adding jsonata_validate prototype

mars-cli/mars_lib/jsonata_validate.py

@@ -0,0 +1,77 @@
+import jsonata
+import requests
+import csv
+import json
+import argparse
+
+def main(filepath='../test-data/biosamples-original-isa.json', 
+         table_url='https://docs.google.com/spreadsheets/d/e/2PACX-1vQvgQoUByiJgGcJ4jtD8bG9AyQrh4TYVQE8aq7AqJRxLdfyLFATKspu_vkyqbVsTyEnNIBHqWtpgV6X/pub?gid=0&single=true&output=csv'): 
+    """
+    Main function to validate JSON data using a JSONata expression extracted from a CSV file.
+
+    Parameters:
+    filepath (str): The path to the JSON file to be validated.
+    table_url (str): The URL of the CSV file hosted online that contains JSONata expressions.
+
+    Returns:
+    None: This function prints the index and value of invalid JSONata expressions.
+    """
+
+    try:
+        # Fetch CSV data from the provided URL
+        res = requests.get(table_url)
+        res.raise_for_status()  # Check for HTTP request errors
+    except requests.exceptions.RequestException as e:
+        print(f"Error fetching the table from the URL: {e}")
+        return
+
+    try:
+        # Parse the fetched CSV data into a list of rows
+        table = csv.reader(res.text.split('\n'))
+        jsonata_list = list(table)
+    except Exception as e:
+        print(f"Error reading CSV data: {e}")
+        return
+
+    try:
+        # Open and load the JSON file
+        with open(filepath, 'r') as file:
+            data = json.load(file)
+    except FileNotFoundError:
+        print(f"Error: The file '{filepath}' was not found.")
+        return
+    except json.JSONDecodeError as e:
+        print(f"Error parsing JSON data: {e}")
+        return
+
+    # Loop through each row in the JSONata list starting from index 3
+    for index, ele in enumerate(jsonata_list): 
+        if len(ele) > 6 and ele[6] != "" and index > 2:  # Check if there is a valid JSONata expression
+            try:
+                # Evaluate the JSONata expression
+                expr = jsonata.Jsonata("'"+ele[6])  # Correcting the JSONata expression input
+                result = expr.evaluate(data)
+
+                if result == False:  # If the evaluation fails, print details
+                    print(f"Validation failed at row {index}:")
+                    print(f"Sample ID: {ele[0]}")
+                    print(f"Expression: {ele[6]}")
+                    print(f"Result: {result}")
+            except Exception as e:
+                print(f"Error evaluating JSONata at row {index}: {e}")
+                continue
+
+if __name__ == '__main__':
+    # help(main)
+    # Argument parser for command line inputs
+    parser = argparse.ArgumentParser(description='Validate JSON data using JSONata expressions from a CSV file.')
+
+    # Define command-line arguments
+    parser.add_argument('filepath', type=str, help='Path to the JSON file to be validated.')
+    parser.add_argument('--table_url', type=str, required=False, help='URL of the CSV file containing JSONata expressions.', default='https://docs.google.com/spreadsheets/d/e/2PACX-1vQvgQoUByiJgGcJ4jtD8bG9AyQrh4TYVQE8aq7AqJRxLdfyLFATKspu_vkyqbVsTyEnNIBHqWtpgV6X/pub?gid=0&single=true&output=csv')
+
+    # Parse the arguments
+    args = parser.parse_args()
+
+    # Call the main function with arguments from the command line
+    main(filepath=args.filepath, table_url=args.table_url)

mars-cli/requirements.txt

@@ -4,3 +4,4 @@ keyring
 pydantic
 click
 retry
+jsonata-python

repository-services/isajson-biosamples/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/controller/BioSampleSubmissionController.java

@@ -36,7 +36,7 @@ public class BioSampleSubmissionController {
       @ApiResponse(responseCode = "408", description = "Request Timeout"),
       @ApiResponse(responseCode = "415", description = "Unsupported media type")
   })
-  @CrossOrigin(origins = "http://localhost:8000")
+ // @CrossOrigin(origins = "http://localhost:8000")
   @PostMapping(
     value = "/submit",
     consumes = { APPLICATION_JSON_VALUE, APPLICATION_XML_VALUE })