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import-csv-to-conceptmap is failing unexpectedly. #1320

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dmuylwyk opened this issue May 27, 2019 · 7 comments

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@dmuylwyk
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commented May 27, 2019

I've tested this using the contents of the CSV provided and the import worked without issue. I believe it is the file itself (some encoding issue).


loinc-to-phenx.csv.zip


Testing out the CSV importer for ConceptMaps today on our dev server, and got stuck b/c of this error:

ubuntu@fhir-dev:~/smilecdr/bin$ ./smileutil import-csv-to-conceptmap -v "r4" -t "http://localhost" -f "/home/ubuntu/tmp/loinc-to-phenx.csv" -l -u "http://loinc.org/cm/loinc-to-phenx" -i "http://loinc.org" -o "http://phenxtoolkit.org"
------------------------------------------------------------
🔥  Smile CDR CLI 2019.02.PRE - Command Line Tool
------------------------------------------------------------
Process ID                      : 2976@fhir-dev
Max configured JVM memory (Xmx) : 878.5MB
Detected Java version           : 1.8.0_201
------------------------------------------------------------
2019-03-21 17:54:54 [main] INFO  c.u.f.c.AbstractImportExportCsvConceptMapCommand Specified ConceptMap URL (ConceptMap.url): http://loinc.org/cm/loinc-to-phenx
2019-03-21 17:54:54 [main] INFO  c.u.f.c.ImportCsvToConceptMapCommand Specified source value set (i.e. ConceptMap.sourceUri): http://loinc.org
2019-03-21 17:54:54 [main] INFO  c.u.f.c.ImportCsvToConceptMapCommand Specified target value set (i.e. ConceptMap.targetUri): http://phenxtoolkit.org
2019-03-21 17:54:54 [main] INFO  c.u.f.c.ImportCsvToConceptMapCommand Converting CSV to ConceptMap...
2019-03-21 17:54:54 [main] ERROR ca.uhn.fhir.cli.App Error during execution: 
java.lang.IllegalArgumentException: Mapping for SOURCE_CODE_SYSTEM not found, expected one of [COMMENT, EQUIVALENCE, SOURCE_CODE, SOURCE_CODE_SYSTEM_VERSION, SOURCE_DISPLAY, TARGET_CODE, TARGET_CODE_SYSTEM, TARGET_CODE_SYSTEM_VERSION, TARGET_DISPLAY, SOURCE_CODE_SYSTEM]
    at org.apache.commons.csv.CSVRecord.get(CSVRecord.java:104)
    at org.apache.commons.csv.CSVRecord.get(CSVRecord.java:70)
    at ca.uhn.fhir.cli.ImportCsvToConceptMapCommand.parseCsvRecords(ImportCsvToConceptMapCommand.java:298)
    at ca.uhn.fhir.cli.ImportCsvToConceptMapCommand.convertCsvToConceptMapR4(ImportCsvToConceptMapCommand.java:193)
    at ca.uhn.fhir.cli.ImportCsvToConceptMapCommand.searchForConceptMapByUrl(ImportCsvToConceptMapCommand.java:139)
    at ca.uhn.fhir.cli.ImportCsvToConceptMapCommand.process(ImportCsvToConceptMapCommand.java:118)
    at ca.uhn.fhir.cli.AbstractImportExportCsvConceptMapCommand.run(AbstractImportExportCsvConceptMapCommand.java:107)
    at ca.uhn.fhir.cli.BaseApp.run(BaseApp.java:243)
    at ca.cdr.cli.App.main(App.java:56)
2019-03-21 17:54:54 [Thread-0] INFO  ca.uhn.fhir.cli.App Smile CDR CLI is shutting down...

You'll note in the file I was trying to load (attached), there is exactly the column SOURCE_CODE_SYSTEM, with is in the expected list.

@dmuylwyk dmuylwyk added the bug label May 27, 2019

@dmuylwyk dmuylwyk self-assigned this May 27, 2019

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commented May 27, 2019

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commented May 27, 2019

I'm able to reproduce this in a unit test. : )

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commented May 27, 2019

The first header value is preceded by: \uFEFF/65279

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commented May 27, 2019

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commented May 27, 2019

I'll need to check for this and convert to UTF-8.

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commented May 27, 2019

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commented May 28, 2019

Pull request: #1322

@dmuylwyk dmuylwyk closed this in aed5bb8 Jun 3, 2019

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