--- a
+++ b/src/main.py
@@ -0,0 +1,184 @@
+# main.py
+"""
+Clinical Trial Processing Application
+
+This module serves as the entry point for the clinical trial processing application.
+It provides a command-line interface for selecting and processing clinical trials.
+
+The application can:
+1. Process trials specified manually by NCT ID
+2. Process all cancer trials from the CHIA dataset
+3. Exit the application
+
+Each trial is processed to extract and structure its eligibility criteria.
+"""
+import logging
+import os
+from concurrent.futures import ThreadPoolExecutor, as_completed
+from typing import Generator
+
+from src.services.trial_manager import process_trial
+from src.utils.config import DEFAULT_OUTPUT_DIR, setup_logging
+from src.utils.helpers import curl_with_status_check
+
+# Configure application logging
+setup_logging(log_to_file=True, log_level=logging.DEBUG)
+
+
+def getChiaCancerTrials() -> list[str]:
+    """
+    Retrieve a list of all cancer trial NCT IDs from the CHIA dataset.
+
+    Returns:
+        list[str]: List of NCT IDs for cancer trials.
+    """
+    onlyCancerFolder = os.path.join("..", "Trials", "CHIA", "OnlyCancerTrials")
+    return [
+        file.split(".")[0]
+        for file in os.listdir(onlyCancerFolder)
+        if file.endswith(".json")
+    ]
+
+
+def getTrialsFromUser() -> list[str]:
+    """
+    Prompt the user to enter trial NCT IDs manually.
+
+    Returns:
+        list[str]: List of user-specified NCT IDs.
+    """
+    trials = []
+    while nct_id := input(
+        "Enter the NCT ID of the trial you want to process (or press Enter to finish): "
+    ).strip():
+        trials.append(nct_id)
+    return trials
+
+
+def get_all_nct_ids_from_folder(folder_path: str) -> list[str]:
+    """
+    Retrieve all NCT IDs from the first 11 characters of JSON file names in the specified folder.
+
+    Args:
+        folder_path (str): Path to the folder containing JSON files.
+
+    Returns:
+        list[str]: List of NCT IDs.
+    """
+    return [
+        file_name[:11]
+        for file_name in os.listdir(folder_path)
+        if file_name.endswith(".json")
+    ]
+
+
+def getAllCancerTrials(n: int) -> Generator[str, None, None]:
+    """
+    Retrieve a generator of all cancer trial NCT IDs available in clinicaltrials.gov.
+
+    Yields:
+        str: NCT ID for a cancer trial.
+    """
+    url = f"https://clinicaltrials.gov/api/v2/studies?query.cond=cancer&query.term=cancer&query.titles=Cancer&fields=NCTId&pageSize={n}"
+
+    folder_path = os.path.join(DEFAULT_OUTPUT_DIR, "allTrials", "logical")
+    nct_ids = get_all_nct_ids_from_folder(folder_path)
+    response = curl_with_status_check(url)
+    studies = response.get("studies", [])
+    nextToken = response.get("nextPageToken", "")
+
+    while True:
+        for study in [
+            s
+            for s in studies
+            if s["protocolSection"]["identificationModule"]["nctId"] not in nct_ids
+        ]:
+            yield study["protocolSection"]["identificationModule"]["nctId"]
+
+        if not nextToken:
+            break
+
+        next_url = f"{url}&pageToken={nextToken}"
+        response = curl_with_status_check(next_url)
+        studies = response.get("studies", [])
+        nextToken = response.get("nextPageToken", "")
+
+
+def get_trials(n: int = 100) -> list[str] | Generator[str] | None:
+    """
+    Present options to the user for selecting trials to process.
+
+    Returns:
+        list[str] | None: List of NCT IDs to process, or None if user chooses to quit.
+    """
+    while True:
+        user_choice = (
+            input(
+                "Please choose one of the following\n'm' for manual input\n'c' to process all cancer trials from CHIA\n'a' for all cancer trials\n'q' to quit: "
+            )
+            .strip()
+            .lower()
+        )
+
+        if user_choice == "m":
+            return getTrialsFromUser()
+        elif user_choice == "c":
+            return getChiaCancerTrials()
+        elif user_choice == "a":
+            return getAllCancerTrials(n)
+        elif user_choice == "q":
+            return None
+        else:
+            print("Invalid choice. Please try again.")
+
+
+def process_trial_wrapper(nct_id: str):
+    """
+    Wrapper function to process a trial and handle exceptions.
+
+    Args:
+        nct_id (str): NCT ID of the trial to process.
+    """
+    logger = logging.getLogger(__name__)
+    try:
+        process_trial(nct_id, os.path.join(DEFAULT_OUTPUT_DIR, "allTrials"))
+        logger.info(f"Successfully processed trial {nct_id}")
+    except Exception as e:
+        logger.error(f"Failed to process trial {nct_id}: {str(e)}")
+
+
+def main():
+    """
+    Main application function. Handles user interaction and processes selected trials.
+    """
+    logger = logging.getLogger(__name__)
+    logger.info("Application started...")
+    parallelMultiplier = 100
+
+    trials = get_trials(parallelMultiplier)
+    if not trials:
+        logger.info("No trials selected, exiting...")
+        return
+
+    if isinstance(trials, list):
+        logger.info(f"Selected {len(trials)} trials for processing")
+        logger.info("These are the trials selected: %s", trials)
+        parallelMultiplier = min(parallelMultiplier, len(trials))
+
+    # Process each trial in parallel using ThreadPoolExecutor
+    with ThreadPoolExecutor(max_workers=parallelMultiplier) as executor:
+        future_to_nct_id = {
+            executor.submit(process_trial_wrapper, nct_id): nct_id for nct_id in trials
+        }
+        for future in as_completed(future_to_nct_id):
+            nct_id = future_to_nct_id[future]
+            try:
+                future.result()
+            except Exception as e:
+                logger.error(f"Error processing trial {nct_id}: {str(e)}")
+
+    logger.info("Processing complete")
+
+
+if __name__ == "__main__":
+    main()