コード例 #1
0
ファイル: core.py プロジェクト: xogeny/PyFMI
def get_temp_location():
    if sys.platform == 'win32':
        return os.path.join(tempfile._get_default_tempdir(),'JModelica.org')
    elif sys.platform == 'darwin':
        return os.path.join(tempfile._get_default_tempdir(),'JModelica.org')
    else:
        return os.path.join(tempfile._get_default_tempdir(),os.environ['USER'],'JModelica.org')
コード例 #2
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ファイル: osutils.py プロジェクト: Acidburn0zzz/chromite
def _TempDirSetup(self, prefix='tmp', update_env=True, base_dir=None):
  """Generate a tempdir, modifying the object, and env to use it.

  Specifically, if update_env is True, then from this invocation forward,
  python and all subprocesses will use this location for their tempdir.

  The matching _TempDirTearDown restores the env to what it was.
  """
  # Stash the old tempdir that was used so we can
  # switch it back on the way out.
  self.tempdir = tempfile.mkdtemp(prefix=prefix, dir=base_dir)
  os.chmod(self.tempdir, 0o700)

  if update_env:
    with tempfile._once_lock:
      self._tempdir_value = tempfile._get_default_tempdir()
      self._tempdir_env = tuple((x, os.environ.get(x))
                                for x in _TEMPDIR_ENV_VARS)
      # Now update TMPDIR/TEMP/TMP, and poke the python
      # internal to ensure all subprocess/raw tempfile
      # access goes into this location.
      os.environ.update((x, self.tempdir) for x in _TEMPDIR_ENV_VARS)
      # Finally, adjust python's cached value (we know it's cached by here
      # since we invoked _get_default_tempdir from above).  Note this
      # is necessary since we want *all* output from that point
      # forward to go to this location.
      tempfile.tempdir = self.tempdir
コード例 #3
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ファイル: test_acceptance.py プロジェクト: xmendez/wfuzz
    def test(self):
        if not expected_list:
            return
        temp_name = next(tempfile._get_candidate_names())
        defult_tmp_dir = tempfile._get_default_tempdir()

        filename = os.path.join(defult_tmp_dir, temp_name)

        # Wfuzz results
        with wfuzz.FuzzSession(url=url, **dict(list(params.items()) + list(dict(save=filename).items()))) as s:
            if payloads is None:
                fuzzed = s.fuzz()
            else:
                fuzzed = s.get_payloads(payloads).fuzz()

            ret_list = [(x.code, x.history.urlparse.path) for x in fuzzed]

        # repeat test with performaing same saved request
        with wfuzz.FuzzSession(payloads=[("wfuzzp", dict(fn=filename))], url="FUZZ") as s:
            same_list = [(x.code, x.history.urlparse.path) for x in s.fuzz()]

        self.assertEqual(sorted(ret_list), sorted(same_list))

        # repeat test with performaing FUZZ[url] saved request
        with wfuzz.FuzzSession(payloads=[("wfuzzp", dict(fn=filename))], url="FUZZ[url]") as s:
            same_list = [(x.code, x.history.urlparse.path) for x in s.fuzz()]

        self.assertEqual(sorted(ret_list), sorted(same_list))
コード例 #4
0
ファイル: test_acceptance.py プロジェクト: xmendez/wfuzz
    def test(self):
        temp_name = next(tempfile._get_candidate_names())
        defult_tmp_dir = tempfile._get_default_tempdir()

        filename = os.path.join(defult_tmp_dir, temp_name)

        # Wfuzz results
        with wfuzz.FuzzSession(url=url, **params) as s:
            s.export_to_file(filename)

            if payloads is None:
                fuzzed = s.fuzz()
            else:
                fuzzed = s.get_payloads(payloads).fuzz()

            ret_list = [(x.code, x.history.urlparse.path) for x in fuzzed]

        # repeat test with recipe as only parameter
        with wfuzz.FuzzSession(recipe=[filename]) as s:
            if payloads is None:
                same_list = [(x.code, x.history.urlparse.path) for x in s.fuzz()]
            else:
                same_list = [(x.code, x.history.urlparse.path) for x in s.get_payloads(payloads).fuzz()]

        self.assertEqual(sorted(ret_list), sorted(same_list))
コード例 #5
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def get_temp_aln(aln):
    tfname = os.path.join(tempfile._get_default_tempdir(),
                          next(tempfile._get_candidate_names()))
    aln.write(tfname,alignment_format='PIR')
    seqs = get_seqs_from_pir(tfname)
    os.unlink(tfname)
    return seqs
コード例 #6
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ファイル: screenshot.py プロジェクト: digininja/wfuzz
    def process(self, fuzzresult):
        temp_name = next(tempfile._get_candidate_names())
        defult_tmp_dir = tempfile._get_default_tempdir()

        filename = os.path.join(defult_tmp_dir, temp_name + ".png")

        subprocess.call(['cutycapt', '--url=%s' % pipes.quote(fuzzresult.url), '--out=%s' % filename])
        self.add_result("Screnshot taken, output at %s" % filename)
コード例 #7
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def _get_temp_file_name():
    """Generate a temporary file name with an absolute path.
    
    :rtype: str
    """
    return (tempfile._get_default_tempdir()
        + os.sep
        + next(tempfile._get_candidate_names()))
コード例 #8
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 def tmpName() -> str:
     '''
     Return the path to a temporary file.
     '''
     
     tempdir = tempfile._get_default_tempdir()
     name = next(tempfile._get_candidate_names())
     return '{}/{}'.format(tempdir, name)
コード例 #9
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def genTempFilePath(subdir=''):
    tempFileName = next(tempfile._get_candidate_names())
    tempDir = tempfile._get_default_tempdir()
    if subdir == '':
        return os.path.join(tempDir, tempFileName)
    else:
        dir = os.path.join(tempDir, subdir)
        os.makedirs(dir, exist_ok=True)
        return os.path.join(dir, tempFileName)
コード例 #10
0
def render_mm(self, code, options, format, prefix='mermaid'):
    """Render mermaid code into a PNG or PDF output file."""

    if format == 'raw':
        format = 'png'

    mermaid_cmd = self.builder.config.mermaid_cmd
    hashkey = (
        code + str(options) +
        str(self.builder.config.mermaid_sequence_config)).encode('utf-8')

    basename = '%s-%s' % (prefix, sha1(hashkey).hexdigest())
    fname = '%s.%s' % (basename, format)
    relfn = posixpath.join(self.builder.imgpath, fname)
    outdir = os.path.join(self.builder.outdir, self.builder.imagedir)
    outfn = os.path.join(outdir, fname)
    tmpfn = os.path.join(_get_default_tempdir(), basename)

    if os.path.isfile(outfn):
        return relfn, outfn

    ensuredir(os.path.dirname(outfn))

