109807: Live Import - PubMed - support optional apiKey config

atmire · Jan 30, 2025 · c25433e · c25433e
1 parent ca7851f
commit c25433e
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Showing 3 changed files with 28 additions and 1 deletion.
diff --git a/...va/org/dspace/importer/external/pubmed/service/PubmedImportMetadataSourceServiceImpl.java b/...va/org/dspace/importer/external/pubmed/service/PubmedImportMetadataSourceServiceImpl.java
@@ -54,6 +54,7 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat
 
     private String urlFetch;
     private String urlSearch;
+    private String apiKey;
 
     private int attempt = 3;
 
@@ -209,6 +210,9 @@ public GetNbRecords(Query query) {
         @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>>();
@@ -282,6 +286,9 @@ public Collection<ImportRecord> call() throws Exception {
             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());
@@ -312,6 +319,9 @@ public Collection<ImportRecord> call() throws Exception {
             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());
@@ -386,6 +396,9 @@ public GetRecord(Query q) {
         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));
@@ -426,6 +439,9 @@ public FindMatchingRecords(Query q) {
         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));
@@ -455,6 +471,9 @@ public Collection<ImportRecord> call() throws Exception {
             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);
@@ -530,4 +549,8 @@ public void setUrlSearch(String urlSearch) {
         this.urlSearch = urlSearch;
     }
 
+    public void setApiKey(String apiKey) {
+        this.apiKey = apiKey;
+    }
+
 }
diff --git a/dspace-api/src/main/resources/spring/spring-dspace-addon-import-services.xml b/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">

diff --git a/dspace/config/modules/external-providers.cfg b/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
 #################################################################
@@ -96,4 +99,4 @@ datacite.timeout = 180000
 #---------------------------------------------------------------#
 
 ror.orgunit-import.api-url = https://api.ror.org/organizations
-#################################################################
+#################################################################