Add S3Handle using minio 5.0.0

[joshmoore]

URLs starting with s3:// will now be passed to the
S3Handle. ./showinfo s3://bucket/path/file.tiff then
opens the file as expected.

• add login information
• introduce caching: https://trello.com/c/KKZCpvaV/64-s3-url-to-take-parameters
• add documentation

[joshmoore]

Caching looks like this:

        s3Client.getObject(
                "bucket",
                "/browse/formatted/20180823/iss_breast/dots-fov_000-Z0-H0-C0.tiff",
                "/tmp/cache-dir");

[joshmoore]

With the latest 2 commits, we can now read from our own minio server (as opposed to AWS) but there seems to be some corruption:

loci.formats.in.TiffReader.initFile(s3://local-bucket.localhost:9000/hybridization-fov_000_Z0_T0_C0.ome.tiff)
Reading IFDs
Error reading IFD type at: 206

loci.common.enumeration.EnumException: Unable to find IFDType with code: 0
	at loci.formats.tiff.IFDType.get(IFDType.java:90) ~[bioformats_package.jar:5.10.0-SNAPSHOT]
	at loci.formats.tiff.TiffParser.readTiffIFDEntry(TiffParser.java:1320) [bioformats_package.jar:5.10.0-SNAPSHOT]
	at loci.formats.tiff.TiffParser.getIFD(TiffParser.java:440) [bioformats_package.jar:5.10.0-SNAPSHOT]
	at loci.formats.tiff.TiffParser.getMainIFDs(TiffParser.java:224) [bioformats_package.jar:5.10.0-SNAPSHOT]
	at loci.formats.in.MinimalTiffReader.initFile(MinimalTiffReader.java:459) [bioformats_package.jar:5.10.0-SNAPSHOT]
	at loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:583) [bioformats_package.jar:5.10.0-SNAPSHOT]
	at loci.formats.FormatReader.setId(FormatReader.java:1397) [bioformats_package.jar:5.10.0-SNAPSHOT]
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650) [bioformats_package.jar:5.10.0-SNAPSHOT]
	at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:1034) [bioformats_package.jar:5.10.0-SNAPSHOT]
	at loci.formats.tools.ImageInfo.main(ImageInfo.java:1120) [bioformats_package.jar:5.10.0-SNAPSHOT]

[joshmoore]

Ah, minio is compiled for JDK8+. cc: @sbesson @melissalinkert @dgault @manics

[sbesson]

Under some conditions this seem to trigger a NPE - see https://web-proxy.openmicroscopy.org/east-ci/job/BIOFORMATS-test-folder/35481/console

[joshmoore]

Ha. Ok. That's interesting.

https://github.com/snoopycrimecop/bioformats/blob/develop/merge/daily/components/formats-gpl/src/loci/formats/in/InCellReader.java#L863 does

      else if (qName.equals("Image")) {
        String file = attributes.getValue("filename");
        String thumb = attributes.getValue("thumbnail");
        Location current = new Location(currentId).getAbsoluteFile();

        Location imageFile = new Location(current.getParentFile(), file);
        currentImageFile = imageFile.getAbsolutePath();
        currentThumbnail =
          new Location(current.getParentFile(), thumb).getAbsolutePath();
      }

and https://github.com/ome/ome-common-java/blob/master/src/main/java/loci/common/Location.java#L148 does:

    this(parent + File.separator + child);

so I assume the current behavior is to return a Location ending in "null". I'll add the test for null here, but this probably could use further review.

[sbesson]

Closing as superseded by #33