    # mermaid expects UTF-8 by default
    if isinstance(code, text_type):
        code = code.encode('utf-8')

    with open(tmpfn, 'wb') as t:
        t.write(code)

    mm_args = [mermaid_cmd, '-i', tmpfn, '-o', outfn]
    mm_args.extend(self.builder.config.mermaid_params)
    if self.builder.config.mermaid_sequence_config:
        mm_args.extend('--configFile',
                       self.builder.config.mermaid_sequence_config)

    try:
        p = Popen(mm_args, stdout=PIPE, stdin=PIPE, stderr=PIPE)
    except OSError as err:
        if err.errno != ENOENT:  # No such file or directory
            raise
        logger.warning('command %r cannot be run (needed for mermaid '
                       'output), check the mermaid_cmd setting' % mermaid_cmd)
        return None, None

    stdout, stderr = p.communicate(code)
    if self.builder.config.mermaid_verbose:
        logger.info(stdout)

    if p.returncode != 0:
        raise MermaidError('Mermaid exited with error:\n[stderr]\n%s\n'
                           '[stdout]\n%s' % (stderr, stdout))
    if not os.path.isfile(outfn):
        raise MermaidError(
            'Mermaid did not produce an output file:\n[stderr]\n%s\n'
            '[stdout]\n%s' % (stderr, stdout))
    return relfn, outfn
コード例 #11
0
def make_temp_filename(tmpdir=None, extension=""):
    """
    Get a random filename in a tmpdir with an optional extension
    """
    if tmpdir is None:
        tmpdir = tempfile._get_default_tempdir()  # pylint: disable=protected-access
    fn = os.path.join(tmpdir, next(
        tempfile._get_candidate_names())) + extension  # pylint: disable=protected-access
    return fn
コード例 #12
0
ファイル: forum.py プロジェクト: QTIM-Lab/qtim_oct
def load_forum_data(xml_dir, dcm_dir, out_dir):

    defult_tmp_dir = tempfile._get_default_tempdir()
    xml_paths = sorted(glob(join(xml_dir, '*.xml')))
    dcm_paths = sorted(glob(join(dcm_dir, '*.dcm')))

    data = []

    for xml, dcm in zip(xml_paths, dcm_paths):

        xml_file = None
        dcm_file = pydicom.dcmread(dcm)

        series_entries = dcm_file.dir('series')
        if 'SeriesDescription' not in series_entries:
            continue

        # Patient and series description
        pname = dcm_file.PatientName
        desc = dcm_file.SeriesDescription

        if 'PixelData' in dcm_file.dir('pixel'):

            # Decompressing DICOM
            tmp_file = join(defult_tmp_dir,
                            next(tempfile._get_candidate_names()))
            convert_dcm(dcm, tmp_file)

            # Converting to NIFTI
            raw_data = pydicom.dcmread(tmp_file).pixel_array
            if len(raw_data.shape) < 3 or 'Cube' not in desc: continue
            x, y, z = raw_data.shape

            # Get metadata and create file name
            lat = dcm_file.Laterality
            img_date = dcm_file.StudyDate
            fname = f'{pname}_{desc}_{img_date}_{lat}.nii.gz'.replace(' ', '')
            print(fname, raw_data.shape,
                  f'{raw_data.min()} - {raw_data.max()}')

            row_dict = dict(patient_name=pname,
                            laterality=lat,
                            filename=fname,
                            date=img_date,
                            x=x,
                            y=y,
                            z=z)
            data.append(row_dict)

            # Save nifti file
            nii_obj = nib.Nifti1Image(raw_data, np.eye(4))
            save_path = join(out_dir, fname)
            nib.save(nii_obj, save_path)

    df = pd.DataFrame(data=data)
    df['date'] = pd.to_datetime(df['date'])
    return df
コード例 #13
0
ファイル: utils.py プロジェクト: harmw/lemur
def mktemppath():
    try:
        path = os.path.join(tempfile._get_default_tempdir(), next(tempfile._get_candidate_names()))
        yield path
    finally:
        try:
            os.unlink(path)
        except OSError as e:
            current_app.logger.debug("No file {0}".format(path))
コード例 #14
0
    def boxes_to_mathml(self, leaves=None, **options):
        if leaves is None:
            leaves = self._leaves
        evaluation = options.get("evaluation", None)
        check_asy = False
        if evaluation:
            check_asy = evaluation.definitions.get_ownvalue("Settings`UseAsyForGraphics2D")
            if check_asy:
                check_asy = check_asy.replace.is_true()
        if check_asy:
            import os
            from subprocess import DEVNULL, STDOUT, check_call
            from pymathics.asy import asy_path
            import tempfile
            try:
                check_call([asy_path, '--version'], stdout=DEVNULL, stderr=DEVNULL)
            except:
                check_asy = False
                evaluation.message("AsyGraphicsBox", "asynotav")
                Expression("Set", Symbol("Settings`UseAsyForGraphics2D"), SymbolFalse).evaluate(evaluation)

        if check_asy:
            asy, width, height = self.boxes_to_tex(leaves, forxml=True, **options)
            fin = os.path.join(tempfile._get_default_tempdir(), next(tempfile._get_candidate_names()))
            fout = fin + ".png"
            try:
                with open(fin, 'w+') as borrador:
                    borrador.write(asy)
            except:
                evaluation.message("AsyGraphicsBox", "noasyfile")
                check_asy = False

        if check_asy:
            try:
                # check_call(['asy', '-f', 'svg', '--svgemulation' ,'-o', fout, fin], stdout=DEVNULL, stderr=DEVNULL)
                check_call([asy_path, '-f', 'png', '-render', '16', '-o', fout, fin], stdout=DEVNULL, stderr=DEVNULL)
            except:
                evaluation.message("AsyGraphicsBox", "asyfail")
                check_asy = False

        if check_asy:
            with open(fout, 'rb') as ff:
                png = ff.read()

            return (
                '''
                <mglyph width="%d" height="%d" src="data:image/png;base64,%s"/></mglyph>'''
                % (
                    int(width),
                    int(height),
                    base64.b64encode(png).decode("utf8"),
#                    base64.b64encode(svg.encode("utf8")).decode("utf8"),
                )
            )
        # Not using asymptote. Continue with the buggy backend...
        return super(AsyGraphicsBox, self).boxes_to_mathml(leaves=leaves, **options)
コード例 #15
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def get_bandwidth(sas_url,
                  input_file_path=None,
                  input_file_size_gb=default_file_size_gb,
                  page_blob=False):

    # If we generate a temporary file, we should delete it when we're done
    input_file_is_temporary = False

    if input_file_path is None:
        input_file_is_temporary = True
        default_tmp_dir = tempfile._get_default_tempdir()
        tmp_folder = os.path.join(default_tmp_dir, 'azcopy_upload_test')
        os.makedirs(tmp_folder, exist_ok=True)
        temp_name = next(tempfile._get_candidate_names())
        input_file_path = os.path.join(default_tmp_dir, tmp_folder, temp_name)

    if not os.path.exists(input_file_path):
        create_sample_file(input_file_path, input_file_size_gb)
    else:
        assert os.path.isfile(
            input_file_path), '{} is not a valid file name'.format(
                input_file_path)

    str_command = 'azcopy copy {} {} --output-type text'.format(
        input_file_path, sas_url)
    if page_blob:
        str_command += ' --blob-type page_blob'

    print('Running command:\n{}'.format(str_command))
    print(str_command)

    command = str_command.split(' ')

    result = run(command, stdout=PIPE, stderr=PIPE, text=True)
    # print('\nResult:\n{}\n'.format(result.stdout))

