import argparse
import Bio
import Bio.Phylo
import gzip
import os, json, sys
import pandas as pd
import subprocess
import shlex
from contextlib import contextmanager
from treetime.utils import numeric_date
from collections import defaultdict
from pkg_resources import resource_stream
from io import TextIOWrapper
from .__version__ import __version__

from augur.io import open_file

from augur.util_support.color_parser import ColorParser
from augur.util_support.date_disambiguator import DateDisambiguator
from augur.util_support.metadata_file import MetadataFile
from augur.util_support.node_data_reader import NodeDataReader
from augur.util_support.shell_command_runner import ShellCommandRunner


class AugurException(Exception):
    pass


def is_vcf(fname):
    """Convenience method to check if a file is a vcf file.

    >>> is_vcf("./foo")
    False
    >>> is_vcf("./foo.vcf")
    True
    >>> is_vcf("./foo.vcf.GZ")
    True
    """
    return fname.lower().endswith(".vcf") or fname.lower().endswith(".vcf.gz")

def myopen(fname, mode):
    if fname.endswith('.gz'):
        import gzip
        return gzip.open(fname, mode, encoding='utf-8')
    else:
        return open(fname, mode, encoding='utf-8')

def get_json_name(args, default=None):
    if args.output_node_data:
        return args.output_node_data
    else:
        if default:
            print("WARNING: no name for the output file was specified. Writing results to %s."%default, file=sys.stderr)
            return default
        else:
            raise ValueError("Please specify a name for the JSON file containing the results.")


def ambiguous_date_to_date_range(uncertain_date, fmt, min_max_year=None):
    return DateDisambiguator(uncertain_date, fmt=fmt, min_max_year=min_max_year).range()

def read_metadata(fname, query=None):
    return MetadataFile(fname, query).read()

def is_date_ambiguous(date, ambiguous_by="any"):
    """
    Returns whether a given date string in the format of YYYY-MM-DD is ambiguous by a given part of the date (e.g., day, month, year, or any parts).

    Parameters
    ----------
    date : str
        Date string in the format of YYYY-MM-DD
    ambiguous_by : str
        Field of the date string to test for ambiguity ("day", "month", "year", "any")
    """
    date_components = date.split('-', 2)

    if len(date_components) == 3:
        year, month, day = date_components
    elif len(date_components) == 2:
        year, month = date_components
        day = "XX"
    else:
        year = date_components[0]
        month = "XX"
        day = "XX"

    # Determine ambiguity hierarchically such that, for example, an ambiguous
    # month implicates an ambiguous day even when day information is available.
    return any((
        "X" in year,
        "X" in month and ambiguous_by in ("any", "month", "day"),
        "X" in day and ambiguous_by in ("any", "day")
    ))

def get_numerical_dates(meta_dict, name_col = None, date_col='date', fmt=None, min_max_year=None):
    if fmt:
        from datetime import datetime
        numerical_dates = {}
        for k,m in meta_dict.items():
            v = m[date_col]
            if type(v)!=str:
                print("WARNING: %s has an invalid data string:"%k,v)
                continue
            elif 'XX' in v:
                ambig_date = ambiguous_date_to_date_range(v, fmt, min_max_year)
                if ambig_date is None or None in ambig_date:
                    numerical_dates[k] = [None, None] #don't send to numeric_date or will be set to today
                else:
                    numerical_dates[k] = [numeric_date(d) for d in ambig_date]
            else:
                try:
                    numerical_dates[k] = numeric_date(datetime.strptime(v, fmt))
                except:
                    numerical_dates[k] = None
    else:
        numerical_dates = {k:float(v) for k,v in meta_dict.items()}

    return numerical_dates


class InvalidTreeError(Exception):
    """Represents an error loading a phylogenetic tree from a filename.
    """
    pass


def read_tree(fname, min_terminals=3):
    """Safely load a tree from a given filename or raise an error if the file does
    not contain a valid tree.

    Parameters
    ----------
    fname : str
        name of a file containing a phylogenetic tree

    min_terminals : int
        minimum number of terminals required for the parsed tree as a sanity
        check on the tree

    Raises
    ------
    InvalidTreeError
        If the given file exists but does not seem to contain a valid tree format.

