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Improve handling of OME-TIFF multi-file filesets with partial metadata blocks #2314

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merged 2 commits into from
Apr 4, 2016
Merged

Improve handling of OME-TIFF multi-file filesets with partial metadata blocks #2314

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ccc77fc
Improve handling of OME-TIFF multi-file filesets with partial metadat…
sbesson Mar 29, 2016
10391fb
Do not store meta to prevent unexpected interference with initFile()
sbesson Mar 29, 2016
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26 changes: 23 additions & 3 deletions components/formats-bsd/src/loci/formats/in/OMETiffReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -163,6 +163,27 @@ public boolean isThisType(String name, boolean open) {
}
metaFile = new Location(name).getAbsolutePath();
boolean valid = super.isThisType(name, open);
if (metadataFile != null) {
// this is a binary-only file
// overwrite XML with what is in the companion OME-XML file
String dir = new File(metaFile).getParent();
Location path = new Location(dir, metadataFile);
LOGGER.debug("Checking metadata file {}", path);
if (!path.exists()) return false;
metadataFile = path.getAbsolutePath();

try {
String xml = readMetadataFile();
service.createOMEXMLMetadata(xml);
} catch (ServiceException se) {
LOGGER.debug("OME-XML parsing failed", se);
return false;
} catch (IOException e) {
return false;
} catch (NullPointerException e) {
return false;
}
}
if (valid && !isGroupFiles()) {
try {
return isSingleFile(metaFile);
Expand Down Expand Up @@ -215,11 +236,10 @@ else if (description instanceof String) {
meta = service.createOMEXMLMetadata(comment);

try {
String metadataFile = meta.getBinaryOnlyMetadataFile();
metadataFile = meta.getBinaryOnlyMetadataFile();
// check the suffix to make sure that the MetadataFile is not
// referencing the current OME-TIFF
if (metadataFile != null && !checkSuffix(metadataFile, "ome.tiff") &&
!checkSuffix(metadataFile, "ome.tif"))
if (metadataFile != null)
{
return true;
}
Expand Down