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pyHuibl_dev.py
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#!/usr/local/bin/python3
import re
import os
import pickle
#import ads.sandbox as ads
import ads
import codecs
import time
import sys
import matplotlib
matplotlib.use('TkAgg')
import matplotlib.pyplot as pl
import numpy as np
#import pylab as pl
import datetime as dt
import argparse as ap
from shutil import copyfile
from operator import itemgetter
'''
Read huibl data file, for maintaining publications, web side and monitor citations
v19 cleaned up some reporting new citations, purge multiple entries on same day
- note wrote a cleanup routine to delete redundant citation entries.
todo
- v9: check 4 cits, check excel
-v10: also compare to last run
- check -1 counts for sources with temp arXiV
- Because the arXiv counts make the citations go up and down, it is alos useful to have a csv of the last run and
compare new citations against the last run. Otherwise the count going down can mas a new citation
- write docx?
'''
rootdir = os.environ['HOME']
monthdir = rootdir+'/Work/Docs/Huib/Publists'
dailydir = rootdir+'/Work/Mondata/Huibl'
dostatsupdate = False
verbose = False
debug = False
Nadspol = 0
#doAdsPol = False
#exAdsPol = ['2017ApJ...848L..12A']
#maxpolads = 500
if debug: print('Counting:',Nadspol)
sorttype = ['paper','confer','book','popular','poster','memo','other']
pubencoding = 'utf-8'
version = 'v3'
arroot = rootdir+'/Work/Web/Live/Archive'
arref = 'Archive'
def GetArgs():
'''
Get the arguments to reading the data
'''
parser = ap.ArgumentParser(description='Update list of publications & citations')
# parser.add_argument('integers', metavar='N', type=int, nargs='+',
# help='an integer for the accumulator')
parser.add_argument('-n','--noupdate', action = 'store_true',
help='do not update from ads')
parser.add_argument('-c','--compare', choices=['month','recent','day'],
default = 'month',
help='compare to monthly savings or most recent (yesterday?)')
parser.add_argument('-y','--yscale', choices=['linear','log','root'],
default = 'linear',
help ='scale on y axis, lin, log or root')
parser.add_argument('-p','--plot', choices=['papsel','citsum','allpap','hindex','hinnow','none'],
default = 'none',
help='plot todo, papsel, citsum, allpap, hindex,none')
parser.add_argument('-w','--window', choices=['all','adecade','ayear','amonth','aweek'],
default = 'all',
help='plot window constrained to last ...')
parser.add_argument('-s','--sort', choices=['original','reverse','byyear','bycits',
'typeyear','typecits'], default = 'reverse',
help='sort order for html output')
parser.add_argument('-x','--maxpolads',type=int,default=500)
args = parser.parse_args()
return args
class CitStats():
class CitPaper():
def __init__(self,bib='',author='',tag='',type='memo',cits=[]):
self.bib=bib
self.ids={}
self.ids['author']=author
self.ids['tag']=tag
self.ids['type']=type
self.cits=cits
def __init__(self, papers=None,dates=None):
if (papers == None): papers = []
if (dates == None): dates = []
self.fields=['author','tag','type']
self.papers = papers
self.dates = dates
return
def dtDates(self):
dtdates = []
for date in self.dates:
tmp = date.split('/')
year = int(tmp[2])
if (year > 50 ): year += 1900
else: year += 2000
dtdates.append(dt.datetime(year,int(tmp[1]),int(tmp[0])))
return dtdates
def dump(self,output):
#write header
output.write('{:20}'.format('Header'))
for field in self.fields:
output.write('{:20}'.format(field))
for day in self.dates:
output.write('{:8}'.format(day))
output.write('\n')
for pap in self.papers:
output.write('{:20}'.format(pap.bib))
for field in self.fields:
output.write('{:20}'.format(pap.ids[field]))
for count in pap.cits:
output.write('{:8}'.format(count))
output.write('\n')
def addPaper(self,paper,author,tag,type,newcit):
