from biocypher import BioCypher
import networkx as nx
import json
import os
import uuid
from graphCreation import create_graph
from graphCreation.process_references import process_references
from graphCreation.property_convolution import property_convolution

from schema_config_generation import write_automated_schema
from graphCreation.node_typing import set_resource_type



def load_multiple_fhir_bundles(directory_path):
    graph = nx.DiGraph()
    init = True

    # Iterate over all files in the directory
    for filename in os.listdir(directory_path):
        if filename.endswith('.json'):  # Assuming FHIR bundles are in JSON format
            file_path = os.path.join(directory_path, filename)
            with open(file_path, 'r') as f:
                bundle_json = json.load(f)

                #fix all strings to to enable ' in neo4j
                fixed_quotes = replace_single_quotes(bundle_json)
            if init:
                #print(bundle_json, filename, graph)
                create_graph.json_to_networkx(fixed_quotes, filename, graph)
                init = False
            else:
                create_graph.add_json_to_networkx(fixed_quotes, filename, graph)
        print("Imported: ", filename)

    return graph

def replace_single_quotes(obj):
    if isinstance(obj, str):  # If it's a string, replace single quotes
        return obj.replace("'", "''")
    elif isinstance(obj, dict):  # If it's a dictionary, process each key-value pair
        return {key: replace_single_quotes(value) for key, value in obj.items()}
    elif isinstance(obj, list):  # If it's a list, process each item
        return [replace_single_quotes(item) for item in obj]
    else:
        return obj  # Leave other data types unchanged

def main():
    #get a list of nodes that should be imported
    ## create networkX and run improvement scripts
    print("Creating the graph...", flush=True)
    nx_graph = load_multiple_fhir_bundles('./testData/') # 'mockData' for unit test data, 'testData' for Synthea files
    print(nx_graph)

    print("Reducing references...", flush=True)
    process_references(nx_graph)
    print(nx_graph)

    print("Convolute references...", flush=True)
    property_convolution(nx_graph)
    print(nx_graph)

    print("Generate auto schema...")
    write_automated_schema(nx_graph, 'config/automated_schema.yaml', None)


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

    bc.show_ontology_structure()

    #BioCypher preperation
    ## node generator: extract id, label and property dictionary
    def node_generator():
        for node in nx_graph.nodes():

            """             #single qoutes break neo4j import, e.g. 'CHILDREN'S Hospital'
            checkDisplay = nx_graph.nodes[node].get('display')
            if checkDisplay:
                checkDisplay = checkDisplay.replace("'", "''")
                nx_graph.nodes[node]['display'] = checkDisplay
                #print("------->", nx_graph.nodes[node].get('display'))
            
            checkName = nx_graph.nodes[node].get('name')
            if checkName:
                checkName = checkName.replace("'", "''")
                nx_graph.nodes[node]['name'] = checkName
                #print("------->", nx_graph.nodes[node].get('name')) """

            label = nx_graph.nodes[node].get('label')
           
            if label == "resource":
                label = nx_graph.nodes[node].get('resourceType')
            '''
            elif label == 'identifier':
                label = nx_graph.nodes[node].get('system')
                print('/' in label)
                if '/' in label:
                    lastSlash = label.rfind('/') + 1
                    label = label[lastSlash:] + '-ID'
            elif label == 'telecom':
                label = nx_graph.nodes[node].get('system')
                print('/' in label)
                if '/' in label:
                    lastSlash = label.rfind('/') + 1
                    label = 'telecom-' + label[lastSlash:]
            elif label == 'address':
                extension = nx_graph.nodes[node].get('extension_url')
                print("EX!: ", extension)
                if extension:
                    lastSlash = extension.rfind('/') + 1
                    label = label + '-' + extension[lastSlash:]
            '''

            yield(
                nx_graph.nodes[node].get('id', node), #remark: this returns the node id if this attribute exists. otherwise it returns node which equals the identifier that is used by nx
                label,
                nx_graph.nodes[node] # get properties
            )

    def edge_generator():
        for edge in nx_graph.edges(data = True):
            source, target, attributes = edge

            s_label = nx_graph.nodes[source].get('label')
            if s_label == 'resource':
                s_label = nx_graph.nodes[source].get('resourceType')
            t_label = nx_graph.nodes[target].get('label')
            if t_label == 'resource':
                t_label = nx_graph.nodes[target].get('resourceType')
            label = s_label + '_to_' + t_label

            yield(
                attributes.get('id', str(uuid.uuid4())),  # Edge ID (if exists, otherwise use nx internal id)
                nx_graph.nodes[source].get('id', source),
                nx_graph.nodes[target].get('id', target),
                label,
                attributes  # All edge attributes
            )

    bc.write_nodes(node_generator())
    bc.write_edges(edge_generator())

    #write the import script
    bc.write_import_call()

if __name__ == "__main__":
    #print("Called import script. Should run its main function now...")
    main()