PubmedSpreadsheet Generation Code - Revision history

Public: /* reload.py */

2011-09-19T10:53:38Z

reload.py

← Older revision		Revision as of 10:53, 19 September 2011
Line 313:		Line 313:
	</pre></code>		</pre></code>
	==reload.py==		==reload.py==
			<code><pre>
	#!/usr/bin/python		#!/usr/bin/python
	~~<code><pre>~~
	from NEWGoogleSpreadsheet import GoogleSpreadsheet, SpreadsheetRow		from NEWGoogleSpreadsheet import GoogleSpreadsheet, SpreadsheetRow

Public at 10:53, 19 September 2011

2011-09-19T10:53:20Z

@@ Line 311: / Line 311: @@
 	def __len__(self):
 		return len(self.rows)
 </pre></code>

Public: /* NewGoogleSpreadSheet.py */

2011-09-16T11:24:03Z

NewGoogleSpreadSheet.py

← Older revision		Revision as of 11:24, 16 September 2011
Line 200:		Line 200:

	==NewGoogleSpreadSheet.py==		==NewGoogleSpreadSheet.py==
	#!/usr/bin/python		<code><pre>
			#!/usr/bin/python
	import gdata.spreadsheet.service		import gdata.spreadsheet.service
	class GoogleSpreadsheetException(Exception):		class GoogleSpreadsheetException(Exception):
Line 310:		Line 311:
	def __len__(self):		def __len__(self):
	return len(self.rows)		return len(self.rows)
			</pre></code>

Public: /* NewGoogleSpreadSheet.py */

2011-09-16T11:23:18Z

NewGoogleSpreadSheet.py

← Older revision		Revision as of 11:23, 16 September 2011
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	pass		pass
	class SpreadsheetRow:		class SpreadsheetRow:
	"""Row in a GoogleSpreadsheet"""		"""Row in a GoogleSpreadsheet"""
			def __init__(self, index, row_dict):
	def __init__(self, index, row_dict):
	"""Inits SpreadsheetRow.		"""Inits SpreadsheetRow.

Public: /* NewGoogleSpreadSheet.py */

2011-09-16T11:22:53Z

NewGoogleSpreadSheet.py

← Older revision		Revision as of 11:22, 16 September 2011
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	class GoogleSpreadsheetException(Exception):		class GoogleSpreadsheetException(Exception):
	pass		pass

	class SpreadsheetRow:		class SpreadsheetRow:
	"""Row in a GoogleSpreadsheet"""		"""Row in a GoogleSpreadsheet"""

Public: /* NewGoogleSpreadSheet.py */

2011-09-16T11:22:39Z

NewGoogleSpreadSheet.py

← Older revision		Revision as of 11:22, 16 September 2011
Line 203:		Line 203:
	import gdata.spreadsheet.service		import gdata.spreadsheet.service
	class GoogleSpreadsheetException(Exception):		class GoogleSpreadsheetException(Exception):
	pass		pass

	class SpreadsheetRow:		class SpreadsheetRow:

Public: /* NewGoogleSpreadSheet.py */

2011-09-16T11:22:17Z

NewGoogleSpreadSheet.py

← Older revision		Revision as of 11:22, 16 September 2011
Line 201:		Line 201:
	==NewGoogleSpreadSheet.py==		==NewGoogleSpreadSheet.py==
	#!/usr/bin/python		#!/usr/bin/python

	import gdata.spreadsheet.service		import gdata.spreadsheet.service

	class GoogleSpreadsheetException(Exception):		class GoogleSpreadsheetException(Exception):
	pass		pass
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	def __init__(self, index, row_dict):		def __init__(self, index, row_dict):
	"""Inits SpreadsheetRow.		"""Inits SpreadsheetRow.

	Args:		Args:
	index: Row position in spreadsheet.		index: Row position in spreadsheet.
Line 224:		Line 222:
	return str(self.row_dict)		return str(self.row_dict)

	class GoogleSpreadsheet:		class GoogleSpreadsheet:
	"""An iterable Google Spreadsheet."""		"""An iterable Google Spreadsheet."""

			def __init__(self, spreadsheet_id, worksheet_id, user='***********', password='************'):
			"""Inits GoogleSpreadsheet.

	~~def __init__(self, spreadsheet_id, worksheet_id, user='programmer@gersteinlab.org', password='alpaca'):~~
	~~"""Inits GoogleSpreadsheet.~~

	Args:		Args:
	spreadsheet_id: Google-assigned unique id for spreadsheet		spreadsheet_id: Google-assigned unique id for spreadsheet
Line 240:		Line 238:
	self.gd_client.password = password		self.gd_client.password = password
	self.gd_client.ProgrammaticLogin()		self.gd_client.ProgrammaticLogin()

	self.count = 0		self.count = 0
	self.spreadsheet_id = spreadsheet_id		self.spreadsheet_id = spreadsheet_id
Line 246:		Line 244:
	self.feed = self.gd_client.GetListFeed(self.spreadsheet_id, self.worksheet_id)		self.feed = self.gd_client.GetListFeed(self.spreadsheet_id, self.worksheet_id)
	self.rows = self.form_rows(self.feed)		self.rows = self.form_rows(self.feed)

	def form_rows(self, ListFeed):		def form_rows(self, ListFeed):
	"""Builds row data from the Google Spreadsheet.		"""Builds row data from the Google Spreadsheet.

