1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
|
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Referencer plugin to expand/shorten Journal names using a database file
#
# Copyright 2014 Dominik Kriegner <dominik.kriegner@gmail.com>
"""
Referencer - plugin for expanding and shortening journal names.
The short and long versions of the journal names are read from a database.
The journal name database syntax follows the one used by JabRef
see http://jabref.sourceforge.net/resources.php for details
Example files with a lot of already defined Abbreviations can be found at this
webpage
Briefly: lines starting with '#' are considered comments
and a typical entry is
<full name> = <abbreviation>
currently this means the names are not allowed to contain a '='
example of an entry would be:
Physical Review B = Phys. Rev. B
The database file is read from the plugin directory were also the Python source code
is located.
after a lot of new Journal names were added the journal database can be sorted easily using
cat expj_journaldb.txt | sort > expj_journaldb_ordered.txt
mv expj_journaldb_ordered.txt expj_journaldb.txt
"""
import os
import urllib2
import referencer
from referencer import _
import gtk # for dialogs
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>
<toolbar name='ToolBar'>
<placeholder name='PluginToolBarActions'>
<toolitem action='_plugin_expj_expand'/>
</placeholder>
<placeholder name='PluginToolBarActions'>
<toolitem action='_plugin_expj_shorten'/>
</placeholder>
</toolbar>
</ui>
"""
}
referencer_plugin_actions = [
{
"name": "_plugin_expj_expand",
"label": _("Expand Journal Name"),
"tooltip": _("Expand the Journal title to the long form"),
"icon": "expj_expand.svg",
"callback": "do_expand",
"accelerator": "<control><shift>E"
},
{
"name": "_plugin_expj_shorten",
"label": _("Shorten Journal Name"),
"tooltip": _("Shorten the Journal title to the abbreviated form"),
"icon": "expj_shorten.svg",
"callback": "do_shorten",
"accelerator": "<control><shift>C"
}
]
# try opening the database
# when this fails the plugin will still be loaded and a hint will be shown in all the dialogs
DISPHINT = True
for fname in DBs:
try:
with open(fname) as fh:
DISPHINT = False
except IOError:
pass
# create the lists for expansion and shortening
expanded = []
contracted = []
def do_expand (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
shortv = doc.get_field('journal')
repl = shortv
if shortv != "":
try:
# try direct lookup in database
idx = map(string.lower,contracted).index(shortv.strip().lower())
repl = expanded[idx]
except ValueError:
try: # check if journal name is already the expanded version
idx = map(string.lower,expanded).index(shortv.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(shortv,contracted,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'"%(shortv))
else:
label = gtk.Label(_("No exact match found!\nChoose correct entry for journal") + " '%s'"%(shortv))
dialog.vbox.pack_start(label)
for i in range(len(match)):
if i==0:
rb = gtk.RadioButton(None,expanded[contracted.index(match[i])])
rb.set_active(True)
else:
rb = gtk.RadioButton(rb,expanded[contracted.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 name"))
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(repl)
contracted.append(shortv)
save_db()
# change the journal name
doc.set_field('journal',repl)
if DEBUG:
print("expj: changed journal entry from '%s' to '%s'"%(shortv,repl))
return True
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
def load_db():
"""
Load Journal names from database file upon first use of the module
"""
global expanded,contracted,DISPHINT
for fname in DBs:
try:
with open(fname) as fh:
for line in fh.readlines():
splitline = line.strip().split('=')
if len(splitline) == 2:
longv,shortv = splitline
expanded.append(longv.strip())
contracted.append(shortv.strip())
elif DEBUG:
print("expj: unparseable line in Journal name database (%s)"%line.strip())
DISPHINT = False # at least one file was loaded so remove the hint
except IOError:
pass #raise IOError("Database file for plugin expj could not be loaded.")
def save_db():
"""
Save current database to text file to keep changes for next
start of Referencer
"""
global expanded,contracted
try:
with open(DBs[0],'a') as fh:
newentry = expanded[-1]
newentry += " = "
newentry += contracted[-1]
fh.write(newentry + '\n')
except IOError:
if DEBUG:
print("expj: changes to Journal name database could not be written! (File: %s)"%DBs[0])
#raise IOError("Database file for plugin expj could not be written.")
def download_db(link):
"""
Download Journal name database from the given link and save it to the database file,
afterwards trigger a reread of all databases
"""
global expanded,contracted
if DEBUG:
print("expj: Download link '%s'"%link)
try:
response = urllib2.urlopen(link)
except ValueError, err:
downloadException(err.message)
return
# assume download was fine
# check typ of download before proceeding
if response.headers.type != 'text/plain':
downloadException("Document type must be text/plain and not %s"%response.headers.type)
return
# write to base database
with open(DBs[1],'w') as fh:
fh.write(response.read())
# clean old databases to trigger reload upon next usage
expanded = []
contracted = []
class downloadException(gtk.Dialog):
def __init__(self, parent=None):
gtk.Dialog.__init__(self,errmsg,"expj plugin",
parent,
gtk.DIALOG_MODAL |
gtk.DIALOG_DESTROY_WITH_PARENT,
(gtk.STOCK_OK, gtk.RESPONSE_OK))
text = """
<b> expj Download Error</b>
The error message is:
"%s"
Check the specified link and try again
""" %errmsg
label = gtk.Label()
label.set_markup(text)
self.vbox.pack_start(label)
self.vbox.show_all()
class preferencesDialog(gtk.Dialog):
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 webpage 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 costom 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()
# Main referencer preferences function
def referencer_config():
"""
function run by the referencer plugin configure button found in
Edit -> Preferences
"""
prefs = preferencesDialog()
response = prefs.run()
if response == int(gtk.RESPONSE_OK):
download_db(prefs.dllink.get_text())
prefs.destroy()
|
