<gh_stars>0
import tempfile
import os
import sys
import shlex
import subprocess as sp
import logging
from . import track
from . import genome
from . import base
from . import trackdb

logging.basicConfig(level=logging.INFO)
logger = logging.getLogger(__name__)

RSYNC_OPTIONS = '--progress -rvL'


def run(cmds, **kwargs):
    """
    Wrapper around subprocess.run, with unicode decoding of output.

    Additional kwargs are passed to subprocess.run.
    """
    proc = sp.Popen(cmds, bufsize=-1, stdout=sp.PIPE, stderr=sp.STDOUT,
                    close_fds=sys.platform != 'win32')
    for line in proc.stdout:
        print(line[:-1].decode())
    retcode = proc.wait()
    if retcode:
        raise sp.CalledProcessError(retcode, cmds)


def symlink(target, linkname):
    """
    Create a symlink to `target` called `linkname`.

    Converts `target` and `linkname` to absolute paths; creates
    `dirname(linkname)` if needed.
    """
    target = os.path.abspath(target)
    linkname = os.path.abspath(linkname)
    if not os.path.exists(target):
        raise ValueError("target {} not found".format(target))

    link_dir = os.path.dirname(linkname)
    if not os.path.exists(link_dir):
        os.makedirs(link_dir)

    run(['ln', '-s', '-f', target, linkname])
    return linkname


def upload(host, user, local_dir, remote_dir, rsync_options=RSYNC_OPTIONS):
    """
    Upload a file or directory via rsync.

    Parameters
    ----------
    host : str or None
        If None, omit the host part and just transfer locally

    user : str or None
        If None, omit the user part

    local_dir : str
        If a directory, a trailing "/" will be added.

    remote_dir : str
        If a directory, a trailing "/" will be added.
    """
    if user is None:
        user = ""
    else:
        user = user + "@"
    if host is None or host == 'localhost':
        host = ""
    else:
        host = host + ":"

    if not local_dir.endswith('/'):
        local_dir = local_dir + '/'

    if not remote_dir.endswith('/'):
        remote_dir = remote_dir + '/'

    remote_string = '{user}{host}{remote_dir}'.format(**locals())
    cmds = ['rsync']
    cmds += shlex.split(rsync_options)
    cmds += [local_dir, remote_string]
    run(cmds)
    return [remote_string]


def local_link(local_fn, remote_fn, staging):
    """
    Creates a symlink to a local staging area.

    The link name is built from `remote_fn`, but the absolute path is put
    inside the staging directory.

    Example
    -------

    If we have the following initial setup::

        cwd="/home/user"
        local="data/sample1.bw"
        remote="/hubs/hg19/a.bw"
        staging="__staging__"

    Then this function does the equivalent of::

        mkdir -p __staging__/hubs/hg19
        ln -sf \\
            /home/user/data/sample1.bw \\
            /home/user/__staging__/hubs/hg19/a.bw
    """
    linkname = os.path.join(staging, remote_fn.lstrip(os.path.sep))
    return symlink(local_fn, linkname)


def stage(x, staging):
    """
    Stage an object to the `staging` directory.

    If the object is a Track and is one of the types that needs an index file
    (bam, vcfTabix), then the index file will be staged as well.

    Returns a list of the linknames created.
    """
    linknames = []

    # Objects that don't represent a file shouldn't be staged
    non_file_objects = (
        track.ViewTrack,
        track.CompositeTrack,
        track.AggregateTrack,
        track.SuperTrack,
        genome.Genome,
    )
    if isinstance(x, non_file_objects):
        return linknames

    # If it's an object representing a file, then render it.
    #
    # Track objects don't represent files, but their documentation does
    linknames.append(x.render(staging))

    if hasattr(x, 'source') and hasattr(x, 'filename'):
        def _stg(x, ext=''):
            # A remote track hosted elsewhere does not need staging. This is
            # defined by a track with a url, but no source or filename.
            if (
                x.source is None
                and x.filename is None
                and getattr(x, 'url', None) is not None
            ):
                return

            linknames.append(
                local_link(x.source + ext, x.filename + ext, staging)
            )

