forked from jkitchin/org-ref
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathorg-ref-bibtex.el
1213 lines (1075 loc) · 41.7 KB
/
org-ref-bibtex.el
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
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
;;; org-ref-bibtex.el -- org-ref-bibtex utilities
;; Copyright(C) 2014 John Kitchin
;; Author: John Kitchin <[email protected]>
;; URL: https://github.com/jkitchin/org-ref
;; Version: 0.1
;; Keywords: org-mode, bibtex
;; Package-Requires: ((org-ref) (s) (dash) (doi-utils) (key-chord))
;; This file is not currently part of GNU Emacs.
;; This program is free software; you can redistribute it and/or
;; modify it under the terms of the GNU General Public License as
;; published by the Free Software Foundation; either version 2, or (at
;; your option) any later version.
;; This program is distributed in the hope that it will be useful, but
;; WITHOUT ANY WARRANTY; without even the implied warranty of
;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;; General Public License for more details.
;; You should have received a copy of the GNU General Public License
;; along with this program ; see the file COPYING. If not, write to
;; the Free Software Foundation, Inc., 59 Temple Place - Suite 330,
;; Boston, MA 02111-1307, USA.
;;; Commentary:
;; org-ref-bibtex-generate-longtitles
;; org-ref-bibtex-generate-shorttitles
;; org-ref-stringify-journal-name :: replace a journal name with a string in
;; `org-ref-bibtex-journal-abbreviations'
;; org-ref-set-journal-string :: in a bibtex entry run this to replace the
;; journal with a string
;;
;; org-ref-title-case-article :: title case the title in an article
;; org-ref-sentence-case-article :: sentence case the title in an article.
;; org-ref-replace-nonascii :: replace nonascii characters in a bibtex
;; entry. Replacements are in `org-ref-nonascii-latex-replacements'.
;;
;; org-ref-title-case-article
;; org-ref-sentence-case-article
;;
;; org-ref-bibtex-next-entry :: bound to M-n
;; org-ref-bibtex-previous-entry :: bound to M-p
;;
;; Functions to act on a bibtex entry or file
;; org-ref-bibtex-hydra/body gives a hydra menu to a lot of useful functions.
;; org-ref-bibtex-new-entry/body gives a hydra menu to add new bibtex entries.
;; org-ref-bibtex-file/body gives a hydra menu of actions for the bibtex file
;;
;; org-ref-bibtex :: a deprecated menu of actions
(require 'bibtex)
(require 'dash)
(require 'hydra)
(require 'key-chord nil 'no-error)
(require 'message)
(require 's)
(require 'org-ref-citeproc)
;;; Code:
;; This is duplicated from org-ref-core to try to avoid a byte-compile error.
(add-to-list 'load-path
(expand-file-name
"citeproc"
(file-name-directory (or load-file-name (buffer-file-name)))))
(add-to-list 'load-path
(expand-file-name
"citeproc/csl"
(file-name-directory (or load-file-name (buffer-file-name)))))
;;* Custom variables
(defgroup org-ref-bibtex nil
"Customization group for org-ref-bibtex."
:group 'org-ref-bibtex)
(defcustom org-ref-bibtex-hydra-key-chord
nil
"Key-chord to run `org-ref-bibtex-hydra'.
I like \"jj\""
:type 'string
:group 'org-ref-bibtex)
(defcustom org-ref-bibtex-hydra-key-binding
nil
"Key-binding to run `org-ref-bibtex-hydra'.
I like \C-cj."
:type 'string
:group 'org-ref-bibtex)
(defcustom org-ref-helm-cite-shorten-authors nil
"If non-nil show only last names in the helm selection buffer."
:type 'boolean
:group 'org-ref-bibtex)
;;* Journal abbreviations
(defvar org-ref-bibtex-journal-abbreviations
'()
"List of (string journal-full-name journal-abbreviation). Find
new abbreviations at http://cassi.cas.org/search.jsp.")
(defcustom org-ref-bibtex-assoc-pdf-with-entry-move-function 'rename-file
"Function to use when associating pdf files with bibtex entries.
The value should be either `rename-file' or `copy-file'. The former
will move and rename the original file. The latter will leave the
original file in place while creating a renamed copy in
`org-ref-pdf-directory'."
:type 'function
:group 'org-ref-bibtex)
(setq org-ref-bibtex-journal-abbreviations
'(("ACR" "Accounts of Chemical Research" "Acc. Chem. Res.")
("ACAT" "ACS Catalysis" "ACS Catal.")
("AM" "Acta Materialia" "Acta Mater.")
("AMM" "Acta Metallurgica et Materialia" "Acta Metall. Mater.")
("AEM" "Advanced Energy Materials" "Adv. Energy Mater.")
("AAMI" "ACS Applied Materials \\& Interfaces"
"ACS Appl. Mater. Interfaces")
("AMiner" "American Mineralogist" "Am. Mineral.")
("AngC" "Angewandte Chemie-International Edition"
"Angew. Chem. Int. Edit.")
