clean

.gitignore

@@ -195,10 +195,9 @@ Endobest Reporting/
 jsons history/
 nul
 
-# Ignore all json, exe, log, txt and xlsx files
+# Ignore all json, exe, log and xlsx files
 *.json
 *.exe
 *.log
-*.txt
 /*.xlsx
 !eb_org_center_mapping.xlsx

eb_dashboard.py

@@ -21,7 +21,7 @@
 # identification, and support for complex data extraction using JSON path expressions.
 import json
 import logging
-import msvcrt
+
 import os
 import re
 import sys
@@ -118,10 +118,6 @@ access_token = ""
 refresh_token = ""
 threads_list = []
 _token_refresh_lock = threading.Lock()
-on_retry_exhausted = "ask"  # "ask" | "ignore" | "abort" — set at startup
-fetch_six_month_visit = False   # Whether to fetch 6-month visit data (slow, ~5s per patient)
-_stored_username = ""       # Credentials stored at login for automatic re-login
-_stored_password = ""
 _threads_list_lock = threading.Lock()
 global_pbar = None
 _global_pbar_lock = threading.Lock()
@@ -190,10 +186,8 @@ def new_token():
             finally:
                 if attempt < ERROR_MAX_RETRY - 1:
                     sleep(WAIT_BEFORE_RETRY)
-        # Refresh token exhausted — attempt full re-login with stored credentials
+        logging.critical("Persistent error in refresh_token")
-        logging.warning("Refresh token exhausted. Attempting re-login with stored credentials.")
+        raise httpx.RequestError(message="Persistent error in refresh_token")
-        _do_login(_stored_username, _stored_password)
-        logging.info("Re-login successful. New tokens acquired.")
 
 
 def api_call_with_retry(func):
@@ -218,10 +212,7 @@ def api_call_with_retry(func):
                     
                     if isinstance(exc, httpx.HTTPStatusError) and exc.response.status_code == 401:
                         logging.info(f"Token expired for {func_name}. Refreshing token.")
-                        try:
                         new_token()
-                        except (httpx.RequestError, httpx.HTTPStatusError) as token_exc:
-                            logging.warning(f"Token refresh/re-login failed for {func_name}: {token_exc}")
                     
                     if attempt < ERROR_MAX_RETRY - 1:
                         sleep(WAIT_BEFORE_RETRY)
@@ -234,18 +225,8 @@ def api_call_with_retry(func):
                             sleep(WAIT_BEFORE_NEW_BATCH_OF_RETRIES)
                             break # Exit for loop to restart batch in while True
                         else:
-                            # All automatic batches exhausted — apply on_retry_exhausted policy
+                            # All automatic batches exhausted, ask the user
                             with _user_interaction_lock:
-                                if on_retry_exhausted == "ignore":
-                                    ctx = getattr(thread_local_storage, "current_patient_context", {"id": "Unknown", "pseudo": "Unknown"})
-                                    logging.warning(f"[AUTO-IGNORE] Skipping {func_name} for Patient {ctx['id']} ({ctx['pseudo']}). Error: {exc}")
-                                    return None
-
-                                elif on_retry_exhausted == "abort":
-                                    logging.critical(f"[AUTO-ABORT] Stopping script after persistent error in {func_name}. Error: {exc}")
-                                    raise httpx.RequestError(message=f"Persistent error in {func_name} (auto-aborted)")
-
-                                else:  # "ask" — display error then interactive prompt
                                 console.print(f"\n[bold red]Persistent error in {func_name} after {batch_count} batches ({total_attempts} attempts).[/bold red]")
                                 console.print(f"[red]Exception: {exc}[/red]")
                                 
@@ -263,6 +244,7 @@ def api_call_with_retry(func):
                                     batch_count = 1 # Reset batch counter for the next interactive round
                                     break # Exit for loop to restart batch in while True
                                 elif choice == "Ignore (return None and continue)":
+                                    # Retrieve context if available
                                     ctx = getattr(thread_local_storage, "current_patient_context", {"id": "Unknown", "pseudo": "Unknown"})
                                     logging.warning(f"[IGNORE] User opted to skip {func_name} for Patient {ctx['id']} ({ctx['pseudo']}). Error: {exc}")
                                     return None
@@ -277,37 +259,8 @@ def api_call_with_retry(func):
 # BLOCK 3: AUTHENTICATION
 # ============================================================================
 
