- #4556 - Unable to access PMC BioC service

- Fix PubAnnotation document access - Re-enable tests
inception-project · Mar 4, 2024 · 215083f · 215083f
1 parent 4631370
commit 215083f
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Showing 3 changed files with 19 additions and 25 deletions.
diff --git a/...java/de/tudarmstadt/ukp/inception/externalsearch/pubannotation/PubAnnotationProvider.java b/...java/de/tudarmstadt/ukp/inception/externalsearch/pubannotation/PubAnnotationProvider.java
@@ -67,7 +67,7 @@ public PubAnnotationProvider(EntrezClient aEntrezClient)
     List<PubAnnotationDocumentHandle> query(PubAnnotationProviderTraits aTraits, String aQuery,
             int aPage, int aPageSize)
     {
-        Map<String, String> variables = new HashMap<>();
+        var variables = new HashMap<String, String>();
         variables.put("keywords", aQuery);
         variables.put("page", Integer.toString(aPage));
         variables.put("per", Integer.toString(aPageSize));
@@ -84,12 +84,12 @@ List<PubAnnotationDocumentHandle> query(PubAnnotationProviderTraits aTraits, Str
     public List<ExternalSearchResult> executeQuery(DocumentRepository aDocumentRepository,
             PubAnnotationProviderTraits aTraits, String aQuery)
     {
-        List<PubAnnotationDocumentHandle> response = query(aTraits, aQuery, 1, 100);
+        var response = query(aTraits, aQuery, 1, 100);
 
         var documentSummaries = lookupDocumentSummaries(response);
 
-        List<ExternalSearchResult> results = new ArrayList<>();
-        for (PubAnnotationDocumentHandle handle : response) {
+        var results = new ArrayList<ExternalSearchResult>();
+        for (var handle : response) {
             var summary = documentSummaries
                     .get(Pair.of(handle.getSourceDb(), parseInt(handle.getSourceId())));
             var result = new ExternalSearchResult(aDocumentRepository, handle.getSourceDb(),
@@ -112,7 +112,7 @@ public List<ExternalSearchResult> executeQuery(DocumentRepository aDocumentRepos
     private Map<Pair<String, Integer>, DocSum> lookupDocumentSummaries(
             List<PubAnnotationDocumentHandle> response)
     {
-        Map<Pair<String, Integer>, DocSum> documentDetails = new HashMap<>();
+        var documentDetails = new HashMap<Pair<String, Integer>, DocSum>();
         var groupedByDb = response.stream()
                 .collect(groupingBy(PubAnnotationDocumentHandle::getSourceDb));
         for (var group : groupedByDb.entrySet()) {
@@ -133,25 +133,24 @@ public ExternalSearchResult getDocumentResult(DocumentRepository aRepository,
             PubAnnotationProviderTraits aTraits, String aCollectionId, String aDocumentId)
         throws IOException
     {
-        ExternalSearchResult result = new ExternalSearchResult(aRepository, aCollectionId,
-                aDocumentId);
-        return result;
+        return new ExternalSearchResult(aRepository, aCollectionId, aDocumentId);
     }
 
     @Override
     public String getDocumentText(DocumentRepository aDocumentRepository,
             PubAnnotationProviderTraits aTraits, String aCollectionId, String aDocumentId)
     {
         return getSections(aDocumentRepository, aTraits, aCollectionId, aDocumentId).stream()
-                .map(PubAnnotationDocumentSection::getText).collect(Collectors.joining("\n\n"));
+                .map(PubAnnotationDocumentSection::getText) //
+                .collect(Collectors.joining("\n\n"));
     }
 
     @Override
     public InputStream getDocumentAsStream(DocumentRepository aDocumentRepository,
             PubAnnotationProviderTraits aTraits, String aCollectionId, String aDocumentId)
         throws IOException
     {
-        String json = JSONUtil.toJsonString(
+        var json = JSONUtil.toJsonString(
                 getSections(aDocumentRepository, aTraits, aCollectionId, aDocumentId));
 
         return IOUtils.toInputStream(json, UTF_8);
@@ -160,18 +159,16 @@ public InputStream getDocumentAsStream(DocumentRepository aDocumentRepository,
     private List<PubAnnotationDocumentSection> getSections(DocumentRepository aDocumentRepository,
             PubAnnotationProviderTraits aTraits, String aCollectionId, String aDocumentId)
     {
-        Map<String, String> variables = new HashMap<>();
+        var variables = new HashMap<String, String>();
         variables.put("collectionId", aCollectionId);
         variables.put("documentId", aDocumentId);
 