("APLM" "APL Materials" "APL Mat.")
("ACBE" "Applied Catalysis B: Environmental" "Appl. Catal. B-Environ.")
("APL" "Applied Physics Letters" "Appl. Phys. Lett.")
("ASS" "Applied Surface Science" "Appl. Surf. Sci.")
("CL" "Catalysis Letters" "Catal. Lett.")
("CC" "Catalysis Communications" "Catal. Commun.")
("CST" "Catalysis Science & Technology" "Catal. Sci. Technol.")
("CT" "Catalysis Today" "Catal. Today")
("ChC" "Chemical Communications" "Chem. Commun.")
("CPL" "Chemical Physics Letters" "Chem. Phys. Lett")
("CR" "Chemical Reviews" "Chem. Rev.")
("CSR" "Chemical Society Reviews" "Chem. Soc. Rev.")
("CSR" "Chemical Society Reviews" "Chem. Soc. Rev.")
("CM" "Chemistry of Materials" "Chem. Mater.")
("CSA" "Colloids and Surfaces, A: Physicochemical and Engineering Aspects"
"Colloids Surf., A")
("CF" "Combustion and Flame" "Combust. Flame")
("CPMS" "Computational Materials Science" "Comp. Mater. Sci.")
("CPC" "Computer Physics Communications" "Comput. Phys. Commun.")
("CSE" "Computing in Science \\& Engineering" "Comput. Sci. Eng.")
("CGD" "Crystal Growth \\& Design" "Cryst. Growth Des.")
("CEC" "CrystEngComm" "CrystEngComm")
("EA" "Electrochimica Acta" "Electrochim. Acta")
("ECST" "ECS Transactions" "ECS Trans.")
("EES" "Energy \\& Environmental Science" "Energy Environ. Sci.")
("HPR" "High Pressure Research" "High Pressure Res.")
("IC" "Inorganic Chemistry" "Inorg. Chem.")
("IECR" "Industrial \\& Engineering Chemistry Research"
"Ind. Eng. Chem. Res.")
("JJAP" "Japanese Journal of Applied Physics" "Jpn. J. Appl. Phys.")
("JMatR" "Journal of Materials Research" "J. Mater. Res.")
("JALC" "Journal of Alloys and Compounds" "J. Alloy Compd.")
("JAC" "Journal of Applied Crystallography" "J. Appl. Crystallogr.")
("JAE" "Journal of Applied Electrochemistry" "J. Appl. Electrochem.")
("JAP" "Journal of Applied Physics" "J. Appl. Phys.")
("JC" "Journal of Catalysis" "J. Catal.")
("JCP" "Journal of Chemical Physics" "J. Chem. Phys.")
("JCC" "Journal of Computational Chemistry" "J. Comput. Chem.")
("JCG" "Journal of Crystal Growth" "J. Crys. Growth")
("JMC" "Journal of Materials Chemistry" "J. Mater. Chem.")
("JMC" "Journal of Materials Chemistry" "J. Mater. Chem.")
("JMSL" "Journal of Materials Science Letters" "J. Mater. Sci. Lett.")
("JMS" "Journal of Membrane Science" "J. Memb. Sci.")
("JPE" "Journal of Phase Equilibria" "J. Phase Equilib.")
("JPCS" "Journal of Physics and Chemistry of Solids"
"J. Phys. Chem. Solids")
("JPCM" "Journal of Physics: Condensed Matter"
"J. Phys.: Condens. Matter")
("JPS" "Journal of Power Sources" "J. Power Sources")
("JSSC" "Journal of Solid State Chemistry" "J. Solid State Chem.")
("JACerS" "Journal of the American Ceramic Society" "J. Am. Ceram. Soc.")
("JACS" "Journal of the American Chemical Society" "J. Am. Chem. Soc.")
("JASIST" "Journal of the American Society for Information Science and Technology"
"J. Am. Soc. Inf. Sci. Technol.")
("JES" "Journal of The Electrochemical Society" "J. Electrochem. Soc.")
("JEaC" "Journal of Electroanalytical Chemistry" "J. Electroanal. Chem.")
("JMS" "Journal of Membrane Science" "J. Memb. Sci.")
("JRS" "Journal of Raman Spectroscopy" "J. Raman Spectrosc.")
("JVST" "Journal of Vacuum Science \\& Technology A"
"J. Vac. Sci. Technol. A")
("ML" "Materials Letters" "Mater. Lett.")
("MSE-BS" "Materials Science and Engineering B" "Mat. Sci. Eng. B-Solid")
("MOLSIM" "Molecular Simulation" "Mol. Sim.")
("Nature" "Nature" "Nature")
("NM" "Nature Materials" "Nat. Mater.")
("NC" "Nature Chemistry" "Nat. Chem.")
("PML" "Philosophical Magazine Letters" "Phil. Mag. Lett.")
("PMA" "Philosophical Magazine A" "Phil. Mag. A")
("PA" "Physica A: Statistical Mechanics and its Applications" "Physica A")
("PB" "Physica B-Condensed Matter" "Physica B")
("PCCP" "Physical Chemistry Chemical Physics" "Phys. Chem. Chem. Phys.")
