@@ -0,0 +1,2674 @@
+/*%0A * Copyright (C) 2003 EBI, GRL%0A * %0A * This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by%0A * the Free Software Foundation; either 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, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or%0A * FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.%0A * %0A * You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation,%0A * 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 no genes are named after numeric EntrezGene identifiers.%0A */%0A%0Apublic class EntrezGeneNumeric extends SingleDatabaseTestCase %7B%0A%0A%09%0A%09/**%0A%09 * Create a new EntrezGeneNumeric testcase.%0A%09 */%0A%09public EntrezGeneNumeric() %7B%0A%0A%09%09addToGroup(%22release%22);%0A%09%09setDescription(%22Check that no genes are named after numeric EntrezGene identifiers.%22);%0A%09%09setPriority(Priority.AMBER);%0A%09%09setEffect(%22Causes genes to be displayed with numeric EntrezGene 'names', which is potentially confusing.%22);%0A%09%09%0A%09%7D%0A%0A%09/**%0A%09 * Only run on core databases.%0A%09 */%0A%09public void types() %7B%0A%0A%09%09removeAppliesToType(DatabaseType.CDNA);%0A%09%09removeAppliesToType(DatabaseType.VEGA);%0A%09%09removeAppliesToType(DatabaseType.OTHERFEATURES);%0A%09%09%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%09%09%0A%09%09Connection con = dbre.getConnection();%0A%09%09%0A%09%09int rows = getRowCount(con, %22SELECT COUNT(*) FROM gene g, external_db e, xref x WHERE g.display_xref_id=x.xref_id AND e.external_db_id=x.external_db_id AND e.db_name='EntrezGene' AND x.display_label REGEXP '%5E%5B0-9%5D+$'%22);%0A%0A%09%09if (rows %3E 0) %7B%0A%09%09%09%0A%09%09%09ReportManager.problem(this, con, rows + %22 genes are named after numeric EntrezGene identifiers%22);%0A%09%09%09result = false;%0A%09%09%09%0A%09%09%7D else %7B%0A%09%09%09%0A%09%09%09ReportManager.correct(this, con, %22No genes are named after numeric EntrezGene identifiers%22);%0A%09%09%09%0A%09%09%7D%0A%09%09%0A%09%09return result;%0A%09%09%0A%09%7D // run%0A%0A%09//----------------------------------------------------------------------%0A%0A%7D // EntrezGeneNumeric%0A%0A

Check that no genes are named after numeric EntrezGene identifiers.