refactoring

src/HowBadIsMyBatch.ipynb

@@ -439,8 +439,8 @@
    "outputs": [],
    "source": [
     "from SymptomsCausedByVaccines.HtmlUpdater import updateHtmlFile\n",
-    "from SymptomsCausedByVaccines.PrrByVaccineBySymptomFactory import PrrByVaccineBySymptomFactory\n",
+    "from src.SymptomsCausedByVaccines.PrrSeriesFactory import PrrSeriesFactory\n",
-    "from SymptomsCausedByVaccines.PrrByVaccineBySymptomTransformer import PrrByVaccineBySymptomTransformer\n",
+    "from src.SymptomsCausedByVaccines.PrrSeriesTransformer import PrrSeriesTransformer\n",
     "from SymptomsCausedByVaccines.ProportionalReportingRatiosPersister import saveProportionalReportingRatios\n",
     "import os\n",
     "import pandas as pd"
@@ -467,10 +467,21 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "prrByVaccineBySymptom = PrrByVaccineBySymptomFactory.getPrrByVaccineBySymptom(prrByVaccineAndSymptom)\n",
+    "prrByVaccineBySymptom = PrrSeriesFactory.getPrrByVaccineBySymptom(prrByVaccineAndSymptom)\n",
     "prrByVaccineBySymptom"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "0f247c64",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "prrBySymptomByVaccine = PrrSeriesFactory.getPrrBySymptomByVaccine(prrByVaccineAndSymptom)\n",
+    "prrBySymptomByVaccine"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -478,10 +489,21 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "prrByVaccineBySymptomWithoutZeroPrrs = PrrByVaccineBySymptomTransformer.removeNonZeroPrrs(prrByVaccineBySymptom)\n",
+    "prrByVaccineBySymptomWithoutZeroPrrs = PrrSeriesTransformer.filterByNonZeroPrrs(prrByVaccineBySymptom)\n",
     "prrByVaccineBySymptomWithoutZeroPrrs"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f07203e4",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "prrBySymptomByVaccineWithHighPrrs = PrrSeriesTransformer.filterByHighPrrs(prrBySymptomByVaccine)\n",
+    "prrBySymptomByVaccineWithHighPrrs"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -491,7 +513,19 @@
    "source": [
     "saveProportionalReportingRatios(\n",
     "    prrByVaccineBySymptomWithoutZeroPrrs,\n",
-    "    directory = os.path.normpath(os.getcwd() + '/../docs/data/ProportionalReportingRatios/'))"
+    "    directory = os.path.normpath(os.getcwd() + '/../docs/data/ProportionalReportingRatios/symptoms'))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "fac4b34f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "saveProportionalReportingRatios(\n",
+    "    prrBySymptomByVaccineWithHighPrrs,\n",
+    "    directory = os.path.normpath(os.getcwd() + '/../docs/data/ProportionalReportingRatios/vaccines'))"
    ]
   },
   {

src/SymptomsCausedByVaccines/PrrByVaccineBySymptomFactory.py

@@ -1,5 +0,0 @@
-class PrrByVaccineBySymptomFactory:
-
-    @staticmethod
-    def getPrrByVaccineBySymptom(prrByVaccineAndSymptom):
-        return prrByVaccineAndSymptom.apply(lambda prrByVaccine: prrByVaccine.to_dict())

src/SymptomsCausedByVaccines/PrrByVaccineBySymptomFactoryTest.py

@@ -1,32 +0,0 @@
-import unittest
-from pandas.testing import assert_series_equal
-from TestHelper import TestHelper
-import pandas as pd
-from SymptomsCausedByVaccines.PrrByVaccineBySymptomFactory import PrrByVaccineBySymptomFactory
-
-class PrrByVaccineBySymptomFactoryTest(unittest.TestCase):
-
-    def test_getPrrByVaccineBySymptom(self):
-        # Given
-        prrByVaccineAndSymptom = TestHelper.createDataFrame(
-                columns = ['11-beta-hydroxylase deficiency', '17-hydroxyprogesterone'],
-                data = [  [0.6,                              1.5],
-                          [0.3,                              3.0]],
-                index = pd.Index(
-                    name = 'VAX_TYPE',
-                    data = [
-                        '6VAX-F',
-                        'ADEN'
-                        ]))
-        
-        # When
-        prrByVaccineBySymptom = PrrByVaccineBySymptomFactory.getPrrByVaccineBySymptom(prrByVaccineAndSymptom)
-        
-        # Then
-        assert_series_equal(
-            prrByVaccineBySymptom,
-            pd.Series(
-                {
-                    '11-beta-hydroxylase deficiency': {'6VAX-F': 0.6, 'ADEN': 0.3},
-                    '17-hydroxyprogesterone': {'6VAX-F': 1.5, 'ADEN': 3.0}
-                }))