#add a paper, set cits to zero, but most recent to newcit
tmpcits = []
for day in range(len(self.dates)-1):
tmpcits.append(0)
tmpcits.append(newcit)
self.papers.append(self.CitPaper(paper,author,tag,type,tmpcits))
def delCol(self,id):
del self.dates[id]
for pap in self.papers:
del pap.cits[id]
return
def addDate(self,date):
self.dates.append(date)
for pap in self.papers:
pap.cits.append(-1)
def updCits(self, code, newc ):
#updates the most recent cit
for pap in self.papers:
if (pap.bib == code):
pap.cits[-1] = newc
def readStats(self,file):
stafile = open(file,'r',encoding='ascii')
readheader = True
for line in stafile:
fields = line.rstrip('\r\n').split(',')
ncols = len(fields)
if (readheader):
for i in range(len(self.fields)):
#print('Test:',i,fields[0],fields[1])
if ( fields[i+1] != self.fields[i] ): print('WARN fields',i, fields, self.fields)
for i in range(len(self.fields)+1,ncols):
self.dates.append(fields[i])
readheader = False
else:
tmpcits = []
for i in range(len(self.fields)+1,ncols):
#print('debug:',i,fields[i])
tmpcits.append(int(fields[i]))
self.papers.append(self.CitPaper(fields[0],fields[1],fields[2],fields[3],tmpcits))
def writeStats(self,file):
#first check whether the new column has same date as one but last
if (self.dates[-1] == self.dates[-2]):
print('Rerunning on ',self.dates[-2],' cleaning up')
self.delCol(-2)
outp = open(file,'w',encoding='ascii',errors='ignore')
outp.write('{},'.format('bibcode'))
for field in self.fields:
outp.write('{},'.format(field))
for entry in self.dates[:-1]:
outp.write('{},'.format(entry))
outp.write('{}\n'.format(self.dates[-1]))
#for pap in self.papers:
for pap in sorted(self.papers, key = lambda num: num.cits[-1], reverse=True):
#for cit in sorted(cits, key = lambda numb: numb[-1], reverse=True ):
outp.write('{},'.format(pap.bib))
for id in self.fields:
#print('debug',pap.ids[id])
outp.write('{},'.format((pap.ids[id])))
for cit in pap.cits[:-1]:
outp.write('{},'.format(cit))
outp.write('{}\n'.format(pap.cits[-1]))
def mostRecent(self):
return self.dates[-1]
def extrPlots(self, top):
x = self.dtDates()
y = []
name = ''
for pap in self.papers:
if (pap.bib == top):
y = pap.cits
name = pap.bib+':'+pap.ids['author']+' ('+pap.ids['tag']+')'
return name, x, y
def sumPlots(self):
x = self.dtDates()
y = []
for idt in range(len(self.dates)):
sumcit = 0
for pap in self.papers:
sumcit += pap.cits[idt]
y.append(sumcit)
return 'Sum Citations',x,y
def indexH(self):
x = self.dtDates()
y = []
hinnow = []
for idt in range(len(self.dates)):
tmph = []
#print 'rset',tmph
for pap in self.papers:
tmph.append(pap.cits[idt])
#print idt,pap.bib,pap.cits[idt]
tmph.sort(reverse = True)
#print '1 dim',tmph
hindex = 0
#print 'hin on date', idt, tmph
if(idt == len(self.dates)-1):
hinnow = tmph
for ih in range(len(tmph)):
if (ih+1 <= tmph[ih]):
#print('Ha:',ih,ih+1,tmph[ih])
hindex = ih+1
y.append(hindex)
print('Current H index: ',y[-1])
#huib hier
best = 0
for pap in self.papers:
#print the nearest paper to increase H and those within 3
if (pap.cits[-1] <= y[-1] and pap.cits[-1] > best):
best = pap.cits[-1]
for pap in self.papers:
if (pap.cits[-1] <= y[-1] and (best - pap.cits[-1]) < 3):
print('Close to increase Hindex: {:19}, {:20} at {:3}'.format(
pap.bib, pap.ids['author'],pap.cits[-1]))
return 'H index',x,y, hinnow
def findSteepest(self,deltad,exclude):
'''return the steepest riser in deltad, taking into account exclude'''
recedate = self.dtDates()[-1]
ilast = 0
idt = 0
for dtdate in self.dtDates():
if (recedate-dtdate>dt.timedelta(deltad)):
ilast = idt
idt += 1
steeppap = self.papers[0]
steepest = 0
for pap in self.papers:
if ((pap.cits[-1]-pap.cits[ilast])>steepest and pap.bib not in exclude ):
steeppap = pap
steepest = pap.cits[-1]-pap.cits[ilast]
