'http://localhost:8090/service/disambiguate' -X POST -F "query={ 'text': 'The army, led by general Paul von Hindenburg defeated Russia in a series of battles collectively known as the First Battle of Tannenberg. But the failed Russian invasion, causing the fresh German troops to move to the east, allowed the tactical Allied victory at the First Battle of the Marne.', 'processSentence': [ 1 ], 'sentences': [ { 'offsetStart': 0, 'offsetEnd': 138 }, { 'offsetStart': 138, 'offsetEnd': 293 } ], 'entities': [ { 'rawName': 'Russian', 'type': 'NATIONAL', 'offsetStart': 153, 'offsetEnd': 160 } ] }"
from entity-fishing.
Hello @lfoppiano
Find the attached screenshot of the address of http://localhost:8090/ and the error it shows
from entity-fishing.
The error in the first screenshot is correct, as you cannot GET from that entry point.
The rest is due to the problem we've got in the tests, indeed. We need to solve this first.
Could you give me the list of target/WEB-INF/lib
from your nerd root directory?
from entity-fishing.
Hello @lfoppiano
Find the list below from WEB-INF/lib folder
tree
.
├── ant-1.6.5.jar
├── args4j-2.0.16.jar
├── asm-3.1.jar
├── avro-1.7.5.jar
├── clearnlp-1.3.1.jar
├── com
│ └── cybozu
│ └── language-detection
│ ├── 09-13-2011
│ │ ├── language-detection-09-13-2011.jar
│ │ └── language-detection-09-13-2011.pom
│ └── maven-metadata-local.xml
├── commons-beanutils-1.7.0.jar
├── commons-beanutils-core-1.8.0.jar
├── commons-cli-1.2.jar
├── commons-codec-1.9.jar
├── commons-collections-3.2.2.jar
├── commons-collections4-4.1.jar
├── commons-compress-1.4.1.jar
├── commons-configuration-1.6.jar
├── commons-digester-1.8.jar
├── commons-el-1.0.jar
├── commons-httpclient-3.0.1.jar
├── commons-io-2.5.jar
├── commons-lang-2.4.jar
├── commons-lang3-3.6.jar
├── commons-logging-1.2.jar
├── commons-math-2.1.jar
├── commons-net-1.4.1.jar
├── core-3.1.1.jar
├── fr
│ └── limsi
│ └── wapiti
│ └── wapiti
│ ├── 1.5.0
│ │ ├── wapiti-1.5.0.jar
│ │ └── wapiti-1.5.0.pom
│ └── maven-metadata-local.xml
├── fst-2.50.jar
├── grobid-core-0.4.3-SNAPSHOT.jar
├── grobid-ner-0.4.3-SNAPSHOT.jar
├── grobid-trainer-0.4.3-SNAPSHOT.jar
├── guava-19.0.jar
├── hadoop-core-1.2.1.jar
├── hppc-0.4.1.jar
├── hsqldb-1.8.0.10.jar
├── httpclient-4.5.3.jar
├── httpcore-4.4.6.jar
├── httpmime-4.5.3.jar
├── jackson-annotations-2.9.0.jar
├── jackson-core-2.9.0.jar
├── jackson-core-asl-1.9.13.jar
├── jackson-databind-2.9.0.jar
├── jackson-dataformat-yaml-2.9.0.jar
├── jackson-jaxrs-1.7.1.jar
├── jackson-mapper-asl-1.9.13.jar
├── jackson-xc-1.7.1.jar
├── jasper-compiler-5.5.12.jar
├── jasper-runtime-5.5.12.jar
├── javassist-3.21.0-GA.jar
├── java-util-1.9.0.jar
├── jaxb-impl-2.2.5.jar
├── jersey-client-1.8.jar
├── jersey-core-1.8.jar
├── jersey-json-1.8.jar
├── jersey-multipart-1.8.jar
├── jersey-server-1.8.jar
├── jets3t-0.6.1.jar
├── jettison-1.1.jar
├── jetty-6.1.26.jar
├── jetty-util-6.1.26.jar
├── jregex-1.2_01.jar
├── jsonic-1.3.10.jar
├── json-io-2.5.1.jar
├── jsp-2.1-6.1.14.jar
├── jsp-api-2.1-6.1.14.jar
├── language-detection-09-13-2011.jar
├── lmdbjni-0.4.6.jar
├── lmdbjni-linux64-0.4.6.jar
├── lmdbjni-osx64-0.4.6.jar
├── lmdbjni-win64-0.4.6.jar
├── log4j-1.2.17.jar
├── lucene-analyzers-common-4.5.1.jar
├── lucene-analyzers-kuromoji-4.5.1.jar
├── lucene-analyzers-smartcn-4.5.1.jar
├── lucene-core-4.5.1.jar
├── mimepull-1.4.jar
├── naming-core-0.8.jar
├── naming-java-0.8.jar
├── objenesis-2.5.1.jar
├── org
│ ├── grobid
│ │ ├── grobid-core
│ │ │ ├── 0.4.2-SNAPSHOT
│ │ │ │ └── grobid-core-0.4.2-SNAPSHOT.jar
│ │ │ └── 0.4.3-SNAPSHOT
│ │ │ ├── grobid-core-0.4.3-SNAPSHOT.jar
│ │ │ ├── grobid-core-0.4.3-SNAPSHOT.pom
│ │ │ ├── maven-metadata-local.xml
│ │ │ └── _remote.repositories
│ │ ├── grobid-parent
│ │ │ └── 0.4.3-SNAPSHOT
│ │ │ └── grobid-parent-0.4.3-SNAPSHOT.pom
│ │ ├── ner
│ │ │ └── grobid-ner
│ │ │ ├── 0.4.2-SNAPSHOT
│ │ │ │ └── grobid-ner-0.4.2-SNAPSHOT.jar
│ │ │ └── 0.4.3-SNAPSHOT
│ │ │ └── grobid-ner-0.4.3-SNAPSHOT.jar
│ │ └── trainer
│ │ └── grobid-trainer
│ │ ├── 0.4.2-SNAPSHOT
│ │ │ └── grobid-trainer-0.4.2-SNAPSHOT.jar
│ │ └── 0.4.3-SNAPSHOT
│ │ ├── grobid-trainer-0.4.3-SNAPSHOT.jar
│ │ ├── grobid-trainer-0.4.3-SNAPSHOT.pom
│ │ ├── maven-metadata-local.xml
│ │ └── _remote.repositories
│ └── wipo
│ └── analysers
│ └── wipo-analysers
│ ├── 0.0.1
│ │ ├── _maven.repositories
│ │ ├── wipo-analysers-0.0.1.jar
│ │ └── wipo-analysers-0.0.1.pom
│ └── maven-metadata-local.xml
├── oro-2.0.8.jar
├── paranamer-2.3.jar
