[
https://issues.apache.org/jira/browse/CTAKES-539?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17611347#comment-17611347
]
Ritika Maheshwari commented on CTAKES-539:
------------------------------------------
Attaching the uima log. Although in case of the error reported by santanu he
probably did not download the umls resources as he was getting the following
error
16 moreCaused by: java.io.FileNotFoundException: No File exists at
org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml at
But that is not the case with me as I have downloaded the code. Although I had
to change an import statement in DrugMentionAnotator.xml as it was not able to
find the TypeSystem.xml
<typeSystemDescription>
<imports>
<!-- <import name="org.apache.ctakes.drugner.types.TypeSystem"/ -->
<import location
="../../src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml"/>
</imports>
Some how not able to attach the log file it complains about missing token.
Putting it here
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!DOCTYPE log SYSTEM "logger.dtd">
<log>
<record>
<date>2022-09-29T18:11:35</date>
<millis>1664500295309</millis>
<sequence>0</sequence>
<logger>org.apache.uima</logger>
<level>SEVERE</level>
<class>org.apache.uima.tools.cvd.MainFrame</class>
<method>handleException(527)</method>
<thread>24</thread>
<message>Initialization of annotator class
"org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.
(Descriptor:
file:/Users/ritikamaheshwari/cTakesL/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)</message>
<exception>
<message>org.apache.uima.resource.ResourceInitializationException:
Initialization of annotator class
"org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.
(Descriptor:
file:/Users/ritikamaheshwari/cTakesL/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)</message>
<frame>
<class>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl</class>
<method>initializeAnalysisComponent</method>
<line>274</line>
</frame>
<frame>
<class>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl</class>
<method>initialize</method>
<line>172</line>
</frame>
<frame>
<class>org.apache.uima.impl.AnalysisEngineFactory_impl</class>
<method>produceResource</method>
<line>94</line>
</frame>
<frame>
<class>org.apache.uima.impl.CompositeResourceFactory_impl</class>
<method>produceResource</method>
<line>62</line>
</frame>
<frame>
<class>org.apache.uima.UIMAFramework</class>
<method>produceResource</method>
<line>279</line>
</frame>
<frame>
<class>org.apache.uima.UIMAFramework</class>
<method>produceAnalysisEngine</method>
<line>407</line>
</frame>
<frame>
<class>org.apache.uima.analysis_engine.asb.impl.ASB_impl</class>
<method>setup</method>
<line>256</line>
</frame>
<frame>
<class>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl</class>
<method>initASB</method>
<line>435</line>
</frame>
<frame>
<class>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl</class>
<method>initializeAggregateAnalysisEngine</method>
<line>379</line>
</frame>
<frame>
<class>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl</class>
<method>initialize</method>
<line>192</line>
</frame>
<frame>
<class>org.apache.uima.impl.AnalysisEngineFactory_impl</class>
<method>produceResource</method>
<line>94</line>
</frame>
<frame>
<class>org.apache.uima.impl.CompositeResourceFactory_impl</class>
<method>produceResource</method>
<line>62</line>
</frame>
<frame>
<class>org.apache.uima.UIMAFramework</class>
<method>produceResource</method>
<line>279</line>
</frame>
<frame>
<class>org.apache.uima.UIMAFramework</class>
<method>produceAnalysisEngine</method>
<line>371</line>
</frame>
<frame>
<class>org.apache.uima.tools.cvd.MainFrame</class>
<method>setupAE</method>
<line>1486</line>
</frame>
<frame>
<class>org.apache.uima.tools.cvd.MainFrame</class>
<method>loadAEDescriptor</method>
<line>477</line>
</frame>
<frame>
<class>org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler</class>
<method>actionPerformed</method>
<line>52</line>
</frame>
<frame>
<class>javax.swing.AbstractButton</class>
<method>fireActionPerformed</method>
<line>2022</line>
</frame>
<frame>
<class>javax.swing.AbstractButton$Handler</class>
<method>actionPerformed</method>
<line>2348</line>
</frame>
<frame>
<class>javax.swing.DefaultButtonModel</class>
<method>fireActionPerformed</method>
<line>402</line>
</frame>
<frame>
<class>javax.swing.DefaultButtonModel</class>
