import_igc_data.py

#!/usr/bin/env python
import argparse
import logging
import os
import sys
from itertools import islice

from bioapi import MetageneDBCatalogGeneAPI, MetageneDBCatalogTaxonomyAPI
from requests.exceptions import HTTPError
from slugify import slugify

from metagenedb.common.utils.parsers import IGCLineParser

logging.basicConfig(format='[%(asctime)s] %(levelname)s:%(name)s:%(message)s')
logger = logging.getLogger()


class ImportIGCGenes(object):
    METAGENEDB_GENE_API = MetageneDBCatalogGeneAPI
    METAGENEDB_TAXONOMY_API = MetageneDBCatalogTaxonomyAPI

    PHYLUM_COL = 'taxo_phylum'
    GENUS_COL = 'taxo_genus'
    SELECTED_KEYS = ['gene_id', 'length', 'kegg_ko', PHYLUM_COL, GENUS_COL]

    def __init__(self, annotation_file, url, skip_tax=False, skip_functions=False):
        self.annotation_file = annotation_file
        self.url = url
        self.metagenedb_gene_api = self.METAGENEDB_GENE_API(base_url=self.url)
        self.metagenedb_taxonomy_api = self.METAGENEDB_TAXONOMY_API(base_url=self.url)
        self.total_genes = self._get_number_genes()
        self._reset_counters()
        # Skip some insertion if specified in script options
        self.skip_tax = skip_tax
        self.skip_functions = skip_functions

    def _reset_counters(self):
        self.processed_genes = 0
        self.created_genes = 0
        self.updated_genes = 0
        self.skipped_genes = 0

    def _get_number_genes(self):
        if not os.path.isfile(self.annotation_file):
            return 0
        with open(self.annotation_file) as f:
            for i, l in enumerate(f):
                pass
        return i + 1

    def _select_taxonomy(self, gene_dict, unknown_val='unknown'):
        """
        Select the taxonomy to be assigned for the gene.
        genus has priority on phylum. If both unknow, remove the taxonomy key
        """
        phylum = gene_dict.pop(self.PHYLUM_COL)
        genus = gene_dict.pop(self.GENUS_COL)
        if self.skip_tax:
            return gene_dict
        resp_dict = {}
        if genus != unknown_val:
            resp_dict = self.metagenedb_taxonomy_api.get_all(params={'name': genus, 'rank': 'genus'})
            if len(resp_dict['results']) > 1:
                logger.warning(f"More than 1 result found for genus {genus}. First result is kept.")
        elif phylum != unknown_val:
            resp_dict = self.metagenedb_taxonomy_api.get_all(params={'name': phylum, 'rank': 'phylum'})
            if len(resp_dict['results']) > 1:
                logger.warning(f"More than 1 result found for phylum {phylum}. First result is kept.")
        if resp_dict.get('count', 0) > 0:
            gene_dict.update({'taxonomy': resp_dict['results'][0]['tax_id']})
        return gene_dict

    def _parse_gene(self, raw_line, selected_keys=SELECTED_KEYS):
        """
        Use IGCLineParser and return selected keys
        """
        gene_parser = IGCLineParser()
        all_dict = gene_parser.gene(raw_line)
        selected_dict = {k: v for k, v in all_dict.items() if k in selected_keys}
        return selected_dict

    def _clean_gene(self, gene_dict):
        gene_dict['gene_name'] = gene_dict['gene_id']
        gene_dict['gene_id'] = slugify(gene_dict['gene_id'])
        gene_dict['functions'] = gene_dict.pop('kegg_ko')
        gene_dict = self._select_taxonomy(gene_dict)
        if self.skip_functions or 'unknown' in gene_dict['functions']:
            gene_dict.pop('functions')
        return gene_dict

    def load_annotation_file_to_db_in_chunks(self, chunk_size=1000, test=False):
        with open(self.annotation_file, 'r') as file:
            while True:
                chunk_genes = list(islice(file, chunk_size))
                if not chunk_genes:
                    break
                genes = [self._clean_gene(self._parse_gene(i)) for i in chunk_genes]
                try:
                    response = self.metagenedb_gene_api.put(genes)
                    self.created_genes += response.get('created').get('count')
                    self.updated_genes += response.get('updated').get('count')
                except HTTPError as http_error:
                    logging.warning("%s: %s; %s", http_error, http_error.response.json(), genes)
                    self.skipped_genes += len(genes)
                self.processed_genes += len(chunk_genes)
                logger.info("%s Genes processed so far...", self.processed_genes)
                if test is True:
                    break
        logger.info("[DONE] %s/%s Genes created.", self.created_genes, self.total_genes)
        logger.info("[DONE] %s/%s Genes updated.", self.updated_genes, self.total_genes)
        logger.info("[DONE] %s/%s Genes skipped.", self.skipped_genes, self.total_genes)


def parse_arguments():
    """
    Defines parser.
    """
    parser = argparse.ArgumentParser(description='Populate database from a given IGC annotation file.')
    # Common arguments for analysis and annotations
    parser.add_argument('annotation', help='IGC annotation file')
    parser.add_argument('--url', help='base URL of the instance.', default='http://localhost/')
    parser.add_argument('--chunk_size', type=int, default=1000, help='How many genes to handle and create in the same time.')
    parser.add_argument('--skip_taxonomy', action='store_true', help='Skip taxonomy information from genes.')
    parser.add_argument('--skip_functions', action='store_true', help='Skip functions information from genes.')
    parser.add_argument('--test', action='store_true', help='Run only on first chunk.')
    parser.add_argument('-v', '--verbose', action='store_true')

    try:
        return parser.parse_args()
    except SystemExit:
        sys.exit(1)


def run():
    args = parse_arguments()
    if args.verbose:
        logger.setLevel(logging.INFO)
    import_igc_genes = ImportIGCGenes(args.annotation, args.url,
                                      skip_tax=args.skip_taxonomy, skip_functions=args.skip_functions)
    import_igc_genes.load_annotation_file_to_db_in_chunks(chunk_size=args.chunk_size, test=args.test)


if __name__ == "__main__":
    run()