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Default application.json not found in classpath in precompiled jar on github (affecting multiple releases tested version 86 and 85).
Tested to not be affected version 79/56. Main error below. Should be an easy fix.
Exception in thread "main" com.typesafe.config.ConfigException$IO: application: application.conf: java.io.IOException: resource not found on classpath: application.conf, application.json: java.io.IOException: resource not found on classpath: application.json, application.properties: java.io.IOException: resource not found on classpath: application.properties
at com.typesafe.config.impl.SimpleIncluder.fromBasename(SimpleIncluder.java:236)
at com.typesafe.config.impl.ConfigImpl.parseResourcesAnySyntax(ConfigImpl.java:133)
at com.typesafe.config.ConfigFactory.parseResourcesAnySyntax(ConfigFactory.java:1083)
at com.typesafe.config.impl.SimpleIncluder.includeResourceWithoutFallback(SimpleIncluder.java:123)
at com.typesafe.config.impl.SimpleIncluder.includeResources(SimpleIncluder.java:109)
at com.typesafe.config.impl.ConfigParser$ParseContext.parseInclude(ConfigParser.java:181)
at com.typesafe.config.impl.ConfigParser$ParseContext.parseObject(ConfigParser.java:237)
at com.typesafe.config.impl.ConfigParser$ParseContext.parseValue(ConfigParser.java:103)
at com.typesafe.config.impl.ConfigParser$ParseContext.parse(ConfigParser.java:415)
at com.typesafe.config.impl.ConfigParser.parse(ConfigParser.java:25)
at com.typesafe.config.impl.Parseable.rawParseValue(Parseable.java:263)
at com.typesafe.config.impl.Parseable.rawParseValue(Parseable.java:250)
at com.typesafe.config.impl.Parseable.parseValue(Parseable.java:180)
at com.typesafe.config.impl.Parseable.parseValue(Parseable.java:174)
at com.typesafe.config.impl.Parseable.parse(Parseable.java:301)
at com.typesafe.config.ConfigFactory.parseFile(ConfigFactory.java:793)
at com.typesafe.config.ConfigFactory.parseApplicationReplacement(ConfigFactory.java:1166)
at com.typesafe.config.DefaultConfigLoadingStrategy.parseApplicationConfig(DefaultConfigLoadingStrategy.java:11)
at com.typesafe.config.ConfigFactory.defaultApplication(ConfigFactory.java:532)
at com.typesafe.config.ConfigFactory$1.call(ConfigFactory.java:264)
at com.typesafe.config.ConfigFactory$1.call(ConfigFactory.java:261)
at com.typesafe.config.impl.ConfigImpl$LoaderCache.getOrElseUpdate(ConfigImpl.java:66)
at com.typesafe.config.impl.ConfigImpl.computeCachedConfig(ConfigImpl.java:93)
at com.typesafe.config.ConfigFactory.load(ConfigFactory.java:261)
at com.typesafe.config.ConfigFactory.load(ConfigFactory.java:237)
at cromwell.languages.util.ImportResolver$HttpResolver$.apply(ImportResolver.scala:237)
at womtool.input.WomGraphMaker$.importResolvers$lzycompute$1(WomGraphMaker.scala:28)
at womtool.input.WomGraphMaker$.importResolvers$1(WomGraphMaker.scala:27)
at womtool.input.WomGraphMaker$.$anonfun$getBundleAndFactory$1(WomGraphMaker.scala:39)
at scala.util.Either.flatMap(Either.scala:352)
at womtool.input.WomGraphMaker$.getBundleAndFactory(WomGraphMaker.scala:30)
at womtool.input.WomGraphMaker$.fromFiles(WomGraphMaker.scala:46)
at womtool.validate.Validate$.validate(Validate.scala:26)
at womtool.WomtoolMain$.dispatchCommand(WomtoolMain.scala:54)
at womtool.WomtoolMain$.runWomtool(WomtoolMain.scala:161)
at womtool.WomtoolMain$.delayedEndpoint$womtool$WomtoolMain$1(WomtoolMain.scala:166)
at womtool.WomtoolMain$delayedInit$body.apply(WomtoolMain.scala:27)
at scala.Function0.apply$mcV$sp(Function0.scala:42)
at scala.Function0.apply$mcV$sp$(Function0.scala:42)
at scala.runtime.AbstractFunction0.apply$mcV$sp(AbstractFunction0.scala:17)
at scala.App.$anonfun$main$1(App.scala:98)
at scala.App.$anonfun$main$1$adapted(App.scala:98)
at scala.collection.IterableOnceOps.foreach(IterableOnce.scala:575)
at scala.collection.IterableOnceOps.foreach$(IterableOnce.scala:573)
at scala.collection.AbstractIterable.foreach(Iterable.scala:933)
at scala.App.main(App.scala:98)
at scala.App.main$(App.scala:96)
at womtool.WomtoolMain$.main(WomtoolMain.scala:27)
at womtool.WomtoolMain.main(WomtoolMain.scala)
Caused by: com.typesafe.config.ConfigException$IO: application.conf: java.io.IOException: resource not found on classpath: application.conf
at com.typesafe.config.impl.Parseable.parseValue(Parseable.java:190)
at com.typesafe.config.impl.Parseable.parseValue(Parseable.java:174)
at com.typesafe.config.impl.Parseable.parse(Parseable.java:152)
at com.typesafe.config.impl.SimpleIncluder.fromBasename(SimpleIncluder.java:185)
... 48 more
Caused by: java.io.IOException: resource not found on classpath: application.conf
at com.typesafe.config.impl.Parseable$ParseableResources.rawParseValue(Parseable.java:726)
at com.typesafe.config.impl.Parseable$ParseableResources.rawParseValue(Parseable.java:701)
at com.typesafe.config.impl.Parseable.parseValue(Parseable.java:180)
... 51 more
Default application.json not found in classpath in precompiled jar on github (affecting multiple releases tested version 86 and 85).
Tested to not be affected version 79/56. Main error below. Should be an easy fix.
The backend I'm running on is slurm and local
Workflow link
https://github.com/mmterpstra/Bestie
Below are the first few lines of the config shown.
OS and java version
Centos7 and Java/11.0.16 (openjdk)
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