{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/cromwell/pulls/comments/51483837","id":51483837,"diff_hunk":"@@ -104,10 +104,10 @@ case class WorkflowDescriptor(id: WorkflowId,\n     val logger = backend.workflowLogger(this)\n \n     def copyFile(file: WdlFile): Try[Unit] = {\n-      val src = file.valueString.toPath(workflowLogger, gcsFilesystem)\n-      val wfPath = wfContext.root.toPath(workflowLogger, gcsFilesystem).toAbsolutePath\n+      val src = file.valueString.toPath(gcsFilesystem)\n+      val wfPath = wfContext.root.toPath(gcsFilesystem).toAbsolutePath\n       val relativeFilePath = src.subpath(wfPath.getNameCount, src.getNameCount)\n-      val dest = destDirectory.toPath(workflowLogger, gcsOutputsFilesystem).resolve(relativeWorkflowRootPath).resolve(relativeFilePath)\n+      val dest = destDirectory.toPath(gcsOutputsFilesystem).resolve(relativeWorkflowRootPath).resolve(relativeFilePath)","path":"src/main/scala/cromwell/engine/WorkflowDescriptor.scala","position":56,"original_position":56,"commit_id":"5ac44146d597c6339170a5d885de18caca3b8418","original_commit_id":"5ac44146d597c6339170a5d885de18caca3b8418","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":"Also pre-existing but I wonder if the double-resolve is necessary or can it somehow be done in one pass","created_at":"2016-02-01T21:31:52Z","updated_at":"2016-02-01T21:31:52Z","html_url":"https://github.com/broadinstitute/cromwell/pull/412#discussion_r51483837","pull_request_url":"https://api.github.com/repos/broadinstitute/cromwell/pulls/412","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/cromwell/pulls/comments/51483837"},"html":{"href":"https://github.com/broadinstitute/cromwell/pull/412#discussion_r51483837"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/cromwell/pulls/412"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/cromwell/pulls/412","id":57719833,"html_url":"https://github.com/broadinstitute/cromwell/pull/412","diff_url":"https://github.com/broadinstitute/cromwell/pull/412.diff","patch_url":"https://github.com/broadinstitute/cromwell/pull/412.patch","issue_url":"https://api.github.com/repos/broadinstitute/cromwell/issues/412","number":412,"state":"open","locked":false,"title":"Preemptible VMs","user":{"login":"Horneth","id":2978948,"avatar_url":"https://avatars.githubusercontent.com/u/2978948?v=3","gravatar_id":"","url":"https://api.github.com/users/Horneth","html_url":"https://github.com/Horneth","followers_url":"https://api.github.com/users/Horneth/followers","following_url":"https://api.github.com/users/Horneth/following{/other_user}","gists_url":"https://api.github.com/users/Horneth/gists{/gist_id}","starred_url":"https://api.github.com/users/Horneth/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Horneth/subscriptions","organizations_url":"https://api.github.com/users/Horneth/orgs","repos_url":"https://api.github.com/users/Horneth/repos","events_url":"https://api.github.com/users/Horneth/events{/privacy}","received_events_url":"https://api.github.com/users/Horneth/received_events","type":"User","site_admin":false},"body":"","created_at":"2016-01-29T23:59:27Z","updated_at":"2016-02-01T21:31:52Z","closed_at":null,"merged_at":null,"merge_commit_sha":"875de8f795d9077e169e8d485f3b2c625feb54e3","assignee":{"login":"cjllanwarne","id":13006282,"avatar_url":"https://avatars.githubusercontent.com/u/13006282?v=3","gravatar_id":"","url":"https://api.github.com/users/cjllanwarne","html_url":"https://github.com/cjllanwarne","followers_url":"https://api.github.com/users/cjllanwarne/followers","following_url":"https://api.github.com/users/cjllanwarne/following{/other_user}","gists_url":"https://api.github.com/users/cjllanwarne/gists{/gist_id}","starred_url":"https://api.github.com/users/cjllanwarne/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cjllanwarne/subscriptions","organizations_url":"https://api.github.com/users/cjllanwarne/orgs","repos_url":"https://api.github.com/users/cjllanwarne/repos","events_url":"https://api.github.com/users/cjllanwarne/events{/privacy}","received_events_url":"https://api.github.com/users/cjllanwarne/received_events","type":"User","site_admin":false},"milestone":null,"commits_url":"https://api.github.com/repos/broadinstitute/cromwell/pulls/412/commits