print('Steepest riser over {:6.2f} yr: {:19}, {:20} from {:3} to {:3}'.format(deltad/365,
steeppap.bib, steeppap.ids['author'],steeppap.cits[ilast],steeppap.cits[-1]))
return steeppap.bib
def allCodes(self):
#all papers with a cit
mypapers = []
for pap in self.papers:
if (pap.cits[-1] > 0):
mypapers.append(pap.bib)
return mypapers
def selBibCodes(self):
'''
print som<e articles with interesting stats
and return a list of fav articles for plotting
'''
minimal = ['2006ASPC..351..497K','1995ApJ...448L.123V','2017ApJ...834L...8M']
exclude = ['2017ApJ...848L..12A','2017Natur.541...58C','2017ApJ...834L...7T']
for code in minimal:
for pap in self.papers:
if (pap.bib == code):
print('Favourite paper : {:19}, {:20} now at {:3}'.format(pap.bib,
pap.ids['author'],pap.cits[-1]))
for code in exclude:
for pap in self.papers:
if (pap.bib == code):
print('Exlude from stats: {:19}, {:20} now at {:3}'.format(pap.bib,
pap.ids['author'],pap.cits[-1]))
#find most cited
maxcit = 0
maxpap = self.papers[0]
for pap in self.papers:
if (pap.cits[-1] > maxcit and pap.bib not in exclude):
maxcit = pap.cits[-1]
maxpap = pap
print('Max cited paper: {:19}, {:20} now at {:3}'.format(maxpap.bib,
maxpap.ids['author'],maxpap.cits[-1]))
#maintain a list with papers to plot:
plotlist = minimal
if (not maxpap.bib in plotlist): plotlist.append(maxpap.bib)
#find fastest increase
steeppap = self.findSteepest(16*365,exclude)
if (not steeppap in plotlist): plotlist.append(steeppap)
steeppap = self.findSteepest(4*365,exclude)
if (not steeppap in plotlist): plotlist.append(steeppap)
steeppap = self.findSteepest(365,exclude)
if (not steeppap in plotlist): plotlist.append(steeppap)
steeppap = self.findSteepest(0.25*365,exclude)
if (not steeppap in plotlist): plotlist.append(steeppap)
#find all first author with more than 20
for pap in self.papers:
if (pap.cits[-1] > 35 and (pap.ids['author'].find('angeveld')>0)):
if (not pap.bib in plotlist): plotlist.append(pap.bib)
return plotlist
def reportCits(self, pltype, plwindow, yscale ):
'''
Generate report on citations by plotting
'''
def plotHinnow(hinnow):
x = np.array(range(len(hinnow)))+1
hsel = np.where( x < hinnow )
ih=hsel[0][-1]
#print('paper:',papcits['pap'][ih],' has:',papcits['cits'][ih])
#print('paper:',papcits['pap'][ih+1],' has:',papcits['cits'][ih+1])
hindex=x[ih]
x1, y1 = [hindex, 0], [hindex, hindex]
x2, y2 = [hindex, hindex], [0, hindex]
pl.plot(x1, y1, x2, y2,'k-')
pl.plot(x,hinnow)
pl.yscale('log')
pl.show()
def plotCits( taglist, xlistx, ylisty, xmin, ymin, yscale ):
print ('yscale:',yscale)
myscale = 'linear'
if (yscale=='log'): myscale= 'log'
x = np.array(xlistx)
y = np.array(ylisty)
mycol=['r','g','b','k','m',
'darkcyan','orange','maroon',
'navy','teal', 'gray', 'purple'] #omitting 'y' and 'w'
pl.title("Huib's citation extract")
pl.ylabel('citations')
pl.xlabel('date')
print(type(x),x.shape,type(y),y.shape)
#for xval in
ibeg = (abs(x - xmin)).argmin()
pl.xlim(right=x[0][-1],left=xmin)
pl.ylim(bottom=max(1,0.99*np.min(y[:,ibeg:-1])), top=1.01*np.max(y[:,ibeg:-1]))
print('YLim:',np.min(y[:,ibeg:-1]),np.max(y[:,ibeg:-1]))
ic = 0
for ipl in range(len(x)):
pl.plot(x[ipl],y[ipl],c=mycol[ic],lw=2,label=taglist[ipl])
ic += 1
if (ic > len(mycol)-1): ic = 0
ax = pl.subplot(111)
ax.set_yscale(myscale)
box = ax.get_position()
ax.set_position([box.x0-0.1*box.width, box.y0 + box.height * 0.2,
1.2*box.width, box.height * 0.8])
ax.legend(loc='upper center', bbox_to_anchor=(0.5, -0.07), ncol=4, fontsize=8)
wm = pl.get_current_fig_manager()
wm.window.wm_geometry("1400x400+5+5")
pl.show()
x = []
y = []
tag = []
sumtag,sumx,sumy = self.sumPlots()
hixtag,hix,hiy,hinnow = self.indexH()
arts = self.selBibCodes()
if( pltype == 'hinnow' ):
plotHinnow(hinnow)
elif (pltype == 'papsel'):
for art in arts:
tmptag,tmpx,tmpy = self.extrPlots(art)
tag.append(tmptag)
