Re: format of citation keys

hello dave


this looks promising.

i did what you suggested. followingly, i created a new pybliographic
database and importet a medline file. success -> keys look nice now!


however, my existing database are still with the old key format, and
that is not changed. so i tried exporting the database to medline
format, and import it into a new database. this gives the following
error:


maasha@krusty:~$ pybliographic 
Traceback (most recent call last):
  File "/usr/share/pybliographer/Pyblio/GnomeUI/Document.py", line 578, in ui_open_document
    self.open_document (url, how)
  File "/usr/share/pybliographer/Pyblio/GnomeUI/Document.py", line 592, in open_document
    data = Open.bibopen (url, how = how)
  File "/usr/share/pybliographer/Pyblio/Open.py", line 113, in bibopen
    base = simple_try (url, how)
  File "/usr/share/pybliographer/Pyblio/Open.py", line 95, in simple_try
    base = opener (url, 0)
  File "/usr/share/pybliographer/Pyblio/Format/Medline.py", line 279, in opener
    base = Medline (url)
  File "/usr/share/pybliographer/Pyblio/Format/Medline.py", line 206, in __init__
    self.add (entry)
  File "/usr/share/pybliographer/Pyblio/Base.py", line 188, in add
    entry.key = Autoload.get_by_name ('key', keytype).data (entry, self)
  File "/home/maasha/.pybrc.py", line 65, in generate_key_new2
    key = 'entry-%d' % __entry
NameError: global name '__entry' is not defined


now, what is this?

i should say it comes from the script .pybrc.py ?


# DAE new type of key format AuthorBCDEYY

from string import *

from Pyblio import Key, Autoload, recode

_flat = recode.recode ('latin1..flat')

def generate_key_new (entry, table):

    if   entry.has_key ('author'): aut = entry ['author']
    elif entry.has_key ('editor'): aut = entry ['editor']
    else:                          aut = ()

    if len (aut) == 0:
        global __entry
        key = 'entry-%d' % __entry
        __entry = __entry + 1
    else:
        honorific, first, last, lineage = aut [0].format ()
        key = join (split (last, ' '), '')
        nextkey = ''
        if len (aut) > 1:
            for a in aut:
                honorific, first, last, lineage = a.format ()
                nextkey = nextkey + join (map (lambda x:
                                       x [0], split (last, ' ')), '')
	nextkey = str (nextkey) [1:]
        key = key + join (nextkey, '')
        
        if entry.has_key ('date'):
            year = entry ['date'].year
            
            if year: key = key + str (year) [2:]


    base = _flat (key)
    key  = Key.Key (table, base)
    
    if table.has_key (key):
	suff = ord ('a')
	
        while table.has_key (key):
            suff = suff + 1
            
            if suff > ord ('z'):
                suff = ord ('a')
                base = base + 'a'

            key  = Key.Key (table, base + chr (suff))
            
    return Key.Key (table, key)

Autoload.register ('key', 'New', generate_key_new)

def generate_key_new2 (entry, table):

    if   entry.has_key ('author'): aut = entry ['author']
    elif entry.has_key ('editor'): aut = entry ['editor']
    else:                          aut = ()

    if len (aut) == 0:
        global __entry
        key = 'entry-%d' % __entry
        __entry = __entry + 1
    else:
        honorific, first, last, lineage = aut [0].format ()
        key = join (split (last, ' '), '')
        
        if entry.has_key ('date'):
            year = entry ['date'].year
            
            if year: key = key + str(year)


    base = _flat (key)
    key  = Key.Key (table, base)
    
    if table.has_key (key):
	suff = ord ('a')
	
        while table.has_key (key):
            suff = suff + 1
            
            if suff > ord ('z'):
                suff = ord ('a')
                base = base + 'a'

            key  = Key.Key (table, base + chr (suff))
            
    return Key.Key (table, key)

Autoload.register ('key', 'New2', generate_key_new2)


suggestions for a fix?



best regards


martin




On Mon, Jan 31, 2005 at 03:09:10PM +0000, david.evans-I9fZos/[email protected] wrote:
> If you use the attached .pybrc.py file (put it in your home directory
> before starting pybliographic), and select the imaginatively named
> New2 keyformat in Preferences, then I think that does what you want.
> If not, you should be able to edit that file to change it.
> 
> hope that helps
> 
> Dave
> 
> ---- Message from [email protected] (Martin A. Hansen) at 2005-01-31
> 15:50:50 ------
> >hello
> >
> >
> >the following is cut & pasted from a pybliographic entry:
> >
> >Article     [BDD+98] 
> >Author      Bork, P.; Dandekar, T.; Diaz-Lazcoz, Y.; Eisenhaber, F.;
> Huynen, M.; Yuan, Y.
> >Title       Predicting function: from genes to genomes and back.
> >Journal     J Mol Biol
> >Date        1998
> >Volume      283
> >Number      4
> >Pages       707-25
> >
> >
> >the format of the citation key is [BDD+98]. it is clear to me that
> the idea behind this
> >abbreviation is that the BDD is the first letter in the first three
> authors, and the + denotes
> >that there are more than three authors, and 98 denotes the year of
> the publication. this
> >format may seem logical enough, however, it is very un-intuitive and
> frustrating to work with,
> >when citing references in latex or lyx. the reason is that i
> remember all the papers being
> >cited by the first author - that is the above paper is Bork 1998 in
> my mind. thus i think it
> >would make much more sense to change the format of the citaion key
> to the name of the first
> >author along with the publication year so that [BDD+98] becomes
> [BORK1998]. if dr bork authors
> >more than one paper a year, then the succeeding papers should have
> a, b, c ... suffixed. eg.
> >[BORK1998a], [BORK1998b] ...
> >
> >
> >can this be done without too much trouble?
> >
> >
> >best regards
> >
> >
> >martin
> >
> >
> >-------------------------------------------------------
> >This SF.Net email is sponsored by: IntelliVIEW -- Interactive
> Reporting
> >Tool for open source databases. Create drag-&-drop reports. Save time
> >by over 75%! Publish reports on the web. Export to DOC, XLS, RTF,
> etc.
> >Download a FREE copy at http://www.intelliview.com/go/osdn_nl
> >_______________________________________________
> >Pybliographer-general mailing list
> >Pybliographer-general-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
> >https://lists.sourceforge.net/lists/listinfo/pybliographer-general
> >
> >
> >
> 




-------------------------------------------------------
This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting
Tool for open source databases. Create drag-&-drop reports. Save time
by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc.
Download a FREE copy at http://www.intelliview.com/go/osdn_nl