+;;; jmax-bibtex.el --- jmax-bibtex utilities
+
+;;; Commentary:
+;; Requires: s.el, dash.el, org-ref.el, doi-utils.el
+
+;;; Code:
+
+(defvar jmax-bibtex-journal-abbreviations
+ '(("ACAT" "ACS Catalysis" "ACS Catal.")
+ ("AM" "Acta Materialia" "Acta Mater.")
+ ("AMM" "Acta Metallurgica et Materialia" "Acta Metall. Mater.")
+ ("AMiner" "American Mineralogist" "Am. Mineral.")
+ ("AngC" "Angewandte Chemie-International Edition" "Angew. Chem. Int. Edit.")
+ ("APLM" "APL Materials" "APL Mat.")
+ ("ACBE" "Applied Catalysis B: Environmental" "Appl. Catal. B-Environ.")
+ ("APL" "Applied Physics Letters" "Appl. Phys. Lett.")
+ ("ASS" "Applied Surface Science" "Appl. Surf. Sci.")
+ ("CL" "Catalysis Letters" "Catal. Lett.")
+ ("CST" "Catalysis Science & Technology" "Catal. Sci. Technol.")
+ ("CT" "Catalysis Today" "Catal. Today")
+ ("CPL" "Chemical Physics Letters" "Chem. Phys. Lett")
+ ("CR" "Chemical Reviews" "Chem. Rev.")
+ ("CSR" "Chemical Society Reviews" "Chem. Soc. Rev.")
+ ("CSR" "Chemical Society Reviews" "Chem. Soc. Rev.")
+ ("CM" "Chemistry of Materials" "Chem. Mater.")
+ ("CSA" "Colloids and Surfaces, A: Physicochemical and Engineering Aspects" "Colloids Surf., A")
+ ("CPMS" "Computational Materials Science" "Comp. Mater. Sci.")
+ ("CPC" "Computer Physics Communications" "Comput. Phys. Commun.")
+ ("CGD" "Crystal Growth \\& Design" "Cryst. Growth Des.")
+ ("CEC" "CrystEngComm" "CrystEngComm")
+ ("ECST" "ECS Transactions" "ECS Trans.")
+ ("EES" "Energy \\& Environmental Science" "Energy Environ. Sci.")
+ ("HPR" "High Pressure Research" "High Pressure Res.")
+ ("IC" "Inorganic Chemistry" "Inorg. Chem.")
+ ("IECR" "Industrial \\& Engineering Chemistry Research" "Ind. Eng. Chem. Res.")
+ ("JJAP" "Japanese Journal of Applied Physics" "Jpn. J. Appl. Phys.")
+ ("JMatR" "Journal of Materials Research" "J. Mater. Res.")
+ ("JALC" "Journal of Alloys and Compounds" "J. Alloy Compd.")
+ ("JAC" "Journal of Applied Crystallography" "J. Appl. Crystallogr.")
+ ("JAP" "Journal of Applied Physics" "J. Appl. Phys.")
+ ("JC" "Journal of Catalysis" "J. Catal.")
+ ("JCP" "Journal of Chemical Physics" "J. Chem. Phys.")
+ ("JCC" "Journal of Computational Chemistry" "J. Comput. Chem.")
+ ("JCG" "Journal of Crystal Growth" "J. Crys. Growth")
+ ("JMC" "Journal of Materials Chemistry" "J. Mater. Chem.")
+ ("JMC" "Journal of Materials Chemistry" "J. Mater. Chem.")
+ ("JMSL" "Journal of Materials Science Letters" "J. Mater. Sci. Lett.")
+ ("JMS" "Journal of Membrane Science" "J. Memb. Sci.")
+ ("JPE" "Journal of Phase Equilibria" "J. Phase Equilib.")
+ ("JPCS" "Journal of Physics and Chemistry of Solids" "J. Phys. Chem. Solids")
+ ("JPCM" "Journal of Physics: Condensed Matter" "J. Phys.: Condens. Matter")
+ ("JSSC" "Journal of Solid State Chemistry" "J. Solid State Chem.")
+ ("JACerS" "Journal of the American Ceramic Society" "J. Am. Ceram. Soc.")
+ ("JACS" "Journal of the American Chemical Society" "J. Am. Chem. Soc.")
