import copy
import re
from dataclasses import dataclass, field
from datetime import datetime
from pathlib import Path
from typing import ClassVar, Dict, List, Optional, Pattern, Set, Tuple, Union

import requests
from bs4 import BeautifulSoup, NavigableString, Tag
from dateutil import parser
from tabula import read_pdf

import sec_certs.constants as constants
from sec_certs import helpers
from sec_certs.cert_rules import REGEXEC_SEP, fips_common_rules, fips_rules
from sec_certs.config.configuration import config
from sec_certs.constants import LINE_SEPARATOR
from sec_certs.dataset.cpe import CPEDataset
from sec_certs.helpers import fips_dgst, load_cert_file, normalize_match_string, save_modified_cert_file
from sec_certs.model.cpe_matching import CPEClassifier
from sec_certs.sample.certificate import Certificate, logger
from sec_certs.sample.cpe import CPE
from sec_certs.serialization.json import ComplexSerializableType


class FIPSCertificate(Certificate, ComplexSerializableType):
    FIPS_BASE_URL: ClassVar[str] = "https://csrc.nist.gov"
    FIPS_MODULE_URL: ClassVar[
        str
    ] = "https://csrc.nist.gov/projects/cryptographic-module-validation-program/certificate/"

    @dataclass(eq=True)
    class State(ComplexSerializableType):
        sp_path: Path
        html_path: Path
        fragment_path: Path
        tables_done: bool
        file_status: Optional[bool]
        txt_state: bool

        def __init__(
            self,
            sp_path: Union[str, Path],
            html_path: Union[str, Path],
            fragment_path: Union[str, Path],
            tables_done: bool,
            file_status: Optional[bool],
            txt_state: bool,
        ):
            self.sp_path = Path(sp_path)
            self.html_path = Path(html_path)
            self.fragment_path = Path(fragment_path)
            self.tables_done = tables_done
            self.file_status = file_status
            self.txt_state = txt_state

    def set_local_paths(
        self,
        sp_dir: Optional[Union[str, Path]],
        html_dir: Optional[Union[str, Path]],
        fragment_dir: Optional[Union[str, Path]],
    ):
        if sp_dir is not None:
            self.state.sp_path = (Path(sp_dir) / (str(self.cert_id))).with_suffix(".pdf")
        if html_dir is not None:
            self.state.html_path = (Path(html_dir) / (str(self.cert_id))).with_suffix(".html")
        if fragment_dir is not None:
            self.state.fragment_path = (Path(fragment_dir) / (str(self.cert_id))).with_suffix(".txt")

    @dataclass(eq=True)
    class Algorithm(ComplexSerializableType):
        cert_id: str
        vendor: str
        implementation: str
        type: str
        date: str

        @property
        def dgst(self):
            # certs in dataset are in format { id: [FIPSAlgorithm] }, there is only one type of algorithm
            # for each id
            return self.type

        def __repr__(self):
            return self.type + " algorithm #" + self.cert_id + " created by " + self.vendor

        def __str__(self):
            return str(self.type + " algorithm #" + self.cert_id + " created by " + self.vendor)

    @dataclass(eq=True)
    class WebScan(ComplexSerializableType):
        module_name: Optional[str]
        standard: Optional[str]
        status: Optional[str]
        date_sunset: Optional[datetime]
        date_validation: Optional[List[datetime]]
        level: Optional[str]
        caveat: Optional[str]
        exceptions: Optional[List[str]]
        module_type: Optional[str]
        embodiment: Optional[str]
        algorithms: Optional[List[Dict[str, str]]]
        tested_conf: Optional[List[str]]
        description: Optional[str]
        mentioned_certs: Optional[Dict[str, Dict[str, int]]]
        vendor: Optional[str]
        vendor_www: Optional[str]
        lab: Optional[str]
        lab_nvlap: Optional[str]
        historical_reason: Optional[str]
        security_policy_www: Optional[str]
        certificate_www: Optional[str]
        hw_version: Optional[str]
        fw_version: Optional[str]
        revoked_reason: Optional[str]
        revoked_link: Optional[str]
        sw_versions: Optional[str]
        product_url: Optional[str]
        connections: List[str]

