Minor check in run_parser for collection_type

Fixes on documentation

Author: JosePizarro3

bam_masterdata/cli/cli.py

@@ -622,7 +622,7 @@ def push_to_openbis(file_path, datamodel_path):
     "collection_type",  # alias
     type=click.Choice(["COLLECTION", "DEFAULT_EXPERIMENT"], case_sensitive=False),
     default="COLLECTION",
-    help='Type of collection to create in openBIS. Options are "COLLECTION" or "DEFAULT_EXPERIMENT". Defaults to "COLLECTION".',
+    help="Type of collection to create in openBIS. Options are 'COLLECTION' or 'DEFAULT_EXPERIMENT'. Defaults to 'COLLECTION'.",
 )
 def parser(files_parser, project_name, collection_name, space_name, collection_type):
     parser_map = {}  # TODO load from configuration from yaml file

bam_masterdata/cli/run_parser.py

@@ -43,6 +43,12 @@ def run_parser(
             "No files or parsers to parse. Please provide valid file paths or contact an Admin to add missing parser."
         )
         return
+    # Ensure collection_type is valid
+    if collection_type not in ["COLLECTION", "DEFAULT_EXPERIMENT"]:
+        logger.error(
+            f"Invalid collection_type '{collection_type}'. Must be either 'COLLECTION' or 'DEFAULT_EXPERIMENT'."
+        )
+        return
 
     # Specify the space
     try:

docs/tutorials/parsing.md

@@ -203,8 +203,8 @@ run_parser(
     You can choose between two collection types:
     - `"COLLECTION"` (default): A general-purpose collection type
     - `"DEFAULT_EXPERIMENT"`: A collection type designed for experiments with additional metadata fields like start/end dates, experimental goals, etc.
-    
-    If you don't specify `collection_type`, it defaults to `"COLLECTION"`.
+
+    If you don't specify `collection_type`, it defaults to `"COLLECTION"`. We recommend keeping the default `collection_type`, as future openBIS releases will get rid of the collection concept and we will, as a result, deprecate this feature.
 
 ### What Happens Next?
 
@@ -245,7 +245,6 @@ run_parser(
     project_name="MY_PROJECT",
     collection_name="MULTI_DATA_COLLECTION",
     files_parser=files_parser,
-    collection_type="DEFAULT_EXPERIMENT"  # Use DEFAULT_EXPERIMENT for experiment data
 )
 ```
 
@@ -467,7 +466,6 @@ def main():
         project_name="AUTOMATION_TEST",
         collection_name="BATCH_EXPERIMENTS",
         files_parser=files_parser,
-        collection_type="DEFAULT_EXPERIMENT"
     )
 
     print("Metadata injection complete!")