annotate lisp/org/org-bibtex.el @ 101458:36abe982e7cd

2009-01-25 Carsten Dominik <[e-mail]> * org-exp.el (org-export-as-html): Turn \par into a paragraph. * org.el (org-agenda-tags-todo-honor-ignore-options): Declare variable. * org-table.el (org-table-insert-hline): Fix typo in fuction call to `backward-char'. * org-exp.el (org-export-as-html): Remove the initial space from colon examples. * org.el (org-scan-tags): Call `org-agenda-check-for-timestamp-as-reason-to-ignore-todo-item'. * org-agenda.el (org-agenda-todo-list, org-agenda-match-view): New customization groups. (org-agenda-tags-todo-honor-ignore-options): New option. (org-agenda-check-for-timestamp-as-reason-to-ignore-todo-item): New function. (org-agenda-get-todos): Use `org-agenda-check-for-timestamp-as-reason-to-ignore-todo-item'. 2009-01-25 Carsten Dominik <[e-mail]> * org-exp.el (org-export-format-source-code-or-example): Escape HTML characters also in examples that anre not treated with htmlize. Also, just switch to EXAMPLE processing if we do not have a good version of htmlize. * org-rmail.el: Fix copyright notice. * org.el (org-activate-footnote-links): Improve footnote link highlighting. * org-footnote.el (org-footnote-normalize): Fix finding the end of a footnote definition at the end of the file. * org-table.el (org-table-get-specials): Add an imagined hline at the end of the table. This can be useful for references that want to go to the end of the table. Also fix bug when computing last row constants, in tables that do not start right at the right margin. (org-table-eval-formula): Match and replace remove references. (org-table-formula-substitute-names): Make sure that names inside a "remote" call are left alone, the will be replaced later when the remote call is handled. (org-table-convert-refs-to-rc): Do not convert things that might look like a reference, but are really part of an ID or namei n a remote reference. (org-table-get-remote-range): New function. 2009-01-25 Carsten Dominik <[e-mail]> * org-faces.el (org-clock-overlay): Fix bug in face definition. * org-clock.el (org-clock-put-overlay): Use new face instead of `secondary-selection'. * org-faces.el (org-clock-overlay): New face. 2009-01-25 Carsten Dominik <[e-mail]> * org-exp.el (org-get-current-options): Include the option for publishing time stamps. * org.el (org-toggle-heading): Renamed from `org-toggel-region-headings'. No longer needs a region defined, but will use it if there is one. (org-ctrl-c-star): Simplified, relying more on the internal workings of `org-toggle-heading'. (org-toggle-item): Renamed from `org-toggle-region-items'. No longer needs a region defined, but will use it if there is one. (org-ctrl-c-minus): Simplified, relying more on the inernal workings of `org-toggle-item'. * org-export-latex.el (org-export-latex-preprocess): Fix bug in environment detection. Also, do real changes only in unprotected places. 2009-01-25 Carsten Dominik <[e-mail]> * org-export-latex.el (org-export-latex-quotation-marks): Use `org-if-unprotected-1'. (org-export-latex-set-initial-vars): Check for class definition in property. * org-macs.el (org-if-unprotected-1): New macro. 2009-01-25 Carsten Dominik <[e-mail]> * org-compat.el (org-count-lines): New function. * org-exp.el (org-export-format-source-code-or-example): Handle switches related to text areas. * org.el (org-activate-footnote-links): Don't allow match inside a link. * org-footnote.el (org-footnote-re): Don't allow match inside a link. * org-export-latex.el (org-export-latex-links): Keep a relative path relative also after export. * org-exp.el (org-export-html-scripts): Fix HTML snippet. * org.el (org-make-tags-matcher): Never use IDO for completing the tags matcher match string. (org-completing-read): Also remove the special biding for "?". * org-attach.el (org-attach-allow-inheritance): New option. (org-attach-inherited): New variable. (org-attach-dir): Handle properties related to the attachment directory. (org-attach-check-absolute-path): New function. (org-attach-set-directory, org-attach-set-inherit): New commands. (org-attach): Accommodate the new commands in the dispatcher. 2009-01-25 Carsten Dominik <[e-mail]> * org-compat.el (org-fit-window-to-buffer): Fix bug with using `window-full-width-p'. * org-exp.el (org-export-as-html): Only check for images files that really can be inlined * org.el (org-image-file-name-regexp, org-file-image-p): Allow the list of extensions to be a parameter. * org-exp.el (org-export-html-inline-image-extensions): New variable. * org-agenda.el (org-prepare-agenda): Use `org-agenda-block-separator'. (org-agenda-block-separator): New option. 2009-01-25 Carsten Dominik <[e-mail]> * org-export-latex.el (org-export-latex-tables): Call `org-table-clean-before-export' with the new optional argument. * org-exp.el (org-table-clean-before-export): New optional parameter MAYBE-QUOTED, allows for quoted characters like \# in first column. 