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OHDSI / Vocabulary-v5.0

Build process for the OHDSI Standardized Vocabularies. Currently not available as independent release.
The Unlicense
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Issue while running JAR file #1046

Open clairblacketer opened 2 months ago

clairblacketer commented 2 months ago

i have downloaded vocabularies and extracted the files and while running cpt.sh i am facing issues running the JAR file using the API key. please let me know what are the prerequisite to be installed to run this JAR fie in databricks environment. also the JAR file is running perfectly in command prompt and CPT4 records also got updated. but throwing error while running in databricks environment ERROR: "Separator not found and chunk size limit exceeded"

any suggestion that would be very helpful folks!

**transferring this issue from the CDM github

@Fyaz92a

YaroslavTir commented 2 months ago

@clairblacketer

JAR file is running perfectly in the command prompt, and CPT4 records also got updated, but throwing an error while running n the Databricks environment.

I am not fully sure where the issue is occurring. It can be interpreted in two ways:

  1. The JAR is being executed in the Databricks environment:

    • Can you provide the complete logfile.log to better understand the issue?
    • A possible workaround could be to copy the updated CPT4 CSV files directly into Databricks.

  2. CSV files are being imported into Databricks:

    • I need clarification on which commands are being used to import the CSV files.