1 ;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10 -*-
2 ;;;; *************************************************************************
3 ;;;; FILE IDENTIFICATION
5 ;;;; Name: pubmed-src.lisp
6 ;;;; Purpose: Library to access PubMed web application
7 ;;;; Programmer: Kevin M. Rosenberg
8 ;;;; Date Started: Jun 2001
12 ;;;; This file, part of cl-pubmed, is Copyright (c) 2002 by Kevin M. Rosenberg
14 ;;;; cl-pubmed users are granted the rights to distribute and use this software
15 ;;;; as governed by the terms of the GNU Lesser General Public License
16 ;;;; (http://www.gnu.org/licenses/lgpl.html)
17 ;;;; *************************************************************************
22 (defparameter +pubmed-host+ "www.ncbi.nlm.nih.gov")
23 (defparameter +pubmed-query-url+ "/entrez/utils/pmqty.fcgi")
24 (defparameter +pubmed-fetch-url+ "/entrez/utils/pmfetch.fcgi")
25 (defparameter *proxy-host* nil)
28 (define-condition pubmed-condition ()
32 (define-condition pubmed-server-error (error pubmed-condition)
33 ((response :initarg :response
35 :reader pubmed-condition-response))
36 (:report (lambda (c stream)
37 (format stream "A PubMed server error occurred.")
38 (awhen (pubmed-condition-response c)
39 (format stream " The server response was:~&~S" it)))))
41 (define-condition pubmed-query-error (error pubmed-condition)
42 ((response :initarg :response
44 :reader pubmed-condition-response))
45 (:report (lambda (c stream)
46 (format stream "A PubMed server error occurred.")
47 (awhen (pubmed-condition-response c)
48 (format stream " The server response was:~&~S" it)))))
50 ;;; Article-Set and Article Classes
52 (defclass pm-article-set ()
53 ((query :type string :initarg :query :accessor articles-query)
54 (articles :type list :initarg :articles :accessor articles)
55 (total :type fixnum :initarg :total :accessor articles-total)
56 (count :type fixnum :initarg :count :accessor articles-count)
57 (start :type fixnum :initarg :start :accessor articles-start))
58 (:documentation "Pubmed Article Set Class")
59 (:default-initargs :total 0 :start 0 :count 0
60 :query nil :articles nil))
62 (defclass pm-article ()
64 (pmid :type integer :accessor article-pmid)
65 (title :type string :accessor article-title)
66 (authors :type list :accessor article-authors)
67 (affiliation :type string :accessor article-affiliation)
68 (journal :type string :accessor article-journal)
69 (date :type string :accessor article-date)
70 (volume :type string :accessor article-volume)
71 (issue :type string :accessor article-issue)
72 (pages :type string :accessor article-pages)
73 (abstract :type string :accessor article-abstract)
74 (mesh-headings :type list :accessor article-mesh-headings))
75 (:documentation "Pubmed Article Class"))
77 (defmethod print-object ((obj pm-article-set) (s stream))
78 (print-unreadable-object (obj s :type t :identity t)
79 (format s "~d total articles, ~d articles starting at #~d"
85 (defmethod print-object ((obj pm-article) (s stream))
86 (print-unreadable-object (obj s :type t :identity t)
87 (format s "pmid:~d, title:~S" (article-pmid obj)
88 (article-title obj))))
90 (defun article-equal-p (a b)
91 (check-type a pm-article)
92 (check-type b pm-article)
93 (eql (article-pmid a) (article-pmid b)))
95 (defun article-ref (art)
96 "Return a string of publication data for an article"
98 (awhen (article-date art)
99 (string-append ref (format nil "~a; " it)))
100 (awhen (article-volume art)
101 (string-append ref it))
102 (awhen (article-issue art)
103 (string-append ref (format nil "(~a)" it)))
104 (awhen (article-pages art)
105 (string-append ref (format nil ":~a" it)))
108 (defmethod print-article-set ((artset pm-article-set)
109 &key (os *standard-output*) (format :text)
110 (complete nil) (print-link nil))
111 "Display an article set to specified stream in specified format"
112 (dotimes (i (articles-count artset) artset)
113 (if (nth i (articles artset))
114 (print-article (nth i (articles artset)) :os os :format format
115 :complete complete :print-link print-link)
