{"action":"created","comment":{"url":"https://api.github.com/repos/genomicsengland/GelReportModels/pulls/comments/211916802","pull_request_review_id":148435987,"id":211916802,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDIxMTkxNjgwMg==","diff_hunk":"@@ -71,6 +71,73 @@ def _migrate_tumour_sample(self, old_instance):\n         )\n \n \n+class MigrationParticipants110To100(BaseMigration):\n+    old_model = participant_1_1_0\n+    new_model = participant_1_0_0\n+\n+    def migrate_pedigree(self, old_instance):\n+        new_instance = self.convert_class(self.new_model.Pedigree, old_instance)\n+        new_instance.versionControl = self.new_model.VersionControl()\n+        new_instance.members = [self.migrate_member(member) for member in old_instance.members]\n+        if new_instance.validate(new_instance.toJsonDict()):\n+            return new_instance\n+        else:\n+            raise MigrationError(\n+                'This model can not be converted: ', handle_avro_errors(new_instance.validate_parts())\n+            )\n+\n+    def migrate_member(self, old_instance):\n+        new_instance = self.convert_class(self.new_model.PedigreeMember, old_instance)\n+        if old_instance.hpoTermList is not None:\n+            new_instance.hpoTermList = [self.migrate_hpo(hpo) for hpo in old_instance.hpoTermList]\n+        if old_instance.disorderList is not None:\n+            new_instance.disorderList = [self.migrate_disorder(disorder) for disorder in old_instance.disorderList]\n+        if old_instance.ancestries is not None:\n+            new_instance.ancestries = self.migrate_ancestries(old_instance.ancestries)\n+        if old_instance.samples is not None:\n+            new_instance.samples= [self.migrate_sample(sample) for sample in old_instance.samples]\n+        return new_instance\n+\n+    def migrate_hpo(self, old_instance):\n+        new_instance = self.convert_class(self.new_model.HpoTerm, old_instance)\n+        new_instance.modifiers = {}\n+        if old_instance.modifiers.laterality is not None:\n+            new_instance.modifiers['laterality'] = old_instance.modifiers.laterality\n+        if old_instance.modifiers.progression is not None:\n+            new_instance.modifiers['progression'] = old_instance.modifiers.progression\n+        if old_instance.modifiers.severity is not None:\n+            new_instance.modifiers['severity'] = old_instance.modifiers.severity\n+        if old_instance.modifiers.spatialPattern is not None:\n+            new_instance.modifiers['spatialPattern'] = old_instance.modifiers.spatialPattern\n+        return new_instance\n+\n+    def migrate_disorder(self, old_instance):\n+        new_instance = self.convert_class(self.new_model.Disorder, old_instance)\n+        new_instance.ageOfOnset = str(old_instance.ageOfOnset)\n+        return new_instance\n+\n+    def migrate_ancestries(self, old_instance):\n+        new_instance = self.convert_class(self.new_model.Ancestries, old_instance)\n+        if old_instance.chiSquare1KGenomesPhase3Pop is not None:\n+            new_instance.chiSquare1KGenomesPhase3Pop = [self.migrate_chiblahblah(chi)\n+                                                        for chi in old_instance.chiSquare1KGenomesPhase3Pop]\n+        return new_instance\n+\n+    def migrate_chiblahblah(self, old_instance):","path":"protocols/migration/participants.py","position":56,"original_position":56,"commit_id":"47b49689ad5a0fe57ce5dbfc30277ae90c85caa3","original_commit_id":"47b49689ad5a0fe57ce5dbfc30277ae90c85caa3","user":{"login":"greglever","id":9075983,"node_id":"MDQ6VXNlcjkwNzU5ODM=","avatar_url":"https://avatars1.githubusercontent.com/u/9075983?v=4","gravatar_id":"","url":"https://api.github.com/users/greglever","html_url":"https://github.com/greglever","followers_url":"https://api.github.com/users/greglever/followers","following_url":"https://api.github.com/users/greglever/following{/other_user}","gists_url":"https://api.github.com/users/greglever/gists{/gist_id}","starred_url":"https://api.github.com/users/greglever/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/greglever/subscriptions","organizations_url":"https://api.github.com/users/greglever/orgs","repos_url":"https://api.github.com/users/greglever/repos","events_url":"https://api.github.com/users/greglever/events{/privacy}","received_events_url":"https://api.github.com/users/greglever/received_events","type":"User","site_admin":false},"body":"please