added QC logic, security fixes as well

Author: miloswrath

.github/workflows/main.yml

@@ -33,7 +33,10 @@ jobs:
           if [ -f code/requirements.txt ]; then pip install -r code/requirements.txt; fi
 
       - name: Run Python script
-        run: python code/main.py
+        env:
+          RC_TOKEN: ${{ secrets.RC_TOKEN }}
+        run: |
+          python code/main.py 1 "$RC_TOKEN"
 
       - name: Commit and push changes to main
         run: |
@@ -43,7 +46,3 @@ jobs:
           git add .
           git commit -m "Automated changes from GitHub Actions"
           git push origin main
-
-
-
-

code/core/gg.py

@@ -15,14 +15,18 @@ def __init__(self, matched, intdir, obsdir):
             obsdir (str): Path to the observational directory.
         """
         self.matched = matched
-        self.INTDIR = intdir+'/'
-        self.OBSDIR = obsdir+'/'
+        self.INTDIR = intdir.rstrip('/') + '/'
+        self.OBSDIR = obsdir.rstrip('/') + '/'
         self.DERIVATIVES = "/derivatives/GGIR-3.1.4"  # Defined within the class
 
     def run_gg(self):
         """
         Run GGIR for both the internal and observational project directories.
+        After each GGIR run, invoke the QC pipeline for that project.
         """
+        # Assume QC is available at this import path
+        from utils.qc import QC 
+
         for project_dir in [self.INTDIR, self.OBSDIR]:
             command = f"Rscript core/acc.R --project_dir {project_dir} --deriv_dir {self.DERIVATIVES}"
 
@@ -47,3 +51,30 @@ def run_gg(self):
 
                 if process.returncode != 0:
                     raise subprocess.CalledProcessError(process.returncode, command)
+
+                print(f"GGIR completed successfully for {project_dir}.")
+
+                # Determine project type for QC ('int' for internal, 'obs' for observational)
+                if project_dir.rstrip('/') == self.INTDIR.rstrip('/'):
+                    project_type = 'int'
+                else:
+                    project_type = 'obs'
+
+                # Run QC for this project
+                print(f"Starting QC pipeline for {project_type} project.")
+                qc_runner = QC(project_type)
+                qc_runner.qc()
+                print(f"QC pipeline finished for {project_type} project.")
+
+            except subprocess.CalledProcessError as e:
+                print(f"Error running GGIR for {project_dir}: {e}")
+                # Optionally, continue to next project or break, depending on desired behavior
+            except Exception as e:
+                print(f"Unexpected error when processing {project_dir}: {e}")
+                # Optionally, continue to next project or break
+
+
+# Example usage:
+# matched_dict = {...}
+# gg = GG(matched_dict, "/path/to/internal", "/path/to/observational")
+# gg.run_gg()

code/main.py

@@ -8,31 +8,50 @@
 RDSS_DIR = '/mnt/nfs/rdss/vosslab/Repositories/Accelerometer_Data'
 
 class pipe:
-    def __init__(self, daysago=None):
+    def __init__(self, token, daysago):
+        self.token = token
         self.daysago = daysago
 
     def run_pipe(self):
         self._create_syms()
-        matched = Save(intdir=INT_DIR, obsdir=OBS_DIR, rdssdir=RDSS_DIR, daysago=self.daysago).save()
+        matched = Save(
+            intdir=INT_DIR,
+            obsdir=OBS_DIR,
+            rdssdir=RDSS_DIR,
+            token=self.token,
+            daysago=self.daysago
+        ).save()
+
         with open('code/res/data.json', 'w') as file:
             file.write('{\n}')
             file.write(',\n'.join(f'   "{key}": "{value}"' for key, value in matched.items()))
-        #GG(matched=matched, intdir=INT_DIR, obsdir=OBS_DIR).run_gg()
+
+        # GG(matched=matched, intdir=INT_DIR, obsdir=OBS_DIR).run_gg()
         return None
 
     def _create_syms(self):
         return create_symlinks('../mnt')
 
 
 if __name__ == '__main__':
-    if len(sys.argv) > 1:  # Ensure there's an argument
-        try:
-            daysago = int(sys.argv[1])  # Convert argument to integer
-        except ValueError:
-            print("Error: daysago must be an integer")
-            sys.exit(1)  # Exit script with error
-    else:
-        daysago = None  # Default to None if no argument is provided
-
-    p = pipe(daysago=daysago)
+    # Expect exactly 2 arguments: daysago (integer) and token (string)
+    if len(sys.argv) != 3:
+        print("Usage: python main.py <daysago> <token>")
+        print("  <daysago> must be an integer, <token> must be a non-empty string.")
+        sys.exit(1)
+
+    # Parse daysago
+    try:
+        daysago = int(sys.argv[1])
+    except ValueError:
+        print("Error: <daysago> must be an integer.")
+        sys.exit(1)
+
+    # Parse token
+    token = sys.argv[2]
+    if not token:
+        print("Error: <token> cannot be empty.")
+        sys.exit(1)
+
+    p = pipe(token, daysago)
     p.run_pipe()

code/utils/comparison_utils.py

@@ -9,8 +9,8 @@
 
 class ID_COMPARISONS:
 
-    def __init__(self, mnt_dir, daysago=None) -> None:
-       self.token = 'DE4E2DB72778DACA9B8848574107D2F5'
+    def __init__(self, mnt_dir, token, daysago=None) -> None:
+       self.token = token
        self.mnt_dir = mnt_dir
        self.INT_DIR = '/Volumes/vosslabhpc/Projects/BOOST/InterventionStudy/3-experiment/data/act-int-test'
        self.OBS_DIR = '/Volumes/vosslabhpc/Projects/BOOST/ObservationalStudy/3-experiment/data/act-obs-test'