diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile index 624e73ea..48989171 100755 --- a/.devcontainer/Dockerfile +++ b/.devcontainer/Dockerfile @@ -1,9 +1,11 @@ FROM scilus/scilus:2.0.2 ARG NFTEST_VERSION +ARG POETRY_VERSION ENV NODE_MAJOR=18 ENV NFTEST_VERSION=${NFTEST_VERSION:-0.9.0-rc1} +ENV POETRY_VERSION=${POETRY_VERSION:-1.8.*} RUN apt update && apt install -y \ curl \ @@ -14,7 +16,13 @@ RUN apt update && apt install -y \ RUN python3 -m pip install pipx && \ python3 -m pipx ensurepath && \ - pipx install poetry + pipx install poetry==${POETRY_VERSION} RUN curl -fsSL https://deb.nodesource.com/setup_${NODE_MAJOR}.x | bash - &&\ - apt-get install -y nodejs + apt-get install -y nodejs && \ + groupadd --gid 501 yeoman && \ + useradd --uid 501 --gid yeoman --shell /bin/bash --create-home yeoman && \ + echo "yeoman ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers + +RUN mkdir /generated && chown yeoman:yeoman /generated +WORKDIR /generated diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 6412e4d1..923e3e6d 100755 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -3,13 +3,17 @@ "build": { "dockerfile": "Dockerfile", "args": { - "NFTEST_VERSION": "0.9.0-rc1" + "NFTEST_VERSION": "0.9.0-rc1", + "POETRY_VERSION": "1.8.*" } }, "forwardPorts": [3000], "onCreateCommand": "bash .devcontainer/onCreateCommand.sh", "updateContentCommand": "bash .devcontainer/updateContentCommand.sh", "postStartCommand": "git config --global --add safe.directory ${containerWorkspaceFolder}", + "containerEnv": { + "WORKSPACE": "${containerWorkspaceFolder}" + }, "features": { "ghcr.io/devcontainers/features/git:1": {}, "ghcr.io/devcontainers/features/git-lfs:1": {}, diff --git a/.devcontainer/onCreateCommand.sh b/.devcontainer/onCreateCommand.sh index 011dd957..946c505a 100755 --- a/.devcontainer/onCreateCommand.sh +++ b/.devcontainer/onCreateCommand.sh @@ -1,5 +1,7 @@ #!/usr/bin/env bash +# Setup for NF-CORE + npm install -g --save-dev --save-exact prettier npm install -g editorconfig npm install -g --save-dev editorconfig-checker @@ -12,3 +14,10 @@ mkdir -p /nf-test/bin cd /nf-test/bin/ curl -fsSL https://code.askimed.com/install/nf-test | bash -s ${NFTEST_VERSION} echo "PATH=$PATH:/nf-test/bin" >> ~/.bashrc + + +# Setup for VSCODE Extensions Development + +npm install -g typescript +npm install -g tslint +npm install -g yo generator-code diff --git a/.github/workflows/checks.yml b/.github/workflows/checks.yml index 29b61745..264a0c6b 100755 --- a/.github/workflows/checks.yml +++ b/.github/workflows/checks.yml @@ -1,6 +1,22 @@ name: nf-scil checks on: workflow_call: + inputs: + nextflow_version: + description: "Nextflow version to use" + required: false + type: string + default: "24.04.4" + nf_core_version: + description: "nf-core version to use" + required: false + type: string + default: "2.14.*" + nf_test_version: + description: "nf-test version to use" + required: false + type: string + default: "0.9.0-rc1" env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} @@ -11,6 +27,8 @@ jobs: steps: - uses: actions/checkout@v4 - uses: actions/setup-python@v5 + with: + cache: 'pip' - uses: pre-commit/action@v3.0.1 # FIXME Flip this off once we get to less than a couple hundred. Adding # this so it will only run against changed files. It'll make it much @@ -21,34 +39,32 @@ jobs: prettier: runs-on: ubuntu-latest steps: - - name: Check out repository - uses: actions/checkout@v4 - - - name: Install NodeJS - uses: actions/setup-node@v4 + - uses: actions/checkout@v4 + - uses: actions/setup-node@v4 with: node-version: "20" + cache: 'npm' - name: Install Prettier - run: npm install -g prettier@3.1.0 + run: npm ci - name: Run Prettier --check - run: prettier --check . + run: npx prettier --check . editorconfig: runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 - - uses: actions/setup-node@v4 with: node-version: "20" + cache: 'npm' - name: Install editorconfig-checker - run: npm install -g editorconfig-checker + run: npm ci - name: Run ECLint check - run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test) + run: npx editorconfig-checker -exclude README.md $(git ls-files | grep -v test) nf-test-changes: name: compute - changes @@ -95,6 +111,7 @@ jobs: with: type: "module" component: ${{ matrix.module }} + nextflow_version: ${{ inputs.nextflow_version }} secrets: inherit lint-subworkflows: @@ -111,6 +128,7 @@ jobs: with: type: "subworkflow" component: ${{ matrix.subworkflow }} + nextflow_version: ${{ inputs.nextflow_version }} secrets: inherit nf-test: @@ -133,12 +151,29 @@ jobs: profile: ${{ matrix.profile }} paths: ${{ matrix.path }} runner: ${{ matrix.runner }} + nextflow_version: ${{ inputs.nextflow_version }} + nf_test_version: ${{ inputs.nf_test_version }} secrets: inherit + upload-reports: + name: upload reports + needs: [nf-test-changes, nf-test] + if: ${{ ( needs.nf-test-changes.outputs.paths != '[]' ) }} + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: actions/upload-artifact/merge@v4 + with: + name: nf-test-reports + pattern: reports-* + delete-merged: true + retention-days: 10 + compression-level: 9 + confirm-pass: name: status runs-on: ubuntu-latest - needs: [prettier, editorconfig, nf-test-changes, lint-modules, lint-subworkflows, nf-test] + needs: [prettier, editorconfig, nf-test-changes, lint-modules, lint-subworkflows, nf-test, upload-reports] if: ${{ !cancelled() }} steps: - name: All tests ok diff --git a/.github/workflows/code_linting.yml b/.github/workflows/code_linting.yml deleted file mode 100755 index b595d5a7..00000000 --- a/.github/workflows/code_linting.yml +++ /dev/null @@ -1,70 +0,0 @@ -name: Code Linting -run-name: Code Linting (automated) -on: - issue_comment: - types: [created] - -jobs: - fix-linting: - # Only run if comment is on a PR with the main repo, and if it contains the magic keywords - if: > - contains(github.event.comment.html_url, '/pull/') && - contains(github.event.comment.body, '@nf-scil-bot fix linting') && - github.repository == 'scilus/nf-scil' - runs-on: scilus-nf-scil-runners - steps: - # Use the @nf-scil-bot token to check out so we can push later - - uses: actions/checkout@v4 - with: - token: ${{ secrets.GITHUB_TOKEN }} - - # indication that the linting is being fixed - - name: React on comment - uses: peter-evans/create-or-update-comment@v3 - with: - comment-id: ${{ github.event.comment.id }} - reactions: eyes - - # Action runs on the issue comment, so we don't get the PR by default - # Use the gh cli to check out the PR - - name: Checkout Pull Request - run: gh pr checkout ${{ github.event.issue.number }} - env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - - - uses: actions/setup-node@v4 - - - name: Install Prettier - run: npm install -g prettier @prettier/plugin-php - - # Check that we actually need to fix something - - name: Run 'prettier --check' - id: prettier_status - run: | - if prettier --check ${GITHUB_WORKSPACE}; then - echo "::set-output name=result::pass" - else - echo "::set-output name=result::fail" - fi - - name: Run 'prettier --write' - if: steps.prettier_status.outputs.result == 'fail' - run: prettier --write ${GITHUB_WORKSPACE} - - - name: Post nothing-to-do comment - if: steps.prettier_status.outputs.result == 'pass' - uses: peter-evans/create-or-update-comment@v3 - with: - issue-number: ${{ github.event.issue.number }} - body: | - Nothing for me to do here! :shrug: - This is probably because the linting errors come from `nf-core lint` and have to be fixed manually (or with `nf-core lint --fix`). - - name: Commit & push changes - if: steps.prettier_status.outputs.result == 'fail' - run: | - git config user.email "scil@nf-sc.il" - git config user.name "nf-scil-bot" - git config push.default upstream - git add . - git status - git commit -m "[automated] Fix linting with Prettier" - git push diff --git a/.github/workflows/lint_module.yml b/.github/workflows/lint_module.yml index 225840a1..108b91f4 100755 --- a/.github/workflows/lint_module.yml +++ b/.github/workflows/lint_module.yml @@ -14,6 +14,11 @@ on: options: - module - subworkflow + nextflow_version: + description: "Nextflow version to use" + required: false + type: string + default: "24.04.4" workflow_call: inputs: component: @@ -24,6 +29,11 @@ on: description: "Type of component" required: true type: string + nextflow_version: + description: "Nextflow version to use" + required: false + type: string + default: "24.04.4" run-name: Lint ${{ inputs.component }} jobs: @@ -33,36 +43,30 @@ jobs: steps: - uses: actions/checkout@v4 - - - name: Set up Python - uses: actions/setup-python@v5 + - uses: abatilo/actions-poetry@v2 with: - python-version: "3.11" - - - uses: actions/cache@v4 + poetry-version: "1.8.*" + - uses: actions/setup-python@v5 with: - path: ~/.cache/pip - key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} - restore-keys: | - ${{ runner.os }}-pip - ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} - - - name: Install pip - run: python -m pip install --upgrade pip - + python-version: "3.11" + cache: 'poetry' - uses: actions/setup-java@v4 with: distribution: "temurin" java-version: "17" - - - name: Setup Nextflow - uses: nf-core/setup-nextflow@v2 + - uses: nf-core/setup-nextflow@v2 + with: + version: ${{ inputs.nextflow_version }} - name: Install nf-core tools run: | - python -m pip install --upgrade --force-reinstall nf-core==2.14.* + poetry install --no-root - name: Lint ${{ inputs.type }} ${{ inputs.component }} env: GIT_CLONE_PROTECTION_ACTIVE: false - run: nf-core --verbose ${{ inputs.type }}s --git-remote https://github.com/scilus/nf-scil.git lint ${{ inputs.component }} + run: | + poetry run nf-core --verbose ${{ inputs.type }}s \ + --git-remote https://github.com/${{ github.repository }}.git \ + --branch ${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}} \ + lint ${{ inputs.component }} diff --git a/.github/workflows/nf-test_module.yml b/.github/workflows/nf-test_module.yml index 0faf0841..7bb7e027 100644 --- a/.github/workflows/nf-test_module.yml +++ b/.github/workflows/nf-test_module.yml @@ -15,9 +15,19 @@ on: - docker - singularity runner: - description: "Runner label to use for the test run" - default: 'ubuntu-latest' - type: string + description: "Runner label to use for the test run" + default: 'ubuntu-latest' + type: string + nextflow_version: + description: "Nextflow version to use" + required: false + type: string + default: "24.04.4" + nf_test_version: + description: "nf-test version to use" + required: false + type: string + default: "0.9.0-rc1" workflow_call: inputs: profile: @@ -35,6 +45,16 @@ on: description: "Runner label to use for the test run" default: 'ubuntu-latest' type: string + nextflow_version: + description: "Nextflow version to use" + required: false + type: string + default: "24.04.4" + nf_test_version: + description: "nf-test version to use" + required: false + type: string + default: "0.9.0-rc1" env: NXF_SINGULARITY_CACHEDIR: /home/runner/.singularity_cache/.singularity @@ -48,63 +68,63 @@ jobs: if: inputs.paths != '' && inputs.profile != '' env: NXF_ANSI_LOG: false - NFTEST_VER: "0.9.0-rc1" - NFSCIL_TEST_DATA_HOME: /home/runner/_work - + NXF_DISABLE_CHECK_LATEST: true + NFTEST_VERSION: "${{ inputs.nf_test_version }}" + # nf-test directories need to be placed on an ephemeral disk accessible to docker. + # In our case, it's only the _work workspace for security reasons + NXF_WORKDIR: /home/runner/_work steps: - uses: actions/checkout@v4 - + - uses: actions/setup-python@v5 + with: + python-version: "3.11" + cache: 'pip' - uses: actions/setup-java@v4 with: distribution: "temurin" java-version: "17" - - - name: Setup Nextflow - uses: nf-core/setup-nextflow@v2 - + - uses: nf-core/setup-nextflow@v2 + with: + version: ${{ inputs.nextflow_version }} - name: Setup nf-test uses: AlexVCaron/setup-nf-test@2c5a31b90b34d97abf155b57ee0f79c7f5aa118a # Used to make the action executable on our runners. Related to how the home # and work directories are set up from ephemeral disks. See nf-core/setup-nf-test/issues/6 with: - version: ${{ env.NFTEST_VER }} + version: ${{ inputs.nf_test_version }} + + - name: Install Python dependencies + run: python -m pip install --upgrade pip pdiff cryptography - name: Fix nf-test launching jvm with too much memory run: | sed -i 's/-Xmx10g//' $(which nf-test) - - name: Set up Python - uses: actions/setup-python@v5 - with: - python-version: "3.11" - - - uses: actions/cache@v4 - id: cache-pip-pdiff - with: - path: ~/.cache/pip - key: ${{ runner.os }}-pip-pdiff - restore-keys: | - ${{ runner.os }}-pip-pdiff - - - uses: actions/github-script@v7 + - name: Compute test run UID + uses: actions/github-script@v7 id: test-run-identifier with: script: | identifier='${{ inputs.paths }}'.toLowerCase().replaceAll(/[/. ]+/g, '-').trim('-'); - core.setOutput('tag', identifier); + core.setOutput('uid', identifier); - - uses: actions/cache@v4 + - name: Cache test archives under test UID + uses: actions/cache@v4 with: - path: ${{ env.NFSCIL_TEST_DATA_HOME }}/nf-scil-test-archives - key: nf-scil-test-data-cache-${{ steps.test-run-identifier.outputs.tag }} - - - name: Install Python dependencies - run: python -m pip install --upgrade pip pdiff cryptography + path: ${{ env.NXF_WORKDIR }}/nf-scil-test-archives + key: | + nf-scil-test-data-cache-${{ steps.test-run-identifier.outputs.uid }} + nf-scil-test-data-cache- - name: Run nf-test env: NFT_DIFF: "pdiff" NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2" + TMPDIR: ${{ env.NXF_WORKDIR }}/tmpdir + NFT_WORKDIR: ${{ env.NXF_WORKDIR }}/.nf-test + NXF_CACHE_DIR: ${{ env.NXF_WORKDIR }}/.nextflow + NXF_TEMP: ${{ env.NXF_WORKDIR }}/tmpdir + NFSCIL_TEST_DATA_HOME: ${{ env.NXF_WORKDIR }} run: | # use "docker_self_hosted" if it runs on self-hosted runner and inputs.profile=docker if [ "${{ inputs.profile }}" == "docker" ]; then @@ -113,12 +133,7 @@ jobs: PROFILE=${{ inputs.profile }} fi - # nf-test directories need to be placed on an ephemeral disk accessible to docker. - # In our case, it's only the _work workspace for security reasons - mkdir -p /home/runner/_work/tmpdir - - TMPDIR=/home/runner/_work/tmpdir \ - NFT_WORKDIR=/home/runner/_work \ + mkdir -p ${{ env.TMPDIR }} nf-test test \ --profile=$PROFILE \ --tap=test.tap \ @@ -134,26 +149,59 @@ jobs: - name: Tests logs if: failure() run: | - shopt -s globstar - for f in /home/runner/_work/tests/**/work/**/.command.log - do + shopt -s globstar + for f in ${{ env.NXF_WORKDIR }}/.nf-test/tests/**/work/**/.command.log + do - echo "$(sed '3q;d' $(dirname $f)/.command.run)" - cat $f + echo "$(sed '3q;d' $(dirname $f)/.command.run)" + cat $f - done + done - - name: Upload images as artifacts + - name: Collect test reports + if: always() + run: | + mkdir -p tests_reports + i=1 + for t in ${{ env.NXF_WORKDIR }}/.nf-test/tests/* + do + tag=$(cat $t/meta/mock.nf | grep -E 'include \{.*' | tail -1 | cut -d' ' -f3)_$i + cp $t/report.html tests_reports/${tag}.html + i=$((i+1)) + done + + - name: Upload test reports if: always() uses: actions/upload-artifact@v4 with: - name: image_artifacts-${{ steps.test-run-identifier.outputs.tag }} - path: /home/runner/_work/tests/**/work/**/*.nii.gz + name: reports-${{ steps.test-run-identifier.outputs.uid }} + path: tests_reports/ + overwrite: true + retention-days: 1 + compression-level: 9 + + - name: Collect test working directories + if: failure() + run: | + mkdir -p tests_workdir + for t in ${{ env.NXF_WORKDIR }}/.nf-test/tests/**/work/**/.command.log + do + tag=$(sed -n '3p' $(dirname $t)/.command.run | cut -d' ' -f3 | tr -d "'") + cp -R $(dirname $t) tests_workdir/$tag + done + + - name: Upload test working directories + if: failure() + uses: actions/upload-artifact@v4 + with: + name: tests-workdir-${{ steps.test-run-identifier.outputs.uid }} + path: tests_workdir/ overwrite: true - retention-days: 2 + retention-days: 1 compression-level: 9 + include-hidden-files: true - name: Clean up if: always() run: | - sudo rm -rf /home/ubuntu/tests/ + sudo rm -rf ${{ env.NXF_WORKDIR }}/.nf-test diff --git a/.github/workflows/publish_extension.yml b/.github/workflows/publish_extension.yml new file mode 100644 index 00000000..576660ba --- /dev/null +++ b/.github/workflows/publish_extension.yml @@ -0,0 +1,50 @@ +name: Publish Extension + +on: + workflow_dispatch: + inputs: + name: + description: "Name of the extension to deploy" + required: true + type: string + workflow_call: + inputs: + name: + description: "Name of the extension to deploy" + required: true + type: string + +jobs: + deploy: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + with: + sparse-checkout: | + nf-scil-extensions/${{ inputs.name }} + sparse-checkout-cone-mode: false + + - uses: actions/setup-node@v4 + with: + node-version: 20 + cache: "npm" + cache-dependency-path: nf-scil-extensions/${{ inputs.name }}/package-lock.json + + - name: npm clean install + working-directory: nf-scil-extensions/${{ inputs.name }} + run: npm ci + + # - name: Publish to Open VSX Registry + # uses: HaaLeo/publish-vscode-extension@v1 + # with: + # packagePath: nf-scil-extensions/${{ inputs.name }} + # pat: ${{ secrets.OPEN_VSX_TOKEN }} + # skipDuplicate: true + + - name: Publish to Visual Studio Marketplace + uses: HaaLeo/publish-vscode-extension@v1 + with: + packagePath: nf-scil-extensions/${{ inputs.name }} + pat: ${{ secrets.VSCE_TOKEN }} + registryUrl: https://marketplace.visualstudio.com + skipDuplicate: true diff --git a/.github/workflows/update_main.yml b/.github/workflows/update_main.yml index 75a3d937..89b5bb3a 100755 --- a/.github/workflows/update_main.yml +++ b/.github/workflows/update_main.yml @@ -13,3 +13,17 @@ jobs: checks: uses: ./.github/workflows/checks.yml secrets: inherit + + publish-test-data-treeview-extension: + if: github.repository == 'scilus/nf-scil' + uses: ./.github/workflows/publish_extension.yml + with: + name: "test-data-treeview" + secrets: inherit + + publish-extension-package: + if: github.repository == 'scilus/nf-scil' + uses: ./.github/workflows/publish_extension.yml + with: + name: "extension-package" + secrets: inherit diff --git a/.prettierignore b/.prettierignore index 4c1267e2..cd823bb4 100755 --- a/.prettierignore +++ b/.prettierignore @@ -5,6 +5,7 @@ docs/api/_build testing nf_core/module-template/modules/meta.yml nf_core/module-template/tests/test.yml +**/package-lock.json .github .devcontainer .vscode diff --git a/README.md b/README.md index 4ea9e67d..3f3a0ed4 100755 --- a/README.md +++ b/README.md @@ -138,7 +138,7 @@ run the following commands : ```bash pip install pipx pipx ensurepath -pipx install poetry +pipx install poetry==1.8.