summaryrefslogtreecommitdiff
path: root/bog.el
blob: 48ee41b749a0075bfb11b109d19c91e30133293f (plain)
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
;;; bog.el --- Extensions for research notes in Org mode

;; Copyright (C) 2013 Kyle Meyer <kyle@kyleam.com>

;; Author: Kyle Meyer <kyle@kyleam.com>
;; URL: https://github.com/kyleam/bog
;; Keywords: BibTeX, org-mode
;; Version: 0.5.0
;; Package-Requires: ((org "8.0.0") (dash "2.5.0"))

;; 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 3, 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 GNU Emacs.  If not, see <http://www.gnu.org/licenses/>.

;;; Commentary:
;;
;; Bog provides a few convenience functions for taking research notes in
;; Org mode. Many of these commands center around a citekey, the unique
;; identifier for a study. Some of the main commands are listed below.
;;
;; - `bog-find-citekey-pdf'
;; - `bog-find-citekey-bib'
;; - `bog-search-citekey-on-web'
;; - `bog-rename-staged-pdf-to-citekey'
;; - `bog-goto-citekey-heading-in-buffer'
;; - `bog-goto-citekey-heading-in-notes'
;; - `bog-search-notes-for-citekey'
;; - `bog-clean-and-rename-staged-bibs'
;; - `bog-refile'
;; - `bog-search-notes'
;; - `bog-sort-topic-headings-in-buffer'
;; - `bog-sort-topic-headings-in-notes'
;;
;; See README (or bog-readme.org) for more information.

;;; Code:

(require 'dash)
(require 'org)


;;; Customization

(defgroup bog nil
  "Extensions for research notes in Org mode"
  :group 'org)

(defcustom bog-citekey-format
  "\\([0-9]*[a-z]+[-a-z]*\\)\\([0-9]\\{4\\}\\)\\([a-z][a-z0-9]*\\)"
  "Regex used to match study citekey.

By default, this matches any sequence of lower case
letters (allowing hyphenation) that is followed by 4 digits and
then lower case letters.

The default format corresponds to the following BibTeX autokey
settings:

  (setq bibtex-autokey-year-length 4
        bibtex-autokey-titleword-length nil
        bibtex-autokey-titlewords-stretch 0
        bibtex-autokey-titlewords 1
        bibtex-autokey-year-title-separator \"\")"
  :group 'bog
  :type 'string)

(defcustom bog-citekey-func 'bog-citekey-from-heading-title
  "Function used to get citekey from study notes.

By default, this is `bog-citekey-from-heading-title', which
selects the citekey from the first parent heading whose title
matches `bog-citekey-format'.

The other option is `bog-citekey-from-property', which selects
the citekey from the first parent that has the property
`bog-citekey-property'."
  :group 'bog
  :type 'function)

(defcustom bog-citekey-property "CUSTOM_ID"
  "Property name used to store citekey.
This is only used if `bog-citekey-func' is set to
`bog-citekey-from-property'. The default corresponds to the
default value of `org-bibtex-key-property'."
  :group 'bog
  :type 'string)

(defcustom bog-notes-directory "~/bib"
  "The name of the directory that Org files are stored in."
  :group 'bog
  :type 'string)

(defcustom bog-pdf-directory
  (expand-file-name "pdfs" bog-notes-directory)
  "The name of the directory that PDF files are stored in."
  :group 'bog
  :type 'string)

(defcustom bog-stage-directory
  (expand-file-name "stage" bog-notes-directory)
  "The name of the directory to search for new files.
`bog-rename-staged-pdf-to-citekey' and
`bog-rename-staged-bib-to-citekey' will search here for files to
rename."
  :group 'bog
  :type 'string)

(defcustom bog-find-citekey-bib-func 'bog-find-citekey-bib-file
  "Function used to find BibTeX entry for citekey.

Default is `bog-find-citekey-bib-file' that locates single entry
BibTeX files in `bog-bib-directory'.

