biojava · josemduarte · Mar 8, 2019 · Feb 18, 2019 · Feb 19, 2019 · Feb 19, 2019
diff --git a/.gitattributes b/.gitattributes
@@ -37,7 +37,7 @@
 *.sto   text
 *.tsv   text
 *.txt   text
-*.xml   text
+*.xml   text eol=lf #Causing decompression test to fail when line endings in org/biojava/nbio/core/util/build.xml are crlf
 *.xsd   text
 *.yml   text
 

diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java
@@ -26,15 +26,8 @@
 package org.biojava.nbio.core.sequence.io;
 
 import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
-import org.biojava.nbio.core.sequence.DNASequence;
 import org.biojava.nbio.core.sequence.DataSource;
-import org.biojava.nbio.core.sequence.ProteinSequence;
 import org.biojava.nbio.core.sequence.TaxonomyID;
-import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
-import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
-import org.biojava.nbio.core.sequence.compound.DNACompoundSet;
-import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
-import org.biojava.nbio.core.sequence.features.AbstractFeature;
 import org.biojava.nbio.core.sequence.features.DBReferenceInfo;
 import org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface;
 import org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface;
@@ -43,13 +36,20 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.*;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
+import java.util.List;
 
 /**
- * Use GenbankReaderHelper as an example of how to use this class where GenbankReaderHelper should be the
+ * Use {@link GenbankReaderHelper} as an example of how to use this class where {@link GenbankReaderHelper} should be the
  * primary class used to read Genbank files
  *
  */
@@ -66,9 +66,9 @@ public boolean isClosed() {
 	}
 
 	/**
-	 * If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about
-	 * local file offsets for quick reads. InputStreams does not give you the name of the stream to access quickly via file seek. A seek in
-	 * an inputstream is forced to read all the data so you don't gain anything.
+	 * If you are going to use {@link FileProxyProteinSequenceCreator} then do not use this constructor because we need details about
+	 * local file offsets for quick reads. {@link InputStream} does not give you the name of the stream to access quickly via file seek. A seek in
+	 * an {@link InputStream} is forced to read all the data so you don't gain anything.
 	 * @param is
 	 * @param headerParser
 	 * @param sequenceCreator
@@ -107,18 +107,21 @@ public GenbankReader(
 
 	/**
 	 * The parsing is done in this method.<br>
-	 * This method tries to process all the available Genbank records
+	 * This method will return all the available Genbank records
 	 * in the File or InputStream, closes the underlying resource,
 	 * and return the results in {@link LinkedHashMap}.<br>
-	 * You don't need to call {@link #close()} after calling this method.
+	 * You don't need to call {@link GenbankReader#close()} after calling this method.
 	 * @see #process(int)
 	 * @return {@link HashMap} containing all the parsed Genbank records
 	 * present, starting current fileIndex onwards.
 	 * @throws IOException
 	 * @throws CompoundNotFoundException
+	 * @throws OutOfMemoryError if the input resource is larger than the allocated heap.
 	 */
 	public LinkedHashMap<String,S> process() throws IOException, CompoundNotFoundException {
-		return process(-1);
+		LinkedHashMap<String,S> result = process(-1);
+		close();
+		return result;
 	}
 
 	/**
@@ -137,13 +140,18 @@ public LinkedHashMap<String,S> process() throws IOException, CompoundNotFoundExc
 	 * @see #process()
 	 * @author Amr AL-Hossary
 	 * @since 3.0.6
-	 * @param max maximum number of records to return, <code>-1</code> for infinity.
+	 * @param max maximum number of records to return.
 	 * @return {@link HashMap} containing maximum <code>max</code> parsed Genbank records
 	 * present, starting current fileIndex onwards.
 	 * @throws IOException
 	 * @throws CompoundNotFoundException
 	 */
 	public LinkedHashMap<String,S> process(final int max) throws IOException, CompoundNotFoundException {
+
+		if(closed){
+			throw new IOException("Cannot perform action: resource has been closed.");
+		}
+
 		LinkedHashMap<String,S> sequences = new LinkedHashMap<>();
 		@SuppressWarnings("unchecked")
 		int i=0;
@@ -158,12 +166,9 @@ public LinkedHashMap<String,S> process(final int max) throws IOException, Compou
 			genbankParser.getSequenceHeaderParser().parseHeader(genbankParser.getHeader(), sequence);
 
