{"action":"created","issue":{"url":"https://api.github.com/repos/keeps/roda/issues/547","repository_url":"https://api.github.com/repos/keeps/roda","labels_url":"https://api.github.com/repos/keeps/roda/issues/547/labels{/name}","comments_url":"https://api.github.com/repos/keeps/roda/issues/547/comments","events_url":"https://api.github.com/repos/keeps/roda/issues/547/events","html_url":"https://github.com/keeps/roda/issues/547","id":177480136,"number":547,"title":"Running roda-core from command line doesn't init 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Description\r\n\r\nRunning roda-core jar from command line doesn't init RodaCoreFactory properly. \r\nThe log shows this error:\r\n```\r\ncom.typesafe.config.ConfigException$IO: reference.conf @ jar:file:/home/tobias/work/keeps/roda.git/roda-core/roda-core/target/roda-core-2.0.0-SNAPSHOT-jar-with-dependencies.jar!/reference.conf: read error: Stream closed\r\n```\r\nThe variable `RodaCoreFactory.ldapUtility` is `null`.\r\n\r\n**Running RodaCoreFactory from inside IntelliJ works fine. So, maybe the problem has something to do with the way roda-core-...with-dependencies.jar is produced.**\r\n\r\n### Steps to reproduce\r\n\r\n1. `mvn -Proda-core-jar clean package`\r\n2. `java -jar roda-core/roda-core/target/roda-core-2.0.0-SNAPSHOT-jar-with-dependencies.jar`\r\n\r\nThe `roda-core.log` shows:\r\n```\r\n2016-09-16 18:34:58,453 [main] DEBUG org.roda.core.RodaCoreFactory - RODA HOME is /home/tobias/.roda\r\n2016-09-16 18:34:58,804 [main] INFO  org.roda.core.RodaCoreFactory - Copy files from classpath prefix=config/, destination=/home/tobias/.roda/example-config, removePrefix=true, excludePaths=[config/ldap, config/index], #resources=152\r\n2016-09-16 18:34:58,856 [main] DEBUG org.roda.core.RodaCoreFactory - Finished instantiating essential directories\r\n2016-09-16 18:34:58,921 [main] DEBUG org.roda.core.RodaCoreFactory - Finished loading roda-core.properties & roda-core-formats.properties\r\n2016-09-16 18:34:58,933 [main] DEBUG org.roda.core.RodaCoreFactory - Finished loading roda-roles.properties\r\n2016-09-16 18:34:58,941 [main] DEBUG org.roda.core.RodaCoreFactory - Going to instantiate Filesystem on '/home/tobias/.roda/data/storage'\r\n2016-09-16 18:34:58,946 [main] DEBUG org.roda.core.RodaCoreFactory - Finished instantiating storage...\r\n2016-09-16 18:34:58,960 [main] DEBUG org.roda.core.RodaCoreFactory - Finished instantiating model...\r\n2016-09-16 18:34:58,960 [main] DEBUG org.roda.core.RodaCoreFactory - Finished instantiating storage & model\r\n2016-09-16 18:34:59,176 [main] INFO  org.roda.core.RodaCoreFactory - Copy files from classpath prefix=config/index/, destination=/tmp/index6613177610829922652, removePrefix=false, excludePaths=[], #resources=121\r\n2016-09-16 18:34:59,255 [main] INFO  org.roda.core.RodaCoreFactory - Using SOLR home: /tmp/index6613177610829922652/config/index\r\n2016-09-16 18:35:04,884 [main] DEBUG org.roda.core.RodaCoreFactory - Finished instantiating solr & index\r\n2016-09-16 18:35:04,895 [main] INFO  org.roda.core.plugins.PluginManager - PluginManager init OK\r\n2016-09-16 18:35:04,897 [main] DEBUG org.roda.core.RodaCoreFactory - Finished instantiating plugin manager\r\n2016-09-16 18:35:05,217 [main] ERROR org.roda.core.RodaCoreFactory - Error instantiating RodaCoreFactory\r\ncom.typesafe.config.ConfigException$IO: reference.conf @ jar:file:/home/tobias/work/keeps/roda.git/roda-core/roda-core/target/roda-core-2.0.0-SNAPSHOT-jar-with-dependencies.jar!