feat(api): collect AI shown/hidden flag for cases and fix assign cases shell script

README.md

@@ -65,7 +65,8 @@ Clone the repository if you haven't done so already, then follow these steps to
 
 To run the application locally, follow these steps:
 
-> Note: Ensure you have activated your pipenv shell by running `pipenv shell`.
+> [!IMPORTANT]
+> Ensure you have activated your pipenv shell by running `pipenv shell`.
 
 1. Ensure all dependencies are installed using Pipenv.
    ```bash
@@ -82,7 +83,8 @@ To run the application locally, follow these steps:
    flask run --host=127.0.0.1 --port=5001
    ```
 
-> **NOTE:** If your frontend is also running, ensure it is configured to communicate with this backend API. You may need to set the API URL in your frontend configuration.
+> [!NOTE]
+> If your frontend is also running, ensure it is configured to communicate with this backend API. You may need to set the API URL in your frontend configuration.
 > Also, you might need to use CORS (Cross-Origin Resource Sharing) if your frontend and backend are served from different origins. You can use the `flask-cors` package to handle this:
 > ```shell
 > pipenv install flask-cors
@@ -122,6 +124,16 @@ pipenv install flake8
 flake8 src
 ```
 
+## Black Formatting
+
+It is highly encouraged to use [Black](https://black.readthedocs.io/en/stable/) for code formatting before every commit. You can run it as follows:
+
+```shell
+pipenv run black .
+```
+
+Run this inside a pipenv shell, from the root directory of the project. This will format all Python files in the project.
+
 ## Database Setup and Migrations
 
 ### Local Database
@@ -146,6 +158,10 @@ flask db migrate -m "Create user table"
 flask db upgrade  # Execute this if you pull new changes that alter the schema remotely.
 ```
 
+> [!IMPORTANT]
+> When you run `flask db migrate`, it generates a new migration script in the `src/migrations/versions` directory. Review this script to ensure it accurately reflects the changes you made to the models. If necessary, modify the script before running `flask db upgrade`.
+> This is very crucial because the migration script might contain errors or false commands, like `drop_table`, which can lead to data loss. Always double-check the generated migration script before applying it.
+
 ## Git Hooks
 
 Configure your local hooks as follows:
@@ -163,6 +179,7 @@ Specifically, the application is deployed to an AWS ECS cluster using Fargate. T
 
 It also uses Terraform to manage the infrastructure as code. 
 
+> [!TIP]
 > **Visit the [augmed-infra repository](https://github.com/DHEPLab/augmed-infra) for more details on the infrastructure setup and deployment process.**
 
 ## License

pyproject.toml

@@ -1,7 +1,13 @@
 [tool.black]
+line-length = 88
+target-version = ['py38']
 exclude = '''
 /(
-    src/migrations/*
+    \.venv         # skip your virtual-env
+  | src/migrations  # skip all files under migrations
+  | \.git          # skip git dir
+  | build          # skip build/
+  | dist           # skip dist/
 )/
 '''
 

script/assign_cases/generate_config.sh

@@ -1,4 +1,4 @@
-#!/usr/bin/env sh
+#!/usr/bin/env bash
 
 # ---------------------------------------------------------------------------------------------------------------
 # generate_config.sh
@@ -26,8 +26,8 @@
 #
 # To run:
 # 1. Change directory to the script's location: cd script/assign_cases
-# 1. Run: chmod +x generate_config.sh
-# 2. Run the script: (Remember to remove the # symbols at the beginning of each line)
+# 2. Run: chmod +x generate_config.sh
+# 3. Run the script: (Remember to remove the # symbols at the beginning of each line)
 #   ./generate_config.sh \
 #     <db_host> \
 #     <db_port> \
@@ -63,28 +63,33 @@ CASES_PER_USER="$6"
 RISK_CASES_PER_USER="$7"
 OUT="$8"
 
+# Prompt for database password once, export to PGPASSWORD for all subsequent psql invocations
+printf 'Password for user %s: ' "$DB_USER"
+stty -echo
+read DB_PASS
+stty echo
+echo
+export PGPASSWORD="$DB_PASS"
+
 # 1) Print a single header line.  (The CSV parser expects exactly these columns.)
 printf 'User,Case No.,Path,Collapse,Highlight,Top\n' > "$OUT"
 
