- #JAVA JAR FILE IN PYTHON WINDOWS 10#
- #JAVA JAR FILE IN PYTHON CODE#
- #JAVA JAR FILE IN PYTHON WINDOWS#
ENV JAVA_OPTS="nfigurationFile=/opt/amazon/lib/log4j2.xml" However, I am setting JAVA_OPTS environment variable in the Dockerfile to pass the log4j configuration file to JVM. So I modified the variable 'shell=False" and I pass in the command and arguments as a list to the subprocess. runnable_command = "java $JAVA_OPTS " \īut for that I had to make the variable "shell=True" which has a security risk. When I pass the entire command with arguments as a string to subprocess, it works fine. ENV CLASSPATH /path/to/dir/containing/jar/file I set the CLASSPATH environment variable in the Dockerfile to include the directory containing the jar file.
#JAVA JAR FILE IN PYTHON CODE#
I am running the python code on a docker container in AWS Batch. Log.I am trying to make a subprocess call from my python script to a java class built inside a jar. Log.info('Save Results to : ' + rtsavelocation)įilesaveOK = os.path.exists(rtsavelocation)
Rtsavelocation = AnalyzeTools.create_resultfilename(imagefile, Log.info('Saving Processed Image to : ' + savepath_pastack) Savepath_pastack = ExportTools.savedata(pastack, imagefile, I could really need help here since I currently have no workaround to save the table otherwise yet. But I can still remember seen it working also in headless a while ago. The respective part of the python script is shown beloe and works fine when running the script from the Fiji Script Editor, but not in headless mode.
Save Results to : c:\Users\m1srh\Downloads\test\OverViewScan_Test_raw_stitched_RESULTS.txt Saving Processed Image to : c:\Users\m1srh\Downloads\test\OverViewScan_Test_raw_stitched_PA.ome.tiff Filename : c:\Users\m1srh\Downloads\test\OverViewScan_Test_raw_i Script Directory: c:\Users\m1srh\Documents\Fiji\ScriptsĬ:\Users\m1srh\Downloads\test\OverViewScan_Test_raw_i
#JAVA JAR FILE IN PYTHON WINDOWS#
Windows RegCreateKeyEx(.) returned error code 5. WARNING: Could not open/create prefs root node Software\JavaSoft\Prefs at root 0x80000002. Overriding Save Image As Tiff Without Prompt identifier: script:ZenIntegration/Save_Image_As_Tiff_Without_Prompt.java jar: file:/c:/Users/m1srh/DOCUME~1/Fiji/jars/scijava-common-2.65.0.jarĥ:34:48 PM identifier: command:ch._Run_Macro jar: file:/c:/Users/m1srh/DOCUME~1/Fiji/plugins/BIOP/B_Run_Macro-1.0.0-SNAPSHOT.jar SLF4J: Found binding in ġ7:34:44,981 |-INFO in ch. - Found resource at ġ7:34:44,982 |-WARN in ch. - Resource occurs multiple times on the classpath.ġ7:34:44,982 |-WARN in ch. - Resource occurs at ġ7:34:45,008 |-INFO in - URL is not of type fileġ7:34:45,154 |-INFO in ch.action.ConfigurationAction - debug attribute not setġ7:34:45,157 |-INFO in ch.action.AppenderAction - About to instantiate appender of type ġ7:34:45,168 |-INFO in ch.action.AppenderAction - Naming appender as ġ7:34:45,178 |-INFO in ch.action.NestedComplexPropertyIA - Assuming default type for propertyġ7:34:45,267 |-INFO in ch.action.RootLoggerAction - Setting level of ROOT logger to ERRORġ7:34:45,267 |-INFO in ch.action.AppenderRefAction - Attaching appender named to Loggerġ7:34:45,268 |-INFO in ch.action.ConfigurationAction - End of configuration.ġ7:34:45,269 |-INFO in - Registering current configuration as safe fallback point SLF4J: Class path contains multiple SLF4J bindings. Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release Λ Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m support was removed in 8.0 There is no error message or something, but the TXT file is just not saved. When I run the script now in headless mode from the commandline i get the output below.
The script works fine when started from Fiji itself.
#JAVA JAR FILE IN PYTHON WINDOWS 10#
I created a python script for Fiji, which is up-to date on my Windows 10 system. I have a strange problem, where I need help.
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