{"action":"created","comment":{"url":"https://api.github.com/repos/griffithlab/civic-api-client/pulls/comments/57097930","id":57097930,"diff_hunk":"@@ -27,26 +27,61 @@ deactivate\n ```\n \n ##Usage\n-Very basic functionality for now, this will run a web-server on\n-http://127.0.0.1:5000/ , this page will list the items that need work.\n+Command options:\n+1. variants-list\n+2. evidence-items-list\n+3. action-items-web-view\n+4. tsv-creat\n+\n+1. List variants errors\n+Basic usage (check for all variants and print out all errors):\n ```\n-civic-api-client action-items-web-view\n+civic-api-client variants-list\n ```\n-\n-Here's the usage for drug search:\n-\n+Error type can be specified, for example:\n+```\n+civic-api-client variants-list --wrong-base\n+```\n+Command above will print variants where ref/var base is not in [A,C,G,T,N,None]\n+For more error types, see help manu with following command:\n+```\n+civic-api-client variants-list -h\n+```\n+2. List evidence errors\n+Basic usage (check for all evidence and print out all errors):\n+```\n+civic-api-client evidence-items-list\n+```\n+Error type can be specified, for example, search for missing drug items:\n Print out on screen(All types):\n+```\n civic-api-client evidence-items-list --drug \n-\n-Print out on web(All types):\n-civic-api-client evidence-items-list --drug --web\n-\n-Specify evidence types(Prognostic,for example):\n-civic-api-client evidence-items-list --drug --evi-type Predictive\n-\n+```\n Specify evidence types and print on web page(Predictive,for example):\n+```\n civic-api-client evidence-items-list --drug --evi-type Predictive --web\n-\n+```\n+For more error types, see help manu with following command:\n+```\n+civic-api-client evidence-items-list -h\n+```\n+3. Check for variants or evidences errors on web\n+Basic functionality for now, this will run a web-server on\n+http://127.0.0.1:5000/ , this page will list the items that need work.\n+```\n+civic-api-client action-items-web-view\n+```\n+Can also be done by following command:\n+```\n+civic-api-client variants-list --web\n+```\n+```\n+civic-api-client evidence-items-list --web\n+```\n+4. Export all evidence items as tsv file \n+```\n+civic-api-client tsv-creat","path":"README.md","position":71,"original_position":71,"commit_id":"3c77738e0f37afaade76a01d9e291087675a84b3","original_commit_id":"3c77738e0f37afaade76a01d9e291087675a84b3","user":{"login":"gatoravi","id":764948,"avatar_url":"https://avatars.githubusercontent.com/u/764948?v=3","gravatar_id":"","url":"https://api.github.com/users/gatoravi","html_url":"https://github.com/gatoravi","followers_url":"https://api.github.com/users/gatoravi/followers","following_url":"https://api.github.com/users/gatoravi/following{/other_user}","gists_url":"https://api.github.com/users/gatoravi/gists{/gist_id}","starred_url":"https://api.github.com/users/gatoravi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gatoravi/subscriptions","organizations_url":"https://api.github.com/users/gatoravi/orgs","repos_url":"https://api.github.com/users/gatoravi/repos","events_url":"https://api.github.com/users/gatoravi/events{/privacy}","received_events_url":"https://api.github.com/users/gatoravi/received_events","type":"User","site_admin":false},"body":"should be `tsv-create` here and in the code :space_invader: ","created_at":"2016-03-23T01:33:17Z","updated_at":"2016-03-23T01:33:17Z","html_url":"https://github.com/griffithlab/civic-api-client/pull/20#discussion_r57097930","pull_request_url":"https://api.github.com/repos/griffithlab/civic-api-client/pulls/20","_links":{"self":{"href":"https://api.github.com/repos/griffithlab/civic-api-client/pulls/comments/57097930"},"html":{"href":"https://github.com/griffithlab/civic-api-client/pull/20#discussion_r57097930"},"pull_request":{"href":"https://api.github.com/repos/griffithlab/civic-api-client/pulls/20"}}},"pull_request":{"url":"https://api.github.com/repos/griffithlab/civic-api-client/pulls/20","id":63619244,"html_url":"https://github.com/griffithlab/civic-api-client/pull/20","diff_url":"https://github.com/griffithlab/civic-api-client/pull/20.diff","patch_url":"https://github.com/griffithlab/civic-api-client/pull/20.patch","issue_url":"https://api.github.com/repos/griffithlab/civic-api-client/issues/20","number":20,"state":"open","locked":false,"title":"Eliminated variants without accepted evidence","user":{"login":"LeiChen0218","id":17259687,"avatar_url":"https://avatars.githubusercontent.com/u/17259687?v=3","gravatar_id":"","url":"https://api.github.com/users/LeiChen0218","html_url":"https://github.com/LeiChen0218","followers_url":"https://api.github.com/users/LeiChen0218/followers","following_url":"https://api.github.com/users/LeiChen0218/following{/other_user}","gists_url":"https://api.github.com/users/LeiChen0218/gists{/gist_id}","starred_url":"https://api.github.com/users/LeiChen0218/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/LeiChen0218/subscriptions","organizations_url":"https://api.github.com/users/LeiChen0218/orgs","repos_url":"https://api.github.com/users/LeiChen0218/repos","events_url":"https://api.github.com/users/LeiChen0218/events{/privacy}","received_events_url":"https://api.github.com/users/LeiChen0218/received_events","type":"User","site_admin":false},"body":"Fixed #19.  @gatoravi @malachig ","created_at":"2016-03-21T19:31:43Z","updated_at":"2016-03-23T01:33:17Z","closed_at":null,"merged_at":null,"merge_commit_sha":"e8569cb53643d27c215eb823ebccc50720d03043","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/griffithlab/civic-api-client/pulls/20/commits","review_comments_url":"https://api.github.com/repos/griffithlab/civic-api-client/pulls/20/comments","review_comment_url":"https://api.github.com/repos/griffithlab/civic-api-client/pulls/comments{/number}","comments_url":"https://api.github.com/repos/griffithlab/civic-api-client/issues/20/comments","statuses_url":"https://api.github.com/repos/griffithlab/civic-api-client/statuses/3c77738e0f37afaade76a01d9e291087675a84b3","head":{"label":"griffithlab:vl-valid-filter","ref":"vl-valid-filter","sha":"3c77738e0f37afaade76a01d9e291087675a84b3","user":{"login":"griffithlab","id":8323084,"avatar_url":"https://avatars.githubusercontent.com/u/8323084?v=3","gravatar_id":"","url":"https://api.github.com/users/griffithlab","html_url":"https://github.com/griffithlab","followers_url":"https://api.github.com/users/griffithlab/followers","following_url":"https://api.github.com/users/griffithlab/following{/other_user}","gists_url":"https://api.github.com/users/griffithlab/gists{/gist_id}","starred_url":"https://api.github.com/users/griffithlab/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/griffithlab/subscriptions","organizations_url":"https://api.github.com/users/griffithlab/orgs","repos_url":"https://api.github.com/users/griffithlab/repos","events_url":"https://api.github.com/users/griffithlab/events{/privacy}","received_events_url":"https://api.github.com/users/griffithlab/received_events","type":"Organization","site_admin":false},"repo":{"id":49983578,"name":"civic-api-client","full_name":"griffithlab/civic-api-client","owner":{"login":"griffithlab","id":8323084,"avatar_url":"https://avatars.githubusercontent.com/u/8323084?v=3","gravatar_id":"","url":"https://api.github.com/users/griffithlab","html_url":"https://github.com/griffithlab","followers_url":"https://api.github.com/users/griffithlab/followers","following_url":"https://api.github.com/users/griffithlab/following{/other_user}","gists_url":"https://api.github.com/users/griffithlab/gists{/gist_id}","starred_url":"https://api.github.com/users/griffithlab/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/griffithlab/subscriptions","organizations_url":"https://api.github.com/users/griffithlab/orgs","repos_url":"https://api.github.com/users/griffithlab/repos","events_url":"https://api.github.com/users/griffithlab/events{/privacy}","received_events_url":"https://api.github.com/users/griffithlab/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/griffithlab/civic-api-client","description":"Example tools using the CIVIC API","fork":false,"url":"https://api.github.com/repos/griffithlab/civic-api-client","forks_url":"https://api.github.com/repos/griffithlab/civic-api-client/forks","keys_url":"https://api.github.com/repos/griffithlab/civic-api-client/keys{/key_id}","collaborators_url":"https://api.github.com/repos/griffithlab/civic-api-client/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/griffithlab/civic-api-client/teams","hooks_url":"https://api.github.com/repos/griffithlab/civic-api-client/hooks","issue_events_url":"https://api.github.com/repos/griffithlab/civic-api-client/issues/events{/number}","events_url":"https://api.github.com/repos/griffithlab/civic-api-client/events","assignees_url":"https://api.github.com/repos/griffithlab/civic-api-client/assignees{/user}","branches_url":"https://api.github.com/repos/griffithlab/civic-api-client/branches{/branch}","tags_url":"https://api.github.com/repos/griffithlab/civic-api-client/tags","blobs_url":"https://api.github.com/repos/griffithlab/civic-api-client/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/griffithlab/civic-api-client/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/griffithlab/civic-api-client/git/refs{/sha}","trees_url":"https://api.github.com/repos/