Python util.run_command函数代码示例

def get_dev(user_mod=''):
    '''
        use v4l-info to determine device for a given driver module
    '''
    if user_mod == 'bttv0':
        user_mod = 'bttv'

    with run_command('ls /dev/video*', do_popen=True) as pop_:
        for line in pop_:
            devname = line.strip()
            if hasattr(devname, 'decode'):
                devname = devname.decode()

            if not os.path.exists('/usr/bin/v4l-info'):
                print('YOU NEED TO INSTALL v4l-conf')
                exit(0)
            driver = ''
            with run_command('v4l-info %s 2> /dev/null | grep driver'
                             % devname, do_popen=True) as v4linfo:
                for line in v4linfo:
                    if hasattr(line, 'decode'):
                        line = line.decode()
                    if line != '':
                        driver = line.split()[2].strip('"')
                if user_mod in driver or (not user_mod and driver == 'em28xx'):
                    return devname

def build_ns3(config, build_examples, build_tests, args, build_options):
    cmd = [sys.executable, "waf", "configure"] + args

    if build_examples:
        cmd.append("--enable-examples")

    if build_tests:
        cmd.append("--enable-tests")

    try:
        ns3_traces, = config.getElementsByTagName("ns-3-traces")
    except ValueError:
        # Don't print a warning message here since regression traces
        # are no longer used.
        pass
    else:
        cmd.extend([
                "--with-regression-traces", os.path.join("..", ns3_traces.getAttribute("dir")),
                ])

    try:
        pybindgen, = config.getElementsByTagName("pybindgen")
    except ValueError:
        print "Note: configuring ns-3 without pybindgen"
    else:
        cmd.extend([
                "--with-pybindgen", os.path.join("..", pybindgen.getAttribute("dir")),
        ])

    run_command(cmd) # waf configure ...
    run_command([sys.executable, "waf", "build"] + build_options)

 def install_pkgs(self, pkg_lst, mnt_pt):     
     
     for pkg in pkg_lst:
         self.install_package(mnt_pt, pkg)
         
     #clean apt package cache
     util.run_command("chroot %s /usr/bin/apt-get clean" % mnt_pt)

 def run(self,input):
     filename = tempfile.mktemp()
     f = open(filename,'wb')
     cmd = self.command
     if input: cmd += '< %s' % input.pathname
     util.run_command(cmd, f.write, self.callback.log)
     f.close()
     return {'output': File(filename)}

 def _disable_ttys(self, mnt_pt):
     
     #disable gettys
     util.run_command("sed -i -e 's/^\([1-6].*:respawn*\)/#\1/' -e 's/^T/#\t/' %s/etc/inittab" % mnt_pt)
     
     text = "S0:12345:respawn:/sbin/getty -L console 9600 vt100\n"
     util.write_to_file("%s/etc/inittab" % mnt_pt, "a", text)
     
     

 def copy_kernel_modules(self, mnt_pt):
     #disable hw clock
     #os.chmod("%s/etc/init.d/hwclock.sh" % mnt_pt, 0644)
     
     #copy kernek modules
     kernel_version = os.path.basename(self._kernel)[8:]
     util.run_command("cp -r /lib/modules/%s \
                 %s/lib/modules/%s" % (kernel_version, mnt_pt, kernel_version)) 
     

 def netanim_download():
     local_file = required_netanim_version + ".tar.bz2"
     remote_file = constants.NETANIM_RELEASE_URL + "/" + local_file
     print "Retrieving NetAnim from " + remote_file
     urllib.urlretrieve(remote_file, local_file)
     print "Uncompressing " + local_file
     run_command(["tar", "-xjf", local_file])
     print "Rename %s as %s" % (required_netanim_version, constants.LOCAL_NETANIM_PATH)
     os.rename(required_netanim_version, constants.LOCAL_NETANIM_PATH)

 def run(self, **k):
     input = k["test data"]
     model = k["model"]
     filename = tempfile.mktemp()
     cmd = "%s %s %s %s" % (svm_predict_pathname, input.pathname, model.pathname, filename)
     log = self.callback.log
     log("# Running %s\n" % cmd)
     util.run_command(cmd, log, log)
     return {"output": TextFile(filename, autodel=True)}

def pipeline_monogenic_validation(work_dir=os.environ['OBER_OUT'] + '/requests/monogenic/work',
                                  index_segments_dir=os.environ['OBER_OUT'] + '/requests/monogenic/work/index_segments',
                                  region_size=100,
                                  theta_affinity=0.95,
                                  theta_weight=0.5,
                                  regenerate_segments=True,
                                  snps=None,  # np.array([6, 8]),
                                  debug=1,
                                  debug_sample=512):
    # Load SNPs
    problem = im.io.read_plink(prefix=work_dir + '/monogenic.12', pedigree=im.itu.HUTT_PED, haplotype=None, frames=None)
    # Testing: simulate aligned samples output (hap types should be 2 in the imputed genotype output line)
    problem.haplotype.poo_phase = np.zeros((problem.num_samples,), dtype=np.byte)
    problem.haplotype.poo_phase[np.array([0, 1])] = 1
    problem.haplotype.poo_phase[np.array([2, 3])] = -1
    