2009-01-25 Carsten Dominik <[e-mail]> * org-plot.el (org-plot/gnuplot): Fix text-ind parameter for histograms. * org-colview.el (org-colview-construct-allowed-dates): Better error catching when a date/time property does not have allowed values defined. * org-colview-xemacs.el (org-colview-construct-allowed-dates): Better error catching when a date/time property does not have allowed values defined. 2009-01-25 Carsten Dominik <[e-mail]> * org.el (org-map-entries): Restore point and restriction after `org-map-entries'. 2009-01-25 Carsten Dominik <[e-mail]> * org.el (org-time=, org-time<, org-time<=, org-time>) (org-time>=, org-time<>): Make sure both values are dates. 2009-01-25 Carsten Dominik <[e-mail]> * org-archive.el (org-extract-archive-heading): Allow %s for file name also in achive location heading. 2009-01-25 Carsten Dominik <[e-mail]> * org-archive.el (org-add-archive-files): Uniquify the list before returning it. 2009-01-25 Carsten Dominik <[e-mail]> * org-compat.el (org-fit-window-to-buffer): Use `window-full-width-p'. * org-export-latex.el (org-export-latex-fixed-width): Enforce the space after the colon in short examples. * org-exp.el (org-export-protect-colon-examples): Rewritten, to enforce a space after the colon. However, we also allow lines that are *only* a colon. (org-export-as-html): Enforce the space after the colon in short examples. (org-export-preprocess-string): Do the colon example protection earlier. (org-export-remove-timestamps): Do not check for protection at the end of the line. 2009-01-25 Carsten Dominik <[e-mail]> * org.el (org-format-latex-options): Add new matcher for single letters between dollars. (org-get-header): Function removed. (org-heading-components): New function. * org-exp.el (org-export-define-heading-targets): Record ID's also as alternative targets. (org-export-as-html): Interpret "id:" links to other files by preserving the relative path. * org-jsinfo.el (org-infojs-handle-options): Catch the case if v is nil. * org-exp.el (org-export-normalize-links): Protect the main link, to avoid special character processing. * org-export-latex.el (org-export-latex-special-keyword-regexp): New variable. (org-export-latex-special-string-regexps): Variable removed. (org-export-latex-keywords): Use the new regexp. * org-exp.el (org-export-handle-include-files): Fetch switches and put them into the BEGIN statement. * org-timer.el (org-timer-mode-line-string): New variable. * org-clock.el (org-clock-mode-line-map): Renamed from `org-clock-mode-map'. (org-clock-mode-line-timer): Renamed from `org-mode-line-timer'. (org-clock-update-mode-line): Renamed from `org-update-mode-line'. (org-clock-put-overlay): Renamed from `org-put-clock-overlay'. (org-clock-remove-overlays): Renamed from `org-remove-clock-overlays'. * org-timer.el (org-timer-pause-or-continue): Implement stopping and mode line display. (org-timer-stop): New command. (org-timer-seconds): Return correct time when timer is paused. (org-timer-mode-line-timer): New variable. (org-timer-set-mode-line, org-timer-update-mode-line): New functions. * org.el (org-insert-heading): Handle new value `auto' for `org-blank-before-new-entry'. (org-org-menu): Add new items for timer functions. * org-list.el (org-insert-item): Handle new value `auto' for `org-blank-before-new-entry'. * org.el (org-blank-before-new-entry): New value `auto', made default. 2009-01-25 Carsten Dominik <[e-mail]> * org-exp.el (org-export-normalize-links): If the link is also used as the description, protect the description. 2009-01-25 Carsten Dominik <[e-mail]> * org.el (org-closest-date): Fix bug with yearly repeats, in combination with preference of the past as it is used for deadline and scheduling search. * org-exp.el (org-html-handle-time-stamps): No longer check for the `org-export-with-timestamps' option, because the preprocesser has taken care of this already. * org.el (org-entry-properties): Catch the case when this is called in a non-org-mode file. * org-export-latex.el (org-export-latex-remove-from-headlines): Variable made obsolete, also LaTeX export now uses the standard variables. (org-export-as-latex): Add the timestamps parameter to the preprocessor parameter list. (org-export-latex-content): Export the remaining keywords without considering to remove them. (org-export-latex-keywords-maybe): Make the REMOVE-LIST optional. Use bold font instead of tt font for the keywords. (org-export-latex-fontify-headline): Format headlines, assuming that all keywords still present should be published. (org-export-latex-keywords): Remove argument TIMESTAMPS and just publish what ever remains of the time stamps. (org-export-latex-list-parameters): New option. (org-export-latex-lists): Pass additional parameters to the list