{"action":"created","comment":{"url":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/comments/91473078","pull_request_review_id":11980494,"id":91473078,"diff_hunk":"@@ -0,0 +1,42 @@\n+/*\n+ * Copyright (c) 2016 Memorial Sloan Kettering Cancer Center.\n+ *\n+ * This library is distributed in the hope that it will be useful, but WITHOUT\n+ * ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS\n+ * FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder\n+ * is on an \"as is\" basis, and Memorial Sloan-Kettering Cancer Center has no\n+ * obligations to provide maintenance, support, updates, enhancements or\n+ * modifications. In no event shall Memorial Sloan-Kettering Cancer Center be\n+ * liable to any party for direct, indirect, special, incidental or\n+ * consequential damages, including lost profits, arising out of the use of this\n+ * software and its documentation, even if Memorial Sloan-Kettering Cancer\n+ * Center has been advised of the possibility of such damage.\n+ */\n+\n+/*\n+ * This file is part of cBioPortal.\n+ *\n+ * cBioPortal is free software: you can redistribute it and/or modify\n+ * it under the terms of the GNU Affero General Public License as\n+ * published by the Free Software Foundation, either version 3 of the\n+ * License.\n+ *\n+ * This program is distributed in the hope that it will be useful,\n+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\n+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\n+ * GNU Affero General Public License for more details.\n+ *\n+ * You should have received a copy of the GNU Affero General Public License\n+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.\n+*/\n+package org.cbioportal.persistence;\n+\n+import org.cbioportal.model.GeneticEntity;\n+import org.cbioportal.model.GeneticEntity.EntityType;\n+\n+public interface GeneticEntityRepository {","path":"persistence/persistence-api/src/main/java/org/cbioportal/persistence/GeneticEntityRepository.java","position":37,"original_position":37,"commit_id":"e840806e6afb2c08e695c95299643ec25db7eefb","original_commit_id":"e840806e6afb2c08e695c95299643ec25db7eefb","user":{"login":"pieterlukasse","id":2900303,"avatar_url":"https://avatars.githubusercontent.com/u/2900303?v=3","gravatar_id":"","url":"https://api.github.com/users/pieterlukasse","html_url":"https://github.com/pieterlukasse","followers_url":"https://api.github.com/users/pieterlukasse/followers","following_url":"https://api.github.com/users/pieterlukasse/following{/other_user}","gists_url":"https://api.github.com/users/pieterlukasse/gists{/gist_id}","starred_url":"https://api.github.com/users/pieterlukasse/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pieterlukasse/subscriptions","organizations_url":"https://api.github.com/users/pieterlukasse/orgs","repos_url":"https://api.github.com/users/pieterlukasse/repos","events_url":"https://api.github.com/users/pieterlukasse/events{/privacy}","received_events_url":"https://api.github.com/users/pieterlukasse/received_events","type":"User","site_admin":false},"body":"I agree that it should at least not be called *Mybatis because it does not interact with mybatis directly. I changed the name of the class and documented its purpose. We could also move it to the persistence package directly instead of having it in persistence-mybatis.","created_at":"2016-12-08T09:14:06Z","updated_at":"2016-12-08T09:14:06Z","html_url":"https://github.com/cBioPortal/cbioportal/pull/1972#discussion_r91473078","pull_request_url":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/1972","_links":{"self":{"href":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/comments/91473078"},"html":{"href":"https://github.com/cBioPortal/cbioportal/pull/1972#discussion_r91473078"},"pull_request":{"href":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/1972"}}},"pull_request":{"url":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/1972","id":96762101,"html_url":"https://github.com/cBioPortal/cbioportal/pull/1972","diff_url":"https://github.com/cBioPortal/cbioportal/pull/1972.diff","patch_url":"https://github.com/cBioPortal/cbioportal/pull/1972.patch","issue_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/1972","number":1972,"state":"open","locked":false,"title":"Adding API implementation for GeneticData","user":{"login":"pieterlukasse","id":2900303,"avatar_url":"https://avatars.githubusercontent.com/u/2900303?v=3","gravatar_id":"","url":"https://api.github.com/users/pieterlukasse","html_url":"https://github.com/pieterlukasse","followers_url":"https://api.github.com/users/pieterlukasse/followers","following_url":"https://api.github.com/users/pieterlukasse/following{/other_user}","gists_url":"https://api.github.com/users/pieterlukasse/gists{/gist_id}","starred_url":"https://api.github.com/users/pieterlukasse/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pieterlukasse/subscriptions","organizations_url":"https://api.github.com/users/pieterlukasse/orgs","repos_url":"https://api.github.com/users/pieterlukasse/repos","events_url":"https://api.github.com/users/pieterlukasse/events{/privacy}","received_events_url":"https://api.github.com/users/pieterlukasse/received_events","type":"User","site_admin":false},"body":"# What? Why?