+ ("JES" "Journal of The Electrochemical Society" "J. Electrochem. Soc.")
+ ("JEaC" "Journal of Electroanalytical Chemistry" "J. Electroanal. Chem.")
+ ("JMS" "Journal of Membrane Science" "J. Memb. Sci.")
+ ("JVST" "Journal of Vacuum Science \\& Technology A" "J. Vac. Sci. Technol. A")
+ ("ML" "Materials Letters" "Mater. Lett.")
+ ("MSE-BS" "Materials Science and Engineering B" "Mat. Sci. Eng. B-Solid")
+ ("MOLSIM" "Molecular Simulation" "Mol. Sim.")
+ ("Nature" "Nature" "Nature")
+ ("NM" "Nature Materials" "Nat. Mater.")
+ ("PML" "Philosophical Magazine Letters" "Phil. Mag. Lett.")
+ ("PMA" "Philosophical Magazine A" "Phil. Mag. A")
+ ("PA" "Physica A: Statistical Mechanics and its Applications" "Physica A")
+ ("PB" "Physica B-Condensed Matter" "Physica B")
+ ("PCCP" "Physical Chemistry Chemical Physics" "Phys. Chem. Chem. Phys.")
+ ("PSSB" "physica status solidi (b)" "Phys. Status Solidi B")
+ ("PRA" "Physical Review A" "Phys. Rev. A")
+ ("PRB" "Physical Review B" "Phys. Rev. B")
+ ("PRL" "Physical Review Letters" "Phys. Rev. Lett.")
+ ("PCM" "Physics and Chemistry of Minerals" "Phys. Chem. Miner.")
+ ("PSurfSci" "Progress in Surface Science" "Prog. Surf. Sci.")
+ ("Science" "Science" "Science")
+ ("SABC" "Sensors and Actuators B: Chemical" "Sensor. Actuat. B-Chem.")
+ ("SS" "Surface Science" "Surf. Sci.")
+ ("EPJB" "The European Physical Journal B" "Eur. Phys. J. B")
+ ("JPC" "The Journal of Physical Chemistry" "J. Phys. Chem.")
+ ("JPCB" "The Journal of Physical Chemistry B" "J. Phys. Chem. B")
+ ("JPCC" "The Journal of Physical Chemistry C" "J. Phys. Chem. C")
+ ("JPCL" "The Journal of Physical Chemistry Letters" "J. Phys. Chem. Lett.")
+ ("JCP" "The Journal of Chemical Physics" "J. Chem. Phys.")
+ ("TSF" "Thin Solid Films" "Thin Solid Films")
+ ("TC" "Topics in Catalysis" "Top. Catal.")
+ ("WR" "Water Research" "Water Res."))
+ "List of (string journal-full-name journal-abbreviation). Find abbreviations at http://cassi.cas.org/search.jsp.")
+
+
+(defun jmax-bibtex-generate-longtitles ()
+ "Generate longtitles.bib which are @string definitions.
+The full journal names are in `jmax-bibtex-journal-abbreviations'."
+ (interactive)
+ (with-temp-file "longtitles.bib"
+ (dolist (row jmax-bibtex-journal-abbreviations)
+ (insert (format "@string{%s=\"%s\"}\n"
+ (nth 0 row)
+ (nth 1 row))))))
+
+
+(defun jmax-bibtex-generate-shorttitles ()
+ "Generate shorttitles.bib which are @string definitions.
+The abbreviated journal names in `jmax-bibtex-journal-abbreviations'."
+ (interactive)
+ (with-temp-file "shorttitles.bib"
+ (dolist (row jmax-bibtex-journal-abbreviations)
+ (insert (format "@string{%s=\"%s\"}\n"
+ (nth 0 row)
+ (nth 2 row))))))
+
+
+(defun jmax-stringify-journal-name (&optional key start end)
+ "Replace journal name in a bibtex entry with a string.
