UMLSFileReader.java

/* 
 * 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.
 *
 * Contributions from 2013-2017 where performed either by US government 
 * employees, or under US Veterans Health Administration contracts. 
 *
 * US Veterans Health Administration contributions by government employees
 * are work of the U.S. Government and are not subject to copyright
 * protection in the United States. Portions contributed by government 
 * employees are USGovWork (17USC §105). Not subject to copyright. 
 * 
 * Contribution by contractors to the US Veterans Health Administration
 * during this period are contractually contributed under the
 * Apache License, Version 2.0.
 *
 * See: https://www.usa.gov/government-works
 * 
 * Contributions prior to 2013:
 *
 * Copyright (C) International Health Terminology Standards Development Organisation.
 * Licensed under the Apache License, Version 2.0.
 *
 */



package sh.isaac.converters.sharedUtils.umlsUtils;

//~--- JDK imports ------------------------------------------------------------

import java.io.BufferedReader;
import java.io.IOException;

import java.util.ArrayList;
import java.util.List;

//~--- non-JDK imports --------------------------------------------------------

import sh.isaac.converters.sharedUtils.sql.TerminologyFileReader;

//~--- classes ----------------------------------------------------------------

/**
 * The Class UMLSFileReader.
 */
public class UMLSFileReader
         implements TerminologyFileReader {
   /** The reader. */
   private final BufferedReader reader;

   /** The next line. */
   private List<String> nextLine;

   //~--- constructors --------------------------------------------------------

   /**
    * Instantiates a new UMLS file reader.
    *
    * @param reader the reader
    */
   public UMLSFileReader(BufferedReader reader) {
      this.reader = reader;
   }

   //~--- methods -------------------------------------------------------------

   /**
    * Close.
    *
    * @throws IOException Signals that an I/O exception has occurred.
    * @see sh.isaac.converters.sharedUtils.sql.TerminologyFileReader#close()
    */
   @Override
   public void close()
            throws IOException {
      this.reader.close();
   }

   /**
    * Read next line.
    *
    * @throws IOException Signals that an I/O exception has occurred.
    */
   private void readNextLine()
            throws IOException {
      final String line = this.reader.readLine();

      if (line != null) {
         final String[] cols = line.split("\\|", -1);

         // remove the last because the files have a trailing separator, with no data after it
         this.nextLine = new ArrayList<>(cols.length - 1);

         for (final String s: cols) {
            if ((this.nextLine.size() == cols.length - 1) && ((s.length() == 0) || (s == null))) {
               break;
            }

            this.nextLine.add(s);
         }
      }
   }

   //~--- get methods ---------------------------------------------------------

   /**
    * Gets the next row.
    *
    * @return the next row
    * @throws IOException Signals that an I/O exception has occurred.
    * @see sh.isaac.converters.sharedUtils.sql.TerminologyFileReader#getNextRow()
    */
   @Override
   public List<String> getNextRow()
            throws IOException {
      if (this.nextLine == null) {
         readNextLine();
      }

      final List<String> temp = this.nextLine;

      this.nextLine = null;
      return temp;
   }

   /**
    * Checks for next row.
    *
    * @return true, if successful
    * @throws IOException Signals that an I/O exception has occurred.
    * @see sh.isaac.converters.sharedUtils.sql.TerminologyFileReader#hasNextRow()
    */
   @Override
   public boolean hasNextRow()
            throws IOException {
      if (this.nextLine == null) {
         readNextLine();
      }

      return this.nextLine != null;
   }
}