\r\nThis adds new endpoints and respective implementations for retrieving genetic data (aka genetic alteration data). It uses the new genetic entity data model introduced in #1902. \r\n\r\nChanges proposed in this pull request:\r\n- implementation of existing endpoint: `/api/genetic-profiles/{geneticProfileId}/genetic-data`\r\n- created new endpoint with respective implementation: ` /genetic-profiles/{geneticProfileId}/fetch`\r\n\r\nSee also [proposal document](https://docs.google.com/document/d/12T0gTzArDdjxn74xcdXfdbxeeo_yDK6Kp24S9UWVFjs/edit). \r\n\r\n# Checks\r\n- test still fail because #1902 needs to be merged in `rc` first\r\n\r\n# Notify reviewers\r\n@ersinciftci @sheridancbio ","created_at":"2016-12-06T16:51:09Z","updated_at":"2016-12-08T09:14:06Z","closed_at":null,"merged_at":null,"merge_commit_sha":"0a6e35276ecd611de068aa312322082ae9666330","assignee":null,"assignees":[],"milestone":null,"commits_url":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/1972/commits","review_comments_url":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/1972/comments","review_comment_url":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/comments{/number}","comments_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/1972/comments","statuses_url":"https://api.github.com/repos/cBioPortal/cbioportal/statuses/e840806e6afb2c08e695c95299643ec25db7eefb","head":{"label":"thehyve:genetic_alteration_api","ref":"genetic_alteration_api","sha":"e840806e6afb2c08e695c95299643ec25db7eefb","user":{"login":"thehyve","id":1502440,"avatar_url":"https://avatars.githubusercontent.com/u/1502440?v=3","gravatar_id":"","url":"https://api.github.com/users/thehyve","html_url":"https://github.com/thehyve","followers_url":"https://api.github.com/users/thehyve/followers","following_url":"https://api.github.com/users/thehyve/following{/other_user}","gists_url":"https://api.github.com/users/thehyve/gists{/gist_id}","starred_url":"https://api.github.com/users/thehyve/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/thehyve/subscriptions","organizations_url":"https://api.github.com/users/thehyve/orgs","repos_url":"https://api.github.com/users/thehyve/repos","events_url":"https://api.github.com/users/thehyve/events{/privacy}","received_events_url":"https://api.github.com/users/thehyve/received_events","type":"Organization","site_admin":false},"repo":{"id":37332427,"name":"cbioportal","full_name":"thehyve/cbioportal","owner":{"login":"thehyve","id":1502440,"avatar_url":"https://avatars.githubusercontent.com/u/1502440?v=3","gravatar_id":"","url":"https://api.github.com/users/thehyve","html_url":"https://github.com/thehyve","followers_url":"https://api.github.com/users/thehyve/followers","following_url":"https://api.github.com/users/thehyve/following{/other_user}","gists_url":"https://api.github.com/users/thehyve/gists{/gist_id}","starred_url":"https://api.github.com/users/thehyve/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/thehyve/subscriptions","organizations_url":"https://api.github.com/users/thehyve/orgs","repos_url":"https://api.github.com/users/thehyve/repos","events_url":"https://api.github.com/users/thehyve/events{/privacy}","received_events_url":"https://api.github.com/users/thehyve/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/thehyve/cbioportal","description":"cBioPortal topic branches at The