You need to create HS.SDA3.Container object in Transform method before using it. Something like this:

Class Hosiptal.SDA3.DataTrans Extends Ens.DataTransform
{

ClassMethod Transform(source As EnsLib.HL7.Message, ByRef target As HS.SDA3.Container, aux) As %Status
{
    #Dim sc As %Status = $$$OK
    Set sc =  ##class(HS.Gateway.HL7.HL7ToSDA3).GetSDA(source, .xml)
    Quit:$$$ISERR(sc) sc
    Set target = ##class(HS.SDA3.Container).%New()
    Set sc = target.InitializeXMLParse(.xml)
    Quit sc
}

}

If I'm using an objectgenerator, is there a way to check the compile flags and have it behave differently based on which flags are set?

A very exciting way to introduce some unexpected behavior down the line.

What is your use case?

And as a tangent, is there a list somewhere of what compile flags there are?

Sure:

do $system.OBJ.ShowFlags()
do $system.OBJ.ShowQualifiers()

If you get access error on Linux:

javaldx failed! Warning: failed to read path from javaldx LibreOffice 7.3 - Fatal Error: The application cannot be started. User installation could not be completed.
LibreOffice user installation could not be processed due to missing access rights. Please make sure that you have sufficient access rights for the following location and restart LibreOffice.

Add this to LibreOffice parameters:

set args($i(args)) = "-env:UserInstallation=file:///tmp/libreofficehome/"

where /tmp/libreofficehome is any empty folder InterSystems IRIS has write access to.

If there's a text layer use LibreOffice to convert to txt (InterSystems IRIS wrapper), for OCR you'll need some thirdparty tool, for example Tesseract can be easily used with Embedded Python.

UPD: LibreOffice can't extract text from PDFs unfortunately. Here's Embedded Python solution:

Class User.PDF
{

/// zw ##class(User.PDF).GetText("/tmp/example.pdf", .text)
ClassMethod GetText(file, Output text) As %Status
{
  try {
    #dim sc As %Status = $$$OK
    kill text
    set dir = $system.Util.ManagerDirectory()_ "python"
    do ##class(%File).CreateDirectoryChain(dir)
    // pip3 install --target /data/db/mgr/python --ignore-requires-python typing==3.10.0.0
    try {
      set pypdf2 = $system.Python.Import("PyPDF2")
    } catch {
      set cmd = "pip3"
      set args($i(args)) = "install"
      set args($i(args)) = "--target"
      set args($i(args)) = dir
      set args($i(args)) = "PyPDF2==2.10.0"
      set args($i(args)) = "dataclasses"
      set args($i(args)) = "typing-extensions==3.10.0.1" 
      set args($i(args)) = "--upgrade"
      set sc = $ZF(-100,"", cmd, .args)
      set pypdf2 = $system.Python.Import("PyPDF2")
    }
    return:'$d(pypdf2) $$$ERROR($$$GeneralError, "Unable to load PyPDF2")
    kill pypdf2
    set text = ..GetTextPy(file)
  } catch ex {
    set sc = ex.AsStatus()
  }
  quit sc
}

ClassMethod GetTextPy(file) [ Language = python ]
{
  from PyPDF2 import PdfReader

  reader = PdfReader(file)
  text = ""
  for page in reader.pages:
    text += page.extract_text() + "\n"

  return text
}

}

Try to reload like this:

set importlib = ##class(%SYS.Python).Import("importlib")
do importlib.reload(helloWorld)

Also, it not an IRIS-specific behavior, you'll get the same results in any python interpreter:

import helloWorld
helloWorld.helloWorld()
>'Hello world'
del helloWorld

# modify helloWorld.py in text editor

import helloWorld
helloWorld.helloWorld()
>'Hello world'