 			// add features to new sequence
-			for (String k: genbankParser.getFeatures().keySet()){
-				for (AbstractFeature f: genbankParser.getFeatures(k)){
-					//f.getLocations().setSequence(sequence);  // can't set proper sequence source to features. It is actually needed? Don't think so...
-					sequence.addFeature(f);
-				}
-			}
+			genbankParser.getFeatures().values().stream()
+			.flatMap(List::stream)
+			.forEach(sequence::addFeature);
 
 			// add taxonomy ID to new sequence
 			ArrayList<DBReferenceInfo> dbQualifier = genbankParser.getDatabaseReferences().get("db_xref");
@@ -175,10 +180,6 @@ public LinkedHashMap<String,S> process(final int max) throws IOException, Compou
 			sequences.put(sequence.getAccession().getID(), sequence);
 		}
 
-		if (max < 0) {
-			close();
-		}
-
 		return sequences;
 	}
 
@@ -187,33 +188,9 @@ public void close() {
 			bufferedReader.close();
 			this.closed = true;
 		} catch (IOException e) {
-			logger.error("Couldn't close the reader. {}", e.getMessage());
+			logger.error("Couldn't close the reader.", e);
 			this.closed = false;
 		}
 	}
-
-	public static void main(String[] args) throws Exception {
-		String proteinFile = "src/test/resources/BondFeature.gb";
-		FileInputStream is = new FileInputStream(proteinFile);
-
-		GenbankReader<ProteinSequence, AminoAcidCompound> proteinReader = new GenbankReader<>(is, new GenericGenbankHeaderParser<>(), new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
-		LinkedHashMap<String,ProteinSequence> proteinSequences = proteinReader.process();
-		System.out.println(proteinSequences);
-
-		String inputFile = "src/test/resources/NM_000266.gb";
-		is = new FileInputStream(inputFile);
-		GenbankReader<DNASequence, NucleotideCompound> dnaReader = new GenbankReader<>(is, new GenericGenbankHeaderParser<>(), new DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
-		LinkedHashMap<String,DNASequence> dnaSequences = dnaReader.process();
-		System.out.println(dnaSequences);
-
-		String crazyFile = "src/test/resources/CraftedFeature.gb";
-		is = new FileInputStream(crazyFile);
-		GenbankReader<DNASequence, NucleotideCompound> crazyReader = new GenbankReader<>(is, new GenericGenbankHeaderParser<>(), new DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
-		LinkedHashMap<String,DNASequence> crazyAnnotatedSequences = crazyReader.process();
-
-		is.close();
-		System.out.println(crazyAnnotatedSequences);
-	}
-
 }
 
diff --git a/...-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java b/...-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
@@ -32,7 +32,11 @@
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
 import org.biojava.nbio.core.sequence.compound.DNACompoundSet;
 import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
-import org.biojava.nbio.core.sequence.features.*;
+import org.biojava.nbio.core.sequence.features.AbstractFeature;
+import org.biojava.nbio.core.sequence.features.DBReferenceInfo;
+import org.biojava.nbio.core.sequence.features.DatabaseReferenceInterface;
+import org.biojava.nbio.core.sequence.features.FeatureRetriever;
+import org.biojava.nbio.core.sequence.features.FeaturesKeyWordInterface;
 import org.biojava.nbio.core.sequence.io.GenbankSequenceParser;
 import org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser;
 import org.biojava.nbio.core.sequence.template.AbstractSequence;
@@ -41,7 +45,14 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.*;
+import java.io.BufferedInputStream;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
 import java.net.URL;
 import java.net.URLConnection;
 import java.util.ArrayList;
@@ -54,7 +65,7 @@
  */
 public class GenbankProxySequenceReader<C extends Compound> extends StringProxySequenceReader<C> implements FeaturesKeyWordInterface, DatabaseReferenceInterface, FeatureRetriever {
 
