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openalex.el
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;;; openalex.el --- Org-ref interface to OpenAlex
;;; Commentary:
;; This is an elisp interface to OpenAlex (https://docs.openalex.org/) for org-ref.
;;
;; This provides functionality for the OpenAlex APIs.
;;
;; `oa-query' provides a general interface to all the endpoints with a filter.
;; It is not interactive though.
;;
;; `oa-author' provides an interactive way to search for an author and then see
;; a Google Scholar like org buffer with information about the author.
;;
;; `oa-fulltext-search' provides an interactive full text search of Works in
;; OpenAlex. You get an org-buffer of results, with links to subsequent pages of
;; results.
;;
;; `oa-coa' is an interactive command to generate the NSF COA form data for
;; coauthors.
;;
;; `oa-get-bibtex-entries' is an interactive command to download all bibtex
;; entries from headings in the current buffer with a DOI property.
;;
;; if you have an OpenAlex API you can set `oa-api-key' to use it. The
;; `user-mail-address' value will be added to the queries if it exists so you
;; will get the polite pool.
;;
;; This library extends the `org-ref-citation-hydra' and adds keys to get to
;; cited by, references and related documents in OpenAlex.
(require 'dash)
(require 's)
(require 'request)
(require 'doi-utils)
(require 'org-ref-citation-links)
(declare-function org-ref-possible-bibfiles "org-ref-core")
(declare-function org-ref-find-bibliography "org-ref-core")
(declare-function org-ref-get-bibtex-key-and-file "org-ref-core")
(declare-function bibtex-completion-show-entry "bibtex-completion")
(declare-function bibtex-completion-apa-format-reference "bibtex-completion")
(declare-function ivy-read "ivy")
(defcustom oa-api-key
nil
"Your API key if you have one."
:group 'openalex
:type 'string)
;;; Code:
(defun oa--response-parser ()
"Parse the response from json to elisp."
(let ((json-array-type 'list)
(json-object-type 'plist)
(json-key-type 'keyword)
(json-false nil)
(json-encoding-pretty-print nil))
(json-read)))
(defun oa-get (data query &optional iterable)
"Get fields from DATA with QUERY.
QUERY is a dot notation string.
key1.key2.key3 represents a nested item.
key1.key2[].key3 represents key3 on all items in key1.key2.
Tested with up to two [] in the query.
Assumes data is in plist form."
(let* ((fields (and query (split-string query "\\.")))
(current-field (and fields (pop fields))))
(cond
;; return condition
((null query)
data)
;; query[] means get query then turn iteration on
((and (s-ends-with-p "[]" current-field) (null iterable))
(setq current-field (substring current-field 0 -2))
(oa-get (plist-get data (intern-soft (concat ":" current-field)))
(when fields
(string-join fields "."))
t))
;; this means another level of iteration. You already have a collection. we
;; have to iterate over each one I think.
((and (s-ends-with-p "[]" current-field) iterable)
(setq current-field (substring current-field 0 -2))
(cl-loop for item in data collect
(oa-get (plist-get item (intern-soft (concat ":" current-field)))
(when fields
(string-join fields "."))
t)))
;; single keyword, iterate over collection
(iterable
(oa-get (cl-loop for item in data collect
(plist-get item (intern-soft (concat ":" current-field))))
(when fields
(string-join fields "."))
t))
;; single keyword
(t
(oa-get (plist-get data (intern-soft (concat ":" current-field)))
(when fields
(string-join fields ".")))))))
