Closed mattshardlow closed 6 years ago
@reckart done at guidelines; should we add in any other place in the documentation of github?
@pennyl67 I think the guidelines is sufficient.
I've now updated the UIMA versions throughout my components and released new artefacts to maven central. (I'm waiting for them to filter through).
I've updated the metadata of my component using the form at test.openminted.eu. However,changing the location under the 'distribution' section has only affected the componentInfo->distributionInfos->componentDistributionInfo->distributionLocation field in the metadata. This is now out of sync with the componentInfo->identificationInfo->resourceIdentifiers->resourceIdentifier field, which still has the old version (0.0.1).
Is there any way of forcing this change on the uploaded version of the component's metadata? Or do I need to start the process again?
I think that you need to re-register components from scratch in order to retrieve the new maven project, generate the docker image and the respective galaxy wrappers.
ok, will give it a go
Tried that, but it says 'already added'. Does this mean that it's not possible to upload a new version of a component to the framework if an older version has already been registered?
ah, ok maybe I misinterpreted the message. Apparently it's added it to the 'my components' section (3 times!)
I've now registered the component. But when I try to create a new workflow, I don't have the option to create a workflow using v2. There is a button in the galaxy interface to switch to version 0.0.2, but this doesn't appear to do anything. Is it disabled? One option would be to delete v0.0.1. Is that the right way to go about this?
I tried deleting the older version from 'my components' and runnning an updated workflow with the new version, but it errored again. Please can you send me the log, in case there's anything helpful in there. Any support you can offer to get this running is appreciated (especially given the short deadline to the launch).
Here is the log from your component
Using default installation dir /opt/omtd-component-executor
ocoord:uk.ac.mmu.tdmlab.journalism:TextMiningForJournalismApplication:0.0.1
15:58:31.277 [main] INFO eu.openminted.workflows.componentdependencies.DependenciesFetcherMain - ...
. ____ _ __ _ _
/\\ / ___'_ __ _ _(_)_ __ __ _ \ \ \ \
( ( )\___ | '_ | '_| | '_ \/ _` | \ \ \ \
\\/ ___)| |_)| | | | | || (_| | ) ) ) )
' |____| .__|_| |_|_| |_\__, | / / / /
=========|_|==============|___/=/_/_/_/
:: Spring Boot :: (v1.4.2.RELEASE)
2018-05-11 15:58:35.904 INFO 16 --- [ main] e.o.w.c.DependenciesFetcherMain : Starting DependenciesFetcherMain v0.0.1-SNAPSHOT on snf-774931 with PID 16 (/opt/omtd-component-executor/omtd-component-dependencies-fetcher/target/omtd-component-dependencies-fetcher-0.0.1-SNAPSHOT-exec.jar started by root in /opt/omtd-component-executor)
2018-05-11 15:58:35.911 INFO 16 --- [ main] e.o.w.c.DependenciesFetcherMain : No active profile set, falling back to default profiles: default
2018-05-11 15:58:36.398 INFO 16 --- [ main] s.c.a.AnnotationConfigApplicationContext : Refreshing org.springframework.context.annotation.AnnotationConfigApplicationContext@22d8cfe0: startup date [Fri May 11 15:58:36 UTC 2018]; root of context hierarchy
2018-05-11 15:58:40.296 INFO 16 --- [ main] o.s.j.e.a.AnnotationMBeanExporter : Registering beans for JMX exposure on startup
2018-05-11 15:58:40.351 INFO 16 --- [ main] e.o.w.c.DependenciesFetcherMain : uk.ac.mmu.tdmlab.journalism:TextMiningForJournalismApplication:0.0.1
classPathListFileName:./TDMClasspathLists/classpath.uk.ac.mmu.tdmlab.journalism_TextMiningForJournalismApplication_0.0.1
uk.ac.mmu.tdmlab.journalism:TextMiningForJournalismApplication:0.0.1
length:72
FIlTER/opt/TDMlocalRepo/org/springframework/spring-core/3.2.16.RELEASE/spring-core-3.2.16.RELEASE.jar
FIlTER/opt/TDMlocalRepo/org/springframework/spring-context/3.2.16.RELEASE/spring-context-3.2.16.RELEASE.jar
FIlTER/opt/TDMlocalRepo/org/springframework/spring-aop/3.2.16.RELEASE/spring-aop-3.2.16.RELEASE.jar
FIlTER/opt/TDMlocalRepo/org/springframework/spring-expression/3.2.16.RELEASE/spring-expression-3.2.16.RELEASE.jar
FIlTER/opt/TDMlocalRepo/org/springframework/spring-beans/3.2.16.RELEASE/spring-beans-3.2.16.RELEASE.jar
2018-05-11 15:59:38.663 INFO 16 --- [ main] e.o.w.c.DependenciesFetcherMain : Started DependenciesFetcherMain in 65.993 seconds (JVM running for 69.581)
2018-05-11 15:59:38.664 INFO 16 --- [ main] e.o.w.c.DependenciesFetcherMain : DONE!
2018-05-11 15:59:38.667 INFO 16 --- [ Thread-1] s.c.a.AnnotationConfigApplicationContext : Closing org.springframework.context.annotation.AnnotationConfigApplicationContext@22d8cfe0: startup date [Fri May 11 15:58:36 UTC 2018]; root of context hierarchy
2018-05-11 15:59:38.686 INFO 16 --- [ Thread-1] o.s.j.e.a.AnnotationMBeanExporter : Unregistering JMX-exposed beans on shutdown
coordinates:uk.ac.mmu.tdmlab.journalism_TextMiningForJournalismApplication_0.0.1
inDir:tmp
otDir:/srv/galaxy/database/jobs_directory/001/1408/working/out/
uimaParams:
15:59:41.524 [main] INFO eu.openminted.workflows.uima.executor.PipelineCommandLineRunner - ...
. ____ _ __ _ _
/\\ / ___'_ __ _ _(_)_ __ __ _ \ \ \ \
( ( )\___ | '_ | '_| | '_ \/ _` | \ \ \ \
\\/ ___)| |_)| | | | | || (_| | ) ) ) )
' |____| .__|_| |_|_| |_\__, | / / / /
=========|_|==============|___/=/_/_/_/
:: Spring Boot :: (v1.4.2.RELEASE)
2018-05-11 15:59:46.179 INFO 45 --- [ main] e.o.w.u.e.PipelineCommandLineRunner : Starting PipelineCommandLineRunner v0.0.1-SNAPSHOT on snf-774931 with PID 45 (/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar started by root in /opt/omtd-component-executor/scripts/working)
2018-05-11 15:59:46.182 INFO 45 --- [ main] e.o.w.u.e.PipelineCommandLineRunner : No active profile set, falling back to default profiles: default
2018-05-11 15:59:46.656 INFO 45 --- [ main] s.c.a.AnnotationConfigApplicationContext : Refreshing org.springframework.context.annotation.AnnotationConfigApplicationContext@6e5e91e4: startup date [Fri May 11 15:59:46 UTC 2018]; root of context hierarchy
2018-05-11 15:59:49.687 INFO 45 --- [ main] f.a.AutowiredAnnotationBeanPostProcessor : JSR-330 'javax.inject.Inject' annotation found and supported for autowiring
2018-05-11 15:59:50.648 INFO 45 --- [ main] o.s.j.e.a.AnnotationMBeanExporter : Registering beans for JMX exposure on startup
parsing...
input tmp
output /srv/galaxy/database/jobs_directory/001/1408/working/out/
className uk.ac.mmu.tdmlab.journalism.TextMiningForJournalismApplication
2018-05-11 15:59:50.735 INFO 45 --- [ main] e.o.w.u.e.PipelineCommandLineRunner :
Executing..