griffithlab/civic-api-client/git/trees{/sha}","statuses_url":"https://api.github.com/repos/griffithlab/civic-api-client/statuses/{sha}","languages_url":"https://api.github.com/repos/griffithlab/civic-api-client/languages","stargazers_url":"https://api.github.com/repos/griffithlab/civic-api-client/stargazers","contributors_url":"https://api.github.com/repos/griffithlab/civic-api-client/contributors","subscribers_url":"https://api.github.com/repos/griffithlab/civic-api-client/subscribers","subscription_url":"https://api.github.com/repos/griffithlab/civic-api-client/subscription","commits_url":"https://api.github.com/repos/griffithlab/civic-api-client/commits{/sha}","git_commits_url":"https://api.github.com/repos/griffithlab/civic-api-client/git/commits{/sha}","comments_url":"https://api.github.com/repos/griffithlab/civic-api-client/comments{/number}","issue_comment_url":"https://api.github.com/repos/griffithlab/civic-api-client/issues/comments{/number}","contents_url":"https://api.github.com/repos/griffithlab/civic-api-client/contents/{+path}","compare_url":"https://api.github.com/repos/griffithlab/civic-api-client/compare/{base}...{head}","merges_url":"https://api.github.com/repos/griffithlab/civic-api-client/merges","archive_url":"https://api.github.com/repos/griffithlab/civic-api-client/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/griffithlab/civic-api-client/downloads","issues_url":"https://api.github.com/repos/griffithlab/civic-api-client/issues{/number}","pulls_url":"https://api.github.com/repos/griffithlab/civic-api-client/pulls{/number}","milestones_url":"https://api.github.com/repos/griffithlab/civic-api-client/milestones{/number}","notifications_url":"https://api.github.com/repos/griffithlab/civic-api-client/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/griffithlab/civic-api-client/labels{/name}","releases_url":"https://api.github.com/repos/griffithlab/civic-api-client/releases{/id}","deployments_url":"https://api.github.com/repos/griffithlab/civic-api-client/deployments","created_at":"2016-01-19T21:14:16Z","updated_at":"2016-02-22T21:21:01Z","pushed_at":"2016-03-22T21:53:35Z","git_url":"git://github.com/griffithlab/civic-api-client.git","ssh_url":"git@github.com:griffithlab/civic-api-client.git","clone_url":"https://github.com/griffithlab/civic-api-client.git","svn_url":"https://github.com/griffithlab/civic-api-client","homepage":null,"size":1099,"stargazers_count":0,"watchers_count":0,"language":"Python","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":1,"mirror_url":null,"open_issues_count":9,"forks":1,"open_issues":9,"watchers":0,"default_branch":"master"}},"base":{"label":"griffithlab:master","ref":"master","sha":"5008fcc5fcf3cd29bb90bd312530e00db4069e62","user":{"login":"griffithlab","id":8323084,"avatar_url":"https://avatars.githubusercontent.com/u/8323084?v=3","gravatar_id":"","url":"https://api.github.com/users/griffithlab","html_url":"https://github.com/griffithlab","followers_url":"https://api.github.com/users/griffithlab/followers","following_url":"https://api.github.com/users/griffithlab/following{/other_user}","gists_url":"https://api.github.com/users/griffithlab/gists{/gist_id}","starred_url":"https://api.github.com/users/griffithlab/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/griffithlab/subscriptions","organizations_url":"https://api.github.com/users/griffithlab/orgs","repos_url":"https://api.github.com/users/griffithlab/repos","events_url":"https://api.github.com/users/griffithlab/events{/privacy}","received_events_url":"https://api.github.com/users/griffithlab/received_events","type":"Organization","site_admin":false},"repo":{"id":49983578,"name":"civic-api-client","full_name":"griffithlab/civic-api-client","owner":{"login":"griffithlab","id":8323084,"avatar_url":"https://avatars.githubusercontent.com/u/8323084?v=3","gravatar_id":"","url":"https://api.github.com/users/griffithlab","html_url":"https://github.com/griffithlab","followers_url":"https://api.github.com/users/griffithlab/followers","following_url":"https://api.github.com/users/griffithlab/following{/other_user}","gists_url":"https://api.github.com/users/griffithlab/gists{/gist_id}","starred_url":"https://api.github.com/users/griffithlab/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/griffithlab/subscriptions","organizations_url":"https://api.github.com/users/griffithlab/orgs","repos_url":"https://api.github.com/users/griffithlab/repos","events_url":"https://api.github.com/users/griffithlab/events{/privacy}","received_events_url":"https://api.github.com/users/griffithlab/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/griffithlab/civic-api-client","description":"Example