93 lines
3.3 KiB
Python
93 lines
3.3 KiB
Python
from scrapy.http import Request
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from scrapy import log
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from source import Source
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from scrapy.selector import Selector
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from FourmiCrawler.items import Result
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import re
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class PubChem(Source):
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""" PubChem scraper for chemical properties
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This parser parses the part on PubChem pages that gives Chemical and Physical properties of a substance.
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"""
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website = 'https://*.ncbi.nlm.nih.gov/*'
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website_www = 'https://www.ncbi.nlm.nih.gov/*'
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website_pubchem = 'https://pubchem.ncbi.nlm.nih.gov/*'
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search = 'pccompound?term=%s'
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data_url = 'toc/summary_toc.cgi?tocid=27&cid=%s'
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__spider = None
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searched_compounds = set()
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def __init__(self, config):
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Source.__init__(self, config)
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self.cfg = config
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def parse(self, response):
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""" Distributes the above described behaviour """
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requests = []
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log.msg('A response from %s just arrived!' % response.url, level=log.DEBUG)
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sel = Selector(response)
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compound = sel.xpath('//h1/text()').extract()[0]
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if compound in self.searched_compounds:
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return None
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self.searched_compounds.update(compound)
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raw_synonyms = sel.xpath('//div[@class="smalltext"]/text()').extract()[0]
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for synonym in raw_synonyms.strip().split(', '):
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log.msg('PubChem synonym found: %s' % synonym, level=log.DEBUG)
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self.searched_compounds.update(synonym)
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self._spider.get_synonym_requests(synonym)
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log.msg('Raw synonyms found: %s' % raw_synonyms, level=log.DEBUG)
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n = re.search(r'cid=(\d+)',response.url)
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if n:
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cid = n.group(1)
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log.msg('cid: %s' % cid, level=log.DEBUG)
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requests.append(Request(url=self.website_pubchem[:-1] + self.data_url % cid, callback=self.parse_data))
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return requests
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def parse_data(self, response):
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log.msg('parsing data', level=log.DEBUG)
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requests = []
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sel = Selector(response)
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props = sel.xpath('//div')
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for prop in props:
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prop_name = ''.join(prop.xpath('b/text()').extract())
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if prop.xpath('a'):
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prop_source = ''.join(prop.xpath('a/@title').extract())
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prop_value = ''.join(prop.xpath('a/text()').extract())
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new_prop = Result({
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'attribute': prop_name,
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'value': prop_value,
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'source': prop_source,
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'reliability': 'Unknown',
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'conditions': ''
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})
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requests.append(new_prop)
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elif prop.xpath('ul'):
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prop_values = prop.xpath('ul//li')
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for prop_li in prop_values:
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prop_value = ''.join(prop_li.xpath('a/text()').extract())
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prop_source = ''.join(prop_li.xpath('a/@title').extract())
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new_prop = Result({
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'attribute': prop_name,
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'value': prop_value,
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'source': prop_source,
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'reliability': 'Unknown',
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'conditions': ''
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})
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requests.append(new_prop)
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return requests
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def new_compound_request(self, compound):
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return Request(url=self.website_www[:-1] + self.search % compound, callback=self.parse)
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