add missing variable and quotes

NOEL-MNI · Sep 19, 2023 · 38fb44f · 38fb44f
1 parent d162856
commit 38fb44f
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/.github/workflows/test-inference-pipeline.yml b/.github/workflows/test-inference-pipeline.yml
@@ -5,6 +5,7 @@ on: [push, pull_request]
 
 env:
   CI_TESTING: True
+  CI_TESTING_PATIENT_ID: "sub-00055"
 
 jobs:
   build:
@@ -39,12 +40,11 @@ jobs:
           wget ${BASE_URL}/${CI_TESTING_PATIENT_ID}_acq-tse3dvfl_FLAIR.nii.gz\?versionId\=HmzYoUuYkdbyd8jkpdJjVkZydRHNSqUX -O ~/io/${CI_TESTING_PATIENT_ID}/flair.nii.gz
           wget ${BASE_URL}/${CI_TESTING_PATIENT_ID}_acq-tse3dvfl_FLAIR_roi.nii.gz\?versionId\=ulmEU3nb8WCvGwcwTbkcdNSVr07PMPQN -O ~/io/${CI_TESTING_PATIENT_ID}/label.nii.gz
         env:
-          CI_TESTING_PATIENT_ID: sub-00055
-          BASE_URL: https://s3.amazonaws.com/openneuro.org/ds004199/${CI_TESTING_PATIENT_ID}/anat
+          BASE_URL: "https://s3.amazonaws.com/openneuro.org/ds004199/${CI_TESTING_PATIENT_ID}/anat"
 
       - name: Run inference for deepFCD
         run: |
-          ./app/inference.py sub-00055 t1.nii.gz flair.nii.gz ~/io cuda 1 1
+          ./app/inference.py ${CI_TESTING_PATIENT_ID} t1.nii.gz flair.nii.gz ~/io cuda 1 1
         env:
           CI_TESTING_GT: "./tests/segmentations/${CI_TESTING_PATIENT_ID}/${CI_TESTING_PATIENT_ID}_label_dilated_final.nii.gz"
           CI_TESTING_PRED_DIR: "/home/ga/io"