{"action":"created","issue":{"url":"https://api.github.com/repos/ClinGen/clincoded/issues/861","repository_url":"https://api.github.com/repos/ClinGen/clincoded","labels_url":"https://api.github.com/repos/ClinGen/clincoded/issues/861/labels{/name}","comments_url":"https://api.github.com/repos/ClinGen/clincoded/issues/861/comments","events_url":"https://api.github.com/repos/ClinGen/clincoded/issues/861/events","html_url":"https://github.com/ClinGen/clincoded/pull/861","id":167497433,"number":861,"title":"Connects to #827. Codon data display.","user":{"login":"jimmyzhen","id":6956310,"avatar_url":"https://avatars.githubusercontent.com/u/6956310?v=3","gravatar_id":"","url":"https://api.github.com/users/jimmyzhen","html_url":"https://github.com/jimmyzhen","followers_url":"https://api.github.com/users/jimmyzhen/followers","following_url":"https://api.github.com/users/jimmyzhen/following{/other_user}","gists_url":"https://api.github.com/users/jimmyzhen/gists{/gist_id}","starred_url":"https://api.github.com/users/jimmyzhen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jimmyzhen/subscriptions","organizations_url":"https://api.github.com/users/jimmyzhen/orgs","repos_url":"https://api.github.com/users/jimmyzhen/repos","events_url":"https://api.github.com/users/jimmyzhen/events{/privacy}","received_events_url":"https://api.github.com/users/jimmyzhen/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/ClinGen/clincoded/labels/in%20progress","name":"in progress","color":"ededed"}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-07-26T00:44:54Z","updated_at":"2016-07-27T00:36:17Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/ClinGen/clincoded/pulls/861","html_url":"https://github.com/ClinGen/clincoded/pull/861","diff_url":"https://github.com/ClinGen/clincoded/pull/861.diff","patch_url":"https://github.com/ClinGen/clincoded/pull/861.patch"},"body":"This PR consists of changes pertinent to the handling of UI display in the variant codon table on the computational tab.\r\n\r\n**Technical details:**\r\n1. Abstracted the repetitive code from index.js and created a helper method to get HGVS notation in the formats required by either myvariant.info or Ensembl VEP.\r\n2. Created a helper method to set the primary transcript based on the logical filtering of properties such as 'canonical', 'source' and 'hgvsc' in the Ensembl VEP response.\r\n3. Added '&canonical=1&merged=1' params to Ensembl VEP API request to expose **canonical** flags and **RefSeq** transcripts in response.\r\n4. Decoupled the Eutils/Esearch combo fetch method since the Esearch method for codon data relies on Ensembl VEP response going forward.\r\n5. Updated the handling of UI display in the variant codon table given different test cases.\r\n\r\n**Steps to test:**\r\nVia the variant selection interface, try the following example IDs. Verify the expected display given the different test cases.\r\n\r\nTest case 1 - No protein change, such as amino acid and/or location not found in VEP.\r\nExpected display - **The current variant is in a non-coding region.**\r\nExample IDs: 139214, CA501097\r\n\r\nTest case 2 - Has protein change, but ClinVar response returns count of 0.\r\nExpected display - **No variants have been found at this codon in ClinVar.**\r\nExample IDs: 55847, CA501096\r\n\r\nTest case 3 - Has protein change, and ClinVar response returns count of 1.\r\nExpected display - **The current variant is the only variant found at this codon in ClinVar.**\r\nExample IDs: 35824, CA501104\r\n\r\nTest case 4 - Has protein change, and ClinVar response returns count of more than 1. \r\nExpected display - **Additional ClinVar variants found in the same codon: count (Search ClinVar for variants in this codon)**\r\nExample IDs: 35816, 53423"},"comment":{"url":"https://api.github.com/repos/ClinGen/clincoded/issues/comments/235448147","html_url":"https://github.com/ClinGen/clincoded/pull/861#issuecomment-235448147","issue_url":"https://api.github.com/repos/ClinGen/clincoded/issues/861","id":235448147,"user":{"login":"jimmyzhen","id":6956310,"avatar_url":"https://avatars.githubusercontent.com/u/6956310?v=3","gravatar_id":"","url":"https://api.github.com/users/jimmyzhen","html_url":"https://github.com/jimmyzhen","followers_url":"https://api.github.com/users/jimmyzhen/followers","following_url":"https://api.github.com/users/jimmyzhen/following{/other_user}","gists_url":"https://api.github.com/users/jimmyzhen/gists{/gist_id}","starred_url":"https://api.github.com/users/jimmyzhen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jimmyzhen/subscriptions","organizations_url":"https://api.github.com/users/jimmyzhen/orgs","repos_url":"https://api.github.com/users/jimmyzhen/repos","events_url":"https://api.github.com/users/jimmyzhen/events{/privacy}","received_events_url":"https://api.github.com/users/jimmyzhen/received_events","type":"User","site_admin":false},"created_at":"2016-07-27T00:36:17Z","updated_at":"2016-07-27T00:36:17Z","body":"@kilodalton Thank you for catching the bug! It's been now fixed and committed back to the PR."}}
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