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Merge pull request #31 from josemduarte/master
Removing ParseException
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292 changes: 144 additions & 148 deletions
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mmtf-codec/src/main/java/org/rcsb/mmtf/decoder/ReaderUtils.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,148 +1,144 @@ | ||
| package org.rcsb.mmtf.decoder; | ||
|
|
||
| import java.io.ByteArrayInputStream; | ||
| import java.io.ByteArrayOutputStream; | ||
| import java.io.IOException; | ||
| import java.io.InputStream; | ||
| import java.net.URL; | ||
| import java.nio.file.Files; | ||
| import java.nio.file.Path; | ||
| import java.text.ParseException; | ||
| import java.util.zip.GZIPInputStream; | ||
|
|
||
| import org.rcsb.mmtf.dataholders.MmtfStructure; | ||
| import org.rcsb.mmtf.serialization.MessagePackSerialization; | ||
| import org.rcsb.mmtf.utils.CodecUtils; | ||
|
|
||
| /** | ||
| * A class of static utility methods for reading data. | ||
| * | ||
| * @author Anthony Bradley | ||
| * | ||
| */ | ||
| public class ReaderUtils { | ||
|
|
||
| /** | ||
| * The size of a chunk for a byte buffer. | ||
| */ | ||
| private static final int BYTE_BUFFER_CHUNK_SIZE = 4096; | ||
|
|
||
| /** | ||
| * Find the message pack byte array from the web using the input code and a base url. Caches the | ||
| * file if possible. | ||
| * | ||
| * @param pdbCode the pdb code for the desired structure. | ||
| * @return the MMTFBean of the deserialized data | ||
| * @throws java.text.ParseException if MessagePack cannot be parsed | ||
| * @throws IOException if the data cannot be read from the URL | ||
| */ | ||
| public static MmtfStructure getDataFromUrl(String pdbCode) | ||
| throws ParseException, IOException { | ||
| // Get these as an inputstream | ||
| byte[] bytes = getByteArrayFromUrl(pdbCode); | ||
| // Now return the gzip deflated and deserialized byte array | ||
| MessagePackSerialization mmtfBeanSeDeMessagePackImpl | ||
| = new MessagePackSerialization(); | ||
| return mmtfBeanSeDeMessagePackImpl.deserialize(new ByteArrayInputStream( | ||
| deflateGzip(bytes))); | ||
| } | ||
|
|
||
| /** | ||
| * Get the GZIP compressed and messagepack serialized data from the MMTF servers | ||
| * | ||
| * @param pdbCode the PDB code for the data required | ||
| * @return the byte array (GZIP compressed) of the data from the URL | ||
| * @throws IOException an error reading the URL | ||
| */ | ||
| public static byte[] getByteArrayFromUrl(String pdbCode) | ||
| throws IOException { | ||
| URL url = new URL(getUrl(pdbCode)); | ||
| try (InputStream inputStream = url.openStream(); | ||
| ByteArrayOutputStream baos = new ByteArrayOutputStream();) { | ||
| byte[] byteChunk = new byte[BYTE_BUFFER_CHUNK_SIZE]; | ||
| // Or whatever size you want to read in at a time. | ||
| int n; | ||
| while ((n = inputStream.read(byteChunk)) > 0) { | ||
| baos.write(byteChunk, 0, n); | ||
| } | ||
| return baos.toByteArray(); | ||
| } | ||
| } | ||
|
|
||
| /** | ||
| * Deflate a gzip byte array. | ||
| * | ||
| * @param inputBytes a gzip compressed byte array | ||
| * @return a deflated byte array | ||
| * @throws IOException error in gzip input stream | ||
| */ | ||
| public static byte[] deflateGzip(byte[] inputBytes) throws IOException { | ||
| ByteArrayOutputStream byteArrayOutputStream | ||
| = new ByteArrayOutputStream(); | ||
| try (GZIPInputStream gzipInputStream = new GZIPInputStream( | ||
| new ByteArrayInputStream(inputBytes))) { | ||
| byte[] buffer = new byte[BYTE_BUFFER_CHUNK_SIZE]; | ||
| while (gzipInputStream.available() == 1) { | ||