<method>setPressed</method>
<line>259</line>
</frame>
<frame>
<class>javax.swing.AbstractButton</class>
<method>doClick</method>
<line>376</line>
</frame>
<frame>
<class>javax.swing.plaf.basic.BasicMenuItemUI</class>
<method>doClick</method>
<line>842</line>
</frame>
<frame>
<class>javax.swing.plaf.basic.BasicMenuItemUI$Handler</class>
<method>mouseReleased</method>
<line>886</line>
</frame>
<frame>
<class>java.awt.Component</class>
<method>processMouseEvent</method>
<line>6539</line>
</frame>
<frame>
<class>javax.swing.JComponent</class>
<method>processMouseEvent</method>
<line>3324</line>
</frame>
<frame>
<class>java.awt.Component</class>
<method>processEvent</method>
<line>6304</line>
</frame>
<frame>
<class>java.awt.Container</class>
<method>processEvent</method>
<line>2239</line>
</frame>
<frame>
<class>java.awt.Component</class>
<method>dispatchEventImpl</method>
<line>4889</line>
</frame>
<frame>
<class>java.awt.Container</class>
<method>dispatchEventImpl</method>
<line>2297</line>
</frame>
<frame>
<class>java.awt.Component</class>
<method>dispatchEvent</method>
<line>4711</line>
</frame>
<frame>
<class>java.awt.LightweightDispatcher</class>
<method>retargetMouseEvent</method>
<line>4904</line>
</frame>
<frame>
<class>java.awt.LightweightDispatcher</class>
<method>processMouseEvent</method>
<line>4535</line>
</frame>
<frame>
<class>java.awt.LightweightDispatcher</class>
<method>dispatchEvent</method>
<line>4476</line>
</frame>
<frame>
<class>java.awt.Container</class>
<method>dispatchEventImpl</method>
<line>2283</line>
</frame>
<frame>
<class>java.awt.Window</class>
<method>dispatchEventImpl</method>
<line>2746</line>
</frame>
<frame>
<class>java.awt.Component</class>
<method>dispatchEvent</method>
<line>4711</line>
</frame>
<frame>
<class>java.awt.EventQueue</class>
<method>dispatchEventImpl</method>
<line>760</line>
</frame>
<frame>
<class>java.awt.EventQueue</class>
<method>access$500</method>
<line>97</line>
</frame>
<frame>
<class>java.awt.EventQueue$3</class>
<method>run</method>
<line>709</line>
</frame>
<frame>
<class>java.awt.EventQueue$3</class>
<method>run</method>
<line>703</line>
</frame>
<frame>
<class>java.security.AccessController</class>
<method>doPrivileged</method>
</frame>
<frame>
<class>java.security.ProtectionDomain$JavaSecurityAccessImpl</class>
<method>doIntersectionPrivilege</method>
<line>74</line>
</frame>
<frame>
<class>java.security.ProtectionDomain$JavaSecurityAccessImpl</class>
<method>doIntersectionPrivilege</method>
<line>84</line>
</frame>
<frame>
<class>java.awt.EventQueue$4</class>
<method>run</method>
<line>733</line>
</frame>
<frame>
<class>java.awt.EventQueue$4</class>
<method>run</method>
<line>731</line>
</frame>
<frame>
<class>java.security.AccessController</class>
<method>doPrivileged</method>
</frame>
<frame>
<class>java.security.ProtectionDomain$JavaSecurityAccessImpl</class>
<method>doIntersectionPrivilege</method>
<line>74</line>
</frame>
<frame>
<class>java.awt.EventQueue</class>
<method>dispatchEvent</method>
<line>730</line>
</frame>
<frame>
<class>java.awt.EventDispatchThread</class>
<method>pumpOneEventForFilters</method>
<line>205</line>
</frame>
<frame>
<class>java.awt.EventDispatchThread</class>
<method>pumpEventsForFilter</method>
<line>116</line>
</frame>
<frame>
<class>java.awt.EventDispatchThread</class>
<method>pumpEventsForHierarchy</method>
<line>105</line>
</frame>
<frame>
<class>java.awt.EventDispatchThread</class>
<method>pumpEvents</method>
<line>101</line>
</frame>
<frame>
<class>java.awt.EventDispatchThread</class>
<method>pumpEvents</method>
<line>93</line>
</frame>
<frame>
<class>java.awt.EventDispatchThread</class>
<method>run</method>
<line>82</line>
</frame>
</exception>
</record>
<record>
<date>2022-09-29T18:34:01</date>
<millis>1664501641759</millis>
<sequence>1</sequence>
<logger>org.apache.uima.resource.impl.ConfigurationManager_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.impl.ConfigurationManager_impl</class>
<method>declareParameters</method>
<thread>24</thread>
<message>Parameter "ChunkCreatorClass" in context / =
"org.apache.ctakes.chunker.ae.PhraseTypeChunkCreator" </message>
</record>
<record>
<date>2022-09-29T18:34:01</date>
<millis>1664501641761</millis>
<sequence>2</sequence>
<logger>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl</class>
<method>initialize</method>
<thread>24</thread>