;; * General query
(defun oa--query-all-data (endpoint &rest filter)
(let* ((page 1)
(url (concat "https://api.openalex.org/" endpoint))
(filter-string (string-join (cl-loop for key in (plist-get-keys filter) collect
(concat (substring (symbol-name key) 1)
":"
(url-hexify-string
(plist-get filter key))))
","))
(params `(("mailto" . ,user-mail-address)
("api_key" . ,oa-api-key)
("filter" . ,filter-string)
("page" . ,page)))
(req (request url :sync t :parser 'oa--response-parser :params params))
(data (request-response-data req))
(meta (plist-get data :meta))
(count (plist-get meta :count))
(per-page (plist-get meta :per_page))
(pages (ceiling (/ (float count) per-page)))
(results (plist-get data :results)))
(cl-loop for i from 2 to pages do
(setf (cdr (assoc "page" params)) i)
(setq req (request purl :sync t :parser 'oa--response-parser :params params)
data (request-response-data req)
results (append results (plist-get data :results))))
results))
(defun oa-query (endpoint &rest filter)
"Run a query at ENDPOINT with FILTER.
ENDPOINT can be works, authors, sources, institutions, concepts,
publishers, or funders.
FILTER is a plist (:field value) where :field is a valid filter
field (see
https://docs.openalex.org/how-to-use-the-api/get-lists-of-entities/filter-entity-lists),
and value is what you want to filter on. The following logic is supported:
!value is negation
<value is less than
>value is greater than
value1+value2 is and within a field
value1|value2 is or within a field
Your email address will be added if `user-mail-address' is
non-nil, and `oa-api-key' if it is non-nil to the API url."
(let* ((page (if (plist-get filter :page)
(prog1
(string-to-number (plist-get filter :page))
(setq filter (org-plist-delete filter :page)))
1))
(base-url "https://api.openalex.org")
(url (concat base-url "/" endpoint "?filter="))
(filter-string (string-join
(cl-loop for key in (plist-get-keys filter) collect
(concat (substring (symbol-name key) 1)
":"
(url-hexify-string
(plist-get filter key))))
","))
(req (request url :sync t :parser 'oa--response-parser
:params `(("mailto" . ,user-mail-address)
("api_key" . ,oa-api-key)
("filter" . ,filter-string)
("page" . ,page))))
(data (request-response-data req))
(meta (plist-get data :meta))
(count (plist-get meta :count))
(per-page (plist-get meta :per_page))
(pages (ceiling (/ (float count) per-page)))
(results (plist-get data :results))
(next-page (format "[[elisp:(oa-query \"%s\" %s :page \"%s\")][Next page: %s]]"
endpoint
(string-join (cl-loop for x in filter
collect
(if (keywordp x)
(format "%s" x)
(format "%S" x)))
" ")
(+ page 1)
(+ page 1)))
(buf (generate-new-buffer "*OpenAlex - Query*")))
(with-current-buffer buf
(erase-buffer)
(org-mode)
(insert (concat
(format "#+title: %s
** Results
:PROPERTIES:
:FILTER: %s
:COUNT: %s
:END:
%s
\n\n"
filter-string
filter-string
count
next-page)
(cond
((string= endpoint "works")
(string-join
(cl-loop for wrk in results collect
(s-format "*** ${title}
:PROPERTIES:
:HOST: ${primary_location.source.display_name}
:YEAR: ${publication_year}
:CITED_BY_COUNT: ${cited_by_count}
:AUTHOR: ${authors}
:DOI: ${doi}
:OPENALEX: ${id}
:CREATED_DATE: ${created_date}
:END:
${get-bibtex}
- ${oa-refs}
- ${oa-related}
- ${oa-cited}
${abstract}
"
(lambda (key data)
(or (cdr (assoc key data)) ""))
`(("title" . ,(oa--title wrk))
("primary_location.source.display_name" . ,(oa-get wrk "primary_location.source.display_name"))
("publication_year" . ,(oa-get wrk "publication_year"))
("cited_by_count" . ,(oa-get wrk "cited_by_count"))
("authors" . ,(oa--authors wrk))
("doi" . ,(oa-get wrk "doi"))
("id" . ,(oa-get wrk "id"))
("created_date" . ,(oa-get wrk "created_date"))
("get-bibtex" . ,(oa--elisp-get-bibtex wrk))
("oa-refs" . ,(oa--elisp-get-oa-refs wrk))
("oa-related" . ,(oa--elisp-get-oa-related wrk))
("oa-cited" . ,(oa--elisp-get-oa-cited-by wrk))
("abstract" . ,(oa--abstract wrk)))))
"\n"))
(t
(format "%s" results)
)))))
(pop-to-buffer buf)
(goto-char (point-min))))
;; * Work object
(defun oa--work (entity-id &optional filter)
"Retrieve json data for a Work object for ENTITY-ID.