x.append(tmpx)
y.append(tmpy)
elif (pltype == 'citsum'):
x.append(sumx)
y.append(sumy)
tag.append(sumtag)
elif (pltype == 'hindex'):
x.append(hix)
y.append(hiy)
tag.append(hixtag)
elif (pltype == 'allpap'):
arts = self.allCodes()
for art in arts:
tmptag,tmpx,tmpy = self.extrPlots(art)
tag.append(tmptag)
x.append(tmpx)
y.append(tmpy)
elif (pltype == 'none'):
pass
else:
print('Unknown plot type:',pltype)
if (len(x)>0):
xmin = x[0][0]
if (plwindow != 'all'):
if (plwindow=='adecade'): deltaday = 3653
if (plwindow=='ayear'): deltaday = 365
if (plwindow=='amonth'): deltaday = 30
if (plwindow=='aweek'): deltaday = 7
xmin = dt.datetime.now() - dt.timedelta(deltaday)
ymin = 5000
plotCits( tag, x, y, xmin, ymin, yscale )
return
class Paper():
'''Local storage class for papers'''
def __init__(self,bibcode='.'*19,tag='notag',year='0000',authors=[],
pubmag='unknown',pubpag=0,pubvol=0, matched=False):
self.bibcode = bibcode
self.tag = tag
self.year = year
self.authors = authors
self.pubmag = pubmag
self.pubvol = pubvol
self.pubpag = pubpag
self.pubful = 'Somewhere'
self.cits = -1
self.citlist = []
self.oldcits = -1
self.type = ''
self.files = []
self.actions = []
self.links = []
self.comments = []
self.altbibcodes = []
self.matched = False
def __lt__(self,pap2):
return str(self.bibcode)<str(pap2.bibcode)
def strSum(self):
firsta = self.authors[0].split(',')[0]
outstr = '{:16}: {:19} ({:20})'.format(firsta,self.bibcode,self.tag)
#print self.bibcode, self.tag, self.year, self.authors[0]
return outstr
def PubHtml(self,output):
#print('debug:','<LI>{}'.format(self.authors[0]).encode('ascii', 'xmlcharrefreplace'))
#print('debug:',u'<LI>{}'.format(self.authors[0]))
output.write(u'<LI>{}'.format(self.authors[0]))
if (len(self.authors)>25):
huib = ''
for name in self.authors:
if (name.find('angeveld')>0):
huib = name
for name in self.authors[1:4]:
output.write('; {}'.format(name))
output.write(', and {} authors including {},'.format((len(self.authors)-4), huib))
else:
for name in self.authors[1:]:
output.write('; {}'.format(name))
output.write('\n')
output.write('<CITE>"{}"</CITE>,\n'.format(self.title))
output.write('{}, {}<BR>\n'.format(self.year,self.pubful))
for link in self.files:
rlink = arref+'/'+link
output.write('<A HREF={}> PDF file</A> availabe.\n'.format(rlink))
output.write('<P>\n\n')
def Full(self,output):
'''Print in same format v3'''
output.write('HuiBl-v3: {}, {}, {}\n'.format(self.bibcode, self.tag, self.type))
for name in self.authors:
if (name == self.authors[-1]):
output.write('{};\n'.format(name))
else:
output.write('{}; '.format(name))
output.write('"{}"\n'.format(self.title))
if (self.type != 'paper' or self.pubmag == 'unknown'):
output.write('{}, {}\n'.format(self.year, self.pubful))
else:
if hasattr( self, 'pubspecial'):
output.write('{}, {} ({}) {}, {}\n'.format(self.year, self.pubmag, self.pubspecial, self.pubvol, self.pubpag))
else:
output.write('{}, {} {}, {}\n'.format(self.year, self.pubmag, self.pubvol, self.pubpag))
for pub in self.files:
output.write('file: {}\n'.format(pub))
if hasattr( self, 'preprint'):
output.write('preprint: {}\n'.format(self.preprint))
for reas in self.comments:
output.write('#{}\n'.format(reas))
for code in self.altbibcodes:
output.write('altbibcode: {}\n'.format(code))
for date in self.actions:
output.write('{} {}\n'.format(date[0],date[1]))
for url in self.links:
output.write('link: {}\n'.format(url))
def ParsePub(self, line):
'''Parse publication line, once needed for finding bib code v3'''
repubarxiv = re.compile(r'^\d{4}\,?\s+(arXiv)\:(\d{4})\.(\d{3,5})')
repubart = re.compile(r'^\d{4}\,?\s+(\S+\_?\S)\,?\s+(\d{1,6})\,?\s+(A|L|P)?(\d{1,6})')
respecial = re.compile(r'^\d{4}\,?\s+(\S+)\,?\s+\((.+)\)\s+(\d{1,6})\,?\s+(A|L|P)?(\d{1,6})')
