使用ElementTree难以解析XML文件的一部分 [英] Difficulty parsing a section of XML file with ElementTree
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问题描述
我已经编写了以下代码来解析此 XML文件。您可以看到它仍然有些混乱，但是我在大多数情况下都处于正确的轨道上。
I have written the code below to parse this XML file. You can see it's still a bit messy, but that I'm on the right track for most of it.
您可以看到我被困的一部分是目标部分（我在本节中尝试过的代码在这里用三引号引起来，但是您可以看到该节不起作用。）
You can see one part that I'm stuck on is the 'targets' section (I've left the code that I've tried for this section in here with triple quotes, but you can see that section doesn't work).
我想知道是否有人可以帮助我告诉我我哪里出问题了/如何解析目标部分？如果您在此处中查看XML文件的HTML，我基本上只是想提取信息在目标部分中，针对每个基因/条目（或者，如果可能的话，XML文件的目标部分中似乎有更多信息，所以我可以选择其中一个）？
I'm wondering if someone could help show me where I'm going wrong/how to parse the targets section? If you look at the HTML of the XML file here, I basically just want to extract the information in the targets section, for each gene/entry (or if it was possible, there seems to be more info in the targets section of the XML file, so if I could take that either)?
谢谢
import requests
import xml.etree.ElementTree as ET
import urllib2
#get the XML file
#response = requests.get('https://www.drugbank.ca/drugs/DB01048.xml')
#with open('output.txt', 'w') as input:
# input.write(response.content)
tree = ET.parse('output.txt')
root = tree.getroot()
val = lambda x: "{http://www.drugbank.ca}" + str(x)
key_list = ['drugbank-id','name','description','cas-number','unii','average-mass','monoisotopic-mass','state','indication','pharmacodynamics','mechanism-of-action','toxicity','metabolism','absorption','half-life','protein-binding','route-of-elimination','volume-of-distribution','fda-label','msds']
key_dict = {}
for i in key_list:
for child in root.getchildren():
key_dict[i] = child.find(val(i)).text.encode('utf-8')
#print key_dict
def method1(str_name,list_name):
if subnode.tag == str_name:
list_name = []
for i in subnode:
list_name.append(i.text)
return list_name
def method2(list1_name,list2_name,list3_name,list4_name):
if subnode.tag == list1_name:
for i in subnode:
if i.tag == list2_name:
for a in i:
if a.tag == list3_name:
for u in a:
if u.tag == list4_name:
yield u.text
def method3(list1_name, list2_name):
list_of_tuples = []
if subnode.tag == list1_name:
for i in subnode:
if i.tag == list2_name:
temp_list = []
for a in i:
temp_list.append(a.text)
list_of_tuples.append(temp_list)
return list_of_tuples
alternative_parents = []
substituents = []
list_to_run_thru = ['description','direct-parent','kingdom','superclass','class','subclass']
ap_sub = lambda x:'{http://www.drugbank.ca}'+ x
for node in root:
for subnode in node:
print method1('{http://www.drugbank.ca}groups','group_list')
print method1('{http://www.drugbank.ca}synonyms','synonym_list')
print method1('{http://www.drugbank.ca}patent','patent_list')
print method2('{http://www.drugbank.ca}general-references','{http://www.drugbank.ca}articles','{http://www.drugbank.ca}article','{http://www.drugbank.ca}pubmed-id')#
if subnode.tag == '{http://www.drugbank.ca}classification':
for each_item in list_to_run_thru:
for i in subnode:
if i.tag == ap_sub(each_item):
print i.text
if i.tag == '{http://www.drugbank.ca}alternative-parent':
alternative_parents.append(i.text)
if i.tag == '{http://www.drugbank.ca}substituent':
substituents.append(i.text)
print method3('{http://www.drugbank.ca}salts','{http://www.drugbank.ca}salt')
print method3('{http://www.drugbank.ca}products','{http://www.drugbank.ca}product')
print method3('{http://www.drugbank.ca}mixtures','{http://www.drugbank.ca}mixture')
