{"action":"created","issue":{"url":"https://api.github.com/repos/RGLab/LabKeyModules/issues/21","repository_url":"https://api.github.com/repos/RGLab/LabKeyModules","labels_url":"https://api.github.com/repos/RGLab/LabKeyModules/issues/21/labels{/name}","comments_url":"https://api.github.com/repos/RGLab/LabKeyModules/issues/21/comments","events_url":"https://api.github.com/repos/RGLab/LabKeyModules/issues/21/events","html_url":"https://github.com/RGLab/LabKeyModules/issues/21","id":192468070,"number":21,"title":"GeneExpressionExplorer is broken","user":{"login":"ldash","id":1403489,"avatar_url":"https://avatars.githubusercontent.com/u/1403489?v=3","gravatar_id":"","url":"https://api.github.com/users/ldash","html_url":"https://github.com/ldash","followers_url":"https://api.github.com/users/ldash/followers","following_url":"https://api.github.com/users/ldash/following{/other_user}","gists_url":"https://api.github.com/users/ldash/gists{/gist_id}","starred_url":"https://api.github.com/users/ldash/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ldash/subscriptions","organizations_url":"https://api.github.com/users/ldash/orgs","repos_url":"https://api.github.com/users/ldash/repos","events_url":"https://api.github.com/users/ldash/events{/privacy}","received_events_url":"https://api.github.com/users/ldash/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-11-30T03:43:10Z","updated_at":"2016-12-05T21:22:31Z","closed_at":null,"body":"@SRenan \r\nGEE is broken on Production - I'm assuming it has been, ever since you left, because none of us touched it or the data really: https://www.immunespace.org/GeneExpressionExplorer/Studies/begin.view\r\nTime point: 0 hours (1 cohort)\r\nCohorts: Study group 2 2009-2010 Fluzone (SDY180) <- the only one there\r\nGenes: A1BG <- the first one\r\nThere is no filtering on the \"Data Finder\"\r\n\r\nError is:\r\n\r\nError in merge.data.table(data, PD, by = \"biosample_accession\") : Elements listed in `by` must be valid column names in x and y\r\n\r\nAfer some investigation I can tell the following:\r\n\r\nThe resulting error on line 128 is because data does not have the `biosample_accesssion` column, though line 127 suggests it should.\r\nThe above is due to line 120, because `PD$biosample_accession` is an empty column, I mean, the whole `PD` is empty.\r\nIt is empty, because `merge(PD, HAI, by = \"participant_id\")` in line 117 makes it empty.\r\nAnd the reason, why it's impty is that the sets of participant_id-s from the 2 data frames do not overlap.\r\nThe JOIN in line 113 reduces the number of unique PTIDs from 21 down to just 3 within HAI.\r\n\r\nNot sure, if it's the correct approach/fix, but If we keep non-matched rows on the left by adding in line 113 `, all.x = TRUE`, then things seem to work (it appears we get the same result as if running the module from just within SDY180)\r\n\r\nCould you, please, investigate and if the above fix is not correct, then add some extra logiс either to fix it (not sure how) or to fail gracefully with an info message?\r\n\r\nReproducible on test as well, of course..."},"comment":{"url":"https://api.github.com/repos/RGLab/LabKeyModules/issues/comments/264981182","html_url":"https://github.com/RGLab/LabKeyModules/issues/21#issuecomment-264981182","issue_url":"https://api.github.com/repos/RGLab/LabKeyModules/issues/21","id":264981182,"user":{"login":"ldash","id":1403489,"avatar_url":"https://avatars.githubusercontent.com/u/1403489?v=3","gravatar_id":"","url":"https://api.github.com/users/ldash","html_url":"https://github.com/ldash","followers_url":"https://api.github.com/users/ldash/followers","following_url":"https://api.github.com/users/ldash/following{/other_user}","gists_url":"https://api.github.com/users/ldash/gists{/gist_id}","starred_url":"https://api.github.com/users/ldash/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ldash/subscriptions","organizations_url":"https://api.github.com/users/ldash/orgs","repos_url":"https://api.github.com/users/ldash/repos","events_url":"https://api.github.com/users/ldash/events{/privacy}","received_events_url":"https://api.github.com/users/ldash/received_events","type":"User","site_admin":false},"created_at":"2016-12-05T21:22:31Z","updated_at":"2016-12-05T21:22:31Z","body":"Thanks, @gfinak Not sure, if you saw Renan's comment on Slack in the IS channel about this, but he wrote: \"I don't think that the suggested fix is correct because it wouldn't limit the data to peak immunogenicty. I can't check exactly how it would behave but it would likely end with multiple points per subject.\""}}
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