Merge pull request #4398 from inception-project/feature/4397-Better-e…

…rror-message-when-PMC-document-cannot-be-found #4397 - Better error message when PMC document cannot be found
inception-project · Dec 27, 2023 · 546e37f · 546e37f
2 parents 3446478 + fa191af
commit 546e37f
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Showing 6 changed files with 53 additions and 18 deletions.
diff --git a/inception/inception-external-search-pubmed/pom.xml b/inception/inception-external-search-pubmed/pom.xml
@@ -90,6 +90,10 @@
       <groupId>com.fasterxml.jackson.core</groupId>
       <artifactId>jackson-annotations</artifactId>
     </dependency>
+    <dependency>
+      <groupId>com.fasterxml.jackson.core</groupId>
+      <artifactId>jackson-databind</artifactId>
+    </dependency>
     <dependency>
       <groupId>com.fasterxml.jackson.dataformat</groupId>
       <artifactId>jackson-dataformat-xml</artifactId>

diff --git a/...d/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/pmcoa/PmcOaClient.java b/...d/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/pmcoa/PmcOaClient.java
@@ -17,10 +17,12 @@
  */
 package de.tudarmstadt.ukp.inception.externalsearch.pubmed.pmcoa;
 
+import java.io.IOException;
 import java.util.Map;
 
 import org.springframework.http.HttpMethod;
 import org.springframework.http.converter.xml.MappingJackson2XmlHttpMessageConverter;
+import org.springframework.web.client.HttpClientErrorException.NotFound;
 import org.springframework.web.client.RestTemplate;
 
 import de.tudarmstadt.ukp.inception.externalsearch.pubmed.traits.PubMedProviderTraits;
@@ -40,14 +42,25 @@ public PmcOaClient()
         restTemplate.getMessageConverters().add(new MappingJackson2XmlHttpMessageConverter());
     }
 
-    public byte[] bioc(PubMedProviderTraits aTraits, String aID)
+    public byte[] bioc(PubMedProviderTraits aTraits, String aID) throws IOException
     {
-        var variables = Map.of( //
-                PARAM_ID, aID);
+        try {
+            var variables = Map.of( //
+                    PARAM_ID, aID);
 
-        var response = restTemplate.exchange(BIOC_URL, HttpMethod.GET, null, byte[].class,
-                variables);
+            var response = restTemplate.exchange(BIOC_URL, HttpMethod.GET, null, byte[].class,
+                    variables);
 
-        return response.getBody();
+            return response.getBody();
+        }
+        catch (NotFound e) {
+            throw new IOException("BioC version of document [" + aID + "] not found at ["
+                    + BIOC_URL.replace("{id}", aID)
+                    + "]. The Open Access files and BioC versions are not updated  as "
+                    + "quickly as the PMC website itself is updated. It may take a couple of days until "
+                    + "a particular file is available as BioC. Another reason could be that the document you "
+                    + "are looking for is not included in the Open Access set. Try adding "
+                    + "`\"open access\"[filter]` without \"`\" to your search to filter by Open Access files.");
+        }
     }
 }
diff --git a/.../java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/traits/PubMedProviderTraits.java b/.../java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/traits/PubMedProviderTraits.java
@@ -19,6 +19,13 @@
 
 import java.io.Serializable;
 
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.databind.annotation.JsonSerialize;
+
+//The @JsonSerialize annotation avoid the "InvalidDefinitionException: No serializer found"
+//exception without having to set SerializationFeature.FAIL_ON_EMPTY_BEANS
+@JsonSerialize
+@JsonIgnoreProperties(ignoreUnknown = true)
 public class PubMedProviderTraits
     implements Serializable
 {

diff --git a/...src/main/java/de/tudarmstadt/ukp/inception/app/ui/externalsearch/DocumentDetailsPage.java b/...src/main/java/de/tudarmstadt/ukp/inception/app/ui/externalsearch/DocumentDetailsPage.java
@@ -23,8 +23,6 @@
 import static de.tudarmstadt.ukp.inception.app.ui.externalsearch.DocumentDetailsPage.PAGE_PARAM_DOCUMENT_ID;
 import static de.tudarmstadt.ukp.inception.app.ui.externalsearch.DocumentDetailsPage.PAGE_PARAM_REPOSITORY_ID;
 