converter. * org-exp.el (org-export-preprocess-string): Remove clock lines and timestamps already in the preprocesor. (org-export-remove-timestamps, org-export-remove-clock-lines): New functions. (org-export-as-ascii, org-export-as-html): Add the timestamps parameter to the preprocessor parameter list. * org-list.el (org-list-parse-list): Parse for checkboxes. (org-list-to-generic): Introduce and handle new parameters :cbon and :cboff. (org-list-to-latex, org-list-to-html, org-list-to-texinfo): Add optional parameter PARAMS. * org-export-latex.el (org-export-latex-special-chars): Fix problems with interpreting dollar signs. (org-inside-latex-math-p): New function. (org-export-latex-preprocess): Protect all the math fragments. * org.el (org-latex-regexps): Allow a dash after a dollar. * org-w3m.el (org-w3m-copy-for-org-mode): Always deactivate the mark after copying. * org-agenda.el (org-run-agenda-series): Have series options set when finalizing the agenda. * org-exp.el (org-export-format-source-code-or-example): Protect the converted examples. * org.el (org-set-regexps-and-options): Fix the regexp `org-complex-heading-regexp'. 2009-01-25 Carsten Dominik <[e-mail]> * org.el (org-edit-src-get-label-format): New function. (org-coderef-label-format): New option. (org-edit-src-code, org-edit-src-find-region-and-lang): Parse for a label format specification and make sure it is used in the edit buffer. (org-edit-src-get-label-format): New function. (org-store-link): Handle new coderef formats. (org-link-search): Handle new coderef formats. * org-footnote.el (org-footnote-create-definition) (org-footnote-goto-local-insertion-point): Make footnote insertion work correctly when the "Footnotes" headline is the last line in the buffer. * org.el (org-goto-marker-or-bmk): Expose context after jumping to the location. 2009-01-25 Carsten Dominik <[e-mail]> * org-w3m.el (org-w3m): New customization group. (org-w3m-deactivate-mark): New option. (org-w3m-copy-for-org-mode): Deactivate region, unless the user option say not to. 2009-01-25 Carsten Dominik <[e-mail]> * org.el (org-set-font-lock-defaults): Trigger footnote fontification. (org-activate-footnote-links): New function. (org-activate-links): New entry `footnote'. * org-faces.el (org-footnote): New face. 2009-01-25 Carsten Dominik <[e-mail]> * org-macs.el (org-re): Handle the [:word:] class. * org-exp.el (org-export-preprocess-string): Call `org-export-protect-colon-examples'. (org-export-protect-colon-examples): Renamed from `org-export-protect-examples', and scope limited to lines starting with a colon. 2009-01-25 Carsten Dominik <[e-mail]> * org-exp.el (org-export-preprocess-string): Move the preprocess hook to after turning on Org-mode. (org-export-preprocess-after-include-files-hook) (org-export-preprocess-after-tree-selection-hook) (org-export-preprocess-before-backend-specifics-hook) (org-export-preprocess-final-hook): New hooks. (org-export-preprocess-string): Run the new hooks. * org.el (org-ctrl-c-minus): Fix indentation for new items. * org-footnote.el: New file. * org.el (org-footnote): Require footnote code. (org-startup-options): Add new footnote options. (org-mode-map): New keybindig for footnotes. (org-ctrl-c-ctrl-c): Add function at footnotes. (org-org-menu): New menu entries for footnotes. * org-export-latex.el (org-export-as-latex): Pass footnote variable to preprocessor. (org-export-latex-preprocess): Treat multiple references to a footnote. * org-exp.el (org-export-preprocess-string): Call `org-footnote-normalize'. (org-export-as-ascii, org-export-as-html): Pass footnote variable to preprocessor. (org-export-as-html): Treat multiple references to a footnote. 2009-01-25 Carsten Dominik <[e-mail]> * org-export-latex.el (org-export-latex-links): Handle coderef links. * org.el (org-bracket-link-analytic-regexp++): New variable. (org-make-link-regexps): Initialize `org-bracket-link-analytic-regexp++'. (org-store-link): Implement special case in edit-src buffer. (org-insert-link): No use of ide to insert stored links. (org-link-search): Implement special case for coderefs. * org-exp.el (org-export-html-scripts): New constant. (org-export-html-style-default): Add a new style for highlighted code. (org-export-code-refs): New variable. (org-export-preprocess-string): Initialize `org-export-code-refs'. Call `org-export-replace-src-segments-and-examples' No longer call `org-export-protect-examples'. (org-export-target-internal-links): Take care of coderef targets. (org-export-last-code-line-counter-value): New variable. (org-export-replace-src-segments-and-examples): Renamed from `org-export-replace-src-segments', and modified. (org-export-format-source-code-or-example): Renamed from `org-export-format-source-code'. (org-export-number-lines): New function. (org-export-as-ascii, org-export-as-html): Handle coderef links.