| int size = gzipInputStream.read(buffer); | ||
| if (size == -1) { | ||
| break; | ||
| } | ||
| byteArrayOutputStream.write(buffer, 0, size); | ||
| } | ||
| return byteArrayOutputStream.toByteArray(); | ||
| } | ||
| } | ||
|
|
||
| /** | ||
| * A function to get MMTF data from a file path. | ||
| * | ||
| * @param filePath the full path of the file to be read | ||
| * @return the deserialized {@link MmtfStructure} | ||
| * @throws IOException an error reading the file | ||
| * @throws java.text.ParseException if MessagePack cannot be parsed | ||
| */ | ||
| public static MmtfStructure getDataFromFile(Path filePath) | ||
| throws IOException, ParseException { | ||
| // Now return the gzip deflated and deserialized byte array | ||
| try (InputStream is = new ByteArrayInputStream(readFile(filePath))) { | ||
| return getDataFromInputStream(is); | ||
| } | ||
| } | ||
|
|
||
| /** | ||
| * Read a byte array from a file | ||
| * | ||
| * @param path the input file path | ||
| * @return the returned byte array | ||
| * @throws IOException an error reading the file | ||
| */ | ||
| private static byte[] readFile(Path path) throws IOException { | ||
| byte[] data = Files.readAllBytes(path); | ||
| return data; | ||
| } | ||
|
|
||
| /** | ||
| * Read an input stream to an {@link MmtfStructure} object. | ||
| * | ||
| * @param inStream the {@link InputStream} to read. | ||
| * @return the {@link MmtfStructure} to be returned | ||
| * @throws java.text.ParseException if MessagePack cannot be parsed | ||
| * @throws java.io.IOException if the inStream cannot be read | ||
| */ | ||
| public static MmtfStructure getDataFromInputStream(InputStream inStream) | ||
| throws ParseException, IOException { | ||
| MessagePackSerialization mmtfBeanSeDeMessagePackImpl | ||
| = new MessagePackSerialization(); | ||
| return mmtfBeanSeDeMessagePackImpl.deserialize(inStream); | ||
| } | ||
|
|
||
| /** | ||
| * Get the URL to return a given PDB id | ||
| * | ||
| * @param pdbId the input PDB id | ||
| * @return the URL {@link String} to get data from | ||
| */ | ||
| public static String getUrl(String pdbId) { | ||
| return CodecUtils.BASE_URL + pdbId; | ||
| } | ||
| } | ||
| package org.rcsb.mmtf.decoder; | ||
|
|
||
| import java.io.ByteArrayInputStream; | ||
| import java.io.ByteArrayOutputStream; | ||
| import java.io.IOException; | ||
| import java.io.InputStream; | ||
| import java.net.URL; | ||
| import java.nio.file.Files; | ||
| import java.nio.file.Path; | ||
| import java.util.zip.GZIPInputStream; | ||
|
|
||
| import org.rcsb.mmtf.dataholders.MmtfStructure; | ||
| import org.rcsb.mmtf.serialization.MessagePackSerialization; | ||
| import org.rcsb.mmtf.utils.CodecUtils; | ||
|
|
||
| /** | ||
| * A class of static utility methods for reading data. | ||
| * | ||
| * @author Anthony Bradley | ||
| * | ||
| */ | ||
| public class ReaderUtils { | ||
|
|
||
| /** | ||
| * The size of a chunk for a byte buffer. | ||
| */ | ||
| private static final int BYTE_BUFFER_CHUNK_SIZE = 4096; | ||
|
|
||
| /** | ||
| * Find the message pack byte array from the web using the input code and a base url. Caches the | ||
| * file if possible. | ||
| * | ||
| * @param pdbCode the pdb code for the desired structure. | ||
| * @return the MMTFBean of the deserialized data | ||
| * @throws IOException if the data cannot be read from the URL | ||
| */ | ||
| public static MmtfStructure getDataFromUrl(String pdbCode) | ||
| throws IOException { | ||
| // Get these as an inputstream | ||
| byte[] bytes = getByteArrayFromUrl(pdbCode); | ||
| // Now return the gzip deflated and deserialized byte array | ||
| MessagePackSerialization mmtfBeanSeDeMessagePackImpl | ||
