I'm trying to generate documentation of my HL7 FHIR profiles using IG Publisher (publisher.jar). I'm running it on command line on macOS. I've uploaded the IG resource on Simplifier and it validates with no errors.
The problem is that i'm getting java.lang.NullPointerException. Full output below:
java -jar publisher.jar -ig fsh-generated/resources/ImplementationGuide-nfz.pozplus.json -tx n/a
FHIR IG Publisher Version 1.1.120 (Git# 210e48f945ad). Built 2022-05-13T15:20:39.709Z (8 days old)
Detected Java version: 11.0.10 from /Library/Java/JavaVirtualMachines/adoptopenjdk-11.jdk/Contents/Home on Mac OS X/x86_64 (64bit). 2048MB available
dir = /Users/marcingrudzien/Library/CloudStorage/OneDrive-Osobisty/Praca/iEHReu/NFZ/POZ-Plus/FHIR/sushi-test/NfzTest, path = /Users/marcingrudzien/.gem/ruby/3.1.2/bin:/Users/marcingrudzien/.rubies/ruby-3.1.2/lib/ruby/gems/3.1.0/bin:/Users/marcingrudzien/.rubies/ruby-3.1.2/bin:/opt/homebrew/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/share/dotnet:~/.dotnet/tools:/Library/Frameworks/Mono.framework/Versions/Current/Commands:/Applications/Postgres.app/Contents/Versions/latest/bin
Parameters: -ig fsh-generated/resources/ImplementationGuide-nfz.pozplus.json -tx n/a
Start Clock # sobota, 21 maja 2022 20:56:04 czas środkowoeuropejski letni (2022-05-21T20:56:04+02:00)
API keys loaded from /Users/marcingrudzien/fhir-api-keys.ini (00:00.0027)
Package Cache: /Users/marcingrudzien/.fhir/packages (00:00.0030)
Load Configuration from /Users/marcingrudzien/Library/CloudStorage/OneDrive-Osobisty/Praca/iEHReu/NFZ/POZ-Plus/FHIR/sushi-test/NfzTest/fsh-generated/resources/ImplementationGuide-nfz.pozplus.json (00:00.0053)
Root directory: /Users/marcingrudzien/Library/CloudStorage/OneDrive-Osobisty/Praca/iEHReu/NFZ/POZ-Plus/FHIR/sushi-test/NfzTest/fsh-generated/resources (00:00.0084)
Publishing Content Failed: null (00:00.0086)
(00:00.0087)
Use -? to get command line help (00:00.0087)
(00:00.0087)
Stack Dump (for debugging): (00:00.0088)
java.lang.NullPointerException
at org.hl7.fhir.igtools.publisher.Publisher.initializeFromJson(Publisher.java:2947)
at org.hl7.fhir.igtools.publisher.Publisher.initialize(Publisher.java:2168)
at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:854)
at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:10144)
I hope someone here could help me. I could provide any additional information, if needed.
From the stack dump, you are missing a "path" property in your json config file, but I highly recommend that you switch to using the new set up, a ini file that points to a template and a IG resource. Use something like the sample-ig as a starter (https://github.com/FHIR/sample-ig) or see the how-to (https://build.fhir.org/ig/FHIR/ig-guidance/index.html)
sh jmeter.sh -n -t filePath.jmx -l outFilePath.jtl -e -o folderPath
Error generating the report: org.apache.jmeter.report.dashboard.GenerationException: Error while processing samples: Consumer failed with message :Consumer failed with message :Consumer failed with message :Consumer failed with message :Begin size 0 is not equal to fixed size 5
In resume
Consumer failed with message :Begin size 0 is not equal to fixed size 5
currently using Java version "17" 2021-09-14 LTS
MacOS big SUR version 11.4
the properties files are fresh and values are equal to the default ones
Jmeter 5.4.1
outFile.jtl
timeStamp,elapsed,label,responseCode,responseMessage,threadName,dataType,success,failureMessage,bytes,sentBytes,grpThreads,allThreads,URL,Latency,IdleTime,Connect
1632430450882,1117,HTTP Request,200,OK,FIRST_Jmeter_Test 1-3,text,true,,3824,557,3,3,Url_hidden,1111,0,256
1632430450448,1755,HTTP Request,200,OK,FIRST_Jmeter_Test 1-2,text,true,,3836,557,3,3,Url_hidden,1755,0,690
1632430450448,1755,HTTP Request,200,OK,FIRST_Jmeter_Test 1-1,text,true,,3828,557,3,3,Url_hidden,1755,0,690
1632430452312,585,HTTP Request,200,OK,FIRST_Jmeter_Test 1-2,text,true,,3836,557,3,3,Url_hidden,585,0,144
1632430452238,758,HTTP Request,200,OK,FIRST_Jmeter_Test 1-3,text,true,,3832,557,3,3,Url_hidden,757,0,137
1632430452301,806,HTTP Request,200,OK,FIRST_Jmeter_Test 1-1,text,true,,3828,557,3,3,Url_hidden,805,0,136
1632430452962,550,HTTP Request,200,OK,FIRST_Jmeter_Test 1-2,text,true,,3824,557,3,3,Url_hidden,550,0,152
1632430453328,593,HTTP Request,200,OK,FIRST_Jmeter_Test 1-1,text,true,,3828,557,2,2,Url_hidden,592,0,135
1632430453276,815,HTTP Request,200,OK,FIRST_Jmeter_Test 1-3,text,true,,3840,557,1,1,Url_hidden,814,0,142
The thread run successfully and the jtl file is created as well.
