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valentin-pinkaunormanrz
valentin-pinkau
authored and
normanrz
committed
Refactor tests (#56)
* use test scripts * make executable * add local test script
1 parent 7f982a2 commit 9300ea8

16 files changed

+198
-178
lines changed

‎.circleci/config.yml‎

Lines changed: 14 additions & 178 deletions
Original file line numberDiff line numberDiff line change
@@ -13,56 +13,23 @@ jobs:
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- run:
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name: Build docker image
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command: docker build -t "scalableminds/webknossos-cuber:${CIRCLE_BUILD_NUM}" .
16+
command: tests/scripts/build_docker_image.sh
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name: Decompress test data
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command: tar -xzvf testdata/WT1_wkw.tar.gz
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command: tests/scripts/decompress_test_data.sh
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- run:
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name: Check formatting
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command: |
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set -x
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docker run \
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--rm \
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--entrypoint "/bin/bash" \
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-w "/" \
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scalableminds/webknossos-cuber:${CIRCLE_BUILD_NUM} \
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-c "black --check /app/wkcuber"
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command: tests/scripts/check_formatting.sh
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- run:
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name: Python tests
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command: |
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set -x
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mkdir -p testoutput
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docker run \
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-v "${PWD}/testdata:/testdata" \
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-v "${PWD}/testoutput:/testoutput" \
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--rm \
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--entrypoint "/bin/bash" \
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-w "/" \
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scalableminds/webknossos-cuber:${CIRCLE_BUILD_NUM} \
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-c "py.test /app/tests"
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command: tests/scripts/python_tests.sh
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- run:
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name: Test tiff cubing
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command: |
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set -x
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mkdir -p testoutput/tiff
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docker run \
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-v "${PWD}/testdata:/testdata" \
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-v "${PWD}/testoutput:/testoutput" \
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--rm \
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scalableminds/webknossos-cuber:${CIRCLE_BUILD_NUM} \
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wkcuber.cubing \
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--verbose \
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--jobs 2 \
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--batch_size 8 \
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--layer_name color \
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/testdata/tiff /testoutput/tiff
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[ -d testoutput/tiff/color ]
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[ -d testoutput/tiff/color/1 ]
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[ $(find testoutput/tiff/color/1 -mindepth 3 -name "*.wkw" | wc -l) -eq 1 ]
32+
command: tests/scripts/tiff_cubing.sh
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# - run:
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# name: Test DM3 cubing
@@ -88,170 +55,39 @@ jobs:
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- run:
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name: Test tile cubing
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command: |
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set -x
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mkdir -p testoutput/temca2
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docker run \
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-v "${PWD}/testdata:/testdata" \
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-v "${PWD}/testoutput:/testoutput" \
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--rm \
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scalableminds/webknossos-cuber:${CIRCLE_BUILD_NUM} \
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wkcuber.tile_cubing \
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--verbose \
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--jobs 2 \
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--batch_size 8 \
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--layer_name color \
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/testdata/temca2 /testoutput/temca2
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[ -d testoutput/temca2/color ]
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[ -d testoutput/temca2/color/1 ]
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[ $(find testoutput/temca2/color/1 -mindepth 3 -name "*.wkw" | wc -l) -eq 8 ]
58+
command: tests/scripts/tile_cubing.sh
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- run:
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name: Test simple tiff cubing
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command: |
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set -x
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mkdir -p testoutput/tiff2
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docker run \
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-v "${PWD}/testdata:/testdata" \
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-v "${PWD}/testoutput:/testoutput" \
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--rm \
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scalableminds/webknossos-cuber:${CIRCLE_BUILD_NUM} \
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wkcuber \
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--verbose \
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--jobs 2 \
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--batch_size 8 \
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--layer_name color \
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--max_mag 4 \
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--scale 11.24,11.24,25 \
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--name awesome_data \
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/testdata/tiff /testoutput/tiff2
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[ -d testoutput/tiff2/color ]
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[ -d testoutput/tiff2/color/1 ]
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[ $(find testoutput/tiff2/color/1 -mindepth 3 -name "*.wkw" | wc -l) -eq 1 ]
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[ -e testoutput/tiff2/datasource-properties.json ]
62+
command: tests/scripts/simple_tiff_cubing.sh
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- run:
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name: Test simple tiff cubing (no compression)
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command: |
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set -x
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mkdir -p testoutput/tiff3
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docker run \
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-v "${PWD}/testdata:/testdata" \
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-v "${PWD}/testoutput:/testoutput" \
