/*
* 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.
*/
/*
* 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 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;
import org.ensembl.healthcheck.util.Utils;
/**
* Check that unrpoejcted GO xrefs exist, and that there are no blank or null
* linkage types.
*/
public class GOXrefs extends SingleDatabaseTestCase {
/**
* Create a new GOXrefs testcase.
*/
public GOXrefs() {
setDescription("Check that unrpoejcted GO xrefs exist, and that there are no blank or null linkage types.");
setTeamResponsible(Team.GENEBUILD);
}
/**
* This only really applies to core databases
*/
public void types() {
removeAppliesToType(DatabaseType.OTHERFEATURES);
removeAppliesToType(DatabaseType.ESTGENE);
removeAppliesToType(DatabaseType.VEGA);
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;
// only check for GO xrefs for human, mouse, rat & drosophila
// if (dbre.getSpecies().equals(Species.HOMO_SAPIENS) ||
// dbre.getSpecies().equals(Species.MUS_MUSCULUS) ||
// dbre.getSpecies().equals(Species.RATTUS_NORVEGICUS) ||
// dbre.getSpecies().equals(Species.DROSOPHILA_MELANOGASTER)) {
Connection con = dbre.getConnection();
if (true) {
// check that they exist in the xref table
String sql = "SELECT COUNT(*) FROM external_db edb, xref x WHERE edb.db_name like 'go%' AND edb.external_db_id = x.external_db_id AND (x.info_type IS NULL OR x.info_type != 'PROJECTION')";
int xref_rows = DBUtils.getRowCount(con, sql);
if (xref_rows == 0) {
ReportManager.problem(this, con,
"No unprojected GO xrefs found.");
result = false;
} else {
ReportManager.correct(this, con, "Found " + xref_rows
+ " unprojected GO xrefs");
// if GO xrefs exist, check that the ontology_xref table is
// populated
int ontology_xref_rows = DBUtils.getRowCount(con,
"SELECT COUNT(*) FROM ontology_xref");
if (ontology_xref_rows == 0) {
ReportManager
.problem(
this,
con,
"Found "
+ xref_rows
+ " GO xrefs in xref table but ontology_xref table is empty");
result = false;
} else {
ReportManager.correct(this, con, "ontology_xref table has "
+ ontology_xref_rows + " rows");
}
}
}
// check for blank or null linkage_type
int blank = DBUtils
.getRowCount(
con,
"SELECT COUNT(*) FROM ontology_xref WHERE linkage_type IS NULL OR linkage_type=''");
if (blank > 0) {
ReportManager
.problem(
this,
con,
blank
+ " rows in ontology_xref have null or blank ('') linkage_type");
result = false;
} else {
ReportManager.correct(this, con,
"No blank or null linkage_types in ontology_xref");
}
// check that linkage_type values are one of the allowable values
String[] allowable_linkage_types = { "IC", "IBA", "IDA", "IEA", "IEP",
"IGI", "IMP", "IPI", "ISS", "NAS", "ND", "TAS", "NR", "RCA",
"EXP", "ISO", "ISA", "ISM", "IGC" };
String[] linkage_types = DBUtils
.getColumnValues(
con,
"SELECT DISTINCT(linkage_type) FROM ontology_xref WHERE linkage_type != '' AND linkage_type NOT IN ('"
+ Utils.arrayToString(allowable_linkage_types,
"','") + "')");
if (linkage_types.length > 0) {
ReportManager
.problem(
this,
con,
"Linkage type(s): "
+ Utils.arrayToString(linkage_types, ", ")
+ " incorrect. Allowable values are: "
+ Utils.arrayToString(
allowable_linkage_types, ", "));
result = false;
} else {
ReportManager.correct(this, con,
"Linkage type values in ontology_xref are correct");
}
// check that *only* GO xrefs have linkage types assigned
String[] dbs = DBUtils
.getColumnValues(
con,
"SELECT DISTINCT(e.db_name) FROM external_db e, xref x, object_xref ox, ontology_xref g WHERE e.external_db_id=x.external_db_id AND x.xref_id=ox.xref_id AND ox.object_xref_id=g.object_xref_id AND e.db_name not like 'GO%' ");
if (dbs.length > 0) {
ReportManager
.problem(
this,
con,
"Some "
+ Utils.arrayToString(dbs, ", ")
+ " xrefs have entries in linkage_type - should only be GO xrefs");
result = false;
} else {
ReportManager.correct(this, con,
"No non-GO xrefs have linkage types assigned");
}
return result;
} // run
} // GOXrefs