The other option is `bog-find-citekey-entry' that searches within
a single BibTeX file, `bog-bib-file', for the citekey entry."
  :group 'bog
  :type 'function)

(defcustom bog-bib-directory
  (expand-file-name "bibs" bog-notes-directory)
  "The name of the directory that BibTeX files are stored in.
This is only meaningful if `bog-find-citekey-bib-func' set to
`bog-find-citekey-bib-file'."
  :group 'bog
  :type 'string)

(defcustom bog-bib-file nil
  "BibTeX file name.
This is only meaningful if `bog-find-citekey-bib-func' set to
`bog-find-citekey-entry'."
  :group 'bog
  :type 'string)

(defcustom bog-read-file-name 'read-file-name
  "A function that will be used to promtp for file name.
The function should accept one arguments, a string to use for the
prompt. A good alternative is `ido-read-file-name'."
  :group 'bog
  :type 'function)

(defcustom bog-completing-read 'completing-read
  "A function that will be used for completion prompts.
The function should accept two arguments, a string to use for the
prompt and a list of strings to offer as choices. A good
alternative is `ido-completing-read'."
  :group 'bog
  :type 'function)

(defcustom bog-pdf-opener "xdg-open"
  "Program to open PDF files with."
  :group 'bog
  :type 'string)

(defcustom bog-pdf-file-name-separators '("-" "_")
  "Characters allowed to follow the citekey in PDF file names.
When `bog-find-citekey-pdf' is run on <citekey>, it will find
files with the format <citekey><sep>*.pdf, where <sep> is one of
the characters in `bog-pdf-file-name-separators'.")

(defcustom bog-pdf-renaming-func 'bog-pdf-ask-on-conflict
  "Function used to rename stage PDF files.
This function should accept a PDF file name and a citekey as
arguments and return the name of the final PDF file. Currently
the only built-in function is `bog-pdf-ask-on-conflict'.")

(defcustom bog-pdf-secondary-name "-supplement"
  "Modification to make to PDF file name on renaming confict.
When a staged PDF is being renamed with
`bog-pdf-ask-on-conflict', the user will be prompted if
<citekey>.pdf already exists.
<citekey>`bog-pdf-secondary-name'.pdf will be the default value
for the prompt.")

(defcustom bog-web-search-url
  "http://scholar.google.com/scholar?q=%s"
  "URL to use for CITEKEY search.
It should contain the placeholder \"%s\" for the query."
  :group 'bog
  :type 'string)

(defcustom  bog-topic-heading-level 1
  "Consider headings at this level to be topic headings.
Topic headings for studies may be at any level, but
`bog-sort-topic-headings' uses this variable to determine what
level to operate on."
  :group 'bog
  :type 'integer)

(defcustom  bog-refile-maxlevel bog-topic-heading-level
  "Consider up to this level when refiling with `bog-refile'."
  :group 'bog
  :type 'integer)

(defcustom bog-keymap-prefix (kbd "C-c \"")
  "Bog keymap prefix."
  :group 'bog
  :type 'string)

(defcustom bog-agenda-custom-command-key "b"
  "Key to use for Bog notes search key in agenda dispatch.
If nil, a custom command will not be added to Org agenda
dispatch, but searching Bog notes through the agenda interface
will still be available through `bog-search-notes' and
`bog-search-notes-for-citekey'."
  :group 'bog
  :type '(choice
          (const :tag "Don't display in agenda dispatch" nil)
          (string :tag "Key for agenda dispatch")))


;;; General utilities

(defun bog-select-citekey (citekeys)
  "Prompt for citekey from CITEKEYS"
  (funcall bog-completing-read "Select citekey: " citekeys))

(defun bog-citekey-groups-with-delim (citekey &optional delim groups)
  "Return groups of `bog-citekey-format', seperated by DELIM.

If DELIM is nil, space is used.

If GROUPS is nil, groups 1, 2, and 3 are selected (which
corresponds to the last name of the first author, the publication
year, and the first meaningful word in the title)."
  (let ((groups (or groups '(1 2 3)))
        (delim (or delim " ")))
    (string-match bog-citekey-format citekey)
    (mapconcat #'(lambda (g) (match-string-no-properties g citekey))
               groups delim)))

(defun bog-citekey-at-point ()
  (let ((maybe-citekey (thing-at-point 'word)))
    (when (and maybe-citekey
               (bog-citekey-only-p maybe-citekey))
      (substring-no-properties maybe-citekey))))

(defun bog-citekey-from-notes ()
  "Get the citekey from the context of the Org file."
  (or (bog-citekey-at-point)
      (funcall bog-citekey-func)))

(defun bog-citekey-from-heading-title ()
  "Retrieve citekey from first parent heading that matches
`bog-citekey-format'."
  (save-excursion
    (save-restriction
      (widen)
      (let ((heading (org-no-properties (org-get-heading t t))))
        (while (and (not (bog-citekey-only-p heading))
                    (org-up-heading-safe))
          (setq heading (org-no-properties (org-get-heading t t))))
        (when (not (bog-citekey-only-p heading))
          (error "Citekey not found"))
        heading))))

(defun bog-citekey-from-property ()
  "Retrieve citekey from first parent heading that has the
 property `bog-citekey-property'."
  (save-excursion
    (save-restriction
      (widen)
      (let ((citekey (org-entry-get (point) bog-citekey-property)))
        (while (and (not citekey)
                    (org-up-heading-safe))
          (setq citekey (org-entry-get (point) bog-citekey-property)))
        (when (not citekey)
          (error "Citekey not found"))
        citekey))))

(defun bog-citekey-heading-p ()
  (let ((heading (org-no-properties (org-get-heading t t))))
    (or (bog-citekey-only-p heading)
        (org-entry-get (point) bog-citekey-property))))

(defun bog-citekey-p (text)
  "Indicate if TEXT matches `bog-citekey-format'."
  (when (string-match bog-citekey-format text)
    t))

(defun bog-citekey-only-p (text)
  "Indicate if all of TEXT matches `bog-citekey-format'."
  (string-match bog-citekey-format text)
  (when (equal (length text) (match-end 0))
    t))


;;; PDF-related

;;;###autoload
(defun bog-find-citekey-pdf (arg)
  "Open PDF file for a citekey.
If a prefix argument is given, a prompt will open to select from
available citekeys. Otherwise, the citekey will be taken from the
text under point if it matches `bog-citekey-format' or using
`bog-citekey-func'."
  (interactive "P")
  (let ((citekey (or (and arg (bog-select-citekey (bog-pdf-citekeys)))
                     (bog-citekey-from-notes))))
    (bog-open-citekey-pdf citekey)))

(defun bog-open-citekey-pdf (citekey)
  (let* (citekey-pdf
         (citekey-pdfs (bog-citekey-pdfs citekey))
         (citekey-pdfs-names (-map 'file-name-nondirectory citekey-pdfs))
         (num-choices (length citekey-pdfs-names)))
    (cond
     ((= 0 num-choices)
      (error "No PDF found for %s" citekey))
     ((= 1 num-choices)
      (setq citekey-pdf (car citekey-pdfs)))
     (t
      (setq citekey-pdf
            (expand-file-name (funcall bog-completing-read
                                       "Select PDF file: "
                                       citekey-pdfs-names)
                              bog-pdf-directory))))
    (start-process "bog-pdf" nil bog-pdf-opener citekey-pdf)))

(defun bog-citekey-pdfs (citekey)
  (let* ((patterns (--map (concat it "*") bog-pdf-file-name-separators))
         (patterns (cons "" patterns)))
    (--mapcat (file-expand-wildcards
               (concat (file-name-as-directory bog-pdf-directory)
                       citekey it ".pdf"))
              patterns)))

;;;###autoload
(defun bog-rename-staged-pdf-to-citekey ()
  "Rename PDF in `bog-stage-directory' to `bog-pdf-directory'/<citekey>.pdf.
The citekey will be taken from the text under point if it matches
`bog-citekey-format' or using `bog-citekey-func'."
  (interactive)
  (let ((citekey (bog-citekey-from-notes)))
    (bog-rename-staged-pdf citekey)))

(defun bog-rename-staged-pdf (citekey)
  (let* ((staged-pdfs
          (file-expand-wildcards
           (concat (file-name-as-directory bog-stage-directory) "*.pdf")))
         (staged-pdfs-names (-map 'file-name-nondirectory staged-pdfs))
         (num-choices (length staged-pdfs-names))
         staged-pdf)
    (cond
     ((= 0 num-choices)
      (setq staged-pdf (funcall bog-read-file-name
                                "Select PDF file to rename: ")))
     ((= 1 num-choices)
      (setq staged-pdf (car staged-pdfs)))
     (t
      (setq staged-pdf
            (expand-file-name (funcall bog-completing-read
                                       "Select PDF file to rename: "
                                       staged-pdfs-names)
                              bog-stage-directory))))
    (message "Renamed %s to %s" staged-pdf
             (funcall bog-pdf-renaming-func staged-pdf citekey))))

