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Enable ZarrReader tests #16

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Enable ZarrReader tests #16

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14ff471
Enable ZarrReader tests
joshmoore Sep 17, 2021
2d4d55e
Passing zarr_reader_open
joshmoore Sep 19, 2021
7ed18c7
Set format to prevent long searches over HTTP
joshmoore Sep 19, 2021
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31 changes: 31 additions & 0 deletions scripts/zarr_reader_open
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Original file line number Diff line number Diff line change
@@ -0,0 +1,31 @@
#!/usr/bin/env bash

set -e
set -u
set -x

export INVOCATION_DIR=${INVOCATION_DIR:-$PWD}

echo =======================
echo Current Directory: $PWD
echo Invocation Directory: ${INVOCATION_DIR}
echo =======================

# Install bftools if missing
test -e ${INVOCATION_DIR}/bftools || {
pushd ${INVOCATION_DIR}
test -e bftools.zip || wget https://downloads.openmicroscopy.org/bio-formats/latest/artifacts/bftools.zip
unzip bftools
popd
}

# Build ZarrReader if not built
test -e ${INVOCATION_DIR}/ZarrReader || {
git clone git://github.com/ome/ZarrReader ${INVOCATION_DIR}/ZarrReader
pushd ${INVOCATION_DIR}ZarrReader
mvn package -DskipTests # 1>&2
popd
}

export BF_CP=${INVOCATION_DIR}/ZarrReader/target/\*
${INVOCATION_DIR}/bftools/showinf -format Zarr -nopix "$@"/.zattrs
3 changes: 3 additions & 0 deletions suites.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,3 +7,6 @@

- name: checksum
script: zarr_checksum

- name: reader
script: zarr_reader_open
4 changes: 3 additions & 1 deletion test_suite.py
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Expand Up @@ -180,7 +180,9 @@ def source(request: SubRequest, tmpdir: py.path.local) -> typing.Iterator[Source
def suite(request: SubRequest, tmpdir: os.PathLike) -> typing.Iterator[Suite]:
doc = request.param
script = doc["script"]
script = f"{request.config.invocation_dir}/scripts/{script}"
idir = f"{request.config.invocation_dir}"
os.environ["INVOCATION_DIR"] = idir
script = f"{idir}/scripts/{script}"
yield Suite(script)


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