ENTITY-ID is an OpenAlex ID, DOI, Pubmed id,etc.
ENTITY-ID may also be a list of ids with a filter.
If FILTER is non-nil it should be a string like \"filter=openalex:\"
https://docs.openalex.org/api-entities/works"
(let* ((url (concat "https://api.openalex.org/works"
;; This is hackier than I prefer, but sometimes entity-id
;; is nil, or starts with ? for a filter, and I couldn't
;; see a cleaner way to solve this. this function is used
;; in a lot of places.
(cond
((string-prefix-p "?" entity-id)
entity-id)
(t
(format "/%s" entity-id)))))
(req (request url :sync t :parser 'oa--response-parser
:params `(("mailto" . ,user-mail-address)
("api_key" . ,oa-api-key)
("filter" . ,filter))))
(data (request-response-data req)))
;; 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))
;; * autocomplete works
(defun oa--works-candidates (query)
"Retrieve autocomplete works from OpenAlex."
(or
(ivy-more-chars)
(let* ((url "https://api.openalex.org/autocomplete/works")
(req (request url :sync t :parser 'oa--response-parser
:params `(("mailto" . ,user-mail-address)
("api_key" . ,oa-api-key)
("q" . ,query))))
(data (request-response-data req))
(results (plist-get data :results)))
(cl-loop for work in results collect
(propertize
(format "%s, %s"
(plist-get work :display_name)
(plist-get work :hint))
'oaid (plist-get work :id))))))
(defun oa-works ()
"Autocomplete works.
This doesn't seem as useful as it could be."
(interactive)
(ivy-read "Work: " #'oa--works-candidates
:dynamic-collection t
:action
'(1
("o" (lambda (candidate)
(browse-url (get-text-property 0 'oaid candidate)))
"Open in browser"))))
;; * Viewing works
;; ** help functions for complex data
;;
;; Some things like authors need to be constructed, and cannot just be looked
;; up. In other cases, I want logic, e.g. if data is there provide something,
;; and if not return an empty string. These functions do that work.
(defun oa--authors (wrk)
"Return an author string for WRK.
The string is a comma-separated list of links to author pages in OpenAlex."
(s-join ", " (cl-loop for author in (plist-get wrk :authorships)
collect
(format "[[elisp:(oa--author-org \"%s\")][%s]]"
(plist-get
(plist-get author :author)
:id)
(plist-get
(plist-get author :author)
:display_name)))))
(defun oa--title (wrk)
"Return a title from WRK with linebreaks removed."
(string-replace "\n" " " (plist-get wrk :title)))
;; I want some links if they can be made so the buffer is interactive. It might
;; be nice to integrate M-, navigation.
(defun oa--elisp-get-bibtex (wrk)
"Return a elisp link to get a bibtex entry for WRK if there is a doi."
(if-let ((doi (plist-get wrk :doi)))
(format "[[elisp:(doi-add-bibtex-entry \"%s\")][Get bibtex entry]]" doi)
""))
(defun oa--elisp-get-oa-related (wrk)
"Return a elisp link to get related works for WRK."
(format "[[elisp:(progn (xref--push-markers (current-buffer) (point)) (oa--related-works \"%s\"))][Get related work (%s)]]"
(plist-get wrk :id)
(length (plist-get wrk :related_works))))
(defun oa--elisp-get-oa-refs (wrk)
"Return a elisp link to get references for WRK."
