Fixing an issue with Pubmed entries without abstracts

Any Pubmed entries that is lacking an abstract text causes an error during the parsing of the XML file. As example use this article: http://www.ncbi.nlm.nih.gov/pubmed/22442467 You can download its XML file with $ curl "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=$22442467&retmode=xml" > 22442467.xml The is no "Abstract" and "AbstractText" element in there. The modification circumvent the error and an empty string is returned by the modified function.
konrad · Apr 1, 2012 · 0168464 · 0168464 · konrad · Apr 1, 2012
1 parent 4f37b15
commit 0168464
Showing 1 changed file with 4 additions and 0 deletions.
diff --git a/PubmedParserFetcher.body.php b/PubmedParserFetcher.body.php
@@ -295,6 +295,10 @@ function doi()
 		 *  as it is a PHP keyword.
 		 */
 		function abstr() {
+		        // Some Pubmed entries are missing an abtract
+		        if (is_array($this->medline->PubmedArticle->MedlineCitation->Article->Abstract->AbstractText) == FALSE){
+			   return "";
+                        }
 			foreach ( $this->medline->PubmedArticle->MedlineCitation->Article->Abstract->AbstractText as $p ) {
 					// Abstract paragraphs may be preceded by a label.
 					// The label is given as an XML parameter, e.g.: