*/
package jalview.io;
-import jalview.api.AlignExportSettingI;
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.util.MessageManager;
-
+import java.io.BufferedInputStream;
import java.io.BufferedReader;
+import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileReader;
import java.io.InputStreamReader;
import java.io.Reader;
import java.io.StringReader;
+import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.net.URL;
+import java.net.URLConnection;
import java.util.zip.GZIPInputStream;
+import jalview.api.AlignExportSettingsI;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureSettingsModelI;
+import jalview.bin.Cache;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
/**
* implements a random access wrapper around a particular datasource, for
* passing to identifyFile and AlignFile objects.
*/
public class FileParse
{
+ protected static final String SPACE = " ";
+
+ protected static final String TAB = "\t";
+
/**
* text specifying source of data. usually filename or url.
*/
public File inFile = null;
+ private byte[] bytes; // from JavaScript
+
+ public byte[] getBytes()
+ {
+ return bytes;
+ }
+
/**
* a viewport associated with the current file operation. May be null. May
* move to different object.
/**
* specific settings for exporting data from the current context
*/
- private AlignExportSettingI exportSettings;
+ private AlignExportSettingsI exportSettings;
/**
* sequence counter for FileParse object created from same data source
*/
protected String suffix = null;
- protected String type = null;
+ protected DataSourceType dataSourceType = null;
protected BufferedReader dataIn = null;
{
if (from == null)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_null_fileparse"));
+ throw new Error(MessageManager
+ .getString("error.implementation_error_null_fileparse"));
}
if (from == this)
{
suffix = from.suffix;
errormessage = from.errormessage; // inherit potential error messages
error = false; // reset any error condition.
- type = from.type;
+ dataSourceType = from.dataSourceType;
dataIn = from.dataIn;
if (dataIn != null)
{
}
if (!error)
{
- if (fileStr.toLowerCase().endsWith(".gz"))
+ try
{
- try
- {
- dataIn = tryAsGzipSource(new FileInputStream(fileStr));
- dataName = fileStr;
- return error;
- } catch (Exception x)
- {
- warningMessage = "Failed to resolve as a GZ stream ("
- + x.getMessage() + ")";
- // x.printStackTrace();
- }
- ;
+ dataIn = checkForGzipStream(new FileInputStream(fileStr));
+ dataName = fileStr;
+ } catch (Exception x)
+ {
+ warningMessage = "Failed to resolve " + fileStr
+ + " as a data source. (" + x.getMessage() + ")";
+ // x.printStackTrace();
+ error = true;
}
-
- dataIn = new BufferedReader(new FileReader(fileStr));
- dataName = fileStr;
+ ;
}
return error;
}
- private BufferedReader tryAsGzipSource(InputStream inputStream)
+ /**
+ * Recognise the 2-byte magic header for gzip streams
+ *
+ * https://recalll.co/ask/v/topic/java-How-to-check-if-InputStream-is-Gzipped/555aadd62bd27354438b90f6
+ *
+ * @param bytes
+ * - at least two bytes
+ * @return
+ * @throws IOException
+ */
+ public static boolean isGzipStream(InputStream input) throws IOException
+ {
+ if (!input.markSupported())
+ {
+ Cache.error(
+ "FileParse.izGzipStream: input stream must support mark/reset");
+ return false;
+ }
+ input.mark(4);
+
+ // get first 2 bytes or return false
+ byte[] bytes = new byte[2];
+ int read = input.read(bytes);
+ input.reset();
+ if (read != bytes.length)
+ {
+ return false;
+ }
+
+ int header = (bytes[0] & 0xff) | ((bytes[1] << 8) & 0xff00);
+ return (GZIPInputStream.GZIP_MAGIC == header);
+ }
+
+ /**
+ * Returns a Reader for the given input after wrapping it in a buffered input
+ * stream, and then checking if it needs to be wrapped by a GZipInputStream
+ *
+ * @param input
+ * @return
+ */
+ private BufferedReader checkForGzipStream(InputStream input)
throws Exception
{
- BufferedReader inData = new BufferedReader(new InputStreamReader(
- new GZIPInputStream(inputStream)));
+ // NB: stackoverflow
+ // https://stackoverflow.com/questions/4818468/how-to-check-if-inputstream-is-gzipped
+ // could use a PushBackInputStream rather than a BufferedInputStream
+ if (!input.markSupported())
+ {
+ input = new BufferedInputStream(input, 16);
+ }
+ if (isGzipStream(input))
+ {
+ return getGzipReader(input);
+ }
+ // return a buffered reader for the stream.