(format "[[elisp:(progn (xref--push-markers (current-buffer) (point)) (oa--referenced-works \"%s\"))][Get references (%s)]]"
(plist-get wrk :id)
(length (plist-get wrk :referenced_works))))
(defun oa--elisp-get-oa-cited-by (wrk)
"Return a elisp link to get works that cite WRK."
(format "[[elisp:(progn (xref--push-markers (current-buffer) (point)) (oa--cited-by-works \"%s\"))][Get cited by (%s)]]"
(plist-get wrk :id)
(plist-get wrk :cited_by_count)))
(defun oa--works-entries (works)
"Return a list of org-formatted entries in WORKS.
WORKS is a list of results from OpenAlex."
(cl-loop for wrk in (plist-get works :results)
collect
(s-format "** ${title}
:PROPERTIES:
:HOST: ${primary_location.source.display_name}
:YEAR: ${publication_year}
:CITED_BY_COUNT: ${cited_by_count}
:AUTHOR: ${authors}
:DOI: ${doi}
:OPENALEX: ${id}
:END:
${get-bibtex}
- ${oa-refs}
- ${oa-related}
- ${oa-cited}
"
(lambda (key data)
(or (cdr (assoc key data)) ""))
`(("title" . ,(oa-get wrk "title"))
("primary_location.source.display_name" . ,(oa-get wrk "primary_location.source.display_name"))
("publication_year" . ,(oa-get wrk "publication_year"))
("cited_by_count" . ,(oa-get wrk "cited_by_count"))
("authors" . ,(oa--authors wrk))
("doi" . ,(oa-get wrk "doi"))
("id" . ,(oa-get wrk "id"))
("get-bibtex" . ,(oa--elisp-get-bibtex wrk))
("oa-refs" . ,(oa--elisp-get-oa-refs wrk))
("oa-related" . ,(oa--elisp-get-oa-related wrk))
("oa-cited" . ,(oa--elisp-get-oa-cited-by wrk))))))
(defun oa--works-buffer (bufname header entries)
"Create an org-buffer with BUFNAME representing the results in WORKS.
HEADER is the first thing in the buffer
WORKS is usually a list of results from OpenAlex.
Argument ENTRIES A list of strings for each org entry."
(let ((buf (get-buffer-create bufname)))
(with-current-buffer buf
(erase-buffer)
(insert header)
(insert "#+COLUMNS: %25ITEM %YEAR %CITED_BY_COUNT
elisp:org-columns elisp:org-columns-quit
#+caption: Sort
| year | [[elisp:(oa-buffer-sort-year t)][old first]] | [[elisp:(oa-buffer-sort-year)][new first]] |
| cited by | [[elisp:(oa-buffer-sort-cited-by-count t)][low first]] | [[elisp:(oa-buffer-sort-cited-by-count)][high first]] |
")
(insert (s-join "\n" entries))
(org-mode)
(goto-char (point-min))
(org-next-visible-heading 1))
;; (display-buffer-in-side-window buf '((side . right)))
(pop-to-buffer buf)))
(defun oa--related-works (entity-id)
"Show the Related works buffer for ENTITY-ID."
(let* ((wrk (oa--work entity-id))
(related-work (plist-get wrk :related_works))
split
entries)
(while related-work
(setq split (-split-at 25 related-work)
related-work (nth 1 split))
;; split is what we process now
(setq entries (append entries
(oa--works-entries
(oa--work (format "?filter=openalex:%s" (s-join "|" (nth 0 split))))))))
(oa--works-buffer
"*OpenAlex - Related works*"
(format "* OpenAlex - Related works for %s ([[%s][json]])
%s\n\n"
entity-id
(plist-get wrk :oa-url)
(s-format ":PROPERTIES:
:TITLE: ${title}
:HOST: ${primary_location.source.display_name}
:AUTHOR: ${authors}
:DOI: ${doi}
:YEAR: ${publication_year}
:OPENALEX: ${id}
:END:
Found ${nentries} results.
