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TamerGeziciTamerGezici
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Add localpipeline to testing workflow
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‎.github/workflows/aa_use_case_test.yml‎

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@@ -417,6 +417,86 @@ jobs:
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path: |
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${{github.workspace}}/developer/aa_test.log
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aatest_ds000114_fmri_localpipeline:
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name: Testing fMRI using local pipeline connection
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# The type of runner that the job will run on
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runs-on: ubuntu-20.04
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# Steps represent a sequence of tasks that will be executed as part of the job
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steps:
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- name: Maximize build space
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uses: easimon/maximize-build-space@master
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with:
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root-reserve-mb: ${{ env.DISKSIZE }}
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swap-size-mb: 1024
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remove-dotnet: 'true'
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remove-android: 'true'
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remove-haskell: 'true'
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- name: Set git to use LF
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run: |
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git config --global core.autocrlf false
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git config --global core.eol lf
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- name: Check out repository under $GITHUB_WORKSPACE
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uses: actions/checkout@v2
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- name: Set up Python 3.6
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uses: actions/setup-python@v2
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with:
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# Semantic version range syntax or exact version of a Python version
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python-version: '3.6'
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# Optional - x64 or x86 architecture, defaults to x64
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architecture: 'x64'
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- name: Set up MATLAB
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uses: matlab-actions/setup-matlab@v1
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with:
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# MATLAB release to set up R2020a
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release: R2020a
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- name: Install tools and configure aa
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run: |
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python trigger_install.py
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working-directory: ${{github.workspace}}/.github/workflows
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env:
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LOAD_FSL: 0
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LOAD_FREESURFER: 0
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PARAMETER_XML: aap_parameters_defaults_GitHub.xml
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- name: Retrive test data under $HOME/data/aa_demo
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run: |
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mkdir -p $HOME/data/aa_demo
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aws s3 cp s3://openneuro.org/ds000114 $HOME/data/aa_demo/ds000114 --quiet --recursive --exclude "*" --include "task-*" --no-sign-request
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aws s3 cp s3://openneuro.org/ds000114 $HOME/data/aa_demo/ds000114 --quiet --recursive --exclude "*" --include "dwi*" --no-sign-request
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aws s3 cp s3://openneuro.org/ds000114/sub-01 $HOME/data/aa_demo/ds000114/sub-01 --quiet --recursive --no-sign-request
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aws s3 cp s3://openneuro.org/ds000114/sub-02 $HOME/data/aa_demo/ds000114/sub-02 --quiet --recursive --no-sign-request
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aws s3 cp s3://openneuro.org/ds000114/sub-03 $HOME/data/aa_demo/ds000114/sub-03 --quiet --recursive --no-sign-request
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env:
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AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
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AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
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AWS_EC2_METADATA_DISABLED: true
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- name: Run script
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uses: matlab-actions/run-command@v1
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with:
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command: addpath(getenv('GITHUB_WORKSPACE')); aa_ver5; SPM = spmClass(fullfile(getenv('HOME'),'tools','spm12')); SPM.load; aa_test('glob','aatest_ds000114_fmri_localpipeline','haltonerror',true)
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- name: Archive data
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uses: actions/upload-artifact@v2
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with:
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name: aatest_ds000114_fmri
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path: |
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~/projects/
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- name: Archive log
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uses: actions/upload-artifact@v2
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with:
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name: testlog_${{github.job}}
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path: |
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${{github.workspace}}/developer/aa_test.log
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aatest_ds000114_scrubbing:
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name: Testing fMRI frame censoring
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