+The strings are defined in
+`jmax-bibtex-journal-abbreviations'. The optional arguments KEY,
+START and END allow you to use this with `bibtex-map-entries'"
+ (interactive)
+ (bibtex-beginning-of-entry)
+ (when
+ (string= "article"
+ (downcase
+ (cdr (assoc "=type=" (bibtex-parse-entry)))))
+ (let* ((full-names (mapcar
+ (lambda (row)
+ (cons (nth 1 row) (nth 0 row)))
+ jmax-bibtex-journal-abbreviations))
+ (abbrev-names (mapcar
+ (lambda (row)
+ (cons (nth 2 row) (nth 0 row)))
+ jmax-bibtex-journal-abbreviations))
+ (journal (s-trim (bibtex-autokey-get-field "journal")))
+ (bstring (or
+ (cdr (assoc journal full-names))
+ (cdr (assoc journal abbrev-names)))))
+ (when bstring
+ (bibtex-set-field "journal" bstring t)
+ (bibtex-fill-entry)))))
+
+(defun jmax-set-journal-string (full-journal-name)
+ "Set a bibtex journal name to the string that represents FULL-JOURNAL-NAME.
+This is defined in `jmax-bibtex-journal-abbreviations'."
+ (interactive (list
+ (ido-completing-read
+ "Journal: "
+ (mapcar
+ (lambda (x)
+ (nth 1 x))
+ jmax-bibtex-journal-abbreviations))))
+ ;; construct data alist for the string lookup.
+ (let ((alist (mapcar
+ (lambda (x)
+ (cons (nth 1 x) (nth 0 x)))
+ jmax-bibtex-journal-abbreviations)))
+ (bibtex-set-field "journal" (cdr (assoc full-journal-name alist)) t)
+ (bibtex-fill-entry)
+ (bibtex-clean-entry)))
+
+;; see https://github.com/fxcoudert/tools/blob/master/doi2bib for more replacements
+(defvar jmax-nonascii-latex-replacements
+ '()
+ "Cons list of non-ascii characters and their LaTeX representations.")
+
+(setq jmax-nonascii-latex-replacements
+ '(("í" . "{\\\\'i}")
+ ("æ" . "{\\\\ae}")
+ ("ć" . "{\\\\'c}")
+ ("é" . "{\\\\'e}")
+ ("ä" . "{\\\\\"a}")
+ ("è" . "{\\\\`e}")
+ ("à" . "{\\\\`a}")
+ ("á" . "{\\\\'a}")
+ ("ø" . "{\\\\o}")
+ ("ë" . "{\\\\\"e}")
+ ("ü" . "{\\\\\"u}")
+ ("ñ" . "{\\\\~n}")
+ ("å" . "{\\\\aa}")
+ ("ö" . "{\\\\\"o}")
+ ("í" . "{\\\\'i}")
+ ("ó" . "{\\\\'o}")
+ ("ó" . "{\\\\'o}")
+ ("ú" . "{\\\\'u}")
+ ("ú" . "{\\\\'u}")
+ ("š" . "{\\\\v{s}}")
+ ("İ" . "{\\\\.I}")
+ ("ğ" . "{\\\\u{g}}")
+ ("δ" . "$\\\\delta$")
+ ("ç" . "{\\\\c{c}}")
+ ("ß" . "{\\\\ss}")
+ ("≤" . "$\\\\le$")
+ ("<" . "$\\\\lt$")
+ ("θ" . "$\\\\theta$")
+ ("μ" . "$\\\\mu$")
+ ("→" . "$\\\\rightarrow$")
+ ("⇌" . "$\\\\leftrightharpoons$")
+ ("×" . "$\\\\times$")
+ ("°" . "$\\\\deg$")
+ ;; I think these are non-ascii spaces. there seems to be more than one.
+ (" " . " ")
+ (" " . " ")
+ ("–" . "-")
+ ("−" . "-")
+ ("–" . "-")
+ ("‘" . "'")
+ ("’" . "'")
+ ("“" . "\"")
+ ("”" . "\"")))
+
+(defun jmax-replace-nonascii ()
+ "Hook function to replace non-ascii characters in a bibtex entry."
+
+ (interactive)
+ (save-restriction
+ (bibtex-narrow-to-entry)
+ (goto-char (point-min))
+ (dolist (char (mapcar (lambda (x) (car x)) jmax-nonascii-latex-replacements))
+ (while (re-search-forward char nil t)
+ (replace-match (cdr (assoc char jmax-nonascii-latex-replacements))))
+ (goto-char (point-min)))))
+
+(add-hook 'org-ref-clean-bibtex-entry-hook 'jmax-replace-nonascii)
+
+
+(defvar jmax-lower-case-words
+ '("a" "an" "on" "and" "for"
+ "the" "of" "in")
+ "List of words to keep lowercase when changing case in a title.")
