diff --git a/.gitignore b/.gitignore index 836dc6ca842..fb12341fb23 100644 --- a/.gitignore +++ b/.gitignore @@ -14,4 +14,5 @@ src/HowBadIsMyBatch.nbconvert.html src/__pycache__/ src/intensivstationen/__pycache__/ google-chrome-stable_current_amd64* -src/captcha/__pycache__ \ No newline at end of file +src/captcha/__pycache__ +src/GoogleAnalytics/__pycache__ diff --git a/src/GoogleAnalytics/ResolutionProvider.py b/src/GoogleAnalytics/ResolutionProvider.py new file mode 100644 index 00000000000..ea9b87dac24 --- /dev/null +++ b/src/GoogleAnalytics/ResolutionProvider.py @@ -0,0 +1,15 @@ +from enum import Enum +import linecache + + +class Resolution(Enum): + CITY = 1 + COUNTRY = 2 + + +class ResolutionProvider: + + @staticmethod + def getResolution(file): + columns = linecache.getline(file, 7) + return Resolution.CITY if 'City' in columns else Resolution.COUNTRY diff --git a/src/GoogleAnalytics/ResolutionProviderTest.py b/src/GoogleAnalytics/ResolutionProviderTest.py new file mode 100644 index 00000000000..ddf7d49b007 --- /dev/null +++ b/src/GoogleAnalytics/ResolutionProviderTest.py @@ -0,0 +1,23 @@ +import unittest +from GoogleAnalytics.ResolutionProvider import Resolution, ResolutionProvider + + +class ResolutionProviderTest(unittest.TestCase): + + def test_getResolution_COUNTRY(self): + # Given + + # When + resolution = ResolutionProvider.getResolution('src/testdata/GoogleAnalytics/CountryByBatchcode 20230302-20230430.csv') + + # Then + self.assertEqual(resolution, Resolution.COUNTRY) + + def test_getResolution_CITY(self): + # Given + + # When + resolution = ResolutionProvider.getResolution('src/testdata/GoogleAnalytics/CountryByBatchcode 20230730-20230929.csv') + + # Then + self.assertEqual(resolution, Resolution.CITY) diff --git a/src/GoogleAnalytics/__init__.py b/src/GoogleAnalytics/__init__.py new file mode 100644 index 00000000000..e69de29bb2d diff --git a/src/GoogleAnalyticsReaderTest.py b/src/GoogleAnalyticsReaderTest.py index afd28f534be..13ac554bb1d 100644 --- a/src/GoogleAnalyticsReaderTest.py +++ b/src/GoogleAnalyticsReaderTest.py @@ -12,4 +12,4 @@ class GoogleAnalyticsReaderTest(unittest.TestCase): dateRange = googleAnalyticsReader.getDateRange() # Then - self.assertEqual(dateRange, (date(2023, 3, 2), date(2023, 5, 31))) + self.assertEqual(dateRange, (date(2023, 3, 2), date(2023, 9, 29))) diff --git a/src/HowBadIsMyBatch.ipynb b/src/HowBadIsMyBatch.ipynb index e07504bd44f..e8ea731aa03 100644 --- a/src/HowBadIsMyBatch.ipynb +++ b/src/HowBadIsMyBatch.ipynb @@ -2,10 +2,19 @@ "cells": [ { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "id": "9de5907f-18f5-4cb1-903e-26028ff1fa03", "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "2023-10-03 00:48:04.102691: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: SSE4.1 SSE4.2 AVX AVX2 FMA\n", + "To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.\n" + ] + } + ], "source": [ "from CountryCountsByBatchcodeTable2BarChartDescriptionTableConverter import CountryCountsByBatchcodeTable2BarChartDescriptionTableConverter\n", "from JensenShannonDistance2BarChartDescriptionColumnAdder import JensenShannonDistance2BarChartDescriptionColumnAdder\n", @@ -32,20 +41,38 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 2, "id": "d1e4fa9e", "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "03.10.2023, 00:48:07 Uhr\n" + ] + } + ], "source": [ "print(datetime.now().strftime(\"%d.%m.%Y, %H:%M:%S Uhr\"))" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "id": "ffad1c04", "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " lastUpdated: 2023-09-29 00:00:00\n", + "lastUpdatedDataSource: 2023-09-29 00:00:00\n", + "needsUpdate: False\n" + ] + } + ], "source": [ "dateProvider = DateProvider()\n", "print(' lastUpdated:', dateProvider.getLastUpdated())\n", @@ -56,7 +83,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 4, "id": "194b7357", "metadata": {}, "outputs": [], @@ -78,7 +105,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 5, "id": "58333a19", "metadata": {}, "outputs": [], @@ -88,30 +115,649 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 6, "id": "f10b558f", "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "
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VAERS_ID
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2684965COVID19PFIZER\\BIONTECHHD98351<NA>
2684975COVID19MODERNA216C453<NA>
2684979COVID19MODERNA037A22B1<NA>
2684982COVID19MODERNA30046753<NA>
2684990COVID19MODERNANDC:80777-0102-1<NA>
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SYMPTOM1SYMPTOM2SYMPTOM3SYMPTOM4SYMPTOM5
VAERS_ID
855017ArthralgiaChillsInjection site painPyrexiaNaN
855018ChillsFatigueHypertensionHypoaesthesiaInjected limb mobility decreased
855018Muscular weaknessPain in extremityPyrexiaTremorVertigo
855019PainPruritusRashNaNNaN
855020ChillsInfluenza like illnessMyalgiaPain in extremityPyrexia
..................