don't call it `migrate_chiblahblah`...","created_at":"2018-08-22T11:16:35Z","updated_at":"2018-08-22T11:16:39Z","html_url":"https://github.com/genomicsengland/GelReportModels/pull/328#discussion_r211916802","pull_request_url":"https://api.github.com/repos/genomicsengland/GelReportModels/pulls/328","author_association":"COLLABORATOR","_links":{"self":{"href":"https://api.github.com/repos/genomicsengland/GelReportModels/pulls/comments/211916802"},"html":{"href":"https://github.com/genomicsengland/GelReportModels/pull/328#discussion_r211916802"},"pull_request":{"href":"https://api.github.com/repos/genomicsengland/GelReportModels/pulls/328"}}},"pull_request":{"url":"https://api.github.com/repos/genomicsengland/GelReportModels/pulls/328","id":209861317,"node_id":"MDExOlB1bGxSZXF1ZXN0MjA5ODYxMzE3","html_url":"https://github.com/genomicsengland/GelReportModels/pull/328","diff_url":"https://github.com/genomicsengland/GelReportModels/pull/328.diff","patch_url":"https://github.com/genomicsengland/GelReportModels/pull/328.patch","issue_url":"https://api.github.com/repos/genomicsengland/GelReportModels/issues/328","number":328,"state":"open","locked":false,"title":"IP-1880 - Migrate IR RD from 5 to 4","user":{"login":"priesgo","id":3140648,"node_id":"MDQ6VXNlcjMxNDA2NDg=","avatar_url":"https://avatars1.githubusercontent.com/u/3140648?v=4","gravatar_id":"","url":"https://api.github.com/users/priesgo","html_url":"https://github.com/priesgo","followers_url":"https://api.github.com/users/priesgo/followers","following_url":"https://api.github.com/users/priesgo/following{/other_user}","gists_url":"https://api.github.com/users/priesgo/gists{/gist_id}","starred_url":"https://api.github.com/users/priesgo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/priesgo/subscriptions","organizations_url":"https://api.github.com/users/priesgo/orgs","repos_url":"https://api.github.com/users/priesgo/repos","events_url":"https://api.github.com/users/priesgo/events{/privacy}","received_events_url":"https://api.github.com/users/priesgo/received_events","type":"User","site_admin":false},"body":"[IP-1880 - Migrate IR RD from 5 to 4](https://jira.extge.co.uk/browse/IP-1880)\r\n===========\r\n\r\nDo not merge a test is still failing, please review, I will continue tomorrow.\r\n\r\nAdditionally:\r\n* Using some factories to create appropriate mocked data\r\n* Fixed an issue on validation of map fields","created_at":"2018-08-21T15:12:42Z","updated_at":"2018-08-22T11:16:39Z","closed_at":null,"merged_at":null,"merge_commit_sha":"823ca574452b701f899adbff00853205c50f5447","assignee":{"login":"priesgo","id":3140648,"node_id":"MDQ6VXNlcjMxNDA2NDg=","avatar_url":"https://avatars1.githubusercontent.com/u/3140648?v=4","gravatar_id":"","url":"https://api.github.com/users/priesgo","html_url":"https://github.com/priesgo","followers_url":"https://api.github.com/users/priesgo/followers","following_url":"https://api.github.com/users/priesgo/following{/other_user}","gists_url":"https://api.github.com/users/priesgo/gists{/gist_id}","starred_url":"https://api.github.com/users/priesgo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/priesgo/subscriptions","organizations_url":"https://api.github.com/users/priesgo/orgs","repos_url":"https://api.github.com/users/priesgo/repos","events_url":"https://api.github.com/users/priesgo/events{/privacy}","received_events_url":"https://api.github.com/users/priesgo/received_events","type