diff --git a/src/HowBadIsMyBatch.nbconvert.ipynb b/src/HowBadIsMyBatch.nbconvert.ipynb new file mode 100644 index 00000000000..58195d460ae --- /dev/null +++ b/src/HowBadIsMyBatch.nbconvert.ipynb @@ -0,0 +1,1657 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "id": "9de5907f-18f5-4cb1-903e-26028ff1fa03", + "metadata": { + "execution": { + "iopub.execute_input": "2023-01-15T21:46:10.677136Z", + "iopub.status.busy": "2023-01-15T21:46:10.676811Z", + "iopub.status.idle": "2023-01-15T21:46:12.906899Z", + "shell.execute_reply": "2023-01-15T21:46:12.906289Z" + } + }, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "2023-01-15 21:46:11.039889: 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", + "2023-01-15 21:46:12.789155: 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", + "2023-01-15 21:46:12.790873: 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": "2023-01-15T21:46:12.910035Z", + "iopub.status.busy": "2023-01-15T21:46:12.909438Z", + "iopub.status.idle": "2023-01-15T21:46:12.914644Z", + "shell.execute_reply": "2023-01-15T21:46:12.914111Z" + } + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "15.01.2023, 21:46:12 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": "2023-01-15T21:46:12.917614Z", + "iopub.status.busy": "2023-01-15T21:46:12.917299Z", + "iopub.status.idle": "2023-01-15T21:46:13.202943Z", + "shell.execute_reply": "2023-01-15T21:46:13.202283Z" + } + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " lastUpdated: 2023-01-13 00:00:00\n", + "lastUpdatedDataSource: 2023-01-13 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": "2023-01-15T21:46:13.206252Z", + "iopub.status.busy": "2023-01-15T21:46:13.205699Z", + "iopub.status.idle": "2023-01-15T21:46:13.210050Z", + "shell.execute_reply": "2023-01-15T21:46:13.209514Z" + } + }, + "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": "2023-01-15T21:46:13.212481Z", + "iopub.status.busy": "2023-01-15T21:46:13.212278Z", + "iopub.status.idle": "2023-01-15T21:47:50.513385Z", + "shell.execute_reply": "2023-01-15T21:47:50.512158Z" + } + }, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "[WDM] - Downloading: 100%|██████████| 6.96M/6.96M [00:00<00:00, 215MB/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" + ] + }, + { + "data": { + "text/plain": [ + "'textInCaptchaImage: '" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/plain": [ + "'7d26e9'" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1/1 [==============================] - 0s 38ms/step\n" + ] + }, + { + "data": { + "text/plain": [ + "'textInCaptchaImage: '" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/plain": [ + "'ad8AE8'" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1/1 [==============================] - 0s 39ms/step\n" + ] + }, + { + "data": { + "text/plain": [ + "'textInCaptchaImage: '" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/plain": [ + "'470368'" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1/1 [==============================] - 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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
..........................................
25520962023-01-0600000NaNCOVID19MODERNANaN3Unknown Country0
25520972023-01-0600000NaNCOVID19PFIZER\\BIONTECHFC31431Unknown Country0
25520982023-01-0600000NaNCOVID19MODERNANaNUNKUnknown Country0
25520992023-01-0600000NaNCOVID19MODERNANaN2Unknown Country0
25521002023-01-0600001NaNCOVID19PFIZER\\BIONTECHGD68004Unknown Country1
\n", + "

1498524 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", + "2552096 2023-01-06 0 0 0 0 0 NaN \n", + "2552097 2023-01-06 0 0 0 0 0 NaN \n", + "2552098 2023-01-06 0 0 0 0 0 NaN \n", + "2552099 2023-01-06 0 0 0 0 0 NaN \n", + "2552100 2023-01-06 0 0 0 0 1 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", + "2552096 COVID19 MODERNA NaN 3 Unknown Country \n", + "2552097 COVID19 PFIZER\\BIONTECH FC3143 1 Unknown Country \n", + "2552098 COVID19 MODERNA NaN UNK Unknown Country \n", + "2552099 COVID19 MODERNA NaN 2 Unknown Country \n", + "2552100 COVID19 PFIZER\\BIONTECH GD6800 4 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", + "2552096 0 \n", + "2552097 0 \n", + "2552098 0 \n", + "2552099 0 \n", + "2552100 1 \n", + "\n", + "[1498524 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": "2023-01-15T21:48:17.805073Z", + "iopub.status.busy": "2023-01-15T21:48:17.804487Z", + "iopub.status.idle": "2023-01-15T21:48:18.061433Z", + "shell.execute_reply": "2023-01-15T21:48:18.060653Z" + } + }, + "outputs": [], + "source": [ + "updateBatchCodeTableHtmlFile(internationalVaersCovid19, batchCodeTableHtmlFile=\"../docs/batchCodeTable.html\")" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "id": "0915aa5a", + "metadata": { + "execution": { + "iopub.execute_input": "2023-01-15T21:48:18.065363Z", + "iopub.status.busy": "2023-01-15T21:48:18.064897Z", + "iopub.status.idle": "2023-01-15T21:48:34.052744Z", + "shell.execute_reply": "2023-01-15T21:48:34.051603Z" + } + }, + "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": 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