Add non-interactive mode to build-schema module

CHANGELOG.md

@@ -30,6 +30,7 @@ Code contributions to the release:
 - Auto-fill tax_id and host_disease based on organism fields [#407](https://github.com/BU-ISCIII/relecov-tools/pull/407)
 - Implement Pull Request Template [#410](https://github.com/BU-ISCIII/relecov-tools/pull/410)
 - Now pipeline-manager splits by organism-template first [#412](https://github.com/BU-ISCIII/relecov-tools/pull/412)
+- Implement non-interactive execution of build-schema module [#416](https://github.com/BU-ISCIII/relecov-tools/pull/416)
 
 #### Fixes
 

README.md

@@ -343,8 +343,13 @@ Options:
   -v, --draft_version TEXT  Version of the JSON schema specification to be
                             used. Example: '2020-12'. See: https://json-
                             schema.org/specification-links
-  --version                 Specifies the version of the metadata template to generate.
-  -d, --diff BOOLEAN        Prints a changelog/diff between the base and
+  --version           TEXT  Specifies the version of the metadata template to 
+                            generate.
+  -p, --project       TEXT  Specify the project you want to generate the schema   
+                            and template for.
+  --non-interactive BOOLEAN executes the module by assigning the default interactive 
+                            parameters
+  -d, --diff        BOOLEAN Prints a changelog/diff between the base and
                             incoming versions of the schema. Required for the generation 
                             of the JSON schema.
   -o, --out_dir PATH        Path to save output file/s

relecov_tools/__main__.py

@@ -710,15 +710,34 @@ def pipeline_manager(input, templates_root, output, config, folder_names):
 @click.option(
     "-p", "--project", help="Specficy the project to build the metadata template."
 )
+@click.option(
+    "--non-interactive",
+    is_flag=True,
+    help="Run the script without user interaction, using default values.",
+)
 @click.option("-o", "--out_dir", type=click.Path(), help="Path to save output file/s")
 def build_schema(
-    input_file, schema_base, draft_version, diff, out_dir, version, project
+    input_file,
+    schema_base,
+    draft_version,
+    diff,
+    out_dir,
+    version,
+    project,
+    non_interactive,
 ):
     """Generates and updates JSON Schema files from Excel-based database definitions."""
     # Build new schema
     try:
         schema_update = relecov_tools.build_schema.SchemaBuilder(
-            input_file, schema_base, draft_version, diff, out_dir, version, project
+            input_file,
+            schema_base,
+            draft_version,
+            diff,
+            out_dir,
+            version,
+            project,
+            non_interactive,
         )
 
         # Build new schema

relecov_tools/build_schema.py

@@ -39,12 +39,14 @@ def __init__(
         out_dir=None,
         version=None,
         project=None,
+        non_interactive=False,
     ):
         """
         Initialize the SchemaBuilder class. This class generates a JSON Schema file based on the provided draft version.
         It reads the database definition from an Excel file and allows customization of the schema generation process.
         """
         self.excel_file_path = excel_file_path
+        self.non_interactive = non_interactive
         # Validate input data
         if not self.excel_file_path or not os.path.isfile(self.excel_file_path):
             log.error("A valid Excel file path must be provided.")
@@ -111,11 +113,19 @@ def __init__(
             self.show_diff = True
 
         # Validate json schema draft version
-        self.draft_version = (
-            relecov_tools.assets.schema_utils.jsonschema_draft.check_valid_version(
-                draft_version
+        if not draft_version:
+            if self.non_interactive:
+                self.draft_version = "2020-12"
+            else:
+                self.draft_version = relecov_tools.assets.schema_utils.jsonschema_draft.check_valid_version(
+                    draft_version
+                )
+        else:
+            self.draft_version = (
+                relecov_tools.assets.schema_utils.jsonschema_draft.check_valid_version(
+                    draft_version
+                )
             )
-        )
 
         # Validate base schema
         if base_schema_path is not None:
@@ -267,9 +277,11 @@ def validate_database_definition(self, json_data):
             stderr.print(f"\t- Log errors saved to:\n\t{error_file_path}")
 
             # Ask user whether to continue or stop execution
-            if not relecov_tools.utils.prompt_yn_question(
+            if self.non_interactive or relecov_tools.utils.prompt_yn_question(
                 "Errors found in database values. Do you want to continue? (Y/N)"
             ):
+                pass
+            else:
                 return log_errors
         else:
             stderr.print("[green]\t- Database validation passed")
@@ -608,8 +620,12 @@ def get_schema_diff(self, base_schema, new_schema):
     def print_save_schema_diff(self, diff_lines=None):
         # Set user's choices
         choices = ["Print to standard output (stdout)", "Save to file", "Both"]
-        diff_output_choice = relecov_tools.utils.prompt_selection(
-            "How would you like to print the diff between schemes?:", choices
+        diff_output_choice = (
+            "Save to file"
+            if self.non_interactive
+            else relecov_tools.utils.prompt_selection(
+                "How would you like to print the diff between schemes?:", choices
+            )
         )
         if diff_output_choice in ["Print to standard output (stdout)", "Both"]:
             for line in diff_lines:
@@ -671,8 +687,12 @@ def create_metadatalab_excel(self, json_schema):
         try:
             # Retrieve existing files in the output directory
             output_files = os.listdir(self.output_folder)
-            notes_control_input = input(
-                "\033[93mEnter a note about changes made to the schema: \033[0m"
+            notes_control_input = (
+                "Auto-generated update"
+                if self.non_interactive
+                else input(
+                    "\033[93mEnter a note about changes made to the schema: \033[0m"
+                )
             )
             # Identify existing template files
             template_files = [
@@ -1175,10 +1195,9 @@ def handle_build_schema(self):
         self.save_new_schema(new_schema_json)
 
         # Create metadata lab template
-        promp_answ = relecov_tools.utils.prompt_yn_question(
+        if self.non_interactive or relecov_tools.utils.prompt_yn_question(
             "Do you want to create a metadata lab file?:"
-        )
-        if promp_answ:
+        ):
             self.create_metadatalab_excel(new_schema_json)
 
         # Return new schema