@@ -0,0 +1,2607 @@
+/*%0A Copyright (C) 2003 EBI, GRL%0A %0A This library is free software; you can redistribute it and/or%0A modify it under the terms of the GNU Lesser General Public%0A License as published by the Free Software Foundation; either%0A version 2.1 of the License, or (at your option) any later version.%0A %0A This library is distributed in the hope that it will be useful,%0A but WITHOUT ANY WARRANTY; without even the implied warranty of%0A MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU%0A Lesser General Public License for more details.%0A %0A You should have received a copy of the GNU Lesser General Public%0A License along with this library; if not, write to the Free Software%0A Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA%0A */%0Apackage org.ensembl.healthcheck.testcase.generic;%0A%0Aimport java.sql.Connection;%0A%0Aimport org.ensembl.healthcheck.DatabaseRegistryEntry;%0Aimport org.ensembl.healthcheck.ReportManager;%0Aimport org.ensembl.healthcheck.testcase.SingleDatabaseTestCase;%0A%0A/**%0A * Check that there are no duplicates in the assembly table.%0A */%0A%0Apublic class DuplicateAssembly extends SingleDatabaseTestCase %7B%0A%0A%09/**%0A%09 * Create a new DuplicateAssembly testcase.%0A%09 */%0A%09public DuplicateAssembly() %7B%0A%0A%09%09addToGroup(%22post_genebuild%22);%0A%09%09addToGroup(%22release%22);%0A%09%09setDescription(%22Check that there are no duplicates in the assembly table%22);%0A%0A%09%7D%0A%0A%09/**%0A%09 * Run the test.%0A%09 * %0A%09 * @param dbre%0A%09 *          The database to use.%0A%09 * @return true if the test pased.%0A%09 * %0A%09 */%0A%09public boolean run(DatabaseRegistryEntry dbre) %7B%0A%0A%09%09boolean result = true;%0A%0A%09%09Connection con = dbre.getConnection();%0A%0A%09%09int rows = getRowCount(%0A%09%09%09%09con,%0A%09%09%09%09%22SELECT *, COUNT(*) AS c FROM assembly GROUP BY asm_seq_region_id, cmp_seq_region_id, asm_start, asm_end, cmp_start, cmp_end, ori HAVING c %3E 1%22);%0A%0A%09%09if (rows %3E 0) %7B%0A%0A%09%09%09ReportManager.problem(this, con, rows + %22 duplicate rows in assembly table%22);%0A%09%09%09result = false;%0A%0A%09%09%7D else %7B%0A%0A%09%09%09ReportManager.correct(this, con, %22No duplicate rows in the assembly table%22);%0A%0A%09%09%7D%0A%0A%09%09return result;%0A%0A%09%7D // run%0A%0A%09/**%0A%09 * Note more details can be obtained via: %0A%09 * %0A%09 * SELECT a.*, sr1.name, cs1.name, sr2.name, cs2.name, COUNT(*) AS c %0A%09 * FROM assembly a, seq_region sr1, seq_region sr2, coord_system cs1, coord_system cs2 %0A%09 * WHERE a.cmp_seq_region_id = sr1.seq_region_id AND%0A%09 *       sr1.coord_system_id = cs1.coord_system_id AND%0A%09 *       a.asm_seq_region_id = sr2.seq_region_id AND%0A%09 *       sr2.coord_system_id = cs2.coord_system_id %0A%09 * GROUP BY asm_seq_region_id,  cmp_seq_region_id, asm_start, asm_end, cmp_start, cmp_end, ori%0A%09 * HAVING c %3E 1;%0A%09 */%0A%09%0A%7D // DuplicateAssembly%0A

Check for duplicate rows in the assembly table.