Hi Ryan,
It looks like either --source.adam or --source.sdtm is pointing to a non-existing directory or directory that cannot be accessed by your user.
Thanks,
Philipp Strigunov
I thought I’d checked this, but it’s possible. I’ll confirm and try again at the first opportunity. Thank you for your help!
Hi
I also have same Warning in CLI log as following. I wonder how to solve this issue or if the warning is ignorable.
WARNING: Could not open/create prefs root node Software\JavaSoft\Prefs at root 0x80000002. Windows RegCreateKeyEx(…) returned error code 5.
Thank you for your supporting!
Hello Kaori,
I am assuming this is related to your comment in How to add CTs to the Pinnacle21 community version (in CLI) | Pinnacle 21. Did you manually add CT to the configs folder? This should not be done. What versions did you add?
Kind regards,
Matt
Hi Matt,
Thank you for your comment. This is very helpful!
I believe this warning is not related the issue of CT. Even though CT exists, the warning occurs. And I do not add CT file manually so far.
My version of P21C is v4.1.0, using in Citrix.
I am not familier with Java, I have no idea what causes this warning ,config or PC environment.
Regarding CT, I have noticed that CT can be added when I validate datasets with P21C with the CT which I want to add. But I wonder if there is option of CLI or command line to add CT when it does not exist, or other solution to solve it.
Thank you again for your help!
Hi Kaori,
Please email the full CLI log file to community@pinnacle21.com for further review/assistance.
Kind regards,
Matt
Thank you for your help! I have sent the log file via email! I hope that will help to solve our issue.
Thank you again for your great support!
I tried to use the example ADaM CLI code from https://www.pinnacle21.com/projects/validator/community-cli, but it failed. Complete command-line output from PowerShell is shown at the bottom. To save reading, I’ve highlighted some messages that seem important. Can anybody suggest what might be wrong here? Thanks in advance for any help.
The worst-looking thing I saw was
WARNING: Could not open/create prefs root node Software\JavaSoft\Prefs at root 0x80000002. Windows RegCreateKeyEx(…) returned error code 5.
I don’t have the permissions to create registry keys. Is this going to be a dealbreaker?
Other highlights include:
13:47:42,995 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.groovy]
13:47:42,995 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
log4j:WARN No appenders could be found for logger (com.amazonaws.AmazonWebServiceClient).
log4j:WARN Please initialize the log4j system properly.
13:47:43,223 |-WARN in ch.qos.logback.core.ConsoleAppender[STDOUT] - This appender no longer admits a layout as a sub-co
mponent, set an encoder instead.
13:47:43,223 |-WARN in ch.qos.logback.core.ConsoleAppender[STDOUT] - To ensure compatibility, wrapping your layout in La
youtWrappingEncoder.
13:47:43,223 |-WARN in ch.qos.logback.core.ConsoleAppender[STDOUT] - See also Logback Error Codes
teadOfEncoder for details2019-06-21 13:47:55 [main] WARN net.pinnacle21.oce.utils.DataSources - ‘config’ folder or file is not found.
2019-06-21 13:47:55 [main] INFO net.pinnacle21.oce.utils.DataSources - Found ‘configs’ folder in local dir C:\Users\rm1
132\Documents\Pinnacle 21 Community\configs. Will use it
Full log:
PS C:\Users\USER\Documents\Pinnacle 21 Community> java -jar p21-client-1.0.0.jar --engine.version=“FDA 1903.1” --stand
ard=adam --standard.version=1.1 --source.sdtm=“c:\sdtmpath” --source.adam = “C:\adampath” --source.define=“C:\adampath\define.xml” --cdisc.ct.sdtm.version=2017-12-22 --cdisc.ct.