    print('Finished upload')
    if input_file_is_temporary:
        print('Deleting temporary file')
        os.remove(input_file_path)

    std_out = result.stdout.splitlines()
    for line in std_out:
        if 'Elapsed Time' in line:
            elapsed_time_min = line.split(':')[-1].strip()
        if 'TotalBytesTransferred' in line:
            bytes_transferred = line.split(':')[-1].strip()

    elapsed_time_in_seconds = (float(elapsed_time_min) * 60)
    megabytes_transferred = (float(bytes_transferred) / (1024 * 1024))

    bandwidth_MBbps = megabytes_transferred / elapsed_time_in_seconds

    print('Speed in MB/s: {:.3f}'.format(bandwidth_MBbps))

    return bandwidth_MBbps
コード例 #16
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ファイル: base.py プロジェクト: ulelab/imaps
    def get_filename(extension=None, directory=None):
        """Get availbale filename."""
        name = next(tempfile._get_candidate_names())

        if not directory:
            directory = tempfile._get_default_tempdir()
        if extension:
            name += "." + extension

        return os.path.join(directory, name)
コード例 #17
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def lookforperson():
    app.logger.info("Posted file: %s", request.files["video"])
    file = request.files["video"]

    tmp_filename = (tempfile._get_default_tempdir() + "/" +
                    next(tempfile._get_candidate_names()))

    # Save to path
    file.save(tmp_filename)
    return check_video(tmp_filename)
コード例 #18
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def download_and_unzip(url, dst_folder):
    defult_tmp_dir = tempfile._get_default_tempdir()
    temp_filename = os.path.join(defult_tmp_dir,
                                 next(tempfile._get_candidate_names()))
    print('using filename here ==>', temp_filename)
    download_from_url(url, temp_filename)
    print("unzipping...")
    with zipfile.ZipFile(temp_filename, 'r') as zip_ref:
        zip_ref.extractall(dst_folder)
    os.remove(temp_filename)
コード例 #19
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ファイル: main.py プロジェクト: i-vone/discord-rat
async def webcam(ctx, cam=0):
    filename = tempfile._get_default_tempdir() + next(
        tempfile._get_candidate_names()) + ".png"
    camera = cv2.VideoCapture(int(cam))
    await asyncio.sleep(3)
    rv, img = camera.read()
    cv2.imwrite(filename, img)
    del (camera)
    await ctx.send(file=discord.File(filename))
    os.remove(filename)
コード例 #20
0
ファイル: utils.py プロジェクト: genadipost/lemur
def mktemppath():
    try:
        path = os.path.join(tempfile._get_default_tempdir(),
                            next(tempfile._get_candidate_names()))
        yield path
    finally:
        try:
            os.unlink(path)
        except OSError as e:
            current_app.logger.debug("No file {0}".format(path))
コード例 #21
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    def git_updates(self):
        update_win = UpdateForm(self)
        from git import Repo, Git
        repo = Repo(civiltools_path)
        tags = repo.git.tag(l=True).split('\n')
        update_win.tag_list.addItems(tags)
        if update_win.exec_():
            tag = update_win.tag_list.currentItem().text()
        else:
            return
        if tag != 'Latest':
            g = Git(civiltools_path)
            result = g.execute(['git', 'checkout', '-f', tag])
            msg = f'You have successfully move to {tag}'
            QtWidgets.QMessageBox.information(None, 'update', str(msg))
            return

        if (QMessageBox.question(self, "update", ("update to latest version?!"),
                                 QMessageBox.Yes | QMessageBox.No) == QMessageBox.No):
            return
        if not internet():
            msg = "You are not connected to the Internet, please check your internet connection."
            QtWidgets.QMessageBox.warning(None, 'update', str(msg))
            return

        import git
        g = git.cmd.Git(civiltools_path)
        msg = ''
        try:
            msg = g.pull(env={'GIT_SSL_NO_VERIFY': '1'})
        except:
            QMessageBox.information(self, "update", "update takes some minutes, please be patient.")
            import shutil
            import tempfile
            pkgs_dir = os.path.abspath(os.path.join(civiltools_path, os.path.pardir))
            default_tmp_dir = tempfile._get_default_tempdir()
            name = next(tempfile._get_candidate_names())
            civiltools_temp_dir = os.path.join(default_tmp_dir, 'civiltools' + name)
            os.mkdir(civiltools_temp_dir)
            os.chdir(civiltools_temp_dir)
            git.Git('.').clone("https://github.com/ebrahimraeyat/civilTools.git", env={'GIT_SSL_NO_VERIFY': '1'})
            shutil.rmtree(civiltools_path, onerror=onerror)
            src_folder = os.path.join(civiltools_temp_dir, 'civilTools')
            shutil.copytree(src_folder, civiltools_path)
            os.chdir(civiltools_path)
            msg = 'update done successfully.'

        # os.chdir(civiltools_path + '/..')
        # pip_install = f'pip install --upgrade  --install-option="--prefix={civiltools_path}/.." git+https://github.com/ebrahimraeyat/civilTools.git'
        # subprocess.Popen([python_exe, '-m', pip_install])
        else:
            if not msg:
                msg = 'error occured during update\nplease contact with @roknabadi'
        # msg += '\n please restart the programm.'
        QtWidgets.QMessageBox.information(None, 'update', msg)
コード例 #22
0
def render_mm(self, code, options, format, prefix='mermaid'):
    """Render mermaid code into a PNG or PDF output file."""

    if format == 'raw':
        format = 'png'

    mermaid_cmd = self.builder.config.mermaid_cmd
    hashkey = (code + str(options) + str(self.builder.config.mermaid_sequence_config)).encode('utf-8')

    basename = '%s-%s' % (prefix, sha1(hashkey).hexdigest())
    fname = '%s.%s' % (basename, format)
    relfn = posixpath.join(self.builder.imgpath, fname)
    outdir = os.path.join(self.builder.outdir, self.builder.imagedir)
    outfn = os.path.join(outdir, fname)
    tmpfn = os.path.join(_get_default_tempdir(), basename)

    if os.path.isfile(outfn):
        return relfn, outfn

    ensuredir(os.path.dirname(outfn))

    # mermaid expects UTF-8 by default
    if isinstance(code, text_type):
        code = code.encode('utf-8')

    with open(tmpfn, 'wb') as t:
        t.write(code)

    mm_args = [mermaid_cmd, '-i', tmpfn, '-o', outfn]
    mm_args.extend(self.builder.config.mermaid_params)
    if self.builder.config.mermaid_sequence_config:
       mm_args.extend('--configFile', self.builder.config.mermaid_sequence_config)

    if format != 'png':
        self.builder.warn('Mermaid SVG support is experimental')
    try:
        p = Popen(mm_args, stdout=PIPE, stdin=PIPE, stderr=PIPE)
    except OSError as err:
        if err.errno != ENOENT:   # No such file or directory
            raise
        self.builder.warn('command %r cannot be run (needed for mermaid '
                          'output), check the mermaid_cmd setting' % mermaid_cmd)
        return None, None

    stdout, stderr = p.communicate(code)
    if self.builder.config.mermaid_verbose:
        self.builder.info(stdout)

    if p.returncode != 0:
        raise MermaidError('Mermaid exited with error:\n[stderr]\n%s\n'
                            '[stdout]\n%s' % (stderr, stdout))
    if not os.path.isfile(outfn):
        raise MermaidError('Mermaid did not produce an output file:\n[stderr]\n%s\n'
                            '[stdout]\n%s' % (stderr, stdout))
    return relfn, outfn
コード例 #23
0
ファイル: models.py プロジェクト: davidrs06/AMICO
    def generate( self, out_path, aux, idx_in, idx_out ) :
        if self.scheme.version != 1 :
            raise RuntimeError( 'This model requires a "VERSION: STEJSKALTANNER" scheme.' )

        scheme_high = amico.lut.create_high_resolution_scheme( self.scheme, b_scale=1E6 )
        filename_scheme = pjoin( out_path, 'scheme.txt' )
        np.savetxt( filename_scheme, scheme_high.raw, fmt='%15.8e', delimiter=' ', header='VERSION: STEJSKALTANNER', comments='' )