========================
className:uk.ac.mmu.tdmlab.journalism.TextMiningForJournalismApplication
inputDir:tmp
outputDir:/srv/galaxy/database/jobs_directory/001/1408/working/out/
**parameters
========================
========================
2018-05-11 15:59:52.358 WARN 45 --- [ main] org.apache.uima : SAXTransformerFactory didn't recognize setting attribute http://javax.xml.XMLConstants/property/accessExternalDTD
2018-05-11 15:59:52.359 WARN 45 --- [ main] org.apache.uima : SAXTransformerFactory didn't recognize setting attribute http://javax.xml.XMLConstants/property/accessExternalStylesheet
2018-05-11 15:59:53.130 WARN 45 --- [ main] org.apache.uima : Skipping adding "" to URLs because it is not a directory or a JAR
2018-05-11 15:59:53.257 INFO 45 --- [ main] o.a.u.r.metadata.impl.Import_impl : Import by name: jar:file:/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar!/BOOT-INF/lib/de.tudarmstadt.ukp.dkpro.core.api.lexmorph-asl-1.8.0.jar!/desc/type/POS.xml
2018-05-11 15:59:53.348 INFO 45 --- [ main] o.a.u.r.metadata.impl.Import_impl : Import by name: jar:file:/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar!/BOOT-INF/lib/de.tudarmstadt.ukp.dkpro.core.api.lexmorph-asl-1.8.0.jar!/desc/type/Morpheme.xml
2018-05-11 15:59:53.471 INFO 45 --- [ main] o.a.u.r.metadata.impl.Import_impl : Import by name: jar:file:/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar!/BOOT-INF/lib/de.tudarmstadt.ukp.dkpro.core.api.segmentation-asl-1.8.0.jar!/desc/type/LexicalUnits.xml
2018-05-11 15:59:53.544 INFO 45 --- [ main] o.a.u.r.metadata.impl.Import_impl : Import by name: jar:file:/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar!/BOOT-INF/lib/de.tudarmstadt.ukp.dkpro.core.api.lexmorph-asl-1.8.0.jar!/desc/type/POS.xml
2018-05-11 15:59:53.550 INFO 45 --- [ main] o.a.u.r.metadata.impl.Import_impl : Import by name: jar:file:/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar!/BOOT-INF/lib/de.tudarmstadt.ukp.dkpro.core.api.lexmorph-asl-1.8.0.jar!/desc/type/Morpheme.xml
2018-05-11 15:59:53.948 WARN 45 --- [ main] org.apache.uima : Skipping adding "" to URLs because it is not a directory or a JAR
2018-05-11 15:59:54.081 INFO 45 --- [ main] o.a.u.r.impl.ConfigurationManager_impl : Parameter "lenient" in context / = "false"
2018-05-11 15:59:54.093 INFO 45 --- [ main] o.a.u.r.impl.ConfigurationManager_impl : Parameter "sourceLocation" in context / = "tmp"
2018-05-11 15:59:54.097 INFO 45 --- [ main] o.a.u.r.impl.ConfigurationManager_impl : Parameter "patterns" in context / = "[[+]**/*.xmi]"
2018-05-11 15:59:54.103 INFO 45 --- [ main] o.a.u.r.impl.ConfigurationManager_impl : Parameter "useDefaultExcludes" in context / = "true"
2018-05-11 15:59:54.105 INFO 45 --- [ main] o.a.u.r.impl.ConfigurationManager_impl : Parameter "includeHidden" in context / = "false"
2018-05-11 15:59:54.144 INFO 45 --- [ main] d.t.ukp.dkpro.core.io.xmi.XmiReader : Scanning [file:/opt/omtd-component-executor/scripts/working/tmp/]
2018-05-11 15:59:54.173 INFO 45 --- [ main] d.t.ukp.dkpro.core.io.xmi.XmiReader : Found [0] resources to be read
2018-05-11 15:59:54.495 WARN 45 --- [ main] org.apache.uima : Skipping adding "" to URLs because it is not a directory or a JAR
2018-05-11 15:59:54.498 INFO 45 --- [ main] o.a.u.r.metadata.impl.Import_impl : Import by name: jar:file:/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar!/BOOT-INF/lib/de.tudarmstadt.ukp.dkpro.core.api.lexmorph-asl-1.8.0.jar!/desc/type/POS.xml
2018-05-11 15:59:54.520 INFO 45 --- [ main] o.a.u.r.metadata.impl.Import_impl : Import by name: jar:file:/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar!/BOOT-INF/lib/de.tudarmstadt.ukp.dkpro.core.api.lexmorph-asl-1.8.0.jar!/desc/type/Morpheme.xml
2018-05-11 15:59:54.542 INFO 45 --- [ main] o.a.u.r.metadata.impl.Import_impl : Import by name: jar:file:/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar!/BOOT-INF/lib/de.tudarmstadt.ukp.dkpro.core.api.segmentation-asl-1.8.0.jar!/desc/type/LexicalUnits.xml
2018-05-11 15:59:54.565 INFO 45 --- [ main] o.a.u.r.metadata.impl.Import_impl : Import by name: jar:file:/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar!/BOOT-INF/lib/de.tudarmstadt.ukp.dkpro.core.api.lexmorph-asl-1.8.0.jar!/desc/type/POS.xml
2018-05-11 15:59:54.567 INFO 45 --- [ main] o.a.u.r.metadata.impl.Import_impl : Import by name: jar:file:/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar!/BOOT-INF/lib/de.tudarmstadt.ukp.dkpro.core.api.lexmorph-asl-1.8.0.jar!/desc/type/Morpheme.xml
2018-05-11 15:59:54.598 WARN 45 --- [ main] org.apache.uima : Skipping adding "" to URLs because it is not a directory or a JAR
2018-05-11 15:59:54.647 WARN 45 --- [ main] org.apache.uima : Skipping adding "" to URLs because it is not a directory or a JAR
2018-05-11 15:59:54.681 WARN 45 --- [ main] org.apache.uima : Skipping adding "" to URLs because it is not a directory or a JAR
2018-05-11 15:59:54.849 INFO 45 --- [ main] o.a.u.a.i.PrimitiveAnalysisEngine_impl : AnalysisEngine [uk.ac.mmu.tdmlab.journalism.TextMiningForJournalismApplication] initialization begin
2018-05-11 15:59:55.328 INFO 45 --- [ main] o.a.u.r.metadata.impl.Import_impl : Import by name: jar:file:/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar!/BOOT-INF/lib/de.tudarmstadt.ukp.dkpro.core.api.lexmorph-asl-1.8.0.jar!/desc/type/POS.xml
2018-05-11 15:59:55.361 INFO 45 --- [ main] o.a.u.r.metadata.impl.Import_impl : Import by name: jar:file:/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar!/BOOT-INF/lib/de.tudarmstadt.ukp.dkpro.core.api.lexmorph-asl-1.8.0.jar!/desc/type/Morpheme.xml
2018-05-11 15:59:55.396 INFO 45 --- [ main] o.a.u.r.metadata.impl.Import_impl : Import by name: jar:file:/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar!/BOOT-INF/lib/de.tudarmstadt.ukp.dkpro.core.api.segmentation-asl-1.8.0.jar!/desc/type/LexicalUnits.xml
2018-05-11 15:59:55.449 INFO 45 --- [ main] o.a.u.r.metadata.impl.Import_impl : Import by name: jar:file:/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar!/BOOT-INF/lib/de.tudarmstadt.ukp.dkpro.core.api.lexmorph-asl-1.8.0.jar!/desc/type/POS.xml
2018-05-11 15:59:55.463 INFO 45 --- [ main] o.a.u.r.metadata.impl.Import_impl : Import by name: jar:file:/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar!/BOOT-INF/lib/de.tudarmstadt.ukp.dkpro.core.api.lexmorph-asl-1.8.0.jar!/desc/type/Morpheme.xml
2018-05-11 15:59:55.990 INFO 45 --- [ main] o.a.u.a.i.PrimitiveAnalysisEngine_impl : AnalysisEngine [uk.ac.mmu.tdmlab.journalism.StanfordNLPTagger] initialization begin
2018-05-11 15:59:56.540 INFO 45 --- [ main] e.stanford.nlp.pipeline.StanfordCoreNLP : Adding annotator tokenize
2018-05-11 15:59:56.597 INFO 45 --- [ main] e.s.nlp.pipeline.TokenizerAnnotator : No tokenizer type provided. Defaulting to PTBTokenizer.
2018-05-11 15:59:56.684 INFO 45 --- [ main] e.stanford.nlp.pipeline.StanfordCoreNLP : Adding annotator ssplit
2018-05-11 15:59:56.713 INFO 45 --- [ main] e.stanford.nlp.pipeline.StanfordCoreNLP : Adding annotator pos
2018-05-11 16:00:01.390 INFO 45 --- [ main] e.s.nlp.tagger.maxent.MaxentTagger : Loading POS tagger from edu/stanford/nlp/models/pos-tagger/english-left3words/english-left3words-distsim.tagger ... done [4.6 sec].