","review_comments_url":"https://api.github.com/repos/broadinstitute/cromwell/pulls/412/comments","review_comment_url":"https://api.github.com/repos/broadinstitute/cromwell/pulls/comments{/number}","comments_url":"https://api.github.com/repos/broadinstitute/cromwell/issues/412/comments","statuses_url":"https://api.github.com/repos/broadinstitute/cromwell/statuses/5ac44146d597c6339170a5d885de18caca3b8418","head":{"label":"broadinstitute:tj_PreemptibleVMs","ref":"tj_PreemptibleVMs","sha":"5ac44146d597c6339170a5d885de18caca3b8418","user":{"login":"broadinstitute","id":393552,"avatar_url":"https://avatars.githubusercontent.com/u/393552?v=3","gravatar_id":"","url":"https://api.github.com/users/broadinstitute","html_url":"https://github.com/broadinstitute","followers_url":"https://api.github.com/users/broadinstitute/followers","following_url":"https://api.github.com/users/broadinstitute/following{/other_user}","gists_url":"https://api.github.com/users/broadinstitute/gists{/gist_id}","starred_url":"https://api.github.com/users/broadinstitute/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/broadinstitute/subscriptions","organizations_url":"https://api.github.com/users/broadinstitute/orgs","repos_url":"https://api.github.com/users/broadinstitute/repos","events_url":"https://api.github.com/users/broadinstitute/events{/privacy}","received_events_url":"https://api.github.com/users/broadinstitute/received_events","type":"Organization","site_admin":false},"repo":{"id":34136406,"name":"cromwell","full_name":"broadinstitute/cromwell","owner":{"login":"broadinstitute","id":393552,"avatar_url":"https://avatars.githubusercontent.com/u/393552?v=3","gravatar_id":"","url":"https://api.github.com/users/broadinstitute","html_url":"https://github.com/broadinstitute","followers_url":"https://api.github.com/users/broadinstitute/followers","following_url":"https://api.github.com/users/broadinstitute/following{/other_user}","gists_url":"https://api.github.com/users/broadinstitute/gists{/gist_id}","starred_url":"https://api.github.com/users/broadinstitute/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/broadinstitute/subscriptions","organizations_url":"https://api.github.com/users/broadinstitute/orgs","repos_url":"https://api.github.com/users/broadinstitute/repos","events_url":"https://api.github.com/users/broadinstitute/events{/privacy}","received_events_url":"https://api.github.com/users/broadinstitute/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/broadinstitute/cromwell","description":"Workflow Execution Engine using WDL","fork":false,"url":"https://api.github.com/repos/broadinstitute/cromwell","forks_url":"https://api.github.com/repos/broadinstitute/cromwell/forks","keys_url":"https://api.github.com/repos/broadinstitute/cromwell/keys{/key_id}","collaborators_url":"https://api.github.com/repos/broadinstitute/cromwell/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/broadinstitute/cromwell/teams","hooks_url":"https://api.github.com/repos/broadinstitute/cromwell/hooks","issue_events_url":"https://api.github.com/repos/broadinstitute/cromwell/issues/events{/number}","events_url":"https://api.github.com/repos/broadinstitute/cromwell/events","assignees_url":"https://api.github.com/repos/broadinstitute/cromwell/assignees{/user}","branches_url":"https://api.github.com/repos/broadinstitute/cromwell/branches{/branch}","tags_url":"https://api.github.com/repos/broadinstitute/cromwell/tags","blobs_url":"https://api.github.com/repos/broadinstitute/cromwell/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/broadinstitute/cromwell/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/broadinstitute/cromwell/git/refs{/sha}","trees_url":"https://api.github.com/repos/broadinstitute/cromwell/git/trees{/sha}","statuses_url":"https://api.github.com/repos/broadinstitute/cromwell/statuses/{sha}","languages_url":"https://api.github.com/repos/broadinstitute/cromwell/languages","stargazers_url":"https://api.github.com/repos/broadinstitute/cromwell/stargazers","contributors_url":"https://api.github.com/repos/broadinstitute/cromwell/contributors","subscribers_url":"https://api.github.com/repos/broadinstitute/cromwell/subscribers","subscription_url":"https://api.github.com/repos/broadinstitute/cromwell/subscription","commits_url":"https://api.github.com/repos/broadinstitute/cromwell/commits{/sha}","git_commits_url":"https://api.github.com/repos/broadinstitute/cromwell/git/commits{/sha}","comments_url":"https://api.github.com/repos/broadinstitute/cromwell/comments{/number}","issue_comment_url":"https://api.github.com/repos/broadinstitute/cromwell/issues/comments{/number}","contents_url":"https://api.github.com/repos/broadinstitute/cromwell/contents/{+path}","compare_url":"https://api.github.com/repos/broadinstitute/cromwell/compare/{base}...