{"action":"created","issue":{"url":"https://api.github.com/repos/ga4gh/compliance/issues/192","repository_url":"https://api.github.com/repos/ga4gh/compliance","labels_url":"https://api.github.com/repos/ga4gh/compliance/issues/192/labels{/name}","comments_url":"https://api.github.com/repos/ga4gh/compliance/issues/192/comments","events_url":"https://api.github.com/repos/ga4gh/compliance/issues/192/events","html_url":"https://github.com/ga4gh/compliance/issues/192","id":157719049,"number":192,"title":"Protobuf compliance problem","user":{"login":"macieksmuga","id":6685511,"avatar_url":"https://avatars.githubusercontent.com/u/6685511?v=3","gravatar_id":"","url":"https://api.github.com/users/macieksmuga","html_url":"https://github.com/macieksmuga","followers_url":"https://api.github.com/users/macieksmuga/followers","following_url":"https://api.github.com/users/macieksmuga/following{/other_user}","gists_url":"https://api.github.com/users/macieksmuga/gists{/gist_id}","starred_url":"https://api.github.com/users/macieksmuga/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/macieksmuga/subscriptions","organizations_url":"https://api.github.com/users/macieksmuga/orgs","repos_url":"https://api.github.com/users/macieksmuga/repos","events_url":"https://api.github.com/users/macieksmuga/events{/privacy}","received_events_url":"https://api.github.com/users/macieksmuga/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-05-31T16:50:28Z","updated_at":"2016-05-31T17:41:25Z","closed_at":null,"body":"I feel like I'm tripping over an old issue here, but I can't get several compliance tests to pass.\r\n\r\nThe error pattern is always as follows:\r\n```\r\ncom.google.protobuf.InvalidProtocolBufferException: Expect message object but got: [\"<some content here>\"]\r\n```\r\nFor example for tests like searchReadsWithOneReadGroupIdSucceeds, I get the error: `com.google.protobuf.InvalidProtocolBufferException: Expect message object but got: [\"60\"]`\r\n\r\nFWIW, the alignments JSON object that I receive as a response from the server for the above test looks as follows:\r\n```\r\n{\"alignments\":[{\"failedVendorQualityChecks\":false,\"improperPlacement\":false,\"fragmentLength\":186,\"alignedQuality\":[15,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,37,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,40,37,37,37,37,37,37,33,37,37,37,33,33],\"numberReads\":2,\"duplicateFragment\":false,\"secondaryAlignment\":false,\"readNumber\":1,\"readGroupId\":\"WyJicmNhMSIsInJncyIsIkhHMDAwOTYiLCJTUlIwNjI2MzQiXQ\",\"fragmentName\":\"HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram:117428991\",\"alignedSequence\":\"CAGTCCTGGATAATGGGTTTATGAAAAACACTTTTTCTTCCTTCAGCAAGCAAAATTATTTATGAAGCTGTATGGTTTCAGCAACAGGGAGCAAAGGAAA\",\"id\":\"WyJicmNhMSIsInJncyIsIkhHMDAwOTYiLCJIRzAwMDk2Lm1hcHBlZC5JTExVTUlOQS5id2EuR0JSLmxvd19jb3ZlcmFnZS4yMDEyMDUyMi5iYW0uY3JhbToxMTc0Mjg5OTEiXQ\",\"alignment\":{\"mappingQuality\":60,\"cigar\":[{\"operationLength\":\"100\",\"operation\":\"ALIGNMENT_MATCH\",\"referenceSequence\":\"\"}],\"position\":{\"strand\":\"POS_STRAND\",\"position\":\"136\",\"referenceName\":\"ref_brca1\"}},\"info\":{\"MQ\":[\"60\"],\"RG\":[\"SRR062634\"],\"MD\":[\"100\"],\"X0\":[\"1\"],\"X1\":[\"0\"],\"SM\":[\"37\"],\"AM\":[\"37\"],\"XT\":[\"U\"],\"NM\":[\"0\"]},\"supplementaryAlignment\":false,\"nextMatePosition\":{\"strand\":\"NEG_STRAND\",\"position\":\"222\",\"referenceName\":\"ref_brca1\"}}],\"nextPageToken\":\"\"}\r\nSo either my server (that I believe is running the latest protobuf branch) is emitting stale JSON or the compliance suite is somehow being overly picky.\r\n```\r\nAny help with this would be greatly appreciated."},"comment":{"url":"https://api.github.com/repos/ga4gh/compliance/issues/comments/222763868","html_url":"https://github.com/ga4gh/compliance/issues/192#issuecomment-222763868","issue_url":"https://api.github.com/repos/ga4gh/compliance/issues/192","id":222763868,"user":{"login":"macieksmuga","id":6685511,"avatar_url":"https://avatars.githubusercontent.com/u/6685511?v=3","gravatar_id":"","url":"https://api.github.com/users/macieksmuga","html_url":"https://github.com/macieksmuga","followers_url":"https://api.github.com/users/macieksmuga/followers","following_url":"https://api.github.com/users/macieksmuga/following{/other_user}","gists_url":"https://api.github.com/users/macieksmuga/gists{/gist_id}","starred_url":"https://api.github.com/users/macieksmuga/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/macieksmuga/subscriptions","organizations_url":"https://api.github.com/users/macieksmuga/orgs","repos_url":"https://api.github.com/users/macieksmuga/repos","events_url":"https://api.github.com/users/macieksmuga/events{/privacy}","received_events_url":"https://api.github.com/users/macieksmuga/received_events","type":"User","site_admin":false},"created_at":"2016-05-31T17:41:25Z","updated_at":"2016-05-31T17:41:25Z","body":"Figured it out. The version of protobuf used in the server is newer than the version used here. To fix, update `parent/pom.xml` as follows:\r\n```\r\n        <proto.version>3.0.0-beta-3</proto.version>\r\n```\r\nThis resolves the issue."}}
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