Source code for tool.validate_fastqc

"""
.. See the NOTICE file distributed with this work for additional information
   regarding copyright ownership.

   Licensed under the Apache License, Version 2.0 (the "License");
   you may not use this file except in compliance with the License.
   You may obtain a copy of the License at

       http://www.apache.org/licenses/LICENSE-2.0

   Unless required by applicable law or agreed to in writing, software
   distributed under the License is distributed on an "AS IS" BASIS,
   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
   See the License for the specific language governing permissions and
   limitations under the License.
"""

from __future__ import print_function

import os
import shlex
import subprocess
import sys

from utils import logger

try:
    if hasattr(sys, '_run_from_cmdl') is True:
        raise ImportError
    from pycompss.api.parameter import FILE_IN, FILE_OUT
    from pycompss.api.task import task
    # from pycompss.api.api import compss_wait_on
except ImportError:
    logger.warn("[Warning] Cannot import \"pycompss\" API packages.")
    logger.warn("          Using mock decorators.")

    from utils.dummy_pycompss import FILE_IN, FILE_OUT  # pylint: disable=ungrouped-imports
    from utils.dummy_pycompss import task  # pylint: disable=ungrouped-imports
    # from utils.dummy_pycompss import compss_wait_on

from basic_modules.metadata import Metadata
from basic_modules.tool import Tool

# ------------------------------------------------------------------------------


class fastqcTool(Tool):  # pylint: disable=invalid-name
    """
    Tool for running indexers over a genome FASTA file
    """

    def __init__(self, configuration=None):
        """
        Initialise the tool with its configuration.


        Parameters
        ----------
        configuration : dict
            a dictionary containing parameters that define how the operation
            should be carried out, which are specific to each Tool.
        """
        logger.info("FastQC")
        Tool.__init__(self)

        if configuration is None:
            configuration = {}

        self.configuration.update(configuration)

    @task(returns=bool, fastq_file=FILE_IN, report_file=FILE_OUT, isModifier=False)
    def validate(self, fastq_file, report_file):  # pylint: disable=unused-argument, no-self-use
        """
        FastQC Validator

        Parameters
        ----------
        FastQC_file : str
            Location of the FastQ file
        report_loc : str
            Location of the output report file
        """
        command_line = 'fastqc ' + fastq_file
        logger.info("FastQC COMMAND: {0}".format(command_line))
        try:
            args = shlex.split(command_line)
            process = subprocess.Popen(args)
            process.wait()
        except (OSError, IOError) as error:
            logger.fatal("FastQC error: {0}".format(error))
            return False

        try:
            fastq_file_tmp = os.path.split(fastq_file)

            tail_substring = "fastq"
            if ".fq" in fastq_file_tmp[1]:
                tail_substring = "fq"

            gzipped = ""
            if fastq_file_tmp[1][-3:] == ".gz":
                gzipped = ".gz"

            fastq_file_tmp_name = fastq_file_tmp[1].replace(
                "." + tail_substring + gzipped, "_fastqc.html")
            fastq_file_tmp = os.path.join(fastq_file_tmp[0], fastq_file_tmp_name)

            with open(report_file, "wb") as f_out:
                with open(fastq_file_tmp, "rb") as f_in:
                    f_out.write(f_in.read())
        except (OSError, IOError) as error:
            logger.fatal("I/O error({0}): {1}".format(error.errno, error.strerror))
            return False

        return True

    def run(self, input_files, input_metadata, output_files):
        """
        Tool for assessing the quality of reads in a FastQ file

        Parameters
        ----------
        input_files : dict
            fastq : str
                List of file locations
        metadata : dict
            fastq : dict
                Required meta data
        output_files : dict
            report : str
                Location of the HTML

        Returns
        -------
        array : list
            First element is a list of the index files. Second element is a
            list of the matching metadata
        """

        # input and output share most metadata
        self.validate(
            input_files['fastq'],
            output_files['report']
        )

        output_metadata = {
            "report": Metadata(
                data_type="xml",
                file_type="HTML",
                file_path=output_files['report'],
                sources=[input_metadata["fastq"].file_path],
                taxon_id=input_metadata["fastq"].taxon_id,
                meta_data={
                    "tool": "fastqc_validator"
                }
            )
        }

        return (output_files, output_metadata)

# ------------------------------------------------------------------------------