adam.version =2017-12-22 --meddra.version=19.0 --report=“C:\Users\USER\Desktop\report.xlsx”
13:47:42,995 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.groovy]
13:47:42,995 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
13:47:42,995 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [jar:file:/C:/Use
rs/USER/Documents/Pinnacle%2021%20Community/p21-client-1.0.0.jar!/logback.xml]
13:47:43,006 |-INFO in ch.qos.logback.core.joran.spi.ConfigurationWatchList@9b1010 - URL [jar:file:/C:/Users/USER/Docu
ments/Pinnacle%2021%20Community/p21-client-1.0.0.jar!/logback.xml] is not of type file
13:47:43,096 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - debug attribute not set
13:47:43,106 |-INFO in ch.qos.logback.core.joran.action.DefinePropertyAction - About to instantiate property definer of
type [net.pinnacle21.oce.logging.JarNameDefiner]
13:47:43,106 |-INFO in ch.qos.logback.core.joran.action.DefinePropertyAction - Popping property definer for property nam
ed [jarName] from the object stack
13:47:43,160 |-INFO in ch.qos.logback.core.joran.action.DefinePropertyAction - About to instantiate property definer of
type [net.pinnacle21.oce.logging.LogLevelDefiner]
13:47:43,163 |-INFO in ch.qos.logback.core.joran.action.DefinePropertyAction - Popping property definer for property nam
ed [logLevel] from the object stack
13:47:43,163 |-INFO in ch.qos.logback.core.joran.action.DefinePropertyAction - About to instantiate property definer of
type [net.pinnacle21.oce.logging.LogAppendFlagDefiner]
13:47:43,163 |-INFO in ch.qos.logback.core.joran.action.DefinePropertyAction - Popping property definer for property nam
ed [appendFlag] from the object stack
13:47:43,163 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - About to instantiate appender of type [ch.qos.l
ogback.core.FileAppender]
13:47:43,168 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - Naming appender as [CLI-APPENDER]
13:47:43,183 |-INFO in ch.qos.logback.core.joran.action.NestedComplexPropertyIA - Assuming default type [ch.qos.logback.
classic.encoder.PatternLayoutEncoder] for [encoder] property
13:47:43,211 |-INFO in ch.qos.logback.core.FileAppender[CLI-APPENDER] - File property is set to [C:\Users\USER\Documen
ts\Pinnacle 21 Community\logs\p21-client-1.0.0]
13:47:43,213 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - About to instantiate appender of type [ch.qos.l
ogback.core.ConsoleAppender]
13:47:43,219 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - Naming appender as [STDOUT]
13:47:43,223 |-WARN in ch.qos.logback.core.ConsoleAppender[STDOUT] - This appender no longer admits a layout as a sub-co
mponent, set an encoder instead.
13:47:43,223 |-WARN in ch.qos.logback.core.ConsoleAppender[STDOUT] - To ensure compatibility, wrapping your layout in La
youtWrappingEncoder.
13:47:43,223 |-WARN in ch.qos.logback.core.ConsoleAppender[STDOUT] - See also Logback Error Codes
teadOfEncoder for details
13:47:43,223 |-INFO in ch.qos.logback.classic.joran.action.RootLoggerAction - Setting level of ROOT logger to INFO
13:47:43,223 |-INFO in ch.qos.logback.core.joran.action.AppenderRefAction - Attaching appender named [CLI-APPENDER] to L
ogger[ROOT]
13:47:43,224 |-INFO in ch.qos.logback.core.joran.action.AppenderRefAction - Attaching appender named [STDOUT] to Logger[
ROOT]
13:47:43,224 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - End of configuration.
13:47:43,224 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@3708b3 - Registering current configuration as safe
fallback pointSLF4J: net.pinnacle21.oce.utils.DataSources
SLF4J: The following set of substitute loggers may have been accessed
SLF4J: during the initialization phase. Logging calls during this
SLF4J: phase were not honored. However, subsequent logging calls to these
SLF4J: loggers will work as normally expected.
SLF4J: See also SLF4J Error Codes
Jun 21, 2019 1:47:43 PM java.util.prefs.WindowsPreferences
WARNING: Could not open/create prefs root node Software\JavaSoft\Prefs at root 0x80000002. Windows RegCreateKeyEx(…) r
eturned error code 5.
2019-06-21 13:47:44 [main] INFO net.pinnacle21.oce.model.input.Input - Use default value 2
log4j:WARN No appenders could be found for logger (com.amazonaws.AmazonWebServiceClient).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See Apache log4j 1.2 - Frequently Asked Technical Questions for more info.
