{"action":"created","comment":{"url":"https://api.github.com/repos/biocore/qiita/pulls/comments/46440312","id":46440312,"diff_hunk":"@@ -0,0 +1,73 @@\n+# -----------------------------------------------------------------------------\n+# Copyright (c) 2014--, The Qiita Development Team.\n+#\n+# Distributed under the terms of the BSD 3-clause License.\n+#\n+# The full license is in the file LICENSE, distributed with this software.\n+# -----------------------------------------------------------------------------\n+\n+from subprocess import Popen, PIPE\n+from os.path import join\n+\n+from qiita_core.qiita_settings import qiita_config\n+from qiita_db.processing_job import ProcessingJob\n+from qiita_db.util import get_work_base_dir\n+from qiita_db.logger import LogEntry\n+\n+\n+def system_call(cmd):\n+    \"\"\"Call command and return (stdout, stderr, return_value)","path":"qiita_ware/executor.py","position":19,"original_position":19,"commit_id":"404a1e8921c37bc6db4a9f28396e38eda0f283b6","original_commit_id":"404a1e8921c37bc6db4a9f28396e38eda0f283b6","user":{"login":"antgonza","id":2014559,"avatar_url":"https://avatars.githubusercontent.com/u/2014559?v=3","gravatar_id":"","url":"https://api.github.com/users/antgonza","html_url":"https://github.com/antgonza","followers_url":"https://api.github.com/users/antgonza/followers","following_url":"https://api.github.com/users/antgonza/following{/other_user}","gists_url":"https://api.github.com/users/antgonza/gists{/gist_id}","starred_url":"https://api.github.com/users/antgonza/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/antgonza/subscriptions","organizations_url":"https://api.github.com/users/antgonza/orgs","repos_url":"https://api.github.com/users/antgonza/repos","events_url":"https://api.github.com/users/antgonza/events{/privacy}","received_events_url":"https://api.github.com/users/antgonza/received_events","type":"User","site_admin":false},"body":"Call cmd and return ... ","created_at":"2015-12-02T16:50:12Z","updated_at":"2015-12-02T16:50:12Z","html_url":"https://github.com/biocore/qiita/pull/1558#discussion_r46440312","pull_request_url":"https://api.github.com/repos/biocore/qiita/pulls/1558","_links":{"self":{"href":"https://api.github.com/repos/biocore/qiita/pulls/comments/46440312"},"html":{"href":"https://github.com/biocore/qiita/pull/1558#discussion_r46440312"},"pull_request":{"href":"https://api.github.com/repos/biocore/qiita/pulls/1558"}}},"pull_request":{"url":"https://api.github.com/repos/biocore/qiita/pulls/1558","id":52357892,"html_url":"https://github.com/biocore/qiita/pull/1558","diff_url":"https://github.com/biocore/qiita/pull/1558.diff","patch_url":"https://github.com/biocore/qiita/pull/1558.patch","issue_url":"https://api.github.com/repos/biocore/qiita/issues/1558","number":1558,"state":"open","locked":false,"title":"WIP: Plugin connect everything","user":{"login":"josenavas","id":2501478,"avatar_url":"https://avatars.githubusercontent.com/u/2501478?v=3","gravatar_id":"","url":"https://api.github.com/users/josenavas","html_url":"https://github.com/josenavas","followers_url":"https://api.github.com/users/josenavas/followers","following_url":"https://api.github.com/users/josenavas/following{/other_user}","gists_url":"https://api.github.com/users/josenavas/gists{/gist_id}","starred_url":"https://api.github.com/users/josenavas/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/josenavas/subscriptions","organizations_url":"https://api.github.com/users/josenavas/orgs","repos_url":"https://api.github.com/users/josenavas/repos","events_url":"https://api.github.com/users/josenavas/events{/privacy}","received_events_url":"https://api.github.com/users/josenavas/received_events","type":"User","site_admin":false},"body":"This is built on top of #1557 so review/merge that one first.\r\n\r\nThis PR connects all the plugin bits so the system should be all functional again.\r\n\r\nCurrently, there are still some reference to the data objects (RawData, PreprocessedData and ProcessData) done in qiita_pet (which I thought were already removed); and some parts of the interface is acting up.\r\n\r\nTomorrow I will need to shift for some time to work in some of my class homeworks, so doing a WIP in case that somebody else can also take a look. The vast majority of the work is already done, and the only missing bits in here is to fix the interface to be compliant with the underlying 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