added new test, modified structure to allow disabling of push to dataverse

Author: Benedikt Ehinger

lslautobids/config_globals.py

@@ -13,6 +13,7 @@ def __init__(self):
             "redo_bids_conversion": False,
             "reupload": False,
             "redo_other_pc": False,
+            "push_to_dataverse": True,
         }
 
     def init(self, args):

lslautobids/convert_to_bids_and_upload.py

@@ -364,7 +364,7 @@ def convert_to_bids(self, xdf_path,subject_id,session_id, run_id, task_id,other,
         # Validate BIDS data
         logger.info("Validating BIDS data...")
         # Validate the BIDS data
-        val = self.validate_bids(bids_root+project_name,subject_id,session_id, logger)
+        val = self.validate_bids(os.path.join(bids_root,project_name),subject_id,session_id, logger)
         return val
 
     def validate_bids(self,bids_path,subject_id,session_id, logger):
@@ -482,26 +482,29 @@ def bids_process_and_upload(processed_files,logger):
     bids.populate_dataset_description_json(project_name, logger)
     logger.info('Generating metadatafiles........')   
     generate_json_file(project_name, logger)
-    logger.info('Generating dataverse dataset........')
 
-    doi, status = create_dataverse(project_name)
 
-    logger.info("Creating and adding files to Dataverse dataset...")
-    create_and_add_files_to_datalad_dataset(bids_root+project_name,status, logger)
+    logger.info("Creating and adding files to Datalad dataset...")
+    create_and_add_files_to_datalad_dataset(os.path.join(bids_root,project_name),logger)
 
-    if status == 0:
-        logger.info('Linking dataverse dataset with datalad')
-        add_sibling_dataverse_in_folder(doi, logger)
-
-    if cli_args.yes:
-        logger.info('Pushing files to dataverse........')
-        push_files_to_dataverse(project_name, logger)
-    else:
-        user_input = get_user_input("Do you want to push the files to Dataverse? ",logger)
+    if cli_args.push_to_dataverse:
+        logger.info('Generating dataverse dataset........')
+        doi, status = create_dataverse(project_name, logger)
+        if status == 0: # run only if a new dataverse was created
+            logger.info('Linking dataverse dataset with datalad')
+            add_sibling_dataverse_in_folder(doi, logger)
+
+        if cli_args.yes:
+            user_input = "y"
+        else:
+            user_input = get_user_input("Do you want to push the files to Dataverse? ",logger)
+        
         if user_input == "y":
             logger.info('Pushing files to dataverse........')
             push_files_to_dataverse(project_name, logger)
         elif user_input == "n":
             logger.info("Program aborted.")
         else:
             logger.error("Invalid Input.")
+    else:
+        logger.info('cli.push_to_dataverse was false, not pushing.')

lslautobids/datalad_create.py

@@ -2,29 +2,33 @@
 import os
 
 
-def create_and_add_files_to_datalad_dataset(dataset_path,flag, logger):
+def create_and_add_files_to_datalad_dataset(dataset_path,logger):
     message = "LSL Auto BIDS: new files found and added"
-    if flag==0:
+    #if flag==0:
+    
+    try:
+        dl.Dataset(dataset_path)
+    except:
         message ="LSL Auto BIDS: new datalad dataset created"
         # Create a new dataset
         logger.info('Creating a new datalad dataset........')
         try:
             dl.create(dataset_path, force=True) # files already exist, so we eforce it
+
+            # make sure only large files are saved
+            with open(os.path.join(dataset_path,".gitattributes"), "a") as f:
+                f.write("* annex.largefiles=largerthan=100kb")
+                f.write("\n*.csv annex.largefiles=nothing")
+                f.write("\n*.log annex.largefiles=nothing")
+                f.write("\n*.tsv annex.largefiles=nothing")
+                f.write("\n*.md annex.largefiles=nothing")
+                f.write("\n*.json annex.largefiles=nothing")
+
         except:
             logger.info("Could not create a new dataset, maybe it exists already?")
 
-    # Commit changes
-    # Change to dataset path
-    os.chdir(dataset_path)
-    if flag==0:
-    	# needed to modify participants.tsv etc. later
-    	with open(os.path.join(dataset_path,".gitattributes"), "a") as f:
-            f.write("* annex.largefiles=largerthan=100kb")
-            f.write("\n*.csv annex.largefiles=nothing")
-            f.write("\n*.log annex.largefiles=nothing")
-            f.write("\n*.tsv annex.largefiles=nothing")
-            f.write("\n*.md annex.largefiles=nothing")
-            f.write("\n*.json annex.largefiles=nothing")
+
+    # commit current files
     logger.info('Committing current changes........')
-    dl.save(path = '.', message=message)
+    dl.save(path = dataset_path, message=message)
 

lslautobids/dataverse_dataset_create.py

@@ -12,7 +12,7 @@
 logger = logging.getLogger(__name__)
 logging.basicConfig(level=logging.INFO, format='%(levelname)s: %(message)s')
 
-def create_dataverse(project_name):
+def create_dataverse(project_name, logger):
     """
     Creates a Dataverse dataset and returns the PID and dataset ID.
     

pyproject.toml

@@ -6,5 +6,11 @@ build-backend = "setuptools.build_meta"
 # Ref: https://github.com/codespell-project/codespell#using-a-config-file
 skip = '.git*,*.svg,*.bib'
 check-hidden = true
+
+[dependency-groups]
+dev = [
+    "git-annex>=10.20251114",
+    "pytest>=9.0.1",
+]
 # ignore-regex = ''
 # ignore-words-list = ''

tests/run_all_tests.py renamed to tests/run_all_tests.py.deactivate

@@ -18,3 +18,16 @@ def get_root_paths(test_file: str):
     }
 
 
+
+
+# Dummy CLI argument simulation
+class DummyCLIArgs:
+    def __init__(self):
+        self.project_name = "test-project"
+        self.yes = True
+        self.redo_bids_conversion = False 
+        self.redo_other_pc = False   
+        self.push_to_dataverse = False
+    def init(self, args):
+        # you can store the args or ignore
+        pass

tests/test_utils/path_config.py

@@ -0,0 +1,4 @@
+time	event	what
+00:00 	cap size selection	
+00:00	camera working y/n	
+

tests/testcases/test_main_functionality/__init__.py

@@ -0,0 +1 @@
+id	age	gender	handedness	dom_eye	no_preex_conditions	visual_acuity_test	remarks