"
(lambda (key data)
(or (cdr (assoc key data)) ""))
`(("title" . ,(oa-get wrk "title"))
("primary_location.source.display_name" . ,(oa-get wrk "primary_location.source.display_name"))
("authors" . ,(oa--authors wrk))
("doi" . ,(oa-get wrk "doi"))
("publication_year" . ,(oa-get wrk "publication_year"))
("id" . ,(oa-get wrk "id"))
("nentries" . ,(length entries)))))
entries)))
(defun oa--referenced-works (entity-id)
"Show the Referenced work for ENTITY-ID."
(let* ((wrk (oa--work entity-id))
(referenced-work (plist-get wrk :referenced_works))
split
(entries '()))
(while referenced-work
(setq split (-split-at 25 referenced-work)
referenced-work (nth 1 split))
;; split is what we process now
(setq entries (append entries
(oa--works-entries
(oa--work (format "?filter=openalex:%s"
(s-join "|" (nth 0 split))))))))
(oa--works-buffer
"*OpenAlex - References*"
(format "* OpenAlex - References from %s ([[%s][json]])
%s\n\n"
entity-id
(plist-get wrk :oa-url)
(s-format ":PROPERTIES:
:TITLE: ${title}
:HOST: ${primary_location.source.display_name}
:AUTHOR: ${authors}
:DOI: ${doi}
:YEAR: ${publication_year}
:OPENALEX: ${id}
:END:
Found ${nentries} results.
"
(lambda (key data)
(or (cdr (assoc key data)) ""))
`(("title" . ,(oa-get wrk "title"))
("primary_location.source.display_name" . ,(oa-get wrk "primary_location.source.display_name"))
("authors" . ,(oa--authors wrk))
("doi" . ,(oa-get wrk "doi"))
("publication_year" . ,(oa-get wrk "publication_year"))
("id" . ,(oa-get wrk "id"))
("nentries" . ,(length entries)))))
entries)))
;; This function is different than the previous two. First we follow a URL
;; provided by the data, and second, here we do follow pages.
(defun oa--cited-by-works (entity-id)
"Show the Cited by buffer for ENTITY-ID."
(let* ((wrk (oa--work entity-id))
(url (plist-get wrk :cited_by_api_url))
(cited-by-works (request-response-data
(request url
:sync t
:parser 'oa--response-parser
:params `(("mailto" . ,user-mail-address)
("api_key" . ,oa-api-key)))))
(count (plist-get (plist-get cited-by-works :meta) :count))
(per-page (plist-get (plist-get cited-by-works :meta) :per_page))
(entries '())
(page 2))
;; get first page
(setq entries (oa--works-entries cited-by-works))
(while (> count (* per-page (- page 1)))
(setq cited-by-works (request-response-data
(request url
:sync t
:parser 'oa--response-parser
:params `(("mailto" . ,user-mail-address)
("api_key" . ,oa-api-key)
("page" . ,page)))))
(setq entries (append entries (oa--works-entries cited-by-works)))
(cl-incf page))
(oa--works-buffer
"*OpenAlex - Cited by*"
(format "* OpenAlex - %s Cited by ([[%s][json]])
%s"
entity-id
url
(s-format ":PROPERTIES:
:TITLE: ${title}
:HOST: ${primary_location.source.display_name}
:AUTHOR: ${authors}
:DOI: ${doi}
:YEAR: ${publication_year}
:OPENALEX: ${id}
:END:
Found ${nentries} results.