(defun bog-pdf-ask-on-conflict (staged-pdf citekey)
  "Prompt for a new name of PDF file for CITEKEY already exists.
STAGED-PDF will be renamed to <citekey>.pdf within
`bog-pdf-directory'. If this file already exists, the user will
be prompted for another name. `bog-pdf-secondary-name' can be
used to control the default string used in the prompt."
  (let ((pdf-file (bog-citekey-as-pdf citekey)))
    (condition-case nil
        (rename-file staged-pdf pdf-file)
      (file-error
       (let ((new-file-name
              (replace-regexp-in-string ".pdf"
                                        (concat bog-pdf-secondary-name ".pdf")
                                        (file-name-nondirectory pdf-file))))
         (setq new-file-name
               (read-string
                (format "File %s already exists. Name to use instead: "
                        pdf-file)
                new-file-name nil nil '(new-file-name)))
         (setq pdf-file (expand-file-name new-file-name bog-pdf-directory))
         (rename-file staged-pdf pdf-file))))
    pdf-file))

(defun bog-citekey-as-pdf (citekey)
  (expand-file-name (concat citekey ".pdf") bog-pdf-directory))

(defun bog-pdf-citekeys ()
  "Return a list citekeys for all pdf files in
`bog-pdf-directory'."
  (-map 'file-name-base
        (file-expand-wildcards (concat
                                (file-name-as-directory bog-pdf-directory)
                                "*.pdf"))))


;;; BibTeX-related

;;;###autoload
(defun bog-find-citekey-bib (arg)
  "Open BibTeX file for a citekey.
If a prefix argument is given, a prompt will open to select from
available citekeys. Otherwise, the citekey will be taken from the
text under point if it matches `bog-citekey-format' or using
`bog-citekey-func'."
  (interactive "P")
  (let ((citekey (or (and arg (bog-select-citekey (bog-pdf-citekeys)))
                     (bog-citekey-from-notes))))
    (funcall bog-find-citekey-bib-func citekey)))

(defun bog-find-citekey-bib-file (citekey)
  "Open BibTeX file of CITEKEY contained in `bog-bib-directory'."
  (let ((bib-file (bog-citekey-as-bib citekey)))
    (unless (file-exists-p bib-file)
      (error "%s does not exist" bib-file))
    (find-file-other-window bib-file)))

(defun bog-find-citekey-entry (citekey)
  "Search for CITEKEY in `bog-bib-file'."
  (find-file-other-window bog-bib-file)
  (bibtex-search-entry citekey))

;;;###autoload
(defun bog-clean-and-rename-staged-bibs ()
  "Clean and rename BibTeX files in `bog-stage-directory'.

New BibTeX files are searched for in `bog-stage-directory', and
`bog-prepare-bib-file' will be run one each file before it is
moved to `bog-bib-directory'/<citekey>.bib.

This function is only useful if you use the non-standard setup of
one entry per BibTeX file."
  (interactive)
  (let ((staged
         (file-expand-wildcards
          (concat (file-name-as-directory bog-stage-directory) "*.bib"))))
    (--each staged
      (bog-prepare-bib-file it t bog-bib-directory))))

(defun bog-prepare-bib-file (file &optional new-key new-directory)
  (save-excursion
    (let ((was-open (get-file-buffer file))
          (buffer (find-file-noselect file)))
      (with-current-buffer buffer
        (goto-char (point-min))
        (bibtex-skip-to-valid-entry)
        (bibtex-clean-entry new-key)
        (let* ((citekey (bibtex-key-in-head))
               (bib-file
                (expand-file-name (concat citekey ".bib") new-directory)))
          (when (get-buffer bib-file)
            (error "Buffer for %s already exists" bib-file))
          (rename-file file bib-file)
          (rename-buffer bib-file)
          (set-visited-file-name bib-file)
          (save-buffer)))
      (unless was-open
        (kill-buffer buffer)))))

