我使用Entrez Utilities Web Service库（使用pubmed标识符）从Java应用程序访问已发布的文章。Renaud在github上发布了如何使用该工具的完整工作示例。在大多数情况下，一切都很好，但最近我发现了一个pubmed id，这让库崩溃了。
我使用的代码如下：
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 < res2.getPubmedArticleSet().getPubmedArticleSetChoice().length; j++) {
PubmedArticleType art = res2.getPubmedArticleSet().getPubmedArticleSetChoice()[j].getPubmedArticle();
if (art != null) {
return art;
}
}
return null;
}
当我用id = 22363258调用这个函数时，我得到了一个根本没有信息的错误：
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
所以，我有两个问题：
- 原因是什么？我能做些什么来修复它
- 有没有其他java API可以用来访问公共摘要？我知道我可以解析html页面，但我真的不想这么做，因为它带来的问题比解决的问题多
这里有一个RESTful API，它允许从pubmed数据库中检索摘要和所有元信息。
检索我需要的所有数据的确切链接如下所示：http://www.ebi.ac.uk/europepmc/webservices/rest/search/resulttype=core&query=ext_id:222363258