+
+
+(defun jmax-title-case-article (&optional key start end)
+ "Convert a bibtex entry article title to title-case.
+The arguments KEY, START and END are optional, and are only there
+so you can use this function with `bibtex-map-entries' to change
+all the title entries in articles."
+ (interactive)
+ (bibtex-beginning-of-entry)
+
+ (let* ((title (bibtex-autokey-get-field "title"))
+ (words (split-string title))
+ (start 0))
+ (when
+ (string= "article" (downcase (cdr (assoc "=type=" (bibtex-parse-entry)))))
+ (setq words (mapcar
+ (lambda (word)
+ (if (or
+ ;; match words containing {} or \ which are probably
+ ;; LaTeX or protected words
+ (string-match "\\$\\|{\\|}\\|\\\\" word)
+ ;; these words should not be capitalized, unless they
+ ;; are the first word
+ (-contains? jmax-lower-case-words (s-downcase word)))
+ word
+ (s-capitalize word)))
+ words))
+
+ ;; Check if first word should be capitalized
+ (when (-contains? jmax-lower-case-words (car words))
+ (setf (car words) (s-capitalize (car words))))
+
+ (setq title (mapconcat 'identity words " "))
+
+ ;; Capitalize letters after a dash
+ (while
+ (string-match "[a-zA-Z]-\\([a-z]\\)" title start)
+ (let ((char (substring title (match-beginning 1) (match-end 1))))
+ (setf (substring title (match-beginning 1) (match-end 1))
+ (format "%s" (upcase char)))
+ (setq start (match-end 1))))
+
+ ;; this is defined in doi-utils
+ (bibtex-set-field
+ "title"
+ title)
+ (bibtex-fill-entry))))
+
+(add-hook 'org-ref-clean-bibtex-entry-hook 'jmax-title-case-article)
+
+
+(defun jmax-sentence-case-article (&optional key start end)
+ "Convert a bibtex entry article title to sentence-case.
+The arguments KEY, START and END are optional, and are only there
+so you can use this function with `bibtex-map-entries' to change
+all the title entries in articles."
+ (interactive)
+ (bibtex-beginning-of-entry)
+
+ (let* ((title (bibtex-autokey-get-field "title"))
+ (words (split-string title))
+ (start 0))
+ (when
+ (string= "article" (downcase (cdr (assoc "=type=" (bibtex-parse-entry)))))
+ (setq words (mapcar
+ (lambda (word)
+ (if
+ ;; match words containing {} or \ which are probably
+ ;; LaTeX or protected words
+ (string-match "\\$\\|{\\|}\\|\\\\" word)
+ word
+ (s-downcase word)))
+ words))
+
+ ;; capitalize first word
+ (setf (car words) (s-capitalize (car words)))
+
+ ;; join the words
+ (setq title (mapconcat 'identity words " "))
+
+ ;; capitalize a word after a :, eg. a subtitle, and protect it
+ (while
+ (string-match "[a-z]:\\s-+\\([A-Z]\\)" title start)
+ (let ((char (substring title (match-beginning 1) (match-end 1))))
+ (setf (substring title (match-beginning 1) (match-end 1))
+;; (format "{%s}" (upcase char)))
+ (format "%s" (upcase char)))
+ (setq start (match-end 1))))
+
+ ;; this is defined in doi-utils
+ (bibtex-set-field
+ "title" title)
+
+ ;; clean and refill entry so it looks nice
+ (bibtex-clean-entry)
+ (bibtex-fill-entry))))
+
+
+
+
+(defun jmax-bibtex-next-entry (&optional n)
+ "Jump to the beginning of the next bibtex entry.
+N is a prefix argument. If it is numeric, jump that many entries
+forward. Negative numbers do nothing."
+ (interactive "P")
+ ;; Note if we start at the beginning of an entry, nothing
+ ;; happens. We need to move forward a char, and call again.
+ (when (= (point) (save-excursion
+ (bibtex-beginning-of-entry)))
+ (forward-char)
+ (jmax-bibtex-next-entry))
+
+ ;; search forward for an entry
+ (when
+ (re-search-forward bibtex-entry-head nil t (and (numberp n) n))
+ ;; go to beginning of the entry
+ (bibtex-beginning-of-entry)))
+
+
+(defun jmax-bibtex-previous-entry (&optional n)
+ "Jump to beginning of the previous bibtex entry.
