def get_citation_from_doi(query,
email='*****@*****.**',
tool='Referencer',
database='pubmed'):
params = {
'db': database,
'tool': tool,
'email': email,
'term': query + "[doi]",
'usehistory': 'y',
'retmax': 1
}
# try to resolve the PubMed ID of the DOI
url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?' + urllib.urlencode(
params)
data = referencer.download(_("Resolving DOI"),
_("Finding PubMed ID from DOI %s") % query, url)
# parse XML output from PubMed...
xmldoc = minidom.parseString(data)
ids = xmldoc.getElementsByTagName('Id')
# nothing found, exit
if len(ids) == 0:
raise "pubmed.get_citation_from_doi: DOI not found"
# get ID
id = ids[0].childNodes[0].data
print "pubmed.get_citation_from_doi: DOI ", query, " has PubMed ID ", id
return get_citation_from_pmid(id)
def get_citation_from_doi(query, email='*****@*****.**', tool='Referencer', database='pubmed'):
params = {
'db':database,
'tool':tool,
'email':email,
'term':query + "[doi]",
'usehistory':'y',
'retmax':1
}
# try to resolve the PubMed ID of the DOI
url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?' + urllib.urlencode(params)
data = referencer.download (_("Resolving DOI"), _("Finding PubMed ID from DOI %s") % query , url);
# parse XML output from PubMed...
xmldoc = minidom.parseString(data)
ids = xmldoc.getElementsByTagName('Id')
# nothing found, exit
if len(ids) == 0:
raise "pubmed.get_citation_from_doi: DOI not found"
# get ID
id = ids[0].childNodes[0].data
print "pubmed.get_citation_from_doi: DOI ", query, " has PubMed ID ", id
return get_citation_from_pmid (id)
def __init__(self, parent = None):
gtk.Dialog.__init__(self,"expj plugin configuration",
parent,
gtk.DIALOG_MODAL |
gtk.DIALOG_DESTROY_WITH_PARENT,
(gtk.STOCK_CANCEL, gtk.RESPONSE_REJECT,
gtk.STOCK_OK, gtk.RESPONSE_OK))
#vbox = gtk.VBox()
label = gtk.Label(_("Journal name database download link:"))
self.dllink = gtk.Entry()
self.dllink.set_text(DEFAULTDOWNLOAD)
self.vbox.pack_start(label,padding=3)
self.vbox.pack_start(self.dllink,padding=3)
hbox = gtk.HBox()
text = _('The above link should direct to a text file following the syntax described on the JabRef web page where also other possible useful Journal name database files can be found.\n<a href="http://jabref.sourceforge.net/resources.php">http://jabref.sourceforge.net/resources.php</a>\nBe aware that the downloaded file will replace your current Journal name database. Your custom entries saved in a separate file will remain unchanged!')
label = gtk.Label()
label.set_markup(text)
label.set_line_wrap(True)
image = gtk.Image()
image.set_from_stock(gtk.STOCK_DIALOG_INFO,gtk.ICON_SIZE_DIALOG)
hbox.pack_start(image)
hbox.pack_start(label)
self.vbox.pack_start(hbox,padding=3)
self.vbox.show_all()
def resolve_metadata (doc, method):
if method != "doi":
return False
doi = doc.get_field("doi")
params = {
'data_type':"XML",
'doi':doi
}
url = "http://adsabs.harvard.edu/cgi-bin/nph-bib_query?" + urllib.urlencode (params)
data = referencer.download (_("Resolving DOI"), _("Fetching metadata from NASA ADS for DOI %s") % doi, url);
if data.find ("retrieved=\"1\"") == -1:
print "Couldn't get info from ADS"
return False
fields = []
try:
xmldoc = minidom.parseString (data)
fields.append (["journal", get_field(xmldoc, "journal")])
fields.append (["title", get_field(xmldoc, "title")])
fields.append (["volume", get_field(xmldoc, "volume")])
authors = xmldoc.getElementsByTagName('author')
authorString = ""
first = True
for author in authors:
name = author.childNodes[0].data.encode("utf-8")
if (first == False):
authorString += " and "
print "got author", name
authorString += name
first = False
fields.append (["author", authorString])
print "appended authors"
