Merge pull request #4 from Medical-Image-Analysis-Laboratory/dev-hk

Integration of automatic DL-based brain extraction
Medical-Image-Analysis-Laboratory · Oct 20, 2020 · 74bb016 · 74bb016
2 parents 69c920d + 98cb9a4
commit 74bb016
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -1,4 +1,7 @@
-version: 2
+version: 2.1
+
+orbs:
+  coverage-reporter: codacy/coverage-reporter@11.0.1
 
 jobs:
 
@@ -117,7 +120,12 @@ jobs:
               docker images
             fi
       - run:
-          name: Run super-resolution pipelines on sample testing dataset
+          name: Create the data/test folder
+          no_output_timeout: 1h
+          command: |
+            mkdir -p /tmp/src/mialsuperresolutiontoolkit/data/test
+      - run:
+          name: Test-01 - Run super-resolution pipelines on sample testing dataset with manual masks
           no_output_timeout: 6h
           command: |
             # Get version, update files.
@@ -128,24 +136,60 @@ jobs:
             ls -la  /tmp/src/mialsuperresolutiontoolkit/data/derivatives
 
             #Execute BIDS App
-            docker run -it --rm \
+            docker run -it --rm --entrypoint /app/run_srr_coverage.sh \
                 -v /tmp/src/mialsuperresolutiontoolkit/data:/bids_dir \
                 -v /tmp/src/mialsuperresolutiontoolkit/data/derivatives:/output_dir \
                 sebastientourbier/mialsuperresolutiontoolkit-bidsapp \
                 /bids_dir /output_dir participant --participant_label 01 \
-                --param_file /bids_dir/code/participants_params.json 
+                --param_file /bids_dir/code/participants_params.json \
+                --manual 
+
+            # Rename log
+            mv /tmp/src/mialsuperresolutiontoolkit/data/code/log.txt /tmp/src/mialsuperresolutiontoolkit/data/test/test-01_log.txt
 