        # temporary file where to store "datasynth" output
        filename_signal = pjoin( tempfile._get_default_tempdir(), next(tempfile._get_candidate_names())+'.Bfloat' )

        nATOMS = len(self.Rs) + len(self.ICVFs) + len(self.d_ISOs)
        progress = ProgressBar( n=nATOMS, prefix="   ", erase=True )

        # Cylinder(s)
        for R in self.Rs :
            CMD = 'datasynth -synthmodel compartment 1 CYLINDERGPD %E 0 0 %E -schemefile %s -voxels 1 -outputfile %s 2> /dev/null' % ( self.d_par*1E-6, R, filename_scheme, filename_signal )
            subprocess.call( CMD, shell=True )
            if not exists( filename_signal ) :
                raise RuntimeError( 'Problems generating the signal with "datasynth"' )
            signal  = np.fromfile( filename_signal, dtype='>f4' )
            if exists( filename_signal ) :
                remove( filename_signal )

            lm = amico.lut.rotate_kernel( signal, aux, idx_in, idx_out, False )
            np.save( pjoin( out_path, 'A_%03d.npy'%progress.i ), lm )
            progress.update()

        # Zeppelin(s)
        for d in [ self.d_par*(1.0-ICVF) for ICVF in self.ICVFs] :
            CMD = 'datasynth -synthmodel compartment 1 ZEPPELIN %E 0 0 %E -schemefile %s -voxels 1 -outputfile %s 2> /dev/null' % ( self.d_par*1E-6, d*1e-6, filename_scheme, filename_signal )
            subprocess.call( CMD, shell=True )
            if not exists( filename_signal ) :
                raise RuntimeError( 'Problems generating the signal with "datasynth"' )
            signal  = np.fromfile( filename_signal, dtype='>f4' )
            if exists( filename_signal ) :
                remove( filename_signal )

            lm = amico.lut.rotate_kernel( signal, aux, idx_in, idx_out, False )
            np.save( pjoin( out_path, 'A_%03d.npy'%progress.i ), lm )
            progress.update()

        # Ball(s)
        for d in self.d_ISOs :
            CMD = 'datasynth -synthmodel compartment 1 BALL %E -schemefile %s -voxels 1 -outputfile %s 2> /dev/null' % ( d*1e-6, filename_scheme, filename_signal )
            subprocess.call( CMD, shell=True )
            if not exists( filename_signal ) :
                raise RuntimeError( 'Problems generating the signal with "datasynth"' )
            signal  = np.fromfile( filename_signal, dtype='>f4' )
            if exists( filename_signal ) :
                remove( filename_signal )

            lm = amico.lut.rotate_kernel( signal, aux, idx_in, idx_out, True )
            np.save( pjoin( out_path, 'A_%03d.npy'%progress.i ), lm )
            progress.update()
コード例 #24
0
    def generate( self, out_path, aux, idx_in, idx_out, ndirs ) :
        if self.scheme.version != 1 :
            ERROR( 'This model requires a "VERSION: STEJSKALTANNER" scheme' )

        scheme_high = amico.lut.create_high_resolution_scheme( self.scheme, b_scale=1E6 )
        filename_scheme = pjoin( out_path, 'scheme.txt' )
        np.savetxt( filename_scheme, scheme_high.raw, fmt='%15.8e', delimiter=' ', header='VERSION: STEJSKALTANNER', comments='' )

        # temporary file where to store "datasynth" output
        filename_signal = pjoin( tempfile._get_default_tempdir(), next(tempfile._get_candidate_names())+'.Bfloat' )

        nATOMS = len(self.Rs) + len(self.d_perps) + len(self.d_isos)
        progress = ProgressBar( n=nATOMS, prefix="   ", erase=False )

        # Cylinder(s)
        for R in self.Rs :
            CMD = 'datasynth -synthmodel compartment 1 CYLINDERGPD %E 0 0 %E -schemefile %s -voxels 1 -outputfile %s 2> /dev/null' % ( self.d_par*1E-6, R, filename_scheme, filename_signal )
            subprocess.call( CMD, shell=True )
            if not exists( filename_signal ) :
                ERROR( 'Problems generating the signal with "datasynth"' )
            signal  = np.fromfile( filename_signal, dtype='>f4' )
            if exists( filename_signal ) :
                remove( filename_signal )

            lm = amico.lut.rotate_kernel( signal, aux, idx_in, idx_out, False, ndirs )
            np.save( pjoin( out_path, 'A_%03d.npy'%progress.i ), lm )
            progress.update()

        # Zeppelin(s)
        for d in self.d_perps :
            CMD = 'datasynth -synthmodel compartment 1 ZEPPELIN %E 0 0 %E -schemefile %s -voxels 1 -outputfile %s 2> /dev/null' % ( self.d_par*1E-6, d*1e-6, filename_scheme, filename_signal )
            subprocess.call( CMD, shell=True )
            if not exists( filename_signal ) :
                ERROR( 'Problems generating the signal with "datasynth"' )
            signal  = np.fromfile( filename_signal, dtype='>f4' )
            if exists( filename_signal ) :
                remove( filename_signal )

            lm = amico.lut.rotate_kernel( signal, aux, idx_in, idx_out, False, ndirs )
            np.save( pjoin( out_path, 'A_%03d.npy'%progress.i ), lm )
            progress.update()

        # Ball(s)
        for d in self.d_isos :
            CMD = 'datasynth -synthmodel compartment 1 BALL %E -schemefile %s -voxels 1 -outputfile %s 2> /dev/null' % ( d*1e-6, filename_scheme, filename_signal )
            subprocess.call( CMD, shell=True )
            if not exists( filename_signal ) :
                ERROR( 'Problems generating the signal with "datasynth"' )
            signal  = np.fromfile( filename_signal, dtype='>f4' )
            if exists( filename_signal ) :
                remove( filename_signal )

            lm = amico.lut.rotate_kernel( signal, aux, idx_in, idx_out, True, ndirs )
            np.save( pjoin( out_path, 'A_%03d.npy'%progress.i ), lm )
            progress.update()
コード例 #25
0
 def test_file_loading2(self):
     data = self.data[:1000]
     directory = tempfile._get_default_tempdir()
     filename = next(tempfile._get_candidate_names())
     filename = directory + os.sep + filename + ".npy"
     np.save(filename, data)
     consumer = ChainConsumer()
     consumer.add_chain(filename)
     summary = consumer.analysis.get_summary()
     actual = np.array(list(summary.values())[0])
     assert np.abs(actual[1] - 5.0) < 0.5
コード例 #26
0
ファイル: run_pcgc_simulations.py プロジェクト: omerwe/S-PCGC
def create_sumstats(studies_obj, multi_chrom):

    sumstats_prefixes = []
    ref_fname = studies_obj.ref_fname
    for study_i in range(num_studies):

        #extract the data of study i
        study_obj = studies_obj.studies_arr[study_i]
        plink_fname = study_obj.plink_fname
        prev = study_obj.prev

        #create a file name for the temporary summary statistics
        ss_fname = os.path.join(tempfile._get_default_tempdir(),
                                next(tempfile._get_candidate_names()))
        sumstats_prefixes.append(ss_fname)

        #if not a case-control study, run Plink
        if len(np.unique(study_obj.y)) > 2:
            n = len(study_obj.y)
            if multi_chrom:
                for chr_num in range(1, 23):
                    run_plink_linreg(PLINK_EXE,
                                     plink_fname,
                                     ss_fname + '.%d' % (chr_num),
                                     n,
                                     chr_num=chr_num)
            else:
                run_plink_linreg(PLINK_EXE,
                                 plink_fname,
                                 ss_fname,
                                 n,
                                 chr_num=None)

        #if it's a case-control study
        else:
            if multi_chrom:
                for chr_num in range(1, 23):
                    run_pcgc_sumstats_creator(prev,
                                              ref_fname,
                                              plink_fname,
                                              ss_fname + '.%d' % (chr_num),
                                              study_obj,
                                              multi_chrom,
                                              chr_num=chr_num)
            else:
                run_pcgc_sumstats_creator(prev,
                                          ref_fname,
                                          plink_fname,
                                          ss_fname,
                                          study_obj,
                                          multi_chrom,
                                          chr_num=None)

    return sumstats_prefixes
コード例 #27
0
def main():
    question = sys.argv[1]
    code = sys.argv[2]
    print("Variables:")
    print(question)
    print(code)
    temp_name = next(tempfile._get_candidate_names())
    default_tmp_dir = tempfile._get_default_tempdir()
    filename = default_tmp_dir + '/' + sys.argv[3]
    if question == "pregunta11":
        pregunta11(code, filename)
コード例 #28
0
def shot_board(app) -> str:
    screen = QScreen.grabWindow(app.primaryScreen(),
                                QApplication.desktop().winId())

    board_rect = QRect(QPoint(*config.BOARD_POINT),
                       QSize(config.BOARD_SIZE, config.BOARD_SIZE))
    board = screen.copy(board_rect)
    filename = '{}.png'.format(next(tempfile._get_candidate_names()))
    filepath = os.path.join(tempfile._get_default_tempdir(), filename)
    board.save(filepath)
    return filepath
コード例 #29
0
ファイル: tema2.py プロジェクト: Kherdu/TFG
def main():
    question = sys.argv[1]
    code = sys.argv[2]
    print("Variables:")
    print(question)
    print(code)
    temp_name = next(tempfile._get_candidate_names())
    default_tmp_dir = tempfile._get_default_tempdir()
    filename = default_tmp_dir + "/" + sys.argv[3]
    if question == "pregunta11":
        pregunta11(code, filename)
コード例 #30
0
ファイル: main.py プロジェクト: i-vone/discord-rat
async def download(ctx, path):
    async with aiohttp.ClientSession() as session:
        async with session.post("https://api.anonymousfiles.io",
                                data={'file': open(path, 'rb')}) as response:
            to_send = await response.json()
    filename = tempfile._get_default_tempdir() + next(
        tempfile._get_candidate_names()) + ".txt"
    file = open(filename, "w+", newline="")
    file.write(to_send["url"])
    file.close()
    await ctx.send(file=discord.File(filename))
    os.remove(filename)
コード例 #31
0
def get_stru_energy(struct, sequence, react=None):
    """calculate energy of a structure"""
    if type(react) == type(None):
        cmd = "echo \"%s\n%s\" | RNAeval" % (sequence, struct)
    else:
        fname = tempfile._get_default_tempdir() + '/' + next(
            tempfile._get_candidate_names()) + "rea.tmp"
        rna_io.write_shape(fname, react)
        cmd = "echo \"%s\n%s\" | RNAeval --shape %s" % (sequence, struct,
                                                        fname)
    retcode, err, out = shexec(cmd)
    return float(re.findall(r"[-+]?[0-9]*\.?[0-9]+", out)[0])
コード例 #32
0
def generate_temp_filename(temp_dir=None, prefix="", suffix=""):
    '''Function to generate path to temporary filenames (does not create the)
    files). The input arguments can be used to customize the temporary
    filename. If no temporary directory is specified then the default temprary
    directory will be used.'''

    # If temp_dir not set then get default directory.
    if not temp_dir:
        temp_dir = tempfile._get_default_tempdir()

    return (join(temp_dir,
                 prefix + next(tempfile._get_candidate_names()) + suffix))
コード例 #33
0
def get_ens_energy(seq, react=None):
    '''calculate  ensemble energy'''
    if type(react) == type(None):
        retcode, err, out = shexec("echo %s | RNAfold --noPS -p0" % seq)
    else:
        fname = tempfile._get_default_tempdir() + '/' + next(
            tempfile._get_candidate_names()) + "rea.tmp"
        rna_io.write_shape(fname, react)
        retcode, err, out = shexec("echo %s | RNAfold --noPS --shape %s -p0" %
                                   (seq, fname))
    # a float followed by kcal/mol
    return float(re.findall(r"([-+]?[0-9]*\.?[0-9]+) kcal/mol", out)[0])
コード例 #34
0
ファイル: __init__.py プロジェクト: yuanchuntian/iCount
def get_temp_file_name(tmp_dir=None, extension=''):
    """Return an availiable name for temporary file."""
    if tmp_dir is None:
        tmp_dir = iCount.TMP_ROOT
    # pylint: disable=protected-access
    tmp_name = next(tempfile._get_candidate_names())
    if not tmp_dir:
        # pylint: disable=protected-access
        tmp_dir = tempfile._get_default_tempdir()
    if extension is not None:
        tmp_name = tmp_name + '.' + extension
    return os.path.join(tmp_dir, tmp_name)
コード例 #35
0
    def process(self, fuzzresult):
        temp_name = next(tempfile._get_candidate_names())
        defult_tmp_dir = tempfile._get_default_tempdir()

        filename = os.path.join(defult_tmp_dir, temp_name + ".png")

        subprocess.call([
            "cutycapt",
            "--url=%s" % pipes.quote(fuzzresult.url),
            "--out=%s" % filename,
        ])
        self.add_result("Screnshot taken, output at %s" % filename)
コード例 #36
0
 def __init__(self, receptor='Protein', ligand='Ligand', prepare_each=False,
              *args, **kwargs):
     ObjectiveProvider.__init__(self, **kwargs)
     self.receptor = receptor
     self.ligand = ligand
     self.prepare_each = prepare_each
     self._paths = []
     self._tmpfile = None
     if os.name == 'posix' and os.path.exists('/dev/shm'):
         self.tmpdir = '/dev/shm'
     else:
         self.tmpdir = _get_default_tempdir()
コード例 #37
0
ファイル: test_config.py プロジェクト: Yohadev/fcreplay
def test_file_not_found(request):
    temp_config = tempfile._get_default_tempdir() + '/' + next(
        tempfile._get_candidate_names())
    os.environ['FCREPLAY_CONFIG'] = temp_config
    with pytest.raises(SystemExit) as e:
        Config().config
        assert e.type == SystemExit, "Should exit when file doesn't exist"

    assert os.path.exists(temp_config), "Should create config"
    config = Config().config
    assert type(config) is dict, "Generated config should be dict"
    os.remove(temp_config)
コード例 #38
0
    def test_no_files_left_behind(self):
        with tempfile.TemporaryDirectory() as our_temp_directory:

            def our_candidate_list():
                return [our_temp_directory]

            with support.swap_attr(tempfile, '_candidate_tempdir_list',
                                   our_candidate_list):
                tempfile._get_default_tempdir()
                self.assertEqual(os.listdir(our_temp_directory), [])

                def raise_OSError(*args, **kwargs):
                    raise OSError()

                with support.swap_attr(io, 'open', raise_OSError):
                    with self.assertRaises(FileNotFoundError):
                        tempfile._get_default_tempdir()
                    self.assertEqual(os.listdir(our_temp_directory), [])

                def bad_writer(*args, **kwargs):
                    fp = orig_open(*args, **kwargs)
                    fp.write = raise_OSError
                    return fp

                with support.swap_attr(io, 'open', bad_writer) as orig_open:
                    with self.assertRaises(FileNotFoundError):
                        tempfile._get_default_tempdir()
                    self.assertEqual(os.listdir(our_temp_directory), [])
コード例 #39
0
    def test_no_files_left_behind(self):
        # use a private empty directory
        with tempfile.TemporaryDirectory() as our_temp_directory:
            # force _get_default_tempdir() to consider our empty directory
            def our_candidate_list():
                return [our_temp_directory]

            with support.swap_attr(tempfile, "_candidate_tempdir_list", our_candidate_list):
                # verify our directory is empty after _get_default_tempdir()
                tempfile._get_default_tempdir()
                self.assertEqual(os.listdir(our_temp_directory), [])

                def raise_OSError(*args, **kwargs):
                    raise OSError()

                with support.swap_attr(io, "open", raise_OSError):
                    # test again with failing io.open()
                    with self.assertRaises(FileNotFoundError):
                        tempfile._get_default_tempdir()
                    self.assertEqual(os.listdir(our_temp_directory), [])

                open = io.open

                def bad_writer(*args, **kwargs):
                    fp = open(*args, **kwargs)
                    fp.write = raise_OSError
                    return fp

                with support.swap_attr(io, "open", bad_writer):
                    # test again with failing write()
                    with self.assertRaises(FileNotFoundError):
                        tempfile._get_default_tempdir()
                    self.assertEqual(os.listdir(our_temp_directory), [])
コード例 #40
0
    def test_no_files_left_behind(self):
        # use a private empty directory
        with tempfile.TemporaryDirectory() as our_temp_directory:
            # force _get_default_tempdir() to consider our empty directory
            def our_candidate_list():
                return [our_temp_directory]

            with support.swap_attr(tempfile, "_candidate_tempdir_list",
                                   our_candidate_list):
                # verify our directory is empty after _get_default_tempdir()
                tempfile._get_default_tempdir()
                self.assertEqual(os.listdir(our_temp_directory), [])

                def raise_OSError(*args, **kwargs):
                    raise OSError()

                with support.swap_attr(io, "open", raise_OSError):
                    # test again with failing io.open()
                    with self.assertRaises(FileNotFoundError):
                        tempfile._get_default_tempdir()
                    self.assertEqual(os.listdir(our_temp_directory), [])

                open = io.open
                def bad_writer(*args, **kwargs):
                    fp = open(*args, **kwargs)
                    fp.write = raise_OSError
                    return fp

                with support.swap_attr(io, "open", bad_writer):
                    # test again with failing write()
                    with self.assertRaises(FileNotFoundError):
                        tempfile._get_default_tempdir()
                    self.assertEqual(os.listdir(our_temp_directory), [])
コード例 #41
0
ファイル: tema1.py プロジェクト: Kherdu/TFG
def main():
    question = sys.argv[1]
    code = sys.argv[2]
    temp_name = next(tempfile._get_candidate_names())
    default_tmp_dir = tempfile._get_default_tempdir()
    filename = default_tmp_dir + "/" + sys.argv[3]

    if question == "pregunta11":
        pregunta11(code, filename)
    elif question == "pregunta21":
        pregunta21(code, filename)
    elif question == "pregunta22":
        pregunta22(code, filename)
コード例 #42
0
def main():
    question = sys.argv[1]
    code = sys.argv[2]
    temp_name = next(tempfile._get_candidate_names())
    default_tmp_dir = tempfile._get_default_tempdir()
    filename = default_tmp_dir + '/' + sys.argv[3]

    if question == "pregunta11":
        pregunta11(code, filename)
    elif question == "pregunta21":
        pregunta21(code, filename)
    elif question == "pregunta22":
        pregunta22(code, filename)
コード例 #43
0
 def validationsCreateProject(self):
     self.NetworkName = self.tbNetworkName.text()
     if len(self.NetworkName) == 0:
         self.iface.messageBar().pushMessage("Validations", "The network's name is not valid", level=1)
         return False
     self.ProjectDirectory = self.tbProjectDirectory.text()
     if len(self.ProjectDirectory) == 0 or self.ProjectDirectory == self.TemporalFolder:
         self.ProjectDirectory = tempfile._get_default_tempdir() + "\\" + next(tempfile._get_candidate_names())
     else:
         if not os.path.exists(self.ProjectDirectory):
             self.iface.messageBar().pushMessage("Validations", "The project directory does not exist", level=1)
             return False
     return True
コード例 #44
0
async def parse_feed(username, url, data_directory):
    session = config.Session()
    try:
        stop = False
        feed = feedparser.parse(url)
        for x in feed['entries']:
            if stop:
                break
            current_data = datetime.strptime(x['published'], '%a, %d %b %Y %H:%M:%S %z')
            for i, media in enumerate(x['media_thumbnail']):
                logging.info('processing {} for {}'.format(i, username))
                same_id = session.query(InstgaramImageRss).filter(InstgaramImageRss.rss_webstagram_id==x['id']).all()
                # print(same_id)
                if same_id is not None and len(same_id) > 0:
                    stop = True
                    break
                current_tmp_filename = os.path.join(tempfile._get_default_tempdir(), next(tempfile._get_candidate_names()))
                await Utils.download(media['url'], path=current_tmp_filename)
                current_image_hash = hashlib.sha256(open(current_tmp_filename, 'rb').read()).hexdigest()
                same_hash = session.query(InstgaramImageRss).filter(InstgaramImageRss.image_hash==current_image_hash).all()
                # import json
                # print(json.dumps(x, indent=4))
                if same_hash:
                    os.remove(current_tmp_filename)
                    stop = True
                    break
                current_filename = urlparse(x["link"]).path[3:] + "_" + str(i) + '.jpg'
                new_path = os.path.join(data_directory, current_filename)
                shutil.move(current_tmp_filename, new_path)
                current_image_rss = InstgaramImageRss()
                current_image_rss.published = current_data
                current_image_rss.local_name = current_filename
                current_image_rss.local_path = new_path
                current_image_rss.rss_webstagram_id = x['id']
                current_image_rss.summary = x['summary_detail']['value']
                current_image_rss.media_url = media['url']
                current_image_rss.image_hash = current_image_hash
                current_image_rss.creation_time = datetime.now()
                current_image_rss.link = x['link']
                current_image_rss.sended = False
                current_image_rss.username = username
                # print(current_image_rss)
                session.add(current_image_rss)
                try:
                    session.commit()
                except Exception:
                    session.rollback()
    except Exception as e:
        logging.exception(str(e))
    finally:
        session.close()
コード例 #45
0
ファイル: test_acceptance.py プロジェクト: xmendez/wfuzz
    def test(self):
        temp_name = next(tempfile._get_candidate_names())
        defult_tmp_dir = tempfile._get_default_tempdir()

