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Guide for running tests

Download Slicer

  • Download a fresh Slicer-4.11.20200930-linux-amd64 locally
  • Install SlicerDMRI extension module. It can be found at ~/.config/NA-MIC/Extensions-29402/SlicerDMRI
  • You can copy both the Slicer-4.11.20200930-linux-amd64 and SlicerDMRI into /root directory for ease of mounting.

Download test data

This step is intended for eliminating sluggishness involved in downloading test data from Dropbox repeatedly. You can have both luigi-pnlpipe-test-data and luigi-pnlpipe-g-truth downloaded in your machine. This approach is particularly useful when you would have to rebuild the Docker container. If you download them inside the container, then they would be lost during rebuild. But if they are downloaded locally once, you can mount them into your container after a rebuild.

  • Test data

      d=luigi-pnlpipe-test-data.tar.gz
  # download locally
  wget https://www.dropbox.com/s/pzloevkr8h3kyac/$d
  # mount as
  docker run ... -v ~/$d:/home/pnlbwh/$d ...

  • Ground truth

      r=luigi-pnlpipe-g-truth.tar.gz
  # download locally
  wget https://www.dropbox.com/s/gi7kukud44bl6p2/$r
  # mount as
  docker run ... -v ~/$r:/home/pnlbwh/luigi-pnlpipe/tests/$r ...

Download IITmean_b0_256.nii.gz

wget https://www.nitrc.org/frs/download.php/11290/IITmean_b0_256.nii.gz

Set up log directory

  • .gitconfig

Define the following ~/.gitconfig:

[color]
    ui = auto
[user]
    email = your_email
    name = your_name
  • .ssh

Define the following ~/.ssh/config:

Host github.com
    IdentityFile ~/.ssh/your_private_key
    StrictHostKeyChecking no
  • clone

Clone the private repo with SSH protocol:

git clone git@github.com:pnlbwh/pnlpipe-nightly-tests.git

NOTE Users outside PNL will not have access to this repository. They can create a repository named pnlpipe-nightly-tests in their GitHub and adjust the above pnlbwh/pnlpipe-nightly-tests.git with their remote. In the simplest manner, just mkdir pnlpipe-nightly-tests and forget about .gitconfig or .ssh. If you do not set up a repository, you will not be able to upload the test logs to GitHub. Yet, you will be able to access them within pnlpipe-nightly-tests folder.

Launch container

To set up test environment, we shall mount SlicerDMRI, FreeSurfer license, IITmean_b0_256.nii.gz for CNN-Diffusion-MRIBrain-Segmentation, .ssh, .gitconfig, pnlpipe-nightly-tests into the container:

docker run --rm -ti \
-v ~/Slicer-4.11.20200930-linux-amd64:/Slicer-4.11 \
-v ~/SlicerDMRI:/SlicerDMRI \
-v ~/license.txt:/home/pnlbwh/freesurfer-7.1.0/license.txt \
-v ~/IITmean_b0_256.nii.gz:/home/pnlbwh/CNN-Diffusion-MRIBrain-Segmentation/model_folder/IITmean_b0_256.nii.gz \
-v ~/.ssh:/root/.ssh \
-v ~/.gitconfig:/home/pnlbwh/.gitconfig \
-v ~/pnlpipe-nightly-tests:/home/pnlbwh/luigi-pnlpipe/pnlpipe-nightly-tests \
tbillah/pnlpipe

Run tests

luigi-pnlpipe/pipeline_test.sh -h

Local pull request

Let's say want to test the PR hcp<--provenance. Before merging on GitHub, we want to merge locally and test. Upon successful testing, we can merge the PR on GitHub. For this purpose, the following commands would come handy:

  • PR when the local branch is hcp

      git reset --hard
  git pull origin hcp --ff-only
  git pull origin provenance --rebase

  • PR when the local branch is not hcp

      git reset --hard
  git checkout --orphan hcp
  git rm -rf .
  git pull origin hcp --ff-only
  git pull origin azure --rebase

Appendix

  • It is safe to ignore failures of test_json and test_html provenance files. Every now and then, there is a parameter update in Luigi configuration files. For the above tests to pass, we need to update ground truth data with new provenance files comprising the updated parameters. Provenance files themselves are only a few kilobytes. However, given the large size of ground truth data and the slowness of Dropbox upload, it is quite problematic to update the remote ground truth data. Hence, we let the failures to occur. If the rest of the tests succeed, we satisfactorily conclude that the nightly tests have succeeded.