        _stg(x)

        if isinstance(x, track.Track):
            if x.tracktype == 'bam':
                _stg(x, ext='.bai')
            if x.tracktype == 'vcfTabix':
                _stg(x, ext='.tbi')

        if isinstance(x, track.CompositeTrack):
            if x._html:
                _stg(x._html)

    return linknames



def stage_hub(hub, staging=None):
    """
    Stage a hub by symlinking all its connected files to a local directory.
    """
    linknames = []
    if staging is None:
        staging = tempfile.mkdtemp()
    for obj, level in hub.leaves(base.HubComponent, intermediate=True):
        linknames.extend(stage(obj, staging))

    return staging, linknames


def upload_hub(hub, host, remote_dir, user=None, port=22, rsync_options=RSYNC_OPTIONS, staging=None):
    """
    Renders, stages, and uploads a hub.
    """
    hub.render()
    if staging is None:
        staging = tempfile.mkdtemp()
    staging, linknames = stage_hub(hub, staging=staging)
    local_dir = os.path.join(staging)
    upload(host, user, local_dir=local_dir, remote_dir=remote_dir, rsync_options=rsync_options)
    return linknames

import tempfile
import os
import sys
import shlex
import subprocess as sp
import logging
from . import track
from . import genome
from . import base
from . import trackdb

logging.basicConfig(level=logging.INFO)
logger = logging.getLogger(__name__)

RSYNC_OPTIONS = '--progress -rvL'


def run(cmds, **kwargs):
    """
    Wrapper around subprocess.run, with unicode decoding of output.

    Additional kwargs are passed to subprocess.run.
    """
    proc = sp.Popen(cmds, bufsize=-1, stdout=sp.PIPE, stderr=sp.STDOUT,
                    close_fds=sys.platform != 'win32')
    for line in proc.stdout:
        print(line[:-1].decode())
    retcode = proc.wait()
    if retcode:
        raise sp.CalledProcessError(retcode, cmds)


def symlink(target, linkname):
    """
    Create a symlink to `target` called `linkname`.

    Converts `target` and `linkname` to absolute paths; creates
    `dirname(linkname)` if needed.
    """
    target = os.path.abspath(target)
    linkname = os.path.abspath(linkname)
    if not os.path.exists(target):
        raise ValueError("target {} not found".format(target))

    link_dir = os.path.dirname(linkname)
    if not os.path.exists(link_dir):
        os.makedirs(link_dir)

    run(['ln', '-s', '-f', target, linkname])
    return linkname


def upload(host, user, local_dir, remote_dir, rsync_options=RSYNC_OPTIONS):
    """
    Upload a file or directory via rsync.

    Parameters
    ----------
    host : str or None
        If None, omit the host part and just transfer locally

    user : str or None
        If None, omit the user part

    local_dir : str
        If a directory, a trailing "/" will be added.

    remote_dir : str
        If a directory, a trailing "/" will be added.
    """
    if user is None:
        user = ""
    else:
        user = user + "@"
    if host is None or host == 'localhost':
        host = ""
    else:
        host = host + ":"

    if not local_dir.endswith('/'):
        local_dir = local_dir + '/'

    if not remote_dir.endswith('/'):
        remote_dir = remote_dir + '/'

    remote_string = '{user}{host}{remote_dir}'.format(**locals())
    cmds = ['rsync']
    cmds += shlex.split(rsync_options)
    cmds += [local_dir, remote_string]
    run(cmds)
    return [remote_string]


def local_link(local_fn, remote_fn, staging):
    """
    Creates a symlink to a local staging area.

    The link name is built from `remote_fn`, but the absolute path is put
    inside the staging directory.

