/*
* 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.variation;
import java.sql.Connection;
import java.util.List;
import org.ensembl.healthcheck.DatabaseRegistryEntry;
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.RowMapper;
import org.ensembl.healthcheck.util.SqlTemplate;
/**
* Checks phenotype_feature_attrib entries do not contain unsupported characters or unhelpful values.
*/
public class PhenotypeFeatureAttrib extends CheckChar {
public PhenotypeFeatureAttrib() {
setDescription("Check that imported phenotype_feature_attrib values are reasonable");
setTeamResponsible(Team.VARIATION);
}
/**
* Check phenotype_feature_attrib table
*
* @param dbre
* The database to check.
* @return True if the test passed
*/
public boolean run(final DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
try {
/*
* Will extract a list of phenotype_feature_attrib.values and check for oddness
*/
boolean char_ok = true;
List<String> data = getSqlTemplate(con).queryForDefaultObjectList(
"select value from phenotype_feature_attrib", String.class);
for (int i = 0; i < data.size(); i++) {
String input = data.get(i);
// skip 'not provided' as it is a ClinVar status
if( input.equalsIgnoreCase( "not provided" ) ){continue;}
// check for descriptions suggesting no data
boolean name_ok = checkNonTerms(input);
if(name_ok == false){
result = false;
ReportManager.problem(this, con, "phenotype_feature_attrib : " + input + " is not useful");
}
// check for unsupported individual characters
char_ok = checkUnsupportedChar(input);
if(char_ok == false){
result = false;
ReportManager.problem(this, con, "phenotype_feature_attrib: \""+ input +"\" has unsupported characters or starts oddly");
}
}
} catch (Exception e) {
ReportManager.problem(this, con, "HealthCheck generated an exception: " + e.getMessage());
result = false;
}
if (result) {
// if there were no problems, just inform for the interface to pick the HC
ReportManager.correct(this, con, "PhenotypeFeatureAttrib healthcheck passed without any problem");
}
return result;
}
// --------------------------------------
}