-	private final static Logger logger = LoggerFactory.getLogger(GenbankProxySequenceReader.class);
+	private static final Logger logger = LoggerFactory.getLogger(GenbankProxySequenceReader.class);
 
 	private static final String eutilBaseURL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"; //
 	private String genbankDirectoryCache = null;

diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java
@@ -20,13 +20,6 @@
  */
 package org.biojava.nbio.core.sequence.io;
 
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.ArrayList;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-
 import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
 import org.biojava.nbio.core.sequence.DNASequence;
 import org.biojava.nbio.core.sequence.ProteinSequence;
@@ -46,8 +39,20 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.BufferedInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
 import static org.hamcrest.CoreMatchers.is;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.assertTrue;
 
 /**
  *
@@ -161,7 +166,7 @@ public void testProcess() throws Exception {
 	 */
 	@Test
 	public void testPartialProcess() throws IOException, CompoundNotFoundException, NoSuchFieldException {
-		InputStream inStream = this.getClass().getResourceAsStream("/two-dnaseqs.gb");
+		CheckableInputStream inStream = new CheckableInputStream(this.getClass().getResourceAsStream("/two-dnaseqs.gb"));
 
 		GenbankReader<DNASequence, NucleotideCompound> genbankDNA
 				= new GenbankReader<>(
@@ -173,27 +178,29 @@ public void testPartialProcess() throws IOException, CompoundNotFoundException,
 		// First call to process(1) returns the first sequence
 		LinkedHashMap<String, DNASequence> dnaSequences = genbankDNA.process(1);
 
+		assertFalse(inStream.isclosed());
 		assertNotNull(dnaSequences);
 		assertEquals(1, dnaSequences.size());
 		assertNotNull(dnaSequences.get("vPetite"));
 
 		// Second call to process(1) returns the second sequence
 		dnaSequences = genbankDNA.process(1);
+		assertFalse(inStream.isclosed());
 		assertNotNull(dnaSequences);
 		assertEquals(1, dnaSequences.size());
 		assertNotNull(dnaSequences.get("sbFDR"));
 
 		assertFalse(genbankDNA.isClosed());
 		genbankDNA.close();
 		assertTrue(genbankDNA.isClosed());
-
+		assertTrue(inStream.isclosed());
 	}
 
 	@Test
 	public void CDStest() throws Exception {
 		logger.info("CDS Test");
 
-		InputStream inStream = this.getClass().getResourceAsStream("/BondFeature.gb");
+		CheckableInputStream inStream = new CheckableInputStream(this.getClass().getResourceAsStream("/BondFeature.gb"));
 		assertNotNull(inStream);
 
 		GenbankReader<ProteinSequence, AminoAcidCompound> GenbankProtein
@@ -203,7 +210,7 @@ public void CDStest() throws Exception {
 						new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet())
 				);
 		LinkedHashMap<String, ProteinSequence> proteinSequences = GenbankProtein.process();
-		inStream.close();
+		assertTrue(inStream.isclosed());
 
 
 		Assert.assertTrue(proteinSequences.size() == 1);
@@ -260,4 +267,27 @@ public void testNcbiExpandedAccessionFormats() throws Exception {
 		DNASequence header2 = readGenbankResource("/empty_header2.gb");
 		assertEquals("AZZZAA02123456789 10000000000 bp    DNA     linear   PRI 15-OCT-2018", header2.getOriginalHeader());
 	}
+
+	/**
+	 * Helper class to be able to verify the closed state of the input stream.
+	 */
+	private class CheckableInputStream extends BufferedInputStream {
+
+		private boolean closed;
+
+		CheckableInputStream(InputStream in) {
+			super(in);
+			closed = false;
+		}
+
+		@Override
+		public void close() throws IOException {
+			super.close();
+			closed = true;
+		}
+
+		boolean isclosed() {
+			return closed;
+		}
+	}
 }