<reponame>alliance-genome/agr_genedescriptions
import logging
import re
from collections import defaultdict
from typing import Set, List, Tuple, Dict, Union
from ontobio import Ontology
from genedescriptions.commons import Sentence, DataType, Module
from genedescriptions.config_parser import GenedescConfigParser

logger = logging.getLogger(__name__)


def compose_sentence(prefix: str, additional_prefix: str, term_names: List[str], postfix: str,
                     config: GenedescConfigParser, ancestors_with_multiple_children: Set[str] = None,
                     rename_cell: bool = False, put_anatomy_male_at_end: bool = False) -> str:
    """compose the text of a sentence given its prefix, terms, and postfix

    Args:
        prefix (str): the prefix of the sentence
        term_names (List[str]): a list of term names
        postfix (str): the postfix of the sentence
        config (GenedescConfigParser): a gene description configuration object
        additional_prefix (str): an additional prefix to be used for special cases
        ancestors_with_multiple_children (Set[str]): set containing labels of terms that cover more than one children
            term in the original set and which will appear with the label '(multiple)'
        rename_cell (bool): rename 'cell' into 'the cell'
        put_anatomy_male_at_end (bool): move 'male' to the end of the sentence (for anatomy), and change it to
            'in male'
    Returns:
        str: the text of the sentence
    """
    if additional_prefix:
        additional_prefix = " " + additional_prefix
    new_prefix = prefix + additional_prefix + " "
    term_names = sorted(term_names)
    if ancestors_with_multiple_children:
        term_names = [term_name + " (multiple)" if term_name in ancestors_with_multiple_children else term_name for
                      term_name in term_names]
    if postfix != "":
        postfix = " " + postfix
    if rename_cell:
        if "cell" in term_names or "Cell" in term_names:
            if len(term_names) == 1:
                new_prefix = prefix[0:-2]
                term_names = ["widely"]
            else:
                if not additional_prefix:
                    new_prefix += "several structures, including "
                term_names = [term for term in term_names if term != "cell" and term != "Cell"]
    if put_anatomy_male_at_end and "male" in term_names and len(term_names) > 1:
        term_names = [term for term in term_names if term != "male"]
        term_names.append("in male")
    return new_prefix + concatenate_words_with_oxford_comma(term_names,
                                                            separator=config.get_terms_delimiter()) + postfix


def _get_single_sentence(initial_terms_ids: List[str], node_ids: List[str], ontology: Ontology, aspect: str,
                         evidence_group: str, qualifier: str, prepostfix_sentences_map: Dict[str, Tuple[str, str]],
                         config: GenedescConfigParser, terms_merged: bool = False, add_others: bool = False,
                         truncate_others_generic_word: str = "several",
                         truncate_others_aspect_words: Dict[str, str] = None,
                         ancestors_with_multiple_children: Set[str] = None, rename_cell: bool = False,
                         trimmed: bool = False, put_anatomy_male_at_end: bool = False) -> Union[Sentence, None]:
    """build a sentence object

    Args:
        node_ids (List[str]): list of ids for the terms to be combined in the sentence
        ontology (Ontology): the ontology containing the nodes
        aspect (str): aspect
        evidence_group (str): evidence group
        qualifier (str): qualifier
        prepostfix_sentences_map (Dict[str, Tuple[str, str]]): map for prefix and postfix phrases
        config (GenedescConfigParser): a gene description configuration object
        terms_merged (bool): whether the terms set has been merged to reduce its size
        add_others (bool): whether to say that there are other terms which have been omitted from the sentence
        truncate_others_generic_word (str): a generic word to indicate that the set of terms reported in the sentence is
            only a subset of the original terms, e.g., 'several'
        truncate_others_aspect_words (Dict[str, str]): one word for each aspect describing the kind of terms that are
            included in the aspect
        ancestors_with_multiple_children (Set[str]): set containing labels of terms that cover more than one children
            term in the original set and which will appear with the label '(multiple)'
        rename_cell (bool): whether to rename the term 'cell'
    Returns:
        Union[Sentence,None]: the combined go sentence
    """
    if len(node_ids) > 0:
        prefix = prepostfix_sentences_map[aspect + "|" + evidence_group + "|" + qualifier][0]
        additional_prefix = ""
        others_word = "entities"
        if aspect in truncate_others_aspect_words:
            others_word = truncate_others_aspect_words[aspect]
        if add_others:
            additional_prefix += truncate_others_generic_word + " " + others_word + ", including"
        postfix = prepostfix_sentences_map[aspect + "|" + evidence_group + "|" + qualifier][1]
        term_labels = [ontology.label(node_id, id_if_null=True) for node_id in node_ids]
        if ancestors_with_multiple_children is None:
            ancestors_with_multiple_children = set()
        return Sentence(prefix=prefix, initial_terms_ids=initial_terms_ids, terms_ids=node_ids, postfix=postfix,
                        text=compose_sentence(prefix=prefix, term_names=term_labels, postfix=postfix,
                                              additional_prefix=additional_prefix,
                                              ancestors_with_multiple_children=ancestors_with_multiple_children,
                                              rename_cell=rename_cell, config=config,
                                              put_anatomy_male_at_end=put_anatomy_male_at_end),
                        aspect=aspect, evidence_group=evidence_group, terms_merged=terms_merged,
                        additional_prefix=additional_prefix, qualifier=qualifier,
                        ancestors_covering_multiple_terms=ancestors_with_multiple_children, trimmed=trimmed)
    else:
        return None


def rename_human_ortholog_name(ortholog_name: str):
    new_name = ortholog_name
    if " family member " in ortholog_name:
        new_name = new_name.replace(" family member ", " ")
    new_name = re.sub(r"[,]? kDa$", "", new_name)
    return new_name


def is_human_ortholog_name_valid(ortholog_name: str):
    if "human uncharacterized protein" in ortholog_name.lower():
        return False
    return True


def concatenate_words_with_oxford_comma(words: List[str], separator: str = ","):
    """concatenate words by separating them with commas and a final oxford comma if more than two or by 'and' if two

    Args:
        words (List[str]): a list of words
        separator: the separator to be used between words, default to 'comma'

    Returns:
        str: a concatenated string representing the list of words
    """
    if len(words) > 2:
        return (separator + " ").join(words[0:-1]) + separator + " and " + words[-1]
    else:
        return " and ".join(words)


def get_best_human_ortholog_for_info_poor(human_orthologs, evidence_codes, human_df_agr, config):
    best_orth = ""
    if len(human_orthologs) > 0:
        ev_codes_group_map = config.get_evidence_codes_groups_map(module=Module.GO)
        exp_orthologs = defaultdict(int)
        predicted_orthologs = defaultdict(int)
        for ortholog in human_orthologs:
            orth_id = ortholog[0]
            ortholog_annotations = human_df_agr.get_annotations_for_gene(gene_id="RGD:" + orth_id,
                                                                         annot_type=DataType.GO,
                                                                         priority_list=evidence_codes)
            for annotation in ortholog_annotations:
                if annotation['aspect'] == 'F':
                    if "EXPERIMENTAL" in ev_codes_group_map[annotation["evidence"]['type']]:
                        exp_orthologs[ortholog[0]] += 1
                    else:
                        predicted_orthologs[ortholog[0]] += 1
        if len(exp_orthologs) > 0:
            best_orth = sorted([(key, value) for key, value in exp_orthologs.items()], key=lambda x: x[1],
                               reverse=True)[0][0]
        elif len(predicted_orthologs) > 0:
            best_orth = sorted([(key, value) for key, value in predicted_orthologs.items()], key=lambda x: x[1],
                               reverse=True)[0][0]
    return best_orth

import logging
import re
from collections import defaultdict
from typing import Set, List, Tuple, Dict, Union
from ontobio import Ontology
from genedescriptions.commons import Sentence, DataType, Module
from genedescriptions.config_parser import GenedescConfigParser

logger = logging.getLogger(__name__)


def compose_sentence(prefix: str, additional_prefix: str, term_names: List[str], postfix: str,
                     config: GenedescConfigParser, ancestors_with_multiple_children: Set[str] = None,
                     rename_cell: bool = False, put_anatomy_male_at_end: bool = False) -> str:
    """compose the text of a sentence given its prefix, terms, and postfix

