Exemple #1
0
def get_mount_points():
    """return system mount points as list of (mountpoint, device, fstype).
    Compatible with linux and solaris"""
    try:
        buf = get_shell_output('mount')
    except (IOError, os.error), (errno, strerror):
        return (strerror, errno)
 def check_progs(self):
     for k, v in defaultprogs.items():
         r = get_shell_output('which \"%s\"' %v)
         if r:
             self.progs[k] = v
         else:
             self.progs[k] = ''
Exemple #3
0
def get_mount_points():
    """return system mount points as list of (mountpoint, device, fstype).
    Compatible with linux and solaris"""
    try:
        buf = get_shell_output('mount')
    except (IOError, os.error), (errno, strerror):
        return (strerror, errno)
 def check_progs(self):
     for k, v in defaultprogs.items():
         r = get_shell_output('which \"%s\"' % v)
         if r:
             self.progs[k] = v
         else:
             self.progs[k] = ''
Exemple #5
0
 def get_rdev(f):
     """'ls -la' to get mayor and minor number of devices"""
     try:
         buf = get_shell_output('ls -la %s' % encode(f))
     except:
         return 0
     else:
         try:
             return int(buf[4][:-1]), int(buf[5])
         except:
             # HACK: found 0xff.. encoded device numbers, ignore them...
             return 0, 0
Exemple #6
0
 def get_rdev(f):
     """'ls -la' to get mayor and minor number of devices"""
     try:
         buf = get_shell_output('ls -la %s' % encode(f))
     except:
         return 0
     else:
         try:
             return int(buf[4][:-1]), int(buf[5])
         except:
             # HACK: found 0xff.. encoded device numbers, ignore them...
             return 0, 0
def kill_app():
    cmd = "yarn application -list | awk -F ' ' '{print $1,$4}'"
    output = utils.get_shell_output(cmd)
    kill_cmd = "yarn application -kill "

    for line in output:
        field = line.strip().split(" ")
        appId = field[0]
        user = field[1]
        if user == "go2data_rank":
            kill_app = kill_cmd + appId
            utils.execute_command(kill_app)
            logger.info("application:{app} kill done".format(app=appId))
Exemple #8
0
def async_data(environment):
    try:
        cmd = "wc -l /search/odin/taoyongbo/rank/rankResult/multiRank"
        output = utils.get_shell_output(cmd)
        total_count = 0
        for line in output:
            field = line.strip().split(" ")
            total_count = int(field[0])

        if total_count > 0 and environment == "prod":
            subprocess.Popen("python async.py", shell=True)
    except:
        logger.info("GpsCustomStatisticTask excute failed")
Exemple #9
0
def test_assemblyvalidation():
    bamasm = get_testfile('cm-500pgun-asm-b2mv31-bam')
    contigfa = get_testfile('cm-500pgun-asm-b2mv31-fa')
    bamref = get_testfile('cm-500pgun-ref-bam')
    refstatsfile = get_testfile('cm-500pgun-ref-stats')
    refphylfile = get_testfile('cm-ref-phyl')
    nucmercoords = get_testfile('cm-500pgun-val-nucmer')

    val = AssemblyValidation(bamref, bamasm, refphylfile, refstatsfile, contigfa, nucmercoords)
    assert(len(val.contigs) == int(get_shell_output("grep -c '^>' " + contigfa)[0]))

    make_dir(get_outdir() + "masm")
    val.write_contig_purity(get_outdir() + "masm" + "/contig-purity.tsv")
    val.write_general_stats(get_outdir() + "masm" + "/asm-stats.tsv")
    val.write_genome_contig_cov(get_outdir() + "masm" + "/genome-contig-coverage.tsv")
Exemple #10
0
def pan_regenerate(tab):
    """regenerate vfs pan file: copy files"""

    dir_src = tab.path
    dir_dest = tab.vbase.replace('#vfs', '')
    # check if can copy files
    out = utils.get_shell_output('touch ' + utils.encode(dir_dest))
    if out:
        return ''.join(out.split(':')[1:])[1:]
    # copy files
    for f in glob(os.path.join(dir_src, '*')):
        f = os.path.basename(f)
        try:
            files.copy_bulk(os.path.join(dir_src, f), os.path.join(dir_dest, f))
        except (IOError, os.error), (errno, strerror):
            app.display()
            messages.error('Cannot regenerating vfs (closing panelize)\n%s (%s)' % (strerror, errno))
Exemple #11
0
def pan_regenerate(tab):
    """regenerate vfs pan file: copy files"""

    dir_src = tab.path
    dir_dest = tab.vbase.replace('#vfs', '')
    # check if can copy files
    out = utils.get_shell_output('touch ' + utils.encode(dir_dest))
    if out:
        return ''.join(out.split(':')[1:])[1:]
    # copy files
    for f in glob(os.path.join(dir_src, '*')):
        f = os.path.basename(f)
        try:
            files.copy_bulk(os.path.join(dir_src, f),
                            os.path.join(dir_dest, f))
        except (IOError, os.error), (errno, strerror):
            app.display()
            messages.error(
                'Cannot regenerating vfs (closing panelize)\n%s (%s)' %
                (strerror, errno))
Exemple #12
0
 def check_progs(self):
     for k, v in defaultprogs.items():
         r = get_shell_output('%s \"%s\"' % (sysprogs['which'], v))
         self.progs[k] = v if r else ''
Exemple #13
0
    def __execute_command(self):

        cmd = 'mountavfs'
        get_shell_output(cmd)
        self.base = self.avfs + self.server
Exemple #14
0
    def __execute_command(self):

        cmd = 'mountavfs'
        get_shell_output(cmd)
        self.base = self.avfs + self.server