Hyve","fork":true,"url":"https://api.github.com/repos/thehyve/cbioportal","forks_url":"https://api.github.com/repos/thehyve/cbioportal/forks","keys_url":"https://api.github.com/repos/thehyve/cbioportal/keys{/key_id}","collaborators_url":"https://api.github.com/repos/thehyve/cbioportal/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/thehyve/cbioportal/teams","hooks_url":"https://api.github.com/repos/thehyve/cbioportal/hooks","issue_events_url":"https://api.github.com/repos/thehyve/cbioportal/issues/events{/number}","events_url":"https://api.github.com/repos/thehyve/cbioportal/events","assignees_url":"https://api.github.com/repos/thehyve/cbioportal/assignees{/user}","branches_url":"https://api.github.com/repos/thehyve/cbioportal/branches{/branch}","tags_url":"https://api.github.com/repos/thehyve/cbioportal/tags","blobs_url":"https://api.github.com/repos/thehyve/cbioportal/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/thehyve/cbioportal/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/thehyve/cbioportal/git/refs{/sha}","trees_url":"https://api.github.com/repos/thehyve/cbioportal/git/trees{/sha}","statuses_url":"https://api.github.com/repos/thehyve/cbioportal/statuses/{sha}","languages_url":"https://api.github.com/repos/thehyve/cbioportal/languages","stargazers_url":"https://api.github.com/repos/thehyve/cbioportal/stargazers","contributors_url":"https://api.github.com/repos/thehyve/cbioportal/contributors","subscribers_url":"https://api.github.com/repos/thehyve/cbioportal/subscribers","subscription_url":"https://api.github.com/repos/thehyve/cbioportal/subscription","commits_url":"https://api.github.com/repos/thehyve/cbioportal/commits{/sha}","git_commits_url":"https://api.github.com/repos/thehyve/cbioportal/git/commits{/sha}","comments_url":"https://api.github.com/repos/thehyve/cbioportal/comments{/number}","issue_comment_url":"https://api.github.com/repos/thehyve/cbioportal/issues/comments{/number}","contents_url":"https://api.github.com/repos/thehyve/cbioportal/contents/{+path}","compare_url":"https://api.github.com/repos/thehyve/cbioportal/compare/{base}...{head}","merges_url":"https://api.github.com/repos/thehyve/cbioportal/merges","archive_url":"https://api.github.com/repos/thehyve/cbioportal/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/thehyve/cbioportal/downloads","issues_url":"https://api.github.com/repos/thehyve/cbioportal/issues{/number}","pulls_url":"https://api.github.com/repos/thehyve/cbioportal/pulls{/number}","milestones_url":"https://api.github.com/repos/thehyve/cbioportal/milestones{/number}","notifications_url":"https://api.github.com/repos/thehyve/cbioportal/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/thehyve/cbioportal/labels{/name}","releases_url":"https://api.github.com/repos/thehyve/cbioportal/releases{/id}","deployments_url":"https://api.github.com/repos/thehyve/cbioportal/deployments","created_at":"2015-06-12T16:27:05Z","updated_at":"2016-11-02T12:53:16Z","pushed_at":"2016-12-07T16:57:05Z","git_url":"git://github.com/thehyve/cbioportal.git","ssh_url":"git@github.com:thehyve/cbioportal.git","clone_url":"https://github.com/thehyve/cbioportal.git","svn_url":"https://github.com/thehyve/cbioportal","homepage":"","size":189478,"stargazers_count":2,"watchers_count":2,"language":null,"has_issues":false,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":1,"mirror_url":null,"open_issues_count":0,"forks":1,"open_issues":0,"watchers":2,"default_branch":"default"}},"base":{"label":"cBioPortal:rc","ref":"rc","sha":"6584c4531023752548ff7e77bb378020244b4a42","user":{"login":"cBioPortal","id":9876251,"avatar_url":"https://avatars.githubusercontent.com/u/9876251?v=3","gravatar_id":"","url":"https://api.github.com/users/cBioPortal","html_url":"https://github.com/cBioPortal","followers_url":"https://api.github.com/users/cBioPortal/followers","following_url":"https://api.github.com/users/cBioPortal/following{/other_user}","gists_url":"https://api.github.com/users/cBioPortal/gists{/gist_id}","starred_url":"https://api.github.com/users/cBioPortal/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cBioPortal/subscriptions","organizations_url":"https://api.github.com/users/cBioPortal/orgs","repos_url":"https://api.github.com/users/cBioPortal/repos","events_url":"https://api.github.com/users/cBioPortal/events{/privacy}","received_events_url":"https://api.github.com/users/cBioPortal/received_events","type":"Organization","site_admin":false},"repo":{"id":32481543,"name":"cbioportal","full_name":"cBioPortal/cbioportal","owner":{"login":"cBioPortal","id":9876251,"avatar_url":"https://avatars.githubusercontent.com/u/9876251?v=3","gravatar_id":"","url":"https://api.github.com/users/cBioPortal","html_url":"https://github.com/cBioPortal","followers_url":"https://api.github.com/users/cBioPortal/followers","following_url":"https://api.github.com/users/cBioPortal/following{/other_user}","gists_url":"https://api.github.com/users/cBioPortal/gists{/gist_id}","starred_url":"https://api.github.com/users/cBioPortal/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cBioPortal/subscriptions","organizations_url":"https://api.github.com/users/cBioPortal/orgs","repos_url":"https://api.github.com/users/cBioPortal/repos","events_url":"https://api.github.com/users/cBioPortal/events{/privacy}","received_events_url":"https://api.github.com/users/cBioPortal/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/cBioPortal/cbioportal","description":"cBioPortal for Cancer Genomics","fork":false,"url":"https://api.github.com/repos/cBioPortal/cbioportal","forks_url":"https://api.github.com/repos/cBioPortal/cbioportal/forks","keys_url":"https://api.github.com/repos/cBioPortal/cbioportal/keys{/key_id}","collaborators_url":"https://api.github.com/repos/cBioPortal/cbioportal/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/cBioPortal/cbioportal/teams","hooks_url":"https://api.github.com/repos/cBioPortal/cbioportal/hooks","issue_events_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/events{/number}","events_url":"https://api.github.com/repos/cBioPortal/cbioportal/events","assignees_url":"https://api.github.com/repos/cBioPortal/cbioportal/assignees{/user}","branches_url":"https://api.github.com/repos/cBioPortal/cbioportal/branches{/branch}","tags_url":"https://api.github.com/repos/cBioPortal/cbioportal/tags","blobs_url":"https://api.github.com/repos/cBioPortal/cbioportal/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/cBioPortal/cbioportal/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/cBioPortal/cbioportal/git/refs{/sha}","trees_url":"https://api.github.com/repos/cBioPortal/cbioportal/git/trees{/sha}","statuses_url":"https://api.github.com/repos/cBioPortal/cbioportal/statuses/{sha}","languages_url":"https://api.github.com/repos/cBioPortal/cbioportal/languages","stargazers_url":"https://api.github.com/repos/cBioPortal/cbioportal/stargazers","contributors_url":"https://api.github.com/repos/cBioPortal/cbioportal/contributors","subscribers_url":"https://api.github.com/repos/cBioPortal/cbioportal/subscribers","subscription_url":"https://api.github.com/repos/cBioPortal/cbioportal/subscription","commits_url":"https://api.github.com/repos/cBioPortal/cbioportal/commits{/sha}","git_commits_url":"https://api.github.com/repos/cBioPortal/cbioportal/git/commits{/sha}","comments_url":"https://api.github.com/repos/cBioPortal/cbioportal/comments{/number}","issue_comment_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/comments{/number}","contents_url":"https://api.github.com/repos/cBioPortal/cbioportal/contents/{+path}","compare_url":"https://api.github.com/repos/cBioPortal/cbioportal/compare/{base}...{head}","merges_url":"https://api.github.com/repos/cBioPortal/cbioportal/merges","archive_url":"https://api.github.com/repos/cBioPortal/cbioportal/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/cBioPortal/cbioportal/downloads","issues_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues{/number}","pulls_url":"https://api.github.com/repos/cBioPortal/cbioportal/pulls{/number}","milestones_url":"https://api.github.com/repos/cBioPortal/cbioportal/milestones{/number}","notifications_url":"https://api.github.com/repos/cBioPortal/cbioportal/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/cBioPortal/cbioportal/labels{/name}","releases_url":"https://api.github.com/repos/cBioPortal/cbioportal/releases{/id}","deployments_url":"https://api.github.com/repos/cBioPortal/cbioportal/deployments","created_at":"2015-03-18T20:09:09Z","updated_at":"2016-11-28T20:25:37Z","pushed_at":"2016-12-08T00:11:33Z","git_url":"git://github.com/cBioPortal/cbioportal.git","ssh_url":"git@github.com:cBioPortal/cbioportal.git","clone_url":"https://github.com/cBioPortal/cbioportal.git","svn_url":"https://github.com/cBioPortal/cbioportal","homepage":"http://cbioportal.org","size":273363,"stargazers_count":80,"watchers_count":80,"language":"JavaScript","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":true,"forks_count":116,"mirror_url":null,"open_issues_count":351,"forks":116,"open_issues":351,"watchers":80,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/1972"},"html":{"href":"https://github.com/cBioPortal/cbioportal/pull/1972"},"issue":{"href":"https://api.github.com/repos/cBioPortal/cbioportal/issues/1972"},"comments":{"href":"https://api.github.com/repos/cBioPortal/cbioportal/issues/1972/comments"},"review_comments":{"href":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/1972/comments"},"review_comment":{"href":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/1972/commits"},"statuses":{"href":"https://api.github.com/repos/cBioPortal/cbioportal/statuses/e840806e6afb2c08e695c95299643ec25db7eefb"}}}}
{"actor":{"display_login":"pieterlukasse"}}