	Args:		Args:
	listFeed: SpreadsheetsListFeed object for the spreadsheet		listFeed: SpreadsheetsListFeed object for the spreadsheet
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	rows.append(SpreadsheetRow(i, d))		rows.append(SpreadsheetRow(i, d))
	return rows		return rows

	def reload(self):		def reload(self):
	"""Refreshes object with current state of the remote spreadsheet"""		"""Refreshes object with current state of the remote spreadsheet"""
	self.feed = self.gd_client.GetListFeed(self.spreadsheet_id, self.worksheet_id)		self.feed = self.gd_client.GetListFeed(self.spreadsheet_id, self.worksheet_id)
	self.rows = self.form_rows(self.feed)		self.rows = self.form_rows(self.feed)

	def update_row(self, row):		def update_row(self, row):
	"""Replaces a row on the remote spreadsheet and updates current object.		"""Replaces a row on the remote spreadsheet and updates current object.

	Args:		Args:
	row: SpreadsheetRow object to be updated		row: SpreadsheetRow object to be updated
Line 276:		Line 274:
	raise GoogleSpreadsheetException("Error updating row")		raise GoogleSpreadsheetException("Error updating row")
	self.reload()		self.reload()


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

	Args:		Args:
	row: SpreadsheetRow object to be added		row: SpreadsheetRow object to be added
Line 289:		Line 286:
	raise GoogleSpreadsheetException("Error updating row")		raise GoogleSpreadsheetException("Error updating row")
	self.reload()		self.reload()

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

	Args:		Args:
	row: SpreadsheetRow object to be deleted		row: SpreadsheetRow object to be deleted
Line 298:		Line 295:
	entry = self.gd_client.DeleteRow(self.feed.entry[row.index])		entry = self.gd_client.DeleteRow(self.feed.entry[row.index])
	self.reload()		self.reload()

	def __iter__(self):		def __iter__(self):
	return self		return self

	def next(self):		def next(self):
	if self.count >= len(self.rows):		if self.count >= len(self.rows):
Line 309:		Line 306:
	self.count += 1		self.count += 1
	return self.rows[self.count - 1]		return self.rows[self.count - 1]

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

	def __len__(self):		def __len__(self):
	return len(self.rows)		return len(self.rows)

Public at 11:20, 16 September 2011

2011-09-16T11:20:09Z

@@ Line 1: / Line 1: @@
 ==parse_pmids.py==
   <code>
   #!/usr/bin/python
@@ Line 199: / Line 198: @@
      cmd = "sed -e 's/ä/\&#228;/g' -e 's/ç/\&#231;/g' -e 's/ü/\&#252;/g' -e 's/ó/\&#243;/g' -e 's/ö/\&#246;/g' -e 's/ş/\&#351;/g' -e 's/í/\&#237;/g' -e 's/é/\&#233;/g' -e 's/ô/\&#244;/g' -e 's/è/\&#232;/g' export.tab > export_out.tab"
      os.system(cmd)

Public: /* import.py */

2011-09-16T11:18:04Z

import.py

← Older revision		Revision as of 11:18, 16 September 2011
Line 183:		Line 183:
	import sys		import sys
	import os		import os
			def main(input_file,output_file) :
	def main(input_file,output_file) :
	parser = sax.make_parser()		parser = sax.make_parser()
	handler = PubmedHandler(output_file)		handler = PubmedHandler(output_file)

Public: /* import.py */

2011-09-16T11:17:46Z

import.py

← Older revision		Revision as of 11:17, 16 September 2011
Line 184:		Line 184:
	import os		import os

	def main(input_file,output_file) :		def main(input_file,output_file) :
	parser = sax.make_parser()		parser = sax.make_parser()
	handler = PubmedHandler(output_file)		handler = PubmedHandler(output_file)
	parser.setContentHandler(handler)		parser.setContentHandler(handler)
	parser.parse(input_file)		parser.parse(input_file)

			if __name__ == '__main__':
	if __name__ == '__main__':
	input_file = 'NCBIData.xml'		input_file = 'NCBIData.xml'
	output_file = 'export.tab'		output_file = 'export.tab'
Line 198:		Line 197:
	if len(sys.argv) > 2:		if len(sys.argv) > 2:
	output_file = sys.argv[2]		output_file = sys.argv[2]

	main(input_file,output_file)		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"		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)		os.system(cmd)