--- /dev/null
+;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10 -*-
+;;;; *************************************************************************
+;;;; FILE IDENTIFICATION
+;;;;
+;;;; Name: pubmed-src.lisp
+;;;; Purpose: Library to access PubMed web application
+;;;; Programmer: Kevin M. Rosenberg
+;;;; Date Started: Jun 2001
+;;;;
+;;;; $Id: pubmed-src.lisp,v 1.1 2003/06/06 22:04:05 kevin Exp $
+;;;;
+;;;; This file, part of cl-pubmed, is Copyright (c) 2002 by Kevin M. Rosenberg
+;;;;
+;;;; cl-pubmed users are granted the rights to distribute and use this software
+;;;; as governed by the terms of the GNU Lesser General Public License
+;;;; (http://www.gnu.org/licenses/lgpl.html)
+;;;; *************************************************************************
+
+(in-package #:pubmed)
+
+
+(defparameter +pubmed-host+ "www.ncbi.nlm.nih.gov")
+(defparameter +pubmed-query-url+ "/entrez/utils/pmqty.fcgi")
+(defparameter +pubmed-fetch-url+ "/entrez/utils/pmfetch.fcgi")
+
+
+(define-condition pubmed-condition ()
+ ())
+
+
+(define-condition pubmed-server-error (error pubmed-condition)
+ ((response :initarg :response
+ :initform nil
+ :reader pubmed-server-error-response))
+ (:report (lambda (c stream)
+ (format stream "A PubMed server error occurred.")
+ (awhen (pubmed-server-error-response c)
+ (format stream " The server response was:~&~S" it)))))
+
+(define-condition pubmed-query-error (error pubmed-condition)
+ ((response :initarg :response
+ :initform nil
+ :reader pubmed-query-error-response))
+ (:report (lambda (c stream)
+ (format stream "A PubMed server error occurred.")
+ (awhen (pubmed-query-error-response c)
+ (format stream " The server response was:~&~S" it)))))
+
+;;; Article-Set and Article Classes
+
+(defclass pm-article-set ()
+ ((query :type string :initarg :query :accessor articles-query)
+ (articles :type list :initarg :articles :accessor articles)
+ (total :type fixnum :initarg :total :accessor articles-total)
+ (count :type fixnum :initarg :count :accessor articles-count)
+ (start :type fixnum :initarg :start :accessor articles-start))
+ (:documentation "Pubmed Article Set Class")
+ (:default-initargs :total 0 :start 0 :count 0
+ :query nil :articles nil))
+
+(defclass pm-article ()
+ (
+ (pmid :type integer :accessor article-pmid)
+ (title :type string :accessor article-title)
+ (authors :type list :accessor article-authors)
+ (affiliation :type string :accessor article-affiliation)
+ (journal :type string :accessor article-journal)
+ (date :type string :accessor article-date)
+ (volume :type string :accessor article-volume)
+ (issue :type string :accessor article-issue)
+ (pages :type string :accessor article-pages)
+ (abstract :type string :accessor article-abstract)
+ (mesh-headings :type list :accessor article-mesh-headings))
+ (:documentation "Pubmed Article Class"))
+
+(defmethod print-object ((obj pm-article-set) (s stream))
+ (print-unreadable-object (obj s :type t :identity t)
+ (format s "~d total articles, ~d articles starting at #~d"
+ (articles-total obj)
+ (articles-count obj)
+ (articles-start obj)
+ )))
+
+(defmethod print-object ((obj pm-article) (s stream))
+ (print-unreadable-object (obj s :type t :identity t)
+ (format s "pmid:~d, title:~S" (article-pmid obj)
+ (article-title obj))))
+
+(defun article-equal-p (a b)
+ (check-type a pm-article)
+ (check-type b pm-article)
+ (eql (article-pmid a) (article-pmid b)))
+
+(defun article-ref (art)
+ "Return a string of publication data for an article"
+ (let ((ref ""))
+ (awhen (article-date art)
+ (string-append ref (format nil "~a; " it)))
+ (awhen (article-volume art)
+ (string-append ref it))
+ (awhen (article-issue art)
+ (string-append ref (format nil "(~a)" it)))
+ (awhen (article-pages art)
+ (string-append ref (format nil ":~a" it)))
+ ref))
+
+(defmethod print-article-set ((artset pm-article-set) &key (os *standard-output*) (format :text)
+ (complete nil) (print-link t))
+ "Display an article set to specified stream in specified format"
+ (dotimes (i (articles-count artset))
+ (print-article (nth i (articles artset)) :os os :format format
+ :complete complete :print-link print-link))
+ artset)
+
+(defmethod print-article ((art pm-article) &key (os *standard-output*)
+ (format :text) (complete nil) (print-link t))
