Fix NumPy deprecation warning by replacing np.float with float

Dockerfile

@@ -1,9 +1,44 @@
-FROM python:2.7-slim
+# Use slim Python 3.10 image
+FROM python:3.10.12-slim
 
-RUN mkdir -p /usr/src/app
-WORKDIR /usr/src/app
-COPY requirements.txt /usr/src/app/
-RUN pip install --no-cache-dir -r requirements.txt
-COPY . /usr/src/app
+# Set Flask environment variables
+ENV FLASK_ENV=development
+ENV FLASK_APP=calculators.py
+ENV FLASK_DEBUG=1
+
+WORKDIR /app
+RUN mkdir /uwsgi_log
+
+# Copy project files
+COPY . /app
+
+# Install system dependencies for building packages (numpy, scipy, uwsgi)
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    build-essential \
+    gfortran \
+    python3-dev \
+    libatlas-base-dev \
+    libopenblas-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+# Upgrade pip, setuptools, wheel
+RUN pip install --upgrade pip setuptools wheel
+
+# Install prebuilt wheels for numpy/scipy to avoid build errors
+RUN pip install numpy==1.25.2 scipy==1.11.1
+
+# Install Flask, Jinja2, MarkupSafe compatible versions
+RUN pip install Flask>=2.2.5 Jinja2>=3.1.2 MarkupSafe>=2.1.2
+
+# Install remaining dependencies from requirements.txt excluding numpy/scipy/Flask/Jinja2/MarkupSafe
+RUN pip install --use-pep517 --no-build-isolation $(grep -vE "numpy|scipy|Flask|Jinja2|MarkupSafe" requirements.txt)
+
+# Install uwsgi if needed
+RUN apt-get update && apt-get install -y uwsgi \
+    && rm -rf /var/lib/apt/lists/*
+
+# Expose Flask port
 EXPOSE 5000
-CMD ["gunicorn", "--workers=4", "-b 0.0.0.0:5000","wsgi:app"]
+
+# Run the Flask app
+CMD ["flask", "run", "--host=0.0.0.0"]