2018-05-11 16:00:01.395 INFO 45 --- [ main] e.stanford.nlp.pipeline.StanfordCoreNLP : Adding annotator lemma
2018-05-11 16:00:01.401 INFO 45 --- [ main] e.stanford.nlp.pipeline.StanfordCoreNLP : Adding annotator ner
2018-05-11 16:00:04.815 INFO 45 --- [ main] e.s.nlp.ie.AbstractSequenceClassifier : Loading classifier from edu/stanford/nlp/models/ner/english.all.3class.distsim.crf.ser.gz ... done [3.1 sec].
2018-05-11 16:00:10.764 INFO 45 --- [ main] e.s.nlp.ie.AbstractSequenceClassifier : Loading classifier from edu/stanford/nlp/models/ner/english.muc.7class.distsim.crf.ser.gz ... done [5.9 sec].
2018-05-11 16:00:12.024 INFO 45 --- [ main] e.s.nlp.ie.AbstractSequenceClassifier : Loading classifier from edu/stanford/nlp/models/ner/english.conll.4class.distsim.crf.ser.gz ... done [1.3 sec].
2018-05-11 16:00:12.034 INFO 45 --- [ main] edu.stanford.nlp.time.JollyDayHolidays : Initializing JollyDayHoliday for SUTime from classpath edu/stanford/nlp/models/sutime/jollyday/Holidays_sutime.xml as sutime.binder.1.
2018-05-11 16:00:12.729 INFO 45 --- [ main] e.s.n.time.TimeExpressionExtractorImpl : Using following SUTime rules: edu/stanford/nlp/models/sutime/defs.sutime.txt,edu/stanford/nlp/models/sutime/english.sutime.txt,edu/stanford/nlp/models/sutime/english.holidays.sutime.txt
2018-05-11 16:00:28.215 INFO 45 --- [ main] e.s.n.pipeline.TokensRegexNERAnnotator : TokensRegexNERAnnotator ner.fine.regexner: Read 580641 unique entries out of 581790 from edu/stanford/nlp/models/kbp/regexner_caseless.tab, 0 TokensRegex patterns.
2018-05-11 16:00:28.372 INFO 45 --- [ main] e.s.n.pipeline.TokensRegexNERAnnotator : TokensRegexNERAnnotator ner.fine.regexner: Read 4857 unique entries out of 4868 from edu/stanford/nlp/models/kbp/regexner_cased.tab, 0 TokensRegex patterns.
2018-05-11 16:00:28.376 INFO 45 --- [ main] e.s.n.pipeline.TokensRegexNERAnnotator : TokensRegexNERAnnotator ner.fine.regexner: Read 585498 unique entries from 2 files
2018-05-11 16:01:04.828 INFO 45 --- [ main] o.a.u.a.i.PrimitiveAnalysisEngine_impl : AnalysisEngine [uk.ac.mmu.tdmlab.journalism.StanfordNLPTagger] initialization successful
2018-05-11 16:01:05.015 INFO 45 --- [ main] o.a.u.r.metadata.impl.Import_impl : Import by name: jar:file:/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar!/BOOT-INF/lib/de.tudarmstadt.ukp.dkpro.core.api.lexmorph-asl-1.8.0.jar!/desc/type/POS.xml
2018-05-11 16:01:05.016 INFO 45 --- [ main] o.a.u.r.metadata.impl.Import_impl : Import by name: jar:file:/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar!/BOOT-INF/lib/de.tudarmstadt.ukp.dkpro.core.api.lexmorph-asl-1.8.0.jar!/desc/type/Morpheme.xml
2018-05-11 16:01:05.017 INFO 45 --- [ main] o.a.u.r.metadata.impl.Import_impl : Import by name: jar:file:/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar!/BOOT-INF/lib/de.tudarmstadt.ukp.dkpro.core.api.segmentation-asl-1.8.0.jar!/desc/type/LexicalUnits.xml
2018-05-11 16:01:05.024 INFO 45 --- [ main] o.a.u.a.i.PrimitiveAnalysisEngine_impl : AnalysisEngine [uk.ac.mmu.tdmlab.journalism.WhereAnnotator] initialization begin
2018-05-11 16:01:05.030 INFO 45 --- [ main] o.a.u.a.i.PrimitiveAnalysisEngine_impl : AnalysisEngine [uk.ac.mmu.tdmlab.journalism.WhereAnnotator] initialization successful
2018-05-11 16:01:05.136 INFO 45 --- [ main] o.a.u.r.metadata.impl.Import_impl : Import by name: jar:file:/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar!/BOOT-INF/lib/de.tudarmstadt.ukp.dkpro.core.api.lexmorph-asl-1.8.0.jar!/desc/type/POS.xml
2018-05-11 16:01:05.138 INFO 45 --- [ main] o.a.u.r.metadata.impl.Import_impl : Import by name: jar:file:/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar!/BOOT-INF/lib/de.tudarmstadt.ukp.dkpro.core.api.lexmorph-asl-1.8.0.jar!/desc/type/Morpheme.xml
2018-05-11 16:01:05.139 INFO 45 --- [ main] o.a.u.r.metadata.impl.Import_impl : Import by name: jar:file:/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar!/BOOT-INF/lib/de.tudarmstadt.ukp.dkpro.core.api.segmentation-asl-1.8.0.jar!/desc/type/LexicalUnits.xml
2018-05-11 16:01:05.142 INFO 45 --- [ main] o.a.u.a.i.PrimitiveAnalysisEngine_impl : AnalysisEngine [uk.ac.mmu.tdmlab.journalism.WhoAnnotator] initialization begin
2018-05-11 16:01:05.144 INFO 45 --- [ main] o.a.u.a.i.PrimitiveAnalysisEngine_impl : AnalysisEngine [uk.ac.mmu.tdmlab.journalism.WhoAnnotator] initialization successful
2018-05-11 16:01:05.288 INFO 45 --- [ main] o.a.u.r.metadata.impl.Import_impl : Import by name: jar:file:/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar!/BOOT-INF/lib/de.tudarmstadt.ukp.dkpro.core.api.lexmorph-asl-1.8.0.jar!/desc/type/POS.xml
2018-05-11 16:01:05.290 INFO 45 --- [ main] o.a.u.r.metadata.impl.Import_impl : Import by name: jar:file:/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar!/BOOT-INF/lib/de.tudarmstadt.ukp.dkpro.core.api.lexmorph-asl-1.8.0.jar!/desc/type/Morpheme.xml
2018-05-11 16:01:05.291 INFO 45 --- [ main] o.a.u.r.metadata.impl.Import_impl : Import by name: jar:file:/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar!/BOOT-INF/lib/de.tudarmstadt.ukp.dkpro.core.api.segmentation-asl-1.8.0.jar!/desc/type/LexicalUnits.xml
2018-05-11 16:01:05.296 INFO 45 --- [ main] o.a.u.a.i.PrimitiveAnalysisEngine_impl : AnalysisEngine [uk.ac.mmu.tdmlab.journalism.WhenAnnotator] initialization begin
2018-05-11 16:01:05.298 INFO 45 --- [ main] o.a.u.a.i.PrimitiveAnalysisEngine_impl : AnalysisEngine [uk.ac.mmu.tdmlab.journalism.WhenAnnotator] initialization successful
2018-05-11 16:01:05.302 INFO 45 --- [ main] o.a.u.a.i.PrimitiveAnalysisEngine_impl : AnalysisEngine [uk.ac.mmu.tdmlab.journalism.TextMiningForJournalismApplication] initialization successful
2018-05-11 16:01:05.469 WARN 45 --- [ main] org.apache.uima : Skipping adding "" to URLs because it is not a directory or a JAR
2018-05-11 16:01:05.471 INFO 45 --- [ main] o.a.u.r.metadata.impl.Import_impl : Import by name: jar:file:/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar!/BOOT-INF/lib/de.tudarmstadt.ukp.dkpro.core.api.lexmorph-asl-1.8.0.jar!/desc/type/POS.xml
2018-05-11 16:01:05.483 INFO 45 --- [ main] o.a.u.r.metadata.impl.Import_impl : Import by name: jar:file:/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar!/BOOT-INF/lib/de.tudarmstadt.ukp.dkpro.core.api.lexmorph-asl-1.8.0.jar!/desc/type/Morpheme.xml
2018-05-11 16:01:12.745 INFO 45 --- [ main] o.a.u.r.metadata.impl.Import_impl : Import by name: jar:file:/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar!/BOOT-INF/lib/de.tudarmstadt.ukp.dkpro.core.api.segmentation-asl-1.8.0.jar!/desc/type/LexicalUnits.xml
2018-05-11 16:01:12.767 INFO 45 --- [ main] o.a.u.r.metadata.impl.Import_impl : Import by name: jar:file:/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar!/BOOT-INF/lib/de.tudarmstadt.ukp.dkpro.core.api.lexmorph-asl-1.8.0.jar!/desc/type/POS.xml