I quite new on Jmeter and tried to see where that "size" attribute is currently locate to see how change it, but could not find it on any *.properties file
any though how can be this fixed, what the message is referring to?
thanks
This error is likely due to an incompatibility of JMeter with Java 17 (as mentioned by Dmitri T).
Whilst we wait for a fix, a workaround would be downgrading to Java 16. I can confirm this solved the issue for me.
I had the same issue with:
MacOS big SUR version 11.6
Jmeter 5.4.1 (installed via brew)
Temurin 11 (LTS) OpenJDK & Temurin 8 (LTS) OpenJDK
Running Jmeter with Java 8 solved my issue. The problem was, that Jmeter always used Java 11. I struggled some days to find out, how to set the Jmeter Java version:
set the correct Java 8 Home in: /usr/local/Cellar/jmeter/5.4.1/bin/jmeter:
JAVA_HOME=$JAVA_8_HOME exec "/usr/local/Cellar/jmeter/5.4.1/libexec/bin/jmeter" "$#"
Maybe there are easier ways to set Java 8 for Jmeter - but this was the only solution which worked for me.
I had Java 8 installed however, the JMeter was picking up Java 1.17 which was nowhere in my system. So uninstalling and reinstalling jmeter, worked like a charm for me.
I cannot reproduce your issue using:
openjdk:8-jre-alpine docker image
JMeter 5.4.1
Test plan Test.jmx from extras folder of JMeter
Demo:
If you cannot reproduce the above behaviour I think you made some changes either to Results File Configuration or to Reporting Configuration or both so you need to inspect all the JMeter Properties which differ from the defaults and restore their values to the original ones.
If you need further support you need to share at least first 2 lines of your outFilePath.jtl results file. Better if possible the full file and all the .properties files from JMeter's "bin" folder.
exec commandline /usr/libexec/java_home -V
enter image description here
replace bin of jmeter JAVA_HOME
enter image description here
and then ,it is success.
i try to install Oracle Forms and Reports 12.2.1.4, but everytime I run setup.fmw.12.2.1.4.0_fr_win64.exe file Oracle Universal Installer window shows up for a moment with communicate "Preparing the installer...". After that it dissappears and shows again with another communicate: "Cleaning up...". After this communicate, the installer window turns off and there are no other steps.
Screens below
first communicate
second communicate
Did anybody have this problem also? My JAVA_HOME is set as C:\Java\jdk1.8.0_241 and PATH=%JAVA_HOME%\bin.