;;;###autoload
(defun bog-create-combined-bib ()
  "Create buffer that has entries for all citekeys in buffer."
  (interactive)
  (let ((bib-buffer (get-buffer-create "*Bib*"))
        (refs (-map 'bog-citekey-as-bib (bog-collect-references))))
    (--each refs (unless (file-exists-p it) (error "%s does not exist" it)))
    (switch-to-buffer-other-window bib-buffer)
    (--each refs
      (insert "\n")
      (insert-file-contents it)
      (goto-char (point-max)))
    (bibtex-mode)
    (goto-char (point-min))))

(defun bog-collect-references (&optional no-sort)
  "Return names in buffer that match `bog-citekey-format'.
If NO-SORT, citekeys are returned in reverse order that they
occur in buffer instead of alphabetical order."
  (let (refs)
    (save-excursion
      (goto-char (point-min))
      (while (re-search-forward bog-citekey-format nil t)
        (add-to-list 'refs (match-string-no-properties 0)))
      (if no-sort
          refs
        (--sort (string-lessp it other) refs)))))

(defun bog-citekey-as-bib (citekey)
  (expand-file-name (concat citekey ".bib") bog-bib-directory))

(defun bog-bib-citekeys ()
  "Return a list citekeys for all BibTeX files in `bog-bib-directory'."
  (-map 'file-name-base
        (file-expand-wildcards (concat
                                (file-name-as-directory bog-bib-directory)
                                "*.bib"))))


;;; Web

;;;###autoload
(defun bog-search-citekey-on-web ()
  "Open browser and perform query based for a citekey.

The URL will be taken from `bog-web-search-url'.

The citekey is split by groups in `bog-citekey-format' and joined by
\"+\" to form the query string."
  (interactive)
  (let ((citekey (bog-citekey-from-notes)))
    (bog-open-citekey-on-web citekey)))

(defun bog-open-citekey-on-web (citekey)
  (let ((url (bog-citekey-as-search-url citekey)))
    (browse-url url)))

(defun bog-citekey-as-search-url (citekey)
  "Return URL to use for search."
  (let ((query (bog-citekey-groups-with-delim citekey "+")))
    (format bog-web-search-url query)))


;;; Notes-related

(defun bog-goto-citekey-heading-in-buffer ()
  "Find citekey heading in this buffer.
The citekey will be taken from the text under point if it matches
`bog-citekey-format'."
  (interactive)
  (let* ((citekey (or (bog-citekey-at-point)
                      (read-string "Enter citekey: ")))
         (pos (org-find-exact-headline-in-buffer citekey nil t)))
    (if pos
        (progn
          (org-mark-ring-push)
          (goto-char pos)
          (org-show-context))
      (message "Heading for %s not found in buffer" citekey))))

(defun bog-goto-citekey-heading-in-notes ()
  "Find citekey heading in notes.
All org files in `bog-notes-directory' will be searched. The
citekey will be taken from the text under point if it matches
`bog-citekey-format'."
  (interactive)
  (let* ((citekey (or (bog-citekey-at-point)
                      (read-string "Enter citekey: ")))
        (marker
         (org-find-exact-heading-in-directory citekey bog-notes-directory)))
    (if marker
        (progn
          (switch-to-buffer (marker-buffer marker))
          (goto-char (marker-position marker))
          (org-show-context))
      (message "Heading for %s not found in notes" citekey))))

(defun bog-refile ()
  "Refile heading within notes.
All headings from Org files in `bog-notes-directory' at or above
level `bog-refile-maxlevel' are considered."
  (interactive)
  (let ((org-refile-targets `((,(bog-notes-files)
                               :maxlevel . ,bog-refile-maxlevel))))
    (org-refile)))

(defun bog-notes-files ()
  (file-expand-wildcards
   (concat (file-name-as-directory bog-notes-directory)
           "*.org")))

(defun bog-search-notes (&optional todo-only)
  "Search notes using `org-search-view'.
With prefix argument TODO-ONLY, only TODO entries are searched."
  (interactive "P")
  (let ((lprops (nth 4 bog-agenda-custom-command)))
    (put 'org-agenda-redo-command 'org-lprops lprops)
    (org-let lprops '(org-search-view todo-only))))

