[MNT] Update help text and fix formatting issues in user messages (#217)

* fix missing whitespaces in user messages

* add more info to help text

* provide example value for --name

bagel/bids_utils.py

@@ -16,8 +16,8 @@ def check_unique_bids_subjects(pheno_subjects: list, bids_subjects: list):
     unique_bids_subjects = set(bids_subjects).difference(pheno_subjects)
     if len(unique_bids_subjects) > 0:
         raise LookupError(
-            "The specified BIDS directory contains subject IDs not found in"
-            f"the provided phenotypic json-ld file: {unique_bids_subjects}"
+            "The specified BIDS directory contains subject IDs not found in "
+            f"the provided phenotypic json-ld file: {unique_bids_subjects}. "
             "Please check that the specified BIDS and phenotypic datasets match."
         )
 

bagel/cli.py

@@ -10,7 +10,13 @@
 from bagel import mappings, models
 from bagel.utility import check_overwrite, load_json
 
-bagel = typer.Typer()
+bagel = typer.Typer(
+    help="""
+    A command-line tool for creating valid, subject-level instances of the Neurobagel graph data model.
+
+    To view the arguments for a specific command, run: bagel [COMMAND] --help
+    """
+)
 
 
 @bagel.command()
@@ -34,8 +40,8 @@ def pheno(
     name: str = typer.Option(
         ...,
         help="A descriptive name for the dataset the input belongs to. "
-        "This name is expected to match the name field in the BIDS "
-        "dataset_description.json file.",
+        "This name is expected to match the name field in the BIDS dataset_description.json file. "
+        'Should be enclosed in quotes, e.g.: --name "my dataset name"',
     ),
     portal: str = typer.Option(
         default=None,
@@ -60,8 +66,8 @@ def pheno(
     with the Neurobagel annotation tool. The annotations are expected to be stored
     in a data dictionary (.json).
 
-    This tool will create a valid, subject-level instance of the Neurobagel
-    graph datamodel for the provided phenotypic file in the .jsonld format.
+    This command will create a valid, subject-level instance of the Neurobagel
+    graph data model for the provided phenotypic file in the .jsonld format.
     You can upload this .jsonld file to the Neurobagel graph.
     """
     # Check if output file already exists
@@ -188,8 +194,8 @@ def bids(
     with phenotypic metadata (.jsonld) created in a previous step using the
     bagel pheno command.
 
-    This tool will create a valid, subject-level instance of the Neurobagel
-    graph datamodel for the combined metadata in the .jsonld format.
+    This command will create a valid, subject-level instance of the Neurobagel
+    graph data model for the combined metadata in the .jsonld format.
     You can upload this .jsonld file to the Neurobagel graph.
     """
     # Check if output file already exists

bagel/pheno_utils.py

@@ -389,7 +389,7 @@ def validate_data_dict(data_dict: dict) -> None:
         > 1
     ):
         raise ValueError(
-            "The provided data dictionary has more than one column about participant ID or session ID."
+            "The provided data dictionary has more than one column about participant ID or session ID. "
             "Please make sure that only one column is annotated for participant and session IDs."
         )
 
@@ -446,6 +446,6 @@ def validate_inputs(data_dict: dict, pheno_df: pd.DataFrame) -> None:
     if row_indices := get_rows_with_empty_strings(pheno_df, columns_about_ids):
         raise LookupError(
             "We have detected missing values in participant or session id columns. "
-            "Please make sure that every row has a non-empty participant id (and session id where applicable)."
+            "Please make sure that every row has a non-empty participant id (and session id where applicable). "
             f"We found missing values in the following rows (first row is zero): {row_indices}."
         )