{"action":"created","comment":{"url":"https://api.github.com/repos/ga4gh/server/pulls/comments/41787500","id":41787500,"diff_hunk":"@@ -192,6 +192,18 @@ def getAllReadGroupSets(self):\n             for readGroupSet in iterator:\n                 yield readGroupSet\n \n+    def getAllReadGroups(self):\n+        \"\"\"\n+        Get all read groups in a read group set\n+        \"\"\"\n+        for dataset in self.getAllDatasets():\n+            iterator = self._client.searchReadGroupSets(\n+                datasetId=dataset.id)\n+            for readGroupSet in iterator:\n+                rgs = self._client.getReadGroupSet(readGroupSet.id)\n+                for rg in rgs.readGroups:\n+                    yield rg.id","path":"ga4gh/cli.py","position":14,"original_position":14,"commit_id":"d0ff5030b25e80bcd8760536db1b1e4a1a49fc6f","original_commit_id":"d0ff5030b25e80bcd8760536db1b1e4a1a49fc6f","user":{"login":"jeromekelleher","id":2664569,"avatar_url":"https://avatars.githubusercontent.com/u/2664569?v=3","gravatar_id":"","url":"https://api.github.com/users/jeromekelleher","html_url":"https://github.com/jeromekelleher","followers_url":"https://api.github.com/users/jeromekelleher/followers","following_url":"https://api.github.com/users/jeromekelleher/following{/other_user}","gists_url":"https://api.github.com/users/jeromekelleher/gists{/gist_id}","starred_url":"https://api.github.com/users/jeromekelleher/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jeromekelleher/subscriptions","organizations_url":"https://api.github.com/users/jeromekelleher/orgs","repos_url":"https://api.github.com/users/jeromekelleher/repos","events_url":"https://api.github.com/users/jeromekelleher/events{/privacy}","received_events_url":"https://api.github.com/users/jeromekelleher/received_events","type":"User","site_admin":false},"body":"We should yield the readgroup object here rather than the ID to keep symmetry with the other methods.","created_at":"2015-10-12T18:41:27Z","updated_at":"2015-10-12T18:41:27Z","html_url":"https://github.com/ga4gh/server/pull/738#discussion_r41787500","pull_request_url":"https://api.github.com/repos/ga4gh/server/pulls/738","_links":{"self":{"href":"https://api.github.com/repos/ga4gh/server/pulls/comments/41787500"},"html":{"href":"https://github.com/ga4gh/server/pull/738#discussion_r41787500"},"pull_request":{"href":"https://api.github.com/repos/ga4gh/server/pulls/738"}}},"pull_request":{"url":"https://api.github.com/repos/ga4gh/server/pulls/738","id":47449858,"html_url":"https://github.com/ga4gh/server/pull/738","diff_url":"https://github.com/ga4gh/server/pull/738.diff","patch_url":"https://github.com/ga4gh/server/pull/738.patch","issue_url":"https://api.github.com/repos/ga4gh/server/issues/738","number":738,"state":"open","locked":false,"title":"Added support for finding all read groups when no read group specified","user":{"login":"pkrusche","id":1199561,"avatar_url":"https://avatars.githubusercontent.com/u/1199561?v=3","gravatar_id":"","url":"https://api.github.com/users/pkrusche","html_url":"https://github.com/pkrusche","followers_url":"https://api.github.com/users/pkrusche/followers","following_url":"https://api.github.com/users/pkrusche/following{/other_user}","gists_url":"https://api.github.com/users/pkrusche/gists{/gist_id}","starred_url":"https://api.github.com/users/pkrusche/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pkrusche/subscriptions","organizations_url":"https://api.github.com/users/pkrusche/orgs","repos_url":"https://api.github.com/users/pkrusche/repos","events_url":"https://api.github.com/users/pkrusche/events{/privacy}","received_events_url":"https://api.github.com/users/pkrusche/received_events","type":"User","site_admin":false},"body":"Fixes issue #702","created_at":"2015-10-12T18:25:25Z","updated_at":"2015-10-12T18:41:27Z","closed_at":null,"merged_at":null,"merge_commit_sha":"d1e112baca9b7073c7bd7d3d9245d6f9ae3e84bd","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/ga4gh/server/pulls/738/commits","review_comments_url":"https://api.github.com/repos/ga4gh/server/pulls/738/comments","review_comment_url":"https://api.github.com/repos/ga4gh/server/pulls/comments{/number}","comments_url":"https://api.github.com/repos/ga4gh/server/issues/738/comments","statuses_url":"https://api.github.com/repos/ga4gh/server/statuses/d0ff5030b25e80bcd8760536db1b1e4a1a49fc6f","head":{"label":"pkrusche:702-better-default-cli-read-search","ref":"702-better-default-cli-read-search","sha":"d0ff5030b25e80bcd8760536db1b1e4a1a49fc6f","user":{"login":"pkrusche","id":1199561,"avatar_url":"https://avatars.githubusercontent.com/u/1199561?v=3","gravatar_id":"","url":"https://api.github.com/users/pkrusche","html_url":"https://github.com/pkrusche","followers_url":"https://api.github.com/users/pkrusche/followers","following_url":"https://api.github.com/users/pkrusche/following{/other_user}","gists_url":"https://api.github.com/users/pkrusche/gists{/gist_id}","starred_url":"https://api.github.com/users/pkrusche/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pkrusche/subscriptions","organizations_url":"https://api.github.com/users/pkrusche/orgs","repos_url":"https://api.github.com/users/pkrusche/repos","events_url":"https://api.github.com/users/pkrusche/events{/privacy}","received_events_url":"https://api.github.com/users/pkrusche/received_events","type":"User","site_admin":false},"repo":{"id":44114728,"name":"server","full_name":"pkrusche/server","owner":{"login":"pkrusche","id":1199561,"avatar_url":"https://avatars.githubusercontent.com/u/1199561?v=3","gravatar_id":"","url":"https://api.github.com/users/pkrusche","html_url":"https://github.com/pkrusche","followers_url":"https://api.github.com/users/pkrusche/followers","following_url":"https://api.github.com/users/pkrusche/following{/other_user}","gists_url":"https://api.github.com/users/pkrusche/gists{/gist_id}","starred_url":"https://api.github.com/users/pkrusche/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pkrusche/subscriptions","organizations_url":"https://api.github.com/users/pkrusche/orgs","repos_url":"https://api.github.com/users/pkrusche/repos","events_url":"https://api.github.com/users/pkrusche/events{/privacy}","received_events_url":"https://api.github.com/users/pkrusche/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/pkrusche/server","description":"A reference implementation of the APIs defined in the schemas repository.","fork":true,"url":"https://api.github.com/repos/pkrusche/server","forks_url":"https://api.github.com/repos/pkrusche/server/forks","keys_url":"https://api.github.com/repos/pkrusche/server/keys{/key_id}","collaborators_url":"https://api.github.com/repos/pkrusche/server/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/pkrusche/server/teams","hooks_url":"https://api.github.com/repos/pkrusche/server/hooks","issue_events_url":"https://api.github.com/repos/pkrusche/server/issues/events{/number}","events_url":"https://api.github.com/repos/pkrusche/server/events","assignees_url":"https://api.github.com/repos/pkrusche/server/assignees{/user}","branches_url":"https://api.github.com/repos/pkrusche/server/branches{/branch}","tags_url":"https://api.github.com/repos/pkrusche/server/tags","blobs_url":"https://api.github.com/repos/pkrusche/server/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/pkrusche/server/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/pkrusche/server/git/refs{/sha}","trees_url":"https://api.github.com/repos/pkrusche/server/git/trees{/sha}","statuses_url":"https://api.github.com/repos/pkrusche/server/statuses/{sha}","languages_url":"https://api.github.com/repos/pkrusche/server/languages","stargazers_url":"https://api.github.com/repos/pkrusche/server/stargazers","contributors_url":"https://api.github.com/repos/pkrusche/server/contributors","subscribers_url":"https://api.github.com/repos/pkrusche/server/subscribers","subscription_url":"https://api.github.com/repos/pkrusche/server/subscription","commits_url":"https://api.github.com/repos/pkrusche/server/commits{/sha}","git_commits_url":"https://api.github.com/repos/pkrusche/server/git/commits{/sha}","comments_url":"https://api.github.com/repos/pkrusche/server/comments{/number}","issue_comment_url":"https://api.github.com/repos/pkrusche/server/issues/comments{/number}","contents_url":"https://api.github.com/repos/pkrusche/server/contents/{+path}","compare_url":"https://api.github.com/repos/pkrusche/server/compare/{base}...{head}","merges_url":"https://api.github.com/repos/pkrusche/server/merges","archive_url":"https://api.github.com/repos/pkrusche/server/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/pkrusche/server/downloads","issues_url":"https://api.github.com/repos/pkrusche/server/issues{/number}","pulls_url":"https://api.github.com/repos/pkrusche/server/pulls{/number}","milestones_url":"https://api.github.com/repos/pkrusche/server/milestones{/number}","notifications_url":"https://api.github.com/repos/pkrusche/server/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/pkrusche/server/labels{/name}","releases_url":"https://api.github.com/repos/pkrusche/server/releases{/id}","created_at":"2015-10-12T15:00:49Z","updated_at":"2015-10-12T15:00:50Z","pushed_at":"2015-10-12T18:24:33Z","git_url":"git://github.com/pkrusche/server.git","ssh_url":"git@github.com:pkrusche/server.git","clone_url":"https://github.com/pkrusche/server.git","svn_url":"https://github.com/pkrusche/server","homepage":null,"size":4154,"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":"develop"}},"base":{"label":"ga4gh:develop","ref":"develop","sha":"562d12f5e8ab582bf28cfc7195bbcdac37adc659","user":{"login":"ga4gh","id":6921777,"avatar_url":"https://avatars.githubusercontent.com/u/6921777?v=3","gravatar_id":"","url":"https://api.github.com/users/ga4gh","html_url":"https://github.com/ga4gh","followers_url":"https://api.github.com/users/ga4gh/followers","following_url":"https://api.github.com/users/ga4gh/following{/other_user}","gists_url":"https://api.github.com/users/ga4gh/gists{/gist_id}","starred_url":"https://api.github.com/users/ga4gh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ga4gh/subscriptions","organizations_url":"https://api.github.com/users/ga4gh/orgs","repos_url":"https://api.github.com/users/ga4gh/repos","events_url":"https://api.github.com/users/ga4gh/events{/privacy}","received_events_url":"https://api.github.com/users/ga4gh/received_events","type":"Organization","site_admin":false},"repo":{"id":22882621,"name":"server","full_name":"ga4gh/server","owner":{"login":"ga4gh","id":6921777,"avatar_url":"https://avatars.githubusercontent.com/u/6921777?v=3","gravatar_id":"","url":"https://api.github.com/users/ga4gh","html_url":"https://github.com/ga4gh","followers_url":"https://api.github.com/users/ga4gh/followers","following_url":"https://api.github.com/users/ga4gh/following{/other_user}","gists_url":"https://api.github.com/users/ga4gh/gists{/gist_id}","starred_url":"https://api.github.com/users/ga4gh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ga4gh/subscriptions","organizations_url":"https://api.github.com/users/ga4gh/orgs","repos_url":"https://api.github.com/users/ga4gh/repos","events_url":"https://api.github.com/users/ga4gh/events{/privacy}","received_events_url":"https://api.github.com/users/ga4gh/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/ga4gh/server","description":"A reference implementation of the APIs defined in the schemas