("PSSB" "physica status solidi (b)" "Phys. Status Solidi B")
("PRA" "Physical Review A" "Phys. Rev. A")
("PRB" "Physical Review B" "Phys. Rev. B")
("PRL" "Physical Review Letters" "Phys. Rev. Lett.")
("PCM" "Physics and Chemistry of Minerals" "Phys. Chem. Miner.")
("PNAS" "Proceedings of the National Academy of Sciences of the United States of America"
"Proc. Natl. Acad. Sci. U. S. A.")
("PSurfSci" "Progress in Surface Science" "Prog. Surf. Sci.")
("Science" "Science" "Science")
("SM" "Scripta Materialia" "Scr. Mater.")
("SABC" "Sensors and Actuators B: Chemical" "Sensor. Actuat. B-Chem.")
("SS" "Surface Science" "Surf. Sci.")
("EPJB" "The European Physical Journal B" "Eur. Phys. J. B")
("JPC" "The Journal of Physical Chemistry" "J. Phys. Chem.")
("JPCB" "The Journal of Physical Chemistry B" "J. Phys. Chem. B")
("JPCC" "The Journal of Physical Chemistry C" "J. Phys. Chem. C")
("JPCL" "The Journal of Physical Chemistry Letters"
"J. Phys. Chem. Lett.")
("JCP" "The Journal of Chemical Physics" "J. Chem. Phys.")
("MSMSE" "Modelling and Simulation in Materials Science and Engineering"
"Modell. Simul. Mater. Sci. Eng.")
("TSF" "Thin Solid Films" "Thin Solid Films")
("TC" "Topics in Catalysis" "Top. Catal.")
("WR" "Water Research" "Water Res.")))
;;;###autoload
(defun org-ref-bibtex-generate-longtitles ()
"Generate longtitles.bib which are @string definitions.
The full journal names are in `org-ref-bibtex-journal-abbreviations'."
(interactive)
(with-temp-file "longtitles.bib"
(dolist (row org-ref-bibtex-journal-abbreviations)
(insert (format "@string{%s=\"%s\"}\n"
(nth 0 row)
(nth 1 row))))))
;;;###autoload
(defun org-ref-bibtex-generate-shorttitles ()
"Generate shorttitles.bib which are @string definitions.
The abbreviated journal names in `org-ref-bibtex-journal-abbreviations'."
(interactive)
(with-temp-file "shorttitles.bib"
(dolist (row org-ref-bibtex-journal-abbreviations)
(insert (format "@string{%s=\"%s\"}\n"
(nth 0 row)
(nth 2 row))))))
;;;###autoload
(defun org-ref-stringify-journal-name (&optional key start end)
"Replace journal name in a bibtex entry with a string.
The strings are defined in
`org-ref-bibtex-journal-abbreviations'. The optional arguments KEY,
START and END allow you to use this with `bibtex-map-entries'"
(interactive)
(bibtex-beginning-of-entry)
(when
(string= "article"
(downcase
(cdr (assoc "=type=" (bibtex-parse-entry)))))
(let* ((full-names (mapcar
(lambda (row)
(cons (nth 1 row) (nth 0 row)))
org-ref-bibtex-journal-abbreviations))
(abbrev-names (mapcar
(lambda (row)
(cons (nth 2 row) (nth 0 row)))
org-ref-bibtex-journal-abbreviations))
(journal (s-trim (bibtex-autokey-get-field "journal")))
(bstring (or
(cdr (assoc journal full-names))
(cdr (assoc journal abbrev-names)))))
(when bstring
(bibtex-set-field "journal" bstring t)
(bibtex-fill-entry)))))
;;;###autoload
(defun org-ref-helm-set-journal-string ()
"Helm interface to set a journal string in a bibtex entry.
Entries come from `org-ref-bibtex-journal-abbreviations'."
(interactive)
(bibtex-set-field
"journal"
(helm :sources
`((name . "journal")
(candidates . ,(mapcar
(lambda (x)
(cons (format "%s | %s" (nth 1 x) (nth 2 x))
(car x)))
org-ref-bibtex-journal-abbreviations))
(action . (lambda (x) (identity x))))
:input (s-trim (bibtex-autokey-get-field "journal")))
t)
(bibtex-fill-entry)
(bibtex-clean-entry))
;;;###autoload
(defun org-ref-set-journal-string (full-journal-name)
"Set a bibtex journal name to the string that represents FULL-JOURNAL-NAME.
This is defined in `org-ref-bibtex-journal-abbreviations'."
(interactive (list
(completing-read
"Journal: "
(mapcar
(lambda (x)
(nth 1 x))
org-ref-bibtex-journal-abbreviations))))
;; construct data alist for the string lookup.
