PubmedSpreadsheet Generation Code

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(PubmedHandler.py)
Line 26: Line 26:
==PubmedHandler.py==
==PubmedHandler.py==
  <code>
  <code>
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#!/usr/bin/python
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#!/usr/bin/python
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# -*- coding: utf-8 -*-
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# -*- coding: utf-8 -*-
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from datetime import date
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from datetime import date
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from xml.sax import ContentHandler
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from xml.sax import ContentHandler
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import xml.sax.saxutils<br \>
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import xml.sax.saxutils<br \>
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class PubmedHandler(ContentHandler):
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class PubmedHandler(ContentHandler):
     def __init__(self,output_file = 'export.tab'):
     def __init__(self,output_file = 'export.tab'):
         self.file = file(output_file,'w')
         self.file = file(output_file,'w')

Revision as of 11:11, 16 September 2011

parse_pmids.py


#!/usr/bin/python
import os, sys
from GoogleSpreadsheet import GoogleSpreadsheet
from datetime import datetime
master_spreadsheet_id = "******************" worksheet_id = "od6" master_spreadsheet = GoogleSpreadsheet(master_spreadsheet_id, worksheet_id)
ncbiquery = "/home/mpw6/new_papers/ncbiquery.txt" ncbiFile = open(ncbiquery,'w')
def buildQuery(master_spreadsheet, ncbiFile): start = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=" pmids = end = "&rettype=xml&retmode=file" for row in master_spreadsheet: if row['pmid']: pmids += row['pmid'].lstrip('\) + ',' pmids = pmids[:-1] out = start + pmids + end + '\n' ncbiFile.write(out)
buildQuery(master_spreadsheet, ncbiFile)

PubmedHandler.py


#!/usr/bin/python
# -*- coding: utf-8 -*-
from datetime import date
from xml.sax import ContentHandler
import xml.sax.saxutils
class PubmedHandler(ContentHandler): def __init__(self,output_file = 'export.tab'): self.file = file(output_file,'w') self.sep = '\t' self.data = {} self.key = self.pmid = False self.authors = [] self.handling = False self.elements = ['Initials', #multiple, name unique 'LastName', #multiple, name unique 'MedlineTA', #unique 'PMID', #unique 'OtherID', #unique 'MedlinePgn', #unique 'Volume', #unique 'Issue', #unique 'Year', #inside PubDate 'Month', #inside PubDate 'Day', #inside PubDate 'ArticleTitle', #unique 'CollectiveName',#unique 'ArticleId', 'PubDate', ] self.file.write(self.get_header())
def __del__(self): self.file.close()
def startElement(self,name,attrs): if name == 'PubmedArticle': self.data = {'PMID':} self.authors = [] self.is_articledate = False self.is_pubdate = False self.pmid = 0 self.handling = False elif name == 'PubDate': self.is_pubdate = True self.data['Year'] = self.data['Month']= self.data['Day'] = elif name in self.elements: if name == 'ArticleId': if attrs.getValue('IdType') == 'pmc': self.key = 'PMCID' self.data['PMCID'] = self.handling = True else: self.key = name self.handling = True if name == 'PMID': self.pmid += 1 if name not in ['Year','Month','Day','PMID']: self.data[name] =
def endElement(self,name): if name == 'PubmedArticle': self.write_to_file() elif name == 'PubDate': self.is_pubdate = False elif name == 'Author': #merge author if self.get_data('Initials'): self.authors.append(self.get_data('Initials') + ' ' + self.get_data('LastName')) if self.get_data('CollectiveName'): self.authors.append(self.get_data('CollectiveName')) self.data['CollectiveName'] = self.handling = False
def characters(self,content): if self.handling: if self.key in ['Year','Month','Day']: if self.is_pubdate: self.data[self.key] += content elif self.key == 'PMID': if self.pmid == 1: self.data[self.key] += content else: self.data[self.key] += xml.sax.saxutils.escape(content)
def write_to_file(self): try: self.file.write(self.get_row().encode('utf-8')) except UnicodeEncodeError as anomerr: print anomerr print self.get_row() return[]
def get_row(self): return self.sep.join([', '.join(self.authors), self.get_data('MedlineTA'), self.get_data('PMID'), self.get_data('MedlinePgn'), self.get_data('Volume'), self.get_data('Year'), self.get_citation(), self.get_data('ArticleTitle'), self.get_data('PMCID')]) + '\n'
def get_citation(self):

citation = if self.get_data('Year'): citation += '(' + self.get_data('Year') + ').' + ' '

       citation += '' + self.get_data('MedlineTA') + '' + ' '
       date_str = 
       ref_str = 
       #build date string
       if self.get_data('Year'):
           date_str += self.get_data('Year')
       if self.get_data('Month'):
           date_str += ' ' + self.get_data('Month')
       if self.get_int_data('Day'):
           date_str += ' %d' % self.get_int_data('Day')
       date_str = date_str.strip()
       
       #build ref string
       if self.get_data('Volume'):
           ref_str += self.get_data('Volume')
       #if self.get_data('Issue'):
       #    ref_str += '('+self.get_data('Issue')+')'
       if self.get_data('MedlinePgn'):
           ref_str += ':' + self.get_data('MedlinePgn')
           
       ref_str = ref_str.strip()
       
       #if date_str:
           #citation += date_str
       if ref_str:
           #if date_str:
               #citation += ';'
           citation += ref_str
       if citation[-1] != '.':
           citation += '.'
       return citation
               
   def get_data(self,key):
       if self.data.has_key(key):
           return self.data[key]
       return 
   
   def get_int_data(self,key):
       val = self.get_data(key)
       try:
           val = int(val)
           return val
       except ValueError:
           pass
       return 0
       
   def get_header(self):
       return self.sep.join(['Authors','Journal','PMID','Pages','Volume','Year','Citation','Title','PMCID']) + '\n'

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