    Returns
    -------
    Bio.Phylo :
        BioPython tree instance

    """
    T = None
    supported_tree_formats = ["newick", "nexus"]
    for fmt in supported_tree_formats:
        try:
            T = Bio.Phylo.read(fname, fmt)

            # Check the sanity of the parsed tree to handle cases when non-tree
            # data are still successfully parsed by BioPython. Too few terminals
            # in a tree indicates that the input is not valid.
            if T.count_terminals() < min_terminals:
                T = None
            else:
                break
        except ValueError:
            # We cannot open the tree in the current format, so we will try
            # another.
            pass

    # If the tree cannot be loaded, raise an error to that effect.
    if T is None:
        raise InvalidTreeError(
            "Could not read the given tree %s using the following supported formats: %s" % (fname, ", ".join(supported_tree_formats))
        )

    return T


def read_node_data(fnames, tree=None):
    return NodeDataReader(fnames, tree).read()


def write_json(data, file_name, indent=(None if os.environ.get("AUGUR_MINIFY_JSON") else 2), include_version=True):
    """
    Write ``data`` as JSON to the given ``file_name``, creating parent directories
    if necessary. The augur version is included as a top-level key "augur_version".

    Parameters
    ----------
    data : dict
        data to write out to JSON
    file_name : str
        file name to write to
    indent : int or None, optional
        JSON indentation level. Default is `None` if the environment variable `AUGUR_MINIFY_JSON`
        is truthy, else 1
    include_version : bool, optional
        Include the augur version. Default: `True`.

    Raises
    ------
    OSError
    """
    #in case parent folder does not exist yet
    parent_directory = os.path.dirname(file_name)
    if parent_directory and not os.path.exists(parent_directory):
        try:
            os.makedirs(parent_directory)
        except OSError: #Guard against race condition
            if not os.path.isdir(parent_directory):
                raise

    if include_version:
        data["generated_by"] = {"program": "augur", "version": get_augur_version()}

    with open(file_name, 'w', encoding='utf-8') as handle:
        json.dump(data, handle, indent=indent, sort_keys=True)


def load_features(reference, feature_names=None):
    #read in appropriately whether GFF or Genbank
    #checks explicitly for GFF otherwise assumes Genbank
    if not os.path.isfile(reference):
        print("ERROR: reference sequence not found. looking for", reference)
        return None

    features = {}
    if '.gff' in reference.lower():
        #looks for 'gene' and 'gene' as best for TB
        try:
            from BCBio import GFF #Package name is confusing - tell user exactly what they need!
        except ImportError:
            print("ERROR: Package BCBio.GFF not found! Please install using \'pip install bcbio-gff\' before re-running.")
            return None
        limit_info = dict( gff_type = ['gene'] )

        with open(reference, encoding='utf-8') as in_handle:
            for rec in GFF.parse(in_handle, limit_info=limit_info):
                for feat in rec.features:
                    if feature_names is not None: #check both tags; user may have used either
                        if "gene" in feat.qualifiers and feat.qualifiers["gene"][0] in feature_names:
                            fname = feat.qualifiers["gene"][0]
                        elif "locus_tag" in feat.qualifiers and feat.qualifiers["locus_tag"][0] in feature_names:
                            fname = feat.qualifiers["locus_tag"][0]
                        else:
                            fname = None
                    else:
                        if "gene" in feat.qualifiers:
                            fname = feat.qualifiers["gene"][0]
                        else:
                            fname = feat.qualifiers["locus_tag"][0]
                    if fname:
                        features[fname] = feat

            if feature_names is not None:
                for fe in feature_names:
                    if fe not in features:
                        print("Couldn't find gene {} in GFF or GenBank file".format(fe))

    else:
        from Bio import SeqIO
        for feat in SeqIO.read(reference, 'genbank').features:
            if feat.type=='CDS':
                if "locus_tag" in feat.qualifiers:
                    fname = feat.qualifiers["locus_tag"][0]
                    if feature_names is None or fname in feature_names:
                        features[fname] = feat
                elif "gene" in feat.qualifiers:
                    fname = feat.qualifiers["gene"][0]
                    if feature_names is None or fname in feature_names:
                        features[fname] = feat
            elif feat.type=='source': #read 'nuc' as well for annotations - need start/end of whole!
                features['nuc'] = feat

    return features

def read_config(fname):
    if not (fname and os.path.isfile(fname)):
        print("ERROR: config file %s not found."%fname)
        return defaultdict(dict)

    try:
        with open(fname, 'rb') as ifile:
            config = json.load(ifile)
    except json.decoder.JSONDecodeError as err:
        print("FATAL ERROR:")
        print("\tCouldn't parse the JSON file {}".format(fname))
        print("\tError message: '{}'".format(err.msg))
        print("\tLine number: '{}'".format(err.lineno))
        print("\tColumn number: '{}'".format(err.colno))
        print("\tYou must correct this file in order to proceed.")
        sys.exit(2)

