X-Git-Url: http://git.kpe.io/?p=pubmed.git;a=blobdiff_plain;f=pubmed-src.lisp;fp=pubmed-src.lisp;h=0000000000000000000000000000000000000000;hp=ad18ca963760f14fbc2b9b9268a35d0866e8b132;hb=5ce187bd43a9280f16a315121967f39b9d2d1e10;hpb=3163cad3295c4353f62c0fb0b94a76031369aa82 diff --git a/pubmed-src.lisp b/pubmed-src.lisp deleted file mode 100644 index ad18ca9..0000000 --- a/pubmed-src.lisp +++ /dev/null @@ -1,355 +0,0 @@ -;;;; -*- 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 "" (funcall print-link - (article-pmid art)))) - (format os "
~a
~%" - (article-title art)) - (when (and print-link has-link) - (format os "")) - (format os "
~a
~%" - (list-to-delimited-string (article-authors art) ", ")) - (format os "
~a ~a
~%" - (article-journal art) (article-ref art)) - (when (and complete (article-abstract art)) - (format os "
~a
~%" - (article-abstract art))) - (when (and complete (article-mesh-headings art)) - (format os "
Mesh Headings:
") - (dolist (mh (article-mesh-headings art)) - (format os "
~a
~%" mh))) - (format os "

~%")))) - 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 "" results) - (error 'pubmed-query-error :response results)) - ((search "

Server Error

" results) - (error 'pubmed-server-error :response results)) - (t - (awhen (xml-tag-contents "Id" results) - (delimited-string-to-list it #\space))))) - - -