+ * 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; + } }