    return config

def read_lat_longs(overrides=None, use_defaults=True):
    coordinates = {}
    # TODO: make parsing of tsv files more robust while allow for whitespace delimiting for backwards compatibility
    def add_line_to_coordinates(line):
        if line.startswith('#') or line.strip() == "":
            return
        fields = line.strip().split() if not '\t' in line else line.strip().split('\t')
        if len(fields) == 4:
            geo_field, loc = fields[0].lower(), fields[1].lower()
            lat, long = float(fields[2]), float(fields[3])
            coordinates[(geo_field, loc)] = {
                "latitude": lat,
                "longitude": long
            }
        else:
            print("WARNING: geo-coordinate file contains invalid line. Please make sure not to mix tabs and spaces as delimiters (use only tabs):",line)
    if use_defaults:
        with resource_stream(__package__, "data/lat_longs.tsv") as stream:
            with TextIOWrapper(stream, "utf-8") as defaults:
                for line in defaults:
                    add_line_to_coordinates(line)
    if overrides:
        if os.path.isfile(overrides):
            with open(overrides, encoding='utf-8') as ifile:
                for line in ifile:
                    add_line_to_coordinates(line)
        else:
            print("WARNING: input lat/long file %s not found." % overrides)
    return coordinates

def read_colors(overrides=None, use_defaults=True):
    return ColorParser(mapping_filename=overrides, use_defaults=use_defaults).mapping

def write_VCF_translation(prot_dict, vcf_file_name, ref_file_name):
    """
    Writes out a VCF-style file (which seems to be minimally handleable
    by vcftools and pyvcf) of the AA differences between sequences and the reference.
    This is a similar format created/used by read_in_vcf except that there is one
    of these dicts (with sequences, reference, positions) for EACH gene.

    Also writes out a fasta of the reference alignment.

    EBH 12 Dec 2017
    """
    import numpy as np

    #for the header
    seqNames = list(prot_dict[list(prot_dict.keys())[0]]['sequences'].keys())

    #prepare the header of the VCF & write out
    header=["#CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO","FORMAT"]+seqNames
    with open(vcf_file_name, 'w', encoding='utf-8') as the_file:
        the_file.write( "##fileformat=VCFv4.2\n"+
                        "##source=NextStrain_Protein_Translation\n"+
                        "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n")
        the_file.write("\t".join(header)+"\n")

    refWrite = []
    vcfWrite = []

    #go through for every gene/protein
    for fname, prot in prot_dict.items():
        sequences = prot['sequences']
        ref = prot['reference']
        positions = prot['positions']

        #write out the reference fasta
        refWrite.append(">"+fname)
        refWrite.append(ref)

        #go through every variable position
        #There are no deletions here, so it's simpler than for VCF nuc sequenes!
        for pi in positions:
            pos = pi+1 #change numbering to match VCF not python
            refb = ref[pi] #reference base at this position

            #try/except is (much) faster than list comprehension!
            pattern = []
            for k,v in sequences.items():
                try:
                    pattern.append(sequences[k][pi])
                except KeyError:
                    pattern.append('.')
            pattern = np.array(pattern)

            #get the list of ALTs - minus any '.'!
            uniques = np.unique(pattern)
            uniques = uniques[np.where(uniques!='.')]

            #Convert bases to the number that matches the ALT
            j=1
            for u in uniques:
                pattern[np.where(pattern==u)[0]] = str(j)
                j+=1
            #Now convert these calls to #/# (VCF format)
            calls = [ j+"/"+j if j!='.' else '.' for j in pattern ]
            if len(uniques)==0:
                print("UNEXPECTED ERROR WHILE CONVERTING TO VCF AT POSITION {}".format(str(pi)))
                break

            #put it all together and write it out
            output = [fname, str(pos), ".", refb, ",".join(uniques), ".", "PASS", ".", "GT"] + calls

            vcfWrite.append("\t".join(output))

    #write it all out
    with open(ref_file_name, 'w', encoding='utf-8') as the_file:
        the_file.write("\n".join(refWrite))

    with open(vcf_file_name, 'a', encoding='utf-8') as the_file:
        the_file.write("\n".join(vcfWrite))

    if vcf_file_name.lower().endswith('.gz'):
        import os
        #must temporarily remove .gz ending, or gzip won't zip it!
        os.rename(vcf_file_name, vcf_file_name[:-3])
        call = ["gzip", vcf_file_name[:-3]]
        run_shell_command(" ".join(call), raise_errors = True)

shquote = shlex.quote

def run_shell_command(cmd, raise_errors=False, extra_env=None):
    """
    Run the given command string via Bash with error checking.