calculators.py

@@ -1,18 +1,143 @@
 from flask import Flask, jsonify, request
 from flask import abort, render_template
 from flask_bootstrap import Bootstrap
-from gail import gail, gail_api
+
+# DEBUG: Add debugging information before imports
+import os
+import sys
+
+print("=== DEBUGGING IMPORT ISSUES ===")
+print("Current working directory:", os.getcwd())
+print("Python path:")
+for path in sys.path:
+    print(f"  {path}")
+
+print("\nContents of current directory:")
+for item in os.listdir('.'):
+    print(f"  {item}")
+
+print("\nLooking for gail directory...")
+if os.path.exists('./gail'):
+    print("✓ gail directory found at ./gail")
+    print("Contents of gail directory:")
+    for item in os.listdir('./gail'):
+        print(f"  {item}")
+
+    # Check if __init__.py exists
+    if os.path.exists('./gail/__init__.py'):
+        print("✓ __init__.py found in gail directory")
+    else:
+        print("✗ __init__.py NOT found in gail directory")
+
+    # Check for the specific files we need
+    if os.path.exists('./gail/gail.py'):
+        print("✓ gail.py found")
+    else:
+        print("✗ gail.py NOT found")
+
+    if os.path.exists('./gail/gail_api.py'):
+        print("✓ gail_api.py found")
+    else:
+        print("✗ gail_api.py NOT found")
+
+else:
+    print("✗ gail directory NOT found at ./gail")
+
+# Also check absolute path
+if os.path.exists('/app/gail'):
+    print("✓ gail directory found at /app/gail")
+    print("Contents of /app/gail directory:")
+    for item in os.listdir('/app/gail'):
+        print(f"  {item}")
+else:
+    print("✗ gail directory NOT found at /app/gail")
+
+print("=== END DEBUGGING INFO ===\n")
+
+# Try different import approaches
+print("=== TESTING IMPORTS ===")
+
+try:
+    print("Attempting: import gail.gail_api as gail_api")
+    import gail.gail_api as gail_api
+    print("✓ SUCCESS: gail.gail_api imported successfully")
+except ImportError as e:
+    print(f"✗ FAILED: {e}")
+
+    # Try alternative approach
+    try:
+        print("Attempting: sys.path.insert approach")
+        gail_path = os.path.join(os.path.dirname(__file__), 'gail')
+        if gail_path not in sys.path:
+            sys.path.insert(0, gail_path)
+        import gail_api
+        print("✓ SUCCESS: gail_api imported with sys.path.insert")
+    except ImportError as e2:
+        print(f"✗ FAILED: {e2}")
+
+        # Try direct file import
+        try:
+            print("Attempting: direct file path import")
+            import importlib.util
+            spec = importlib.util.spec_from_file_location("gail_api", "./gail/gail_api.py")
+            gail_api = importlib.util.module_from_spec(spec)
+            spec.loader.exec_module(gail_api)
+            print("✓ SUCCESS: gail_api imported directly from file")
+        except Exception as e3:
+            print(f"✗ FAILED: {e3}")
+            print("All import attempts failed!")
+            gail_api = None
+
+try:
+    print("Attempting: from gail.gail import GailRiskCalculator")
+    from gail.gail import GailRiskCalculator
+    print("✓ SUCCESS: GailRiskCalculator imported successfully")
+except ImportError as e:
+    print(f"✗ FAILED: {e}")
+
+    # Try alternative approach
+    try:
+        print("Attempting: GailRiskCalculator with sys.path.insert")
+        if 'gail' not in sys.modules:
+            gail_path = os.path.join(os.path.dirname(__file__), 'gail')
+            if gail_path not in sys.path:
+                sys.path.insert(0, gail_path)
+        import gail
+        from gail import GailRiskCalculator
+        print("✓ SUCCESS: GailRiskCalculator imported with sys.path.insert")
+    except ImportError as e2:
+        print(f"✗ FAILED: {e2}")
+
+        # Try direct file import
+        try:
+            print("Attempting: GailRiskCalculator direct file path import")
+            import importlib.util
+            spec = importlib.util.spec_from_file_location("gail", "./gail/gail.py")
+            gail_module = importlib.util.module_from_spec(spec)
+            spec.loader.exec_module(gail_module)
+            GailRiskCalculator = gail_module.GailRiskCalculator
+            print("✓ SUCCESS: GailRiskCalculator imported directly from file")
+        except Exception as e3:
+            print(f"✗ FAILED: {e3}")
+            print("All GailRiskCalculator import attempts failed!")
+            GailRiskCalculator = None
+
 import numpy as np
 from RiskAssessment import BasicRiskAssessment as assessment
 
+print("=== END TESTING IMPORTS ===\n")
 
 app = Flask(__name__)
 Bootstrap(app)
 
 
 def get_calculator(calculator_name):
     if calculator_name.lower() == "gail":
-        return gail_api.GailAPI()
+        if gail_api is not None:
+            return gail_api.GailAPI()
+        else:
+            print("ERROR: gail_api is None, cannot create GailAPI instance")
+            return None
     return None
 
 @app.route('/')
@@ -53,7 +178,6 @@ def getFieldDescrptions(calculator):
     # gailapi = gail_api.GailAPI()
     return render_template("api_doc.html", name=calc.get_name(), version="2.0", apidef=calc.get_input_fields_json())
 
-
 @app.route('/api/v1.0/gail', methods=['POST'])
 def doGailCalc():
     """
@@ -72,7 +196,10 @@ def doGailCalc():
         abort(400)
     else:
         # print request.json
-        calc = gail.GailRiskCalculator()
+        if GailRiskCalculator is None:
+            return jsonify({"error": "GailRiskCalculator not available due to import issues"}), 500
+
+        calc = GailRiskCalculator()
         calc.Initialize()  # TODO: look into moving this into the instantion of the object
 
