nxmlreader error

Question

nxmlreader error

Closed this issue a year ago · 14 comments

Don't know why messages like the below popped out:
Any solution to fix that?

¡¡¡ NxmlReader error !!!

paper: PMC9911860

error:
java.lang.NullPointerException

stack trace:
java.base/java.io.Reader.(Reader.java:167)
java.base/java.io.InputStreamReader.(InputStreamReader.java:125)
scala.io.BufferedSource.reader(BufferedSource.scala:26)
scala.io.BufferedSource.bufferedReader(BufferedSource.scala:27)
scala.io.BufferedSource.charReader$lzycompute(BufferedSource.scala:37)
scala.io.BufferedSource.charReader(BufferedSource.scala:35)
scala.io.BufferedSource.scala$io$BufferedSource$$decachedReader(BufferedSource.scala:64)
scala.io.BufferedSource$BufferedLineIterator.(BufferedSource.scala:69)
scala.io.BufferedSource.getLines(BufferedSource.scala:88)
org.clulab.reach.grounding.TsvIMKBFactory.loadFromKBDir(TsvIMKBFactory.scala:48)
org.clulab.reach.grounding.TsvIMKBFactory.$anonfun$make$1(TsvIMKBFactory.scala:25)
org.clulab.reach.grounding.TsvIMKBFactory.$anonfun$make$1$adapted(TsvIMKBFactory.scala:24)
scala.Option.foreach(Option.scala:274)
org.clulab.reach.grounding.TsvIMKBFactory.make(TsvIMKBFactory.scala:24)
org.clulab.reach.grounding.ReachIMKBMentionLookups$.buildKb(ReachIMKBMentionLookups.scala:127)
org.clulab.reach.grounding.ReachIMKBMentionLookups$.$anonfun$configuredKBML$1(ReachIMKBMentionLookups.scala:143)
scala.collection.Iterator.foreach(Iterator.scala:941)
scala.collection.Iterator.foreach$(Iterator.scala:941)
scala.collection.AbstractIterator.foreach(Iterator.scala:1429)
scala.collection.IterableLike.foreach(IterableLike.scala:74)
scala.collection.IterableLike.foreach$(IterableLike.scala:73)
scala.collection.AbstractIterable.foreach(Iterable.scala:56)
org.clulab.reach.grounding.ReachIMKBMentionLookups$.configuredKBML$lzycompute(ReachIMKBMentionLookups.scala:141)
org.clulab.reach.grounding.ReachIMKBMentionLookups$.configuredKBML(ReachIMKBMentionLookups.scala:134)
org.clulab.reach.grounding.ReachGrounder.(ReachGrounder.scala:23)
org.clulab.reach.ReachSystem.(ReachSystem.scala:41)
org.clulab.reach.PaperReader$.reachSystem$lzycompute(PaperReader.scala:44)
org.clulab.reach.PaperReader$.reachSystem(PaperReader.scala:41)
org.clulab.reach.PaperReader$.getMentionsFromEntry(PaperReader.scala:141)
org.clulab.reach.ReachCLI.processPaper(ReachCLI.scala:112)
org.clulab.reach.CLI.$anonfun$processPapers$5(CLI.scala:83)
org.clulab.reach.CLI.$anonfun$processPapers$5$adapted(CLI.scala:77)
scala.collection.parallel.AugmentedIterableIterator.map2combiner(RemainsIterator.scala:116)
scala.collection.parallel.AugmentedIterableIterator.map2combiner$(RemainsIterator.scala:113)
scala.collection.parallel.immutable.ParVector$ParVectorIterator.map2combiner(ParVector.scala:66)
scala.collection.parallel.ParIterableLike$Map.leaf(ParIterableLike.scala:1056)
scala.collection.parallel.Task.$anonfun$tryLeaf$1(Tasks.scala:53)
scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:23)
scala.util.control.Breaks$$anon$1.catchBreak(Breaks.scala:67)
scala.collection.parallel.Task.tryLeaf(Tasks.scala:56)
scala.collection.parallel.Task.tryLeaf$(Tasks.scala:50)
scala.collection.parallel.ParIterableLike$Map.tryLeaf(ParIterableLike.scala:1053)
scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask.internal(Tasks.scala:170)
scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask.internal$(Tasks.scala:157)
scala.collection.parallel.AdaptiveWorkStealingForkJoinTasks$WrappedTask.internal(Tasks.scala:440)
scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask.compute(Tasks.scala:150)
scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask.compute$(Tasks.scala:149)
scala.collection.parallel.AdaptiveWorkStealingForkJoinTasks$WrappedTask.compute(Tasks.scala:440)
java.base/java.util.concurrent.RecursiveAction.exec(RecursiveAction.java:189)
java.base/java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:290)
java.base/java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(ForkJoinPool.java:1020)
java.base/java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656)
java.base/java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594)
java.base/java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183)

Answer 1 · 2023-09-06T15:57:15.000Z

The program is trying to read a resource that should be in its own jar file (or one nearby), but the resource is not there. If it were trying to read a simple file, there would be a file not found error, but with a resource a null is returned and it eventually causes a crash. It would be very unusual for a resource to disappear and it might be that the program is not being built correctly. The missing resource is probably in the bioresources subproject among the files in src/main/resources/org/clulab/reach/kb, but they should all be placed into jars during the build process and made available via the classpath or whatever mechanism is used to start up the program. Perhaps it's just the startup that's the problem. How is that being done?

Answer 2 · 2023-09-06T16:13:10.000Z

Do you mean how I install REACH? I just downloaded the reach master branch, installing SBT and Scala. Do I need to put a jar file into a specific folder?

Answer 3 · 2023-09-06T17:10:15.000Z

It can be installed anywhere, but there are lots of ways to run the program and some are sensitive to where the current directory is in relation to the installed files. Can you say how you are running the program (e.g., shell script, sbt, java, IntelliJ), what the current directory is, and where the file version.sbt (just to pick one) is located? I'll try to do the same thing and see if it works.

Answer 4 · 2023-09-06T18:20:27.000Z

I used sbt
here are the directories:
current directory: /Users/luohaomiao/reach
version.sbt: /Users/luohaomiao/reach

btw, I don't know if CMU format is still available since reach is iterating.

Answer 5 · 2023-09-06T21:19:07.000Z

It looks like you are using a Mac, so I'm testing on one, but not finding any problems. Did you use a command like sbt 'runMain org.clulab.reach.RunReachCLI'? That should work. Can you check the java version?

Answer 6 · 2023-09-06T21:43:19.000Z

Yes, I used the command line you mentioned.
here is my java version:
openjdk version "11.0.20.1" 2023-08-24
OpenJDK Runtime Environment Homebrew (build 11.0.20.1+0)
OpenJDK 64-Bit Server VM Homebrew (build 11.0.20.1+0, mixed mode)
also scala version is:
Scala code runner version 2.12.2 -- Copyright 2002-2017, LAMP/EPFL and Lightbend, Inc.
sbt version:
sbt version in this project: 1.9.4
sbt script version: 1.9.4

============================
By the way, will you make cmu format compatible with REACH in the future?

Answer 7 · 2023-09-07T15:37:44.000Z

As far as I can tell, everything is correct with your installation. I'm going to try to find a JDK that matches, in case that is the problem. If that doesn't help, I will make a branch with some better exception handling that can hopefully tell us more about what is going wrong inside the program.

It doesn't seem like this is at all related to CMU format. I don't understand that question.

Answer 8 · 2023-09-07T17:21:56.000Z

It works for me using a JVM fairly close:

openjdk version "11.0.20.1" 2023-08-24 LTS
OpenJDK Runtime Environment (build 11.0.20.1+1-LTS)
OpenJDK 64-Bit Server VM (build 11.0.20.1+1-LTS, mixed mode)

Can you run sbt test on reach and see whether it tests OK before I try anything else?

