improve json parsing from OAI output

core/openai/prompts/model_card.py

@@ -42,5 +42,4 @@
 Use the following research paper as a reference: ---PAPER START---{research_paper}---PAPER END--. Ensure that the output follows the below model card format.\n
 TEMPLATE: {model_card_template}\n
 Make sure that the following text can be serialized as a JSON object:\n
-```json
 {{"""

core/openai/prompts/petrinet_config.py

@@ -3,8 +3,6 @@
       Use the following petri net json file as a reference: {petrinet}.
       Assume that parameter fields with missing values may have multiple different sets values discussed in the research paper for different conditions.\n
       Return the different sets of initial parameters for the petri net model file like so:
-      ```
-      json
 	  {{"conditions": {{"condition_1": "description of condition_1", "condition_2": "description of condition_2", ...}},
 	  "parameters": [{{
       "id": "beta",
@@ -18,6 +16,5 @@
       Only use parameters found in the reference petrinet file provided above.
       Ensure that the output follows the above petri net format and can be serialized as a JSON. Specifically populate parameters and initials. Use the following
       research paper to answer the user's query: {research_paper}\n\n Answer:
-      ```json
          {{
 """

core/utils.py

@@ -16,21 +16,14 @@ def remove_references(text: str) -> str:
 	return new_text.strip()
 
 
-def extract_json(text: str):
-	try:
-		matches = re.findall(r'\{.*\}', text, re.DOTALL)
-
-		if matches:
-			for match in matches:
-				try:
-					json_obj = json.loads(match)
-					return json_obj
-				except json.JSONDecodeError:
-					continue
-		return None
-	except Exception as e:
-		print(f"An error occurred while parsing JSON: {e}")
-		return None
+def extract_json(text: str) -> dict:
+    corrected_text = text.replace('{{', '{').replace('}}', '}')
+    print(corrected_text)
+    try:
+        json_obj = json.loads(corrected_text)
+        return json_obj
+    except json.JSONDecodeError as e:
+        raise ValueError(f"Error decoding JSON: {e}\nfrom text {text}")
 
 def normalize_greek_alphabet(text: str) -> str:
 	greek_to_english = {
@@ -62,7 +55,7 @@ def model_config_adapter(model_config: dict) -> dict:
 	"""
 
 	output_json = {'conditions': []}
-
+	print(model_config)
 	for condition_name, description in model_config['conditions'].items():
 		condition_data = {'name': condition_name, 'description': description, 'parameters': []}
 		for param_data in model_config['parameters']: