Build Papers Page Code - Revision history

Public: /* update.py */

2011-09-16T11:42:36Z

update.py

← Older revision		Revision as of 11:42, 16 September 2011
Line 532:		Line 532:
	printSubject(master_spreadsheet,header)		printSubject(master_spreadsheet,header)
	printPapers(master_spreadsheet, summaryFile, header)		printPapers(master_spreadsheet, summaryFile, header)
	</pre><code>		</pre></code>

Public: /* update.py */

2011-09-16T11:42:13Z

update.py

← Older revision		Revision as of 11:42, 16 September 2011
Line 352:		Line 352:
	simpleFile.write(out)		simpleFile.write(out)
	</pre></code>		</pre></code>
			Generate Subject Main Page and page for each Subject
			<code><pre>
	def printSubject(master_spreadsheet,header):		def printSubject(master_spreadsheet,header):
	allsubjects = []		allsubjects = []

Public: /* update.py */

2011-09-16T11:40:49Z

update.py

← Older revision		Revision as of 11:40, 16 September 2011
Line 32:		Line 32:
	'''		'''
	</pre></code>		</pre></code>
			Generate Main Page and page for each Paper
			<code><pre>
	def printPapers(master_spreadsheet,summaryFile, header):		def printPapers(master_spreadsheet,summaryFile, header):
	out = "<HTML>\n"		out = "<HTML>\n"
Line 350:		Line 351:
	out += row['citation'].lstrip('\'') + '</DL>\n'		out += row['citation'].lstrip('\'') + '</DL>\n'
	simpleFile.write(out)		simpleFile.write(out)
			</pre></code>

	def printSubject(master_spreadsheet,header):		def printSubject(master_spreadsheet,header):

Public: /* update.py */

2011-09-16T11:38:36Z

update.py

@@ Line 28: / Line 28: @@
 subjectSummaryFile = open(subjectSummaryIndex,'w')
-header = '''<STYLE TYPE="text/css">
+header = '''
-A { text-decoration:none; }
+***********
 '''
 </pre></code>

Public: /* update.py */

2011-09-16T11:37:52Z

update.py

← Older revision		Revision as of 11:37, 16 September 2011
Line 51:		Line 51:
	<!-- Buttons for individual sections -->		<!-- Buttons for individual sections -->
	<FONT FACE='sans-serif, Arial, Helvetica' COLOR="#993333">		<FONT FACE='sans-serif, Arial, Helvetica' COLOR="#993333">
	<SPAN CLASS="headerMenu"><A HREF="/">Main</A></SPAN>		<SPAN CLASS="headerMenu"><A HREF="/">Main</A></SPAN> •
	•		<SPAN CLASS="headerMenu"><A HREF="/subject">By Subject</A></SPAN> •
	<SPAN CLASS="headerMenu"><A HREF="/subject">By Subject</A></SPAN>		<SPAN CLASS="headerMenu"><A HREF="http://oldpapers.gersteinlab.org/search/labquery.pl?query=default">Medline</A></SPAN> •
	•		<SPAN CLASS="headerMenu"><A HREF="http://info.gersteinlab.org/Papers_Page_Code">Code</A></SPAN> •
	<SPAN CLASS="headerMenu"><A HREF="http://oldpapers.gersteinlab.org/search/labquery.pl?query=default">Medline</A></SPAN>
	•
	<SPAN CLASS="headerMenu"><A HREF="http://info.gersteinlab.org/Papers_Page_Code">Code</A></SPAN>
	•
	</FONT>		</FONT>
	</CENTER>		</CENTER>

Public: /* update.py */

2011-09-16T11:36:24Z

update.py

← Older revision		Revision as of 11:36, 16 September 2011
Line 63:		Line 63:
	<HR>		<HR>
	'''		'''
	</pre><code>		</pre></code>

	def printPapers(master_spreadsheet,summaryFile, header):		def printPapers(master_spreadsheet,summaryFile, header):

Public: /* update.py */

2011-09-16T11:35:50Z

update.py

← Older revision		Revision as of 11:35, 16 September 2011
Line 63:		Line 63:
	<HR>		<HR>
	'''		'''
	</pre><~~Code~~>		</pre><code>

	def printPapers(master_spreadsheet,summaryFile, header):		def printPapers(master_spreadsheet,summaryFile, header):

Public: /* update.py */

2011-09-16T11:35:14Z

update.py

← Older revision		Revision as of 11:35, 16 September 2011
Line 1:		Line 1:
	==update.py==		==update.py==
			Basic Setup