Answer 9 · 2023-09-07T22:57:45.000Z

(base) MacBook-Pro-81:reach luohaomiao$ sbt test
OpenJDK 64-Bit Server VM warning: Option UseConcMarkSweepGC was deprecated in version 9.0 and will likely be removed in a future release.
OpenJDK 64-Bit Server VM warning: Option UseConcMarkSweepGC was deprecated in version 9.0 and will likely be removed in a future release.
[info] welcome to sbt 1.4.0 (Homebrew Java 11.0.20.1)
[info] loading settings for project reach-build from plugins.sbt ...
[info] loading project definition from /Users/luohaomiao/reach/project
[info] loading settings for project root from build.sbt,version.sbt ...
[info] loading settings for project bioresources from build.sbt ...
[info] loading settings for project processors from build.sbt ...
[info] loading settings for project main from build.sbt ...
[info] loading settings for project causalAssembly from build.sbt ...
[info] loading settings for project context from build.sbt ...
[info] loading settings for project export from build.sbt ...
[info] set current project to reach-exe (in build file:/Users/luohaomiao/reach/
[warn] there are 2 keys that are not used by any other settings/tasks:
[warn]
[warn] * bioresources / releaseProcess
[warn] +- /Users/luohaomiao/reach/bioresources/build.sbt:11
[warn] * root / releaseProcess
[warn] +- /Users/luohaomiao/reach/build.sbt:125
[warn]
[warn] note: a setting might still be used by a command; to exclude a key from this lintUnused check
[warn] either append it to Global / excludeLintKeys or call .withRank(KeyRanks.Invisible) on the key
[warn] Getting the hostname MacBook-Pro-81.local was slow (5002.640167 ms). This is likely because the computer's hostname is not set. You can set the hostname with the command: scutil --set HostName $(scutil --get LocalHostName).
[info] compiling 6 Scala sources to /Users/luohaomiao/reach/processors/target/scala-2.12/test-classes ...
[warn] /Users/luohaomiao/reach/processors/src/test/scala/org/clulab/processors/TestCompactLexiconNER.scala:182:23: method findFiles in object Files is deprecated (since 8.3.3): This call to findFiles is deprecated. Please use org.clulab.utils.FileUtils.findFiles() instead.
[warn] val files = Files.findFiles("kbs", "tsv")
[warn] ^
[warn] one warning found
17:33:45.023 [pool-5-thread-7-ScalaTest-running-TestBioNLPTokenizer] DEBUG org.clulab.dynet.Utils - Initializing DyNet...6s
[dynet] Checking /Users/luohaomiao/reach for libdynet_swig.jnilib...
[dynet] Checking /Users/luohaomiao for libdynet_swig.jnilib...
[dynet] Extracting resource intel-libdynet_swig.jnilib to /var/folders/my/28hyn3s92ld0r5f3gpk4kbj80000gn/T/libdynet_swig-18442456197711360756.jnilib...
[dynet] Loading DyNet from /var/folders/my/28hyn3s92ld0r5f3gpk4kbj80000gn/T/libdynet_swig-18442456197711360756.jnilib...19s
[dynet] random seed: 2522620396
[dynet] allocating memory: 512MB
[dynet] memory allocation done.
17:33:48.586 [pool-5-thread-7-ScalaTest-running-TestBioNLPTokenizer] DEBUG org.clulab.dynet.Utils - DyNet initialization complete.
17:33:51.310 [pool-5-thread-7-ScalaTest-running-TestBioNLPTokenizer] INFO edu.stanford.nlp.pipeline.StanfordCoreNLP - Adding annotator pos
17:33:54.153 [pool-5-thread-7-ScalaTest-running-TestBioNLPTokenizer] INFO edu.stanford.nlp.tagger.maxent.MaxentTagger - Loading POS tagger from edu/stanford/nlp/models/pos-tagger/english-left3words/english-left3words-distsim.tagger ... done [2.5 sec].
17:33:54.576 [pool-5-thread-7-ScalaTest-running-TestBioNLPTokenizer] INFO edu.stanford.nlp.pipeline.StanfordCoreNLP - Adding annotator lemma
17:33:54.918 [pool-5-thread-7-ScalaTest-running-TestBioNLPTokenizer] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - macro=true
17:33:54.919 [pool-5-thread-7-ScalaTest-running-TestBioNLPTokenizer] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - featureFactory=org.clulab.processors.bionlp.ner.BioNERFactory
17:33:55.146 [pool-5-thread-7-ScalaTest-running-TestBioNLPTokenizer] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - macro=true
17:33:55.147 [pool-5-thread-7-ScalaTest-running-TestBioNLPTokenizer] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - featureFactory=org.clulab.processors.bionlp.ner.BioNERFactory
17:33:55.158 [pool-5-thread-7-ScalaTest-running-TestBioNLPTokenizer] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - macro=true
17:33:55.159 [pool-5-thread-7-ScalaTest-running-TestBioNLPTokenizer] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - featureFactory=org.clulab.processors.bionlp.ner.BioNERFactory
17:33:55.172 [pool-5-thread-7-ScalaTest-running-TestBioNLPTokenizer] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - macro=true
17:33:55.172 [pool-5-thread-7-ScalaTest-running-TestBioNLPTokenizer] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - featureFactory=org.clulab.processors.bionlp.ner.BioNERFactory
17:33:55.224 [pool-5-thread-7-ScalaTest-running-TestBioNLPTokenizer] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - macro=true
17:33:55.224 [pool-5-thread-7-ScalaTest-running-TestBioNLPTokenizer] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - featureFactory=org.clulab.processors.bionlp.ner.BioNERFactory
17:33:55.252 [pool-5-thread-7-ScalaTest-running-TestBioNLPTokenizer] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - macro=true
17:33:55.252 [pool-5-thread-7-ScalaTest-running-TestBioNLPTokenizer] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - featureFactory=org.clulab.processors.bionlp.ner.BioNERFactory
17:33:55.272 [pool-5-thread-7-ScalaTest-running-TestBioNLPTokenizer] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - macro=true
17:33:55.273 [pool-5-thread-7-ScalaTest-running-TestBioNLPTokenizer] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - featureFactory=org.clulab.processors.bionlp.ner.BioNERFactory
17:33:55.283 [pool-5-thread-7-ScalaTest-running-TestBioNLPTokenizer] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - macro=true
17:33:55.284 [pool-5-thread-7-ScalaTest-running-TestBioNLPTokenizer] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - featureFactory=org.clulab.processors.bionlp.ner.BioNERFactory
[info] TestBioNLPTokenizer:
[info] BioNLPProcessor
[info] - should NOT tokenize slashes if they are part of measurement units *** FAILED *** (10 seconds, 743 milliseconds)
[info] java.io.IOException: Unable to open "org/clulab/processors/bionlp/ner/bioner.dat" as class path, filename or URL
[info] at edu.stanford.nlp.io.IOUtils.getInputStreamFromURLOrClasspathOrFileSystem(IOUtils.java:480)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1503)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1495)
[info] at org.clulab.processors.bionlp.ner.CRFNER$.load(CRFNER.scala:164)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer$lzycompute(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3(HybridNER.scala:62)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3$adapted(HybridNER.scala:47)
[info] at scala.collection.TraversableLike$WithFilter.$anonfun$foreach$1(TraversableLike.scala:792)
[info] at scala.collection.Iterator.foreach(Iterator.scala:941)
[info] ...
[info] - should tokenize ERK/MAPK-signaling into "ERK and MAPK signaling" *** FAILED *** (26 milliseconds)
[info] java.io.IOException: Unable to open "org/clulab/processors/bionlp/ner/bioner.dat" as class path, filename or URL
[info] at edu.stanford.nlp.io.IOUtils.getInputStreamFromURLOrClasspathOrFileSystem(IOUtils.java:480)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1503)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1495)
[info] at org.clulab.processors.bionlp.ner.CRFNER$.load(CRFNER.scala:164)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer$lzycompute(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3(HybridNER.scala:62)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3$adapted(HybridNER.scala:47)
[info] at scala.collection.TraversableLike$WithFilter.$anonfun$foreach$1(TraversableLike.scala:792)
[info] at scala.collection.Iterator.foreach(Iterator.scala:941)
[info] ...
[info] - should reattach / and tokenize it properly *** FAILED *** (9 milliseconds)
[info] java.io.IOException: Unable to open "org/clulab/processors/bionlp/ner/bioner.dat" as class path, filename or URL
[info] at edu.stanford.nlp.io.IOUtils.getInputStreamFromURLOrClasspathOrFileSystem(IOUtils.java:480)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1503)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1495)
[info] at org.clulab.processors.bionlp.ner.CRFNER$.load(CRFNER.scala:164)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer$lzycompute(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3(HybridNER.scala:62)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3$adapted(HybridNER.scala:47)
[info] at scala.collection.TraversableLike$WithFilter.$anonfun$foreach$1(TraversableLike.scala:792)
[info] at scala.collection.Iterator.foreach(Iterator.scala:941)
[info] ...
[info] - should NOT tokenize names of protein families around slash *** FAILED *** (8 milliseconds)
[info] java.io.IOException: Unable to open "org/clulab/processors/bionlp/ner/bioner.dat" as class path, filename or URL
[info] at edu.stanford.nlp.io.IOUtils.getInputStreamFromURLOrClasspathOrFileSystem(IOUtils.java:480)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1503)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1495)
[info] at org.clulab.processors.bionlp.ner.CRFNER$.load(CRFNER.scala:164)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer$lzycompute(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3(HybridNER.scala:62)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3$adapted(HybridNER.scala:47)
[info] at scala.collection.TraversableLike$WithFilter.$anonfun$foreach$1(TraversableLike.scala:792)
[info] at scala.collection.Iterator.foreach(Iterator.scala:941)
[info] ...
[info] - should tokenize complex names around slash *** FAILED *** (47 milliseconds)
[info] java.io.IOException: Unable to open "org/clulab/processors/bionlp/ner/bioner.dat" as class path, filename or URL
[info] at edu.stanford.nlp.io.IOUtils.getInputStreamFromURLOrClasspathOrFileSystem(IOUtils.java:480)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1503)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1495)
[info] at org.clulab.processors.bionlp.ner.CRFNER$.load(CRFNER.scala:164)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer$lzycompute(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3(HybridNER.scala:62)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3$adapted(HybridNER.scala:47)
[info] at scala.collection.TraversableLike$WithFilter.$anonfun$foreach$1(TraversableLike.scala:792)
[info] at scala.collection.Iterator.foreach(Iterator.scala:941)
[info] ...
[info] - should tokenize complex names around dash *** FAILED *** (20 milliseconds)
[info] java.io.IOException: Unable to open "org/clulab/processors/bionlp/ner/bioner.dat" as class path, filename or URL
[info] at edu.stanford.nlp.io.IOUtils.getInputStreamFromURLOrClasspathOrFileSystem(IOUtils.java:480)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1503)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1495)
[info] at org.clulab.processors.bionlp.ner.CRFNER$.load(CRFNER.scala:164)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer$lzycompute(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3(HybridNER.scala:62)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3$adapted(HybridNER.scala:47)
[info] at scala.collection.TraversableLike$WithFilter.$anonfun$foreach$1(TraversableLike.scala:792)
[info] at scala.collection.Iterator.foreach(Iterator.scala:941)
[info] ...
[info] - should tokenize n-ary complexes correctly around dash or slash *** FAILED *** (18 milliseconds)
[info] java.io.IOException: Unable to open "org/clulab/processors/bionlp/ner/bioner.dat" as class path, filename or URL
[info] at edu.stanford.nlp.io.IOUtils.getInputStreamFromURLOrClasspathOrFileSystem(IOUtils.java:480)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1503)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1495)
[info] at org.clulab.processors.bionlp.ner.CRFNER$.load(CRFNER.scala:164)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer$lzycompute(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3(HybridNER.scala:62)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3$adapted(HybridNER.scala:47)
[info] at scala.collection.TraversableLike$WithFilter.$anonfun$foreach$1(TraversableLike.scala:792)
[info] at scala.collection.Iterator.foreach(Iterator.scala:941)
[info] ...
[info] - should not tokenize up, down, re *** FAILED *** (6 milliseconds)
[info] java.io.IOException: Unable to open "org/clulab/processors/bionlp/ner/bioner.dat" as class path, filename or URL
[info] at edu.stanford.nlp.io.IOUtils.getInputStreamFromURLOrClasspathOrFileSystem(IOUtils.java:480)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1503)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1495)
[info] at org.clulab.processors.bionlp.ner.CRFNER$.load(CRFNER.scala:164)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer$lzycompute(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3(HybridNER.scala:62)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3$adapted(HybridNER.scala:47)
[info] at scala.collection.TraversableLike$WithFilter.$anonfun$foreach$1(TraversableLike.scala:792)
[info] at scala.collection.Iterator.foreach(Iterator.scala:941)
[info] ...
17:33:56.595 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor2] INFO edu.stanford.nlp.pipeline.StanfordCoreNLP - Adding annotator pos
17:33:56.893 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor2] INFO edu.stanford.nlp.pipeline.StanfordCoreNLP - Adding annotator lemma
17:33:56.898 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor2] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - macro=true
17:33:56.898 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor2] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - featureFactory=org.clulab.processors.bionlp.ner.BioNERFactory
17:33:58.676 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor2] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - macro=true
17:33:58.677 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor2] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - featureFactory=org.clulab.processors.bionlp.ner.BioNERFactory
[info] TestBioNLPProcessor2:
[info] BioNLPProcessor
[info] - should parse abstract text *** FAILED *** (388 milliseconds)
[info] java.io.IOException: Unable to open "org/clulab/processors/bionlp/ner/bioner.dat" as class path, filename or URL
[info] at edu.stanford.nlp.io.IOUtils.getInputStreamFromURLOrClasspathOrFileSystem(IOUtils.java:480)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1503)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1495)
[info] at org.clulab.processors.bionlp.ner.CRFNER$.load(CRFNER.scala:164)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer$lzycompute(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3(HybridNER.scala:62)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3$adapted(HybridNER.scala:47)
[info] at scala.collection.TraversableLike$WithFilter.$anonfun$foreach$1(TraversableLike.scala:792)
[info] at scala.collection.Iterator.foreach(Iterator.scala:941)
[info] ...
[info] - should parse body text *** FAILED *** (1 second, 775 milliseconds)
[info] java.io.IOException: Unable to open "org/clulab/processors/bionlp/ner/bioner.dat" as class path, filename or URL
[info] at edu.stanford.nlp.io.IOUtils.getInputStreamFromURLOrClasspathOrFileSystem(IOUtils.java:480)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1503)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1495)
[info] at org.clulab.processors.bionlp.ner.CRFNER$.load(CRFNER.scala:164)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer$lzycompute(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3(HybridNER.scala:62)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3$adapted(HybridNER.scala:47)
[info] at scala.collection.TraversableLike$WithFilter.$anonfun$foreach$1(TraversableLike.scala:792)
[info] at scala.collection.Iterator.foreach(Iterator.scala:941)
[info] ...
17:33:59.181 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO edu.stanford.nlp.pipeline.StanfordCoreNLP - Adding annotator pos
17:33:59.204 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO edu.stanford.nlp.pipeline.StanfordCoreNLP - Adding annotator lemma
17:33:59.205 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] DEBUG org.clulab.processors.bionlp.ner.KBLoader - Loading LexiconNER from knowledge bases...
17:33:59.559 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.sequences.LexiconNER - Beginning to load the KBs for the rule-based NER...
17:33:59.795 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.sequences.LexiconNER - Loaded OVERRIDE matchers for all labels. The number of entries added to the first layer was 750.
17:33:59.805 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Loading BioProcess...
17:34:04.051 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Done. Read 68227 lines from bio_process.tsv
17:34:04.051 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.sequences.LexiconNER - Loaded matcher for label BioProcess. The number of entries added to the first layer was 5556.
17:34:04.051 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Loading Cellular_component...
17:34:04.207 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Done. Read 2 lines from biopax-cellular_component.tsv
17:34:04.207 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Loading Cellular_component...