2684975Haemodynamic testHypoaesthesiaLaboratory testMagnetic resonance imaging abdominalMagnetic resonance imaging thoracic
2684975Nervous system disorderRash macularRenal cystRespiratory distressRespiratory failure
2684975VomitingNaNNaNNaNNaN
2684982Anaemia macrocyticBlood magnesiumHypercalcaemiaHypomagnesaemiaMagnesium deficiency
2684982Nerve injuryParaesthesiaSARS-CoV-2 testNaNNaN
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2584689 rows × 5 columns

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RECVDATEDIEDL_THREATER_VISITHOSPITALDISABLESPLTTYPEVAX_TYPEVAX_MANUVAX_LOTVAX_DOSE_SERIESCOUNTRYSEVERE
VAERS_ID
9024182020-12-1500000NaNCOVID19PFIZER\\BIONTECHEH98991United States0
9024402020-12-1500000NaNCOVID19PFIZER\\BIONTECHEH 98991United States0
9024462020-12-1500000NaNCOVID19PFIZER\\BIONTECHEH98991United States0
9024642020-12-1500000NaNCOVID19PFIZER\\BIONTECHEH9899UNKUnited States0
9024652020-12-1500000NaNCOVID19PFIZER\\BIONTECHEH98991United States0
..........................................
26849152023-09-2101010NZPFIZER INCPV20230015804COVID19PFIZER\\BIONTECH<NA>1New Zealand1
26849162023-09-2100010NZPFIZER INCPV20230015804COVID19PFIZER\\BIONTECH<NA>1New Zealand0
26849192023-09-2100001NaNCOVID19PFIZER\\BIONTECHFA46321<NA>1
26849752023-09-2200000NaNCOVID19MODERNA216C453<NA>0
26849822023-09-2200010NaNCOVID19MODERNA30046753<NA>0
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1596698 rows × 13 columns

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RECVDATEDIEDL_THREATER_VISITHOSPITALDISABLESPLTTYPEVAX_TYPEVAX_MANUVAX_LOTVAX_DOSE_SERIESSEVERECOUNTRY
VAERS_ID
9024182020-12-1500000NaNCOVID19PFIZER\\BIONTECHEH989910United States
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9024462020-12-1500000NaNCOVID19PFIZER\\BIONTECHEH989910United States
9024642020-12-1500000NaNCOVID19PFIZER\\BIONTECHEH9899UNK0United States
9024652020-12-1500000NaNCOVID19PFIZER\\BIONTECHEH989910United States
..........................................
