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MassBank / MassBank-data

Official repository of open data MassBank records
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Problem with command line validator #30

Closed tsufz closed 5 years ago

tsufz commented 5 years ago

Hi, my validator does not work correctly. There is maybe a problem with the illegal method?

root@massbank2:/MassBank-data# mvn -q -f .scripts/MassBank-web/MassBank-Project/MassBank-lib/pom.xml install WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access by com.google.inject.internal.cglib.core.$ReflectUtils$1 (file:/usr/share/maven/lib/guice.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain) WARNING: Please consider reporting this to the maintainers of com.google.inject.internal.cglib.core.$ReflectUtils$1 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release root@massbank2:/MassBank-data# mc MobaXterm X11 proxy: Unsupported authorisation protocol

root@massbank2:/MassBank-data# mc MobaXterm X11 proxy: Unsupported authorisation protocol

root@massbank2:/MassBank-data# root@massbank2:/MassBank-data# ./.scripts/validate.sh ./ Validating 43 files Exception in thread "main" java.io.IOException: File 'AAFC' exists but is a directory at org.apache.commons.io.FileUtils.openInputStream(FileUtils.java:291) at org.apache.commons.io.FileUtils.readFileToString(FileUtils.java:1805) at massbank.Validator.main(Validator.java:230) root@massbank2:/MassBank-data# ./.scripts/validate.sh /MassBank-data/ Validating 43 files Exception in thread "main" java.io.IOException: File 'AAFC' exists but is a directory at org.apache.commons.io.FileUtils.openInputStream(FileUtils.java:291) at org.apache.commons.io.FileUtils.readFileToString(FileUtils.java:1805) at massbank.Validator.main(Validator.java:230)

meier-rene commented 5 years ago

Please use either .scripts/validate.sh with a directory containing record files, e.g. .scripts/validate.sh AAFC. Using a directory containig directories with record files is not possible. To validate the complete data repo please use .scripts/validate_all_local.sh. I updated the README to make this more clear.