{"action":"created","issue":{"url":"https://api.github.com/repos/clulab/reach/issues/549","repository_url":"https://api.github.com/repos/clulab/reach","labels_url":"https://api.github.com/repos/clulab/reach/issues/549/labels{/name}","comments_url":"https://api.github.com/repos/clulab/reach/issues/549/comments","events_url":"https://api.github.com/repos/clulab/reach/issues/549/events","html_url":"https://github.com/clulab/reach/issues/549","id":260395563,"number":549,"title":"Reach jarfile not using given config file.","user":{"login":"pagreene","id":25346565,"avatar_url":"https://avatars3.githubusercontent.com/u/25346565?v=4","gravatar_id":"","url":"https://api.github.com/users/pagreene","html_url":"https://github.com/pagreene","followers_url":"https://api.github.com/users/pagreene/followers","following_url":"https://api.github.com/users/pagreene/following{/other_user}","gists_url":"https://api.github.com/users/pagreene/gists{/gist_id}","starred_url":"https://api.github.com/users/pagreene/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pagreene/subscriptions","organizations_url":"https://api.github.com/users/pagreene/orgs","repos_url":"https://api.github.com/users/pagreene/repos","events_url":"https://api.github.com/users/pagreene/events{/privacy}","received_events_url":"https://api.github.com/users/pagreene/received_events","type":"User","site_admin":false},"labels":[{"id":604092963,"url":"https://api.github.com/repos/clulab/reach/labels/support","name":"support","color":"b60205","default":false}],"state":"open","locked":false,"assignee":{"login":"hickst","id":22797,"avatar_url":"https://avatars3.githubusercontent.com/u/22797?v=4","gravatar_id":"","url":"https://api.github.com/users/hickst","html_url":"https://github.com/hickst","followers_url":"https://api.github.com/users/hickst/followers","following_url":"https://api.github.com/users/hickst/following{/other_user}","gists_url":"https://api.github.com/users/hickst/gists{/gist_id}","starred_url":"https://api.github.com/users/hickst/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hickst/subscriptions","organizations_url":"https://api.github.com/users/hickst/orgs","repos_url":"https://api.github.com/users/hickst/repos","events_url":"https://api.github.com/users/hickst/events{/privacy}","received_events_url":"https://api.github.com/users/hickst/received_events","type":"User","site_admin":false},"assignees":[{"login":"hickst","id":22797,"avatar_url":"https://avatars3.githubusercontent.com/u/22797?v=4","gravatar_id":"","url":"https://api.github.com/users/hickst","html_url":"https://github.com/hickst","followers_url":"https://api.github.com/users/hickst/followers","following_url":"https://api.github.com/users/hickst/following{/other_user}","gists_url":"https://api.github.com/users/hickst/gists{/gist_id}","starred_url":"https://api.github.com/users/hickst/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hickst/subscriptions","organizations_url":"https://api.github.com/users/hickst/orgs","repos_url":"https://api.github.com/users/hickst/repos","events_url":"https://api.github.com/users/hickst/events{/privacy}","received_events_url":"https://api.github.com/users/hickst/received_events","type":"User","site_admin":false}],"milestone":null,"comments":6,"created_at":"2017-09-25T19:54:53Z","updated_at":"2017-09-26T21:54:44Z","closed_at":null,"author_association":"NONE","body":"We create a jar file to run reach (for portability), using the following in the top reach directory:\r\n```\r\necho 'mainClass in assembly := Some(\"org.clulab.reach.RunReachCLI\")' >> build.sbt\r\n[sudo] sbt assembly\r\n```\r\n(Thus sudo is supposedly not needed, but sbt won't run on my system without it) We would then like to be able to run the script via\r\n```\r\njava -jar <name of the jarfile>.jar <config file>\r\n```\r\nThis has worked with previous versions of reach, however, it does not work for 1.3.4 or 1.3.5. I have verified that the conf file is valid, by running (successfully in both versions)\r\n```\r\n[sudo] sbt -Dconfig.file=<path to config file> \"runMain org.clulab.reach.RunReachCLI\"\r\n```\r\nNote that\r\n```\r\n[sudo] sbt \"runMain org.clulab.reach.RunReachCLI <path to config file>\"\r\n```\r\nShows essentially the same problem as with running with the jar file.\r\n\r\nThe actual failure occurs when the system tries to access '[Home]/reach/papers', which of course does not exist."},"comment":{"url":"https://api.github.com/repos/clulab/reach/issues/comments/332347595","html_url":"https://github.com/clulab/reach/issues/549#issuecomment-332347595","issue_url":"https://api.github.com/repos/clulab/reach/issues/549","id":332347595,"user":{"login":"hickst","id":22797,"avatar_url":"https://avatars3.githubusercontent.com/u/22797?v=4","gravatar_id":"","url":"https://api.github.com/users/hickst","html_url":"https://github.com/hickst","followers_url":"https://api.github.com/users/hickst/followers","following_url":"https://api.github.com/users/hickst/following{/other_user}","gists_url":"https://api.github.com/users/hickst/gists{/gist_id}","starred_url":"https://api.github.com/users/hickst/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hickst/subscriptions","organizations_url":"https://api.github.com/users/hickst/orgs","repos_url":"https://api.github.com/users/hickst/repos","events_url":"https://api.github.com/users/hickst/events{/privacy}","received_events_url":"https://api.github.com/users/hickst/received_events","type":"User","site_admin":false},"created_at":"2017-09-26T21:54:44Z","updated_at":"2017-09-26T21:54:44Z","author_association":"CONTRIBUTOR","body":"This has to do with some resources internal to the Malt parser whose version has to match the version of Malt used. Since you are reverting Reach you have to revert (and locally compile) Processors. In reviewing the checkins, I believe you have to revert Processors to version 97f4f79e1bc022cee38f733dcc3e3916a8ce4f81 or earlier.\r\n\r\nBut I still think this is opening a can of worms. Unless you have absolutely no time to wait on this issue, I would recommend that we discuss what I can do for you from this end. Feel free to call me directly and we can discuss the schedule and parameters of a solution."}}
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