    Args:
        prefix (str): the prefix of the sentence
        term_names (List[str]): a list of term names
        postfix (str): the postfix of the sentence
        config (GenedescConfigParser): a gene description configuration object
        additional_prefix (str): an additional prefix to be used for special cases
        ancestors_with_multiple_children (Set[str]): set containing labels of terms that cover more than one children
            term in the original set and which will appear with the label '(multiple)'
        rename_cell (bool): rename 'cell' into 'the cell'
        put_anatomy_male_at_end (bool): move 'male' to the end of the sentence (for anatomy), and change it to
            'in male'
    Returns:
        str: the text of the sentence
    """
    if additional_prefix:
        additional_prefix = " " + additional_prefix
    new_prefix = prefix + additional_prefix + " "
    term_names = sorted(term_names)
    if ancestors_with_multiple_children:
        term_names = [term_name + " (multiple)" if term_name in ancestors_with_multiple_children else term_name for
                      term_name in term_names]
    if postfix != "":
        postfix = " " + postfix
    if rename_cell:
        if "cell" in term_names or "Cell" in term_names:
            if len(term_names) == 1:
                new_prefix = prefix[0:-2]
                term_names = ["widely"]
            else:
                if not additional_prefix:
                    new_prefix += "several structures, including "
                term_names = [term for term in term_names if term != "cell" and term != "Cell"]
    if put_anatomy_male_at_end and "male" in term_names and len(term_names) > 1:
        term_names = [term for term in term_names if term != "male"]
        term_names.append("in male")
    return new_prefix + concatenate_words_with_oxford_comma(term_names,
                                                            separator=config.get_terms_delimiter()) + postfix


def _get_single_sentence(initial_terms_ids: List[str], node_ids: List[str], ontology: Ontology, aspect: str,
                         evidence_group: str, qualifier: str, prepostfix_sentences_map: Dict[str, Tuple[str, str]],
                         config: GenedescConfigParser, terms_merged: bool = False, add_others: bool = False,
                         truncate_others_generic_word: str = "several",
                         truncate_others_aspect_words: Dict[str, str] = None,
                         ancestors_with_multiple_children: Set[str] = None, rename_cell: bool = False,
                         trimmed: bool = False, put_anatomy_male_at_end: bool = False) -> Union[Sentence, None]:
    """build a sentence object

    Args:
        node_ids (List[str]): list of ids for the terms to be combined in the sentence
        ontology (Ontology): the ontology containing the nodes
        aspect (str): aspect
        evidence_group (str): evidence group
        qualifier (str): qualifier
        prepostfix_sentences_map (Dict[str, Tuple[str, str]]): map for prefix and postfix phrases
        config (GenedescConfigParser): a gene description configuration object
        terms_merged (bool): whether the terms set has been merged to reduce its size
        add_others (bool): whether to say that there are other terms which have been omitted from the sentence
        truncate_others_generic_word (str): a generic word to indicate that the set of terms reported in the sentence is
            only a subset of the original terms, e.g., 'several'
        truncate_others_aspect_words (Dict[str, str]): one word for each aspect describing the kind of terms that are
            included in the aspect
        ancestors_with_multiple_children (Set[str]): set containing labels of terms that cover more than one children
            term in the original set and which will appear with the label '(multiple)'
        rename_cell (bool): whether to rename the term 'cell'
    Returns:
        Union[Sentence,None]: the combined go sentence
    """
    if len(node_ids) > 0:
        prefix = prepostfix_sentences_map[aspect + "|" + evidence_group + "|" + qualifier][0]
        additional_prefix = ""
        others_word = "entities"
        if aspect in truncate_others_aspect_words:
            others_word = truncate_others_aspect_words[aspect]
        if add_others:
            additional_prefix += truncate_others_generic_word + " " + others_word + ", including"
        postfix = prepostfix_sentences_map[aspect + "|" + evidence_group + "|" + qualifier][1]
        term_labels = [ontology.label(node_id, id_if_null=True) for node_id in node_ids]
        if ancestors_with_multiple_children is None:
            ancestors_with_multiple_children = set()
        return Sentence(prefix=prefix, initial_terms_ids=initial_terms_ids, terms_ids=node_ids, postfix=postfix,
                        text=compose_sentence(prefix=prefix, term_names=term_labels, postfix=postfix,
                                              additional_prefix=additional_prefix,
                                              ancestors_with_multiple_children=ancestors_with_multiple_children,
                                              rename_cell=rename_cell, config=config,
                                              put_anatomy_male_at_end=put_anatomy_male_at_end),
                        aspect=aspect, evidence_group=evidence_group, terms_merged=terms_merged,
                        additional_prefix=additional_prefix, qualifier=qualifier,
                        ancestors_covering_multiple_terms=ancestors_with_multiple_children, trimmed=trimmed)
    else:
        return None


