summaryrefslogtreecommitdiff
path: root/bog.el
blob: 130a1c1fdced080a25b71c13609915874f3a34a0 (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
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
;;; bog.el --- Extensions for research notes in Org mode

;; Copyright (C) 2013-2014 Kyle Meyer <kyle@kyleam.com>

;; Author: Kyle Meyer <kyle@kyleam.com>
;; URL: https://github.com/kyleam/bog
;; Keywords: bib, outlines
;; Version: 0.6.0
;; Package-Requires: ((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.  See the README
;; (https://github.com/kyleam/bog) 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-allowed-before-citekey
  "\\(\n\\|\\s-\\|(\\|\\[\\|{\\|<\\|,\\)"
  "Regex that specifies characters allowed before a citekey.
This may need to be modified if you have a custom
`bog-citekey-format' or if you tend to used a certain character
before citekeys that isn't included above."
  :group 'bog
  :type 'string)

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

(defcustom bog-root-directory "~/bib"
  "Root directory for default values of other Bog directories."
  :group 'bog
  :type 'string)

(defcustom bog-notes-directory
  (expand-file-name "notes" bog-root-directory)
  "Directory with Org research notes."
  :group 'bog
  :type 'string)

(defcustom bog-file-directory
  (expand-file-name "citekey-files" bog-root-directory)
  "Directory with citekey-associated files."
  :group 'bog
  :type 'string)

(defcustom bog-stage-directory
  (expand-file-name "stage" bog-root-directory)
  "Directory to search for new files.
`bog-rename-staged-file-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', which locates single
entry BibTeX files in `bog-bib-directory'.

The other option is `bog-find-citekey-entry', which 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-root-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-citekey-file-name-separators '("-" "_")
  "Characters allowed to follow the citekey in file names.
When `bog-find-citekey-file' is run on <citekey>, it will find
files with the format <citekey>.* and <citekey><sep>*.<ext>,
where <sep> is one of these characters.")

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

(defcustom bog-file-secondary-name "-supplement"
  "Modification to make to file name on renaming confict.
When a staged file is being renamed with
`bog-file-ask-on-conflict', the user will be prompted if
<citekey>.<ext> already exists.
<citekey>`bog-file-secondary-name'.<ext> 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-use-citekey-cache nil
  "Cache list of all citekeys.
Depending on the number of citekeys present in notes, enabling
this can make functions that prompt with a list of all
citekeys (or all heading citekeys) noticeably faster.  However,
no attempt is made to update the list of citekeys.  To see newly
added citekeys, clear the cache with `bog-clear-citekey-cache'."
  :group 'bog
  :type 'boolean)


;;; Citekey methods

(defmacro bog-selection-method (name context-method collection-method)
  "Create citekey selection function.
Function will be named bog-citekey-from-NAME and will take one
argument (NO-CONTEXT).  If NO-CONTEXT is nil, CONTEXT-METHOD will
be called with no arguments.  If CONTEXT-METHOD returns nil or if
NO-CONTEXT is non-nil, the user will be prompted with citekeys
gathered by COLLECTION-METHOD."
  `(defun ,(intern (concat "bog-citekey-from-" name)) (no-context)
     ,(format "Select citekey with `%s', falling back on `%s'.
If NO-CONTEXT is non-nil, immediately fall back."
              (symbol-name context-method)
              (symbol-name collection-method))
      (or (and no-context (bog-select-citekey (,collection-method)))
          (,context-method)
          (bog-select-citekey (,collection-method)))))

(bog-selection-method "notes-or-files"
                      bog-citekey-from-notes
                      bog-all-file-citekeys)

(bog-selection-method "notes-or-bibs"
                      bog-citekey-from-notes
                      bog-bib-citekeys)

(bog-selection-method "notes-or-all"
                      bog-citekey-from-notes
                      bog-all-citekeys)

(bog-selection-method "point-or-buffer-headings"
                      bog-citekey-at-point
                      bog-heading-citekeys-in-wide-buffer)

(bog-selection-method "point-or-all-headings"
                      bog-citekey-at-point
                      bog-all-heading-citekeys)