-        RestTemplate restTemplate = new RestTemplate();
+        var restTemplate = new RestTemplate();
 
-        var url = aTraits.getUrl() + "/docs/sourcedb/{collectionId}/sourceid/{documentId}.json";
+        var url = aTraits.getUrl() + "/docs/sourcedb/{collectionId}/sourceid/{documentId}";
         try {
             // If the document has multiple sections, a list is returned...
-            ResponseEntity<List<PubAnnotationDocumentSection>> response = restTemplate.exchange(url,
-                    GET, null, SPRING_LIST_TYPE_REF, variables);
-
+            var response = restTemplate.exchange(url, GET, null, SPRING_LIST_TYPE_REF, variables);
             return response.getBody();
         }
         catch (RestClientException e) {

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
@@ -35,7 +35,6 @@
 
 import org.apache.uima.UIMAException;
 
-import de.tudarmstadt.ukp.clarin.webanno.model.Project;
 import de.tudarmstadt.ukp.inception.externalsearch.ExternalSearchProvider;
 import de.tudarmstadt.ukp.inception.externalsearch.ExternalSearchResult;
 import de.tudarmstadt.ukp.inception.externalsearch.model.DocumentRepository;
@@ -81,10 +80,10 @@ public List<ExternalSearchResult> executeQuery(DocumentRepository aDocumentRepos
         var summaryResponse = entrezClient.esummary(DB_PUB_MED_CENTRAL,
                 searchResponse.getIdList().stream().mapToInt(i -> i).toArray());
 
-        List<ExternalSearchResult> results = new ArrayList<>();
+        var results = new ArrayList<ExternalSearchResult>();
         for (var summary : summaryResponse.getDocSumaries()) {
-            ExternalSearchResult result = new ExternalSearchResult(aDocumentRepository,
-                    DB_PUB_MED_CENTRAL, summary.getId() + EXT_XML);
+            var result = new ExternalSearchResult(aDocumentRepository, DB_PUB_MED_CENTRAL,
+                    summary.getId() + EXT_XML);
             result.setOriginalUri(
                     "https://www.ncbi.nlm.nih.gov/pmc/articles/" + PMCID_PREFIX + summary.getId());
             result.setOriginalSource(summary.source());
@@ -110,9 +109,7 @@ public ExternalSearchResult getDocumentResult(DocumentRepository aRepository,
             PubMedProviderTraits aTraits, String aCollectionId, String aDocumentId)
         throws IOException
     {
-        ExternalSearchResult result = new ExternalSearchResult(aRepository, aCollectionId,
-                aDocumentId);
-        return result;
+        return new ExternalSearchResult(aRepository, aCollectionId, aDocumentId);
     }
 
     @Override
@@ -123,7 +120,7 @@ public String getDocumentText(DocumentRepository aDocumentRepository,
         var biocXml = pmcoaClient.bioc(aTraits, PMCID_PREFIX + stripExtension(aDocumentId));
 
         try {
-            Project project = aDocumentRepository.getProject();
+            var project = aDocumentRepository.getProject();
             var cas = WebAnnoCasUtil.createCas(schemaService.getFullProjectTypeSystem(project));
             new BioCToCas().parseXml(new ByteArrayInputStream(biocXml), cas.getJCas());
             return cas.getDocumentText();

diff --git a/.../src/test/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/PubMedProviderTest.java b/.../src/test/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/PubMedProviderTest.java
@@ -74,7 +74,7 @@ public void thatGetDocumentTextWorks() throws Exception
         when(annotationService.getFullProjectTypeSystem(any()))
                 .thenReturn(createTypeSystemDescription());
 
-        String results = sut.getDocumentText(repo, traits, "PMC", "PMC7096989");
+        String results = sut.getDocumentText(repo, traits, "PMC", "7096989");
 
         // System.out.println(results);