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update packages

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Daniel Weschke
2022-01-04 21:35:17 +01:00
parent 1d5275c946
commit 8de00e5202
700 changed files with 42441 additions and 85378 deletions
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lisp/org-ref/org-ref-pubmed.el
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@@ -1,6 +1,6 @@
;;; org-ref-pubmed.el --- Links and functions for Pubmed and NIH databases -*- lexical-binding: t; -*-
;; Copyright (C) 2015 John Kitchin
;; Copyright (C) 2015-2021 John Kitchin
;; Author: John Kitchin <jkitchin@andrew.cmu.edu>
;; Keywords: convenience
@@ -53,15 +53,15 @@
(require 'org)
(require 'org-ref-utils)
(org-ref-link-set-parameters "pmid"
:follow (lambda (link-string) (browse-url (format "http://www.ncbi.nlm.nih.gov/pubmed/%s" link-string)))
:export (lambda (keyword desc format)
(cond
((eq format 'html)
(format "<a href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/mid/%s\">pmid:%s</a>" keyword (or desc keyword))) ; no output for html
((eq format 'latex)
;; write out the latex command
(format "\\url{http://www.ncbi.nlm.nih.gov/pmc/articles/mid/%s}{%s}" keyword (or desc keyword))))))
(org-link-set-parameters "pmid"
:follow (lambda (link-string) (browse-url (format "http://www.ncbi.nlm.nih.gov/pubmed/%s" link-string)))
:export (lambda (keyword desc format)
(cond
((eq format 'html)
(format "<a href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/mid/%s\">pmid:%s</a>" keyword (or desc keyword))) ; no output for html
((eq format 'latex)
;; write out the latex command
(format "\\url{http://www.ncbi.nlm.nih.gov/pmc/articles/mid/%s}{%s}" keyword (or desc keyword))))))
;;** Get MEDLINE metadata
@@ -72,16 +72,15 @@
"Get MEDLINE text for PMID as a string."
(with-current-buffer
(url-retrieve-synchronously
(format "http://www.ncbi.nlm.nih.gov/pubmed/%s/?report=medline&format=text" pmid))
(format "https://pubmed.ncbi.nlm.nih.gov/%s/?format=pubmed" pmid))
(goto-char (point-min))
(let ((p1 (search-forward "<pre>"))
(let ((p1 (search-forward "<pre class=\"article-details\" id=\"article-details\">"))
(p2 (search-forward "</pre>")))
(buffer-substring (+ 1 p1) (- p2 6)))))
(replace-regexp-in-string "
" "" (buffer-substring (+ 1 p1) (- p2 6))))))
;;** Parse the PMID MEDLINE data
;; We can parse this into a data structure.
(defun pubmed-parse-medline (pmid)
"Parse the medline text for PMID and return a list of cons cells."
@@ -153,31 +152,6 @@ You must clean the entry after insertion."
You must clean the entry after insertion."
(interactive "sPMID: ")
(insert (pubmed-pmid-to-bibtex pmid)))
;;** PMID to xml
;; We can also get xml of the MEDLINE data. The web page here also wraps the xml
;; in a <pre> block and escapes the <> with &lt; and &gt;, which we have to
;; undo. I have not used this code for anything, so I am not sure how good the
;; xml code is.
;;;###autoload
(defun pubmed-get-medline-xml (pmid)
"Get MEDLINE xml for PMID as a string."
(interactive)
(with-current-buffer
(url-retrieve-synchronously
(format "http://www.ncbi.nlm.nih.gov/pubmed/%s/?report=xml&format=text" pmid))
(goto-char (point-min))
(while (search-forward "&lt;" nil t)
(replace-match "<"))
(goto-char (point-min))
(while (search-forward "&gt;" nil t)
(replace-match ">"))
(goto-char (point-min))
(let ((p1 (search-forward "<pre>"))
(p2 (search-forward "</pre>")))
(buffer-substring (+ 1 p1) (- p2 6)))))
;;* Pubmed Central (PMC) link
@@ -190,14 +164,14 @@ You must clean the entry after insertion."
;; Here we define a new link. Clicking on it simply opens a webpage to the
;; article.
(org-ref-link-set-parameters "pmcid"
:follow (lambda (link-string) (browse-url (format "http://www.ncbi.nlm.nih.gov/pmc/articles/%s" link-string)))
:export (lambda (keyword desc format)
(cond
((eq format 'html)
(format "<a href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/%s\">pmcid:%s</a>" keyword (or desc keyword)))
((eq format 'latex)
(format "\\url{http://www.ncbi.nlm.nih.gov/pmc/articles/%s}{%s}" keyword (or desc keyword))))))
(org-link-set-parameters "pmcid"
:follow (lambda (link-string) (browse-url (format "http://www.ncbi.nlm.nih.gov/pmc/articles/%s" link-string)))
:export (lambda (keyword desc format)
(cond
((eq format 'html)
(format "<a href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/%s\">pmcid:%s</a>" keyword (or desc keyword)))
((eq format 'latex)
(format "\\url{http://www.ncbi.nlm.nih.gov/pmc/articles/%s}{%s}" keyword (or desc keyword))))))
;;* NIHMSID
@@ -208,15 +182,15 @@ You must clean the entry after insertion."