-import java.io.IOException;
-
 import org.apache.wicket.markup.html.basic.Label;
 import org.apache.wicket.model.LoadableDetachableModel;
 import org.apache.wicket.request.mapper.parameter.PageParameters;
@@ -95,7 +93,7 @@ private String getDocumentText()
         try {
             return externalSearchService.getDocumentText(repo, collectionId, documentId);
         }
-        catch (IOException e) {
+        catch (Exception e) {
             return "ERROR: " + e.getMessage();
         }
     }
@@ -105,7 +103,7 @@ private ExternalSearchResult getDocumentResult()
         try {
             return externalSearchService.getDocumentResult(repo, collectionId, documentId);
         }
-        catch (IOException e) {
+        catch (Exception e) {
             return new ExternalSearchResult(repo, collectionId, documentId);
         }
     }

diff --git a/...earch/src/main/java/de/tudarmstadt/ukp/inception/app/ui/externalsearch/ResultRowView.html b/...earch/src/main/java/de/tudarmstadt/ukp/inception/app/ui/externalsearch/ResultRowView.html
@@ -19,11 +19,11 @@
 <html xmlns:wicket="http://wicket.apache.org">
 <body>
   <wicket:panel>
-    <div class="flex-h-container">
-      <div class="fs-1 me-4">
-        <i wicket:id="icon"/>
+    <div class="d-flex">
+      <div class="fs-1 mx-2">
+        <i wicket:id="icon" class="text-muted"/>
       </div>
-      <a wicket:id="titleLink" class="flex-content text-decoration-none text-reset">
+      <a wicket:id="titleLink" class="flex-grow-1 text-decoration-none text-reset mx-2">
         <h5>
           <wicket:container wicket:id="title"/>
         </h5>
@@ -33,12 +33,12 @@ <h5>
           </li>
         </ul>
       </a>
-      <div class="flex-v-container">
-        <a wicket:id="importLink" class="btn btn-secondary">
+      <div class="flex-v-container mx-2 flex-shrink-0">
+        <a wicket:id="importLink" class="btn btn-outline-secondary">
           <i class="fas fa-plus"></i>
           <wicket:message key="import"/>
         </a>
-        <a wicket:id="openLink" class="btn btn-secondary">
+        <a wicket:id="openLink" class="btn btn-outline-secondary">
           <i class="fas fa-folder-open"></i>
           <wicket:message key="open"/>
         </a>

diff --git a/...l-search/src/main/java/de/tudarmstadt/ukp/inception/app/ui/externalsearch/SearchPage.html b/...l-search/src/main/java/de/tudarmstadt/ukp/inception/app/ui/externalsearch/SearchPage.html
@@ -16,6 +16,19 @@
   limitations under the License.
 -->
 <html xmlns:wicket="http://wicket.apache.org/dtds.data/wicket-xhtml1.4-strict.dtd">
+<head>
+  <wicket:head>
+    <style>
+      .results-table thead {
+        position: sticky;
+        top: 0px;
+      }
+      .results-table thead td {
+        border-bottom: 0px;
+      }
+    </style>
+  </wicket:head>
+</head>
 <body>
   <wicket:extend>
     <div class="flex-content flex-v-container flex-gutter">
@@ -40,7 +53,7 @@
       </form>
       <div class="scrolling flex-content flex-h-container mb-0">
         <div wicket:id="dataTableContainer" class="w-100">
-          <table wicket:id="resultsTable" class="table" cellspacing="0" >
+          <table wicket:id="resultsTable" class="table results-table" cellspacing="0" >
             [Results table]
           </table>
         </div>