├── ptk-common-3.0.6.jar
├── rats-runtime-1.15.0.jar
├── scala-library-2.10.3.jar
├── servlet-api-2.5-20081211.jar
├── servlet-api-2.5-6.1.14.jar
├── slf4j-api-1.7.25.jar
├── slf4j-log4j12-1.7.25.jar
├── smile-core-1.3.1.jar
├── smile-data-1.3.1.jar
├── smile-graph-1.3.1.jar
├── smile-math-1.3.1.jar
├── snakeyaml-1.17.jar
├── snappy-java-1.0.5.jar
├── stax-api-1.0.1.jar
├── stringmetric-core_2.10-0.27.3.jar
├── swc-engine-3.1.5.jar
├── swc-parser-lazy-3.1.5.jar
├── utils-3.0.6.jar
├── wapiti-1.5.0.jar
├── wipo-analysers-0.0.1.jar
├── xmlenc-0.52.jar
├── xmlpull-1.1.3.1.jar
├── xpp3_min-1.1.4c.jar
├── xstream-1.4.10.jar
└── xz-1.0.jar
28 directories, 125 files
from entity-fishing.
Hello @lfoppiano
Does you updated the Grobid and Grobid-ner , now during nerd build process it is showing POM is missing
See the below result after mvn clean install
mvn clean install
[INFO] Scanning for projects...
[WARNING]
[WARNING] Some problems were encountered while building the effective model for com.scienceminer.nerd:nerd-service:war:0.0.2
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 47, column 21
[WARNING]
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING]
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING]
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building (N)ERD 0.0.2
[INFO] ------------------------------------------------------------------------
[WARNING] The POM for org.grobid:grobid-ner:jar:0.5.0.2-SNAPSHOT is missing, no dependency information available
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 2.983 s
[INFO] Finished at: 2018-01-10T19:57:57+05:30
[INFO] Final Memory: 10M/153M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal on project nerd-service: Could not resolve dependencies for project com.scienceminer.nerd:nerd-service:war:0.0.2: Failure to find org.grobid:grobid-ner:jar:0.5.0.2-SNAPSHOT in file:////home/grid/Desktop/uf/nerd/lib/ was cached in the local repository, resolution will not be reattempted until the update interval of 3rd-party-local-repo has elapsed or updates are forced -> [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/DependencyResolutionException
from entity-fishing.
Hi @asdf5252, indeed I wrongly commit the pom.xml. It should be back as before.
I haven't had time to check your maven log. I'll try to do it before the end of the week.
from entity-fishing.
Hi @asdf5252 I've checked and re-checked and I didn't find any issue with nerd on master...
from entity-fishing.
Hello @lfoppiano
I am installing everything from the beginning , if any issue occur , I will let you know.
from entity-fishing.
Hi @asdf5252 actually, I've managed to reproduce the error while trying to solve another problem you might have by pulling the code from master, I should be able to solve this issue today.
from entity-fishing.
@asdf5252 could you try now? pull or re-clone the master repository
from entity-fishing.
Hello @lfoppiano
Thanks , now the build issue is solved and I am getting the output from http://localhost:8090/.
from entity-fishing.
Hello @lfoppiano
Can we build GROBID quantities locally ?
from entity-fishing.
Yes but if you have any issue with that please open an issue on the relative project.
from entity-fishing.
Related Issues (20)
- Impact of text length on identified entities HOT 3
- Problem of disambiguation of ENs according to the case or spelling of terms HOT 1
- Sometimes entity fishing returns "Invalid id or excluded via caching" as rawName of preferredForm HOT 1
- Different results when supplying entity spans HOT 2
- Named Entity Recognition and Classification for languages other than EN/FR HOT 4
- Case and term selection for French
- Bad formatting of json response HOT 1
- Add an option to make a warm-up of lower/upper KB databases at startup HOT 1
- EF display of French dates HOT 1
- Add an option to retrieve a text only wikidata definition from entity ? HOT 7
- not able to build entity-fishing HOT 2
- Support for Swedish language HOT 6
- Japanese language alpha 2 misconifgured HOT 3
- Docker HOT 2
- HTTP 2.0 support or support for request batching? HOT 1
- installation failes (at arm64) HOT 2
- Dutch language support HOT 2
- General Statistics of Retrievable Wiki Entities HOT 4
- The first request to disambiguate is slow and also memory is growing as more requests are coming in HOT 1
- Entity Fishing Service Randomly not Yielding Wiki Link HOT 6
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from entity-fishing.