X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileParse.java;h=d0b61e450debf163cc0349ee583fc75a107d9798;hb=9c127c47a7bf73c3e538815635f525fe59f7faba;hp=dc0418fb04d6cae7571d730d65864baeca4ded64;hpb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;p=jalview.git diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java index dc0418f..d0b61e4 100755 --- a/src/jalview/io/FileParse.java +++ b/src/jalview/io/FileParse.java @@ -20,13 +20,14 @@ */ package jalview.io; -import jalview.api.AlignExportSettingI; -import jalview.api.AlignViewportI; +import jalview.api.AlignExportSettingsI; import jalview.api.AlignmentViewPanel; import jalview.api.FeatureSettingsModelI; 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; @@ -35,16 +36,24 @@ import java.io.InputStream; 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.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. */ @@ -52,6 +61,13 @@ public class FileParse 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. @@ -61,7 +77,7 @@ public class FileParse /** * 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 @@ -125,9 +141,8 @@ public class FileParse { 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) { @@ -179,79 +194,151 @@ public class FileParse } 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; } + + /** + * 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 + */ + private static boolean isGzipStream(byte[] bytes) { + int head = ((int) bytes[0] & 0xff) | ((bytes[1] << 8) & 0xff00); + return (GZIPInputStream.GZIP_MAGIC == head); + } - private BufferedReader tryAsGzipSource(InputStream inputStream) + /** + * 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 { + + // NB: stackoverflow https://stackoverflow.com/questions/4818468/how-to-check-if-inputstream-is-gzipped + // could use a PushBackInputStream rather than a BufferedInputStream + + BufferedInputStream bufinput; + if (!input.markSupported()) { + bufinput= new BufferedInputStream(input,16); + input = bufinput; + } + input.mark(4); + byte[] bytes=input.readNBytes(2); + input.reset(); + if (bytes.length==2 && isGzipStream(bytes)) { + 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))); + 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. + *

+ * If the response status includes + * + *

+   * Content-Type : application/x-gzip
+   * 
+ * + * 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) { - try + HttpURLConnection conn = (HttpURLConnection) _conn; + int rc = conn.getResponseCode(); + if (rc != HttpURLConnection.HTTP_OK) { - InputStream inputStream = url.openStream(); - dataIn = tryAsGzipSource(inputStream); - dataName = fileStr; - return false; + throw new IOException( + "Response status from " + urlStr + " was " + rc); + } + } else { + try { + 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; } /** @@ -302,22 +389,45 @@ public class FileParse * Create a datasource for input to Jalview. See AppletFormatAdapter for the * types of sources that are handled. * - * @param fileStr - * - datasource locator/content + * @param file + * - datasource locator/content as File or String * @param sourceType * - protocol of source * @throws MalformedURLException * @throws IOException */ - public FileParse(String fileStr, DataSourceType sourceType) + public FileParse(Object file, DataSourceType sourceType) throws MalformedURLException, IOException { - this.dataSourceType = sourceType; + 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 (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) @@ -326,18 +436,27 @@ public class FileParse { 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 (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 @@ -384,8 +503,7 @@ public class FileParse 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); @@ -396,7 +514,7 @@ public class FileParse } if (is != null) { - dataIn = new BufferedReader(new java.io.InputStreamReader(is)); + dataIn = new BufferedReader(new InputStreamReader(is)); dataName = fileStr; } else @@ -414,8 +532,8 @@ public class FileParse { // 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); @@ -446,9 +564,9 @@ public class FileParse { 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 })); } /** @@ -501,9 +619,8 @@ public class FileParse } 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")); } } @@ -584,7 +701,7 @@ public class FileParse /** * @return the currently configured exportSettings for writing data. */ - public AlignExportSettingI getExportSettings() + public AlignExportSettingsI getExportSettings() { return exportSettings; } @@ -595,7 +712,7 @@ public class FileParse * @param exportSettings * the exportSettings to set */ - public void setExportSettings(AlignExportSettingI exportSettings) + public void setExportSettings(AlignExportSettingsI exportSettings) { this.exportSettings = exportSettings; } @@ -630,4 +747,61 @@ public class FileParse { 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; + } }