-# 2) Run one big psql‐COPY that:
-#    • Picks N random users
-#    • Picks M random cases per user (only person_ids that exist in visit_occurrence)
-#    • For each sampled (user,case_id), fetch all leaf‐observations but filter them at random() < 0.5
-#      → emit only those chosen leaves, with Collapse=FALSE, Highlight=TRUE
-#    • Separately, pick K random “risk cases” per user → emit exactly one "CRC risk assessments" row for each
-#      of those, again with Collapse=FALSE, Highlight=TRUE
-psql -h "$DB_HOST" \
-     -p "$DB_PORT" \
-     -U "$DB_USER" \
-     -d "$DB_NAME" \
-     -A -F',' -t <<SQL >> "$OUT"
+# 2) Loop over each of N random users, generate their cases, and append to CSV with progress logging
+count=0
+while IFS= read -r user; do
+  count=$((count + 1))
+  echo "[${count}/${NUM_USERS}] Processing user: $user"
+
+  psql -h "$DB_HOST" \
+       -p "$DB_PORT" \
+       -U "$DB_USER" \
+       -d "$DB_NAME" \
+       -w \
+       -A -F',' -t <<SQL >> "$OUT"
 WITH
-  -- STEP A: Pick N random users
+  -- STEP A: Single user context
   users AS (
-    SELECT email
-    FROM public."user"
-    ORDER BY random()
-    LIMIT $NUM_USERS
+    SELECT '$user' AS email
   ),
 
   -- STEP B: All person_ids that actually have at least one visit (so get_case_by_user won't blow up)
@@ -329,10 +334,26 @@ WITH
     FROM risk_cases rc
   )
 
--- UNION together leaf_rows + risk_rows
-SELECT * FROM leaf_rows
-UNION ALL
-SELECT * FROM risk_rows;
+-- UNION together leaf_rows + risk_rows and randomize order for this user
+SELECT * FROM (
+  SELECT * FROM leaf_rows
+  UNION ALL
+  SELECT * FROM risk_rows
+) AS all_rows
+ORDER BY random();
+SQL
+
+done < <(psql -h "$DB_HOST" \
+           -p "$DB_PORT" \
+           -U "$DB_USER" \
+           -d "$DB_NAME" \
+           -w \
+           -A -t <<SQL
+SELECT email
+FROM public."user"
+ORDER BY random()
+LIMIT $NUM_USERS;
 SQL
+)
 
-echo "Wrote $OUT"
+echo "Done – wrote $OUT"

src/analytics/controller/analytics_controller.py

@@ -5,7 +5,10 @@
 from src.user.repository.display_config_repository import DisplayConfigRepository
 from src.common.model.ApiResponse import ApiResponse
 from src.user.utils.auth_utils import jwt_validation_required
-from src.common.exception.BusinessException import BusinessException, BusinessExceptionEnum
+from src.common.exception.BusinessException import (
+    BusinessException,
+    BusinessExceptionEnum,
+)
 from datetime import datetime, timezone
 
 # Give the blueprint its full prefix; no strict_slashes here
@@ -15,31 +18,36 @@
     url_prefix="/api/analytics",
 )
 
+
 @analytics_blueprint.route("/", methods=["POST"], strict_slashes=False)
 @jwt_validation_required()
 def record():  # pragma: no cover
     payload = request.get_json() or {}
-    case_config_id    = payload.get("caseConfigId")
-    case_open_str     = payload.get("caseOpenTime")
-    answer_open_str   = payload.get("answerOpenTime")
+    case_config_id = payload.get("caseConfigId")
+    case_open_str = payload.get("caseOpenTime")
+    answer_open_str = payload.get("answerOpenTime")
     answer_submit_str = payload.get("answerSubmitTime")
 
     if not all([case_config_id, case_open_str, answer_open_str, answer_submit_str]):
         ex = BusinessException(
             BusinessExceptionEnum.RenderTemplateError,
-            "Missing analytics metrics fields"
+            "Missing analytics metrics fields",
         )
         return jsonify(ApiResponse.error(ex)), 400
 
