Java tutorial
/* Copyright 2010 Massachusetts General Hospital 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.sc.probro.servlets; import java.io.BufferedReader; import java.io.File; import java.io.IOException; import java.io.InputStream; import java.io.InputStreamReader; import java.io.PrintWriter; import java.io.StringReader; import java.util.Collection; import java.util.LinkedList; import java.util.List; import java.util.Map; import java.util.Set; import java.util.TreeSet; import java.util.regex.*; import javax.servlet.ServletContext; import javax.servlet.ServletException; import javax.servlet.http.HttpServletRequest; import javax.servlet.http.HttpServletResponse; import org.apache.commons.fileupload.FileItem; import org.apache.commons.fileupload.FileUploadException; import org.apache.commons.fileupload.disk.DiskFileItemFactory; import org.apache.commons.fileupload.servlet.FileCleanerCleanup; import org.apache.commons.fileupload.servlet.ServletFileUpload; import org.apache.commons.io.FileCleaningTracker; import org.eclipse.jetty.util.log.Log; import org.sc.obo.*; import org.sc.probro.Broker; import org.sc.probro.BrokerProperties; import org.sc.probro.Ontology; import org.sc.probro.UserCredentials; import org.sc.probro.data.BrokerModel; import org.sc.probro.data.DBModelException; import org.sc.probro.exceptions.BadRequestException; import org.sc.probro.exceptions.BrokerException; import org.sc.probro.lucene.IndexCreator; import org.sc.probro.sparql.BindingTable; import org.sc.probro.sparql.OBOBuilder; import org.sc.probro.sparql.OBOSparql; import org.sc.probro.sparql.Prefixes; import com.hp.hpl.jena.rdf.model.Literal; import com.hp.hpl.jena.rdf.model.RDFNode; public class IndexCreatorServlet extends BrokerServlet { private OBOSparql oboSparql; public IndexCreatorServlet(BrokerProperties ps) { super(ps); oboSparql = new OBOSparql(ps); } public void init() throws ServletException { super.init(); } public void destroy() { super.destroy(); } public static final int MB = 1024 * 1024; protected void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { try { OBOBuilder builder = new OBOBuilder(oboSparql); String oboName = getRequiredParam(request, "obo", String.class); try { String oboText = builder.loadOBO(oboName); response.setStatus(HttpServletResponse.SC_OK); response.setContentType("text"); PrintWriter writer = response.getWriter(); writer.println(oboText); } catch (IOException e) { throw new BrokerException(e); } } catch (BrokerException e) { handleException(response, e); return; } } public static DiskFileItemFactory newDiskFileItemFactory(ServletContext context, File repository) { FileCleaningTracker fileCleaningTracker = FileCleanerCleanup.getFileCleaningTracker(context); DiskFileItemFactory factory = new DiskFileItemFactory(10 * MB, repository); factory.setFileCleaningTracker(fileCleaningTracker); return factory; } protected void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { try { OBOParser parser = null; Map<String, String[]> params = decodedParams(request); UserCredentials creds = new UserCredentials(); String ontologyName = null; boolean isMultipart = ServletFileUpload.isMultipartContent(request); if (!isMultipart) { throw new BrokerException(HttpServletResponse.SC_BAD_REQUEST, "No multipart form data."); } try { File repository = new File(System.getProperty("java.io.tmpdir")); // Create a factory for disk-based file items //DiskFileItemFactory factory = new DiskFileItemFactory(); DiskFileItemFactory factory = newDiskFileItemFactory(getServletContext(), repository); // Set factory constraints factory.setSizeThreshold(10 * MB); //factory.setRepository(yourTempDirectory); // Create a new file upload handler ServletFileUpload upload = new ServletFileUpload(factory); upload.setSizeMax(50 * MB); // Parse the request List<FileItem> items = upload.parseRequest(request); for (FileItem item : items) { if (item.isFormField()) { String formName = item.getFieldName(); String formValue = item.getString(); Log.info(String.format("%s=%s", formName, formValue)); if (formName.equals("ontology_name")) { ontologyName = formValue; } } else { String formName = item.getFieldName(); String fileName = item.getName(); String contentType = item.getContentType(); boolean isInMemory = item.isInMemory(); long sizeInBytes = item.getSize(); if (formName.equals("ontology_file")) { Log.info(String.format("fileName=%s, contentType=%s, size=%d", fileName, contentType, sizeInBytes)); if (fileName.length() > 0) { InputStream uploadedStream = item.getInputStream(); BufferedReader reader = new BufferedReader(new InputStreamReader(uploadedStream)); parser = new OBOParser(); parser.parse(reader); reader.close(); } } else { Log.warn(String.format("unknown file: %s", formName)); } } } } catch (IOException e) { throw new BrokerException(HttpServletResponse.SC_BAD_REQUEST, e.getMessage()); } catch (FileUploadException e) { throw new BrokerException(e); } if (ontologyName == null) { throw new BadRequestException("No ontology_name field given."); } OBOOntology ontology = null; try { if (parser != null) { Log.info(String.format("Retrieving OBO ontology from file.")); // file was uploaded ontology = parser.getOntology(); } else { // try to get it from teh sparql endpoint Log.info(String.format("No OBO file uploaded, reading from Sparql endpoint instead.")); OBOBuilder builder = new OBOBuilder(oboSparql); ontology = builder.buildOntology(ontologyName); } } catch (IOException e) { throw new BrokerException(e); } Broker broker = getBroker(); try { Ontology ont = broker.createOntology(creds, ontologyName, ontology); response.setStatus(HttpServletResponse.SC_OK); response.setContentType("text"); response.getWriter().print(ont.id); } finally { broker.close(); } } catch (BrokerException e) { handleException(response, e); return; } } }