17:34:04.560 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Done. Read 3386 lines from GO-subcellular-locations.tsv
17:34:04.560 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Loading Cellular_component...
17:34:04.745 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Done. Read 956 lines from uniprot-subcellular-locations.tsv
17:34:04.745 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.sequences.LexiconNER - Loaded matcher for label Cellular_component. The number of entries added to the first layer was 470.
17:34:04.745 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Loading Gene_or_gene_product...
17:34:04.848 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] DEBUG org.clulab.processors.bionlp.ner.KBLoader - Loading LexiconNER from knowledge bases...
17:34:04.853 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.sequences.LexiconNER - Beginning to load the KBs for the rule-based NER...
17:34:04.859 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.sequences.LexiconNER - Loaded OVERRIDE matchers for all labels. The number of entries added to the first layer was 750.
17:34:04.859 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Loading BioProcess...
17:34:07.851 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Done. Read 68227 lines from bio_process.tsv
17:34:07.851 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.sequences.LexiconNER - Loaded matcher for label BioProcess. The number of entries added to the first layer was 5556.
17:34:07.851 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Loading Cellular_component...
17:34:07.977 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Done. Read 2 lines from biopax-cellular_component.tsv
17:34:07.977 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Loading Cellular_component...
17:34:08.223 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Done. Read 3386 lines from GO-subcellular-locations.tsv
17:34:08.223 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Loading Cellular_component...
17:34:08.375 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Done. Read 956 lines from uniprot-subcellular-locations.tsv
17:34:08.375 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.sequences.LexiconNER - Loaded matcher for label Cellular_component. The number of entries added to the first layer was 470.
17:34:08.376 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Loading Gene_or_gene_product...
17:34:08.613 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] DEBUG org.clulab.processors.bionlp.ner.KBLoader - Loading LexiconNER from knowledge bases...
17:34:08.646 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.sequences.LexiconNER - Beginning to load the KBs for the rule-based NER...
17:34:08.655 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.sequences.LexiconNER - Loaded OVERRIDE matchers for all labels. The number of entries added to the first layer was 750.
17:34:08.655 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Loading BioProcess...
17:34:11.785 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Done. Read 68227 lines from bio_process.tsv
17:34:11.786 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.sequences.LexiconNER - Loaded matcher for label BioProcess. The number of entries added to the first layer was 5556.
17:34:11.786 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Loading Cellular_component...
17:34:11.893 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Done. Read 2 lines from biopax-cellular_component.tsv
17:34:11.894 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Loading Cellular_component...
17:34:12.080 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Done. Read 3386 lines from GO-subcellular-locations.tsv
17:34:12.080 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Loading Cellular_component...
17:34:12.194 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Done. Read 956 lines from uniprot-subcellular-locations.tsv
17:34:12.195 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.sequences.LexiconNER - Loaded matcher for label Cellular_component. The number of entries added to the first layer was 470.
17:34:12.195 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Loading Gene_or_gene_product...
17:34:12.338 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] DEBUG org.clulab.processors.bionlp.ner.KBLoader - Loading LexiconNER from knowledge bases...
17:34:12.342 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.sequences.LexiconNER - Beginning to load the KBs for the rule-based NER...
17:34:12.344 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.sequences.LexiconNER - Loaded OVERRIDE matchers for all labels. The number of entries added to the first layer was 750.
17:34:12.345 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Loading BioProcess...
17:34:15.700 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Done. Read 68227 lines from bio_process.tsv
17:34:15.700 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.sequences.LexiconNER - Loaded matcher for label BioProcess. The number of entries added to the first layer was 5556.
17:34:15.701 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Loading Cellular_component...
17:34:15.830 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Done. Read 2 lines from biopax-cellular_component.tsv
17:34:15.830 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Loading Cellular_component...
17:34:16.148 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Done. Read 3386 lines from GO-subcellular-locations.tsv
17:34:16.148 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Loading Cellular_component...
17:34:16.332 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Done. Read 956 lines from uniprot-subcellular-locations.tsv
17:34:16.332 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.sequences.LexiconNER - Loaded matcher for label Cellular_component. The number of entries added to the first layer was 470.
17:34:16.332 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Loading Gene_or_gene_product...
17:34:16.538 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] DEBUG org.clulab.processors.bionlp.ner.KBLoader - Loading LexiconNER from knowledge bases...
17:34:16.541 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.sequences.LexiconNER - Beginning to load the KBs for the rule-based NER...
17:34:16.546 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.sequences.LexiconNER - Loaded OVERRIDE matchers for all labels. The number of entries added to the first layer was 750.
17:34:16.547 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Loading BioProcess...
17:34:37.639 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Done. Read 68227 lines from bio_process.tsv
17:34:37.656 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.sequences.LexiconNER - Loaded matcher for label BioProcess. The number of entries added to the first layer was 5556.
17:34:37.657 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Loading Cellular_component...
17:34:38.191 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Done. Read 2 lines from biopax-cellular_component.tsv
17:34:38.192 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Loading Cellular_component...
17:34:38.572 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Done. Read 3386 lines from GO-subcellular-locations.tsv
17:34:38.632 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Loading Cellular_component...
17:34:39.386 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Done. Read 956 lines from uniprot-subcellular-locations.tsv
17:34:39.386 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.sequences.LexiconNER - Loaded matcher for label Cellular_component. The number of entries added to the first layer was 470.
17:34:39.386 [pool-5-thread-7-ScalaTest-running-TestFastBioNLPProcessor] INFO org.clulab.processors.bionlp.BioNLPProcessor - Loading Gene_or_gene_product...
[info] TestFastBioNLPProcessor:
[info] FastBioNLPProcessor
[info] - should recognize correct NEs in text 0 *** FAILED *** (5 seconds, 666 milliseconds)
[info] java.lang.RuntimeException: ERROR: cannot find resource org/clulab/reach/kb/uniprot-proteins-0_F.tsv.gz in classpath!
[info] at org.clulab.utils.Files$.loadStreamFromClasspath(Files.scala:123)
[info] at org.clulab.processors.bionlp.ner.ReachSingleStandardKbSource.$anonfun$withTokens$6(ReachStandardKbSource.scala:52)
[info] at scala.util.Failure.getOrElse(Try.scala:222)
[info] at org.clulab.processors.bionlp.ner.ReachSingleStandardKbSource.$anonfun$withTokens$4(ReachStandardKbSource.scala:52)
[info] at scala.util.Failure.getOrElse(Try.scala:222)
[info] at org.clulab.processors.bionlp.ner.ReachSingleStandardKbSource.$anonfun$withTokens$2(ReachStandardKbSource.scala:51)
[info] at scala.util.Failure.getOrElse(Try.scala:222)
[info] at org.clulab.processors.bionlp.ner.ReachSingleStandardKbSource.withTokens(ReachStandardKbSource.scala:50)
[info] at org.clulab.processors.bionlp.ner.ReachMultiStandardKbSource.$anonfun$withTokens$8(ReachStandardKbSource.scala:78)
[info] at org.clulab.processors.bionlp.ner.ReachMultiStandardKbSource.$anonfun$withTokens$8$adapted(ReachStandardKbSource.scala:77)
[info] ...
[info] FastBioNLPProcessor
[info] - should recognize correct NEs in text 1 *** FAILED *** (3 seconds, 734 milliseconds)
[info] java.lang.RuntimeException: ERROR: cannot find resource org/clulab/reach/kb/uniprot-proteins-0_F.tsv.gz in classpath!
[info] at org.clulab.utils.Files$.loadStreamFromClasspath(Files.scala:123)
[info] at org.clulab.processors.bionlp.ner.ReachSingleStandardKbSource.$anonfun$withTokens$6(ReachStandardKbSource.scala:52)
[info] at scala.util.Failure.getOrElse(Try.scala:222)
[info] at org.clulab.processors.bionlp.ner.ReachSingleStandardKbSource.$anonfun$withTokens$4(ReachStandardKbSource.scala:52)
[info] at scala.util.Failure.getOrElse(Try.scala:222)
[info] at org.clulab.processors.bionlp.ner.ReachSingleStandardKbSource.$anonfun$withTokens$2(ReachStandardKbSource.scala:51)
[info] at scala.util.Failure.getOrElse(Try.scala:222)
[info] at org.clulab.processors.bionlp.ner.ReachSingleStandardKbSource.withTokens(ReachStandardKbSource.scala:50)
[info] at org.clulab.processors.bionlp.ner.ReachMultiStandardKbSource.$anonfun$withTokens$8(ReachStandardKbSource.scala:78)
[info] at org.clulab.processors.bionlp.ner.ReachMultiStandardKbSource.$anonfun$withTokens$8$adapted(ReachStandardKbSource.scala:77)
[info] ...
[info] - should recognize correct NEs in text 2 *** FAILED *** (3 seconds, 759 milliseconds)
[info] java.lang.RuntimeException: ERROR: cannot find resource org/clulab/reach/kb/uniprot-proteins-0_F.tsv.gz in classpath!
[info] at org.clulab.utils.Files$.loadStreamFromClasspath(Files.scala:123)
[info] at org.clulab.processors.bionlp.ner.ReachSingleStandardKbSource.$anonfun$withTokens$6(ReachStandardKbSource.scala:52)
[info] at scala.util.Failure.getOrElse(Try.scala:222)
[info] at org.clulab.processors.bionlp.ner.ReachSingleStandardKbSource.$anonfun$withTokens$4(ReachStandardKbSource.scala:52)
[info] at scala.util.Failure.getOrElse(Try.scala:222)
[info] at org.clulab.processors.bionlp.ner.ReachSingleStandardKbSource.$anonfun$withTokens$2(ReachStandardKbSource.scala:51)
[info] at scala.util.Failure.getOrElse(Try.scala:222)
[info] at org.clulab.processors.bionlp.ner.ReachSingleStandardKbSource.withTokens(ReachStandardKbSource.scala:50)
[info] at org.clulab.processors.bionlp.ner.ReachMultiStandardKbSource.$anonfun$withTokens$8(ReachStandardKbSource.scala:78)
[info] at org.clulab.processors.bionlp.ner.ReachMultiStandardKbSource.$anonfun$withTokens$8$adapted(ReachStandardKbSource.scala:77)
[info] ...
[info] - should recognize correct species in text 3 *** FAILED *** (4 seconds, 200 milliseconds)
[info] java.lang.RuntimeException: ERROR: cannot find resource org/clulab/reach/kb/uniprot-proteins-0_F.tsv.gz in classpath!
[info] at org.clulab.utils.Files$.loadStreamFromClasspath(Files.scala:123)
[info] at org.clulab.processors.bionlp.ner.ReachSingleStandardKbSource.$anonfun$withTokens$6(ReachStandardKbSource.scala:52)
[info] at scala.util.Failure.getOrElse(Try.scala:222)
[info] at org.clulab.processors.bionlp.ner.ReachSingleStandardKbSource.$anonfun$withTokens$4(ReachStandardKbSource.scala:52)
[info] at scala.util.Failure.getOrElse(Try.scala:222)
[info] at org.clulab.processors.bionlp.ner.ReachSingleStandardKbSource.$anonfun$withTokens$2(ReachStandardKbSource.scala:51)
[info] at scala.util.Failure.getOrElse(Try.scala:222)
[info] at org.clulab.processors.bionlp.ner.ReachSingleStandardKbSource.withTokens(ReachStandardKbSource.scala:50)
[info] at org.clulab.processors.bionlp.ner.ReachMultiStandardKbSource.$anonfun$withTokens$8(ReachStandardKbSource.scala:78)
[info] at org.clulab.processors.bionlp.ner.ReachMultiStandardKbSource.$anonfun$withTokens$8$adapted(ReachStandardKbSource.scala:77)
[info] ...
[info] - should parse dependencies correctly *** FAILED *** (23 seconds, 609 milliseconds)
[info] java.lang.RuntimeException: ERROR: cannot find resource org/clulab/reach/kb/uniprot-proteins-0_F.tsv.gz in classpath!
[info] at org.clulab.utils.Files$.loadStreamFromClasspath(Files.scala:123)
[info] at org.clulab.processors.bionlp.ner.ReachSingleStandardKbSource.$anonfun$withTokens$6(ReachStandardKbSource.scala:52)
[info] at scala.util.Failure.getOrElse(Try.scala:222)
[info] at org.clulab.processors.bionlp.ner.ReachSingleStandardKbSource.$anonfun$withTokens$4(ReachStandardKbSource.scala:52)
[info] at scala.util.Failure.getOrElse(Try.scala:222)
[info] at org.clulab.processors.bionlp.ner.ReachSingleStandardKbSource.$anonfun$withTokens$2(ReachStandardKbSource.scala:51)
[info] at scala.util.Failure.getOrElse(Try.scala:222)
[info] at org.clulab.processors.bionlp.ner.ReachSingleStandardKbSource.withTokens(ReachStandardKbSource.scala:50)
[info] at org.clulab.processors.bionlp.ner.ReachMultiStandardKbSource.$anonfun$withTokens$8(ReachStandardKbSource.scala:78)
[info] at org.clulab.processors.bionlp.ner.ReachMultiStandardKbSource.$anonfun$withTokens$8$adapted(ReachStandardKbSource.scala:77)
[info] ...
17:34:41.924 [pool-5-thread-7] DEBUG org.clulab.processors.bionlp.ner.KBLoader - Loading LexiconNER from knowledge bases...
17:34:42.002 [pool-5-thread-7] INFO org.clulab.sequences.LexiconNER - Beginning to load the KBs for the rule-based NER...4s
17:34:42.017 [pool-5-thread-7] INFO org.clulab.sequences.LexiconNER - Loaded OVERRIDE matchers for all labels. The number of entries added to the first layer was 750.
17:34:42.017 [pool-5-thread-7] INFO org.clulab.processors.bionlp.BioNLPProcessor - Loading BioProcess... / executeTests 74s
17:35:04.667 [pool-5-thread-7] INFO org.clulab.processors.bionlp.BioNLPProcessor - Done. Read 68227 lines from bio_process.tsv
17:35:04.672 [pool-5-thread-7] INFO org.clulab.sequences.LexiconNER - Loaded matcher for label BioProcess. The number of entries added to the first layer was 5556.
17:35:04.673 [pool-5-thread-7] INFO org.clulab.processors.bionlp.BioNLPProcessor - Loading Cellular_component...teTests 96s
17:35:05.970 [pool-5-thread-7] INFO org.clulab.processors.bionlp.BioNLPProcessor - Done. Read 2 lines from biopax-cellular_component.tsv
17:35:05.971 [pool-5-thread-7] INFO org.clulab.processors.bionlp.BioNLPProcessor - Loading Cellular_component...teTests 97s
17:35:06.685 [pool-5-thread-7] INFO org.clulab.processors.bionlp.BioNLPProcessor - Done. Read 3386 lines from GO-subcellular-locations.tsv
17:35:06.715 [pool-5-thread-7] INFO org.clulab.processors.bionlp.BioNLPProcessor - Loading Cellular_component...teTests 98s
17:35:07.397 [pool-5-thread-7] INFO org.clulab.processors.bionlp.BioNLPProcessor - Done. Read 956 lines from uniprot-subcellular-locations.tsv
17:35:07.397 [pool-5-thread-7] INFO org.clulab.sequences.LexiconNER - Loaded matcher for label Cellular_component. The number of entries added to the first layer was 470.
17:35:07.397 [pool-5-thread-7] INFO org.clulab.processors.bionlp.BioNLPProcessor - Loading Gene_or_gene_product...Tests 99s
[info] TestCompactLexiconNER:
[info] org.clulab.processors.TestCompactLexiconNER *** ABORTED *** (12 milliseconds)
[info] java.lang.RuntimeException: ERROR: cannot find resource org/clulab/reach/kb/uniprot-proteins-0_F.tsv.gz in classpath!
[info] at org.clulab.utils.Files$.loadStreamFromClasspath(Files.scala:123)
[info] at org.clulab.processors.bionlp.ner.ReachSingleStandardKbSource.$anonfun$withTokens$6(ReachStandardKbSource.scala:52)
[info] at scala.util.Failure.getOrElse(Try.scala:222)
[info] at org.clulab.processors.bionlp.ner.ReachSingleStandardKbSource.$anonfun$withTokens$4(ReachStandardKbSource.scala:52)
[info] at scala.util.Failure.getOrElse(Try.scala:222)
[info] at org.clulab.processors.bionlp.ner.ReachSingleStandardKbSource.$anonfun$withTokens$2(ReachStandardKbSource.scala:51)
[info] at scala.util.Failure.getOrElse(Try.scala:222)
[info] at org.clulab.processors.bionlp.ner.ReachSingleStandardKbSource.withTokens(ReachStandardKbSource.scala:50)
[info] at org.clulab.processors.bionlp.ner.ReachMultiStandardKbSource.$anonfun$withTokens$8(ReachStandardKbSource.scala:78)
[info] at org.clulab.processors.bionlp.ner.ReachMultiStandardKbSource.$anonfun$withTokens$8$adapted(ReachStandardKbSource.scala:77)
[info] ...
17:35:08.242 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.pipeline.StanfordCoreNLP - Adding annotator pos
17:35:08.340 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.pipeline.StanfordCoreNLP - Adding annotator lemma