"
(lambda (key data)
(or (cdr (assoc key data)) ""))
`(("title" . ,(oa-get wrk "title"))
("primary_location.source.display_name" . ,(oa-get wrk "primary_location.source.display_name"))
("authors" . ,(oa--authors wrk))
("doi" . ,(oa-get wrk "doi"))
("publication_year" . ,(oa-get wrk "publication_year"))
("id" . ,(oa-get wrk "id"))
("nentries" . ,(length entries)))))
entries)))
;; ** buffer utilities for sorting entries
(defun oa-buffer-sort-year (&optional ascending)
"Sort org headings by year in descending order (new to old).
With prefix arg ASCENDING, sort in ascending order (old to new)"
(interactive "P")
(if ascending
(org-sort-entries nil ?f
(lambda () (string-to-number (or (org-entry-get (point) "YEAR") "0")))
(lambda (y1 y2)
(< y1 y2)))
(org-sort-entries nil ?f
(lambda () (string-to-number (or (org-entry-get (point) "YEAR") "0")))
(lambda (y1 y2)
(> y1 y2))))
(org-fold-show-all))
(defun oa-buffer-sort-cited-by-count (&optional ascending)
"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
(org-sort-entries nil ?f
(lambda ()
(string-to-number
(or (org-entry-get (point) "CITED_BY_COUNT")
"0")))
#'<)
(org-sort-entries nil ?f
(lambda ()
(string-to-number
(or
(org-entry-get (point) "CITED_BY_COUNT")
"0")))
#'>))
(org-fold-show-all))
;; * Interactive versions for org-ref citations
(defun oa-related-works ()
"Open the side window for Related works on cite at point."
(interactive)
(oa--related-works (concat "https://doi.org/" (org-ref-get-doi-at-point))))
(defun oa-referenced-works ()
"Open the side window for References from the cite at point."
(interactive)
(oa--referenced-works (concat "doi:" (org-ref-get-doi-at-point))))
(defun oa-cited-by-works ()
"Open the side window for Citing works for the cite at point."
(interactive)
(oa--cited-by-works (concat "doi:" (org-ref-get-doi-at-point))))
(defun oa-open ()
"Open the cite at point in OpenAlex."
(interactive)
(let* ((url (concat
"https://api.openalex.org/works/https://doi.org/"
(org-ref-get-doi-at-point)))
(req (request url :sync t :parser 'oa--response-parser))
(data (request-response-data req)))
(browse-url (plist-get data :id))))
(defhydra+ org-ref-citation-hydra ()
"Add open from action to `org-ref-citation-hydra'."
("xa" oa-open "Open in OpenAlex" :column "OpenAlex")
("xr" oa-related-works "Related documents" :column "OpenAlex")
("xc" oa-cited-by-works "Cited by documents" :column "OpenAlex")
("xf" oa-referenced-works "References from" :column "OpenAlex"))
;; * Author object
(defun oa--author (entity-id &optional filter)
"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"
entity-id))
(req (request url :sync t :parser 'oa--response-parser
:params `(("mailto" . ,user-mail-address)
("api_key" . ,oa-api-key)
("filter" . ,filter))))
(data (request-response-data req)))
;; this is for convenience to inspect data in a browser.
(plist-put data :oa-url url)
data))
(defun oa--author-entries (works-data url)
"Get entries from WORKS-DATA."
