'''
Benjamin Langley

Usage: python3 R4CapStatement_NarrativeMaker.py [json file]
Dependecies: 
    fhirclient
    pandas
    xlrd
    openpyxl
    stringcase
    jinja2
    commonmark
    lxml

To install all dependencies: pip3 install -r requirements.txt
to run on windows: python -m pip ...

NOTE: this requires the r4models to be installed in the fhirclient pip site-package, to be installed in [installdir]/lib/python/site-packages/fhirclient
Email Eric Haas for these models (the _element extension elements are not supported in that version. Corety Spears can provide a modified set or rfmodels for 
the capabilitystatement element level extension )

Modified from: 
https://github.com/Healthedata1/MyNotebooks/blob/master/CapStatement/R4CapStatement_Maker.ipynb
and jinja template from
https://github.com/Healthedata1/MyNotebooks/blob/master/CapStatement/R4capabilitystatement-server.j2
'''
import sys
import os
import os.path
from os import path
import glob
import validators
import fhirclient.r4models.capabilitystatement as CS
import fhirclient.r4models.implementationguide as IG
import fhirclient.r4models.structuredefinition as SD
import fhirclient.r4models.codeableconcept as CC
import fhirclient.r4models.fhirdate as D
import fhirclient.r4models.extension as X
import fhirclient.r4models.contactdetail as CD
import fhirclient.r4models.narrative as N
import fhirclient.r4models.bundle as B
import re 

import tarfile
# import fhirclient.r4models.narrative as N
import json
from json import dumps, loads
from requests import post, get
from pathlib import Path
from collections import namedtuple
from pandas import *
from datetime import datetime, date
from stringcase import snakecase, titlecase
from jinja2 import Environment, FileSystemLoader, select_autoescape
from commonmark import commonmark
from lxml import etree


# GLOBALS
fhir_base_url = 'http://hl7.org/fhir/'
f_jurisdiction = CC.CodeableConcept({
    "coding": [
        {
            "system": "urn:iso:std:iso:3166",
            "code": "US"
        }
    ]
})
conf_url = 'http://hl7.org/fhir/StructureDefinition/capabilitystatement-expectation'
combo_url = 'http://hl7.org/fhir/StructureDefinition/capabilitystatement-search-parameter-combination'
# dict to for SP to get right canonicals, may use spreadsheet or package file in future.
sp_specials = {
    'us-core-includeprovenance': 'http://hl7.org/fhir/us/core/SearchParameter/us-core-includeprovenance'}
#this should be a map to the common
sp_common_list = ["address", "address-city", "address-country", "address-postalcode", "address-state", "address-use", "birthdate", "code", "context", "context-quantity", "context-type", "context-type-quantity", "context-type-value", "date", "description", "email", "encounter", "family", "gender", "given", "identifier", "jurisdiction", "medication", "name", "patient", "phone", "phonetic", "publisher", "status", "status", "telecom", "title", "type", "url", "version"]
none_list = ['', ' ', 'none', 'n/a', 'N/A', 'N', 'False']
sep_list = (',', ';', ' ', ', ', '; ')
f_now = D.FHIRDate(str(date.today()))



class bcolors:
    HEADER = '\033[95m'
    OKBLUE = '\033[94m'
    OKCYAN = '\033[96m'
    OKGREEN = '\033[92m'
    WARNING = '\033[93m'
    FAIL = '\033[91m'
    ENDC = '\033[0m'
    BOLD = '\033[1m'
    UNDERLINE = '\033[4m'

def markdown(text, *args, **kwargs):
    return commonmark(text, *args, **kwargs)

def main():
    if (len(sys.argv) < 2):
        print(
            "Error: missing json file - correct usage is:\n\tpython3 R4CapStatement_NarrativeMaker.py [json file] {[Artifacts Folder]}")
        return

    xls = sys.argv[1]

    in_json_file = sys.argv[1]
    artifacts_folder = ""
    
    if len(sys.argv) > 2:
        artifacts_folder = sys.argv[2]
   
    print('....Generating CapabilityStatement Narrative.....')



    with open(in_json_file, 'r') as h:
        pjs = json.load(h)
    capStatement = CS.CapabilityStatement(pjs)
    #print(dumps(capStatement.as_json(), indent=3))    # %% [markdown]

    # CapabilityStatement loaded

    in_path = ''
    in_file = 'R4capabilitystatement-server.j2'

    env = Environment(
        loader=FileSystemLoader(searchpath=in_path),
        autoescape=select_autoescape(['html', 'xml', 'xhtml', 'j2', 'md'])
    )

    env.filters['markdown'] = markdown


    template = env.get_template(in_file)

    pname_map = {}
    igname_map = {}
    csname_map = {}
    # Load name maps
    if artifacts_folder != "":
        print('....Retrieving Artifact Names .....')
        artifacts_folder = os.path.abspath(artifacts_folder)
        struct_def_files = glob.glob(artifacts_folder + "/StructureDefinition-*.json")
        imp_guide_files = glob.glob(artifacts_folder + "/ImplementationGuide-*.json")
        cap_stmt_files = glob.glob(artifacts_folder + "/CapabilityStatement-*.json")
        
        pname_map = get_pname_map(struct_def_files)
        igname_map = get_igname_map(imp_guide_files)
        csname_map = get_csname_map(cap_stmt_files)

    # Check access to hl7.org/fhir
    r = get (fhir_base_url)
    if r.status_code == 200:
        print('....Retrieving Online Artifact Names .....')
        # Loop through all references in the CapabilityStatement and attempt to retried the artifacts to load the names into the map
        

        # Instantiates
        if capStatement.instantiates:
            for url in capStatement.instantiates:
                if url not in csname_map:
                    csname_map[url] = get_url_title(url, "instantiates CapabilityStatement")

        # Imports
        if capStatement.imports:
            for url in capStatement.imports:
                if url not in csname_map:
                    csname_map[url] = get_url_title(url, "imports CapabilityStatement")

        # Implementation Guides
        if capStatement.implementationGuide:
            for url in capStatement.implementationGuide:
                if url not in igname_map:
                    igname_map[url] = get_url_title(url, "ImplementationGuide")

        # Iterate through rest resources
        if capStatement.rest:
            for rest in capStatement.rest:
                if rest.resource:
                    for resource in rest.resource:
                        if resource.profile:
                            url = resource.profile
                            if url not in pname_map:
                                pname_map[url] = get_url_title(url, resource.type + " profile")
                                
                        if resource.supportedProfile:
                            for url in resource.supportedProfile:
                                if url not in pname_map:
                                    pname_map[url] = get_url_title(url, resource.type + " supported profile")

    else:
        print("Unable to connect to " + fhir_base_url + ". Will not attempt to load online artifacts to retrieve artifact names.")




    rendered = template.render(cs=capStatement, path_map='', pname_map=pname_map, purl_map='', sp_map='', 
                            csname_map=csname_map, csurl_map='', sp_url_map='', igname_map=igname_map, igurl_map='')
    
    #template.render(cs=cs, path_map=path_map, pname_map=pname_map, purl_map=purl_map, sp_map=sp_map, 
    #                       csname_map=csname_map, csurl_map=csurl_map, igname_map=igname_map, igurl_map=igurl_map)

    tempPath = Path.cwd() / "test.html"
    tempPath.write_text(rendered)
    #print(rendered)
    

    parser = etree.XMLParser(remove_blank_text=True)
    root = etree.fromstring(rendered, parser=parser)

    div = (etree.tostring(root[1][0], encoding='unicode', method='html'))

    print("\n####################################################\n")
    #print(etree.tostring(root[1][0], encoding='unicode', method='html'))
    print("\n####################################################\n")
    narr = N.Narrative()
    narr.status = 'generated'


    #div = re.sub('https://paciowg.github.io/advance-directives-ig/StructureDefinition-', 'SSSSSSSSSSSSSSSSS', div)
    # replace all of the supported profile urls in link text with just the profile name from inside the cononical url
    #######div = re.sub('">\(https?://.*/StructureDefinition-(.*)\.html\)</a>', '">\\1</a>', div)
    #div = re.sub('">\(https://paciowg.github.io/advance-directives-ig/StructureDefinition-PADI-(PersonalGoal.html)</a>', '\\1', div)
    # For some reason <br /> is being replaced with <br></br>, which is wrong. Convert it back.
    #div = div.replace("<br></br>", "<br />")
    #print(div)
    narr.div = div

    #print(dumps(narr.div, indent=3))    # %% [markdown]
    capStatement.text = narr
    outfile = 'Narrative-' + in_json_file
    path = Path.cwd() / outfile
    tempOut = dumps(capStatement.as_json(), indent=4)
    tempOut = tempOut.replace("<sup>+</sup>", "<sup>&#8224;</sup>")
    #tempOut = tempOut.replace(“<sup>t</sup>”, “<sup>&#8224;</sup>”)
    #print(tempOut)
    path.write_text(tempOut)


    print('.............validating..............')
    r = validate(capStatement)
    if (r.status_code != 200):
        print("Error: Unable to validate - status code {}".format(r.status_code))
    path = Path.cwd() / 'validation.html'
    path.write_text(
        f'<h1>Validation output</h1><h3>Status Code = {r.status_code}</h3> {r.json()["text"]["div"]}')
    print(f"HTML webpage of validation saved to:\n\t {path}")

