/* $RCSfile$ * $Author: egonw $ * $Date: 2007-01-04 18:46:10 +0100 (Thu, 04 Jan 2007) $ * $Revision: 7636 $ * * Copyright (C) 2001-2007 The Chemistry Development Kit (CDK) project * * Contact: cdk-devel@lists.sourceforge.net * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU Lesser General Public License * as published by the Free Software Foundation; either version 2.1 * of the License, or (at your option) any later version. * All we ask is that proper credit is given for our work, which includes * - but is not limited to - adding the above copyright notice to the beginning * of your source code files, and to any copyright notice that you may distribute * with programs based on this work. * * 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 Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. * */ package org.openscience.cdk.internet; import java.io.BufferedReader; import java.io.FileNotFoundException; import java.io.IOException; import java.io.InputStreamReader; import java.io.Reader; import java.net.MalformedURLException; import java.net.URI; import java.net.URISyntaxException; import java.net.URL; import java.net.URLConnection; import java.util.Enumeration; import java.util.Vector; import org.openscience.cdk.ChemFile; import org.openscience.cdk.ChemObject; import org.openscience.cdk.Molecule; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.exception.UnsupportedChemObjectException; import org.openscience.cdk.io.IChemObjectReader; import org.openscience.cdk.io.ReaderFactory; import org.openscience.cdk.io.formats.IChemFormat; import org.openscience.cdk.tools.DataFeatures; import org.openscience.cdk.tools.LoggingTool; import org.openscience.dadml.DATABASE; import org.openscience.dadml.DBDEF; import org.openscience.dadml.DBLIST; import org.openscience.dadml.FIELD; import org.openscience.dadml.INDEX; import org.openscience.dadml.filereaders.DBDEFFileReader; import org.openscience.dadml.filereaders.DBLISTFileReader; import org.openscience.dadml.tools.DBDEFInfo; /** * Reads a molecule from a DADML super database. * * <p>Database Access Definition Markup Language (DADML) is an XML * application that makes it possible to define how databases can be accessed * via URLs. * * @author Egon Willighagen <egonw@sci.kun.nl> * @cdk.created 2001-12-18 * * @cdk.keyword internet * @cdk.keyword database * @cdk.builddepends dadml.jar * @cdk.require dadml */ 00078 public class DADMLReader { private String superdb; private LoggingTool logger; private URI query; /** * Contructs a new DADMLReader that can read Molecule from the internet. * * @param superdb DADML super database to look up structure from */ 00090 public DADMLReader(String superdb) { logger = new LoggingTool(this); this.superdb = superdb; this.query = null; } public IChemFormat getFormat() { return new IChemFormat() { public String getFormatName() { return "DADML network"; } public String getMIMEType() { return null; }; public String getPreferredNameExtension() { return null; }; public String[] getNameExtensions() { return new String[0]; }; public String getReaderClassName() { return null; }; public String getWriterClassName() { return null; } public boolean isXMLBased() { return true; }; public int getSupportedDataFeatures() { return DataFeatures.NONE; }; public int getRequiredDataFeatures() { return DataFeatures.NONE; }; }; } public void setReader(Reader input) throws CDKException { throw new CDKException("This Reader does not read from a Reader but from internet nodes"); } /** * Sets the query. * * @param indexType Index type (e.g. CAS-NUMBER) * @param value Index of molecule to download (e.g. 50-00-0) */ 00122 public void setQuery(String indexType, String value) { try { this.query = new URI("dadml://any/" + indexType + "?" + value); } catch (URISyntaxException exception) { logger.error("Serious error: ", exception.getMessage()); logger.debug(exception); } } /** * Sets the query in the form of an URI. * An example URI is: <code>dadml://any/CAS-NUMBER?50-00-0</code>. * * @param query URI query. */ 00137 public void setQuery(URI query) throws URISyntaxException { this.query = query; } /** * Takes an object which subclasses IChemObject, e.g.Molecule, and will read this * (from file, database, internet etc). If the specific implementation does not * support a specific IChemObject it will throw an Exception. * * @param object The object that subclasses IChemObject * @return The IChemObject read * @exception UnsupportedChemObjectException */ 00150 public ChemObject read(ChemObject object) throws UnsupportedChemObjectException { if (object instanceof Molecule) { return (ChemObject)readMolecule(); } else { throw new UnsupportedChemObjectException("Only supported is Molecule."); } } /** * Read a Molecule from a DADML super database. * * @return The Molecule that was read */ 00163 private org.openscience.cdk.interfaces.IMolecule readMolecule() { org.openscience.cdk.interfaces.IMolecule molecule = null; try { URL resource = this.resolveLink(query); // this has to be reformulated molecule = this.downloadURL(resource); } catch (Exception exception) { logger.error("File Not Found: ", exception.getMessage()); logger.debug(exception); } return molecule; } /** * Resolved the given DADML URI into a URL from which content can possibly be * downloaded. * * @param dadmlRI The DADML URI to be resolved. */ 00182 public URL resolveLink(URI dadmlRI) { Vector links = resolveLinks(dadmlRI); if (links.size() > 0) { return ((DADMLResult)links.elementAt(0)).getURL(); } // else return null; } /** * Resolved the given DADML URI into a list of URLs from which content can possibly be * downloaded. The URL classes returned are of type <code>DADMLResult</code>. * * @param dadmlRI The DADML URI to be resolved. * * @see org.openscience.cdk.internet.DADMLResult */ 00198 public Vector resolveLinks(URI dadmlRI) { logger.debug("Resolving URI: ", dadmlRI); Vector links = new Vector(); boolean found = false; // this is true when a structure is downloaded boolean done = false; // this is true when all URLS have been tested String indexType = dadmlRI.getPath().substring(1); String index = dadmlRI.getQuery(); DBLIST dblist = new DBLIST(); try { logger.info("Downloading DADML super database: ", this.superdb); // Proxy authorization has to be ported from Chemistry Development Kit (CDK) // for now, do without authorization DBLISTFileReader reader = new DBLISTFileReader(); dblist = reader.read(this.superdb); } catch (Exception supererror) { logger.error("Exception while reading super db: ", supererror.getMessage()); logger.debug(supererror); } Enumeration dbases = dblist.databases(); while (!found && !done && dbases.hasMoreElements()) { DATABASE database = (DATABASE)dbases.nextElement(); String dburl = database.getURL() + database.getDefinition(); DBDEF dbdef = new DBDEF(); // Proxy authorization has to be ported from Chemistry Development Kit (CDK) // for now, do without authorization try { logger.info("Downloading: ", dburl); // do without authorization DBDEFFileReader reader = new DBDEFFileReader(); dbdef = reader.read(dburl); } catch (Exception deferror) { System.err.println(deferror.toString()); } if (DBDEFInfo.hasINDEX(dbdef, indexType)) { // oke, find a nice URL to use for download logger.debug("Trying: ", dbdef.getTITLE()); Enumeration fields = dbdef.fields(); while (fields.hasMoreElements()) { FIELD field = (FIELD)fields.nextElement(); String mime = field.getMIMETYPE(); String ftype = field.getTYPE(); if ((mime.equals("chemical/x-mdl-mol") || mime.equals("chemical/x-pdb") || mime.equals("chemical/x-cml")) && (ftype.equals("3DSTRUCTURE") || ftype.equals("2DSTRUCTURE"))) { logger.info("Accepted: ", field.getMIMETYPE(), ",", field.getTYPE()); Enumeration indices = field.getINDEX(); while (indices.hasMoreElements()) { INDEX ind = (INDEX)indices.nextElement(); if (ind.getTYPE().equals(indexType)) { // here is the URL composed String url = dbdef.getURL() + ind.getACCESS_PREFIX() + index + ind.getACCESS_SUFFIX(); logger.debug("Adding to resolved links: ", url); try { links.add(new DADMLResult(new URL(url), field)); } catch (MalformedURLException exception) { logger.error("Malformed URL: ", exception.getMessage()); logger.debug(exception); } } } } else { // reject other mime types && type structures logger.info("Rejected: ", field.getMIMETYPE(), ",", field.getTYPE()); } } } else { logger.warn("Database does not have indexType: ", indexType); } } return links; } private org.openscience.cdk.interfaces.IMolecule downloadURL(URL resource) { org.openscience.cdk.interfaces.IMolecule molecule = new Molecule(); logger.debug("Downloading from URL: ", resource); try { URLConnection connection = resource.openConnection(); BufferedReader bufReader = new BufferedReader( new InputStreamReader(connection.getInputStream()) ); IChemObjectReader reader = new ReaderFactory().createReader(bufReader); ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile()); logger.debug("#sequences: ", chemFile.getChemSequenceCount()); org.openscience.cdk.interfaces.IChemSequence chemSequence = chemFile.getChemSequence(0); logger.debug("#models in sequence: ", chemSequence.getChemModelCount()); org.openscience.cdk.interfaces.IChemModel chemModel = chemSequence.getChemModel(0); org.openscience.cdk.interfaces.IMoleculeSet moleculeSet = chemModel.getMoleculeSet(); logger.debug("#mols in model: ", moleculeSet.getMoleculeCount()); molecule = moleculeSet.getMolecule(0); } catch (UnsupportedChemObjectException exception) { logger.error("Unsupported IChemObject type: ", exception.getMessage()); logger.debug(exception); } catch (FileNotFoundException exception) { logger.error("File not found: ", exception.getMessage()); logger.debug(exception); } catch (Exception exception) { logger.error(exception.getMessage()); logger.debug(exception); } return molecule; } public void close() throws IOException { } }