	<code><pre>		<code><pre>
	#!/usr/bin/python		#!/usr/bin/python
Line 57:		Line 59:
	<SPAN CLASS="headerMenu"><A HREF="http://info.gersteinlab.org/Papers_Page_Code">Code</A></SPAN>		<SPAN CLASS="headerMenu"><A HREF="http://info.gersteinlab.org/Papers_Page_Code">Code</A></SPAN>
	•		•
	~~<!--~~
	~~<SPAN CLASS="headerMenu"><A HREF="http://wiki.gersteinlab.org/pubinfo/Paper_search">Search</A></SPAN>~~
	~~ • ~~
	~~--><SPAN CLASS="headerMenu"><A HREF="http://wiki.gersteinlab.org/pubinfo/Other_Papers">Other Writings</A></SPAN>~~
	</FONT>		</FONT>
	</CENTER>		</CENTER>

Public: Created page with '==update.py==

 #!/usr/bin/python import os, sys, re from GoogleSpreadsheet import GoogleSpreadsheet from datetime import datetime  pubmed_spreadsheet_id = "***********…'


2011-09-16T11:34:14Z
Created page with '==update.py== <code><pre> #!/usr/bin/python import os, sys, re from GoogleSpreadsheet import GoogleSpreadsheet from datetime import datetime  pubmed_spreadsheet_id = "***********…'
New page
==update.py==

<code><pre>

#!/usr/bin/python

import os, sys, re

from GoogleSpreadsheet import GoogleSpreadsheet

from datetime import datetime



pubmed_spreadsheet_id = "*******************"

master_spreadsheet_id = "********************"

subject_spreadsheet_id = "*************************"

worksheet_id = "od6"

pubmed_spreadsheet = GoogleSpreadsheet(pubmed_spreadsheet_id, worksheet_id)

master_spreadsheet = GoogleSpreadsheet(master_spreadsheet_id, worksheet_id)

subject_spreadsheet = GoogleSpreadsheet(subject_spreadsheet_id, worksheet_id)

timestamp = str(datetime.now().ctime())



summaryPath = "************"

summaryIndex = "*********************"

summaryFile = open(summaryIndex,'w')

simpleIndex = "*************"

simpleFile = open(simpleIndex,'w')

subjectPath = "********************"

subjectIndex = subjectPath + "index.html"

subjectFile = open(subjectIndex,'w')

subjectSummaryIndex = "******************"

subjectSummaryFile = open(subjectSummaryIndex,'w')



header = '''<STYLE TYPE="text/css">

A { text-decoration:none; }

.headerMenu A:link { color:#993333; }

.headerMenu A:visited { color:#993333; }

.headerMenu A:active { color:#334499; }

.headerMenu A:hover { color:#334499; }

.headerMenu A:sansserif{ font-family:Arial,Helvetica,sans-serif; }

.papersList { margin-left:0px; }

.paperTitle { margin-left:50px; }

.paperTitle A:link { color:#000000; }

.paperTitle A:visited { color:#000000; }

.paperTitle A:active { color:#000000; }

.paperTitle A:hover { color:#000000; }

.paperCite { margin-left:100px; }

</STYLE>

</HEAD>

<BODY BGCOLOR="white">

<CENTER>

<BR />

<FONT SIZE=+2 FACE='sans-serif, Arial, Helvetica' COLOR="#334499">Gerstein Lab Publications</FONT>

<BR /><BR />

<!-- Buttons for individual sections -->

<FONT FACE='sans-serif, Arial, Helvetica' COLOR="#993333">

<SPAN CLASS="headerMenu"><A HREF="/">Main</A></SPAN>

&nbsp;&#8226;&nbsp;

<SPAN CLASS="headerMenu"><A HREF="/subject">By Subject</A></SPAN>

&nbsp;&#8226;&nbsp;

<SPAN CLASS="headerMenu"><A HREF="http://oldpapers.gersteinlab.org/search/labquery.pl?query=default">Medline</A></SPAN>

&nbsp;&#8226;&nbsp;

<SPAN CLASS="headerMenu"><A HREF="http://info.gersteinlab.org/Papers_Page_Code">Code</A></SPAN>

&nbsp;&#8226;&nbsp;

<!--

<SPAN CLASS="headerMenu"><A HREF="http://wiki.gersteinlab.org/pubinfo/Paper_search">Search</A></SPAN>

&nbsp;&#8226;&nbsp;

--><SPAN CLASS="headerMenu"><A HREF="http://wiki.gersteinlab.org/pubinfo/Other_Papers">Other Writings</A></SPAN>

</FONT>

</CENTER>

<HR>

'''

