X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FFileParse.java;h=1f51d8c8ad1a0c3cf93628793bab09c40f56b79c;hb=f1b00517fe5f888f3213d70270e27a83dffe1695;hp=809bc8f2d13a3ebb9b48877c8cfc9b41a377b314;hpb=dd8112aefe2c3a08c51f1684d5cda16be938c74f;p=jalview.git diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java index 809bc8f..1f51d8c 100755 --- a/src/jalview/io/FileParse.java +++ b/src/jalview/io/FileParse.java @@ -20,12 +20,7 @@ */ package jalview.io; -import jalview.api.AlignExportSettingsI; -import jalview.api.AlignViewportI; -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; @@ -36,10 +31,20 @@ 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.api.AlignExportSettingsI; +import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; +import jalview.api.FeatureSettingsModelI; +import jalview.bin.Console; +import jalview.util.MessageManager; +import jalview.util.Platform; + /** * implements a random access wrapper around a particular datasource, for * passing to identifyFile and AlignFile objects. @@ -63,6 +68,7 @@ public class FileParse { return bytes; } + /** * a viewport associated with the current file operation. May be null. May * move to different object. @@ -189,29 +195,92 @@ 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; } - 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()) + { + Console.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 + { + // 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( @@ -222,44 +291,79 @@ public class FileParse return inData; } - private boolean checkURLSource(String fileStr) + /** + * 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) + { + 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) + || contentType.endsWith("gzip") || "gzip".equals(encoding); + Exception e = null; + InputStream inputStream = _conn.getInputStream(); + if (isgzipped) { - if (e != null) + try + { + 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; } /** @@ -276,7 +380,7 @@ public class FileParse if (sfpos > -1 && sfpos < fileStr.length() - 1) { suffix = fileStr.substring(sfpos + 1); - // System.err.println("DEBUG: Found Suffix:"+suffix); + // jalview.bin.Console.errPrintln("DEBUG: Found Suffix:"+suffix); return fileStr.substring(0, sfpos); } return null; @@ -331,15 +435,10 @@ public class FileParse } private void parse(File file, String fileStr, DataSourceType sourceType, - boolean isFileObject) throws MalformedURLException, IOException - { - /** - * @j2sNative - * - * this.bytes = file && file._bytes; - * - */ - this.dataSourceType = sourceType; + boolean isFileObject) throws IOException + { + bytes = Platform.getFileBytes(file); + dataSourceType = sourceType; error = false; if (sourceType == DataSourceType.FILE) @@ -349,7 +448,8 @@ public class FileParse { // this will be from JavaScript inFile = file; - dataIn = new BufferedReader(new InputStreamReader(new ByteArrayInputStream(bytes))); + dataIn = new BufferedReader( + new InputStreamReader(new ByteArrayInputStream(bytes))); dataName = fileStr; } else if (checkFileSource(fileStr)) @@ -375,16 +475,10 @@ public class FileParse } else if (sourceType == DataSourceType.RELATIVE_URL) { - /** - * BH 2018 hack for no support for access-origin - * - * @j2sNative - * - * this.bytes = swingjs.JSUtil.getFileAsBytes$O(fileStr); - * - */ - - dataIn = new BufferedReader(new java.io.InputStreamReader(new ByteArrayInputStream(bytes))); + // BH 2018 hack for no support for access-origin + bytes = Platform.getFileAsBytes(fileStr); + dataIn = new BufferedReader( + new InputStreamReader(new ByteArrayInputStream(bytes))); dataName = fileStr; } @@ -434,8 +528,7 @@ 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); @@ -446,7 +539,7 @@ public class FileParse } if (is != null) { - dataIn = new BufferedReader(new java.io.InputStreamReader(is)); + dataIn = new BufferedReader(new InputStreamReader(is)); dataName = fileStr; } else @@ -464,8 +557,7 @@ 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[] + "exception.failed_to_read_data_from_source", new String[] { errormessage })); } error = false; @@ -542,7 +634,7 @@ public class FileParse { if (bytesRead >= READAHEAD_LIMIT) { - System.err.println(String.format( + jalview.bin.Console.errPrintln(String.format( "File reset error: read %d bytes but reset limit is %d", bytesRead, READAHEAD_LIMIT)); } @@ -680,4 +772,61 @@ 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; + } }