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fix paths of the output notebook
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.github/workflows/test_colab.yml

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@@ -89,7 +89,7 @@ jobs:
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for nb in part1_prerequisites part2_searching_basics part3_exploring_cohorts; do
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docker run -d --name colab -v "$(pwd):/content" -e GOOGLE_APPLICATION_CREDENTIALS="${{ env.GOOGLE_APPLICATION_CREDENTIALS }}" imagingdatacommons/idc-testing-colab:latest
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docker exec -t colab /bin/bash -c "pip install papermill"
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docker exec -t colab /bin/bash -c "set -o xtrace && set -o errexit && set -o pipefail && set -o nounset && set +o errexit && cd content/ && papermill /content/notebooks/getting_started/${nb}.ipynb /content/outputs/output_${nb}.ipynb && set -o errexit && ls -A || echo \"The previous command has some errors..Continuing\""
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docker exec -t colab /bin/bash -c "set -o xtrace && set -o errexit && set -o pipefail && set -o nounset && set +o errexit && cd content/ && papermill /content/notebooks/getting_started/${nb}.ipynb /content/test/outputs/output_${nb}.ipynb && set -o errexit && ls -A || echo \"The previous command has some errors..Continuing\""
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#docker exec -t colab /bin/bash -c "jupyter nbconvert --to html --ExtractOutputPreprocessor.enabled=False /content/test/outputs/output_${nb}.ipynb"
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docker stop colab
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docker rm colab

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