#reproc = re.compile(r'^\d{4}\,?\s+(?:in\s*)(?:the\s*)?Proceedings\ of\s+(\".*\")\,?\s*(.*)\,?\s+p?\.?\s*(\d{1,4})\s*(\-\s*\d{1,4})?\s*$')
matchpubart = repubart.match(line)
matchspecial = respecial.match(line)
matcharxiv = repubarxiv.match(line)
#matchproc = reproc.match(line)
#print '>>',line
if (matchpubart):
self.pubmag =matchpubart.group(1)
self.pubvol =matchpubart.group(2)
self.pubpag =matchpubart.group(4)
#self.GenBibcode()
return True
elif matchspecial:
#1989, A&A (Letters) 216 L1-L4
self.pubmag =matchspecial.group(1)
self.pubspecial = matchspecial.group(2)
self.pubvol =matchspecial.group(3)
self.pubpag =matchspecial.group(5)
#self.GenBibcode()
return True
elif matcharxiv:
self.pubmag =matcharxiv.group(1)
self.pubvol =matcharxiv.group(2)
self.pubpag =matcharxiv.group(3)
else:
if verbose: print('WARN: Decoding v3 data, pubs not recognised: {}'.format(line))
return False
def GenBibcode(self):
self.pubmag = self.pubmag.rstrip(',')
self.bibcode = self.year+self.pubmag
pad = '.'*(5-len(self.pubmag)+4-len(self.pubvol))
self.bibcode += pad + self.pubvol
if hasattr(self, 'pubspecial'):
self.bibcode += self.pubspecial[0]
else:
self.bibcode += '.'
pad = '.'*(4-len(self.pubpag))
self.bibcode += pad + self.pubpag + self.authors[0][0].upper()
def __setitem__(self,key,value):
self.__dict__[key] = value
def fillFromAds(self, ads):
self.bibcode = ads.bibcode
self.authors = ads.author
self.year = ads.year
self.title = ads.title[0]
#Trying this Huib, some papers have not resolved this v13
try:
self.pubful = '{} {}, {}'.format(ads.pub, ads.volume, ads.page[0])
tmpdate = str(ads.pubdate)
adsdate = tmpdate[8:10]+tmpdate[5:7]+tmpdate[2:4]
self.actions.append((adsdate,'adsdate'))
except:
pass
def UpdateByADS(self, ads):
'''deprecated for now'''
self.authors = ads.author
self.title = ads.title[0]
#print ads.pubdate, type(ads.pubdate)
try:
tmpdate = str(ads.pubdate)
adsdate = tmpdate[8:10]+tmpdate[5:7]+tmpdate[2:4]
self.actions.append((adsdate,'adsdate'))
except:
pass
class ListPapers():
def __init__(self):
self.list = []
def Insert(self,paper=Paper()):
self.list.append(paper)
def SumList(self):
for paper in self.list:
print(paper.strSum())
def FullList(self, outfile, mycoding):
output = open(outfile,'w', encoding = mycoding)
for paper in self.list:
output.write('\n')
paper.Full(output)
def getCits(self,item):
return self.list[item].cits
def addStats(self, stats):
for paper in self.list:
for citpap in stats.papers:
if ( paper.bibcode == citpap.bib ):
paper.oldcits = citpap.cits[-1]
paper.cits = paper.oldcits
def ReadPubV3(self,file, myencoding ):
'''parsing v3 file and filling list of papers'''
v3lines = {
'comment': re.compile(r'^\#(.*)'),
'header': re.compile(r'^HuiBl-v3:\s(.{19})\,\s*(\S+),\s*(\S+)\s*(.*)?\s*$'),
'author': re.compile(r'^((.*)\,\s*(.*)\;)+$'),
'title': re.compile(r'^\"(.*)\"\s*$'),
'pub': re.compile(r'^(\d{4})\,?\s+(.*)$'),
'action': re.compile(r'^(\d{6})\s+((in\s)?\S+)\s*(\S*)?\s*$'),
'file': re.compile(r'^file\:\s*(\S+\.\w+)\s*$'),
'altbibcode' : re.compile(r'altbibcode\:\s*(\S*)\s*$'),
'preprint' : re.compile(r'preprint\:\s*(\S*)\s*$'),
'link': re.compile(r'^link\:\s*(http\S+)\s*$'),
'blank': re.compile(r'^\s*$') }
datain = open(file,'r', encoding = myencoding)
inblock = False
nwarn = 0
nhead = 0
for line in datain:
line = line.rstrip('\n')
if debug: print(line)
foundmatch = False
for ltype in list(v3lines.keys()):
#print ltype, oldlines[ltype]
match = v3lines[ltype].match(line)
#first determine if in block
if (match):
#print ltype,':',line
foundmatch = True
if (ltype == 'blank'):
inblock == False
elif (ltype == 'header'):
inblock = True
if (match and inblock):
#time to modify data
if (ltype == 'header'):
nhead += 1
curpap = Paper(bibcode=match.group(1))
self.Insert(curpap)
curpap.tag = match.group(2)
curpap.type =match.group(3)
elif (ltype == 'comment'):
