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OHDSI / WhiteRabbit

WhiteRabbit is a small application that can be used to analyse the structure and contents of a database as preparation for designing an ETL. It comes with RabbitInAHat, an application for interactive design of an ETL to the OMOP Common Data Model with the help of the the scan report generated by White Rabbit.
http://ohdsi.github.io/WhiteRabbit
Apache License 2.0
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Bug creating ScanReport in WhiteRabbit v0.10.8 #375

Closed elisahenke closed 1 year ago

elisahenke commented 1 year ago

Cannot create ScanReport based on csv files in WhiteRabbit v0.10.8.

Steps to reproduce the behavior for WhiteRabbit:

  1. Defined working folder
  2. Defined delimiter
  3. Added csv file to scan
  4. Scan tables
  5. Error:

Generating scan report Exception in thread "Thread-3" java.lang.NoClassDefFoundError: org.apache.commons.compress.archivers.ArchiveOutputStream at org.ohdsi.whiteRabbit.scan.SourceDataScan.generateReport(SourceDataScan.java:172) at org.ohdsi.whiteRabbit.scan.SourceDataScan.process(SourceDataScan.java:117) at org.ohdsi.whiteRabbit.WhiteRabbitMain$ScanThread.run(WhiteRabbitMain.java:1054) Caused by: java.lang.ClassNotFoundException: org.apache.commons.compress.archivers.ArchiveOutputStream at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:788) at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178) at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:1081) ... 3 more

We tested this with own csv-files as well as with the test csv-files in the WhiteRabbit repository. The error is displayed for both.

janblom commented 1 year ago

One dependency (commons-compress) fell victim to the dependencies update (a version containing vulnerabilities was a transient dependency before). I added a newer version back explicitly. I also verified that all other dependencies compared to version 0.10.7 are unaffected.

@elisahenke could you please test with version 0.10.8a?

elisahenke commented 1 year ago

Hi @janblom, the described error is solved with version 0.10.8a. Thank you very much for solving it!

However, the error described in Issue #376 still remains.

janblom commented 1 year ago

Solved with release 0.10.8a (included in release 0.10.8).