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Fix #1329 : stowrs utility : Ignore probing content type of file(s) i…
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…f it is explicitly specified by --contentType flag
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@vrindanayak
vrindanayak committed Aug 2, 2023
1 parent 73510b3 commit 0765b42
Showing 1 changed file with 35 additions and 42 deletions.
77 changes: 35 additions & 42 deletions dcm4che-tool/dcm4che-tool-stowrs/src/main/java/org/dcm4che3/tool/stowrs/StowRS.java
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Original file line number Diff line number Diff line change
Expand Up @@ -364,7 +364,7 @@ private void doNecessaryChecks(CommandLine cl, List<String> files)
disableTM = cl.hasOption("disableTM");
encapsulatedDocLength = cl.hasOption("encapsulatedDocLength");
if (cl.hasOption("contentType"))
bulkdataFileContentType = fileContentTypeFromCL = fileContentType(cl.getOptionValue("contentType"));
fileContentTypeFromCL = fileContentType(cl.getOptionValue("contentType"));
limit = Integer.parseInt(cl.getOptionValue("limit", "0"));
configureTmpFile(cl);
processFirstFile(cl);
Expand All @@ -380,19 +380,22 @@ private void configureTmpFile(CommandLine cl) {

private void processFirstFile(CommandLine cl) throws Exception {
if (cl.getArgList().isEmpty()) {
setContentAndAcceptType(cl, false);
setRequestContentAndAcceptTypes(cl, false);
return;
}

applyFunctionToFile(cl.getArgList().get(0), false, path -> {
String contentType = Files.probeContentType(path);
if (contentType == null || !contentType.equals(MediaTypes.APPLICATION_DICOM)) {
firstBulkdataFileContentType = FileContentType.valueOf(contentType, path);
if (fileContentTypeFromCL == null)
bulkdataFileContentType = firstBulkdataFileContentType;
}
setContentAndAcceptType(cl, contentType != null && contentType.equals(MediaTypes.APPLICATION_DICOM));
});
if (fileContentTypeFromCL == null)
applyFunctionToFile(cl.getArgList().get(0), false, path -> {
String contentType = Files.probeContentType(path);
setRequestContentAndAcceptTypes(cl, contentType != null && contentType.equals(MediaTypes.APPLICATION_DICOM));
if (contentType == null || !contentType.equals(MediaTypes.APPLICATION_DICOM))
firstBulkdataFileContentType = bulkdataFileContentType = FileContentType.valueOf(contentType, path);
});
else {
LOG.info("Ignoring checking of content type of first file");
firstBulkdataFileContentType = bulkdataFileContentType = fileContentTypeFromCL;
setRequestContentAndAcceptTypes(cl, false);
}
}

private static FileContentType fileContentType(String s) {
Expand Down Expand Up @@ -526,7 +529,7 @@ static FileContentType valueOf(String contentType, Path path) {
}
}

private static void setContentAndAcceptType(CommandLine cl, boolean dicom) {
private static void setRequestContentAndAcceptTypes(CommandLine cl, boolean dicom) {
if (dicom) {
requestContentType = MediaTypes.APPLICATION_DICOM;
requestAccept = cl.hasOption("a") ? getOptionValue("a", cl) : MediaTypes.APPLICATION_DICOM_XML;
Expand Down Expand Up @@ -603,13 +606,9 @@ private void pixelMetadata(String contentLoc, StowRSBulkdata stowRSBulkdata, Att
private Attributes createStaticMetadata() throws Exception {
LOG.info("Creating static metadata. Set defaults, if essential attributes are not present.");
Attributes metadata;
if (firstBulkdataFileContentType == null)
metadata = SAXReader.parse(StreamUtils.openFileOrURL(metadataFilePathStr));
else {
metadata = SAXReader.parse(StreamUtils.openFileOrURL(firstBulkdataFileContentType.getSampleMetadataResourceURL()));
addAttributesFromFile(metadata);
supplementSOPClass(metadata, firstBulkdataFileContentType.getSOPClassUID());
}
metadata = SAXReader.parse(StreamUtils.openFileOrURL(firstBulkdataFileContentType.getSampleMetadataResourceURL()));
addAttributesFromFile(metadata);
supplementSOPClass(metadata, firstBulkdataFileContentType.getSOPClassUID());
metadata.addAll(attrs);
if (!url.endsWith("studies"))
metadata.setString(Tag.StudyInstanceUID, VR.UI, url.substring(url.lastIndexOf("/") + 1));
Expand Down Expand Up @@ -1001,18 +1000,11 @@ private void writeMetadataAndBulkData(OutputStream out, List<String> files, fina