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--rm \
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scalableminds/webknossos-cuber:${CIRCLE_BUILD_NUM} \
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wkcuber \
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--verbose \
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--jobs 2 \
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--batch_size 8 \
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--layer_name color \
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--max_mag 4 \
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--no_compress \
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--scale 11.24,11.24,25 \
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--name awesome_data \
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/testdata/tiff /testoutput/tiff3
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[ -d testoutput/tiff3/color ]
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[ -d testoutput/tiff3/color/1 ]
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[ $(find testoutput/tiff3/color/1 -mindepth 3 -name "*.wkw" | wc -l) -eq 1 ]
156-
[ -e testoutput/tiff3/datasource-properties.json ]
66+
command: tests/scripts/simple_tiff_cubing_no_compression.sh
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- run:
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name: Test KNOSSOS conversion
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command: |
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set -x
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mkdir -p testoutput/knossos
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docker run \
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-v "${PWD}/testdata:/testdata" \
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-v "${PWD}/testoutput:/testoutput" \
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--rm \
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scalableminds/webknossos-cuber:${CIRCLE_BUILD_NUM} \
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wkcuber.convert_knossos \
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--verbose \
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--jobs 2 \
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--dtype uint8 \
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--layer_name color \
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--mag 1 \
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/testdata/knossos/color/1 /testoutput/knossos
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[ -d testoutput/knossos/color ]
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[ -d testoutput/knossos/color/1 ]
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[ $(find testoutput/knossos/color/1 -mindepth 3 -name "*.wkw" | wc -l) -eq 1 ]
70+
command: tests/scripts/knossos_conversion.sh
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- run:
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name: Decompress reference magnification data
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command: mkdir -p testdata/tiff_mag_2_reference && tar -xzvf testdata/tiff_mag_2_reference.tar.gz -C testdata/tiff_mag_2_reference
74+
command: tests/scripts/decompress_reference_mag.sh
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- run:
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name: Test downsampling
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command: |
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set -x
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docker run \
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-v "${PWD}/testoutput:/testoutput" \
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--rm \
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scalableminds/webknossos-cuber:${CIRCLE_BUILD_NUM} \
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wkcuber.downsampling \
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--verbose \
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--jobs 2 \
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--max 8 \
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--buffer_cube_size 128 \
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--layer_name color \
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/testoutput/tiff
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[ -d testoutput/tiff/color/2 ]
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[ -d testoutput/tiff/color/4 ]
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[ -d testoutput/tiff/color/8 ]
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[ -n testoutput/tiff/color/16 ]
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[ $(find testoutput/tiff/color/2 -mindepth 3 -name "*.wkw" | wc -l) -eq 1 ]
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[ $(find testoutput/tiff/color/4 -mindepth 3 -name "*.wkw" | wc -l) -eq 1 ]
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[ $(find testoutput/tiff/color/8 -mindepth 3 -name "*.wkw" | wc -l) -eq 1 ]
205-
cmp --silent testoutput/tiff/color/2/z0/y0/x0.wkw testdata/tiff_mag_2_reference/color/2/z0/y0/x0.wkw
78+
command: tests/scripts/downsampling.sh
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20780
- run:
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name: Test compression
209-
command: |
210-
set -x
211-
docker run \
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-v "${PWD}/testoutput:/testoutput" \
213-
--rm \
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scalableminds/webknossos-cuber:${CIRCLE_BUILD_NUM} \
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wkcuber.compress \
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--verbose \
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--jobs 2 \
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--layer_name color \
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/testoutput/tiff /testoutput/tiff_compress
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[ -d testoutput/tiff_compress/color/1 ]
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[ -d testoutput/tiff_compress/color/2 ]
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[ -d testoutput/tiff_compress/color/4 ]
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[ -d testoutput/tiff_compress/color/8 ]
82+
command: tests/scripts/compression.sh
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- run:
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name: Test in-place compression
227-
command: |
228-
set -x
229-
cp -r testoutput/tiff testoutput/tiff_compress2
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docker run \
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-v "${PWD}/testoutput:/testoutput" \
232-
--rm \
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scalableminds/webknossos-cuber:${CIRCLE_BUILD_NUM} \
234-
wkcuber.compress \
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--verbose \
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--jobs 2 \
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--layer_name color \
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/testoutput/tiff_compress2
86+
command: tests/scripts/in_place_compression.sh
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- run:
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name: Test metadata generation
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command: |
243-
set -x
244-
docker run \
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-v "${PWD}/testoutput:/testoutput" \
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--rm \
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scalableminds/webknossos-cuber:${CIRCLE_BUILD_NUM} \
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wkcuber.metadata \
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--name test_dataset \
250-
--scale 11.24,11.24,25 \
251-
/testoutput/tiff
252-
[ -e testoutput/tiff/datasource-properties.json ]
253-
jq --argfile a testdata/tiff/datasource-properties.fixture.json --argfile b testoutput/tiff/datasource-properties.json -n '$a == $b'
254-
# diff testdata/tiff/datasource-properties.fixture.json testoutput/tiff/datasource-properties.json
90+
command: tests/scripts/meta_generation.sh
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- run:
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name: Push docker images