2018-05-11 16:01:12.786 INFO 45 --- [ main] o.a.u.r.metadata.impl.Import_impl : Import by name: jar:file:/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar!/BOOT-INF/lib/de.tudarmstadt.ukp.dkpro.core.api.lexmorph-asl-1.8.0.jar!/desc/type/Morpheme.xml
2018-05-11 16:01:12.796 WARN 45 --- [ main] org.apache.uima : Skipping adding "" to URLs because it is not a directory or a JAR
2018-05-11 16:01:12.818 WARN 45 --- [ main] org.apache.uima : Skipping adding "" to URLs because it is not a directory or a JAR
2018-05-11 16:01:12.822 WARN 45 --- [ main] org.apache.uima : Skipping adding "" to URLs because it is not a directory or a JAR
2018-05-11 16:01:12.825 INFO 45 --- [ main] o.a.u.r.impl.ConfigurationManager_impl : Parameter "targetLocation" in context / = "/srv/galaxy/database/jobs_directory/001/1408/working/out/"
2018-05-11 16:01:12.826 INFO 45 --- [ main] o.a.u.r.impl.ConfigurationManager_impl : Parameter "singularTarget" in context / = "false"
2018-05-11 16:01:12.827 INFO 45 --- [ main] o.a.u.r.impl.ConfigurationManager_impl : Parameter "compression" in context / = "NONE"
2018-05-11 16:01:12.827 INFO 45 --- [ main] o.a.u.r.impl.ConfigurationManager_impl : Parameter "stripExtension" in context / = "false"
2018-05-11 16:01:12.828 INFO 45 --- [ main] o.a.u.r.impl.ConfigurationManager_impl : Parameter "useDocumentId" in context / = "false"
2018-05-11 16:01:12.828 INFO 45 --- [ main] o.a.u.r.impl.ConfigurationManager_impl : Parameter "escapeDocumentId" in context / = "true"
2018-05-11 16:01:12.829 INFO 45 --- [ main] o.a.u.r.impl.ConfigurationManager_impl : Parameter "overwrite" in context / = "true"
2018-05-11 16:01:12.841 INFO 45 --- [ main] o.a.u.a.i.PrimitiveAnalysisEngine_impl : AnalysisEngine [de.tudarmstadt.ukp.dkpro.core.io.xmi.XmiWriter] initialization begin
2018-05-11 16:01:12.909 INFO 45 --- [ main] o.a.u.a.i.PrimitiveAnalysisEngine_impl : AnalysisEngine [de.tudarmstadt.ukp.dkpro.core.io.xmi.XmiWriter] initialization successful
2018-05-11 16:01:12.921 WARN 45 --- [ main] org.apache.uima : Skipping adding "" to URLs because it is not a directory or a JAR
2018-05-11 16:01:13.250 INFO 45 --- [ main] utoConfigurationReportLoggingInitializer :
Error starting ApplicationContext. To display the auto-configuration report re-run your application with 'debug' enabled.
2018-05-11 16:01:13.272 ERROR 45 --- [ main] o.s.boot.SpringApplication : Application startup failed
java.lang.ExceptionInInitializerError: null
at org.apache.uima.cas.admin.CASFactory.createTypeSystem(CASFactory.java:126) ~[uimaj-core-3.0.0.jar!/:3.0.0]
at org.apache.uima.cas.impl.CASImpl.<init>(CASImpl.java:937) ~[uimaj-core-3.0.0.jar!/:3.0.0]
at org.apache.uima.cas.impl.CASImpl.<init>(CASImpl.java:960) ~[uimaj-core-3.0.0.jar!/:3.0.0]
at org.apache.uima.cas.admin.CASFactory.createCAS(CASFactory.java:48) ~[uimaj-core-3.0.0.jar!/:3.0.0]
at org.apache.uima.util.CasCreationUtils.doCreateCas(CasCreationUtils.java:611) ~[uimaj-core-3.0.0.jar!/:3.0.0]
at org.apache.uima.util.CasCreationUtils.createCas(CasCreationUtils.java:292) ~[uimaj-core-3.0.0.jar!/:3.0.0]
at eu.openminted.workflows.uima.executor.UIMAFitRunner.runPipeline(UIMAFitRunner.java:119) ~[classes!/:0.0.1-SNAPSHOT]
at eu.openminted.workflows.uima.executor.UIMAFitRunner.uimaFitRun(UIMAFitRunner.java:106) ~[classes!/:0.0.1-SNAPSHOT]
at eu.openminted.workflows.uima.executor.PipelineCommandLineRunner.run(PipelineCommandLineRunner.java:41) [classes!/:0.0.1-SNAPSHOT]
at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:800) ~[spring-boot-1.4.2.RELEASE.jar!/:1.4.2.RELEASE]
at org.springframework.boot.SpringApplication.callRunners(SpringApplication.java:784) ~[spring-boot-1.4.2.RELEASE.jar!/:1.4.2.RELEASE]
at org.springframework.boot.SpringApplication.afterRefresh(SpringApplication.java:771) ~[spring-boot-1.4.2.RELEASE.jar!/:1.4.2.RELEASE]
at org.springframework.boot.SpringApplication.run(SpringApplication.java:316) ~[spring-boot-1.4.2.RELEASE.jar!/:1.4.2.RELEASE]
at eu.openminted.workflows.uima.executor.PipelineCommandLineRunner.main(PipelineCommandLineRunner.java:29) [classes!/:0.0.1-SNAPSHOT]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_161]
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:1.8.0_161]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_161]
at java.lang.reflect.Method.invoke(Method.java:498) ~[na:1.8.0_161]
at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:48) [omtd-component-uima-0.0.1-SNAPSHOT-exec.jar:0.0.1-SNAPSHOT]
at org.springframework.boot.loader.Launcher.launch(Launcher.java:87) [omtd-component-uima-0.0.1-SNAPSHOT-exec.jar:0.0.1-SNAPSHOT]
at org.springframework.boot.loader.Launcher.launch(Launcher.java:50) [omtd-component-uima-0.0.1-SNAPSHOT-exec.jar:0.0.1-SNAPSHOT]
at org.springframework.boot.loader.PropertiesLauncher.main(PropertiesLauncher.java:521) [omtd-component-uima-0.0.1-SNAPSHOT-exec.jar:0.0.1-SNAPSHOT]
Caused by: org.apache.uima.cas.CASRuntimeException: The JCas cannot be initialized. The following errors occurred:
JCas Class "org.apache.uima.jcas.tcas.DocumentAnnotation", loaded from "jar:file:/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar!/BOOT-INF/lib/uimaj-document-annotation-2.8.1.jar!/org/apache/uima/jcas/tcas/DocumentAnnotation.class", is missing required constructor; likely cause is wrong version (UIMA version 3 or later JCas required).
at org.apache.uima.cas.impl.FSClassRegistry.reportErrors(FSClassRegistry.java:1284) ~[uimaj-core-3.0.0.jar!/:3.0.0]
at org.apache.uima.cas.impl.FSClassRegistry.loadJCasForTSandClassLoader(FSClassRegistry.java:400) ~[uimaj-core-3.0.0.jar!/:3.0.0]
at org.apache.uima.cas.impl.FSClassRegistry.getGeneratorsForClassLoader(FSClassRegistry.java:1320) ~[uimaj-core-3.0.0.jar!/:3.0.0]
at org.apache.uima.cas.impl.TypeSystemImpl.getGeneratorsForClassLoader(TypeSystemImpl.java:2888) ~[uimaj-core-3.0.0.jar!/:3.0.0]
at org.apache.uima.cas.impl.TypeSystemImpl.commit(TypeSystemImpl.java:1435) ~[uimaj-core-3.0.0.jar!/:3.0.0]
at org.apache.uima.cas.impl.TypeSystemImpl.commit(TypeSystemImpl.java:1358) ~[uimaj-core-3.0.0.jar!/:3.0.0]
at org.apache.uima.cas.impl.TypeSystemImpl.<clinit>(TypeSystemImpl.java:2735) ~[uimaj-core-3.0.0.jar!/:3.0.0]
... 22 common frames omitted
2018-05-11 16:01:13.277 INFO 45 --- [ main] s.c.a.AnnotationConfigApplicationContext : Closing org.springframework.context.annotation.AnnotationConfigApplicationContext@6e5e91e4: startup date [Fri May 11 15:59:46 UTC 2018]; root of context hierarchy
2018-05-11 16:01:13.280 INFO 45 --- [ main] o.s.j.e.a.AnnotationMBeanExporter : Unregistering JMX-exposed beans on shutdown
I don't have the option to create a workflow using v2. There is a button in the galaxy interface to switch to version 0.0.2, but this doesn't appear to do anything. Is it disabled? One option would be to delete v0.0.1. Is that the right way to go about this?