2019-06-21 13:47:45 [RxIoScheduler-2] INFO net.bootstrap.core.AbstractCommand - command=‘cmd-aws-healthCheck’, runTime=
436
2019-06-21 13:47:45 [RxIoScheduler-2] INFO net.bootstrap.utils.S3Loader - Services are healthy
2019-06-21 13:47:45 [main] INFO net.bootstrap.utils.S3Loader - Downloading from s3 p21-community-resources
2019-06-21 13:47:45 [RxIoScheduler-2] INFO net.bootstrap.utils.S3Loader - Downloading from s3 p21-community-resources
2019-06-21 13:47:45 [main] INFO net.bootstrap.core.AbstractCommand - command=‘cmd-aws-download’, runTime=56
2019-06-21 13:47:45 [main] INFO net.bootstrap.utils.Libs - Loading engine version 1511.5
2019-06-21 13:47:45 [main] INFO net.bootstrap.core.AbstractCommand - command=‘cmd-aws-download’, runTime=55
2019-06-21 13:47:45 [main] INFO net.bootstrap.utils.Libs - Loading engine version 1903.1
2019-06-21 13:47:45 [main] INFO n.p.oce.model.input.ParseResults - Loaded parameters |Command line: --engine.version=FD
A 1903.1 --standard=adam --standard.version=1.1 --source.sdtm=c:\sdtmpath --source.adam = C:\adampath --source.define=C:\adampath\define.xml --cdisc.ct.sdtm.version=2017-12-22 -
-cdisc.ct.adam.version =2017-12-22 --meddra.version=19.0 --report=C:\Users\USER\Desktop\report.xlsx|
2019-06-21 13:47:45 [main] INFO net.pinnacle21.oce.utils.DataSources - Folder multi://sources contains XPT files. Setti
ng format to XPT by default
2019-06-21 13:47:45 [main] INFO n.p.o.m.r.StandardRequestBuilder - Source format is determined as ‘xport’
2019-06-21 13:47:45 [RxIoScheduler-2] INFO net.bootstrap.core.AbstractCommand - command=‘cmd-aws-download’, runTime=2752019-06-21 13:47:46 [RxIoScheduler-2] INFO net.bootstrap.utils.S3Loader - Downloading from s3 p21-community-resources
2019-06-21 13:47:46 [RxIoScheduler-4] INFO net.bootstrap.core.AbstractCommand - command=‘cmd-aws-download’, runTime=48
2019-06-21 13:47:46 [RxIoScheduler-4] INFO net.bootstrap.utils.Libs - Loading engine version 1511.5
2019-06-21 13:47:46 [RxIoScheduler-3] INFO net.bootstrap.core.AbstractCommand - command=‘cmd-aws-download’, runTime=2872019-06-21 13:47:46 [RxIoScheduler-4] INFO net.bootstrap.core.AbstractCommand - command=‘cmd-aws-download’, runTime=256
2019-06-21 13:47:46 [RxIoScheduler-4] INFO net.bootstrap.utils.Libs - Loading engine version 1903.1
2019-06-21 13:47:46 [RxIoScheduler-5] INFO net.bootstrap.core.AbstractCommand - command=‘cmd-aws-download’, runTime=2982019-06-21 13:47:55 [main] INFO n.p.o.m.r.StandardRequestBuilder - Determine filter FDA from engine FDA
2019-06-21 13:47:55 [main] INFO n.p.o.m.r.StandardRequestBuilder - Determined engine version 1903.1
2019-06-21 13:47:55 [main] INFO n.p.o.m.r.ValidatorRequestBuilder - Build validator request
2019-06-21 13:47:55 [main] INFO net.pinnacle21.oce.model.FormatType - Cannot determine output format type. Set to defau
lt ‘excel’
2019-06-21 13:47:55 [main] INFO net.pinnacle21.oce.model.FormatType - Failed to find format type for file ‘report’ and
extension ‘xlsx’. Trying default ‘excel’
2019-06-21 13:47:55 [main] INFO net.pinnacle21.oce.model.FormatType - Output format type is determined as ‘excel’
2019-06-21 13:47:55 [main] INFO net.pinnacle21.oce.model.FormatType - Failed to find format type for file ‘report’ and
extension ‘xlsx’. Trying default ‘excel’
2019-06-21 13:47:55 [main] INFO net.pinnacle21.oce.model.FormatType - Output format type is default as ‘excel’
2019-06-21 13:47:55 [main] INFO net.pinnacle21.oce.model.input.Input - Use default value 1000
2019-06-21 13:47:55 [main] INFO n.p.o.m.r.ValidatorRequestBuilder - No output provided. Report URL will be written to s
tandard output
2019-06-21 13:47:55 [main] INFO n.p.o.m.r.StandardRequestBuilder - Source format is determined as ‘xport’
2019-06-21 13:47:55 [main] INFO n.p.o.m.r.StandardRequestBuilder - Determine filter FDA from engine FDA
2019-06-21 13:47:55 [main] INFO n.p.o.m.r.StandardRequestBuilder - Determined engine version 1903.1
2019-06-21 13:47:55 [main] INFO net.pinnacle21.oce.utils.DataSources - Found ‘lib’ folder in local dir C:\Users\USER
Documents\Pinnacle 21 Community\lib. Will use it
2019-06-21 13:47:55 [main] WARN net.pinnacle21.oce.utils.DataSources - ‘config’ folder or file is not found.