pages = get_field (xmldoc, "page")
print "getting lastPage"
lastPage = get_field (xmldoc, "lastpage")
if (len(lastPage) > 0):
pages += "-"
pages += lastPage
print "got pages " , pages
fields.append (["page", pages])
print "appended pages"
except:
print "exception"
return False
for field in fields:
if len(field[1]) > 0:
doc.set_field(field[0], field[1])
# TODO: parse pubdata element for "Jul 1989" (month and year fields)
return True
def get_citation_from_pmid (pmid, email='*****@*****.**', tool='Referencer', database='pubmed'):
params = {
'db':database,
'tool':tool,
'email':email,
'id':pmid,
'retmode':'xml'
}
# get citation info:
url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?' + urllib.urlencode(params)
data = referencer.download (_("Resolving PubMed ID"), _("Fetching metadata from NCBI for PubMed ID %s") % pmid, url);
return data
def get_number_of_records (document):
title = document.get_field("title")
year = document.get_field ("year")
author= document.get_field ("author")
url0='http://estipub.isiknowledge.com/esti/cgi?databaseID=WOS&rspType=xml&method=search&firstRec=1&numRecs=1'
url0+= '&query='+get_query(document)
data0 = referencer.download(
_("Obtaining data from ISI-WebOfScience"),
_("Fetching number of ocurrences for %s/%s/%s") % (author,title,year),
url0)
print data0
xmldoc0 = minidom.parseString(data0)
recordsFound=get_field(xmldoc0,"recordsFound")
return int(recordsFound)
def get_data(self,document, firstrec=None, numrecs=None):
title = document.get_field("title")
year = document.get_field ("year")
author= document.get_field ("author")
if firstrec is None:
firstrec = 1
if numrecs is None:
numrecs = 1
url='http://estipub.isiknowledge.com/esti/cgi?databaseID=WOS&SID=Q1mNFhCECOk6c8aELLh&rspType=xml&method=searchRetrieve'
url += \
'&firstRec=' + str(firstrec) + \
'&numRecs=' + str(numrecs) + \
'&query=' + get_query(document)
data = referencer.download(_("Obtaining data from ISI-WebOfScience"),
_("Fetching data for %s/%s/%s")
% (author,title,year), url);
return data
def do_search(document):
title = document.get_field("title")
year = document.get_field("year")
author = document.get_field("author")
url0 = 'http://estipub.isiknowledge.com/esti/cgi?action=search&viewType=xml&mode=GeneralSearch&product=WOS&ServiceName=GeneralSearch&filter=&Start=&End=%d&DestApp=WOS' % (
get_MAXRECORDS())
url0 += "&" + get_query(document)
print "isi query url:", url0
if False: #debugging
#data0 = open("plugins/isi-plugin-testdata.txt").read()
data0 = open("plugins/isi-plugin-testdata2.txt").read()
else:
data0 = referencer.download(
_("Obtaining data from ISI-WebOfScience"),
_("Querying for %s/%s/%s") % (author, title, year), url0)
print data0
xmldoc0 = minidom.parseString(data0)
return xmldoc0
def resolve_metadata(doc, method=None):
# try with title, otherwise try with author + year
title = doc.get_field("title")
if title:
searchTerms = [title]
else:
searchTerms = [get_first_author(doc.get_field("author"))]
searchTerms += [doc.get_field("year")]
searchTerm = " ".join(searchTerms)
for c in "(),.{}!\"':=#%$/&[]+":
searchTerm = searchTerm.replace(c, "")
searchTerm = searchTerm.replace("-", " ")
while searchTerm.find(" ") > 0: #remove double spaces
searchTerm = searchTerm.replace(" ", " ")
#print "DBLP:searchTerm:", repr(searchTerm)
url = "http://www.dblp.org/search/api/?%s&h=1000&c=0&f=0&format=xml" % (
urllib.urlencode({'q': searchTerm}))
print "DBLP:url:", repr(url)
data = referencer.download(
_("Searching DBLP"),
_("Fetching metadata from DBLP for search query '%s'") % searchTerm,
url)
if not data:
return False
hits = parse_hits_get_urls(data)
print "DBLP:hits:", hits
if len(hits) != 1:
#XXX, display UI?