17:35:08.343 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - macro=true
17:35:08.346 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - featureFactory=org.clulab.processors.bionlp.ner.BioNERFactory
17:35:08.365 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - macro=true
17:35:08.368 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - featureFactory=org.clulab.processors.bionlp.ner.BioNERFactory
17:35:08.729 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - macro=true
17:35:08.730 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - featureFactory=org.clulab.processors.bionlp.ner.BioNERFactory
17:35:08.761 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - macro=true
17:35:08.761 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - featureFactory=org.clulab.processors.bionlp.ner.BioNERFactory
17:35:08.766 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - macro=true
17:35:08.766 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - featureFactory=org.clulab.processors.bionlp.ner.BioNERFactory
17:35:09.161 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - macro=true
17:35:09.188 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - featureFactory=org.clulab.processors.bionlp.ner.BioNERFactory
17:35:09.195 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - macro=true
17:35:09.196 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - featureFactory=org.clulab.processors.bionlp.ner.BioNERFactory
17:35:09.200 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - macro=true
17:35:09.207 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - featureFactory=org.clulab.processors.bionlp.ner.BioNERFactory
17:35:09.240 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - macro=true
17:35:09.240 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - featureFactory=org.clulab.processors.bionlp.ner.BioNERFactory
17:35:09.247 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - macro=true
17:35:09.247 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - featureFactory=org.clulab.processors.bionlp.ner.BioNERFactory
17:35:09.250 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - macro=true
17:35:09.251 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - featureFactory=org.clulab.processors.bionlp.ner.BioNERFactory
17:35:09.311 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - macro=true
17:35:09.312 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - featureFactory=org.clulab.processors.bionlp.ner.BioNERFactory
17:35:09.351 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - macro=true
17:35:09.351 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - featureFactory=org.clulab.processors.bionlp.ner.BioNERFactory
17:35:09.388 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - macro=true
17:35:09.388 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - featureFactory=org.clulab.processors.bionlp.ner.BioNERFactory
17:35:09.397 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - macro=true
17:35:09.397 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - featureFactory=org.clulab.processors.bionlp.ner.BioNERFactory
17:35:09.407 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - macro=true
17:35:09.407 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - featureFactory=org.clulab.processors.bionlp.ner.BioNERFactory
17:35:09.510 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - macro=true
17:35:09.510 [pool-5-thread-7-ScalaTest-running-TestBioNLPProcessor] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - featureFactory=org.clulab.processors.bionlp.ner.BioNERFactory
[info] TestBioNLPProcessor:
[info] BioNLPProcessor
[info] - should recognize some tricky entity names *** FAILED *** (118 milliseconds)
[info] java.io.IOException: Unable to open "org/clulab/processors/bionlp/ner/bioner.dat" as class path, filename or URL
[info] at edu.stanford.nlp.io.IOUtils.getInputStreamFromURLOrClasspathOrFileSystem(IOUtils.java:480)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1503)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1495)
[info] at org.clulab.processors.bionlp.ner.CRFNER$.load(CRFNER.scala:164)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer$lzycompute(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3(HybridNER.scala:62)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3$adapted(HybridNER.scala:47)
[info] at scala.collection.TraversableLike$WithFilter.$anonfun$foreach$1(TraversableLike.scala:792)
[info] at scala.collection.Iterator.foreach(Iterator.scala:941)
[info] ...
[info] BioNLPProcessor
[info] - should recognize correct NEs in text 1 *** FAILED *** (16 milliseconds
[info] java.io.IOException: Unable to open "org/clulab/processors/bionlp/ner/bioner.dat" as class path, filename or URL
[info] at edu.stanford.nlp.io.IOUtils.getInputStreamFromURLOrClasspathOrFileSystem(IOUtils.java:480)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1503)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1495)
[info] at org.clulab.processors.bionlp.ner.CRFNER$.load(CRFNER.scala:164)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer$lzycompute(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3(HybridNER.scala:62)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3$adapted(HybridNER.scala:47)
[info] at scala.collection.TraversableLike$WithFilter.$anonfun$foreach$1(TraversableLike.scala:792)
[info] at scala.collection.Iterator.foreach(Iterator.scala:941)
[info] ...
[info] - should recognize correct NEs in text 2 *** FAILED *** (357 milliseconds)
[info] java.io.IOException: Unable to open "org/clulab/processors/bionlp/ner/bioner.dat" as class path, filename or URL
[info] at edu.stanford.nlp.io.IOUtils.getInputStreamFromURLOrClasspathOrFileSystem(IOUtils.java:480)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1503)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1495)
[info] at org.clulab.processors.bionlp.ner.CRFNER$.load(CRFNER.scala:164)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer$lzycompute(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3(HybridNER.scala:62)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3$adapted(HybridNER.scala:47)
[info] at scala.collection.TraversableLike$WithFilter.$anonfun$foreach$1(TraversableLike.scala:792)
[info] at scala.collection.Iterator.foreach(Iterator.scala:941)
[info] ...
[info] - should recognize correct species in text 3 *** FAILED *** (29 milliseconds)
[info] java.io.IOException: Unable to open "org/clulab/processors/bionlp/ner/bioner.dat" as class path, filename or URL
[info] at edu.stanford.nlp.io.IOUtils.getInputStreamFromURLOrClasspathOrFileSystem(IOUtils.java:480)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1503)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1495)
[info] at org.clulab.processors.bionlp.ner.CRFNER$.load(CRFNER.scala:164)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer$lzycompute(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3(HybridNER.scala:62)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3$adapted(HybridNER.scala:47)
[info] at scala.collection.TraversableLike$WithFilter.$anonfun$foreach$1(TraversableLike.scala:792)
[info] at scala.collection.Iterator.foreach(Iterator.scala:941)
[info] ...
[info] - should recognize protein families *** FAILED *** (3 milliseconds)
[info] java.io.IOException: Unable to open "org/clulab/processors/bionlp/ner/bioner.dat" as class path, filename or URL
[info] at edu.stanford.nlp.io.IOUtils.getInputStreamFromURLOrClasspathOrFileSystem(IOUtils.java:480)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1503)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1495)
[info] at org.clulab.processors.bionlp.ner.CRFNER$.load(CRFNER.scala:164)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer$lzycompute(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3(HybridNER.scala:62)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3$adapted(HybridNER.scala:47)
[info] at scala.collection.TraversableLike$WithFilter.$anonfun$foreach$1(TraversableLike.scala:792)
[info] at scala.collection.Iterator.foreach(Iterator.scala:941)
[info] ...
[info] - should fixup POS tags correctly for bio-verbs (100 milliseconds)
[info] - should fixup POS tags correctly for reverse bio-verbs (183 milliseconds)
[info] - should Correct the tags of His and Pro to NN (26 milliseconds)
[info] - should not annotate NEs from the stop list *** FAILED *** (97 milliseconds)
[info] java.io.IOException: Unable to open "org/clulab/processors/bionlp/ner/bioner.dat" as class path, filename or URL
[info] at edu.stanford.nlp.io.IOUtils.getInputStreamFromURLOrClasspathOrFileSystem(IOUtils.java:480)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1503)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1495)
[info] at org.clulab.processors.bionlp.ner.CRFNER$.load(CRFNER.scala:164)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer$lzycompute(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3(HybridNER.scala:62)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3$adapted(HybridNER.scala:47)
[info] at scala.collection.TraversableLike$WithFilter.$anonfun$foreach$1(TraversableLike.scala:792)
[info] at scala.collection.Iterator.foreach(Iterator.scala:941)
[info] ...
[info] - should not annotate NEs from the stop list when upper initial *** FAILED *** (2 milliseconds)
[info] java.io.IOException: Unable to open "org/clulab/processors/bionlp/ner/bioner.dat" as class path, filename or URL
[info] at edu.stanford.nlp.io.IOUtils.getInputStreamFromURLOrClasspathOrFileSystem(IOUtils.java:480)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1503)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1495)
[info] at org.clulab.processors.bionlp.ner.CRFNER$.load(CRFNER.scala:164)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer$lzycompute(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3(HybridNER.scala:62)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3$adapted(HybridNER.scala:47)
[info] at scala.collection.TraversableLike$WithFilter.$anonfun$foreach$1(TraversableLike.scala:792)
[info] at scala.collection.Iterator.foreach(Iterator.scala:941)
[info] ...
[info] - should tokenize complexes correctly *** FAILED *** (9 milliseconds)
[info] java.io.IOException: Unable to open "org/clulab/processors/bionlp/ner/bioner.dat" as class path, filename or URL
[info] at edu.stanford.nlp.io.IOUtils.getInputStreamFromURLOrClasspathOrFileSystem(IOUtils.java:480)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1503)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1495)
[info] at org.clulab.processors.bionlp.ner.CRFNER$.load(CRFNER.scala:164)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer$lzycompute(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3(HybridNER.scala:62)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3$adapted(HybridNER.scala:47)
[info] at scala.collection.TraversableLike$WithFilter.$anonfun$foreach$1(TraversableLike.scala:792)
[info] at scala.collection.Iterator.foreach(Iterator.scala:941)
[info] ...
[info] - should override named entities *** FAILED *** (9 milliseconds)
[info] java.io.IOException: Unable to open "org/clulab/processors/bionlp/ner/bioner.dat" as class path, filename or URL
[info] at edu.stanford.nlp.io.IOUtils.getInputStreamFromURLOrClasspathOrFileSystem(IOUtils.java:480)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1503)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1495)
[info] at org.clulab.processors.bionlp.ner.CRFNER$.load(CRFNER.scala:164)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer$lzycompute(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3(HybridNER.scala:62)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3$adapted(HybridNER.scala:47)
[info] at scala.collection.TraversableLike$WithFilter.$anonfun$foreach$1(TraversableLike.scala:792)
[info] at scala.collection.Iterator.foreach(Iterator.scala:941)
[info] ...
[info] - should recognize 'Smad 2' as a protein *** FAILED *** (5 milliseconds)
[info] java.io.IOException: Unable to open "org/clulab/processors/bionlp/ner/bioner.dat" as class path, filename or URL
[info] at edu.stanford.nlp.io.IOUtils.getInputStreamFromURLOrClasspathOrFileSystem(IOUtils.java:480)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1503)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1495)
[info] at org.clulab.processors.bionlp.ner.CRFNER$.load(CRFNER.scala:164)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer$lzycompute(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3(HybridNER.scala:62)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3$adapted(HybridNER.scala:47)
[info] at scala.collection.TraversableLike$WithFilter.$anonfun$foreach$1(TraversableLike.scala:792)
[info] at scala.collection.Iterator.foreach(Iterator.scala:941)
[info] ...
[info] - should recognize 'Smad' as a family *** FAILED *** (2 milliseconds)
[info] java.io.IOException: Unable to open "org/clulab/processors/bionlp/ner/bioner.dat" as class path, filename or URL
[info] at edu.stanford.nlp.io.IOUtils.getInputStreamFromURLOrClasspathOrFileSystem(IOUtils.java:480)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1503)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1495)
[info] at org.clulab.processors.bionlp.ner.CRFNER$.load(CRFNER.scala:164)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer$lzycompute(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3(HybridNER.scala:62)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3$adapted(HybridNER.scala:47)
[info] at scala.collection.TraversableLike$WithFilter.$anonfun$foreach$1(TraversableLike.scala:792)
[info] at scala.collection.Iterator.foreach(Iterator.scala:941)
[info] ...
[info] - should not label XREFs as entities *** FAILED *** (82 milliseconds)
[info] java.io.IOException: Unable to open "org/clulab/processors/bionlp/ner/bioner.dat" as class path, filename or URL
[info] at edu.stanford.nlp.io.IOUtils.getInputStreamFromURLOrClasspathOrFileSystem(IOUtils.java:480)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1503)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1495)
[info] at org.clulab.processors.bionlp.ner.CRFNER$.load(CRFNER.scala:164)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer$lzycompute(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3(HybridNER.scala:62)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3$adapted(HybridNER.scala:47)
[info] at scala.collection.TraversableLike$WithFilter.$anonfun$foreach$1(TraversableLike.scala:792)
[info] at scala.collection.Iterator.foreach(Iterator.scala:941)
[info] ...
[info] - should label E2F as a family *** FAILED *** (8 milliseconds)
[info] java.io.IOException: Unable to open "org/clulab/processors/bionlp/ner/bioner.dat" as class path, filename or URL
[info] at edu.stanford.nlp.io.IOUtils.getInputStreamFromURLOrClasspathOrFileSystem(IOUtils.java:480)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1503)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1495)
[info] at org.clulab.processors.bionlp.ner.CRFNER$.load(CRFNER.scala:164)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer$lzycompute(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3(HybridNER.scala:62)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3$adapted(HybridNER.scala:47)
[info] at scala.collection.TraversableLike$WithFilter.$anonfun$foreach$1(TraversableLike.scala:792)
[info] at scala.collection.Iterator.foreach(Iterator.scala:941)
[info] ...
[info] - should not produce empty tokens *** FAILED *** (29 milliseconds)
[info] java.io.IOException: Unable to open "org/clulab/processors/bionlp/ner/bioner.dat" as class path, filename or URL
[info] at edu.stanford.nlp.io.IOUtils.getInputStreamFromURLOrClasspathOrFileSystem(IOUtils.java:480)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1503)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1495)
[info] at org.clulab.processors.bionlp.ner.CRFNER$.load(CRFNER.scala:164)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer$lzycompute(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3(HybridNER.scala:62)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3$adapted(HybridNER.scala:47)
[info] at scala.collection.TraversableLike$WithFilter.$anonfun$foreach$1(TraversableLike.scala:792)
[info] at scala.collection.Iterator.foreach(Iterator.scala:941)
[info] ...
[info] - should recognize "insulin receptor substrate-1" as an entity *** FAILED *** (9 milliseconds)
[info] java.io.IOException: Unable to open "org/clulab/processors/bionlp/ner/bioner.dat" as class path, filename or URL
[info] at edu.stanford.nlp.io.IOUtils.getInputStreamFromURLOrClasspathOrFileSystem(IOUtils.java:480)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1503)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1495)
[info] at org.clulab.processors.bionlp.ner.CRFNER$.load(CRFNER.scala:164)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer$lzycompute(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3(HybridNER.scala:62)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3$adapted(HybridNER.scala:47)
[info] at scala.collection.TraversableLike$WithFilter.$anonfun$foreach$1(TraversableLike.scala:792)
[info] at scala.collection.Iterator.foreach(Iterator.scala:941)
[info] ...
[info] - should NOT recognize "Mdm2 binding" as a protein family *** FAILED *** (9 milliseconds)
[info] java.io.IOException: Unable to open "org/clulab/processors/bionlp/ner/bioner.dat" as class path, filename or URL