* ``` > [!NOTE] diff --git a/modules/nf-scil/reconst/dtimetrics/tests/main.nf.test b/modules/nf-scil/reconst/dtimetrics/tests/main.nf.test index 91ddbfd6..a18fe531 100644 --- a/modules/nf-scil/reconst/dtimetrics/tests/main.nf.test +++ b/modules/nf-scil/reconst/dtimetrics/tests/main.nf.test @@ -18,8 +18,7 @@ nextflow_process { script "../../../../../subworkflows/nf-scil/load_test_data/main.nf" process { """ - input[0] = Channel.from( [ "DWIss1000-dir32.zip", - "segmentation.zip" ] ) + input[0] = Channel.from( [ "DWIss1000-dir32.zip", "segmentation.zip" ] ) input[1] = "test.load-test-data" """ } diff --git a/modules/nf-scil/segmentation/fastseg/tests/main.nf.test b/modules/nf-scil/segmentation/fastseg/tests/main.nf.test index 0299f948..9114b5e9 100644 --- a/modules/nf-scil/segmentation/fastseg/tests/main.nf.test +++ b/modules/nf-scil/segmentation/fastseg/tests/main.nf.test @@ -20,7 +20,7 @@ nextflow_process { script "../../../../../subworkflows/nf-scil/load_test_data/main.nf" process { """ - input[0] = Channel.from( [ "heavy.zip" ] ) + input[0] = Channel.from( [ "T1w.zip" ] ) input[1] = "test.load-test-data" """ } @@ -34,7 +34,7 @@ nextflow_process { input[0] = LOAD_DATA.out.test_data_directory.map{ test_data_directory -> [ [ id:'test', single_end:false ], // meta map - file("\${test_data_directory}/anat/anat_image.nii.gz", checkIfExists: true,), + file("\${test_data_directory}/T1w.nii.gz", checkIfExists: true,), [] ] } @@ -45,7 +45,15 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + niftiMD5SUM(process.out.wm_mask.get(0).get(1)), + niftiMD5SUM(process.out.gm_mask.get(0).get(1)), + niftiMD5SUM(process.out.csf_mask.get(0).get(1)), + niftiMD5SUM(process.out.wm_map.get(0).get(1)), + niftiMD5SUM(process.out.gm_map.get(0).get(1)), + niftiMD5SUM(process.out.csf_map.get(0).get(1)), + process.out.versions + ).match() } ) } } @@ -56,8 +64,8 @@ nextflow_process { input[0] = LOAD_DATA.out.test_data_directory.map{ test_data_directory -> [ [ id:'test', single_end:false ], // meta map - file("\${test_data_directory}/anat/anat_image.nii.gz", checkIfExists: true,), - file("\${test_data_directory}/anat/anat_mask.nii.gz", checkIfExists: true) + file("\${test_data_directory}/T1w.nii.gz", checkIfExists: true,), + file("\${test_data_directory}/T1w_mask.nii.gz", checkIfExists: true) ] } """ @@ -67,8 +75,16 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + niftiMD5SUM(process.out.wm_mask.get(0).get(1)), + niftiMD5SUM(process.out.gm_mask.get(0).get(1)), + niftiMD5SUM(process.out.csf_mask.get(0).get(1)), + niftiMD5SUM(process.out.wm_map.get(0).get(1)), + niftiMD5SUM(process.out.gm_map.get(0).get(1)), + niftiMD5SUM(process.out.csf_map.get(0).get(1)), + process.out.versions + ).match() } ) } } -} \ No newline at end of file +} diff --git a/modules/nf-scil/segmentation/fastseg/tests/main.nf.test.snap b/modules/nf-scil/segmentation/fastseg/tests/main.nf.test.snap index 7ae441af..7778861a 100644 --- a/modules/nf-scil/segmentation/fastseg/tests/main.nf.test.snap +++ b/modules/nf-scil/segmentation/fastseg/tests/main.nf.test.snap @@ -1,252 +1,38 @@ { "segmentation - fastseg - lesion": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test__mask_wm.nii.gz:md5,2b2ced42fcf870d68ff44bf90d2701d4" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test__mask_gm.nii.gz:md5,39396421c6d1d32ea7943a5ec7a49dce" - ] - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "test__mask_csf.nii.gz:md5,d0fbc088059f17faff38fbcd33257d27" - ] - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test__map_wm.nii.gz:md5,1d5a9655d4e3c832b14c83e9424b00fc" - ] - ], - "4": [ - [ - { - "id": "test", - "single_end": false - }, - "test__map_gm.nii.gz:md5,f7e51eb14af645c687db5d2c6a4f5bf4" - ] - ], - "5": [ - [ - { - "id": "test", - "single_end": false - }, - "test__map_csf.nii.gz:md5,9c14d8f70e69d641d9c214d0d52b3663" - ] - ], - "6": [ - "versions.yml:md5,d42da2620c5aa82292375b0f9d8d7092" - ], - "csf_map": [ - [ - { - "id": "test", - "single_end": false - }, - "test__map_csf.nii.gz:md5,9c14d8f70e69d641d9c214d0d52b3663" - ] - ], - "csf_mask": [ - [ - { - "id": "test", - "single_end": false - }, - "test__mask_csf.nii.gz:md5,d0fbc088059f17faff38fbcd33257d27" - ] - ], - "gm_map": [ - [ - { - "id": "test", - "single_end": false - }, - "test__map_gm.nii.gz:md5,f7e51eb14af645c687db5d2c6a4f5bf4" - ] - ], - "gm_mask": [ - [ - { - "id": "test", - "single_end": false - }, - "test__mask_gm.nii.gz:md5,39396421c6d1d32ea7943a5ec7a49dce" - ] - ], - "versions": [ - "versions.yml:md5,d42da2620c5aa82292375b0f9d8d7092" - ], - "wm_map": [ - [ - { - "id": "test", - "single_end": false - }, - "test__map_wm.nii.gz:md5,1d5a9655d4e3c832b14c83e9424b00fc" - ] - ], - "wm_mask": [ - [ - { - "id": "test", - "single_end": false - }, - "test__mask_wm.nii.gz:md5,2b2ced42fcf870d68ff44bf90d2701d4" - ] - ] - } + "test__mask_wm.nii.gz:md5:header,18e02970ee42367e0ee9f81b36cde160,data,e4d00ba5559d32119050e6afe77b627c", + "test__mask_gm.nii.gz:md5:header,cb2d88714675fc7d8c450de4db5227c6,data,d713974dbe87760182112e10f96a7f82", + "test__mask_csf.nii.gz:md5:header,cb2d88714675fc7d8c450de4db5227c6,data,29599fab55e3ee75318cef36563684a4", + "test__map_wm.nii.gz:md5:header,58dc3623694060dace951ba8073d5e01,data,62a268dbc74814d62ed9f9596b5a72e5", + "test__map_gm.nii.gz:md5:header,58dc3623694060dace951ba8073d5e01,data,420e7664f81a5899f7007f71c08f28d8", + "test__map_csf.nii.gz:md5:header,58dc3623694060dace951ba8073d5e01,data,2bde307c6dae36a5fc00eba7a2ca7933", + [ + "versions.yml:md5,d42da2620c5aa82292375b0f9d8d7092" + ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0-rc1", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-17T13:59:58.264241" + "timestamp": "2024-09-04T20:12:08.928978" }, "segmentation - fastseg": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test__mask_wm.nii.gz:md5,f849e268007a747714e342162f13f631" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test__mask_gm.nii.gz:md5,39396421c6d1d32ea7943a5ec7a49dce" - ] - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "test__mask_csf.nii.gz:md5,d0fbc088059f17faff38fbcd33257d27" - ] - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test__map_wm.nii.gz:md5,1d5a9655d4e3c832b14c83e9424b00fc" - ] - ], - "4": [ - [ - { - "id": "test", - "single_end": false - }, - "test__map_gm.nii.gz:md5,f7e51eb14af645c687db5d2c6a4f5bf4" - ] - ], - "5": [ - [ - { - "id": "test", - "single_end": false - }, - "test__map_csf.nii.gz:md5,9c14d8f70e69d641d9c214d0d52b3663" - ] - ], - "6": [ - "versions.yml:md5,d42da2620c5aa82292375b0f9d8d7092" - ], - "csf_map": [ - [ - { - "id": "test", - "single_end": false - }, - "test__map_csf.nii.gz:md5,9c14d8f70e69d641d9c214d0d52b3663" - ] - ], - "csf_mask": [ - [ - { - "id": "test", - "single_end": false - }, - "test__mask_csf.nii.gz:md5,d0fbc088059f17faff38fbcd33257d27" - ] - ], - "gm_map": [ - [ - { - "id": "test", - "single_end": false - }, - "test__map_gm.nii.gz:md5,f7e51eb14af645c687db5d2c6a4f5bf4" - ] - ], - "gm_mask": [ - [ - { - "id": "test", - "single_end": false - }, - "test__mask_gm.nii.gz:md5,39396421c6d1d32ea7943a5ec7a49dce" - ] - ], - "versions": [ - "versions.yml:md5,d42da2620c5aa82292375b0f9d8d7092" - ], - "wm_map": [ - [ - { - "id": "test", - "single_end": false - }, - "test__map_wm.nii.gz:md5,1d5a9655d4e3c832b14c83e9424b00fc" - ] - ], - "wm_mask": [ - [ - { - "id": "test", - "single_end": false - }, - "test__mask_wm.nii.gz:md5,f849e268007a747714e342162f13f631" - ] - ] - } + "test__mask_wm.nii.gz:md5:header,cb2d88714675fc7d8c450de4db5227c6,data,08b5c8665f0a07c182eb63f045d01855", + "test__mask_gm.nii.gz:md5:header,cb2d88714675fc7d8c450de4db5227c6,data,d713974dbe87760182112e10f96a7f82", + "test__mask_csf.nii.gz:md5:header,cb2d88714675fc7d8c450de4db5227c6,data,29599fab55e3ee75318cef36563684a4", + "test__map_wm.nii.gz:md5:header,58dc3623694060dace951ba8073d5e01,data,62a268dbc74814d62ed9f9596b5a72e5", + "test__map_gm.nii.gz:md5:header,58dc3623694060dace951ba8073d5e01,data,420e7664f81a5899f7007f71c08f28d8", + "test__map_csf.nii.gz:md5:header,58dc3623694060dace951ba8073d5e01,data,2bde307c6dae36a5fc00eba7a2ca7933", + [ + "versions.yml:md5,d42da2620c5aa82292375b0f9d8d7092" + ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0-rc1", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-13T19:52:04.291343" + "timestamp": "2024-09-04T20:03:24.730234" } } \ No newline at end of file diff --git a/nf-scil-extensions/.vscode/launch.json