{head}","merges_url":"https://api.github.com/repos/broadinstitute/cromwell/merges","archive_url":"https://api.github.com/repos/broadinstitute/cromwell/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/broadinstitute/cromwell/downloads","issues_url":"https://api.github.com/repos/broadinstitute/cromwell/issues{/number}","pulls_url":"https://api.github.com/repos/broadinstitute/cromwell/pulls{/number}","milestones_url":"https://api.github.com/repos/broadinstitute/cromwell/milestones{/number}","notifications_url":"https://api.github.com/repos/broadinstitute/cromwell/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/broadinstitute/cromwell/labels{/name}","releases_url":"https://api.github.com/repos/broadinstitute/cromwell/releases{/id}","deployments_url":"https://api.github.com/repos/broadinstitute/cromwell/deployments","created_at":"2015-04-17T19:39:36Z","updated_at":"2016-02-01T21:02:57Z","pushed_at":"2016-02-01T21:16:15Z","git_url":"git://github.com/broadinstitute/cromwell.git","ssh_url":"git@github.com:broadinstitute/cromwell.git","clone_url":"https://github.com/broadinstitute/cromwell.git","svn_url":"https://github.com/broadinstitute/cromwell","homepage":"","size":4937,"stargazers_count":27,"watchers_count":27,"language":"Scala","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":true,"forks_count":7,"mirror_url":null,"open_issues_count":8,"forks":7,"open_issues":8,"watchers":27,"default_branch":"develop"}},"base":{"label":"broadinstitute:develop","ref":"develop","sha":"950d6cf4339f88677fed1eeaa86c3f6fca80560b","user":{"login":"broadinstitute","id":393552,"avatar_url":"https://avatars.githubusercontent.com/u/393552?v=3","gravatar_id":"","url":"https://api.github.com/users/broadinstitute","html_url":"https://github.com/broadinstitute","followers_url":"https://api.github.com/users/broadinstitute/followers","following_url":"https://api.github.com/users/broadinstitute/following{/other_user}","gists_url":"https://api.github.com/users/broadinstitute/gists{/gist_id}","starred_url":"https://api.github.com/users/broadinstitute/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/broadinstitute/subscriptions","organizations_url":"https://api.github.com/users/broadinstitute/orgs","repos_url":"https://api.github.com/users/broadinstitute/repos","events_url":"https://api.github.com/users/broadinstitute/events{/privacy}","received_events_url":"https://api.github.com/users/broadinstitute/received_events","type":"Organization","site_admin":false},"repo":{"id":34136406,"name":"cromwell","full_name":"broadinstitute/cromwell","owner":{"login":"broadinstitute","id":393552,"avatar_url":"https://avatars.githubusercontent.com/u/393552?v=3","gravatar_id":"","url":"https://api.github.com/users/broadinstitute","html_url":"https://github.com/broadinstitute","followers_url":"https://api.github.com/users/broadinstitute/followers","following_url":"https://api.github.com/users/broadinstitute/following{/other_user}","gists_url":"https://api.github.com/users/broadinstitute/gists{/gist_id}","starred_url":"https://api.github.com/users/broadinstitute/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/broadinstitute/subscriptions","organizations_url":"https://api.github.com/users/broadinstitute/orgs","repos_url":"https://api.github.com/users/broadinstitute/repos","events_url":"https://api.github.com/users/broadinstitute/events{/privacy}","received_events_url":"https://api.github.com/users/broadinstitute/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/broadinstitute/cromwell","description":"Workflow Execution Engine using