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    copied!<p>Wow, I was working on a similar project myself just a week or so ago! </p> <p><strong>Edit:</strong> I recently updated the code to take advantage of <a href="https://www.crummy.com/software/BeautifulSoup/" rel="nofollow noreferrer" title="BeautifulSoup">BeautifulSoup</a>. I have my own virtualenv for it, but you can install it with pip.</p> <p>Basically, my program takes a pubmed ID, a DOI, or a text file of lines of pubmed IDs and/or DOIs, and grabs information about the article. It can easily be tweaked for your own needs to obtain the abstract, but here's my code:</p> <pre><code>import re import sys import traceback from bs4 import BeautifulSoup import requests class PubMedObject(object): soup = None url = None # pmid is a PubMed ID # url is the url of the PubMed web page # search_term is the string used in the search box on the PubMed website def __init__(self, pmid=None, url='', search_term=''): if pmid: pmid = pmid.strip() url = "http://www.ncbi.nlm.nih.gov/pubmed/%s" % pmid if search_term: url = "http://www.ncbi.nlm.nih.gov/pubmed/?term=%s" % search_term page = requests.get(url).text self.soup = BeautifulSoup(page, "html.parser") # set the url to be the fixed one with the PubMedID instead of the search_term if search_term: try: url = "http://www.ncbi.nlm.nih.gov/pubmed/%s" % self.soup.find("dl",class_="rprtid").find("dd").text except AttributeError as e: # NoneType has no find method print("Error on search_term=%s" % search_term) self.url = url def get_title(self): return self.soup.find(class_="abstract").find("h1").text #auths is the string that has the list of authors to return def get_authors(self): result = [] author_list = [a.text for a in self.soup.find(class_="auths").findAll("a")] for author in author_list: lname, remainder = author.rsplit(' ', 1) #add periods after each letter in the first name fname = ".".join(remainder) + "." result.append(lname + ', ' + fname) return ', '.join(result) def get_citation(self): return self.soup.find(class_="cit").text def get_external_url(self): url = None doi_string = self.soup.find(text=re.compile("doi:")) if doi_string: doi = doi_string.split("doi:")[-1].strip().split(" ")[0][:-1] if doi: url = "http://dx.doi.org/%s" % doi else: doi_string = self.soup.find(class_="portlet") if doi_string: doi_string = doi_string.find("a")['href'] if doi_string: return doi_string return url or self.url def render(self): template_text = '' with open('template.html','r') as template_file: template_text = template_file.read() try: template_text = template_text.replace("{{ external_url }}", self.get_external_url()) template_text = template_text.replace("{{ citation }}", self.get_citation()) template_text = template_text.replace("{{ title }}", self.get_title()) template_text = template_text.replace("{{ authors }}", self.get_authors()) template_text = template_text.replace("{{ error }}", '') except AttributeError as e: template_text = template_text.replace("{{ external_url }}", '') template_text = template_text.replace("{{ citation }}", '') template_text = template_text.replace("{{ title }}", '') template_text = template_text.replace("{{ authors }}", '') template_text = template_text.replace("{{ error }}", '&lt;!-- Error --&gt;') return template_text.encode('utf8') def start_table(f): f.write('\t\t\t\t\t\t\t\t\t&lt;div class="resourcesTable"&gt;\n'); f.write('\t\t\t\t\t\t\t\t\t\t&lt;table border="0" cellspacing="0" cellpadding="0"&gt;\n'); def end_table(f): f.write('\t\t\t\t\t\t\t\t\t\t&lt;/table&gt;\n'); f.write('\t\t\t\t\t\t\t\t\t&lt;/div&gt;\n'); def start_accordion(f): f.write('\t\t\t\t\t\t\t\t\t&lt;div class="accordion"&gt;\n'); def end_accordion(f): f.write('\t\t\t\t\t\t\t\t\t&lt;/div&gt;\n'); def main(args): try: # program's main code here print("Parsing pmids.txt...") with open('result.html', 'w') as sum_file: sum_file.write('&lt;!--\n') with open('pmids.txt','r') as pmid_file: with open('result.html','a') as sum_file: for pmid in pmid_file: sum_file.write(pmid) sum_file.write('\n--&gt;\n') with open('pmids.txt','r') as pmid_file: h3 = False h4 = False table_mode = False accordion_mode = False with open('result.html', 'a') as sum_file: for pmid in pmid_file: if pmid[:4] == "####": if h3 and not accordion_mode: start_accordion(sum_file) accordion_mode = True sum_file.write('\t\t\t\t\t\t\t\t\t&lt;h4&gt;&lt;a href="#"&gt;%s&lt;/a&gt;&lt;/h4&gt;\n' % pmid[4:].strip()) h4 = True elif pmid[:3] == "###": if h4: if table_mode: end_table(sum_file) table_mode = False end_accordion(sum_file) h4 = False accordion_mode = False elif h3: end_table(sum_file) table_mode = False sum_file.write('\t\t\t\t\t\t\t\t&lt;h3&gt;&lt;a href="#"&gt;%s&lt;/a&gt;&lt;/h3&gt;\n' % pmid[3:].strip()) h3 = True elif pmid.strip(): if (h3 or h4) and not table_mode: start_table(sum_file) table_mode = True if pmid[:4] == "http": if pmid[:18] == "http://dx.doi.org/": sum_file.write(PubMedObject(search_term=pmid[18:]).render()) else: print("url=%s" % pmid) p = PubMedObject(url=pmid).render() sum_file.write(p) print(p) elif pmid.isdigit(): sum_file.write(PubMedObject(pmid).render()) else: sum_file.write(PubMedObject(search_term=pmid).render()) if h3: if h4: end_table(sum_file) end_accordion(sum_file) else: end_table(sum_file) pmid_file.close() print("Done!") except BaseException as e: print traceback.format_exc() print "Error: %s %s" % (sys.exc_info()[0], e.args) return 1 except: # error handling code here print "Error: %s" % sys.exc_info()[0] return 1 # exit on error else: raw_input("Press enter to exit.") return 0 # exit errorlessly if __name__ == '__main__': sys.exit(main(sys.argv)) </code></pre> <p>It now returns a HTML file based on the information it downloaded. Here is the template.txt:</p> <pre><code>&lt;tr&gt;{{ error }} &lt;td valign="top" class="resourcesICO"&gt;&lt;a href="{{ external_url }}" target="_blank"&gt;&lt;img src="/image/ico_sitelink.gif" width="24" height="24" /&gt;&lt;/a&gt;&lt;/td&gt; &lt;td&gt;&lt;a href="{{ external_url }}"&gt;{{ title }}&lt;/a&gt;&lt;br /&gt; {{ authors }}&lt;br /&gt; &lt;em&gt;{{ citation }}&lt;/em&gt;&lt;/td&gt; &lt;/tr&gt; </code></pre> <p>When you run it, the program will ask you for the DOI or the Pubmed ID. If you do not provide one, it will read pmids.txt.Feel free to use the code as you see fit.</p>
 

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