         # TODO: move the rhyp and age indicator logic into the gail calculator, all it's logic should live in there.
@@ -82,7 +209,7 @@ def doGailCalc():
             if request.json['ihyp'] == 0:
                 rhyp = np.float64(0.93)
             elif request.json['ihyp'] == 1:
-                rhyp = np.float(1.82)
+                rhyp = float(1.82)
 
         fiveYearABS = calc.CalculateAbsoluteRisk(request.json['age'],
                                                  request.json['age'] + 5,
@@ -136,4 +263,4 @@ def doGailCalc():
 
 
 if __name__ == "__main__":
-    app.run(debug=False)
+    app.run(debug=False, host="0.0.0.0", port=5070)

calculators_tests.py

@@ -85,7 +85,7 @@ def get_NCI(self,
                 utils.roundLikeNCI(cgvLifetimeRiskAVE))
 
     def test_bad_calc_name(self):
-        print "Testing Unknown Calculator Name (For v2.0)"
+        print("Testing Unknown Calculator Name (For v2.0)")
         # test getting the docs for a bad calc
         rv = self.app.get('/api/v2.0/bad_calc')
         assert rv.status_code == 501
@@ -95,7 +95,7 @@ def test_bad_calc_name(self):
         assert rv.status_code == 501
 
     def test_gail_calc_doc(self):
-        print "Testing GAIL Doc URLs (For v2.0)"
+        print("Testing GAIL Doc URLs (For v2.0)")
         rv = self.app.get('/api/v2.0/gail')
         assert rv.status_code == 200
         assert "VisExcell API For GAIL - version 2.0" in rv.get_data()
@@ -104,7 +104,7 @@ def test_gail_calc_doc(self):
         assert rv.mimetype == "application/json"
 
     def test_gail_calc_post(self):
-        print "Testing getting GAIL results for (v2.0)"
+        print("Testing getting GAIL results for (v2.0)")
         post_data = {
             "age": 48,
             "menarch_age": 2,
@@ -132,7 +132,7 @@ def test_gail_calc_post(self):
     # TODO: Add bad post data to check error responses
 
     def test_unknown_biopsies(self):
-        print "Testing for unknown biopsy bug (using v1.0)"
+        print("Testing for unknown biopsy bug (using v1.0)")
         post_data = {
             "age": 40,
             "menarch_age": 2,
@@ -176,7 +176,7 @@ def test_unknown_biopsies(self):
                     self.assertEqual((fyr, fyra, ltr, ltra),(nci_fyr,nci_fyra,nci_ltr,nci_ltra), "Inputs: %r" % post_data)
 
     def test_calculations_valid_inputs(self):
-        print "Testing for valid inputs (using v1.0)"
+        print("Testing for valid inputs (using v1.0)")
         test_inputs = [{"age": 42, "menarch_age": 2, "live_birth_age": 0, "ever_had_biopsy": 0, "num_biopsy": 0, "first_deg_relatives": 0, "ihyp": 99, "race": 1},
                        {"age": 50, "menarch_age": 2, "live_birth_age": 0, "ever_had_biopsy": 0, "num_biopsy": 0, "first_deg_relatives": 0, "ihyp": 99, "race": 1},
                        {"age": 68, "menarch_age": 2, "live_birth_age": 0, "ever_had_biopsy": 0, "num_biopsy": 0, "first_deg_relatives": 0, "ihyp": 99, "race": 1},

