{"action":"created","issue":{"url":"https://api.github.com/repos/pombase/pombase-chado/issues/504","labels_url":"https://api.github.com/repos/pombase/pombase-chado/issues/504/labels{/name}","comments_url":"https://api.github.com/repos/pombase/pombase-chado/issues/504/comments","events_url":"https://api.github.com/repos/pombase/pombase-chado/issues/504/events","html_url":"https://github.com/pombase/pombase-chado/issues/504","id":116517917,"number":504,"title":"Incorrectly loaded with/from values","user":{"login":"markmcdowall","id":462902,"avatar_url":"https://avatars.githubusercontent.com/u/462902?v=3","gravatar_id":"","url":"https://api.github.com/users/markmcdowall","html_url":"https://github.com/markmcdowall","followers_url":"https://api.github.com/users/markmcdowall/followers","following_url":"https://api.github.com/users/markmcdowall/following{/other_user}","gists_url":"https://api.github.com/users/markmcdowall/gists{/gist_id}","starred_url":"https://api.github.com/users/markmcdowall/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/markmcdowall/subscriptions","organizations_url":"https://api.github.com/users/markmcdowall/orgs","repos_url":"https://api.github.com/users/markmcdowall/repos","events_url":"https://api.github.com/users/markmcdowall/events{/privacy}","received_events_url":"https://api.github.com/users/markmcdowall/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"kimrutherford","id":90474,"avatar_url":"https://avatars.githubusercontent.com/u/90474?v=3","gravatar_id":"","url":"https://api.github.com/users/kimrutherford","html_url":"https://github.com/kimrutherford","followers_url":"https://api.github.com/users/kimrutherford/followers","following_url":"https://api.github.com/users/kimrutherford/following{/other_user}","gists_url":"https://api.github.com/users/kimrutherford/gists{/gist_id}","starred_url":"https://api.github.com/users/kimrutherford/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kimrutherford/subscriptions","organizations_url":"https://api.github.com/users/kimrutherford/orgs","repos_url":"https://api.github.com/users/kimrutherford/repos","events_url":"https://api.github.com/users/kimrutherford/events{/privacy}","received_events_url":"https://api.github.com/users/kimrutherford/received_events","type":"User","site_admin":false},"milestone":null,"comments":20,"created_at":"2015-11-12T10:09:42Z","updated_at":"2015-11-18T10:29:12Z","closed_at":null,"body":"The loading of the with/from values seems to have failed. In previous releases where there have been multiple with/from gene stable_ids these have existed as separate rows. In Chadov56 they are now getting included as a single row with comma separation.\r\n\r\n```sql\r\nSELECT\r\n  f1.uniquename,\r\n  f1.feature_cvterm_id,\r\n  f1.value,\r\n  f2.uniquename\r\nFROM\r\n  (\r\n    SELECT\r\n      f.uniquename,\r\n      fcp.value,\r\n      fc.feature_cvterm_id\r\n    FROM\r\n      feature f\r\n      JOIN feature_cvterm fc ON (f.feature_id=fc.feature_id)\r\n      JOIN cvterm fcc ON (fc.cvterm_id=fcc.cvterm_id)\r\n      JOIN dbxref fccx ON (fcc.dbxref_id=fccx.dbxref_id)\r\n      JOIN db fccd ON (fccx.db_id=fccd.db_id)\r\n      LEFT JOIN feature_cvtermprop fcp ON (fc.feature_cvterm_id=fcp.feature_cvterm_id)\r\n      LEFT JOIN cvterm fcpt ON (fcp.type_id=fcpt.cvterm_id)\r\n    WHERE\r\n      fcpt.name IN ('with') AND\r\n      fcp.value LIKE 'PomBase:%') AS f1\r\n  LEFT JOIN feature f2 ON (f1.value='PomBase:' || f2.uniquename)\r\nWHERE\r\n  f2.uniquename IS NULL;\r\n```\r\n\r\n   uniquename   | feature_cvterm_id |                                        value                                        | uniquename \r\n----------------|-------------------|-------------------------------------------------------------------------------------|------------\r\n SPAC2G11.12.1  |              4515 | PomBase:SPBC336.01,PomBase:SPAC20H4.07                                              | \r\n SPBC16E9.18.1  |             44625 | PomBase:SPAC25B8.03,PomBase:SPAC31G5.15                                             | \r\n SPBC16E9.18.1  |             44627 | PomBase:SPAC25B8.03,PomBase:SPAC31G5.15                                             | \r\n SPAC1610.03c.1 |             10467 | PomBase:SPBC16A3.05c,PomBase:SPAP27G11.10c                                          | \r\n SPAC2G11.12.1  |              4519 | PomBase:SPAC16A10.07c,PomBase:SPBC660.13c                                           | \r\n SPAC2F3.01.1   |             23486 | PomBase:SPCC4F11.04c,PomBase:SPAC17G8.11c                                           | \r\n SPAC17H9.19c.1 |             11904 | PomBase:SPAC29B12.03,PomBase:SPAC17H9.10c                                           | \r\n SPCC4F11.04c.1 |             70773 | PomBase:SPAC2F3.01,PomBase:SPAC17G8.11c                                             | \r\n SPCC4F11.04c.1 |             70774 | PomBase:SPAC2F3.01,PomBase:SPAC17G8.11c                                             | \r\n SPAC3A12.09c.1 |              8293 | PomBase:SPAC3A12.09c,PomBase:SPCPB16A4.05c,PomBase:SPAC29A4.13,PomBase:SPAC1952.11c | \r\n\r\nIn Chadov55 these annotations where on separate row:\r\n```sql\r\nSELECT\r\n  f1.uniquename,\r\n  f1.feature_cvterm_id,\r\n  f1.value,\r\n  f2.uniquename\r\nFROM\r\n  (\r\n    SELECT\r\n      f.uniquename,\r\n      fcp.value,\r\n      fc.feature_cvterm_id\r\n    FROM\r\n      feature f\r\n      JOIN feature_cvterm fc ON (f.feature_id=fc.feature_id)\r\n      JOIN cvterm fcc ON (fc.cvterm_id=fcc.cvterm_id)\r\n      JOIN dbxref fccx ON (fcc.dbxref_id=fccx.dbxref_id)\r\n      JOIN db fccd ON (fccx.db_id=fccd.db_id)\r\n      LEFT JOIN feature_cvtermprop fcp ON (fc.feature_cvterm_id=fcp.feature_cvterm_id)\r\n      LEFT JOIN cvterm fcpt ON (fcp.type_id=fcpt.cvterm_id)\r\n    WHERE\r\n      fcpt.name IN ('with') AND\r\n      fcp.value LIKE 'PomBase:%') AS f1\r\n  LEFT JOIN feature f2 ON (f1.value='PomBase:' || f2.uniquename)\r\nWHERE\r\n   f1.feature_cvterm_id=36334;\r\n```\r\n\r\n  uniquename   | feature_cvterm_id |        value        | uniquename  \r\n---------------|-------------------|---------------------|-------------\r\n SPBC1706.01.1 |             36334 | PomBase:SPCC895.05  | SPCC895.05\r\n SPBC1706.01.1 |             36334 | PomBase:SPCC1223.06 | SPCC1223.06"},"comment":{"url":"https://api.github.com/repos/pombase/pombase-chado/issues/comments/157672521","html_url":"https://github.com/pombase/pombase-chado/issues/504#issuecomment-157672521","issue_url":"https://api.github.com/repos/pombase/pombase-chado/issues/504","id":157672521,"user":{"login":"kimrutherford","id":90474,"avatar_url":"https://avatars.githubusercontent.com/u/90474?v=3","gravatar_id":"","url":"https://api.github.com/users/kimrutherford","html_url":"https://github.com/kimrutherford","followers_url":"https://api.github.com/users/kimrutherford/followers","following_url":"https://api.github.com/users/kimrutherford/following{/other_user}","gists_url":"https://api.github.com/users/kimrutherford/gists{/gist_id}","starred_url":"https://api.github.com/users/kimrutherford/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kimrutherford/subscriptions","organizations_url":"https://api.github.com/users/kimrutherford/orgs","repos_url":"https://api.github.com/users/kimrutherford/repos","events_url":"https://api.github.com/users/kimrutherford/events{/privacy}","received_events_url":"https://api.github.com/users/kimrutherford/received_events","type":"User","site_admin":false},"created_at":"2015-11-18T10:29:12Z","updated_at":"2015-11-18T10:29:12Z","body":"> Kim, if you could do the fix as a fallback that would be great.\r\n\r\nI'm having a bit of trouble keeping up.  Which fix do you mean?  It looks like you've removed all the commas from the contig file with= qualifiers, which is great.  I need to fix the loader to store the pipe separated withs sensibly in Chado.  Is that the fix you mean?"}}