{"action":"created","issue":{"url":"https://api.github.com/repos/clulab/eidos/issues/443","repository_url":"https://api.github.com/repos/clulab/eidos","labels_url":"https://api.github.com/repos/clulab/eidos/issues/443/labels{/name}","comments_url":"https://api.github.com/repos/clulab/eidos/issues/443/comments","events_url":"https://api.github.com/repos/clulab/eidos/issues/443/events","html_url":"https://github.com/clulab/eidos/issues/443","id":362745330,"node_id":"MDU6SXNzdWUzNjI3NDUzMzA=","number":443,"title":"Time normalization config in eidos.conf and reference.conf","user":{"login":"bgyori","id":5939016,"node_id":"MDQ6VXNlcjU5MzkwMTY=","avatar_url":"https://avatars0.githubusercontent.com/u/5939016?v=4","gravatar_id":"","url":"https://api.github.com/users/bgyori","html_url":"https://github.com/bgyori","followers_url":"https://api.github.com/users/bgyori/followers","following_url":"https://api.github.com/users/bgyori/following{/other_user}","gists_url":"https://api.github.com/users/bgyori/gists{/gist_id}","starred_url":"https://api.github.com/users/bgyori/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bgyori/subscriptions","organizations_url":"https://api.github.com/users/bgyori/orgs","repos_url":"https://api.github.com/users/bgyori/repos","events_url":"https://api.github.com/users/bgyori/events{/privacy}","received_events_url":"https://api.github.com/users/bgyori/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-09-21T19:26:22Z","updated_at":"2018-09-21T20:14:33Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"I've been trying to configure Eidos to use the time normalization feature and I'm running into some issues. These are 3 issues here but they are related so I'm putting them all here.\r\n\r\nFirst, I am wondering if some of the differences in `eidos.conf` and `reference.conf` are on purpose or not.\r\n\r\n1. In reference.conf timeNormModelPath is set to\r\n```\r\ntimeNormModelPath = /org/clulab/wm/eidos/english/models/timenorm_model.hdf5                                                \r\n```\r\nwhereas in eidos.conf it is set to\r\n```\r\ntimeNormModelPath = /org/clulab/wm/eidos/models/timenorm_model.hdf5\r\n```\r\nI think between the two, the latter is the better default setting since timenorm_model.hdf is part of the repo at org/clulab/wm/eidos/models/timenorm_model.hdf5. Should I update the default reference.conf to use this path?\r\n\r\n2. Another inconsistency between the two conf files is that in `reference.conf`\r\n```\r\nuseTimeNorm = false\r\n```\r\nis set but there is no `useTimeNorm` row in `eidos.conf`. Would it make sense to include the same row with the same default value in eidos.conf as well?\r\n\r\n3. Now, using the settings as follows:\r\n```\r\ntimeNormModelPath = /org/clulab/wm/eidos/models/timenorm_model.hdf5\r\n...\r\nuseTimeNorm = true\r\n```\r\nand running\r\n```\r\njava -Xmx12G -cp /Users/ben/tmp/eidos/target/scala-2.12/eidos-assembly-0.2.2-SNAPSHOT.jar org.clulab.wm.eidos.apps.ExtractFromDirectory /Users/ben/tmp/eidos/docs /Users/ben/tmp/eidos/docs\r\n```\r\nI get\r\n\r\n```\r\n15:22:16.328 [scala-execution-context-global-11] INFO  e.s.nlp.pipeline.StanfordCoreNLP - Adding annotator pos\r\n15:22:17.500 [scala-execution-context-global-11] INFO  e.s.nlp.tagger.maxent.MaxentTagger - Loading POS tagger from edu/stanford/nlp/models/pos-tagger/english-left3words/english-left3words-distsim.tagger ... done [1.2 sec].