X-Git-Url: https://git.donarmstrong.com/?p=org-ref.git;a=blobdiff_plain;f=org-ref.el;h=86a3e5aa93654c19f0a5911c2d3e26025ee593f4;hp=939b8ee7102ee218574b0fac89f6616c3ec2177f;hb=f6a6ac450ac52f98255ef184800775a2163414b7;hpb=2e9a984b86534dc777b8099e628620afdc44f2a3;ds=sidebyside diff --git a/org-ref.el b/org-ref.el index 939b8ee..86a3e5a 100644 --- a/org-ref.el +++ b/org-ref.el @@ -326,7 +326,7 @@ You will see a message in the minibuffer when on a cite, ref or label link." (replace-regexp-in-string "\*" "\\\\*" x) ) org-ref-cite-types "\\|") "\\)" - ":\\([a-zA-Z0-9-_:]*,?\\)*")) + ":\\([a-zA-Z0-9-_:\\./]*,?\\)*")) (setq org-ref-label-re @@ -504,7 +504,8 @@ Format according to the type in `org-ref-bibliography-entry-format'." (loop for file in org-ref-bibliography-files do (if (org-ref-key-in-file-p key (file-truename file)) (throw 'result file) - (message "%s not found in %s" key (file-truename file)))))) + (message "%s not found in %s" + key (file-truename file)))))) (with-temp-buffer (insert-file-contents file) @@ -611,45 +612,53 @@ Format according to the type in `org-ref-bibliography-entry-format'." ;; may contain multiple files. this code finds the ;; one you clicked on and opens it. (lambda (link-string) - ;; get link-string boundaries - ;; we have to go to the beginning of the line, and then search forward - + ;; get link-string boundaries we have to go to the + ;; beginning of the line, and then search forward (let* ((bibfile) ;; object is the link you clicked on (object (org-element-context)) (link-string-beginning) - (link-string-end)) - + (link-string-end) + (cp (point))) (save-excursion (goto-char (org-element-property :begin object)) (search-forward link-string nil nil 1) (setq link-string-beginning (match-beginning 0)) (setq link-string-end (match-end 0))) - ;; We set the reftex-default-bibliography - ;; here. it should be a local variable only in - ;; the current buffer. We need this for using - ;; reftex to do citations. - (set (make-local-variable 'reftex-default-bibliography) - (split-string (org-element-property :path object) ",")) - - ;; now if we have comma separated bibliographies - ;; we find the one clicked on. we want to - ;; search forward to next comma from point - (save-excursion - (if (search-forward "," link-string-end 1 1) - (setq key-end (- (match-end 0) 1)) ; we found a match - (setq key-end (point)))) ; no comma found so take the point - ;; and backward to previous comma from point - (save-excursion - (if (search-backward "," link-string-beginning 1 1) - (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match - (setq key-beginning (point)))) ; no match found + ;; Make sure point is in the link-path. + (if (< cp link-string-beginning) + (goto-char link-string-beginning)) + ;; We set the reftex-default-bibliography + ;; here. it should be a local variable only in + ;; the current buffer. We need this for using + ;; reftex to do citations. + (set (make-local-variable 'reftex-default-bibliography) + (split-string + (org-element-property :path object) ",")) + + ;; now if we have comma separated bibliographies + ;; we find the one clicked on. we want to + ;; search forward to next comma from point + (save-excursion + (if (search-forward "," link-string-end 1 1) + ;; we found a match + (setq key-end (- (match-end 0) 1)) + ;; no comma found so take the point + (setq key-end (point)))) + ;; and backward to previous comma from point + (save-excursion + (if (search-backward "," link-string-beginning 1 1) + ;; we found a match + (setq key-beginning (+ (match-beginning 0) 1)) + (setq key-beginning (point)))) ; no match found ;; save the key we clicked on. - (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end))) - (find-file bibfile))) ; open file on click + (setq bibfile (org-ref-strip-string + (buffer-substring key-beginning key-end))) + ;; open file on click + (find-file bibfile))) - ;; formatting code + ;; formatting code (lambda (keyword desc format) (cond ((eq format 'org) (org-ref-get-org-bibliography)) @@ -657,10 +666,14 @@ Format according to the type in `org-ref-bibliography-entry-format'." ((eq format 'html) (org-ref-get-html-bibliography)) ((eq format 'latex) ;; write out the latex bibliography command - (format "\\bibliography{%s}" (replace-regexp-in-string "\\.bib" "" (mapconcat 'identity - (mapcar 'expand-file-name - (split-string keyword ",")) - ","))))))) + (format "\\bibliography{%s}" + (replace-regexp-in-string + "\\.bib" "" + (mapconcat + 'identity + (mapcar 'expand-file-name + (split-string keyword ",")) + ","))))))) (org-add-link-type "nobibliography" ;; this code is run on clicking. The bibliography @@ -714,20 +727,11 @@ Format according to the type in `org-ref-bibliography-entry-format'." ((eq format 'html) (org-ref-get-html-bibliography)) ((eq format 'latex) ;; write out the latex bibliography command - -; (format "{\\setbox0\\vbox{\\bibliography{%s}}}" -; (replace-regexp-in-string "\\.bib" "" (mapconcat 'identity -; (mapcar 'expand-file-name -; (split-string keyword ",")) -; ","))) - (format "\\nobibliography{%s}" (replace-regexp-in-string "\\.bib" "" (mapconcat 'identity (mapcar 'expand-file-name (split-string keyword ",")) - ","))) - - )))) + ","))))))) (org-add-link-type "printbibliography" (lambda (arg) (message "Nothing implemented for clicking here.")) @@ -737,8 +741,7 @@ Format according to the type in `org-ref-bibliography-entry-format'." ((eq format 'html) (org-ref-get-html-bibliography)) ((eq format 'latex) ;; write out the biblatex bibliography command - "\\printbibliography")) -)) + "\\printbibliography")))) (org-add-link-type "bibliographystyle" (lambda (arg) (message "Nothing implemented for clicking here.")) @@ -748,11 +751,26 @@ Format according to the type in `org-ref-bibliography-entry-format'." ;; write out the latex bibliography command (format "\\bibliographystyle{%s}" keyword))))) + +(defun org-bibliographystyle-complete-link (&optional arg) + "Completion function for bibliographystyle link. +ARG does nothing." + (format "bibliographystyle:%s" (ido-completing-read + "style: " + '("unsrt" "plain" "alpha" + ;; natbib + ;; https://www.sharelatex.com/learn/Natbib_bibliography_styles + "dinat" "humannat" "plainnat" + "abbrnat" "unsrtnat" "rusnat" + "ksfhnat")))) + + (defun org-bibliography-complete-link (&optional arg) "Completion function for bibliography link. ARG does nothing." (format "bibliography:%s" (read-file-name "enter file: " nil nil t))) + (defun org-ref-insert-bibliography-link () "Insert a bibliography with completion." (interactive) @@ -900,6 +918,8 @@ ARG does nothing." ((eq format 'latex) (format "\\listoftables"))))) + +;; ** label link (defun org-ref-count-labels (label) "Counts number of matches for LABEL in the document." (+ (count-matches (format "label:%s\\b[^-:]" label) (point-min) (point-max)) @@ -916,7 +936,6 @@ ARG does nothing." (setq custom-id-count (+ 1 custom-id-count))))) custom-id-count))) -;; ** label link (org-add-link-type "label" (lambda (label) @@ -951,21 +970,21 @@ ARG does nothing." :type "ref" :link (concat "ref:" (org-element-property :name object)))) -;; it turns out this does not work. you can already store a link to a heading with a CUSTOM_ID ;; store link on heading with custom_id -; (when (and (equal (org-element-type object) 'headline) -; (org-entry-get (point) "CUSTOM_ID")) -; (org-store-link-props -; :type "ref" -; :link (concat "ref:" (org-entry-get (point) "CUSTOM_ID")))) + ;; this is not a ref link, but it is still what you want + (when (and (equal (org-element-type object) 'headline) + (org-entry-get (point) "CUSTOM_ID")) + (org-store-link-props + :type "custom_id" + :link (format "[[#%s]]" (org-entry-get (point) "CUSTOM_ID")))) ;; and to #+label: lines + (when (and (equal (org-element-type object) 'paragraph) (org-element-property :name object)) (org-store-link-props :type "ref" - :link (concat "ref:" (org-element-property :name object)))) -)) + :link (concat "ref:" (org-element-property :name object)))))) (add-hook 