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rokroskar/removing_liquid_names.ipynb

Created November 26, 2015 13:56
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removing_liquid_names.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 136,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"import xml.etree.ElementTree as ET"
]
},
{
"cell_type": "code",
"execution_count": 137,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"with open('/Users/rok/Downloads/liquidnames.txt') as f: \n",
" liquid_names = {liquid_name.rstrip() for liquid_name in f.readlines()}"
]
},
{
"cell_type": "code",
"execution_count": 138,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"tree = ET.parse('/Users/rok/Downloads/LiquidDescription.xml')"
]
},
{
"cell_type": "code",
"execution_count": 139,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"root = tree.getroot()"
]
},
{
"cell_type": "code",
"execution_count": 140,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"previous_length = 0\n",
"current_length = len(root)"
]
},
{
"cell_type": "code",
"execution_count": 142,
"metadata": {
"collapsed": false,
"scrolled": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"<Element 'liquid' at 0x1074148d0>\n",
"A-beta diluted sample 1/20\n",
"IBL Serum 1mm\n",
"Predilution Amyloid-beta\n",
"\n",
" \n",
"<Element 'liquid' at 0x1073f27d0>\n",
"B12 diluted samples\n",
"IBL Serum 1mm\n",
"Predilution Active B12\n",
"\n",
" \n",
"<Element 'liquid' at 0x1072e1b90>\n",
"diluted samples_Test\n",
"IBL Water 1mm_mix@asp\n",
"Predilution_Test\n",
"\n",
" \n",
"<Element 'liquid' at 0x1072e1290>\n",
"Dilution 1 Cystatin C CAL B\n",
"IBL Serum 1mm\n",
"Predilution Cystatin C\n",
"\n",
" \n",
"<Element 'liquid' at 0x1071fe550>\n",
"Dilution 1 Cystatin C CAL D\n",
"IBL Serum 1mm\n",
"Predilution Cystatin C\n",
"\n",
" \n",
"<Element 'liquid' at 0x1071d2950>\n",
"Dilution 1 Cystatin C CAL F\n",
"IBL Serum 1mm\n",
"Predilution Cystatin C\n",
"\n",
" \n",
"<Element 'liquid' at 0x1071d2510>\n",
"Dilution 1 Cystatin C CONTROL High End\n",
"IBL Serum 1mm\n",
"Predilution Cystatin C\n",
"\n",
" \n",
"<Element 'liquid' at 0x1071d2110>\n",
"Dilution 1 Cystatin C CONTROL Low End\n",
"IBL Serum 1mm\n",
"Predilution Cystatin C\n",
"\n",
" \n",
"<Element 'liquid' at 0x1071c7f90>\n",
"Dilution 2 Cystatin C Cal A\n",
"IBL Serum 1mm\n",
"Predilution Cystatin C\n",
"\n",
" \n",
"<Element 'liquid' at 0x1071c7d90>\n",
"Dilution 2 Cystatin C Cal C\n",
"IBL Serum 1mm\n",
"Predilution Cystatin C\n",
"\n",
" \n",
"<Element 'liquid' at 0x1071c7210>\n",
"Dilution 2 Cystatin C Cal E\n",
"IBL Serum 1mm\n",
"Predilution Cystatin C\n",
"\n",
" \n",
"<Element 'liquid' at 0x1071bc750>\n",
"Dilution 2 Cystatin C Control High\n",
"IBL Serum 1mm\n",
"Predilution Cystatin C\n",
"\n",
" \n",
"<Element 'liquid' at 0x1071bcb90>\n",
"Dilution 2 Cystatin C Control Low\n",
"IBL Serum 1mm\n",
"Predilution Cystatin C\n",
"\n",
" \n",
"<Element 'liquid' at 0x1071a8990>\n",
"Dilution 2 Cystatin C Samples\n",
"IBL Serum 1mm\n",
"Predilution Cystatin C\n",
"\n",
" \n",
"<Element 'liquid' at 0x1071a8910>\n",
"DOP CAL A diluted\n",
"IBL Water 1mm\n",
"Predilution Dopamin\n",
"\n",
" \n",
"<Element 'liquid' at 0x107237210>\n",
"DOP CAL C diluted\n",
"IBL Water 1mm\n",
"Predilution Dopamin\n",
"\n",
" \n",
"<Element 'liquid' at 0x10724c190>\n",
