"""
MultiQC config module. Holds a single copy of config variables to be used
across all other modules.

On import, only loads defaults from config_defaults.yaml. To populate from
custom parameters, call load_user_config() from the user_config module
"""

import itertools

# Default logger will be replaced by caller
import logging
import os
import subprocess
import sys
from datetime import datetime
from pathlib import Path
from typing import Any, Dict, List, Optional, Set, Tuple, Union

import importlib_metadata
import yaml
from importlib_metadata import EntryPoint

from multiqc.types import Anchor, ModuleId, SectionId
from multiqc.utils import pyaml_env
from multiqc.utils.util_functions import strtobool, update_dict

logger = logging.getLogger(__name__)

# Get the MultiQC version
version = importlib_metadata.version("multiqc")
short_version = version
git_hash = None
git_hash_short = None

MODULE_DIR = Path(__file__).parent.absolute()
script_path = str(MODULE_DIR)  # dynamically used by report.multiqc_dump_json()
REPO_DIR = MODULE_DIR.parent.absolute()

# noinspection PyBroadException
try:
    git_root = Path(
        subprocess.check_output(
            ["git", "rev-parse", "--show-toplevel"], cwd=script_path, stderr=subprocess.STDOUT, universal_newlines=True
        ).strip()
    )
    # .git
    # multiqc/
    #   utils/
    #     config.py  <- __file__
    expected_git_root = Path(script_path).parent.parent
    if git_root == expected_git_root:
        git_hash = subprocess.check_output(
            ["git", "rev-parse", "HEAD"], cwd=script_path, stderr=subprocess.STDOUT, universal_newlines=True
        ).strip()
        git_hash_short = git_hash[:7]
        version = f"{version} ({git_hash_short})"
except:  # noqa: E722
    pass

CleanPatternT = Union[str, Dict[str, Union[str, List[str]]]]


title: str
subtitle: str
intro_text: str
report_comment: str
report_header_info: List[Dict[str, str]]
show_analysis_paths: bool
show_analysis_time: bool
custom_logo: str
custom_logo_url: str
custom_logo_title: str
custom_css_files: List[str]
simple_output: bool
template: str
profile_runtime: bool
profile_memory: bool
pandoc_template: str
read_count_multiplier: float
read_count_prefix: str
read_count_desc: str
long_read_count_multiplier: float
long_read_count_prefix: str
long_read_count_desc: str
base_count_multiplier: float
base_count_prefix: str
base_count_desc: str
output_fn_name: str
data_dir_name: str
plots_dir_name: str
data_format: str
force: bool
verbose: bool
no_ansi: bool
quiet: bool
prepend_dirs: bool
prepend_dirs_depth: int
prepend_dirs_sep: str
file_list: bool
require_logs: bool
version_check_url: str

make_data_dir: bool
zip_data_dir: bool
data_dump_file: bool
data_dump_file_write_raw: Optional[bool]
megaqc_url: str
megaqc_access_token: Optional[str]
megaqc_timeout: float
export_plots: bool
make_report: bool
make_pdf: bool

plots_force_flat: bool
plots_export_font_scale: float
plots_force_interactive: bool
plots_flat_numseries: int
plots_defer_loading_numseries: int
num_datasets_plot_limit: int  # DEPRECATED in favour of plots_number_of_series_to_defer_loading
lineplot_number_of_points_to_hide_markers: int
barplot_legend_on_bottom: bool
violin_downsample_after: Optional[int]
violin_min_threshold_outliers: int
violin_min_threshold_no_points: int