repository.","fork":false,"url":"https://api.github.com/repos/ga4gh/server","forks_url":"https://api.github.com/repos/ga4gh/server/forks","keys_url":"https://api.github.com/repos/ga4gh/server/keys{/key_id}","collaborators_url":"https://api.github.com/repos/ga4gh/server/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/ga4gh/server/teams","hooks_url":"https://api.github.com/repos/ga4gh/server/hooks","issue_events_url":"https://api.github.com/repos/ga4gh/server/issues/events{/number}","events_url":"https://api.github.com/repos/ga4gh/server/events","assignees_url":"https://api.github.com/repos/ga4gh/server/assignees{/user}","branches_url":"https://api.github.com/repos/ga4gh/server/branches{/branch}","tags_url":"https://api.github.com/repos/ga4gh/server/tags","blobs_url":"https://api.github.com/repos/ga4gh/server/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/ga4gh/server/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/ga4gh/server/git/refs{/sha}","trees_url":"https://api.github.com/repos/ga4gh/server/git/trees{/sha}","statuses_url":"https://api.github.com/repos/ga4gh/server/statuses/{sha}","languages_url":"https://api.github.com/repos/ga4gh/server/languages","stargazers_url":"https://api.github.com/repos/ga4gh/server/stargazers","contributors_url":"https://api.github.com/repos/ga4gh/server/contributors","subscribers_url":"https://api.github.com/repos/ga4gh/server/subscribers","subscription_url":"https://api.github.com/repos/ga4gh/server/subscription","commits_url":"https://api.github.com/repos/ga4gh/server/commits{/sha}","git_commits_url":"https://api.github.com/repos/ga4gh/server/git/commits{/sha}","comments_url":"https://api.github.com/repos/ga4gh/server/comments{/number}","issue_comment_url":"https://api.github.com/repos/ga4gh/server/issues/comments{/number}","contents_url":"https://api.github.com/repos/ga4gh/server/contents/{+path}","compare_url":"https://api.github.com/repos/ga4gh/server/compare/{base}...{head}","merges_url":"https://api.github.com/repos/ga4gh/server/merges","archive_url":"https://api.github.com/repos/ga4gh/server/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/ga4gh/server/downloads","issues_url":"https://api.github.com/repos/ga4gh/server/issues{/number}","pulls_url":"https://api.github.com/repos/ga4gh/server/pulls{/number}","milestones_url":"https://api.github.com/repos/ga4gh/server/milestones{/number}","notifications_url":"https://api.github.com/repos/ga4gh/server/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/ga4gh/server/labels{/name}","releases_url":"https://api.github.com/repos/ga4gh/server/releases{/id}","created_at":"2014-08-12T15:31:49Z","updated_at":"2015-09-16T11:44:20Z","pushed_at":"2015-10-12T18:25:25Z","git_url":"git://github.com/ga4gh/server.git","ssh_url":"git@github.com:ga4gh/server.git","clone_url":"https://github.com/ga4gh/server.git","svn_url":"https://github.com/ga4gh/server","homepage":null,"size":7014,"stargazers_count":41,"watchers_count":41,"language":"Python","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":67,"mirror_url":null,"open_issues_count":96,"forks":67,"open_issues":96,"watchers":41,"default_branch":"develop"}},"_links":{"self":{"href":"https://api.github.com/repos/ga4gh/server/pulls/738"},"html":{"href":"https://github.com/ga4gh/server/pull/738"},"issue":{"href":"https://api.github.com/repos/ga4gh/server/issues/738"},"comments":{"href":"https://api.github.com/repos/ga4gh/server/issues/738/comments"},"review_comments":{"href":"https://api.github.com/repos/ga4gh/server/pulls/738/comments"},"review_comment":{"href":"https://api.github.com/repos/ga4gh/server/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/ga4gh/server/pulls/738/commits"},"statuses":{"href":"https://api.github.com/repos/ga4gh/server/statuses/d0ff5030b25e80bcd8760536db1b1e4a1a49fc6f"}}}}