;;; org-bibtex.el --- Org links to BibTeX entries
;;
;; Copyright (C) 2007, 2008, 2009 Free Software Foundation, Inc.
;;
;; Author: Bastien Guerry <bzg at altern dot org>
;;         Carsten Dominik <carsten dot dominik at gmail dot com>
;; Keywords: org, wp, remember
;; Version: 6.19a
;;
;; This file is part of GNU Emacs.
;;
;; GNU Emacs 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 of the License, or
;; (at your option) any later version.

;; GNU Emacs 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:
;;
;; This file implements links to database entries in BibTeX files.
;; Instead of defining a special link prefix, it uses the normal file
;; links combined with a custom search mechanism to find entries
;; by reference key.  And it constructs a nice description tag for
;; the link that contains the author name, the year and a short title.
;;
;; It also stores detailed information about the entry so that
;; remember templates can access and enter this information easily.
;;
;; The available properties for each entry are listed here:
;;
;; :author        :publisher      :volume      :pages
;; :editor        :url            :number      :journal
;; :title         :year           :series      :address
;; :booktitle     :month          :annote      :abstract
;; :key           :btype
;;
;; Here is an example of a remember template that use some of this
;; information (:author :year :title :journal :pages):
;;
;; (setq org-remember-templates
;;   '((?b "* READ %?\n\n%a\n\n%:author (%:year): %:title\n   \
;;          In %:journal, %:pages.")))
;;
;; Let's say you want to remember this BibTeX entry:
;;
;; @Article{dolev83,
;;   author = 	 {Danny Dolev and Andrew C. Yao},
;;   title = 	 {On the security of public-key protocols},
;;   journal = 	 {IEEE Transaction on Information Theory},
;;   year = 	 1983,
;;   volume =	 2,
;;   number =	 29,
;;   pages =	 {198--208},
;;   month =	 {Mars}
;; }
;;
;; M-x `org-remember' on this entry will produce this buffer:
;;
;; =====================================================================
;; * READ <== [point here]
;;
;; [[file:/file.bib::dolev83][Dolev & Yao 1983: security of public key protocols]]
;;
;; Danny Dolev and Andrew C. Yao (1983): On the security of public-key protocols
;; In IEEE Transaction on Information Theory, 198--208.
;; =====================================================================
;;
;;; History:
;;
;; The link creation part has been part of Org-mode for a long time.
;;
;; Creating better remember template information was inspired by a request
;; of Austin Frank: http://article.gmane.org/gmane.emacs.orgmode/4112
;; and then imlemented by Bastien Guerry.
;;
;; Org-mode loads this module by default - if this is not what you want,
;; configure the variable `org-modules'.

;;; Code:

(require 'org)

(defvar description nil) ; dynamically scoped from org.el

(declare-function bibtex-beginning-of-entry "bibtex" ())
(declare-function bibtex-generate-autokey "bibtex" ())
(declare-function bibtex-parse-entry "bibtex" (&optional content))
(declare-function bibtex-url "bibtex" (&optional pos no-browse))

(org-add-link-type "bibtex" 'org-bibtex-open)
(add-hook 'org-store-link-functions 'org-bibtex-store-link)

;; (defun org-bibtex-publish (path)
;;   "Build the description of the BibTeX entry for publishing."
;;   (let* ((search (when (string-match "::\\(.+\\)\\'" path)
;; 		   (match-string 1 path)))
;; 	 (path (substring path 0 (match-beginning 0)))
;; 	 key)
;;     (with-temp-buffer
;;       (org-open-file path t nil search)
;;       (setq key (org-create-file-search-functions)))
;;     (or description key)))

(defun org-bibtex-open (path)
  "Visit the bibliography entry on PATH."
  (let* ((search (when (string-match "::\\(.+\\)\\'" path)
		   (match-string 1 path)))
	 (path (substring path 0 (match-beginning 0))))
    (org-open-file path t nil search)))