\r\njar:file:/Users/ben/tmp/eidos/target/scala-2.12/eidos-assembly-0.2.2-SNAPSHOT.jar!/org/clulab/wm/eidos/models/timenorm_model.hdf5\r\nException in thread \"main\" java.nio.file.FileSystemNotFoundException\r\n\tat com.sun.nio.zipfs.ZipFileSystemProvider.getFileSystem(ZipFileSystemProvider.java:171)\r\n\tat com.sun.nio.zipfs.ZipFileSystemProvider.getPath(ZipFileSystemProvider.java:157)\r\n\tat java.nio.file.Paths.get(Paths.java:143)\r\n\tat org.clulab.wm.eidos.EidosSystem$LoadableAttributes$.apply(EidosSystem.scala:129)\r\n\tat org.clulab.wm.eidos.EidosSystem.<init>(EidosSystem.scala:153)\r\n\tat org.clulab.wm.eidos.apps.ExtractFromDirectory$.delayedEndpoint$org$clulab$wm$eidos$apps$ExtractFromDirectory$1(ExtractFromDirectory.scala:14)\r\n\tat org.clulab.wm.eidos.apps.ExtractFromDirectory$delayedInit$body.apply(ExtractFromDirectory.scala:9)\r\n\tat scala.Function0.apply$mcV$sp(Function0.scala:34)\r\n\tat scala.Function0.apply$mcV$sp$(Function0.scala:34)\r\n\tat scala.runtime.AbstractFunction0.apply$mcV$sp(AbstractFunction0.scala:12)\r\n\tat scala.App.$anonfun$main$1$adapted(App.scala:76)\r\n\tat scala.collection.immutable.List.foreach(List.scala:389)\r\n\tat scala.App.main(App.scala:76)\r\n\tat scala.App.main$(App.scala:74)\r\n\tat org.clulab.wm.eidos.apps.ExtractFromDirectory$.main(ExtractFromDirectory.scala:9)\r\n\tat org.clulab.wm.eidos.apps.ExtractFromDirectory.main(ExtractFromDirectory.scala)\r\n\r\n```\r\n\r\nNote that I added a debug print: ```println(timeNormResource)``` on EidosSystem.scala line 127 to produce this line\r\n```\r\njar:file:/Users/ben/tmp/eidos/target/scala-2.12/eidos-assembly-0.2.2-SNAPSHOT.jar!/org/clulab/wm/eidos/models/timenorm_model.hdf5\r\n```\r\nI also confirmed by browsing the jar file itself that /org/clulab/wm/eidos/models/timenorm_model.hdf5 is at the specified location within the JAR.\r\n\r\nThanks for your help!"},"comment":{"url":"https://api.github.com/repos/clulab/eidos/issues/comments/423658029","html_url":"https://github.com/clulab/eidos/issues/443#issuecomment-423658029","issue_url":"https://api.github.com/repos/clulab/eidos/issues/443","id":423658029,"node_id":"MDEyOklzc3VlQ29tbWVudDQyMzY1ODAyOQ==","user":{"login":"bgyori","id":5939016,"node_id":"MDQ6VXNlcjU5MzkwMTY=","avatar_url":"https://avatars0.githubusercontent.com/u/5939016?v=4","gravatar_id":"","url":"https://api.github.com/users/bgyori","html_url":"https://github.com/bgyori","followers_url":"https://api.github.com/users/bgyori/followers","following_url":"https://api.github.com/users/bgyori/following{/other_user}","gists_url":"https://api.github.com/users/bgyori/gists{/gist_id}","starred_url":"https://api.github.com/users/bgyori/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bgyori/subscriptions","organizations_url":"https://api.github.com/users/bgyori/orgs","repos_url":"https://api.github.com/users/bgyori/repos","events_url":"https://api.github.com/users/bgyori/events{/privacy}","received_events_url":"https://api.github.com/users/bgyori/received_events","type":"User","site_admin":false},"created_at":"2018-09-21T20:14:33Z","updated_at":"2018-09-21T20:14:33Z","author_association":"CONTRIBUTOR","body":"Thanks, so if I understand correctly, if I put the hdf5 file outside the JAR and reference it by its absolute path it should work. Let me try that and I'll report back!"}}
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