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Merge pull request #27 from AgPipeline/develop
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,67 @@ | ||
| #!/usr/bin/env bash | ||
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| # Checking the results of running the docker commands | ||
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| # Define expected results | ||
| EXPECTED_FILES=("result.json") | ||
| EXPECTED_CANOPYCOVER_VALUES=(99.75714285714285 20.91874906479126) | ||
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| # What folder are we looking in for outputs | ||
| if [[ ! "${1}" == "" ]]; then | ||
| TARGET_FOLDER="${1}" | ||
| else | ||
| TARGET_FOLDER="./outputs" | ||
| fi | ||
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| # What our target file to read is | ||
| if [[ ! "${2}" == "" ]]; then | ||
| CHECK_FILE="${2}" | ||
| else | ||
| CHECK_FILE="canopycover.csv" | ||
| fi | ||
| EXPECTED_FILES+=("${CHECK_FILE}") | ||
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| # Check if expected files are found | ||
| for i in $(seq 0 $(( ${#EXPECTED_FILES[@]} - 1 ))) | ||
| do | ||
| if [[ ! -f "${TARGET_FOLDER}/${EXPECTED_FILES[$i]}" ]]; then | ||
| echo "Expected file ${EXPECTED_FILES[$i]} is missing" | ||
| exit 10 | ||
| fi | ||
| done | ||
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| # Check the results of the canopy cover calculation | ||
| RESULT_VALUES=(`gawk ' | ||
| BEGIN { | ||
| FPAT = "([^,]+)|(\"[^\"]+\")" | ||
| } | ||
| { | ||
| if ($1 != "local_datetime") { # Skipping the header line | ||
| printf("%s\n", $2) | ||
| } | ||
| } | ||
| END { | ||
| } | ||
| ' "${TARGET_FOLDER}/${CHECK_FILE}"`) | ||
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| echo "Result counts: ${#EXPECTED_CANOPYCOVER_VALUES[@]} vs ${#RESULT_VALUES[@]}" | ||
| if [[ ${#EXPECTED_CANOPYCOVER_VALUES[@]} != ${#RESULT_VALUES[@]} ]]; then | ||
| echo "Number of results found in file (${#RESULT_VALUES[@]}) don't match expected count (${#EXPECTED_CANOPYCOVER_VALUES[@]})" | ||
| if [[ ${#RESULT_VALUES[@]} > 0 ]]; then | ||
| for i in $(seq 0 $(( ${#RESULT_VALUES[@]} - 1 ))) | ||
| do | ||
| echo "${i}: ${RESULT_VALUES[$i]}" | ||
| done | ||
| fi | ||
| exit 20 | ||
| fi | ||
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| for i in $(seq 0 $(( ${#EXPECTED_CANOPYCOVER_VALUES[@]} - 1 ))) | ||
| do | ||
| if [[ "${EXPECTED_CANOPYCOVER_VALUES[$i]}" == "${RESULT_VALUES[$i]}" ]]; then | ||
| echo "Values for index ${i} match: '${RESULT_VALUES[$i]}' '${EXPECTED_CANOPYCOVER_VALUES[$i]}'" | ||
| else | ||
| echo "Result value for index ${i}: '${RESULT_VALUES[$i]}' doesn't match expected: '${EXPECTED_CANOPYCOVER_VALUES[$i]}'" | ||
| exit 30 | ||
| fi | ||
| done |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,65 @@ | ||
| name: Testing Docker image | ||
| on: | ||
| push: | ||
| branches: | ||
| - master | ||
| - develop | ||
| pull_request: | ||
| branches: | ||
| - master | ||
| - develop | ||
| tags: | ||
| - v* | ||
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| jobs: | ||
| docker_testing: | ||
| runs-on: ubuntu-latest | ||
| name: Running Docker testing | ||
| steps: | ||
| - name: Fetch source code | ||
| uses: actions/checkout@v2 | ||
| - name: Create folders | ||
| run: | | ||
| mkdir ./inputs && chmod 777 ./inputs | ||
| mkdir ./outputs && chmod 777 ./outputs | ||
| - name: List folder contents | ||
| run: | | ||
| echo "Current folder" && ls -la | ||
| echo "test_data" && ls -l ./test_data | ||
| - name: Copy testing data files | ||