(defun bog-select-citekey (citekeys)
  "Prompt for citekey from CITEKEYS."
  (org-icompleting-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 ()
  "Return citekey at point.
The citekey must have the format specified by
`bog-citekey-format' and, if not at the beginning of the buffer,
be preceded by a characters in `bog-allowed-before-citekey'."
  (save-excursion
    (unless (bobp)
      (re-search-backward bog-allowed-before-citekey)
      (forward-char 1))
    (when (looking-at bog-citekey-format)
      (match-string-no-properties 0))))

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

(defun bog-citekey-from-tree ()
  "Retrieve citekey from first parent heading associated with citekey."
  (org-with-wide-buffer
   (let (maybe-citekey)
     (while (and (not (setq maybe-citekey (bog-citekey-from-heading)))
                 ;; This isn't actually safe in Org mode <= 8.2.10.
                 ;; Fixed in Org mode commit
                 ;; 9ba9f916e87297d863c197cb87199adbb39da894.
                 (ignore-errors (org-up-heading-safe))))
     maybe-citekey)))

(defun bog-citekey-from-heading ()
  "Retrieve citekey from current heading title or property."
  (or (bog-citekey-from-heading-title)
      (bog-citekey-from-property)))

(defun bog-citekey-from-heading-title ()
  "Retrieve citekey from heading title."
  (unless (org-before-first-heading-p)
    (let ((heading (org-no-properties (org-get-heading t t))))
      (when (bog-citekey-p heading) heading))))

(defun bog-citekey-from-property ()
  "Retrieve citekey from `bog-citekey-property'."
  (--when-let (org-entry-get (point) bog-citekey-property)
    (when (bog-citekey-p it) it)))

(defun bog-citekey-p (text)
  "Does TEXT match `bog-citekey-format'?"
  (when (string-match-p (format "^%s$" bog-citekey-format) text)
    t))

(defvar bog--all-citekeys nil)
(defun bog-all-citekeys ()
  "Return all citekeys in `bog-notes-files'."
  (or (and bog-use-citekey-cache bog--all-citekeys)
      (setq bog--all-citekeys (apply 'append
                                    (-map 'bog-citekeys-in-file
                                          (bog-notes-files))))))

(defvar bog--all-heading-citekeys nil)
(defun bog-all-heading-citekeys ()
  "Return all citekeys in headings of `bog-notes-files'."
  (or (and bog-use-citekey-cache bog--all-heading-citekeys)
      (setq bog--all-heading-citekeys (-mapcat 'bog-heading-citekeys-in-file
                                               (bog-notes-files)))))

(defun bog-clear-citekey-cache ()
  "Clear cache of citekeys contained in `bog-notes-files'."
  (interactive)
  (setq bog--all-citekeys nil
        bog--all-heading-citekeys nil))

(defun bog-citekeys-in-file (file)
  "Return all citekeys in FILE."
  (let (refs)
    (with-temp-buffer
      (org-mode)
      (insert-file-contents file)
      (while (re-search-forward bog-citekey-format nil t)
        (push (match-string-no-properties 0) refs)))
    (-distinct refs)))

(defun bog-heading-citekeys-in-file (file)
  "Return all citekeys in headings of FILE."
  (with-temp-buffer
    (org-mode)
    (insert-file-contents file)
    (setq citekeys (bog-heading-citekeys-in-buffer))))

(defun bog-heading-citekeys-in-buffer ()
  "Return all citekeys in current buffer."
  (--keep it
          (org-map-entries 'bog-citekey-from-heading)))

(defun bog-heading-citekeys-in-wide-buffer ()
  "Return all citekeys in current buffer, without any narrowing."
  (--keep it
          (org-map-entries 'bog-citekey-from-heading nil 'file)))


;;; Citekey-associated files

;;;###autoload
(defun bog-find-citekey-file (&optional no-context)
  "Open citekey-associated file.

The citekey will be taken from the text under point if it matches
`bog-citekey-format' or from the current tree.

