Merge pull request #32 from alexpron/fix-dup-underscore

Fix dup underscore

shanoir2bids.py

@@ -24,6 +24,7 @@
 import shanoir_downloader
 from dotenv import load_dotenv
 from heudiconv.main import workflow
+from heudiconv.bids import sanitize_label
 
 import bids_validator
 
@@ -199,9 +200,35 @@ def generate_bids_heuristic_file(
 
     heuristic = f"""from heudiconv.heuristics.reproin import create_key
 
+
 def create_bids_key(dataset):
 
-    template = create_key(subdir=dataset['bidsDir'],file_suffix="_".join(dataset['bidsName'].split('_')[:-1]) + '_' + r"run-{{item:02d}}_" + dataset['bidsName'].split('_')[-1],outtype={outtype})
+    from heudiconv.bids import BIDSFile 
+    
+    # check if run key is already used in filename 
+    # (could be done in Pybids or using heudiconv utils?) 
+    
+    if not '_run-' in  dataset['bidsName']:
+        bids_entities = BIDSFile._known_entities 
+        # insert additional run key to dissociate identical scans
+        # check where to insert run key 
+        split_keyword = '_' # default
+        for entity in bids_entities[bids_entities.index('run') + 1 :]:
+            if entity in dataset['bidsName']:
+                split_keyword = '_' + entity
+                break 
+        split_filename = dataset['bidsName'].split(split_keyword)
+        if split_keyword != '_':
+            file_suffix = "".join(split_filename[:-1]) + '_' +  r"run-{{item:02d}}" +  split_keyword  +  split_filename[-1]
+        else:
+      
+            file_suffix = "_".join(split_filename[:-1]) + '_' + r"run-{{item:02d}}" + split_keyword + split_filename[-1]
+            if len(split_filename) == 1:
+                # remove unwanted first "_" 
+                file_suffix = file_suffix[1:]
+    else:
+        file_suffix = dataset['bidsName']
+    template = create_key(subdir=dataset['bidsDir'],file_suffix=file_suffix,outtype={outtype})
     return template
 
 def get_dataset_to_key_mapping(shanoir2bids):
@@ -214,7 +241,9 @@ def get_dataset_to_key_mapping(shanoir2bids):
 def simplify_runs(info):
     info_final = dict()
     for key in info.keys():
+        print(key)
         if len(info[key])==1:
+            print('Simplified key', key)
             new_template = key[0].replace('run-{{item:02d}}_','')
             new_key = (new_template, key[1], key[2])
             info_final[new_key] = info[key]
@@ -449,12 +478,12 @@ def is_mapping_bids(self):
             paths = (
                 "/"
                 + "sub-"
-                + subject
+                + sanitize_label(subject)
                 + "/"
                 + map["bidsDir"]
                 + "/"
                 + "sub-"
-                + subject
+                + sanitize_label(subject)
                 + "_"
                 + map["bidsName"]
                 + extension
@@ -465,18 +494,18 @@ def is_mapping_bids(self):
             paths = (
                 "/"
                 + "sub-"
-                + subject
+                + sanitize_label(subject)
                 + "/"
                 + "ses-"
-                + map["bidsSession"]
+                + sanitize_label(map["bidsSession"])
                 + "/"
                 + map["bidsDir"]
                 + "/"
                 + "sub-"
-                + subject
+                + sanitize_label(subject)
                 + "_"
                 + "ses-"
-                + map["bidsSession"]
+                + sanitize_label(map["bidsSession"])
                 + "_"
                 + map["bidsName"]
                 + extension
@@ -721,7 +750,7 @@ def escape_solr_special_characters(s):
                     "overwrite": True,
                 }
 
-                if self.longitudinal:
+                if self.longitudinal and bids_seq_session is not None:
                     workflow_params["session"] = bids_seq_session
                 try:
                     workflow(**workflow_params)