gga_get_data.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-

import bioblend
import argparse
import os
import subprocess
import logging
import sys
import fnmatch
import time
import json
import re
import stat
import shutil

from bioblend.galaxy.objects import GalaxyInstance
from bioblend import galaxy

import utilities
import speciesData

""" 
gga_get_data.py

Usage: $ python3 gga_get_data.py -i input_example.yml [OPTIONS]

"""


class GetData(speciesData.SpeciesData):
    """
    Child of SpeciesData

    Contains methods and attributes to copy data into the src_data subfolders of an organism

    """

    def goto_species_dir(self):
        """
        Go to the species directory (starting from the main dir)

        :return:
        """

        os.chdir(self.main_dir)
        species_dir = os.path.join(self.main_dir, self.genus_species) + "/"
        try:
            os.chdir(species_dir)
        except OSError:
            logging.critical("Cannot access %s" % species_dir)
            sys.exit(0)
        return 1



    def make_directory_tree(self):
        """
        Generate the directory tree for an organism

        :return:
        """

        os.chdir(self.main_dir)

        try:
            os.chdir(self.species_dir)
        except OSError as exc:
            logging.critical("Cannot access %s" % self.genus_species)
            sys.exit(exc)

        # Creation (or updating) of the src_data directory tree
        try:
            os.mkdir("./src_data")
        except FileExistsError:
            logging.debug("'src_data' directory already exist for %s" % self.full_name)
        except PermissionError as exc:
            logging.critical("Insufficient permission to create src_data directory tree")
            sys.exit(exc)

        # List of all the directories to create in src_data
        src_data_dirs_li = ["./src_data", "./src_data/annotation", "./src_data/genome", "./src_data/tracks",
                            "./src_data/annotation/%s" % self.species_folder_name,
                            "./src_data/genome/%s" % self.species_folder_name,
                            "./src_data/annotation/{0}/OGS{1}/".format(self.species_folder_name, self.ogs_version),
                            "./src_data/genome/{0}/v{1}".format(self.species_folder_name, self.genome_version)]
        make_dirs(dir_paths_li=src_data_dirs_li)

        # Return to main directory
        os.chdir(self.main_dir)

        logging.info("src_data directory tree generated for %s" % self.full_name)


    def get_source_data_files_from_path(self):
        """
        Find source data files and copy them into the src_data dir tree

        :return:
        """

        try:
            os.chdir(self.species_dir)
        except OSError:
            logging.critical("Cannot access " + self.species_dir)
            sys.exit(0)

        organism_annotation_dir = os.path.abspath("./src_data/annotation/{0}/OGS{1}".format(self.species_folder_name, self.ogs_version))
        organism_genome_dir = os.path.abspath("./src_data/genome/{0}/v{1}".format(self.species_folder_name, self.genome_version))

        datasets_to_get = {"genome_path": self.genome_path,
                           "gff_path": self.gff_path, 
                           "transcripts_path": self.transcripts_path,
                           "proteins_path": self.proteins_path,
                           "interpro_path": self.interpro_path, 
                           "orthofinder_path": self.orthofinder_path, 
                           "blastp_path": self.blastp_path, 
                           "blastx_path": self.blastx_path}

        genome_datasets = ["genome_path"]
        annotation_datasets = ["gff_path", "transcripts_path", "proteins_path", "orthofinder_path", "interpro_path", "blastp_path", "blastx_path"]  
        # Where to store blast results?