(let* ((meta (plist-get works-data :meta))
(per-page (plist-get meta :per_page))
(count (plist-get meta :count))
(pages (/ count per-page))
(entries '())
purl)
;; if there is a remainder we need to get the rest
(when (> (mod count per-page) 0) (cl-incf pages))
;; Now we have to loop through the pages
(cl-loop for i from 1 to pages
do
(setq works-data (request-response-data
(request url
:sync t
:parser 'oa--response-parser
:params `(("mailto" . ,user-mail-address)
("api_key" . ,oa-api-key)
("page" . ,i))))
entries (append entries
(cl-loop for result in (plist-get works-data :results)
collect
(s-format "*** ${title}
:PROPERTIES:
:ID: ${id}
:DOI: ${ids.doi}
:PDF: ${primary_location.pdf_url}
:LANDING_PAGE: ${primary_location.landing_page_url}
:YEAR: ${publication_year}
:HOST_VENUE: ${primary_location.source.display_name}
:AUTHORS: ${authors}
:CITED_BY_COUNT: ${cited_by_count}
:END:
${get-bibtex}
- ${oa-refs}
- ${oa-related}
- ${oa-cited}
${abstract}
" (lambda (key data)
(or (cdr (assoc key data)) ""))
`(("title" . ,(oa--title result))
("id" . ,(oa-get result "id"))
("ids.doi" . ,(oa-get result "ids.doi"))
("publication_year" . ,(oa-get result "publication_year"))
("primary_location.pdf_url" . ,(oa-get result "primary_location.pdf_url"))
("primary_location.landing_page_url" . ,(oa-get result "primary_location.landing_page_url"))
("primary_location.source.display_name" . ,(oa-get result "primary_location.source.display_name"))
("authors" . ,(oa--authors result))
("cited_by_count" . ,(oa-get result "cited_by_count"))
("get-bibtex" . ,(oa--elisp-get-bibtex result))
("oa-refs" . ,(oa--elisp-get-oa-refs result))
("oa-related" . ,(oa--elisp-get-oa-related result))
("oa-cited" . ,(oa--elisp-get-oa-cited-by result))
("abstract" . ,(oa--abstract result))))))))
entries))
(defun oa--abstract (wrk)
"Construct an abstract from a WRK."
(let* ((aii (plist-get wrk :abstract_inverted_index))
(word_index '())
sorted)
(cl-loop for (k v) on aii by 'cddr
do
(cl-loop for index in v
do
(push (list k index) word_index)))
(setq sorted (sort
word_index
(lambda (a b)
(<
(nth 1 a)
(nth 1 b)))))
(string-join (mapcar
(lambda (x)
(substring
(symbol-name (car x))
1))
sorted)
" ")))
(defun oa--author-candidates (query)
"Retrieve autocomplete authors from OpenAlex."
(or
(ivy-more-chars)
(let* ((url "https://api.openalex.org/autocomplete/authors")
(req (request url :sync t :parser 'oa--response-parser
:params `(("mailto" . ,user-mail-address)
("api_key" . ,oa-api-key)
("q" . ,query))))
(data (request-response-data req))
(results (plist-get data :results)))
(cl-loop for author in results collect
(propertize
(format "%s - %s"
(plist-get author :display_name)
(plist-get
author :hint))
'oaid (plist-get author :id))))))
(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\"
set y2tics nomirror
set key left top
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))
(shell-command shellcmd)
(delete-file cmdfile)
(format "[[%s]]" pngfile))
"Gnuplot required to see citation graph. Please install it."))
(defun oa--author-org (entity-id)
"Generate an org-buffer for an author with ENTITY-ID."
(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
(request works-url
:sync t
:parser 'oa--response-parser
:params `(("mailto" . ,user-mail-address)
("api_key" . ,oa-api-key))))))
(with-current-buffer buf
(erase-buffer)
(insert (s-format "* ${display_name} ([[${oa-url}][json]])
:PROPERTIES:
:OPENALEX: ${id}
:ORCID: ${orcid}
:SCOPUS: ${ids.scopus}
:WORKS_COUNT: ${works_count}
:CITED_BY_COUNT: ${cited_by_count}
:INSTITUTION: ${last_known_institution.display_name}, ${last_known_institution.country_code}
:END:
#+COLUMNS: %25ITEM %YEAR %CITED_BY_COUNT
elisp:org-columns elisp:org-columns-quit
${citations-image}
** Articles
#+caption: Sort
| year | [[elisp:(oa-buffer-sort-year t)][old first]] | [[elisp:(oa-buffer-sort-year)][new first]] |
| cited by | [[elisp:(oa-buffer-sort-cited-by-count t)][low first]] | [[elisp:(oa-buffer-sort-cited-by-count)][high first]] |
"
(lambda (key data)
(or (cdr (assoc key data)) ""))
`(("display_name" . ,(oa-get data "display_name"))
("oa-url" . ,(oa-get data "oa-url"))
("id" . ,(oa-get data "id"))
("orcid" . ,(oa-get data "orcid"))
("ids.scopus" . ,(oa-get data "ids.scopus"))
("works_count" . ,(oa-get data "works_count"))
("last_known_institution.display_name" . ,(oa-get data "last_known_institution.display_name"))
("last_known_institution.country_code" . ,(oa-get data "last_known_institution.country_code"))
("citations-image" . ,citations-image))))
(insert (s-join "\n" (oa--author-entries works-data works-url)))
(org-mode)
(goto-char (point-min))
(org-next-visible-heading 1))
(pop-to-buffer buf)))
(defun oa-author ()
"Get data and act on it for an author."
