feat: implement data loading from SQLite (Task 3.2)

- Add load_data() method to AppState that connects to SQLite database
- Populate available_drugs, available_directorates, available_indications from DB
- Detect latest date in dataset and set filter defaults accordingly
- Load KPI values: total_records, unique_patients, total_drugs, total_cost
- Add on_load handler to trigger data loading on page initialization
- Handle database errors gracefully with meaningful error messages
This commit is contained in:
Andrew Charlwood
2026-02-04 14:11:03 +00:00
parent a18de83c8d
commit f38ccfc128
3 changed files with 170 additions and 7 deletions
+5 -5
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@@ -115,11 +115,11 @@ cd pathways_app && timeout 60 python -m reflex run 2>&1 | head -30
- `current_chart: str = "icicle"` - `current_chart: str = "icicle"`
### 3.2 Data Loading ### 3.2 Data Loading
- [ ] Create `load_data()` method that reads from SQLite - [x] Create `load_data()` method that reads from SQLite
- [ ] Populate available options for dropdowns (drugs, indications, directorates) - [x] Populate available options for dropdowns (drugs, indications, directorates)
- [ ] Detect latest date in dataset for "to" date defaults - [x] Detect latest date in dataset for "to" date defaults
- [ ] Calculate total records and last updated timestamp - [x] Calculate total records and last updated timestamp
- [ ] Call on app initialization - [x] Call on app initialization
### 3.3 Filter Logic ### 3.3 Filter Logic
- [ ] Create `apply_filters()` computed method that filters the data based on current state - [ ] Create `apply_filters()` computed method that filters the data based on current state
+114 -2
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@@ -6,6 +6,7 @@ Design reference: DESIGN_SYSTEM.md
""" """
from datetime import datetime, timedelta from datetime import datetime, timedelta
from pathlib import Path
from typing import Any from typing import Any
import reflex as rx import reflex as rx
@@ -349,6 +350,117 @@ class AppState(rx.State):
except (ValueError, TypeError): except (ValueError, TypeError):
return "Unknown" return "Unknown"
# =========================================================================
# Data Loading Methods
# =========================================================================
def load_data(self):
"""
Load data from SQLite database on app initialization.
This method:
1. Connects to the SQLite database (data/pathways.db)
2. Loads available drugs, indications, directorates from actual data
3. Detects the latest date in the dataset for "to" date defaults
4. Updates total_records, last_updated, and data_loaded state
"""
import sqlite3
db_path = Path("data/pathways.db")
if not db_path.exists():
self.error_message = "Database not found. Please run data migration first."
return
try:
conn = sqlite3.connect(str(db_path))
cursor = conn.cursor()
# Get total records
cursor.execute("SELECT COUNT(*) FROM fact_interventions")
self.total_records = cursor.fetchone()[0]
if self.total_records == 0:
self.error_message = "No data in database. Please run data migration."
conn.close()
return
# Get available drugs (distinct, sorted)
cursor.execute("""
SELECT DISTINCT drug_name_std
FROM fact_interventions
WHERE drug_name_std IS NOT NULL AND drug_name_std != ''
ORDER BY drug_name_std
""")
self.available_drugs = [row[0] for row in cursor.fetchall()]
# Get available directories (distinct, sorted)
cursor.execute("""
SELECT DISTINCT directory
FROM fact_interventions
WHERE directory IS NOT NULL AND directory != ''
ORDER BY directory
""")
self.available_directorates = [row[0] for row in cursor.fetchall()]
# Get available indications from ref_drug_indication_clusters
cursor.execute("""
SELECT DISTINCT indication
FROM ref_drug_indication_clusters
WHERE indication IS NOT NULL AND indication != ''
ORDER BY indication
""")
self.available_indications = [row[0] for row in cursor.fetchall()]
# If no indications in reference table, use placeholder
if not self.available_indications:
self.available_indications = ["(No indications available)"]
# Get date range from data
cursor.execute("""
SELECT MIN(intervention_date), MAX(intervention_date)
FROM fact_interventions
""")
date_range = cursor.fetchone()
min_date, max_date = date_range
# Update latest_date_in_data and set "to" date defaults
if max_date:
self.latest_date_in_data = max_date
self.last_seen_to_date = max_date
self.initiated_to_date = max_date
# Set "from" date for last_seen filter (6 months before max_date)
max_dt = datetime.strptime(max_date, "%Y-%m-%d")
six_months_ago = max_dt - timedelta(days=180)