</pre><Code>



def printPapers(master_spreadsheet,summaryFile, header):

	out = "<HTML>\n"

	out += "<HEAD>\n"

	out += "<TITLE>Gerstein Lab Publications</TITLE>\n"

	out += header

	out += "\n"

	out += "<CENTER>\n"

	out += "<FONT FACE='sans-serif, Arial, Helvetica'><FONT SIZE=+2 COLOR=993333>Main Scientific Publications</FONT>\n"

	out += "\n"

	out += "<H3><FONT SIZE=\"4\" COLOR=\"#334499\">Total papers: " + str(len(master_spreadsheet)) + "</FONT></H3></FONT>\n"

	out += "<p>(Last updated " + timestamp + ")</CENTER>\n"

	years = {}

	currentYear = 0

	for row in master_spreadsheet:

		rowYear = row['year']

		if years.has_key(rowYear):

			years[rowYear] += 1

		else:

			years[rowYear] = 1

	for row in master_spreadsheet:

		pubmed = pubmed_spreadsheet

		if currentYear != row['year']:

			currentYear = row['year']

			out += "<H3 ALIGN=center><FONT FACE='arial,helvetica,sans-serif' COLOR=334499 SIZE=4>-- " + currentYear + " (" + str(years[currentYear]) + ") --</FONT></H3>"

		summaryFile.write(out)

		simpleFile.write(out)

		simpleFile2.write(out)	

		out = ""

		printPaperEntry(row, summaryFile, pubmed)

		printSimpleEntry(row, simpleFile, pubmed)

		printSimpleEntry(row,simpleFile2,pubmed)	

		printEntrySummary(row, header, pubmed)

		printEntryExtended(row)

	out = "</BODY></HTML>"

	summaryFile.write(out)

	simpleFile.write(out)



def printEntrySummary(row,header,pubmed):

	#if row['pmid']:

		#print 'pES first: ' + row['pmid']

	#else:

		#print 'pES first: no pmid'

	pubmed.count = 0

	for pubmed_row in pubmed:

		#print 'pES pubmed: ' + pubmed_row['pmid']

		if row['pmid'] == pubmed_row['pmid']:

			row['title'] = pubmed_row['title']

			row['citation'] = pubmed_row['citation']

			row['authors'] = pubmed_row['authors']

			row['year'] = pubmed_row['year']

			break

	# create summary directory

	entrySummary = summaryPath + row['labid'].lstrip('\'')

	if not os.path.exists(entrySummary):

		os.makedirs(entrySummary)

	entrySummaryIndex = entrySummary + "/index.html"

	entrySummaryFile = open(entrySummaryIndex,'w')

    

	out = "<HTML>\n"

	out += "<HEAD>\n"

	out += "<TITLE>" + row['title'].lstrip('\'') + "</TITLE>"

	out += header

	out += "\n"

	out += "<blockquote>\n"

	out += "<font size=+3><tt>" + row['labid'] + "</tt></font><p />"

	out += "\n"

	# print title and citation

	out += "<DIV CLASS=\"paperTitle\"><FONT SIZE=+1><B><A HREF=\"/papers/" + row['labid'].lstrip('\'') + "/index.html\">" + row['title'].lstrip('\'') + "</A></B></FONT></DIV>\n"

	if row.has_key('authors'):		

		out += "<DIV CLASS=\"paperCite\">" +row['authors'].lstrip('\'')+ " " +row['citation'].lstrip('\'') + "</DIV>\n"	

	else:		

		out += "<DIV CLASS=\"paperCite\">" + " " + row['citation'].lstrip('\'') + "</DIV>\n"	

	# print links

	out += "<DIV CLASS=\"paperCite\">"

	if not row['website']:

		out += "<IMG SRC=\"/papers/null.gif\" HEIGHT=\"23\" WIDTH=\"56\" BORDER=\"0\">"

	else:

		out += "<A HREF=\"" + row['website'].lstrip('\'')  + "\"><IMG SRC=\"/papers/website.jpg\" HEIGHT=\"23\" WIDTH=\"56\" BORDER=\"0\"></A>"

	if not row['preprint']:

		out += "<IMG SRC=\"/papers/null.gif\" HEIGHT=\"23\" WIDTH=\"56\" BORDER=\"0\">"

	else:

		out += "<A HREF=\"" + row['preprint'].lstrip('\'') + "\"><IMG BORDER=\"0\" HEIGHT=\"23\" WIDTH=\"56\" SRC=\"/papers/preprint.jpg\"></A>"

	if not row['pmid']:

		out += "<IMG SRC=\"/papers/null.gif\" HEIGHT=\"23\" WIDTH=\"56\" BORDER=\"0\">"

	else:

		out += "<A HREF=\"http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=" + row['pmid'].lstrip('\'') + "&dopt=Abstract\"><IMG BORDER=\"0\" HEIGHT=\"23\" WIDTH=\"56\" SRC=\"/papers/medline.jpg\"></A>"

	#if not labid:

	#	out += "<A HREF=\"#\">" + "<IMG BORDER=\"0\" WIDTH=\"23\" HEIGHT=\"23\" SRC=\"/papers/more.gif\"></A>"

	#else:

	out += "<A HREF=\"/papers/" + row['labid'].lstrip('\'') + "/index-all.html\">" + "<IMG BORDER=\"0\" WIDTH=\"23\" HEIGHT=\"23\" SRC=\"/papers/more.gif\"></A>"

	out += "</DIV>\n<P />\n"