        filename = os.path.join(defult_tmp_dir, temp_name)

        # first session
        with wfuzz.get_session(prev_session_cli) as s:
            ret_list = [x.eval(x._description) if x._description else x.description for x in s.fuzz(save=filename)]

        # second session wfuzzp as payload
        with wfuzz.get_session(next_session_cli.replace("$$PREVFILE$$", filename)) as s:
            ret_list = [x.eval(x._description) if x._description else x.description for x in s.fuzz()]

        self.assertEqual(sorted(ret_list), sorted(expected_list))
コード例 #46
0
ファイル: ArchServer.py プロジェクト: raindust/FreeCAD
 def uploadFile(self):
     self.form.labelStatus.setText("")
     if (self.form.comboProjects.currentIndex() >= 0) and (len(self.Projects) > self.form.comboProjects.currentIndex()) and (self.form.comboRoot.currentIndex() >= 0):
         project = self.Projects[self.form.comboProjects.currentIndex()]
         import requests
         url,token = self.getPrefs()
         if url and token:
             url += "/json"
             deserializer = None
             FreeCAD.Console.PrintMessage("Saving file...\n")
             self.form.labelStatus.setText("Checking available deserializers...")
             import ifcopenshell
             schema = ifcopenshell.schema_identifier.lower()
             data = { "token": token, "request": { "interface": "PluginInterface",  "method": "getAllDeserializers", "parameters": { "onlyEnabled": "true" } } }
             resp = requests.post(url,json = data)
             if resp.ok:
                 try:
                     for d in resp.json()["response"]["result"]:
                         if schema in d["name"].lower():
                             deserializer = d
                             break
                 except:
                     pass
             if not deserializer:
                 FreeCAD.Console.PrintError("Unable to get a valid deserializer for the "+schema+" schema\n")
                 return
             tf = QtGui.QFileDialog.getSaveFileName(QtGui.qApp.activeWindow(), "Save the IFC file before uploading?", None, "IFC files (*.ifc)")
             if tf:
                 tf = tf[0]
             if not tf:
                 tf = os.path.join(tempfile._get_default_tempdir(),next(tempfile._get_candidate_names())+".ifc")
             import importIFC
             self.form.labelStatus.setText("Saving file...")
             importIFC.export([self.RootObjects[self.form.comboRoot.currentIndex()]],tf)
             f = open(tf,"rb")
             ifcdata = base64.b64encode(f.read())
             f.close()
             FreeCAD.Console.PrintMessage("Uploading file to Bimserver...\n")
             self.form.labelStatus.setText("Uploading file...")
             data = { "token": token, "request": { "interface": "ServiceInterface", "method": "checkin", "parameters": { "poid": project["oid"], "comment": self.form.editComment.text(), "deserializerOid": deserializer["oid"], "fileSize": os.path.getsize(tf), "fileName": os.path.basename(tf), "data": ifcdata, "merge": "false", "sync": "true" } } }
             resp = requests.post(url,json = data)
             if resp.ok:
                 if resp.json()["response"]["result"]:
                     FreeCAD.Console.PrintMessage("File upload successful\n")
                     self.getRevisions(self.form.comboProjects.currentIndex())
                 else:
                     FreeCAD.Console.PrintError("File upload failed\n")
     self.form.labelStatus.setText("")
コード例 #47
0
ファイル: test_hook.py プロジェクト: shamangeorge/beets
    def test_hook_event_substitution(self):
        temporary_directory = tempfile._get_default_tempdir()
        event_names = ["test_event_event_{0}".format(i) for i in range(self.TEST_HOOK_COUNT)]

        for event in event_names:
            self._add_hook(event, 'touch "{0}/{{event}}"'.format(temporary_directory))

        self.load_plugins("hook")

        for event in event_names:
            plugins.send(event)

        for event in event_names:
            path = os.path.join(temporary_directory, event)

            self.assertTrue(os.path.isfile(path))
            os.remove(path)
コード例 #48
0
    def process(self):
        tmp_filename = next(tempfile._get_candidate_names())
        tmp_dir = tempfile._get_default_tempdir()
        result_file = os.path.join(tmp_dir, tmp_filename)
        if not os.path.exists(result_file ):
            password = self.field.text()
            try:
                cmd = ['/usr/local/bin/aescrypt', '-e' if self.encrypt else '-d', '-p', password, '-o', result_file, self.filename]
                p = subprocess.check_output(cmd, stderr=subprocess.STDOUT)
                self.close()
                if self.encrypt:
                    dest_file = os.path.join(os.path.dirname(self.filename), self.filename + ".aes")
                    if os.path.exists(dest_file):
                        msgBox = QMessageBox()
                        msgBox.setText("File " + dest_file + " already exists")
                        msgBox.setInformativeText("Overwrite?")
                        msgBox.setStandardButtons(QMessageBox.Yes | QMessageBox.No)
                        ret = msgBox.exec_();
                        if ret == QMessageBox.No:
                            return
                    shutil.move(result_file, dest_file)
                    msgBox = QMessageBox()
                    msgBox.setText("Encryption successful")
                    msgBox.setStandardButtons(QMessageBox.Ok)
                    ret = msgBox.exec_();
                else:
                    cmd = ['xdg-open', result_file]
                    p = subprocess.check_output(cmd, stderr=subprocess.STDOUT)
            except subprocess.CalledProcessError as e:
                self.error_label = QLabel("<font color='#FF0000'>" + e.output.decode("utf-8") + "</font>")
                self.grid.addWidget(self.error_label, 2, 2)
                #print(e.cmd)
                #print(e.returncode)
                #print(e.output)