        @property
        def dgst(self):
            # certs in dataset are in format { id: [FIPSAlgorithm] }, there is only one type of algorithm
            # for each id
            return helpers.get_first_16_bytes_sha256(self.product_url + self.vendor_www)

        def __repr__(self):
            return self.module_name + " created by " + self.vendor

        def __str__(self):
            return str(self.module_name + " created by " + self.vendor)

    @dataclass(eq=True)
    class PdfScan(ComplexSerializableType):
        cert_id: int
        keywords: Dict
        algorithms: List
        connections: List[str]

        @property
        def dgst(self):
            # certs in dataset are in format { id: [FIPSAlgorithm] }, there is only one type of algorithm
            # for each id
            return helpers.get_first_16_bytes_sha256(str(self.keywords))

        def __repr__(self):
            return self.cert_id

        def __str__(self):
            return str(self.cert_id)

    @dataclass(eq=True)
    class FIPSHeuristics(ComplexSerializableType):
        keywords: Optional[Dict[str, Dict]]
        algorithms: List[Dict[str, Dict]]
        connections: List[str]
        unmatched_algs: int

        extracted_versions: Optional[List[str]] = field(default=None)
        cpe_matches: Optional[Set[str]] = field(default=None)
        verified_cpe_matches: Optional[Set[CPE]] = field(default=None)
        related_cves: Optional[List[str]] = field(default=None)
        cpe_candidate_vendors: Optional[List[str]] = field(init=False)

        directly_affected_by: Optional[Set] = field(default=None)
        indirectly_affected_by: Optional[Set] = field(default=None)
        directly_affecting: Optional[Set] = field(default=None)
        indirectly_affecting: Optional[Set] = field(default=None)

        @property
        def serialized_attributes(self) -> List[str]:
            all_vars = copy.deepcopy(super().serialized_attributes)
            all_vars.remove("cpe_candidate_vendors")
            return all_vars

        def __post_init__(self):
            self.cpe_candidate_vendors = None

        @property
        def dgst(self):
            # certs in dataset are in format { id: [FIPSAlgorithm] }, there is only one type of algorithm
            # for each id
            return helpers.get_first_16_bytes_sha256(str(self.keywords))

    def __str__(self) -> str:
        return str(self.cert_id)

    @property
    def dgst(self) -> str:
        return fips_dgst(self.cert_id)

    @property
    def label_studio_title(self):
        return (
            "Vendor: "
            + str(self.web_scan.vendor)
            + "\n"
            + "Module name: "
            + str(self.web_scan.module_name)
            + "\n"
            + "HW version: "
            + str(self.web_scan.hw_version)
            + "\n"
            + "FW version: "
            + str(self.web_scan.fw_version)
        )

    @staticmethod
    def download_security_policy(cert: Tuple[str, Path]) -> None:
        exit_code = helpers.download_file(*cert, delay=1)
        if exit_code != requests.codes.ok:
            logger.error(f"Failed to download security policy from {cert[0]}, code: {exit_code}")

    def __init__(
        self,
        cert_id: int,
        web_scan: "FIPSCertificate.WebScan",
        pdf_scan: "FIPSCertificate.PdfScan",
        heuristics: "FIPSCertificate.FIPSHeuristics",
        state: State,
    ):
        super().__init__()
        self.cert_id = cert_id
        self.web_scan = web_scan
        self.pdf_scan = pdf_scan
        self.heuristics = heuristics
        self.state = state

    @classmethod
    def from_dict(cls, dct: Dict) -> "FIPSCertificate":
        new_dct = dct.copy()

        if new_dct["web_scan"].date_validation:
            new_dct["web_scan"].date_validation = [parser.parse(x).date() for x in new_dct["web_scan"].date_validation]

        if new_dct["web_scan"].date_sunset:
            new_dct["web_scan"].date_sunset = parser.parse(new_dct["web_scan"].date_sunset).date()
        return super(cls, FIPSCertificate).from_dict(new_dct)

