{"action":"created","comment":{"url":"https://api.github.com/repos/biocore/qiita/pulls/comments/26878829","id":26878829,"diff_hunk":"@@ -237,6 +237,98 @@ def test_get_preprocess_fasta_cmd_sff_run_prefix(self):\n         self.assertTrue(obs_cmds[6].startswith('cat'))\n         self.assertTrue('seqs_filtered.qual' in obs_cmds[6])\n \n+    def test_get_preprocess_fasta_cmd_sff_run_prefix_match(self):\n+        # Test that the run prefixes in the prep_template and the file names\n+        # actually match and raise an error if not\n+        conn_handler = SQLConnectionHandler()\n+        sql = (\"\"\"\n+            INSERT INTO qiita.filepath (filepath_id, filepath,\n+                filepath_type_id, checksum, checksum_algorithm_id,\n+                data_directory_id) VALUES (19, 'new.sff', 17, 852952723, 1, 5);\n+            INSERT INTO qiita.raw_filepath (raw_data_id , filepath_id) VALUES\n+                (3, 19);\n+            UPDATE qiita.prep_1 SET run_prefix='preprocess_test';\n+            UPDATE qiita.prep_1 SET run_prefix='new' WHERE\n+                sample_id = '1.SKB8.640193';\n+        \"\"\")\n+        conn_handler.execute(sql)\n+\n+        raw_data = RawData(3)\n+        params = Preprocessed454Params(1)\n+        prep_template = PrepTemplate(1)\n+\n+        obs_cmd, obs_output_dir = _get_preprocess_fasta_cmd(\n+            raw_data, prep_template, params)\n+\n+        obs_cmds = obs_cmd.split('; ')\n+        # assumming that test_get_preprocess_fasta_cmd_sff_no_run_prefix is\n+        # working we only need to test for the commands being ran and\n+        # that n is valid\n+        self.assertTrue(len(obs_cmds) == 9)","path":"qiita_ware/test/test_processing_pipeline.py","position":42,"original_position":42,"commit_id":"6f5340fe0ec670e04050b23210bd8c9f2decb76e","original_commit_id":"6f5340fe0ec670e04050b23210bd8c9f2decb76e","user":{"login":"wasade","id":474290,"avatar_url":"https://avatars.githubusercontent.com/u/474290?v=3","gravatar_id":"","url":"https://api.github.com/users/wasade","html_url":"https://github.com/wasade","followers_url":"https://api.github.com/users/wasade/followers","following_url":"https://api.github.com/users/wasade/following{/other_user}","gists_url":"https://api.github.com/users/wasade/gists{/gist_id}","starred_url":"https://api.github.com/users/wasade/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wasade/subscriptions","organizations_url":"https://api.github.com/users/wasade/orgs","repos_url":"https://api.github.com/users/wasade/repos","events_url":"https://api.github.com/users/wasade/events{/privacy}","received_events_url":"https://api.github.com/users/wasade/received_events","type":"User","site_admin":false},"body":"`assertEqual`","created_at":"2015-03-20T21:41:14Z","updated_at":"2015-03-20T21:41:14Z","html_url":"https://github.com/biocore/qiita/pull/1008#discussion_r26878829","pull_request_url":"https://api.github.com/repos/biocore/qiita/pulls/1008","_links":{"self":{"href":"https://api.github.com/repos/biocore/qiita/pulls/comments/26878829"},"html":{"href":"https://github.com/biocore/qiita/pull/1008#discussion_r26878829"},"pull_request":{"href":"https://api.github.com/repos/biocore/qiita/pulls/1008"}}},"pull_request":{"url":"https://api.github.com/repos/biocore/qiita/pulls/1008","id":31653846,"html_url":"https://github.com/biocore/qiita/pull/1008","diff_url":"https://github.com/biocore/qiita/pull/1008.diff","patch_url":"https://github.com/biocore/qiita/pull/1008.patch","issue_url":"https://api.github.com/repos/biocore/qiita/issues/1008","number":1008,"state":"open","locked":false,"title":"fixing new 454 issue","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":"This solves an issue when you have 3 sff files, where 2 are from the same run (prefix aaa) and the 3rd one has a different prefix (prefix bbb). This is aaa1.sff, aaa2.sff, bbb.sff. In this case we need to split at the same time aaa1-2 and then bbb. \r\n\r\nNote that this is blocking some analysis so quick reviews are greatly appreciated. @biocore/qiita-dev ","created_at":"2015-03-20T21:33:13Z","updated_at":"2015-03-20T21:41:14Z","closed_at":null,"merged_at":null,"merge_commit_sha":"4036291be4f2d653df4dfeea3d973e60b71ecaf8","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/biocore/qiita/pulls/1008/commits","review_comments_url":"https://api.github.com/repos/biocore/qiita/pulls/1008/comments","review_comment_url":"https://api.github.com/repos/biocore/qiita/pulls/comments{/number}","comments_url":"https://api.github.com/repos/biocore/qiita/issues/1008/comments","statuses_url":"https://api.github.com/repos/biocore/qiita/statuses/6f5340fe0ec670e04050b23210bd8c9f2decb76e","head":{"label":"antgonza:454-issue","ref":"454-issue","sha":"6f5340fe0ec670e04050b23210bd8c9f2decb76e","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},"repo":{"id":16964638,"name":"qiita","full_name":"antgonza/qiita","owner":{"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},"private":false,"html_url":"https://github.com/antgonza/qiita","description":"Qiita - A QIIME databasing effort","fork":true,"url":"https://api.github.com/repos/antgonza/qiita","forks_url":"https://api.github.com/repos/antgonza/qiita/forks","keys_url":"https://api.github.com/repos/antgonza/qiita/keys{/key_id}","collaborators_url":"https://api.github.com/repos/antgonza/qiita/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/antgonza/qiita/teams","hooks_url":"https://api.github.com/repos/antgonza/qiita/hooks","issue_events_url":"https://api.github.com/repos/antgonza/qiita/issues/events{/number}","events_url":"https://api.github.com/repos/antgonza/qiita/events","assignees_url":"https://api.github.com/repos/antgonza/qiita/assignees{/user}","branches_url":"https://api.github.com/repos/antgonza/qiita/branches{/branch}","tags_url":"https://api.github.com/repos/antgonza/qiita/tags","blobs_url":"https://api.github.com/repos/antgonza/qiita/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/antgonza/qiita/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/antgonza/qiita/git/refs{/sha}","trees_url":"https://api.github.com/repos/antgonza/qiita/git/trees{/sha}","statuses_url":"https://api.github.com/repos/antgonza/qiita/statuses/{sha}","languages_url":"https://api.github.com/repos/antgonza/qiita/languages","stargazers_url":"https://api.github.com/repos/antgonza/qiita/stargazers","contributors_url":"https://api.github.com/repos/antgonza/qiita/contributors","subscribers_url":"https://api.github.com/repos/antgonza/qiita/subscribers","subscription_url":"https://api.github.com/repos/antgonza/qiita/subscription","commits_url":"https://api.github.com/repos/antgonza/qiita/commits{/sha}","git_commits_url":"https://api.github.com/repos/antgonza/qiita/git/commits{/sha}","comments_url":"https://api.github.com/repos/antgonza/qiita/comments{/number}","issue_comment_url":"https://api.github.com/repos/antgonza/qiita/issues/comments{/number}","contents_url":"https://api.github.com/repos/antgonza/qiita/contents/{+path}","compare_url":"https://api.github.com/repos/antgonza/qiita/compare/{base}...{head}","merges_url":"https://api.github.com/repos/antgonza/qiita/merges","archive_url":"https://api.github.com/repos/antgonza/qiita/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/antgonza/qiita/downloads","issues_url":"https://api.github.com/repos/antgonza/qiita/issues{/number}","pulls_url":"https://api.github.com/repos/antgonza/qiita/pulls{/number}","milestones_url":"https://api.github.com/repos/antgonza/qiita/milestones{/number}","notifications_url":"https://api.github.com/repos/antgonza/qiita/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/antgonza/qiita/labels{/name}","releases_url":"https://api.github.com/repos/antgonza/qiita/releases{/id}","created_at":"2014-02-18T21:38:48Z","updated_at":"2015-03-20T16:35:11Z","pushed_at":"2015-03-20T21:30:30Z","git_url":"git://github.com/antgonza/qiita.git","ssh_url":"git@github.com:antgonza/qiita.git","clone_url":"https://github.com/antgonza/qiita.git","svn_url":"https://github.com/antgonza/qiita","homepage":"","size":122955,"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:master","ref":"master","sha":"e937609cb72f65e59fc488091f2efe09fe9ed412","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":"2015-03-20T12:16:36Z","pushed_at":"2015-03-20T21:33:13Z","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":126616,"stargazers_count":14,"watchers_count":14,"language":"Python","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":17,"mirror_url":null,"open_issues_count":193,"forks":17,"open_issues":193,"watchers":14,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/biocore/qiita/pulls/1008"},"html":{"href":"https://github.com/biocore/qiita/pull/1008"},"issue":{"href":"https://api.github.com/repos/biocore/qiita/issues/1008"},"comments":{"href":"https://api.github.com/repos/biocore/qiita/issues/1008/comments"},"review_comments":{"href":"https://api.github.com/repos/biocore/qiita/pulls/1008/comments"},"review_comment":{"href":"https://api.github.com/repos/biocore/qiita/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/biocore/qiita/pulls/1008/commits"},"statuses":{"href":"https://api.github.com/repos/biocore/qiita/statuses/6f5340fe0ec670e04050b23210bd8c9f2decb76e"}}}}