[info] at edu.stanford.nlp.io.IOUtils.getInputStreamFromURLOrClasspathOrFileSystem(IOUtils.java:480)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1503)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1495)
[info] at org.clulab.processors.bionlp.ner.CRFNER$.load(CRFNER.scala:164)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer$lzycompute(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3(HybridNER.scala:62)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3$adapted(HybridNER.scala:47)
[info] at scala.collection.TraversableLike$WithFilter.$anonfun$foreach$1(TraversableLike.scala:792)
[info] at scala.collection.Iterator.foreach(Iterator.scala:941)
[info] ...
[info] - should recognize correct NEs in text with parentheses *** FAILED *** (101 milliseconds)
[info] java.io.IOException: Unable to open "org/clulab/processors/bionlp/ner/bioner.dat" as class path, filename or URL
[info] at edu.stanford.nlp.io.IOUtils.getInputStreamFromURLOrClasspathOrFileSystem(IOUtils.java:480)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1503)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1495)
[info] at org.clulab.processors.bionlp.ner.CRFNER$.load(CRFNER.scala:164)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer$lzycompute(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3(HybridNER.scala:62)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3$adapted(HybridNER.scala:47)
[info] at scala.collection.TraversableLike$WithFilter.$anonfun$foreach$1(TraversableLike.scala:792)
[info] at scala.collection.Iterator.foreach(Iterator.scala:941)
[info] ...
17:35:10.190 [pool-5-thread-7-ScalaTest-running-TestHeadlessDependencies] INFO edu.stanford.nlp.pipeline.StanfordCoreNLP - Adding annotator pos
17:35:10.216 [pool-5-thread-7-ScalaTest-running-TestHeadlessDependencies] INFO edu.stanford.nlp.pipeline.StanfordCoreNLP - Adding annotator lemma
17:35:10.217 [pool-5-thread-7-ScalaTest-running-TestHeadlessDependencies] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - macro=true
17:35:10.217 [pool-5-thread-7-ScalaTest-running-TestHeadlessDependencies] INFO edu.stanford.nlp.sequences.SeqClassifierFlags - featureFactory=org.clulab.processors.bionlp.ner.BioNERFactory
[info] TestHeadlessDependencies:
[info] BioNLPProcessor
[info] - should handle cycles in dependency tree robustly *** FAILED *** (35 milliseconds)
[info] java.io.IOException: Unable to open "org/clulab/processors/bionlp/ner/bioner.dat" as class path, filename or URL
[info] at edu.stanford.nlp.io.IOUtils.getInputStreamFromURLOrClasspathOrFileSystem(IOUtils.java:480)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1503)
[info] at edu.stanford.nlp.ie.AbstractSequenceClassifier.loadClassifier(AbstractSequenceClassifier.java:1495)
[info] at org.clulab.processors.bionlp.ner.CRFNER$.load(CRFNER.scala:164)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer$lzycompute(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.bioNer(HybridNER.scala:22)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3(HybridNER.scala:62)
[info] at org.clulab.processors.bionlp.ner.HybridNER.$anonfun$recognizeNamedEntities$3$adapted(HybridNER.scala:47)
[info] at scala.collection.TraversableLike$WithFilter.$anonfun$foreach$1(TraversableLike.scala:792)
[info] at scala.collection.Iterator.foreach(Iterator.scala:941)
[info] ...
[info] compiling 56 Scala sources to /Users/luohaomiao/reach/main/target/scala-2.12/test-classes ...
[info] Run completed in 3 minutes, 31 seconds.
[info] Total number of tests run: 36
[info] Suites: completed 5, aborted 1
[info] Tests: succeeded 3, failed 33, canceled 0, ignored 0, pending 0
[info] *** 1 SUITE ABORTED ***
[info] *** 33 TESTS FAILED ***
[error] Failed tests:
[error] org.clulab.processors.TestBioNLPTokenizer
[error] org.clulab.processors.TestBioNLPProcessor2
[error] org.clulab.processors.TestFastBioNLPProcessor
[error] org.clulab.processors.TestBioNLPProcessor
[error] org.clulab.processors.TestHeadlessDependencies
[error] Error during tests:
[error] org.clulab.processors.TestCompactLexiconNER
[dynet] Checking /Users/luohaomiao/reach for libdynet_swig.jnilib...
[dynet] Checking /Users/luohaomiao for libdynet_swig.jnilib...
[dynet] Extracting resource intel-libdynet_swig.jnilib to /var/folders/my/28hyn3s92ld0r5f3gpk4kbj80000gn/T/libdynet_swig-52315725025211103.jnilib...
[dynet] Loading DyNet from /var/folders/my/28hyn3s92ld0r5f3gpk4kbj80000gn/T/libdynet_swig-52315725025211103.jnilib...s
[dynet] random seed: 1236199978
[dynet] allocating memory: 512,512,512,512MB
[dynet] memory allocation done.
17:39:13.261 [pool-5-thread-9-ScalaTest-running-TestPaperReader] INFO o.c.p.m.DeepLearningPolarityClassifier - Loading saved model SavedLSTM_WideBound_u_tag ...
17:39:15.532 [pool-5-thread-9-ScalaTest-running-TestPaperReader] INFO o.c.p.m.DeepLearningPolarityClassifier - Loading model finished!
[info] TestPaperReader:
[info] PaperReader
[info] - should read plain text files *** FAILED *** (2 minutes, 19 seconds)
[info] java.lang.NullPointerException:
[info] at java.base/java.io.Reader.(Reader.java:167)
[info] at java.base/java.io.InputStreamReader.(InputStreamReader.java:125)
[info] at scala.io.BufferedSource.reader(BufferedSource.scala:26)
[info] at scala.io.BufferedSource.bufferedReader(BufferedSource.scala:27)
[info] at scala.io.BufferedSource.charReader$lzycompute(BufferedSource.scala:37)
[info] at scala.io.BufferedSource.charReader(BufferedSource.scala:35)
[info] at scala.io.BufferedSource.scala$io$BufferedSource$$decachedReader(BufferedSource.scala:64)
[info] at scala.io.BufferedSource$BufferedLineIterator.(BufferedSource.scala:69)
[info] at scala.io.BufferedSource.getLines(BufferedSource.scala:88)
[info] at org.clulab.reach.grounding.TsvIMKBFactory.loadFromKBDir(TsvIMKBFactory.scala:48)
[info] ...
[dynet] random seed: 0
17:39:18.189 [pool-5-thread-9] INFO o.c.p.m.DeepLearningPolarityClassifier - Loading saved model SavedLSTM_WideBound_u_tag ...
17:39:20.190 [pool-5-thread-9] INFO o.c.p.m.DeepLearningPolarityClassifier - Loading model finished!executeTests 142s
[info] DemoTests2:
[info] org.clulab.reach.DemoTests2 *** ABORTED *** (1 millisecond)
[info] java.lang.ExceptionInInitializerError:
[info] at org.clulab.reach.DemoTests2.(DemoTests.scala:39)
[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
[info] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
[info] at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
[info] at java.base/java.lang.Class.newInstance(Class.java:584)
[info] at org.scalatest.tools.Framework$ScalaTestTask.execute(Framework.scala:435)
[info] at sbt.TestRunner.runTest$1(TestFramework.scala:139)
[info] at sbt.TestRunner.run(TestFramework.scala:154)
[info] at sbt.TestFramework$$anon$3$$anonfun$$lessinit$greater$1.$anonfun$apply$1(TestFramework.scala:317)
[info] ...
[info] Cause: java.lang.NullPointerException:
[info] at java.base/java.io.Reader.(Reader.java:167)
[info] at java.base/java.io.InputStreamReader.(InputStreamReader.java:125)
[info] at scala.io.BufferedSource.reader(BufferedSource.scala:26)
[info] at scala.io.BufferedSource.bufferedReader(BufferedSource.scala:27)
[info] at scala.io.BufferedSource.charReader$lzycompute(BufferedSource.scala:37)
[info] at scala.io.BufferedSource.charReader(BufferedSource.scala:35)
[info] at scala.io.BufferedSource.scala$io$BufferedSource$$decachedReader(BufferedSource.scala:64)
[info] at scala.io.BufferedSource$BufferedLineIterator.(BufferedSource.scala:69)
[info] at scala.io.BufferedSource.getLines(BufferedSource.scala:88)
[info] at org.clulab.reach.grounding.TsvIMKBFactory.loadFromKBDir(TsvIMKBFactory.scala:48)
[info] ...
[info] compiling 4 Scala sources to /Users/luohaomiao/reach/assembly/target/scala-2.12/test-classes ...
[info] compiling 8 Scala sources to /Users/luohaomiao/reach/export/target/scala-2.12/test-classes ...
[info] TestAssemblyRules:
[info] /org/clulab/reach/assembly/grammars/intrasentential.yml
[info] - should compile without error (4 seconds, 287 milliseconds)
[info] /org/clulab/reach/assembly/grammars/intersentential.yml
[info] - should compile without error (708 milliseconds)
[info] /org/clulab/reach/assembly/grammars/biodrb-patterns.yml
[info] - should compile without error (464 milliseconds)
[info] /org/clulab/reach/assembly/grammars/mihaila-causal-discourse.yml
[info] - should compile without error (128 milliseconds)
[dynet] Checking /Users/luohaomiao/reach for libdynet_swig.jnilib...
[dynet] Checking /Users/luohaomiao for libdynet_swig.jnilib...
[dynet] Extracting resource intel-libdynet_swig.jnilib to /var/folders/my/28hyn3s92ld0r5f3gpk4kbj80000gn/T/libdynet_swig-13072292625081415830.jnilib...
[dynet] Loading DyNet from /var/folders/my/28hyn3s92ld0r5f3gpk4kbj80000gn/T/libdynet_swig-13072292625081415830.jnilib...
[dynet] random seed: 1895505492
[dynet] allocating memory: 512,512,512,512MB
[dynet] memory allocation done.
17:39:45.513 [pool-5-thread-11] INFO o.c.p.m.DeepLearningPolarityClassifier - Loading saved model SavedLSTM_WideBound_u_tag ...
17:39:47.690 [pool-5-thread-11] INFO o.c.p.m.DeepLearningPolarityClassifier - Loading model finished!/ Test / executeTests 12s
[info] TestAssemblyManager:
[info] org.clulab.reach.assembly.TestAssemblyManager *** ABORTED *** (4 milliseconds)
[info] java.lang.NullPointerException:
[info] at java.base/java.io.Reader.(Reader.java:167)
[info] at java.base/java.io.InputStreamReader.(InputStreamReader.java:125)
[info] at scala.io.BufferedSource.reader(BufferedSource.scala:26)
[info] at scala.io.BufferedSource.bufferedReader(BufferedSource.scala:27)
[info] at scala.io.BufferedSource.charReader$lzycompute(BufferedSource.scala:37)
[info] at scala.io.BufferedSource.charReader(BufferedSource.scala:35)
[info] at scala.io.BufferedSource.scala$io$BufferedSource$$decachedReader(BufferedSource.scala:64)
[info] at scala.io.BufferedSource$BufferedLineIterator.(BufferedSource.scala:69)
[info] at scala.io.BufferedSource.getLines(BufferedSource.scala:88)
[info] at org.clulab.reach.grounding.TsvIMKBFactory.loadFromKBDir(TsvIMKBFactory.scala:48)
[info] ...
[dynet] random seed: 0
17:39:49.196 [pool-5-thread-11-ScalaTest-running-TestAssemblySieves] INFO o.c.p.m.DeepLearningPolarityClassifier - Loading saved model SavedLSTM_WideBound_u_tag ...
17:39:51.005 [pool-5-thread-11-ScalaTest-running-TestAssemblySieves] INFO o.c.p.m.DeepLearningPolarityClassifier - Loading model finished!
[dynet] random seed: 0
17:39:51.966 [pool-5-thread-11-ScalaTest-running-TestAssemblySieves] INFO o.c.p.m.DeepLearningPolarityClassifier - Loading saved model SavedLSTM_WideBound_u_tag ...
17:39:53.713 [pool-5-thread-11-ScalaTest-running-TestAssemblySieves] INFO o.c.p.m.DeepLearningPolarityClassifier - Loading model finished!
[dynet] random seed: 0
17:39:54.748 [pool-5-thread-11-ScalaTest-running-TestAssemblySieves] INFO o.c.p.m.DeepLearningPolarityClassifier - Loading saved model SavedLSTM_WideBound_u_tag ...
17:39:56.875 [pool-5-thread-11-ScalaTest-running-TestAssemblySieves] INFO o.c.p.m.DeepLearningPolarityClassifier - Loading model finished!
[dynet] random seed: 0
17:39:57.832 [pool-5-thread-11-ScalaTest-running-TestAssemblySieves] INFO o.c.p.m.DeepLearningPolarityClassifier - Loading saved model SavedLSTM_WideBound_u_tag ...
17:40:00.150 [pool-5-thread-11-ScalaTest-running-TestAssemblySieves] INFO o.c.p.m.DeepLearningPolarityClassifier - Loading model finished!
[dynet] random seed: 0
17:40:01.289 [pool-5-thread-11-ScalaTest-running-TestAssemblySieves] INFO o.c.p.m.DeepLearningPolarityClassifier - Loading saved model SavedLSTM_WideBound_u_tag ...
17:40:03.087 [pool-5-thread-11-ScalaTest-running-TestAssemblySieves] INFO o.c.p.m.DeepLearningPolarityClassifier - Loading model finished!
[dynet] random seed: 0
17:40:03.891 [pool-5-thread-11-ScalaTest-running-TestAssemblySieves] INFO o.c.p.m.DeepLearningPolarityClassifier - Loading saved model SavedLSTM_WideBound_u_tag ...
17:40:05.856 [pool-5-thread-11-ScalaTest-running-TestAssemblySieves] INFO o.c.p.m.DeepLearningPolarityClassifier - Loading model finished!
[dynet] random seed: 0
17:40:06.857 [pool-5-thread-11-ScalaTest-running-TestAssemblySieves] INFO o.c.p.m.DeepLearningPolarityClassifier - Loading saved model SavedLSTM_WideBound_u_tag ...
17:40:09.070 [pool-5-thread-11-ScalaTest-running-TestAssemblySieves] INFO o.c.p.m.DeepLearningPolarityClassifier - Loading model finished!
[dynet] random seed: 0
17:40:10.051 [pool-5-thread-11-ScalaTest-running-TestAssemblySieves] INFO o.c.p.m.DeepLearningPolarityClassifier - Loading saved model SavedLSTM_WideBound_u_tag ...
17:40:12.592 [pool-5-thread-11-ScalaTest-running-TestAssemblySieves] INFO o.c.p.m.DeepLearningPolarityClassifier - Loading model finished!
[dynet] random seed: 0
17:40:13.756 [pool-5-thread-11-ScalaTest-running-TestAssemblySieves] INFO o.c.p.m.DeepLearningPolarityClassifier - Loading saved model SavedLSTM_WideBound_u_tag ...
17:40:15.964 [pool-5-thread-11-ScalaTest-running-TestAssemblySieves] INFO o.c.p.m.DeepLearningPolarityClassifier - Loading model finished!
[info] TestAssemblySieves:
[info] Once BEF had been phosphorylated, AFT was ubiquitinated
[info] - should be annotated with the phosphorylation preceding the ubiquitination *** FAILED *** (2 seconds, 785 milliseconds)
[info] java.lang.NullPointerException:
[info] at java.base/java.io.Reader.(Reader.java:167)
[info] at java.base/java.io.InputStreamReader.(InputStreamReader.java:125)
[info] at scala.io.BufferedSource.reader(BufferedSource.scala:26)
[info] at scala.io.BufferedSource.bufferedReader(BufferedSource.scala:27)
[info] at scala.io.BufferedSource.charReader$lzycompute(BufferedSource.scala:37)
[info] at scala.io.BufferedSource.charReader(BufferedSource.scala:35)
[info] at scala.io.BufferedSource.scala$io$BufferedSource$$decachedReader(BufferedSource.scala:64)
[info] at scala.io.BufferedSource$BufferedLineIterator.(BufferedSource.scala:69)
[info] at scala.io.BufferedSource.getLines(BufferedSource.scala:88)
[info] at org.clulab.reach.grounding.TsvIMKBFactory.loadFromKBDir(TsvIMKBFactory.scala:48)
[info] ...
[info] AFT will be ubiquitinated only if BEF is first phosphorylated
[info] - should be annotated with the phosphorylation preceding the ubiquitination *** FAILED *** (2 seconds, 750 milliseconds)
[info] java.lang.NullPointerException:
[info] at java.base/java.io.Reader.(Reader.java:167)
[info] at java.base/java.io.InputStreamReader.(InputStreamReader.java:125)
[info] at scala.io.BufferedSource.reader(BufferedSource.scala:26)
[info] at scala.io.BufferedSource.bufferedReader(BufferedSource.scala:27)
[info] at scala.io.BufferedSource.charReader$lzycompute(BufferedSource.scala:37)
[info] at scala.io.BufferedSource.charReader(BufferedSource.scala:35)
[info] at scala.io.BufferedSource.scala$io$BufferedSource$$decachedReader(BufferedSource.scala:64)
[info] at scala.io.BufferedSource$BufferedLineIterator.(BufferedSource.scala:69)
[info] at scala.io.BufferedSource.getLines(BufferedSource.scala:88)
[info] at org.clulab.reach.grounding.TsvIMKBFactory.loadFromKBDir(TsvIMKBFactory.scala:48)
[info] ...
[info] AFT was ubiquitinated when BEF had been phosphorylated
[info] - should be annotated with the phosphorylation preceding the ubiquitination *** FAILED *** (3 seconds, 102 milliseconds)
[info] java.lang.NullPointerException:
[info] at java.base/java.io.Reader.(Reader.java:167)
[info] at java.base/java.io.InputStreamReader.(InputStreamReader.java:125)
[info] at scala.io.BufferedSource.reader(BufferedSource.scala:26)
[info] at scala.io.BufferedSource.bufferedReader(BufferedSource.scala:27)
[info] at scala.io.BufferedSource.charReader$lzycompute(BufferedSource.scala:37)
[info] at scala.io.BufferedSource.charReader(BufferedSource.scala:35)
[info] at scala.io.BufferedSource.scala$io$BufferedSource$$decachedReader(BufferedSource.scala:64)
[info] at scala.io.BufferedSource$BufferedLineIterator.(BufferedSource.scala:69)
[info] at scala.io.BufferedSource.getLines(BufferedSource.scala:88)
[info] at org.clulab.reach.grounding.TsvIMKBFactory.loadFromKBDir(TsvIMKBFactory.scala:48)
[info] ...
[info] Together these data demonstrate that E2-induced SRC-3 phosphorylation is dependent on a direct interaction between SRC-3 and ERα and can occur outside of the nucleus.
[info] - should be annotated with the binding preceding the phosphorylation *** FAILED *** (3 seconds, 426 milliseconds)
[info] java.lang.NullPointerException:
[info] at java.base/java.io.Reader.(Reader.java:167)
[info] at java.base/java.io.InputStreamReader.(InputStreamReader.java:125)
[info] at scala.io.BufferedSource.reader(BufferedSource.scala:26)
[info] at scala.io.BufferedSource.bufferedReader(BufferedSource.scala:27)
[info] at scala.io.BufferedSource.charReader$lzycompute(BufferedSource.scala:37)
[info] at scala.io.BufferedSource.charReader(BufferedSource.scala:35)
[info] at scala.io.BufferedSource.scala$io$BufferedSource$$decachedReader(BufferedSource.scala:64)
[info] at scala.io.BufferedSource$BufferedLineIterator.(BufferedSource.scala:69)
[info] at scala.io.BufferedSource.getLines(BufferedSource.scala:88)
[info] at org.clulab.reach.grounding.TsvIMKBFactory.loadFromKBDir(TsvIMKBFactory.scala:48)
[info] ...
[info] BEF was phosphorylated. Then, AFT was ubiquitinated.
[info] - should be annotated with the phosphorylation preceding the ubiquitination *** FAILED *** (2 seconds, 615 milliseconds)
[info] java.lang.NullPointerException:
[info] at java.base/java.io.Reader.(Reader.java:167)
[info] at java.base/java.io.InputStreamReader.(InputStreamReader.java:125)
[info] at scala.io.BufferedSource.reader(BufferedSource.scala:26)
[info] at scala.io.BufferedSource.bufferedReader(BufferedSource.scala:27)