(interactive)
(ivy-read "Author: " #'oa--author-candidates
:dynamic-collection t
:action
'(1
("o" (lambda (candidate)
(oa--author-org (get-text-property 0 'oaid candidate)))
"Open org file")
("l" (lambda (candidate)
(insert (format "[[%s][%s]]"
(get-text-property 0 'oaid candidate)
candidate))))
("u" (lambda (candidate)
(browse-url (get-text-property 0 'oaid candidate)))
"Open in browser"))))
;; * Full text search
(defun oa-fulltext-search (query &optional page)
"Perform a fulltext search on QUERY.
PAGE is optional, and loads that page of results. Defaults to 1."
(interactive (list (read-string "Query: ")
nil))
(when (null page) (setq page 1))
(let* ((url "https://api.openalex.org/works")
(req (request url
:sync t
:parser #'oa--response-parser
:params `(("mailto" . ,user-mail-address)
("api_key" . ,oa-api-key)
("page" . ,page)
("filter" . ,(format "fulltext.search:%s" query)))))
(data (request-response-data req))
(metadata (plist-get data :meta))
(count (plist-get metadata :count))
(per-page (plist-get metadata :per_page))
(npages (+ (/ count per-page) (if (= 0 (mod count per-page)) 0 1)))
(results (plist-get data :results))
(next-page (format "[[elisp:(oa-fulltext-search \"%s\" %s)][Next page: %s of %s]]"
query
(+ page 1)
(+ page 1)
npages))
(buf (get-buffer-create "*OpenAlex Full-text search*")))
(with-current-buffer buf
(erase-buffer)
(org-mode)
(insert (s-format "#+title: Full-text search: ${query}
[[elisp:(oa-fulltext-search \"${query}\" ${page})]]"
'aget
`(("query" . ,query)
("page" . ,page))))
(insert (s-format
"
${meta.count} results: Page ${meta.page} of ${s1} ${s2}
\n\n"
(lambda (key data)
(or (cdr (assoc key data)) ""))
`(("meta.page" . ,(oa-get data "meta.page"))
("s1" . ,(format "%s" npages))
("s2" . ,(format "%s" next-page)))))
(insert
(cl-loop for result in results concat
(s-format "* ${title}
:PROPERTIES:
:JOURNAL: ${primary_location.source.display_name}
:AUTHOR: ${authors}
:YEAR: ${publication_year}
:OPENALEX: ${id}
:DOI: ${ids.doi}
:END:
${get-bibtex}
- ${oa-refs}
- ${oa-related}
- ${oa-cited}
" (lambda (key data)
(or (cdr (assoc key data)) ""))
`(("title" . ,(oa--title result))
("primary_location.source.display_name" . ,(oa-get result "primary_location.source.display_name"))
("authors" . ,(oa--authors result))
("publication_year" . ,(oa-get result "publication_year"))
("id" . ,(oa-get result "id"))
("ids.doi" . ,(oa-get result "ids.doi"))