bd2konfhir / nlp2fhir Goto Github PK

Is there a publicly available file for this resource? If I have "Medication List Resources" checked I get an error that it can't find the file referenced here:

It doesn't look like it's part of any of the dependency packages.

@qqndrew
Hi Where can I get SNOMEDCT US Edition resource files (downloadable with a UMLS license, placed in ./SNOMEDCT_US) ?

Hi,

I created an FHIR server and I want to connect to this server through your app and use my own data.
Is it possible? If yes, could you please guide me and tell me how?

LG
Sohrab

To update dictionaries for cTAKES and MedTagger

Hi @qqndrew,
When I run NLP2FHIR-GUI-1.0-SNAPSHOT.jar, I got this error. Also which project can I run to get this rest API http://52.252.147.136:8080/submit?

java -jar NLP2FHIR-GUI-1.0-SNAPSHOT.jar
java.util.concurrent.ExecutionException: java.lang.RuntimeException: org.apache.uima.util.InvalidXMLException: An import could not be resolved. No file with name "medxndesc/aggregate_analysis_engine/MedXNAggregateTAE.xml" was found in the class path or data path. (Descriptor: )
at java.base/java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.base/java.util.concurrent.FutureTask.get(FutureTask.java:191)
at edu.mayo.bsi.nlp2fhir.gui.GUI.lambda$createExecuteButton$2(GUI.java:166)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: java.lang.RuntimeException: org.apache.uima.util.InvalidXMLException: An import could not be resolved. No file with name "medxndesc/aggregate_analysis_engine/MedXNAggregateTAE.xml" was found in the class path or data path. (Descriptor: )
at edu.mayo.bsi.nlp2fhir.pipelines.resources.ResourcePipelineBuilder.(ResourcePipelineBuilder.java:69)
at edu.mayo.bsi.nlp2fhir.pipelines.resources.ResourcePipelineBuilder.newBuilder(ResourcePipelineBuilder.java:274)
at edu.mayo.bsi.nlp2fhir.gui.model.pipelinebuilder.tasks.ResourceTask.construct(ResourceTask.java:66)
at edu.mayo.bsi.nlp2fhir.gui.GUI.buildAndExecutePipeline(GUI.java:181)
at edu.mayo.bsi.nlp2fhir.gui.GUI.lambda$createExecuteButton$1(GUI.java:145)
... 5 more
Caused by: org.apache.uima.util.InvalidXMLException: An import could not be resolved. No file with name "medxndesc/aggregate_analysis_engine/MedXNAggregateTAE.xml" was found in the class path or data path. (Descriptor: )
at org.apache.uima.resource.metadata.impl.Import_impl.findAbsoluteUrl(Import_impl.java:122)
at org.apache.uima.fit.factory.AnalysisEngineFactory.createEngineDescription(AnalysisEngineFactory.java:875)
at edu.mayo.bsi.nlp2fhir.pipelines.resources.ResourcePipelineBuilder.initializeSourceSystems(ResourcePipelineBuilder.java:75)
at edu.mayo.bsi.nlp2fhir.pipelines.resources.ResourcePipelineBuilder.(ResourcePipelineBuilder.java:65)

What is the meaning of the fields Section Definition Directory and Section Definition File? We're trying to use and change the software (add language support), but can not figure out how to exactly. Could you please reach out and help us? We've tried e-mail but got no response.

@gqjiang

Hi, could you please provide some example clinical narrative for some sections to try out these app http://52.252.147.136:8080/?iss=http%3A%2F%2Flaunch.smarthealthit.org%2Fv%2Fr3%2Ffhir&launch=eyJhIjoxLCJmIjpmYWxzZSwiZyI6ZmFsc2UsImQiOi0xfQ

Thanks!

@qqndrew I am getting this error while running Annotator main class

Exception in thread "main" org.apache.uima.resource.ResourceInitializationException: Invalid value for parameter "InputDirectory" in component "edu.mayo.bsi.nlp2fhir.preprocessors.FHIRXMIFileSystemReader" -- directory "xmis" does not exist.
at org.apache.ctakes.core.cr.XmiCollectionReaderCtakes.initialize(XmiCollectionReaderCtakes.java:81)
at org.apache.uima.collection.CollectionReader_ImplBase.initialize(CollectionReader_ImplBase.java:70)
at org.apache.uima.impl.CollectionReaderFactory_impl.produceResource(CollectionReaderFactory_impl.java:103)
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.produceResource(UIMAFramework.java:331)
at org.apache.uima.UIMAFramework.produceCollectionReader(UIMAFramework.java:812)
at org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:133)
at edu.mayo.bsi.nlp2fhir.Pipeline.main(Pipeline.java:114)

Looks like the Interface UIMA-Stream-Server/UIMA-Server-Core/src/main/java/edu/mayo/dhs/uima/server/api/UIMANLPResultSerializer.java

has been updated so the return type of serializeNLPResult is JsonNode.

The implementation in this project at:
NLP2FHIR-STREAM/src/main/java/edu/mayo/bsi/nlp2fhir/stream/NLP2FHIRResourceBundleSerializer.java

has the return type Serializable. There isn't a version number change so it's a little difficult to roll back but I will try to git co an older version of UIMA-Stream-Server as a workaround for now.