<message>AnalysisEngine [AggregatePlaintextFastUMLSProcessor] initialization
begin</message>
</record>
<record>
<date>2022-09-29T18:34:01</date>
<millis>1664501641761</millis>
<sequence>3</sequence>
<logger>org.apache.uima.resource.metadata.impl.Import_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by location:
file:/Users/ritikamaheshwari/cTakesL/ctakes-chunker/desc/Chunker.xml</message>
</record>
<record>
<date>2022-09-29T18:34:01</date>
<millis>1664501641768</millis>
<sequence>4</sequence>
<logger>org.apache.uima.resource.metadata.impl.Import_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by name:
file:/Users/ritikamaheshwari/cTakesL/ctakes-type-system/target/classes/org/apache/ctakes/typesystem/types/TypeSystem.xml</message>
</record>
<record>
<date>2022-09-29T18:34:01</date>
<millis>1664501641781</millis>
<sequence>5</sequence>
<logger>org.apache.uima.resource.metadata.impl.Import_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by location:
file:/Users/ritikamaheshwari/cTakesL/ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml</message>
</record>
<record>
<date>2022-09-29T18:34:01</date>
<millis>1664501641786</millis>
<sequence>6</sequence>
<logger>org.apache.uima.resource.metadata.impl.Import_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by name:
file:/Users/ritikamaheshwari/cTakesL/ctakes-type-system/target/classes/org/apache/ctakes/typesystem/types/TypeSystem.xml</message>
</record>
<record>
<date>2022-09-29T18:34:01</date>
<millis>1664501641786</millis>
<sequence>7</sequence>
<logger>org.apache.uima.resource.metadata.impl.Import_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by location:
file:/Users/ritikamaheshwari/cTakesL/ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml</message>
</record>
<record>
<date>2022-09-29T18:34:01</date>
<millis>1664501641791</millis>
<sequence>8</sequence>
<logger>org.apache.uima.resource.metadata.impl.Import_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by location:
file:/Users/ritikamaheshwari/cTakesL/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml</message>
</record>
<record>
<date>2022-09-29T18:34:01</date>
<millis>1664501641796</millis>
<sequence>9</sequence>
<logger>org.apache.uima.resource.metadata.impl.Import_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by location:
file:/Users/ritikamaheshwari/cTakesL/ctakes-ne-contexts/desc/StatusAnnotator.xml</message>
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<record>
<date>2022-09-29T18:34:01</date>
<millis>1664501641802</millis>
<sequence>10</sequence>
<logger>org.apache.uima.resource.metadata.impl.Import_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by location:
file:/Users/ritikamaheshwari/cTakesL/ctakes-ne-contexts/desc/NegationAnnotator.xml</message>
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<record>
<date>2022-09-29T18:34:01</date>
<millis>1664501641807</millis>
<sequence>11</sequence>
<logger>org.apache.uima.resource.metadata.impl.Import_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by location:
file:/Users/ritikamaheshwari/cTakesL/ctakes-clinical-pipeline/desc/analysis_engine/ExtractionPrepAnnotator.xml</message>
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<record>
<date>2022-09-29T18:34:01</date>
<millis>1664501641811</millis>
<sequence>12</sequence>
<logger>org.apache.uima.resource.metadata.impl.Import_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by location:
file:/Users/ritikamaheshwari/cTakesL/ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.xml</message>
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<record>
<date>2022-09-29T18:34:01</date>
<millis>1664501641815</millis>
<sequence>13</sequence>
<logger>org.apache.uima.resource.metadata.impl.Import_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by location:
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<record>
<date>2022-09-29T18:34:01</date>
<millis>1664501641820</millis>
<sequence>14</sequence>
<logger>org.apache.uima.resource.metadata.impl.Import_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by location:
file:/Users/ritikamaheshwari/cTakesL/ctakes-chunker/desc/AdjustNounPhraseToIncludeFollowingPPNP.xml</message>
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<record>
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<millis>1664501641825</millis>
<sequence>15</sequence>
<logger>org.apache.uima.resource.metadata.impl.Import_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by location:
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<date>2022-09-29T18:34:01</date>
<millis>1664501641829</millis>
<sequence>16</sequence>
<logger>org.apache.uima.resource.metadata.impl.Import_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by name:
file:/Users/ritikamaheshwari/cTakesL/ctakes-type-system/target/classes/org/apache/ctakes/typesystem/types/TypeSystem.xml</message>
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<date>2022-09-29T18:34:01</date>
<millis>1664501641829</millis>
<sequence>17</sequence>
<logger>org.apache.uima.resource.metadata.impl.Import_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by location:
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<millis>1664501641834</millis>
<sequence>18</sequence>
<logger>org.apache.uima.resource.metadata.impl.Import_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by name:
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<date>2022-09-29T18:34:01</date>
<millis>1664501641834</millis>
<sequence>19</sequence>
<logger>org.apache.uima.resource.metadata.impl.Import_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by location:
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<date>2022-09-29T18:34:01</date>
<millis>1664501641840</millis>
<sequence>20</sequence>
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<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by name:
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<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by location:
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<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by location:
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<millis>1664501641848</millis>
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<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by location:
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<record>
<date>2022-09-29T18:34:01</date>
<millis>1664501641852</millis>
<sequence>24</sequence>
<logger>org.apache.uima.resource.metadata.impl.Import_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by location:
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<record>
<date>2022-09-29T18:34:01</date>
<millis>1664501641856</millis>
<sequence>25</sequence>
<logger>org.apache.uima.resource.metadata.impl.Import_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by location:
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<record>
<date>2022-09-29T18:34:01</date>
<millis>1664501641860</millis>
<sequence>26</sequence>
<logger>org.apache.uima.resource.metadata.impl.Import_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by location:
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<record>
<date>2022-09-29T18:34:01</date>
<millis>1664501641864</millis>
<sequence>27</sequence>
<logger>org.apache.uima.resource.metadata.impl.Import_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by location:
file:/Users/ritikamaheshwari/cTakesL/ctakes-assertion/desc/analysis_engine/UncertaintyCleartkAnalysisEngine.xml</message>
</record>
<record>
<date>2022-09-29T18:34:01</date>
<millis>1664501641869</millis>
<sequence>28</sequence>
<logger>org.apache.uima.resource.metadata.impl.Import_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by location:
file:/Users/ritikamaheshwari/cTakesL/ctakes-dependency-parser/desc/analysis_engine/ClearNLPDependencyParserAE.xml</message>
</record>
<record>
<date>2022-09-29T18:34:01</date>
<millis>1664501641873</millis>
<sequence>29</sequence>
<logger>org.apache.uima.resource.metadata.impl.Import_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by name:
file:/Users/ritikamaheshwari/cTakesL/ctakes-type-system/target/classes/org/apache/ctakes/typesystem/types/TypeSystem.xml</message>
</record>
<record>
<date>2022-09-29T18:34:01</date>
<millis>1664501641874</millis>
<sequence>30</sequence>
<logger>org.apache.uima.resource.metadata.impl.Import_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by location:
file:/Users/ritikamaheshwari/cTakesL/ctakes-dependency-parser/desc/analysis_engine/ClearNLPSemanticRoleLabelerAE.xml</message>
</record>
<record>
<date>2022-09-29T18:34:01</date>
<millis>1664501641878</millis>
<sequence>31</sequence>
<logger>org.apache.uima.resource.metadata.impl.Import_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by name:
