/*
* 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 java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
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;
/**
* Check that analyses (e.g. havana) and their associated xref types (e.g. OTTT) exist, and vice versa.
*/
public class AnalysisXrefs extends SingleDatabaseTestCase {
/**
* Creates a new instance of AnalysisXrefs
*/
public AnalysisXrefs() {
setDescription("Check that analyses (e.g. havana) and their associated xref types (e.g. OTTT) exist, and vice versa");
setPriority(Priority.AMBER);
setEffect("Will cause problems/miscoloring on web display.");
setFix("Possibly indicates a problem with the Havana/Ensembl merge pipeline");
setTeamResponsible(Team.GENEBUILD);
}
/**
* This only applies to core and Vega databases.
*/
public void types() {
removeAppliesToType(DatabaseType.ESTGENE);
removeAppliesToType(DatabaseType.CDNA);
removeAppliesToType(DatabaseType.OTHERFEATURES);
removeAppliesToType(DatabaseType.RNASEQ);
}
/**
* Run the test.
*
* @param dbre
* The database registry containing all the specified databases.
*/
public boolean run(DatabaseRegistryEntry dbre) {
boolean result = true;
// --------------------------------
// havana/OTTT
result &= checkAnalysisAndSource( dbre, "Transcript",
"havana", "ensembl_havana_transcript",
"havana_ig_gene", "ensembl_havana_lincrna",
"proj_havana", "proj_ensembl_havana_transcript",
"proj_ensembl_havana_lincrna", "proj_havana_ig_gene",
"ensembl_havana_ig_gene", "proj_ensembl_havana_ig_gene",
"OTTT" );
// --------------------------------
// other pairs here
// --------------------------------
return result;
} // run
// --------------------------------------------------------------------------
private boolean checkAnalysisAndSource(DatabaseRegistryEntry dbre, String objectType, String analysis1, String analysis2, String analysis3, String analysis4, String analysis5, String analysis6, String analysis7, String analysis8, String analysis9, String analysis10, String source) {
boolean result = true;
Connection con = dbre.getConnection();
String table = objectType.toLowerCase();
// find objects with the analysis logic name that don't have any xrefs of a
// particular type (e.g. transcripts with an analysis of 'havana' should
// have at least one xref from 'OTTT')
String sql = "SELECT COUNT(*) FROM "
+ table
+ " t, analysis a WHERE t.analysis_id=a.analysis_id AND a.logic_name like '%havana%' AND t."
+ table
+ "_id NOT IN (SELECT DISTINCT(ox.ensembl_id) FROM xref x, object_xref ox WHERE x.xref_id=ox.xref_id AND ox.ensembl_object_type=? AND x.display_label like '%OTT%')";
try {
PreparedStatement stmt = con.prepareStatement(sql);
stmt.setString(1, objectType);
ResultSet rs = stmt.executeQuery();
rs.first();
int rows = rs.getInt(1);
if (rows > 0) {
result = false;
ReportManager.problem(this, con, rows + " " + table + "s with source " + analysis1 + " do not have any associated xrefs of display OTT ");
} else {
ReportManager.correct(this, con, "All " + table + "s with analysis " + analysis1 + " have associated " + source + " xrefs");
}
rs.close();
stmt.close();
} catch (SQLException e) {
System.err.println("Error executing:\n" + sql);
e.printStackTrace();
}
// and vice-versa - check for objects that have particular types of xref but
// are the wrong analysis
// e.g. all transcripts that have an OTTT xref should be of analysis type
// 'havana' or 'ensembl_havana_transcript'.
sql = "SELECT COUNT(DISTINCT(t." + table + "_id)) FROM xref x, object_xref ox, external_db e, " + table
+ " t, analysis a WHERE x.xref_id=ox.xref_id AND x.external_db_id=e.external_db_id AND ox.ensembl_id=t." + table
+ "_id AND a.logic_name not in (?, ?, ?, ?, ?, ?, ?, ?, ?, ?) AND e.db_name=? AND t.analysis_id=a.analysis_id AND ox.ensembl_object_type=?";
try {
PreparedStatement stmt = con.prepareStatement(sql);
stmt.setString(1, analysis1);
stmt.setString(2, analysis2);
stmt.setString(3, analysis3);
stmt.setString(4, analysis4);
stmt.setString(5, analysis5);
stmt.setString(6, analysis6);
stmt.setString(7, analysis7);
stmt.setString(8, analysis8);
stmt.setString(9, analysis9);
stmt.setString(10, analysis10);
stmt.setString(11, source);
stmt.setString(12, objectType);
ResultSet rs = stmt.executeQuery();
rs.first();
int rows = rs.getInt(1);
if (rows > 0) {
result = false;
ReportManager.problem(this, con, rows + " " + table + "s with " + source + " xrefs do not have an analysis named " + analysis1 + ", " + analysis2 + ", " + analysis3 + ", " + analysis4 + ", " + analysis5 + ", " + analysis6 + ", " + analysis7 + ", " + analysis8 + ", " + analysis9 + " or " + analysis10);
} else {
ReportManager.correct(this, con, "All " + table + "s with " + source + " xrefs have analyses of type " + analysis1 + ", " + analysis2 + ", " + analysis3 + ", " + analysis4 + ", " + analysis5 + ", " + analysis6 + ", " + analysis7 + ", " + analysis8 + ", " + analysis9 + " or " + analysis10);
}
rs.close();
stmt.close();
} catch (SQLException e) {
System.err.println("Error executing:\n" + sql);
e.printStackTrace();
}
return result;
}
// --------------------------------------------------------------------------
} // AnalysisXrefs