116 (princ "NULL Article" os))))
118 (defmethod print-article ((art pm-article) &key (os *standard-output*)
119 (format :text) (complete nil) (print-link nil))
123 (format os "~a~%~a~%~a~a ~a~%~a~%"
125 (list-to-delimited-string (article-authors art) ", ")
126 (aif (article-affiliation art)
127 (format nil "~a~%" it) "")
128 (article-journal art) (article-ref art)
129 (aif (article-abstract art)
132 "Abstract available")
133 "No abstract available")
135 (format os "~a~%" (article-mesh-headings art)))))
137 (let ((has-link (or (article-abstract art) (article-mesh-headings art))))
138 (when (and print-link has-link)
139 (format os "<a href=\"~A\">" (funcall print-link
140 (article-pmid art))))
141 (format os "<div class=\"article-title\">~a</div>~%"
143 (when (and print-link has-link)
145 (format os "<div class=\"article-authors\">~a</div>~%"
146 (list-to-delimited-string (article-authors art) ", "))
147 (format os "<div class=\"article-reference\">~a ~a</div>~%"
148 (article-journal art) (article-ref art))
149 (when (and complete (article-abstract art))
150 (format os "<div class=\"article-abstract\">~a</div>~%"
151 (article-abstract art)))
152 (when (and complete (article-mesh-headings art))
153 (format os "<div class=\"mesh-heading-title\">Mesh Headings:</div>")
154 (dolist (mh (article-mesh-headings art))
155 (format os "<div class=\"mesh-heading\">~a</div>~%" mh)))
156 (format os "<p/>~%"))))
160 ;;; PubMed Query Functions
162 (defun pm-query (searchstr &key maximum start)
163 "Performs PubMed query and fetch and returns article-set structure"
166 (pubmed-search-xml searchstr :maximum maximum :start start)
167 (when (xml-tag-contents "Count" status)
168 (let ((as (make-instance 'pm-article-set)))
170 (articles-total as) (parse-integer (xml-tag-contents "Count" status))
171 (articles-query as) searchstr
172 (articles-start as) (parse-integer (xml-tag-contents "DispStart" status))
173 (articles-count as) (parse-integer (xml-tag-contents "DispMax" status))
174 (articles as) (extract-article-set results))
177 (defun pm-fetch-ids (pmids)
178 "Fetchs list of Pubmed ID's and returns pm-article-set class"
179 (setq pmids (mklist pmids))
180 (let ((results (pubmed-fetch-pmids-xml pmids)))
181 (unless (xml-tag-contents "Error" results)
182 (let ((as (make-instance 'pm-article-set)))
184 (articles-total as) (length pmids)
185 (articles-query as) (list-to-delimited-string pmids #\,)
186 (articles-start as) 0
187 (articles-count as) (length pmids)
188 (articles as) (extract-article-set results))
192 (defun pubmed-search-tree (searchstr &key maximum start)
193 "Performs a pubmed search and returns two values:
194 tree of PubMed search results and tree of PubMed search status"
196 (xml-search-results xml-search-status)
197 (pubmed-search-xml searchstr :maximum maximum :start start)
198 (if xml-search-results
199 (values (parse-xml-no-ws xml-search-results)
200 (parse-xml-no-ws xml-search-status))
201 (values nil (parse-xml-no-ws xml-search-status)))))
203 (defun pubmed-search-xml (searchstr &key maximum start)
204 "Performs a Pubmed search and returns two values:
205 XML string of PubMed search results and XML search status"
207 (pmids search-status)
208 (pubmed-query-xml searchstr :maximum maximum :start start)
209 (values (pubmed-fetch-pmids-xml pmids) search-status)))
211 (defun pubmed-query-xml (searchstr &key maximum start)
212 "Performs a Pubmed search and returns two values:
213 list of PubMed ID's that match search string and XML search status"
214 (let ((search-results (pubmed-query-status searchstr :maximum maximum :start start)))
215 (values (extract-pmid-list search-results) search-results)))
217 (defun pubmed-query-status (searchstr &key start maximum)
218 "Performs a Pubmed search and returns XML results of PubMed search
219 which contains PubMed ID's and status results"
220 (let ((query-alist `(("db" . "m") ("term" . ,searchstr) ("mode" . "xml"))))
221 (when maximum (push (cons "dispmax" maximum) query-alist))
222 (when start (push (cons "dispstart" start) query-alist))
223 (net.aserve.client:do-http-request
224 (format nil "http://~a~a" +pubmed-host+ +pubmed-query-url+)
227 :proxy *proxy-host*)))
229 (defun pubmed-fetch-pmids-xml (pmids)
230 "Fetch articles for a list of PubMed ID's and return XML string"
231 (setq pmids (mklist pmids)) ;; Ensure list
233 (net.aserve.client:do-http-request
234 (format nil "http://~a~a" +pubmed-host+ +pubmed-fetch-url+)
237 `(("db" . "PubMed") ("report" . "xml") ("mode" . "text")
238 ("id" . ,(list-to-delimited-string pmids #\,)))
239 :proxy *proxy-host*)))
241 ;;; XML Extraction Routines
243 (defun extract-article-set (results)
244 "Extract article set from PubMed XML string, return results in pm-article-set class"
245 (multiple-value-bind (as-start as-end as-next)
246 (positions-xml-tag-contents "PubmedArticleSet" results)
247 (declare (ignore as-end as-next))
254 (a-start a-end a-next)
255 (positions-xml-tag-contents "PubmedArticle" results pos)
258 (push (extract-article results a-start a-end) articles)
262 (nreverse articles)))))
264 (defun extract-article (xmlstr a-start a-end)
265 "Extract article contents from PubMed XML string and return results in pm-article class"
266 (let ((article (make-instance 'pm-article)))
268 (article-pmid article) (parse-integer (xml-tag-contents "PMID" xmlstr a-start a-end))
269 (article-title article) (xml-tag-contents "ArticleTitle" xmlstr a-start a-end)
270 (article-journal article) (xml-tag-contents "MedlineTA" xmlstr a-start a-end)
271 (article-pages article) (xml-tag-contents "MedlinePgn" xmlstr a-start a-end)
272 (article-affiliation article) (xml-tag-contents "Affiliation" xmlstr a-start a-end)
273 (article-abstract article) (xml-tag-contents "AbstractText" xmlstr a-start a-end))
274 (multiple-value-bind (ji-start ji-end ji-next)
275 (positions-xml-tag-contents "JournalIssue" xmlstr a-start a-end)
276 (declare (ignore ji-next))
278 (article-volume article) (xml-tag-contents "Volume" xmlstr ji-start ji-end)
279 (article-issue article) (xml-tag-contents "Issue" xmlstr ji-start ji-end))
280 (aif (xml-tag-contents "MedlineDate" xmlstr ji-start ji-end)
281 (setf (article-date article) it)
282 (setf (article-date article)
283 (concatenate 'string (xml-tag-contents "Year" xmlstr ji-start ji-end)
284 (aif (xml-tag-contents "Month" xmlstr ji-start ji-end)
285 (format nil " ~a" it)
288 (multiple-value-bind (al-start al-end al-next)
289 (positions-xml-tag-contents "AuthorList" xmlstr a-start a-end)
290 (declare (ignore al-next))
291 (setf (article-authors article)
298 (au-start au-end au-next)
299 (positions-xml-tag-contents "Author" xmlstr pos al-end)
302 (push (extract-author xmlstr au-start au-end) authors)
305 (nreverse authors)))))
307 (multiple-value-bind (mhl-start mhl-end mhl-next)
308 (positions-xml-tag-contents "MeshHeadingList" xmlstr a-start a-end)
309 (declare (ignore mhl-next))
310 (setf (article-mesh-headings article)
317 (mh-start mh-end mh-next)
318 (positions-xml-tag-contents "MeshHeading" xmlstr pos mhl-end)
321 (push (extract-mesh-heading xmlstr mh-start mh-end) mesh-headings)
325 (nreverse mesh-headings)))))
329 (defun extract-author (xmlstr start end)
330 "Extract author name from XML string"
331 (let ((last-name (xml-tag-contents "LastName" xmlstr start end))
332 (initials (xml-tag-contents "Initials" xmlstr start end)))
333 (concatenate 'string last-name " " initials)))
335 (defun extract-mesh-heading (xmlstr start end)
336 "Extract and format mesh headings from XML string"
337 (let ((desc (xml-tag-contents "DescriptorName" xmlstr start end))
338 (sh (xml-tag-contents "SubHeading" xmlstr start end)))
340 (format nil "~a(~a)" desc sh)
343 (defun extract-pmid-list (results)
344 "Returns list of PubMed ID's from XML result string"
346 ((search "<ERROR>" results)
347 (error 'pubmed-query-error :response results))
348 ((search "<H1>Server Error</H1>" results)
349 (error 'pubmed-server-error :response results))
351 (awhen (xml-tag-contents "Id" results)
352 (delimited-string-to-list it #\space)))))