+++ /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
-;;;;
-;;;; $Id$
-;;;;
-;;;; 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")
-(defparameter *proxy-host* nil)
-
-
-(define-condition pubmed-condition ()
- ())
-
-
-(define-condition pubmed-server-error (error pubmed-condition)
- ((response :initarg :response
- :initform nil
- :reader pubmed-condition-response))
- (:report (lambda (c stream)
- (format stream "A PubMed server error occurred.")
- (awhen (pubmed-condition-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-condition-response))
- (:report (lambda (c stream)
- (format stream "A PubMed server error occurred.")
- (awhen (pubmed-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)
- (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 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)
-
-
-;;; 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
- :proxy *proxy-host*)))
-
-(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 #\,)))
- :proxy *proxy-host*)))
-
-;;; 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