我正在尝试访问uniprot网站以检索蛋白质序列列表，并将其配置文件作为XML文件。文件很大。我正在使用JBPM全包附带的eclipse。另外，我在虚拟盒子下使用ubuntu。现在当我运行我的代码时，我得到了这个堆栈跟踪：
java.io.IOException: Premature EOF
at sun.net.www.http.ChunkedInputStream.fastRead(ChunkedInputStream.java:234)
at sun.net.www.http.ChunkedInputStream.read(ChunkedInputStream.java:662)
at java.io.FilterInputStream.read(FilterInputStream.java:116)
at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:2512)
at edu.uga.uniprot.amna.QueryExecuter.ExecuteQuery(QueryExecuter.java:40)
at edu.uga.uniprot.amna.Uniprot.getProteenStringByDFamily(Uniprot.java:40)
at edu.uga.uniprot.amna.Uniprot.getProteensByDFamily(Uniprot.java:55)
at org.drools.bpmn2.Process_org_drools_bpmn2_Hello_World_0.action4(Process_org_drools_bpmn2_Hello_World_0.java:60)
at org.drools.bpmn2.Process_org_drools_bpmn2_Hello_World_0Action4Invoker.execute(Process_org_drools_bpmn2_Hello_World_0Action4Invoker.java:14)
at org.jbpm.workflow.instance.node.ActionNodeInstance.internalTrigger(ActionNodeInstance.java:47)
at org.jbpm.workflow.instance.impl.NodeInstanceImpl.trigger(NodeInstanceImpl.java:122)
at org.jbpm.workflow.instance.impl.NodeInstanceImpl.triggerConnection(NodeInstanceImpl.java:185)
at org.jbpm.workflow.instance.impl.NodeInstanceImpl.triggerCompleted(NodeInstanceImpl.java:150)
at org.jbpm.workflow.instance.node.StartNodeInstance.triggerCompleted(StartNodeInstance.java:49)
at org.jbpm.workflow.instance.node.StartNodeInstance.internalTrigger(StartNodeInstance.java:41)
at org.jbpm.workflow.instance.impl.NodeInstanceImpl.trigger(NodeInstanceImpl.java:122)
at org.jbpm.ruleflow.instance.RuleFlowProcessInstance.internalStart(RuleFlowProcessInstance.java:35)
at org.jbpm.process.instance.impl.ProcessInstanceImpl.start(ProcessInstanceImpl.java:188)
at org.jbpm.workflow.instance.impl.WorkflowProcessInstanceImpl.start(WorkflowProcessInstanceImpl.java:302)
at org.jbpm.process.instance.ProcessRuntimeImpl.startProcessInstance(ProcessRuntimeImpl.java:154)
at org.jbpm.process.instance.ProcessRuntimeImpl.startProcess(ProcessRuntimeImpl.java:124)
at org.drools.common.AbstractWorkingMemory.startProcess(AbstractWorkingMemory.java:1095)
at org.drools.impl.StatefulKnowledgeSessionImpl.startProcess(StatefulKnowledgeSessionImpl.java:306)
at com.sample.ProcessTest.main(ProcessTest.java:49)
java.lang.RuntimeException: unable to execute Action
at org.jbpm.workflow.instance.node.ActionNodeInstance.internalTrigger(ActionNodeInstance.java:49)
at org.jbpm.workflow.instance.impl.NodeInstanceImpl.trigger(NodeInstanceImpl.java:122)
at org.jbpm.workflow.instance.impl.NodeInstanceImpl.triggerConnection(NodeInstanceImpl.java:185)
at org.jbpm.workflow.instance.impl.NodeInstanceImpl.triggerCompleted(NodeInstanceImpl.java:150)
at org.jbpm.workflow.instance.node.StartNodeInstance.triggerCompleted(StartNodeInstance.java:49)
at org.jbpm.workflow.instance.node.StartNodeInstance.internalTrigger(StartNodeInstance.java:41)
at org.jbpm.workflow.instance.impl.NodeInstanceImpl.trigger(NodeInstanceImpl.java:122)
at org.jbpm.ruleflow.instance.RuleFlowProcessInstance.internalStart(RuleFlowProcessInstance.java:35)