b/nf-scil-extensions/extension-package/.vscode/launch.json similarity index 100% rename from nf-scil-extensions/.vscode/launch.json rename to nf-scil-extensions/extension-package/.vscode/launch.json diff --git a/nf-scil-extensions/.vscodeignore b/nf-scil-extensions/extension-package/.vscodeignore similarity index 100% rename from nf-scil-extensions/.vscodeignore rename to nf-scil-extensions/extension-package/.vscodeignore diff --git a/nf-scil-extensions/CHANGELOG.md b/nf-scil-extensions/extension-package/CHANGELOG.md similarity index 100% rename from nf-scil-extensions/CHANGELOG.md rename to nf-scil-extensions/extension-package/CHANGELOG.md diff --git a/nf-scil-extensions/README.md b/nf-scil-extensions/extension-package/README.md similarity index 100% rename from nf-scil-extensions/README.md rename to nf-scil-extensions/extension-package/README.md diff --git a/nf-scil-extensions/icon.avif b/nf-scil-extensions/extension-package/icon.avif similarity index 100% rename from nf-scil-extensions/icon.avif rename to nf-scil-extensions/extension-package/icon.avif diff --git a/nf-scil-extensions/extension-package/package-lock.json b/nf-scil-extensions/extension-package/package-lock.json new file mode 100644 index 00000000..43a1cb55 --- /dev/null +++ b/nf-scil-extensions/extension-package/package-lock.json @@ -0,0 +1,15 @@ +{ + "name": "nf-scil-extensions", + "version": "0.1.0", + "lockfileVersion": 3, + "requires": true, + "packages": { + "": { + "name": "nf-scil-extensions", + "version": "0.1.0", + "engines": { + "vscode": "^1.84.0" + } + } + } +} diff --git a/nf-scil-extensions/package.json b/nf-scil-extensions/extension-package/package.json similarity index 78% rename from nf-scil-extensions/package.json rename to nf-scil-extensions/extension-package/package.json index 3b190d55..2cbf2df8 100755 --- a/nf-scil-extensions/package.json +++ b/nf-scil-extensions/extension-package/package.json @@ -7,7 +7,7 @@ "url": "https://github.com/scilus/nf-scil.git" }, "icon": "icon.avif", - "version": "0.0.2", + "version": "0.1.0", "publisher": "AlexVCaron", "engines": { "vscode": "^1.84.0" @@ -46,6 +46,15 @@ "nf-core.nf-core-extensionpack", "twxs.cmake", "yahyabatulu.vscode-markdown-alert", - "yzhang.markdown-all-in-one" + "yzhang.markdown-all-in-one", + "onnovalkering.vscode-singularity", + "nextflow.nextflow", + "KorbinianEckstein.niivue", + "mutantdino.resourcemonitor", + "christian-kohler.npm-intellisense", + "dbaeumer.vscode-eslint", + "connor4312.esbuild-problem-matchers", + "ms-vscode.extension-test-runner", + "AlexVCaron.nf-scil-test-data-treeview" ] } diff --git a/nf-scil-extensions/vsc-extension-quickstart.md b/nf-scil-extensions/extension-package/vsc-extension-quickstart.md similarity index 100% rename from nf-scil-extensions/vsc-extension-quickstart.md rename to nf-scil-extensions/extension-package/vsc-extension-quickstart.md diff --git a/nf-scil-extensions/test-data-treeview/.eslintignore b/nf-scil-extensions/test-data-treeview/.eslintignore new file mode 100644 index 00000000..868f47fa --- /dev/null +++ b/nf-scil-extensions/test-data-treeview/.eslintignore @@ -0,0 +1 @@ +vscode.proposed.d.ts diff --git a/nf-scil-extensions/test-data-treeview/.eslintrc.json b/nf-scil-extensions/test-data-treeview/.eslintrc.json new file mode 100644 index 00000000..10565a2e --- /dev/null +++ b/nf-scil-extensions/test-data-treeview/.eslintrc.json @@ -0,0 +1,24 @@ +{ + "root": true, + "parser": "@typescript-eslint/parser", + "parserOptions": { + "ecmaVersion": 6, + "sourceType": "module" + }, + "plugins": ["@typescript-eslint"], + "rules": { + "@typescript-eslint/naming-convention": [ + "warn", + { + "selector": "import", + "format": ["camelCase", "PascalCase"] + } + ], + "@typescript-eslint/semi": "warn", + "curly": "warn", + "eqeqeq": "warn", + "no-throw-literal": "warn", + "semi": "off" + }, + "ignorePatterns": ["out", "dist", "**/*.d.ts"] +} diff --git a/nf-scil-extensions/test-data-treeview/.gitignore b/nf-scil-extensions/test-data-treeview/.gitignore new file mode 100644 index 00000000..da385c69 --- /dev/null +++ b/nf-scil-extensions/test-data-treeview/.gitignore @@ -0,0 +1,5 @@ +out +node_modules +yarn.lock +.vscode-test +dist diff --git a/nf-scil-extensions/test-data-treeview/.vscode-test.mjs b/nf-scil-extensions/test-data-treeview/.vscode-test.mjs new file mode 100644 index 00000000..36a79aef --- /dev/null +++ b/nf-scil-extensions/test-data-treeview/.vscode-test.mjs @@ -0,0 +1,5 @@ +import { defineConfig } from "@vscode/test-cli"; + +export default defineConfig({ + files: "out/test/**/*.test.js", +}); diff --git a/nf-scil-extensions/test-data-treeview/.vscode/extensions.json b/nf-scil-extensions/test-data-treeview/.vscode/extensions.json new file mode 100644 index 00000000..9a9d640e --- /dev/null +++ b/nf-scil-extensions/test-data-treeview/.vscode/extensions.json @@ -0,0 +1,5 @@ +{ + // See http://go.microsoft.com/fwlink/?LinkId=827846 + // for the documentation about the extensions.json format + "recommendations": ["dbaeumer.vscode-eslint", "connor4312.esbuild-problem-matchers", "ms-vscode.extension-test-runner"] +} diff --git a/nf-scil-extensions/test-data-treeview/.vscode/launch.json b/nf-scil-extensions/test-data-treeview/.vscode/launch.json new file mode 100644 index 00000000..909a38b5 --- /dev/null +++ b/nf-scil-extensions/test-data-treeview/.vscode/launch.json @@ -0,0 +1,21 @@ +// A launch configuration that compiles the extension and then opens it inside a new window +// Use IntelliSense to learn about possible attributes. +// Hover to view descriptions of existing attributes. +// For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387 +{ + "version": "0.2.0", + "configurations": [ + { + "name": "Run Extension", + "type": "extensionHost", + "request": "launch", + "args": [ + "--extensionDevelopmentPath=${workspaceFolder}" + ], + "outFiles": [ + "${workspaceFolder}/dist/**/*.js" + ], + "preLaunchTask": "${defaultBuildTask}" + } + ] +} diff --git a/nf-scil-extensions/test-data-treeview/.vscode/settings.json b/nf-scil-extensions/test-data-treeview/.vscode/settings.json new file mode 100644 index 00000000..0873375e --- /dev/null +++ b/nf-scil-extensions/test-data-treeview/.vscode/settings.json @@ -0,0 +1,13 @@ +// Place your settings in this file to overwrite default and user settings. +{ + "files.exclude": { + "out": false, // set this to true to hide the "out" folder with the compiled JS files + "dist": false // set this to true to hide the "dist" folder with the compiled JS files + }, + "search.exclude": { + "out": true, // set this to false to include "out" folder in search results + "dist": true // set this to false to include "dist" folder in search results + }, + // Turn off tsc task auto detection since we have the necessary tasks as npm scripts + "typescript.tsc.autoDetect": "off" +} diff --git a/nf-scil-extensions/test-data-treeview/.vscode/tasks.json b/nf-scil-extensions/test-data-treeview/.vscode/tasks.json new file mode 100644 index 00000000..07b32ad3 --- /dev/null +++ b/nf-scil-extensions/test-data-treeview/.vscode/tasks.json @@ -0,0 +1,64 @@ +// See https://go.microsoft.com/fwlink/?LinkId=733558 +// for the documentation about the tasks.json format +{ + "version": "2.0.0", + "tasks": [ + { + "label": "watch", + "dependsOn": [ + "npm: watch:tsc", + "npm: watch:esbuild" + ], + "presentation": { + "reveal": "never" + }, + "group": { + "kind": "build", + "isDefault": true + } + }, + { + "type": "npm", + "script": "watch:esbuild", + "group": "build", + "problemMatcher": "$esbuild-watch", + "isBackground": true, + "label": "npm: watch:esbuild", + "presentation": { + "group": "watch", + "reveal": "never" + } + }, + { + "type": "npm", + "script": "watch:tsc", + "group": "build", + "problemMatcher": "$tsc-watch", + "isBackground": true, + "label": "npm: watch:tsc", + "presentation": { + "group": "watch", + "reveal": "never" + } + }, + { + "type": "npm", + "script": "watch-tests", + "problemMatcher": "$tsc-watch", + "isBackground": true, + "presentation": { + "reveal": "never", + "group": "watchers" + }, + "group": "build" + }, + { + "label": "tasks: watch-tests", + "dependsOn": [ + "npm: watch", + "npm: watch-tests" + ], + "problemMatcher": [] + } + ] +} diff --git a/nf-scil-extensions/test-data-treeview/.vscodeignore b/nf-scil-extensions/test-data-treeview/.vscodeignore new file mode 100644 index 00000000..db4b55ab --- /dev/null +++ b/nf-scil-extensions/test-data-treeview/.vscodeignore @@ -0,0 +1,7 @@ +.vscode +node_modules +out/ +src/ +tsconfig.json +webpack.config.js +esbuild.js diff --git a/nf-scil-extensions/test-data-treeview/CHANGELOG.md b/nf-scil-extensions/test-data-treeview/CHANGELOG.md new file mode 100644 index 00000000..df400792 --- /dev/null +++ b/nf-scil-extensions/test-data-treeview/CHANGELOG.md @@ -0,0 +1,9 @@ +# Change Log + +All notable changes to the "test-data-treeview" extension will be documented in this file. + +Check [Keep a Changelog](http://keepachangelog.com/) for recommendations on how to structure this