Opening non-existing files throws NPE

[dscho]

It shows this exception:

(Fiji Is Just) ImageJ 2.0.0-rc-2; Java 1.6.0_24 [64-bit]; Linux 3.2.0-64-generic; 27MB of 10279MB (<1%)

java.lang.UnsupportedOperationException: Attempting to read or write from a io.scif.io.VirtualHandle. There is no source to operate on.
    at io.scif.io.VirtualHandle.readFully(VirtualHandle.java:141)
    at io.scif.io.RandomAccessInputStream.readFully(RandomAccessInputStream.java:474)
    at io.scif.io.RandomAccessInputStream.readString(RandomAccessInputStream.java:397)
    at io.scif.ome.formats.OMEXMLFormat$Checker.isFormat(OMEXMLFormat.java:232)
    at io.scif.AbstractChecker.isFormat(AbstractChecker.java:91)
    at io.scif.services.DefaultFormatService.getFormatList(DefaultFormatService.java:289)
    at io.scif.services.DefaultFormatService.getFormat(DefaultFormatService.java:271)
    at net.imagej.DefaultDatasetService.canOpen(DefaultDatasetService.java:215)
    at net.imagej.io.DatasetIOPlugin.supportsOpen(DatasetIOPlugin.java:66)
    at org.scijava.io.DefaultIOService.getOpener(DefaultIOService.java:66)
    at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:129)
    at net.imagej.legacy.DefaultLegacyHooks.interceptFileOpen(DefaultLegacyHooks.java:427)
    at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:156)
    at ij.IJ.runPlugIn(IJ.java)
    at ij.Executer.runCommand(Executer.java:131)
    at ij.Executer.run(Executer.java:64)
    at java.lang.Thread.run(Thread.java:662)

and the console shows a lot of similar stack traces like the following (with different formats):

11:51:56.167 [Open...] DEBUG loci.formats.FormatHandler - 
java.io.FileNotFoundException: /tmp/a1.pg (No such file or directory)
    at java.io.RandomAccessFile.open(Native Method) ~[na:1.6.0_24]
    at java.io.RandomAccessFile.<init>(RandomAccessFile.java:212) ~[na:1.6.0_24]
    at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:127) ~[formats-common-5.0.2.jar:na]
    at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:143) ~[formats-common-5.0.2.jar:na]
    at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:152) ~[formats-common-5.0.2.jar:na]
    at loci.common.Location.getHandle(Location.java:323) ~[formats-common-5.0.2.jar:na]
    at loci.common.Location.getHandle(Location.java:293) ~[formats-common-5.0.2.jar:na]
    at loci.common.Location.getHandle(Location.java:283) ~[formats-common-5.0.2.jar:na]
    at loci.common.Location.getHandle(Location.java:273) ~[formats-common-5.0.2.jar:na]
    at loci.common.RandomAccessInputStream.<init>(RandomAccessInputStream.java:102) ~[formats-common-5.0.2.jar:na]
    at loci.formats.FormatReader.isThisType(FormatReader.java:612) ~[formats-api-5.0.2.jar:na]
    at loci.formats.ImageReader.isThisType(ImageReader.java:247) [formats-api-5.0.2.jar:na]
    at io.scif.bf.BioFormatsFormat$Checker.isFormat(BioFormatsFormat.java:199) [scifio-bf-compat-1.7.2.jar:1.7.2]
    at io.scif.services.DefaultFormatService.getFormatList(DefaultFormatService.java:289) [scifio-0.14.1.jar:0.14.1]
    at io.scif.services.DefaultFormatService.getFormat(DefaultFormatService.java:271) [scifio-0.14.1.jar:0.14.1]
    at net.imagej.DefaultDatasetService.canOpen(DefaultDatasetService.java:215) [imagej-common-0.7.2.jar:0.7.2]
    at net.imagej.io.DatasetIOPlugin.supportsOpen(DatasetIOPlugin.java:66) [imagej-common-0.7.2.jar:0.7.2]
    at org.scijava.io.DefaultIOService.getOpener(DefaultIOService.java:66) [scijava-common-2.22.3.jar:2.22.3]
    at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:129) [imagej-legacy-0.5.3.jar:0.5.3]
    at net.imagej.legacy.DefaultLegacyHooks.interceptFileOpen(DefaultLegacyHooks.java:427) [imagej-legacy-0.5.3.jar:0.5.3]
    at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:156) [imagej-legacy-0.5.3.jar:0.5.3]
    at ij.IJ.runPlugIn(IJ.java) [na:1.49b]
    at ij.Executer.runCommand(Executer.java:131) [na:1.49b]
    at ij.Executer.run(Executer.java:64) [na:1.49b]
    at java.lang.Thread.run(Thread.java:662) [na:1.6.0_24]

@hinerm I fear that we need something clever here, to be able to pass virtual handles as well as real files...

[ctrueden]

Maybe we should just bite the bullet and tackle scifio/scifio#181?

[hinerm]

Since these formats (OMEXML and BioFormats) weren't in the main SCIFIO component I didn't review them when I was updating checkers to ensure valid streams before reading.

Should be simple fixes in both cases.

[hinerm]

... should be simple fix in the OMEXMLFormat case...

[hinerm]

The formats are now fixed. And with imagej/imagej-plugins-commands@0086d09 we will now actually display the error when it happens. I don't think there's anything else to do for this issue right now.