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0827183 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 | {
"cells": [
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [],
"source": [
"import os,re,zipfile\n",
"import pandas as pd"
]
},
{
"cell_type": "code",
"execution_count": 46,
"metadata": {},
"outputs": [],
"source": [
"file1=\"/home/itai/Downloads/Spec - Manually file prepared by Bioforum PM (1).xlsx\"\n",
"file2=\"/home/itai/Downloads/ALS - Export of metadata from Rave.xlsx\"\n",
"file3=\"/home/itai/Downloads/Database Validation Tracker_General Checks_v10 (1).xlsm\""
]
},
{
"cell_type": "code",
"execution_count": 47,
"metadata": {},
"outputs": [],
"source": [
"def fetch_sheet_names(path):\n",
" sheets=[]\n",
" with zipfile.ZipFile(path,'r') as zip_ref:\n",
" xml=zip_ref.read(\"xl/workbook.xml\").decode(\"utf-8\")\n",
" for s_tag in re.findall(\"<sheet [^>]*\",xml) : sheets.append(re.search('name=\"[^\"]*',s_tag).group(0)[6:])\n",
"\n",
" return sheets"
]
},
{
"cell_type": "code",
"execution_count": 48,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"['CRFDraft',\n",
" 'Forms',\n",
" 'Fields',\n",
" 'Folders',\n",
" 'DataDictionaries',\n",
" 'DataDictionaryEntries',\n",
" 'UnitDictionaries',\n",
" 'UnitDictionaryEntries',\n",
" 'Matrices',\n",
" 'Matrix1#1YEAR',\n",
" 'Matrix2#30DAY',\n",
" 'Matrix3#90DAY',\n",
" 'Matrix4#90DAYREPEAT',\n",
" 'Matrix5#BASELINEDOV',\n",
" 'Matrix6#COMPLETE',\n",
" 'Matrix7#COMPLETEUS',\n",
" 'Matrix8#DISCHARGE',\n",
" 'Matrix9#DMREGISTRY',\n",
" 'Matrix10#ENROLLED',\n",
" 'Matrix11#INDEX',\n",
" 'Matrix12#LBCHEMISTRY',\n",
" 'Matrix13#POSTOPICU',\n",
" 'Matrix14#PRIMARY',\n",
" 'Matrix15#REGISTRY',\n",
" 'Matrix16#REGISTRYFU',\n",
" 'Matrix17#UNIQUE',\n",
" 'Matrix18#UNS',\n",
" 'Checks',\n",
" 'CheckSteps',\n",
" 'CheckActions',\n",
" 'Derivations',\n",
" 'DerivationSteps',\n",
" 'LabVariableMappings',\n",
" 'CustomFunctions',\n",
" 'EmailAlerts',\n",
" 'CoderConfiguration',\n",
" 'CoderSupplementalTerms',\n",
" 'CoderComponentTerms']"
]
},
"execution_count": 48,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"fetch_sheet_names(file2)"
]
},
{
"cell_type": "code",
"execution_count": 25,
"metadata": {},
"outputs": [],
"source": [
"def process_excel_files(files):\n",
" temp_list=[(file,fetch_sheet_names(file)) for file in files]\n",
" df = [pd.read_excel(tup[0],sheet) for tup in temp_list for sheet in tup[1]]\n",
" return df\n",
"\n",
"def fetch_sheet_names(path):\n",
" sheets=[]\n",
" with zipfile.ZipFile(path,'r') as zip_ref:\n",
" xml=zip_ref.read(\"xl/workbook.xml\").decode(\"utf-8\")\n",
" for s_tag in re.findall(\"<sheet [^>]*\",xml) : sheets.append(re.search('name=\"[^\"]*',s_tag).group(0)[6:])\n",
"\n",
" return sheets"
]
},
{
"cell_type": "code",
"execution_count": 44,
"metadata": {},
"outputs": [
{
"ename": "BadZipFile",
"evalue": "File is not a zip file",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mBadZipFile\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[44], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43mprocess_excel_files\u001b[49m\u001b[43m(\u001b[49m\u001b[43m[\u001b[49m\u001b[43mfile2\u001b[49m\u001b[43m]\u001b[49m\u001b[43m)\u001b[49m\n",
"Cell \u001b[0;32mIn[25], line 2\u001b[0m, in \u001b[0;36mprocess_excel_files\u001b[0;34m(files)\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mprocess_excel_files\u001b[39m(files):\n\u001b[0;32m----> 2\u001b[0m temp_list\u001b[38;5;241m=\u001b[39m\u001b[43m[\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfile\u001b[49m\u001b[43m,\u001b[49m\u001b[43mfetch_sheet_names\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfile\u001b[49m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mfor\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43mfile\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;129;43;01min\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43mfiles\u001b[49m\u001b[43m]\u001b[49m\n\u001b[1;32m 3\u001b[0m df \u001b[38;5;241m=\u001b[39m [pd\u001b[38;5;241m.\u001b[39mread_excel(tup[\u001b[38;5;241m0\u001b[39m],sheet) \u001b[38;5;28;01mfor\u001b[39;00m tup \u001b[38;5;129;01min\u001b[39;00m temp_list \u001b[38;5;28;01mfor\u001b[39;00m sheet \u001b[38;5;129;01min\u001b[39;00m tup[\u001b[38;5;241m1\u001b[39m]]\n\u001b[1;32m 4\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m df\n",