curpap.comments.append(match.group(1))
elif (ltype == 'altbibcode'):
curpap.altbibcodes.append(match.group(1))
elif (ltype == 'preprint'):
curpap.preprint = match.group(1)
elif (ltype == 'author'):
curpap.authors = line.rstrip(';').split('; ')
elif ( ltype == 'title'):
curpap.title =match.group(1)
elif ( ltype == 'pub' ):
curpap.year = match.group(1)
curpap.pubful = match.group(2)
if (curpap.type == 'paper'):
curpap.ParsePub(line)
elif ( ltype == 'file' ):
curpap.files.append(match.group(1))
elif ( ltype == 'link' ):
curpap.links.append(match.group(1))
elif ( ltype == 'action' ):
curpap.actions.append((match.group(1),match.group(2)))
elif (match and not inblock):
if (ltype == 'comment' ):
if verbose: print('#{}'.format(match.group(1)))
elif (ltype == 'blank'):
pass
else:
if verbose: print('WARN: unexpected line of type {}: {}'.format(ltype,line))
nwarn += 1
if ( not foundmatch):
inblock = False
if verbose: print('WARN: unmatched line: {}'.format(line))
nwarn += 1
print('Read {} headers, {} unexpected lines'.format(nhead,nwarn))
def checkFiles(self):
stats = {}
for type in sorttype:
stats[type] = {'nent':0, 'nhas':0, 'nlnk':0, 'nps':0}
for pap in self.list:
#papers should have links
if (len(pap.files)<1 and pap.type == 'paper'):
print('WARN, no file for {}'.format(pap.strSum()))
#all files should exist
for link in pap.files:
linkf = arroot+'/'+link
if (not os.path.isfile(linkf)):
print('WARN cannot find {}!'.format(link))
#add stats
stats[pap.type]['nent'] +=1
if (len(pap.files) > 0): stats[pap.type]['nhas'] += 1
stats[pap.type]['nlnk'] += len(pap.files)
for link in pap.files:
if (link.find('.ps') >0 ):
stats[pap.type]['nps'] +=1
for type in sorttype:
print('type {:8}, total {:3}, with file {:3}, total files {:3}, {:3} ps ext'.format(
type,stats[type]['nent'],stats[type]['nhas'],stats[type]['nlnk'],stats[type]['nps']))
def writeHtml(self, sort, dir, outroot):
if debug: print('debug, sort is:',sort)
htmlout = open(dir+'/'+outroot+'.html','w',encoding='ascii',errors='xmlcharrefreplace')
print('Writing:'+dir+'/'+outroot+'.html')
htmlout.write('<CITE>Last updated: {}</CITE><BR>\n<OL>\n'.format(dt.datetime.now().strftime("%a %d/%m/%Y %H:%M %Z")))
if (sort == 'typeyear'):
for pap in sorted(self.list, key =lambda x: (-1*sorttype.index(x.type), x.year), reverse=(True) ):
pap.PubHtml(htmlout)
elif (sort == 'typecits'):
for pap in sorted(self.list, key =lambda x: (-1*sorttype.index(x.type), x.cits), reverse=(True) ):
pap.PubHtml(htmlout)
elif (sort == 'bycits'):
for pap in sorted(self.list, key =lambda x: (x.cits), reverse=(True) ):
pap.PubHtml(htmlout)
elif (sort == 'byyear'):
for pap in sorted(self.list, key =lambda x: (x.year), reverse=(True) ):
pap.PubHtml(htmlout)
elif (sort == 'original'):
for pap in self.list:
pap.PubHtml(htmlout)
elif (sort == 'reverse'):
for pap in reversed(self.list):
pap.PubHtml(htmlout)
else:
print("ERROR, not implemented")
def ReadADS_Pickle(dir,file):
papers = list(ads.SearchQuery(author="Langevelde, H.", sort="pubdate asc", rows=400))
print('From ADS retrieved {} papers'.format(len(papers)))
output = open(dir+'/'+file,'wb')
pickle.dump(papers, output, pickle.HIGHEST_PROTOCOL)
output.close()
def ReadADS4Huib():
try:
papers = list(ads.SearchQuery(author="van Langevelde,", sort="pubdate asc", rows=400, fl=['id', 'bibcode', 'title', 'date','citation_count', 'author', 'citation', 'pubdate', 'year', 'pub', 'volume', 'page']))
print('From ADS retrieved {} van Langevelde papers'.format(len(papers)))
papers += list(ads.SearchQuery(author="Langevelde, H.", sort="pubdate asc", rows=400, fl=['id', 'bibcode', 'title', 'date','citation_count', 'author', 'citation', 'pubdate', 'year', 'pub', 'volume', 'page']))
print('From ADS retrieved total {} papers'.format(len(papers)))
except:
print('No connection with ADS, no updates...')