2019-06-21 13:47:55 [main] INFO net.pinnacle21.oce.utils.DataSources - Found ‘configs’ folder in local dir C:\Users\rm1
132\Documents\Pinnacle 21 Community\configs. Will use it
2019-06-21 13:47:55 [main] INFO n.p.oce.model.input.ConfigInfo - Config ‘C:\Users\USER\Documents\Pinnacle 21 Communit
y\configs’ is a directory. Cannot parse for standard, version, and filter
2019-06-21 13:47:55 [main] INFO n.pinnacle21.oce.utils.ResourceUtils - Looking for config file in folder=C:\Users\rm113
2\Documents\Pinnacle 21 Community\configs
2019-06-21 13:47:55 [main] INFO n.pinnacle21.oce.utils.ResourceUtils - Checking config file=C:\Users\USER\Documents\P
innacle 21 Community\configs\ADaM-IG 1.1 (FDA).xml
2019-06-21 13:47:55 [main] INFO n.p.oce.model.input.ConfigInfo - Config C:\Users\USER\Documents\Pinnacle 21 Community
\configs\ADaM-IG 1.1 (FDA).xml does not exist. Looking up in engine versioned folder C:\Users\USER\Documents\Pinnacle
21 Community\configs\1903.1
2019-06-21 13:47:55 [main] INFO n.pinnacle21.oce.utils.ResourceUtils - Looking for config file in folder=C:\Users\rm113
2\Documents\Pinnacle 21 Community\configs\1903.1
2019-06-21 13:47:55 [main] INFO n.pinnacle21.oce.utils.ResourceUtils - Checking config file=C:\Users\USER\Documents\P
innacle 21 Community\configs\1903.1\ADaM-IG 1.1 (FDA).xml
2019-06-21 13:47:55 [main] ERROR n.pinnacle21.oce.utils.ProcessUtils - CLI.4.1::Data source is invalid::Cannot run local
validation. Data source=‘multi://sources’ does not exist
net.pinnacle21.oce.exceptions.CLIException: Cannot run local validation. Data source=‘multi://sources’ does not exist
at net.pinnacle21.oce.model.request.ValidatorRequestBuilder.build(ValidatorRequestBuilder.java:128) ~[p21-client
-1.0.0.jar:1.0.0]
at net.pinnacle21.oce.model.request.RequestType.lambda$static$1(RequestType.java:24) ~[p21-client-1.0.0.jar:1.0.
0]
at net.pinnacle21.oce.model.request.RequestType.toRequest(RequestType.java:97) ~[p21-client-1.0.0.jar:1.0.0]
at net.pinnacle21.oce.utils.InputUtils.from(InputUtils.java:51) ~[p21-client-1.0.0.jar:1.0.0]
at net.pinnacle21.oce.utils.ProcessUtils.start(ProcessUtils.java:143) ~[p21-client-1.0.0.jar:1.0.0]
at net.pinnacle21.oce.utils.ProcessUtils.startFromCommandLine(ProcessUtils.java:131) ~[p21-client-1.0.0.jar:1.0.
0]
at net.pinnacle21.oce.utils.ProcessUtils.startFromCommandLine(ProcessUtils.java:102) ~[p21-client-1.0.0.jar:1.0.
0]
at net.pinnacle21.oce.Main.main(Main.java:16) [p21-client-1.0.0.jar:1.0.0]
PS C:\Users\USER\Documents\Pinnacle 21 Community>