ProductionAnalysisLogicName.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 java.util.Collection;
import java.util.HashSet;
import java.util.List;
import java.util.Set;

import org.ensembl.healthcheck.DatabaseRegistryEntry;
import org.ensembl.healthcheck.DatabaseType;
import org.ensembl.healthcheck.ReportManager;
import org.ensembl.healthcheck.Team;
import org.ensembl.healthcheck.Species;
import org.ensembl.healthcheck.testcase.AbstractTemplatedTestCase;
import org.ensembl.healthcheck.testcase.Priority;
import org.ensembl.healthcheck.util.DBUtils;
import org.ensembl.healthcheck.util.SqlTemplate;

public class ProductionAnalysisLogicName extends AbstractTemplatedTestCase {
  
  public ProductionAnalysisLogicName() {
    addToGroup("production");
    addToGroup("pre-compara-handover");
    addToGroup("post-compara-handover");
    addToGroup("post-projection");
    
    setDescription("Check that the content of the analysis logic names in the core databases are subsets of production");
    setPriority(Priority.AMBER);
    setEffect("Discrepancies between tables can cause problems");
    setFix("Resync tables");
    setTeamResponsible(Team.GENEBUILD);
    setSecondTeamResponsible(Team.RELEASE_COORDINATOR);
  }

  public void types() {
    removeAppliesToType(DatabaseType.SANGER_VEGA);
    removeAppliesToType(DatabaseType.VEGA);
  }
  
  @Override
  protected boolean runTest(DatabaseRegistryEntry dbre) {
    boolean result = true;
    Species dbSpecies = dbre.getSpecies();
    String species = dbSpecies.toString();
    if (species == null || species.equalsIgnoreCase("unknown")) {
      species = dbre.getAlias();
    }    
    String databaseType = dbre.getType().getName();
    Set<String> coreLogicNames = getLogicNamesDb(dbre);
    Set<String> productionLogicNames = getLogicNamesFromProduction(dbre, species, databaseType);
    Set<String> coreDbVersion = getDbVersionCore(dbre);
    Set<String> productionDbVersion = getDbVersionProduction(dbre, coreLogicNames);
    result &= checkHasDbVersion(dbre, productionDbVersion, coreDbVersion, databaseType);
    result &= checkHasDbVersion(dbre, coreDbVersion, productionDbVersion, "production");
    if(!dbre.isMultiSpecies()) {
    	// checks are inappropriate for a multispecies database where individual mappings
    	// are not stored in the production database
    	result &= testForIdentity(dbre, coreLogicNames, productionLogicNames, "production");
    	result &= testForIdentity(dbre, productionLogicNames, coreLogicNames, databaseType);
    }
    return result;
  }
  
  /**
   * Minuses the elements in the second collection from the first. Anything
   * remaining in the first collection cannot exist in the second set 
   */
  private <T extends CharSequence> boolean testForIdentity(DatabaseRegistryEntry dbre, Collection<T> core, Collection<T> toRemove, String type) {
    Set<T> missing = new HashSet<T>(core);
    missing.removeAll(toRemove);
    if(missing.isEmpty()) {
      return true;
    }
    for(CharSequence name: missing) {
      String msg = String.format("The logic name '%s' is missing from %s", name, type);
      ReportManager.problem(this, dbre.getConnection(), msg);
    }
    return false;
  }

  private <T extends CharSequence> boolean checkHasDbVersion(DatabaseRegistryEntry dbre, Collection<T> core, Collection<T> production, String type) {
    Set<T> missing = new HashSet<T>(core);
    missing.removeAll(production);
    if(missing.isEmpty()) {
      return true;
    }
    for(CharSequence name: missing) {
      String msg = String.format("Analysis '%s' in %s db should have a dbversion", name, type);
      ReportManager.problem(this, dbre.getConnection(), msg);
    }
    return false;
  }
  
  private Set<String> getLogicNamesDb(DatabaseRegistryEntry dbre) {
    SqlTemplate t = DBUtils.getSqlTemplate(dbre);
    String sql = "select logic_name from analysis join analysis_description using (analysis_id)";
    List<String> results = t.queryForDefaultObjectList(sql, String.class);
    return new HashSet<String>(results);
  }
  
  private Set<String> getLogicNamesFromProduction(DatabaseRegistryEntry dbre, String species, String databaseType) {
    SqlTemplate t = DBUtils.getSqlTemplate(getProductionDatabase());
    String sql = "select logic_name from analysis_description ad, species s, analysis_web_data aw where ad.analysis_description_id = aw.analysis_description_id and aw.species_id = s.species_id and s.db_name = '" + species + "' and aw.db_type = '" + databaseType + "' and s.is_current = 1 and ad.is_current = 1";
    List<String> results = t.queryForDefaultObjectList(sql, String.class);
    return new HashSet<String>(results);
  }

  private Set<String> getDbVersionCore(DatabaseRegistryEntry dbre) {
    SqlTemplate t = DBUtils.getSqlTemplate(dbre);
    String sql = "SELECT logic_name FROM analysis where !isnull(db_version)";
    List<String> results = t.queryForDefaultObjectList(sql, String.class);
    return new HashSet<String>(results);
  }

  private Set<String> getDbVersionProduction(DatabaseRegistryEntry dbre, Set<String> analysisList) {
    SqlTemplate t = DBUtils.getSqlTemplate(getProductionDatabase());
    Set<String> results = new HashSet<String>();
    for (String analysis : analysisList) {
      String sql = "SELECT logic_name FROM analysis_description where logic_name = '" + analysis + "' and db_version = 1";
      results.addAll(t.queryForDefaultObjectList(sql, String.class));
    }
    return results;
  }

}