-def _do_login(username, password):
-    """Performs the two-step authentication (IAM → RC) with the given credentials.
-    Updates global access_token and refresh_token on success.
-    Raises httpx.RequestError or httpx.HTTPStatusError on failure.
-    Must NOT acquire _token_refresh_lock (caller's responsibility).
-    """
-    global access_token, refresh_token
-
-    client = get_httpx_client()
-    client.base_url = IAM_URL
-    response = client.post(API_AUTH_LOGIN_ENDPOINT,
-                           json={"username": username, "password": password},
-                           timeout=20)
-    response.raise_for_status()
-    master_token = response.json()["access_token"]
-    user_id = response.json()["userId"]
-
-    client = get_httpx_client()
-    client.base_url = RC_URL
-    response = client.post(API_AUTH_CONFIG_TOKEN_ENDPOINT,
-                           headers={"Authorization": f"Bearer {master_token}"},
-                           json={"userId": user_id, "clientId": RC_APP_ID,
-                                 "userAgent": "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/137.0.0.0 Safari/537.36"},
-                           timeout=20)
-    response.raise_for_status()
-    access_token = response.json()["access_token"]
-    refresh_token = response.json()["refresh_token"]
-
-
 def login():
-    global _stored_username, _stored_password
+    global access_token, refresh_token
 
     user_name = (questionary.text("login :", default=DEFAULT_USER_NAME).ask())
     password = (questionary.password("password :", default=DEFAULT_PASSWORD).ask())
@@ -315,18 +268,42 @@ def login():
         return "Exit"
 
     try:
-        _do_login(user_name, password)
+        client = get_httpx_client()
+        client.base_url = IAM_URL
+        response = client.post(API_AUTH_LOGIN_ENDPOINT, json={"username": user_name, "password": password},
+                               timeout=20)
+        response.raise_for_status()
+        master_token = response.json()["access_token"]
+        user_id = response.json()["userId"]
     except httpx.RequestError as exc:
         print(f"Login Error : {exc}")
         logging.warning(f"Login Error : {exc}")
         return "Error"
     except httpx.HTTPStatusError as exc:
         print(f"Login Error : {exc.response.status_code} for Url {exc.request.url}")
-        logging.warning(f"Login Error : {exc.response.status_code} for Url {exc.request.url}")
+        logging.warning(
+            f"Login Error : {exc.response.status_code} for Url {exc.request.url}")
+        return "Error"
+
+    try:
+        client = get_httpx_client()
+        client.base_url = RC_URL
+        response = client.post(API_AUTH_CONFIG_TOKEN_ENDPOINT, headers={"Authorization": f"Bearer {master_token}"},
+                              json={"userId": user_id, "clientId": RC_APP_ID,
+                                    "userAgent": "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/137.0.0.0 Safari/537.36"},
+                              timeout=20)
+        response.raise_for_status()
+        access_token = response.json()["access_token"]
+        refresh_token = response.json()["refresh_token"]
+    except httpx.RequestError as exc:
+        print(f"Login Error : {exc}")
+        logging.warning(f"Login Error : {exc}")
+        return "Error"
+    except httpx.HTTPStatusError as exc:
+        print(f"Login Error : {exc.response.status_code} for Url {exc.request.url}")
+        logging.warning(f"Login Error : {exc}")
         return "Error"
 
-    _stored_username = user_name
-    _stored_password = password
     print()
     print("Login Success")
     return "Success"
@@ -336,100 +313,6 @@ def login():
 # BLOCK 3B: FILE UTILITIES
 # ============================================================================
 