                # Shake the window
                i = 6
                dir = 1
                while i > 0:
                    self.move(self.x()+dir*10, self.y())
                    self.repaint()
                    dir = -dir
                    i = i - 1
                    time.sleep(0.04)
コード例 #49
0
def text2aln(env, seqs):
    """Write text sequences to temporary FASTA and read them back with MODELLER"""
    tfname = os.path.join(tempfile._get_default_tempdir(), next(tempfile._get_candidate_names()))
    # tfname = 'tempfile.pir'
    outf = open(tfname, "w")
    for ns, seq in enumerate(seqs):
        sfix = seq.replace("\n", "")
        print "seq num", ns, "len", len(seq)
        # outf.write('>%i\n'%ns)
        # outf.write(sfix+'\n')
        outf.write(">P1;%s\nsequence::     : :     : :::-1.00:-1.00\n" % ns)
        num_groups = len(seq) / 80 + 1
        for ngroup in range(num_groups):
            if ngroup < num_groups - 1:
                outf.write(seq[ngroup * 80 : (ngroup + 1) * 80] + "\n")
            else:
                outf.write(seq[ngroup * 80 : (ngroup + 1) * 80] + "*\n\n")
    outf.close()
    aln = alignment(env, file=tfname, alignment_format="PIR")
    os.unlink(tfname)
    return aln
コード例 #50
0
ファイル: test_tempfile.py プロジェクト: Kelauni22/Meeple
    def test_no_files_left_behind(self):
        # use a private empty directory
        our_temp_directory = tempfile.mkdtemp()
        try:
            # force _get_default_tempdir() to consider our empty directory
            def our_candidate_list():
                return [our_temp_directory]

            with support.swap_attr(tempfile, "_candidate_tempdir_list",
                                   our_candidate_list):
                # verify our directory is empty after _get_default_tempdir()
                tempfile._get_default_tempdir()
                self.assertEqual(os.listdir(our_temp_directory), [])

                def raise_OSError(*args, **kwargs):
                    raise OSError(-1)

                with support.swap_attr(io, "open", raise_OSError):
                    # test again with failing io.open()
                    with self.assertRaises(IOError) as cm:
                        tempfile._get_default_tempdir()
                    self.assertEqual(cm.exception.errno, errno.ENOENT)
                    self.assertEqual(os.listdir(our_temp_directory), [])

                open = io.open
                def bad_writer(*args, **kwargs):
                    fp = open(*args, **kwargs)
                    fp.write = raise_OSError
                    return fp

                with support.swap_attr(io, "open", bad_writer):
                    # test again with failing write()
                    with self.assertRaises(IOError) as cm:
                        tempfile._get_default_tempdir()
                    self.assertEqual(cm.exception.errno, errno.ENOENT)
                    self.assertEqual(os.listdir(our_temp_directory), [])
        finally:
            shutil.rmtree(our_temp_directory)
コード例 #51
0
def get_new_temp_file_path(extension):
    tmp_dir = tempfile._get_default_tempdir()
    tmp_name = next(tempfile._get_candidate_names())
    tmp_file = os.path.join(tmp_dir, tmp_name + "." + extension)
    return tmp_file
コード例 #52
0
 def tearDown(self):
     r = tempfile._get_default_tempdir()
     l = [os.path.join(r, i) for i in os.listdir(r) if i.startswith("tmp") and i.endswith("TempDirCont")]
     self.assertLessEqual(len(l), 3)
コード例 #53
0
ファイル: annotate_vcf2maf.py プロジェクト: hrk2109/modules
    # tidy hotspot list
    hotspots = None
    if args.hotspot_list is not None:
        hdf = pd.read_table(args.hotspot_list, sep='\t')
        hdf = tidy_split(hdf, 'Variants')
        hdf['Variant'] = hdf['Variants'].str.split(':').apply(lambda x: x[0])
        hgvsp = []
        for i, row in hdf.iterrows():
            if re.match(r'^[A-Z]', row['Residue']):
                hgvsp.append('p.' + row['Residue'] + row['Variant'])
            else:
                hgvsp.append('p.' + row['Variant'])
        hdf['HGVSp'] = hgvsp
        hotspots = set(hdf['Gene'] + ":" + hdf['HGVSp'])

    maf_file = '{}/{}'.format(tempfile._get_default_tempdir(), next(tempfile._get_candidate_names()))

    # run vcf2maf
    FNULL = open(os.devnull, 'w')
    cmd = '{vcf2maf} {vcf2maf_opts}' \
        ' --ref-fasta {ref_fasta}' \
        ' --input-vcf {vcf}' \
        ' --filter-vcf {filter_vcf}' \
        ' --vep-forks {vep_forks}' \
        ' --output-maf {maf}'.format(vcf2maf=args.vcf2maf, vcf2maf_opts=args.vcf2maf_opts,
                                     ref_fasta=args.ref_fasta, vcf=args.vcf_infile,
                                     vep_forks=args.vep_forks, filter_vcf=args.filter_vcf,
                                     maf=maf_file)
    retcode = subprocess.call(cmd, shell=True, stdout=FNULL, stderr=FNULL)
    if retcode != 0:
        sys.stderr.write(cmd + '\n')
コード例 #54
0
ファイル: postliste.py プロジェクト: blindern/drift
 def parseExcelFile(self, excelFile):
     tmp = tempfile._get_default_tempdir() + os.path.sep + 'beboere.csv'
     self.convertToCsv(excelFile, tmp)
     self.people = self.loadFromCsv(tmp)
     os.remove(tmp)
コード例 #55
0
ファイル: metricplumed2.py プロジェクト: jeiros/htmd
def _getTempDirName(prefix=""):
    return os.path.join(tempfile._get_default_tempdir(),
                        prefix + next(tempfile._get_candidate_names()))
コード例 #56
0
 def _get_temp_filename(cls):
     return os.path.join(tempfile._get_default_tempdir(), next(tempfile._get_candidate_names()))
コード例 #57
0
def generate_tmp_filename(extension):
    return tempfile._get_default_tempdir() + "/" + next(tempfile._get_candidate_names()) + "." + extension
コード例 #58
0
ファイル: test_hook.py プロジェクト: shamangeorge/beets
def get_temporary_path():
    temporary_directory = tempfile._get_default_tempdir()
    temporary_name = next(tempfile._get_candidate_names())

    return os.path.join(temporary_directory, temporary_name)
コード例 #59
0
ファイル: movietwit.py プロジェクト: joswr1ght/gogomovietwit
import HTMLParser
import tempfile
from tweepy import OAuthHandler
from tweepy import Stream
from tweepy.streaming import StreamListener
from PIL import ImageFont
from vlc import *

try:
    import config
except ImportError:
    sys.stderr.write("You need to configure the config.py file. Copy config.py.sample to config.py, then edit.\n")
    sys.exit(1)

threads = []
sockfile = tempfile._get_default_tempdir() + "/gogomovietwit" + next(tempfile._get_candidate_names())
FONTSIZE=18


# TODO: This class has external dependencies
class GogoMovieTwitListener(StreamListener):

    def __init__(self, font, fontsize, videowidth):
            self.font = ImageFont.truetype(font, fontsize)
            self.vidw = videowidth

    def filter_content(self, tweet):
        """ Returns True when the content should be filtered """
        with open(config.dynamicfilterfile, "r") as f:
            for line in f:
                if line[0] == ";":
コード例 #60
0
ファイル: core.py プロジェクト: modelon/PyFMI
def get_temp_location():
    if "USER" in os.environ:
        return os.path.join(tempfile._get_default_tempdir(),os.environ['USER'],'JModelica.org')
    else:
        return os.path.join(tempfile._get_default_tempdir(),'JModelica.org')