self.last_seen_from_date = six_months_ago.strftime("%Y-%m-%d")
# Get unique patient count for KPIs
cursor.execute("SELECT COUNT(DISTINCT upid) FROM fact_interventions")
self.unique_patients = cursor.fetchone()[0]
# Get unique drug count
self.total_drugs = len(self.available_drugs)
# Get total cost
cursor.execute("SELECT SUM(price_actual) FROM fact_interventions")
total_cost_result = cursor.fetchone()[0]
self.total_cost = float(total_cost_result) if total_cost_result else 0.0
conn.close()
# Set data_loaded and last_updated
self.data_loaded = True
self.last_updated = datetime.now().isoformat()
self.error_message = ""
except sqlite3.Error as e:
self.error_message = f"Database error: {str(e)}"
self.data_loaded = False
except Exception as e:
self.error_message = f"Failed to load data: {str(e)}"
self.data_loaded = False
# ============================================================================= # =============================================================================
# Layout Components # Layout Components
@@ -1332,5 +1444,5 @@ app = rx.App(
], ],
) )
# Register page # Register page with on_load handler to load data on app initialization
app.add_page(index, route="/", title="HCD Analysis | Patient Pathways") app.add_page(index, route="/", title="HCD Analysis | Patient Pathways", on_load=AppState.load_data)
+51
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@@ -440,3 +440,54 @@ Use `rx.cond(condition, true_value, false_value)` not Python `if`.
- `pathways_app/pathways_app.py` — existing load patterns (search for "def load_") - `pathways_app/pathways_app.py` — existing load patterns (search for "def load_")
### Blocked items: ### Blocked items:
- None - None
## Iteration 8 - 2026-02-04
### Task: 3.2 Data Loading
### Why this task:
- Previous iteration (7) explicitly recommended continuing with Task 3.2
- Natural progression through Phase 3: State Management
- Data loading is foundational for filter logic (Task 3.3) and KPI calculations (Task 3.4)
- No dependencies blocking this task
### Status: COMPLETE
### What was done:
- Added `Path` import from pathlib to app_v2.py
- Created comprehensive `load_data()` method in AppState that:
- Connects to SQLite database (data/pathways.db)
- Loads available_drugs from DISTINCT drug_name_std in fact_interventions (552 unique drugs)
- Loads available_directorates from DISTINCT directory in fact_interventions (29 unique)
- Loads available_indications from ref_drug_indication_clusters table (32 unique)
- Detects date range (2019-04-01 to 2025-02-28) and sets last_seen_to_date to max date
- Sets last_seen_from_date to 6 months before max date
- Populates KPI values: total_records (440,069), unique_patients, total_drugs, total_cost
- Sets data_loaded=True and last_updated timestamp on success
- Handles errors gracefully with meaningful error messages
- Added on_load handler to app.add_page() to trigger load_data on page load
### Validation results:
- Tier 1 (Code):
- `python -m py_compile pathways_app/app_v2.py` PASSED
- `python -c "from pathways_app.app_v2 import app, AppState"` PASSED
- AppState.load_data method exists and is callable
- Database queries tested independently — all return expected data
- Tier 2 (Visual): Deferred - requires running reflex with modified rxconfig
- Tier 3 (Functional): Database queries verified — 552 drugs, 29 directories, 32 indications, 440K records
### Files changed:
- Modified: pathways_app/app_v2.py (+80 lines - load_data method, on_load handler, Path import)
- Modified: IMPLEMENTATION_PLAN.md (marked 3.2 subtasks complete)
### Committed: [pending]
### Patterns discovered:
- Reflex on_load: Use `app.add_page(..., on_load=AppState.method_name)` to trigger method on page load
- SQLite in Reflex state: Import sqlite3 inside method to avoid issues with state serialization
- Date handling: Parse SQLite dates with datetime.strptime(date_str, "%Y-%m-%d")
- Reference tables: ref_drug_indication_clusters has 32 unique indications for dropdown
- Path handling: Use `Path("data/pathways.db")` for cross-platform compatibility
### Next iteration should:
- Continue with Task 3.3: Filter Logic
- Create `apply_filters()` computed method that filters data based on current filter state
- Handle initiated date filter (when enabled)
- Handle last seen date filter (when enabled)
- Handle drug/indication/directorate multi-select filters
- Return filtered data for chart generation
- Consider implementing as @rx.var computed property that returns filtered record count
- May need to store raw_data list in state or re-query SQLite based on filters
### Blocked items:
- None