-def ask_on_retry_exhausted():
-    """Asks the user what to do when all API retry batches are exhausted."""
-    global on_retry_exhausted
-    choice = questionary.select(
-        "On retry exhausted :",
-        choices=[
-            "Ask (interactive prompt)",
-            "Ignore (return None and continue)",
-            "Abort (stop script)"
-        ]
-    ).ask()
-    if choice is None or choice == "Ask (interactive prompt)":
-        on_retry_exhausted = "ask"
-    elif choice == "Ignore (return None and continue)":
-        on_retry_exhausted = "ignore"
-    else:
-        on_retry_exhausted = "abort"
-
-
-def ask_fetch_six_month_visit():
-    """Asks the user whether to fetch 6-month visit data (slow API call, ~5s per patient)."""
-    global fetch_six_month_visit
-    choice = questionary.select(
-        "Fetch 6-month visit progress data? (slow, ~5s per patient) :",
-        choices=[
-            "No (skip, faster execution)",
-            "Yes (fetch 6-month visit data)"
-        ]
-    ).ask()
-    fetch_six_month_visit = (choice == "Yes (fetch 6-month visit data)")
-
-
-def wait_for_scheduled_launch():
-    """Asks the user when to start the processing and waits if needed.
-    Options: Immediately / In X minutes / At HH:MM
-    """
-    choice = questionary.select(
-        "When to start processing ?",
-        choices=["Immediately", "In X minutes", "At HH:MM"]
-    ).ask()
-
-    if choice is None or choice == "Immediately":
-        return
-
-    if choice == "In X minutes":
-        minutes_str = questionary.text(
-            "Number of minutes :",
-            validate=lambda x: x.isdigit() and int(x) > 0
-        ).ask()
-        if not minutes_str:
-            return
-        target_time = datetime.now() + timedelta(minutes=int(minutes_str))
-
-    else:  # "At HH:MM"
-        time_str = questionary.text(
-            "Start time (HH:MM) :",
-            validate=lambda x: bool(re.match(r'^\d{2}:\d{2}$', x)) and
-                               0 <= int(x.split(':')[0]) <= 23 and
-                               0 <= int(x.split(':')[1]) <= 59
-        ).ask()
-        if not time_str:
-            return
-        now = datetime.now()
-        h, m = int(time_str.split(':')[0]), int(time_str.split(':')[1])
-        target_time = now.replace(hour=h, minute=m, second=0, microsecond=0)
-        if target_time <= now:
-            console.print("[yellow]⚠ Specified time is already past. Starting immediately.[/yellow]")
-            return
-
-    print()
-    try:
-        while True:
-            remaining = target_time - datetime.now()
-            if remaining.total_seconds() <= 0:
-                break
-            total_secs = int(remaining.total_seconds())
-            h = total_secs // 3600
-            m = (total_secs % 3600) // 60
-            s = total_secs % 60
-            target_str = target_time.strftime('%H:%M:%S')
-            print(f"\r  Starting in {h:02d}:{m:02d}:{s:02d}... (at {target_str}) — Ctrl+C to cancel  ",
-                  end="", flush=True)
-            sleep(1)
-            # Flush keyboard buffer to prevent stray keystrokes from polluting subsequent prompts
-            while msvcrt.kbhit():
-                msvcrt.getwch()
-        print()
-        console.print("[green]✓ Starting processing.[/green]")
-    except KeyboardInterrupt:
-        print()
-        console.print("[bold red]Launch cancelled by user.[/bold red]")
-        raise SystemExit(0)
-
-
 def load_json_file(filename):
     """
     Load a JSON file from disk.
@@ -617,12 +500,6 @@ def _find_questionnaire_by_id(qcm_dict, qcm_id):
     if not isinstance(qcm_dict, dict):
         return None
     qcm_data = qcm_dict.get(qcm_id)
-    if qcm_data and qcm_data.get("_count", 1) > 1:
-        ctx = getattr(thread_local_storage, "current_patient_context", {"id": "Unknown", "pseudo": "Unknown"})
-        logging.error(
-            f"[DUPLICATE QCM] Patient {ctx['id']} ({ctx['pseudo']}): "
-            f"Questionnaire id='{qcm_id}' appeared {qcm_data['_count']} times in API response — using last received copy"
-        )
     return qcm_data.get("answers") if qcm_data else None
 
 
@@ -630,32 +507,20 @@ def _find_questionnaire_by_name(qcm_dict, name):
     """Finds a questionnaire by name (sequential search, returns first match)."""
     if not isinstance(qcm_dict, dict):
         return None
-    matches = [qcm for qcm in qcm_dict.values()
+    for qcm in qcm_dict.values():
-               if get_nested_value(qcm, ["questionnaire", "name"]) == name]
+        if get_nested_value(qcm, ["questionnaire", "name"]) == name:
-    if len(matches) > 1:
+            return qcm.get("answers")
-        ctx = getattr(thread_local_storage, "current_patient_context", {"id": "Unknown", "pseudo": "Unknown"})
+    return None
-        ids = [get_nested_value(q, ["questionnaire", "id"]) for q in matches]
-        logging.error(
-            f"[DUPLICATE QCM] Patient {ctx['id']} ({ctx['pseudo']}): "
-            f"Questionnaire name='{name}' matches {len(matches)} entries (ids: {ids}) — returning first match"
-        )
-    return matches[0].get("answers") if matches else None
 
