Build Papers Page Code

From GersteinInfo

(Difference between revisions)
Revision as of 11:35, 16 September 2011

update.py

Basic Setup
#!/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>
 • 
<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>
 • 
</FONT>
</CENTER>
<HR>
'''
<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 += "\n"
	out += "Main Scientific Publications\n"
	out += "\n"

	out += " Total papers: " + str(len(master_spreadsheet)) + "\n"
	out += "(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 += "
 -- " + currentYear + " (" + str(years[currentYear]) + ") --"
		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 += "\n"
	out += "" + row['labid'] + "<p />"
	out += "\n"
	# print title and citation
	out += "<A HREF=\"/papers/" + row['labid'].lstrip('\) + "/index.html\">" + row['title'].lstrip('\) + "</A>\n"
	if row.has_key('authors'):		

		out += "" +row['authors'].lstrip('\)+ " " +row['citation'].lstrip('\) + "\n"	
	else:		

		out += "" + " " + row['citation'].lstrip('\) + "
\n"	
	# print links

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

<a href=index-all.html>View all citation information</a>
<a href='/'>Return to papers index</a>
 </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 += "\n"
	if not row['labid']:
		out += "" + row['pmid'].lstrip('\) + "<p />"
	else:
		out += "" + row['labid'] + "<p />"
	out += "\n"
	# print title and citation
	if not title:
		out += "<A HREF=\"/papers/" + row['labid'].lstrip('\) + "/index.html\">" + row['title'].lstrip('\) + "</A>\n"
	else:

		out += "<A HREF=\"/papers/" + row['labid'].lstrip('\) + "/index.html\">" + title.lstrip('\) + "</A>\n"
	if not citation:
	 	if not row.has_key('authors'):		

	 		out += "" + " " + row['citation'].lstrip('\) + "
\n"	
	#	out += "" + " " + row['citation'].lstrip('\) + "
\n"	
	 	else:		

	 		out += "" + row['authors'].lstrip('\) + " " +row['citation'].lstrip('\) + "\n"	
	else:

		out += "" + authors.lstrip('\) + ' ' + citation.lstrip('\) + "\n"
	# print links

	out += ""
	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 += "\n<P />\n"
	out += '<A HREF="index.html">Switch to compact view</A>\n\n'
	if not authors:

		out += '\n'
	else:

		out += '\n'
	if not journal:
		out += '\n'
	else:

		out += ''
	if not row['pmid']:
		out += "\n"
	else:

		out += '\n'
	if not pages:
		out += "\n"
	else:

		out += "\n"	if not volume:

		out += "\n"
	else:

		out += "\n"	if not year:

		out += "\n"
	else:

		out += "\n"
	out += "\n"	if not row['labid']:

		out += "\n"
	else:

		out += "\n"	if not title:

		out += "\n"
	else:

		out += "\n"	if not row['subject']:

		out += "\n"
	else:
		subjects = row['subject'].split(',')
		num_subjects = len(subjects)

		out += '\n'
	if not row['website']:
		out += "\n"
	else:

		out += '\n'
	out += "Authors  
Authors '
		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 += '
Journal  
Journal '
		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>
PMID  
PMID '
		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>
Pages  
Pages " + pages.lstrip('\) + "
Volume  
Volume " + volume.lstrip('\) + "
Year  
Year " + year.lstrip('\) + "
labcite " + citation.lstrip('\) + "
labid  
labid " + row['labid'].lstrip('\) + "
labtitle  
labtitle " + title.lstrip('\) + "
subject  
subject '
		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 += '
website  
website <A HREF="'+row['website'].lstrip('\)+'">'+row['website'].lstrip('\)+'</A>

