InterproFeatures.java

/*
 * 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.generic;

import java.sql.Connection;

import org.ensembl.healthcheck.DatabaseRegistryEntry;
import org.ensembl.healthcheck.DatabaseType;
import org.ensembl.healthcheck.ReportManager;
import org.ensembl.healthcheck.Team;
import org.ensembl.healthcheck.testcase.SingleDatabaseTestCase;
import org.ensembl.healthcheck.util.DBUtils;

/**
 * Check that there the interpro table is populated and there are interpro protein features
 */

public class InterproFeatures extends SingleDatabaseTestCase {
	

	/**
	 * Create a new InterproFeatures testcase.
	 */
	public InterproFeatures() {

		setDescription("Check that there the interpro table is populated and there are interpro protein features");
		setTeamResponsible(Team.GENEBUILD);
		removeAppliesToType(DatabaseType.OTHERFEATURES);

	}

	/**
	 * This only really applies to core & vega databases
	 */
	public void types() {

		removeAppliesToType(DatabaseType.OTHERFEATURES);
		removeAppliesToType(DatabaseType.ESTGENE);
		removeAppliesToType(DatabaseType.CDNA);
		removeAppliesToType(DatabaseType.RNASEQ);

	}

	/**
	 * Run the test.
	 * 
	 * @param dbre
	 *            The database to use.
	 * @return true if the test passed.
	 * 
	 */
	public boolean run(DatabaseRegistryEntry dbre) {

		boolean result = true;
		
		Connection con = dbre.getConnection();

		if (DBUtils.getRowCount(con, "SELECT COUNT(*) FROM interpro") == 0) {

			ReportManager.problem(this, con,
					"InterPro table is empty");
			result &= false;

		}
		
		if(DBUtils.getRowCount(con, "SELECT COUNT(*) FROM protein_feature JOIN interpro ON (id=hit_name)") == 0) {

			ReportManager.problem(this, con,
					"No InterPro protein features found");
			result &= false;
			
		}
		
		return result;


	} // run

}