Java tutorial
/* * Copyright (C) 2015 SeqWare * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package io.seqware.pipeline.engines.whitestar; import com.google.gson.FieldNamingPolicy; import com.google.gson.Gson; import com.google.gson.GsonBuilder; import com.google.gson.reflect.TypeToken; import java.io.File; import java.io.IOException; import java.lang.reflect.Type; import java.util.SortedSet; import java.util.TreeSet; import net.sourceforge.seqware.common.metadata.Metadata; import net.sourceforge.seqware.common.metadata.MetadataFactory; import net.sourceforge.seqware.common.metadata.MetadataInMemory; import net.sourceforge.seqware.common.model.Workflow; import net.sourceforge.seqware.common.model.WorkflowParam; import net.sourceforge.seqware.common.model.WorkflowRun; import net.sourceforge.seqware.common.util.Log; import static net.sourceforge.seqware.common.util.Rethrow.rethrow; import net.sourceforge.seqware.common.util.configtools.ConfigTools; import org.apache.commons.io.FileUtils; /** * This is a KISS implementation of persistence for WhiteStar relying upon JSON text files in the working directory. * * @author dyuen */ public class Persistence { public static final String PERSISTENT_DIR = "whitestar"; public static final String WORKFLOW_RUN_FILENAME = "workflowRun.json"; public static final String WORKFLOW_FILENAME = "workflow.json"; public static final String STATE_FILENAME = "state.json"; private final File persistDir; /** * * @param nfsWorkDir */ public Persistence(File nfsWorkDir) { if (!nfsWorkDir.exists()) { throw new RuntimeException("Unable to locate working directory"); } this.persistDir = new File(nfsWorkDir, Persistence.PERSISTENT_DIR); boolean dircreated = persistDir.exists() || persistDir.mkdir(); boolean writeable = persistDir.setWritable(true, false); if (!dircreated || !writeable) { throw new RuntimeException("Unable to write to working directory"); } } public synchronized SortedSet<String> readCompletedJobs() { try { Gson gson = new GsonBuilder().setFieldNamingPolicy(FieldNamingPolicy.LOWER_CASE_WITH_UNDERSCORES) .setPrettyPrinting().create(); String statesString = FileUtils.readFileToString(new File(persistDir, STATE_FILENAME)); Type collectionType = new TypeToken<SortedSet<String>>() { }.getType(); SortedSet<String> states = gson.fromJson(statesString, collectionType); return states; } catch (IOException ex) { Log.stdoutWithTime("Unable to read workflowrun state"); rethrow(ex); } return null; } public synchronized WorkflowRun readWorkflowRun() { try { Gson gson = new GsonBuilder().setFieldNamingPolicy(FieldNamingPolicy.LOWER_CASE_WITH_UNDERSCORES) .setPrettyPrinting().create(); String workflowRunString = FileUtils.readFileToString(new File(persistDir, WORKFLOW_RUN_FILENAME)); String workflowString = FileUtils.readFileToString(new File(persistDir, WORKFLOW_FILENAME)); WorkflowRun workflowRun = gson.fromJson(workflowRunString, WorkflowRun.class); Workflow workflow = gson.fromJson(workflowString, Workflow.class); workflowRun.setWorkflow(workflow); SortedSet<WorkflowRun> runs = new TreeSet<>(); runs.add(workflowRun); workflow.setWorkflowRuns(runs); // load into persistence store if needed Metadata metadata = MetadataFactory.get(ConfigTools.getSettings()); if (metadata instanceof MetadataInMemory) { MetadataInMemory mim = (MetadataInMemory) metadata; mim.loadEntity(workflow); mim.loadEntity(workflowRun); } return workflowRun; } catch (IOException ex) { Log.stdoutWithTime("Unable to read workflowrun state"); rethrow(ex); } return null; } public synchronized void persistState(int swid, SortedSet<String> completedJobs) { try { // write state of workflow run Gson gson = new GsonBuilder().setFieldNamingPolicy(FieldNamingPolicy.LOWER_CASE_WITH_UNDERSCORES) .setPrettyPrinting().create(); Metadata ws = MetadataFactory.get(ConfigTools.getSettings()); WorkflowRun workflowRun = ws.getWorkflowRunWithWorkflow(String.valueOf(swid)); Workflow workflow = workflowRun.getWorkflow(); workflowRun.setWorkflow(null); workflow.setWorkflowRuns(null); if (workflow.getWorkflowParams() != null) { for (WorkflowParam param : workflow.getWorkflowParams()) { param.setWorkflow(null); } } // ugly, need to avoid circular reference before serialization FileUtils.write(new File(persistDir, WORKFLOW_RUN_FILENAME), gson.toJson(workflowRun)); FileUtils.write(new File(persistDir, WORKFLOW_FILENAME), gson.toJson(workflow)); FileUtils.write(new File(persistDir, STATE_FILENAME), gson.toJson(completedJobs)); workflowRun.setWorkflow(workflow); SortedSet<WorkflowRun> set = new TreeSet<>(); set.add(workflowRun); workflow.setWorkflowRuns(set); if (workflow.getWorkflowParams() != null) { for (WorkflowParam param : workflow.getWorkflowParams()) { param.setWorkflow(workflow); } } } catch (IOException ex) { Log.stdoutWithTime("Unable to write workflowrun state"); rethrow(ex); } } }