    # Create segments only for the regions around each snp
    if regenerate_segments:
        for row in (problem.info.snp[snps] if snps is not None else problem.info.snp):
            # Find SNP's region (the one containing its base-pair position) 
            chrom, bp = row['chrom'], row['base_pair']
            phasing_dir = '%s/phasing/chr%d' % (os.environ['OBER_OUT'], chrom)
            index_segments_chrom_dir = '%s/chr%d' % (index_segments_dir, chrom)
            info_file = '%s/hutt.phased.info.npz' % (phasing_dir,)
            info = im.io.read_info_npz(info_file)
            snp_bp = info.snp['base_pair']
            snp_index = util.nearest_neighbor_in_list_tree(bp, snp_bp, util.list_index_tree(snp_bp))
            snp_index = snp_index if snp_bp[snp_index] <= bp else snp_index - 1
            start = region_size * (snp_index / region_size)
            stop = start + region_size
            segment_file = '%s/segments-%d-%d.out' % (index_segments_chrom_dir, start, stop)
            if not os.path.exists(segment_file):
                util.mkdir_if_not_exists(index_segments_chrom_dir)
                util.run_command('find-segments-of-snp-range %d %d < %s/segments.out > %s' % (start, stop, phasing_dir, segment_file)) 
            
            # Index segments
            if regenerate_segments or \
            not os.path.exists('%s/metadata.npz' % (index_segments_chrom_dir,)) or \
            not os.path.exists('%s/region-%d.npz' % (index_segments_chrom_dir, start)):
                index_segments_beagle.main(segment_file, info_file, segment_file, index_segments_chrom_dir,
                                           snp_index=snp_index, debug=2,
                                           theta_affinity=theta_affinity, theta_weight=theta_weight)
    
    # Impute using the newly generated segment index
    _, t = im.v.iv.impute_problem(problem, debug=debug, remove_partial_calls=True,
                                  segment_location=index_segments_dir,  # if regenerate_segments else None,
                                  snps=snps, debug_sample=debug_sample)

    im.io.write_plink(im.Problem(genotype=t.imputed, pedigree=im.examples.hutt_pedigree(), haplotype=None, frames=None),
                      work_dir + '/imputed.12', save_frames=False, save_haplotype=False)
    im.cgi.io_cgi.write_imputed(t, sys.stdout, poo_phase=problem.haplotype.poo_phase)
    with open(work_dir + '/imputed.12.lgen', 'wb') as f:
        im.cgi.io_cgi.write_imputed_lgen(t, f)
    return t

 def install(self):
     """mount disk image and download base system"""
     
     #mount disk image
     mnt_pt = "/mnt/%s" % self._name
     os.mkdir(mnt_pt)
     util.run_command("mount -o loop %s %s" % (self._path, mnt_pt))
     
     #download base system
     print "Downloading %s base system\n" % self._release
     return util.run_command("debootstrap --arch %s %s %s %s" % 
               (self._arch, self._release, mnt_pt, self._location))

    def post_install(self):
        # create /etc/fstab, /etc/hostname, /etc/network/interfaces, /etc/hosts
        # create xen config file, unmount disk image

        mnt_pt = "/mnt/%s" % self._name

        print "Setting up guest OS %s\n" % self._name

        print "Copying kernel modules\n"
        self.copy_kernel_modules(mnt_pt)

        print "Disabling extra ttys\n"
        self._disable_ttys(mnt_pt)

        print "Setting up apt\n"
        text = """# %s/stable
deb http://archive.ubuntu.com/ubuntu/ %s main restricted universe multiverse
deb http://security.ubuntu.com/ubuntu %s-security main restricted universe multiverse

""" % (
            self._release,
            self._release,
            self._release,
        )

        self._apt_setup(text, mnt_pt)

        print "installing libc6-xen, udev, ssh\n"
        self.install_pkgs(["libc6-xen", "openssh-server", "udev"], mnt_pt)

        # create /etc/fstab
        print "Setting up filesystem table\n"
        self.create_fstab(mnt_pt)

        print "Setting up networking\n"
        self.network_setup(mnt_pt)

        # hack to prevent nash-hotplug from hogging cpu
        self.kill_nash_hotplug(mnt_pt)

        print "Creating initrd for %s\n" % self._name
        self.create_initrd()

        print "Generating xen configuration file /etc/xen/%s\n" % self._name
        self.create_xen_config()

        # unmount filesystem
        util.run_command("umount %s" % mnt_pt)
        os.rmdir(mnt_pt)

        print "Installation of guest domain %s complete!!!" % self._name
        return 0

    def list_auto_snapshot_sets(self, tag = None):
        """
        Returns a list of zfs filesystems and volumes tagged with
        the "com.sun:auto-snapshot" property set to "true", either
        set locally or inherited. Snapshots are excluded from the
        returned result.