I am not sure where exactly are you looking. Could you please about which button are you talking about?
There was a button in the Galaxy interface to switch from v0.0.1 to v0.0.2, although I didn't screenshot it and it has disappeared since I deleted the older version of the component.
It looks from the log (and from a conversation I just had with Mark on Skype) like the old version of the component was still running. We've cleared out the old version of the component and I've set a new workflow running with the correct version.
It's still running, which I assume means the workflow is hanging. I don't have any info to debug with. Any thoughts on what the problem might be @gkirtzou or @galanisd ?
@mattshardlow I've just had a look and I can see the new wrokflow and that it called v0.0.2 correctly. From the galaxy logs it appears that the workflow completed successfully, although strangely I can't see any output having been produced. Does it still show as running in the UI? Does your component write out the XMI files when it's finished?
Here is the log from the latest run of your component. The image has finished without an error, but it seems that no input has been provided. Your component consumes XMI files, right? Have you created a workflow where you used TIKA or PDFReader to generate xmi from pdf files? You can check here for information how you can build a workflow in OMTD : https://openminted.github.io/releases/workflow-editor/1.0.0/workflow
Using default installation dir /opt/omtd-component-executor
ocoord:uk.ac.mmu.tdmlab.journalism:TextMiningForJournalismApplication:0.0.2
19:07:37.070 [main] INFO eu.openminted.workflows.componentdependencies.DependenciesFetcherMain - ...
. ____ _ __ _ _
/\\ / ___'_ __ _ _(_)_ __ __ _ \ \ \ \
( ( )\___ | '_ | '_| | '_ \/ _` | \ \ \ \
\\/ ___)| |_)| | | | | || (_| | ) ) ) )
' |____| .__|_| |_|_| |_\__, | / / / /
=========|_|==============|___/=/_/_/_/
:: Spring Boot :: (v1.4.2.RELEASE)
2018-05-11 19:07:38.834 INFO 16 --- [ main] e.o.w.c.DependenciesFetcherMain : Starting DependenciesFetcherMain v0.0.1-SNAPSHOT on snf-774932 with PID 16 (/opt/omtd-component-executor/omtd-component-dependencies-fetcher/target/omtd-component-dependencies-fetcher-0.0.1-SNAPSHOT-exec.jar started by root in /opt/omtd-component-executor)
2018-05-11 19:07:38.842 INFO 16 --- [ main] e.o.w.c.DependenciesFetcherMain : No active profile set, falling back to default profiles: default
2018-05-11 19:07:39.058 INFO 16 --- [ main] s.c.a.AnnotationConfigApplicationContext : Refreshing org.springframework.context.annotation.AnnotationConfigApplicationContext@22d8cfe0: startup date [Fri May 11 19:07:39 UTC 2018]; root of context hierarchy
2018-05-11 19:07:41.194 INFO 16 --- [ main] o.s.j.e.a.AnnotationMBeanExporter : Registering beans for JMX exposure on startup
2018-05-11 19:07:41.225 INFO 16 --- [ main] e.o.w.c.DependenciesFetcherMain : uk.ac.mmu.tdmlab.journalism:TextMiningForJournalismApplication:0.0.2
classPathListFileName:./TDMClasspathLists/classpath.uk.ac.mmu.tdmlab.journalism_TextMiningForJournalismApplication_0.0.2
uk.ac.mmu.tdmlab.journalism:TextMiningForJournalismApplication:0.0.2
length:70
FIlTER/opt/TDMlocalRepo/org/springframework/spring-core/3.2.16.RELEASE/spring-core-3.2.16.RELEASE.jar
FIlTER/opt/TDMlocalRepo/org/springframework/spring-context/3.2.16.RELEASE/spring-context-3.2.16.RELEASE.jar
FIlTER/opt/TDMlocalRepo/org/springframework/spring-aop/3.2.16.RELEASE/spring-aop-3.2.16.RELEASE.jar
FIlTER/opt/TDMlocalRepo/org/springframework/spring-expression/3.2.16.RELEASE/spring-expression-3.2.16.RELEASE.jar
FIlTER/opt/TDMlocalRepo/org/springframework/spring-beans/3.2.16.RELEASE/spring-beans-3.2.16.RELEASE.jar
2018-05-11 19:08:27.814 INFO 16 --- [ main] e.o.w.c.DependenciesFetcherMain : Started DependenciesFetcherMain in 50.042 seconds (JVM running for 52.07)
2018-05-11 19:08:27.815 INFO 16 --- [ main] e.o.w.c.DependenciesFetcherMain : DONE!
2018-05-11 19:08:27.818 INFO 16 --- [ Thread-1] s.c.a.AnnotationConfigApplicationContext : Closing org.springframework.context.annotation.AnnotationConfigApplicationContext@22d8cfe0: startup date [Fri May 11 19:07:39 UTC 2018]; root of context hierarchy
2018-05-11 19:08:27.823 INFO 16 --- [ Thread-1] o.s.j.e.a.AnnotationMBeanExporter : Unregistering JMX-exposed beans on shutdown
coordinates:uk.ac.mmu.tdmlab.journalism_TextMiningForJournalismApplication_0.0.2
inDir:tmp
otDir:/srv/galaxy/database/jobs_directory/001/1414/working/out/
uimaParams:
19:08:29.149 [main] INFO eu.openminted.workflows.uima.executor.PipelineCommandLineRunner - ...
. ____ _ __ _ _
/\\ / ___'_ __ _ _(_)_ __ __ _ \ \ \ \
( ( )\___ | '_ | '_| | '_ \/ _` | \ \ \ \
\\/ ___)| |_)| | | | | || (_| | ) ) ) )
' |____| .__|_| |_|_| |_\__, | / / / /
=========|_|==============|___/=/_/_/_/
:: Spring Boot :: (v1.4.2.RELEASE)
2018-05-11 19:08:31.304 INFO 45 --- [ main] e.o.w.u.e.PipelineCommandLineRunner : Starting PipelineCommandLineRunner v0.0.1-SNAPSHOT on snf-774932 with PID 45 (/opt/omtd-component-executor/omtd-component-uima/target/omtd-component-uima-0.0.1-SNAPSHOT-exec.jar started by root in /opt/omtd-component-executor/scripts/working)
2018-05-11 19:08:31.311 INFO 45 --- [ main] e.o.w.u.e.PipelineCommandLineRunner : No active profile set, falling back to default profiles: default
2018-05-11 19:08:31.542 INFO 45 --- [ main] s.c.a.AnnotationConfigApplicationContext : Refreshing org.springframework.context.annotation.AnnotationConfigApplicationContext@6e5e91e4: startup date [Fri May 11 19:08:31 UTC 2018]; root of context hierarchy
2018-05-11 19:08:33.923 INFO 45 --- [ main] f.a.AutowiredAnnotationBeanPostProcessor : JSR-330 'javax.inject.Inject' annotation found and supported for autowiring
2018-05-11 19:08:34.617 INFO 45 --- [ main] o.s.j.e.a.AnnotationMBeanExporter : Registering beans for JMX exposure on startup
parsing...
input tmp
output /srv/galaxy/database/jobs_directory/001/1414/working/out/
className uk.ac.mmu.tdmlab.journalism.TextMiningForJournalismApplication
2018-05-11 19:08:34.692 INFO 45 --- [ main] e.o.w.u.e.PipelineCommandLineRunner :
Executing..