+ "Display an article"
+ (ecase format
+ (:text
+ (format os "~a~%~a~%~a~a ~a~%~a~%"
+ (article-title art)
+ (list-to-delimited-string (article-authors art) ", ")
+ (aif (article-affiliation art)
+ (format nil "~a~%" it) "")
+ (article-journal art) (article-ref art)
+ (aif (article-abstract art)
+ (if complete
+ it
+ "Abstract available")
+ "No abstract available")
+ (when complete
+ (format os "~a~%" (article-mesh-headings art)))))
+ (:html
+ (let ((has-link (or (article-abstract art) (article-mesh-headings art))))
+ (when (and print-link has-link)
+ (format os "<a href=\"~a?key=~a\">" (make-url "print-article") (article-pmid art)))
+ (format os "<div class=\"article-title\">~a</div>~%" (article-title art))
+ (when (and print-link has-link)
+ (format os "</a>"))
+ (format os "<div class=\"article-authors\">~a</div>~%"
+ (list-to-delimited-string (article-authors art) ", "))
+ (format os "<div class=\"article-reference\">~a ~a</div>~%"
+ (article-journal art) (article-ref art))
+ (when (and complete (article-abstract art))
+ (format os "<div class=\"article-abstract\">~a</div>~%"
+ (article-abstract art)))
+ (when (and complete (article-mesh-headings art))
+ (format os "<div class=\"mesh-heading-title\">Mesh Headings:</div>")
+ (dolist (mh (article-mesh-headings art))
+ (format os "<div class=\"mesh-heading\">~a</div>~%" mh)))
+ (format os "<p/>~%"))))
+ art)
+
+
+;;; PubMed Query Functions
+
+(defun pm-query (searchstr &key maximum start)
+ "Performs PubMed query and fetch and returns article-set structure"
+ (multiple-value-bind
+ (results status)
+ (pubmed-search-xml searchstr :maximum maximum :start start)
+ (when (xml-tag-contents "Count" status)
+ (let ((as (make-instance 'pm-article-set)))
+ (setf
+ (articles-total as) (parse-integer (xml-tag-contents "Count" status))
+ (articles-query as) searchstr
+ (articles-start as) (parse-integer (xml-tag-contents "DispStart" status))
+ (articles-count as) (parse-integer (xml-tag-contents "DispMax" status))
+ (articles as) (extract-article-set results))
+ as))))
+
+(defun pm-fetch-ids (pmids)
+ "Fetchs list of Pubmed ID's and returns pm-article-set class"
+ (setq pmids (mklist pmids))
+ (let ((results (pubmed-fetch-pmids-xml pmids)))
+ (unless (xml-tag-contents "Error" results)
+ (let ((as (make-instance 'pm-article-set)))
+ (setf
+ (articles-total as) (length pmids)
+ (articles-query as) (list-to-delimited-string pmids #\,)
+ (articles-start as) 0
+ (articles-count as) (length pmids)
+ (articles as) (extract-article-set results))
+ as))))
+
+#+ignore
+(defun pubmed-search-tree (searchstr &key maximum start)
+ "Performs a pubmed search and returns two values:
+tree of PubMed search results and tree of PubMed search status"
+ (multiple-value-bind
+ (xml-search-results xml-search-status)
+ (pubmed-search-xml searchstr :maximum maximum :start start)
+ (if xml-search-results
+ (values (parse-xml-no-ws xml-search-results)
+ (parse-xml-no-ws xml-search-status))
+ (values nil (parse-xml-no-ws xml-search-status)))))
+
+(defun pubmed-search-xml (searchstr &key maximum start)
+ "Performs a Pubmed search and returns two values:
+XML string of PubMed search results and XML search status"
+ (multiple-value-bind
+ (pmids search-status)
+ (pubmed-query-xml searchstr :maximum maximum :start start)
+ (values (pubmed-fetch-pmids-xml pmids) search-status)))
+
+(defun pubmed-query-xml (searchstr &key maximum start)
+ "Performs a Pubmed search and returns two values:
+ list of PubMed ID's that match search string and XML search status"
+ (let ((search-results (pubmed-query-status searchstr :maximum maximum :start start)))
+ (values (extract-pmid-list search-results) search-results)))
+
+(defun pubmed-query-status (searchstr &key start maximum)
+ "Performs a Pubmed search and returns XML results of PubMed search
+ which contains PubMed ID's and status results"
+ (let ((query-alist `(("db" . "m") ("term" . ,searchstr) ("mode" . "xml"))))
+ (when maximum (push (cons "dispmax" maximum) query-alist))
+ (when start (push (cons "dispstart" start) query-alist))
+ (net.aserve.client:do-http-request
+ (format nil "http://~a~a" +pubmed-host+ +pubmed-query-url+)
+ :method :get
+ :query query-alist)))
+
+(defun pubmed-fetch-pmids-xml (pmids)
+ "Fetch articles for a list of PubMed ID's and return XML string"
