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update to replacer, make oa-author interactive, add graph
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Your Name committed Jan 13, 2024
1 parent d56a6c2 commit 980cbad
Showing 1 changed file with 102 additions and 16 deletions.
118 changes: 102 additions & 16 deletions openalex.el
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,8 @@ https://docs.openalex.org/api-entities/works"
"")))
(req (request url :sync t :parser 'oa--response-parser))
(data (request-response-data req)))
;; this is for convenience to inspect data in a browser.
;; this is for convenience to inspect data in a browser, e.g. you can click
;; on the url in Emacs and it opens in a browser.
(plist-put data :oa-url url)
data))

Expand All @@ -57,9 +58,6 @@ https://docs.openalex.org/api-entities/works"
;; This section provides a replacer and helper function to format org-entries
;; from the results returned in OpenAlex.




(defun oa--replacer (key object)
"Replacer function for `s-format'.
QUERY is a string that is either a sexp for a function to
Expand All @@ -68,19 +66,31 @@ sexp, it is read and evaluated. Otherwise, the path is split, and
looked up sequentially in object.
OBJECT is a plist, usually from a Work request."
(if (or (s-starts-with? "(" key)
(boundp (intern-soft key)))
;; this is a function we should evaluate
;; it is kind of janky and might miss context.
(eval (read key) t)
(cond
((s-starts-with? "(" key)
;; this is potentially janky and might mess up things with dynamic scoping
;; and other lexical things. It does seem to work.
(eval (read key)))

;; in principle this should be a variable you want to put in the template. it
;; is tricky though, and I don't understand why, sometimes it appears that
;; something is bound, but then it isn't. I wonder if it is related to
;; lexical binding or something. This seems to do what I want.
((and (boundp (intern-soft key))
(symbol-value (intern-soft key)))
(symbol-value (intern-soft key)))

(t
;; just get data
(let ((fields (s-split "\\." key))
result)
;; sequentially process the dot-notation field by field
(while fields
(setq object (plist-get object (intern-soft (concat ":" (pop fields))))))
(or (string-replace "\\n" "" (format "%s" object)) "Not found"))))


(or
;; I find it useful to remove line breaks
(string-replace "\\n" "" (format "%s" object))
"Not found")))))


;; ** help functions for complex data
Expand Down Expand Up @@ -312,7 +322,7 @@ With prefix arg ASCENDING, sort in ascending order (old to new)"


(defun oa-buffer-sort-cited-by-count (&optional ascending)
"Sort orgheadings by cited by count in descending order high to low.
"Sort org headings by cited by count in descending order high to low.
With prefix arg ASCENDING sort from low to high."
(interactive "P")
(if ascending
Expand Down Expand Up @@ -351,15 +361,16 @@ With prefix arg ASCENDING sort from low to high."
(oa--cited-by-works (concat "doi:" (org-ref-get-doi-at-point))))



(defhydra+ org-ref-citation-hydra ()
"Add related documents action to `org-ref-citation-hydra'."
("xr" oa-related-works "Related documents" :column "OpenAlex"))


(defhydra+ org-ref-citation-hydra ()
"Add cited by documents action to `org-ref-citation-hydra'."
("xc" oa-cited-by-works "Cited by documents" :column "OpenAlex"))


(defhydra+ org-ref-citation-hydra ()
"Add references from action to `org-ref-citation-hydra'."
("xf" oa-referenced-works "References from" :column "OpenAlex"))
Expand All @@ -378,7 +389,8 @@ With prefix arg ASCENDING sort from low to high."
;; * Author object

(defun oa--author (entity-id &optional filter)
"Get an Author object for entity-id"
"Get an Author object for ENTITY-ID.
FILTER is an optional string to add to the URL."
(let* ((url (concat "https://api.openalex.org/authors"
(if filter
(concat "?" filter entity-id)
Expand Down Expand Up @@ -435,10 +447,81 @@ ${(oa--elisp-get-bibtex result)}
entries))


(defun oa--author-candidates ()
(let* ((str (read-string "Author: "))
(url (format "https://api.openalex.org/autocomplete/authors?q=%s"
(url-hexify-string str)))
(req (request url :sync t :parser 'oa--response-parser))
(data (request-response-data req))
(results (plist-get data :results))
(candidates (cl-loop for author in results collect
(cons
(format "%s - %s"
(plist-get author :display_name)
(plist-get
author :hint))
(plist-get author :id)))))
candidates))


(defun oa--counts-by-year (data)
"Get citation counts by year and make a graph.
DATA is an author from OpenAlex.
Requires gnuplot. Generates a temporary file."
(if (executable-find "gnuplot")
(let* ((pngfile (make-temp-file "oa-" nil ".png"))
(counts (sort
(cl-loop for i from 1 for item in (plist-get data :counts_by_year)
collect
(list
(plist-get item :year)
(plist-get item :cited_by_count)
(plist-get item :works_count)))
(lambda (a b)
(< (nth 0 a)
(nth 0 b)))))
(count-string (cl-loop for i from 1 for (year cites works) in counts
concat
(format "%s \"%s\" %s %s\n"
i year cites works)))
(gnuplot (format "set terminal \"png\" size 800,400
set output \"%s\"
$counts << EOD
%s
EOD
set boxwidth 0.5
set style fill solid noborder
set style line 1 lc rgb \"grey\"
set ylabel \"Citation count\"
set y2label \"Document count\"
plot $counts using 1:3:xtic(2) with boxes lc rgb \"grey\" title \"Citations per year\", \"\" using 1:4 axes x1y2 with lines title \"Document count\"
"
pngfile
count-string))
(cmdfile (make-temp-file "gnuplot-cmds-" nil ".gpl"))
(shellcmd (format "gnuplot --persist -c \"%s\"" cmdfile)))
(with-temp-file cmdfile
(insert gnuplot)
(message (buffer-string)))
(shell-command shellcmd)
(delete-file cmdfile)
(format "[[%s]]" pngfile))
"Gnuplot required to see citation graph. Please install it."))


(defun oa-author (entity-id)
"View Author for ENTITY-ID in an org-buffer."
"View Author for ENTITY-ID in an org-buffer.
ENTITY-ID is usually a url, e.g. to OpenAlex or orcid.
See https://docs.openalex.org/api-entities/authors/get-a-single-author.
When run interactively, you are queried for a name and an
autocomplete set of candidates is provided."
(interactive
(list (let ((candidates (oa--author-candidates)))
(cdr (assoc (completing-read "Author: " candidates) candidates)))))
(let* ((buf (get-buffer-create "*OpenAlex - Author*"))
(data (oa--author entity-id))
(citations-image (oa--counts-by-year data))
(works-count (plist-get data :works_count))
(works-url (plist-get data :works_api_url))
(works-data (request-response-data
Expand All @@ -449,6 +532,7 @@ ${(oa--elisp-get-bibtex result)}
(erase-buffer)
(insert (s-format "* ${display_name} ([[${oa-url}][json]])
:PROPERTIES:
:OPENALEX: ${id}
:ORCID: ${orcid}
:SCOPUS: ${ids.scopus}
:WORKS_COUNT: ${works_count}
Expand All @@ -459,6 +543,8 @@ ${(oa--elisp-get-bibtex result)}
#+COLUMNS: %25ITEM %YEAR %CITED_BY_COUNT
elisp:org-columns elisp:org-columns-quit
${citations-image}
** Articles
#+caption: Sort
Expand Down

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