{"action":"created","comment":{"url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/pulls/comments/238996924","pull_request_review_id":181671036,"id":238996924,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDIzODk5NjkyNA==","diff_hunk":"@@ -226,14 +233,19 @@ def test_demultiplexing(self):\n         assert self._test_success\n \n     def test_demultiplexing_aborted(self):\n-        self.setup_test('sample', 'test_demultiplexing', 'demultiplexing')\n-        with patch('analysis_driver.pipelines.demultiplexing.Setup._run', side_effect=SequencingRunError):\n+        self.setup_test('sample', 'test_demultiplexing_aborted', 'demultiplexing')\n+\n+        mocked_clarity_run = MockedRunProcess(udf={'Run Status': 'RunAborted'}, container=mocked_flowcell_pooling)\n+        with patch('egcg_core.clarity.get_run', return_value=mocked_clarity_run):\n             exit_status = client.main(['--run'])\n-            self.assertEqual('exit status', exit_status, 0)\n \n-            self.expect_equal(\n-                rest_communication.get_document('analysis_driver_procs')['status'], 'aborted'\n-            )\n+        self.assertEqual('exit status', exit_status, 0)\n+        ad_proc = rest_communication.get_document('analysis_driver_procs', where={'dataset_name': self.run_id})\n+\n+        self.expect_equal(\n+            ad_proc['status'], 'aborted', 'pipeline status'\n+        )\n+        self.expect_stage_data([('setup', 9)], analysis_driver_proc=ad_proc['proc_id'])","path":"integration_tests/integration_test.py","position":null,"original_position":71,"commit_id":"6345d792d06eec6f73f1f663c86510095393da2d","original_commit_id":"0e84237b499bf5dbb54e8c472a6140c5499f277e","user":{"login":"tcezard","id":650891,"node_id":"MDQ6VXNlcjY1MDg5MQ==","avatar_url":"https://avatars0.githubusercontent.com/u/650891?v=4","gravatar_id":"","url":"https://api.github.com/users/tcezard","html_url":"https://github.com/tcezard","followers_url":"https://api.github.com/users/tcezard/followers","following_url":"https://api.github.com/users/tcezard/following{/other_user}","gists_url":"https://api.github.com/users/tcezard/gists{/gist_id}","starred_url":"https://api.github.com/users/tcezard/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tcezard/subscriptions","organizations_url":"https://api.github.com/users/tcezard/orgs","repos_url":"https://api.github.com/users/tcezard/repos","events_url":"https://api.github.com/users/tcezard/events{/privacy}","received_events_url":"https://api.github.com/users/tcezard/received_events","type":"User","site_admin":false},"body":"This is fixed now. Tests did pass cause there is only one stage at this point","created_at":"2018-12-05T09:56:28Z","updated_at":"2018-12-05T09:56:28Z","html_url":"https://github.com/EdinburghGenomics/Analysis-Driver/pull/362#discussion_r238996924","pull_request_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/pulls/362","author_association":"CONTRIBUTOR","_links":{"self":{"href":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/pulls/comments/238996924"},"html":{"href":"https://github.com/EdinburghGenomics/Analysis-Driver/pull/362#discussion_r238996924"},"pull_request":{"href":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/pulls/362"}},"in_reply_to_id":238989185},"pull_request":{"url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/pulls/362","id":234317682,"node_id":"MDExOlB1bGxSZXF1ZXN0MjM0MzE3Njgy","html_url":"https://github.com/EdinburghGenomics/Analysis-Driver/pull/362","diff_url":"https://github.com/EdinburghGenomics/Analysis-Driver/pull/362.diff","patch_url":"https://github.com/EdinburghGenomics/Analysis-Driver/pull/362.patch","issue_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/issues/362","number":362,"state":"open","locked":false,"title":"Support for multiprocessing when raising exceptions","user":{"login":"tcezard","id":650891,"node_id":"MDQ6VXNlcjY1MDg5MQ==","avatar_url":"https://avatars0.githubusercontent.com/u/650891?v=4","gravatar_id":"","url":"https://api.github.com/users/tcezard","html_url":"https://github.com/tcezard","followers_url":"https://api.github.com/users/tcezard/followers","following_url":"https://api.github.com/users/tcezard/following{/other_user}","gists_url":"https://api.github.com/users/tcezard/gists{/gist_id}","starred_url":"https://api.github.com/users/tcezard/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tcezard/subscriptions","organizations_url":"https://api.github.com/users/tcezard/orgs","repos_url":"https://api.github.com/users/tcezard/repos","events_url":"https://api.github.com/users/tcezard/events{/privacy}","received_events_url":"https://api.github.com/users/tcezard/received_events","type":"User","site_admin":false},"body":"Exception raised in stages are now stored in a multiprocessing.Queue.\r\nIn order to receive them when multiprocessing is active\r\nThis includes PipelineError which is raised when a stage returns non 0 exist code.\r\nThis will closes #335 but is not very elegant, especially the fact that there are Run specific action in the `client.py` which should be process type agnostic.\r\nIf you can think of a better solution do let me know.