@@ -0,0 +1,2386 @@
+/*%0A Copyright (C) 2004 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 */%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 if protein_coding genes have a canonical transcript that has a valid translation. See also canonical_transcript checks in%0A * CoreForeignKeys.%0A */%0Apublic class CanonicalTranscriptCoding extends SingleDatabaseTestCase %7B%0A%0A%09/**%0A%09 * Create a new instance of CanonicalTranscriptCoding.%0A%09 */%0A%09public CanonicalTranscriptCoding() %7B%0A%0A%09%09addToGroup(%22release%22);%0A%09%09addToGroup(%22post_genebuild%22);%0A%09%09setDescription(%22Check if protein_coding genes have a canonical transcript that has a valid translation. See also canonical_transcript checks in CoreForeignKeys.%22);%0A%09%09setTeamResponsible(%22compara%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%09Connection con = dbre.getConnection();%0A%0A%09%09int rows = getRowCount(con, %22SELECT COUNT(*) FROM gene g LEFT JOIN translation tr ON g.canonical_transcript_id=tr.transcript_id WHERE g.biotype='protein_coding' AND tr.transcript_id IS NULL%22);%0A%0A%09%09if (rows %3E 0) %7B%0A%0A%09%09%09result = false;%0A%09%09%09ReportManager.problem(this, con, rows + %22 protein_coding genes have canonical transcripts that do not have valid translations%22);%0A%0A%09%09%7D else %7B%0A%0A%09%09%09ReportManager.correct(this, con, %22All protein_coding genes have canonical_transcripts that translate%22);%0A%09%09%7D%0A%0A%09%09return result;%0A%0A%09%7D // run%0A%0A%7D // CanonicalTranscriptCoding%0A

Check for protein coding genes with invalid translations