ZarrReader: Add Unit tests

dgault commented 3 years ago

Adds some initial unit tests for the ZarrReader and the JZarrServiceimpl

joshmoore commented 3 years ago

Using my ome_zarr_test_suite script:

#!/usr/bin/env bash
set -e
set -u
test -e ZarrReader  || git clone git://github.com/ome/ZarrReader 1>&2
cd ZarrReader
mvn package -DskipTests # 1>&2
cd ..
java -jar ZarrReader/target/*.jar -nopix "$@"

(pinned to your branch)

I'm seeing

ZarrReader initializing fake.zarr/.zattrs
Exception in thread "main" java.lang.IndexOutOfBoundsException: Index 0 out of bounds for length 0
    at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)
    at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)
    at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)
    at java.base/java.util.Objects.checkIndex(Objects.java:372)
    at java.base/java.util.ArrayList.get(ArrayList.java:459)
    at loci.formats.in.ZarrReader.openZarr(ZarrReader.java:423)
    at loci.formats.in.ZarrReader.initializeZarrService(ZarrReader.java:354)
    at loci.formats.in.ZarrReader.initFile(ZarrReader.java:132)
    at loci.formats.FormatReader.setId(FormatReader.java:1421)
    at loci.formats.ImageReader.setId(ImageReader.java:849)
    at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
    at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:1035)
    at loci.formats.tools.ImageInfo.main(ImageInfo.java:1121)
    at loci.formats.in.ZarrReader.main(ZarrReader.java:667)

for fake.zarr/.zattrs, fake.zarr/.zgroup, and fake.zarr/0/0.0.0.0.0

joshmoore commented 3 years ago

Copied a few of the pom.xml changes over to #4 and added an --exclude to the description of this PR.

joshmoore commented 3 years ago

Green!

ome / ZarrReader

ZarrReader: Add Unit tests #3