/reference.conf: read error: Stream closed\r\n\tat com.typesafe.config.impl.Tokenizer$TokenIterator.nextCharRaw(Tokenizer.java:159)\r\n\tat com.typesafe.config.impl.Tokenizer$TokenIterator.pullUnquotedText(Tokenizer.java:340)\r\n\tat com.typesafe.config.impl.Tokenizer$TokenIterator.pullNextToken(Tokenizer.java:637)\r\n\tat com.typesafe.config.impl.Tokenizer$TokenIterator.queueNextToken(Tokenizer.java:660)\r\n\tat com.typesafe.config.impl.Tokenizer$TokenIterator.next(Tokenizer.java:678)\r\n\tat com.typesafe.config.impl.Tokenizer$TokenIterator.next(Tokenizer.java:63)\r\n\tat com.typesafe.config.impl.ConfigDocumentParser$ParseContext.popToken(ConfigDocumentParser.java:45)\r\n\tat com.typesafe.config.impl.ConfigDocumentParser$ParseContext.nextToken(ConfigDocumentParser.java:51)\r\n\tat com.typesafe.config.impl.ConfigDocumentParser$ParseContext.checkElementSeparator(ConfigDocumentParser.java:124)\r\n\tat com.typesafe.config.impl.ConfigDocumentParser$ParseContext.parseObject(ConfigDocumentParser.java:462)\r\n\tat com.typesafe.config.impl.ConfigDocumentParser$ParseContext.parseValue(ConfigDocumentParser.java:247)\r\n\tat com.typesafe.config.impl.ConfigDocumentParser$ParseContext.parseObject(ConfigDocumentParser.java:405)\r\n\tat com.typesafe.config.impl.ConfigDocumentParser$ParseContext.parseValue(ConfigDocumentParser.java:247)\r\n\tat com.typesafe.config.impl.ConfigDocumentParser$ParseContext.parseObject(ConfigDocumentParser.java:405)\r\n\tat com.typesafe.config.impl.ConfigDocumentParser$ParseContext.parseValue(ConfigDocumentParser.java:247)\r\n\tat com.typesafe.config.impl.ConfigDocumentParser$ParseContext.parseObject(ConfigDocumentParser.java:405)\r\n\tat com.typesafe.config.impl.ConfigDocumentParser$ParseContext.parse(ConfigDocumentParser.java:595)\r\n\tat com.typesafe.config.impl.ConfigDocumentParser.parse(ConfigDocumentParser.java:14)\r\n\tat com.typesafe.config.impl.Parseable.rawParseValue(Parseable.java:260)\r\n\tat com.typesafe.config.impl.Parseable.rawParseValue(Parseable.java:248)\r\n\tat com.typesafe.config.impl.Parseable.parseValue(Parseable.java:180)\r\n\tat com.typesafe.config.impl.Parseable.parseValue(Parseable.java:174)\r\n\tat com.typesafe.config.impl.Parseable.parseValue(Parseable.java:307)\r\n\tat com.typesafe.config.impl.Parseable$ParseableResources.rawParseValue(Parseable.java:747)\r\n\tat com.typesafe.config.impl.Parseable$ParseableResources.rawParseValue(Parseable.java:710)\r\n\tat com.typesafe.config.impl.Parseable.parseValue(Parseable.java:180)\r\n\tat com.typesafe.config.impl.Parseable.parseValue(Parseable.java:174)\r\n\tat com.typesafe.config.impl.Parseable.parse(Parseable.java:299)\r\n\tat com.typesafe.config.impl.ConfigImpl$1.call(ConfigImpl.java:373)\r\n\tat com.typesafe.config.impl.ConfigImpl$1.call(ConfigImpl.java:367)\r\n\tat com.typesafe.config.impl.ConfigImpl$LoaderCache.getOrElseUpdate(ConfigImpl.java:65)\r\n\tat com.typesafe.config.impl.ConfigImpl.computeCachedConfig(ConfigImpl.java:92)\r\n\tat com.typesafe.config.impl.ConfigImpl.defaultReference(ConfigImpl.java:367)\r\n\tat com.typesafe.config.ConfigFactory.defaultReference(ConfigFactory.java:413)\r\n\tat akka.actor.ActorSystem$Settings.