    @staticmethod
    def download_html_page(cert: Tuple[str, Path]) -> Optional[Tuple[str, Path]]:
        exit_code = helpers.download_file(*cert, delay=1)
        if exit_code != requests.codes.ok:
            logger.error(f"Failed to download html page from {cert[0]}, code: {exit_code}")
            return cert
        return None

    @staticmethod
    def initialize_dictionary() -> Dict:
        return {
            "module_name": None,
            "standard": None,
            "status": None,
            "date_sunset": None,
            "date_validation": None,
            "level": None,
            "caveat": None,
            "exceptions": None,
            "module_type": None,
            "embodiment": None,
            "tested_conf": None,
            "description": None,
            "vendor": None,
            "vendor_www": None,
            "lab": None,
            "lab_nvlap": None,
            "historical_reason": None,
            "revoked_reason": None,
            "revoked_link": None,
            "algorithms": [],
            "mentioned_certs": {},
            "tables_done": False,
            "security_policy_www": None,
            "certificate_www": None,
            "hw_versions": None,
            "fw_versions": None,
            "sw_versions": None,
            "product_url": None,
        }

    @staticmethod
    def parse_caveat(current_text: str) -> Dict[str, Dict[str, int]]:
        """
        Parses content of "Caveat" of FIPS CMVP .html file
        :param current_text: text of "Caveat"
        :return: dictionary of all found algorithm IDs
        """
        ids_found: Dict[str, Dict[str, int]] = {}
        r_key = r"(?P<word>\w+)?\s?(?:#\s?|Cert\.?(?!.\s)\s?|Certificate\s?)+(?P<id>\d+)"
        for m in re.finditer(r_key, current_text):
            if m.group("word") and m.group("word").lower() in {"rsa", "shs", "dsa", "pkcs", "aes"}:
                continue
            if m.group("id") in ids_found:
                ids_found[m.group("id")]["count"] += 1
            else:
                ids_found[m.group("id")] = {"count": 1}

        return ids_found

    @staticmethod
    def extract_algorithm_certificates(current_text: str, in_pdf: bool = False) -> List:
        """
        Parses table of FIPS (non) allowed algorithms
        :param current_text: Contents of the table
        :param in_pdf: Specifies whether the table was found in a PDF security policies file
        :return: List containing one element - dictionary with all parsed algorithm cert ids
        """
        set_items = set()
        if in_pdf:
            reg = r"(?:#?\s?|(?:Cert)\.?[^. ]*?\s?)(?:[CcAa]\s)?(?P<id>[CcAa]? ?\d+)"
        else:
            reg = r"(?:#[CcAa]?\s?|(?:Cert)\.?[^. ]*?\s?)(?:[CcAa]\s)?(?P<id>\d+)"
        for m in re.finditer(reg, current_text):
            set_items.add(m.group())

        return [{"Certificate": list(set_items)}] if len(set_items) > 0 else []

    @staticmethod
    def parse_table(element: Union[Tag, NavigableString]) -> List[Dict]:
        """
        Parses content of <table> tags in FIPS .html CMVP page
        :param element: text in <table> tags
        :return: list of all found algorithm IDs
        """
        found_items = []
        trs = element.find_all("tr")
        for tr in trs:
            tds = tr.find_all("td")
            cert = FIPSCertificate.extract_algorithm_certificates(tds[1].text)
            found_items.append(
                {
                    "Name": tds[0].text,
                    "Certificate": cert[0]["Certificate"] if cert != [] else [],
                    "Links": [str(x) for x in tds[1].find_all("a")],
                    "Raw": str(tr),
                }
            )

        return found_items

    @staticmethod
    def parse_html_main(current_div: Tag, html_items_found: Dict, pairs: Dict):
        title = current_div.find("div", class_="col-md-3").text.strip()
        content = (
            current_div.find("div", class_="col-md-9")
            .text.strip()
            .replace("\n", "")
            .replace("\t", "")
            .replace("    ", " ")
        )

        if title in pairs:
            if "date_sunset" == pairs[title]:
                html_items_found[pairs[title]] = parser.parse(content).date()

            elif "caveat" in pairs[title]:
                html_items_found[pairs[title]] = content
                html_items_found["mentioned_certs"].update(FIPSCertificate.parse_caveat(content))

