Operation overhaul

[c-schuler]

Description

• Github Issue:
• I've read the contribution guidelines
• Code compiles without errors
• Tests are created / updated
• Documentation is created / updated

By creating this PR you acknowledge that your contribution will be licensed under Apache 2.0

[ddieppois]

The project build is successful following the latest changes

[ddieppois]

So with all the changes in main I'm not able to run the script from dtr-content-r4

daviddieppois@Davids-MBP dtr-content-r4 % JAVA -jar "input-cache/tooling-2.6.0-SNAPSHOT.jar" -ProcessAcceleratorKit -s=ASLP -pts=input/l2/DTR.xlsx -op=./ -dep="ASLP.A1 Adult Sleep Studies"
no main manifest attribute, in input-cache/tooling-2.6.0-SNAPSHOT.jar

[ddieppois]

daviddieppois@Davids-MBP dtr-content-r4 % JAVA -jar "/Users/daviddieppois/Documents/git/cqf-tooling/tooling-cli/target/tooling-cli-2.6.0-SNAPSHOT.jar" -ProcessAcceleratorKit -s=ASLP -pts=input/l2/DTR.xlsx -op=./ -dep="ASLP.A1 Adult Sleep Studies"
ERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using SimpleLogger to log to the console...
Exception in thread "main" java.lang.reflect.InvocationTargetException
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:48)
at org.springframework.boot.loader.Launcher.launch(Launcher.java:87)
at org.springframework.boot.loader.Launcher.launch(Launcher.java:50)
at org.springframework.boot.loader.JarLauncher.main(JarLauncher.java:51)
Caused by: java.lang.NullPointerException
at java.base/java.lang.String.startsWith(String.java:1428)
at java.base/java.lang.String.startsWith(String.java:1470)
at org.opencds.cqf.tooling.acceleratorkit.Processor.getFhirCodes(Processor.java:661)
at org.opencds.cqf.tooling.acceleratorkit.Processor.getDataElementCodes(Processor.java:894)
at org.opencds.cqf.tooling.acceleratorkit.Processor.getPrimaryCodes(Processor.java:708)
at org.opencds.cqf.tooling.acceleratorkit.Processor.createDataElement(Processor.java:800)
at org.opencds.cqf.tooling.acceleratorkit.Processor.processDataElementPage(Processor.java:1086)
at org.opencds.cqf.tooling.acceleratorkit.Processor.processScope(Processor.java:261)
at org.opencds.cqf.tooling.acceleratorkit.Processor.execute(Processor.java:193)
at org.opencds.cqf.tooling.cli.Main.main(Main.java:287)
... 8 more
daviddieppois@Davids-MBP dtr-content-r4 %

[ddieppois]

After adding the fix that I did for the previous branch it seems to be working as expected, still with the CQL bug that we need to fix with other tickets ! I'll approve

Fix: setCanonicalBase("http://example.org/sdh"); - Processor.java line 661

daviddieppois@Davids-MBP dtr-content-r4 % JAVA -jar "/Users/daviddieppois/Documents/git/cqf-tooling/tooling-cli/target/tooling-cli-2.6.0-SNAPSHOT.jar" -ProcessAcceleratorKit -s=ASLP -pts=input/l2/DTR.xlsx -op=./ -dep="ASLP.A1 Adult Sleep Studies" ERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using SimpleLogger to log to the console... Nov. 28, 2023 9:39:10 A.M. ca.uhn.fhir.util.VersionUtil initialize INFO: HAPI FHIR version 6.8.0 - Rev f33627087f Nov. 28, 2023 9:39:10 A.M. ca.uhn.fhir.context.FhirContext <init> INFO: Creating new FHIR context for FHIR version [R4] daviddieppois@Davids-MBP dtr-content-r4 %