file. + +## [Unreleased] + +- Initial release diff --git a/nf-scil-extensions/test-data-treeview/README.md b/nf-scil-extensions/test-data-treeview/README.md new file mode 100644 index 00000000..d6a9faa9 --- /dev/null +++ b/nf-scil-extensions/test-data-treeview/README.md @@ -0,0 +1,9 @@ +# test-data-treeview README + +This extension is designed to provide a treeview of test data files for **nf-scil**. It adds a new view to the **Explorer** sidebar that displays the test data files in the workspace. Through it, the user can explore available packages' contents, open files for visualization and download them locally. + +## Release Notes + +No release notes yet. + +--- diff --git a/nf-scil-extensions/test-data-treeview/esbuild.js b/nf-scil-extensions/test-data-treeview/esbuild.js new file mode 100644 index 00000000..95ab0413 --- /dev/null +++ b/nf-scil-extensions/test-data-treeview/esbuild.js @@ -0,0 +1,54 @@ +const esbuild = require("esbuild"); + +const production = process.argv.includes("--production"); +const watch = process.argv.includes("--watch"); + +/** + * @type {import('esbuild').Plugin} + */ +const esbuildProblemMatcherPlugin = { + name: "esbuild-problem-matcher", + + setup(build) { + build.onStart(() => { + console.log("[watch] build started"); + }); + build.onEnd((result) => { + result.errors.forEach(({ text, location }) => { + console.error(`✘ [ERROR] ${text}`); + console.error(` ${location.file}:${location.line}:${location.column}:`); + }); + console.log("[watch] build finished"); + }); + }, +}; + +async function main() { + const ctx = await esbuild.context({ + entryPoints: ["src/extension.ts"], + bundle: true, + format: "cjs", + minify: production, + sourcemap: !production, + sourcesContent: false, + platform: "node", + outfile: "dist/extension.js", + external: ["vscode"], + logLevel: "silent", + plugins: [ + /* add to the end of plugins array */ + esbuildProblemMatcherPlugin, + ], + }); + if (watch) { + await ctx.watch(); + } else { + await ctx.rebuild(); + await ctx.dispose(); + } +} + +main().catch((e) => { + console.error(e); + process.exit(1); +}); diff --git a/nf-scil-extensions/test-data-treeview/icon.avif b/nf-scil-extensions/test-data-treeview/icon.avif new file mode 100755 index 00000000..3bf48d77 Binary files /dev/null and b/nf-scil-extensions/test-data-treeview/icon.avif differ diff --git a/nf-scil-extensions/test-data-treeview/package-lock.json b/nf-scil-extensions/test-data-treeview/package-lock.json new file mode 100644 index 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"nfscilTestData", + "name": "nf-scil Test Data" + } + ] + }, + "menus": { + "view/title": [ + { + "command": "nfscilTestData.clearCache", + "when": "view == nfscilTestData", + "group": "navigation" + }, + { + "command": "nfscilTestData.loadListing", + "when": "view == nfscilTestData", + "group": "navigation" + }, + { + "command": "nfscilTestData.forceDownloadListing", + "when": "view == nfscilTestData", + "group": "navigation" + }, + { + "command": "nfscilTestData.refreshEntry", + "when": "view == nfscilTestData", + "group": "navigation" + } + ], + "view/item/context": [ + { + "command": "nfscilTestData.openInEditor", + "when": "view == nfscilTestData && viewItem == testDataFile", + "group": "inline" + }, + { + "command": "nfscilTestData.saveAs", + "when": "view == nfscilTestData && viewItem == testDataFile", + "group": "inline" + } + ] + }, + "commands": [ + { + "command": "nfscilTestData.refreshEntry", + "title": "Refresh packages", + "icon": "$(refresh)" + }, + { + "command": "nfscilTestData.clearCache", + "title": "Clear cache", + "icon": "$(trash)" + }, + { + "command": "nfscilTestData.loadListing", + "title": "Load package listing", + "icon": "$(list-tree)" + }, + { + "command": "nfscilTestData.forceDownloadListing", + "title": "Force online package listing", + "icon": "$(cloud-download)" + }, + { + "command": "nfscilTestData.openInEditor", + "title": "Open file in the editor", + "icon": "$(eye)" + }, + { + "command": "nfscilTestData.saveAs", + "title": "Save as...", + "icon": "$(desktop-download)" + } + ] + }, + "scripts": { + "vscode:prepublish": "npm run package", + "compile": "npm run check-types && npm run lint && node esbuild.js", + "watch": "npm-run-all -p watch:*", + "watch:esbuild": "node esbuild.js --watch", + "watch:tsc": "tsc --noEmit --watch --project tsconfig.json", + "package": "npm run check-types && npm run lint && node esbuild.js --production", + "compile-tests": "tsc -p . --outDir out", + "watch-tests": "tsc -p . -w --outDir out", + "pretest": "npm run compile-tests && npm run compile && npm run lint", + "check-types": "tsc --noEmit", + "lint": "eslint src --ext ts", + "test": "vscode-test" + }, + "devDependencies": { + "@types/adm-zip": "^0.5.5", + "@types/mocha": "^10.0.7", + "@types/node": "20.x", + "@types/vscode": "^1.92.0", + "@typescript-eslint/eslint-plugin": "^7.14.1", + "@typescript-eslint/parser": "^7.11.0", + "@vscode/test-cli": "^0.0.9", + "@vscode/test-electron": "^2.4.0", + "esbuild": "^0.21.5", + "eslint": "^8.57.0", + "npm-run-all": "^4.1.5", + "typescript": "^5.4.5" + }, + "dependencies": { + "adm-zip": "^0.5.15" + } +} diff --git a/nf-scil-extensions/test-data-treeview/src/extension.ts b/nf-scil-extensions/test-data-treeview/src/extension.ts new file mode 100644 index 00000000..307b36c8 --- /dev/null +++ b/nf-scil-extensions/test-data-treeview/src/extension.ts @@ -0,0 +1,47 @@ +"use strict"; + +import * as vscode from "vscode"; + +import { TestDataProvider } from "./nfscilTestData"; + +export function activate(context: vscode.ExtensionContext) { + const rootPath = + vscode.workspace.workspaceFolders && vscode.workspace.workspaceFolders.length > 0 + ? vscode.workspace.workspaceFolders[0].uri.fsPath + : undefined; + + const storagePath = context.globalStorageUri.fsPath; + + const testDataProvider = new TestDataProvider(rootPath, storagePath); + + vscode.window.registerTreeDataProvider("nfscilTestData", testDataProvider); + + vscode.commands.registerCommand("nfscilTestData.refreshEntry", () => testDataProvider.refresh()); + vscode.commands.registerCommand("nfscilTestData.clearCache", () => testDataProvider.clear(false)); + vscode.commands.registerCommand("nfscilTestData.loadListing", () => { + vscode.window + .showOpenDialog({ + canSelectFiles: true, + canSelectFolders: false, + canSelectMany: false, + openLabel: "Load package listing", + filters: { + "JSON files": ["json"], + }, + defaultUri: rootPath ? vscode.Uri.file(rootPath) : undefined, + }) + .then((uri) => { + if (uri && uri[0]) { + testDataProvider.loadListing(uri[0].fsPath); + } else { + vscode.window.showErrorMessage("No file selected"); + } + }); + }); + vscode.commands.registerCommand("nfscilTestData.forceDownloadListing", () => + testDataProvider.forceDownloadListing(), + ); + + vscode.commands.registerCommand("nfscilTestData.openInEditor", (element) => testDataProvider.openInEditor(element)); + vscode.commands.registerCommand("nfscilTestData.saveAs", (element) => testDataProvider.saveAs(element)); +} diff --git a/nf-scil-extensions/test-data-treeview/src/nfscilTestData.ts b/nf-scil-extensions/test-data-treeview/src/nfscilTestData.ts new file mode 100644 index 00000000..8a23e630 --- /dev/null +++ b/nf-scil-extensions/test-data-treeview/src/nfscilTestData.ts @@ -0,0 +1,318 @@ +import * as vscode from "vscode"; +import * as fs from "fs"; +import * as https from "https"; +import * as fpath from "path"; +import * as url from "url"; +import AdmZip = require("adm-zip"); + +const NFSCIL_REPOSITORY = "AlexVCaron/nf-scil"; +const NFSCIL_REF_BRANCH = "test/data"; +const TEST_DATA_REPOSITORY = "scil_test_data/dvc-store/files/md5"; + +const NFSCIL_RAW_URL = url.format({ + protocol: "https", + hostname: "raw.githubusercontent.com", + pathname: NFSCIL_REPOSITORY, +}); +const TEST_DATA_URL = url.format({ + protocol: "https", + hostname: "scil.usherbrooke.ca", + pathname: TEST_DATA_REPOSITORY, +}); + +export class TestDataProvider implements vscode.TreeDataProvider { + private _onDidChangeTreeData: vscode.EventEmitter = new vscode.EventEmitter< + TestDataItem | undefined | void + >(); + readonly onDidChangeTreeData: vscode.Event = this._onDidChangeTreeData.event; + + temp: string; + storagePath: string; + packagePath: string; + contentPath: string; + + listing: string = ""; + pullOnline: boolean = true; + + constructor( + private workspaceRoot: string | undefined, + storagePath: string, + ) { + // Get temporary directory to store transitory files + this.workspaceRoot = workspaceRoot; + this.storagePath = storagePath; + this.temp = storagePath; + this.packagePath = fpath.join(this.temp, "packages"); + this.contentPath = fpath.join(this.temp, "unpacked"); + + if (workspaceRoot) { + this.listing = fpath.join(workspaceRoot, "tests", "config", "test_data.json"); + } + + fs.mkdirSync(storagePath, { recursive: true }); + fs.mkdirSync(this.packagePath, { recursive: true }); + fs.mkdirSync(this.contentPath, { recursive: true }); + } + + refresh(all: boolean = true): void { + if (all) { + this.pullOnline = true; + + if (this.workspaceRoot) { + this.listing = fpath.join(this.workspaceRoot, "tests", "config", "test_data.json"); + } + } + + this._onDidChangeTreeData.fire(); + } + + clear(all: boolean = true): void { + fs.rmdirSync(this.packagePath, { recursive: true }); + fs.rmdirSync(this.contentPath, { recursive: true }); + fs.mkdirSync(this.packagePath, { recursive: true }); + fs.mkdirSync(this.contentPath, { recursive: true }); + + if (all) { + this.listing = ""; + this.pullOnline = false; + } + + this.refresh(false); + } + + forceDownloadListing() { + if (this.listing || !this.pullOnline) { + this.clear(true); + this.listing = ""; + this.pullOnline = true; + this.refresh(false); + } + } + + loadListing(listing: string) { + if (!fs.existsSync(listing)) { + vscode.window.showErrorMessage("Listing does not exist"); + return; + } + + this.listing = listing; + this.refresh(false); + } + + getTreeItem(element: TestDataItem): vscode.TreeItem { + return element; + } + + getChildren(element?: TestDataItem): Thenable { + if (!this.workspaceRoot) { + return Promise.resolve([]); + } + + if (element) { + return Promise.resolve(this.getChildrenItems(element)); + } else { + return Promise.resolve(this.getTestDataPackages()); + } + } + + downloadFile(source: string, target: string): Thenable { + if (fs.existsSync(target)) { + return Promise.resolve(); + } + + const file = fs.createWriteStream(target); + console.log("Downloading file from: " + source); + + return new Promise((resolve, reject) => { + const request = https + .get(source, function (response) { + response + .on("error", (err) => { + fs.unlink(target, () => { + console.log("Failed to download file: " + err.message); + vscode.window.showErrorMessage("Failed to download file: " + source); + }); + reject(err); + }) + .pipe(file); + file.on("finish", () => { + file.close(() => { + console.log("Downloaded file to: " + target); + }); + resolve(); + }); + }) + .on("error", (err) => { + fs.unlink(target, () => { + console.log("Failed to download file: " + err.message); + vscode.window.showErrorMessage("Failed to download file: " + source); + }); + reject(err); + }); + request.end(); + }); + } + + loadTestDataListing(listing?: string): Thenable | void { + if (this.workspaceRoot) { + let listingPromise: Promise; + + if (listing && fs.existsSync(listing)) { + listingPromise = Promise.resolve(listing); + } else if (this.pullOnline) { + console.log("Fetching listing from nf-scil/" + NFSCIL_REF_BRANCH); + const listing = fpath.join(this.temp, "test_data.json"); + fs.rmSync(listing, { force: true }); + listingPromise = new Promise((resolve) => { + this.downloadFile( + fpath.join(NFSCIL_RAW_URL, NFSCIL_REF_BRANCH, "tests", "config", "test_data.json"), + listing, + ).then(() => { + resolve(listing); + }); + }); + } else { + return Promise.resolve([]); + } + + return listingPromise.then((listing) => { + const testPackages: TestDataPackage[] = []; + const data = JSON.parse(fs.readFileSync(listing, "utf8")); + + for (const key in data) { + const value = data[key]; + testPackages.push(new TestDataPackage(key, vscode.TreeItemCollapsibleState.Collapsed, "", value)); + } + + return testPackages; + }); + } + } + + getTestDataPackages(): Thenable { + return Promise.resolve(this.loadTestDataListing(this.listing) || []); + } + + unpackArchive(archive: string): Thenable { + const zip = new AdmZip(archive); + const name = fpath.basename(archive, fpath.extname(archive)); + const content = fpath.join(this.contentPath, name); + + if (fs.existsSync(content)) { + return Promise.resolve(content); + } + + return new Promise((resolve, reject) => { + try { + zip.extractAllTo(this.contentPath, true); + resolve(content); + } catch (err) { + vscode.window.showErrorMessage("Failed to unpack archive: " + name + ".zip"); + reject(err); + } + }); + } + + getFolderContents(folder: string): TestDataItem[] { + const contents: TestDataItem[] = []; + + for (const file of fs.readdirSync(folder)) { + const filePath = fpath.join(folder, file); + const stat = fs.statSync(filePath); + const relPath = fpath.relative(this.contentPath, filePath); + if (stat.isFile()) { + contents.push(new TestDataFile(file, vscode.TreeItemCollapsibleState.None, relPath)); + } else if (stat.isDirectory()) { + contents.push(new TestDataFolder(file, vscode.TreeItemCollapsibleState.Collapsed, relPath)); + } + } + + return contents; + } + + getTestDataPackageContents(element: TestDataPackage): Thenable { + const location = fpath.join(element.md5sum.substring(0, 2), element.md5sum.substring(2)); + const packagePath = fpath.join(this.packagePath, element.label); + + return new Promise((resolve) => { + this.downloadFile(fpath.join(TEST_DATA_URL, location), packagePath).then(() => { + this.unpackArchive(packagePath).then((location) => { + resolve(this.getFolderContents(location)); + }); + }); + }); + } + + getChildrenItems(element: TestDataItem): Thenable { + if (element instanceof TestDataPackage) { + return this.getTestDataPackageContents(element); + } else if (element instanceof TestDataFolder) { + return Promise.resolve(this.getFolderContents(fpath.join(this.contentPath, element.path))); + } + + return Promise.resolve([]); + } + + openInEditor(element: TestDataItem): void { + Promise.resolve( + vscode.commands.executeCommand("vscode.open", vscode.Uri.file(fpath.join(this.contentPath, element.path))), + ); + } + + saveAs(element: TestDataItem): void { + if (this.workspaceRoot) { + vscode.window + .showSaveDialog({ + defaultUri: vscode.Uri.file(this.workspaceRoot), + filters: { + "All files": ["*"], + }, + }) + .then((uri) => { + if (uri) { + fs.copyFileSync(fpath.join(this.contentPath, element.path), uri.fsPath); + } + }); + } + } +} + +export abstract class TestDataItem extends vscode.TreeItem { + constructor( + public readonly label: string, + public readonly collapsibleState: vscode.TreeItemCollapsibleState, + public readonly path: string, + public readonly command?: vscode.Command, + ) { + super(label, collapsibleState); + this.path = path; + } + + abstract iconPath: { light: string; dark: string } | string; + + contextValue = "testDataItem"; +} + +export class TestDataPackage extends TestDataItem { + constructor( + public readonly label: string, + public readonly collapsibleState: vscode.TreeItemCollapsibleState, + public readonly path: string, + public readonly md5sum: string, + public readonly command?: vscode.Command, + ) { + super(label, collapsibleState, path, command); + this.md5sum = md5sum; + } + + iconPath = "$(archive)"; +} + +export class TestDataFolder extends TestDataItem { + iconPath = "$(file-directory)"; +} + +export class TestDataFile extends TestDataItem { + contextValue = "testDataFile"; + iconPath = "$(file)"; +} diff --git a/nf-scil-extensions/test-data-treeview/src/test/extension.test.ts b/nf-scil-extensions/test-data-treeview/src/test/extension.test.ts new file mode 100644 index 00000000..8bcfbcdb --- /dev/null +++ b/nf-scil-extensions/test-data-treeview/src/test/extension.test.ts @@ -0,0 +1,15 @@ +import * as assert from "assert"; + +// You can import and use all API from the 'vscode' module +// as well as import your extension to test it +import * as vscode from "vscode"; +// import * as myExtension from '../../extension'; + +suite("Extension Test Suite", () => { + vscode.window.showInformationMessage("Start all tests."); + + test("Sample test", () => { + assert.strictEqual(-1, [1, 2, 3].indexOf(5)); + assert.strictEqual(-1, [1, 2, 3].indexOf(0)); + }); +}); diff --git a/nf-scil-extensions/test-data-treeview/tsconfig.json b/nf-scil-extensions/test-data-treeview/tsconfig.json new file mode 100644 index 00000000..081d57c6 --- /dev/null +++ b/nf-scil-extensions/test-data-treeview/tsconfig.json @@ -0,0 +1,12 @@ +{ + "compilerOptions": { + "module": "commonjs", + "target": "es2020", + "lib": ["es2020"], + "outDir": "out", + "sourceMap": true, + "rootDir": "src", + "strict": true + }, + "exclude": ["node_modules", ".vscode-test"] +} diff --git a/nf-scil-extensions/test-data-treeview/vsc-extension-quickstart.md b/nf-scil-extensions/test-data-treeview/vsc-extension-quickstart.md new file mode 100644 index 00000000..e2d793c2 --- /dev/null +++ b/nf-scil-extensions/test-data-treeview/vsc-extension-quickstart.md @@ -0,0 +1,46 @@ +# Welcome to your VS Code Extension + +## What's in the folder + +- This folder contains all of the files necessary for your extension. +- `package.json` - this is the manifest file in which you declare your extension and command. + - The sample plugin registers a command and defines its title and command name. With this information VS Code can show the command in the command palette. It doesn’t yet need to load the plugin. +- `src/extension.ts` - this is the main file where you will provide the implementation of your command. + - The file exports one function, `activate`, which is called the very first time your extension is activated (in this case by executing