Here's also -debug log below
m_szTempDirectory: C:\Windows\Temp
Extract to C:\Windows\Temp\sfxCD9A.tmp
Extracting sfx.ini from D:\setup_fmw_12.2.1.4.0_fr_win64.exe to C:\Windows\Temp\sfxCD9A.tmp
Wiz_SingleEntryUnzip (extractAutorun) return code: 0
Total uncompressed size: 2447428290
m_szTempDirectory: C:\Windows\Temp
Extract to same C:\Windows\Temp\sfxCD9A.tmp
Extracting installer files
Wiz_SingleEntryUnzip() result: 0
Total disks: 1 (1)
Finished extracting Disk1
Using version 1.8.0.211.12 of component Disk1\stage\Components\oracle.jre
Jar list: Disk1\stage\Components\oracle.jre\1.8.0.211.12\DataFiles\filegroup1.jar
New command: oracle.jre\.\jdk\jre\bin\java.exe -jar install/modules/ora-launcher.jar
Unzipping Java jars Disk1\stage\Components\oracle.jre\1.8.0.211.12\DataFiles\filegroup1.jar to oracle.jre
Getting size of Disk1\stage\Components\oracle.jre\1.8.0.211.12\DataFiles\filegroup1.jar
Size of Disk1\stage\Components\oracle.jre\1.8.0.211.12\DataFiles\filegroup1.jar: 201205655
Checking space for Java components in C:\Windows\Temp
Unzipping Java jars: Disk1\stage\Components\oracle.jre\1.8.0.211.12\DataFiles\filegroup1.jar
Unzipping Disk1\stage\Components\oracle.jre\1.8.0.211.12\DataFiles\filegroup1.jar
Launch command length: 278
Launch command: "C:\Windows\Temp\sfxCD9A.tmp\oracle.jre\jdk\jre\bin\java.exe" "-Djava.io.tmpdir=C:\Windows\Temp" "-Dsfx.installer.launcher.home=D:\" "-Dsfx.extract.path=C:\Windows\Temp\sfxCD9A.tmp" "-Dsfx.exe=D:\setup_fmw_12.2.1.4.0_fr_win64.exe" -jar install/modules/ora-launcher.jar "-debug"
cmdLine: "C:\Windows\Temp\sfxCD9A.tmp\oracle.jre\jdk\jre\bin\java.exe" "-Djava.io.tmpdir=C:\Windows\Temp" "-Dsfx.installer.launcher.home=D:\" "-Dsfx.extract.path=C:\Windows\Temp\sfxCD9A.tmp" "-Dsfx.exe=D:\setup_fmw_12.2.1.4.0_fr_win64.exe" -jar install/modules/ora-launcher.jar "-debug"
Command successfully started; waiting for completion
Usage: java [-options] class [args...]
(to execute a class)
or java [-options] -jar jarfile [args...]
(to execute a jar file)
where options include:
-d32 use a 32-bit data model if available
-d64 use a 64-bit data model if available
-server to select the "server" VM
The default VM is server.
-cp <class search path of directories and zip/jar files>
-classpath <class search path of directories and zip/jar files>
A ; separated list of directories, JAR archives,
and ZIP archives to search for class files.
-D<name>=<value>
set a system property
-verbose:[class|gc|jni]
enable verbose output
-version print product version and exit
-version:<value>
Warning: this feature is deprecated and will be removed
in a future release.
require the specified version to run
-showversion print product version and continue
-jre-restrict-search | -no-jre-restrict-search
Warning: this feature is deprecated and will be removed
in a future release.
include/exclude user private JREs in the version search
-? -help print this help message
-X print help on non-standard options
-ea[:<packagename>...|:<classname>]
-enableassertions[:<packagename>...|:<classname>]
enable assertions with specified granularity
-da[:<packagename>...|:<classname>]
-disableassertions[:<packagename>...|:<classname>]
disable assertions with specified granularity
-esa | -enablesystemassertions
enable system assertions
-dsa | -disablesystemassertions
disable system assertions
-agentlib:<libname>[=<options>]
load native agent library <libname>, e.g. -agentlib:hprof
see also, -agentlib:jdwp=help and -agentlib:hprof=help
-agentpath:<pathname>[=<options>]
load native agent library by full pathname
-javaagent:<jarpath>[=<options>]
load Java programming language agent, see java.lang.instrument
-splash:<imagepath>
show splash screen with specified image
See http://www.oracle.com/technetwork/java/javase/documentation/index.html for more details.
dwExitCode: 1
myspawn() result: 1
Press any key to exit
To be clear, you need to start the installer using an elevated shell. This is not the same as being a member of the Windows "Administrator" group. Right-click on the exe and click on "Run as administrator".