"DOP CAL E diluted\n",
"IBL Water 1mm\n",
"Predilution Dopamin\n",
"\n",
" \n",
"<Element 'liquid' at 0x1071351d0>\n",
"DOP CONTROL 1 diluted\n",
"IBL Water 1mm\n",
"Predilution Dopamin\n",
"\n",
" \n",
"<Element 'liquid' at 0x107135990>\n",
"DOP CONTROL 2 diluted\n",
"IBL Water 1mm\n",
"Predilution Dopamin\n",
"\n",
" \n",
"<Element 'liquid' at 0x107135e10>\n",
"DOP Sample diluted\n",
"IBL Water 1mm\n",
"Predilution Dopamin\n",
"\n",
" \n",
"<Element 'liquid' at 0x107326d90>\n",
"GLUT CAL A\n",
"IBL Serum 1mm\n",
"Predilution Glutamate\n",
"\n",
" \n",
"<Element 'liquid' at 0x1073301d0>\n",
"GLUT CAL C\n",
"IBL Serum 1mm\n",
"Predilution Glutamate\n",
"\n",
" \n",
"<Element 'liquid' at 0x107330650>\n",
"GLUT CAL E\n",
"IBL Serum 1mm\n",
"Predilution Glutamate\n",
"\n",
" \n",
"<Element 'liquid' at 0x1073462d0>\n",
"GLUT CONTROL 1\n",
"IBL Serum 1mm\n",
"Predilution Glutamate\n",
"\n",
" \n",
"<Element 'liquid' at 0x107346690>\n",
"GLUT CONTROL 2\n",
"IBL Serum 1mm\n",
"Predilution Glutamate\n",
"\n",
" \n",
"<Element 'liquid' at 0x107346ad0>\n",
"GLUT SAMPLE\n",
"IBL Serum 1mm\n",
"Predilution Glutamate\n",
"\n",
" \n",
"<Element 'liquid' at 0x10737b210>\n",
"hTau total dil samples ditis\n",
"IBL Water 1mm_mix@asp\n",
"Predilution hTau total_ditis_v1\n",
"\n",
" \n",
"<Element 'liquid' at 0x10737b910>\n",
"hTau total diluted samples\n",
"IBL Water 1mm_mix@asp\n",
"Predilution hTau total_v2\n",
"\n",
" \n",
"<Element 'liquid' at 0x107390510>\n",
"hTau total diluted samples_Test4\n",
"IBL Water 1mm_mix@asp\n",
"Predilution hTau total_Test4\n",
"\n",
" \n",
"<Element 'liquid' at 0x106f93ad0>\n",
"NAD diluted samples\n",
"IBL Water 1mm\n",
"Predilution Noradrenalin\n",
"\n",
" \n",
"<Element 'liquid' at 0x1072f8050>\n",
"Predil LC verify\n",
"IBL Water 1mm_tiptouch\n",
"predil_LC verify\n",
"\n",
" \n",
"<Element 'liquid' at 0x1072f8510>\n",
"Predil Precise ditis\n",
"IBL Water 3mm_tiptouch\n",
"Predil Precise ditis\n",
"\n",
" \n",
"<Element 'liquid' at 0x1072f8a90>\n",
"Predilution pTau\n",
"IBL Water 1mm_mix@asp\n",
"Predilution pTau_v1\n",
"\n",
" \n",
"<Element 'liquid' at 0x1071ba0d0>\n",
"Test_Mix_Dilution\n",
"IBL Serum 1mm_mix@asp\n",
"Mix Test\n",
"\n",
" \n",
"<Element 'liquid' at 0x1073f2390>\n",
"Borrelia diluted samples\n",
"IBL Serum 2mm\n",
"Predilution Borrelia IgG\n",
"\n",
" \n",
"<Element 'liquid' at 0x1072e17d0>\n",
"Dilution 1 Cystatin C CAL A\n",
"IBL Serum 1mm\n",
"Predilution Cystatin C\n",
"\n",
" \n",
"<Element 'liquid' at 0x1071fe110>\n",
"Dilution 1 Cystatin C CAL E\n",
"IBL Serum 1mm\n",
"Predilution Cystatin C\n",
"\n",
" \n",
"<Element 'liquid' at 0x1072b5690>\n",
"Dilution 1 Cystatin C CONTROL Low\n",
"IBL Serum 1mm\n",
"Predilution Cystatin C\n",
"\n",
" \n",
"<Element 'liquid' at 0x1071c7690>\n",
"Dilution 2 Cystatin C Cal B\n",
"IBL Serum 1mm\n",
"Predilution Cystatin C\n",
"\n",
" \n",
"<Element 'liquid' at 0x1071bc210>\n",
"Dilution 2 Cystatin C Cal F\n",
"IBL Serum 1mm\n",
"Predilution Cystatin C\n",
"\n",
" \n",
"<Element 'liquid' at 0x1071bc410>\n",
"Dilution 2 Cystatin C Control Low End\n",
"IBL Serum 1mm\n",
"Predilution Cystatin C\n",
"\n",
" \n",
"<Element 'liquid' at 0x107237290>\n",
"DOP CAL B diluted\n",
"IBL Water 1mm\n",
"Predilution Dopamin\n",
"\n",
" \n",
"<Element 'liquid' at 0x107135310>\n",
"DOP CAL F diluted\n",
