Moved to Monika's private repository.

sql/delete_duplicates.sql

-CREATE PROCEDURE delete_duplicates()
-BEGIN
- 
-DECLARE v_identifier varChar(255);
-DECLARE v_unmapped_object_id INT;
-DECLARE existing_object_id INT DEFAULT 0;
-DECLARE v_parent varChar(255);
-DECLARE v_ensembl_id INT;
-DECLARE v_unmapped_reason_id INT;
-DECLARE v_ensembl_object_type varChar(15);
-DECLARE v_external_db_id INT;
-DECLARE done INT DEFAULT 0;
-DECLARE row_count INT DEFAULT 0;
-
-DECLARE cur1 CURSOR FOR SELECT unmapped_object_id, identifier, ensembl_id, parent, unmapped_reason_id, ensembl_object_type, external_db_id from unmapped_object where ensembl_id is not null and parent is not null and ensembl_object_type is not null and external_db_id is not null order by unmapped_object_id;
-DECLARE CONTINUE HANDLER FOR NOT FOUND SET done = TRUE;
-
-OPEN cur1;
-
-main_loop: LOOP
-
-	SET done = FALSE;
-	FETCH cur1 INTO v_unmapped_object_id,v_identifier, v_ensembl_id, v_parent, v_unmapped_reason_id, v_ensembl_object_type, v_external_db_id;
-
-	IF done THEN
-   		LEAVE main_loop;
-	END IF;
-
-	SET row_count = 0;
-	SELECT COUNT(1) INTO row_count FROM unmapped_object WHERE identifier = v_identifier and ensembl_id = v_ensembl_id and parent = v_parent and unmapped_reason_id = v_unmapped_reason_id and ensembl_object_type = v_ensembl_object_type and external_db_id = v_external_db_id;
-	IF row_count > 1 THEN
-		DELETE FROM unmapped_object where unmapped_object_id <> v_unmapped_object_id and identifier = v_identifier and ensembl_id = v_ensembl_id and parent = v_parent and unmapped_reason_id = v_unmapped_reason_id and ensembl_object_type = v_ensembl_object_type and external_db_id = v_external_db_id;
-
-	END IF;
-END LOOP;
-
-CLOSE cur1;
-
-END
-

sql/link_xrefs_to_genes.sql

-CREATE PROCEDURE link_xrefs_to_genes()
-BEGIN
- 
-DECLARE count_deleted, count_updated INT DEFAULT 0;
-DECLARE v_object_xref_id INT;
-DECLARE existing_object_xref INT DEFAULT 0;
-DECLARE v_ensembl_id INT;
-DECLARE v_ensembl_object_type varChar(15);
-DECLARE v_xref_id INT;
-DECLARE v_gene_id INT DEFAULT 0;
-DECLARE done INT DEFAULT 0;
-
-DECLARE cur1 CURSOR FOR SELECT object_xref_id, ensembl_id, ensembl_object_type, o.xref_id FROM object_xref o INNER JOIN xref x on o.xref_id = x.xref_id INNER JOIN external_db e on e.external_db_id =x.external_db_id WHERE db_name in ('UniGene', 'Uniprot_genename','DBASS3', 'DBASS5') AND ensembl_object_type <> 'Gene';
-DECLARE CONTINUE HANDLER FOR NOT FOUND SET done = TRUE;
-
-OPEN cur1;
-
-main_loop: LOOP
-
-	SET done = FALSE;
-	FETCH cur1 INTO v_object_xref_id,v_ensembl_id, v_ensembl_object_type, v_xref_id;
-
-	IF done THEN
-   		LEAVE main_loop;
-	END IF;
-	-- find the corresponding gene_id
-	SET v_gene_id = 0;
-	CASE
-		WHEN v_ensembl_object_type = 'Transcript' THEN
-			SELECT COALESCE(gene_id,0) INTO v_gene_id FROM transcript where transcript_id = v_ensembl_id;
-		WHEN v_ensembl_object_type = 'Translation' THEN
-			SELECT COALESCE(gene_id,0) INTO v_gene_id FROM transcript tp inner join translation tl where tp.transcript_id = tl.transcript_id and translation_id = v_ensembl_id;
-	END CASE;
-	SET existing_object_xref = 0;
-	IF v_gene_id > 0 THEN
-    		SELECT COALESCE(object_xref_id,0) INTO existing_object_xref FROM object_xref where ensembl_id = v_gene_id AND xref_id = v_xref_id AND ensembl_object_type = 'Gene';
-		IF existing_object_xref > 0 THEN
-        		
-			-- if gene_id already linked to this xref_id delete the object_xref
-			DELETE FROM object_xref WHERE object_xref_id = v_object_xref_id;
-			SET count_deleted = count_deleted + 1;
-			DELETE FROM identity_xref WHERE object_xref_id = v_object_xref_id;
-			DELETE FROM dependent_xref WHERE object_xref_id = v_object_xref_id;
-    		ELSE
-        		-- if not linked update the current object_xref
-			UPDATE object_xref SET ensembl_id = v_gene_id, ensembl_object_type = 'Gene' WHERE object_xref_id = v_object_xref_id;
-			SET count_updated = count_updated + 1;
-    		END IF;
-	END IF;
-END LOOP;
-
-CLOSE cur1;
-
--- populate the meta table with patch id and counts for updated rows
-INSERT INTO meta (species_id, meta_key, meta_value) 
-VALUES (NULL, 'data_changes', CONCAT('link_xrefs_to_genes.sql|updated ',count_updated,' xrefs, deleted ',count_deleted,' xrefs'));
-
-END
-