    Example
    -------

    If we have the following initial setup::

        cwd="/home/user"
        local="data/sample1.bw"
        remote="/hubs/hg19/a.bw"
        staging="__staging__"

    Then this function does the equivalent of::

        mkdir -p __staging__/hubs/hg19
        ln -sf \\
            /home/user/data/sample1.bw \\
            /home/user/__staging__/hubs/hg19/a.bw
    """
    linkname = os.path.join(staging, remote_fn.lstrip(os.path.sep))
    return symlink(local_fn, linkname)


def stage(x, staging):
    """
    Stage an object to the `staging` directory.

    If the object is a Track and is one of the types that needs an index file
    (bam, vcfTabix), then the index file will be staged as well.

    Returns a list of the linknames created.
    """
    linknames = []

    # Objects that don't represent a file shouldn't be staged
    non_file_objects = (
        track.ViewTrack,
        track.CompositeTrack,
        track.AggregateTrack,
        track.SuperTrack,
        genome.Genome,
    )
    if isinstance(x, non_file_objects):
        return linknames

    # If it's an object representing a file, then render it.
    #
    # Track objects don't represent files, but their documentation does
    linknames.append(x.render(staging))

    if hasattr(x, 'source') and hasattr(x, 'filename'):
        def _stg(x, ext=''):
            # A remote track hosted elsewhere does not need staging. This is
            # defined by a track with a url, but no source or filename.
            if (
                x.source is None
                and x.filename is None
                and getattr(x, 'url', None) is not None
            ):
                return

            linknames.append(
                local_link(x.source + ext, x.filename + ext, staging)
            )

        _stg(x)

        if isinstance(x, track.Track):
            if x.tracktype == 'bam':
                _stg(x, ext='.bai')
            if x.tracktype == 'vcfTabix':
                _stg(x, ext='.tbi')

        if isinstance(x, track.CompositeTrack):
            if x._html:
                _stg(x._html)

    return linknames



def stage_hub(hub, staging=None):
    """
    Stage a hub by symlinking all its connected files to a local directory.
    """
    linknames = []
    if staging is None:
        staging = tempfile.mkdtemp()
    for obj, level in hub.leaves(base.HubComponent, intermediate=True):
        linknames.extend(stage(obj, staging))

    return staging, linknames


def upload_hub(hub, host, remote_dir, user=None, port=22, rsync_options=RSYNC_OPTIONS, staging=None):
    """
    Renders, stages, and uploads a hub.
    """
    hub.render()
    if staging is None:
        staging = tempfile.mkdtemp()
    staging, linknames = stage_hub(hub, staging=staging)
    local_dir = os.path.join(staging)
    upload(host, user, local_dir=local_dir, remote_dir=remote_dir, rsync_options=rsync_options)
    return linknames
Wrapper around subprocess.run, with unicode decoding of output.      Additional kwargs are passed to subprocess.run. Create a symlink to `target` called `linkname`.      Converts `target` and `linkname` to absolute paths; creates     `dirname(linkname)` if needed. Upload a file or directory via rsync.      Parameters     ----------     host : str or None         If None, omit the host part and just transfer locally      user : str or None         If None, omit the user part      local_dir : str         If a directory, a trailing "/" will be added.      remote_dir : str         If a directory, a trailing "/" will be added. Creates a symlink to a local staging area.      The link name is built from `remote_fn`, but the absolute path is put     inside the staging directory.      Example     -------      If we have the following initial setup::          cwd="/home/user"         local="data/sample1.bw"         remote="/hubs/hg19/a.bw"         staging="__staging__"      Then this function does the equivalent of::          mkdir -p __staging__/hubs/hg19         ln -sf \\             /home/user/data/sample1.bw \\             /home/user/__staging__/hubs/hg19/a.bw Stage an object to the `staging` directory.      If the object is a Track and is one of the types that needs an index file     (bam, vcfTabix), then the index file will be staged as well.      Returns a list of the linknames created. # Objects that don't represent a file shouldn't be staged # If it's an object representing a file, then render it. # # Track objects don't represent files, but their documentation does # A remote track hosted elsewhere does not need staging. This is # defined by a track with a url, but no source or filename. Stage a hub by symlinking all its connected files to a local directory. Renders, stages, and uploads a hub.