========================
className:uk.ac.mmu.tdmlab.journalism.TextMiningForJournalismApplication
inputDir:tmp
outputDir:/srv/galaxy/database/jobs_directory/001/1414/working/out/
**parameters
========================
========================
2018-05-11 19:08:35.521 WARN 45 --- [ main] org.apache.uima : SAXTransformerFactory didn't recognize setting attribute http://javax.xml.XMLConstants/property/accessExternalDTD
2018-05-11 19:08:35.521 WARN 45 --- [ main] org.apache.uima : SAXTransformerFactory didn't recognize setting attribute http://javax.xml.XMLConstants/property/accessExternalStylesheet
2018-05-11 19:08:36.326 INFO 45 --- [ main] d.t.ukp.dkpro.core.io.xmi.XmiReader : Scanning [file:/opt/omtd-component-executor/scripts/working/tmp/]
2018-05-11 19:08:36.329 INFO 45 --- [ main] d.t.ukp.dkpro.core.io.xmi.XmiReader : Found [0] resources to be read
2018-05-11 19:08:38.034 INFO 45 --- [ main] e.stanford.nlp.pipeline.StanfordCoreNLP : Adding annotator tokenize
2018-05-11 19:08:38.078 INFO 45 --- [ main] e.s.nlp.pipeline.TokenizerAnnotator : No tokenizer type provided. Defaulting to PTBTokenizer.
2018-05-11 19:08:38.116 INFO 45 --- [ main] e.stanford.nlp.pipeline.StanfordCoreNLP : Adding annotator ssplit
2018-05-11 19:08:38.146 INFO 45 --- [ main] e.stanford.nlp.pipeline.StanfordCoreNLP : Adding annotator pos
2018-05-11 19:08:39.945 INFO 45 --- [ main] e.s.nlp.tagger.maxent.MaxentTagger : Loading POS tagger from edu/stanford/nlp/models/pos-tagger/english-left3words/english-left3words-distsim.tagger ... done [1.7 sec].
2018-05-11 19:08:39.947 INFO 45 --- [ main] e.stanford.nlp.pipeline.StanfordCoreNLP : Adding annotator lemma
2018-05-11 19:08:39.951 INFO 45 --- [ main] e.stanford.nlp.pipeline.StanfordCoreNLP : Adding annotator ner
2018-05-11 19:08:45.445 INFO 45 --- [ main] e.s.nlp.ie.AbstractSequenceClassifier : Loading classifier from edu/stanford/nlp/models/ner/english.all.3class.distsim.crf.ser.gz ... done [3.4 sec].
2018-05-11 19:08:50.700 INFO 45 --- [ main] e.s.nlp.ie.AbstractSequenceClassifier : Loading classifier from edu/stanford/nlp/models/ner/english.muc.7class.distsim.crf.ser.gz ... done [5.3 sec].
2018-05-11 19:08:51.767 INFO 45 --- [ main] e.s.nlp.ie.AbstractSequenceClassifier : Loading classifier from edu/stanford/nlp/models/ner/english.conll.4class.distsim.crf.ser.gz ... done [1.1 sec].
2018-05-11 19:08:51.780 INFO 45 --- [ main] edu.stanford.nlp.time.JollyDayHolidays : Initializing JollyDayHoliday for SUTime from classpath edu/stanford/nlp/models/sutime/jollyday/Holidays_sutime.xml as sutime.binder.1.
2018-05-11 19:08:52.455 INFO 45 --- [ main] e.s.n.time.TimeExpressionExtractorImpl : Using following SUTime rules: edu/stanford/nlp/models/sutime/defs.sutime.txt,edu/stanford/nlp/models/sutime/english.sutime.txt,edu/stanford/nlp/models/sutime/english.holidays.sutime.txt
2018-05-11 19:09:04.099 INFO 45 --- [ main] e.s.n.pipeline.TokensRegexNERAnnotator : TokensRegexNERAnnotator ner.fine.regexner: Read 580641 unique entries out of 581790 from edu/stanford/nlp/models/kbp/regexner_caseless.tab, 0 TokensRegex patterns.
2018-05-11 19:09:04.151 INFO 45 --- [ main] e.s.n.pipeline.TokensRegexNERAnnotator : TokensRegexNERAnnotator ner.fine.regexner: Read 4857 unique entries out of 4868 from edu/stanford/nlp/models/kbp/regexner_cased.tab, 0 TokensRegex patterns.
2018-05-11 19:09:04.152 INFO 45 --- [ main] e.s.n.pipeline.TokensRegexNERAnnotator : TokensRegexNERAnnotator ner.fine.regexner: Read 585498 unique entries from 2 files
2018-05-11 19:09:32.837 INFO 45 --- [ main] e.o.w.u.e.PipelineCommandLineRunner : Started PipelineCommandLineRunner in 63.143 seconds (JVM running for 64.893)
2018-05-11 19:09:32.838 INFO 45 --- [ main] e.o.w.u.e.PipelineCommandLineRunner : DONE!
2018-05-11 19:09:32.842 INFO 45 --- [ Thread-1] s.c.a.AnnotationConfigApplicationContext : Closing org.springframework.context.annotation.AnnotationConfigApplicationContext@6e5e91e4: startup date [Fri May 11 19:08:31 UTC 2018]; root of context hierarchy
2018-05-11 19:09:32.848 INFO 45 --- [ Thread-1] o.s.j.e.a.AnnotationMBeanExporter : Unregistering JMX-exposed beans on shutdown
See image of my workflow attached. I'm very surprised that it didn't find any input.
My component is a standard UIMA Analysis Engine, so the docker wrapping process should configure it correctly right?
It's not clear to me why the application didn't show that it had finished? It still says that it is running in the 'my operations' section. Is this a known bug?
It's not clear to me why the application didn't show that it had finished? It still says that it is running in the 'my operations' section. Is this a known bug?
Not a known bug but I can guess what's happened. Essentially the workflow service waits for the final job to be finished and then waits for the output to appear. Given there is no output I'm guessing it's still sat waiting. I'll have a look and see if I can find a solution (the problem of spotting a workflow having finished is awkward via the API and hence we were relying in part on outputs being produced).
Thanks Mark.
I've tried to run the application with a few other corpora (a brand new testing corpus by penny, Named Entity Recognition Corpus for Social Science Publications) - but in both cases I got an error, the first one saying that the corpus could not be found and the second one saying that the corpus was empty. I'll keep looking for a solution.
see:
I changed the TIKA pattern from */.pdf to */.* as it says in the documentation at: https://openminted.github.io/releases/workflow-editor/1.0.0/workflow
This is now running - however I have no way to tell whether it is running and has completed with no output.
On a separate note, I don't seem to be able to edit the parameters of components when I return to a workflow. See attached image, with Tika highlighted, but no details on the right hand side.
On a separate note, I don't seem to be able to edit the parameters of components when I return to a workflow. See attached image, with Tika highlighted, but no details on the right hand side.
that's a known bug in Galaxy which we hope will be fixed soon. See issue #10 for all the gory details. The current workaround is to delete and re-add the component you want to edit.
Thanks Mark. Good to know.
I changed the TIKA pattern from */.pdf to /. as it says in the documentation at: https://openminted.github.io/releases/workflow-editor/1.0.0/workflow
This is now running - however I have no way to tell whether it is running and has completed with no output.
Not sure if it's an error in copy-paste or not but to select PDF files you need the pattern **/*.pdf
your example misses the * after the /. In the same way to select all files I would assume you need **/*
or more likely **/*.*
.
I've had a look at the logs and on this occasion it failed when running the omtdImporter suggesting something wrong with the corpus, although I can't see what exactly. What's weird is I would expect it to report the failure in the UI. Does it still show as running?
Yeah, that's an issue with the markdown swallowing some of the characters. It should read
"*\*\/*.*"
I originally had the */.pdf, but changed it following the docs at https://openminted.github.io/releases/workflow-editor/1.0.0/workflow, which say:
Caution! For both converters you need to configure the pattern parameter (displayed in the right column): for the Tika Multi-Format Reader, set the pattern to "*\*\/*.*" and for PDFReader, set the pattern to "*/.pdf".
