X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileParse.java;h=2dec5592664b9889095ed0d9f4618696cc1524d1;hb=cb8e52fbbc5f725e3f7f48c672cdddb0690bd978;hp=7117d0fcf537a5ae211577c0e290a59d8404af84;hpb=acf9118bba86938c8406e7041b4e5a507f4f37a3;p=jalview.git diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java index 7117d0f..2dec559 100755 --- a/src/jalview/io/FileParse.java +++ b/src/jalview/io/FileParse.java @@ -20,13 +20,9 @@ */ package jalview.io; -import jalview.api.AlignExportSettingI; -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; import java.io.FileInputStream; import java.io.FileReader; @@ -35,10 +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. @@ -56,6 +62,13 @@ 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. @@ -65,7 +78,7 @@ 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 @@ -182,29 +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( @@ -215,44 +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) + || "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; } /** @@ -303,22 +414,45 @@ 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) @@ -339,6 +473,15 @@ public class FileParse } } } + 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 @@ -385,8 +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); @@ -397,7 +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 @@ -584,7 +726,7 @@ public class FileParse /** * @return the currently configured exportSettings for writing data. */ - public AlignExportSettingI getExportSettings() + public AlignExportSettingsI getExportSettings() { return exportSettings; } @@ -595,7 +737,7 @@ public class FileParse * @param exportSettings * the exportSettings to set */ - public void setExportSettings(AlignExportSettingI exportSettings) + public void setExportSettings(AlignExportSettingsI exportSettings) { this.exportSettings = exportSettings; } @@ -630,4 +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; + } }