WDL","fork":false,"url":"https://api.github.com/repos/broadinstitute/cromwell","forks_url":"https://api.github.com/repos/broadinstitute/cromwell/forks","keys_url":"https://api.github.com/repos/broadinstitute/cromwell/keys{/key_id}","collaborators_url":"https://api.github.com/repos/broadinstitute/cromwell/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/broadinstitute/cromwell/teams","hooks_url":"https://api.github.com/repos/broadinstitute/cromwell/hooks","issue_events_url":"https://api.github.com/repos/broadinstitute/cromwell/issues/events{/number}","events_url":"https://api.github.com/repos/broadinstitute/cromwell/events","assignees_url":"https://api.github.com/repos/broadinstitute/cromwell/assignees{/user}","branches_url":"https://api.github.com/repos/broadinstitute/cromwell/branches{/branch}","tags_url":"https://api.github.com/repos/broadinstitute/cromwell/tags","blobs_url":"https://api.github.com/repos/broadinstitute/cromwell/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/broadinstitute/cromwell/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/broadinstitute/cromwell/git/refs{/sha}","trees_url":"https://api.github.com/repos/broadinstitute/cromwell/git/trees{/sha}","statuses_url":"https://api.github.com/repos/broadinstitute/cromwell/statuses/{sha}","languages_url":"https://api.github.com/repos/broadinstitute/cromwell/languages","stargazers_url":"https://api.github.com/repos/broadinstitute/cromwell/stargazers","contributors_url":"https://api.github.com/repos/broadinstitute/cromwell/contributors","subscribers_url":"https://api.github.com/repos/broadinstitute/cromwell/subscribers","subscription_url":"https://api.github.com/repos/broadinstitute/cromwell/subscription","commits_url":"https://api.github.com/repos/broadinstitute/cromwell/commits{/sha}","git_commits_url":"https://api.github.com/repos/broadinstitute/cromwell/git/commits{/sha}","comments_url":"https://api.github.com/repos/broadinstitute/cromwell/comments{/number}","issue_comment_url":"https://api.github.com/repos/broadinstitute/cromwell/issues/comments{/number}","contents_url":"https://api.github.com/repos/broadinstitute/cromwell/contents/{+path}","compare_url":"https://api.github.com/repos/broadinstitute/cromwell/compare/{base}...{head}","merges_url":"https://api.github.com/repos/broadinstitute/cromwell/merges","archive_url":"https://api.github.com/repos/broadinstitute/cromwell/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/broadinstitute/cromwell/downloads","issues_url":"https://api.github.com/repos/broadinstitute/cromwell/issues{/number}","pulls_url":"https://api.github.com/repos/broadinstitute/cromwell/pulls{/number}","milestones_url":"https://api.github.com/repos/broadinstitute/cromwell/milestones{/number}","notifications_url":"https://api.github.com/repos/broadinstitute/cromwell/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/broadinstitute/cromwell/labels{/name}","releases_url":"https://api.github.com/repos/broadinstitute/cromwell/releases{/id}","deployments_url":"https://api.github.com/repos/broadinstitute/cromwell/deployments","created_at":"2015-04-17T19:39:36Z","updated_at":"2016-02-01T21:02:57Z","pushed_at":"2016-02-01T21:16:15Z","git_url":"git://github.com/broadinstitute/cromwell.git","ssh_url":"git@github.com:broadinstitute/cromwell.git","clone_url":"https://github.com/broadinstitute/cromwell.git","svn_url":"https://github.com/broadinstitute/cromwell","homepage":"","size":4937,"stargazers_count":27,"watchers_count":27,"language":"Scala","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":true,"forks_count":7,"mirror_url":null,"open_issues_count":8,"forks":7,"open_issues":8,"watchers":27,"default_branch":"develop"}},"_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/cromwell/pulls/412"},"html":{"href":"https://github.com/broadinstitute/cromwell/pull/412"},"issue":{"href":"https://api.github.com/repos/broadinstitute/cromwell/issues/412"},"comments":{"href":"https://api.github.com/repos/broadinstitute/cromwell/issues/412/comments"},"review_comments":{"href":"https://api.github.com/repos/broadinstitute/cromwell/pulls/412/comments"},"review_comment":{"href":"https://api.github.com/repos/broadinstitute/cromwell/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/broadinstitute/cromwell/pulls/412/commits"},"statuses":{"href":"https://api.github.com/repos/broadinstitute/cromwell/statuses/5ac44146d597c6339170a5d885de18caca3b8418"}}}}