collapse_tables: bool
max_table_rows: int
table_columns_visible: Dict[str, Union[bool, Dict[str, bool]]]
table_columns_placement: Dict[str, Dict[str, float]]
table_columns_name: Dict[str, Union[str, Dict[str, str]]]
table_cond_formatting_colours: List[Dict[str, str]]
table_cond_formatting_rules: Dict[str, Dict[str, List[Dict[str, Union[str, int, float]]]]]
decimalPoint_format: str
thousandsSep_format: str
remove_sections: List[str]
section_comments: Dict[str, str]
lint: bool  # Deprecated since v1.17
strict: bool
development: bool
custom_plot_config: Dict
custom_table_header_config: Dict
software_versions: Dict
ignore_symlinks: bool
ignore_images: bool
fn_ignore_dirs: List[str]
fn_ignore_paths: List[str]
sample_names_ignore: List[str]
sample_names_ignore_re: List[str]
sample_names_rename_buttons: List[str]
sample_names_replace: Dict[str, str]
sample_names_replace_regex: bool
sample_names_replace_exact: bool
sample_names_replace_complete: bool
sample_names_rename: List
show_hide_buttons: List
show_hide_patterns: List
show_hide_regex: List
show_hide_mode: List
no_version_check: bool
log_filesize_limit: int
filesearch_lines_limit: int
report_readerrors: int
skip_generalstats: int
skip_versions_section: int
disable_version_detection: int
versions_table_group_header: str
data_format_extensions: Dict[str, str]
export_plot_formats: List[str]
filesearch_file_shared: List[str]
custom_content: Dict
fn_clean_sample_names: bool
use_filename_as_sample_name: bool
fn_clean_exts: List[CleanPatternT]
fn_clean_trim: List[str]
fn_ignore_files: List[str]
top_modules: List[Union[str, Dict[str, Dict[str, str]]]]
module_order: List[Union[str, Dict[str, Dict[str, Union[str, List[str]]]]]]
preserve_module_raw_data: Optional[bool]
table_sample_merge: Dict[str, List[CleanPatternT]]

# Module filename search patterns
sp: Dict = {}

# Other defaults that can't be set in YAML
modules_dir: str
creation_date: str
working_dir: str
analysis_dir: List[str]
output_dir: str
kwargs: Dict = {}

# Other variables that set only through the CLI
run_modules: List[str]
custom_content_modules: List[str]
exclude_modules: List[str]
data_dir: Optional[str]
plots_dir: Optional[str]
custom_data: Dict
report_section_order: Dict[
    Union[SectionId, ModuleId, Anchor], Union[str, Dict[str, int], Dict[str, Union[SectionId, ModuleId, Anchor]]]
]
output_fn: Optional[str]
filename: Optional[str]
megaqc_upload: bool

avail_modules: Dict[str, EntryPoint]
avail_templates: Dict[str, EntryPoint]


def load_defaults():
    """
    Load config from defaults. Happens before even logger is created
    """
    config_defaults_path = MODULE_DIR / "config_defaults.yaml"
    with config_defaults_path.open() as f:
        _default_config = yaml.safe_load(f)
    for c, v in _default_config.items():
        globals()[c] = v

    # Module filename search patterns
    with (Path(MODULE_DIR) / "search_patterns.yaml").open() as f:
        global sp
        sp = yaml.safe_load(f)

    # Other defaults that can't be set in defaults YAML
    global modules_dir, creation_date, working_dir, analysis_dir, output_dir, megaqc_access_token, kwargs
    modules_dir = str(Path(MODULE_DIR) / "modules")
    creation_date = datetime.now().astimezone().strftime("%Y-%m-%d, %H:%M %Z")
    working_dir = os.getcwd()
    analysis_dir = [os.getcwd()]
    output_dir = os.path.realpath(os.getcwd())
    megaqc_access_token = os.environ.get("MEGAQC_ACCESS_TOKEN")
    kwargs = {}

    # Other variables that set only through the CLI
    global \
        run_modules, \
        custom_content_modules, \
        exclude_modules, \
        data_dir, \
        plots_dir, \
        custom_data, \
        report_section_order, \
        output_fn, \
        filename, \
        megaqc_upload
    run_modules = []
    custom_content_modules = []
    exclude_modules = []
    data_dir = None
    plots_dir = None
    custom_data = {}
    report_section_order = {}
    output_fn = None
    filename = None
    megaqc_upload = False

    # Available modules.
    global avail_modules
    # Modules must be listed in pyproject.toml under entry_points['multiqc.modules.v1']
    # Get all modules, including those from other extension packages
    avail_modules = dict()
    for entry_point in importlib_metadata.entry_points(group="multiqc.modules.v1"):
        nice_name = entry_point.name
        avail_modules[nice_name] = entry_point

    # Available templates.
    global avail_templates
    # Templates must be listed in pyproject.toml under entry_points['multiqc.templates.v1']
    # Get all templates, including those from other extension packages
    avail_templates = {}
    for entry_point in importlib_metadata.entry_points(group="multiqc.templates.v1"):
        nice_name = entry_point.name
        avail_templates[nice_name] = entry_point