+ InputStreamReader isReader = new InputStreamReader(input);
+ BufferedReader toReadFrom = new BufferedReader(isReader);
+ return toReadFrom;
+ }
+
+ /**
+ * Returns a {@code BufferedReader} which wraps the input stream with a
+ * GZIPInputStream. Throws a {@code ZipException} if a GZIP format error
+ * occurs or the compression method used is unsupported.
+ *
+ * @param inputStream
+ * @return
+ * @throws Exception
+ */
+ private BufferedReader getGzipReader(InputStream inputStream)
+ throws Exception
+ {
+ BufferedReader inData = new BufferedReader(
+ new InputStreamReader(new GZIPInputStream(inputStream)));
inData.mark(2048);
inData.read();
inData.reset();
return inData;
}
- private boolean checkURLSource(String fileStr) throws IOException,
- MalformedURLException
+ /**
+ * Tries to read from the given URL. If successful, saves a reader to the
+ * response in field {@code dataIn}, otherwise (on exception, or HTTP response
+ * status not 200), throws an exception.
+ * <p>
+ * If the response status includes
+ *
+ * <pre>
+ * Content-Type : application/x-gzip
+ * </pre>
+ *
+ * then tries to read as gzipped content.
+ *
+ * @param urlStr
+ * @throws IOException
+ * @throws MalformedURLException
+ */
+ private void checkURLSource(String urlStr)
+ throws IOException, MalformedURLException
{
errormessage = "URL NOT FOUND";
- URL url = new URL(fileStr);
- //
- // GZIPInputStream code borrowed from Aquaria (soon to be open sourced) via
- // Kenny Sabir
- Exception e = null;
- if (fileStr.toLowerCase().endsWith(".gz"))
+ URL url = new URL(urlStr);
+ URLConnection _conn = url.openConnection();
+ if (_conn instanceof HttpURLConnection)
+ {
+ HttpURLConnection conn = (HttpURLConnection) _conn;
+ int rc = conn.getResponseCode();
+ if (rc != HttpURLConnection.HTTP_OK)
+ {
+ throw new IOException(
+ "Response status from " + urlStr + " was " + rc);
+ }
+ }
+ else
{
try
{
- InputStream inputStream = url.openStream();
- dataIn = tryAsGzipSource(inputStream);
- dataName = fileStr;
- return false;
+ dataIn = checkForGzipStream(_conn.getInputStream());
+ dataName = urlStr;
+ } catch (IOException ex)
+ {
+ throw new IOException("Failed to handle non-HTTP URI stream", ex);
} catch (Exception ex)
{
- e = ex;
+ throw new IOException(
+ "Failed to determine type of input stream for given URI",
+ ex);
}
+ return;
}
-
- try
- {
- dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
- } catch (IOException q)
+ String encoding = _conn.getContentEncoding();
+ String contentType = _conn.getContentType();
+ boolean isgzipped = "application/x-gzip".equalsIgnoreCase(contentType)
+ || "gzip".equals(encoding);
+ Exception e = null;
+ InputStream inputStream = _conn.getInputStream();
+ if (isgzipped)
{
- if (e != null)
+ try
{
- throw new IOException(
- MessageManager
- .getString("exception.failed_to_resolve_gzip_stream"),
- e);
+ dataIn = getGzipReader(inputStream);
+ dataName = urlStr;
+ } catch (Exception e1)
+ {
+ throw new IOException(MessageManager
+ .getString("exception.failed_to_resolve_gzip_stream"), e);
}
- throw q;
+ return;
}
- // record URL as name of datasource.