| = new MessagePackSerialization(); | ||
| return mmtfBeanSeDeMessagePackImpl.deserialize(new ByteArrayInputStream( | ||
| deflateGzip(bytes))); | ||
| } | ||
|
|
||
| /** | ||
| * Get the GZIP compressed and messagepack serialized data from the MMTF servers | ||
| * | ||
| * @param pdbCode the PDB code for the data required | ||
| * @return the byte array (GZIP compressed) of the data from the URL | ||
| * @throws IOException an error reading the URL | ||
| */ | ||
| public static byte[] getByteArrayFromUrl(String pdbCode) | ||
| throws IOException { | ||
| URL url = new URL(getUrl(pdbCode)); | ||
| try (InputStream inputStream = url.openStream(); | ||
| ByteArrayOutputStream baos = new ByteArrayOutputStream();) { | ||
| byte[] byteChunk = new byte[BYTE_BUFFER_CHUNK_SIZE]; | ||
| // Or whatever size you want to read in at a time. | ||
| int n; | ||
| while ((n = inputStream.read(byteChunk)) > 0) { | ||
| baos.write(byteChunk, 0, n); | ||
| } | ||
| return baos.toByteArray(); | ||
| } | ||
| } | ||
|
|
||
| /** | ||
| * Deflate a gzip byte array. | ||
| * | ||
| * @param inputBytes a gzip compressed byte array | ||
| * @return a deflated byte array | ||
| * @throws IOException error in gzip input stream | ||
| */ | ||
| public static byte[] deflateGzip(byte[] inputBytes) throws IOException { | ||
| ByteArrayOutputStream byteArrayOutputStream | ||
| = new ByteArrayOutputStream(); | ||
| try (GZIPInputStream gzipInputStream = new GZIPInputStream( | ||
| new ByteArrayInputStream(inputBytes))) { | ||
| byte[] buffer = new byte[BYTE_BUFFER_CHUNK_SIZE]; | ||
| while (gzipInputStream.available() == 1) { | ||
| int size = gzipInputStream.read(buffer); | ||
| if (size == -1) { | ||
| break; | ||
| } | ||
| byteArrayOutputStream.write(buffer, 0, size); | ||
| } | ||
| return byteArrayOutputStream.toByteArray(); | ||
| } | ||
| } | ||
|
|
||
| /** | ||
| * A function to get MMTF data from a file path. | ||
| * | ||
| * @param filePath the full path of the file to be read | ||
| * @return the deserialized {@link MmtfStructure} | ||
| * @throws IOException an error reading the file | ||
| */ | ||
| public static MmtfStructure getDataFromFile(Path filePath) | ||
| throws IOException { | ||
| // Now return the gzip deflated and deserialized byte array | ||
| try (InputStream is = new ByteArrayInputStream(readFile(filePath))) { | ||
| return getDataFromInputStream(is); | ||
| } | ||
| } | ||
|
|
||
| /** | ||
| * Read a byte array from a file | ||
| * | ||
| * @param path the input file path | ||
| * @return the returned byte array | ||
| * @throws IOException an error reading the file | ||
| */ | ||
| private static byte[] readFile(Path path) throws IOException { | ||
| byte[] data = Files.readAllBytes(path); | ||
| return data; | ||
| } | ||
|
|
||
| /** | ||
| * Read an input stream to an {@link MmtfStructure} object. | ||
| * | ||
| * @param inStream the {@link InputStream} to read. | ||
| * @return the {@link MmtfStructure} to be returned | ||
| * @throws java.io.IOException if the inStream cannot be read | ||
| */ | ||
| public static MmtfStructure getDataFromInputStream(InputStream inStream) | ||
| throws IOException { | ||
| MessagePackSerialization mmtfBeanSeDeMessagePackImpl | ||
| = new MessagePackSerialization(); | ||
| return mmtfBeanSeDeMessagePackImpl.deserialize(inStream); | ||
| } | ||
|
|
||
| /** | ||
| * Get the URL to return a given PDB id | ||
| * | ||
| * @param pdbId the input PDB id | ||
| * @return the URL {@link String} to get data from | ||
| */ | ||
| public static String getUrl(String pdbId) { | ||
| return CodecUtils.BASE_URL + pdbId; | ||
| } | ||
| } |
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