{"action":"created","comment":{"url":"https://api.github.com/repos/biocore/qiita/pulls/comments/31195834","id":31195834,"diff_hunk":"@@ -41,8 +41,73 @@\n class ProcessingPipelineTests(TestCase):\n     def setUp(self):\n         self.db_dir = get_db_files_base_dir()\n-        self.files_to_remove = []\n-        self.dirs_to_remove = []\n+\n+        # Create a SFF dataset: add prep template and a RawData\n+        study = Study(1)\n+        md_dict = {\n+            'SKB8.640193': {'center_name': 'ANL',\n+                            'primer': 'GTGCCAGCMGCCGCGGTAA',\n+                            'barcode': 'GTCCGCAAGTTA',\n+                            'run_prefix': \"preprocess_test\",\n+                            'platform': 'ILLUMINA',\n+                            'library_construction_protocol': 'AAAA',\n+                            'experiment_design_description': 'BBBB'},\n+            'SKD8.640184': {'center_name': 'ANL',\n+                            'primer': 'GTGCCAGCMGCCGCGGTAA',\n+                            'barcode': 'CGTAGAGCTCTC',\n+                            'run_prefix': \"preprocess_test\",\n+                            'platform': 'ILLUMINA',\n+                            'library_construction_protocol': 'AAAA',\n+                            'experiment_design_description': 'BBBB'},\n+            'SKB7.640196': {'center_name': 'ANL',\n+                            'primer': 'GTGCCAGCMGCCGCGGTAA',\n+                            'barcode': 'CCTCTGAGAGCT',\n+                            'run_prefix': \"preprocess_test\",\n+                            'platform': 'ILLUMINA',\n+                            'library_construction_protocol': 'AAAA',\n+                            'experiment_design_description': 'BBBB'}\n+        }\n+        md = pd.DataFrame.from_dict(md_dict, orient='index')\n+        self.sff_prep_template = PrepTemplate.create(md, study, \"16S\")\n+\n+        tmp_dir = mkdtemp()\n+        path_builder = partial(join, tmp_dir)\n+        fp1 = path_builder('preprocess_test1.sff')\n+        with open(fp1, 'w') as f:\n+            f.write('\\n')\n+        fp2 = path_builder('preprocess_test2.sff')\n+        with open(fp2, 'w') as f:\n+            f.write('\\n')\n+        fps = [(fp1, 17), (fp2, 17)]\n+\n+        # Magic number 1: is the filetype id\n+        self.raw_data = RawData.create(1, [self.sff_prep_template], fps)\n+\n+        # Create a SFF dataset with multiple run prefix:\n+        # add prep template and a RawData\n+        md_dict['SKD8.640184']['run_prefix'] = \"new\"\n+        md_rp = pd.DataFrame.from_dict(md_dict, orient='index')\n+        self.sff_prep_template_rp = PrepTemplate.create(md_rp, study, \"16S\")\n+\n+        path_builder = partial(join, tmp_dir)\n+        rp_fp1 = path_builder('preprocess_test1.sff')\n+        with open(rp_fp1, 'w') as f:\n+            f.write('\\n')\n+        rp_fp2 = path_builder('preprocess_test2.sff')\n+        with open(rp_fp2, 'w') as f:\n+            f.write('\\n')\n+        fps = [(rp_fp1, 17), (rp_fp2, 17)]\n+\n+        # Magic number 1: is the filetype id\n+        self.raw_data_rp = RawData.create(1, [self.sff_prep_template_rp], fps)\n+\n+        # Make sure that we clean up all created files\n+        self.files_to_remove = [fp1, fp2, rp_fp1, rp_fp2]","path":"qiita_ware/test/test_processing_pipeline.py","position":67,"original_position":67,"commit_id":"09d0fd72c37ee2bbdad6119a71334fe7b138ad92","original_commit_id":"09d0fd72c37ee2bbdad6119a71334fe7b138ad92","user":{"login":"ElDeveloper","id":375307,"avatar_url":"https://avatars.githubusercontent.com/u/375307?v=3","gravatar_id":"","url":"https://api.github.com/users/ElDeveloper","html_url":"https://github.com/ElDeveloper","followers_url":"https://api.github.com/users/ElDeveloper/followers","following_url":"https://api.github.com/users/ElDeveloper/following{/other_user}","gists_url":"https://api.github.com/users/ElDeveloper/gists{/gist_id}","starred_url":"https://api.github.com/users/ElDeveloper/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ElDeveloper/subscriptions","organizations_url":"https://api.github.com/users/ElDeveloper/orgs","repos_url":"https://api.github.com/users/ElDeveloper/repos","events_url":"https://api.github.com/users/ElDeveloper/events{/privacy}","received_events_url":"https://api.github.com/users/ElDeveloper/received_events","type":"User","site_admin":false},"body":"Nix