{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/cromwell/pulls/comments/30557270","id":30557270,"diff_hunk":"@@ -15,7 +15,9 @@ class LocalEngineFunctions(executionContext: TaskExecutionContext) extends Engin\n   override protected def read_int(params: Seq[Try[WdlValue]]): Try[WdlInteger] = {\n     assertSingleArgument(params).map {\n       case f: WdlFile =>\n-        WdlInteger(io.Source.fromFile(f.value.toFile).mkString.toInt)\n+        WdlInteger(io.Source.fromFile(f.value.toFile).mkString.trim.toInt)","path":"src/main/scala/cromwell/engine/backend/local/LocalEngineFunctions.scala","position":5,"original_position":5,"commit_id":"9e0d039d6b16908c5be7c8d903d0294f0ce5d0b6","original_commit_id":"9e0d039d6b16908c5be7c8d903d0294f0ce5d0b6","user":{"login":"geoffjentry","id":961771,"avatar_url":"https://avatars.githubusercontent.com/u/961771?v=3","gravatar_id":"","url":"https://api.github.com/users/geoffjentry","html_url":"https://github.com/geoffjentry","followers_url":"https://api.github.com/users/geoffjentry/followers","following_url":"https://api.github.com/users/geoffjentry/following{/other_user}","gists_url":"https://api.github.com/users/geoffjentry/gists{/gist_id}","starred_url":"https://api.github.com/users/geoffjentry/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/geoffjentry/subscriptions","organizations_url":"https://api.github.com/users/geoffjentry/orgs","repos_url":"https://api.github.com/users/geoffjentry/repos","events_url":"https://api.github.com/users/geoffjentry/events{/privacy}","received_events_url":"https://api.github.com/users/geoffjentry/received_events","type":"User","site_admin":false},"body":"Hmm. It doesn't look like that's changed from a time back when I know this was the case as people used to bitch about it on the tubez and important ppl would say \"so don't use fromFile, silly!\" *shrug*","created_at":"2015-05-18T23:30:56Z","updated_at":"2015-05-18T23:30:56Z","html_url":"https://github.com/broadinstitute/cromwell/pull/20#discussion_r30557270","pull_request_url":"https://api.github.com/repos/broadinstitute/cromwell/pulls/20","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/cromwell/pulls/comments/30557270"},"html":{"href":"https://github.com/broadinstitute/cromwell/pull/20#discussion_r30557270"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/cromwell/pulls/20"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/cromwell/pulls/20","id":35651824,"html_url":"https://github.com/broadinstitute/cromwell/pull/20","diff_url":"https://github.com/broadinstitute/cromwell/pull/20.diff","patch_url":"https://github.com/broadinstitute/cromwell/pull/20.patch","issue_url":"https://api.github.com/repos/broadinstitute/cromwell/issues/20","number":20,"state":"open","locked":false,"title":"The green step of red/green/refactor, but wow does this need refactoring.","user":{"login":"mcovarr","id":10790523,"avatar_url":"https://avatars.githubusercontent.com/u/10790523?v=3","gravatar_id":"","url":"https://api.github.com/users/mcovarr","html_url":"https://github.com/mcovarr","followers_url":"https://api.github.com/users/mcovarr/followers","following_url":"https://api.github.com/users/mcovarr/following{/other_user}","gists_url":"https://api.github.com/users/mcovarr/gists{/gist_id}","starred_url":"https://api.github.com/users/mcovarr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mcovarr/subscriptions","organizations_url":"https://api.github.com/users/mcovarr/orgs","repos_url":"https://api.github.com/users/mcovarr/repos","events_url":"https://api.github.com/users/mcovarr/events{/privacy}","received_events_url":"https://api.github.com/users/mcovarr/received_events","type":"User","site_admin":false},"body":"This is green and actually does appear to work with a couple of mods to the three-step workflow, one to fake the `ps` for deterministic results, another to fix a bug in the wc command.  But this seriously needs refactoring:\r\n\r\n1. Proper concurrency handling for store updates.  The current code is awful, the mutable stores are just passed around the various concurrently executing actors.  Probably the stores should be behind an actor which the CallActor and WorkflowActor would `ask` for queries or updates, and then compose a `pipeTo` with the `Future` response.\r\n\r\n2. While the potential parallelism of the cgrep and wc calls does appear to work as intended, the current test does not assert this.\r\n\r\n3. The call dependency determination only works for member access expressions and is kind of gross.\r\n\r\n4. The connection of inputs to outputs requires member access expressions and uses logic very much like point 3.  Also the way outputs are copied to inputs in the symbol store seems clunky and wasteful; if the input expressions could be truly evaluated at call invocation it wouldn't be necessary to create copies of this 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