    Returns True if the command exits normally.  Returns False if the command
    exits with failure and "raise_errors" is False (the default).  When
    "raise_errors" is True, exceptions are rethrown.

    If an *extra_env* mapping is passed, the provided keys and values are
    overlayed onto the default subprocess environment.
    """
    return ShellCommandRunner(cmd, raise_errors=raise_errors, extra_env=extra_env).run()


def first_line(text):
    """
    Returns the first line of the given text, ignoring leading and trailing
    whitespace.
    """
    return text.strip().splitlines()[0]


def available_cpu_cores(fallback: int = 1) -> int:
    """
    Returns the number (an int) of CPU cores available to this **process**, if
    determinable, otherwise the number of CPU cores available to the
    **computer**, if determinable, otherwise the *fallback* number (which
    defaults to 1).
    """
    try:
        # Note that this is the correct function to use, not os.cpu_count(), as
        # described in the latter's documentation.
        #
        # The reason, which the documentation does not detail, is that
        # processes may be pinned or restricted to certain CPUs by setting
        # their "affinity".  This is not typical except in high-performance
        # computing environments, but if it is done, then a computer with say
        # 24 total cores may only allow our process to use 12.  If we tried to
        # naively use all 24, we'd end up with two threads across the 12 cores.
        # This would degrade performance rather than improve it!
        return len(os.sched_getaffinity(0))
    except:
        # cpu_count() returns None if the value is indeterminable.
        return os.cpu_count() or fallback


def nthreads_value(value):
    """
    Argument value validation and casting function for --nthreads.
    """

    if value.lower() == 'auto':
        return available_cpu_cores()

    try:
        return int(value)
    except ValueError:
        raise argparse.ArgumentTypeError("'%s' is not an integer or the word 'auto'" % value) from None


def get_parent_name_by_child_name_for_tree(tree):
    '''
    Return dictionary mapping child node names to parent node names
    '''
    parents = {}
    for clade in tree.find_clades(order='level'):
        for child in clade:
            parents[child.name] = clade.name
    return parents


def annotate_parents_for_tree(tree):
    """Annotate each node in the given tree with its parent.

    >>> import io
    >>> tree = Bio.Phylo.read(io.StringIO("(A, (B, C))"), "newick")
    >>> not any([hasattr(node, "parent") for node in tree.find_clades()])
    True
    >>> tree = annotate_parents_for_tree(tree)
    >>> tree.root.parent is None
    True
    >>> all([hasattr(node, "parent") for node in tree.find_clades()])
    True
    """
    tree.root.parent = None
    for node in tree.find_clades(order="level"):
        for child in node.clades:
            child.parent = node

    # Return the tree.
    return tree


def json_to_tree(json_dict, root=True):
    """Returns a Bio.Phylo tree corresponding to the given JSON dictionary exported
    by `tree_to_json`.

    Assigns links back to parent nodes for the root of the tree.

    Test opening a JSON from augur export v1.

    >>> import json
    >>> json_fh = open("tests/data/json_tree_to_nexus/flu_h3n2_ha_3y_tree.json", "r")
    >>> json_dict = json.load(json_fh)
    >>> tree = json_to_tree(json_dict)
    >>> tree.name
    'NODE_0002020'
    >>> len(tree.clades)
    2
    >>> tree.clades[0].name
    'NODE_0001489'
    >>> hasattr(tree, "attr")
    True
    >>> "dTiter" in tree.attr
    True
    >>> tree.clades[0].parent.name
    'NODE_0002020'
    >>> tree.clades[0].branch_length > 0
    True

    Test opening a JSON from augur export v2.

