r9011: new policy

[pubmed.git] / pubmed-src.lisp

diff --git a/pubmed-src.lisp b/pubmed-src.lisp
index a2e832adf321ca31dbb07b257a94a83b3b8ece0d..e53057a716d70c9f7d7935e6bf9eec5ebe42cf56 100644 (file)
--- a/pubmed-src.lisp
+++ b/pubmed-src.lisp
@@ -7,7 +7,7 @@
 ;;;; Programmer:    Kevin M. Rosenberg
 ;;;; Date Started:  Jun 2001
 ;;;;
-;;;; $Id: pubmed-src.lisp,v 1.1 2003/06/06 22:04:05 kevin Exp $
+;;;; $Id$
 ;;;;
 ;;;; This file, part of cl-pubmed, is Copyright (c) 2002 by Kevin M. Rosenberg
 ;;;;
@@ -22,6 +22,7 @@
 (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 ()
@@ -31,19 +32,19 @@
 (define-condition pubmed-server-error (error pubmed-condition)
   ((response :initarg :response
             :initform nil
-            :reader pubmed-server-error-response))
+            :reader pubmed-condition-response))
   (:report (lambda (c stream)
             (format stream "A PubMed server error occurred.")
-            (awhen (pubmed-server-error-response c)
+            (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-query-error-response))
+            :reader pubmed-condition-response))
   (:report (lambda (c stream)
             (format stream "A PubMed server error occurred.")
-            (awhen (pubmed-query-error-response c)
+            (awhen (pubmed-condition-response c)
                    (format stream " The server response was:~&~S" it)))))
   
 ;;; Article-Set and Article Classes
@@ -104,16 +105,18 @@
           (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))
+(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))
-    (print-article (nth i (articles artset)) :os os :format format 
-                  :complete complete :print-link print-link))
-  artset)
+  (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 t))
+                         (format :text) (complete nil) (print-link nil))
   "Display an article"
   (ecase format
     (:text
@@ -133,8 +136,10 @@
      (: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))
+         (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>~%"
@@ -218,7 +223,8 @@ XML string of PubMed search results and XML search status"
     (net.aserve.client:do-http-request
      (format nil "http://~a~a" +pubmed-host+ +pubmed-query-url+)
      :method :get
-     :query query-alist)))
+     :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"
@@ -229,7 +235,8 @@ XML string of PubMed search results and XML search status"
        :method :get
        :query 
        `(("db" . "PubMed") ("report" . "xml") ("mode" . "text")
-        ("id" . ,(list-to-delimited-string pmids #\,))))))
+        ("id" . ,(list-to-delimited-string pmids #\,)))
+       :proxy *proxy-host*)))
 
 ;;; XML Extraction Routines