/*
 * Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
 * Copyright [2016-2018] 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.
 */

/*
 * Copyright (C) 2003 EBI, GRL
 * 
 * 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
 * the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.
 * 
 * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
 * FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
 * 
 * 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,
 * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 */
package org.ensembl.healthcheck.testcase.generic;

import java.sql.Connection;
import java.util.ArrayList;
import java.util.List;
import java.sql.Statement;
import java.sql.ResultSet;

import org.apache.commons.lang.StringUtils;
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.Priority;
import org.ensembl.healthcheck.testcase.SingleDatabaseTestCase;
import org.ensembl.healthcheck.util.DBUtils;

/**
 * Check that transcripts which need supporting features have them.
 */

public class TranscriptSupportingFeatures extends SingleDatabaseTestCase {

	List<String> allowedNoSupporting = new ArrayList<String>();

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

		setDescription("Check that transcripts which need supporting features have them.");
		setPriority(Priority.AMBER);
		setTeamResponsible(Team.GENEBUILD);

		allowedNoSupporting.add("BGI_Augustus_geneset");
		allowedNoSupporting.add("BGI_Genewise_geneset");
		allowedNoSupporting.add("BGI_Genscan_geneset");
		allowedNoSupporting.add("LRG_import");
		allowedNoSupporting.add("MT_genbank_import");
		allowedNoSupporting.add("Medaka_Genome_Project");
		allowedNoSupporting.add("ccds_import");
		allowedNoSupporting.add("havana");
		allowedNoSupporting.add("havana_ig_gene");
		allowedNoSupporting.add("ncRNA");
		allowedNoSupporting.add("oxford_FGU");
		allowedNoSupporting.add("refseq_human_import");
		allowedNoSupporting.add("refseq_mouse_import");
		allowedNoSupporting.add("refseq_import");
		allowedNoSupporting.add("singapore_est");
		allowedNoSupporting.add("singapore_gene");
		allowedNoSupporting.add("ncRNA_pseudogene");
		allowedNoSupporting.add("gsten");
		allowedNoSupporting.add("cyt");
		allowedNoSupporting.add("hox");

	}

	public void types() {

		removeAppliesToType(DatabaseType.VEGA);
		removeAppliesToType(DatabaseType.SANGER_VEGA);

	}

	/**
	 * 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();
                Statement stmt = null;

		// list of transcript analysis logic_names which are allowed to not have supporting features
		String allowed = "'" + StringUtils.join(allowedNoSupporting, "','") + "'";
		// allow all logic_names containing _rnaseq to accomodate all tissue types and species
		String rnaseq = "'%_rnaseq%'";

		String sql = String
				.format(
						"SELECT COUNT(*), a.logic_name FROM transcript t LEFT JOIN transcript_supporting_feature tsf ON t.transcript_id = tsf.transcript_id JOIN analysis a ON a.analysis_id=t.analysis_id WHERE a.analysis_id=t.analysis_id and tsf.transcript_id IS NULL AND LOWER(a.logic_name) NOT LIKE (%s) AND a.logic_name NOT IN  (%s) group by a.logic_name",
						rnaseq, allowed);
                try {
                        stmt = con.createStatement();
                        ResultSet rs = stmt.executeQuery(sql);
        
                        while (rs.next()) {
        
                                long rows = rs.getLong(1);
                                String analysis = rs.getString(2);
        
        			ReportManager.problem(this, con, rows + " transcripts which should have transcript_supporting_features do not have them for analysis " + analysis);
        			result = false;
        		}
                        if (result) {
                                ReportManager.correct(this, con, "All transcripts that require supporting features have them");
                        } else {
                                ReportManager.problem(this, con, "Useful SQL: " + sql);
                        }
                } catch (Exception e) {
                        result = false;
                        e.printStackTrace();
                }

		return result;

	} // run

} // TranscriptSupportingFeatures

@@ -3420,16 +3420,91 @@
 (%22hox%22);
+%0A%09%09allowedNoSupporting.add(%22lincRNA%22);%0A%09%09allowedNoSupporting.add(%22lncRNA%22);
 %0A%0A%09%7D%0A%0A%09p

Update TranscriptSupportingFeatures.java