(let ((alist (mapcar
(lambda (x)
(cons (nth 1 x) (nth 0 x)))
org-ref-bibtex-journal-abbreviations)))
(bibtex-set-field "journal" (cdr (assoc full-journal-name alist)) t)
(bibtex-fill-entry)
(bibtex-clean-entry)))
;;* Non-ascii character replacement
;; see https://github.com/fxcoudert/tools/blob/master/doi2bib for more replacements
(defvar org-ref-nonascii-latex-replacements
'()
"Cons list of non-ascii characters and their LaTeX representations.")
(setq org-ref-nonascii-latex-replacements
'(("í" . "{\\\\'i}")
("æ" . "{\\\\ae}")
("ć" . "{\\\\'c}")
("é" . "{\\\\'e}")
("ä" . "{\\\\\"a}")
("è" . "{\\\\`e}")
("à" . "{\\\\`a}")
("á" . "{\\\\'a}")
("ø" . "{\\\\o}")
("ë" . "{\\\\\"e}")
("ü" . "{\\\\\"u}")
("ñ" . "{\\\\~n}")
("ņ" . "{\\\\c{n}}")
("ñ" . "{\\\\~n}")
("å" . "{\\\\aa}")
("ö" . "{\\\\\"o}")
("Á" . "{\\\\'A}")
("í" . "{\\\\'i}")
("ó" . "{\\\\'o}")
("ó" . "{\\\\'o}")
("ú" . "{\\\\'u}")
("ú" . "{\\\\'u}")
("š" . "{\\\\v{s}}")
("ř" . "{\\\\v{r}}")
("š" . "{\\\\v{s}}")
("İ" . "{\\\\.I}")
("ğ" . "{\\\\u{g}}")
("δ" . "$\\\\delta$")
("ç" . "{\\\\c{c}}")
("ß" . "{\\\\ss}")
("≤" . "$\\\\le$")
("≥" . "$\\\\ge$")
("<" . "$<$")
("θ" . "$\\\\theta$")
("μ" . "$\\\\mu$")
("→" . "$\\\\rightarrow$")
("⇌" . "$\\\\leftrightharpoons$")
("×" . "$\\\\times$")
("°" . "$\\\\deg$")
("ş" . "{\\\\c{s}}")
("γ" . "$\\\\gamma$")
("ɣ" . "$\\\\gamma$")
("º" . "degC")
("η" . "$\\\\eta$")
("µ" . "$\\\\mu$")
("α" . "$\\\\alpha$")
("β" . "$\\\\beta$")
("ɛ" . "$\\\\epsilon$")
("Ⅵ" . "\\textrm{VI}")
("Ⅲ" . "\\textrm{III}")
("Ⅴ" . "\\textrm{V}")
("λ" . "$\\\\lambda$")
("π" . "$\\\\pi$")
("∞" . "$\\\\infty$")
("χ" . "$\\\\chi$")
("∼" . "\\\\textasciitilde{}")
("‑" . "\\\\textemdash{}")
(" " . " ")
("…" . "...")
("•" . "\\\\textbullet ")
;; I think these are non-ascii spaces. there seems to be more than one.
(" " . " ")
(" " . " ")
(" " . " ")
("–" . "-")
("−" . "-")
("–" . "-")
("—" . "-")
("‒" . "\\\\textemdash{}")
("‘" . "'")
("’" . "'")
("’" . "'")
("“" . "\"")
("’" . "'")
("”" . "\"")))
;;;###autoload
(defun org-ref-replace-nonascii ()
"Hook function to replace non-ascii characters in a bibtex entry."
(interactive)
(save-restriction
(bibtex-narrow-to-entry)
(goto-char (point-min))
(dolist (char (mapcar (lambda (x)
(car x))
org-ref-nonascii-latex-replacements))
(while (re-search-forward char nil t)
(replace-match (cdr (assoc char org-ref-nonascii-latex-replacements))))
(goto-char (point-min))))
(occur "[^[:ascii:]]"))
;;* Title case transformations
(defvar org-ref-lower-case-words
'("a" "an" "on" "and" "for"
"the" "of" "in")
"List of words to keep lowercase when changing case in a title.")
;;;###autoload
(defun org-ref-title-case-article (&optional key start end)
"Convert a bibtex entry article title to title-case.
The arguments KEY, START and END are optional, and are only there
so you can use this function with `bibtex-map-entries' to change
all the title entries in articles."
(interactive)
(bibtex-beginning-of-entry)
(let* ((title (bibtex-autokey-get-field "title"))
(words (split-string title))
(start 0))
(when
(string= "article"
(downcase
(cdr (assoc "=type=" (bibtex-parse-entry)))))
(setq words (mapcar
(lambda (word)
(if (or
;; match words containing {} or \ which are probably
;; LaTeX or protected words
(string-match "\\$\\|{\\|}\\|\\\\" word)
;; these words should not be capitalized, unless they
;; are the first word
(-contains? org-ref-lower-case-words
(s-downcase word)))
word
(s-capitalize word)))
words))
;; Check if first word should be capitalized
(when (-contains? org-ref-lower-case-words (car words))
(setf (car words) (s-capitalize (car words))))
(setq title (mapconcat 'identity words " "))
;; Capitalize letters after a dash
(while
(string-match "[a-zA-Z]-\\([a-z]\\)" title start)
(let ((char (substring title (match-beginning 1) (match-end 1))))
(setf (substring title (match-beginning 1) (match-end 1))
(format "%s" (upcase char)))
(setq start (match-end 1))))
;; this is defined in doi-utils
(bibtex-set-field
"title"
title)
(bibtex-fill-entry))))
;;;###autoload
(defun org-ref-sentence-case-article (&optional key start end)
"Convert a bibtex entry article title to sentence-case.
