DataFiles.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 static java.lang.String.format;

import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

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.AbstractTemplatedTestCase;
import org.ensembl.healthcheck.testcase.Priority;

/**
 * Tries to avoid users specifying data files like 
 * "human_frontal_lobe_rnaseq.bam", rhe data files API automatically deals
 * with file extensions, or " human_frontal_lobe_rnaseq" (extrenous spaces)
 * 
 * @author ayates
 */
public class DataFiles extends AbstractTemplatedTestCase {

  public DataFiles() {
    setDescription("Check that the data_file tables are correctly formatted. Includes searching for bad file extensions and spaces in names");
    setPriority(Priority.AMBER);
    setTeamResponsible(Team.GENEBUILD);
  }

  /**
  * This test only applies to rnaseq databases
  */

  public void types() {
    removeAppliesToType(DatabaseType.SANGER_VEGA);
    removeAppliesToType(DatabaseType.OTHERFEATURES);
    removeAppliesToType(DatabaseType.ESTGENE);
    removeAppliesToType(DatabaseType.CORE);
    removeAppliesToType(DatabaseType.CDNA);
  }
  
  @Override
  protected boolean runTest(DatabaseRegistryEntry dbre) {
    boolean ok = runExtensionTest(dbre);
    ok &= runSpaceTest(dbre);
    return ok;
  }
  
  protected boolean testByPattern(DatabaseRegistryEntry dbre, Pattern p, StringCallback callback) {
    boolean ok = true;
    String sql = "select name from data_file";
    List<String> names = getSqlTemplate(dbre).queryForDefaultObjectList(sql, String.class);
    for(String name: names) {
      Matcher m = p.matcher(name);
      if(m.find()) {
        ok = false;
        String msg = callback.report(dbre, name, m);
        ReportManager.problem(this, dbre.getConnection(), msg);
      }
    }
    return ok;
  }

  protected boolean runExtensionTest(DatabaseRegistryEntry dbre) {
    Pattern p = Pattern.compile("\\.([A-Za-z]+)$");
    StringCallback callback = new StringCallback(){
      @Override
      public String report(DatabaseRegistryEntry dbre, String name, Matcher m) {
        return format("The data_file '%s' has a possible extension '%s'. " +
        		"Do not specify extensions in name; The DataFiles API will add " +
        		"this for you", name, m.group(1));
      }
    };
    return testByPattern(dbre, p, callback);
  }
  
  protected boolean runSpaceTest(DatabaseRegistryEntry dbre) {
    Pattern p = Pattern.compile("\\s");
    StringCallback callback = new StringCallback(){
      @Override
      public String report(DatabaseRegistryEntry dbre, String name, Matcher m) {
        return format("The data_file '%s' has a space in the name '%s'. " +
        		"Do not use spaces", name);
      }
    };
    return testByPattern(dbre, p, callback);
  }
  
  private interface StringCallback {
    String report(DatabaseRegistryEntry dbre, String name, Matcher m);
  }
}