;; article. Once the Web version of the NIHMS submission is approved for
;; inclusion in PMC and the corresponding citation is in PubMed, the article
;; will also be assigned a PMCID.
(org-ref-link-set-parameters "nihmsid"
:follow (lambda (link-string) (browse-url (format "http://www.ncbi.nlm.nih.gov/pmc/articles/mid/%s" link-string)))
:export (lambda (keyword desc format)
(cond
((eq format 'html)
(format "<a href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/mid//%s\">nihmsid:%s</a>" keyword (or desc keyword)))
((eq format 'latex)
;; write out the latex command
(format "\\url{http://www.ncbi.nlm.nih.gov/pmc/articles/mid/%s}{%s}" keyword (or desc keyword))))))
(org-link-set-parameters "nihmsid"
:follow (lambda (link-string) (browse-url (format "http://www.ncbi.nlm.nih.gov/pmc/articles/mid/%s" link-string)))
:export (lambda (keyword desc format)
(cond
((eq format 'html)
(format "<a href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/mid//%s\">nihmsid:%s</a>" keyword (or desc keyword)))
((eq format 'latex)
;; write out the latex command
(format "\\url{http://www.ncbi.nlm.nih.gov/pmc/articles/mid/%s}{%s}" keyword (or desc keyword))))))
@@ -243,17 +217,17 @@ You must clean the entry after insertion."
(browse-url
(format "http://www.ncbi.nlm.nih.gov/pubmed/?term=%s" (url-hexify-string query))))
(org-ref-link-set-parameters "pubmed-search"
:follow (lambda (query)
"Open QUERY in a `pubmed-simple-search'."
(pubmed-simple-search query))
:export (lambda (query desc format)
(let ((url (format "http://www.ncbi.nlm.nih.gov/pubmed/?term=%s" (url-hexify-string query))))
(cond
((eq format 'html)
(format "<a href=\"%s\">%s</a>" url (or desc (concat "pubmed-search:" query))))
((eq format 'latex)
(format "\\href{%s}{%s}" url (or desc (concat "pubmed-search:" query))))))))
(org-link-set-parameters "pubmed-search"
:follow (lambda (query)
"Open QUERY in a `pubmed-simple-search'."
(pubmed-simple-search query))
:export (lambda (query desc format)
(let ((url (format "http://www.ncbi.nlm.nih.gov/pubmed/?term=%s" (url-hexify-string query))))
(cond
((eq format 'html)
(format "<a href=\"%s\">%s</a>" url (or desc (concat "pubmed-search:" query))))
((eq format 'latex)
(format "\\href{%s}{%s}" url (or desc (concat "pubmed-search:" query))))))))
;; ** Pubmed clinical
@@ -272,20 +246,20 @@ You must clean the entry after insertion."
(browse-url
(format "https://www.ncbi.nlm.nih.gov/pubmed/clinical?term=%s" (url-hexify-string query))))
(org-ref-link-set-parameters "pubmed-clinical"
:follow (lambda (query)
"Open QUERY in a `pubmed-clinical-search'."
(pubmed-clinical-search query))
:export (lambda (query desc format)
(let ((url (format "http://www.ncbi.nlm.nih.gov/pubmed/clinical?term=%s"
(url-hexify-string query))))
(cond
((eq format 'html)
(format "<a href=\"%s\">%s</a>" url
(or desc (concat "pubmed-clinical-search:" query))))
((eq format 'latex)
(format "\\href{%s}{%s}" url
(or desc (concat "pubmed-clinical-search:" query))))))))
(org-link-set-parameters "pubmed-clinical"
:follow (lambda (query)
"Open QUERY in a `pubmed-clinical-search'."
(pubmed-clinical-search query))
:export (lambda (query desc format)
(let ((url (format "http://www.ncbi.nlm.nih.gov/pubmed/clinical?term=%s"
(url-hexify-string query))))
(cond
((eq format 'html)
(format "<a href=\"%s\">%s</a>" url
(or desc (concat "pubmed-clinical-search:" query))))
((eq format 'latex)
(format "\\href{%s}{%s}" url
(or desc (concat "pubmed-clinical-search:" query))))))))