The arguments KEY, START and END are optional, and are only there
so you can use this function with `bibtex-map-entries' to change
all the title entries in articles."
(interactive)
(bibtex-beginning-of-entry)
(let* ((title (bibtex-autokey-get-field "title"))
(words (split-string title))
(start 0))
(when
(string= "article"
(downcase
(cdr (assoc "=type="
(bibtex-parse-entry)))))
(setq words (mapcar
(lambda (word)
(if
;; match words containing {} or \ which are probably
;; LaTeX or protected words
(string-match "\\$\\|{\\|}\\|\\\\" word)
word
(s-downcase word)))
words))
;; capitalize first word
(setf (car words) (s-capitalize (car words)))
;; join the words
(setq title (mapconcat 'identity words " "))
;; capitalize a word after a :, eg. a subtitle, and protect it
(while
(string-match "[a-z]:\\s-+\\([A-Z]\\)" title start)
(let ((char (substring title (match-beginning 1) (match-end 1))))
(setf (substring title (match-beginning 1) (match-end 1))
(format "%s" (upcase char)))
(setq start (match-end 1))))
;; this is defined in doi-utils
(bibtex-set-field
"title" title)
;; clean and refill entry so it looks nice
(bibtex-clean-entry)
(bibtex-fill-entry))))
;;* Navigation in bibtex file
;;;###autoload
(defun org-ref-bibtex-next-entry (&optional n)
"Jump to the beginning of the next bibtex entry.
N is a prefix argument. If it is numeric, jump that many entries
forward. Negative numbers do nothing."
(interactive "P")
;; Note if we start at the beginning of an entry, nothing
;; happens. We need to move forward a char, and call again.
(when (= (point) (save-excursion
(bibtex-beginning-of-entry)))
(forward-char)
(org-ref-bibtex-next-entry))
;; search forward for an entry
(when
(re-search-forward bibtex-entry-head nil t (and (numberp n) n))
;; go to beginning of the entry
(bibtex-beginning-of-entry)))
;;;###autoload
(defun org-ref-bibtex-previous-entry (&optional n)
"Jump to beginning of the previous bibtex entry.
N is a prefix argument. If it is numeric, jump that many entries back."
(interactive "P")
(bibtex-beginning-of-entry)
(when
(re-search-backward bibtex-entry-head nil t (and (numberp n) n))
(bibtex-beginning-of-entry)))
(defun org-ref-bibtex-mode-keys ()
"Modify keymaps used by `bibtex-mode'."
(local-set-key (kbd "M-n") 'org-ref-bibtex-next-entry)
(local-set-key (kbd "M-p") 'org-ref-bibtex-previous-entry))
;; add to bibtex-mode-hook
(add-hook 'bibtex-mode-hook 'org-ref-bibtex-mode-keys)
;;* Functions to act on an entry with a doi
;;;###autoload
(defun org-ref-bibtex-entry-doi ()
"Get doi from entry at point."
(interactive)
(save-excursion
(bibtex-beginning-of-entry)
(reftex-get-bib-field "doi" (bibtex-parse-entry t))))
;;;###autoload
(defun org-ref-bibtex-wos ()
"Open bibtex entry in Web Of Science if there is a DOI."
(interactive)
(doi-utils-wos (org-ref-bibtex-entry-doi)))
;;;###autoload
(defun org-ref-bibtex-wos-citing ()
"Open citing articles for bibtex entry in Web Of Science if
there is a DOI."
(interactive)
(doi-utils-wos-citing (org-ref-bibtex-entry-doi)))
;;;###autoload
(defun org-ref-bibtex-wos-related ()
"Open related articles for bibtex entry in Web Of Science if
there is a DOI."
(interactive)
(doi-utils-wos-related (org-ref-bibtex-entry-doi)))
;;;###autoload
(defun org-ref-bibtex-crossref ()
"Open the bibtex entry in Crossref by its doi."
(interactive)
(doi-utils-crossref (org-ref-bibtex-entry-doi)))
;;;###autoload
(defun org-ref-bibtex-google-scholar ()
"Open the bibtex entry at point in google-scholar by its doi."
(interactive)
(doi-utils-google-scholar (org-ref-bibtex-entry-doi)))
;;;###autoload
(defun org-ref-bibtex-pubmed ()
"Open the bibtex entry at point in Pubmed by its doi."