    # get from package (json) file in local .fhir directory
    # save to file
    print('...........done............')
    # path = Path.cwd() / f'capabilitystatement-{cs.id.lower()}.json'
    #path = Path.cwd() / f'capabilitystatement-{meta.title.lower()}.json'
    #path.write_text(dumps(cs.as_json(), indent=4))
    #print(f"CapabilityStatement saved to:\n\t {path}")


def get_conf(conf='MAY', as_dict=False):
    if as_dict:
        return [X.Extension(dict(
            url=conf_url,
            valueCode=conf
        )).as_json()]
    else:
        return [X.Extension(dict(
            url=conf_url,
            valueCode=conf
        ))]


def get_addin_ext(py_ext, json_ext):
    if json_ext:   # ie not ''
        addin_ext = X.Extension(loads(json_ext))
        py_ext.append(addin_ext)  # add in other extensions
    return py_ext


def validate(r):

    #fhir_test_server = 'http://test.fhir.org/r4'
    #fhir_test_server = 'http://hapi.fhir.org/baseR4'
    fhir_test_server = 'http://wildfhir4.aegis.net/fhir4-0-1'

    headers = {
        'Accept': 'application/fhir+json',
        'Content-Type': 'application/fhir+json'
    }

    # profile = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient' # The official URL for this profile is: http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient

    params = dict(
        # profile = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient' # The official URL for this profile is: http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient
    )

    r = post(f'{fhir_test_server}/CapabilityStatement/$validate',
             params=params, headers=headers, data=dumps(r.as_json()))
    return r


def get_sys_op(xls):
    op_list = []
    df_op = read_excel(xls, 'ops', na_filter=False)
    for i in df_op.itertuples(index=True):
        if i.type == 'system':
            op = CS.CapabilityStatementRestResourceOperation()
            op.name = i.name
            op.definition = i.definition
            op.extension = get_conf(i.conf)
            op_list.append(op.as_json())
    return op_list


def get_rest_ints(xls):
    ri_list = []
    df_ri = read_excel(xls, 'rest_interactions', na_filter=False)
    for i in df_ri.itertuples(index=True):
        ri = CS.CapabilityStatementRestInteraction()
        ri.code = i.code
        ri.documentation = i.doc if i.doc not in none_list else None
        ri.extension = get_conf(i.conf)
        ri_list.append(ri.as_json())
    return ri_list


def get_igs(xls):
    ig_list = []
    df_igs = read_excel(xls, 'igs', na_filter=False)
    for ig in df_igs.itertuples(index=True):
        ig_list.append(ig.uri)
    return ig_list  # TODO add conformance to this


def kebab_to_pascal(word):
    return ''.join(x.capitalize() for x in word.split('-'))


def create_capabilitystatement(meta, canon, publisher, publisher_endpoint, xls):
    cs = CS.CapabilityStatement()
#    cs.id = meta.id
    cs.id = meta.title.lower()
    cs.url = f'{canon}CapabilityStatement/{meta.title.lower()}'
    cs.version = meta.version
    cs.name = f'{kebab_to_pascal(meta.id)}{cs.resource_type}'
#    cs.title = f'{titlecase(meta.id).replace("Us ", "US ")} {cs.resource_type}'
    cs.title = f'{meta.title} {cs.resource_type}'
    cs.status = 'active'

    cs.experimental = False
    cs.date = f_now  # as FHIRDate
    cs.publisher = publisher
    cs.contact = [CD.ContactDetail({"telecom": [publisher_endpoint]})]
    cs.description = meta.description
    cs.jurisdiction = [f_jurisdiction]
    cs.kind = 'requirements'
    cs.fhirVersion = meta.fhirVersion
    cs.acceptUnknown = 'both'
    cs.format = [
        "xml",
        "json"
    ]
    cs.patchFormat = [
        "application/json-patch+json",
    ]
    cs.implementationGuide = meta.ig.split(",") + get_igs(xls)