print "DBLP: Not exactly one hit, giving up"
return False
bibtex_xml = get_bibtex_xml_from_url(hits[0])
#print bibtex_xml
bibtex = bibtex_xml_to_bibtex(bibtex_xml)
#print bibtex
doc.parse_bibtex(bibtex)
return True
def do_search (document):
title = document.get_field("title")
year = document.get_field ("year")
author= document.get_field ("author")
url0='http://estipub.isiknowledge.com/esti/cgi?action=search&viewType=xml&mode=GeneralSearch&product=WOS&ServiceName=GeneralSearch&filter=&Start=&End=%d&DestApp=WOS' % (get_MAXRECORDS())
url0+= "&" + get_query(document)
print "isi query url:", url0
if False: #debugging
#data0 = open("plugins/isi-plugin-testdata.txt").read()
data0 = open("plugins/isi-plugin-testdata2.txt").read()
else:
data0 = referencer.download(
_("Obtaining data from ISI-WebOfScience"),
_("Querying for %s/%s/%s") % (author,title,year),
url0)
print data0
xmldoc0 = minidom.parseString(data0)
return xmldoc0
def get_citation_from_pmid(pmid,
email='*****@*****.**',
tool='Referencer',
database='pubmed'):
params = {
'db': database,
'tool': tool,
'email': email,
'id': pmid,
'retmode': 'xml'
}
# get citation info:
url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?' + urllib.urlencode(
params)
data = referencer.download(
_("Resolving PubMed ID"),
_("Fetching metadata from NCBI for PubMed ID %s") % pmid, url)
return data
def resolve_metadata (doc, method=None):
# try with title, otherwise try with author + year
title = doc.get_field("title")
if title:
searchTerms = [title]
else:
searchTerms = [get_first_author(doc.get_field("author"))]
searchTerms += [doc.get_field("year")]
searchTerm = " ".join(searchTerms)
for c in "(),.{}!\"':=#%$/&[]+":
searchTerm = searchTerm.replace(c, "")
searchTerm = searchTerm.replace("-", " ")
while searchTerm.find(" ") > 0: #remove double spaces
searchTerm = searchTerm.replace(" ", " ")
#print "DBLP:searchTerm:", repr(searchTerm)
url = "http://www.dblp.org/search/api/?%s&h=1000&c=0&f=0&format=xml" % (urllib.urlencode({'q': searchTerm}))
print "DBLP:url:", repr(url)
data = referencer.download (_("Searching DBLP"), _("Fetching metadata from DBLP for search query '%s'") % searchTerm, url);
if not data:
return False
hits = parse_hits_get_urls(data)
print "DBLP:hits:", hits
if len(hits) != 1:
#XXX, display UI?
print "DBLP: Not exactly one hit, giving up"
return False
bibtex_xml = get_bibtex_xml_from_url(hits[0])
#print bibtex_xml
bibtex = bibtex_xml_to_bibtex(bibtex_xml)
#print bibtex
doc.parse_bibtex(bibtex)
return True
def get_bibtex_xml_from_url(url):
url = url + ".xml"
data = referencer.download (_("Searching DBLP"), _("Fetching metadata from DBLP for url '%s'") % url, url);
return data
def referencer_search_TEST(search_text):
email = '*****@*****.**'
tool = 'Referencer'
database = 'pubmed'
retmax = 100
params = {
'db': database,
'tool': tool,
'email': email,
'term': search_text,
'usehistory': 'y',
'retmax': retmax
}
# try to resolve the PubMed ID of the DOI
url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?' + urllib.urlencode(
params)
data = referencer.download(_("Searching pubmed"),
_("Searching pubmed for '%s'") % search_text,
url)
# parse XML output from PubMed...
print data
xmldoc = minidom.parseString(data)
ids = xmldoc.getElementsByTagName('Id')
# nothing found, exit
# FIXME: not really an error
if len(ids) == 0:
raise "pubmed.referencer_search: no results"
webenv = xmldoc.getElementsByTagName('WebEnv')
if len(webenv) == 0:
raise "pubmed.referencer_search: no webenv"
webenv = webenv[0].childNodes[0].data
query_key = xmldoc.getElementsByTagName('QueryKey')
if len(query_key) == 0:
raise "pubmed.referencer_search: no query_key"
query_key = query_key[0].childNodes[0].data
params = {
'db': database,
'tool': tool,
'email': email,
'webenv': webenv,
'query_key': query_key,
'retmax': retmax
}
url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?' + urllib.urlencode(
params)
data = referencer.download(
_("Retrieving pubmed summaries"),
_("Retrieving summaries for '%s'") % search_text, url)
xmldoc = minidom.parseString(data)
results = []
for docsum in xmldoc.getElementsByTagName('DocSum'):
title = ""
author = ""
pmid = ""
id = docsum.getElementsByTagName("Id")
if len(id) != 0:
pmid = id[0].childNodes[0].data
else:
raise "pubmed.referencer_search: docsum without id"