(interactive)
(doi-utils-pubmed (org-ref-bibtex-entry-doi)))
;;;###autoload
(defun org-ref-bibtex-pdf (doi)
"Open the pdf for the bibtex entry at point.
Thin wrapper to get `org-ref-bibtex' to open pdf, because it
calls functions with a DOI argument."
(interactive)
(org-ref-open-bibtex-pdf))
(defun org-ref-bibtex-get-file-move-func (prefix)
"Determine whether to use `rename-file' or `copy-file' for `org-ref-bibtex-assoc-pdf-with-entry'.
When called with a PREFIX argument,
`org-ref-bibtex-assoc-pdf-with-entry-move-function' switches to the
opposite function from that which is defined in
`org-ref-assoc-pdf-with-entry-move-function'."
(message (format "%s" prefix))
(if (eq prefix nil)
org-ref-bibtex-assoc-pdf-with-entry-move-function
(if (eq org-ref-bibtex-assoc-pdf-with-entry-move-function 'rename-file)
'copy-file
'rename-file)))
;;;###autoload
(defun org-ref-bibtex-assoc-pdf-with-entry (&optional prefix)
"Prompt for pdf associated with entry at point and rename it.
Check whether a pdf already exists in `org-ref-pdf-directory' with the
name '[bibtexkey].pdf'. If the file does not exist, rename it to
'[bibtexkey].pdf' using
`org-ref-bibtex-assoc-pdf-with-entry-move-function' and place it in
`org-ref-pdf-directory'. Optional PREFIX argument toggles between
`rename-file' and `copy-file'."
(interactive "P")
(save-excursion
(bibtex-beginning-of-entry)
(let* ((file (read-file-name "Select file associated with entry: "))
(bibtex-expand-strings t)
(entry (bibtex-parse-entry t))
(key (reftex-get-bib-field "=key=" entry))
(pdf (concat org-ref-pdf-directory (concat key ".pdf")))
(file-move-func (org-ref-bibtex-get-file-move-func prefix)))
(if (file-exists-p pdf)
(message (format "A file named %s already exists" pdf))
(progn
(funcall file-move-func file pdf)
(message (format "Created file %s" pdf)))))))
;;* Hydra menus
;;** Hydra menu for bibtex entries
;; hydra menu for actions on bibtex entries
(defhydra org-ref-bibtex-hydra (:color blue)
"
_p_: Open pdf _y_: Copy key _n_: New entry _w_: WOS
_b_: Open url _f_: Copy formatted entry _o_: Copy entry _c_: WOS citing
_r_: Refile entry _k_: Add keywords _d_: delete entry _a_: WOS related
_e_: Email entry _K_: Edit keywords _L_: clean entry _P_: Pubmed
_U_: Update entry _N_: Open notes _R_: Crossref _g_: Google Scholar
_s_: Sort entry _a_: Remove nonascii _h_: helm-bibtex _q_: quit
_u_: Update field _F_: file funcs _A_: Assoc pdf with entry
_T_: Title case
_S_: Sentence case
"
("p" org-ref-open-bibtex-pdf)
("P" org-ref-bibtex-pubmed)
("w" org-ref-bibtex-wos)
("c" org-ref-bibtex-wos-citing)
("a" org-ref-bibtex-wos-related)
("R" org-ref-bibtex-crossref)
("g" org-ref-bibtex-google-scholar)
("n" org-ref-bibtex-new-entry/body)
("N" org-ref-open-bibtex-notes)
("o" bibtex-copy-entry-as-kill)
("d" bibtex-kill-entry)
("L" org-ref-clean-bibtex-entry)
("y" (kill-new (bibtex-autokey-get-field "=key=")))
("f" (progn
(bibtex-beginning-of-entry)
(kill-new (orhc-formatted-citation (bibtex-parse-entry t)))))
("k" helm-tag-bibtex-entry)
("K" (lambda ()
(interactive)
(org-ref-set-bibtex-keywords
(read-string "Keywords: "
(bibtex-autokey-get-field "keywords"))
t)))
("b" org-ref-open-in-browser)
("r" (lambda ()
(interactive)
(bibtex-beginning-of-entry)
(bibtex-kill-entry)
(find-file (completing-read
"Bibtex file: "
(f-entries "." (lambda (f) (f-ext? f "bib")))))
(goto-char (point-max))
(bibtex-yank)
(save-buffer)
(kill-buffer)))
("e" org-ref-email-bibtex-entry)
("U" (doi-utils-update-bibtex-entry-from-doi (org-ref-bibtex-entry-doi)))
("u" doi-utils-update-field)
("F" org-ref-bibtex-file/body)
("h" helm-bibtex)
("A" org-ref-bibtex-assoc-pdf-with-entry)
("a" org-ref-replace-nonascii)
("s" org-ref-sort-bibtex-entry)
("T" org-ref-title-case-article)
("S" org-ref-sentence-case-article)
("q" nil))
;; create key-chord and key binding for hydra
(when (and (featurep 'key-chord) org-ref-bibtex-hydra-key-chord)
(key-chord-define-global
org-ref-bibtex-hydra-key-chord
'org-ref-bibtex-hydra/body))
(when org-ref-bibtex-hydra-key-binding
(define-key bibtex-mode-map org-ref-bibtex-hydra-key-binding 'org-ref-bibtex-hydra/body))
;;** Hydra menu for new bibtex entries
;; A hydra for adding new bibtex entries.
