/* * Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute * Copyright [2016-2017] EMBL-European Bioinformatics Institute * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package org.ensembl.healthcheck.testcase.compara; import java.sql.Connection; import org.ensembl.healthcheck.DatabaseRegistryEntry; import org.ensembl.healthcheck.ReportManager; import org.ensembl.healthcheck.Team; import org.ensembl.healthcheck.testcase.SingleDatabaseTestCase; /** * An EnsEMBL Healthcheck test case that checks the "sequence" table */ public class CheckSequenceTable extends SingleDatabaseTestCase { public CheckSequenceTable() { setDescription("Check for the sequence table of an ensembl_compara database."); setTeamResponsible(Team.COMPARA); } public boolean run(DatabaseRegistryEntry dbre) { Connection con = dbre.getConnection(); if (tableHasRows(con, "sequence")) { ReportManager.correct(this, con, "NO ENTRIES in sequence table, so nothing to test IGNORED"); return true; } boolean result = true; result &= checkCountIsZero(con, "sequence", "sequence='' or sequence is NULL"); result &= checkCountIsZero(con, "sequence", "length='' or length=0 or length is NULL"); result &= checkCountIsZero(con, "sequence", "length!=length(sequence)"); return result; } } // CheckSequenceTable