import sys
import os

from biocypher import BioCypher
from schema_config_generation import write_automated_schema


# Add submodule to path BEFORE any other imports
sys.path.insert(0, '/app/mdm2neo4j/src')  # Absolute path in Docker
# OR
#sys.path.insert(0, os.path.join(os.path.dirname(__file__), 'mdm2neo4j'))  # Relative path

# Now your imports should work
import mdm2neo4j.src.xml_processor.xml_processor as xp

from import_fhir_to_nx_diGraph import generate_neo4j_import_script


from import_fhir_to_nx_diGraph import load_multiple_fhir_patients
#import mdm2neo4j.src.xml_processor.xml_processor as xp


def main():

    # create Biocypher driver
    bc = BioCypher(
        biocypher_config_path="config/biocypher_config.yaml",
    )

    #bc.show_ontology_structure() #very extensive
    #BioCypher preperation


    ## create networkX and run improvement scripts

    adapter_mode = 0
    xml_file_path = "./odm_models"

    write_automated_schema(None, 'config/automated_schema.yaml', ['config/manual_schema_config.yaml', 'config/ODM_schema.yaml'])

    if(adapter_mode == 0 or adapter_mode == -1):
        n_patients = int(os.getenv('NUMBER_OF_PATIENTS'))
        print("--- load ", n_patients, " fhir patients ---")
        load_multiple_fhir_patients(n_patients)

    if(adapter_mode == 1 or adapter_mode == -1):

        #bc.show_ontology_structure() #very extensive

        bc.write_nodes(xp.parse_xml_generate_nodes(xml_file_path))
        bc.write_edges(xp.parse_xml_generate_edges(xml_file_path))



    print("CREATING THE SCRIPT", flush=True)
    generate_neo4j_import_script()
    with open('/neo4j_import/shell-scipt-complete', 'w') as f:
        f.write('Import completed successfully')

    print("FHIR import completed successfully")

if __name__ == "__main__":
    main()