IFC entities extracted twice

[Larz60+]

Ok, I have managed to isolate where the duplicates are coming from.
To show this, I restructured your code a bit, to my style, so I could move around quicker,
code now looks like:

main module:

import IFCpaths
import ifcopenshell
import sys


class ifc:
    def __init__(self):
        self.ipath = IFCpaths.IFCpaths()
        self.f = ifcopenshell.open(self.ipath.ModelFull)
        self.f2 = ifcopenshell.file()
        self.process()

    def process(self):
        persons = self.f.by_type("IFCPERSON")
        for person in persons:
            self.f2.add(person)

        organizations = self.f.by_type("IFCORGANIZATION")
        for organization in organizations:
            self.f2.add(organization)
        
        personorganizations = self.f.by_type("IFCPERSONANDORGANIZATION")
        for personorganization in personorganizations:
            self.f2.add(personorganization)
        
        self.f2.write("test222.ifc")


if __name__ == '__main__':
    ifc()

IFCpaths.py

import os
from pathlib import Path


class IFCpaths:
    def __init__(self):
        os.chdir(os.path.abspath(os.path.dirname(__file__)))
        self.homepath = Path('.')
        self.rootpath = self.homepath / '..'

        self.datapath = self.rootpath / 'data'
        self.datapath.mkdir(exist_ok=True)

        self.beam_material = self.datapath / 'Beam_Material.ifc'
        self.ModelFull = self.datapath / 'ModelFull.ifc'
        self.testfile = self.datapath / 'test222.ifc'

Now to isolate the duplication, i wrote the output bit by bit
stage 1:

import IFCpaths
import ifcopenshell
import sys


class ifc:
    def __init__(self):
        self.ipath = IFCpaths.IFCpaths()
        self.f = ifcopenshell.open(self.ipath.ModelFull)
        self.f2 = ifcopenshell.file()
        self.process()

    def process(self):
        persons = self.f.by_type("IFCPERSON")
        for person in persons:
            print(f'person: {person}')
            self.f2.add(person)

        self.f2.write("test222.ifc")
        sys.exit(0)
        
        organizations = self.f.by_type("IFCORGANIZATION")
        for organization in organizations:
            print(f'organization: {organization}')
            self.f2.add(organization)
        
        personorganizations = self.f.by_type("IFCPERSONANDORGANIZATION")
        for personorganization in personorganizations:
            print(f'personorganization: {personorganization}')
            self.f2.add(personorganization)
        
        self.f2.write("test222.ifc")


if __name__ == '__main__':
    ifc()

output (all ok):

Output:
ISO-10303-21;
HEADER;
FILE_DESCRIPTION(('ViewDefinition [CoordinationView]'),'2;1');
FILE_NAME('','2019-04-11T19:46:26',(),(),'IfcOpenShell 0.5.0-dev','IfcOpenShell 0.5.0-dev','');
FILE_SCHEMA(('IFC2X3'));
ENDSEC;
DATA;
#1=IFCPERSON($,$,'',$,$,$,$,$);
ENDSEC;
END-ISO-10303-21;

stage 2:

import IFCpaths
import ifcopenshell
import sys


class ifc:
    def __init__(self):
        self.ipath = IFCpaths.IFCpaths()
        self.f = ifcopenshell.open(self.ipath.ModelFull)
        self.f2 = ifcopenshell.file()
        self.process()

    def process(self):
        persons = self.f.by_type("IFCPERSON")
        for person in persons:
            print(f'person: {person}')
            self.f2.add(person)
        
        organizations = self.f.by_type("IFCORGANIZATION")
        for organization in organizations:
            print(f'organization: {organization}')
            self.f2.add(organization)
        
        self.f2.write("test222.ifc")
        sys.exit(0)

        personorganizations = self.f.by_type("IFCPERSONANDORGANIZATION")
        for personorganization in personorganizations:
            print(f'personorganization: {personorganization}')
            self.f2.add(personorganization)
        
        self.f2.write("test222.ifc")


if __name__ == '__main__':
    ifc()

output (all still ok):

Output:
ISO-10303-21;
HEADER;
FILE_DESCRIPTION(('ViewDefinition [CoordinationView]'),'2;1');
FILE_NAME('','2019-04-11T19:48:24',(),(),'IfcOpenShell 0.5.0-dev','IfcOpenShell 0.5.0-dev','');
FILE_SCHEMA(('IFC2X3'));
ENDSEC;
DATA;
#1=IFCPERSON($,$,'',$,$,$,$,$);
#2=IFCORGANIZATION($,'',$,$,$);
ENDSEC;
END-ISO-10303-21;

stage3

import IFCpaths
import ifcopenshell
import sys


class ifc:
    def __init__(self):
        self.ipath = IFCpaths.IFCpaths()
        self.f = ifcopenshell.open(self.ipath.ModelFull)
        self.f2 = ifcopenshell.file()
        self.process()

    def process(self):
        persons = self.f.by_type("IFCPERSON")
        for person in persons:
            print(f'person: {person}')
            self.f2.add(person)
        
        organizations = self.f.by_type("IFCORGANIZATION")
        for organization in organizations:
            print(f'organization: {organization}')
            self.f2.add(organization)
        
        personorganizations = self.f.by_type("IFCPERSONANDORGANIZATION")
        for personorganization in personorganizations:
            print(f'personorganization: {personorganization}')
            self.f2.add(personorganization)

        self.f2.write("test222.ifc")
        sys.exit(0)
        
        self.f2.write("test222.ifc")


if __name__ == '__main__':
    ifc()

output (not ok)

Output:
ISO-10303-21;
HEADER;
FILE_DESCRIPTION(('ViewDefinition [CoordinationView]'),'2;1');
FILE_NAME('','2019-04-11T19:49:57',(),(),'IfcOpenShell 0.5.0-dev','IfcOpenShell 0.5.0-dev','');
FILE_SCHEMA(('IFC2X3'));
ENDSEC;
DATA;
#1=IFCPERSON($,$,'',$,$,$,$,$);
#2=IFCORGANIZATION($,'',$,$,$);
#3=IFCPERSON($,$,'',$,$,$,$,$);
#4=IFCORGANIZATION($,'',$,$,$);
#5=IFCPERSONANDORGANIZATION(#3,#4,$);
ENDSEC;
END-ISO-10303-21;

So why? ...
This file format is totally new to me, but on looking in the model file, i see:

Output:
#3=IFCPERSONANDORGANIZATION(#1,#2,$);

So, and this is a wild guess being totally uneducated on model file structurs, but having experience with other CAD layouts,
I wonder, does (#1, #2, $) mean include #1: (#1=IFCPERSON($,$,'',$,$,$,$,$);) and
include #2: #2=IFCORGANIZATION($,'',$,$,$); and
include $ (self?): #5=IFCPERSONANDORGANIZATION(#3,#4,$);