for childnode in docsum.getElementsByTagName("Item"):
if childnode.getAttribute("Name") == "Title":
title = childnode.childNodes[0].data
if childnode.getAttribute("Name") == "Author":
author = childnode.childNodes[0].data
results.append({"token": pmid, "title": title, "author": author})
print results
return results
#!/usr/bin/env python
# Simple script to query pubmed for a DOI
# (c) Simon Greenhill, 2007
# http://simon.net.nz/
# Modified for integration with referencer by John Spray, 2007
import urllib
import referencer
from referencer import _
from xml.dom import minidom
referencer_plugin_info = {
"longname": _("PubMed DOI resolver"),
"author": "Simon Greenhill, John Spray"
}
referencer_plugin_capabilities = ["doi", "pubmed"]
# Encoding: every PyUnicode that minidom gives us gets
# encoded as utf-8 into a PyString, this is what PyString_AsString on the C++
# side will expect
def get_field (doc, field):
value = doc.getElementsByTagName(field)
if len(value) == 0:
return ""
</menu>
</menubar>
<toolbar name='ToolBar'>
<placeholder name='PluginToolBarActions'>
<toolitem action='_plugin_isi'/>
</placeholder>
</toolbar>
<popup name='DocPopup'>
<placeholder name='PluginDocPopupActions'>
<menuitem action='_plugin_isi'/>
</placeholder>
</popup>
</ui>
""",
"longname": _("ISI Web of Science resolver (requires subscription)"),
"action": _("Get metadata from ISI Web of Science"),
"tooltip": _("ISI Web of Science resolver (requires subscription)")}
referencer_plugin_actions = [{
"name":"_plugin_isi",
"label":_("ISI Info"),
"tooltip":_("Retrieve metadata for the selected documents from ISI Web of Science"),
"icon":"_stock:gtk-edit",
"callback":"do_action",
"sensitivity":"sensitivity_genkey",
"accelerator":"<control>i"
}]
class isiRec:
def __init__(self, document = None, firstrec = None):
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Add quote in lyx using lyxclient
import os
import referencer
from referencer import _
referencer_plugin_info = {
"longname": _("PaperCrop"),
"author": "Taesoobear",
"ui":
"""
<ui>
<menubar name='MenuBar'>
<menu action='DocMenu'>
<placeholder name='PluginDocMenuActions'>
<menuitem action='_plugin_papercrop'/>
</placeholder>
</menu>
</menubar>
<toolbar name='ToolBar'>
<placeholder name='PluginToolBarActions'>
<toolitem action='_plugin_papercrop'/>
</placeholder>
</toolbar>
<popup name='DocPopup'>
<placeholder name='PluginDocPopupActions'>
<menuitem action='_plugin_papercrop'/>
</placeholder>
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Add quote in lyx using lyxclient
import os
import referencer
from referencer import _
referencer_plugin_info = {
"longname": _("Cite in LyX"),
"author": "Aurélien Naldi",
"ui":
"""
<ui>
<menubar name='MenuBar'>
<menu action='DocMenu'>
<placeholder name='PluginDocMenuActions'>
<menuitem action='_plugin_lyx_cite'/>
</placeholder>
</menu>
</menubar>
<toolbar name='ToolBar'>
<placeholder name='PluginToolBarActions'>
<toolitem action='_plugin_lyx_cite'/>
</placeholder>
</toolbar>
<popup name='DocPopup'>
<placeholder name='PluginDocPopupActions'>
<menuitem action='_plugin_lyx_cite'/>
</placeholder>
</menu>
</menubar>
<toolbar name='ToolBar'>
<placeholder name='PluginToolBarActions'>
<toolitem action='_plugin_isi'/>
</placeholder>
</toolbar>
<popup name='DocPopup'>
<placeholder name='PluginDocPopupActions'>
<menuitem action='_plugin_isi'/>
</placeholder>
</popup>
</ui>
""",
"longname": _("ISI Web of Science resolver (requires subscription)"),
"action": _("Get metadata from ISI Web of Science"),
"tooltip": _("ISI Web of Science resolver (requires subscription)")
}
referencer_plugin_actions = [{
"name":
"_plugin_isi",
"label":
_("ISI Info"),
"tooltip":
_("Retrieve metadata for the selected documents from ISI Web of Science"),
"icon":
"_stock:gtk-edit",
"callback":
"do_action",
def resolve_metadata (doc, method):
if method != "doi":
return False
doi = doc.get_field("doi")
params = {
'data_type':"XML",
'doi':doi
}
url = "http://adsabs.harvard.edu/cgi-bin/nph-bib_query?" + urllib.urlencode (params)
data = referencer.download (_("Resolving DOI"), _("Fetching metadata from NASA ADS for DOI %s") % doi, url);
if data.find ("retrieved=\"1\"") == -1:
print "Couldn't get info from ADS"
return False
fields = []
try:
xmldoc = minidom.parseString (data)
fields.append (["title", get_field(xmldoc, "title")])