Unused tags: e-print footnote grant ignore preprint sortval target website2
<a href='/'>Return to papers index</a>
 </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 = "<A HREF=\"/papers/" + row['labid'].lstrip('\) + "/index.html\">" + row['title'] + "</A>
\n"
	else:

		out = "<A HREF=\"/papers/" + row['labid'].lstrip('\) + "/index.html\">" + title.lstrip('\) + "</A>\n"
	if not citation:
		if not row.has_key('authors'):	

			out += "" + row['citation'].lstrip('\) + "
\n"	
		else:	

			out += "" + row['authors'].lstrip('\) + " " + row['citation'].lstrip('\) + "\n"			
	else:

		out += "" + authors.lstrip('\) + " " + citation.lstrip('\) + "\n"
	# print links

	out += ""
	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 += "\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 = '
' + authors.lstrip('\) + ' (' + year.lstrip('\) + '). "' + title.lstrip('\) +'" '
		p = re.compile("\(\d+\)\.")	
		p2 = re.compile(":")
		citation = p.sub("",citation)
		citation = p2.sub(": ",citation)
		out += citation.lstrip('\) + ' [PMID: ' + pmid + '].
\n'
	else:
		#if not row['authors']:
		out = '' +'"' + row['title'].lstrip('\) + '." '
			#out = '' + ' (' + row['year'].lstrip('\) + '). "' + row['title'].lstrip('\) +'" '
		#else:
			#out = '' + row['authors'].lstrip('\) + ' (' + row['year'].lstrip('\) + '). "' + row['title'].lstrip('\) +'" '
		out += row['citation'].lstrip('\) + '
\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>
<A HREF =        "/">Return to front page</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>
<A HREF=       "/">Return to front page</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 = "" + row['title'].lstrip('\) + "</A>
\n"
		else:

                	out = "<A HREF=\"/papers/" + row['labid'].lstrip('\) + "/index.html\">" + row['title'].lstrip('\) + "</A>\n"
        	out += "" + row['authors'].lstrip('\) + " " + row['citation'].lstrip('\) + "\n"  
       	# print links

        	out += ""
       	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 += "\n<P />\n"
		subjectFile.write(out)
def printSubjectSummary(subject_spreadsheet, subjectSummaryFile, header):
	styleSubject = 
	
    
	<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 +=  '\n\n\n'
	for row in subject_spreadsheet:
		if not category == row['category'].lstrip('\):
			if not category == :

				outPart +=       "</TD>\n"
			SubjectNumber +=1
			tableid = str(SubjectNumber)
			category = row['category'].lstrip('\)
			out +='<TD width="86" class="unsel" id="dh'+tableid+'"><A href="javascript:showdh('+tableid+');" _fcksavedurl="javascript:showdh('+tableid+');">'+ row['category'].lstrip('\) + '</A>
</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 +=  "  <A HREF='/subject/" + row['labid'].lstrip('\)+"/index.html' STYLE='text-decoration:none; color:black'>"
		title = str(row['title'])
		outPart +=    "[ "+row['labid'].lstrip('\)+" ]  "+title.lstrip('\)+"</A>
\n"
	outPart += "</TD></TR>\n"     

	out += '</TR></TABLE>\n
\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>


Retrieved from "http://info.gersteinlab.org/Build_Papers_Page_Code"
Authors
Authors	' 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 += '
Journal
Journal	' 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>
PMID
PMID	' 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>
Pages
Pages	" + pages.lstrip('\) + "
Volume
Volume	" + volume.lstrip('\) + "
Year
Year	" + year.lstrip('\) + "
labcite	" + citation.lstrip('\) + "
labid
labid	" + row['labid'].lstrip('\) + "
labtitle
labtitle	" + title.lstrip('\) + "
subject
subject	' 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 += '
website
website	*<A HREF="'+row['website'].lstrip('\)+'">'+row['website'].lstrip('\)+'</A>*
Build Papers Page Code

From GersteinInfo

Revision as of 11:35, 16 September 2011

update.py

Total papers: " + str(len(master_spreadsheet)) + "

-- " + currentYear + " (" + str(years[currentYear]) + ") --

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@@ Line 63: / Line 63: @@
 <HR>
 '''
-</pre><Code>
+</pre><code>
 def printPapers(master_spreadsheet,summaryFile, header):