+            # Rename partial coverage
+            mv /tmp/src/mialsuperresolutiontoolkit/data/code/coverage.xml /tmp/src/mialsuperresolutiontoolkit/data/test/test-01_coverage.xml
       # - save_cache:
       #    key: ds-sample-derivatives-{{ .Branch }}-{{ epoch }}
       #    paths:
       #       - /tmp/data/ds-sample/derivatives
       - run:
-          name: Checking outputs of MIALSRTK BIDS App run
+          name: Test-01 - Checking outputs of MIALSRTK BIDS App run
+          command: |
+            # Get all files in derivatives except the _*.json interface hash generated by nipype (find) / remove the full path of the derivatives (sed) / sort the files and write it to a text file
+            sudo find /tmp/src/mialsuperresolutiontoolkit/data/derivatives -path */figures -prune -o -not -name "_*.json" -type f -print | sed s+/tmp/src/mialsuperresolutiontoolkit/data/derivatives/++ | sort > /tmp/src/mialsuperresolutiontoolkit/data/test/test-01_outputs.out
+            diff /home/circleci/src/mialsuperresolutiontoolkit/.circleci/test-01_outputs.txt /tmp/src/mialsuperresolutiontoolkit/data/test/test-01_outputs.out         
+            exit $?
+      - run:
+          name: Test-02 - Run super-resolution pipelines on sample testing dataset with automatic brain extraction
+          no_output_timeout: 6h
+          command: |
+            # Get version, update files.
+            #THISVERSION=v$( python /home/circleci/src/mialsuperresolutiontoolkit/get_version.py )
+            #echo "THISVERSION : ${THISVERSION}"
+            ls -la  /tmp/src/mialsuperresolutiontoolkit/data
+            ls -la  /tmp/src/mialsuperresolutiontoolkit/data/code
+            ls -la  /tmp/src/mialsuperresolutiontoolkit/data/derivatives
+
+            #Execute BIDS App
+            docker run -it --rm --entrypoint /app/run_srr_coverage.sh \
+                -v /tmp/src/mialsuperresolutiontoolkit/data:/bids_dir \
+                -v /tmp/src/mialsuperresolutiontoolkit/data/derivatives:/output_dir \
+                sebastientourbier/mialsuperresolutiontoolkit-bidsapp \
+                /bids_dir /output_dir participant --participant_label 01 \
+                --param_file /bids_dir/code/participants_params.json
+
+            # Rename log
+            mv /tmp/src/mialsuperresolutiontoolkit/data/code/log.txt /tmp/src/mialsuperresolutiontoolkit/data/test/test-02_log.txt
+
+            # Rename partial coverage
+            mv /tmp/src/mialsuperresolutiontoolkit/data/code/coverage.xml /tmp/src/mialsuperresolutiontoolkit/data/test/test-02_coverage.xml
+      - run:
+          name: Test-02 - Checking outputs of MIALSRTK BIDS App run
           command: |
-            mkdir -p /tmp/src/mialsuperresolutiontoolkit/data/test
             # Get all files in derivatives except the _*.json interface hash generated by nipype (find) / remove the full path of the derivatives (sed) / sort the files and write it to a text file
-            sudo find /tmp/src/mialsuperresolutiontoolkit/data/derivatives -path */figures -prune -o -not -name "_*.json" -type f -print | sed s+/tmp/src/mialsuperresolutiontoolkit/data/derivatives/++ | sort > /tmp/src/mialsuperresolutiontoolkit/data/test/outputs.out
-            diff /home/circleci/src/mialsuperresolutiontoolkit/.circleci/test_outputs.txt /tmp/src/mialsuperresolutiontoolkit/data/test/outputs.out         
+            sudo find /tmp/src/mialsuperresolutiontoolkit/data/derivatives -path */figures -prune -o -not -name "_*.json" -type f -print | sed s+/tmp/src/mialsuperresolutiontoolkit/data/derivatives/++ | sort > /tmp/src/mialsuperresolutiontoolkit/data/test/test-02_outputs.out
+            diff /home/circleci/src/mialsuperresolutiontoolkit/.circleci/test-02_outputs.txt /tmp/src/mialsuperresolutiontoolkit/data/test/test-02_outputs.out         
             exit $?
       - run:
           name: Clean working directory
@@ -154,12 +198,31 @@ jobs:
             sudo chown $(id -un):$(id -gn) -R /tmp/src/mialsuperresolutiontoolkit/data
             find /tmp/src/mialsuperresolutiontoolkit/data/derivatives -not -name "*.svg" -not -name "*.html" -not -name "*.rst" \
                 -not -name "*.mat" -not -name "*.gpickle" -not -name "*.lta" -not -name "*.json" -not -name "*.txt" -not -name "*.pklz" -type f -delete
+      - persist_to_workspace:
+          root: /tmp
+          paths:
+            - src/mialsuperresolutiontoolkit/data/test
+      - store_artifacts:
+          path: /tmp/src/mialsuperresolutiontoolkit/data/code
       - store_artifacts:
           path: /tmp/src/mialsuperresolutiontoolkit/data/test
       - store_artifacts:
           path: /tmp/src/mialsuperresolutiontoolkit/data/derivatives
 
+  codacy-coverage-report:
+    docker:
+      - image: 'circleci/openjdk:8-jdk'
+
+    working_directory: /tmp/src/mialsuperresolutiontoolkit/data/test
 
+    steps:
+      - attach_workspace:
+          at: /tmp
+      - coverage-reporter/send_report:
+          # With parcellation tests
+          # coverage-reports: '/tmp/src/mialsuperresolutiontoolkit/data/test/test-01_coverage.xml'
+          coverage-reports: '/tmp/src/mialsuperresolutiontoolkit/data/test/test-01_coverage.xml,/tmp/src/mialsuperresolutiontoolkit/data/test/test-02_coverage.xml'
+          project-token: ${CODACY_PROJECT_TOKEN}
   # build_docs:
   #   machine:
   #     # Ubuntu 16.04, docker 18.09.3, docker-compose 1.23.1
@@ -311,6 +374,16 @@ workflows:
             tags:
               only: /.*/
 
+      - codacy-coverage-report:
+          requires:
+            - test
+          filters:
+              branches:
+                ignore:
+                  - /docs?\/.*/
+              tags:
+                only: /.*/
+
       - deploy_docker_release:
           requires:
             - build