 
 def _find_questionnaire_by_category(qcm_dict, category):
     """Finds a questionnaire by category (sequential search, returns first match)."""
     if not isinstance(qcm_dict, dict):
         return None
-    matches = [qcm for qcm in qcm_dict.values()
+    for qcm in qcm_dict.values():
-               if get_nested_value(qcm, ["questionnaire", "category"]) == category]
+        if get_nested_value(qcm, ["questionnaire", "category"]) == category:
-    if len(matches) > 1:
+            return qcm.get("answers")
-        ctx = getattr(thread_local_storage, "current_patient_context", {"id": "Unknown", "pseudo": "Unknown"})
+    return None
-        ids = [get_nested_value(q, ["questionnaire", "id"]) for q in matches]
-        logging.error(
-            f"[DUPLICATE QCM] Patient {ctx['id']} ({ctx['pseudo']}): "
-            f"Questionnaire category='{category}' matches {len(matches)} entries (ids: {ids}) — returning first match"
-        )
-    return matches[0].get("answers") if matches else None
 
 
 def _get_field_value_from_questionnaire(all_questionnaires, field_config):
@@ -1097,13 +962,6 @@ def get_all_questionnaires_by_patient(patient_id, record_data):
     response.raise_for_status()
     response_data = response.json()
 
-    # First pass: count occurrences of each q_id to detect duplicates at lookup time
-    q_id_counts = {}
-    for item in response_data:
-        q_id = get_nested_value(item, path=["questionnaire", "id"])
-        if q_id:
-            q_id_counts[q_id] = q_id_counts.get(q_id, 0) + 1
-
     # Build dictionary with questionnaire metadata for searching
     results = {}
     for item in response_data:
@@ -1118,8 +976,7 @@ def get_all_questionnaires_by_patient(patient_id, record_data):
                     "name": q_name,
                     "category": q_category
                 },
-                "answers": answers,
+                "answers": answers
-                "_count": q_id_counts[q_id]
             }
     return results
 
@@ -1278,12 +1135,8 @@ def _process_inclusion_data(inclusion, organization):
     output_inclusion = {}
 
     # --- Prepare all data sources ---
-    # 1. Launch Visit Search asynchronously (it's slow, ~5s) — only if enabled by user
+    # 1. 6-month visit loading disabled on this branch (No-6-Month-Visit)
-    # We use run_with_context to pass the patient identity to the new thread
+    # visit_future = subtasks_thread_pool.submit(run_with_context, search_visit_by_pseudo_and_order, ctx, pseudo, 2)
-    if fetch_six_month_visit:
-        visit_future = subtasks_thread_pool.submit(run_with_context, search_visit_by_pseudo_and_order, ctx, pseudo, 2)
-    else:
-        visit_future = None
 
     # 2. Prepare inclusion_data: enrich inclusion with organization info
     inclusion_data = dict(inclusion)
@@ -1307,10 +1160,7 @@ def _process_inclusion_data(inclusion, organization):
         logging.error(f"Error fetching request data for patient {patient_id}: {e}")
         request_data = None
 
-    try:
+    # 6-month visit loading disabled on this branch (No-6-Month-Visit)
-        six_month_visit_data = visit_future.result() if visit_future is not None else {}
-    except Exception as e:
-        logging.error(f"Error searching 6-month visit for patient {pseudo}: {e}")
     six_month_visit_data = None
 
     # --- Process all fields from configuration ---
@@ -1378,19 +1228,10 @@ def main():
     if login_status == "Exit":
         return
 
-    print()
-    ask_fetch_six_month_visit()
-
     print()
     number_of_threads = int((questionary.text("Number of threads :", default="12",
                                               validate=lambda x: x.isdigit() and 0 < int(x) <= MAX_THREADS).ask()))
 
-    print()
-    ask_on_retry_exhausted()
-
-    print()
-    wait_for_scheduled_launch()
-
     print()
     load_inclusions_mapping_config()
     load_organizations_mapping_config()