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|
;;; 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
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