    

	out += "<hr><br><a href=index-all.html>View all citation information</a><br><a href='/'>Return to papers index</a><br>&nbsp;</blockquote></BODY></HTML>"

	entrySummaryFile.write(out)



def printEntryExtended(row):

	title = ''

	citation = ''

	authors = ''

	journal = ''

	pages = ''

	volume = ''

	year = ''

	pmcid = ''



	for pubmed_row in pubmed_spreadsheet:

		if row['pmid'] == pubmed_row['pmid']:

			title = pubmed_row['title']

			citation = pubmed_row['citation']

			authors = pubmed_row['authors']

			year = pubmed_row['year']

			journal = pubmed_row['journal']

			pages = pubmed_row['pages']

			volume = pubmed_row['volume']

			pmcid = pubmed_row['pmcid']



	# create summary directory

	entryExtended = summaryPath + row['labid'].lstrip('\'')

	if not os.path.exists(entryExtended):

		os.makedirs(entryExtended)

	entryExtendedIndex = entryExtended + "/index-all.html"

	entryExtendedFile = open(entryExtendedIndex,'w')



	out = "<HTML>\n"

	out += "<HEAD>\n"

	if not title:

		out += "<TITLE>" + row['title'].lstrip('\'') + "</TITLE>"

	else:

		out += "<TITLE>" + title.lstrip('\'') + "</TITLE>"

	out += header

	out += "\n"

	out += "<blockquote>\n"

	if not row['labid']:

		out += "<font size=+3><tt>" + row['pmid'].lstrip('\'') + "</tt></font><p />"

	else:

		out += "<font size=+3><tt>" + row['labid'] + "</tt></font><p />"

	out += "\n"

	# print title and citation

	if not title:

		out += "<DIV CLASS=\"paperTitle\"><FONT SIZE=+1><B><A HREF=\"/papers/" + row['labid'].lstrip('\'') + "/index.html\">" + row['title'].lstrip('\'') + "</A></B></FONT></DIV>\n"

	else:

		out += "<DIV CLASS=\"paperTitle\"><FONT SIZE=+1><B><A HREF=\"/papers/" + row['labid'].lstrip('\'') + "/index.html\">" + title.lstrip('\'') + "</A></B></FONT></DIV>\n"

	if not citation:

	 	if not row.has_key('authors'):		

	 		out += "<DIV CLASS=\"paperCite\">" + " " + row['citation'].lstrip('\'') + "</DIV>\n"	

	#	out += "<DIV CLASS=\"paperCite\">" + " " + row['citation'].lstrip('\'') + "</DIV>\n"	

	 	else:		

	 		out += "<DIV CLASS=\"paperCite\">" + row['authors'].lstrip('\'') + " " +row['citation'].lstrip('\'') + "</DIV>\n"	

	else:

		out += "<DIV CLASS=\"paperCite\">" + authors.lstrip('\'') + ' ' + citation.lstrip('\'') + "</DIV>\n"

	# print links

	out += "<DIV CLASS=\"paperCite\">"

	if not row['website']:

		out += "<IMG SRC=\"/papers/null.gif\" HEIGHT=\"23\" WIDTH=\"56\" BORDER=\"0\">"

	else:

		out += "<A HREF=\"" + row['website'].lstrip('\'')  + "\"><IMG SRC=\"/papers/website.jpg\" HEIGHT=\"23\" WIDTH=\"56\" BORDER=\"0\"></A>"

	if not row['preprint']:

		out += "<IMG SRC=\"/papers/null.gif\" HEIGHT=\"23\" WIDTH=\"56\" BORDER=\"0\">"

	else:

		out += "<A HREF=\"" + row['preprint'].lstrip('\'') + "\"><IMG BORDER=\"0\" HEIGHT=\"23\" WIDTH=\"56\" SRC=\"/papers/preprint.jpg\"></A>"

	if not row['pmid']:

		out += "<IMG SRC=\"/papers/null.gif\" HEIGHT=\"23\" WIDTH=\"56\" BORDER=\"0\">"

	else:

		out += "<A HREF=\"http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=" + row['pmid'].lstrip('\'') + "&dopt=Abstract\"><IMG BORDER=\"0\" HEIGHT=\"23\" WIDTH=\"56\" SRC=\"/papers/medline.jpg\"></A>"

	#if not labid:

	#       out += "<A HREF=\"#\">" + "<IMG BORDER=\"0\" WIDTH=\"23\" HEIGHT=\"23\" SRC=\"/papers/more.gif\"></A>"

	#else:

	out += "<A HREF=\"/papers/" + row['labid'].lstrip('\'') + "/index-all.html\">" + "<IMG BORDER=\"0\" WIDTH=\"23\" HEIGHT=\"23\" SRC=\"/papers/more.gif\"></A>"

	out += "</DIV>\n<P />\n"



	out += '<A HREF="index.html">Switch to compact view</A><hr>\n<table>\n'

	if not authors:

		out += '<tr><td width=100><b><font color=gray>Authors</font></b></td><td><b><font color=#000077>&nbsp;</font></b></td></tr>\n'

	else:

		out += '<tr><td width=100><b><font color=gray>Authors</font></b></td><td><b><font color=#000077>'

		link = '<A HREF="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=PureSearch&db=PubMed&details_term=%s">%s</A>'

		authorlinks = [link % (a.lstrip('\'').strip().replace(' ','%20'),a.lstrip('\'').strip()) for a in authors.split(',')]

		# print authorlinks

		out += ', '.join(authorlinks)

		out += '</font></b></td></tr>\n'

	if not journal:

		out += '<tr><td width=100><b><font color=gray>Journal</font></b></td><td><b><font color=#000077>&nbsp;</font></b></td></tr>\n'

	else:

		out += '<tr><td width=100><b><font color=gray>Journal</font></b></td><td><b><font color=#000077>'

		out += '<A HREF="http://locatorplus.gov/cgi-bin/Pwebrecon.cgi?DB=local&v2=1&ti=1,1&Search_Arg=9808944&Search_Code=0359&CNT=20&SID=1">'

		out += journal + '</A></font></b></td></tr>'

	if not row['pmid']:

		out += "<tr><td width=100><b><font color=gray>PMID</font></b></td><td><b><font color=#000077>&nbsp;</font></b></td></tr>\n"

	else:

		out += '<tr><td width=100><b><font color=gray>PMID</font></b></td><td><b><font color=#000077>'

		out += '<A HREF="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=' + row['pmid'].lstrip('\'') + '&dopt=Abstract">'

		out +=  row['pmid'].lstrip('\'') + '</A></font></b></td></tr>\n'

	if not pages:

		out += "<tr><td width=100><b><font color=gray>Pages</font></b></td><td><b><font color=#000077>&nbsp;</font></b></td></tr>\n"

	else:

		out += "<tr><td width=100><b><font color=gray>Pages</font></b></td><td><b><font color=#000077>" + pages.lstrip('\'') + "</font></b></td></tr>\n"

	if not volume:

		out += "<tr><td width=100><b><font color=gray>Volume</font></b></td><td><b><font color=#000077>&nbsp;</font></b></td></tr>\n"

	else:

		out += "<tr><td width=100><b><font color=gray>Volume</font></b></td><td><b><font color=#000077>" + volume.lstrip('\'') + "</font></b></td></tr>\n"

	if not year:

		out += "<tr><td width=100><b><font color=gray>Year</font></b></td><td><b><font color=#000077>&nbsp;</font></b></td></tr>\n"

	else:

		out += "<tr><td width=100><b><font color=gray>Year</font></b></td><td><b><font color=#000077>" + year.lstrip('\'') + "</font></b></td></tr>\n"

	out += "<tr><td width=100><b><font color=gray>labcite</font></b></td><td><b><font color=#000077>" + citation.lstrip('\'') + "</font></b></td></tr>\n"

	if not row['labid']:

		out += "<tr><td width=100><b><font color=gray>labid</font></b></td><td><b><font color=#000077>&nbsp;</font></b></td></tr>\n"

	else:

		out += "<tr><td width=100><b><font color=gray>labid</font></b></td><td><b><font color=#000077>" + row['labid'].lstrip('\'') + "</font></b></td></tr>\n"

	if not title:

		out += "<tr><td width=100><b><font color=gray>labtitle</font></b></td><td><b><font color=#000077>&nbsp;</font></b></td></tr>\n"

	else:

		out += "<tr><td width=100><b><font color=gray>labtitle</font></b></td><td><b><font color=#000077>" + title.lstrip('\'') + "</font></b></td></tr>\n"

	if not row['subject']:

		out += "<tr><td width=100><b><font color=gray>subject</font></b></td><td><b><font color=#000077>&nbsp;</font></b></td></tr>\n"

	else:

		subjects = row['subject'].split(',')

		num_subjects = len(subjects)

		out += '<tr><td width=100><b><font color=gray>subject</font></b></td><td><b><font color=#000077>'

		subject_count = 0

		for subject in subjects:

			out += '<A HREF="/subject/' + subject.lstrip('\' ') + '">' + subject.lstrip('\' ') + '</A>'

			subject_count += 1

			if subject_count < num_subjects:

				out += ', '

		out += '</font></b></td></tr>\n'

	if not row['website']:

		out += "<tr><td width=100><b><font color=gray>website</font></b></td><td><b><font color=#000077>&nbsp;</font></b></td></tr>\n"

	else:

		out += '<tr><td width=100><b><font color=gray>website</font></b></td><td><b><font color=#000077><A HREF="'+row['website'].lstrip('\'')+'">'+row['website'].lstrip('\'')+'</A></font></b></td></tr>\n'

	

	out += "</table><br><font color=gray>Unused tags: <i>e-print footnote grant ignore preprint sortval target website2</i></font><hr><a href='/'>Return to papers index</a><br>&nbsp;</blockquote></BODY></HTML>"

	entryExtendedFile.write(out)



def printPaperEntry(row, summaryFile, pubmed):

	title = ''

	citation = ''

	authors = ''

	year = ''

	for pubmed_row in pubmed:

		if row['pmid'] == pubmed_row['pmid']:

			title = pubmed_row['title']

			citation = pubmed_row['citation']

			authors = pubmed_row['authors']

			year = pubmed_row['year']

			break

	# print title and citation

	if not title:

		out = "<DIV CLASS=\"paperTitle\"><FONT SIZE=+1><B><A HREF=\"/papers/" + row['labid'].lstrip('\'') + "/index.html\">" + row['title'] + "</A></B></FONT></DIV>\n"

	else:

		out = "<DIV CLASS=\"paperTitle\"><FONT SIZE=+1><B><A HREF=\"/papers/" + row['labid'].lstrip('\'') + "/index.html\">" + title.lstrip('\'') + "</A></B></FONT></DIV>\n"

	if not citation:

		if not row.has_key('authors'):	

			out += "<DIV CLASS=\"paperCite\">" + row['citation'].lstrip('\'') + "</DIV>\n"	

		else:	

			out += "<DIV CLASS =\"paperCite\">" + row['authors'].lstrip('\'') + " " + row['citation'].lstrip('\'') + "</DIV>\n"			

	else:

		out += "<DIV CLASS=\"paperCite\">" + authors.lstrip('\'') + "&nbsp;" + citation.lstrip('\'') + "</DIV>\n"

	# print links

	out += "<DIV CLASS=\"paperCite\">"

	if not row['website']:

		out += "<IMG SRC=\"/papers/null.gif\" HEIGHT=\"23\" WIDTH=\"56\" BORDER=\"0\">"

	else:

		out += "<A HREF=\"" + row['website'].lstrip('\'')  + "\"><IMG SRC=\"/papers/website.jpg\" HEIGHT=\"23\" WIDTH=\"56\" BORDER=\"0\"></A>"

	if not row['preprint']:

		out += "<IMG SRC=\"/papers/null.gif\" HEIGHT=\"23\" WIDTH=\"56\" BORDER=\"0\">"

	else:

		out += "<A HREF=\"" + row['preprint'].lstrip('\'') + "\"><IMG BORDER=\"0\" HEIGHT=\"23\" WIDTH=\"56\" SRC=\"/papers/preprint.jpg\"></A>"

	if not row['pmid']:

		out += "<IMG SRC=\"/papers/null.gif\" HEIGHT=\"23\" WIDTH=\"56\" BORDER=\"0\">"

	else:

		out += "<A HREF=\"http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=" + row['pmid'].lstrip('\'') + "&dopt=Abstract\"><IMG BORDER=\"0\" HEIGHT=\"23\" WIDTH=\"56\" SRC=\"/papers/medline.jpg\"></A>"

	#if not labid:

	#	out += "<A HREF=\"#\">" + "<IMG BORDER=\"0\" WIDTH=\"23\" HEIGHT=\"23\" SRC=\"/papers/more.gif\"></A>"

	#else:

	out += "<A HREF=\"/papers/" + row['labid'].lstrip('\'') + "/index-all.html\">" + "<IMG BORDER=\"0\" WIDTH=\"23\" HEIGHT=\"23\" SRC=\"/papers/more.gif\"></A>"

	out += "</DIV>\n<P />\n"

	summaryFile.write(out)



def printSimpleEntry(row, simpleFile, pubmed):

	pmid = ''

	title = ''

	citation = ''

	authors = ''

	year = ''

	#if row['pmid']:

		#print 'pSE first: ' + row['pmid']

	#else:

		#print 'pSE first: no pmid'

	pubmed.count = 0

	for pubmed_row in pubmed:

		#print 'pSE pubmed: ' + pubmed_row['pmid']

		if row['pmid'] == pubmed_row['pmid']:

			pmid = pubmed_row['pmid']

			title = pubmed_row['title']

			citation = pubmed_row['citation']

			authors = pubmed_row['authors']

			year = pubmed_row['year']

			pmcid = pubmed_row['pmcid']

			break

		#else:

			#print 'no match'

	if row['pmid']:

		out = '<DL COMPACT>' + authors.lstrip('\'') + ' (' + year.lstrip('\'') + '). "' + title.lstrip('\'') +'" '

		p = re.compile("\(\d+\)\.")	

		p2 = re.compile(":")

		citation = p.sub("",citation)

		citation = p2.sub(": ",citation)

		out += citation.lstrip('\'') + ' <FONT SIZE=-2>[PMID: ' + pmid + ']</FONT>.</DL>\n'

	else:

		#if not row['authors']:

		out = '<DL COMPACT>' +'"' + row['title'].lstrip('\'') + '." '

			#out = '<DL COMPACT>' + ' (' + row['year'].lstrip('\'') + '). "' + row['title'].lstrip('\'') +'" '

		#else:

			#out = '<DL COMPACT>' + row['authors'].lstrip('\'') + ' (' + row['year'].lstrip('\'') + '). "' + row['title'].lstrip('\'') +'" '

		out += row['citation'].lstrip('\'') + '</DL>\n'

	simpleFile.write(out)



def printSubject(master_spreadsheet,header):

	allsubjects = []

	subjectpapers = []

	for i,row in enumerate(master_spreadsheet):

		if row.has_key('subject') and row['subject']: #and row['pmid'].isdigit():

			subjects = row['subject'].split(',')

			for subject in subjects:

				subject = subject.strip( ) 

				if subject not in allsubjects:

					allsubjects.append(subject)

					subjectpapers.append([i])

				else:

					index = allsubjects.index(subject)

					subjectpapers[index].append(i)

 

	for row in subject_spreadsheet:

		subject = row['labid'].strip( )

		if subject not in allsubjects:

			path = subjectPath + subject

			if not os.path.exists(path):

				os.makedirs(path) 

			subjectFile = open(path + '/index.html', 'w')

			out = '''<HTML>

<HEAD>

<TITLE>%s</TITLE>

'''%subject.capitalize()



			out +=header

			include = ''

			if row['html']:

				include =row['html'].lstrip('\'')

			if include:

				out += include

			subjectFile.write(out)

			subjectFile.write('</FONT><HR><A HREF =        "/"><B>Return to front page</B></A>\n</BODY></HTML>')

			subjectFile.close()

	

	for i,subject in enumerate(allsubjects):

		printSubjectFile(subject,subjectpapers[i])

 

def printSubjectFile(subject,papers):

	path = subjectPath + subject

	if not os.path.exists(path):

		os.makedirs(path)

	subjectFile = open(path + '/index.html','w')

#	subjectInclude = path + '/include.html'

	out = '''<HTML>

<HEAD>

<TITLE>%s</TITLE>

''' % subject.capitalize()

	out += header

	

	#include include file if exists

#	if os.path.exists(subjectInclude):

#		includeFile = open(subjectInclude,'r')

#		for line in includeFile:

#			subjectFile.write(line + '\n')

#		includeFile.close()

#	subjectFile.write('\n\n')

	include = ''

	for row in subject_spreadsheet:

		if row['labid'] == subject:

			if row['html']:

				include	= row['html'].lstrip('\'')

	if include:

		out += include

	subjectFile.write(out)



	for r in papers:

		printSubjectEntry(subjectFile,r)

	subjectFile.write('	</FONT><HR><A HREF=       "/"><B>Return to front page</B></A>\n</BODY></HTML>')

	subjectFile.close()

	

def printSubjectEntry(subjectFile,r):

	row = master_spreadsheet.rows[r]

	found = False

	for sr in pubmed_spreadsheet:

		if row['pmid'] == sr['pmid']:

			#row['labid'] = sr['labid']

			row['title'] = sr['title']

			row['authors'] = sr['authors']

			row['year'] = sr['year']

			row['citation'] = sr['citation']

			#row['website'] = sr['website']

			#row['preprint'] = sr['preprint']

			found = True

		#	break

	if  found:

        	# print title and citation

		if not row['labid']:

                	out = "<DIV CLASS=\"paperTitle\"><FONT SIZE=+1><B>" + row['title'].lstrip('\'') + "</A></B></FONT></DIV>\n"

		else:

                	out = "<DIV CLASS=\"paperTitle\"><FONT SIZE=+1><B><A HREF=\"/papers/" + row['labid'].lstrip('\'') + "/index.html\">" + row['title'].lstrip('\'') + "</A></B></FONT></DIV>\n"

        	out += "<DIV CLASS=\"paperCite\">" + row['authors'].lstrip('\'') + " " + row['citation'].lstrip('\'') + "</DIV>\n"  

