Merge pull request #4413 from inception-project/bugfix/4412-PMC-searc…

…h-returns-some-results-that-cannot-be-imported #4412 - PMC search returns some results that cannot be imported
inception-project · Dec 28, 2023 · c2a8943 · c2a8943
2 parents 3b71116 + 1e9a669
commit c2a8943
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Showing 6 changed files with 25 additions and 12 deletions.
diff --git a/...c/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/PubMedCentralProvider.java b/...c/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/PubMedCentralProvider.java
@@ -73,7 +73,7 @@ public List<ExternalSearchResult> executeQuery(DocumentRepository aDocumentRepos
             PubMedProviderTraits aTraits, String aQuery)
     {
         var date = Instant.now().atZone(ZoneOffset.UTC).minus(Duration.ofHours(24));
-        var query = aQuery + " AND \"free full text\"[filter] AND (\"0001/01/01\"[PubDate] : \""
+        var query = aQuery + " AND \"open access\"[filter] AND (\"0001/01/01\"[PubDate] : \""
                 + date.get(YEAR) + "/" + date.get(MONTH_OF_YEAR) + "/" + date.get(DAY_OF_MONTH)
                 + "\"[PubDate])";
 

diff --git a/...java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/PubMedCentralProviderFactory.java b/...java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/PubMedCentralProviderFactory.java
@@ -21,6 +21,7 @@
 import static de.tudarmstadt.ukp.inception.support.json.JSONUtil.toJsonString;
 
 import java.io.IOException;
+import java.lang.invoke.MethodHandles;
 
 import org.apache.wicket.markup.html.panel.Panel;
 import org.apache.wicket.model.IModel;
@@ -50,7 +51,7 @@
 public class PubMedCentralProviderFactory
     implements BeanNameAware, ExternalSearchProviderFactory<PubMedProviderTraits>
 {
-    private final Logger log = LoggerFactory.getLogger(getClass());
+    private static final Logger LOG = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());
 
     private final EntrezClient entrezClient;
     private final PmcOaClient pmcOaClient;
@@ -81,7 +82,7 @@ public String getBeanName()
     @Override
     public String getDisplayName()
     {
-        return "PubMed Central (experimental)";
+        return "PubMed Central Open Access (experimental)";
     }
 
     @Override
@@ -105,7 +106,7 @@ public PubMedProviderTraits readTraits(DocumentRepository aDocumentRepository)
                     aDocumentRepository.getProperties());
         }
         catch (IOException e) {
-            log.error("Error while reading traits", e);
+            LOG.error("Error while reading traits", e);
         }
 
         if (traits == null) {
@@ -124,7 +125,7 @@ public void writeTraits(DocumentRepository aDocumentRepository,
             aDocumentRepository.setProperties(json);
         }
         catch (IOException e) {
-            log.error("Error while writing traits", e);
+            LOG.error("Error while writing traits", e);
         }
     }
 }
diff --git a/...de/tudarmstadt/ukp/inception/externalsearch/pubmed/traits/PubMedProviderTraitsEditor.html b/...de/tudarmstadt/ukp/inception/externalsearch/pubmed/traits/PubMedProviderTraitsEditor.html
@@ -18,6 +18,12 @@
 <html xmlns="http://www.w3.org/1999/xhtml"
   xmlns:wicket="http://wicket.apache.org/dtds.data/wicket-xhtml1.4-strict.dtd">
 <wicket:panel>
+  <div class="offset-sm-3 d-flex text-muted" role="alert">
+    <i class="fas fa-info-circle mr-2 mt-1"></i>
+    <p class="mb-0 mx-2 small">
+      <wicket:message key="openAccessHint"/>
+    </p>
+  </div>
   <form wicket:id="form">
   </form>
 </wicket:panel>

diff --git a/...armstadt/ukp/inception/externalsearch/pubmed/traits/PubMedProviderTraitsEditor.properties b/...armstadt/ukp/inception/externalsearch/pubmed/traits/PubMedProviderTraitsEditor.properties
@@ -13,3 +13,8 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
+openAccessHint=#(product.name) uses the BioC version of the PMC documents for import. This is only available for \
+      Open Access texts. #(product.name) automatically adds a filter for open access results \
+      (<code>"open access"[filter]</code>) to the query. The BioC version of these texts may be available only with a \
+      delay #(product.name) automatically excludes results that were published in the last 24h to try to keep the \
+      number of non-importable results low. If you are still unable to import a result, try a bit later.
diff --git a/.../src/main/resources/META-INF/asciidoc/user-guide/external-search-repos-pmc.adoc b/.../src/main/resources/META-INF/asciidoc/user-guide/external-search-repos-pmc.adoc
@@ -25,7 +25,8 @@ support for the BioC format used by this repository connector.
 link:https://www.ncbi.nlm.nih.gov/pmc/[PubMed Central]® (PMC) is a free full-text archive of biomedical and life sciences journal literature at the U.S. National Institutes of Health's National Library of Medicine (NIH/NLM). It can be added as an external document repository by
 selecting the **PubMed Central** repository type.
 
-NOTE: {product-name} uses the BioC version of the PMC documents for import. The search tries to
-      consider only documents that have full text available, but the BioC version of these texts may be
-      available only with a delay. Thus, if you cannot import a recently uploaded document from PMC into
-      {product-name}, you may try it again a day later and have more success.
+NOTE: {product-name} uses the BioC version of the PMC documents for import. This is only available for 
+      Open Access texts. {product-name} automatically adds a filter for open access results (`"open access"[filter]`) 
+      to the query. The BioC version of these texts may be available only with a delay {product-name} automatically 
+      excludes results that were published in the last 24h to try to keep the number of non-importable results low. 
+      If you are still unable to import a result, try a bit later.
diff --git a/...-bootstrap/src/main/java/de/tudarmstadt/ukp/inception/bootstrap/BootstrapFeedbackPanel.js b/...-bootstrap/src/main/java/de/tudarmstadt/ukp/inception/bootstrap/BootstrapFeedbackPanel.js
@@ -16,18 +16,18 @@
  * limitations under the License.
  */
  function bootstrapFeedbackPanelCloseAll() {
-  $('.alert').each((i, e) => {
+  $('.feedbackPanel .alert').each((i, e) => {
     console.log("Closing", e);
     bootstrap.Alert.getOrCreateInstance(e).close();
    });
  }
 
 function bootstrapFeedbackPanelFade() {
   setTimeout(function() {
-    $(".alert.alert-success").fadeTo(600, 0, function(){
+    $(".feedbackPanel .alert.alert-success").fadeTo(600, 0, function(){
       $(".alert.alert-success").each((i, e) => bootstrap.Alert.getOrCreateInstance(e).close());
     });
-    $(".alert.alert-info").fadeTo(600, 0, function(){
+    $(".feedbackPanel .alert.alert-info").fadeTo(600, 0, function(){
       $(".alert.alert-info").each((i, e) => bootstrap.Alert.getOrCreateInstance(e).close());
     });
   }, 2000);