'org-store-link-functions 'org-label-store-link) @@ -976,10 +995,8 @@ ARG does nothing." "on clicking goto the label. Navigate back with C-c &" (org-mark-ring-push) ;; next search from beginning of the buffer - ;; it is possible you would not find the label if narrowing is in effect (widen) - (unless (or ;; our label links @@ -995,20 +1012,15 @@ ARG does nothing." ;; #+label: name org-definition (progn (goto-char (point-min)) - (re-search-forward (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t)) + (re-search-forward + (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t)) ;; org tblname (progn (goto-char (point-min)) - (re-search-forward (format "^#\\+tblname:\\s-*\\(%s\\)\\b" label) nil t)) - -;; Commented out because these ref links do not actually translate correctly in LaTeX. -;; you need [[#label]] links. - ;; CUSTOM_ID -; (progn -; (goto-char (point-min)) -; (re-search-forward (format ":CUSTOM_ID:\s-*\\(%s\\)" label) nil t)) - ) + (re-search-forward + (format "^#\\+tblname:\\s-*\\(%s\\)\\b" label) nil t))) + ;; we did not find anything, so go back to where we came (org-mark-ring-goto) (error "%s not found" label)) @@ -1021,14 +1033,20 @@ ARG does nothing." ((eq format 'latex) (format "\\ref{%s}" keyword))))) + (defun org-ref-get-org-labels () "Return a list of #+LABEL: labels." (save-excursion (goto-char (point-min)) (let ((matches '())) (while (re-search-forward "^#\\+label:\\s-+\\(.*\\)\\b" (point-max) t) - (add-to-list 'matches (match-string-no-properties 1) t)) -matches))) + ;; do not do this for tables. We get those in `org-ref-get-tblnames'. + ;; who would have thought you have save match data here? Trust me. When + ;; I wrote this, you did. + (unless (save-match-data (equal (car (org-element-at-point)) 'table)) + (add-to-list 'matches (match-string-no-properties 1) t))) + matches))) + (defun org-ref-get-custom-ids () "Return a list of custom_id properties in the buffer." @@ -1038,7 +1056,8 @@ matches))) (let ((custom_id (org-entry-get (point) "CUSTOM_ID"))) (when (not (null custom_id)) (setq results (append results (list custom_id))))))) -results)) + results)) + (defun org-ref-get-latex-labels () "Return list of matchin LaTeX defined labels in buffer." @@ -1047,7 +1066,8 @@ results)) (let ((matches '())) (while (re-search-forward "\\\\label{\\([a-zA-z0-9:-]*\\)}" (point-max) t) (add-to-list 'matches (match-string-no-properties 1) t)) -matches))) + matches))) + (defun org-ref-get-tblnames () "Return list of table names in the buffer." @@ -1055,6 +1075,7 @@ matches))) (lambda (table) (org-element-property :name table)))) + (defun org-ref-get-labels () "Return a list of labels in the buffer that you can make a ref link to. This is used to complete ref links and in helm menus." @@ -1063,15 +1084,22 @@ This is used to complete ref links and in helm menus." (widen) (goto-char (point-min)) (let ((matches '())) - ;; these are the label:stuff kinds - (while (re-search-forward "[^#+]label:\\([a-zA-z0-9:-]*\\)" (point-max) t) + ;; these are the org-ref label:stuff kinds + (while (re-search-forward + "[^#+]label:\\([a-zA-z0-9:-]*\\)" (point-max) t) (add-to-list 'matches (match-string-no-properties 1) t)) + ;; now add all the other kinds of labels. (append matches + ;; #+label: (org-ref-get-org-labels) + ;; \label{} (org-ref-get-latex-labels) + ;; #+tblname: and actually #+label (org-ref-get-tblnames) + ;; CUSTOM_IDs (org-ref-get-custom-ids)))))) + (defun org-ref-helm-insert-label-link () "Insert a label link. helm just shows you what labels already exist. If you are on a label link, replace it." @@ -1083,7 +1111,8 @@ If you are on a label link, replace it." ;; default action is to open to the label (action . (lambda (label) ;; unfortunately I do not have markers here - (org-open-link-from-string (format "ref:%s" label)))) + (org-open-link-from-string + (format "ref:%s" label)))) ;; if you select a label, replace current one (action . (lambda (label) (switch-to-buffer ,cb) @@ -1145,6 +1174,7 @@ If you are on a label