<init>(ActorSystem.scala:160)\r\n\tat akka.actor.ActorSystemImpl.<init>(ActorSystem.scala:522)\r\n\tat akka.actor.ActorSystem$.apply(ActorSystem.scala:142)\r\n\tat akka.actor.ActorSystem$.apply(ActorSystem.scala:119)\r\n\tat akka.actor.ActorSystem$.create(ActorSystem.scala:67)\r\n\tat akka.actor.ActorSystem.create(ActorSystem.scala)\r\n\tat org.roda.core.plugins.orchestrate.AkkaEmbeddedPluginOrchestrator.<init>(AkkaEmbeddedPluginOrchestrator.java:98)\r\n\tat org.roda.core.RodaCoreFactory.instantiateMasterNodeSpecificObjects(RodaCoreFactory.java:702)\r\n\tat org.roda.core.RodaCoreFactory.instantiateNodeSpecificObjects(RodaCoreFactory.java:664)\r\n\tat org.roda.core.RodaCoreFactory.instantiate(RodaCoreFactory.java:272)\r\n\tat org.roda.core.RodaCoreFactory.instantiateMaster(RodaCoreFactory.java:207)\r\n\tat org.roda.core.RodaCoreFactory.instantiate(RodaCoreFactory.java:196)\r\n\tat org.roda.core.RodaCoreFactory.main(RodaCoreFactory.java:1447)\r\nCaused by: java.io.IOException: Stream closed\r\n\tat java.util.zip.InflaterInputStream.ensureOpen(InflaterInputStream.java:67)\r\n\tat java.util.zip.InflaterInputStream.read(InflaterInputStream.java:142)\r\n\tat java.io.FilterInputStream.read(FilterInputStream.java:133)\r\n\tat sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284)\r\n\tat sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326)\r\n\tat sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178)\r\n\tat java.io.InputStreamReader.read(InputStreamReader.java:184)\r\n\tat java.io.BufferedReader.fill(BufferedReader.java:161)\r\n\tat java.io.BufferedReader.read(BufferedReader.java:182)\r\n\tat com.typesafe.config.impl.Tokenizer$TokenIterator.nextCharRaw(Tokenizer.java:156)\r\n\t... 46 common frames omitted\r\n2016-09-16 18:35:05,220 [main] INFO  org.roda.core.RodaCoreFactory - RODA Core loading completed with some errors!!! See logs because these errors might cause instability in the system.\r\n```"},"comment":{"url":"https://api.github.com/repos/keeps/roda/issues/comments/248241079","html_url":"https://github.com/keeps/roda/issues/547#issuecomment-248241079","issue_url":"https://api.github.com/repos/keeps/roda/issues/547","id":248241079,"user":{"login":"hsilva-keep","id":1315759,"avatar_url":"https://avatars.githubusercontent.com/u/1315759?v=3","gravatar_id":"","url":"https://api.github.com/users/hsilva-keep","html_url":"https://github.com/hsilva-keep","followers_url":"https://api.github.com/users/hsilva-keep/followers","following_url":"https://api.github.com/users/hsilva-keep/following{/other_user}","gists_url":"https://api.github.com/users/hsilva-keep/gists{/gist_id}","starred_url":"https://api.github.com/users/hsilva-keep/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hsilva-keep/subscriptions","organizations_url":"https://api.github.com/users/hsilva-keep/orgs","repos_url":"https://api.github.com/users/hsilva-keep/repos","events_url":"https://api.github.com/users/hsilva-keep/events{/privacy}","received_events_url":"https://api.github.com/users/hsilva-keep/received_events","type":"User","site_admin":false},"created_at":"2016-09-20T08:44:50Z","updated_at":"2016-09-20T08:44:50Z","body":"@rui-castro you've tried but probably you didn't removed your RODA_HOME folder."}}
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