"IBL Water 1mm\n",
"Predilution Dopamin\n",
"\n",
" \n",
"<Element 'liquid' at 0x107135bd0>\n",
"DOP CONTROL 2 End diluted\n",
"IBL Water 1mm\n",
"Predilution Dopamin\n",
"\n",
" \n",
"<Element 'liquid' at 0x107326fd0>\n",
"GLUT CAL B\n",
"IBL Serum 1mm\n",
"Predilution Glutamate\n",
"\n",
" \n",
"<Element 'liquid' at 0x1073308d0>\n",
"GLUT CAL F\n",
"IBL Serum 1mm\n",
"Predilution Glutamate\n",
"\n",
" \n",
"<Element 'liquid' at 0x1073468d0>\n",
"GLUT CONTROL 2 end\n",
"IBL Serum 1mm\n",
"Predilution Glutamate\n",
"\n",
" \n",
"<Element 'liquid' at 0x10737b410>\n",
"hTau total dil samples ditis2\n",
"IBL Water 1mm_mix@asp\n",
"Predilution hTau total_ditis_v2\n",
"\n",
" \n",
"<Element 'liquid' at 0x1071fe410>\n",
"Dilution 1 Cystatin C CAL C\n",
"IBL Serum 1mm\n",
"Predilution Cystatin C\n",
"\n",
" \n",
"<Element 'liquid' at 0x1071c7a90>\n",
"Dilution 1 Cystatin C Sample\n",
"IBL Serum 1mm\n",
"Predilution Cystatin C\n",
"\n",
" \n",
"<Element 'liquid' at 0x1071bc810>\n",
"Dilution 2 Cystatin C Control High End\n",
"IBL Serum 1mm\n",
"Predilution Cystatin C\n",
"\n",
" \n",
"<Element 'liquid' at 0x107237b10>\n",
"DOP CAL D diluted\n",
"IBL Water 1mm\n",
"Predilution Dopamin\n",
"\n",
" \n",
"<Element 'liquid' at 0x107330410>\n",
"GLUT CAL D\n",
"IBL Serum 1mm\n",
"Predilution Glutamate\n",
"\n",
" \n",
"<Element 'liquid' at 0x10737be10>\n",
"hTau total diluted samples_Test3\n",
"IBL Water 1mm_mix@asp\n",
"Predilution hTau total_Test3\n",
"\n",
" \n",
"<Element 'liquid' at 0x1071d2a10>\n",
"Dilution 1 Cystatin C CONTROL High\n",
"IBL Serum 1mm\n",
"Predilution Cystatin C\n",
"\n",
" \n",
"<Element 'liquid' at 0x107135750>\n",
"DOP CONTROL 1 End diluted\n",
"IBL Water 1mm\n",
"Predilution Dopamin\n",
"\n",
" \n",
"<Element 'liquid' at 0x107346490>\n",
"GLUT CONTROL 1 end\n",
"IBL Serum 1mm\n",
"Predilution Glutamate\n",
"\n",
" \n",
"<Element 'liquid' at 0x1071c7890>\n",
"Dilution 2 Cystatin C Cal D\n",
"IBL Serum 1mm\n",
"Predilution Cystatin C\n",
"\n",
" \n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/Users/rok/miniconda/lib/python2.7/site-packages/ipykernel/__main__.py:5: DeprecationWarning: This method will be removed in future versions. Use 'list(elem)' or iteration over elem instead.\n"
]
}
],
"source": [
"while current_length != previous_length:\n",
" for x in root: \n",
" if x.find('name').text in liquid_names:\n",
" print x\n",
" for child in x.getchildren() : \n",
" print child.text\n",
" root.remove(x)\n",
" previous_length = current_length\n",
" current_length = len(root)"
]
},
{
"cell_type": "code",
"execution_count": 143,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"False"
]
},
"execution_count": 143,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"any([t.find('name') in liquid_names for t in root.getiterator()])"
]
},
{
"cell_type": "code",
"execution_count": 144,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"328"
]
},
"execution_count": 144,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"len(root)"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 2",
"language": "python",
"name": "python2"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 2
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython2",
"version": "2.7.10"
}
},
"nbformat": 4,
"nbformat_minor": 0
}
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