link, replace it." (or label helm-pattern)))))))))))) + (defun org-ref-complete-link (&optional arg) "Completion function for ref links. Optional argument ARG Does nothing." @@ -1152,11 +1182,13 @@ Optional argument ARG Does nothing." (setq label (completing-read "label: " (org-ref-get-labels))) (format "ref:%s" label))) + (defun org-ref-insert-ref-link () "Completion function for a ref link." (interactive) (insert (org-ref-complete-link))) + (defun org-ref-helm-insert-ref-link () "Helm menu to insert ref links to labels in the document. If you are on link, replace with newly selected label. @@ -1255,20 +1287,14 @@ Use C-u C-u to insert a [[#custom-id]] link" ;; #+label: name org-definition (progn (goto-char (point-min)) - (re-search-forward (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t)) + (re-search-forward + (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t)) ;; org tblname (progn (goto-char (point-min)) - (re-search-forward (format "^#\\+tblname:\\s-*\\(%s\\)\\b" label) nil t)) - -;; Commented out because these ref links do not actually translate correctly in LaTeX. -;; you need [[#label]] links. - ;; CUSTOM_ID -; (progn -; (goto-char (point-min)) -; (re-search-forward (format ":CUSTOM_ID:\s-*\\(%s\\)" label) nil t)) - ) + (re-search-forward + (format "^#\\+tblname:\\s-*\\(%s\\)\\b" label) nil t))) ;; we did not find anything, so go back to where we came (org-mark-ring-goto) (error "%s not found" label)) @@ -1280,6 +1306,7 @@ Use C-u C-u to insert a [[#custom-id]] link" ((eq format 'latex) (format "\\pageref{%s}" keyword))))) + (defun org-pageref-complete-link (&optional arg) "Completion function for ref links. Optional argument ARG Does nothing." @@ -1287,11 +1314,13 @@ Optional argument ARG Does nothing." (setq label (completing-read "label: " (org-ref-get-labels))) (format "ref:%s" label))) + (defun org-pageref-insert-ref-link () "Insert a pageref link with completion." (interactive) (insert (org-pageref-complete-link))) + ;; *** nameref link (org-add-link-type "nameref" @@ -1388,7 +1417,9 @@ keyword we clicked on. We also strip the text properties." (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match (setq key-beginning link-string-beginning))) ; no match found ;; save the key we clicked on. - (setq bibtex-key (org-ref-strip-string (buffer-substring key-beginning key-end))) + (setq bibtex-key + (org-ref-strip-string + (buffer-substring key-beginning key-end))) (set-text-properties 0 (length bibtex-key) nil bibtex-key) bibtex-key) ;; link with description. assume only one key @@ -2366,7 +2397,7 @@ Makes a new buffer with clickable links." (kill-buffer "*Missing citations*")) (message "No bad cite links found")))) -;; ** helm interface to bad citations, labels, refs in orgfile +;; ** helm interface to bad citations, labels, refs and files in orgfile (defun org-ref-bad-cite-candidates () "Return a list of conses (key . marker) where key does not exist in the known bibliography files, and marker points to the key." (let* ((cp (point)) ; save to return to later @@ -2436,7 +2467,6 @@ Makes a new buffer with clickable links." (while (re-search-forward (format "[^#+]label:%s\\s-" label) nil t) (push (cons label (point-marker)) multiple-labels)) - (goto-char (point-min)) (while (re-search-forward (format "\\label{%s}\\s-?" label) nil t) @@ -2454,6 +2484,29 @@ Makes a new buffer with clickable links." (goto-char cp))))) multiple-labels)) +(defun org-ref-bad-file-link-candidates () + "Return list of conses (link . marker) wehre the file in the link does not exist." + (let* ((bad-files '())) + (org-element-map (org-element-parse-buffer) 'link + (lambda (link) + (let ((type (org-element-property :type link))) + (when (or (string= "file" type) + (string= "attachfile" type)) + (unless (file-exists-p (org-element-property :path link)) + (add-to-list 'bad-files + (cons (org-element-property :path link) + (save-excursion + (goto-char + (org-element-property :begin link)) + (point-marker))))))))) + ;; Let us also check \attachfile{fname} + (save-excursion + (goto-char (point-min)) + (while (re-search-forward "\\attachfile{\\(.