    >>> json_fh = open("tests/data/zika.json", "r")
    >>> json_dict = json.load(json_fh)
    >>> tree = json_to_tree(json_dict)
    >>> hasattr(tree, "name")
    True
    >>> len(tree.clades) > 0
    True
    >>> tree.clades[0].branch_length > 0
    True
    """
    # Check for v2 JSON which has combined metadata and tree data.
    if root and "meta" in json_dict and "tree" in json_dict:
        json_dict = json_dict["tree"]

    node = Bio.Phylo.Newick.Clade()

    # v1 and v2 JSONs use different keys for strain names.
    if "name" in json_dict:
        node.name = json_dict["name"]
    else:
        node.name = json_dict["strain"]

    if "children" in json_dict:
        # Recursively add children to the current node.
        node.clades = [json_to_tree(child, root=False) for child in json_dict["children"]]

    # Assign all non-children attributes.
    for attr, value in json_dict.items():
        if attr != "children":
            setattr(node, attr, value)

    # Only v1 JSONs support a single `attr` attribute.
    if hasattr(node, "attr"):
        node.numdate = node.attr.get("num_date")
        node.branch_length = node.attr.get("div")

        if "translations" in node.attr:
            node.translations = node.attr["translations"]
    elif hasattr(node, "node_attrs"):
        node.branch_length = node.node_attrs.get("div")

    if root:
        node = annotate_parents_for_tree(node)

    return node

def get_augur_version():
    """
    Returns a string of the current augur version.
    """
    return __version__


def read_bed_file(bed_file):
    """Read a BED file and return a list of excluded sites.

    Note: This function assumes the given file is a BED file. On parsing
    failures, it will attempt to skip the first line and retry, but no
    other error checking is attempted. Incorrectly formatted files will
    raise errors.

    Parameters
    ----------
    bed_file : str
        Path to the BED file

    Returns:
    --------
    list[int]:
        Sorted list of unique zero-indexed sites
    """
    mask_sites = []
    try:
        bed = pd.read_csv(bed_file, sep='\t', header=None, usecols=[1,2],
                          dtype={1:int,2:int})
    except ValueError:
        # Check if we have a header row. Otherwise, just fail.
        bed = pd.read_csv(bed_file, sep='\t', header=None, usecols=[1,2],
                          dtype={1:int,2:int}, skiprows=1)
        print("Skipped row 1 of %s, assuming it is a header." % bed_file)
    for _, row in bed.iterrows():
        mask_sites.extend(range(row[1], row[2]))
    return sorted(set(mask_sites))

def read_mask_file(mask_file):
    """Read a masking file and return a list of excluded sites.

    Masking files have a single masking site per line, either alone
    or as the second column of a tab-separated file. These sites
    are assumed to be one-indexed, NOT zero-indexed. Incorrectly
    formatted lines will be skipped.

    Parameters
    ----------
    mask_file : str
        Path to the masking file

    Returns:
    --------
    list[int]:
        Sorted list of unique zero-indexed sites
    """
    mask_sites = []
    with open(mask_file, encoding='utf-8') as mf:
        for idx, line in enumerate(l.strip() for l in mf.readlines()):
            if "\t" in line:
                line = line.split("\t")[1]
            try:
                mask_sites.append(int(line) - 1)
            except ValueError as err:
                print("Could not read line %s of %s: '%s' - %s" %
                      (idx, mask_file, line, err), file=sys.stderr)
                raise
    return sorted(set(mask_sites))

def load_mask_sites(mask_file):
    """Load masking sites from either a BED file or a masking file.

    Parameters
    ----------
    mask_file: str
        Path to the BED or masking file

    Returns
    -------
    list[int]
        Sorted list of unique zero-indexed sites
    """
    if mask_file.lower().endswith(".bed"):
        mask_sites = read_bed_file(mask_file)
    else:
        mask_sites = read_mask_file(mask_file)
    print("%d masking sites read from %s" % (len(mask_sites), mask_file))
    return mask_sites

VALID_NUCLEOTIDES = { # http://reverse-complement.com/ambiguity.html
    "A", "G", "C", "T", "U", "N", "R", "Y", "S", "W", "K", "M", "B", "V", "D", "H", "-",
    "a", "g", "c", "t", "u", "n", "r", "y", "s", "w", "k", "m", "b", "v", "d", "h", "-"
}


def read_strains(*files, comment_char="#"):
    """Reads strain names from one or more plain text files and returns the
    set of distinct strains.

    Strain names can be commented with full-line or inline comments. For
    example, the following is a valid strain names file:

        # this is a comment at the top of the file
        strain1  # exclude strain1 because it isn't sequenced properly
        strain2
          # this is an empty line that will be ignored.

    Parameters
    ----------
    files : one or more str
        one or more names of text files with one strain name per line

    Returns
    -------
    set :
        strain names from the given input files

    """
    strains = set()
    for input_file in files:
        with open_file(input_file, 'r') as ifile:
            for line in ifile:
                # Allow comments anywhere in a given line.
                strain_name = line.split(comment_char)[0].strip()
                if len(strain_name) > 0:
                    strains.add(strain_name)

    return strains
