title: Accessing pubmed abstracts using Entrez Utilities Web Service
body: <p>I use <a href="http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/DOC/esoap_java_help.html" rel="nofollow noreferrer">Entrez Utilities Web Service library</a> to access pubmed articles from my Java application (using pubmed identifier). Full working example how to use this tool was published by <a href="https://stackoverflow.com/users/125617/renaud">Renaud</a> in this <a href="https://stackoverflow.com/questions/5410151/download-pubmed-abstracts-in-java">post</a> on <a href="https://github.com/renaud/pubmed_ws_client" rel="nofollow noreferrer">github</a>. Everything works fine in most cases, however lately I found a pubmed id which makes the library crash.</p>
  
  <p>The code that I use looks like this:</p>
  
  <pre><code>public PubmedArticleType searchById(Integer id) throws RemoteException {
      EUtilsServiceStub.ESearchRequest req = new EUtilsServiceStub.ESearchRequest();
      req.setDb("pubmed");
      req.setTerm(id+"[uid]");
      req.setEmail("gmail@gmail.com");
      req.setUsehistory("y");
      EUtilsServiceStub.ESearchResult res = service.run_eSearch(req);
      String webEnv = res.getWebEnv();
      String query_key = res.getQueryKey();
  
      EFetchPubmedServiceStub.EFetchRequest req2 = new EFetchPubmedServiceStub.EFetchRequest();
      req2.setWebEnv(webEnv);
      req2.setQuery_key(query_key);
  
      EFetchPubmedServiceStub.EFetchResult res2 = service2.run_eFetch(req2);
      for (int j = 0; j &lt; res2.getPubmedArticleSet().getPubmedArticleSetChoice().length; j++) {
  
          PubmedArticleType art = res2.getPubmedArticleSet().getPubmedArticleSetChoice()[j].getPubmedArticle();
          if (art != null) {
              return art;
          }
      }
      return null;
  }
  </code></pre>
  
  <p>When I call this function with <code>id = 22363258</code> I get the error that isn't informative at all:</p>
  
  <pre><code>org.apache.axis2.AxisFault
      at org.apache.axis2.AxisFault.makeFault(AxisFault.java:430)
      at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub.fromOM(EFetchPubmedServiceStub.java)
      at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub.run_eFetch(EFetchPubmedServiceStub.java:189)
      at ch.epfl.bbp.uima.pubmed.PubmedSearch.searchById(PubmedSearch.java:130)
      at ch.epfl.bbp.uima.pubmed.PubmedSearchTest.testPubmedId(PubmedSearchTest.java:14)
      at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
      at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
      at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
      at java.lang.reflect.Method.invoke(Unknown Source)
      at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:45)
      at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:15)
      at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:42)
      at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:20)
      at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:263)
      at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:68)
      at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:47)
      at org.junit.runners.ParentRunner$3.run(ParentRunner.java:231)
      at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:60)
      at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:229)
      at org.junit.runners.ParentRunner.access$000(ParentRunner.java:50)
      at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:222)
      at org.junit.runners.ParentRunner.run(ParentRunner.java:300)
      at org.eclipse.jdt.internal.junit4.runner.JUnit4TestReference.run(JUnit4TestReference.java:50)
      at org.eclipse.jdt.internal.junit.runner.TestExecution.run(TestExecution.java:38)
      at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:467)
      at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:683)
      at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:390)
      at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.main(RemoteTestRunner.java:197)
  Caused by: java.lang.IllegalArgumentException
      at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub$PubModel_type0$Factory.fromString(EFetchPubmedServiceStub.java:20118)
      at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub$PubModel_type0$Factory.fromString(EFetchPubmedServiceStub.java:20129)
      at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub$ArticleType$Factory.parse(EFetchPubmedServiceStub.java)
      at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub$MedlineCitationType$Factory.parse(EFetchPubmedServiceStub.java:28780)
      at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub$PubmedArticleType$Factory.parse(EFetchPubmedServiceStub.java:19147)
      at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub$PubmedArticleSetChoiceE$Factory.parse(EFetchPubmedServiceStub.java)
      at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub$PubmedArticleSet_type0$Factory.parse(EFetchPubmedServiceStub.java:56549)
      at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub$EFetchResult$Factory.parse(EFetchPubmedServiceStub.java:50607)
      ... 27 more
  </code></pre>
  
  <p>So, I have two questions:</p>
  
  <ul>
  <li>What is the reason? What I can do to fix it?</li>
  <li>Is there any other java API that I could use to access pubmed abstracts? I know I can parse html pages, but I realy don't want to do it, because it introduces more problems than it solves...</li>
  </ul>