fields.append (["volume", get_field(xmldoc, "volume")])
fields.append (["issue", get_field(xmldoc, "issue")])
fields.append (["year", get_field(xmldoc, "pubdate").partition(' ')[2]])
fields.append (["Month", str.lower(get_field(xmldoc, "pubdate").partition(' ')[0])])
fields.append (["Adsurl", xmldoc.getElementsByTagName('url')[-1].childNodes[0].data.encode("utf-8")])
fields.append (["Adsbibcode", get_field(xmldoc, "bibcode")])
# ADS include full bibliographic information in the journal XML tag,
# see http://doc.adsabs.harvard.edu/abs_doc/help_pages/taggedformat.html#jnl
journal = get_field(xmldoc, "journal")
journalString = re.sub(', [vV]ol(ume|\.).*', '', journal)
fields.append (["journal", journalString])
authors = xmldoc.getElementsByTagName('author')
authorString = ""
first = True
for author in authors:
name = author.childNodes[0].data.encode("utf-8")
if (first == False):
authorString += " and "
print "got author", name
authorString += name
first = False
fields.append (["author", authorString])
print "appended authors"
pages = get_field (xmldoc, "page")
print "getting lastPage"
lastPage = get_field (xmldoc, "lastpage")
if (len(lastPage) > 0):
pages += "-"
pages += lastPage
print "got pages " , pages
fields.append (["pages", pages])
print "appended pages"
except:
print "exception"
return False
for field in fields:
if len(field[1]) > 0:
doc.set_field(field[0], field[1])
return True
USERPLDIR = os.path.join(
os.path.expanduser("~"), ".referencer",
"plugins") # os.path.dirname(os.path.realpath(__file__))
DBs = []
DBs.append(os.path.join(USERPLDIR, "expj_journaldb_user.txt"))
DBs.append(os.path.join(USERPLDIR, "expj_journaldb_base.txt"))
DEFAULTMAXSUGGESTIONS = 5 # number of suggestions displayed in case no exact match is found
DEFAULTDOWNLOAD = "http://jabref.sourceforge.net/journals/journal_abbreviations_general.txt"
DEBUG = True
referencer_plugin_info = {
"longname":
_("Expand and abbreviate Journal names"),
"author":
"Dominik Kriegner",
"version":
"0.2.0",
"ui":
"""
<ui>
<menubar name='MenuBar'>
<menu action='DocMenu'>
<placeholder name='PluginDocMenuActions'>
<menuitem action='_plugin_expj_expand'/>
</placeholder>
<placeholder name='PluginDocMenuActions'>
<menuitem action='_plugin_expj_shorten'/>
</placeholder>
def do_shorten (library, documents):
"""
perform shortening of Journal names for listed documents
"""
global expanded,contracted
if len(expanded) == 0:
# on first use of the plugin the database has to be loaded
load_db()
for doc in documents:
# check if it is a article
pass # seems this is not necessary because asking for journal name on not articles
# returns an empty string
# get current journal field
longv = doc.get_field('journal')
repl = longv
if longv != "":
try: # look for exact match in database
idx = map(string.lower,expanded).index(longv.strip().lower())
repl = contracted[idx]
except ValueError:
try: # check if journal name is already the shortened version
idx = map(string.lower,contracted).index(longv.strip().lower())
if idx:
continue
except:
pass
# no exact match was found, we will ask the user what to do
match = difflib.get_close_matches(longv,expanded,DEFAULTMAXSUGGESTIONS) # find 5 most likely replacements
# Prompt the user for the correct entry
dialog = gtk.Dialog(buttons=(gtk.STOCK_CANCEL, gtk.RESPONSE_REJECT, gtk.STOCK_OK, gtk.RESPONSE_ACCEPT))
dialog.set_has_separator(False)
dialog.vbox.set_spacing(6)
dialog.set_default_response(gtk.RESPONSE_ACCEPT)
if DISPHINT:
text = _('No Journal name database found: consider checking the plugin configuration dialog to download a prepared list')
label = gtk.Label(text)
label.set_line_wrap(True)
image = gtk.Image()
image.set_from_stock(gtk.STOCK_DIALOG_INFO,gtk.ICON_SIZE_DIALOG)
hbox = gtk.HBox()
hbox.pack_start(image)
hbox.pack_start(label)
dialog.vbox.pack_start(hbox,padding=3)
if len(match)==0:
label = gtk.Label(_("No match found in database!\nEnter replacement entry for journal") + " '%s'"%(longv))
else:
label = gtk.Label(_("No exact match found!\nChoose correct entry for journal") + " '%s'"%(longv))
dialog.vbox.pack_start(label)
for i in range(len(match)):
if i==0:
rb = gtk.RadioButton(None,contracted[expanded.index(match[i])])
rb.set_active(True)
else:
rb = gtk.RadioButton(rb,contracted[expanded.index(match[i])])
dialog.vbox.pack_start(rb)
