X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileParse.java;h=39d8ad432d6a5f5486d7966ee008472aac53a3ac;hb=33fa5014f3b959dc8d331c95699660861b1f4e3a;hp=7e1940fe0b1ca18b14e313bb1a2c00aae6d6be4c;hpb=5969ead0fd401f4435a3435ede9e4e87cf9c1d0b;p=jalview.git diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java index 7e1940f..39d8ad4 100755 --- a/src/jalview/io/FileParse.java +++ b/src/jalview/io/FileParse.java @@ -20,13 +20,15 @@ */ package jalview.io; -import jalview.api.AlignExportSettingI; +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; import java.io.FileInputStream; import java.io.FileReader; @@ -35,11 +37,13 @@ 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 javajs.util.Rdr; +import jalview.util.Platform; /** * implements a random access wrapper around a particular datasource, for @@ -58,7 +62,12 @@ public class FileParse public File inFile = null; - public byte[] bytes; // from JavaScript + private byte[] bytes; // from JavaScript + + public byte[] getBytes() + { + return bytes; + } /** * a viewport associated with the current file operation. May be null. May @@ -69,7 +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 @@ -186,29 +195,73 @@ 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( @@ -219,44 +272,74 @@ 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) { - 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 + { + 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; } /** @@ -307,38 +390,31 @@ 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) - throws MalformedURLException, IOException - { - - this(null, fileStr, sourceType, false); - } - - public FileParse(File file, DataSourceType sourceType) + public FileParse(Object file, DataSourceType sourceType) throws MalformedURLException, IOException { - - this(file, file.getPath(), sourceType, true); + if (file instanceof File) + { + parse((File) file, ((File) file).getPath(), sourceType, true); + } + else + { + parse(null, file.toString(), sourceType, false); + } } - private FileParse(File file, String fileStr, DataSourceType sourceType, - boolean isFileObject) throws MalformedURLException, IOException + private void parse(File file, String fileStr, DataSourceType sourceType, + boolean isFileObject) throws IOException { - - /** - * @j2sNative - * - * this.bytes = file && file._bytes; - * - */ - this.dataSourceType = sourceType; + bytes = Platform.getFileBytes(file); + dataSourceType = sourceType; error = false; if (sourceType == DataSourceType.FILE) @@ -348,7 +424,8 @@ public class FileParse { // this will be from JavaScript inFile = file; - dataIn = new BufferedReader(new StringReader(new String(bytes))); + dataIn = new BufferedReader( + new InputStreamReader(new ByteArrayInputStream(bytes))); dataName = fileStr; } else if (checkFileSource(fileStr)) @@ -374,18 +451,10 @@ public class FileParse } else if (sourceType == DataSourceType.RELATIVE_URL) { - String data = null; - /** - * BH 2018 hack for no support for access-origin - * - * @j2sNative - * - * data = $.ajax({url:fileStr, async:false}).responseText; - * - */ - - System.out.println(data); - dataIn = Rdr.getBR(data); + // BH 2018 hack for no support for access-origin + bytes = Platform.getFileAsBytes(fileStr); + dataIn = new BufferedReader( + new InputStreamReader(new ByteArrayInputStream(bytes))); dataName = fileStr; } @@ -435,8 +504,7 @@ 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); @@ -447,7 +515,7 @@ public class FileParse } if (is != null) { - dataIn = new BufferedReader(new java.io.InputStreamReader(is)); + dataIn = new BufferedReader(new InputStreamReader(is)); dataName = fileStr; } else @@ -465,8 +533,7 @@ 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; @@ -635,7 +702,7 @@ public class FileParse /** * @return the currently configured exportSettings for writing data. */ - public AlignExportSettingI getExportSettings() + public AlignExportSettingsI getExportSettings() { return exportSettings; } @@ -646,7 +713,7 @@ public class FileParse * @param exportSettings * the exportSettings to set */ - public void setExportSettings(AlignExportSettingI exportSettings) + public void setExportSettings(AlignExportSettingsI exportSettings) { this.exportSettings = exportSettings; } @@ -681,4 +748,61 @@ 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; + } }