def rename_human_ortholog_name(ortholog_name: str):
    new_name = ortholog_name
    if " family member " in ortholog_name:
        new_name = new_name.replace(" family member ", " ")
    new_name = re.sub(r"[,]? kDa$", "", new_name)
    return new_name


def is_human_ortholog_name_valid(ortholog_name: str):
    if "human uncharacterized protein" in ortholog_name.lower():
        return False
    return True


def concatenate_words_with_oxford_comma(words: List[str], separator: str = ","):
    """concatenate words by separating them with commas and a final oxford comma if more than two or by 'and' if two

    Args:
        words (List[str]): a list of words
        separator: the separator to be used between words, default to 'comma'

    Returns:
        str: a concatenated string representing the list of words
    """
    if len(words) > 2:
        return (separator + " ").join(words[0:-1]) + separator + " and " + words[-1]
    else:
        return " and ".join(words)


def get_best_human_ortholog_for_info_poor(human_orthologs, evidence_codes, human_df_agr, config):
    best_orth = ""
    if len(human_orthologs) > 0:
        ev_codes_group_map = config.get_evidence_codes_groups_map(module=Module.GO)
        exp_orthologs = defaultdict(int)
        predicted_orthologs = defaultdict(int)
        for ortholog in human_orthologs:
            orth_id = ortholog[0]
            ortholog_annotations = human_df_agr.get_annotations_for_gene(gene_id="RGD:" + orth_id,
                                                                         annot_type=DataType.GO,
                                                                         priority_list=evidence_codes)
            for annotation in ortholog_annotations:
                if annotation['aspect'] == 'F':
                    if "EXPERIMENTAL" in ev_codes_group_map[annotation["evidence"]['type']]:
                        exp_orthologs[ortholog[0]] += 1
                    else:
                        predicted_orthologs[ortholog[0]] += 1
        if len(exp_orthologs) > 0:
            best_orth = sorted([(key, value) for key, value in exp_orthologs.items()], key=lambda x: x[1],
                               reverse=True)[0][0]
        elif len(predicted_orthologs) > 0:
            best_orth = sorted([(key, value) for key, value in predicted_orthologs.items()], key=lambda x: x[1],
                               reverse=True)[0][0]
    return best_orth
compose the text of a sentence given its prefix, terms, and postfix      Args:         prefix (str): the prefix of the sentence         term_names (List[str]): a list of term names         postfix (str): the postfix of the sentence         config (GenedescConfigParser): a gene description configuration object         additional_prefix (str): an additional prefix to be used for special cases         ancestors_with_multiple_children (Set[str]): set containing labels of terms that cover more than one children             term in the original set and which will appear with the label '(multiple)'         rename_cell (bool): rename 'cell' into 'the cell'         put_anatomy_male_at_end (bool): move 'male' to the end of the sentence (for anatomy), and change it to             'in male'     Returns:         str: the text of the sentence build a sentence object      Args:         node_ids (List[str]): list of ids for the terms to be combined in the sentence         ontology (Ontology): the ontology containing the nodes         aspect (str): aspect         evidence_group (str): evidence group         qualifier (str): qualifier         prepostfix_sentences_map (Dict[str, Tuple[str, str]]): map for prefix and postfix phrases         config (GenedescConfigParser): a gene description configuration object         terms_merged (bool): whether the terms set has been merged to reduce its size         add_others (bool): whether to say that there are other terms which have been omitted from the sentence         truncate_others_generic_word (str): a generic word to indicate that the set of terms reported in the sentence is             only a subset of the original terms, e.g., 'several'         truncate_others_aspect_words (Dict[str, str]): one word for each aspect describing the kind of terms that are             included in the aspect         ancestors_with_multiple_children (Set[str]): set containing labels of terms that cover more than one children             term in the original set and which will appear with the label '(multiple)'         rename_cell (bool): whether to rename the term 'cell'     Returns:         Union[Sentence,None]: the combined go sentence concatenate words by separating them with commas and a final oxford comma if more than two or by 'and' if two      Args:         words (List[str]): a list of words         separator: the separator to be used between words, default to 'comma'      Returns:         str: a concatenated string representing the list of words