        	# print links

        	out += "<DIV CLASS=\"paperCite\">"

        	if not row['website']:

                	out += "<IMG SRC=\"/papers/null.gif\" HEIGHT=\"23\" WIDTH=\"56\" BORDER=\"0\">"

        	else:

                	out += "<A HREF=\"" + row['website'].lstrip('\'')  + "\"><IMG SRC=\"/papers/website.jpg\" HEIGHT=\"23\" WIDTH=\"56\" BORDER=\"0\"></A>"

        	if not row['preprint']:

                	out += "<IMG SRC=\"/papers/null.gif\" HEIGHT=\"23\" WIDTH=\"56\" BORDER=\"0\">"

        	else:

                	out += "<A HREF=\"" + row['preprint'].lstrip('\'') + "\"><IMG BORDER=\"0\" HEIGHT=\"23\" WIDTH=\"56\" SRC=\"/papers/preprint.jpg\"></A>"

        	if not row['pmid']:

                	out += "<IMG SRC=\"/papers/null.gif\" HEIGHT=\"23\" WIDTH=\"56\" BORDER=\"0\">"

        	else:

                	out += "<A HREF=\"http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=" + row['pmid'].lstrip('\'') + "&dopt=Abstract\"><IMG BORDER=\"0\" HEIGHT=\"23\" WIDTH=\"56\" SRC=\"/papers/medline.jpg\"></A>"

        	if not row['labid']:

                	out += "<A HREF=\"#\">" + "<IMG BORDER=\"0\" WIDTH=\"23\" HEIGHT=\"23\" SRC=\"/papers/more.gif\"></A>"

        	else:

                	out += "<A HREF=\"/papers/" + row['labid'].lstrip('\'') + "/index-all.html\">" + "<IMG BORDER=\"0\" WIDTH=\"23\" HEIGHT=\"23\" SRC=\"/papers/more.gif\"></A>"

        	out += "</DIV>\n<P />\n"



		subjectFile.write(out)



def printSubjectSummary(subject_spreadsheet, subjectSummaryFile, header):

	styleSubject = '''

	<BR>    

	<STYLE type="text/css">

	.unsel{background-color:#ffffff; background-position:top; background-repeat:repeat-x; color:#FFFFFF; font-weight:normal;}

	.sel {background-color:#3b5998; color:#FFFFFF; font-weight:normal;}

	.content{background-color:#ffffff; height:25px; padding-left:20px; padding-right:20px; padding-top:20px;color:#ffffff;}

        a{text-decoration:none;color:#ffffff;}

	.unsel a:link {color:#888888;text-decoration:none;}

	.sel a:visited {color:#ffffff;text-decoration:none;}

	.sel a:active {color:#ffffff;text-decoration:none;}

	.sel a:hover {color:#ffffff;text-decoration:underline;}

	</STYLE>

	'''



	category = ''

	SubjectNumber = 0

	outPart = ''

	out = "<HTML>\n"

	out += "<HEAD>\n"

	out += "<TITLE>Gerstein Lab Publications</TITLE>\n"

	out += header

	out += "\n"

	out += styleSubject

	out += '<BODY onload="javascript:showdh(3);">\n'

	out +=  '<TABLE width="915" height="30" frame ="hsides" align="center" cellpadding="0" cellspacing="0">\n<TR>\n<TD width="6"></TD>\n'



	for row in subject_spreadsheet:

		if not category == row['category'].lstrip('\''):

			if not category == '':

				outPart +=       "</TD></TR>\n"

			SubjectNumber +=1

			tableid = str(SubjectNumber)

			category = row['category'].lstrip('\'')

			out +='<TD width="86" class="unsel" id="dh'+tableid+'"><DIV align="center"><FONT FACE=" sans-serif,arial, Helvetica" SIZE=3><A href="javascript:showdh('+tableid+');" _fcksavedurl="javascript:showdh('+tableid+');">'+ row['category'].lstrip('\'') + '</A></FONT></DIV></TD>\n'

			out  += ' <TD width="6"></TD>\n'

			outPart +='<TR id="menu'+ tableid+'" style="display:none">\n'

			outPart +='<TD class="content" style="line-height:25px">\n'

		outPart +=  "<FONT FACE='times'>  <A HREF='/subject/" + row['labid'].lstrip('\'')+"/index.html' STYLE='text-decoration:none; color:black'>"

		title = str(row['title'])

		outPart +=    "<TT>[ "+row['labid'].lstrip('\'')+" ]</TT>  "+title.lstrip('\'')+"</A></FONT><BR>\n"

	outPart += "</TD></TR>\n"     

	out += '</TR></TABLE>\n<TABLE width="915" border="0" align="center" cellpadding="0" cellspacing="0">\n'



	out += outPart 

	out += ''' <script language="javascript">

		function showdh(n){

		for(var i=1;i<=''' + tableid+''';i++){

		eval("dh" + i).className="unsel"

		eval("menu"+i).style.display="none";

		}

		eval("dh"+n).className="sel"

		eval("menu"+n).style.display="";

		}

		</script>

		'''

	out += "</BODY></HTML>" 

	subjectSummaryFile.write(out)  



printSubjectSummary(subject_spreadsheet, subjectSummaryFile, header)

printSubject(master_spreadsheet,header)

printPapers(master_spreadsheet, summaryFile, header)

</pre><code>