tools using the CIVIC API","fork":false,"url":"https://api.github.com/repos/griffithlab/civic-api-client","forks_url":"https://api.github.com/repos/griffithlab/civic-api-client/forks","keys_url":"https://api.github.com/repos/griffithlab/civic-api-client/keys{/key_id}","collaborators_url":"https://api.github.com/repos/griffithlab/civic-api-client/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/griffithlab/civic-api-client/teams","hooks_url":"https://api.github.com/repos/griffithlab/civic-api-client/hooks","issue_events_url":"https://api.github.com/repos/griffithlab/civic-api-client/issues/events{/number}","events_url":"https://api.github.com/repos/griffithlab/civic-api-client/events","assignees_url":"https://api.github.com/repos/griffithlab/civic-api-client/assignees{/user}","branches_url":"https://api.github.com/repos/griffithlab/civic-api-client/branches{/branch}","tags_url":"https://api.github.com/repos/griffithlab/civic-api-client/tags","blobs_url":"https://api.github.com/repos/griffithlab/civic-api-client/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/griffithlab/civic-api-client/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/griffithlab/civic-api-client/git/refs{/sha}","trees_url":"https://api.github.com/repos/griffithlab/civic-api-client/git/trees{/sha}","statuses_url":"https://api.github.com/repos/griffithlab/civic-api-client/statuses/{sha}","languages_url":"https://api.github.com/repos/griffithlab/civic-api-client/languages","stargazers_url":"https://api.github.com/repos/griffithlab/civic-api-client/stargazers","contributors_url":"https://api.github.com/repos/griffithlab/civic-api-client/contributors","subscribers_url":"https://api.github.com/repos/griffithlab/civic-api-client/subscribers","subscription_url":"https://api.github.com/repos/griffithlab/civic-api-client/subscription","commits_url":"https://api.github.com/repos/griffithlab/civic-api-client/commits{/sha}","git_commits_url":"https://api.github.com/repos/griffithlab/civic-api-client/git/commits{/sha}","comments_url":"https://api.github.com/repos/griffithlab/civic-api-client/comments{/number}","issue_comment_url":"https://api.github.com/repos/griffithlab/civic-api-client/issues/comments{/number}","contents_url":"https://api.github.com/repos/griffithlab/civic-api-client/contents/{+path}","compare_url":"https://api.github.com/repos/griffithlab/civic-api-client/compare/{base}...{head}","merges_url":"https://api.github.com/repos/griffithlab/civic-api-client/merges","archive_url":"https://api.github.com/repos/griffithlab/civic-api-client/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/griffithlab/civic-api-client/downloads","issues_url":"https://api.github.com/repos/griffithlab/civic-api-client/issues{/number}","pulls_url":"https://api.github.com/repos/griffithlab/civic-api-client/pulls{/number}","milestones_url":"https://api.github.com/repos/griffithlab/civic-api-client/milestones{/number}","notifications_url":"https://api.github.com/repos/griffithlab/civic-api-client/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/griffithlab/civic-api-client/labels{/name}","releases_url":"https://api.github.com/repos/griffithlab/civic-api-client/releases{/id}","deployments_url":"https://api.github.com/repos/griffithlab/civic-api-client/deployments","created_at":"2016-01-19T21:14:16Z","updated_at":"2016-02-22T21:21:01Z","pushed_at":"2016-03-22T21:53:35Z","git_url":"git://github.com/griffithlab/civic-api-client.git","ssh_url":"git@github.com:griffithlab/civic-api-client.git","clone_url":"https://github.com/griffithlab/civic-api-client.git","svn_url":"https://github.com/griffithlab/civic-api-client","homepage":null,"size":1099,"stargazers_count":0,"watchers_count":0,"language":"Python","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":1,"mirror_url":null,"open_issues_count":9,"forks":1,"open_issues":9,"watchers":0,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/griffithlab/civic-api-client/pulls/20"},"html":{"href":"https://github.com/griffithlab/civic-api-client/pull/20"},"issue":{"href":"https://api.github.com/repos/griffithlab/civic-api-client/issues/20"},"comments":{"href":"https://api.github.com/repos/griffithlab/civic-api-client/issues/20/comments"},"review_comments":{"href":"https://api.github.com/repos/griffithlab/civic-api-client/pulls/20/comments"},"review_comment":{"href":"https://api.github.com/repos/griffithlab/civic-api-client/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/griffithlab/civic-api-client/pulls/20/commits"},"statuses":{"href":"https://api.github.com/repos/griffithlab/civic-api-client/statuses/3c77738e0f37afaade76a01d9e291087675a84b3"}}}}