file:/Users/ritikamaheshwari/cTakesL/ctakes-type-system/target/classes/org/apache/ctakes/typesystem/types/TypeSystem.xml</message>
</record>
<record>
<date>2022-09-29T18:34:01</date>
<millis>1664501641878</millis>
<sequence>32</sequence>
<logger>org.apache.uima.resource.metadata.impl.Import_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by location:
file:/Users/ritikamaheshwari/cTakesL/ctakes-constituency-parser/desc/ConstituencyParserAnnotator.xml</message>
</record>
<record>
<date>2022-09-29T18:34:01</date>
<millis>1664501641883</millis>
<sequence>33</sequence>
<logger>org.apache.uima.resource.metadata.impl.Import_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.metadata.impl.Import_impl</class>
<method>findAbsoluteUrl</method>
<thread>24</thread>
<message>Import by name:
file:/Users/ritikamaheshwari/cTakesL/ctakes-type-system/target/classes/org/apache/ctakes/typesystem/types/TypeSystem.xml</message>
</record>
<record>
<date>2022-09-29T18:34:01</date>
<millis>1664501641887</millis>
<sequence>34</sequence>
<logger>org.apache.uima.analysis_engine.asb.impl.ASB_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.analysis_engine.asb.impl.ASB_impl</class>
<method>initialize</method>
<thread>24</thread>
<message>ASB initialization begin</message>
</record>
<record>
<date>2022-09-29T18:34:01</date>
<millis>1664501641887</millis>
<sequence>35</sequence>
<logger>org.apache.uima.analysis_engine.asb.impl.ASB_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.analysis_engine.asb.impl.ASB_impl</class>
<method>initialize</method>
<thread>24</thread>
<message>ASB initialization successful</message>
</record>
<record>
<date>2022-09-29T18:34:01</date>
<millis>1664501641888</millis>
<sequence>36</sequence>
<logger>org.apache.uima.resource.impl.ConfigurationManager_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.impl.ConfigurationManager_impl</class>
<method>declareParameters</method>
<thread>24</thread>
<message>Parameter "ChunkerModelFile" in context /Chunker/ =
"org/apache/ctakes/chunker/models/chunker-model.zip" </message>
</record>
<record>
<date>2022-09-29T18:34:01</date>
<millis>1664501641888</millis>
<sequence>37</sequence>
<logger>org.apache.uima.resource.impl.ConfigurationManager_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.impl.ConfigurationManager_impl</class>
<method>declareParameters</method>
<thread>24</thread>
<message>Parameter "ChunkCreatorClass" in context /Chunker/ =
"org.apache.ctakes.chunker.ae.PhraseTypeChunkCreator" (overridden from
/ChunkCreatorClass)</message>
</record>
<record>
<date>2022-09-29T18:34:01</date>
<millis>1664501641890</millis>
<sequence>38</sequence>
<logger>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl</class>
<method>initialize</method>
<thread>24</thread>
<message>AnalysisEngine [Chunker] initialization begin</message>
</record>
<record>
<date>2022-09-29T18:34:03</date>
<millis>1664501643570</millis>
<sequence>39</sequence>
<logger>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl</class>
<method>initialize</method>
<thread>24</thread>
<message>AnalysisEngine [Chunker] initialization successful</message>
</record>
<record>
<date>2022-09-29T18:34:03</date>
<millis>1664501643571</millis>
<sequence>40</sequence>
<logger>org.apache.uima.resource.impl.ConfigurationManager_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.impl.ConfigurationManager_impl</class>
<method>declareParameters</method>
<thread>24</thread>
<message>Parameter "SegmentsToSkip" in context /TokenizerAnnotator/ = "[]"
</message>
</record>
<record>
<date>2022-09-29T18:34:03</date>
<millis>1664501643572</millis>
<sequence>41</sequence>
<logger>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl</class>
<method>initialize</method>
<thread>24</thread>
<message>AnalysisEngine [TokenizerAnnotatorPTB] initialization begin</message>
</record>
<record>
<date>2022-09-29T18:34:03</date>
<millis>1664501643574</millis>
<sequence>42</sequence>
<logger>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl</class>
<method>initialize</method>
<thread>24</thread>
<message>AnalysisEngine [TokenizerAnnotatorPTB] initialization
successful</message>
</record>
<record>
<date>2022-09-29T18:34:03</date>
<millis>1664501643575</millis>
<sequence>43</sequence>
<logger>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl</class>
<method>initialize</method>
<thread>24</thread>
<message>AnalysisEngine [ContextDependentTokenizerAnnotator] initialization
