无法从 UMLS 检索数据答案

【问题标题】：Can't retrieve data back from UMLS无法从 UMLS 检索数据
【发布时间】：2017-05-30 14:51:58
【问题描述】：

我一直在尝试在 github 上运行 ctakes-temporal-demo。目前我已经正确配置了eclipse中的所有内容。我已经为 UMLS 帐户设置了正确的密码和 ID。当我尝试运行它时，我收到以下错误：

Exception in thread "main" java.lang.Exception: org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.  (Descriptor: <unknown>)
       at com.optum.cda.Main.main(Main.java:103)
Caused by: org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.  (Descriptor: <unknown>)
       at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
       at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
       at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
       at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
       at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
       at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
       at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
       at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
       at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
       at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
       at org.apache.uima.fit.factory.AnalysisEngineFactory.createEngine(AnalysisEngineFactory.java:711)
       at org.apache.uima.fit.factory.AggregateBuilder.createAggregate(AggregateBuilder.java:207)
       at com.optum.cda.Main.main(Main.java:101)
Caused by: org.apache.uima.resource.ResourceInitializationException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key Could not construct org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary
       at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:131)
       at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
       ... 12 more
Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorContextException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key Could not construct org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary
       at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:199)
       at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionaries(DictionaryDescriptorParser.java:156)
       at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:128)
       at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:129)
       ... 13 more
Caused by: java.lang.reflect.InvocationTargetException
       at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
       at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
       at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
       at java.lang.reflect.Constructor.newInstance(Unknown Source)
       at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:196)
       ... 16 more
Caused by: java.lang.StringIndexOutOfBoundsException: String index out of range: -7
       at java.lang.String.substring(Unknown Source)
       at org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnectionUrl(JdbcConnectionFactory.java:110)
       at org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnection(JdbcConnectionFactory.java:63)
       at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:91)
       at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:72)
       at org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary.<init>(UmlsJdbcRareWordDictionary.java:31)
       ... 21 more

熟悉 ctakes 的人可以帮我找出错误。我试过邮件列表，但没有回复。

【问题讨论】：

标签： java uima ctakes

【解决方案1】：

终于找到解决办法了！似乎无法访问快速字典的 XML 描述符的路径。因此，在验证 UMLS 用户后，无法继续进行数据库设置。

我使用的解决方案之一是为数据库使用静态地址（如果项目被移动，我必须始终更改该地址。）。这不是很优雅，但很有效。

很想知道是否有人有其他解决方案。

【讨论】：

@TammayDas 您能否简要介绍一下您对代码所做的哪些更改以使其适用于示例？
@Tanmay 你能解释一下你是如何解决这个问题的吗……我也被这个问题困扰了好几天……

【解决方案2】：

你把ctakesnorx.script的数据入库了吗？
我们还需要更新以下属性值：

<property key="jdbcUrl" value="jdbc:hsqldb:file:org/apache/ctakes/dictionary/lookup/fast/ctakessnorx/ctakessnorx"/>
<property key="jdbcUser" value="sa"/>
<property key="jdbcPass" value=""/>
<property key="rareWordTable" value="cui_terms"/>

【讨论】：