the command). Inside the `activate` function we call `registerCommand`. + - We pass the function containing the implementation of the command as the second parameter to `registerCommand`. + +## Setup + +- install the recommended extensions (amodio.tsl-problem-matcher, ms-vscode.extension-test-runner, and dbaeumer.vscode-eslint) + +## Get up and running straight away + +- Press `F5` to open a new window with your extension loaded. +- Run your command from the command palette by pressing (`Ctrl+Shift+P` or `Cmd+Shift+P` on Mac) and typing `Hello World`. +- Set breakpoints in your code inside `src/extension.ts` to debug your extension. +- Find output from your extension in the debug console. + +## Make changes + +- You can relaunch the extension from the debug toolbar after changing code in `src/extension.ts`. +- You can also reload (`Ctrl+R` or `Cmd+R` on Mac) the VS Code window with your extension to load your changes. + +## Explore the API + +- You can open the full set of our API when you open the file `node_modules/@types/vscode/index.d.ts`. + +## Run tests + +- Install the [Extension Test Runner](https://marketplace.visualstudio.com/items?itemName=ms-vscode.extension-test-runner) +- Run the "watch" task via the **Tasks: Run Task** command. Make sure this is running, or tests might not be discovered. +- Open the Testing view from the activity bar and click the Run Test" button, or use the hotkey `Ctrl/Cmd + ; A` +- See the output of the test result in the Test Results view. +- Make changes to `src/test/extension.test.ts` or create new test files inside the `test` folder. + - The provided test runner will only consider files matching the name pattern `**.test.ts`. + - You can create folders inside the `test` folder to structure your tests any way you want. + +## Go further + +- Reduce the extension size and improve the startup time by [bundling your extension](https://code.visualstudio.com/api/working-with-extensions/bundling-extension). +- [Publish your extension](https://code.visualstudio.com/api/working-with-extensions/publishing-extension) on the VS Code extension marketplace. +- Automate builds by setting up [Continuous Integration](https://code.visualstudio.com/api/working-with-extensions/continuous-integration). diff --git a/package-lock.json b/package-lock.json new file mode 100644 index 00000000..7a2c7965 --- /dev/null +++ b/package-lock.json @@ -0,0 +1,43 @@ +{ + "name": "nf-scil", + "lockfileVersion": 3, + "requires": true, + "packages": { + "": { + "dependencies": { + "editorconfig-checker": "^5.1.8", + "prettier": "^3.1.0" + } + }, + "node_modules/editorconfig-checker": { + "version": "5.1.8", + "resolved": "https://registry.npmjs.org/editorconfig-checker/-/editorconfig-checker-5.1.8.tgz", + "integrity": "sha512-GM/qCbXA8GajSqqjXiWZN49i0nizQV5PjkVKIwWB9rtsm/pztjnBC+4dts5wW2KdrP2zyMPEltWHtWQwoCadqg==", + "bin": { + "ec": "dist/index.js", + "editorconfig-checker": "dist/index.js" + }, + "engines": { + "node": ">=18.0.0" + }, + "funding": { + "type": "buymeacoffee", + "url": "https://www.buymeacoffee.com/mstruebing" + } + }, + "node_modules/prettier": { + "version": "3.1.0", + "resolved": "https://registry.npmjs.org/prettier/-/prettier-3.1.0.tgz", + "integrity": "sha512-TQLvXjq5IAibjh8EpBIkNKxO749UEWABoiIZehEPiY4GNpVdhaFKqSTu+QrlU6D2dPAfubRmtJTi4K4YkQ5eXw==", + "bin": { + "prettier": "bin/prettier.cjs" + }, + "engines": { + "node": ">=14" + }, + "funding": { + "url": "https://github.com/prettier/prettier?sponsor=1" + } + } + } +} diff --git a/package.json b/package.json new file mode 100644 index 00000000..4abce395 --- /dev/null +++ b/package.json @@ -0,0 +1,6 @@ +{ + "dependencies": { + "editorconfig-checker": "^5.1.8", + "prettier": "^3.1.0" + } +} diff --git a/run_tests.sh b/run_tests.sh index 9e5ad4ee..a5a75f9f 100755 --- a/run_tests.sh +++ b/run_tests.sh @@ -75,21 +75,21 @@ ONCE=false PROFILE="docker" while getopts "e:uoph:" opt; do - case $opt in - e) EXCLUDES+=($OPTARG) - ;; - u) UPDATE_SNAPS=true - ;; - o) ONCE=true - ;; - p) PROFILE="$OPTARG" - ;; - h) echo "$DESCRIPTION" - ;; - \?) echo "Invalid option -$OPTARG" >&2 - echo "$DESCRIPTION" - ;; - esac + case $opt in + e) EXCLUDES+=($OPTARG) + ;; + u) UPDATE_SNAPS=true + ;; + o) ONCE=true + ;; + p) PROFILE="$OPTARG" + ;; + h) echo "$DESCRIPTION" + ;; + \?) echo "Invalid option -$OPTARG" >&2 + echo "$DESCRIPTION" + ;; + esac done diff --git a/subworkflows/nf-scil/anatomical_segmentation/tests/main.nf.test b/subworkflows/nf-scil/anatomical_segmentation/tests/main.nf.test index 5a27f842..b3836084 100644 --- a/subworkflows/nf-scil/anatomical_segmentation/tests/main.nf.test +++ b/subworkflows/nf-scil/anatomical_segmentation/tests/main.nf.test @@ -20,7 +20,7 @@ nextflow_workflow { script "../../load_test_data/main.nf" process { """ - input[0] = Channel.from( [ "heavy.zip" ] ) + input[0] = Channel.from( [ "T1w.zip", "freesurfer_nifti.zip" ] ) input[1] = "test.load-test-data" """ } @@ -32,10 +32,15 @@ nextflow_workflow { when { workflow { """ - input[0] = LOAD_DATA.out.test_data_directory.map{ + ch_split_test_data = LOAD_DATA.out.test_data_directory + .branch{ + t1w: it.simpleName == "T1w" + freesurfer: it.simpleName == "freesurfer_nifti" + } + input[0] = ch_split_test_data.t1w.map{ test_data_directory -> [ - [ id:'test', single_end:false ], // meta map - file("\${test_data_directory}/anat/anat_image.nii.gz", checkIfExists: true), + [ id:'test' ], + file("\${test_data_directory}/T1w.nii.gz", checkIfExists: true), [] ]} input[1] = [] @@ -56,12 +61,17 @@ nextflow_workflow { when { workflow { """ + ch_split_test_data = LOAD_DATA.out.test_data_directory + .branch{ + t1w: it.simpleName == "T1w" + freesurfer: it.simpleName == "freesurfer_nifti" + } input[0] = [] - input[1] = LOAD_DATA.out.test_data_directory.map{ + input[1] = ch_split_test_data.freesurfer.map{ test_data_directory -> [ [ id:'test', single_end:false ], // meta map - file("\${test_data_directory}/freesurfer/aparc_aseg.nii.gz", checkIfExists: true), - file("\${test_data_directory}/freesurfer/wmparc.nii.gz", checkIfExists: true), + file("\${test_data_directory}/aparc+aseg.nii.gz", checkIfExists: true), + file("\${test_data_directory}/wmparc.nii.gz", checkIfExists: true), [] ]} """ diff --git a/subworkflows/nf-scil/anatomical_segmentation/tests/main.nf.test.snap b/subworkflows/nf-scil/anatomical_segmentation/tests/main.nf.test.snap index 48d447fe..1974a2a4 100644 --- a/subworkflows/nf-scil/anatomical_segmentation/tests/main.nf.test.snap +++ b/subworkflows/nf-scil/anatomical_segmentation/tests/main.nf.test.snap @@ -8,7 +8,7 @@ "id": "test", "single_end": false }, - "test__mask_wm.nii.gz:md5,2dc635526adb6ef185300acc326ead13" + "test__mask_wm.nii.gz:md5,0ed4a06defc512b1b898d6e0c3ef678a" ] ], "1": [ @@ -17,7 +17,7 @@ "id": "test", "single_end": false }, - "test__mask_gm.nii.gz:md5,247106ed727133078fe262b0b8244071" + "test__mask_gm.nii.gz:md5,a363d6207419b08346a7c05c6525430e" ] ], "2": [ @@ -26,7 +26,7 @@ "id": "test", "single_end": false }, - "test__mask_csf.nii.gz:md5,b92db7e454c95afadea320a143912ce8" + "test__mask_csf.nii.gz:md5,3dbcb3eefb507bedab91fb80ed636f36" ] ], "3": [ @@ -50,7 +50,7 @@ "id": "test", "single_end": false }, - "test__mask_csf.nii.gz:md5,b92db7e454c95afadea320a143912ce8" + "test__mask_csf.nii.gz:md5,3dbcb3eefb507bedab91fb80ed636f36" ] ], "gm_map": [ @@ -62,7 +62,7 @@ "id": "test", "single_end": false }, - "test__mask_gm.nii.gz:md5,247106ed727133078fe262b0b8244071" + "test__mask_gm.nii.gz:md5,a363d6207419b08346a7c05c6525430e" ] ], "versions": [ @@ -77,16 +77,16 @@ "id": "test", "single_end": false }, - "test__mask_wm.nii.gz:md5,2dc635526adb6ef185300acc326ead13" + "test__mask_wm.nii.gz:md5,0ed4a06defc512b1b898d6e0c3ef678a" ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0-rc1", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-09T20:53:29.945493" + "timestamp": "2024-09-05T02:45:52.364394" }, "anatomical_segmentation - fslfast": { "content": [ @@ -94,55 +94,49 @@ "0": [ [ { - "id": "test", - "single_end": false + "id": "test" }, - "test__mask_wm.nii.gz:md5,f849e268007a747714e342162f13f631" + "test__mask_wm.nii.gz:md5,98d75f5c0ddd2b7f2bfff8fbf1877e34" ] ], "1": [ [ { - "id": "test", - "single_end": false + "id": "test" }, - "test__mask_gm.nii.gz:md5,39396421c6d1d32ea7943a5ec7a49dce" + "test__mask_gm.nii.gz:md5,a840f08c5b90cb351d3272d8cab6f00c" ] ], "2": [ [ { - "id": "test", - "single_end": false + "id": "test" }, - "test__mask_csf.nii.gz:md5,d0fbc088059f17faff38fbcd33257d27" + "test__mask_csf.nii.gz:md5,f22037987a38e5132ccbb2887ee71842" ] ], "3": [ [ { - "id": "test", - "single_end": false + "id": "test" }, - "test__map_wm.nii.gz:md5,1d5a9655d4e3c832b14c83e9424b00fc" + "test__map_wm.nii.gz:md5,c7d666c66baea2132d70be38017c6901" ] ], "4": [ [ { - "id": "test", - "single_end": false + "id": "test" }, - "test__map_gm.nii.gz:md5,f7e51eb14af645c687db5d2c6a4f5bf4" + "test__map_gm.nii.gz:md5,6dbc993e43f6efcdd6a3a097df2b4574" ] ], "5": [ [ { - "id": "test", - "single_end": false + "id": "test" }, - "test__map_csf.nii.gz:md5,9c14d8f70e69d641d9c214d0d52b3663" + "test__map_csf.nii.gz:md5,dcc224f10f31ee306491ebbdcfbe5bfe" ] ], "6": [ @@ -151,37 +145,33 @@ "csf_map": [ [ { - "id": "test", - "single_end": false + "id": "test" }, - "test__map_csf.nii.gz:md5,9c14d8f70e69d641d9c214d0d52b3663" + "test__map_csf.nii.gz:md5,dcc224f10f31ee306491ebbdcfbe5bfe" ] ], "csf_mask": [ [ { - "id": "test", - "single_end": false + "id": "test" }, - "test__mask_csf.nii.gz:md5,d0fbc088059f17faff38fbcd33257d27" + "test__mask_csf.nii.gz:md5,f22037987a38e5132ccbb2887ee71842" ] ], "gm_map": [ [ { - "id": "test", - "single_end": false + "id": "test" }, - "test__map_gm.nii.gz:md5,f7e51eb14af645c687db5d2c6a4f5bf4" + "test__map_gm.nii.gz:md5,6dbc993e43f6efcdd6a3a097df2b4574" ] ], "gm_mask": [ [ { - "id": "test", - "single_end": false + "id": "test" }, - "test__mask_gm.nii.gz:md5,39396421c6d1d32ea7943a5ec7a49dce" + "test__mask_gm.nii.gz:md5,a840f08c5b90cb351d3272d8cab6f00c" ] ], "versions": [ @@ -190,27 +180,25 @@ "wm_map": [ [ { - "id": "test", - "single_end": false + "id": "test" }, - "test__map_wm.nii.gz:md5,1d5a9655d4e3c832b14c83e9424b00fc" + "test__map_wm.nii.gz:md5,c7d666c66baea2132d70be38017c6901" ] ], "wm_mask": [ [ { - "id": "test", - "single_end": false + "id": "test" }, - "test__mask_wm.nii.gz:md5,f849e268007a747714e342162f13f631" + "test__mask_wm.nii.gz:md5,98d75f5c0ddd2b7f2bfff8fbf1877e34" ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0-rc1", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-17T14:24:57.988893" + "timestamp": "2024-09-05T02:38:48.75146" } } \ No newline at end of file diff --git a/test.tap b/test.tap new file mode 100644 index 00000000..fdb6e7ec --- /dev/null +++ b/test.tap @@ -0,0 +1,3 @@ +1..2 +ok 1 Test Process DENOISING_NLMEANS: denoising - nlmeans +ok 2 Test Process DENOISING_NLMEANS: denoising - nlmeans - withmask diff --git a/tests/config/nf-test.config b/tests/config/nf-test.config index 4859b9e5..7e9747fe 100644 --- a/tests/config/nf-test.config +++ b/tests/config/nf-test.config @@ -1,3 +1,5 @@ +import groovy.json.JsonSlurper + params { outdir = "output/" publish_dir_mode = "copy" @@ -5,61 +7,15 @@ params { nf_scil_test_data_remote = "https://scil.usherbrooke.ca" nf_scil_test_database_path = "scil_test_data/dvc-store/files/md5" - nf_scil_test_data_associations = [ - "commit_amico.zip": "c190e6b9d22350b51e222c60febe13b4", - "bundles.zip": "6d3ebc21062bf320714483b7314a230a", - "stats.zip": "2aeac4da5ab054b3a460fc5fdc5e4243", - "bst.zip": "eed227fd246255e7417f92d49eb1066a", - "filtering.zip": "19116ff4244d057c8214ee3fe8e05f71", - "ihMT.zip": "08fcf44848ba2649aad5a5a470b3cb06", - "tractometry.zip": "890bfa70e44b15c0d044085de54e00c6", - "bids_json.zip": "97fd9a414849567fbfdfdb0ef400488b", - "MT.zip": "1f4345485248683b3652c97f2630950e", - "btensor_testdata.zip": "7ada72201a767292d56634e0a7bbd9ad", - "tracking.zip": "4793a470812318ce15f1624e24750e4d", - "atlas.zip": "dc34e073fc582476504b3caf127e53ef", - "anatomical_filtering.zip": "5282020575bd485e15d3251257b97e01", - "connectivity.zip": "fe8c47f444d33067f292508d7050acc4", - "plot.zip": "a1dc54cad7e1d17e55228c2518a1b34e", - "others.zip": "82248b4888a63b0aeffc8070cc206995", - "fodf_filtering.zip": "5985c0644321ecf81fd694fb91e2c898", - "processing.zip": "eece5cdbf437b8e4b5cb89c797872e28", - "surface_vtk_fib.zip": "241f3afd6344c967d7176b43e4a99a41", - "tractograms.zip": "5497d0bf3ccc35f8f4f117829d790267", - "registration.zip": "95ebaa64866bac18d8b0fcd96cd10958", - "topup_eddy.zip": "7847496510dc85fb205ba9586f0011ff", - "topup_eddy_light.zip": "54369410cfd0587e1d8916047945c1fd", - "bids.zip": "68b9efa1e009a59a83adef3aeea9b469", - "antsbet.zip": "66850bea7af7c1f3fc4e7d371d12d6e8", - "freesurfer.zip": "3b876fba6fd77d4962243ac9647bc505", - "freesurfer_reslice.zip": "636ee21cd2ed2910a8f64d432b47f578", - "freesurfer_transforms.zip": "5c562afd9dea52eb99f13ab4dffd4113", - "light.zip": "f2a3a8bddf43d1f67a5e8867ce9ebaa2", - "heavy.zip": "6f2cd0bbdb162455e71de1c7d3b4eb18", - "raw_b0.zip": "6e7b8181b3e929f4235a9364aa60656b", - "raw_DWIms300-1000-2000-dir8-32-60.zip": "cfa4cb9cc9595a18272fdb0ef3a08ce5", - "raw_DWIms300-1000-dir8-32.zip": "29dfaba220a1e921f95e16f811977f36", - "raw_DWIms1000-2000-dir32-60.zip": "7fed32798f158ab8118a116fd9a69f52", - "raw_DWIss300-dir8.zip": "33e735bf7514159b803f8302f4d97db8", - "raw_DWIss1000-dir32.zip": "55246c8f6fe8c04cb8538715cad21c38", - "raw_DWIss2000-dir60.zip": "8dc746ccf9eed5f8931265bad379e2e5", - "raw_EPI.zip": "631e9781bda5ae482d92bba1c612bbf5", - "raw_FLAIR.zip": "67663a38ce23120b1b42d73fa9268d2d", - "raw_T1w.zip": "2a4adad9dd05a0fb626cb71945bc11b5", - "raw_segmentation.zip": "6aac249229e1e360d1fca90bc4a4bec2", - "topup_results.zip": "f83628eac00c9851cb015588909c4ef8", - "b0.zip": "fefd7452a61a80f6ceac7352e6231a0d", - "DWIms300-1000-2000-dir8-32-60.zip": "6249618893c832dfb4392c72fd7c81cb", - "DWIms300-1000-dir8-32.zip": "52e67fa54a2494d2ad5b496d25e6ee99", - "DWIms1000-2000-dir32-60.zip": "5db0cc6624da1d5ec99893b08629e45f", - "DWIss300-dir8.zip": "ef1335775c9fbf11452c71e01b097282", - "DWIss1000-dir32.zip": "c72fd590a3f400278299a068eeffd1d0", - "DWIss2000-dir60.zip": "9ad7ccb4e30b39c47f374018db2e6424", - "T1w.zip": "10e27bb2ddd4d01be968a93b2166096c", - "dti.zip": "ba866c59fc4d984f626691a6b941fc32", - "responses.zip": "1a5b862b91c72740bcce0431a1f9254a", - "segmentation.zip": "ab51be6d142ad1a8e30ffb964447d010" - ] + nf_scil_test_data_associations = new JsonSlurper().parse( + new File("$projectDir/tests/config/test_data.json") + ) +} + +report { + enabled = true + file = "$launchDir/report.html" + overwrite = true } process { diff --git a/tests/config/test_data.json b/tests/config/test_data.json new file mode 100644 index 00000000..14fa9597 --- /dev/null +++ b/tests/config/test_data.json @@ -0,0 +1,57 @@ +{ + "commit_amico.zip": "c190e6b9d22350b51e222c60febe13b4", + "bundles.zip": "6d3ebc21062bf320714483b7314a230a", + "stats.zip": "2aeac4da5ab054b3a460fc5fdc5e4243", + "bst.zip": "eed227fd246255e7417f92d49eb1066a", + "filtering.zip": "19116ff4244d057c8214ee3fe8e05f71", + "ihMT.zip": "08fcf44848ba2649aad5a5a470b3cb06", + "tractometry.zip": "890bfa70e44b15c0d044085de54e00c6", + "bids_json.zip": "97fd9a414849567fbfdfdb0ef400488b", + "MT.zip": "1f4345485248683b3652c97f2630950e", + "btensor_testdata.zip": "7ada72201a767292d56634e0a7bbd9ad", + "tracking.zip": "4793a470812318ce15f1624e24750e4d", + "atlas.zip": "dc34e073fc582476504b3caf127e53ef", + "anatomical_filtering.zip": "5282020575bd485e15d3251257b97e01", + "connectivity.zip": "fe8c47f444d33067f292508d7050acc4", + "plot.zip": "a1dc54cad7e1d17e55228c2518a1b34e", + "others.zip": "82248b4888a63b0aeffc8070cc206995", + "fodf_filtering.zip": "5985c0644321ecf81fd694fb91e2c898", + "processing.zip": "eece5cdbf437b8e4b5cb89c797872e28", + "surface_vtk_fib.zip": "241f3afd6344c967d7176b43e4a99a41", + "tractograms.zip": "5497d0bf3ccc35f8f4f117829d790267", + "registration.zip": "95ebaa64866bac18d8b0fcd96cd10958", + "topup_eddy.zip": "7847496510dc85fb205ba9586f0011ff", + "topup_eddy_light.zip": "54369410cfd0587e1d8916047945c1fd", + "bids.zip": "68b9efa1e009a59a83adef3aeea9b469", + "antsbet.zip": "66850bea7af7c1f3fc4e7d371d12d6e8", + "freesurfer.zip": "3b876fba6fd77d4962243ac9647bc505", + "freesurfer_reslice.zip": "636ee21cd2ed2910a8f64d432b47f578", + "freesurfer_transforms.zip": "5c562afd9dea52eb99f13ab4dffd4113", + "light.zip": "f2a3a8bddf43d1f67a5e8867ce9ebaa2", + "heavy.zip": "6f2cd0bbdb162455e71de1c7d3b4eb18", + "raw_b0.zip": "6e7b8181b3e929f4235a9364aa60656b", + "raw_DWIms300-1000-2000-dir8-32-60.zip": "cfa4cb9cc9595a18272fdb0ef3a08ce5", + "raw_DWIms300-1000-dir8-32.zip": "29dfaba220a1e921f95e16f811977f36", + "raw_DWIms1000-2000-dir32-60.zip": "7fed32798f158ab8118a116fd9a69f52", + "raw_DWIss300-dir8.zip": "33e735bf7514159b803f8302f4d97db8", + "raw_DWIss1000-dir32.zip": "55246c8f6fe8c04cb8538715cad21c38", + "raw_DWIss2000-dir60.zip": "8dc746ccf9eed5f8931265bad379e2e5", + "raw_EPI.zip": "631e9781bda5ae482d92bba1c612bbf5", + "raw_FLAIR.zip": "67663a38ce23120b1b42d73fa9268d2d", + "raw_T1w.zip": "2a4adad9dd05a0fb626cb71945bc11b5", + "raw_segmentation.zip": "6aac249229e1e360d1fca90bc4a4bec2", + "topup_results.zip": "f83628eac00c9851cb015588909c4ef8", + "b0.zip": "fefd7452a61a80f6ceac7352e6231a0d", + "DWIms300-1000-2000-dir8-32-60.zip": "6249618893c832dfb4392c72fd7c81cb", + "DWIms300-1000-dir8-32.zip": "52e67fa54a2494d2ad5b496d25e6ee99", + "DWIms1000-2000-dir32-60.zip": "5db0cc6624da1d5ec99893b08629e45f", + "DWIss300-dir8.zip": "ef1335775c9fbf11452c71e01b097282", + "DWIss1000-dir32.zip": "c72fd590a3f400278299a068eeffd1d0", + "DWIss2000-dir60.zip": "9ad7ccb4e30b39c47f374018db2e6424", + "T1w.zip": "8e9cf2beec4595d407732152a19589f5", + "dti.zip": "ba866c59fc4d984f626691a6b941fc32", + "responses.zip": "1a5b862b91c72740bcce0431a1f9254a", + "segmentation.zip": "ab51be6d142ad1a8e30ffb964447d010", + "freesurfer_full.zip": "203e482426065326ff5920368d4d7908", + "freesurfer_nifti.zip": "adb5ac4cf5c45040339e04e7c142e8c9" +}