(defhydra org-ref-bibtex-new-entry (:color blue)
"New Bibtex entry:"
("a" bibtex-Article "Article")
("b" bibtex-Book "Book")
("i" bibtex-InBook "In book")
("l" bibtex-Booklet "Booklet")
("P" bibtex-Proceedings "Proceedings")
("p" bibtex-InProceedings "In proceedings")
("m" bibtex-Misc "Misc.")
("M" bibtex-Manual "Manual")
("T" bibtex-PhdThesis "PhD Thesis")
("t" bibtex-MastersThesis "MS Thesis")
("R" bibtex-TechReport "Report")
("u" bibtex-Unpublished "unpublished")
("c" bibtex-InCollection "Article in collection")
("q" nil "quit"))
;;** Hydra menu of functions to act on a bibtex file.
(defhydra org-ref-bibtex-file (:color blue)
"Bibtex file functions: "
("v" bibtex-validate "Validate entries")
("s" bibtex-sort-buffer "Sort entries")
("r" bibtex-reformat "Reformat entries")
("c" bibtex-count-entries "Count entries")
("p" org-ref-build-full-bibliography "PDF bibliography"))
;;* DEPRECATED bibtex menu
(defvar org-ref-bibtex-menu-funcs '()
"Functions to run in doi menu.
Each entry is a list of (key menu-name function). The function
must take one argument, the doi. This is somewhat deprecated, as
I prefer the hydra interfaces above.")
(setq org-ref-bibtex-menu-funcs
'(("p" "df" org-ref-bibtex-pdf)
("C" "opy" (lambda (doi)
(kill-new (org-ref-bib-citation))
(bury-buffer)))
("w" "os" doi-utils-wos)
("c" "iting articles" doi-utils-wos-citing)
("r" "elated articles" doi-utils-wos-related)
("s" "Google Scholar" doi-utils-google-scholar)
("P" "Pubmed" doi-utils-pubmed)
("f" "CrossRef" doi-utils-crossref)))
;;;###autoload
(defun org-ref-bibtex ()
"Menu command to run in a bibtex entry.
Functions from `org-ref-bibtex-menu-funcs'. They all rely on the
entry having a doi."
(interactive)
;; construct menu string as a message
(message
(concat
(mapconcat
(lambda (tup)
(concat "[" (elt tup 0) "]"
(elt tup 1) " "))
org-ref-bibtex-menu-funcs "") ": "))
(let* ((input (read-char-exclusive))
(choice (assoc
(char-to-string input) org-ref-bibtex-menu-funcs)))
(when choice
(funcall
(elt
choice
2)
(org-ref-bibtex-entry-doi)
))))
(defalias 'jb 'org-ref-bibtex)
;;;###autoload
(defun org-ref-email-bibtex-entry ()
"Email current bibtex entry at point and pdf if it exists."
(interactive)
(save-excursion
(bibtex-beginning-of-entry)
(let* ((key (reftex-get-bib-field "=key=" (bibtex-parse-entry t)))
pdf)
;; when we have org-ref defined we may have pdf to find.
(when (boundp 'org-ref-pdf-directory)
(setq pdf (expand-file-name
(concat key ".pdf")
org-ref-pdf-directory)))
(bibtex-copy-entry-as-kill)
(compose-mail)
(message-goto-body)
(insert (pop bibtex-entry-kill-ring))
(message-goto-subject)
(insert key)
(message "%s exists %s" pdf (file-exists-p pdf))
(when (file-exists-p pdf)
(mml-attach-file pdf))
(message-goto-to))))
;;* org-ref bibtex keywords
;; adapted from bibtex-utils.el
;; these are candidates for selecting keywords/tags
(defun org-ref-bibtex-keywords ()
"Get keywords defined in current bibtex file.
These are in the keywords field, and are comma or semicolon separated."
(save-excursion
(goto-char (point-min))
(let (keywords kstring)
(while (re-search-forward "^\\s-*keywords.*{\\([^}]+\\)}" nil t)
;; TWS - remove newlines/multiple spaces:
(setq kstring (replace-regexp-in-string
"[ \t\n]+" " "
(match-string 1)))
(mapc
(lambda (v)
(add-to-list 'keywords v t))
(split-string kstring "\\(,\\|;\\)[ \n]*\\|{\\|}" t)))
keywords)))
;;;###autoload
(defun org-ref-set-bibtex-keywords (keywords &optional arg)
"Add KEYWORDS to a bibtex entry.
If KEYWORDS is a list, it is converted to a comma-separated
string. The KEYWORDS are added to the beginning of the
field. Otherwise KEYWORDS should be a string of comma-separate
keywords. Optional argument ARG prefix arg to replace keywords."