\r\n","created_at":"2018-11-28T15:25:11Z","updated_at":"2018-12-05T09:56:28Z","closed_at":null,"merged_at":null,"merge_commit_sha":"fd86d2cc0bcd5784fa6b692100aacb302cbd1ae1","assignee":null,"assignees":[],"requested_reviewers":[],"requested_teams":[],"labels":[],"milestone":null,"commits_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/pulls/362/commits","review_comments_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/pulls/362/comments","review_comment_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/pulls/comments{/number}","comments_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/issues/362/comments","statuses_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/statuses/6345d792d06eec6f73f1f663c86510095393da2d","head":{"label":"EdinburghGenomics:exception_in_main_proc","ref":"exception_in_main_proc","sha":"6345d792d06eec6f73f1f663c86510095393da2d","user":{"login":"EdinburghGenomics","id":12951724,"node_id":"MDEyOk9yZ2FuaXphdGlvbjEyOTUxNzI0","avatar_url":"https://avatars0.githubusercontent.com/u/12951724?v=4","gravatar_id":"","url":"https://api.github.com/users/EdinburghGenomics","html_url":"https://github.com/EdinburghGenomics","followers_url":"https://api.github.com/users/EdinburghGenomics/followers","following_url":"https://api.github.com/users/EdinburghGenomics/following{/other_user}","gists_url":"https://api.github.com/users/EdinburghGenomics/gists{/gist_id}","starred_url":"https://api.github.com/users/EdinburghGenomics/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/EdinburghGenomics/subscriptions","organizations_url":"https://api.github.com/users/EdinburghGenomics/orgs","repos_url":"https://api.github.com/users/EdinburghGenomics/repos","events_url":"https://api.github.com/users/EdinburghGenomics/events{/privacy}","received_events_url":"https://api.github.com/users/EdinburghGenomics/received_events","type":"Organization","site_admin":false},"repo":{"id":37849969,"node_id":"MDEwOlJlcG9zaXRvcnkzNzg0OTk2OQ==","name":"Analysis-Driver","full_name":"EdinburghGenomics/Analysis-Driver","private":false,"owner":{"login":"EdinburghGenomics","id":12951724,"node_id":"MDEyOk9yZ2FuaXphdGlvbjEyOTUxNzI0","avatar_url":"https://avatars0.githubusercontent.com/u/12951724?v=4","gravatar_id":"","url":"https://api.github.com/users/EdinburghGenomics","html_url":"https://github.com/EdinburghGenomics","followers_url":"https://api.github.com/users/EdinburghGenomics/followers","following_url":"https://api.github.com/users/EdinburghGenomics/following{/other_user}","gists_url":"https://api.github.com/users/EdinburghGenomics/gists{/gist_id}","starred_url":"https://api.github.com/users/EdinburghGenomics/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/EdinburghGenomics/subscriptions","organizations_url":"https://api.github.com/users/EdinburghGenomics/orgs","repos_url":"https://api.github.com/users/EdinburghGenomics/repos","events_url":"https://api.github.com/users/EdinburghGenomics/events{/privacy}","received_events_url":"https://api.github.com/users/EdinburghGenomics/received_events","type":"Organization","site_admin":false},"html_url":"https://github.com/EdinburghGenomics/Analysis-Driver","description":"Pipelines for Illumina HiSeqX demultiplexing, sequence QC and variant calling.","fork":false,"url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver","forks_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/forks","keys_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/keys{/key_id}","collaborators_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/teams","hooks_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/hooks","issue_events_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/issues/events{/number}","events_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/events","assignees_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/assignees{/user}","branches_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/branches{/branch}","tags_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/tags","blobs_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/git/refs{/sha}","trees_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/git/trees{/sha}","statuses_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/statuses/{sha}","languages_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/languages","stargazers_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/stargazers","contributors_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/contributors","subscribers_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/subscribers","subscription_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/subscription","commits_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/commits{/sha}","git_commits_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/git/commits{/sha}","comments_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/comments{/number}","issue_comment_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/issues/comments{/number}","contents_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/contents/{+path}","compare_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/compare/{base}...{head}","merges_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/merges","archive_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/downloads","issues_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/issues{/number}","pulls_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/pulls{/number}","milestones_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/milestones{/number}","notifications_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/labels{/name}","releases_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/releases{/id}","deployments_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/deployments","created_at":"2015-06-22T10:42:34Z","updated_at":"2018-11-30T23:45:07Z","pushed_at":"2018-12-05T09:55:48Z","git_url":"git://github.com/EdinburghGenomics/Analysis-Driver.git","ssh_url":"git@github.com:EdinburghGenomics/Analysis-Driver.git","clone_url":"https://github.com/EdinburghGenomics/Analysis-Driver.git","svn_url":"https://github.com/EdinburghGenomics/Analysis-Driver","homepage":"","size":4015,"stargazers_count":8,"watchers_count":8,"language":"Python","has_issues":true,"has_projects":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":0,"mirror_url":null,"archived":false,"open_issues_count":26,"license":null,"forks":0,"open_issues":26,"watchers":8,"default_branch":"master"}},"base":{"label":"EdinburghGenomics:master","ref":"master","sha":"4c43a16ea821c0afe3a37fa40a1eac9b7b121666","user":{"login":"EdinburghGenomics","id":12951724,"node_id":"MDEyOk9yZ2FuaXphdGlvbjEyOTUxNzI0","avatar_url":"https://avatars0.githubusercontent.com/u/12951724?v=4","gravatar_id":"","url":"https://api.github.com/users/EdinburghGenomics","html_url":"https://github.com/EdinburghGenomics","followers_url":"https://api.github.com/users/EdinburghGenomics/followers","following_url":"https://api.github.com/users/EdinburghGenomics/following{/other_user}","gists_url":"https://api.github.com/users/EdinburghGenomics/gists{/gist_id}","starred_url":"https://api.github.com/users/EdinburghGenomics/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/EdinburghGenomics/subscriptions","organizations_url":"https://api.github.com/users/EdinburghGenomics/orgs","repos_url":"https://api.github.com/users/EdinburghGenomics/repos","events_url":"https://api.github.com/users/EdinburghGenomics/events{/privacy}","received_events_url":"https://api.github.com/users/EdinburghGenomics/received_events","type":"Organization","site_admin":false},"repo":{"id":37849969,"node_id":"MDEwOlJlcG9zaXRvcnkzNzg0OTk2OQ==","name":"Analysis-Driver","full_name":"EdinburghGenomics/Analysis-Driver","private":false,"owner":{"login":"EdinburghGenomics","id":12951724,"node_id":"MDEyOk9yZ2FuaXphdGlvbjEyOTUxNzI0","avatar_url":"https://avatars0.githubusercontent.com/u/12951724?v=4","gravatar_id":"","url":"https://api.github.com/users/EdinburghGenomics","html_url":"https://github.com/EdinburghGenomics","followers_url":"https://api.github.com/users/EdinburghGenomics/followers","following_url":"https://api.github.com/users/EdinburghGenomics/following{/other_user}","gists_url":"https://api.github.com/users/EdinburghGenomics/gists{/gist_id}","starred_url":"https://api.github.com/users/EdinburghGenomics/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/EdinburghGenomics/subscriptions","organizations_url":"https://api.github.com/users/EdinburghGenomics/orgs","repos_url":"https://api.github.com/users/EdinburghGenomics/repos","events_url":"https://api.github.com/users/EdinburghGenomics/events{/privacy}","received_events_url":"https://api.github.com/users/EdinburghGenomics/received_events","type":"Organization","site_admin":false},"html_url":"https://github.com/EdinburghGenomics/Analysis-Driver","description":"Pipelines for Illumina HiSeqX demultiplexing, sequence QC and variant calling.","fork":false,"url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver","forks_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/forks","keys_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/keys{/key_id}","collaborators_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/teams","hooks_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/hooks","issue_events_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/issues/events{/number}","events_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/events","assignees_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/assignees{/user}","branches_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/branches{/branch}","tags_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/tags","blobs_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/git/refs{/sha}","trees_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/git/trees{/sha}","statuses_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/statuses/{sha}","languages_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/languages","stargazers_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/stargazers","contributors_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/contributors","subscribers_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/subscribers","subscription_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/subscription","commits_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/commits{/sha}","git_commits_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/git/commits{/sha}","comments_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/comments{/number}","issue_comment_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/issues/comments{/number}","contents_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/contents/{+path}","compare_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/compare/{base}...{head}","merges_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/merges","archive_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/downloads","issues_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/issues{/number}","pulls_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/pulls{/number}","milestones_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/milestones{/number}","notifications_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/labels{/name}","releases_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/releases{/id}","deployments_url":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/deployments","created_at":"2015-06-22T10:42:34Z","updated_at":"2018-11-30T23:45:07Z","pushed_at":"2018-12-05T09:55:48Z","git_url":"git://github.com/EdinburghGenomics/Analysis-Driver.git","ssh_url":"git@github.com:EdinburghGenomics/Analysis-Driver.git","clone_url":"https://github.com/EdinburghGenomics/Analysis-Driver.git","svn_url":"https://github.com/EdinburghGenomics/Analysis-Driver","homepage":"","size":4015,"stargazers_count":8,"watchers_count":8,"language":"Python","has_issues":true,"has_projects":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":0,"mirror_url":null,"archived":false,"open_issues_count":26,"license":null,"forks":0,"open_issues":26,"watchers":8,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/pulls/362"},"html":{"href":"https://github.com/EdinburghGenomics/Analysis-Driver/pull/362"},"issue":{"href":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/issues/362"},"comments":{"href":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/issues/362/comments"},"review_comments":{"href":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/pulls/362/comments"},"review_comment":{"href":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/pulls/362/commits"},"statuses":{"href":"https://api.github.com/repos/EdinburghGenomics/Analysis-Driver/statuses/6345d792d06eec6f73f1f663c86510095393da2d"}},"author_association":"CONTRIBUTOR"}}
{"actor":{"display_login":"tcezard"}}