            elif "FIPS Algorithms" in title:
                html_items_found["algorithms"] += FIPSCertificate.parse_table(
                    current_div.find("div", class_="col-md-9")
                )

            elif "Algorithms" in title or "Description" in title:
                html_items_found["algorithms"] += FIPSCertificate.extract_algorithm_certificates(content)
                if "Description" in title:
                    html_items_found["description"] = content

            elif "tested_conf" in pairs[title] or "exceptions" in pairs[title]:
                html_items_found[pairs[title]] = [
                    x.text for x in current_div.find("div", class_="col-md-9").find_all("li")
                ]
            else:
                html_items_found[pairs[title]] = content

    @staticmethod
    def parse_vendor(current_div: Tag, html_items_found: Dict, current_file: Path):
        vendor_string = current_div.find("div", "panel-body").find("a")

        if not vendor_string:
            vendor_string = list(current_div.find("div", "panel-body").children)[0].strip()
            html_items_found["vendor_www"] = ""
        else:
            html_items_found["vendor_www"] = vendor_string.get("href")
            vendor_string = vendor_string.text.strip()

        html_items_found["vendor"] = vendor_string
        if html_items_found["vendor"] == "":
            logger.warning(f"NO VENDOR FOUND {current_file}")

    @staticmethod
    def parse_lab(current_div: Tag, html_items_found: Dict, current_file: Path):
        html_items_found["lab"] = list(current_div.find("div", "panel-body").children)[0].strip()
        html_items_found["nvlap_code"] = (
            list(current_div.find("div", "panel-body").children)[2].strip().split("\n")[1].strip()
        )

        if html_items_found["lab"] == "":
            logger.warning(f"NO LAB FOUND {current_file}")

        if html_items_found["nvlap_code"] == "":
            logger.warning(f"NO NVLAP CODE FOUND {current_file}")

    @staticmethod
    def parse_related_files(current_div: Tag, html_items_found: Dict):
        links = current_div.find_all("a")
        html_items_found["security_policy_www"] = constants.FIPS_BASE_URL + links[0].get("href")

        if len(links) == 2:
            html_items_found["certificate_www"] = constants.FIPS_BASE_URL + links[1].get("href")

    @staticmethod
    def normalize(items: Dict):
        items["module_type"] = items["module_type"].lower().replace("-", " ").title()
        items["embodiment"] = items["embodiment"].lower().replace("-", " ").replace("stand alone", "standalone").title()

    @staticmethod
    def parse_validation_dates(current_div: Tag, html_items_found: Dict):
        table = current_div.find("table")
        rows = table.find("tbody").findAll("tr")
        html_items_found["date_validation"] = [parser.parse(td.text).date() for td in [row.find("td") for row in rows]]

    @classmethod
    def html_from_file(
        cls, file: Path, state: State, initialized: "FIPSCertificate" = None, redo: bool = False
    ) -> "FIPSCertificate":
        pairs = {
            "Module Name": "module_name",
            "Standard": "standard",
            "Status": "status",
            "Sunset Date": "date_sunset",
            "Validation Dates": "date_validation",
            "Overall Level": "level",
            "Caveat": "caveat",
            "Security Level Exceptions": "exceptions",
            "Module Type": "module_type",
            "Embodiment": "embodiment",
            "FIPS Algorithms": "algorithms",
            "Allowed Algorithms": "algorithms",
            "Other Algorithms": "algorithms",
            "Tested Configuration(s)": "tested_conf",
            "Description": "description",
            "Historical Reason": "historical_reason",
            "Hardware Versions": "hw_versions",
            "Firmware Versions": "fw_versions",
            "Revoked Reason": "revoked_reason",
            "Revoked Link": "revoked_link",
            "Software Versions": "sw_versions",
            "Product URL": "product_url",
        }
        if not initialized:
            items_found = FIPSCertificate.initialize_dictionary()
            items_found["cert_id"] = int(file.stem)
        else:
            items_found = initialized.web_scan.__dict__
            items_found["cert_id"] = initialized.cert_id
            items_found["revoked_reason"] = None
            items_found["revoked_link"] = None
            items_found["mentioned_certs"] = {}
            state.tables_done = initialized.state.tables_done
            state.file_status = initialized.state.file_status
            state.txt_state = initialized.state.txt_state
            initialized.heuristics.connections = []