I'll try a few other patterns to see if that's the issue
Hmm, that Tika pattern looks like a typo. It would mean that the directory had to end with a literal * which makes no sense.
@galanisd, I think you wrote the Tika converter, so should the docs for that read **/*.*
instead of *\*/*.*
Now that you mention it, I think @pennyl67 asked me to check that pattern before converting the adoc into HTML and to do a proper escaping... so I guess it is my fault.
so I guess it is my fault.
I just know that for once it't not my fault :rofl:
Should be fixed by this commit (https://github.com/openminted/openminted.github.io/commit/d127bda28997ad3b5b9b3749c5f84db8da9c7604) and that should be live on the website in a jiffy.
@greenwoodma btw, the Tika converter is probably this one: https://dkpro.github.io/dkpro-core/releases/1.9.1/docs/format-reference.html#format-Tika123
@reckart oh yes, I forgot we were using that, I just remember @galanisd talking about the wrapper for Galaxy.
So I currently have a workflow set up with omtdImporter -> PDFReader and nothing after that. So, as far as I uderstand it, the output from the pdf reader (e.g. the serialised cas xmi) should become the output of the workflow. However, having run that workflow a few times, I am getting the same issue as when I had my component in there (e.g., nothing happening). Any thoughts on this? If the very basic workflow doesn't complete, then It's impossible to debug my own component.
@mattshardlow can you give us the OMTD ID (that long alphanumeric string from the bottom of the landing page) for the PDFReader workflow. There is clearly something odd going on that we need to solve
@greenwoodma it's: 0931732053353301-7bdad7b1-673f-4007-a02b-e476fa01aa1a
My thought is that it might be an issue with the corpus. I have been trying to use the Chebi 2 pdf corpus - test 2 (a24f49a0-ade4-4df7-ab03-8086f93a7235). But this one always seems to fail. I've also tried a few other corpora, but with varying errors (see my post above).
Thanks for having a look at this. I've had a look through the other issues, am I right in thinking nobody else has tried to use the pdf reader as part of their application? If somebody else has, I could take a look at their workflow / try using their corpus with the same input configuration and then plug my component at the end.
I've had a look through the other issues, am I right in thinking nobody else has tried to use the pdf reader as part of their application?
I think almost every workflow that's been built and tested so far uses the PDFReader component. As you say I think the problem is going to be with the corpus. Why not upload a couple of PDF files that are relevant to your use case and create your own test corpus? Just remember when you upload a zip file the documents need to be in the fulltext
folder and not in the root of the zip file.
Why not upload a couple of PDF files that are relevant to your use case and create your own test corpus?
I can give it a go. My use case is fairly flexible (as a journalist might be interested in any scientific domain). So I'll try a few of the other domain specific corpora first.
I've uploaded a couple of pdfs and I'm now running both workflows on this new corpus.
I also tried to use the corpus builder. But the corpora seem to get stuck in the 'under construction' phase. (I tried one from OpenAire and one from CORE). I got 'success' emails for both with link(s): https://test.openminted.eu/landingPage/corpus/b42a3789-933a-4813-b0e9-89bfa75a827c
But the 'my corpora' page shows they are still 'under construction'.
Is this a known issue with the corpus builder? It's fairly important to the app that I wanted to develop using omtd.
Hi Matt,
I am trying to create an app for your workflow (omtdImporter -> PDFReader -> Text Mining For Journalism Application (V2)) so that I can test, however, I am getting a "Error saving application (undefined)" message. It seems that is an AAI issue that causes various problems in the Registry but not sure that it is one of them. @courado @antleb are looking into the problem. When everything is back to normal I will create an app and run some tests to see what is happening.
The workflow in Galaxy executor that corresponds to the ID that you sent ( 0931732053353301-7bdad7b1-673f-4007-a02b-e476fa01aa1a ) is the following.
Galaxy-Workflow-0931732053353301-7bdad7b1-673f-4007-a02b-e476fa01aa1a.ga
-->
{"uuid": "8edafe15-ca38-4c35-972c-f7958f79de1b", "tags": [], "format-version": "0.1", "name": "0931732053353301-7bdad7b1-673f-4007-a02b-e476fa01aa1a", "steps": {"0": {"tool_id": "omtdImporter", "tool_version": "1.0.0", "outputs": [{"type": "input", "name": "output"}], "workflow_outputs": [], "input_connections": {}, "tool_state": "{\"omtdStoreCorpusID\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": null}", "id": 0, "uuid": "414fb090-33d8-460c-8254-8ed2c5bacc5c", "errors": null, "name": "omtdImporter", "post_job_actions": {}, "label": null, "inputs": [], "position": {"top": 174, "left": 200}, "annotation": "", "content_id": "omtdImporter", "type": "tool"}, "1": {"tool_id": "mvn:org.dkpro.core:dkpro-core-io-tika-asl:1.9.1-SNAPSHOT#org.dkpro.core.io.tika.TikaReader", "tool_version": "1.9.1-SNAPSHOT", "outputs": [{"type": "input", "name": "output"}], "workflow_outputs": [], "input_connections": {"component_InputFiles": {"output_name": "output", "id": 0}}, "tool_state": "{\"__page__\": null, \"language\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"patterns\": \"\\\"**/*.pdf\\\"\", \"useDefaultExcludes\": \"\\\"true\\\"\", \"component_InputFiles\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"logFreq\": \"\\\"1\\\"\", \"sourceLocation\": \"\\\"\\\"\", \"includeHidden\": \"\\\"false\\\"\"}", "id": 1, "uuid": "bb2a3c4b-d4dc-4a6a-932f-7b134c98b233", "errors": null, "name": "Tika Multi-Format Reader", "post_job_actions": {}, "label": null, "inputs": [{"name": "component_InputFiles", "description": "runtime parameter for tool Tika Multi-Format Reader"}], "position": {"top": 174, "left": 364.5}, "annotation": "", "content_id": "mvn:org.dkpro.core:dkpro-core-io-tika-asl:1.9.1-SNAPSHOT#org.dkpro.core.io.tika.TikaReader", "type": "tool"}, "2": {"tool_id": "mvn:de.tudarmstadt.ukp.dkpro.core:de.tudarmstadt.ukp.dkpro.core.opennlp-asl:1.9.0#de.tudarmstadt.ukp.dkpro.core.opennlp.OpenNlpSegmenter", "tool_version": "1.9.0", "outputs": [{"type": "input", "name": "output"}], "workflow_outputs": [], "input_connections": {"component_InputFiles": {"output_name": "output", "id": 1}}, "tool_state": "{\"__page__\": null, \"writeToken\": \"\\\"true\\\"\", \"language\": \"\\\"\\\"\", \"segmentationModelLocation\": \"\\\"\\\"\", \"strictZoning\": \"\\\"false\\\"\", \"zoneTypes\": \"\\\"de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Div\\\"\", \"writeSentence\": \"\\\"true\\\"\", \"component_InputFiles\": \"null\", \"modelVariant\": \"\\\"\\\"\", \"tokenizationModelLocation\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"writeForm\": \"\\\"true\\\"\"}", "id": 2, "uuid": "0d2d347a-af26-47d1-a4c9-624a833846ed", "errors": null, "name": "OpenNLP Segmenter", "post_job_actions": {}, "label": null, "inputs": [], "position": {"top": 202, "left": 596}, "annotation": "", "content_id": "mvn:de.tudarmstadt.ukp.dkpro.core:de.tudarmstadt.ukp.dkpro.core.opennlp-asl:1.9.0#de.tudarmstadt.ukp.dkpro.core.opennlp.OpenNlpSegmenter", "type": "tool"}}, "annotation": "", "a_galaxy_workflow": "true"}
I thought that you have created a workflow with omtdImporter and PDFReader not OpenNLPSegmenter. Maybe I missed something.
@galanisd Yes, I originally had the Segmenter in as well, but I then deleted it from the workflow to simplify it. Looking at it now, it appears that change wasn't reflected when I saved the workflow previously. I've tried deleting it again and saving it, but the openNLPSegmenter still reappears. Is this a known issue? There is no message to indicate that the save failed.
Thanks for having a look at the debug. That's strange with the AAAI error - could this be related to the workflow not saving? I've had a look at some other workflows and it appears that other changes haven't been saved either.