26849752023-09-2200000NaNCOVID19MODERNA216C4530<NA>
26849792023-09-2200001NaNCOVID19MODERNA037A22B11United States
26849822023-09-2200010NaNCOVID19MODERNA300467530<NA>
26849892023-09-2200000NaNCOVID19MODERNA<NA>UNK0United States
26849902023-09-2200000NaNCOVID19MODERNANDC:80777-0102-10United States
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1596698 rows × 13 columns

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" + ], + "text/plain": [ + " RECVDATE DIED L_THREAT ER_VISIT HOSPITAL DISABLE SPLTTYPE \\\n", + "VAERS_ID \n", + "902418 2020-12-15 0 0 0 0 0 NaN \n", + "902440 2020-12-15 0 0 0 0 0 NaN \n", + "902446 2020-12-15 0 0 0 0 0 NaN \n", + "902464 2020-12-15 0 0 0 0 0 NaN \n", + "902465 2020-12-15 0 0 0 0 0 NaN \n", + "... ... ... ... ... ... ... ... \n", + "2684975 2023-09-22 0 0 0 0 0 NaN \n", + "2684979 2023-09-22 0 0 0 0 1 NaN \n", + "2684982 2023-09-22 0 0 0 1 0 NaN \n", + "2684989 2023-09-22 0 0 0 0 0 NaN \n", + "2684990 2023-09-22 0 0 0 0 0 NaN \n", + "\n", + " VAX_TYPE VAX_MANU VAX_LOT VAX_DOSE_SERIES SEVERE \\\n", + "VAERS_ID \n", + "902418 COVID19 PFIZER\\BIONTECH EH9899 1 0 \n", + "902440 COVID19 PFIZER\\BIONTECH EH 9899 1 0 \n", + "902446 COVID19 PFIZER\\BIONTECH EH9899 1 0 \n", + "902464 COVID19 PFIZER\\BIONTECH EH9899 UNK 0 \n", + "902465 COVID19 PFIZER\\BIONTECH EH9899 1 0 \n", + "... ... ... ... ... ... \n", + "2684975 COVID19 MODERNA 216C45 3 0 \n", + "2684979 COVID19 MODERNA 037A22B 1 1 \n", + "2684982 COVID19 MODERNA 3004675 3 0 \n", + "2684989 COVID19 MODERNA UNK 0 \n", + "2684990 COVID19 MODERNA NDC:80777-0102- 1 0 \n", + "\n", + " COUNTRY \n", + "VAERS_ID \n", + "902418 United States \n", + "902440 United States \n", + "902446 United States \n", + "902464 United States \n", + "902465 United States \n", + "... ... \n", + "2684975 \n", + "2684979 United States \n", + "2684982 \n", + "2684989 United States \n", + "2684990 United States \n", + "\n", + "[1596698 rows x 13 columns]" + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "internationalVaersCovid19 = CountryColumnsMerger.mergeCountryColumnOfSrcIntoDst(\n", " src = getInternationalVaersCovid19BeforeDeletion(),\n", @@ -132,10 +1063,216 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 10, "id": "0915aa5a", "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "
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BatchAdverse Reaction ReportsDeathsDisabilitiesLife Threatening IllnessesCompanySevere reportsLethality
0C2021050263300UNKNOWN MANUFACTURERNaNNaN
1J2021000343300UNKNOWN MANUFACTURERNaNNaN
2JJ-21C14-024040JANSSENNaNNaN
3J2021030113300UNKNOWN MANUFACTURERNaNNaN
4J202103113300UNKNOWN MANUFACTURERNaNNaN
...........................
922621C19-0220000JANSSENNaNNaN
922721C19-056000JANSSENNaNNaN
922821C13-048000JANSSENNaNNaN
922921C11023000JANSSENNaNNaN
923021C14-0510000JANSSENNaNNaN
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9231 rows × 8 columns

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" + ], + "text/plain": [ + " Batch Adverse Reaction Reports Deaths Disabilities \\\n", + "0 C202105026 3 3 0 \n", + "1 J202100034 3 3 0 \n", + "2 JJ-21C14-02 4 0 4 \n", + "3 J202103011 3 3 0 \n", + "4 J20210311 3 3 0 \n", + "... ... ... ... ... \n", + "9226 21C19-02 20 0 0 \n", + "9227 21C19-05 6 0 0 \n", + "9228 21C13-04 8 0 0 \n", + "9229 21C1102 3 0 0 \n", + "9230 21C14-05 10 0 0 \n", + "\n", + " Life Threatening Illnesses Company Severe reports \\\n", + "0 0 UNKNOWN MANUFACTURER NaN \n", + "1 0 UNKNOWN MANUFACTURER NaN \n", + "2 0 JANSSEN NaN \n", + "3 0 UNKNOWN MANUFACTURER NaN \n", + "4 0 UNKNOWN MANUFACTURER NaN \n", + "... ... ... ... \n", + "9226 0 JANSSEN NaN \n", + "9227 0 JANSSEN NaN \n", + "9228 0 JANSSEN NaN \n", + "9229 0 JANSSEN NaN \n", + "9230 0 JANSSEN NaN \n", + "\n", + " Lethality \n", + "0 NaN \n", + "1 NaN \n", + "2 NaN \n", + "3 NaN \n", + "4 NaN \n", + "... ... \n", + "9226 NaN \n", + "9227 NaN \n", + "9228 NaN \n", + "9229 NaN \n", + "9230 NaN \n", + "\n", + "[9231 rows x 8 columns]" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "batchCodeTable = createGlobalBatchCodeTable(\n", " deleteEntriesWithADRsLessThanOrEqual = 2,\n", @@ -193,15 +1330,322 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 11, "id": "70fcc420", "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/home/frankknoll/Dokumente/Corona/projects/HowBadIsMyBatch/src/CountriesByBatchcodeProvider.py:39: FutureWarning: The behavior of indexing on a MultiIndex with a nested sequence of labels is deprecated and will change in a future version. `series.loc[label, sequence]` will raise if any members of 'sequence' or not present in the index's second level. To retain the old behavior, use `series.index.isin(sequence, level=1)`\n", + " return countryCountsByBatchcode.loc[(batchcodes2Retain, slice(None)), :]\n" + ] + }, + { + "data": { + "text/html": [ + "
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COUNTRY_COUNT_BY_VAX_LOT ClickedCOUNTRY_COUNT_BY_VAX_LOT Before Deletion
VAX_LOTCOUNTRY
J202100034Austria10
Germany10
United States10
JJ-21C14-02Belgium13
Poland10
............