        # search_excluded_datasets = ["interpro_path", "orthofinder_path", "blastp_path", "blastx_path"]  
        # # These datasets will not be searched if missing in the input file

        # Copy datasets in the organism src_data dir tree correct folder
        for k, v in datasets_to_get.items():
            if v:  # If dataset is not present in input file, skip copy
                if k in genome_datasets:
                    logging.info("Copying {0} ({1}) into {2}".format(k, v, organism_genome_dir))
                    genome_fname = "v%s.fasta" % self.genome_version
                    try:
                        shutil.copyfile(os.path.abspath(v), os.path.join(organism_genome_dir, genome_fname))
                    except Exception as exc:
                        logging.warning("Could not copy {0} ({1}) - Exit Code: {2})".format(k, v, exc))
                elif k in annotation_datasets:
                    dataset_fname = ""
                    if k == "gff_path":
                        dataset_fname = "OGS%s.gff" % self.ogs_version
                    elif k == "transcripts_path":
                        dataset_fname = "OGS%s_transcripts.fasta" % self.ogs_version
                    elif k == "proteins_path":
                        dataset_fname = "OGS%s_proteins.fasta" % self.ogs_version
                    elif k == "orthofinder_path":
                        dataset_fname = "OGS%s_orthofinder.tsv" % self.ogs_version
                    elif k == "interpro_path":
                        dataset_fname = "OGS%s_interproscan.xml" % self.ogs_version
                    elif k == "blastp_path":
                        dataset_fname = "OGS%s_blastp.xml" % self.ogs_version
                    elif k == "blastx_path":
                        dataset_fname = "OGS%s_blastx.xml" % self.ogs_version
                    logging.info("Copying {0} ({1}) into {2}".format(k, v, organism_annotation_dir))
                    try:
                        shutil.copyfile(os.path.abspath(v), os.path.join(organism_annotation_dir, dataset_fname))
                    except Exception as exc:
                        logging.warning("Could not copy {0} ({1}) - Exit Code: {2}".format(k, v, exc))
                else:
                    pass

        os.chdir(self.main_dir)


def make_dirs(dir_paths_li):
    """
    Recursively create directories from a list of paths with a try-catch condition

    :param dir_paths_li:
    :return:
    """
    created_dir_paths_li = []

    for dir_path in dir_paths_li:
        try:
            os.mkdir(dir_path)
        except FileExistsError:
            logging.debug("%s directory already exists" % dir_path)
        except PermissionError as exc:
            logging.critical("Insufficient permission to create %s" % dir_path)
            sys.exit(exc)
        created_dir_paths_li.append(dir_path)

    return created_dir_paths_li
    
if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="Automatic data loading in containers and interaction "
                                                 "with galaxy instances for GGA"
                                                 ", following the protocol @ "
                                                 "http://gitlab.sb-roscoff.fr/abims/e-infra/gga")

    parser.add_argument("input",
                        type=str,
                        help="Input file (yml)")

    parser.add_argument("-v", "--verbose",
                        help="Increase output verbosity",
                        action="store_false")

    parser.add_argument("--main-directory",
                        type=str,
                        help="Where the stack containers will be located, defaults to working directory")

    args = parser.parse_args()

    if args.verbose:
        logging.basicConfig(level=logging.DEBUG)
    else:
        logging.basicConfig(level=logging.INFO)
    logging.getLogger("urllib3").setLevel(logging.WARNING)

    if not args.main_directory:
        args.main_directory = os.getcwd()
    else:
        args.main_directory = os.path.abspath(args.main_directory)

    sp_dict_list = utilities.parse_input(args.input)

    for sp_dict in sp_dict_list:

        # Creating an instance of get_data_for_current_species object
        get_data_for_current_species = GetData(parameters_dictionary=sp_dict)

        # Starting
        logging.info("gga_load_data.py called for %s" % get_data_for_current_species.full_name)

        # Setting some of the instance attributes
        get_data_for_current_species.main_dir = args.main_directory
        get_data_for_current_species.species_dir = os.path.join(get_data_for_current_species.main_dir,
                                                                 get_data_for_current_species.genus_species +
                                                                 "/")
        # create src_data directory tree
        get_data_for_current_species.make_directory_tree()
        # Retrieve datasets
        logging.info("Finding and copying datasets for %s" % get_data_for_current_species.full_name)
        get_data_for_current_species.get_source_data_files_from_path()
        logging.info("Sucessfully copied datasets for %s" % get_data_for_current_species.full_name)