Merge branch 'Inria-Empenn:main' into main

.github/workflows/pipeline_tests.yml

@@ -51,6 +51,7 @@ jobs:
   pytest:
     needs: identify-tests
     runs-on: self-hosted
+    timeout-minutes: 2880 # 48h
     steps:
     - name: Checkout PR branch
       uses: actions/checkout@v3

.github/workflows/test_changes.yml

@@ -42,6 +42,7 @@ jobs:
   pytest:
     needs: identify-tests
     runs-on: self-hosted
+    timeout-minutes: 2880 # 48h
     steps:
     - name: Checkout PR branch
       uses: actions/checkout@v3

narps_open/data/results/__init__.py

@@ -56,7 +56,7 @@ def get_uid(self):
 
     def get_file_urls(self):
         """ Return a dict containing the download url for each file of the collection.
-        * dict key is the file base name (with no extension)
+        * dict key is the file base name (with extension)
         * dict value is the download url for the file on Neurovault
         """
 
@@ -69,7 +69,7 @@ def get_file_urls(self):
             file_urls = {}
             for result in json['results']:
                 # Get data for a file in the collection
-                file_urls[result['name']] = result['file']
+                file_urls[result['name']+'.nii.gz'] = result['file']
 
         return file_urls
 
@@ -84,7 +84,7 @@ def download(self):
         for file_name, file_url in self.files.items():
             urlretrieve(
                 file_url,
-                join(self.directory, file_name+'.nii.gz'),
+                join(self.directory, file_name),
                 show_download_progress
                 )
 

tests/conftest.py

@@ -58,15 +58,20 @@ def test_pipeline_execution(
         # Get missing subjects
         missing_subjects = set()
         for file in runner.get_missing_first_level_outputs():
-            missing_subjects.add(get_subject_id(file))
+            subject_id = get_subject_id(file)
+            if subject_id is not None:
+                missing_subjects.add(subject_id)
 
         # Leave if no missing subjects
         if not missing_subjects:
             break
 
         # Start pipeline
         runner.subjects = missing_subjects
-        runner.start(True, False)
+        try: # This avoids errors in the workflow to make the test fail
+            runner.start(True, False)
+        except(RuntimeError) as err:
+            print('RuntimeError: ', err)
 
     # Check missing files for the last time
     missing_files = runner.get_missing_first_level_outputs()
@@ -80,15 +85,15 @@ def test_pipeline_execution(
 
     # Indices and keys to the unthresholded maps
     indices = list(range(1, 18, 2))
-    keys = [f'hypo{i}_unthresh.nii.gz' for i in range(1, 10)]
 
     # Retrieve the paths to the reproduced files
     reproduced_files = runner.pipeline.get_hypotheses_outputs()
     reproduced_files = [reproduced_files[i] for i in indices]
 
     # Retrieve the paths to the results files
     collection = ResultsCollection(team_id)
-    results_files = [join(collection.directory, collection.files[k]) for k in keys]
+    results_files = [join(collection.directory, f) for f in collection.files.keys()]
+    results_files = [results_files[i] for i in indices]
 
     # Compute the correlation coefficients
     return [
@@ -142,10 +147,10 @@ def test_pipeline_evaluation(team_id: str):
 
     for subjects in [20, 40, 60, 80, 108]:
         # Execute pipeline
-        results = helpers.test_pipeline_execution(team_id, subjects)
+        results = test_pipeline_execution(team_id, subjects)
 
         # Compute correlation with results
-        passed = helpers.test_correlation_results(results, subjects)
+        passed = test_correlation_results(results, subjects)
 
         # Write values in a file
         with open(file_name, 'a', encoding = 'utf-8') as file:

tests/data/test_results.py

@@ -48,15 +48,15 @@ def test_create():
         assert collection.uid == '4881'
         assert 'results/orig/4881_2T6S' in collection.directory
         test_str = 'http://neurovault.org/media/images/4881/hypo1_thresholded_revised.nii.gz'
-        assert collection.files['hypo1_thresh'] == test_str
+        assert collection.files['hypo1_thresh.nii.gz'] == test_str
 
         collection = ResultsCollection('43FJ')
         assert collection.team_id == '43FJ'
         assert collection.uid == '4824'
         assert 'results/orig/4824_43FJ' in collection.directory
         test_str = 'http://neurovault.org/media/images/4824/'
         test_str += 'Zstat_Thresholded_Negative_Effect_of_Loss_Equal_Indifference.nii.gz'
-        assert collection.files['hypo5_thresh'] == test_str
+        assert collection.files['hypo5_thresh.nii.gz'] == test_str
 
     @staticmethod
     @mark.unit_test