(defun bog-search-notes-for-citekey (&optional todo-only)
  "Search notes for citekey using `org-search-view'.
With prefix argument TODO-ONLY, only TODO entries are searched."
  (interactive "P")
  (let ((citekey (bog-citekey-from-notes))
        (lprops (nth 4 bog-agenda-custom-command)))
    (put 'org-agenda-redo-command 'org-lprops lprops)
    (org-let lprops '(org-search-view todo-only citekey))))

(defun bog-sort-topic-headings-in-buffer (&optional sorting-type)
  "Sort topic headings in this buffer.
SORTING-TYPE is a character passed to `org-sort-entries'. If nil,
?a is used. The level to sort is determined by
`bog-topic-heading-level'."
  (interactive)
  (org-map-entries '(lambda () (bog-sort-if-topic-header sorting-type))))

(defun bog-sort-topic-headings-in-notes (&optional sorting-type)
  "Sort topic headings in notes.
Unlike `bog-sort-topic-headings-in-buffer', sort topic headings
in all Bog notes."
  (interactive)
  (org-map-entries '(lambda ()  (bog-sort-if-topic-header sorting-type))
                   nil (bog-notes-files)))

(defun bog-sort-if-topic-header (sorting-type)
  "Sort heading with `org-sort-entries' according to SORTING-TYPE.
Sorting is only done if the heading's level matches
`bog-topic-heading-level' and it isn't a citekey heading."
  (let ((sorting-type (or sorting-type ?a)))
    (when (and (= (org-current-level) bog-topic-heading-level)
               (not (bog-citekey-heading-p)))
      (org-sort-entries nil sorting-type))))


;;; Font-lock

(defface bog-citekey-face
  '((((class color) (background dark))
     (:bold t))
    (((class color) (background light))
     (:bold t)))
  "Face used to highlight text that matches `bog-citekey-format'.")

(defun bog-non-heading-citekey-p (limit)
  (and (re-search-forward bog-citekey-format limit t)
       (not (org-at-heading-p))))

(defun bog-add-fontlock ()
  (font-lock-add-keywords nil
                          '((bog-non-heading-citekey-p . 'bog-citekey-face)))
  (font-lock-fontify-buffer))

(defun bog-remove-fontlock ()
  (font-lock-remove-keywords nil
                             '((bog-non-heading-citekey-p . 'bog-citekey-face)))
  (font-lock-fontify-buffer))


;;; Minor mode

(defvar bog-mode-map
  (let ((map (make-sparse-keymap)))
    (let ((prefix-map (make-sparse-keymap)))
      (define-key prefix-map "p" 'bog-find-citekey-pdf)
      (define-key prefix-map "r" 'bog-rename-staged-pdf-to-citekey)
      (define-key prefix-map "b" 'bog-find-citekey-bib)
      (define-key prefix-map "s" 'bog-search-notes)
      (define-key prefix-map "c" 'bog-search-notes-for-citekey)
      (define-key prefix-map "h" 'bog-goto-citekey-heading-in-buffer)
      (define-key prefix-map "H" 'bog-goto-citekey-heading-in-notes)
      (define-key prefix-map "w" 'bog-search-citekey-on-web)
      (define-key map bog-keymap-prefix prefix-map))
    map)
  "Keymap for Bog.")

(defvar bog-agenda-custom-command
  `(,(or bog-agenda-custom-command-key "b") "Search Bog notes" search ""
    ((org-agenda-files (bog-notes-files))
     (org-agenda-text-search-extra-files nil))))

;;;###autoload
(define-minor-mode bog-mode
  "Toggle Bog in this buffer.
With a prefix argument ARG, enable `bog-mode' if ARG is positive,
and disable it otherwise. If called from Lisp, enable the mode if
ARG is omitted or nil.

\\{bog-mode-map}"
  :keymap bog-mode-map
  :group 'bog
  :lighter " Bog"
  :require 'bog
  (cond
   (bog-mode
    (bog-add-fontlock)
    (when bog-agenda-custom-command-key
      (add-to-list 'org-agenda-custom-commands
                   bog-agenda-custom-command)))
   (t
    (bog-remove-fontlock)
    (when bog-agenda-custom-command
      (setq org-agenda-custom-commands (delete bog-agenda-custom-command
                                               org-agenda-custom-commands))))))

(provide 'bog)

;; bog.el ends here