"Cell \u001b[0;32mIn[25], line 2\u001b[0m, in \u001b[0;36m<listcomp>\u001b[0;34m(.0)\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mprocess_excel_files\u001b[39m(files):\n\u001b[0;32m----> 2\u001b[0m temp_list\u001b[38;5;241m=\u001b[39m[(file,\u001b[43mfetch_sheet_names\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfile\u001b[49m\u001b[43m)\u001b[49m) \u001b[38;5;28;01mfor\u001b[39;00m file \u001b[38;5;129;01min\u001b[39;00m files]\n\u001b[1;32m 3\u001b[0m df \u001b[38;5;241m=\u001b[39m [pd\u001b[38;5;241m.\u001b[39mread_excel(tup[\u001b[38;5;241m0\u001b[39m],sheet) \u001b[38;5;28;01mfor\u001b[39;00m tup \u001b[38;5;129;01min\u001b[39;00m temp_list \u001b[38;5;28;01mfor\u001b[39;00m sheet \u001b[38;5;129;01min\u001b[39;00m tup[\u001b[38;5;241m1\u001b[39m]]\n\u001b[1;32m 4\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m df\n",
"Cell \u001b[0;32mIn[25], line 8\u001b[0m, in \u001b[0;36mfetch_sheet_names\u001b[0;34m(path)\u001b[0m\n\u001b[1;32m 6\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mfetch_sheet_names\u001b[39m(path):\n\u001b[1;32m 7\u001b[0m sheets\u001b[38;5;241m=\u001b[39m[]\n\u001b[0;32m----> 8\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[43mzipfile\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mZipFile\u001b[49m\u001b[43m(\u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mr\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mas\u001b[39;00m zip_ref:\n\u001b[1;32m 9\u001b[0m xml\u001b[38;5;241m=\u001b[39mzip_ref\u001b[38;5;241m.\u001b[39mread(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mxl/workbook.xml\u001b[39m\u001b[38;5;124m\"\u001b[39m)\u001b[38;5;241m.\u001b[39mdecode(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mutf-8\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 10\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m s_tag \u001b[38;5;129;01min\u001b[39;00m re\u001b[38;5;241m.\u001b[39mfindall(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m<sheet [^>]*\u001b[39m\u001b[38;5;124m\"\u001b[39m,xml) : sheets\u001b[38;5;241m.\u001b[39mappend(re\u001b[38;5;241m.\u001b[39msearch(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mname=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m[^\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m]*\u001b[39m\u001b[38;5;124m'\u001b[39m,s_tag)\u001b[38;5;241m.\u001b[39mgroup(\u001b[38;5;241m0\u001b[39m)[\u001b[38;5;241m6\u001b[39m:])\n",
"File \u001b[0;32m~/.pyenv/versions/3.11.7/lib/python3.11/zipfile.py:1302\u001b[0m, in \u001b[0;36mZipFile.__init__\u001b[0;34m(self, file, mode, compression, allowZip64, compresslevel, strict_timestamps, metadata_encoding)\u001b[0m\n\u001b[1;32m 1300\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 1301\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m mode \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mr\u001b[39m\u001b[38;5;124m'\u001b[39m:\n\u001b[0;32m-> 1302\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_RealGetContents\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1303\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m mode \u001b[38;5;129;01min\u001b[39;00m (\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mw\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mx\u001b[39m\u001b[38;5;124m'\u001b[39m):\n\u001b[1;32m 1304\u001b[0m \u001b[38;5;66;03m# set the modified flag so central directory gets written\u001b[39;00m\n\u001b[1;32m 1305\u001b[0m \u001b[38;5;66;03m# even if no files are added to the archive\u001b[39;00m\n\u001b[1;32m 1306\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_didModify \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mTrue\u001b[39;00m\n",
"File \u001b[0;32m~/.pyenv/versions/3.11.7/lib/python3.11/zipfile.py:1369\u001b[0m, in \u001b[0;36mZipFile._RealGetContents\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 1367\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m BadZipFile(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mFile is not a zip file\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 1368\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m endrec:\n\u001b[0;32m-> 1369\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m BadZipFile(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mFile is not a zip file\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 1370\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdebug \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m1\u001b[39m:\n\u001b[1;32m 1371\u001b[0m \u001b[38;5;28mprint\u001b[39m(endrec)\n",
"\u001b[0;31mBadZipFile\u001b[0m: File is not a zip file"
