@@ -0,0 +1,2440 @@
+/*%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.Priority;%0Aimport org.ensembl.healthcheck.testcase.SingleDatabaseTestCase;%0A%0A/**%0A * %0A */%0A%0Apublic class GeneDescriptions extends SingleDatabaseTestCase %7B%0A%0A%09/**%0A%09 * Create a new GeneDescriptions testcase.%0A%09 */%0A%09public GeneDescriptions() %7B%0A%0A%09%09addToGroup(%22post_genebuild%22);%0A%09%09addToGroup(%22release%22);%0A%09%09addToGroup(%22core_xrefs%22);%0A%09%09setDescription(%22Check gene descriptions; correct capitalisation of UniprotKB/SwissProt%22);%0A%09%09setPriority(Priority.AMBER);%0A%09%09setEffect(%22Capitalisation of Uniprot will be wrong in gene descriptions.%22);%0A%09%09setFix(%22Re-run xref system or manually fix affected xrefs.%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 passed.%0A%09 * %0A%09 */%0A%09public boolean run(DatabaseRegistryEntry dbre) %7B%0A%0A%09%09boolean result = true;%0A%0A%09%09result &= checkSwissprot(dbre);%0A%0A%09%09return result;%0A%0A%09%7D // run%0A%0A%09// --------------------------------------------------------------------------%0A%09%0A%09private boolean checkSwissprot(DatabaseRegistryEntry dbre) %7B%0A%0A%09%09boolean result = true;%0A%0A%09%09Connection con = dbre.getConnection();%0A%09%09%0A%09%09int rows = getRowCount(con, %22SELECT COUNT(*) FROM gene WHERE description like '%25Uniprot/SWISSPROT%25'%22);%0A%0A%09%09if (rows %3E 0) %7B%0A%09%09%09ReportManager.problem(this, con, rows + %22 descriptions have incorrect spelling/capitalisation of Uniprot attribution%22);%0A%09%09%09result = false;%0A%09%09%7D else %7B%0A%09%09%09ReportManager.correct(this, con, %22All Uniprot attributions correct.%22);%0A%09%09%7D%0A%0A%09%09return result;%0A%0A%09%7D%0A%7D // GeneDescriptions%0A

Check for incorrect spelling of UniprotKB/SWISSPROT in gene descriptions.