[info] at scala.io.BufferedSource.charReader$lzycompute(BufferedSource.scala:37)
[info] at scala.io.BufferedSource.charReader(BufferedSource.scala:35)
[info] at scala.io.BufferedSource.scala$io$BufferedSource$$decachedReader(BufferedSource.scala:64)
[info] at scala.io.BufferedSource$BufferedLineIterator.(BufferedSource.scala:69)
[info] at scala.io.BufferedSource.getLines(BufferedSource.scala:88)
[info] at org.clulab.reach.grounding.TsvIMKBFactory.loadFromKBDir(TsvIMKBFactory.scala:48)
[info] ...
[info] BEF was phosphorylated. Subsequently AFT was ubiquitinated.
[info] - should be annotated with the phosphorylation preceding the ubiquitination *** FAILED *** (2 seconds, 978 milliseconds)
[info] java.lang.NullPointerException:
[info] at java.base/java.io.Reader.(Reader.java:167)
[info] at java.base/java.io.InputStreamReader.(InputStreamReader.java:125)
[info] at scala.io.BufferedSource.reader(BufferedSource.scala:26)
[info] at scala.io.BufferedSource.bufferedReader(BufferedSource.scala:27)
[info] at scala.io.BufferedSource.charReader$lzycompute(BufferedSource.scala:37)
[info] at scala.io.BufferedSource.charReader(BufferedSource.scala:35)
[info] at scala.io.BufferedSource.scala$io$BufferedSource$$decachedReader(BufferedSource.scala:64)
[info] at scala.io.BufferedSource$BufferedLineIterator.(BufferedSource.scala:69)
[info] at scala.io.BufferedSource.getLines(BufferedSource.scala:88)
[info] at org.clulab.reach.grounding.TsvIMKBFactory.loadFromKBDir(TsvIMKBFactory.scala:48)
[info] ...
[info] AFT was ubiquitinated. Prior to this, BEF was phosphorylated.
[info] - should be annotated with the phosphorylation preceding the ubiquitination *** FAILED *** (3 seconds, 170 milliseconds)
[info] java.lang.NullPointerException:
[info] at java.base/java.io.Reader.(Reader.java:167)
[info] at java.base/java.io.InputStreamReader.(InputStreamReader.java:125)
[info] at scala.io.BufferedSource.reader(BufferedSource.scala:26)
[info] at scala.io.BufferedSource.bufferedReader(BufferedSource.scala:27)
[info] at scala.io.BufferedSource.charReader$lzycompute(BufferedSource.scala:37)
[info] at scala.io.BufferedSource.charReader(BufferedSource.scala:35)
[info] at scala.io.BufferedSource.scala$io$BufferedSource$$decachedReader(BufferedSource.scala:64)
[info] at scala.io.BufferedSource$BufferedLineIterator.(BufferedSource.scala:69)
[info] at scala.io.BufferedSource.getLines(BufferedSource.scala:88)
[info] at org.clulab.reach.grounding.TsvIMKBFactory.loadFromKBDir(TsvIMKBFactory.scala:48)
[info] ...
[info] AFT was ubiquitinated. Previously, BEF was phosphorylated.
[info] - should be annotated with the phosphorylation preceding the ubiquitination *** FAILED *** (3 seconds, 693 milliseconds)
[info] java.lang.NullPointerException:
[info] at java.base/java.io.Reader.(Reader.java:167)
[info] at java.base/java.io.InputStreamReader.(InputStreamReader.java:125)
[info] at scala.io.BufferedSource.reader(BufferedSource.scala:26)
[info] at scala.io.BufferedSource.bufferedReader(BufferedSource.scala:27)
[info] at scala.io.BufferedSource.charReader$lzycompute(BufferedSource.scala:37)
[info] at scala.io.BufferedSource.charReader(BufferedSource.scala:35)
[info] at scala.io.BufferedSource.scala$io$BufferedSource$$decachedReader(BufferedSource.scala:64)
[info] at scala.io.BufferedSource$BufferedLineIterator.(BufferedSource.scala:69)
[info] at scala.io.BufferedSource.getLines(BufferedSource.scala:88)
[info] at org.clulab.reach.grounding.TsvIMKBFactory.loadFromKBDir(TsvIMKBFactory.scala:48)
[info] ...
[info] AFT was ubiquitinated. There is intervening material and, previously, BEF was phosphorylated.
[info] - should have no precedence relations *** FAILED *** (3 seconds, 88 milliseconds)
[info] java.lang.NullPointerException:
[info] at java.base/java.io.Reader.(Reader.java:167)
[info] at java.base/java.io.InputStreamReader.(InputStreamReader.java:125)
[info] at scala.io.BufferedSource.reader(BufferedSource.scala:26)
[info] at scala.io.BufferedSource.bufferedReader(BufferedSource.scala:27)
[info] at scala.io.BufferedSource.charReader$lzycompute(BufferedSource.scala:37)
[info] at scala.io.BufferedSource.charReader(BufferedSource.scala:35)
[info] at scala.io.BufferedSource.scala$io$BufferedSource$$decachedReader(BufferedSource.scala:64)
[info] at scala.io.BufferedSource$BufferedLineIterator.(BufferedSource.scala:69)
[info] at scala.io.BufferedSource.getLines(BufferedSource.scala:88)
[info] at org.clulab.reach.grounding.TsvIMKBFactory.loadFromKBDir(TsvIMKBFactory.scala:48)
[info] ...
[info] Run completed in 48 seconds, 854 milliseconds.
[info] Total number of tests run: 13
[info] Suites: completed 2, aborted 1
[info] Tests: succeeded 4, failed 9, canceled 0, ignored 0, pending 0
[info] *** 1 SUITE ABORTED ***
[info] *** 9 TESTS FAILED ***
[error] Failed tests:
[error] org.clulab.reach.assembly.TestAssemblySieves
[error] Error during tests:
[error] org.clulab.reach.assembly.TestAssemblyManager
[info] compiling 2 Scala sources to /Users/luohaomiao/reach/target/scala-2.12/test-classes ...
[dynet] Checking /Users/luohaomiao/reach for libdynet_swig.jnilib...
[dynet] Checking /Users/luohaomiao for libdynet_swig.jnilib...
[dynet] Extracting resource intel-libdynet_swig.jnilib to /var/folders/my/28hyn3s92ld0r5f3gpk4kbj80000gn/T/libdynet_swig-3326261776161524919.jnilib...
[dynet] Loading DyNet from /var/folders/my/28hyn3s92ld0r5f3gpk4kbj80000gn/T/libdynet_swig-3326261776161524919.jnilib...
[dynet] random seed: 545920975
[dynet] allocating memory: 512,512,512,512MB
[dynet] memory allocation done.
17:40:23.297 [pool-5-thread-11-ScalaTest-running-TestRuler] INFO o.c.p.m.DeepLearningPolarityClassifier - Loading saved model SavedLSTM_WideBound_u_tag ...
17:40:25.208 [pool-5-thread-11-ScalaTest-running-TestRuler] INFO o.c.p.m.DeepLearningPolarityClassifier - Loading model finished!
[info] TestRuler:
[info] open Ruler.runOpen
[info] org.clulab.reach.export.apis.TestRuler *** ABORTED *** (8 seconds, 26 milliseconds)
[info] java.lang.ExceptionInInitializerError:
[info] at org.clulab.reach.export.apis.TestRuler.$anonfun$new$1(TestRuler.scala:40)
[info] at org.scalatest.OutcomeOf.outcomeOf(OutcomeOf.scala:85)
[info] at org.scalatest.OutcomeOf.outcomeOf$(OutcomeOf.scala:83)
[info] at org.scalatest.OutcomeOf$.outcomeOf(OutcomeOf.scala:104)
[info] at org.scalatest.Transformer.apply(Transformer.scala:22)
[info] at org.scalatest.Transformer.apply(Transformer.scala:20)
[info] at org.scalatest.FlatSpecLike$$anon$1.apply(FlatSpecLike.scala:1682)
[info] at org.scalatest.TestSuite.withFixture(TestSuite.scala:196)
[info] at org.scalatest.TestSuite.withFixture$(TestSuite.scala:195)
[info] at org.scalatest.FlatSpec.withFixture(FlatSpec.scala:1685)
[info] ...
[info] Cause: java.lang.NullPointerException:
[info] at java.base/java.io.Reader.(Reader.java:167)
[info] at java.base/java.io.InputStreamReader.(InputStreamReader.java:125)
[info] at scala.io.BufferedSource.reader(BufferedSource.scala:26)
[info] at scala.io.BufferedSource.bufferedReader(BufferedSource.scala:27)
[info] at scala.io.BufferedSource.charReader$lzycompute(BufferedSource.scala:37)
[info] at scala.io.BufferedSource.charReader(BufferedSource.scala:35)
[info] at scala.io.BufferedSource.scala$io$BufferedSource$$decachedReader(BufferedSource.scala:64)
[info] at scala.io.BufferedSource$BufferedLineIterator.(BufferedSource.scala:69)
[info] at scala.io.BufferedSource.getLines(BufferedSource.scala:88)
[info] at org.clulab.reach.grounding.TsvIMKBFactory.loadFromKBDir(TsvIMKBFactory.scala:48)
[info] ...
[dynet] Checking /Users/luohaomiao/reach for libdynet_swig.jnilib...
[dynet] Checking /Users/luohaomiao for libdynet_swig.jnilib...
[dynet] Extracting resource intel-libdynet_swig.jnilib to /var/folders/my/28hyn3s92ld0r5f3gpk4kbj80000gn/T/libdynet_swig-16621375721652339215.jnilib...
[dynet] Loading DyNet from /var/folders/my/28hyn3s92ld0r5f3gpk4kbj80000gn/T/libdynet_swig-16621375721652339215.jnilib...
[dynet] random seed: 2999814534
[dynet] allocating memory: 512,512,512,512MB
[dynet] memory allocation done.
17:40:32.400 [pool-5-thread-13] INFO o.c.p.m.DeepLearningPolarityClassifier - Loading saved model SavedLSTM_WideBound_u_tag ...
17:40:34.524 [pool-5-thread-13] INFO o.c.p.m.DeepLearningPolarityClassifier - Loading model finished!xecuteTests 6s
[info] TestReachCLI:
[info] org.clulab.reach.export.TestReachCLI *** ABORTED *** (154 milliseconds)
[info] java.lang.ExceptionInInitializerError:
[info] at org.clulab.reach.export.TestReachCLI.(TestReachCLI.scala:16)
[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
[info] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
[info] at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
[info] at java.base/java.lang.Class.newInstance(Class.java:584)
[info] at org.scalatest.tools.Framework$ScalaTestTask.execute(Framework.scala:435)
[info] at sbt.TestRunner.runTest$1(TestFramework.scala:139)
[info] at sbt.TestRunner.run(TestFramework.scala:154)
[info] at sbt.TestFramework$$anon$3$$anonfun$$lessinit$greater$1.$anonfun$apply$1(TestFramework.scala:317)
[info] ...
[info] Cause: java.lang.NullPointerException:
[info] at java.base/java.io.Reader.(Reader.java:167)
[info] at java.base/java.io.InputStreamReader.(InputStreamReader.java:125)
[info] at scala.io.BufferedSource.reader(BufferedSource.scala:26)
[info] at scala.io.BufferedSource.bufferedReader(BufferedSource.scala:27)
[info] at scala.io.BufferedSource.charReader$lzycompute(BufferedSource.scala:37)
[info] at scala.io.BufferedSource.charReader(BufferedSource.scala:35)
[info] at scala.io.BufferedSource.scala$io$BufferedSource$$decachedReader(BufferedSource.scala:64)
[info] at scala.io.BufferedSource$BufferedLineIterator.(BufferedSource.scala:69)
[info] at scala.io.BufferedSource.getLines(BufferedSource.scala:88)
[info] at org.clulab.reach.grounding.TsvIMKBFactory.loadFromKBDir(TsvIMKBFactory.scala:48)
[info] ...
[warn] 7.467 seconds of the last 10 seconds were spent in garbage collection. You may want to increase the project heap size using -Xmx or try a different gc algorithm, e.g. -XX:+UseG1GC, for better performance.
[error] java.lang.ExceptionInInitializerError
[error] at org.clulab.reach.DemoTests2.(DemoTests.scala:39)
[error] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
[error] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
[error] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
[error] at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
[error] at java.base/java.lang.Class.newInstance(Class.java:584)
[error] at org.scalatest.tools.Framework$ScalaTestTask.execute(Framework.scala:435)
[error] at sbt.TestRunner.runTest$1(TestFramework.scala:139)
[error] at sbt.TestRunner.run(TestFramework.scala:154)
[error] at sbt.TestFramework$$anon$3$$anonfun$$lessinit$greater$1.$anonfun$apply$1(TestFramework.scala:317)
[error] at sbt.TestFramework$.sbt$TestFramework$$withContextLoader(TestFramework.scala:277)
[error] at sbt.TestFramework$$anon$3$$anonfun$$lessinit$greater$1.apply(TestFramework.scala:317)
[error] at sbt.TestFramework$$anon$3$$anonfun$$lessinit$greater$1.apply(TestFramework.scala:317)
[error] at sbt.TestFunction.apply(TestFramework.scala:329)
[error] at sbt.Tests$.processRunnable$1(Tests.scala:461)
[error] at sbt.Tests$.$anonfun$makeSerial$1(Tests.scala:467)
[error] at sbt.std.Transform$$anon$3.$anonfun$apply$2(Transform.scala:46)
[error] at sbt.std.Transform$$anon$4.work(Transform.scala:68)
[error] at sbt.Execute.$anonfun$submit$2(Execute.scala:282)
[error] at sbt.internal.util.ErrorHandling$.wideConvert(ErrorHandling.scala:23)
[error] at sbt.Execute.work(Execute.scala:291)
[error] at sbt.Execute.$anonfun$submit$1(Execute.scala:282)
[error] at sbt.ConcurrentRestrictions$$anon$4.$anonfun$submitValid$1(ConcurrentRestrictions.scala:265)
[error] at sbt.CompletionService$$anon$2.call(CompletionService.scala:64)
[error] at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
[error] at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
[error] at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
[error] at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
[error] at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
[error] at java.base/java.lang.Thread.run(Thread.java:829)
[error] Caused by: java.lang.NullPointerException
[error] at java.base/java.io.Reader.(Reader.java:167)
[error] at java.base/java.io.InputStreamReader.(InputStreamReader.java:125)
[error] at scala.io.BufferedSource.reader(BufferedSource.scala:26)
[error] at scala.io.BufferedSource.bufferedReader(BufferedSource.scala:27)
[error] at scala.io.BufferedSource.charReader$lzycompute(BufferedSource.scala:37)
[error] at scala.io.BufferedSource.charReader(BufferedSource.scala:35)
[error] at scala.io.BufferedSource.scala$io$BufferedSource$$decachedReader(BufferedSource.scala:64)
[error] at scala.io.BufferedSource$BufferedLineIterator.(BufferedSource.scala:69)
[error] at scala.io.BufferedSource.getLines(BufferedSource.scala:88)
[error] at org.clulab.reach.grounding.TsvIMKBFactory.loadFromKBDir(TsvIMKBFactory.scala:48)
[error] at org.clulab.reach.grounding.TsvIMKBFactory.$anonfun$make$1(TsvIMKBFactory.scala:25)
[error] at org.clulab.reach.grounding.TsvIMKBFactory.$anonfun$make$1$adapted(TsvIMKBFactory.scala:24)
[error] at scala.Option.foreach(Option.scala:274)
[error] at org.clulab.reach.grounding.TsvIMKBFactory.make(TsvIMKBFactory.scala:24)
[error] at org.clulab.reach.grounding.ReachIMKBMentionLookups$.buildKb(ReachIMKBMentionLookups.scala:127)
[error] at org.clulab.reach.grounding.ReachIMKBMentionLookups$.$anonfun$configuredKBML$1(ReachIMKBMentionLookups.scala:143)
[error] at scala.collection.Iterator.foreach(Iterator.scala:941)
[error] at scala.collection.Iterator.foreach$(Iterator.scala:941)
[error] at scala.collection.AbstractIterator.foreach(Iterator.scala:1429)
[error] at scala.collection.IterableLike.foreach(IterableLike.scala:74)
[error] at scala.collection.IterableLike.foreach$(IterableLike.scala:73
[error] at scala.collection.AbstractIterable.foreach(Iterable.scala:56)
[error] at org.clulab.reach.grounding.ReachIMKBMentionLookups$.configuredKBML$lzycompute(ReachIMKBMentionLookups.scala:141)
[error] at org.clulab.reach.grounding.ReachIMKBMentionLookups$.configuredKBML(ReachIMKBMentionLookups.scala:134)
[error] at org.clulab.reach.grounding.ReachGrounder.(ReachGrounder.scala:23)
[error] at org.clulab.reach.ReachSystem.(ReachSystem.scala:41)
[error] at org.clulab.reach.PaperReader$.reachSystem$lzycompute(PaperReader.scala:44)
[error] at org.clulab.reach.PaperReader$.reachSystem(PaperReader.scala:41)
[error] at org.clulab.reach.TestUtils$.(TestUtils.scala:65)
[error] at org.clulab.reach.TestUtils$.(TestUtils.scala)
[error] at org.clulab.reach.DemoTests2.(DemoTests.scala:39)
[error] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
[error] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
[error] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
[error] at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
[error] at java.base/java.lang.Class.newInstance(Class.java:584)
[error] at org.scalatest.tools.Framework$ScalaTestTask.execute(Framework.scala:435)
[error] at sbt.TestRunner.runTest$1(TestFramework.scala:139)
[error] at sbt.TestRunner.run(TestFramework.scala:154)
[error] at sbt.TestFramework$$anon$3$$anonfun$$lessinit$greater$1.$anonfun$apply$1(TestFramework.scala:317)
[error] at sbt.TestFramework$.sbt$TestFramework$$withContextLoader(TestFramework.scala:277)
[error] at sbt.TestFramework$$anon$3$$anonfun$$lessinit$greater$1.apply(TestFramework.scala:317)
[error] at sbt.TestFramework$$anon$3$$anonfun$$lessinit$greater$1.apply(TestFramework.scala:317)
[error] at sbt.TestFunction.apply(TestFramework.scala:329)
[error] at sbt.Tests$.processRunnable$1(Tests.scala:461)
[error] at sbt.Tests$.$anonfun$makeSerial$1(Tests.scala:467)
[error] at sbt.std.Transform$$anon$3.$anonfun$apply$2(Transform.scala:46)
[error] at sbt.std.Transform$$anon$4.work(Transform.scala:68)
[error] at sbt.Execute.$anonfun$submit$2(Execute.scala:282)
[error] at sbt.internal.util.ErrorHandling$.wideConvert(ErrorHandling.scala:23)
[error] at sbt.Execute.work(Execute.scala:291)
[error] at sbt.Execute.$anonfun$submit$1(Execute.scala:282)
[error] at sbt.ConcurrentRestrictions$$anon$4.$anonfun$submitValid$1(ConcurrentRestrictions.scala:265)
[error] at sbt.CompletionService$$anon$2.call(CompletionService.scala:64)
[error] at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
[error] at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
[error] at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
[error] at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
[error] at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
[error] at java.base/java.lang.Thread.run(Thread.java:829)
[error] java.lang.ExceptionInInitializerError
[error] at org.clulab.reach.export.apis.TestRuler.$anonfun$new$1(TestRuler.scala:40)
[error] at org.scalatest.OutcomeOf.outcomeOf(OutcomeOf.scala:85)
[error] at org.scalatest.OutcomeOf.outcomeOf$(OutcomeOf.scala:83)
[error] at org.scalatest.OutcomeOf$.outcomeOf(OutcomeOf.scala:104)
[error] at org.scalatest.Transformer.apply(Transformer.scala:22)
[error] at org.scalatest.Transformer.apply(Transformer.scala:20)
[error] at org.scalatest.FlatSpecLike$$anon$1.apply(FlatSpecLike.scala:1682)
[error] at org.scalatest.TestSuite.withFixture(TestSuite.scala:196)
[error] at org.scalatest.TestSuite.withFixture$(TestSuite.scala:195)
[error] at org.scalatest.FlatSpec.withFixture(FlatSpec.scala:1685)
[error] at org.scalatest.FlatSpecLike.invokeWithFixture$1(FlatSpecLike.scala:1680)
