public static Attributes parse(InputStream is) throws ParserConfigurationException, SAXException, IOException { return parse(is, null); } }
public static Attributes parse(String uri) throws ParserConfigurationException, SAXException, IOException { return parse(uri, null); }
private static Attributes createSampleMetadata(StowRS instance) throws Exception { return (instance.fileType == FileType.IMAGE || instance.fileType == FileType.PDF) && instance.sampleMetadataResourceURL != null ? SAXReader.parse(StreamUtils.openFileOrURL(instance.sampleMetadataResourceURL)) : new Attributes(); }
private static Attributes createSampleMetadata(StowRS instance) throws Exception { return (instance.fileType == FileType.IMAGE || instance.fileType == FileType.PDF) && instance.sampleMetadataResourceURL != null ? SAXReader.parse(StreamUtils.openFileOrURL(instance.sampleMetadataResourceURL)) : new Attributes(); }
private static Attributes createMetadata(CommandLine cl, File bulkDataFile) throws Exception { String filePath = bulkDataFile.toPath().toString(); boolean pdf = filePath.endsWith("pdf"); boolean cda = filePath.endsWith("xml"); if (!pdf && !cda) throw new IllegalArgumentException("File extension type not supported."); Attributes metadata = cl.hasOption("pdf") ? SAXReader.parse(StreamUtils.openFileOrURL("resource:encapsulatedPDFMetadata.xml")) : cl.hasOption("cda") ? SAXReader.parse(StreamUtils.openFileOrURL("resource:encapsulatedCDAMetadata.xml")) : new Attributes(); if (cl.hasOption("f")) metadata = SAXReader.parse(cl.getOptionValue("f"), metadata); CLIUtils.addAttributes(metadata, cl.getOptionValues("m")); supplementMissingUIDs(metadata); supplementMissingDateTime(metadata, Tag.ContentDateAndTime, new Date()); supplementMissingDateTime(metadata, Tag.AcquisitionDateTime, new Date(bulkDataFile.lastModified())); supplementMissingValue(metadata, Tag.MIMETypeOfEncapsulatedDocument, pdf ? "application/pdf" : "text/XML"); supplementMissingValue(metadata, Tag.SOPClassUID, pdf ? UID.EncapsulatedPDFStorage : UID.EncapsulatedCDAStorage); return metadata; }
private static Attributes createStaticMetadata(StowRS instance) throws Exception { LOG.info("Creating static metadata. Set defaults, if essential attributes are not present."); Attributes metadata = createSampleMetadata(instance); String metadataFile = instance.metadataFile; if (metadataFile != null) { String metadataFileExt = metadataFile.substring(metadataFile.lastIndexOf(".")+1).toLowerCase(); if (!metadataFileExt.equals("xml")) throw new IllegalArgumentException("Metadata file extension not supported. Read -f option in stowrs help"); metadata = SAXReader.parse(Paths.get(metadataFile).toString(), metadata); } metadata.update(Attributes.UpdatePolicy.OVERWRITE, instance.keys, new Attributes()); supplementDefaultValue(metadata, Tag.PatientName, patName); supplementDefaultValue(metadata, Tag.SOPClassUID, instance.sopCUID); return metadata; }
private static Attributes createStaticMetadata(StowRS instance) throws Exception { LOG.info("Creating static metadata. Set defaults, if essential attributes are not present."); Attributes metadata = createSampleMetadata(instance); String metadataFile = instance.metadataFile; if (metadataFile != null) { String metadataFileExt = metadataFile.substring(metadataFile.lastIndexOf(".")+1).toLowerCase(); if (!metadataFileExt.equals("xml")) throw new IllegalArgumentException("Metadata file extension not supported. Read -f option in stowrs help"); metadata = SAXReader.parse(Paths.get(metadataFile).toString(), metadata); } metadata.update(Attributes.UpdatePolicy.OVERWRITE, instance.keys, new Attributes()); supplementDefaultValue(metadata, Tag.PatientName, patName); supplementDefaultValue(metadata, Tag.SOPClassUID, instance.sopCUID); return metadata; }
private static Attributes createMetadata(CommandLine cl, File bulkDataFile) throws Exception { String filePath = bulkDataFile.toPath().toString(); boolean pdf = filePath.endsWith("pdf"); boolean cda = filePath.endsWith("xml"); if (!pdf && !cda) throw new IllegalArgumentException("File extension type not supported."); Attributes metadata = cl.hasOption("pdf") ? SAXReader.parse(StreamUtils.openFileOrURL("resource:encapsulatedPDFMetadata.xml")) : cl.hasOption("cda") ? SAXReader.parse(StreamUtils.openFileOrURL("resource:encapsulatedCDAMetadata.xml")) : new Attributes(); if (cl.hasOption("f")) metadata = SAXReader.parse(cl.getOptionValue("f"), metadata); CLIUtils.addAttributes(metadata, cl.getOptionValues("m")); supplementMissingUIDs(metadata); supplementMissingDateTime(metadata, Tag.ContentDateAndTime, new Date()); supplementMissingDateTime(metadata, Tag.AcquisitionDateTime, new Date(bulkDataFile.lastModified())); supplementMissingValue(metadata, Tag.MIMETypeOfEncapsulatedDocument, pdf ? "application/pdf" : "text/XML"); supplementMissingValue(metadata, Tag.SOPClassUID, pdf ? UID.EncapsulatedPDFStorage : UID.EncapsulatedCDAStorage); return metadata; }