+N is a prefix argument. If it is numeric, jump that many entries back."
+ (interactive "P")
+ (bibtex-beginning-of-entry)
+ (when
+ (re-search-backward bibtex-entry-head nil t (and (numberp n) n))
+ (bibtex-beginning-of-entry)))
+
+
+(defun jmax-bibtex-mode-keys ()
+ "Modify keymaps used by `bibtex-mode'."
+ (local-set-key (kbd "M-n") 'jmax-bibtex-next-entry)
+ (local-set-key (kbd "M-p") 'jmax-bibtex-previous-entry))
+
+;; add to bibtex-mode-hook
+(add-hook 'bibtex-mode-hook 'jmax-bibtex-mode-keys)
+
+
+(defun jmax-bibtex-entry-doi ()
+ "get doi from entry at point"
+ (interactive)
+ (save-excursion
+ (bibtex-beginning-of-entry)
+ (reftex-get-bib-field "doi" (bibtex-parse-entry t))))
+
+
+(defun jmax-bibtex-wos ()
+ "Open bibtex entry in Web Of Science if there is a DOI"
+ (interactive)
+ (doi-utils-wos (jmax-bibtex-entry-doi)))
+
+
+(defun jmax-bibtex-wos-citing ()
+ "Open citing articles for bibtex entry in Web Of Science if there is a DOI"
+ (interactive)
+ (doi-utils-wos-citing (jmax-bibtex-entry-doi)))
+
+
+(defun jmax-bibtex-wos-related ()
+ "Open related articles for bibtex entry in Web Of Science if there is a DOI"
+ (interactive)
+ (doi-utils-wos-related (jmax-bibtex-entry-doi)))
+
+
+(defun jmax-bibtex-wos-citing ()
+ "Open citing articles for bibtex entry in Web Of Science if there is a DOI"
+ (interactive)
+ (doi-utils-wos-citing (jmax-bibtex-entry-doi)))
+
+
+(defun jmax-bibtex-crossref ()
+ (interactive)
+ (doi-utils-crossref (jmax-bibtex-entry-doi)))
+
+
+(defun jmax-bibtex-google-scholar ()
+ (interactive)
+ (doi-utils-google-scholar (jmax-bibtex-entry-doi)))
+
+
+(defun jmax-bibtex-pubmed ()
+ (interactive)
+ (doi-utils-pubmed (jmax-bibtex-entry-doi)))
+
+(defun jmax-bibtex-pdf (doi)
+ "thin wrapper to get `jmax-bibtex' to open pdf"
+ (interactive)
+ (org-ref-open-bibtex-pdf))
+
+
+
+(defvar jmax-bibtex-menu-funcs '()
+ "Functions to run in doi menu. Each entry is a list of (key menu-name function).
+The function must take one argument, the doi.")
+
+(setq jmax-bibtex-menu-funcs
+ '(("p" "df" jmax-bibtex-pdf)
+ ("w" "os" doi-utils-wos)
+ ("c" "iting articles" doi-utils-wos-citing)
+ ("r" "elated articles" doi-utils-wos-related)
+ ("s" "Google Scholar" doi-utils-google-scholar)
+ ("P" "Pubmed" doi-utils-pubmed)
+ ("f" "CrossRef" doi-utils-crossref)))
+
+(defun jmax-bibtex ()
+ "Menu command to run in a bibtex entry.
+Functions from `jmax-bibtex-menu-funcs'."
+
+ (interactive)
+ (message
+ (concat
+ (mapconcat
+ (lambda (tup)
+ (concat "[" (elt tup 0) "]"
+ (elt tup 1) " "))
+ jmax-bibtex-menu-funcs "") ": "))
+ (let* ((input (read-char-exclusive))
+ (choice (assoc
+ (char-to-string input) jmax-bibtex-menu-funcs)))
+ (when choice
+ (funcall
+ (elt
+ choice
+ 2)
+ (jmax-bibtex-entry-doi)
+ ))))
+
+(defalias 'jb 'jmax-bibtex)
+
+(provide 'jmax-bibtex)
+
+;;; jmax-bibtex.el ends here
projects / org-ref.git / commitdiff