"""

We make each coding system a distinct type. The query model's type checking will then

enforce that queries use the appropriate coding system for a given column.

"""

import csv

import dataclasses

import re

from pathlib import Path

class CodelistError(ValueError): ...

@dataclasses.dataclass(frozen=True)

class BaseCode:

    value: str

    def __post_init__(self):

        if not self.regex.fullmatch(self.value):

            raise ValueError(f"Invalid {self.__class__.__name__}: {self.value}")

    @classmethod

    def _primitive_type(cls):

        return str

    # The presence of this method allows query engines to work with values of this type,

    # despite not being explicitly told about them beforehand

    def _to_primitive_type(self):

        return self.value

# A base class for fields that are concatenated lists of clinical codes. This occurs

# in the admitted patient care spell (apcs) table of hospital episode statistics for

# all_diagnoses (ICD10 codes), and all_procedures (OPCS4 codes).

#

# This inherits from str because that's what the underlying data is, but is in this

# file as it's sort of a code. In future a better implementation might be to parse the

# field value into a Set of clinical codes.

class BaseMultiCodeString(str):

    @classmethod

    def _code_type(cls):

        raise NotImplementedError(

            "BaseMultiCodeString subclasses must implement the _code_type method"

        )

    @classmethod

    def _primitive_type(cls):

        return str

class BNFCode(BaseCode):

    "Pseudo BNF"

    regex = re.compile(

        r"""

        # Standard BNF code

          # Chapter, Section, Paragraph, Sub-paragraph

          [01][0-9]{6}

          # Chemical

          [0-9A-Z]{2}

          # Product, strength-formulation, generic equivalent

          ([A-Z][0-9A-Z]){3}

        | # OR

        # Appliances

        2[0-3][0-9]{9}

        """,

        re.VERBOSE,

    )

class CTV3Code(BaseCode):

    "CTV3 (Read v3)"

    # Some of the CTV3 codes in the OpenCodelists coding system database (though not any

    # actually used in codelists) violate the below format, either by having a leading

    # dot or by starting with a tilde. However I have confirmed that, aside from a tiny

    # handful of cases, these invalid codes are not used in the database so there should

    # never be a need to create codelists which use them.

    regex = re.compile(

        r"""

        [0-9A-Za-z]{5}

        | [0-9A-Za-z]{4}\.{1}

        | [0-9A-Za-z]{3}\.{2}

        | [0-9A-Za-z]{2}\.{3}

        """,

        re.VERBOSE,

    )

class ICD10Code(BaseCode):

    "ICD-10"

    regex = re.compile(r"[A-Z][0-9]{2,3}")

class OPCS4Code(BaseCode):

    "OPCS-4"

    # The documented structure requires three digits, and a dot between the 2nd and 3rd

    # digit, but the codes we have in OpenCodelists omit the dot and sometimes have only

    # two digits.

    # https://en.wikipedia.org/wiki/OPCS-4#Code_structure

    regex = re.compile(

        r"""

        # Uppercase letter excluding I

        [ABCDEFGHJKLMNOPQRSTUVWXYZ]

        [0-9]{2,3}

        """,

        re.VERBOSE,

    )

class SNOMEDCTCode(BaseCode):

    "SNOMED-CT"

    # 6-18 digit number with no leading zeros

    # https://confluence.ihtsdotools.org/display/DOCRELFMT/6.1+SCTID+Data+Type

    regex = re.compile(r"[1-9][0-9]{5,17}")

# Dictionary of Medicines and Devices

class DMDCode(BaseCode):

    "dm+d"

    # Syntactically equivalent to SNOMED-CT

    regex = SNOMEDCTCode.regex

#

# ICD10 codelist as concatenated string

#

# This is specifically for fields in the admitted patient care (APC) part

# of the hospital episode statistics (HES) data where there are fields

# that are a concatenation of all diagnosis codes for a patient's episode

# or spell.

class ICD10MultiCodeString(BaseMultiCodeString):

    "Multiple ICD-10 codes"

    @classmethod

    def _code_type(cls):

        return ICD10Code

    # We want to allow prefix searching on this field so users can

    # search this field for a string prefix. This ensures they pass

    # a valid prefix so we can throw an error, rather than silently

    # failing by running but returning 0 records

    regex = re.compile(r"[A-Z][0-9]{0,3}")

#

# OPCS4 codelist as concatenated string

#

# This is specifically for fields in the admitted patient care (APC) part

# of the hospital episode statistics (HES) data where there are fields

# that are a concatenation of all procedure codes for a patient's episode

# or spell.

class OPCS4MultiCodeString(BaseMultiCodeString):

    "Multiple OPCS4 codes"

    @classmethod

    def _code_type(cls):

        return OPCS4Code

    # We want to allow prefix searching on this field so users can

    # search this field for a string prefix. This ensures they pass

    # a valid prefix so we can throw an error, rather than silently

    # failing by running but returning 0 records

    regex = re.compile(r"[A-Z][0-9]{0,3}")

def codelist_from_csv(filename, *, column, category_column=None):

    """

    Read a codelist from a CSV file as either a list or a dictionary (for categorised

    codelists).

    _filename_<br>

    Path to the file on disk, relative to the root of your repository. (Remember to use

    UNIX/style/forward-slashes not Windows\\style\\backslashes.)

    _column_<br>

    Name of the column in the CSV file which contains the codes.

    _category_column_<br>

    Optional name of a column in the CSV file which contains categories to which each

    code should be mapped. If this argument is passed then the resulting codelist will

    be a dictionary mapping each code to its corresponding category. This can be passed

    to the [`to_category()`](#CodePatientSeries.to_category) method to map a series of

    codes to a series of categories.

    For more detail see the [how-to guide](../how-to/examples.md/#using-codelists-with-category-columns).

    """

    filename = Path(filename)

    if not filename.exists():

        # If the character which comes after the backslash in the string literal happens

        # to form a valid escape sequence then no backslash will appear in the compiled

        # string. Checking the repr for backslashes has false positives (e.g. a tab

        # character will trigger it) but that seems OK in this context.

        if "\\" in repr(filename):

            hint = (

                "\n\n"

                "HINT: Use forward slash (/) instead of backslash (\\) in file paths"

            )

        else:

            hint = ""

        raise CodelistError(f"No CSV file at {filename}{hint}")

    with filename.open("r") as f:

        return codelist_from_csv_lines(

            f, column=column, category_column=category_column

        )

def codelist_from_csv_lines(lines, *, column, category_column=None):

    if category_column is None:

        category_column = column

        return_list = True

    else:

        return_list = False

    # Using `restval=""` ensures we never get None instead of string, so we can always

    # call `.strip()` without blowing up

    reader = csv.DictReader(iter(lines), restval="")

    if column not in reader.fieldnames:

        raise CodelistError(f"No column '{column}' in CSV")

    if category_column not in reader.fieldnames:

        raise CodelistError(f"No column '{category_column}' in CSV")

    code_map = {row[column].strip(): row[category_column].strip() for row in reader}

    # Discard any empty codes

    code_map.pop("", None)

    if return_list:

        return list(code_map)

    else:

        return code_map