begin</message>
</record>
<record>
<date>2022-09-29T18:34:03</date>
<millis>1664501643576</millis>
<sequence>44</sequence>
<logger>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl</class>
<method>initialize</method>
<thread>24</thread>
<message>AnalysisEngine [ContextDependentTokenizerAnnotator] initialization
successful</message>
</record>
<record>
<date>2022-09-29T18:34:03</date>
<millis>1664501643576</millis>
<sequence>45</sequence>
<logger>org.apache.uima.resource.impl.ConfigurationManager_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.impl.ConfigurationManager_impl</class>
<method>declareParameters</method>
<thread>24</thread>
<message>Parameter "windowAnnotations" in context
/DictionaryLookupAnnotatorDB/ =
"org.apache.ctakes.typesystem.type.textspan.Sentence" </message>
</record>
<record>
<date>2022-09-29T18:34:03</date>
<millis>1664501643576</millis>
<sequence>46</sequence>
<logger>org.apache.uima.resource.impl.ConfigurationManager_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.impl.ConfigurationManager_impl</class>
<method>declareParameters</method>
<thread>24</thread>
<message>Parameter "exclusionTags" in context /DictionaryLookupAnnotatorDB/ =
"VB,VBD,VBG,VBN,VBP,VBZ,CC,CD,DT,EX,IN,LS,MD,PDT,POS,PP,PP$,PRP,PRP$,RP,TO,WDT,WP,WPS,WRB"
</message>
</record>
<record>
<date>2022-09-29T18:34:03</date>
<millis>1664501643576</millis>
<sequence>47</sequence>
<logger>org.apache.uima.resource.impl.ConfigurationManager_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.impl.ConfigurationManager_impl</class>
<method>declareParameters</method>
<thread>24</thread>
<message>Parameter "minimumSpan" in context /DictionaryLookupAnnotatorDB/ =
"3" </message>
</record>
<record>
<date>2022-09-29T18:34:03</date>
<millis>1664501643576</millis>
<sequence>48</sequence>
<logger>org.apache.uima.resource.impl.ConfigurationManager_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.resource.impl.ConfigurationManager_impl</class>
<method>declareParameters</method>
<thread>24</thread>
<message>Parameter "DictionaryDescriptor" in context
/DictionaryLookupAnnotatorDB/ =
"org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml" </message>
</record>
<record>
<date>2022-09-29T18:34:03</date>
<millis>1664501643576</millis>
<sequence>49</sequence>
<logger>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl</class>
<method>initialize</method>
<thread>24</thread>
<message>AnalysisEngine [UmlsLookupAnnotator] initialization begin</message>
</record>
<record>
<date>2022-09-29T18:34:03</date>
<millis>1664501643583</millis>
<sequence>50</sequence>
<logger>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl</class>
<method>destroy</method>
<thread>24</thread>
<message>AnalysisEngine [Chunker] destroyed.</message>
</record>
<record>
<date>2022-09-29T18:34:03</date>
<millis>1664501643583</millis>
<sequence>51</sequence>
<logger>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl</class>
<method>destroy</method>
<thread>24</thread>
<message>AnalysisEngine [TokenizerAnnotatorPTB] destroyed.</message>
</record>
<record>
<date>2022-09-29T18:34:03</date>
<millis>1664501643583</millis>
<sequence>52</sequence>
<logger>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl</class>
<method>destroy</method>
<thread>24</thread>
<message>AnalysisEngine [ContextDependentTokenizerAnnotator]
destroyed.</message>
</record>
<record>
<date>2022-09-29T18:34:03</date>
<millis>1664501643583</millis>
<sequence>53</sequence>
<logger>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl</logger>
<level>CONFIG</level>
<class>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl</class>
<method>destroy</method>
<thread>24</thread>
<message>AnalysisEngine [AggregatePlaintextFastUMLSProcessor]
destroyed.</message>
</record>
<record>
<date>2022-09-29T18:34:03</date>
<millis>1664501643583</millis>
<sequence>54</sequence>
<logger>org.apache.uima</logger>
<level>SEVERE</level>
<class>org.apache.uima.tools.cvd.MainFrame</class>
<method>handleException(527)</method>
<thread>24</thread>
<message>Initialization of annotator class
"org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.
(Descriptor:
file:/Users/ritikamaheshwari/cTakesL/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)</message>
<exception>
<message>org.apache.uima.resource.ResourceInitializationException:
Initialization of annotator class
"org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.
