<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div><div>Hi, </div><div><br></div><div>again. some patching issues - I try to patch an ensembl-ontology 67 db to 74. </div><div><br></div><div>There are issues with the patch_71_72_e.sql patch - the table TERM does not exist ( but term ) - attached a patch file for the patch. </div><div><br></div><div>Also, some other changes are missing ( there are no patch files for 67-> 68, 68->69, 69->70, 70->71 ). </div><div><br></div><div>I've listed the changes below but haven't run any tests with the 74 api for this. Did anyone else do ? How does this work with the new ontology_id column in the relation and closure tables ? </div><div><br></div><div>Maybe I should consider just downloading the new ontology 74 db … </div><div><br></div><div>Regards, </div><div><br></div><div> Jan Vogel</div><div><div><br></div><div><b>File : ensembl-74/ensembl/misc-scripts/ontology/sql/patch_71_72_e.sql </b></div><div><br></div><div><font face="Menlo"><br></font></div><div><font face="Menlo">ALTER TABLE <b>TERM </b>ADD COLUMN is_obsolete INT NOT NULL DEFAULT 0;</font></div><div><font face="Menlo"><br></font></div><div><font face="Menlo">-- Patch identifier</font></div><div><font face="Menlo">INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_71_72_e.sql|is_obsolete');</font></div><div><br></div><div><br></div><div><br></div><div><br></div><div><b>Additional changes from 67 -> 74 which are not in patch files: </b></div><div><br></div><div>table term is missing the "is_root" column : </div><div><br></div><div><div><font face="Menlo">ALTER TABLE <b>term </b>ADD COLUMN is_root INT NOT NULL DEFAULT 0;</font></div></div><div><br></div><div>table relation and table closure is missing ontology_id column and subsequently the indexes have to be updated:</div><div><br></div><div><div><font face="Menlo">ALTER TABLE <b>relation </b>ADD COLUMN ontology_id INT UNSIGNED NOT NULL;</font></div></div><div><div><font face="Menlo">ALTER TABLE <b>closure </b>ADD COLUMN ontology_id INT UNSIGNED NOT NULL;</font></div></div><div><font face="Menlo"><br></font></div><div><font face="Menlo">DROP INDEX child_parent_idx ON relation; </font></div><div><div><font face="Menlo">CREATE UNIQUE INDEX child_parent_idx ON relation (child_term_id, parent_term_id, relation_type_id, intersection_of, ontology_id) ; </font></div></div><div><font face="Menlo"><br></font></div><div><div><font face="Menlo">DROP INDEX child_parent_idx ON closure; </font></div><div><font face="Menlo">CREATE UNIQUE INDEX child_parent_idx ON closure (child_term_id, parent_term_id, subparent_term_id, ontology_id) ; </font></div></div><div><br></div><div><br></div><div><br></div><div><br></div><div> </div></div></body></html>