PubmedSpreadsheet Generation Code

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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'

import.py

#!/usr/bin/python
# -*- coding: utf-8 -*-
from PubmedHandler import PubmedHandler
from xml import sax
import sys
import os
def main(input_file,output_file) :
   parser = sax.make_parser()
   handler = PubmedHandler(output_file)
   parser.setContentHandler(handler)
   parser.parse(input_file)
 
 if __name__ == '__main__':
   input_file = 'NCBIData.xml'
   output_file = 'export.tab'
   if len(sys.argv) > 1:
       input_file = sys.argv[1]
   if len(sys.argv) > 2:
       output_file = sys.argv[2]
   main(input_file,output_file)
   cmd = "sed -e 's/ä/\ä/g' -e 's/ç/\ç/g' -e 's/ü/\ü/g' -e 's/ó/\ó/g' -e 's/ö/\ö/g' -e 's/ş/\ş/g' -e 's/í/\í/g' -e 's/é/\é/g' -e 's/ô/\ô/g' -e 's/è/\è/g' export.tab > export_out.tab"
   os.system(cmd)

NewGoogleSpreadSheet.py

 
#!/usr/bin/python
 import gdata.spreadsheet.service
 class GoogleSpreadsheetException(Exception):
     pass
 class SpreadsheetRow:
     """Row in a GoogleSpreadsheet"""
        def __init__(self, index, row_dict):
		"""Inits SpreadsheetRow.
	
		Args:
			index:  Row position in spreadsheet.
			row_dict:  Dict with the data for the row in form 
			{'header1' : value1, 'header2' : value2, 'header3' : value3, ...}
		"""
		self.index = index
		self.row_dict = row_dict
		
	def __str__(self):
		return str(self.row_dict)
		
 class GoogleSpreadsheet:
	"""An iterable Google Spreadsheet."""

	def __init__(self, spreadsheet_id, worksheet_id, user='*************', password='**************'):
		"""Inits GoogleSpreadsheet.
	
		Args:
			spreadsheet_id: Google-assigned unique id for spreadsheet
			worksheet_id: Google-assigned unique id for worksheet within spreadsheet
			user: Google account id with access to spreadsheet
			password: Password for Google account
		"""
		self.gd_client = gdata.spreadsheet.service.SpreadsheetsService()
		self.gd_client.email = user
		self.gd_client.password = password
		self.gd_client.ProgrammaticLogin()
	
		self.count = 0
		self.spreadsheet_id = spreadsheet_id
		self.worksheet_id = worksheet_id
		self.feed = self.gd_client.GetListFeed(self.spreadsheet_id, self.worksheet_id)
		self.rows = self.form_rows(self.feed)
	
	def form_rows(self, ListFeed):
		"""Builds row data from the Google Spreadsheet.
	
		Args:
			listFeed: SpreadsheetsListFeed object for the spreadsheet
		"""
		rows = []
		for i, entry in enumerate(ListFeed.entry):
			d = {}
			for key in entry.custom:
				d[key] = entry.custom[key].text
			rows.append(SpreadsheetRow(i, d))
		return rows

	def reload(self):
		"""Refreshes object with current state of the remote spreadsheet"""
		self.feed = self.gd_client.GetListFeed(self.spreadsheet_id, self.worksheet_id)
		self.rows = self.form_rows(self.feed)
	
	def update_row(self, row):
		"""Replaces a row on the remote spreadsheet and updates current object.
	
		Args:
			row: SpreadsheetRow object to be updated
		"""
		entry = self.gd_client.UpdateRow(self.feed.entry[row.index], row.row_dict)
		if not isinstance(entry, gdata.spreadsheet.SpreadsheetsList):
			raise GoogleSpreadsheetException("Error updating row")
		self.reload()

	def add_row(self, row):
		"""Adds an additional row to the remote spreadsheet and updates current
		object.

		Args:
			row: SpreadsheetRow object to be added
		"""
		entry = self.gd_client.InsertRow(row.row_dict, self.spreadsheet_id, self.worksheet_id)
		if not isinstance(entry, gdata.spreadsheet.SpreadsheetsList):
			raise GoogleSpreadsheetException("Error updating row")
		self.reload()

	def delete_row(self, row):
		"""Deletes a row from the remote spreadsheet and updates current object.

		Args:
			row: SpreadsheetRow object to be deleted
		"""
		entry = self.gd_client.DeleteRow(self.feed.entry[row.index])
		self.reload()
							
	def __iter__(self):
		return self

	def next(self):
		if self.count >= len(self.rows):
			self.count = 0
			raise StopIteration
		else:
			self.count += 1
			return self.rows[self.count - 1]

	def __getitem__(self, index):
		return self.rows[index]
	
	def __len__(self):
		return len(self.rows)

reload.py

#!/usr/bin/python
from NEWGoogleSpreadsheet import GoogleSpreadsheet, SpreadsheetRow

spreadsheet_id = '0AiiHlTECOi8edHFxQWRwN0kxeTQ3ZzdCOXhQX2Z1ZGc'
worksheet_id = 'od6'

gs = GoogleSpreadsheet(spreadsheet_id, worksheet_id)
f = open('export_out.tab', 'r')

headers = [str(x).lower() for x in f.readline().rstrip('\n').split('\t')]
total_lines = 0
for line_num, line in enumerate(f):
        total_lines += 1
        fields = line.rstrip('\n').split('\t')
        row_dict = {}
        for i, val in enumerate(fields):
                row_dict[headers[i]] = val
        r = SpreadsheetRow(line_num, row_dict)
        print r.index, r.row_dict
        if line_num < len(gs):
                gs.update_row(r)
        else:
                gs.add_row(r)
# Remove excess
if total_lines < len(gs):
        for r in gs[:total_lines-1:-1]:
                gs.delete_row(r)
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