at org.jbpm.process.instance.impl.ProcessInstanceImpl.start(ProcessInstanceImpl.java:188)
at org.jbpm.workflow.instance.impl.WorkflowProcessInstanceImpl.start(WorkflowProcessInstanceImpl.java:302)
at org.jbpm.process.instance.ProcessRuntimeImpl.startProcessInstance(ProcessRuntimeImpl.java:154)
at org.jbpm.process.instance.ProcessRuntimeImpl.startProcess(ProcessRuntimeImpl.java:124)
at org.drools.common.AbstractWorkingMemory.startProcess(AbstractWorkingMemory.java:1095)
at org.drools.impl.StatefulKnowledgeSessionImpl.startProcess(StatefulKnowledgeSessionImpl.java:306)
at com.sample.ProcessTest.main(ProcessTest.java:49)
Caused by: java.lang.NullPointerException
at java.io.StringReader.<init>(StringReader.java:33)
at edu.uga.uniprot.amna.Uniprot.loadProteenFromString(Uniprot.java:117)
at edu.uga.uniprot.amna.Uniprot.getProteensByDFamily(Uniprot.java:58)
at org.drools.bpmn2.Process_org_drools_bpmn2_Hello_World_0.action4(Process_org_drools_bpmn2_Hello_World_0.java:60)
at org.drools.bpmn2.Process_org_drools_bpmn2_Hello_World_0Action4Invoker.execute(Process_org_drools_bpmn2_Hello_World_0Action4Invoker.java:14)
at org.jbpm.workflow.instance.node.ActionNodeInstance.internalTrigger(ActionNodeInstance.java:47)
... 14 more
任何人都可以帮助解决此错误或导致错误的原因吗？
以下是生成错误的代码：
public static String ExecuteQuery(String queryURL, boolean writeFile) {
URL url;
try {
System.out.println("Strat getting Data");
String output = "";
int read;
RandomAccessFile file = null;
url = new URL(queryURL);
HttpURLConnection connection =
(HttpURLConnection) url.openConnection();
connection.setRequestProperty("Content-Type", "application/xml");
connection.connect();
//read the result from the server
if(writeFile == true) {
file = new RandomAccessFile(fileName, "rw");
}
InputStream stream = connection.getInputStream();
byte[] buffer = new byte[1024];
BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()));
while((read = stream.read(buffer, 0, 1024)) != -1) {
//System.out.println(new String(buffer));
output = output + new String(buffer).substring(0, read);
if(writeFile == true) {
file.write(buffer, 0, read);
}
buffer = new byte[1024];
}
System.out.println(output);
return output;
} catch (MalformedURLException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
return null;
}
答案 0 :(得分：1)
此错误是由您将空值传递到Uniprot.java第117行的新StringReader（）引起的。
你可以通过stacktrace看到这个：
Caused by: java.lang.NullPointerException
at java.io.StringReader.<init>(StringReader.java:33)
at edu.uga.uniprot.amna.Uniprot.loadProteenFromString(Uniprot.java:117)
at edu.uga.uniprot.amna.Uniprot.getProteensByDFamily(Uniprot.java:58)
StringReader的构造函数如下：
public StringReader(String s) {
this.str = s;
this.length = s.length(); // line 33
}
查看更多StringReader。
答案 1 :(得分：1)
如果您尝试在一个http连接中下载大量uniprot条目，则可能会使您的http连接死亡。我建议您查看http://www.uniprot.org/faq/28#retrieving_entries_via_queries并使用http请求中的偏移量和限制参数来限制您尝试一次性检索的条目数。
下载非常大的结果集时，动态http请求往往会失败。另一种选择是通过ftp下载所有条目并处理下载文件。请参阅UniProt FTP site
答案 2 :(得分：-3)
我终于解决了由于快速读取连接速度慢而导致的问题。一旦我添加了System.out.println(new String(buffer))，它就可以了。
println语句会降低读取操作的速度并使其与连接速度兼容。
我希望这对任何面临同样问题的人都有帮助。