001 /** 002 * Copyright (C) 2010 The Roslin Institute <contact andy.law@roslin.ed.ac.uk> 003 * 004 * This file is part of the Ensembl Java API demonstration project developed by the 005 * Bioinformatics Group at The Roslin Institute, The Royal (Dick) School of 006 * Veterinary Studies, University of Edinburgh. 007 * 008 * This is free software: you can redistribute it and/or modify 009 * it under the terms of the GNU General Public License (version 3) as published by 010 * the Free Software Foundation. 011 * 012 * This software is distributed in the hope that it will be useful, 013 * but WITHOUT ANY WARRANTY; without even the implied warranty of 014 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 015 * GNU General Public License for more details. 016 * 017 * You should have received a copy of the GNU General Public License 018 * in this software distribution. If not, see <http://www.gnu.org/licenses/gpl-3.0.html/>. 019 */ 020 021 package uk.ac.roslin.ensembl.model.database; 022 023 import uk.ac.roslin.ensembl.model.core.CollectionOfSpecies; 024 import uk.ac.roslin.ensembl.model.core.CollectionSpecies; 025 import java.util.Collection; 026 import java.util.HashMap; 027 import java.util.List; 028 import java.util.Properties; 029 import java.util.TreeSet; 030 031 import uk.ac.roslin.ensembl.config.DBConnection.DataSource; 032 import uk.ac.roslin.ensembl.config.EnsemblComparaDivision; 033 import uk.ac.roslin.ensembl.exception.ConfigurationException; 034 import uk.ac.roslin.ensembl.exception.DAOException; 035 import uk.ac.roslin.ensembl.model.core.Species; 036 037 public interface Registry { 038 039 public Properties getConfigProperties(); 040 041 public DataSource getDatasourceType() ; 042 043 public String findMybatisSchemaForSchemaVersion(DatabaseType type, String schema_version); 044 045 public String getMostRecentEnsemblVersion() ; 046 047 //public DatabaseDAO getDatabaseDAO(); 048 049 public Database makeDatabase(String db_name) throws ConfigurationException; 050 051 public ComparisonDatabase getComparaDatabase(EnsemblComparaDivision comparaDivision, String db_version); 052 053 public Database getDatabase(String species_name_or_alias) ; 054 055 public Database getDatabase(String species_name_or_alias, String db_version) ; 056 057 public Database getDatabase(String species_name_or_alias, DatabaseType database_type, String db_version) ; 058 059 public Database getDatabaseForFullName(String fullname) ; 060 061 public TreeSet<? extends Database> getDatabasesByType(DatabaseType type) ; 062 063 064 public Species getSpeciesByAlias(String alias_or_name) ; 065 066 public Species getSpeciesByEnsemblName(String ensemblName) ; 067 068 public Collection<? extends Species> getSpecies(); 069 070 public Collection<? extends CollectionSpecies> getCollectionSpecies(); 071 072 public void addSpecies(String dbStyleName, Species species ) ; 073 074 public CollectionOfSpecies getCollection(String name, String dbVersion); 075 076 public Collection<? extends CollectionOfSpecies> getCollectionRegistriesByName(String name) ; 077 078 public Collection<? extends CollectionOfSpecies> getCollectionsByDBVersion(String dbVersion) ; 079 080 public List<? extends CollectionOfSpecies> getCollections() ; 081 082 public int getHighestEnsemblSchemaVersion() ; 083 084 public int getHighestDBVersion() ; 085 086 public String getMostRecentDBVersion(); 087 088 //handling aliases 089 090 public String getEnsemblNameForAlias(String alias); 091 092 public boolean addSessionAlias(String ensembl_genus_species_name, String alias) throws Exception; 093 094 //Reporting 095 096 public StringBuffer printRegistryReport(); 097 098 public String getAssembly(SingleSpeciesDatabase database) throws DAOException ; 099 100 public HashMap<CollectionSpecies,String> getAssemblies(CollectionDatabase database) throws DAOException ; 101 102 public void setCoreDBBuildLevels(SingleSpeciesCoreDatabase database) throws DAOException ; 103 104 105 }