21C13-04Switzerland10
United States10
21C1102France02
Germany30
21C14-05France010
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29310 rows × 2 columns

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" + ], + "text/plain": [ + " COUNTRY_COUNT_BY_VAX_LOT Clicked \\\n", + "VAX_LOT COUNTRY \n", + "J202100034 Austria 1 \n", + " Germany 1 \n", + " United States 1 \n", + "JJ-21C14-02 Belgium 1 \n", + " Poland 1 \n", + "... ... \n", + "21C13-04 Switzerland 1 \n", + " United States 1 \n", + "21C1102 France 0 \n", + " Germany 3 \n", + "21C14-05 France 0 \n", + "\n", + " COUNTRY_COUNT_BY_VAX_LOT Before Deletion \n", + "VAX_LOT COUNTRY \n", + "J202100034 Austria 0 \n", + " Germany 0 \n", + " United States 0 \n", + "JJ-21C14-02 Belgium 3 \n", + " Poland 0 \n", + "... ... \n", + "21C13-04 Switzerland 0 \n", + " United States 0 \n", + "21C1102 France 2 \n", + " Germany 0 \n", + "21C14-05 France 10 \n", + "\n", + "[29310 rows x 2 columns]" + ] + }, + "execution_count": 11, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "countryCountsByBatchcode = filterByBatchcodes(getCountryCountsByBatchcodeTable(), batchCodeTable['Batch'].values)\n", "countryCountsByBatchcode" ] }, + { + "cell_type": "code", + "execution_count": 42, + "id": "0d755bc8", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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COUNTRY_COUNT_BY_VAX_LOT ClickedCOUNTRY_COUNT_BY_VAX_LOT Before Deletion
VAX_LOTCOUNTRY
EX8679Germany10991132
FC3095Germany8711099
FD7958Germany8461049
FD9234Germany759878
ET3045Germany704716
............
026C21AGermany01
000 106AGermany03
0000437Germany03
JO7BX03Germany02
6202Germany01
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2520 rows × 2 columns

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" + ], + "text/plain": [ + " COUNTRY_COUNT_BY_VAX_LOT Clicked \\\n", + "VAX_LOT COUNTRY \n", + "EX8679 Germany 1099 \n", + "FC3095 Germany 871 \n", + "FD7958 Germany 846 \n", + "FD9234 Germany 759 \n", + "ET3045 Germany 704 \n", + "... ... \n", + "026C21A Germany 0 \n", + "000 106A Germany 0 \n", + "0000437 Germany 0 \n", + "JO7BX03 Germany 0 \n", + "6202 Germany 0 \n", + "\n", + " COUNTRY_COUNT_BY_VAX_LOT Before Deletion \n", + "VAX_LOT COUNTRY \n", + "EX8679 Germany 1132 \n", + "FC3095 Germany 1099 \n", + "FD7958 Germany 1049 \n", + "FD9234 Germany 878 \n", + "ET3045 Germany 716 \n", + "... ... \n", + "026C21A Germany 1 \n", + "000 106A Germany 3 \n", + "0000437 Germany 3 \n", + "JO7BX03 Germany 2 \n", + "6202 Germany 1 \n", + "\n", + "[2520 rows x 2 columns]" + ] + }, + "execution_count": 42, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# df = countryCountsByBatchcode.loc[(slice(None), 'Germany'), :][['COUNTRY_COUNT_BY_VAX_LOT Clicked']].sort_values(by = 'COUNTRY_COUNT_BY_VAX_LOT Clicked', ascending = False)\n", + "df = countryCountsByBatchcode.loc[(slice(None), 'Germany'), :].sort_values(by = 'COUNTRY_COUNT_BY_VAX_LOT Clicked', ascending = False)\n", + "df" + ] + }, + { + "cell_type": "code", + "execution_count": 43, + "id": "c0ada157", + "metadata": {}, + "outputs": [], + "source": [ + "df.to_excel('tmp/tst.xlsx')" + ] + }, { "cell_type": "code", "execution_count": null,