    # Check we have modules & templates
    # Check that we were able to find some modules and templates
    # If not, package probably hasn't been installed properly.
    # Need to do this before click, else will throw cryptic error
    # Note: Can't use logger here, not yet initiated.
    if len(avail_modules) == 0 or len(avail_templates) == 0:
        if len(avail_modules) == 0:
            print("Error - No MultiQC modules found.", file=sys.stderr)
        if len(avail_templates) == 0:
            print("Error - No MultiQC templates found.", file=sys.stderr)
        print(
            "Could not load MultiQC - has it been installed? \n\
            Please either install with pip (pip install multiqc) or by using \n\
            the local files (pip install .)",
            file=sys.stderr,
        )
        sys.exit(1)


load_defaults()

# To restore after load_defaults()
explicit_user_config_files: Set[Path] = set()

# To avoid finding same file many times
loaded_user_files: Set[Path] = set()


def reset():
    """
    Reset the interactive session
    """

    explicit_user_config_files.clear()
    load_defaults()


def find_user_files():
    """
    Overwrite config defaults with user config files.

    Not called automatically because needs the logger to be initiated.

    Note that config files are loaded in a specific order and values can overwrite each other.
    """

    def _load_found_file(path: Union[Path, str, None]):
        load_config_file(path, is_explicit_config=False)

    # Load and parse installation config file if we find it
    _load_found_file(REPO_DIR / "multiqc_config.yaml")

    # Load and parse a config file in $XDG_CONFIG_HOME
    # Ref: https://specifications.freedesktop.org/basedir-spec/basedir-spec-latest.html
    _load_found_file(
        os.path.join(os.environ.get("XDG_CONFIG_HOME", os.path.expanduser("~/.config")), "multiqc_config.yaml")
    )

    # Load and parse a user config file if we find it
    _load_found_file(os.path.expanduser("~/.multiqc_config.yaml"))

    # Load and parse a config file path set in an ENV variable if we find it
    if os.environ.get("MULTIQC_CONFIG_PATH") is not None:
        _load_found_file(os.environ.get("MULTIQC_CONFIG_PATH"))

    # Load separate config entries from MULTIQC_* environment variables
    _add_config(_env_vars_config())

    # Load and parse a config file in this working directory if we find it
    _load_found_file("multiqc_config.yaml")


def load_config_file(yaml_config_path: Union[str, Path, None], is_explicit_config=True) -> Optional[Path]:
    """
    Load and parse a config file if we find it.

    `is_explicit_config` config means the function was called directly or through multiqc.load_config(),
    which means we need to keep track of to restore the config update update_defaults.
    """
    if not yaml_config_path:
        return None

    path = Path(yaml_config_path)
    if not path.is_file() and path.with_suffix(".yml").is_file():
        path = path.with_suffix(".yml")

    if not path.is_file():
        return None

    if path.absolute() in loaded_user_files:  # already loaded
        return path

    if is_explicit_config:
        explicit_user_config_files.add(path)

    try:
        # pyaml_env allows referencing environment variables in YAML for default values
        # new_config can be None if the file is empty
        new_config: Optional[Dict] = pyaml_env.parse_config(str(path))
        if new_config:
            logger.info(f"Loading config settings from: {path}")
            _add_config(new_config, str(path))
    except (IOError, AttributeError) as e:
        logger.warning(f"Error loading config {path}: {e}")
        return None
    except yaml.scanner.ScannerError as e:
        logger.error(f"Error parsing config YAML: {e}")
        raise

    loaded_user_files.add(path.absolute())
    return path


def load_cl_config(cl_config: List[str]):
    for clc_str in cl_config:
        try:
            parsed_clc = yaml.safe_load(clc_str)
            # something:var fails as it needs a space. Fix this (a common mistake)
            if isinstance(parsed_clc, str) and ":" in clc_str:
                clc_str = ": ".join(clc_str.split(":"))
                parsed_clc = yaml.safe_load(clc_str)
            assert isinstance(parsed_clc, dict)
        except yaml.scanner.ScannerError as e:
            logger.error(f"Could not parse command line config: {clc_str}\n{e}")
        except AssertionError:
            logger.error(f"Could not parse command line config: {clc_str}")
        else:
            logger.debug(f"Found command line config: {parsed_clc}")
            _add_config(parsed_clc)


