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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# TO DO: make url variable with help of PubChem identifier ID / cid
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#website = "https://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=297" #contains name of compound but not all parsable data
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# website = "https://pubchem.ncbi.nlm.nih.gov/toc/summary_toc.cgi?tocid=27&cid=297" #contains properties to parse
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website = 'https://www.ncbi.nlm.nih.gov/*'
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search = 'pccompound?term=%s'
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__spider = None
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searched_compounds = []
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def __init__(self):
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Source.__init__(self)
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def parse(self, response):
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""" Distributes the above described behaviour """
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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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else:
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# items = self.parse_properties(sel)
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items = []
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self.searched_compounds.append(compound)
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print items
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return items
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def parse_properties(self, sel):
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""" scrape data from 'Chemical and Physical Properties' box on PubChem. """
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items = []
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prop_names = sel.xpath('.//div[@id="d27"//div/b').\
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xpath('normalize-space(string())')
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prop_values = sel.xpath('.//div[@id="d27"//div/a').\
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xpath('normalize-space(string())')
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prop_sources = sel.xpath('.//div[@id="d27"//div/a[@title]').\
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xpath('normalize-space(string())')
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for i, prop_name in enumerate(prop_names):
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item = Result({
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'attribute': prop_name.extract().encode('utf-8'),
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'value': prop_values[i].extract().encode('utf-8'),
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'source': "PubChem: " + prop_sources[i].extract().encode('utf-8'),
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'reliability': "",
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'conditions': ""
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})
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items.append(item)
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print item
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log.msg('PubChem prop: |%s| |%s| |%s|' % (item['attribute'], item['value'], item['source']), level=log.DEBUG)
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items = filter(lambda a: a['value'] != '', items) # remove items with an empty value
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# item_list = self.clean_items(items)
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return items
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def new_compound_request(self, compound):
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return Request(url=self.website[:-1] + self.search % compound, callback=self.parse)
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# @staticmethod
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# def clean_items(items):
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# """ clean up properties using regex, makes it possible to split the values from the units """
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# for item in items:
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# value = item['value']
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# m = re.search('F;\s(\d+[\.,]?\d*)', value) # clean up numerical Kelvin value (after F)
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# if m:
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# item['value'] = m.group(1) + " K"
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# m = re.match('(\d+[\.,]?\d*)\sJ\sK.+mol', value) # clean up J/K/mol values
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# if m:
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# item['value'] = m.group(1) + " J/K/mol"
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# return items
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