":"User","site_admin":false},"assignees":[{"login":"priesgo","id":3140648,"node_id":"MDQ6VXNlcjMxNDA2NDg=","avatar_url":"https://avatars1.githubusercontent.com/u/3140648?v=4","gravatar_id":"","url":"https://api.github.com/users/priesgo","html_url":"https://github.com/priesgo","followers_url":"https://api.github.com/users/priesgo/followers","following_url":"https://api.github.com/users/priesgo/following{/other_user}","gists_url":"https://api.github.com/users/priesgo/gists{/gist_id}","starred_url":"https://api.github.com/users/priesgo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/priesgo/subscriptions","organizations_url":"https://api.github.com/users/priesgo/orgs","repos_url":"https://api.github.com/users/priesgo/repos","events_url":"https://api.github.com/users/priesgo/events{/privacy}","received_events_url":"https://api.github.com/users/priesgo/received_events","type":"User","site_admin":false}],"requested_reviewers":[{"login":"kevinpetersavage","id":983710,"node_id":"MDQ6VXNlcjk4MzcxMA==","avatar_url":"https://avatars1.githubusercontent.com/u/983710?v=4","gravatar_id":"","url":"https://api.github.com/users/kevinpetersavage","html_url":"https://github.com/kevinpetersavage","followers_url":"https://api.github.com/users/kevinpetersavage/followers","following_url":"https://api.github.com/users/kevinpetersavage/following{/other_user}","gists_url":"https://api.github.com/users/kevinpetersavage/gists{/gist_id}","starred_url":"https://api.github.com/users/kevinpetersavage/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kevinpetersavage/subscriptions","organizations_url":"https://api.github.com/users/kevinpetersavage/orgs","repos_url":"https://api.github.com/users/kevinpetersavage/repos","events_url":"https://api.github.com/users/kevinpetersavage/events{/privacy}","received_events_url":"https://api.github.com/users/kevinpetersavage/received_events","type":"User","site_admin":false}],"requested_teams":[],"labels":[],"milestone":null,"commits_url":"https://api.github.com/repos/genomicsengland/GelReportModels/pulls/328/commits","review_comments_url":"https://api.github.com/repos/genomicsengland/GelReportModels/pulls/328/comments","review_comment_url":"https://api.github.com/repos/genomicsengland/GelReportModels/pulls/comments{/number}","comments_url":"https://api.github.com/repos/genomicsengland/GelReportModels/issues/328/comments","statuses_url":"https://api.github.com/repos/genomicsengland/GelReportModels/statuses/47b49689ad5a0fe57ce5dbfc30277ae90c85caa3","head":{"label":"genomicsengland:IP-1880","ref":"IP-1880","sha":"47b49689ad5a0fe57ce5dbfc30277ae90c85caa3","user":{"login":"genomicsengland","id":10168485,"node_id":"MDEyOk9yZ2FuaXphdGlvbjEwMTY4NDg1","avatar_url":"https://avatars0.githubusercontent.com/u/10168485?v=4","gravatar_id":"","url":"https://api.github.com/users/genomicsengland","html_url":"https://github.com/genomicsengland","followers_url":"https://api.github.com/users/genomicsengland/followers","following_url":"https://api.github.com/users/genomicsengland/following{/other_user}","gists_url":"https://api.github.com/users/genomicsengland/gists{/gist_id}","starred_url":"https://api.github.com/users/genomicsengland/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/genomicsengland/subscriptions","organizations_url":"https://api.github.com/users/genomicsengland/orgs","repos_url":"https://api.github.com/users/genomicsengland/repos","events_url":"https://api.github.com/users/genomicsengland/events{/privacy}","received_events_url":"https://api.github.com/users/genomicsengland/received_events","type":"Organization","site_admin":false},"repo":{"id":68630193,"node_id":"MDEwOlJlcG9zaXRvcnk2ODYzMDE5Mw==","name":"GelReportModels","full_name":"genomicsengland/GelReportModels","owner":{"login":"genomicsengland","id":10168485,"node_id":"MDEyOk9yZ2FuaXphdGlvbjEwMTY4NDg1","avatar_url":"https://avatars0.githubuserc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