With prefix argument NO-CONTEXT, a prompt will open to select
from citekeys for all associated files.  This same prompt will be
opened if locating a citekey from context fails."
  (interactive "P")
  (bog--find-citekey-file (bog-citekey-from-notes-or-files no-context)))

(defun bog--find-citekey-file (citekey)
  (let* (citekey-file
         (citekey-files (bog-citekey-files citekey))
         (citekey-file-names (-map 'file-name-nondirectory citekey-files))
         (num-choices (length citekey-file-names)))
    (case num-choices
      (0 (user-error "No file found for %s" citekey))
      (1 (setq citekey-file (car citekey-files)))
      (t (setq citekey-file (expand-file-name
                             (org-icompleting-read "Select file: "
                                                   citekey-file-names)
                             bog-file-directory))))
    (org-open-file citekey-file)))

(defun bog-citekey-files (citekey)
  "Return files in `bog-file-directory' associated with CITEKEY.
These should be named CITEKEY<sep>*.<ext>, where <sep> is a
character in `bog-citekey-file-name-separators'."
  (let* ((patterns (--map (concat it "*") bog-citekey-file-name-separators))
         (patterns (cons ".*" patterns)))
    (--mapcat (file-expand-wildcards
               (concat (file-name-as-directory bog-file-directory)
                       citekey it))
              patterns)))

;;;###autoload
(defun bog-rename-staged-file-to-citekey (&optional no-context)
  "Rename citekey file in `bog-stage-directory' with `bog-file-renaming-func'.

The citekey will be taken from the text under point if it matches
`bog-citekey-format' or from the current tree.

With prefix argument NO-CONTEXT, a prompt will open to select
from all citekeys present in notes.  This same prompt will be
opened if locating a citekey from context fails.

If the citekey file prompt is slow to appear, consider enabling
`bog-use-citekey-cache'."
  (interactive "P")
  (bog--rename-staged-file-to-citekey (bog-citekey-from-notes-or-all no-context)))

(defun bog--rename-staged-file-to-citekey (citekey)
  (let* ((staged-files (bog-staged-files))
         (staged-file-names (-map 'file-name-nondirectory staged-files))
         (num-choices (length staged-file-names))
         staged-file)
    (case num-choices
      (0 (setq staged-file (org-iread-file-name "Select file to rename: ")))
      (1 (setq staged-file (car staged-files)))
      (t (setq staged-file (expand-file-name
                            (org-icompleting-read "Select file to rename: "
                                                  staged-file-names)
                            bog-stage-directory))))
    (message "Renamed %s to %s" staged-file
             (funcall bog-file-renaming-func staged-file citekey))))

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

(defun bog-citekey-as-file (citekey ext)
  "Return file name `bog-file-directory'/CITEKEY.<ext>."
  (expand-file-name (concat citekey "." ext) bog-file-directory))

(defun bog-all-file-citekeys ()
  "Return a list of citekeys for files in `bog-file-directory'."
  (-distinct (-keep 'bog-file-citekey (bog-all-citekey-files))))

(defun bog-file-citekey (file)
  "Return leading citekey part from base name of FILE."
  (let ((fname (file-name-base file)))
    (when (string-match (concat "^" bog-citekey-format) fname)
      (match-string 0 fname))))

(defun bog-all-citekey-files ()
  "Return list of all files in `bog-file-directory'."
  (-remove 'file-directory-p
           (directory-files bog-file-directory
                            t directory-files-no-dot-files-regexp)))

(defun bog-staged-files ()
  "Return files in `bog-stage-directory'."
  (-remove 'file-directory-p
           (directory-files bog-stage-directory
                            t directory-files-no-dot-files-regexp)))


;;; BibTeX-related

;;;###autoload
(defun bog-find-citekey-bib (&optional no-context)
  "Open BibTeX file for a citekey.

The citekey will be taken from the text under point if it matches
`bog-citekey-format' or from the current tree.

The variable `bog-find-citekey-bib-func' determines how the
citekey is found.

With prefix argument NO-CONTEXT, a prompt will open to select
from citekeys for all BibTeX files.  This same prompt will be
opened if locating a citekey from context fails."
  (interactive "P")
  (funcall bog-find-citekey-bib-func
           (bog-citekey-from-notes-or-bibs no-context)))

(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)
      (user-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
`bibtex-clean-entry' 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)
  (let (bib-file)
    (with-temp-buffer
      (bibtex-mode)
      (insert-file-contents file)
      (bibtex-skip-to-valid-entry)
      (bibtex-clean-entry new-key)
      (setq bib-file (expand-file-name (concat (bibtex-key-in-head) ".bib")
                                       new-directory))
      (write-file bib-file))
    ;; If a buffer was visiting the original bib file, point it to the
    ;; new file.
    (--when-let (find-buffer-visiting file)
      (with-current-buffer it
        (when (get-buffer bib-file)
          (user-error "Buffer for %s already exists" bib-file))
        (rename-buffer bib-file)
        (set-visited-file-name bib-file nil t)))
    (delete-file file)))

;;;###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-unique-references))))
    (--each refs (unless (file-exists-p it) (user-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-unique-references ()
  "Return names in buffer that match `bog-citekey-format'.
Duplicates are removed and the entries are sorted
alphabetically."
  (-distinct (--sort (string-lessp it other) (bog-collect-references))))

(defun bog-collect-references ()
  "Return names in buffer that match `bog-citekey-format'."
  (let (refs)
    (save-excursion
      (goto-char (point-min))
      (while (re-search-forward bog-citekey-format nil t)
        (push (match-string-no-properties 0) refs))
      refs)))

(defun bog-citekey-as-bib (citekey)
  "Return file name `bog-bib-directory'/CITEKEY.bib."
  (expand-file-name (concat citekey ".bib") bog-bib-directory))

(defun bog-bib-citekeys ()
  "Return a list citekeys for all BibTeX entries.
If `bog-bib-file' is non-nil, it returns citekeys from this file
instead of citekeys from file names in `bog-bib-directory'."
  (if bog-bib-file
      (with-temp-buffer
        (bibtex-mode)
        (insert-file-contents bog-bib-file)
        (-map 'car (bibtex-parse-keys)))
    (-map 'file-name-base
          (file-expand-wildcards (concat
                                  (file-name-as-directory bog-bib-directory)
                                  "*.bib")))))


;;; Web

;;;###autoload
(defun bog-search-citekey-on-web (&optional no-context)
  "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.

The citekey will be taken from the text under point if it matches
`bog-citekey-format' or from the current tree.

With prefix argument NO-CONTEXT, a prompt will open to select
from all citekeys present in notes.  This same prompt will be
opened if locating a citekey from context fails.

If the citekey file prompt is slow to appear, consider enabling
`bog-use-citekey-cache'."
  (interactive "P")
  (bog--search-citekey-on-web (bog-citekey-from-notes-or-all no-context)))

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

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


;;; Notes-related

(defun bog-goto-citekey-heading-in-buffer (&optional no-context)
  "Find citekey heading in this buffer.

The citekey will be taken from the text under point if it matches
`bog-citekey-format'.

With prefix argument NO-CONTEXT, a prompt will open to select
from all citekeys for headings in the current buffer.  This same
prompt will be opened if locating a citekey from context fails.

This only works for headings that store the citekey as the
heading title (not as a property).

If the heading is found outside any current narrowing of the
buffer, the narrowing is removed."
  (interactive "P")
  (let* ((citekey (bog-citekey-from-point-or-buffer-headings no-context))
         (pos (org-find-exact-headline-in-buffer citekey nil t)))
    (if pos
        (progn
         (when (or (< pos (point-min))
                   (> pos (point-max)))
           (widen))
         (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 (&optional no-context)
  "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'.

With prefix argument NO-CONTEXT, a prompt will open to select
from all citekeys for headings in notes.  This same prompt will
be opened if locating a citekey from context fails.

If the citekey file prompt is slow to appear, consider enabling
`bog-use-citekey-cache'.

This only works for headings that store the citekey as the
heading title (not as a property).