[error] at org.scalatest.FlatSpecLike.$anonfun$runTest$1(FlatSpecLike.scala:1692)
[error] at org.scalatest.SuperEngine.runTestImpl(Engine.scala:289)
[error] at org.scalatest.FlatSpecLike.runTest(FlatSpecLike.scala:1692)
[error] at org.scalatest.FlatSpecLike.runTest$(FlatSpecLike.scala:1674)
[error] at org.scalatest.FlatSpec.runTest(FlatSpec.scala:1685)
[error] at org.scalatest.FlatSpecLike.$anonfun$runTests$1(FlatSpecLike.scala:1750)
[error] at org.scalatest.SuperEngine.$anonfun$runTestsInBranch$1(Engine.scala:396)
[error] at scala.collection.immutable.List.foreach(List.scala:392)
[error] at org.scalatest.SuperEngine.traverseSubNodes$1(Engine.scala:384)
[error] at org.scalatest.SuperEngine.runTestsInBranch(Engine.scala:373)
[error] at org.scalatest.SuperEngine.$anonfun$runTestsInBranch$1(Engine.scala:410)
[error] at scala.collection.immutable.List.foreach(List.scala:392)
[error] at org.scalatest.SuperEngine.traverseSubNodes$1(Engine.scala:384)
[error] at org.scalatest.SuperEngine.runTestsInBranch(Engine.scala:379)
[error] at org.scalatest.SuperEngine.runTestsImpl(Engine.scala:461)
[error] at org.scalatest.FlatSpecLike.runTests(FlatSpecLike.scala:1750)
[error] at org.scalatest.FlatSpecLike.runTests$(FlatSpecLike.scala:1749
[error] at org.scalatest.FlatSpec.runTests(FlatSpec.scala:1685)
[error] at org.scalatest.Suite.run(Suite.scala:1147)
[error] at org.scalatest.Suite.run$(Suite.scala:1129)
[error] at org.scalatest.FlatSpec.org$scalatest$FlatSpecLike$$super$run(FlatSpec.scala:1685)
[error] at org.scalatest.FlatSpecLike.$anonfun$run$1(FlatSpecLike.scala:1795)
[error] at org.scalatest.SuperEngine.runImpl(Engine.scala:521)
[error] at org.scalatest.FlatSpecLike.run(FlatSpecLike.scala:1795)
[error] at org.scalatest.FlatSpecLike.run$(FlatSpecLike.scala:1793)
[error] at org.scalatest.FlatSpec.run(FlatSpec.scala:1685)
[error] at org.scalatest.tools.Framework.org$scalatest$tools$Framework$$runSuite(Framework.scala:314)
[error] at org.scalatest.tools.Framework$ScalaTestTask.execute(Framework.scala:507)
[error] at sbt.TestRunner.runTest$1(TestFramework.scala:139)
[error] at sbt.TestRunner.run(TestFramework.scala:154)
[error] at sbt.TestFramework$$anon$3$$anonfun$$lessinit$greater$1.$anonfun$apply$1(TestFramework.scala:317)
[error] at sbt.TestFramework$.sbt$TestFramework$$withContextLoader(TestFramework.scala:277)
[error] at sbt.TestFramework$$anon$3$$anonfun$$lessinit$greater$1.apply(TestFramework.scala:317)
[error] at sbt.TestFramework$$anon$3$$anonfun$$lessinit$greater$1.apply(TestFramework.scala:317)
[error] at sbt.TestFunction.apply(TestFramework.scala:329)
[error] at sbt.Tests$.processRunnable$1(Tests.scala:461)
[error] at sbt.Tests$.$anonfun$makeSerial$1(Tests.scala:467)
[error] at sbt.std.Transform$$anon$3.$anonfun$apply$2(Transform.scala:46)
[error] at sbt.std.Transform$$anon$4.work(Transform.scala:68)
[error] at sbt.Execute.$anonfun$submit$2(Execute.scala:282)
[error] at sbt.internal.util.ErrorHandling$.wideConvert(ErrorHandling.scala:23)
[error] at sbt.Execute.work(Execute.scala:291)
[error] at sbt.Execute.$anonfun$submit$1(Execute.scala:282)
[error] at sbt.ConcurrentRestrictions$$anon$4.$anonfun$submitValid$1(ConcurrentRestrictions.scala:265)
[error] at sbt.CompletionService$$anon$2.call(CompletionService.scala:64)
[error] at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
[error] at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
[error] at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
[error] at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
[error] at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
[error] at java.base/java.lang.Thread.run(Thread.java:829)
[error] Caused by: java.lang.NullPointerException
[error] at java.base/java.io.Reader.(Reader.java:167)
[error] at java.base/java.io.InputStreamReader.(InputStreamReader.java:125)
[error] at scala.io.BufferedSource.reader(BufferedSource.scala:26)
[error] at scala.io.BufferedSource.bufferedReader(BufferedSource.scala:27)
[error] at scala.io.BufferedSource.charReader$lzycompute(BufferedSource.scala:37)
[error] at scala.io.BufferedSource.charReader(BufferedSource.scala:35)
[error] at scala.io.BufferedSource.scala$io$BufferedSource$$decachedReader(BufferedSource.scala:64)
[error] at scala.io.BufferedSource$BufferedLineIterator.(BufferedSource.scala:69)
[error] at scala.io.BufferedSource.getLines(BufferedSource.scala:88)
[error] at org.clulab.reach.grounding.TsvIMKBFactory.loadFromKBDir(TsvIMKBFactory.scala:48)
[error] at org.clulab.reach.grounding.TsvIMKBFactory.$anonfun$make$1(TsvIMKBFactory.scala:25)
[error] at org.clulab.reach.grounding.TsvIMKBFactory.$anonfun$make$1$adapted(TsvIMKBFactory.scala:24)
[error] at scala.Option.foreach(Option.scala:274)
[error] at org.clulab.reach.grounding.TsvIMKBFactory.make(TsvIMKBFactory.scala:24)
[error] at org.clulab.reach.grounding.ReachIMKBMentionLookups$.buildKb(ReachIMKBMentionLookups.scala:127)
[error] at org.clulab.reach.grounding.ReachIMKBMentionLookups$.$anonfun$configuredKBML$1(ReachIMKBMentionLookups.scala:143)
[error] at scala.collection.Iterator.foreach(Iterator.scala:941)
[error] at scala.collection.Iterator.foreach$(Iterator.scala:941)
[error] at scala.collection.AbstractIterator.foreach(Iterator.scala:1429)
[error] at scala.collection.IterableLike.foreach(IterableLike.scala:74)
[error] at scala.collection.IterableLike.foreach$(IterableLike.scala:73
[error] at scala.collection.AbstractIterable.foreach(Iterable.scala:56)
[error] at org.clulab.reach.grounding.ReachIMKBMentionLookups$.configuredKBML$lzycompute(ReachIMKBMentionLookups.scala:141)
[error] at org.clulab.reach.grounding.ReachIMKBMentionLookups$.configuredKBML(ReachIMKBMentionLookups.scala:134)
[error] at org.clulab.reach.grounding.ReachGrounder.(ReachGrounder.scala:23)
[error] at org.clulab.reach.ReachSystem.(ReachSystem.scala:41)
[error] at org.clulab.reach.export.apis.Ruler$.(Ruler.scala:18)
[error] at org.clulab.reach.export.apis.Ruler$.(Ruler.scala)
[error] at org.clulab.reach.export.apis.TestRuler.$anonfun$new$1(TestRuler.scala:40)
[error] at org.scalatest.OutcomeOf.outcomeOf(OutcomeOf.scala:85)
[error] at org.scalatest.OutcomeOf.outcomeOf$(OutcomeOf.scala:83)
[error] at org.scalatest.OutcomeOf$.outcomeOf(OutcomeOf.scala:104)
[error] at org.scalatest.Transformer.apply(Transformer.scala:22)
[error] at org.scalatest.Transformer.apply(Transformer.scala:20)
[error] at org.scalatest.FlatSpecLike$$anon$1.apply(FlatSpecLike.scala:1682)
[error] at org.scalatest.TestSuite.withFixture(TestSuite.scala:196)
[error] at org.scalatest.TestSuite.withFixture$(TestSuite.scala:195)
[error] at org.scalatest.FlatSpec.withFixture(FlatSpec.scala:1685)
[error] at org.scalatest.FlatSpecLike.invokeWithFixture$1(FlatSpecLike.scala:1680)
[error] at org.scalatest.FlatSpecLike.$anonfun$runTest$1(FlatSpecLike.scala:1692)
[error] at org.scalatest.SuperEngine.runTestImpl(Engine.scala:289)
[error] at org.scalatest.FlatSpecLike.runTest(FlatSpecLike.scala:1692)
[error] at org.scalatest.FlatSpecLike.runTest$(FlatSpecLike.scala:1674)
[error] at org.scalatest.FlatSpec.runTest(FlatSpec.scala:1685)
[error] at org.scalatest.FlatSpecLike.$anonfun$runTests$1(FlatSpecLike.scala:1750)
[error] at org.scalatest.SuperEngine.$anonfun$runTestsInBranch$1(Engine.scala:396)
[error] at scala.collection.immutable.List.foreach(List.scala:392)
[error] at org.scalatest.SuperEngine.traverseSubNodes$1(Engine.scala:384)
[error] at org.scalatest.SuperEngine.runTestsInBranch(Engine.scala:373)
[error] at org.scalatest.SuperEngine.$anonfun$runTestsInBranch$1(Engine.scala:410)
[error] at scala.collection.immutable.List.foreach(List.scala:392)
[error] at org.scalatest.SuperEngine.traverseSubNodes$1(Engine.scala:384)
[error] at org.scalatest.SuperEngine.runTestsInBranch(Engine.scala:379)
[error] at org.scalatest.SuperEngine.runTestsImpl(Engine.scala:461)
[error] at org.scalatest.FlatSpecLike.runTests(FlatSpecLike.scala:1750)
[error] at org.scalatest.FlatSpecLike.runTests$(FlatSpecLike.scala:1749
[error] at org.scalatest.FlatSpec.runTests(FlatSpec.scala:1685)
[error] at org.scalatest.Suite.run(Suite.scala:1147)
[error] at org.scalatest.Suite.run$(Suite.scala:1129)
[error] at org.scalatest.FlatSpec.org$scalatest$FlatSpecLike$$super$run(FlatSpec.scala:1685)
[error] at org.scalatest.FlatSpecLike.$anonfun$run$1(FlatSpecLike.scala:1795)
[error] at org.scalatest.SuperEngine.runImpl(Engine.scala:521)
[error] at org.scalatest.FlatSpecLike.run(FlatSpecLike.scala:1795)
[error] at org.scalatest.FlatSpecLike.run$(FlatSpecLike.scala:1793)
[error] at org.scalatest.FlatSpec.run(FlatSpec.scala:1685)
[error] at org.scalatest.tools.Framework.org$scalatest$tools$Framework$$runSuite(Framework.scala:314)
[error] at org.scalatest.tools.Framework$ScalaTestTask.execute(Framework.scala:507)
[error] at sbt.TestRunner.runTest$1(TestFramework.scala:139)
[error] at sbt.TestRunner.run(TestFramework.scala:154)
[error] at sbt.TestFramework$$anon$3$$anonfun$$lessinit$greater$1.$anonfun$apply$1(TestFramework.scala:317)
[error] at sbt.TestFramework$.sbt$TestFramework$$withContextLoader(TestFramework.scala:277)
[error] at sbt.TestFramework$$anon$3$$anonfun$$lessinit$greater$1.apply(TestFramework.scala:317)
[error] at sbt.TestFramework$$anon$3$$anonfun$$lessinit$greater$1.apply(TestFramework.scala:317)
[error] at sbt.TestFunction.apply(TestFramework.scala:329)
[error] at sbt.Tests$.processRunnable$1(Tests.scala:461)
[error] at sbt.Tests$.$anonfun$makeSerial$1(Tests.scala:467)
[error] at sbt.std.Transform$$anon$3.$anonfun$apply$2(Transform.scala:46)
[error] at sbt.std.Transform$$anon$4.work(Transform.scala:68)
[error] at sbt.Execute.$anonfun$submit$2(Execute.scala:282)
[error] at sbt.internal.util.ErrorHandling$.wideConvert(ErrorHandling.scala:23)
[error] at sbt.Execute.work(Execute.scala:291)
[error] at sbt.Execute.$anonfun$submit$1(Execute.scala:282)
[error] at sbt.ConcurrentRestrictions$$anon$4.$anonfun$submitValid$1(ConcurrentRestrictions.scala:265)
[error] at sbt.CompletionService$$anon$2.call(CompletionService.scala:64)
[error] at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
[error] at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
[error] at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
[error] at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
[error] at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
[error] at java.base/java.lang.Thread.run(Thread.java:829)
[error] java.lang.ExceptionInInitializerError
[error] at org.clulab.reach.export.TestReachCLI.(TestReachCLI.scala:16)
[error] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
[error] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
[error] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
[error] at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
[error] at java.base/java.lang.Class.newInstance(Class.java:584)
[error] at org.scalatest.tools.Framework$ScalaTestTask.execute(Framework.scala:435)
[error] at sbt.TestRunner.runTest$1(TestFramework.scala:139)
[error] at sbt.TestRunner.run(TestFramework.scala:154)
[error] at sbt.TestFramework$$anon$3$$anonfun$$lessinit$greater$1.$anonfun$apply$1(TestFramework.scala:317)
[error] at sbt.TestFramework$.sbt$TestFramework$$withContextLoader(TestFramework.scala:277)
[error] at sbt.TestFramework$$anon$3$$anonfun$$lessinit$greater$1.apply(TestFramework.scala:317)
[error] at sbt.TestFramework$$anon$3$$anonfun$$lessinit$greater$1.apply(TestFramework.scala:317)
[error] at sbt.TestFunction.apply(TestFramework.scala:329)
[error] at sbt.Tests$.processRunnable$1(Tests.scala:461)
[error] at sbt.Tests$.$anonfun$makeSerial$1(Tests.scala:467)
[error] at sbt.std.Transform$$anon$3.$anonfun$apply$2(Transform.scala:46)
[error] at sbt.std.Transform$$anon$4.work(Transform.scala:68)
[error] at sbt.Execute.$anonfun$submit$2(Execute.scala:282)
[error] at sbt.internal.util.ErrorHandling$.wideConvert(ErrorHandling.scala:23)
[error] at sbt.Execute.work(Execute.scala:291)
[error] at sbt.Execute.$anonfun$submit$1(Execute.scala:282)
[error] at sbt.ConcurrentRestrictions$$anon$4.$anonfun$submitValid$1(ConcurrentRestrictions.scala:265)
[error] at sbt.CompletionService$$anon$2.call(CompletionService.scala:64)
[error] at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
[error] at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
[error] at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
[error] at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
[error] at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
[error] at java.base/java.lang.Thread.run(Thread.java:829)
[error] Caused by: java.lang.NullPointerException
[error] at java.base/java.io.Reader.(Reader.java:167)
[error] at java.base/java.io.InputStreamReader.(InputStreamReader.java:125)
[error] at scala.io.BufferedSource.reader(BufferedSource.scala:26)
[error] at scala.io.BufferedSource.bufferedReader(BufferedSource.scala:27)
[error] at scala.io.BufferedSource.charReader$lzycompute(BufferedSource.scala:37)
[error] at scala.io.BufferedSource.charReader(BufferedSource.scala:35)
[error] at scala.io.BufferedSource.scala$io$BufferedSource$$decachedReader(BufferedSource.scala:64)
[error] at scala.io.BufferedSource$BufferedLineIterator.(BufferedSource.scala:69)
[error] at scala.io.BufferedSource.getLines(BufferedSource.scala:88)
[error] at org.clulab.reach.grounding.TsvIMKBFactory.loadFromKBDir(TsvIMKBFactory.scala:48)
[error] at org.clulab.reach.grounding.TsvIMKBFactory.$anonfun$make$1(TsvIMKBFactory.scala:25)
[error] at org.clulab.reach.grounding.TsvIMKBFactory.$anonfun$make$1$adapted(TsvIMKBFactory.scala:24)
[error] at scala.Option.foreach(Option.scala:274)
[error] at org.clulab.reach.grounding.TsvIMKBFactory.make(TsvIMKBFactory.scala:24)
[error] at org.clulab.reach.grounding.ReachIMKBMentionLookups$.buildKb(ReachIMKBMentionLookups.scala:127)
[error] at org.clulab.reach.grounding.ReachIMKBMentionLookups$.$anonfun$configuredKBML$1(ReachIMKBMentionLookups.scala:143)
[error] at scala.collection.Iterator.foreach(Iterator.scala:941)
[error] at scala.collection.Iterator.foreach$(Iterator.scala:941)
[error] at scala.collection.AbstractIterator.foreach(Iterator.scala:1429)
[error] at scala.collection.IterableLike.foreach(IterableLike.scala:74)
[error] at scala.collection.IterableLike.foreach$(IterableLike.scala:73
[error] at scala.collection.AbstractIterable.foreach(Iterable.scala:56)
[error] at org.clulab.reach.grounding.ReachIMKBMentionLookups$.configuredKBML$lzycompute(ReachIMKBMentionLookups.scala:141)
[error] at org.clulab.reach.grounding.ReachIMKBMentionLookups$.configuredKBML(ReachIMKBMentionLookups.scala:134)
[error] at org.clulab.reach.grounding.ReachGrounder.(ReachGrounder.scala:23)
[error] at org.clulab.reach.ReachSystem.(ReachSystem.scala:41)
[error] at org.clulab.reach.PaperReader$.reachSystem$lzycompute(PaperReader.scala:44)
[error] at org.clulab.reach.PaperReader$.reachSystem(PaperReader.scala:41)
[error] at org.clulab.reach.TestUtils$.(TestUtils.scala:65)
[error] at org.clulab.reach.TestUtils$.(TestUtils.scala)
[error] at org.clulab.reach.export.TestReachCLI.(TestReachCLI.scala:16)
[error] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
[error] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
[error] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
[error] at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
[error] at java.base/java.lang.Class.newInstance(Class.java:584)
[error] at org.scalatest.tools.Framework$ScalaTestTask.execute(Framework.scala:435)
[error] at sbt.TestRunner.runTest$1(TestFramework.scala:139)
[error] at sbt.TestRunner.run(TestFramework.scala:154)
[error] at sbt.TestFramework$$anon$3$$anonfun$$lessinit$greater$1.$anonfun$apply$1(TestFramework.scala:317)
[error] at sbt.TestFramework$.sbt$TestFramework$$withContextLoader(TestFramework.scala:277)
[error] at sbt.TestFramework$$anon$3$$anonfun$$lessinit$greater$1.apply(TestFramework.scala:317)
[error] at sbt.TestFramework$$anon$3$$anonfun$$lessinit$greater$1.apply(TestFramework.scala:317)
[error] at sbt.TestFunction.apply(TestFramework.scala:329)
[error] at sbt.Tests$.processRunnable$1(Tests.scala:461)
[error] at sbt.Tests$.$anonfun$makeSerial$1(Tests.scala:467)
[error] at sbt.std.Transform$$anon$3.$anonfun$apply$2(Transform.scala:46)
[error] at sbt.std.Transform$$anon$4.work(Transform.scala:68)
[error] at sbt.Execute.$anonfun$submit$2(Execute.scala:282)
[error] at sbt.internal.util.ErrorHandling$.wideConvert(ErrorHandling.scala:23)
[error] at sbt.Execute.work(Execute.scala:291)
[error] at sbt.Execute.$anonfun$submit$1(Execute.scala:282)
[error] at sbt.ConcurrentRestrictions$$anon$4.$anonfun$submitValid$1(ConcurrentRestrictions.scala:265)
[error] at sbt.CompletionService$$anon$2.call(CompletionService.scala:64)
[error] at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
[error] at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
[error] at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
[error] at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
[error] at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
[error] at java.base/java.lang.Thread.run(Thread.java:829)
[error] (processors / Test / test) sbt.TestsFailedException: Tests unsuccessful
[error] (main / Test / executeTests) java.lang.ExceptionInInitializerError
[error] (causalAssembly / Test / test) sbt.TestsFailedException: Tests unsuccessful
[error] (export / Test / executeTests) java.lang.ExceptionInInitializerError
[error] (Test / executeTests) java.lang.ExceptionInInitializerError
[error] Total time: 623 s (10:23), completed Sep 7, 2023, 5:40:45 PM

