Merge pull request DSpace#10883 from DSpace/backport-10583-to-dspace-7_x

[Port dspace-7_x] Introduce custom contributor for PubMed's abstract format on metadata import

Author: tdonohue

dspace-api/src/main/java/org/dspace/importer/external/pubmed/metadatamapping/contributor/PubmedAbstractMetadatumContributor.java

@@ -0,0 +1,67 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.importer.external.pubmed.metadatamapping.contributor;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.LinkedList;
+import java.util.List;
+
+import org.dspace.importer.external.metadatamapping.MetadatumDTO;
+import org.dspace.importer.external.metadatamapping.contributor.SimpleXpathMetadatumContributor;
+import org.jdom2.Element;
+import org.jdom2.Namespace;
+import org.jdom2.filter.Filters;
+import org.jdom2.xpath.XPathExpression;
+import org.jdom2.xpath.XPathFactory;
+
+/**
+ * This class is responsible for extracting the abstract from a PubMed XML document.
+ * It uses XPath to find the relevant elements and constructs a formatted string for the abstract, respecting
+ * PubMed's labelled abstract format, and including the labels in the output.
+ */
+public class PubmedAbstractMetadatumContributor extends SimpleXpathMetadatumContributor {
+
+    @Override
+    public Collection<MetadatumDTO> contributeMetadata(Element t) {
+        List<MetadatumDTO> values = new LinkedList<>();
+
+        List<Namespace> namespaces = new ArrayList<>();
+        for (String ns : prefixToNamespaceMapping.keySet()) {
+            namespaces.add(Namespace.getNamespace(prefixToNamespaceMapping.get(ns), ns));
+        }
+
+        XPathExpression<Element> xpath = XPathFactory.instance().compile(query, Filters.element(), null, namespaces);
+        List<Element> nodes = xpath.evaluate(t);
+        StringBuilder sb = new StringBuilder();
+
+        for (Element el : nodes) {
+            String label = el.getAttributeValue("Label");
+            String text = el.getTextNormalize();
+
+            if (text == null || text.isEmpty()) {
+                continue;
+            }
+
+            if (sb.length() > 0) {
+                sb.append("\n\n");
+            }
+
+            if (label != null && !label.equalsIgnoreCase("UNLABELLED")) {
+                sb.append(label).append(": ");
+            }
+            sb.append(text);
+        }
+
+        String fullAbstract = sb.toString().trim();
+        if (!fullAbstract.isEmpty()) {
+            values.add(metadataFieldMapping.toDCValue(field, fullAbstract));
+        }
+        return values;
+    }
+}

dspace-server-webapp/src/test/java/org/dspace/app/rest/PubmedImportMetadataSourceServiceIT.java

@@ -101,35 +101,34 @@ private ArrayList<ImportRecord> getRecords() {
         //define first record
         MetadatumDTO title = createMetadatumDTO("dc","title", null,
                 "Teaching strategies of clinical reasoning in advanced nursing clinical practice: A scoping review.");
-        MetadatumDTO description1 = createMetadatumDTO("dc", "description", "abstract", "To report and synthesize"
-                + " the main strategies for teaching clinical reasoning described in the literature in the context of"
-                + " advanced clinical practice and promote new areas of research to improve the pedagogical approach"
-                + " to clinical reasoning in Advanced Practice Nursing.");
-        MetadatumDTO description2 = createMetadatumDTO("dc", "description", "abstract", "Clinical reasoning and"
-                + " clinical thinking are essential elements in the advanced nursing clinical practice decision-making"
-                + " process. The quality improvement of care is related to the development of those skills."
-                + " Therefore, it is crucial to optimize teaching strategies that can enhance the role of clinical"
-                + " reasoning in advanced clinical practice.");
-        MetadatumDTO description3 = createMetadatumDTO("dc", "description", "abstract", "A scoping review was"
-                + " conducted using the framework developed by Arksey and O'Malley as a research strategy."
-                + " Consistent with the nature of scoping reviews, a study protocol has been established.");
-        MetadatumDTO description4 = createMetadatumDTO("dc", "description", "abstract", "The studies included and"
-                + " analyzed in this scoping review cover from January 2016 to June 2022. Primary studies and secondary"
-                + " revision studies, published in biomedical databases, were selected, including qualitative ones."
-                + " Electronic databases used were: CINAHL, PubMed, Cochrane Library, Scopus, and OVID."
-                + " Three authors independently evaluated the articles for titles, abstracts, and full text.");
-        MetadatumDTO description5 = createMetadatumDTO("dc", "description", "abstract", "1433 articles were examined,"
-                + " applying the eligibility and exclusion criteria 73 studies were assessed for eligibility,"
-                + " and 27 were included in the scoping review. The results that emerged from the review were"
-                + " interpreted and grouped into three macro strategies (simulations-based education, art and visual"
-                + " thinking, and other learning approaches) and nineteen educational interventions.");
-        MetadatumDTO description6 = createMetadatumDTO("dc", "description", "abstract", "Among the different"
-                + " strategies, the simulations are the most used. Despite this, our scoping review reveals that is"
-                + " necessary to use different teaching strategies to stimulate critical thinking, improve diagnostic"
-                + " reasoning, refine clinical judgment, and strengthen decision-making. However, it is not possible to"
-                + " demonstrate which methodology is more effective in obtaining the learning outcomes necessary to"
-                + " acquire an adequate level of judgment and critical thinking. Therefore, it will be"
-                + " necessary to relate teaching methodologies with the skills developed.");
+        MetadatumDTO description1 = createMetadatumDTO("dc", "description", "abstract",
+                "AIM/OBJECTIVE: To report and synthesize the main strategies for teaching clinical reasoning " +
+                        "described in the literature in the context of advanced clinical practice and promote new " +
+                        "areas of research to improve the pedagogical approach to clinical reasoning in Advanced " +
+                        "Practice Nursing.\n\nBACKGROUND: Clinical reasoning and clinical thinking are essential " +
+                        "elements in the advanced nursing clinical practice decision-making process. The quality " +
+                        "improvement of care is related to the development of those skills. Therefore, it is crucial " +
+                        "to optimize teaching strategies that can enhance the role of clinical reasoning in advanced " +
+                        "clinical practice.\n\nDESIGN: A scoping review was conducted using the framework developed " +
+                        "by Arksey and O'Malley as a research strategy. Consistent with the nature of scoping reviews" +
+                        ", a study protocol has been established.\n\nMETHODS: The studies included and analyzed in " +
+                        "this scoping review cover from January 2016 to June 2022. Primary studies and secondary " +
+                        "revision studies, published in biomedical databases, were selected, including qualitative " +
+                        "ones. Electronic databases used were: CINAHL, PubMed, Cochrane Library, Scopus, and OVID. " +
+                        "Three authors independently evaluated the articles for titles, abstracts, and full text.\n\n" +
+                        "RESULTS: 1433 articles were examined, applying the eligibility and exclusion criteria 73 " +
+                        "studies were assessed for eligibility, and 27 were included in the scoping review. The " +
+                        "results that emerged from the review were interpreted and grouped into three macro " +
+                        "strategies (simulations-based education, art and visual thinking, and other learning " +
+                        "approaches) and nineteen educational interventions.\n\nCONCLUSIONS: Among the different " +
+                        "strategies, the simulations are the most used. Despite this, our scoping review reveals " +
+                        "that is necessary to use different teaching strategies to stimulate critical thinking, " +
+                        "improve diagnostic reasoning, refine clinical judgment, and strengthen decision-making. " +
+                        "However, it is not possible to demonstrate which methodology is more effective in obtaining " +
+                        "the learning outcomes necessary to acquire an adequate level of judgment and critical " +
+                        "thinking. Therefore, it will be necessary to relate teaching methodologies with the skills " +
+                        "developed.\n\nAn unlabeled section of an abstract.\n\nAn abstract section with no attributes" +
+                        " at all, concerning.");
         MetadatumDTO identifierOther = createMetadatumDTO("dc", "identifier", "other", "36708638");
         MetadatumDTO author1 = createMetadatumDTO("dc", "contributor", "author", "Giuffrida, Silvia");
         MetadatumDTO author2 = createMetadatumDTO("dc", "contributor", "author", "Silano, Verdiana");
@@ -148,11 +147,6 @@ private ArrayList<ImportRecord> getRecords() {
 