     fmt = "%Y-%m-%dT%H:%M:%S.%fZ"
     try:
-        case_open     = datetime.strptime(case_open_str, fmt).replace(tzinfo=timezone.utc)
-        answer_open   = datetime.strptime(answer_open_str, fmt).replace(tzinfo=timezone.utc)
-        answer_submit = datetime.strptime(answer_submit_str, fmt).replace(tzinfo=timezone.utc)
+        case_open = datetime.strptime(case_open_str, fmt).replace(tzinfo=timezone.utc)
+        answer_open = datetime.strptime(answer_open_str, fmt).replace(
+            tzinfo=timezone.utc
+        )
+        answer_submit = datetime.strptime(answer_submit_str, fmt).replace(
+            tzinfo=timezone.utc
+        )
     except ValueError:
         ex = BusinessException(
             BusinessExceptionEnum.RenderTemplateError,
-            "Bad timestamp format for analytics"
+            "Bad timestamp format for analytics",
         )
         return jsonify(ApiResponse.error(ex)), 400
 

src/analytics/model/analytics.py

@@ -2,6 +2,7 @@
 from sqlalchemy import Column, Integer, String, DateTime, Float
 from src import db
 
+
 class Analytics(db.Model):
     __tablename__ = "analytics"
 
@@ -11,22 +12,21 @@ class Analytics(db.Model):
     case_id = Column(Integer, nullable=False)
 
     # these three fields will also accept and store tz-aware UTC datetimes
-    case_open_time    = Column(DateTime(timezone=True), nullable=False)
-    answer_open_time  = Column(DateTime(timezone=True), nullable=False)
-    answer_submit_time= Column(DateTime(timezone=True), nullable=False)
+    case_open_time = Column(DateTime(timezone=True), nullable=False)
+    answer_open_time = Column(DateTime(timezone=True), nullable=False)
+    answer_submit_time = Column(DateTime(timezone=True), nullable=False)
 
     to_answer_open_secs = Column(Float, nullable=False)
-    to_submit_secs      = Column(Float, nullable=False)
+    to_submit_secs = Column(Float, nullable=False)
     total_duration_secs = Column(Float, nullable=False)
 
-    created_timestamp  = Column(
-        DateTime(timezone=True),
-        default=lambda: datetime.now(timezone.utc)
+    created_timestamp = Column(
+        DateTime(timezone=True), default=lambda: datetime.now(timezone.utc)
     )
     modified_timestamp = Column(
         DateTime(timezone=True),
         default=lambda: datetime.now(timezone.utc),
-        onupdate=lambda: datetime.now(timezone.utc)
+        onupdate=lambda: datetime.now(timezone.utc),
     )
 
     __table_args__ = (

src/analytics/repository/analytics_repository.py

@@ -1,5 +1,6 @@
 from src.analytics.model.analytics import Analytics
 
+
 class AnalyticsRepository:
     def __init__(self, session):  # pragma: no cover
         self.session = session

src/analytics/service/analytics_service.py

@@ -1,10 +1,14 @@
 from datetime import datetime
 from src.analytics.model.analytics import Analytics
 from src.analytics.repository.analytics_repository import AnalyticsRepository
-from src.common.exception.BusinessException import BusinessException, BusinessExceptionEnum
+from src.common.exception.BusinessException import (
+    BusinessException,
+    BusinessExceptionEnum,
+)
 from src.user.utils.auth_utils import get_user_email_from_jwt
 from src.user.repository.display_config_repository import DisplayConfigRepository
 
+
 class AnalyticsService:
     def __init__(
         self,
@@ -14,8 +18,13 @@ def __init__(
         self.analytics_repo = analytics_repository
         self.config_repo = display_config_repository
 
-    def record_metrics(self, case_config_id: str, case_open: datetime,
-                       answer_open: datetime, answer_submit: datetime) -> Analytics:  # pragma: no cover
+    def record_metrics(
+        self,
+        case_config_id: str,
+        case_open: datetime,
+        answer_open: datetime,
+        answer_submit: datetime,
+    ) -> Analytics:  # pragma: no cover
 
         # verify user owns this case_config
         config = self.config_repo.get_configuration_by_id(case_config_id)

src/answer/controller/answer_controller.py

@@ -4,10 +4,10 @@
 from src.answer.repository.answer_repository import AnswerRepository
 from src.answer.service.answer_service import AnswerService
 from src.common.model.ApiResponse import ApiResponse
-from src.configration.repository.answer_config_repository import \
-    AnswerConfigurationRepository
-from src.user.repository.display_config_repository import \
-    DisplayConfigRepository
+from src.configration.repository.answer_config_repository import (
+    AnswerConfigurationRepository,
+)
+from src.user.repository.display_config_repository import DisplayConfigRepository
 from src.user.utils.auth_utils import jwt_validation_required
 
 answer_blueprint = Blueprint("answer", __name__)

src/answer/model/answer.py

@@ -1,5 +1,6 @@
 from datetime import datetime
 
+from sqlalchemy import Boolean
 from sqlalchemy.dialects.postgresql import UUID
 
 from src import db
@@ -18,7 +19,7 @@ class Answer(db.Model):
     display_configuration = db.Column(db.JSON, nullable=True)
     answer_config_id = db.Column(UUID(as_uuid=True), nullable=True)
     answer: dict = db.Column(db.JSON, nullable=True)
-
+    ai_score_shown: bool = db.Column(Boolean, nullable=False, default=False)
     created_timestamp: datetime = db.Column(db.DateTime, default=datetime.utcnow)
     modified_timestamp: datetime = db.Column(
         db.DateTime, default=datetime.utcnow, onupdate=datetime.utcnow

src/answer/service/answer_service.py

@@ -1,11 +1,13 @@
 from src.answer.model.answer import Answer
 from src.answer.repository.answer_repository import AnswerRepository
-from src.common.exception.BusinessException import (BusinessException,
-                                                    BusinessExceptionEnum)
-from src.configration.repository.answer_config_repository import \
-    AnswerConfigurationRepository
-from src.user.repository.display_config_repository import \
-    DisplayConfigRepository
+from src.common.exception.BusinessException import (
+    BusinessException,
+    BusinessExceptionEnum,
+)
+from src.configration.repository.answer_config_repository import (
+    AnswerConfigurationRepository,
+)
+from src.user.repository.display_config_repository import DisplayConfigRepository
 from src.user.utils import auth_utils
 
 
@@ -26,6 +28,8 @@ def add_answer_response(self, task_id: int, data: dict):
         answer = data["answer"]
         answer_config_id = data["answerConfigId"]
 
+        ai_shown = data.get("aiScoreShown", False)
+
         configuration = self.configuration_repository.get_configuration_by_id(task_id)
 
         if not configuration or configuration.user_email != user_eamil:
@@ -41,6 +45,7 @@ def add_answer_response(self, task_id: int, data: dict):
             task_id=task_id,
             case_id=configuration.case_id,
             user_email=user_eamil,
+            ai_score_shown=ai_shown,
             display_configuration=configuration.path_config,
             answer_config_id=answer_config.id,
             answer=answer,

src/cases/controller/case_controller.py

@@ -3,19 +3,15 @@
 from src import db
 from src.answer.repository.answer_repository import AnswerRepository
 from src.cases.repository.concept_repository import ConceptRepository
-from src.cases.repository.drug_exposure_repository import \
-    DrugExposureRepository
+from src.cases.repository.drug_exposure_repository import DrugExposureRepository
 from src.cases.repository.measurement_repository import MeasurementRepository
 from src.cases.repository.observation_repository import ObservationRepository
 from src.cases.repository.person_repository import PersonRepository
-from src.cases.repository.visit_occurrence_repository import \
-    VisitOccurrenceRepository
+from src.cases.repository.visit_occurrence_repository import VisitOccurrenceRepository
 from src.cases.service.case_service import CaseService
 from src.common.model.ApiResponse import ApiResponse
-from src.common.repository.system_config_repository import \
-    SystemConfigRepository
-from src.user.repository.display_config_repository import \
-    DisplayConfigRepository
+from src.common.repository.system_config_repository import SystemConfigRepository
+from src.user.repository.display_config_repository import DisplayConfigRepository
 from src.user.utils import auth_utils
 from src.user.utils.auth_utils import jwt_validation_required