        Keyword Arguments:
        tag:
            A string indicating one of the standard auto-snapshot schedules
            tags to check (eg. "frequent" will map to the tag:
            com.sun:auto-snapshot:frequent). If specified as a zfs property
            on a zfs dataset, the property corresponding to the tag will 
            override the wildcard property: "com.sun:auto-snapshot"
            Default value = None
        """
        #Get auto-snap property in two passes. First with the global
        #value, then overriding with the label/schedule specific value

        included = []
        excluded = []

        cmd = [ZFSCMD, "list", "-H", "-t", "filesystem,volume",
               "-o", "name,com.sun:auto-snapshot", "-s", "name"]
        if tag:
            overrideprop = "com.sun:auto-snapshot:" + tag
            scmd = [ZFSCMD, "list", "-H", "-t", "filesystem,volume",
                    "-o", "name," + overrideprop, "-s", "name"]
            outdata,errdata = util.run_command(scmd)
            for line in outdata.rstrip().split('\n'):
                line = line.split()
                if line[1] == "true":
                    included.append(line[0])
                elif line[1] == "false":
                    excluded.append(line[0])
        outdata,errdata = util.run_command(cmd)
        for line in outdata.rstrip().split('\n'):
            line = line.split()
            # Only set values that aren't already set. Don't override
            try:
                included.index(line[0])
                continue
            except ValueError:
                try:
                    excluded.index(line[0])
                    continue
                except ValueError:
                    # Dataset is not listed in either list.
                    if line[1] == "true":
                        included.append(line[0])
        return included

def get_regression_traces(ns3_dir, regression_branch):
    print """
    #
    # Get the regression traces
    #
    """
    # ns3_dir is the directory into which we cloned the repo
    # regression_branch is the repo in which we will find the traces.  Variations like this should work:
    #  ns-3-dev-ref-traces
    #  craigdo/ns-3-dev-ref-traces
    #  craigdo/ns-3-tap-ref-traces
    regression_traces_dir = os.path.split(regression_branch)[-1]
    regression_branch_url = constants.REGRESSION_TRACES_REPO + regression_branch

    print "Synchronizing reference traces using Mercurial."
    try:
        if not os.path.exists(regression_traces_dir):
            run_command(["hg", "clone", regression_branch_url, regression_traces_dir])
        else:
            run_command(["hg", "-q", "pull", "--cwd", regression_traces_dir, regression_branch_url])
            run_command(["hg", "-q", "update", "--cwd", regression_traces_dir])
    except OSError: # this exception normally means mercurial is not found
        if not os.path.exists(regression_traces_dir_name):
            traceball = regression_tbranch + constants.TRACEBALL_SUFFIX
            print "Retrieving " + traceball + " from web."
            urllib.urlretrieve(constants.REGRESSION_TRACES_URL + traceball, traceball)
            run_command(["tar", "-xjf", traceball])
            print "Done."

    return regression_traces_dir

    def _disable_ttys(self, mnt_pt):
        util.run_command("rm -f %s/etc/event.d/tty[2-6]" % mnt_pt)
        lines = util.pipe_command("cat %s/etc/event.d/tty1" % mnt_pt)
        if self._release == "feisty":
            lines[-1] = "exec /sbin/getty -L 9600 console vt100\n"
        else:
            lines[-1] = "respawn /sbin/getty -L 9600 console vt100\n"

        fd = None
        try:
            fd = open("%s/etc/event.d/tty1" % mnt_pt, "w")
            fd.writelines(lines)
        finally:
            if fd is not None:
                fd.close()

def build_ns3(config, build_examples, build_tests):
    cmd = [
        "python", "waf", "configure",
        ]

    if build_examples:
        cmd.append("--enable-examples")

    if build_tests:
        cmd.append("--enable-tests")

    try:
        ns3_traces, = config.getElementsByTagName("ns-3-traces")
    except ValueError:
        # Don't print a warning message here since regression traces
        # are no longer used.
        pass
    else:
        cmd.extend([
                "--with-regression-traces", os.path.join("..", ns3_traces.getAttribute("dir")),
                ])

    try:
        pybindgen, = config.getElementsByTagName("pybindgen")
    except ValueError:
        print "Note: configuring ns-3 without pybindgen"
    else:
        cmd.extend([
                "--with-pybindgen", os.path.join("..", pybindgen.getAttribute("dir")),
        ])

    try:
        nsc, = config.getElementsByTagName("nsc")
    except ValueError:
        print "Note: configuring ns-3 without NSC"
    else:
        # Build NSC if the architecture supports it
        if sys.platform not in ['linux2']:
            arch = None
        else:
            arch = os.uname()[4]
        if arch == 'x86_64' or arch == 'i686' or arch == 'i586' or arch == 'i486' or arch == 'i386':
            cmd.extend(["--with-nsc", os.path.join("..", nsc.getAttribute("dir"))])
        else:
            print "Note: configuring ns-3 without NSC (architecture not supported)"

    run_command(cmd)
    run_command(["python", "waf"])