Java tutorial
/* * Copyright 2015-2016 OpenCB * * 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.opencb.opencga.analysis.execution.plugins; import com.fasterxml.jackson.core.JsonFactory; import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.dataformat.xml.XmlFactory; import com.fasterxml.jackson.dataformat.yaml.YAMLFactory; import org.apache.commons.lang3.StringUtils; import org.opencb.commons.datastore.core.ObjectMap; import org.opencb.opencga.catalog.models.tool.Execution; import org.opencb.opencga.catalog.models.tool.InputParam; import org.opencb.opencga.storage.core.manager.variant.VariantStorageManager; import org.opencb.opencga.storage.core.manager.variant.operations.StorageOperation; import org.opencb.opencga.catalog.models.tool.Manifest; import org.opencb.opencga.catalog.managers.CatalogManager; import org.opencb.opencga.catalog.exceptions.CatalogException; import org.opencb.opencga.catalog.models.DataStore; import org.opencb.opencga.catalog.models.File; import org.opencb.opencga.storage.core.StorageEngineFactory; import org.opencb.opencga.storage.core.alignment.AlignmentDBAdaptor; import org.opencb.opencga.storage.core.exceptions.StorageEngineException; import org.opencb.opencga.storage.core.variant.adaptors.VariantDBAdaptor; import org.slf4j.Logger; import java.io.IOException; import java.io.InputStream; import java.nio.file.Path; import java.nio.file.Paths; import java.util.LinkedHashMap; import java.util.Map; /** * Created on 26/11/15. * * TODO: Move non abstract methods to a Context class * * @author Jacobo Coll <jacobo167@gmail.com> */ public abstract class OpenCGAAnalysis { private Logger logger; private ObjectMap params; private CatalogManager catalogManager; private String sessionId; private boolean initialized; private StorageEngineFactory storageEngineFactory; private long studyId; private String execution; private VariantStorageManager variantStorageManager; public Manifest getManifest() { try { return loadManifest(getIdentifier()); } catch (IOException ignore) { logger.error("Unable to load manifest"); return null; } } public static Manifest loadManifest(String identifier) throws IOException { final String file; JsonFactory factory; if (OpenCGAAnalysis.class.getResource("/" + identifier + "/manifest.yml") != null) { file = "/" + identifier + "/manifest.yml"; factory = new YAMLFactory(); } else if (OpenCGAAnalysis.class.getResource("/" + identifier + "/manifest.json") != null) { file = "/" + identifier + "/manifest.json"; factory = new JsonFactory(); } else if (OpenCGAAnalysis.class.getResource("/" + identifier + "/manifest.xml") != null) { file = "/" + identifier + "/manifest.xml"; factory = new XmlFactory(); } else { return null; } try (InputStream stream = OpenCGAAnalysis.class.getResourceAsStream(file)) { return new ObjectMapper(factory).readValue(stream, Manifest.class); } } /** * Get analysis identifier. * * @return Analysis identifier */ public abstract String getIdentifier(); public int run() throws Exception { Execution execution = getManifest().getExecutions().get(0); for (Execution e : getManifest().getExecutions()) { if (e.getId().equals(this.execution)) { execution = e; break; } } Map<String, Path> inputParams = new LinkedHashMap<>(); Path outdir = Paths.get(params.getString(execution.getOutputParam())); for (InputParam inputParam : execution.getInputParams()) { String inputParamValue = params.getString(inputParam.getName()); if (StringUtils.isNotEmpty(inputParamValue)) { inputParams.put(inputParam.getName(), Paths.get(inputParamValue)); } } return run(inputParams, outdir, params); } public abstract int run(Map<String, Path> input, Path outdir, ObjectMap params) throws Exception; /* * Util methods */ final void init(Logger logger, ObjectMap configuration, CatalogManager catalogManager, StorageEngineFactory storageEngineFactory, long studyId, String execution, String sessionId) { if (initialized) { throw new IllegalStateException("The plugin was already initialized! Can't init twice"); } this.logger = logger; this.params = configuration; this.catalogManager = catalogManager; this.storageEngineFactory = storageEngineFactory; this.variantStorageManager = new VariantStorageManager(catalogManager, this.storageEngineFactory); this.studyId = studyId; this.execution = execution; this.sessionId = sessionId; initialized = true; } protected final Logger getLogger() { return logger; } protected final ObjectMap getParams() { return params; } protected final CatalogManager getCatalogManager() { return catalogManager; } protected final String getSessionId() { return sessionId; } protected final VariantStorageManager getVariantStorageManager() { return variantStorageManager; } //TODO: Return a VariantDBAdaptor which checks catalog permissions @Deprecated protected final VariantDBAdaptor getVariantDBAdaptor(long studyId) throws CatalogException, IllegalAccessException, InstantiationException, ClassNotFoundException, StorageEngineException { StorageEngineFactory storageEngineFactory = this.storageEngineFactory; DataStore dataStore = StorageOperation.getDataStore(catalogManager, studyId, File.Bioformat.VARIANT, sessionId); String storageEngine = dataStore.getStorageEngine(); String dbName = dataStore.getDbName(); return storageEngineFactory.getVariantStorageEngine(storageEngine).getDBAdaptor(dbName); } //TODO: Return an AlignmentDBAdaptor which checks catalog permissions protected final AlignmentDBAdaptor getAlignmentDBAdaptor(long studyId) { throw new UnsupportedOperationException(); } protected final long getStudyId() { return studyId; } public String getExecution() { return execution; } }