Answer 10 · 2023-09-07T23:43:40.000Z

Thanks. There's definitely something wrong. The one message that looks strange is

[warn] Getting the hostname MacBook-Pro-81.local was slow (5002.640167 ms). This is likely because the computer's hostname is not set. You can set the hostname with the command: scutil --set HostName $(scutil --get LocalHostName).

When Java tries to access resources, it does use a URL internally and I wonder whether this problem might be preventing Java from reading from the resources it needs. I assume that you have the file bioner.dat among the source code.

I suggest that you look into fixing the the hostname problem. I'm not sure whether the suggested command is the best one to use. It would be good to see a test run without the warning and then hopefully no failures.

Answer 11 · 2023-09-08T16:01:23.000Z

fixed hostname and rerun the sbt test, it still popped a lot of errors. Actually, there are several files missing under the directory org/clulab/reach. I think it might be the problem about source code( install REACH by zip)

Answer 12 · 2023-09-08T16:39:45.000Z

I downloaded reach-master.zip with 118,238,760 bytes, unzipped, and ran the tests without problem. Perhaps something went wrong in your case, though. I wonder if the hostname problem plus possible disk or downloading issues indicate a problem with the computer there. It's probably worth trying to reinstall reach.

Answer 13 · 2023-09-08T19:53:00.000Z

Yes, it works right now after I reinstall the reach.

Answer 14 · 2023-09-08T20:09:55.000Z

Wonderful! Thanks for your patience.

Don't know why messages like the below popped out: Any solution to fix that?

Don't know why messages like the below popped out:
Any solution to fix that?