*\\)}" nil t) + (unless (file-exists-p (match-string 1)) + (add-to-list 'bad-files (cons (match-string 1) (point-marker)))))) + bad-files)) + ;;;###autoload (defun org-ref () "Opens a helm interface to actions for org-ref. @@ -2462,7 +2515,8 @@ Shows bad citations, ref links and labels" (let ((cb (current-buffer)) (bad-citations (org-ref-bad-cite-candidates)) (bad-refs (org-ref-bad-ref-candidates)) - (bad-labels (org-ref-bad-label-candidates))) + (bad-labels (org-ref-bad-label-candidates)) + (bad-files (org-ref-bad-file-link-candidates))) (helm :sources `(((name . "Bad citations") (candidates . ,bad-citations) @@ -2482,6 +2536,12 @@ Shows bad citations, ref links and labels" (switch-to-buffer (marker-buffer marker)) (goto-char marker)))) ;; + ((name . "Bad file links") + (candidates . ,bad-files) + (lambda (marker) + (switch-to-buffer (marker-buffer marker)) + (goto-char marker))) + ;; ((name . "Utilities") (candidates . (("Check buffer again" . org-ref) ("Insert citation" . helm-bibtex) @@ -2506,8 +2566,7 @@ Shows bad citations, ref links and labels" )) (action . (lambda (x) (switch-to-buffer ,cb) - (funcall x)))) - )))) + (funcall x)))))))) ;; ** Find non-ascii charaters (defun org-ref-find-non-ascii-characters () @@ -2788,87 +2847,88 @@ Shows bad citations, ref links and labels" (defun org-ref-link-message () "Print a minibuffer message about the link that point is on." (interactive) - (when (eq major-mode 'org-mode) - (let* ((object (org-element-context)) - (type (org-element-property :type object))) - (save-excursion - (cond - ;; cite links - ((-contains? org-ref-cite-types type) - (message (org-ref-get-citation-string-at-point))) - - ;; message some context about the label we are referring to - ((string= type "ref") - (message "%scount: %s" - (org-ref-get-label-context - (org-element-property :path object)) - (org-ref-count-labels - (org-element-property :path object)))) - - ((string= type "eqref") - (message "%scount: %s" - (org-ref-get-label-context - (org-element-property :path object)) - (org-ref-count-labels - (org-element-property :path object)))) - - ;; message the count - ((string= type "label") - (let ((count (org-ref-count-labels - (org-element-property :path object)))) - ;; get plurality on occurrence correct - (message (concat - (number-to-string count) - " occurence" - (when (or (= count 0) - (> count 1)) - "s"))))) - - ((string= type "custom-id") - (save-excursion - (org-open-link-from-string - (format "[[#%s]]" (org-element-property :path object))) - (message "%s" (org-get-heading)))) - - ;; check if the bibliography files exist. - ((string= type "bibliography") - (let* ((bibfile) - ;; object is the link you clicked on - (object (org-element-context)) - (link-string (org-element-property :path object)) - (link-string-beginning) - (link-string-end)) - (save-excursion - (goto-char (org-element-property :begin object)) - (search-forward link-string nil nil 1) - (setq link-string-beginning (match-beginning 0)) - (setq link-string-end (match-end 0))) - - ;; make sure we are in link and not before the : - (when (> link-string-beginning (point)) - (goto-char link-string-beginning)) - - ;; now if we have comma separated bibliographies - ;; we find the one clicked on. we want to - ;; search forward to next comma from point + (save-restriction + (widen) + (when (eq major-mode 'org-mode) + (let* ((object (org-element-context)) + (type (org-element-property :type object))) + (save-excursion + (cond + ;; cite links + ((-contains? org-ref-cite-types type) + (message (org-ref-get-citation-string-at-point))) + + ;; message some context about the label we are referring to + ((string= type "ref") + (message "%scount: %s" + (org-ref-get-label-context + (org-element-property :path object)) + (org-ref-count-labels + (org-element-property :path object)))) + + ((string= type "eqref") + (message "%scount: %s" + (org-ref-get-label-context + (org-element-property :path object)) + (org-ref-count-labels + (org-element-property :path object)))) + + ;; message the count + ((string= type "label") + (let ((count (org-ref-count-labels + (org-element-property :path object)))) + ;; get plurality on occurrence correct + (message (concat + (number-to-string count) + " occurence" + (when (or (= count 0) + (> count 1)) + "s"))))) + + ((string= type "custom-id") (save-excursion - (if (search-forward "," link-string-end 1 1) - (setq key-end (- (match-end 0) 1)) ; we found a match - (setq key-end (point)))) ; no comma found so take the point + (org-open-link-from-string + (format "[[#%s]]" (org-element-property :path object))) + (message "%s" (org-get-heading)))) + + ;; check if the bibliography files exist. + ((string= type "bibliography") + (let* ((bibfile) + ;; object is the link you clicked on + (object (org-element-context)) + (link-string (org-element-property :path object)) + (link-string-beginning) + (link-string-end)) + (save-excursion + (goto-char (org-element-property :begin object)) + (search-forward link-string nil nil 1) + (setq link-string-beginning (match-beginning 0)) + (setq link-string-end (match-end 0))) + + ;; make sure we are in link and not before the : + (when (> link-string-beginning (point)) + (goto-char link-string-beginning)) + + ;; now if we have comma separated bibliographies + ;; we find the one clicked on. we want to + ;; search forward to next comma from point + (save-excursion + (if (search-forward "," link-string-end 1 1) + (setq key-end (- (match-end 0) 1)) ; we found a match + (setq key-end (point)))) ; no comma found so take the point - ;; and backward to previous comma from point - (save-excursion - (if (search-backward "," link-string-beginning 1 1) - (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match - (setq key-beginning (point)))) ; no match found - ;; save the key we clicked on. - (setq bibfile - (org-ref-strip-string - (buffer-substring key-beginning key-end))) - (if (file-exists-p bibfile) - (message "%s exists." bibfile) - (message "!!! %s NOT FOUND !!!" bibfile)))) - ))))) + ;; and backward to previous comma from point + (save-excursion + (if (search-backward "," link-string-beginning 1 1) + (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match + (setq key-beginning (point)))) ; no match found + ;; save the key we clicked on. + (setq bibfile + (org-ref-strip-string + (buffer-substring key-beginning key-end))) + (if (file-exists-p bibfile) + (message "%s exists." bibfile) + (message "!!! %s NOT FOUND !!!" bibfile)))))))))) ;; ** aliases (defalias 'oro 'org-ref-open-citation-at-point) @@ -3003,7 +3063,7 @@ first key that partially matches. This version avoids that." User is prompted for tags. This function is called from `helm-bibtex'. Argument CANDIDATES helm candidates." (message "") - (let ((keywords (read-input "Keywords (comma separated): "))) + (let ((keywords (read-string "Keywords (comma separated): "))) (loop for key in (helm-marked-candidates) do (save-window-excursion @@ -3041,11 +3101,13 @@ In the helm-bibtex buffer, C-u will give you a helm menu to select a new link ty C-u C-u will change the key at point to the selected keys." (let* ((object (org-element-context)) (last-char (save-excursion - (goto-char (org-element-property :end object)) - (backward-char) - (if (looking-at " ") - " " - "")))) + (when (org-element-property :end object) + (goto-char (org-element-property :end object)) + (unless (bobp) + (backward-char)) + (if (looking-at " ") + " " + ""))))) (cond ;; case where we are in a link ((and (equal (org-element-type object) 'link) @@ -3079,7 +3141,7 @@ C-u C-u will change the key at point to the selected keys." ;; We are next to a link, and we want to append ;; next to a link means one character back is on a link. ((save-excursion - (backward-char) + (unless (bobp) (backward-char)) (and (equal (org-element-type (org-element-context)) 'link) (-contains? org-ref-cite-types