src/SymptomsCausedByVaccines/PrrByVaccineBySymptomTransformer.py

@@ -1,6 +0,0 @@
-class PrrByVaccineBySymptomTransformer:
-
-    @staticmethod
-    def removeNonZeroPrrs(prrByVaccineBySymptom):
-        return prrByVaccineBySymptom.map(
-            lambda prrByVaccine: {vaccine: prr for vaccine, prr in prrByVaccine.items() if prr != 0})

src/SymptomsCausedByVaccines/PrrByVaccineBySymptomTransformerTest.py

@@ -1,26 +0,0 @@
-import unittest
-from pandas.testing import assert_series_equal
-import pandas as pd
-from SymptomsCausedByVaccines.PrrByVaccineBySymptomTransformer import PrrByVaccineBySymptomTransformer
-
-class PrrByVaccineBySymptomTransformerTest(unittest.TestCase):
-
-    def test_filterByNonZeroPrrs(self):
-        # Given
-        prrByVaccineBySymptom = pd.Series(
-                {
-                    '11-beta-hydroxylase deficiency': {'6VAX-F': 0.0, 'ADEN': 0.3},
-                    '17-hydroxyprogesterone': {'6VAX-F': 1.5, 'ADEN': 0.0}
-                })
-        
-        # When
-        prrByVaccineBySymptomWithoutZeroPrrs = PrrByVaccineBySymptomTransformer.removeNonZeroPrrs(prrByVaccineBySymptom)
-        
-        # Then
-        assert_series_equal(
-            prrByVaccineBySymptomWithoutZeroPrrs,
-            pd.Series(
-                {
-                    '11-beta-hydroxylase deficiency': {'ADEN': 0.3},
-                    '17-hydroxyprogesterone': {'6VAX-F': 1.5}
-                }))

src/SymptomsCausedByVaccines/PrrSeriesFactory.py

@@ -0,0 +1,11 @@
+class PrrSeriesFactory:
+
+    @staticmethod
+    def getPrrByVaccineBySymptom(prrByVaccineAndSymptom):
+        return prrByVaccineAndSymptom.apply(lambda prrByVaccine: prrByVaccine.to_dict())
+
+    @staticmethod
+    def getPrrBySymptomByVaccine(prrByVaccineAndSymptom):
+        return prrByVaccineAndSymptom.apply(
+            lambda prrBySymptom: prrBySymptom.to_dict(),
+            axis = 'columns')

src/SymptomsCausedByVaccines/PrrSeriesFactoryTest.py

@@ -0,0 +1,58 @@
+import unittest
+from pandas.testing import assert_series_equal
+from TestHelper import TestHelper
+import pandas as pd
+from SymptomsCausedByVaccines.PrrSeriesFactory import PrrSeriesFactory
+
+class PrrSeriesFactoryTest(unittest.TestCase):
+
+    def test_getPrrByVaccineBySymptom(self):
+        # Given
+        prrByVaccineAndSymptom = TestHelper.createDataFrame(
+                columns = ['11-beta-hydroxylase deficiency', '17-hydroxyprogesterone'],
+                data = [  [0.6,                              1.5],
+                          [0.3,                              3.0]],
+                index = pd.Index(
+                    name = 'VAX_TYPE',
+                    data = [
+                        '6VAX-F',
+                        'ADEN'
+                        ]))
+        
+        # When
+        prrByVaccineBySymptom = PrrSeriesFactory.getPrrByVaccineBySymptom(prrByVaccineAndSymptom)
+        
+        # Then
+        assert_series_equal(
+            prrByVaccineBySymptom,
+            pd.Series(
+                {
+                    '11-beta-hydroxylase deficiency': {'6VAX-F': 0.6, 'ADEN': 0.3},
+                    '17-hydroxyprogesterone': {'6VAX-F': 1.5, 'ADEN': 3.0}
+                }))
+
+    def test_getPrrBySymptomByVaccine(self):
+        # Given
+        prrByVaccineAndSymptom = TestHelper.createDataFrame(
+                columns = ['11-beta-hydroxylase deficiency', '17-hydroxyprogesterone'],
+                data = [  [0.6,                              1.5],
+                          [1.3,                              2.5]],
+                index = pd.Index(
+                    name = 'VAX_TYPE',
+                    data = [
+                        '6VAX-F',
+                        'ADEN'
+                        ]))
+        
+        # When
+        prrBySymptomByVaccine = PrrSeriesFactory.getPrrBySymptomByVaccine(prrByVaccineAndSymptom)
+        
+        # Then
+        assert_series_equal(
+            prrBySymptomByVaccine,
+            TestHelper.createSeries(
+                indexName = 'VAX_TYPE',
+                data = {
+                    '6VAX-F': {'11-beta-hydroxylase deficiency': 0.6, '17-hydroxyprogesterone': 1.5},
+                    'ADEN':   {'11-beta-hydroxylase deficiency': 1.3, '17-hydroxyprogesterone': 2.5}
+                }))

