--- /dev/null
+;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10 -*-
+;;;; *************************************************************************
+;;;; FILE IDENTIFICATION
+;;;;
+;;;; Name: entrez.lisp
+;;;; Purpose: Library to access NCBI Entrez web application
+;;;; Programmer: Kevin M. Rosenberg
+;;;; Date Started: April 2013
+;;;;
+;;;; This file, part of cl-entrez, is Copyright (c) 2002 by Kevin M. Rosenberg
+;;;;
+;;;; cl-entrez 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 #:entrez)
+
+
+(defparameter +entrez-host+ "eutils.ncbi.nlm.nih.gov")
+(defparameter +entrez-search-url+ "/entrez/eutils/esearch.fcgi")
+(defparameter +entrez-fetch-url+ "/entrez/eutils/efetch.fcgi")
+(defparameter +entrez-summary-url+ "/entrez/eutils/esummary.fcgi")
+(defparameter *proxy-host* nil)
+
+
+(define-condition entrez-condition ()
+ ())
+
+
+(define-condition entrez-server-error (error entrez-condition)
+ ((response :initarg :response
+ :initform nil
+ :reader entrez-condition-response))
+ (:report (lambda (c stream)
+ (format stream "A Entrez server error occurred.")
+ (awhen (entrez-condition-response c)
+ (format stream " The server response was:~&~S" it)))))
+
+(define-condition entrez-query-error (error entrez-condition)
+ ((response :initarg :response
+ :initform nil
+ :reader entrez-condition-response))
+ (:report (lambda (c stream)
+ (format stream "A Entrez server error occurred.")
+ (awhen (entrez-condition-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)
+ (webenv :type string :initarg :webenv :accessor articles-webenv)
+ (qkey :type string :initarg :qkey :accessor articles-qkey)
+ (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 "Entrez Article Set Class")
+ (:default-initargs :total 0 :start 0 :count 0 :query nil
+ :articles nil :qkey nil :webenv nil))
+
+(defclass equery ()
+ ((query :type string :initarg :query :accessor query)
+ (wenv :type string :initarg :webenv :accessor wenv)
+ (qkey :type string :initarg :qkey :accessor qkey)
+ (qcount :type fixnum :initarg :qcount :accessor qcount))
+ (:documentation "Entrez EQuery Results Class")
+ (:default-initargs :qcount 0 :query nil :qkey nil :webenv 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 "Entrez 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 equery) (s stream))
+ (print-unreadable-object (obj s :type t :identity t)
+ (format s "Found ~d with qkey ~a & wenv ~a"
+ (qcount obj)
+ (qkey obj)
+ (wenv 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 nil))
+ "Display an article set to specified stream in specified format"
+ (dotimes (i (articles-count artset) artset)
+ (if (nth i (articles artset))
+ (print-article (nth i (articles artset)) :os os :format format
+ :complete complete :print-link print-link)
+ (princ "NULL Article" os))))
+
+(defmethod print-article ((art pm-article) &key (os *standard-output*)
+ (format :text) (complete nil) (print-link nil))
+ "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\">" (funcall print-link
+ (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)
+
+
+;;; Entrez Query Functions
+
+(defun equery (searchstr &key (db "pubmed") (usehistory t) start max)
+ "Performs Entrez query and returns article-set structure"
+ (multiple-value-bind
+ (xmlres ids) (do-equery searchstr :db db :usehistory usehistory :start start :max max)
+ (when (xml-tag-contents "Count" xmlres)
+ (let ((as (make-instance 'equery)))
+ (setf
+ (qcount as) (parse-integer (xml-tag-contents "Count" xmlres))
+ (query as) searchstr)
+ (kmrcl:awhen (xml-tag-contents "WebEnv" xmlres)
+ (setf (wenv as) kmrcl:it))
+ (kmrcl:awhen (xml-tag-contents "QueryKey" xmlres)
+ (setf (qkey as) kmrcl:it))
+ as))))
+
+(defun esummary (as &key maximum start)
+;; (articles as) (extract-article-set results))
+ as)
+
+(defun pm-fetch-ids (pmids)
+ "Fetchs list of Entrez ID's and returns pm-article-set class"
+ (setq pmids (mklist pmids))
+ (let ((results (entrez-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 entrez-search-tree (searchstr &key maximum start)
+ "Performs a entrez search and returns two values:
+tree of Entrez search results and tree of Entrez search status"
+ (multiple-value-bind
+ (xml-search-results xml-search-status)
+ (entrez-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 do-equery (term &key (db "pubmed") start max (usehistory t))
+ "Performs a Entrez search and returns two values:
+XML string of Entrez search results and XML search status"
+ (let ((res (http-equery term :start start :max max
+ :usehistory usehistory :db db)))
+ (values res (extract-pmid-list res))))
+
+(defun http-equery (term &key start max (usehistory t)
+ (db "pubmed"))
+ "Performs a Entrez search and returns XML results of Entrez search
+ which contains Entrez ID's and status results"
+ (let* ((alist `(("db" . ,db) ("term" . ,term)))
+ (geturl (format nil "http://~a~a" +entrez-host+ +entrez-search-url+)))
+ (when usehistory
+ (setq alist (acons "usehistory" "y" alist)))
+ (when start
+ (setq alist (acons "retstart" start alist)))
+ (when max
+ (setq alist (acons "retmax" max alist)))
+ (multiple-value-bind (xmlres http-code http-server-alist)
+ (net.aserve.client:do-http-request
+ geturl
+ :method :get
+ :query alist
+ :proxy *proxy-host*)
+ (declare (ignore http-server-alist))
+ (when (not (equal http-code 200))
+ (error "HTTP code performing '~A' was ~D." geturl http-code))
+ xmlres)))
+
+(defun entrez-fetch-pmids-xml (pmids &key (db "pubmed"))
+ "Fetch articles for a list of Entrez 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" +entrez-host+ +entrez-fetch-url+)
+ :method :get
+ :query
+ `(("db" . ,db) ("report" . "xml") ("mode" . "text")
+ ("id" . ,(list-to-delimited-string pmids #\,)))
+ :proxy *proxy-host*)))
+
+;;; XML Extraction Routines
+
+(defun extract-article-set (results)
+ "Extract article set from Entrez 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 Entrez 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 Entrez ID's from XML result string"
+ (cond
+ ((search "<ERROR>" results)
+ (error 'entrez-query-error :response results))
+ ((search "<H1>Server Error</H1>" results)
+ (error 'entrez-server-error :response results))
+ (t
+ (awhen (xml-tag-contents "Id" results)
+ (delimited-string-to-list it #\space)))))
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