print method3('{http://www.drugbank.ca}packagers','{http://www.drugbank.ca}packager')
print method3('{http://www.drugbank.ca}categories','{http://www.drugbank.ca}category')
print method3('{http://www.drugbank.ca}dosages','{http://www.drugbank.ca}dosage')
print method3('{http://www.drugbank.ca}atc-codes','{http://www.drugbank.ca}atc-code')
print method3('{http://www.drugbank.ca}ahfs-codes','{http://www.drugbank.ca}ahfs-code')
print method3('{http://www.drugbank.ca}pdb-entries','{http://www.drugbank.ca}pdb-entry')
print method3('{http://www.drugbank.ca}food-interactions','{http://www.drugbank.ca}food-interaction')
print method3('{http://www.drugbank.ca}drug-interactions','{http://www.drugbank.ca}drug-interaction')
print method3('{http://www.drugbank.ca}calculated-properties','{http://www.drugbank.ca}property')
print method3('{http://www.drugbank.ca}external-identifiers','{http://www.drugbank.ca}external-identifier')
print method3('{http://www.drugbank.ca}external-links','{http://www.drugbank.ca}external-link')
print method3('{http://www.drugbank.ca}snp-adverse-drug-reactions','{http://www.drugbank.ca}reaction')
print substituents
print alternative_parents
'''
if subnode.tag == '{http://www.drugbank.ca}pathways':
for i in subnode:
if i.tag == '{http://www.drugbank.ca}pathway':
for a in i:
print a.text
for u in a:
if u.tag == '{http://www.drugbank.ca}drug':
for x in u:
print x.text
#missing a bit of data here
if subnode.tag == '{http://www.drugbank.ca}targets':
for i in subnode:
if i.tag == '{http://www.drugbank.ca}target':
print i.text
for a in i:
print a.text
if a.tag == '{http://www.drugbank.ca}actions':
for u in a:
print u.text
if a.tag == '{http://www.drugbank.ca}references':
for u in a:
if u.tag == '{http://www.drugbank.ca}articles':
for x in u:
if x.tag == '{http://www.drugbank.ca}article':
for z in x:
print z.text
'''
推荐答案
我使用BeautifulSoup进行解析，因为它是一个简单的库。
I used BeautifulSoup for parsing because it is a simple library.
代码：
import pprint
import requests
from bs4 import BeautifulSoup
html = requests.get('https://www.drugbank.ca/drugs/DB01048#BE0004136').text
soup = BeautifulSoup(html, 'html.parser')
div_targets = soup.find('div', class_='bond-list-container targets')
targets = div_targets.find_all('div', class_='bond card')
t = {}
for target in targets:
k = []
v = []
for property in target.find_all('dt'):
k.append(property.get_text())
for property in target.find_all('dd'):
v.append(property.get_text())
t[target.find('strong').get_text()] = dict(zip(k, v))
pprint.pprint(t)
输出：
{'1. Reverse transcriptase/RNaseH': {'Actions': 'Inhibitor',
'Gene Name': 'pol',
'General Function': 'Rna-dna hybrid '
'ribonuclease '
'activity',
'Kind': 'Protein',
'Molecular Weight': '65223.615 Da',
'Organism': 'Human immunodeficiency virus '
'1',
'Pharmacological action': 'Yes',
'Specific Function': 'Not Available',
'Uniprot ID': 'Q72547',
'Uniprot Name': 'Reverse '
'transcriptase/RNaseH'},
'2. HLA class I histocompatibility antigen, B-57 alpha chain': {'Gene Name': 'HLA-B',
'General Function': 'Involved '
'in '
'the '
'presentation '
'of '
'foreign '
'antigens '
'to '
'the '
'immune '
'system.',
'Kind': 'Protein',
'Molecular Weight': '40223.825 '
'Da',
'Organism': 'Human',
'Pharmacological action': 'Unknown',
'Specific Function': 'Peptide '
'antigen '
'binding',
'Uniprot ID': 'P18465',
'Uniprot Name': 'HLA '
'class '
'I '
'histocompatibility '
'antigen, '
'B-57 '
'alpha '
'chain'}}
这篇关于使用ElementTree难以解析XML文件的一部分的文章就介绍到这了，希望我们推荐的答案对大家有所帮助，也希望大家多多支持IT屋！
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