        if redo:
            items_found = FIPSCertificate.initialize_dictionary()
            items_found["cert_id"] = int(file.stem)

        text = helpers.load_cert_html_file(file)
        soup = BeautifulSoup(text, "html.parser")
        for div in soup.find_all("div", class_="row padrow"):
            FIPSCertificate.parse_html_main(div, items_found, pairs)

        for div in soup.find_all("div", class_="panel panel-default")[1:]:
            if div.find("h4", class_="panel-title").text == "Vendor":
                FIPSCertificate.parse_vendor(div, items_found, file)

            if div.find("h4", class_="panel-title").text == "Lab":
                FIPSCertificate.parse_lab(div, items_found, file)

            if div.find("h4", class_="panel-title").text == "Related Files":
                FIPSCertificate.parse_related_files(div, items_found)

            if div.find("h4", class_="panel-title").text == "Validation History":
                FIPSCertificate.parse_validation_dates(div, items_found)

        FIPSCertificate.normalize(items_found)

        return FIPSCertificate(
            items_found["cert_id"],
            FIPSCertificate.WebScan(
                items_found["module_name"] if "module_name" in items_found else None,
                items_found["standard"] if "standard" in items_found else None,
                items_found["status"] if "status" in items_found else None,
                items_found["date_sunset"] if "date_sunset" in items_found else None,
                items_found["date_validation"] if "date_validation" in items_found else None,
                items_found["level"] if "level" in items_found else None,
                items_found["caveat"] if "caveat" in items_found else None,
                items_found["exceptions"] if "exceptions" in items_found else None,
                items_found["type"] if "type" in items_found else None,
                items_found["embodiment"] if "embodiment" in items_found else None,
                items_found["algorithms"] if "algorithms" in items_found else None,
                items_found["tested_conf"] if "tested_conf" in items_found else None,
                items_found["description"] if "description" in items_found else None,
                items_found["mentioned_certs"] if "mentioned_certs" in items_found else None,
                items_found["vendor"] if "vendor" in items_found else None,
                items_found["vendor_www"] if "vendor_www" in items_found else None,
                items_found["lab"] if "lab" in items_found else None,
                items_found["nvlap_code"] if "nvlap_code" in items_found else None,
                items_found["historical_reason"] if "historical_reason" in items_found else None,
                items_found["security_policy_www"] if "security_policy_www" in items_found else None,
                items_found["certificate_www"] if "certificate_www" in items_found else None,
                items_found["hw_versions"] if "hw_versions" in items_found else None,
                items_found["fw_versions"] if "fw_versions" in items_found else None,
                items_found["revoked_reason"] if "revoked_reason" in items_found else None,
                items_found["revoked_link"] if "revoked_link" in items_found else None,
                items_found["sw_versions"] if "sw_versions" in items_found else None,
                items_found["product_url"] if "product_url" in items_found else None,
                [],
            ),  # connections
            FIPSCertificate.PdfScan(
                items_found["cert_id"],
                {} if not initialized else initialized.pdf_scan.keywords,
                [] if not initialized else initialized.pdf_scan.algorithms,
                [],  # connections
            ),
            FIPSCertificate.FIPSHeuristics(None, [], [], 0),
            state,
        )

    @staticmethod
    def convert_pdf_file(tup: Tuple["FIPSCertificate", Path, Path]) -> "FIPSCertificate":
        cert, pdf_path, txt_path = tup
        if not cert.state.txt_state:
            exit_code = helpers.convert_pdf_file(pdf_path, txt_path, ["-raw"])
            if exit_code != constants.RETURNCODE_OK:
                logger.error(f"Cert dgst: {cert.cert_id} failed to convert security policy pdf->txt")
                cert.state.txt_state = False
            else:
                cert.state.txt_state = True
        return cert

    @staticmethod
    def _declare_state(text: str):
        """
        If less then half of the text is formed of alphabet characters,
        we declare the security policy as "non-parsable"
        :param text: security policy content
        :return: True if parsable, otherwise False
        """
        return len(text) * 0.5 <= len("".join(filter(str.isalpha, text)))

    @staticmethod
    def find_keywords(cert: "FIPSCertificate") -> Tuple[Optional[Dict], "FIPSCertificate"]:
        if not cert.state.txt_state:
            return None, cert

        text, text_with_newlines, unicode_error = load_cert_file(
            cert.state.sp_path.with_suffix(".pdf.txt"), -1, LINE_SEPARATOR
        )

        text_to_parse = text_with_newlines if config.use_text_with_newlines_during_parsing else text

        cert.state.txt_state = FIPSCertificate._declare_state(text)

        if config.ignore_first_page:
            text_to_parse = text_to_parse[text_to_parse.index("") :]

        items_found, fips_text = FIPSCertificate.parse_cert_file(FIPSCertificate.remove_platforms(text_to_parse))

        save_modified_cert_file(cert.state.fragment_path.with_suffix(".fips.txt"), fips_text, unicode_error)

        common_items_found, common_text = FIPSCertificate.parse_cert_file_common(
            text_to_parse, text_with_newlines, fips_common_rules
        )

        save_modified_cert_file(cert.state.fragment_path.with_suffix(".common.txt"), common_text, unicode_error)
        items_found.update(common_items_found)

        return items_found, cert

    @staticmethod
    def match_web_algs_to_pdf(cert: "FIPSCertificate") -> int:
        algs_vals = list(cert.pdf_scan.keywords["rules_fips_algorithms"].values())
        table_vals = [x["Certificate"] for x in cert.pdf_scan.algorithms]
        tables = [x.strip() for y in table_vals for x in y]
        iterable = [alg for x in algs_vals for alg in list(x.keys())]
        iterable += tables
        all_algorithms = set()
        for x in iterable:
            if "#" in x:
                # erase everything until "#" included and take digits
                all_algorithms.add("".join(filter(str.isdigit, x[x.index("#") + 1 :])))
            else:
                all_algorithms.add("".join(filter(str.isdigit, x)))
        not_found = []

        if cert.web_scan.algorithms is None:
            raise RuntimeError(f"Algorithms were not found for cert {cert.cert_id} - this should not be happening.")

        for alg_list in [a["Certificate"] for a in cert.web_scan.algorithms]:
            for web_alg in alg_list:
                if "".join(filter(str.isdigit, web_alg)) not in all_algorithms:
                    not_found.append(web_alg)
        return len(not_found)

    @staticmethod
    def remove_platforms(text_to_parse: str):
        pat = re.compile(r"(?:(?:modification|revision|change) history|version control)\n[\s\S]*?", re.IGNORECASE)
        for match in pat.finditer(text_to_parse):
            text_to_parse = text_to_parse.replace(match.group(), "x" * len(match.group()))
        return text_to_parse

    @staticmethod
    def parse_cert_file_common(
        text_to_parse: str, whole_text_with_newlines: str, search_rules: Dict
    ) -> Tuple[Dict[Pattern, Dict], str]:
        # apply all rules
        items_found_all: Dict[Pattern, Dict] = {}
        for rule_group in search_rules.keys():
            if rule_group not in items_found_all:
                items_found_all[rule_group] = {}

            items_found = items_found_all[rule_group]

            for rule in search_rules[rule_group]:
                rule_and_sep: Union[Pattern, str]
                if type(rule) != str:
                    rule_str = rule.pattern
                    rule_and_sep = re.compile(rule.pattern + REGEXEC_SEP)
                else:
                    rule_str = rule
                    rule_and_sep = rule + REGEXEC_SEP

                for m in re.finditer(rule_and_sep, text_to_parse):
                    # insert rule if at least one match for it was found
                    if rule not in items_found:
                        items_found[rule_str] = {}

                    match = m.group()
                    match = normalize_match_string(match)