]
}
],
"source": [
"process_excel_files([file2])"
]
},
{
"cell_type": "code",
"execution_count": 45,
"metadata": {},
"outputs": [
{
"ename": "BadZipFile",
"evalue": "File is not a zip file",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mBadZipFile\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[45], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43mfetch_sheet_names\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfile2\u001b[49m\u001b[43m)\u001b[49m\n",
"Cell \u001b[0;32mIn[25], line 8\u001b[0m, in \u001b[0;36mfetch_sheet_names\u001b[0;34m(path)\u001b[0m\n\u001b[1;32m 6\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mfetch_sheet_names\u001b[39m(path):\n\u001b[1;32m 7\u001b[0m sheets\u001b[38;5;241m=\u001b[39m[]\n\u001b[0;32m----> 8\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[43mzipfile\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mZipFile\u001b[49m\u001b[43m(\u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mr\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mas\u001b[39;00m zip_ref:\n\u001b[1;32m 9\u001b[0m xml\u001b[38;5;241m=\u001b[39mzip_ref\u001b[38;5;241m.\u001b[39mread(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mxl/workbook.xml\u001b[39m\u001b[38;5;124m\"\u001b[39m)\u001b[38;5;241m.\u001b[39mdecode(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mutf-8\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 10\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m s_tag \u001b[38;5;129;01min\u001b[39;00m re\u001b[38;5;241m.\u001b[39mfindall(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m<sheet [^>]*\u001b[39m\u001b[38;5;124m\"\u001b[39m,xml) : sheets\u001b[38;5;241m.\u001b[39mappend(re\u001b[38;5;241m.\u001b[39msearch(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mname=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m[^\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m]*\u001b[39m\u001b[38;5;124m'\u001b[39m,s_tag)\u001b[38;5;241m.\u001b[39mgroup(\u001b[38;5;241m0\u001b[39m)[\u001b[38;5;241m6\u001b[39m:])\n",
"File \u001b[0;32m~/.pyenv/versions/3.11.7/lib/python3.11/zipfile.py:1302\u001b[0m, in \u001b[0;36mZipFile.__init__\u001b[0;34m(self, file, mode, compression, allowZip64, compresslevel, strict_timestamps, metadata_encoding)\u001b[0m\n\u001b[1;32m 1300\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 1301\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m mode \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mr\u001b[39m\u001b[38;5;124m'\u001b[39m:\n\u001b[0;32m-> 1302\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_RealGetContents\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1303\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m mode \u001b[38;5;129;01min\u001b[39;00m (\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mw\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mx\u001b[39m\u001b[38;5;124m'\u001b[39m):\n\u001b[1;32m 1304\u001b[0m \u001b[38;5;66;03m# set the modified flag so central directory gets written\u001b[39;00m\n\u001b[1;32m 1305\u001b[0m \u001b[38;5;66;03m# even if no files are added to the archive\u001b[39;00m\n\u001b[1;32m 1306\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_didModify \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mTrue\u001b[39;00m\n",
"File \u001b[0;32m~/.pyenv/versions/3.11.7/lib/python3.11/zipfile.py:1369\u001b[0m, in \u001b[0;36mZipFile._RealGetContents\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 1367\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m BadZipFile(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mFile is not a zip file\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 1368\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m endrec:\n\u001b[0;32m-> 1369\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m BadZipFile(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mFile is not a zip file\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 1370\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdebug \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m1\u001b[39m:\n\u001b[1;32m 1371\u001b[0m \u001b[38;5;28mprint\u001b[39m(endrec)\n",
"\u001b[0;31mBadZipFile\u001b[0m: File is not a zip file"
]
}
],
"source": [
"fetch_sheet_names(file2)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "gradio",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.7"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
|