{ "cells": [ { "cell_type": "code", "execution_count": 1, "id": "9de5907f-18f5-4cb1-903e-26028ff1fa03", "metadata": { "execution": { "iopub.execute_input": "2023-01-26T17:35:06.918431Z", "iopub.status.busy": "2023-01-26T17:35:06.918006Z", "iopub.status.idle": "2023-01-26T17:35:08.905969Z", "shell.execute_reply": "2023-01-26T17:35:08.904728Z" } }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "2023-01-26 17:35:07.312254: 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 AVX512F FMA\n", "To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.\n", "2023-01-26 17:35:08.776143: 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 AVX512F FMA\n", "To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.\n", "2023-01-26 17:35:08.777381: I tensorflow/core/common_runtime/process_util.cc:146] Creating new thread pool with default inter op setting: 2. Tune using inter_op_parallelism_threads for best performance.\n" ] } ], "source": [ "import pandas as pd\n", "\n", "pd.set_option('display.max_rows', 100)\n", "pd.set_option('display.max_columns', None)\n", "\n", "import os\n", "from VAERSFileDownloader import updateVAERSFiles\n", "from datetime import datetime\n", "from DateProvider import DateProvider\n", "from InternationalVaersCovid19Provider import getInternationalVaersCovid19\n", "from BatchCodeTableHtmlUpdater import updateBatchCodeTableHtmlFile\n", "from BatchCodeTablePersister import createAndSaveBatchCodeTables" ] }, { "cell_type": "code", "execution_count": 2, "id": "d1e4fa9e", "metadata": { "execution": { "iopub.execute_input": "2023-01-26T17:35:08.909136Z", "iopub.status.busy": "2023-01-26T17:35:08.908775Z", "iopub.status.idle": "2023-01-26T17:35:08.914789Z", "shell.execute_reply": "2023-01-26T17:35:08.914173Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "26.01.2023, 17:35:08 Uhr\n" ] } ], "source": [ "print(datetime.now().strftime(\"%d.%m.%Y, %H:%M:%S Uhr\"))" ] }, { "cell_type": "code", "execution_count": 3, "id": "ffad1c04", "metadata": { "execution": { "iopub.execute_input": "2023-01-26T17:35:08.918199Z", "iopub.status.busy": "2023-01-26T17:35:08.917748Z", "iopub.status.idle": "2023-01-26T17:35:09.387800Z", "shell.execute_reply": "2023-01-26T17:35:09.387223Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " lastUpdated: 2023-01-20 00:00:00\n", "lastUpdatedDataSource: 2023-01-20 00:00:00\n", "needsUpdate: False\n" ] } ], "source": [ "dateProvider = DateProvider()\n", "print(' lastUpdated:', dateProvider.getLastUpdated())\n", "print('lastUpdatedDataSource:', dateProvider.getLastUpdatedDataSource())\n", "needsUpdate = dateProvider.needsUpdate()\n", "print('needsUpdate:', needsUpdate)" ] }, { "cell_type": "code", "execution_count": 4, "id": "194b7357", "metadata": { "execution": { "iopub.execute_input": "2023-01-26T17:35:09.390831Z", "iopub.status.busy": "2023-01-26T17:35:09.390454Z", "iopub.status.idle": "2023-01-26T17:35:09.393780Z", "shell.execute_reply": "2023-01-26T17:35:09.393275Z" } }, "outputs": [], "source": [ "years_from_2020_to_present = list(range(2020, datetime.now().year + 1))" ] }, { "cell_type": "code", "execution_count": 5, "id": "a793dff0", "metadata": { "execution": { "iopub.execute_input": "2023-01-26T17:35:09.396766Z", "iopub.status.busy": "2023-01-26T17:35:09.396417Z", "iopub.status.idle": "2023-01-26T17:38:22.248849Z", "shell.execute_reply": "2023-01-26T17:38:22.248161Z" } }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "[WDM] - Downloading: 100%|██████████| 6.96M/6.96M [00:00<00:00, 74.9MB/s]\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "loading model...\n", "Model: \"model\"\n", "_________________________________________________________________\n", " Layer (type) Output Shape Param # \n", "=================================================================\n", " image (InputLayer) [(None, 241, 62, 1)] 0 \n", " \n", " Conv1 (Conv2D) (None, 241, 62, 32) 320 \n", " \n", " pool1 (MaxPooling2D) (None, 120, 31, 32) 0 \n", " \n", " Conv2 (Conv2D) (None, 120, 31, 64) 18496 \n", " \n", " pool2 (MaxPooling2D) (None, 60, 15, 64) 0 \n", " \n", " reshape (Reshape) (None, 60, 960) 0 \n", " \n", " dense1 (Dense) (None, 60, 64) 61504 \n", " \n", " dropout (Dropout) (None, 60, 64) 0 \n", " \n", " bidirectional (Bidirectiona (None, 60, 256) 197632 \n", " l) \n", " \n", " bidirectional_1 (Bidirectio (None, 60, 128) 164352 \n", " nal) \n", " \n", " dense2 (Dense) (None, 60, 24) 3096 \n", " \n", "=================================================================\n", "Total params: 445,400\n", "Trainable params: 445,400\n", "Non-trainable params: 0\n", "_________________________________________________________________\n", "1/1 [==============================] - 1s 1s/step\n", "textInCaptchaImage: 88BB47\n", "1/1 [==============================] - 0s 38ms/step\n", "textInCaptchaImage: 822040\n", "1/1 [==============================] - 0s 39ms/step\n", "textInCaptchaImage: 30943E\n", "1/1 [==============================] - 0s 41ms/step\n", "textInCaptchaImage: aAE662\n", "1/1 [==============================] - 0s 36ms/step\n", "textInCaptchaImage: E49E6e\n" ] } ], "source": [ "updateVAERSFiles(\n", " years = years_from_2020_to_present,\n", " workingDirectory = os.getcwd())" ] }, { "cell_type": "code", "execution_count": 6, "id": "781ac80e", "metadata": { "execution": { "iopub.execute_input": "2023-01-26T17:38:22.252523Z", "iopub.status.busy": "2023-01-26T17:38:22.252151Z", "iopub.status.idle": "2023-01-26T17:38:50.043596Z", "shell.execute_reply": "2023-01-26T17:38:50.042882Z" } }, "outputs": [ { "data": { "text/html": [ "