for (String file : files)
applyFunctionToFile(file, true, path -> {
if (ignoreNonMatchingFileContentTypes(path))
LOG.info(MessageFormat.format(rb.getString(
"ignore-non-matching-file-content-type"),
path,
bulkdataFileContentType,
fileContentTypeFromCL != null
? fileContentTypeFromCL : firstBulkdataFileContentType));
else {
if (!ignoreNonMatchingFileContentTypes(path))
new JSONWriter(gen).write(
supplementMetadataFromFile(path, createMetadata(staticMetadata)));
}
});

gen.writeEnd();
gen.flush();
}
Expand All @@ -1033,19 +1025,13 @@ private void writeXMLMetadataAndBulkdata(final OutputStream out, List<String> fi
}

for (String file : files)
applyFunctionToFile(file, true, path -> writeXMLMetadataAndBulkdataForEach(out, staticMetadata, path, stowChunk));
applyFunctionToFile(file, true, path -> writeXMLMetadataAndBulkdata(out, staticMetadata, path, stowChunk));
}

private void writeXMLMetadataAndBulkdataForEach(OutputStream out, Attributes staticMetadata, Path bulkdataFilePath, StowChunk stowChunk) {
private void writeXMLMetadataAndBulkdata(OutputStream out, Attributes staticMetadata, Path bulkdataFilePath, StowChunk stowChunk) {
try {
if (ignoreNonMatchingFileContentTypes(bulkdataFilePath)) {
LOG.info(MessageFormat.format(rb.getString(
"ignore-non-matching-file-content-type"),
bulkdataFilePath,
bulkdataFileContentType,
fileContentTypeFromCL != null ? fileContentTypeFromCL : firstBulkdataFileContentType));
if (ignoreNonMatchingFileContentTypes(bulkdataFilePath))
return;
}

Attributes metadata = supplementMetadataFromFile(bulkdataFilePath, createMetadata(staticMetadata));
try (ByteArrayOutputStream bOut = new ByteArrayOutputStream()) {
Expand All @@ -1059,11 +1045,18 @@ private void writeXMLMetadataAndBulkdataForEach(OutputStream out, Attributes sta
}

private boolean ignoreNonMatchingFileContentTypes(Path path) throws IOException {
if (fileCount.incrementAndGet() == 1 || fileContentTypeFromCL != null)
return false;

bulkdataFileContentType = FileContentType.valueOf(Files.probeContentType(path), path);
return !firstBulkdataFileContentType.equals(bulkdataFileContentType);
if (fileCount.incrementAndGet() > 1) {
if (fileContentTypeFromCL == null) {
bulkdataFileContentType = FileContentType.valueOf(Files.probeContentType(path), path);
if (!firstBulkdataFileContentType.equals(bulkdataFileContentType)) {
LOG.info(MessageFormat.format(rb.getString("ignore-non-matching-file-content-type"),
path, bulkdataFileContentType, firstBulkdataFileContentType));
return true;
}
} else
LOG.info("Ignoring checking of content type of subsequent file {}", path);
}
return false;
}

private void writeXMLMetadata(OutputStream out, Attributes staticMetadata) {
Expand Down

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