         metadatums.add(title);
         metadatums.add(description1);
-        metadatums.add(description2);
-        metadatums.add(description3);
-        metadatums.add(description4);
-        metadatums.add(description5);
-        metadatums.add(description6);
         metadatums.add(identifierOther);
         metadatums.add(author1);
         metadatums.add(author2);
@@ -210,4 +204,4 @@ private ArrayList<ImportRecord> getRecords2() {
         return records;
     }
 
-}
+}

dspace-server-webapp/src/test/resources/org/dspace/app/rest/pubmedimport-search-test.xml

@@ -41,6 +41,8 @@
                     <AbstractText Label="METHODS" NlmCategory="METHODS">The studies included and analyzed in this scoping review cover from January 2016 to June 2022. Primary studies and secondary revision studies, published in biomedical databases, were selected, including qualitative ones. Electronic databases used were: CINAHL, PubMed, Cochrane Library, Scopus, and OVID. Three authors independently evaluated the articles for titles, abstracts, and full text.</AbstractText>
                     <AbstractText Label="RESULTS" NlmCategory="RESULTS">1433 articles were examined, applying the eligibility and exclusion criteria 73 studies were assessed for eligibility, and 27 were included in the scoping review. The results that emerged from the review were interpreted and grouped into three macro strategies (simulations-based education, art and visual thinking, and other learning approaches) and nineteen educational interventions.</AbstractText>
                     <AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">Among the different strategies, the simulations are the most used. Despite this, our scoping review reveals that is necessary to use different teaching strategies to stimulate critical thinking, improve diagnostic reasoning, refine clinical judgment, and strengthen decision-making. However, it is not possible to demonstrate which methodology is more effective in obtaining the learning outcomes necessary to acquire an adequate level of judgment and critical thinking. Therefore, it will be necessary to relate teaching methodologies with the skills developed.</AbstractText>
+                    <AbstractText Label="UNLABELLED">An unlabeled section of an abstract.</AbstractText>
+                    <AbstractText>An abstract section with no attributes at all, concerning.</AbstractText>
                     <CopyrightInformation>Copyright &#xa9; 2023 Elsevier Ltd. All rights reserved.</CopyrightInformation>
                 </Abstract>
                 <AuthorList CompleteYN="Y">
@@ -191,4 +193,4 @@
             </ArticleIdList>
         </PubmedData>
     </PubmedArticle>
-</PubmedArticleSet>
+</PubmedArticleSet>

dspace/config/spring/api/pubmed-integration.xml

@@ -57,7 +57,7 @@
         <property name="prefixToNamespaceMapping" ref="prefixToNamespaceMapping"/>
     </bean>
 
-    <bean id="abstractContrib" class="org.dspace.importer.external.metadatamapping.contributor.SimpleXpathMetadatumContributor">
+    <bean id="abstractContrib" class="org.dspace.importer.external.pubmed.metadatamapping.contributor.PubmedAbstractMetadatumContributor">
         <property name="field" ref="dc.description.abstract"/>
         <property name="query" value="descendant::AbstractText"/>
         <property name="prefixToNamespaceMapping" ref="prefixToNamespaceMapping"/>