hbox = gtk.HBox (spacing=6)
if len(match)!=0:
rb = gtk.RadioButton(rb,_("Custom:"))
else:
rb = gtk.Label(_("Replacement:"))
def activate_custom(widget,rb):
"""
the custom entry will be activated upon a text entry
"""
rb.set_active(True)
entry = gtk.Entry()
entry.set_text(_("journal abbreviation"))
entry.set_activates_default(True)
entry.select_region(0,len(entry.get_text()))
if len(match)!=0: entry.connect("changed",activate_custom,rb)
dialog.vbox.pack_start(hbox)
hbox.pack_start(rb)
hbox.pack_start(entry)
dialog.vbox.pack_start(hbox)
dialog.set_focus(entry)
cb = gtk.CheckButton(label=_("Add replacement to database"))
dialog.vbox.pack_start(cb)
dialog.show_all()
response = dialog.run()
dialog.hide()
if (response == gtk.RESPONSE_REJECT):
continue # do not change anthing and continue with next document
# obtain users choice
if len(match)!=0:
active_radio = [r for r in rb.get_group() if r.get_active()][0]
if active_radio.get_label() != _("Custom:"):
repl = active_radio.get_label()
else:
repl = entry.get_text()
else:
repl = entry.get_text()
if cb.get_active():
# save the custom entry to the database
expanded.append(longv)
contracted.append(repl)
save_db()
# change the journal name
doc.set_field('journal',repl)
if DEBUG:
print("expj: changed journal entry from '%s' to '%s'"%(longv,repl))
return True
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
import urllib
try:
import referencer
from referencer import _
except:
#for doctesting
referencer = None
_ = lambda x: x
from xml.dom import minidom
referencer_plugin_info = {
"longname": _("DBLP resolver"),
"version": "0.1",
"author": "Mads Chr. Olesen <*****@*****.**>"
}
referencer_plugin_capabilities = ["resolve_metadata"]
def can_resolve_metadata(doc):
author = doc.get_field("author")
#let's pretend this is an easter egg ;-)
if author and "Mads" in author and "Olesen" in author:
return 80
elif "DBLP" in str(doc.get_field("bibsource")):
return 80
elif doc.get_field("title"):
import gtk
import re
import referencer
from referencer import _
# A referencer plugin to get bibtex info for a book from Google Books
#
# Copyright 2011 Phoenix87
# Copyright 2012 Mads Chr. Olesen <*****@*****.**>
referencer_plugin_info = {
"author": "Phoenix87",
"version": "0.2",
"longname": _("Fetch BiBTeX metadata from Google Books")
}
referencer_plugin_capabilities = ["url"]
pattern = r'http://books[.]google[.](.+?)/books.+?id=([a-zA-Z0-9_]+)'
def can_resolve_metadata(doc):
url = doc.get_field("url")
if not url:
return -1
res = re.match(pattern, url)
if res:
return 90
return -1
def get_bibtex_xml_from_url(url):
url = url + ".xml"
data = referencer.download(
_("Searching DBLP"),
_("Fetching metadata from DBLP for url '%s'") % url, url)
return data
# Generate Bob08 Alice99 Alice99b type keys
import os
import referencer
from referencer import _
import gobject
import gtk
referencer_plugin_info = {
"author":
"John Spray",
"version":
"1.1.2",
"longname":
_("Generate keys from metadata"),
"ui":
"""
<ui>
<menubar name='MenuBar'>
<menu action='ToolsMenu'>
<placeholder name ='PluginToolsActions'>
<menuitem action='_plugin_genkey_genkey'/>
</placeholder>
</menu>
</menubar>
<popup name='DocPopup'>
<placeholder name='PluginDocPopupActions'>
<menuitem action='_plugin_genkey_genkey'/>
</placeholder>
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Add quote in lyx using lyxclient
import os
import referencer
from referencer import _
referencer_plugin_info = {
"longname":
_("PaperCrop"),
"author":
"Taesoobear",
"ui":
"""
<ui>
<menubar name='MenuBar'>
<menu action='DocMenu'>
<placeholder name='PluginDocMenuActions'>
<menuitem action='_plugin_papercrop'/>
</placeholder>
</menu>
</menubar>
<toolbar name='ToolBar'>
<placeholder name='PluginToolBarActions'>
<toolitem action='_plugin_papercrop'/>
</placeholder>
</toolbar>
<popup name='DocPopup'>
<placeholder name='PluginDocPopupActions'>
def referencer_search_TEST (search_text):
email='*****@*****.**'
tool='Referencer'
database='pubmed'
retmax = 100
params = {
'db':database,
'tool':tool,
'email':email,
'term':search_text,
'usehistory':'y',
'retmax':retmax
}
# try to resolve the PubMed ID of the DOI
url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?' + urllib.urlencode(params)
data = referencer.download (_("Searching pubmed"), _("Searching pubmed for '%s'") % search_text , url);
