rewrite main() for cli use

README.md

@@ -38,10 +38,11 @@ Commands:
   validate
 ```
 
-## redcap2reproschema.py Usage
+## redcap2reproschema Usage
+The `redcap2reproschema` function is designed to process a given REDCap CSV file and YAML configuration to generate the output in the reproschema format.
 
 ### Prerequisites
-Before using the conversion script, ensure you have the following:
+Before the conversion, ensure you have the following:
 
 1. **GitHub Repository**:
    - [Create a GitHub repository](https://docs.github.com/en/repositories/creating-and-managing-repositories/creating-a-new-repository) named `reproschema` to store all your reproschema protocols.
@@ -67,8 +68,25 @@ user_name: "john_doe"
 repo_name: "reproschema"
 protocol_description: "This protocol is for assessing cognitive skills."
 ```
+### Command-Line Usage
 
-### Using the Script
+The `redcap2reproschema`` function has been integrated into a CLI tool, use the following command:
+```bash
+reproschema redcap2reproschema path/to/your_redcap_data_dic.csv path/to/your_redcap2rs.yaml
+```
+
+### Python Function Usage
+
+You can also use the `redcap2reproschema` function from the `reproschema-py` package in your Python code.
+
+```python
+from reproschema import redcap2reproschema
+
+csv_path = "path-to/your_redcap_data_dic.csv"
+yaml_path = "path-to/your_redcap2rs.yaml"
+
+reproschema2redcap(input_dir_path, output_csv_filename)
+```
 
 After configuring the YAML file:
 

reproschema/cli.py

@@ -1,5 +1,6 @@
 import os
 import click
+import yaml
 
 from . import get_logger, set_logger_level
 from . import __version__
@@ -100,11 +101,10 @@ def serve(port):
 @main.command()
 @click.argument('csv_path', type=click.Path(exists=True, dir_okay=False))
 @click.argument('yaml_path', type=click.Path(exists=True, dir_okay=False))
-@click.option('--schema-url', default='https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic', show_default=True, help='URL of the schema context')
-def redcap2reproschema(csv_path, yaml_path, schema_url):
+def redcap2reproschema(csv_path, yaml_path):
     """
     Convert REDCap CSV files to Reproschema format.
-    
+
     Provide the path to the REDCap CSV file and the YAML configuration file.
     """
     if not os.path.exists(csv_path):
@@ -113,7 +113,7 @@ def redcap2reproschema(csv_path, yaml_path, schema_url):
         raise click.ClickException(f"YAML file not found at {yaml_path}")
 
     try:
-        # Call the redcap2reproschema main function with provided arguments
-        redcap2rs(csv_path, schema_url, yaml_path)
+        redcap2rs(csv_path, yaml_path)
+        click.echo("Converted REDCap data dictionary to Reproschema format.")
     except Exception as e:
-        raise click.ClickException(f"Error during conversion: {e}")
+        raise click.ClickException(f"Error during conversion: {e}")

reproschema/redcap2reproschema.py

@@ -6,19 +6,8 @@
 import json
 import re
 import yaml
-from collections import defaultdict
 from bs4 import BeautifulSoup
 
-
-def parse_arguments():
-    parser = argparse.ArgumentParser(
-        description="Process REDCap data dictionary and reproschema protocol."
-    )
-    parser.add_argument("csv_file", help="Path to the REDCap data dictionary CSV file.")
-    parser.add_argument("yaml_file", help="Path to the reproschema protocol YAML file.")
-    return parser.parse_args()
-
-
 def normalize_condition(condition_str):
     re_parentheses = re.compile(r"\(([0-9]*)\)")
     re_non_gt_lt_equal = re.compile(r"([^>|<])=")
@@ -339,13 +328,28 @@ def process_csv(
     return datas, order, languages
 
 
-def main(
-    csv_path,
-    schema_context_url,
-    protocol_name,
-    protocol_display_name,
-    protocol_description,
-):
+def redcap2reproschema(csv_path, yaml_path, schema_context_url=None):
+    """
+    Convert a REDCap data dictionary to Reproschema format.
+
+    :param csv_path: Path to the REDCap CSV file.
+    :param yaml_path: Path to the YAML configuration file.
+    :param schema_context_url: URL of the schema context. Optional.
+    """
+    if schema_context_url is None:
+        schema_context_url = "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic"
+
+    # Read YAML configuration
+    try:
+        with open(yaml_path, "r") as f:
+            protocol_info = yaml.safe_load(f)
+    except FileNotFoundError:
+        raise FileNotFoundError(f"YAML file '{yaml_path}' not found.")
+
+    protocol_name = protocol.get("protocol_name")
+    protocol_display_name = protocol.get("protocol_display_name")
+    protocol_description = protocol.get("protocol_description")
+
     # Initialize variables
     schema_map = {
         "Variable / Field Name": "@id",  # column A
@@ -447,41 +451,29 @@ def main(
         protocol_visibility_obj,
     )
 
-
-if __name__ == "__main__":
-    schema_context_url = "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc4/contexts/generic"  # we may also want to keep this schema version updated or in the yaml file
-
-    args = parse_arguments()
-
-    # Read the CSV file path
-    csv_path = args.csv_file
+def main():
+    import argparse
+    parser = argparse.ArgumentParser(description="Convert REDCap data dictionary to Reproschema format.")
+    parser.add_argument("csv_file", help="Path to the REDCap data dictionary CSV file.")
+    parser.add_argument("yaml_file", help="Path to the Reproschema protocol YAML file.")
+    args = parser.parse_args()
 
     # Read the YAML configuration
-    yaml_path = args.yaml_file
     try:
-        with open(yaml_path, "r") as f:
+        with open(args.yaml_file, "r") as f:
             protocol = yaml.safe_load(f)
     except FileNotFoundError:
-        print(f"Error: YAML file '{yaml_path}' not found.")
-        sys.exit(1)
+        raise FileNotFoundError(f"YAML file '{args.yaml_file}' not found.")
 
-    # Extract values from YAML file
-    protocol_name = protocol.get("protocol_name")
-    protocol_display_name = protocol.get("protocol_display_name")
-    protocol_description = protocol.get("protocol_description")
     repo_url = protocol.get("repo_url")
 
-    # git clone the repo
+    # Git operations
     subprocess.run(["git", "clone", repo_url])
-    # set up branch and checkout
     subprocess.run(["git", "checkout", "main"])
-    # cd to the repo
     os.chdir(repo_url.split("/")[-1])
 
-    main(
-        csv_path,
-        schema_context_url,
-        protocol_name,
-        protocol_display_name,
-        protocol_description,
-    )
+    # Call the main conversion function
+    redcap2reproschema(args.csv_file, args.yaml_file)
+
+if __name__ == "__main__":
+    main()