def _env_vars_config() -> Dict:
    """
    Check MULTIQC_* environment variables and set to corresponding config values if they are of scalar types.
    """
    RESERVED_NAMES = {"MULTIQC_CONFIG_PATH"}
    PREFIX = "MULTIQC_"  # Prefix for environment variables
    env_config: Dict[str, Union[str, int, float, bool]] = {}
    for k, v in os.environ.items():
        if k.startswith(PREFIX) and k not in RESERVED_NAMES:
            conf_key = k[len(PREFIX) :].lower()
            if conf_key not in globals():
                continue
            if isinstance(globals()[conf_key], bool):
                try:
                    env_config[conf_key] = strtobool(v)
                except ValueError:
                    logger.warning(f"Could not parse a boolean value from the environment variable ${k}={v}")
                    continue
            elif isinstance(globals()[conf_key], int):
                try:
                    env_config[conf_key] = int(v)
                except ValueError:
                    logger.warning(f"Could not parse a int value from the environment variable ${k}={v}")
                    continue
            elif isinstance(globals()[conf_key], float):
                try:
                    env_config[conf_key] = float(v)
                except ValueError:
                    logger.warning(f"Could not parse a float value from the environment variable ${k}={v}")
                    continue
            elif not isinstance(globals()[conf_key], str) and globals()[conf_key] is not None:
                logger.warning(
                    f"Can only set scalar config entries (str, int, float, bool) with environment variable, "
                    f"but config.{conf_key} expects a type '{type(globals()[conf_key]).__name__}'. Ignoring ${k}"
                )
                continue
            logger.debug(f"Setting config.{conf_key} from the environment variable ${k}")
    return env_config


def _add_config(conf: Dict, conf_path=None):
    """
    Add to the global config with given MultiQC config dict
    """
    global custom_css_files, fn_clean_exts, fn_clean_trim
    log_new_config = {}
    log_filename_patterns = []
    log_filename_clean_extensions = []
    log_filename_clean_trimmings = []
    for c, v in conf.items():
        if c == "sp":
            # Merge filename patterns instead of replacing. Add custom pattern to the beginning,
            # so they supersede the default patterns.
            global sp
            sp = update_dict(sp, v, add_in_the_beginning=True)
            log_filename_patterns.append(v)
        elif c == "extra_fn_clean_exts":
            log_filename_clean_extensions.append(v)
        elif c == "extra_fn_clean_trim":
            log_filename_clean_trimmings.append(v)
        elif c in ["custom_logo"] and v:
            # Resolve file paths - absolute or cwd, or relative to config file
            fpath = v
            if os.path.exists(v):
                fpath = os.path.abspath(v)
            elif conf_path is not None and os.path.exists(os.path.join(os.path.dirname(conf_path), v)):
                fpath = os.path.abspath(os.path.join(os.path.dirname(conf_path), v))
            else:
                logger.error(f"Config '{c}' path not found, skipping ({fpath})")
                continue
            log_new_config[c] = fpath
            update({c: fpath})
        elif c == "custom_css_files":
            for fpath in v:
                if os.path.exists(fpath):
                    fpath = os.path.abspath(fpath)
                elif conf_path is not None and os.path.exists(os.path.join(os.path.dirname(conf_path), fpath)):
                    fpath = os.path.abspath(os.path.join(os.path.dirname(conf_path), fpath))
                else:
                    logger.error(f"CSS path '{c}' path not found, skipping ({fpath})")
                    continue
                logger.debug(f"Adding css file '{c}': {fpath}")
                if not custom_css_files:
                    custom_css_files = []
                custom_css_files.append(fpath)
        else:
            log_new_config[c] = v
            update({c: v})
    if len(log_new_config) > 0:
        logger.debug(f"New config: {log_new_config}")
    if len(log_filename_patterns) > 0:
        logger.debug(f"Added to filename patterns: {log_filename_patterns}")
    if len(log_filename_clean_extensions) > 0:
        logger.debug(f"Added to filename clean extensions: {log_filename_clean_extensions}")
        # Prepend to filename cleaning patterns instead of replacing.
        # This must be done after fn_clean_exts is configured if it's specified
        # in the config.
        fn_clean_exts[0:0] = itertools.chain.from_iterable(log_filename_clean_extensions)
    if len(log_filename_clean_trimmings) > 0:
        logger.debug(f"Added to filename clean trimmings: {log_filename_clean_trimmings}")
        # Prepend to filename cleaning patterns instead of replacing
        # This must be done after fn_clean_trim is configured if it's specified
        # in the config.
        fn_clean_trim[0:0] = itertools.chain.from_iterable(log_filename_clean_trimmings)


def load_sample_names(sample_names_file: Path):
    """
    Function to load file containing a list of alternative sample-name swaps.