    return cs


def get_i(type, df_i):
    int_list = []
    for i in df_i.itertuples(index=True):
        if getattr(i, f'conf_{type}') not in none_list:
            int = CS.CapabilityStatementRestResourceInteraction()
            int.code = i.code
            try:
                int.documentation = getattr(i, f'doc_{type}') if getattr(
                    i, f'doc_{type}') not in none_list else None
            except AttributeError:
                pass
            int.extension = get_conf(getattr(i, f'conf_{type}'))
            int_list.append(int.as_json())

    return int_list




def get_combo_ext(r_type, combos):
    x_list = []
    for combo in combos:
        # convert to extension
        combo_ext = X.Extension()
        combo_ext.url = combo_url
        combo_conf_ext = get_conf(combo[1])
        combo_ext.extension = combo_conf_ext
        for param in combo[0].split(','):
            req_combo = X.Extension(
                dict(
                    url='required',
                    valueString=param  # http://hl7.org/fhir/us/core/SearchParameter/us-core-patient-family
                )
            )
            combo_ext.extension.append(req_combo)
        x_list.append(combo_ext)
    return x_list


def get_op(r_type, df_op):
    op_list = []
    for i in df_op.itertuples(index=True):
        if i.type == r_type:
            op = CS.CapabilityStatementRestResourceOperation()
            op.name = i.name
            op.definition = i.definition
            op.documentation = i.documentation if i.documentation not in none_list else None
            op.extension = get_conf(i.conf)
            try:
                op.extension = get_addin_ext(op.extension, i.ext)
            except AttributeError:
                print("---- no addin extensions found-----")
            op_list.append(op.as_json())

    return op_list

def get_pname_map(file_names):
    
    pname_map = {}
    for file_name in file_names:
        print("Searching: " + file_name + "\n")
        with open(file_name, 'r') as file_h:
            sd = SD.StructureDefinition(json.load(file_h))
            pname_map[sd.url] = sd.title
            print("Found title: " + sd.title + " from URL:" + sd.url + "\n")
        file_h.close()
    
    return pname_map

def get_igname_map(file_names):
    igname_map = {}
    for file_name in file_names:
        with open(file_name, 'r') as file_h:
            ig = IG.ImplementationGuide(json.load(file_h))
            igname_map[ig.url] = ig.title
        file_h.close()
    
    return igname_map

def get_csname_map(file_names):
    csname_map = {}
    for file_name in file_names:
        with open(file_name, 'r') as file_h:
            cap_stmt = CS.CapabilityStatement(json.load(file_h))
            csname_map[cap_stmt.url] = cap_stmt.title
        file_h.close()
    
    return csname_map

def get_url_title(url, msg_context):
    print("Retrieving " + msg_context + " at: " + url)
    try:
        r = get(url, headers={"Accept":"application/json"})
        if r.status_code == 200:
            try:
                json_data = json.loads(r.content)
                #Retrieving this as json data instead of from fhirclient objects in case there is a validation error
                if(json_data['title']):
                    return json_data['title']
                else:
                    print(bcolors.BOLD + bcolors.FAIL + "Warning: Unable to retrieve title from online " + msg_context + " artifact (" + url + ") - Title will not show up in rendered narrative." + bcolors.ENDC)
            except ValueError:
                print(bcolors.BOLD + bcolors.FAIL + "Warning: Unable to decode online " + msg_context + " artifact (" + url + ") - Title will not show up in rendered narrative." + bcolors.ENDC)
        else:
            print(bcolors.BOLD + bcolors.FAIL + "Warning: unable to retrieve online " + msg_context + " artifact (" + url + "). Failed with status code: " + str(r.status_code) + " - Title will not show up in rendered narrative." + bcolors.ENDC)
    except ValueError:
        print(bcolors.BOLD + bcolors.FAIL + "Warning: Unable to retrieve " + msg_context + " artifact (" + url + ")." + bcolors.ENDC)



def markdown(text, *args, **kwargs):
    if text:
        return commonmark(text, *args, **kwargs)

def get_si(path):
    with tarfile.open(f'{path}/package.tgz', mode='r') as tf:
        #pprint(tf.getnames())
        f = tf.extractfile('other/spec.internals')
        r = f.read()
        return(loads(r))

def get_si2(path):
    # Get the full path in case a relative path is provided.
    fullpath = os.path.abspath(path)

    with open(f'{path}', 'r', encoding='utf-8-sig') as f:
        r = f.read()
        # encoding for loads was deprecated in 3.9  https://bugs.python.org/issue39377
        if sys.version_info >= (3, 9):
            return(loads(r))
        else:
            return(loads(r, encoding = 'utf-8'))


main()