                    MAX_ALLOWED_MATCH_LENGTH = 300
                    match_len = len(match)
                    if match_len > MAX_ALLOWED_MATCH_LENGTH:
                        logger.warning("Excessive match with length of {} detected for rule {}".format(match_len, rule))

                    if match not in items_found[rule_str]:
                        items_found[rule_str][match] = {}
                        items_found[rule_str][match][constants.TAG_MATCH_COUNTER] = 0
                        if constants.APPEND_DETAILED_MATCH_MATCHES:
                            items_found[rule_str][match][constants.TAG_MATCH_MATCHES] = []
                        # else:
                        #     items_found[rule_str][match][TAG_MATCH_MATCHES] = ['List of matches positions disabled. Set APPEND_DETAILED_MATCH_MATCHES to True']

                    items_found[rule_str][match][constants.TAG_MATCH_COUNTER] += 1
                    match_span = m.span()
                    # estimate line in original text file
                    # line_number = get_line_number(lines, line_length_compensation, match_span[0])
                    # start index, end index, line number
                    # items_found[rule_str][match][TAG_MATCH_MATCHES].append([match_span[0], match_span[1], line_number])
                    if constants.APPEND_DETAILED_MATCH_MATCHES:
                        items_found[rule_str][match][constants.TAG_MATCH_MATCHES].append([match_span[0], match_span[1]])

        # highlight all found strings (by xxxxx) from the input text and store the rest
        all_matches = []
        for rule_group in items_found_all.keys():
            items_found = items_found_all[rule_group]
            for rule in items_found.keys():
                for match in items_found[rule]:
                    all_matches.append(match)

            # if AES string is removed before AES-128, -128 would be left in text => sort by length first
            # sort before replacement based on the length of match
            all_matches.sort(key=len, reverse=True)
            for match in all_matches:
                whole_text_with_newlines = whole_text_with_newlines.replace(match, "x" * len(match))

        return items_found_all, whole_text_with_newlines

    @staticmethod
    def parse_cert_file(text_to_parse: str) -> Tuple[Dict[Pattern, Dict], str]:
        # apply all rules
        items_found_all: Dict = {}

        for rule_group in fips_rules.keys():
            if rule_group not in items_found_all:
                items_found_all[rule_group] = {}

            items_found: Dict[str, Dict] = items_found_all[rule_group]

            for rule in fips_rules[rule_group]:
                for m in rule.finditer(text_to_parse):
                    # for m in re.finditer(rule, whole_text_with_newlines):
                    # insert rule if at least one match for it was found
                    if rule.pattern not in items_found:
                        items_found[rule.pattern] = {}

                    match = m.group()
                    match = normalize_match_string(match)

                    if match == "":
                        continue

                    if match not in items_found[rule.pattern]:
                        items_found[rule.pattern][match] = {}
                        items_found[rule.pattern][match][constants.TAG_MATCH_COUNTER] = 0

                    items_found[rule.pattern][match][constants.TAG_MATCH_COUNTER] += 1

                    text_to_parse = text_to_parse.replace(match, "x" * len(match))

        return items_found_all, text_to_parse

    @staticmethod
    def analyze_tables(tup: Tuple["FIPSCertificate", bool]) -> Tuple[bool, "FIPSCertificate", List]:
        cert, precision = tup
        if (not precision and cert.state.tables_done) or (
            precision and cert.heuristics.unmatched_algs < config.cert_threshold
        ):
            return cert.state.tables_done, cert, []

        cert_file = cert.state.sp_path
        txt_file = cert_file.with_suffix(".pdf.txt")
        with open(txt_file, "r", encoding="utf-8") as f:
            tables = helpers.find_tables(f.read(), txt_file)
        all_pages = precision and cert.heuristics.unmatched_algs > config.cert_threshold  # bool value

        lst: List = []
        if tables:
            try:
                data = read_pdf(cert_file, pages="all" if all_pages else tables, silent=True)
            except Exception as e:
                try:
                    logger.error(e)
                    helpers.repair_pdf(cert_file)
                    data = read_pdf(cert_file, pages="all" if all_pages else tables, silent=True)

                except Exception as ex:
                    logger.error(ex)
                    return False, cert, lst