If the heading is found outside any current narrowing of the
buffer, the narrowing is removed."
  (interactive "P")
  (let* ((citekey (bog-citekey-from-point-or-all-headings no-context))
         (marker (bog--find-exact-heading-in-notes citekey)))
    (if marker
        (progn
          (switch-to-buffer (marker-buffer marker))
          (when (or (< marker (point-min))
                    (> marker (point-max)))
            (widen))
          (goto-char marker)
          (org-show-context))
      (message "Heading for %s not found in notes" citekey))))

(defun bog--find-exact-heading-in-notes (heading)
  "Return the marker of HEADING in Bog notes.
If the current buffer is a Bog notes file, try to find the
heading there first."
  (or (when (member (buffer-file-name) (bog-notes-files))
        (org-find-exact-headline-in-buffer heading))
      (org-find-exact-heading-in-directory heading bog-notes-directory)))

(defun bog-citekey-tree-to-indirect-buffer (&optional no-context)
  "Open subtree for citekey in an indirect buffer.

The citekey will be taken from the text under point if it matches
`bog-citekey-format'.

With prefix argument NO-CONTEXT, a prompt will open to select
from all citekeys for headings in notes.  This same prompt will
be opened if locating a citekey from context fails.

If the citekey file prompt is slow to appear, consider enabling
`bog-use-citekey-cache'."
  (interactive "P")
  (let* ((citekey (bog-citekey-from-point-or-all-headings no-context))
         (marker (bog--find-exact-heading-in-notes citekey)))
    (if marker
        (with-current-buffer (marker-buffer marker)
          (save-excursion
            (save-restriction
              (goto-char marker)
              (org-tree-to-indirect-buffer))))
      (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 ()
  "Return Org files in `bog-notes-directory'"
  (--remove (let ((base-name (file-name-nondirectory it)))
              (or (string-prefix-p "." base-name)
                  (auto-save-file-name-p base-name)))
   (file-expand-wildcards
    (concat (file-name-as-directory bog-notes-directory)
            "*.org"))))

(defun bog-search-notes (&optional todo-only string)
  "Search notes using `org-search-view'.
With prefix argument TODO-ONLY, only TODO entries are searched.
If STRING is non-nil, this will be used as the search
term (instead of prompting the user for one)."
  (interactive "P")
  (let ((lprops '((org-agenda-files (bog-notes-files))
                  (org-agenda-text-search-extra-files nil))))
    (put 'org-agenda-redo-command 'org-lprops lprops)
    (org-let lprops '(org-search-view todo-only string))))

(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.

The citekey will be taken from the text under point if it matches
`bog-citekey-format' or from the current tree.  If a citekey is
not found, a prompt will open to select from all citekeys present
in notes."
  (interactive "P")
  (bog-search-notes todo-only (bog-citekey-from-notes-or-all nil)))

(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-from-heading)))
      (org-sort-entries nil sorting-type))))

(defun bog-insert-heading-citekey (&optional current-buffer)
  "Select a citekey to insert at point.
By default, offer heading citekeys from all files.  With prefix
argument CURRENT-BUFFER, limit to heading citekeys from the
current buffer."
  (interactive "P")
  (let ((citekey-func (if current-buffer
                          'bog-heading-citekeys-in-wide-buffer
                        'bog-all-heading-citekeys)))
    (insert (bog-select-citekey (funcall citekey-func)))))

(defun bog-open-first-citekey-link (&optional no-context)
  "Open first link under citekey heading.

The citekey will be taken from the text under point if it matches
`bog-citekey-format' or from the current tree.

With prefix argument NO-CONTEXT, a prompt will open to select
from all citekeys for headings in notes.  This same prompt will
be opened if locating a citekey from context fails."
  (interactive "P")
  (let* ((citekey (bog-citekey-from-point-or-all-headings no-context))
         (marker (bog--find-exact-heading-in-notes citekey)))
    (if marker
        (with-current-buffer (marker-buffer marker)
          (org-with-wide-buffer
           (goto-char marker)
           (org-narrow-to-subtree)
           (org-next-link)
           (org-open-at-point)))
      (message "Heading for %s not found in notes" citekey))))


;;; Font-lock

(defface bog-citekey-face
  '((t (:inherit org-link :underline nil)))
  "Face used to highlight text that matches `bog-citekey-format'.")