(Descriptor:
file:/Users/ritikamaheshwari/cTakesL/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)</message>
<frame>
<class>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl</class>
<method>initializeAnalysisComponent</method>
<line>274</line>
</frame>
<frame>
<class>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl</class>
<method>initialize</method>
<line>172</line>
</frame>
<frame>
<class>org.apache.uima.impl.AnalysisEngineFactory_impl</class>
<method>produceResource</method>
<line>94</line>
</frame>
<frame>
<class>org.apache.uima.impl.CompositeResourceFactory_impl</class>
<method>produceResource</method>
<line>62</line>
</frame>
<frame>
<class>org.apache.uima.UIMAFramework</class>
<method>produceResource</method>
<line>279</line>
</frame>
<frame>
<class>org.apache.uima.UIMAFramework</class>
<method>produceAnalysisEngine</method>
<line>407</line>
</frame>
<frame>
<class>org.apache.uima.analysis_engine.asb.impl.ASB_impl</class>
<method>setup</method>
<line>256</line>
</frame>
<frame>
<class>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl</class>
<method>initASB</method>
<line>435</line>
</frame>
<frame>
<class>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl</class>
<method>initializeAggregateAnalysisEngine</method>
<line>379</line>
</frame>
<frame>
<class>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl</class>
<method>initialize</method>
<line>192</line>
</frame>
<frame>
<class>org.apache.uima.impl.AnalysisEngineFactory_impl</class>
<method>produceResource</method>
<line>94</line>
</frame>
<frame>
<class>org.apache.uima.impl.CompositeResourceFactory_impl</class>
<method>produceResource</method>
<line>62</line>
</frame>
<frame>
<class>org.apache.uima.UIMAFramework</class>
<method>produceResource</method>
<line>279</line>
</frame>
<frame>
<class>org.apache.uima.UIMAFramework</class>
<method>produceAnalysisEngine</method>
<line>371</line>
</frame>
<frame>
<class>org.apache.uima.tools.cvd.MainFrame</class>
<method>setupAE</method>
<line>1486</line>
</frame>
<frame>
<class>org.apache.uima.tools.cvd.MainFrame</class>
<method>loadAEDescriptor</method>
<line>477</line>
</frame>
<frame>
<class>org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler</class>
<method>actionPerformed</method>
<line>52</line>
</frame>
<frame>
<class>javax.swing.AbstractButton</class>
<method>fireActionPerformed</method>
<line>2022</line>
</frame>
<frame>
<class>javax.swing.AbstractButton$Handler</class>
<method>actionPerformed</method>
<line>2348</line>
</frame>
<frame>
<class>javax.swing.DefaultButtonModel</class>
<method>fireActionPerformed</method>
<line>402</line>
</frame>
<frame>
<class>javax.swing.DefaultButtonModel</class>
<method>setPressed</method>
<line>259</line>
</frame>
<frame>
<class>javax.swing.AbstractButton</class>
<method>doClick</method>
<line>376</line>
</frame>
<frame>
<class>javax.swing.plaf.basic.BasicMenuItemUI</class>
<method>doClick</method>
<line>842</line>
</frame>
<frame>
<class>javax.swing.plaf.basic.BasicMenuItemUI$Handler</class>
<method>mouseReleased</method>
<line>886</line>
</frame>
<frame>
<class>java.awt.Component</class>
<method>processMouseEvent</method>
<line>6539</line>
</frame>
<frame>
<class>javax.swing.JComponent</class>
<method>processMouseEvent</method>
<line>3324</line>
</frame>
<frame>
<class>java.awt.Component</class>
<method>processEvent</method>
<line>6304</line>
</frame>
<frame>
<class>java.awt.Container</class>
<method>processEvent</method>
<line>2239</line>
</frame>
<frame>
<class>java.awt.Component</class>
<method>dispatchEventImpl</method>
<line>4889</line>
</frame>
<frame>
<class>java.awt.Container</class>
<method>dispatchEventImpl</method>
<line>2297</line>
</frame>
<frame>
<class>java.awt.Component</class>
<method>dispatchEvent</method>
<line>4711</line>
</frame>
<frame>
<class>java.awt.LightweightDispatcher</class>
<method>retargetMouseEvent</method>
<line>4904</line>
</frame>
<frame>
<class>java.awt.LightweightDispatcher</class>
<method>processMouseEvent</method>
<line>4535</line>
</frame>
<frame>
<class>java.awt.LightweightDispatcher</class>
<method>dispatchEvent</method>
<line>4476</line>
</frame>
<frame>
<class>java.awt.Container</class>
<method>dispatchEventImpl</method>
<line>2283</line>
</frame>
<frame>
<class>java.awt.Window</class>
<method>dispatchEventImpl</method>
<line>2746</line>
</frame>
<frame>
<class>java.awt.Component</class>
<method>dispatchEvent</method>
<line>4711</line>
</frame>
<frame>
<class>java.awt.EventQueue</class>
<method>dispatchEventImpl</method>
<line>760</line>
</frame>
<frame>
<class>java.awt.EventQueue</class>
<method>access$500</method>
<line>97</line>
</frame>
<frame>