    Essentially a fancy way of loading stuff into the config.sample_names_rename.

    As such, can also be done directly using a config file.
    """

    global sample_names_rename_buttons, sample_names_rename
    num_cols = None
    try:
        with open(sample_names_file) as f:
            logger.debug(f"Loading sample renaming config settings from: {sample_names_file}")
            for line in f:
                s = line.strip().split("\t")
                if len(s) > 1:
                    # Check that we have consistent numbers of columns
                    if num_cols is None:
                        num_cols = len(s)
                    elif num_cols != len(s):
                        logger.warning(
                            "Inconsistent number of columns found in sample names file (skipping line): '{}'".format(
                                line.strip()
                            )
                        )
                    # Parse the line
                    if len(sample_names_rename_buttons) == 0:
                        sample_names_rename_buttons = s
                    else:
                        sample_names_rename.append(s)
                elif len(line.strip()) > 0:
                    logger.warning(f"Sample names file line did not have columns (must use tabs): {line.strip()}")
    except (IOError, AttributeError) as e:
        logger.error(f"Error loading sample names file: {e}")
    logger.debug(f"Found {len(sample_names_rename_buttons)} sample renaming patterns")


def load_replace_names(replace_names_file: Path):
    global sample_names_replace
    try:
        with open(replace_names_file) as f:
            logger.debug(f"Loading sample replace config settings from: {replace_names_file}")
            for line in f:
                s = line.strip().split("\t")
                if len(s) == 2:
                    sample_names_replace[s[0]] = s[1]
    except (IOError, AttributeError) as e:
        logger.error(f"Error loading sample names replacement file: {e}")
    logger.debug(f"Found {len(sample_names_replace)} sample replacing patterns")


def load_show_hide(show_hide_file: Optional[Path] = None):
    global show_hide_buttons, show_hide_patterns, show_hide_mode, show_hide_regex
    if show_hide_file:
        try:
            with open(show_hide_file, "r") as f:
                logger.debug(f"Loading sample renaming config settings from: {show_hide_file}")
                for line in f:
                    s = line.strip().split("\t")
                    if len(s) >= 3 and s[1] in ["show", "hide", "show_re", "hide_re"]:
                        show_hide_buttons.append(s[0])
                        show_hide_mode.append(s[1])
                        show_hide_patterns.append(s[2:])
                        show_hide_regex.append(s[1] not in ["show", "hide"])  # flag whether regex is turned on
        except AttributeError as e:
            logger.error(f"Error loading show patterns file: {e}")

    # Prepend a "Show all" button if we have anything
    # Do this outside of the file load block in case it was set in the config
    if len(show_hide_buttons) > 0:
        logger.debug(f"Found {len(show_hide_buttons)} show/hide patterns")
        show_hide_buttons.insert(0, "Show all")
        show_hide_mode.insert(0, "hide")
        show_hide_patterns.insert(0, [])
        show_hide_regex.insert(0, False)


# Keep track of all changes to the config
nondefault_config: Dict = {}


def update(u: Dict[str, Any]):
    update_dict(nondefault_config, u)
    return update_dict(globals(), u)


def get_cov_thresholds(config_key: str) -> Tuple[List[int], List[int]]:
    """
    Reads coverage thresholds from the config, otherwise sets sensible defaults. Useful for modules like mosdepth, qualimap (BamQC), ngsbits
    """
    covs = globals().get(config_key, {}).get("general_stats_coverage", [])
    if not covs:
        covs = getattr(globals(), "general_stats_coverage", [])

    if covs and isinstance(covs, list):
        covs = [int(t) for t in covs]
        logger.debug(f"Custom coverage thresholds: {', '.join([str(t) for t in covs])}")
    else:
        covs = [1, 5, 10, 30, 50]
        logger.debug(f"Using default coverage thresholds: {', '.join([str(t) for t in covs])}")

    hidden_covs = globals().get(config_key, {}).get("general_stats_coverage_hidden", [])
    if not hidden_covs:
        hidden_covs = getattr(globals(), "general_stats_coverage_hidden", [])

    if hidden_covs and isinstance(hidden_covs, list):
        logger.debug(f"Hiding coverage thresholds: {', '.join([str(t) for t in hidden_covs])}")
    else:
        hidden_covs = [t for t in covs if t != 30]

    return covs, hidden_covs