(interactive
(list
(completing-read "Keyword: " (org-ref-bibtex-keywords))
current-prefix-arg))
(bibtex-set-field
"keywords"
(if arg
;; replace with arg
(if (listp keywords)
(mapconcat 'identity keywords ", ")
keywords)
;; else concatentate
(concat
(if (listp keywords)
(mapconcat 'identity keywords ", ")
keywords)
(when (not (string= "" (bibtex-autokey-get-field "keywords")))
(concat ", " (bibtex-autokey-get-field "keywords"))))))
(when (buffer-file-name)
(save-buffer)))
(defun org-ref-save-all-bibtex-buffers ()
"Save all bibtex-buffers."
(cl-loop for buffer in (buffer-list)
do
(with-current-buffer buffer
(when (and (buffer-file-name) (f-ext? (buffer-file-name) "bib"))
(save-buffer)))))
;;* org-ref bibtex cache
(defvar orhc-bibtex-cache-data
'((hashes . ())
(candidates . ()))
"Cache data as an alist.
'hashes is a list of cons cells (bibfile . hash)
'candidates is a list of cons cells (bibfile . candidates).
Stored persistently in `orhc-bibtex-cache-file'.")
(defvar orhc-bibtex-cache-file
"~/.orhc-bibtex-cache"
"File to store cached data in.")
(defvar org-ref-bibtex-files nil
"List of bibtex files to get entries from.
This is set internally.")
(defvar orhc-candidate-formats
'(("article" . "${pdf}${notes}|${=key=}| ${author}, ${title}, ${journal} (${year}). ${keywords}")
("book" . " |${=key=}| ${author}, ${title} (${year}) ${keywords}.")
("inbook" . " |${=key=}| ${author}, ${chapter} in ${title} (${year}) ${keywords}")
("techreport" . " |${=key=}| ${title}, ${institution} (${year}). ${keywords}")
("inproceedings" . " |${=key=}| ${author}, ${title} in ${booktitle} (${year}). ${keywords}")
("incollection" . " |${=key=}| ${author}, ${title} in ${booktitle} (${year}). ${keywords}")
("phdthesis" . " |${=key=}| ${author}, ${title}, ${school} (${year}). Phd thesis. ${keywords}")
("mastersthesis" . " |${=key=}| ${author}, ${title}, ${school} (${year}). MS thesis. ${keywords}")
("misc" . " |${=key=}| ${author}, ${title}")
("unpublished" . " |${=key=}| ${author}, ${title}"))
"Formats for candidates.
It is an alist of (=type= . s-format-string).")
;; when you load, we should check the hashes and files
(defun orhc-load-cache-file ()
"Load the cache file to set `orhc-bibtex-cache-data'."
(when (file-exists-p orhc-bibtex-cache-file)
(with-current-buffer (find-file-noselect orhc-bibtex-cache-file)
(goto-char (point-min))
(setq orhc-bibtex-cache-data (read (current-buffer))))
(when (find-buffer-visiting orhc-bibtex-cache-file)
(kill-buffer (find-buffer-visiting orhc-bibtex-cache-file)))))
(defun orhc-clear-cache ()
"Clear the cache and delete `orhc-bibtex-cache-file'."
(interactive)
(setq orhc-bibtex-cache-data '((hashes . nil)
(candidates . nil)))
(when (find-buffer-visiting orhc-bibtex-cache-file)
(kill-buffer (find-buffer-visiting orhc-bibtex-cache-file)))
(when (file-exists-p orhc-bibtex-cache-file)
(delete-file orhc-bibtex-cache-file))
(message "org-ref-helm-cite cache cleared."))
(defun orhc-bibtex-cache-up-to-date ()
"Return if bibtex caches are up to date.
This means the hash of each bibfile is equal to the one for it in
the cache."
(-all? 'identity
(cl-loop
for bibfile in org-ref-bibtex-files
collect
(string= (progn
(with-current-buffer (find-file-noselect bibfile)
(secure-hash 'sha256 (current-buffer))))
(or (cdr (assoc
bibfile
(cdr (assoc 'hashes orhc-bibtex-cache-data)))) "")))))
(defun orhc-bibtex-field-formatter (field entry)
"Format FIELD in a bibtex parsed ENTRY.
A few fields are treated specially, e.g. authors are replaced by
comma-separated list, and I put :: around keywords to make it
easier to search specifically for them."
(let ((s (replace-regexp-in-string
"^{\\|}$" ""
(replace-regexp-in-string
"[\n\\|\t\\|\s]+" " "
(or (cdr (assoc field entry))
(and (string= field "author")
(cdr (assoc "editor" entry)))
"")))))
(cond
((string= field "author")
(if org-ref-helm-cite-shorten-authors
;; copied from `helm-bibtex-shorten-authors'
(cl-loop for a in (s-split " and " s)
for p = (s-split "," a t)
for sep = "" then ", "
concat sep
if (eq 1 (length p))