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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
..........................................
25592172023-01-1300000NaNCOVID19MODERNA045G21A3Unknown Country0
25592172023-01-1300000NaNCOVID19PFIZER\\BIONTECHFD79581Unknown Country0
25592172023-01-1300000NaNCOVID19PFIZER\\BIONTECHFE84052Unknown Country0
25592212023-01-1300010NaNCOVID19MODERNANaN2Unknown Country0
25593042021-08-2100000NaNCOVID19MODERNANaN2Unknown Country0
\n", "

1501995 rows × 13 columns

\n", "
" ], "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", "2559217 2023-01-13 0 0 0 0 0 NaN \n", "2559217 2023-01-13 0 0 0 0 0 NaN \n", "2559217 2023-01-13 0 0 0 0 0 NaN \n", "2559221 2023-01-13 0 0 0 1 0 NaN \n", "2559304 2021-08-21 0 0 0 0 0 NaN \n", "\n", " VAX_TYPE VAX_MANU VAX_LOT VAX_DOSE_SERIES COUNTRY \\\n", "VAERS_ID \n", "902418 COVID19 PFIZER\\BIONTECH EH9899 1 United States \n", "902440 COVID19 PFIZER\\BIONTECH EH 9899 1 United States \n", "902446 COVID19 PFIZER\\BIONTECH EH9899 1 United States \n", "902464 COVID19 PFIZER\\BIONTECH EH9899 UNK United States \n", "902465 COVID19 PFIZER\\BIONTECH EH9899 1 United States \n", "... ... ... ... ... ... \n", "2559217 COVID19 MODERNA 045G21A 3 Unknown Country \n", "2559217 COVID19 PFIZER\\BIONTECH FD7958 1 Unknown Country \n", "2559217 COVID19 PFIZER\\BIONTECH FE8405 2 Unknown Country \n", "2559221 COVID19 MODERNA NaN 2 Unknown Country \n", "2559304 COVID19 MODERNA NaN 2 Unknown Country \n", "\n", " SEVERE \n", "VAERS_ID \n", "902418 0 \n", "902440 0 \n", "902446 0 \n", "902464 0 \n", "902465 0 \n", "... ... \n", "2559217 0 \n", "2559217 0 \n", "2559217 0 \n", "2559221 0 \n", "2559304 0 \n", "\n", "[1501995 rows x 13 columns]" ] }, "execution_count": 6, "metadata": {}, "output_type": "execute_result" } ], "source": [ "internationalVaersCovid19 = getInternationalVaersCovid19(years = years_from_2020_to_present)\n", "internationalVaersCovid19" ] }, { "cell_type": "code", "execution_count": 7, "id": "8d6507ca", "metadata": { "execution": { "iopub.execute_input": "2023-01-26T17:38:50.046577Z", "iopub.status.busy": "2023-01-26T17:38:50.046195Z", "iopub.status.idle": "2023-01-26T17:38:50.631913Z", "shell.execute_reply": "2023-01-26T17:38:50.631226Z" } }, "outputs": [], "source": [ "updateBatchCodeTableHtmlFile(internationalVaersCovid19, batchCodeTableHtmlFile=\"../docs/batchCodeTable.html\")" ] }, { "cell_type": "code", "execution_count": 8, "id": "0915aa5a", "metadata": { "execution": { "iopub.execute_input": "2023-01-26T17:38:50.635284Z", "iopub.status.busy": "2023-01-26T17:38:50.634927Z", "iopub.status.idle": "2023-01-26T17:39:07.884083Z", "shell.execute_reply": "2023-01-26T17:39:07.883344Z" } }, "outputs": [ { "data": { "text/plain": [ "'Afghanistan'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Albania'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Algeria'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Andorra'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Argentina'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Australia'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Azerbaijan'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Bahamas'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Bahrain'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Bangladesh'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Barbados'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Bermuda'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Bolivia, Plurinational State of'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Bosnia and Herzegovina'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Brazil'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Brunei Darussalam'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Canada'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Cayman Islands'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Chile'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'China'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Colombia'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Congo, The Democratic Republic of the'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Cook Islands'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Costa Rica'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "\"Côte d'Ivoire\"" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Dominican Republic'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Ecuador'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Egypt'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'El Salvador'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'French