<class>java.awt.EventQueue$3</class>
<method>run</method>
<line>709</line>
</frame>
<frame>
<class>java.awt.EventQueue$3</class>
<method>run</method>
<line>703</line>
</frame>
<frame>
<class>java.security.AccessController</class>
<method>doPrivileged</method>
</frame>
<frame>
<class>java.security.ProtectionDomain$JavaSecurityAccessImpl</class>
<method>doIntersectionPrivilege</method>
<line>74</line>
</frame>
<frame>
<class>java.security.ProtectionDomain$JavaSecurityAccessImpl</class>
<method>doIntersectionPrivilege</method>
<line>84</line>
</frame>
<frame>
<class>java.awt.EventQueue$4</class>
<method>run</method>
<line>733</line>
</frame>
<frame>
<class>java.awt.EventQueue$4</class>
<method>run</method>
<line>731</line>
</frame>
<frame>
<class>java.security.AccessController</class>
<method>doPrivileged</method>
</frame>
<frame>
<class>java.security.ProtectionDomain$JavaSecurityAccessImpl</class>
<method>doIntersectionPrivilege</method>
<line>74</line>
</frame>
<frame>
<class>java.awt.EventQueue</class>
<method>dispatchEvent</method>
<line>730</line>
</frame>
<frame>
<class>java.awt.EventDispatchThread</class>
<method>pumpOneEventForFilters</method>
<line>205</line>
</frame>
<frame>
<class>java.awt.EventDispatchThread</class>
<method>pumpEventsForFilter</method>
<line>116</line>
</frame>
<frame>
<class>java.awt.EventDispatchThread</class>
<method>pumpEventsForHierarchy</method>
<line>105</line>
</frame>
<frame>
<class>java.awt.EventDispatchThread</class>
<method>pumpEvents</method>
<line>101</line>
</frame>
<frame>
<class>java.awt.EventDispatchThread</class>
<method>pumpEvents</method>
<line>93</line>
</frame>
<frame>
<class>java.awt.EventDispatchThread</class>
<method>run</method>
<line>82</line>
</frame>
</exception>
</record>
</log>
> cTakes 4.0 installation error
> -----------------------------
>
> Key: CTAKES-539
> URL: https://issues.apache.org/jira/browse/CTAKES-539
> Project: cTAKES
> Issue Type: Bug
> Reporter: santanu barkakati
> Priority: Major
>
> I am trying to follow the user installation guide, but got error in below
> step1 of
> h3. CAS Visual Debugger (CVD)
> bin\runctakesCVD.bat
> desc\ctakes-clinical-pipeline\desc\analysis_engine\AggregatePlaintextFastUMLSProcessor.xml
> Would appreciate some direction.
> *Below is the error from log file:*
> 12:03:17.219 - 1: org.apache.uima.tools.cvd.MainFrame.handleException(526):
> SEVERE: Initialization of annotator class
> "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator"
> *{color:#FF0000}failed.{color}* (Descriptor:
> file:/C:/Users/sbarkakati/cTakes/apache-ctakes-4.0.0/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)12:03:17.219
> - 1: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE:
> Initialization of annotator class
> "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.
> (Descriptor:
> file:/C:/Users/sbarkakati/cTakes/apache-ctakes-4.0.0/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)org.apache.uima.resource.ResourceInitializationException:
> Initialization of annotator class
> "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.
> (Descriptor:
> file:/C:/Users/sbarkakati/cTakes/apache-ctakes-4.0.0/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:271)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:170)
> 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:279) at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:407)
> at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:256)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:429)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:373)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:186)
> 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:279) at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:371)
> at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484) at
> org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:476) at
> org.apache.uima.tools.cvd.CVD.main(CVD.java:164)Caused by:
> org.apache.uima.resource.ResourceInitializationException 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:266)
> ... 16 moreCaused by: java.io.FileNotFoundException: No File exists at
> org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml at
> org.apache.ctakes.core.resource.FileLocator.getFullPath(FileLocator.java:193)
> at
> org.apache.ctakes.core.resource.FileLocator.locateFile(FileLocator.java:99)
> at
> org.apache.ctakes.core.resource.FileLocator.getAsStream(FileLocator.java:73)
> at
> org.apache.ctakes.core.resource.FileLocator.getAsStream(FileLocator.java:53)
> at
> org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTe
>
> rmAnnotator.java:128) ... 17 more
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