docker-compose.yml

@@ -0,0 +1,37 @@
+version: '3.8'
+
+services:
+  riskmodels-api:
+    container_name: riskmodels-api
+    build: .
+    restart: always
+#    command: uwsgi --http 0.0.0.0:5000 --master -p 1 -w app:app
+    environment:
+      SECRET_KEY: f502c8e1-f4b2-486a-aeb4-85e427a46613
+      JWT_SECRET_KEY: RbXAh3yIaUBJfDh=wtYs-cTPK?EnwG!JGrFgGhYOdqsy/!h2RXZ1PPaAkIGmrA7F
+      CACHE_ENABLED: 1
+      CACHE_TYPE: RedisCache
+      # DATABASE_TYPE: postgresql
+      # DATABASE_HOST: landa-db       # Connect to root-level Postgres
+      # DATABASE_PORT: 5432
+      # DATABASE_USER: postgres
+      # DATABASE_PASS: gofuckYourselfAUG!2024
+      # DATABASE_DB: riskmodels-db      # Project-specific DB in shared container
+      FLASK_DEBUG: 1
+      FLASK_CONFIG: development
+      FLASK_APP: calculators.py
+      LISTEN_HOST: 0.0.0.0
+      LISTEN_PORT: 5000
+      LOG_LEVEL: INFO
+      UPDATE_DAYS_TOKEN: zdMBOJi9f4WlkHuPai4RRwkM6pryEp
+      FILE_UPLOAD_TOKEN: P5boWPJXxrRDlGvtBuP7a5GOoXY8wo
+    ports:
+      - "5030:5000"
+    networks:
+      - landa_network
+
+# Optional Redis section is removed since you don’t use it yet
+
+networks:
+  landa_network:
+    external: true

gail/__init__.py

@@ -0,0 +1,2 @@
+from . import gail
+from . import gail_api

gail/gail.py

@@ -1,3 +1,4 @@
+# Gail model risk calculator
 import numpy as np
 
 class GailRiskCalculator:
@@ -952,7 +953,7 @@ def CalculateRisk(self,
         for k in range(108):    # really is NumCovPattInGailModel / 2
             # /* col2: indicator for age */
             r8iTox2[k, 1] = np.float64(0.0)
-            r8iTox2[108 + k, 1] = np.float(1.0)
+            r8iTox2[108 + k, 1] = float(1.0)
 
         for j in range(1, 3):       # note, since we always subtract 1 from j and k, we could zero base these
             # /* col3: age menarchy cate */
@@ -1200,7 +1201,7 @@ def CalculateRisk(self,
 if __name__ == '__main__':
     gailMod = GailRiskCalculator()
     gailMod.Initialize()
-    print gailMod.CalculateRisk(1,  # riskIndex int    [1 = Abs, 2 = Ave]
+    print(gailMod.CalculateRisk(1,  # riskIndex int    [1 = Abs, 2 = Ave]
                   35,  # CurrentAge int    [t1]
                   40,  # ProjectionAge int    [t2]
                   0,  # AgeIndicator int    [i0]
@@ -1212,4 +1213,4 @@ def CalculateRisk(self,
                   1,  # int    [ihyp]  HyperPlasia
                   np.float64(1.82),  # double [rhyp]  RHyperPlasia
                   1  # irace int    [race]
-                  )
+                ))

gail/gail_api.py

@@ -1,3 +1,4 @@
+# Gail model risk calculator API
 import gail as gail_calc
 from RiskAssessment import BasicRiskAssessment as assessment
 import numpy as np
@@ -151,7 +152,7 @@ def validate_inputs(self, inputs):
 
     def run(self, inputs):
         errors = self.validate_inputs(inputs)
-        print len(errors.keys())
+        print(len(errors.keys()))
         return_obj = {"code": 200}
         ra_obj = None
         # print "out_of_bounds" not in errors.keys()
@@ -174,7 +175,7 @@ def do_calculation(self, inputs):
             if inputs['ihyp'] == 0:
                 rhyp = np.float64(0.93)
             elif inputs['ihyp'] == 1:
-                rhyp = np.float(1.82)
+                rhyp = float(1.82)
         # The rhyp computed here doesn't get used by the following functions - SRM: 3-23-2017
         # The age_indicator doesn't get used by the following either. - SRM: 3-23-2017
         fiveYearABS = self.calc.CalculateAbsoluteRisk(inputs['age'],

utils.py

@@ -3,8 +3,8 @@
 
 def roundLikeNCI(np_float64):
     outval = np.float64(np_float64) * np.float64(1000.0)
-    if outval - outval.astype(np.int) >= np.float(0.5):
+    if outval - outval.astype(np.int) >= float(0.5):
         outval = outval.astype(np.int) + 1
     else:
         outval = outval.astype(np.int)
-    return np.float(outval) / np.float(1000)
+    return float(outval) / float(1000)