109807: Live Import - PubMed - support optional apiKey config

(cherry picked from commit c25433ee17)

dspace-api/src/main/java/org/dspace/importer/external/pubmed/service/PubmedImportMetadataSourceServiceImpl.java

@@ -55,6 +55,7 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat
 
     private String urlFetch;
     private String urlSearch;
+    private String apiKey;
 
     private int attempt = 3;
 
@@ -210,6 +211,9 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat
         @Override
         public Integer call() throws Exception {
             URIBuilder uriBuilder = new URIBuilder(urlSearch);
+            if (StringUtils.isNotBlank(apiKey)) {
+                uriBuilder.addParameter("api_key", apiKey);
+            }
             uriBuilder.addParameter("db", "pubmed");
             uriBuilder.addParameter("term", query.getParameterAsClass("query", String.class));
             Map<String, Map<String, String>> params = new HashMap<String, Map<String,String>>();
@@ -286,6 +290,9 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat
             List<ImportRecord> records = new LinkedList<ImportRecord>();
 
             URIBuilder uriBuilder = new URIBuilder(urlSearch);
+            if (StringUtils.isNotBlank(apiKey)) {
+                uriBuilder.addParameter("api_key", apiKey);
+            }
             uriBuilder.addParameter("db", "pubmed");
             uriBuilder.addParameter("retstart", start.toString());
             uriBuilder.addParameter("retmax", count.toString());
@@ -316,6 +323,9 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat
             String webEnv = getSingleElementValue(response, "WebEnv");
 
             URIBuilder uriBuilder2 = new URIBuilder(urlFetch);
+            if (StringUtils.isNotBlank(apiKey)) {
+                uriBuilder2.addParameter("api_key", apiKey);
+            }
             uriBuilder2.addParameter("db", "pubmed");
             uriBuilder2.addParameter("retstart", start.toString());
             uriBuilder2.addParameter("retmax", count.toString());
@@ -388,6 +398,9 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat
         public ImportRecord call() throws Exception {
 
             URIBuilder uriBuilder = new URIBuilder(urlFetch);
+            if (StringUtils.isNotBlank(apiKey)) {
+                uriBuilder.addParameter("api_key", apiKey);
+            }
             uriBuilder.addParameter("db", "pubmed");
             uriBuilder.addParameter("retmode", "xml");
             uriBuilder.addParameter("id", query.getParameterAsClass("id", String.class));
@@ -428,6 +441,9 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat
         public Collection<ImportRecord> call() throws Exception {
 
             URIBuilder uriBuilder = new URIBuilder(urlSearch);
+            if (StringUtils.isNotBlank(apiKey)) {
+                uriBuilder.addParameter("api_key", apiKey);
+            }
             uriBuilder.addParameter("db", "pubmed");
             uriBuilder.addParameter("usehistory", "y");
             uriBuilder.addParameter("term", query.getParameterAsClass("term", String.class));
@@ -457,6 +473,9 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat
             String queryKey = getSingleElementValue(response, "QueryKey");
 
             URIBuilder uriBuilder2 = new URIBuilder(urlFetch);
+            if (StringUtils.isNotBlank(apiKey)) {
+                uriBuilder.addParameter("api_key", apiKey);
+            }
             uriBuilder2.addParameter("db", "pubmed");
             uriBuilder2.addParameter("retmode", "xml");
             uriBuilder2.addParameter("WebEnv", webEnv);
@@ -532,4 +551,8 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat
         this.urlSearch = urlSearch;
     }
 
+    public void setApiKey(String apiKey) {
+        this.apiKey = apiKey;
+    }
+
 }

dspace-api/src/main/resources/spring/spring-dspace-addon-import-services.xml

@@ -70,6 +70,7 @@
         <property name="metadataFieldMapping" ref="pubmedMetadataFieldMapping"/>
         <property name="urlFetch" value="${pubmed.url.fetch}"/>
         <property name="urlSearch" value="${pubmed.url.search}"/>
+        <property name="apiKey" value="${pubmed.apiKey}"/>
         <property name="generateQueryForItem" ref="pubmedService"></property>
         <property name="interRequestTime" value="500"/>
         <property name="supportedExtensions">

dspace/config/modules/external-providers.cfg

@@ -45,6 +45,9 @@ epo.searchUrl = https://ops.epo.org/rest-services/published-data/search
 #################################################################
 #----------------------   PubMed   -----------------------------#
 #---------------------------------------------------------------#
+# If apiKey is set then it's used, if not set or blank then it's not
+# Max amount of requests per ip per second with apiKey is 10; without 3
+pubmed.apiKey =
 pubmed.url.search = https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi
 pubmed.url.fetch = https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi
 #################################################################