- dataName = fileStr;
- return false;
+
+ dataIn = new BufferedReader(new InputStreamReader(inputStream));
+ dataName = urlStr;
+ return;
}
/**
* configurable values for the origin and the type of the source
*/
public FileParse(BufferedReader source, String originString,
- String typeString)
+ DataSourceType sourceType)
{
- type = typeString;
+ dataSourceType = sourceType;
error = false;
inFile = null;
dataName = originString;
* Create a datasource for input to Jalview. See AppletFormatAdapter for the
* types of sources that are handled.
*
- * @param fileStr
- * - datasource locator/content
- * @param type
+ * @param file
+ * - datasource locator/content as File or String
+ * @param sourceType
* - protocol of source
* @throws MalformedURLException
* @throws IOException
*/
- public FileParse(String fileStr, String type)
+ public FileParse(Object file, DataSourceType sourceType)
throws MalformedURLException, IOException
{
- this.type = type;
+ if (file instanceof File)
+ {
+ parse((File) file, ((File) file).getPath(), sourceType, true);
+ }
+ else
+ {
+ parse(null, file.toString(), sourceType, false);
+ }
+ }
+
+ private void parse(File file, String fileStr, DataSourceType sourceType,
+ boolean isFileObject) throws IOException
+ {
+ bytes = Platform.getFileBytes(file);
+ dataSourceType = sourceType;
error = false;
- if (type.equals(AppletFormatAdapter.FILE))
+ if (sourceType == DataSourceType.FILE)
{
- if (checkFileSource(fileStr))
+
+ if (bytes != null)
+ {
+ // this will be from JavaScript
+ inFile = file;
+ dataIn = new BufferedReader(
+ new InputStreamReader(new ByteArrayInputStream(bytes)));
+ dataName = fileStr;
+ }
+ else if (checkFileSource(fileStr))
{
String suffixLess = extractSuffix(fileStr);
if (suffixLess != null)
{
throw new IOException(MessageManager.formatMessage(
"exception.problem_opening_file_also_tried",
- new String[] { inFile.getName(), suffixLess,
- errormessage }));
+ new String[]
+ { inFile.getName(), suffixLess, errormessage }));
}
}
else
{
throw new IOException(MessageManager.formatMessage(
- "exception.problem_opening_file",
- new String[] { inFile.getName(), errormessage }));
+ "exception.problem_opening_file", new String[]
+ { inFile.getName(), errormessage }));
}
}
}
- else if (type.equals(AppletFormatAdapter.URL))
+ else if (sourceType == DataSourceType.RELATIVE_URL)
+ {
+ // BH 2018 hack for no support for access-origin
+ bytes = Platform.getFileAsBytes(fileStr);
+ dataIn = new BufferedReader(
+ new InputStreamReader(new ByteArrayInputStream(bytes)));
+ dataName = fileStr;
+
+ }
+ else if (sourceType == DataSourceType.URL)
{
try
{
error = true;
}
}
- else if (type.equals(AppletFormatAdapter.PASTE))
+ else if (sourceType == DataSourceType.PASTE)
{
errormessage = "PASTE INACCESSIBLE!";
dataIn = new BufferedReader(new StringReader(fileStr));
dataName = "Paste";
}
- else if (type.equals(AppletFormatAdapter.CLASSLOADER))
+ else if (sourceType == DataSourceType.CLASSLOADER)
{
errormessage = "RESOURCE CANNOT BE LOCATED";
- java.io.InputStream is = getClass()
- .getResourceAsStream("/" + fileStr);
+ InputStream is = getClass().getResourceAsStream("/" + fileStr);
if (is == null)
{
String suffixLess = extractSuffix(fileStr);
}
if (is != null)
{
- dataIn = new BufferedReader(new java.io.InputStreamReader(is));
+ dataIn = new BufferedReader(new InputStreamReader(is));
dataName = fileStr;
}
else
else
{
errormessage = "PROBABLE IMPLEMENTATION ERROR : Datasource Type given as '"
- + (type != null ? type : "null") + "'";
+ + (sourceType != null ? sourceType : "null") + "'";
error = true;
}
if (dataIn == null || error)
{
// pass up the reason why we have no source to read from
throw new IOException(MessageManager.formatMessage(
- "exception.failed_to_read_data_from_source",
- new String[] { errormessage }));
+ "exception.failed_to_read_data_from_source", new String[]
+ { errormessage }));
}
error = false;
dataIn.mark(READAHEAD_LIMIT);
{
return dataIn.readLine();
}
- throw new IOException(MessageManager.formatMessage(
- "exception.invalid_source_stream",
- new String[] { errormessage }));
+ throw new IOException(MessageManager
+ .formatMessage("exception.invalid_source_stream", new String[]
+ { errormessage }));
}
/**
}
/**
- * rewinds the datasource the beginning.
+ * Rewinds the datasource to the marked point if possible
+ *
+ * @param bytesRead
*
*/
- public void reset() throws IOException
+ public void reset(int bytesRead) throws IOException
{
+ if (bytesRead >= READAHEAD_LIMIT)
+ {
+ System.err.println(String.format(
+ "File reset error: read %d bytes but reset limit is %d",
+ bytesRead, READAHEAD_LIMIT));
+ }
if (dataIn != null && !error)
{
dataIn.reset();
}
else
{
- throw new IOException(
- MessageManager
- .getString("error.implementation_error_reset_called_for_invalid_source"));
+ throw new IOException(MessageManager.getString(
+ "error.implementation_error_reset_called_for_invalid_source"));
}
}
/**
* @return the currently configured exportSettings for writing data.
*/
- public AlignExportSettingI getExportSettings()
+ public AlignExportSettingsI getExportSettings()
{
return exportSettings;
}
* @param exportSettings
* the exportSettings to set
*/
- public void setExportSettings(AlignExportSettingI exportSettings)
+ public void setExportSettings(AlignExportSettingsI exportSettings)
{
this.exportSettings = exportSettings;
}
}
// could also set export/import settings
}
+
+ /**
+ * Returns the preferred feature colour configuration if there is one, else
+ * null
+ *
+ * @return
+ */
+ public FeatureSettingsModelI getFeatureColourScheme()
+ {
+ return null;
+ }
+
+ public DataSourceType getDataSourceType()
+ {
+ return dataSourceType;
+ }
+
+ /**
+ * Returns a buffered reader for the input object. Returns null, or throws
+ * IOException, on failure.
+ *
+ * @param file
+ * a File, or a String which is a name of a file
+ * @param sourceType
+ * @return
+ * @throws IOException
+ */
+ public BufferedReader getBufferedReader(Object file,
+ DataSourceType sourceType) throws IOException
+ {
+ BufferedReader in = null;
+ byte[] bytes;
+
+ switch (sourceType)
+ {
+ case FILE:
+ if (file instanceof String)
+ {
+ return new BufferedReader(new FileReader((String) file));
+ }
+ bytes = Platform.getFileBytes((File) file);
+ if (bytes != null)
+ {
+ return new BufferedReader(
+ new InputStreamReader(new ByteArrayInputStream(bytes)));
+ }
+ return new BufferedReader(new FileReader((File) file));
+ case URL:
+ URL url = new URL(file.toString());
+ in = new BufferedReader(new InputStreamReader(url.openStream()));
+ break;
+ case RELATIVE_URL: // JalviewJS only
+ bytes = Platform.getFileAsBytes(file.toString());
+ if (bytes != null)
+ {
+ in = new BufferedReader(
+ new InputStreamReader(new ByteArrayInputStream(bytes)));
+ }
+ break;
+ case PASTE:
+ in = new BufferedReader(new StringReader(file.toString()));
+ break;
+ case CLASSLOADER:
+ InputStream is = getClass().getResourceAsStream("/" + file);
+ if (is != null)
+ {
+ in = new BufferedReader(new InputStreamReader(is));
+ }
+ break;
+ }
+
+ return in;
+ }
}
git://source.jalview.org / jalview.git / blobdiff