(defun org-bibtex-store-link ()
  "Store a link to a BibTeX entry."
  (when (eq major-mode 'bibtex-mode)
    (let* ((search (org-create-file-search-in-bibtex))
	   (link (concat "file:" (abbreviate-file-name buffer-file-name)
			 "::" search))
	   (entry (mapcar ; repair strings enclosed in "..." or {...}
		   (lambda(c)
		     (if (string-match
			  "^\\(?:{\\|\"\\)\\(.*\\)\\(?:}\\|\"\\)$" (cdr c))
			 (cons (car c) (match-string 1 (cdr c))) c))
		   (save-excursion
		     (bibtex-beginning-of-entry)
		     (bibtex-parse-entry)))))
      (org-store-link-props
       :key (cdr (assoc "=key=" entry))
       :author (or (cdr (assoc "author" entry)) "[no author]")
       :editor (or (cdr (assoc "editor" entry)) "[no editor]")
       :title (or (cdr (assoc "title" entry)) "[no title]")
       :booktitle (or (cdr (assoc "booktitle" entry)) "[no booktitle]")
       :journal (or (cdr (assoc "journal" entry)) "[no journal]")
       :publisher (or (cdr (assoc "publisher" entry)) "[no publisher]")
       :pages (or (cdr (assoc "pages" entry)) "[no pages]")
       :url (or (cdr (assoc "url" entry)) "[no url]")
       :year (or (cdr (assoc "year" entry)) "[no year]")
       :month (or (cdr (assoc "month" entry)) "[no month]")
       :address (or (cdr (assoc "address" entry)) "[no address]")
       :volume (or (cdr (assoc "volume" entry)) "[no volume]")
       :number (or (cdr (assoc "number" entry)) "[no number]")
       :annote (or (cdr (assoc "annote" entry)) "[no annotation]")
       :series (or (cdr (assoc "series" entry)) "[no series]")
       :abstract (or (cdr (assoc "abstract" entry)) "[no abstract]")
       :btype (or (cdr (assoc "=type=" entry)) "[no type]")
       :type "bibtex"
       :link link
       :description description))))

(defun org-create-file-search-in-bibtex ()
  "Create the search string and description for a BibTeX database entry."
  ;; Make a good description for this entry, using names, year and the title
  ;; Put it into the `description' variable which is dynamically scoped.
  (let ((bibtex-autokey-names 1)
	(bibtex-autokey-names-stretch 1)
	(bibtex-autokey-name-case-convert-function 'identity)
	(bibtex-autokey-name-separator " & ")
	(bibtex-autokey-additional-names " et al.")
	(bibtex-autokey-year-length 4)
	(bibtex-autokey-name-year-separator " ")
	(bibtex-autokey-titlewords 3)
	(bibtex-autokey-titleword-separator " ")
	(bibtex-autokey-titleword-case-convert-function 'identity)
	(bibtex-autokey-titleword-length 'infty)
	(bibtex-autokey-year-title-separator ": "))
    (setq description (bibtex-generate-autokey)))
  ;; Now parse the entry, get the key and return it.
  (save-excursion
    (bibtex-beginning-of-entry)
    (cdr (assoc "=key=" (bibtex-parse-entry)))))

(defun org-execute-file-search-in-bibtex (s)
  "Find the link search string S as a key for a database entry."
  (when (eq major-mode 'bibtex-mode)
    ;; Yes, we want to do the search in this file.
    ;; We construct a regexp that searches for "@entrytype{" followed by the key
    (goto-char (point-min))
    (and (re-search-forward (concat "@[a-zA-Z]+[ \t\n]*{[ \t\n]*"
				    (regexp-quote s) "[ \t\n]*,") nil t)
	 (goto-char (match-beginning 0)))
    (if (and (match-beginning 0) (equal current-prefix-arg '(16)))
	;; Use double prefix to indicate that any web link should be browsed
	(let ((b (current-buffer)) (p (point)))
	  ;; Restore the window configuration because we just use the web link
	  (set-window-configuration org-window-config-before-follow-link)
	  (save-excursion (set-buffer b) (goto-char p)
	    (bibtex-url)))
      (recenter 0))  ; Move entry start to beginning of window
  ;; return t to indicate that the search is done.
    t))

;; Finally add the link search function to the right hook.
(add-hook 'org-execute-file-search-functions 'org-execute-file-search-in-bibtex)

(provide 'org-bibtex)

;; arch-tag: 83987d5a-01b8-41c7-85bc-77700f1285f5

;;; org-bibtex.el ends here