that, just noticed 110.","created_at":"2015-05-28T01:05:35Z","updated_at":"2015-05-28T01:05:35Z","html_url":"https://github.com/biocore/qiita/pull/1206#discussion_r31195834","pull_request_url":"https://api.github.com/repos/biocore/qiita/pulls/1206","_links":{"self":{"href":"https://api.github.com/repos/biocore/qiita/pulls/comments/31195834"},"html":{"href":"https://github.com/biocore/qiita/pull/1206#discussion_r31195834"},"pull_request":{"href":"https://api.github.com/repos/biocore/qiita/pulls/1206"}}},"pull_request":{"url":"https://api.github.com/repos/biocore/qiita/pulls/1206","id":36105395,"html_url":"https://github.com/biocore/qiita/pull/1206","diff_url":"https://github.com/biocore/qiita/pull/1206.diff","patch_url":"https://github.com/biocore/qiita/pull/1206.patch","issue_url":"https://api.github.com/repos/biocore/qiita/issues/1206","number":1206,"state":"open","locked":false,"title":"1084 qiita ware","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":"Built on top of #1205 \r\n\r\nFixes all tests for qiita-ware. Failures still expected on qiita-pet.","created_at":"2015-05-24T17:11:40Z","updated_at":"2015-05-28T01:05:35Z","closed_at":null,"merged_at":null,"merge_commit_sha":"520ab6154bf571a7edb5ef92b4f96f1879ef7725","assignee":null,"milestone":{"url":"https://api.github.com/repos/biocore/qiita/milestones/8","html_url":"https://github.com/biocore/qiita/milestones/Alpha%200.2","labels_url":"https://api.github.com/repos/biocore/qiita/milestones/8/labels","id":1049807,"number":8,"title":"Alpha 0.2","description":"","creator":{"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},"open_issues":63,"closed_issues":34,"state":"open","created_at":"2015-04-02T04:52:07Z","updated_at":"2015-05-28T00:20:00Z","due_on":"2015-05-26T07:00:00Z","closed_at":null},"commits_url":"https://api.github.com/repos/biocore/qiita/pulls/1206/commits","review_comments_url":"https://api.github.com/repos/biocore/qiita/pulls/1206/comments","review_comment_url":"https://api.github.com/repos/biocore/qiita/pulls/comments{/number}","comments_url":"https://api.github.com/repos/biocore/qiita/issues/1206/comments","statuses_url":"https://api.github.com/repos/biocore/qiita/statuses/09d0fd72c37ee2bbdad6119a71334fe7b138ad92","head":{"label":"josenavas:1084-qiita-ware","ref":"1084-qiita-ware","sha":"09d0fd72c37ee2bbdad6119a71334fe7b138ad92","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},"repo":{"id":13527677,"name":"QiiTa","full_name":"josenavas/QiiTa","owner":{"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},"private":false,"html_url":"https://github.com/josenavas/QiiTa","description":"QiiTa databasing effort","fork":true,"url":"https://api.github.com/repos/josenavas/QiiTa","forks_url":"https://api.github.com/repos/josenavas/QiiTa/forks","keys_url":"https://api.github.com/repos/josenavas/QiiTa/keys{/key_id}","collaborators_url":"https://api.github.com/repos/josenavas/QiiTa/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/josenavas/QiiTa/teams","hooks_url":"https://api.github.com/repos/josenavas/QiiTa/hooks","issue_events_url":"https://api.github.com/repos/josenavas/QiiTa/issues/events{/number}","events_url":"https://api.github.com/repos/josenavas/QiiTa/events","assignees_url":"https://api.github.com/repos/josenavas/QiiTa/assignees{/user}","branches_url":"https://api.github.com/repos/josenavas/QiiTa/branches{/branch}","tags_url":"https://api.github.com/repos/josenavas/QiiTa/tags","blobs_url":"https://api.github.com/repos/josenavas/QiiTa/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/josenavas/QiiTa/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/josenavas/QiiTa/git/refs{/sha}","trees_url":"https://api.github.com/repos/josenavas/QiiTa/git/trees{/sha}","statuses_url":"https://api.github.com/repos/josenavas/QiiTa/statuses/{sha}","languages_url":"https://api.github.com/repos/josenavas/QiiTa/languages","stargazers_url":"https://api.github.com/repos/josenavas/QiiTa/stargazers","contributors_url":"https://api.github.com/repos/josenavas/QiiTa/contributors","subscribers_url":"https://api.github.com/repos/josenavas/QiiTa/subscribers","subscription_url":"https://api.github.com/repos/josenavas/QiiTa/subscription","commits_url":"https://api.github.com/repos/josenavas/QiiTa/commits{/sha}","git_commits_url":"https://api.github.com/repos/josenavas/QiiTa/git/commits{/sha}","comments_url":"https://api.github.com/repos/josenavas/QiiTa/comments{/number}","issue_comment_url":"https://api.github.com/repos/josenavas/QiiTa/issues/comments{/number}","contents_url":"https://api.github.com/repos/josenavas/QiiTa/contents/{+path}","compare_url":"https://api.github.com/repos/josenavas/QiiTa/compare/{base}...{head}","merges_url":"https://api.github.com/repos/josenavas/QiiTa/merges","archive_url":"https://api.github.com/repos/josenavas/QiiTa/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/josenavas/QiiTa/downloads","issues_url":"https://api.github.com/repos/josenavas/QiiTa/issues{/number}","pulls_url":"https://api.github.com/repos/josenavas/QiiTa/pulls{/number}","milestones_url":"https://api.github.com/repos/josenavas/QiiTa/milestones{/number}","notifications_url":"https://api.github.com/repos/josenavas/QiiTa/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/josenavas/QiiTa/labels{/name}","releases_url":"https://api.github.com/repos/josenavas/QiiTa/releases{/id}","created_at":"2013-10-12T19:29:32Z","updated_at":"2015-05-05T22:50:05Z","pushed_at":"2015-05-27T23:16:48Z","git_url":"git://github.com/josenavas/QiiTa.git","ssh_url":"git@github.com:josenavas/QiiTa.git","clone_url":"https://github.com/josenavas/QiiTa.git","svn_url":"https://github.com/josenavas/QiiTa","homepage":null,"size":125090,"stargazers_count":0,"watchers_count":0,"language":"Python","has_issues":false,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":0,"mirror_url":null,"open_issues_count":0,"forks":0,"open_issues":0,"watchers":0,"default_branch":"master"}},"base":{"label":"biocore:fix-1084","ref":"fix-1084","sha":"c1c6f14067bc45bd99d09256192a86aca690a898","user":{"login":"biocore","id":6241857,"avatar_url":"https://avatars.githubusercontent.com/u/6241857?v=3","gravatar_id":"","url":"https://api.github.com/users/biocore","html_url":"https://github.com/biocore","followers_url":"https://api.github.com/users/biocore/followers","following_url":"https://api.github.com/users/biocore/following{/other_user}","gists_url":"https://api.github.com/users/biocore/gists{/gist_id}","starred_url":"https://api.github.com/users/biocore/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/biocore/subscriptions","organizations_url":"https://api.github.com/users/biocore/orgs","repos_url":"https://api.github.com/users/biocore/repos","events_url":"https://api.github.com/users/biocore/events{/privacy}","received_events_url":"https://api.github.com/users/biocore/received_events","type":"Organization","site_admin":false},"repo":{"id":13131245,"name":"qiita","full_name":"biocore/qiita","owner":{"login":"biocore","id":6241857,"avatar_url":"https://avatars.githubusercontent.com/u/6241857?v=3","gravatar_id":"","url":"https://api.github.com/users/biocore","html_url":"https://github.com/biocore","followers_url":"https://api.github.com/users/biocore/followers","following_url":"https://api.github.com/users/biocore/following{/other_user}","gists_url":"https://api.github.com/users/biocore/gists{/gist_id}","starred_url":"https://api.github.com/users/biocore/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/biocore/subscriptions","organizations_url":"https://api.github.com/users/biocore/orgs","repos_url":"https://api.github.com/users/biocore/repos","events_url":"https://api.github.com/users/biocore/events{/privacy}","received_events_url":"https://api.github.com/users/biocore/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/biocore/qiita","description":"Qiita - A QIIME databasing effort","fork":false,"url":"https://api.github.com/repos/biocore/qiita","forks_url":"https://api.github.com/repos/biocore/qiita/forks","keys_url":"https://api.github.com/repos/biocore/qiita/keys{/key_id}","collaborators_url":"https://api.github.com/repos/biocore/qiita/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/biocore/qiita/teams","hooks_url":"https://api.github.com/repos/biocore/qiita/hooks","issue_events_url":"https://api.github.com/repos/biocore/qiita/issues/events{/number}","events_url":"https://api.github.com/repos/biocore/qiita/events","assignees_url":"https://api.github.com/repos/biocore/qiita/assignees{/user}","branches_url":"https://api.github.com/repos/biocore/qiita/branches{/branch}","tags_url":"https://api.github.com/repos/biocore/qiita/tags","blobs_url":"https://api.github.com/repos/biocore/qiita/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/biocore/qiita/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/biocore/qiita/git/refs{/sha}","trees_url":"https://api.github.com/repos/biocore/qiita/git/trees{/sha}","statuses_url":"https://api.github.com/repos/biocore/qiita/statuses/{sha}","languages_url":"https://api.github.com/repos/biocore/qiita/languages","stargazers_url":"https://api.github.com/repos/biocore/qiita/stargazers","contributors_url":"https://api.github.com/repos/biocore/qiita/contributors","subscribers_url":"https://api.github.com/repos/biocore/qiita/subscribers","subscription_url":"https://api.github.com/repos/biocore/qiita/subscription","commits_url":"https://api.github.com/repos/biocore/qiita/commits{/sha}","git_commits_url":"https://api.github.com/repos/biocore/qiita/git/commits{/sha}","comments_url":"https://api.github.com/repos/biocore/qiita/comments{/number}","issue_comment_url":"https://api.github.com/repos/biocore/qiita/issues/comments{/number}","contents_url":"https://api.github.com/repos/biocore/qiita/contents/{+path}","compare_url":"https://api.github.com/repos/biocore/qiita/compare/{base}...{head}","merges_url":"https://api.github.com/repos/biocore/qiita/merges","archive_url":"https://api.github.com/repos/biocore/qiita/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/biocore/qiita/downloads","issues_url":"https://api.github.com/repos/biocore/qiita/issues{/number}","pulls_url":"https://api.github.com/repos/biocore/qiita/pulls{/number}","milestones_url":"https://api.github.com/repos/biocore/qiita/milestones{/number}","notifications_url":"https://api.github.com/repos/biocore/qiita/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/biocore/qiita/labels{/name}","releases_url":"https://api.github.com/repos/biocore/qiita/releases{/id}","created_at":"2013-09-26T18:50:43Z","updated_at":"2015-05-10T01:08:02Z","pushed_at":"2015-05-28T00:20:00Z","git_url":"git://github.com/biocore/qiita.git","ssh_url":"git@github.com:biocore/qiita.git","clone_url":"https://github.com/biocore/qiita.git","svn_url":"https://github.com/biocore/qiita","homepage":"","size":130911,"stargazers_count":19,"watchers_count":19,"language":"Python","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":22,"mirror_url":null,"open_issues_count":266,"forks":22,"open_issues":266,"watchers":19,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/biocore/qiita/pulls/1206"},"html":{"href":"https://github.com/biocore/qiita/pull/1206"},"issue":{"href":"https://api.github.com/repos/biocore/qiita/issues/1206"},"comments":{"href":"https://api.github.com/repos/biocore/qiita/issues/1206/comments"},"review_comments":{"href":"https://api.github.com/repos/biocore/qiita/pulls/1206/comments"},"review_comment":{"href":"https://api.github.com/repos/biocore/qiita/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/biocore/qiita/pulls/1206/commits"},"statuses":{"href":"https://api.github.com/repos/biocore/qiita/statuses/09d0fd72c37ee2bbdad6119a71334fe7b138ad92"}}}}