            # find columns with cert numbers
            for df in data:
                for col in range(len(df.columns)):
                    if "cert" in df.columns[col].lower() or "algo" in df.columns[col].lower():
                        tmp = FIPSCertificate.extract_algorithm_certificates(
                            df.iloc[:, col].to_string(index=False), True
                        )
                        lst += tmp if tmp != [{"Certificate": []}] else []
                # Parse again if someone picks not so descriptive column names
                tmp = FIPSCertificate.extract_algorithm_certificates(df.to_string(index=False))
                lst += tmp if tmp != [{"Certificate": []}] else []
        return True, cert, lst

    def _create_alg_set(self) -> Set:
        result: Set[str] = set()

        if self.web_scan.algorithms is None:
            raise RuntimeError(f"Algorithms were not found for cert {self.cert_id} - this should not be happening.")

        for alg in self.web_scan.algorithms:
            result.update(cert for cert in alg["Certificate"])
        return result

    def remove_algorithms(self):
        self.state.file_status = True
        if not self.pdf_scan.keywords:
            return

        self.heuristics.keywords = copy.deepcopy(self.pdf_scan.keywords)
        # TODO figure out why can't I delete this
        if self.web_scan.mentioned_certs:
            for item, value in self.web_scan.mentioned_certs.items():
                self.heuristics.keywords["rules_cert_id"].update({"caveat_item": {item: value}})

        alg_set = self._create_alg_set()

        for rule in self.heuristics.keywords["rules_cert_id"]:
            to_pop = set()
            rr = re.compile(rule)
            for cert in self.heuristics.keywords["rules_cert_id"][rule]:
                if cert in alg_set:
                    to_pop.add(cert)
                    continue
                for alg in self.heuristics.keywords["rules_fips_algorithms"]:
                    for found in self.heuristics.keywords["rules_fips_algorithms"][alg]:
                        if (
                            rr.search(found)
                            and rr.search(cert)
                            and rr.search(found).group("id") == rr.search(cert).group("id")
                        ):
                            to_pop.add(cert)

                for alg_cert in self.heuristics.algorithms:
                    for cert_no in alg_cert["Certificate"]:
                        if int("".join(filter(str.isdigit, cert_no))) == int("".join(filter(str.isdigit, cert))):
                            to_pop.add(cert)
            for r in to_pop:
                self.heuristics.keywords["rules_cert_id"][rule].pop(r, None)

            self.heuristics.keywords["rules_cert_id"][rule].pop(self.cert_id, None)

    @staticmethod
    def get_compare(vendor: str):
        vendor_split = (
            vendor.replace(",", "").replace("-", " ").replace("+", " ").replace("®", "").replace("(R)", "").split()
        )
        return vendor_split[0][:4] if len(vendor_split) > 0 else vendor

    def compute_heuristics_version(self):
        versions_for_extraction = ""
        if self.web_scan.module_name:
            versions_for_extraction += f" {self.web_scan.module_name}"
        if self.web_scan.hw_version:
            versions_for_extraction += f" {self.web_scan.hw_version}"
        if self.web_scan.fw_version:
            versions_for_extraction += f" {self.web_scan.fw_version}"
        self.heuristics.extracted_versions = helpers.compute_heuristics_version(versions_for_extraction)

    # TODO: This function is probably safe to delete // I'll not type it then - older API probably?
    def compute_heuristics_cpe_vendors(self, cpe_dataset: CPEDataset):
        if self.web_scan.vendor is None:
            raise RuntimeError(f"Vendor for cert {self.cert_id} not found - this should not be happening.")
        self.heuristics.cpe_candidate_vendors = cpe_dataset.get_candidate_list_of_vendors(self.web_scan.vendor)  # type: ignore

    def compute_heuristics_cpe_match(self, cpe_classifier: CPEClassifier):
        if not self.web_scan.module_name:
            self.heuristics.cpe_matches = None
        else:
            self.heuristics.cpe_matches = cpe_classifier.predict_single_cert(
                self.web_scan.vendor, self.web_scan.module_name, self.heuristics.extracted_versions  # type: ignore
            )