papers = []
return papers
def ReadADSBib(bib):
papers = list(ads.SearchQuery(bibcode=bib, sort="pubdate asc", rows=100, fl=['id', 'bibcode', 'title', 'date','citation_count', 'author', 'citation', 'pubdate' ]))
return papers
def procADS(file):
input = open(file,'rb')
inpapers = pickle.load(input)
print('From pickled ADS retrieved {} papers'.format(len(inpapers)))
return inpapers
def CompareYearAuthorsPage( paper, ads):
#print '>',ads.bibcode, paper.pubmag, ads.bibcode.find(paper.pubmag)
if (ads.year == paper.year and
#ads.bibcode.find(paper.pubmag)>0 and
MatchPageno(paper, ads) and
MatchMostAuthors(paper, ads) ):
if verbose: print('Match for {}, in {} and authors: {}'.format(paper.year,paper.pubmag,paper.authors[0]))
return True
else:
return False
def MatchPageno( paper, ads ):
repageno = re.compile(r'\.{1,3}(\d{1,4})[A-Z]$')
#this does not work so well, as the pageno can be subtracted
pageno = False
match = repageno.match(ads.bibcode)
if (match):
if (paper.pubpag == match.group(1)):
pageno = True
return pageno
def MatchMostAuthors(paper, ads):
reauth = [
re.compile(r'^\s*((?:[\w\-]+)+)\,?\s*(\-?[A-Z]\.\s*)+\s*$'),
re.compile(r'^\s*((?:[\w\-\']+)+)\,?\s*([A-Z][a-z\-]+\s*)+\s*$'),
re.compile(r'^\s*((?:[\w\-\']+)+)\,?\s*([A-Z]\w+\s*(\-?[A-Z]\.\s*)*)+\s*$') ]
authmatch = False
#lets see if we can write a regexp that catches all authors
if (debug):
#This is here to test the regexp
for adsauth in ads.author:
tmpauth = adsauth.encode('ascii','ignore')
match = False
for rea in reauth:
match = (match or rea.match(tmpauth))
if (not match):
print('no match: {}'.format(adsauth.encode('ascii', 'ignore')))
for auth in paper.authors:
match == False
for rea in reauth:
match = (match or rea.match(auth))
if (not match):
print('no auth: ',auth)
else:
paplast = []
adslast = []
for auth in paper.authors:
for rea in reauth:
match = rea.match(auth)
if (match): paplast.append(match.group(1))
break
for adsa in ads.author:
tads = adsa.encode('ascii','ignore')
for rea in reauth:
match = rea.match(tads)
if (match): adslast.append(match.group(1))
break
#if (len(paplast) == 0): print 'WHAT?', paper.authors
nsame = 0
for papl in paplast:
for adsl in adslast:
if (papl == adsl): nsame+=1
if ( len(paplast) != 0 and float(nsame)/len(paplast) > 0.74 ):
#print 'YES',nsame,paper.tag, paper.year,paper.authors[0],' - ',ads.year,ads.bibcode,ads.author[0].encode('ascii','ignore')
authmatch = True
return authmatch
def CompareBibcode(adsc, papc):
nsame = 0
for i in range(len(adsc)):
if (papc[i]==adsc[i]): nsame+=1
if (nsame > 16):
print('Same:',adsc,papc)
return True
else:
return False
def CountByYear( ads ):
istart = 1987
#Huib this may need to get fixed...
iend = 2016
citlist = [0 for x in range(iend-istart+1)]
years = []
ncits = 0
if hasattr(ads, 'citation_count'):
ncits = ads.citation_count
if (ncits>0):
for code in ads.citation:
years.append(int(code[0:4]))
iy = 0
year = istart
while (year <= iend ):
for y in years:
if (year >= y): citlist[iy]+=1
iy += 1
year += 1
#print years
#print citlist
return citlist
def getNonBibs(dir,file):
nonfile = open(dir+'/'+file,'r', encoding = 'utf-8')
nonbibs = []
for item in nonfile:
nonbibs.append(item.rstrip('\n'))
return nonbibs
def updatePubs(adslist, mylist, nonbibs ):
#Find whether everything on ads is in also already in our system
nalloc = 0
nalt = 0
nknown = 0
for ads in adslist:
#loop the list on ads
adsalloc = False
for paper in mylist:
#loop the local record
if (paper.bibcode == ads.bibcode):
nalloc += 1
adsalloc = True
#if the ads is not up this fails, but 0 count returns None for
#ads.citation, which also can raise an exception
try:
paper.cits = ads.citation_count
if (ads.citation_count > 0):
paper.citlist = ads.citation
#is this sorted in any way?
