Fix some merging issues

Author: Hyedryn

Diff for: 2_rsyncAndFixJSON.py

@@ -224,11 +224,8 @@ def fixer(img_path):
 
     active_subject_cmd = subprocess.check_output(f"rsync -az {complementary_cluster_login} {scratch_path}/ukbb/scripts/data/active_subjects_{complementary_cluster_name}.json", shell=True, text=True)
     print(active_subject_cmd)
-<<<<<<< Updated upstream
-
-=======
 
->>>>>>> Stashed changes
+    
     active_subject_cmd = subprocess.check_output(f"rsync -az {outside_cluster_login} {scratch_path}/ukbb/scripts/data/active_subjects_{outside_cluster_name}.json", shell=True, text=True)
     print(active_subject_cmd)
 

Diff for: 4.2_runSingleSubject.py

@@ -103,20 +103,13 @@
             else:
                 print(f"unknow state {state} for subject {subject}")
                 continue
-<<<<<<< Updated upstream
 
-=======
-                
->>>>>>> Stashed changes
+        
         if not os.path.exists(os.path.join(scratch_path,"ukbb","ukbb_bids",subject,"func",f"{subject}_task-rest_bold.nii.gz")):
             slurm_jobs[subject] = 2
             print(f"Subject {subject} nifti not found.")
             continue
-<<<<<<< Updated upstream
 
-=======
-            
->>>>>>> Stashed changes
         slurm_cmd = f"sbatch {scratch_path}/ukbb/.slurm/fmriprep_{subject}.sh"
         try:
             sbatch_output = subprocess.check_output(slurm_cmd, shell=True, text=True)

Diff for: stats.py

@@ -133,10 +133,6 @@ def get_job_state(job_id):
     states_dic[0] = "COMPLETED"
     states_dic[1] = "FAILED"
     states_dic[2] = "FAILED"
-<<<<<<< Updated upstream
-=======
-         
->>>>>>> Stashed changes
 
     #### Beginning of connectome ####
     connectomes_status = {}
@@ -223,7 +219,6 @@ def get_job_state(job_id):
         json.dump(subjects_state, json_file, indent=4)
 
 
-<<<<<<< Updated upstream
     update_active_subjects(scratch_path, cluster_name)
 
     active_subject_cmd = subprocess.check_output(f"rsync -az {complementary_cluster_login} {scratch_path}/ukbb/scripts/data/active_subjects_{complementary_cluster_name}.json", shell=True, text=True)
@@ -232,14 +227,17 @@ def get_job_state(job_id):
 
     active_subject_cmd = subprocess.check_output(f"rsync -az {outside_cluster_login} {scratch_path}/ukbb/scripts/data/active_subjects_{outside_cluster_name}.json", shell=True, text=True)
     print("Updating active subjects (outside):",active_subject_cmd)
-=======
     #update_active_subjects(scratch_path, cluster_name)
->>>>>>> Stashed changes
-
-
-    active_subject_cmd = subprocess.check_output(f"rsync -az {complementary_cluster_login} {scratch_path}/ukbb/scripts/data/active_subjects_{complementary_cluster_name}.json", shell=True, text=True)
-    print("Updating active subjects (complementary):",active_subject_cmd)
 
-    active_subject_cmd = subprocess.check_output(f"rsync -az {outside_cluster_login} {scratch_path}/ukbb/scripts/data/active_subjects_{outside_cluster_name}.json", shell=True, text=True)
-    print("Updating active subjects (outside):",active_subject_cmd)
+    try:
+        active_subject_cmd = subprocess.check_output(f"rsync -az {complementary_cluster_login} {scratch_path}/ukbb/scripts/data/active_subjects_{complementary_cluster_name}.json", shell=True, text=True)
+        print("Updating active subjects (complementary):",active_subject_cmd)
+    except Exception as e:
+        print(e)
+    
+    try:
+        active_subject_cmd = subprocess.check_output(f"rsync -az {outside_cluster_login} {scratch_path}/ukbb/scripts/data/active_subjects_{outside_cluster_name}.json", shell=True, text=True)
+        print("Updating active subjects (outside):",active_subject_cmd)
+    except Exception as e:
+        print(e)