@@ -0,0 +1,2606 @@
+/*%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.DatabaseType;%0Aimport org.ensembl.healthcheck.ReportManager;%0Aimport org.ensembl.healthcheck.testcase.Priority;%0Aimport org.ensembl.healthcheck.testcase.SingleDatabaseTestCase;%0A%0A/**%0A * Check that all DNA and protein align features have an external_db_id set.%0A */%0A%0Apublic class AlignFeatureExternalDB extends SingleDatabaseTestCase %7B%0A%0A%09/**%0A%09 * Create a new XrefCategories testcase.%0A%09 */%0A%09public AlignFeatureExternalDB() %7B%0A%0A%09%09addToGroup(%22post_genebuild%22);%0A%09%09addToGroup(%22release%22);%0A%09%09setDescription(%22Check that all DNA and protein align features have an external_db_id set.%22);%0A%09%09setPriority(Priority.AMBER);%0A%09%09setEffect(%22Needed for web display.%22);%0A%09%09setFix(%22Run genebuilder script to set values.%22);%0A%0A%09%7D%0A%0A%09/**%0A%09 * This only applies to core and Vega databases.%0A%09 */%0A%09public void types() %7B%0A%0A%09%09removeAppliesToType(DatabaseType.OTHERFEATURES);%0A%09%09removeAppliesToType(DatabaseType.ESTGENE);%0A%09%09removeAppliesToType(DatabaseType.CDNA);%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 passed.%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%09String%5B%5D tables = %7B %22protein_align_feature%22, %22dna_align_feature%22 %7D;%0A%0A%09%09for (int i = 0; i %3C tables.length; i++) %7B%0A%0A%09%09%09String table = tables%5Bi%5D;%0A%0A%09%09%09int rows = getRowCount(con, %22SELECT COUNT(*) FROM %22 + table + %22 WHERE external_db_id IS NULL;%22);%0A%0A%09%09%09if (rows %3E 0) %7B%0A%09%09%09%09ReportManager.problem(this, con, rows + %22 rows in %22 + table + %22 have NULL external_db_ids%22);%0A%09%09%09%09result = false;%0A%09%09%09%7D else %7B%0A%09%09%09%09ReportManager.correct(this, con, %22All %22 + table + %22s have external_db_ids set%22);%0A%09%09%09%7D%0A%0A%09%09%7D%0A%0A%09%09return result;%0A%0A%09%7D // run%0A%0A%7D%0A

Check that external_db_id is set in dna_ & protein_align_feature tables.