# parse XML output from PubMed...
print data
xmldoc = minidom.parseString(data)
ids = xmldoc.getElementsByTagName('Id')
# nothing found, exit
# FIXME: not really an error
if len(ids) == 0:
raise "pubmed.referencer_search: no results"
webenv = xmldoc.getElementsByTagName('WebEnv')
if len(webenv) == 0:
raise "pubmed.referencer_search: no webenv"
webenv = webenv[0].childNodes[0].data
query_key = xmldoc.getElementsByTagName('QueryKey')
if len(query_key) == 0:
raise "pubmed.referencer_search: no query_key"
query_key = query_key[0].childNodes[0].data
params = {
'db':database,
'tool':tool,
'email':email,
'webenv':webenv,
'query_key':query_key,
'retmax':retmax
}
url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?' + urllib.urlencode(params)
data = referencer.download (_("Retrieving pubmed summaries"), _("Retrieving summaries for '%s'") % search_text , url);
xmldoc = minidom.parseString(data)
results = []
for docsum in xmldoc.getElementsByTagName('DocSum'):
title = ""
author = ""
pmid = ""
id = docsum.getElementsByTagName("Id")
if len(id) !=0:
pmid = id[0].childNodes[0].data
else:
raise "pubmed.referencer_search: docsum without id"
for childnode in docsum.getElementsByTagName("Item"):
if childnode.getAttribute("Name") == "Title":
title = childnode.childNodes[0].data
if childnode.getAttribute("Name") == "Author":
author = childnode.childNodes[0].data
results.append ({"token":pmid,"title":title,"author":author})
print results
return results
import string # for string handling
import difflib # to find closest matching entry for replacement
USERPLDIR = os.path.join(os.path.expanduser("~"), ".referencer","plugins") # os.path.dirname(os.path.realpath(__file__))
DBs = []
DBs.append(os.path.join(USERPLDIR,"expj_journaldb_user.txt"))
DBs.append(os.path.join(USERPLDIR,"expj_journaldb_base.txt"))
DEFAULTMAXSUGGESTIONS = 5 # number of suggestions displayed in case no exact match is found
DEFAULTDOWNLOAD = "http://jabref.sourceforge.net/journals/journal_abbreviations_general.txt"
DEBUG = True
referencer_plugin_info = {
"longname": _("Expand and abbreviate Journal names"),
"author": "Dominik Kriegner",
"version": "0.2.0",
"ui":
"""
<ui>
<menubar name='MenuBar'>
<menu action='DocMenu'>
<placeholder name='PluginDocMenuActions'>
<menuitem action='_plugin_expj_expand'/>
</placeholder>
<placeholder name='PluginDocMenuActions'>
<menuitem action='_plugin_expj_shorten'/>
</placeholder>
</menu>
</menubar>
#!/usr/bin/env python
# Generate Bob08 Alice99 Alice99b type keys
import os
import referencer
from referencer import _
import gobject
import gtk
referencer_plugin_info = {
"author": "John Spray",
"version": "1.1.2",
"longname": _("Generate keys from metadata"),
"ui":
"""
<ui>
<menubar name='MenuBar'>
<menu action='ToolsMenu'>
<placeholder name ='PluginToolsActions'>
<menuitem action='_plugin_genkey_genkey'/>
</placeholder>
</menu>
</menubar>
<popup name='DocPopup'>
<placeholder name='PluginDocPopupActions'>
<menuitem action='_plugin_genkey_genkey'/>
</placeholder>
</popup>
#!/usr/bin/env python
# ADS metadata scraper, Copyright 2008 John Spray
import urllib
import referencer
from referencer import _
from xml.dom import minidom
referencer_plugin_info = {
"author": "John Spray",
"longname": _("NASA Astrophysics Data System DOI resolver")
}
referencer_plugin_capabilities = ["doi"]
# Encoding: every PyUnicode that minidom gives us gets
# encoded as utf-8 into a PyString, this is what PyString_AsString on the C++
# side will expect
def get_field(doc, field):
value = doc.getElementsByTagName(field)
print "get_field: value = ", value
if len(value) == 0:
return ""
else:
return value[0].childNodes[0].data.encode("utf-8")
def can_resolve_metadata(doc):
if doc.get_field("doi"):
def resolve_metadata(doc, method):
if method != "doi":
return False
doi = doc.get_field("doi")
params = {'data_type': "XML", 'doi': doi}
url = "http://adsabs.harvard.edu/cgi-bin/nph-bib_query?" + urllib.urlencode(
params)
data = referencer.download(
_("Resolving DOI"),
_("Fetching metadata from NASA ADS for DOI %s") % doi, url)
if data.find("retrieved=\"1\"") == -1:
print "Couldn't get info from ADS"
return False
fields = []
try:
xmldoc = minidom.parseString(data)
fields.append(["journal", get_field(xmldoc, "journal")])
fields.append(["title", get_field(xmldoc, "title")])
fields.append(["volume", get_field(xmldoc, "volume")])
fields.append(["issue", get_field(xmldoc, "issue")])
fields.append(["year", get_field(xmldoc, "pubdate").partition(' ')[2]])
fields.append([
"Month",
str.lower(get_field(xmldoc, "pubdate").partition(' ')[0])
])
fields.append([
"Adsurl",
xmldoc.getElementsByTagName('url')[-1].childNodes[0].data.encode(
"utf-8")
])
fields.append(["Adsbibcode", get_field(xmldoc, "bibcode")])
authors = xmldoc.getElementsByTagName('author')
authorString = ""
first = True
for author in authors:
name = author.childNodes[0].data.encode("utf-8")
if (first == False):
authorString += " and "
print "got author", name
authorString += name
first = False
fields.append(["author", authorString])
print "appended authors"
pages = get_field(xmldoc, "page")
print "getting lastPage"
lastPage = get_field(xmldoc, "lastpage")
if (len(lastPage) > 0):
pages += "-"
pages += lastPage
print "got pages ", pages
fields.append(["pages", pages])
print "appended pages"
except:
print "exception"
return False
for field in fields:
if len(field[1]) > 0:
doc.set_field(field[0], field[1])
return True
#!/usr/bin/env python
# ADS metadata scraper, Copyright 2008 John Spray
import urllib
import referencer
from referencer import _
from xml.dom import minidom
referencer_plugin_info = {
"author": "John Spray",
"longname": _("NASA Astrophysics Data System DOI resolver")
}
referencer_plugin_capabilities = ["doi"]
# Encoding: every PyUnicode that minidom gives us gets
# encoded as utf-8 into a PyString, this is what PyString_AsString on the C++
# side will expect
def get_field (doc, field):
value = doc.getElementsByTagName(field)
print "get_field: value = ", value
if len(value) == 0:
return ""
else:
return value[0].childNodes[0].data.encode("utf-8")
def resolve_metadata (doc, method):
if method != "doi":
return False
#!/usr/bin/env python
# Simple script to query pubmed for a DOI
# (c) Simon Greenhill, 2007
# http://simon.net.nz/
# Modified for integration with referencer by John Spray, 2007
import urllib
import referencer
from referencer import _
from xml.dom import minidom
referencer_plugin_info = {
"longname": _("PubMed DOI resolver"),
"author": "Simon Greenhill, John Spray"
}
referencer_plugin_capabilities = ["doi", "pubmed"]
# Encoding: every PyUnicode that minidom gives us gets
# encoded as utf-8 into a PyString, this is what PyString_AsString on the C++
# side will expect
def get_field(doc, field):
value = doc.getElementsByTagName(field)
if len(value) == 0:
return ""
else:
if (len(value[0].childNodes) == 0):
import gtk
import re
import referencer
from referencer import _
# A referencer plugin to get bibtex info for a book from Google Books
#
# Copyright 2011 Phoenix87
# Copyright 2012 Mads Chr. Olesen <*****@*****.**>
# Copyright 2015 Gabriele N. Tornetta <*****@*****.**>
referencer_plugin_info = {
"author": "Gabriele N. Tornetta (a.k.a. Phoenix87)",
"version": "1.0",
"longname": _("Fetch BiBTeX metadata from Google Books")
}
referencer_plugin_capabilities = ["url"]
pattern = r'https?://books[.]google[.](.+?)/books.+?id=(.+)'
def can_resolve_metadata (doc):
url = doc.get_field("url")
if not url:
return -1
res = re.match(pattern, url)
if res:
return 90
return -1
def resolve_metadata(doc, method):
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
import urllib
try:
import referencer
from referencer import _
except:
#for doctesting
referencer = None
_ = lambda x: x
from xml.dom import minidom
referencer_plugin_info = {
"longname": _("DBLP resolver"),
"version": "0.1",
"author": "Mads Chr. Olesen <*****@*****.**>"
}
referencer_plugin_capabilities = ["resolve_metadata"]
def can_resolve_metadata (doc):
author = doc.get_field ("author")
#let's pretend this is an easter egg ;-)
if author and "Mads" in author and "Olesen" in author:
return 80
elif "DBLP" in str(doc.get_field("bibsource")):
return 80
elif doc.get_field ("title"):
return 20