if (paper.cits != len(ads.citation)):
print('WARNING for', paper.bibcode,' cits:',paper.cits,' count:',len(ads.citation))
#print 'Check: N_cits:',paper.bibcode,paper.cits
except:
print("No ADS connection, no citations")
paper.cits = 0
paper.citlist = []
if (ads.bibcode in paper.altbibcodes ):
nalt += 1
adsalloc = True
if (ads.bibcode in nonbibs):
nknown +=1
adsalloc = True
if (not adsalloc):
#print('debug',ads.bibcode, paper.altbibcodes)
print('NEW {} :'.format(ads.bibcode ))
newpaper = Paper()
newpaper.fillFromAds(ads)
mylist.append(newpaper)
print('pub has {} papers, ads {}, matched {} primaries, {} alts and {} known non-papers'.format(len(mylist),len(adslist),nalloc,nalt,nknown))
return mylist
def editPaperCits( paper, stats ):
bibc = str(paper.bibcode)
for ifield in range(len(stats['header'])):
if (stats['header'][ifield] == 'author'):
if (stats[bibc][ifield] != paper.authors[0].split(',')[0].encode('ascii','replace')):
stats[bibc][ifield] = paper.authors[0].split(',')[0]
print('updated author',stats[bibc][ifield])
elif (stats['header'][ifield] == 'tag'):
if (stats[bibc][ifield] != paper.tag):
stats[bibc][ifield] = paper.tag
print('updated tag',stats[bibc][ifield])
elif (stats['header'][ifield] == 'type'):
if (stats[bibc][ifield] != paper.type):
stats[bibc][ifield] = paper.type
print('updated type',stats[bibc][ifield])
def updateCits(stats, mylist, update):
def repdifcits(paper):
'''
Report on the mutations in citations on paper, accumulate in ncittot, ncitsnew
'''
def repmostrecent(nnew,paper):
'''
Reports on the new latest papers for paper, which is an ads.entry
'''
def repentry(i,entry):
if (entry['author']):
print(' -{:2}: {} {} [{}], {:60}'.format(i,entry['author'], entry['bibcode'],
entry['pubdate'], entry['title']))
else:
print(' -{:2}: no author {}, {:60}'.format(i, entry['bibcode'],
entry['title']))
#there could be more if the date is not unique
return
global Nadspol
creps = []
for cit in paper.citlist:
try:
Nadspol += 1
citads = ReadADSBib(cit)
if debug: print(Nadspol, cit, citads[0], 'd:',citads[0].pubdate)
entry = { 'bibcode': cit, 'pubdate':citads[0].pubdate,
'author': citads[0].author[0].split(',')[0],
'title':citads[0].title[0]}
except:
if debug: print(Nadspol,' failed...')
entry = { 'bibcode': cit, 'pubdate': '',
'author': '',
'title':''}
creps.append(entry)
newlist = sorted(creps, key=itemgetter('pubdate'))
for i in range(nnew):
repentry(i,newlist[-1-i])
i = nnew
nmore = 0
while (i<(len(newlist)-1) and newlist[-1-i-1]['pubdate'] == newlist[-1-i]['pubdate']):
nmore += 1
repentry(i,newlist[-1-i])
i = i+1
if (nmore > 0): print('Included ',nmore,' entries with same pubdate.')
return
ncittot = 0
ncitsnew = 0
#print 'Consistent?',paper.cits, paper.citlist
if (paper.cits >= 0 ):
#this is a paper for which stats are available
ncittot = paper.cits
#print 'down:',ntotal, paper.cits
if (paper.cits != paper.oldcits):
#some citations could go from -1 to 1, with only one citation
nnew = paper.cits - max(paper.oldcits,0)
ncitsnew += nnew
if (nnew < 0):
print('{} has citation mutations, was {:3d}, now {:3d} (going down, likely arXiv papers resolved)'.format(paper.strSum(),paper.oldcits,paper.cits))
else:
print('{} has citation mutations, was {:3d}, now {:3d}'.format(paper.strSum(),paper.oldcits,paper.cits))
#if you need to know, op ads for bibcode
if (paper.cits > 0 and paper.cits < opts.maxpolads):
repmostrecent(nnew, paper)
elif (paper.cits < 1):