I've had a look at the logs and on this occasion it failed when running the omtdImporter suggesting something wrong with the corpus, although I can't see what exactly. What's weird is I would expect it to report the failure in the UI. Does it still show as running?
I have a suspicion (I didn't have time to verify it) that when there is a workflow with multiple steps (eg 4 step) and an error occurs in one of the inner steps (eg the 2nd), then the workflow engine is not able to understand that something went wrong and propagate the error to the registry correctly.
In general when the error occurs in the final step, the UI shows the "An error occured" message. In the other case, I think it is under the impression that it is still running.
I agree @gkirtzou it appears that way but.... I specifically updated the workflow service a couple of weeks ago to handle this case. It now scans each step, not just the last, for the error state and should report the error in all cases. I'm wondering if the workflow service on test hasn't been updated properly. @antleb do you know when the workflow service was last updated on test and if it's using the latest version or not?
@galanisd have you been able to test the component? Is there anything more I can do from my side? I don;t want to run more tests if they might interfere with your results? Let me know.
Currently there are two issues in the Registry and it is not possible to test the app that I created. Waiting fixes for both of them.
However, locally in my laptop I tested your component using the UIMA executor script that is also used in OMTD platform. As input I used two random XMI files. It finished successfully so I expect the same to happen and in the platform when the issues that I mentioned are resolved. The output contains some "journalism" annotations; see below some examples.
<journalism:Where xmi:id="1679" sofa="720" begin="1448" end="1456"/><journalism:Where xmi:id="1683" sofa="720" begin="5666" end="5674"/><journalism:Where xmi:id="1687" sofa="720" begin="5749" end="5757"/><journalism:Where xmi:id="1691" sofa="720" begin="5805" end="5815"/><journalism:Where xmi:id="1695" sofa="720" begin="10467" end="10473"/><journalism:Where xmi:id="1699" sofa="720" begin="11800" end="11806"/><journalism:Where xmi:id="1703" sofa="720" begin="11902" end="11910"/><journalism:Where xmi:id="1707" sofa="720" begin="13692" end="13700"/><journalism:Where xmi:id="1711" sofa="720" begin="13936" end="13942"/><journalism:Where xmi:id="1715" sofa="720" begin="13943" end="13956"/><journalism:Where xmi:id="1719" sofa="720" begin="14351" end="14359"/><journalism:Where xmi:id="1723" sofa="720" begin="14865" end="14873"/><journalism:Where xmi:id="1727" sofa="720" begin="16122" end="16130"/><journalism:Where xmi:id="1731" sofa="720" begin="16159" end="16166"/><journalism:Where xmi:id="1735" sofa="720" begin="16174" end="16184"/><journalism:Where xmi:id="1739" sofa="720" begin="20922" end="20928"/><journalism:Where xmi:id="1743" sofa="720" begin="21345" end="21353"/><journalism:Where xmi:id="1747" sofa="720" begin="21356" end="21364"/><journalism:Where xmi:id="1751" sofa="720" begin="21486" end="21494"/><journalism:Where xmi:id="1755" sofa="720" begin="22256" end="22264"/><journalism:Where xmi:id="1759" sofa="720" begin="22297" end="22303"/><journalism:Where xmi:id="1763" sofa="720" begin="22731" end="22739"/><journalism:Where xmi:id="1767" sofa="720" begin="22743" end="22752"/><journalism:Where xmi:id="1771" sofa="720" begin="23019" end="23027"/><journalism:Where xmi:id="1775" sofa="720" begin="23684" end="23692"/><journalism:Where xmi:id="1779" sofa="720" begin="23772" end="23794"/><journalism:Where xmi:id="1783" sofa="720" begin="23861" end="23868"/><journalism:Where xmi:id="1787" sofa="720" begin="24900" end="24910"/><journalism:Where xmi:id="1791" sofa="720" begin="26625" end="26630"/><journalism:Where xmi:id="1795" sofa="720" begin="26642" end="26650"/><journalism:Where xmi:id="1799" sofa="720" begin="26687" end="26693"/><journalism:Where xmi:id="1803" sofa="720" begin="26713" end="26721"/><journalism:Where xmi:id="1807" sofa="720" begin="26815" end="26824"/><journalism:Where xmi:id="1811" sofa="720" begin="26894" end="26902"/><journalism:Where xmi:id="1815" sofa="720" begin="27019" end="27027"/><journalism:Where xmi:id="1819" sofa="720" begin="27120" end="27125"/><journalism:Where xmi:id="1823" sofa="720" begin="27147" end="27155"/><journalism:Where xmi:id="1827" sofa="720" begin="27311" end="27319"/><journalism:Where xmi:id="1831" sofa="720" begin="27510" end="27518"/><journalism:Where xmi:id="1835" sofa="720" begin="27531" end="27540"/><journalism:Where xmi:id="1839" sofa="720" begin="27780" end="27786"/><journalism:Where xmi:id="1843" sofa="720" begin="27799" end="27816"/>
So I think that your component (uk.ac.mmu.tdmlab.journalism, TextMiningForJournalismApplication, 0.0.2) is compatible with OMTD software.
Thanks Dimitris, that's excellent news. Yes, those look like the right type of output annotations in the xmi. Is there any time scale on the fixes? Will they be ready before the launch?
My understanding is that the annotation viewer is currently not working on the platform? Is this likely to be resolved before the launch? If not, I will need to think of another way to show the results of my workflow.
@galanisd any update on fixing the issues in the registry? I'd like to have a go with the component soon so as I can make the video for the presentation. Do you think I'll be able to do this by the start of next week?
I have just run a test @ test.openminted.eu. Selected a random corpus + the journalism app that I have created.
The workflow is this.
The workflow has finished successfully. I have checked Galaxy. Output attached. component_output.zip
There is still some issue in Registry and the status of the execution remains "RUNNING" for ever. @antleb @courado are working on it. The good news are that your component is compatible with OMTD software (as I expected). @gkirtzou @mattshardlow. The metadata have been checked?
Thanks for testing this Dimitris, that's good to hear. Does that mean that the output won't be available in the registry whilst the issue with the execution not flagging as finished persists.
My understanding is that this occurs because Galaxy isn't picking up any output from the workflow. If I put an extra component on the end that outputs a file, then would this circumvent the problem for now?
I have a simple component which summarises the annotations in the CAS, that I could upload to the platform for this purpose.
see: https://github.com/MMU-TDMLab/UIMA/tree/master/AnnotationSummariser (not much documentation unfortunately)
My understanding is that this occurs because Galaxy isn't picking up any output from the workflow. If I put an extra component on the end that outputs a file, then would this circumvent the problem for now?
No the issue as I said is in Registry.
One solution is to register your component @ services.openminted.eu; no issues there when a workflow finishes as far as I know. Please keep the component private, download the metadata and send them to us. Katerina (@gkirtzou ) will check them and if required she will suggest some modifications. Then you will be able to make the component public create a workflow and run with some corpus. This way you will be able to create the video that you need for the presentation.
@mattshardlow Could you proceed registering your component to services? Please register it as private, and send me the metadata, so I could provide you feedback.
@gkirtzou Have uploaded. See metadata attached. I checked for consistency with the component on test, so it should be ok. I'll put together an application too and test + send you the metadata.
metadata for the test corpus: 10358254-c42e-4850-8918-5c0b16a7cb22.xml.txt
and for the application: ec177220-f05c-4131-987a-f83003b4315e.xml.txt
I've set the application running (configured as Dimitris showed above). Just waiting for it to finish.
It appeared that the workflow was not stopping as in test. I created a new version with the same config, apart from 2 modifications: 1) I clicked the star next to the output which indicates that the output is a workflow output. 2) I set it to notify me when the application finished via email. I just recieved an email, and indeed the application appears to have finished.
However, although I can see the pdfs, they do not appear to have any annotations on top of them. Is it possible to view the output CAS via the Annotation Viewer that Jacob developed?
Currently we have developed an initial set of components for the text mining for journalism project. These are available via github here: https://github.com/MMU-TDMLab/TextMiningForJournalism
Our next step is to mavenise these components and register them with the platform.
We have had several delays with processing the funding and contract between BSC and MMU, which means we are currently behind schedule.
My feeling is that we would benefit more from the hackathon at a later point (2-3 weeks time), when we have sorted the funding and have had chance to attempt to register and run our components / application.