‎test.sh‎

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@@ -0,0 +1,15 @@
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export CIRCLE_BUILD_NUM=latest
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tests/scripts/build_docker_image.sh
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tests/scripts/decompress_test_data.sh
4+
tests/scripts/check_formatting.sh
5+
tests/scripts/python_tests.sh
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tests/scripts/tiff_cubing.sh
7+
tests/scripts/tile_cubing.sh
8+
tests/scripts/simple_tiff_cubing.sh
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tests/scripts/simple_tiff_cubing_no_compression.sh
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tests/scripts/knossos_conversion.sh
11+
tests/scripts/decompress_reference_mag.sh
12+
tests/scripts/downsampling.sh
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tests/scripts/compression.sh
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tests/scripts/in_place_compression.sh
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tests/scripts/meta_generation.sh

‎tests/scripts/build_docker_image.sh‎

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set -xe
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docker build -t "scalableminds/webknossos-cuber:${CIRCLE_BUILD_NUM}" .

‎tests/scripts/check_formatting.sh‎

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set -xe
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docker run \
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--rm \
4+
--entrypoint "/bin/bash" \
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-w "/" \
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scalableminds/webknossos-cuber:${CIRCLE_BUILD_NUM} \
7+
-c "black --check /app/wkcuber"

‎tests/scripts/compression.sh‎

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set -xe
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docker run \
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-v "${PWD}/testoutput:/testoutput" \
4+
--rm \
5+
scalableminds/webknossos-cuber:${CIRCLE_BUILD_NUM} \
6+
wkcuber.compress \
7+
--verbose \
8+
--jobs 2 \
9+
--layer_name color \
10+
/testoutput/tiff /testoutput/tiff_compress
11+
[ -d testoutput/tiff_compress/color/1 ]
12+
[ -d testoutput/tiff_compress/color/2 ]
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[ -d testoutput/tiff_compress/color/4 ]
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[ -d testoutput/tiff_compress/color/8 ]

‎tests/scripts/decompress_reference_mag.sh‎

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set -xe
2+
mkdir -p testdata/tiff_mag_2_reference && tar -xzvf testdata/tiff_mag_2_reference.tar.gz -C testdata/tiff_mag_2_reference

‎tests/scripts/decompress_test_data.sh‎

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tar -xzvf testdata/WT1_wkw.tar.gz

‎tests/scripts/downsampling.sh‎

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set -xe
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docker run \
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-v "${PWD}/testoutput:/testoutput" \
4+
--rm \
5+
scalableminds/webknossos-cuber:${CIRCLE_BUILD_NUM} \
6+
wkcuber.downsampling \
7+
--verbose \
8+
--jobs 2 \
9+
--max 8 \
10+
--buffer_cube_size 128 \
11+
--layer_name color \
12+
/testoutput/tiff
13+
[ -d testoutput/tiff/color/2 ]
14+
[ -d testoutput/tiff/color/4 ]
15+
[ -d testoutput/tiff/color/8 ]
16+
[ -n testoutput/tiff/color/16 ]
17+
[ $(find testoutput/tiff/color/2 -mindepth 3 -name "*.wkw" | wc -l) -eq 1 ]
18+
[ $(find testoutput/tiff/color/4 -mindepth 3 -name "*.wkw" | wc -l) -eq 1 ]
19+
[ $(find testoutput/tiff/color/8 -mindepth 3 -name "*.wkw" | wc -l) -eq 1 ]
20+
cmp --silent testoutput/tiff/color/2/z0/y0/x0.wkw testdata/tiff_mag_2_reference/color/2/z0/y0/x0.wkw

‎tests/scripts/in_place_compression.sh‎

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set -xe
2+
cp -r testoutput/tiff testoutput/tiff_compress2
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docker run \
4+
-v "${PWD}/testoutput:/testoutput" \
5+
--rm \
6+
scalableminds/webknossos-cuber:${CIRCLE_BUILD_NUM} \
7+
wkcuber.compress \
8+
--verbose \
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--jobs 2 \
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--layer_name color \
11+
/testoutput/tiff_compress2

‎tests/scripts/knossos_conversion.sh‎

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set -xe
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mkdir -p testoutput/knossos
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docker run \
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-v "${PWD}/testdata:/testdata" \
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-v "${PWD}/testoutput:/testoutput" \
6+
--rm \
7+
scalableminds/webknossos-cuber:${CIRCLE_BUILD_NUM} \
8+
wkcuber.convert_knossos \
9+
--verbose \
10+
--jobs 2 \
11+
--dtype uint8 \
12+
--layer_name color \
13+
--mag 1 \
14+
/testdata/knossos/color/1 /testoutput/knossos
15+
[ -d testoutput/knossos/color ]
16+
[ -d testoutput/knossos/color/1 ]
17+
[ $(find testoutput/knossos/color/1 -mindepth 3 -name "*.wkw" | wc -l) -eq 1 ]

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