+ (setq pmids (mklist pmids)) ;; Ensure list
+ (when pmids
+ (net.aserve.client:do-http-request
+ (format nil "http://~a~a" +pubmed-host+ +pubmed-fetch-url+)
+ :method :get
+ :query
+ `(("db" . "PubMed") ("report" . "xml") ("mode" . "text")
+ ("id" . ,(list-to-delimited-string pmids #\,))))))
+
+;;; XML Extraction Routines
+
+(defun extract-article-set (results)
+ "Extract article set from PubMed XML string, return results in pm-article-set class"
+ (multiple-value-bind (as-start as-end as-next)
+ (positions-xml-tag-contents "PubmedArticleSet" results)
+ (declare (ignore as-end as-next))
+ (when as-start
+ (let ((done nil)
+ (articles '())
+ (pos as-start))
+ (until done
+ (multiple-value-bind
+ (a-start a-end a-next)
+ (positions-xml-tag-contents "PubmedArticle" results pos)
+ (if a-start
+ (progn
+ (push (extract-article results a-start a-end) articles)
+ (setq pos a-next)
+ )
+ (setq done t))))
+ (nreverse articles)))))
+
+(defun extract-article (xmlstr a-start a-end)
+ "Extract article contents from PubMed XML string and return results in pm-article class"
+ (let ((article (make-instance 'pm-article)))
+ (setf
+ (article-pmid article) (parse-integer (xml-tag-contents "PMID" xmlstr a-start a-end))
+ (article-title article) (xml-tag-contents "ArticleTitle" xmlstr a-start a-end)
+ (article-journal article) (xml-tag-contents "MedlineTA" xmlstr a-start a-end)
+ (article-pages article) (xml-tag-contents "MedlinePgn" xmlstr a-start a-end)
+ (article-affiliation article) (xml-tag-contents "Affiliation" xmlstr a-start a-end)
+ (article-abstract article) (xml-tag-contents "AbstractText" xmlstr a-start a-end))
+ (multiple-value-bind (ji-start ji-end ji-next)
+ (positions-xml-tag-contents "JournalIssue" xmlstr a-start a-end)
+ (declare (ignore ji-next))
+ (setf
+ (article-volume article) (xml-tag-contents "Volume" xmlstr ji-start ji-end)
+ (article-issue article) (xml-tag-contents "Issue" xmlstr ji-start ji-end))
+ (aif (xml-tag-contents "MedlineDate" xmlstr ji-start ji-end)
+ (setf (article-date article) it)
+ (setf (article-date article)
+ (concatenate 'string (xml-tag-contents "Year" xmlstr ji-start ji-end)
+ (aif (xml-tag-contents "Month" xmlstr ji-start ji-end)
+ (format nil " ~a" it)
+ "")))))
+
+ (multiple-value-bind (al-start al-end al-next)
+ (positions-xml-tag-contents "AuthorList" xmlstr a-start a-end)
+ (declare (ignore al-next))
+ (setf (article-authors article)
+ (when al-start
+ (let ((done nil)
+ (authors '())
+ (pos al-start))
+ (until done
+ (multiple-value-bind
+ (au-start au-end au-next)
+ (positions-xml-tag-contents "Author" xmlstr pos al-end)
+ (if au-start
+ (progn
+ (push (extract-author xmlstr au-start au-end) authors)
+ (setq pos au-next))
+ (setq done t))))
+ (nreverse authors)))))
+
+ (multiple-value-bind (mhl-start mhl-end mhl-next)
+ (positions-xml-tag-contents "MeshHeadingList" xmlstr a-start a-end)
+ (declare (ignore mhl-next))
+ (setf (article-mesh-headings article)
+ (when mhl-start
+ (let ((done nil)
+ (mesh-headings '())
+ (pos mhl-start))
+ (until done
+ (multiple-value-bind
+ (mh-start mh-end mh-next)
+ (positions-xml-tag-contents "MeshHeading" xmlstr pos mhl-end)
+ (if mh-start
+ (progn
+ (push (extract-mesh-heading xmlstr mh-start mh-end) mesh-headings)
+ (setq pos mh-next)
+ )
+ (setq done t))))
+ (nreverse mesh-headings)))))
+
+ article))
+
+(defun extract-author (xmlstr start end)
+ "Extract author name from XML string"
+ (let ((last-name (xml-tag-contents "LastName" xmlstr start end))
+ (initials (xml-tag-contents "Initials" xmlstr start end)))
+ (concatenate 'string last-name " " initials)))
+
+(defun extract-mesh-heading (xmlstr start end)
+ "Extract and format mesh headings from XML string"
+ (let ((desc (xml-tag-contents "DescriptorName" xmlstr start end))
+ (sh (xml-tag-contents "SubHeading" xmlstr start end)))
+ (if sh
+ (format nil "~a(~a)" desc sh)
+ desc)))
+
+(defun extract-pmid-list (results)
+ "Returns list of PubMed ID's from XML result string"
+ (cond
+ ((search "<ERROR>" results)
+ (error 'pubmed-query-error :response results))
+ ((search "<H1>Server Error</H1>" results)
+ (error 'pubmed-server-error :response results))
+ (t
+ (awhen (xml-tag-contents "Id" results)
+ (delimited-string-to-list it #\space)))))
+
+
+
projects / pubmed.git / blobdiff