private static String writeXML(InputStream in, WadoURI main) throws Exception { File file = new File(main.getOutDir(), main.getOutFileName()+".xml"); TransformerHandler th = getTransformerHandler(main); th.getTransformer().setOutputProperty(OutputKeys.INDENT, main.xmlIndent ? "yes" : "no"); th.setResult(new StreamResult(file)); Attributes attrs= SAXReader.parse(in); SAXWriter saxWriter = new SAXWriter(th); saxWriter.setIncludeKeyword(main.xmlIncludeKeyword); saxWriter.write(attrs); return file.getAbsolutePath(); }
private static Attributes createMetadata(CommandLine cl, FileType inFileType) throws Exception { String metadataResource = cl.hasOption("sc") ? "resource:secondaryCaptureImageMetadata.xml" : cl.hasOption("xc") ? "resource:vlPhotographicImageMetadata.xml" : null; Attributes metadata = inFileType == FileType.jpeg && metadataResource != null ? SAXReader.parse(StreamUtils.openFileOrURL(metadataResource)) : new Attributes(); if (cl.hasOption("f")) metadata = SAXReader.parse(cl.getOptionValue("f"), metadata); CLIUtils.addAttributes(metadata, cl.getOptionValues("m")); supplementMissingUIDs(metadata); supplementMissingValue(metadata, Tag.Modality, "XC"); supplementMissingValue(metadata, Tag.SeriesNumber, "999"); supplementMissingValue(metadata, Tag.InstanceNumber, "1"); supplementMissingDateTime(metadata); supplementMissingType2(metadata); return metadata; }
if(qidors.getTimeFirst() == 0) qidors.setTimeFirst(System.currentTimeMillis()); qidors.responseAttrs.add(SAXReader.parse(new ByteArrayInputStream(removeHeader(parts[i]).getBytes("UTF-8")))); qidors.numMatches++; qidors.xmlIndent ? "yes" : "no"); th.setResult(new StreamResult(out)); Attributes attrs= SAXReader.parse(new ByteArrayInputStream(removeHeader(parts[i]).getBytes())); SAXWriter saxWriter = new SAXWriter(th); saxWriter.setIncludeKeyword(qidors.xmlIncludeKeyword);
public void query(File f) throws Exception { Attributes attrs; String filePath = f.getPath(); String fileExt = filePath.substring(filePath.lastIndexOf(".")+1).toLowerCase(); DicomInputStream dis = null; try { attrs = fileExt.equals("xml") ? SAXReader.parse(filePath) : new DicomInputStream(f).readDataset(-1, -1); if (inFilter != null) { attrs = new Attributes(inFilter.length + 1); attrs.addSelected(attrs, inFilter); } } finally { SafeClose.close(dis); } mergeKeys(attrs, keys); query(attrs); }
private static Attributes createMetadata(CommandLine cl, FileType inFileType) throws Exception { String metadataResource = cl.hasOption("sc") ? "resource:secondaryCaptureImageMetadata.xml" : cl.hasOption("xc") ? "resource:vlPhotographicImageMetadata.xml" : null; Attributes metadata = inFileType == FileType.jpeg && metadataResource != null ? SAXReader.parse(StreamUtils.openFileOrURL(metadataResource)) : new Attributes(); if (cl.hasOption("f")) metadata = SAXReader.parse(cl.getOptionValue("f"), metadata); CLIUtils.addAttributes(metadata, cl.getOptionValues("m")); supplementMissingUIDs(metadata); supplementMissingValue(metadata, Tag.Modality, "XC"); supplementMissingValue(metadata, Tag.SeriesNumber, "999"); supplementMissingValue(metadata, Tag.InstanceNumber, "1"); supplementMissingDateTime(metadata); supplementMissingType2(metadata); return metadata; }
public void query(File f) throws Exception { Attributes attrs; String filePath = f.getPath(); String fileExt = filePath.substring(filePath.lastIndexOf(".")+1).toLowerCase(); DicomInputStream dis = null; try { attrs = fileExt.equals("xml") ? SAXReader.parse(filePath) : new DicomInputStream(f).readDataset(-1, -1); if (inFilter != null) { attrs = new Attributes(inFilter.length + 1); attrs.addSelected(attrs, inFilter); } } finally { SafeClose.close(dis); } mergeKeys(attrs, keys); query(attrs); }
Attributes parsedDicomFile = SAXReader.parse(new FileInputStream(f)); if (CLIUtils.updateAttributes(parsedDicomFile, attrs, uidSuffix)) iuid = parsedDicomFile.getString(Tag.SOPInstanceUID);
Attributes parsedDicomFile = SAXReader.parse(new FileInputStream(f)); if (CLIUtils.updateAttributes(parsedDicomFile, attrs, uidSuffix)) iuid = parsedDicomFile.getString(Tag.SOPInstanceUID);