| run: | | ||
| cp "${PWD}/test_data"/* "${PWD}/inputs/" | ||
| echo "inputs" && ls -l ./inputs | ||
| - name: Folder contents | ||
| run: | | ||
| echo "Current folder" && ls -l | ||
| echo "Inputs folder" && ls -l ./inputs | ||
| echo "Outputs folder" && ls -l ./outputs | ||
| - name: Build docker image | ||
| run: docker build -t canopycover_test:latest ./ | ||
| - name: Compress docker image | ||
| run: docker save canopycover_test:latest | gzip -7 -c - > canopycover_test_image.tar.gz | ||
| - name: Upload docker image | ||
| uses: actions/upload-artifact@v2 | ||
| with: | ||
| name: canopycover_test_image | ||
| path: canopycover_test_image.tar.gz | ||
| - name: Run docker test | ||
| run: docker run --rm -v "${PWD}/inputs:/inputs" -v "${PWD}/outputs:/outputs" canopycover_test:latest --working_space /outputs --metadata /inputs/meta.yaml /inputs/rgb_17_7_W.tif /inputs/mask_1.tif | ||
| - name: Output folder contents | ||
| run: echo "Outputs folder" && ls -l ./outputs | ||
| - name: Check outputs | ||
| run: | | ||
| cat outputs/canopycover.csv | ||
| chmod +x "./.github/workflows/docker_test_check_rgb.sh" | ||
| "./.github/workflows/docker_test_check_rgb.sh" | ||
| artifact_cleanup: | ||
| runs-on: ubuntu-latest | ||
| needs: [docker_testing] | ||
| name: Cleanup artifacts upon success | ||
| steps: | ||
| - name: Remove docker artifact | ||
| uses: geekyeggo/delete-artifact@v1 | ||
| with: | ||
| name: canopycover_test_image |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,53 @@ | ||
| FROM agdrone/agpypeline:1.0 | ||
| FROM ubuntu:18.04 | ||
| LABEL maintainer="Chris Schnaufer <[email protected]>" | ||
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| # Add user | ||
| RUN useradd -u 49044 extractor \ | ||
| && mkdir /home/extractor | ||
| RUN chown -R extractor /home/extractor \ | ||
| && chgrp -R extractor /home/extractor | ||
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| # Install the Python version we want | ||
| RUN apt-get update && \ | ||
| apt-get upgrade -y && \ | ||
| apt-get install -y --no-install-recommends \ | ||
| python3.7 \ | ||
| python3-pip && \ | ||
| ln -sfn /usr/bin/python3.7 /usr/bin/python && \ | ||
| ln -sfn /usr/bin/python3.7 /usr/bin/python3 && \ | ||
| ln -sfn /usr/bin/python3.7m /usr/bin/python3m && \ | ||
| apt-get autoremove -y && \ | ||
| apt-get clean && \ | ||
| rm -rf /var/lib/apt/lists/* | ||
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| # Perform some upgrades | ||
| RUN python3 -m pip install --upgrade --no-cache-dir pip | ||
| RUN python3 -m pip install --upgrade --no-cache-dir setuptools | ||
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| # Install applications we need | ||
| RUN apt-get update && \ | ||
| apt-get install -y --no-install-recommends \ | ||
| python3-gdal \ | ||
| gdal-bin \ | ||
| libgdal-dev \ | ||
| gcc \ | ||
| g++ \ | ||
| python3.7-dev && \ | ||
| python3 -m pip install --upgrade --no-cache-dir \ | ||
| wheel && \ | ||
| python3 -m pip install --upgrade --no-cache-dir \ | ||
| numpy && \ | ||
| python3 -m pip install --upgrade --no-cache-dir \ | ||
| pygdal==2.2.3.* && \ | ||
| apt-get remove -y \ | ||
| libgdal-dev \ | ||
| gcc \ | ||
| g++ \ | ||
| python3-dev && \ | ||
| apt-get autoremove -y && \ | ||
| apt-get clean && \ | ||
| rm -rf /var/lib/apt/lists/* | ||
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| COPY requirements.txt packages.txt /home/extractor/ | ||
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| USER root | ||
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