(defun bog-fontify-non-heading-citekeys (limit)
  (while (re-search-forward bog-citekey-format limit t)
    (unless (save-match-data (org-at-heading-p))
      (add-text-properties (match-beginning 0) (match-end 0)
                           '(face bog-citekey-face)))))


;;; Commander

;;; The commander functionality is taken from projectile.
;;; https://github.com/bbatsov/projectile

(defconst bog-commander-help-buffer "*Commander Help*")

(defvar bog-commander-methods nil
  "List of file-selection methods for the `bog-commander' command.
Each element is a list (KEY DESCRIPTION FUNCTION).
DESCRIPTION is a one-line description of what the key selects.")

;;;###autoload
(defun bog-commander ()
  "Execute a Bog command with a single letter.

The user is prompted for a single character indicating the action
to invoke.  Press \"?\" to describe available actions.

See `def-bog-commander-method' for defining new methods."
  (interactive)
  (message "Commander [%s]: "
           (apply #'string (mapcar #'car bog-commander-methods)))
  (let* ((ch (save-window-excursion
               (select-window (minibuffer-window))
               (read-char)))
         (method (cl-find ch bog-commander-methods :key #'car)))
    (cond (method
           (funcall (cl-caddr method)))
          (t
           (message "No method for character: ?\\%c" ch)
           (ding)
           (sleep-for 1)
           (discard-input)
           (bog-commander)))))

(defmacro def-bog-commander-method (key description &rest body)
  "Define a new `bog-commander' method.

KEY is the key the user will enter to choose this method.

DESCRIPTION is a one-line sentence describing the method.

BODY is a series of forms which are evaluated when the method is
chosen."
  (let ((method `(lambda ()
                   ,@body)))
    `(setq bog-commander-methods
           (cl-sort (cons (list ,key ,description ,method)
                          (cl-remove ,key bog-commander-methods :key #'car))
                    #'< :key #'car))))

(def-bog-commander-method ?? "Commander help buffer."
  (ignore-errors (kill-buffer bog-commander-help-buffer))
  (with-current-buffer (get-buffer-create bog-commander-help-buffer)
    (insert "Bog commander methods:\n\n")
    (loop for (key line nil) in bog-commander-methods
          do (insert (format "%c:\t%s\n" key line)))
    (goto-char (point-min))
    (help-mode)
    (display-buffer (current-buffer) t))
  (bog-commander))

(def-bog-commander-method ?b
  "Find citekey BibTeX file."
  (bog-find-citekey-bib t))

(def-bog-commander-method ?f
  "Find citekey file."
  (bog-find-citekey-file t))

(def-bog-commander-method ?h
  "Find citekey heading in notes."
  (bog-goto-citekey-heading-in-notes t))

(def-bog-commander-method ?s
  "Search Bog notes with `org-search-view'."
  (bog-search-notes))


;;; Minor mode

(defvar bog-mode-map
  (let ((map (make-sparse-keymap)))
    (let ((prefix-map (make-sparse-keymap)))
      (define-key prefix-map "b" 'bog-find-citekey-bib)
      (define-key prefix-map "c" 'bog-search-notes-for-citekey)
      (define-key prefix-map "f" 'bog-find-citekey-file)
      (define-key prefix-map "g" 'bog-search-citekey-on-web)
      (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 "i" 'bog-citekey-tree-to-indirect-buffer)
      (define-key prefix-map "l" 'bog-open-first-citekey-link)
      (define-key prefix-map "r" 'bog-rename-staged-file-to-citekey)
      (define-key prefix-map "s" 'bog-search-notes)
      (define-key prefix-map "w" 'bog-refile)
      (define-key prefix-map "y" 'bog-insert-heading-citekey)
      (define-key map bog-keymap-prefix prefix-map))
    map)
  "Keymap for Bog.")

;;;###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
    (add-hook 'org-font-lock-hook 'bog-fontify-non-heading-citekeys)
    (font-lock-fontify-buffer))
   (t
    (remove-hook 'org-font-lock-hook 'bog-fontify-non-heading-citekeys)
    (font-lock-fontify-buffer))))

(provide 'bog)

;;; bog.el ends here