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from pysmiles import read_smiles

import networkx as nx

import random

import requests

import os

import time

import sys

# returns the order number of the edge that appears using nx.edge_list

def getOrder(line):

    # only allow integer bond order values

    order = line.split("{'order': ")[1].rstrip('}\n')

    return int(line.split("{'order': ")[1].rstrip('}\n')) if order.isdigit() else -1

# multiplies the edge pair by the order number

def processContent(content):

    new_content = ""

    for line in content:

        # check if the line contains bond order information

        if "{'order':" in line:

            bond_order = getOrder(line)

            # if bond order is invalid, then return error

            if bond_order == -1:

                return -1

            # duplicate the edge for value of bond order

            vertex_pair = ' '.join(line.split()[:2])

            for i in range(bond_order):

             new_content += vertex_pair + '\n'

        else:

            new_content += line

    return new_content

def writeMolecule(mol_name, smiles):

    mol_with_H = read_smiles(smiles, explicit_hydrogen=True)

    file_path_mol = "./testcases/molecules/" + mol_name + ".txt"

    nx.write_edgelist(mol_with_H, file_path_mol)

    # write metadata for mol

    nodes = mol_with_H.nodes(data='element')

    mol_data = mol_name + '\n' + str(len(nodes)) + '\n'

    for node in nodes:

      mol_data += node[1] + '\n'

    # read the generated edgelist

    with open(file_path_mol, 'r') as file:

        edgelist = file.read()

    # if theres an invalid edgelist, remove it from the file system

    modified_edgelist = processContent(edgelist.split('\n'))

    if modified_edgelist == -1:

        os.remove(file_path_mol)

        return -1

    # write metadata at the beginning and the original content

    with open(file_path_mol, 'w') as file:

        file.write(mol_data + modified_edgelist)

    # print filepath to pick up in Java

    print(file_path_mol)

    return 0

def writePubChem(start, end):

    MAXSTEP = 100

    INCREMENT = min(end - start, MAXSTEP)

    # range(start, end, step) --> Change values for number of molecules required

    for indx in range(start,end,INCREMENT):

        start_time = time.time()

        numbers = [str(i) for i in range(indx, indx + INCREMENT)]

        # if HH in numbers:

        #     numbers.remove(HH)

        indexes = ",".join(numbers)

        # query from pubchem URL

        url = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/' + indexes + '/property/Title,CanonicalSMILES/json'

        response = requests.get(url)

        # Check if the request was successful

        if response.status_code == 200:

            # Extract the json from the response

            page_text = response.json()

            for chemical in page_text['PropertyTable']['Properties']:

                # check if desired keys are in the json

                if 'CanonicalSMILES' in chemical:

                    mol_name = "molecule" + str(chemical['CID'])

                    smiles = chemical['CanonicalSMILES']

                    # ignore Hydrogen Molecules

                    if smiles == "[HH]":

                        continue

                    # print("molecule "+ str(chemical['CID']) + ": " +  mol_name + "\t" + "smiles: " + smiles)

                    writeMolecule(mol_name, smiles)

        else:

            print("Failed to retrieve the page. Status code:", response.status_code)

        while (time.time() - start_time < 0.3):

            pass

if __name__ == "__main__":

    # get start and end index from Java call

    start = int(sys.argv[1])

    end = int(sys.argv[2])

    if start >= end or start < 0:

        pass

    else:

        writePubChem(start, end + 1)