src/SymptomsCausedByVaccines/PrrSeriesTransformer.py

@@ -0,0 +1,18 @@
+class PrrSeriesTransformer:
+
+    @staticmethod
+    def filterByNonZeroPrrs(prrByVaccineBySymptom):
+        return PrrSeriesTransformer._filterPrrsBy(
+            prrByVaccineBySymptom,
+            lambda prr: prr != 0)
+
+    @staticmethod
+    def filterByHighPrrs(prrBySymptomByVaccine):
+        return PrrSeriesTransformer._filterPrrsBy(
+            prrBySymptomByVaccine,
+            lambda prr: prr > 1)
+
+    @staticmethod
+    def _filterPrrsBy(prrByKeyByOtherKey, prrFilter):
+        return prrByKeyByOtherKey.map(
+            lambda prrByKey: {key: prr for key, prr in prrByKey.items() if prrFilter(prr)})

src/SymptomsCausedByVaccines/PrrSeriesTransformerTest.py

@@ -0,0 +1,46 @@
+import unittest
+from pandas.testing import assert_series_equal
+import pandas as pd
+from SymptomsCausedByVaccines.PrrSeriesTransformer import PrrSeriesTransformer
+
+class PrrSeriesTransformerTest(unittest.TestCase):
+
+    def test_filterByNonZeroPrrs(self):
+        # Given
+        prrByVaccineBySymptom = pd.Series(
+                {
+                    '11-beta-hydroxylase deficiency': {'6VAX-F': 0.0, 'ADEN': 0.3},
+                    '17-hydroxyprogesterone': {'6VAX-F': 1.5, 'ADEN': 0.0}
+                })
+        
+        # When
+        prrByVaccineBySymptomWithoutZeroPrrs = PrrSeriesTransformer.filterByNonZeroPrrs(prrByVaccineBySymptom)
+        
+        # Then
+        assert_series_equal(
+            prrByVaccineBySymptomWithoutZeroPrrs,
+            pd.Series(
+                {
+                    '11-beta-hydroxylase deficiency': {'ADEN': 0.3},
+                    '17-hydroxyprogesterone': {'6VAX-F': 1.5}
+                }))
+
+    def test_filterByHighPrrs(self):
+        # Given
+        prrBySymptomByVaccine = pd.Series(
+                {
+                    '6VAX-F': {'11-beta-hydroxylase deficiency': 0.6, '17-hydroxyprogesterone': 1.5},
+                    'ADEN':   {'11-beta-hydroxylase deficiency': 1.3, '17-hydroxyprogesterone': 0.9}
+                })
+        
+        # When
+        prrBySymptomByVaccineWithHighPrrs = PrrSeriesTransformer.filterByHighPrrs(prrBySymptomByVaccine)
+        
+        # Then
+        assert_series_equal(
+            prrBySymptomByVaccineWithHighPrrs,
+            pd.Series(
+                {
+                    '6VAX-F': {'17-hydroxyprogesterone': 1.5},
+                    'ADEN':   {'11-beta-hydroxylase deficiency': 1.3}
+                }))