Polynesia'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Georgia'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Germany'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Ghana'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Guatemala'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Honduras'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Hong Kong'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'India'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Indonesia'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Iran, Islamic Republic of'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Iraq'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Israel'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Jamaica'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Japan'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Jersey'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Jordan'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Kazakhstan'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Kenya'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "\"Korea, Democratic People's Republic of\"" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Korea, Republic of'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Kuwait'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Kyrgyzstan'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "\"Lao People's Democratic Republic\"" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Lebanon'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Lesotho'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Liberia'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Macao'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Malaysia'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Maldives'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Mauritius'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Mexico'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Moldova, Republic of'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Mongolia'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Montenegro'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Montserrat'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Morocco'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Namibia'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Nepal'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'New Caledonia'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'New Zealand'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Nicaragua'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Nigeria'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Niue'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'North Macedonia'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Norway'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Oman'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Pakistan'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Palestine, State of'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Panama'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Paraguay'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Peru'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Philippines'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Qatar'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Russian Federation'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Réunion'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Samoa'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Saudi Arabia'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Senegal'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Serbia'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Singapore'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'South Africa'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Sri Lanka'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Switzerland'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Syrian Arab Republic'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Taiwan, Province of China'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Tanzania, United Republic of'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Thailand'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Tokelau'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Trinidad and Tobago'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Tunisia'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Turkey'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Uganda'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Ukraine'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'United Arab Emirates'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'United States'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Unknown Country'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Uruguay'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Venezuela, Bolivarian Republic of'" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "'Viet 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