Instead of running setup.exe, try execute \install\oui.exe -debug
I have build a very simple project of hello world in
Payara 5 (5.181)
JSF 2.3
JDK 1.8
CDI 2.0
Maven
and encountered a problem
Unable to start server due following issues: Launch process failed with exit code 1
in console it throws an error of :
Error: Could not find or load main class server\payara5\glassfish.lib.grizzly-npn-bootstrap.jar
[PIC] Payara 5 Error
It seems that the Payara Tools for Eclipse suffer by several bugs that may cause this. In my case, the following workarounds helped:
The Payara installation path should not contain spaces (e.g. Program Files\Payara)
It seems that only Java 8 is supported at the time
Open the domain.xml configuration file for the domain you are trying to start (typically payara_install_path/glassfish/domains/domain1/config/domain1.xml) and search for "Xbootclasspath". You should find a couple of lines like
<jvm-options>[1.8.0|1.8.0u120]-Xbootclasspath/p:${com.sun.aas.installRoot}/lib/grizzly-npn-bootstrap-1.6.jar</jvm-options>
<jvm-options>[1.8.0u121|1.8.0u160]-Xbootclasspath/p:${com.sun.aas.installRoot}/lib/grizzly-npn-bootstrap-1.7.jar</jvm-options>
<jvm-options>[1.8.0u161|1.8.0u190]-Xbootclasspath/p:${com.sun.aas.installRoot}/lib/grizzly-npn-bootstrap-1.8.jar</jvm-options>
<jvm-options>[1.8.0u191|1.8.0u500]-Xbootclasspath/p:${com.sun.aas.installRoot}/lib/grizzly-npn-bootstrap-1.8.1.jar</jvm-options>
Depending of your installed Java version (try running java --version) and choose the appropriate line (most likely the last one). Remove the remaining lines and remove the [...] part at the beginning of the chosen line so you will get something like
<jvm-options>-Xbootclasspath/p:${com.sun.aas.installRoot}/lib/grizzly-npn-bootstrap-1.8.1.jar</jvm-options>
After this, the tools seem to start normally.
The Problem is with Java version. The grizzly-npn-bootstrap-1.8.1.jar Jar is placed in bootclasspath, thats why it requires proper java version to start payara server. So remove unnecessary bootstrap jar from domain.xml.
In Windows:
1) Go To ---C:\Users\xxxx\payara5\glassfish\domains\domain1\config\domain.xml
2) According to my java verson(java version "1.8.0_191") I deleted the following lines from domain.xml. So delete according to your java version.
<jvm-options>[1.8.0|1.8.0u120]-Xbootclasspath/p:${com.sun.aas.installRoot}/lib/grizzly-npn-bootstrap-1.6.jar</jvm-options>
<jvm-options>[1.8.0u121|1.8.0u160]-Xbootclasspath/p:${com.sun.aas.installRoot}/lib/grizzly-npn-bootstrap-1.7.jar</jvm-options>
<jvm-options>[1.8.0u161|1.8.0u190]-Xbootclasspath/p:${com.sun.aas.installRoot}/lib/grizzly-npn-bootstrap-1.8.jar</jvm-options>
3) Remove this [1.8.0u191|1.8.0u500] part from jvm-options & Edit the line in your domain.xml(w.r.t java -version) as shown below
<jvm-options>-Xbootclasspath/p:${com.sun.aas.installRoot}/lib/grizzly-npn-bootstrap-1.8.1.jar</jvm-options>
4) restart your server.
As Radkovo said, "The Payara installation path should not contain spaces (e.g. Program Files\Payara)", so I moved the Payara to the Documents folder.
Problem solved!
I am trying my hands on the Stanford dependency parser. I tried running the parser from command line on windows to extract the dependencies using this command:
java -mx100m -cp "stanford-parser.jar" edu.stanford.nlp.trees.EnglishGrammaticalStructure -sentFile english-onesent.txt -collapsedTree -CCprocessed -parserFile englishPCFG.ser.gz
I am getting the following error:
Error occurred during initialization of VM
Too small initial heap
I changed the memory size to -mx1024, -mx2048 as well as -mx4096. It didn't change anything and the error persists.
What am I missing?
Type -Xmx1024m instead of -mx1024.
See https://docs.oracle.com/javase/8/docs/technotes/tools/windows/java.html
It should be -mx1024m. I skipped m.
One more thing: in the -cp, the model jar should also be included.
... -cp "stanford-parser.jar;stanford-parser-3.5.2-models.jar"...
(assuming you are using the latest version).
Otherwise an IO Exception will be thrown.
There may be some arguments that are preexisting in the IDE.
In eclipse:
Go to-> Run as-> run configuration-> Arguments
then Delete the arguments that are used previously.
Restart your eclipse.
Worked for me!