Python tempfile.TemporaryFile类代码示例

    def pyc(self):
        ofile=TemporaryFile('w+t')
        if self.ua:
            dst=ANSWER_PATH+self.id+'.pyc'
        else:
            dst=BINARY_PATH+self.id+'.pyc'
        cmd=['python',dst]
        p=Popen(cmd,stdin=self.ifile,stdout=ofile,universal_newlines=True,
                preexec_fn=Tester.Limiter(self.lcpu,self.lmem),stderr=DEVNULL)
        p.wait()

        self.result=0
        if p.returncode==-9:
            self.result=-5
        elif p.returncode==-11:
            self.result=-6
        elif p.returncode==-25:
            self.result=-4
        elif p.returncode<0:
            self.result=-3
        else:
            ofile.seek(0)
            if self.output!=ofile.read(-1):
                self.result=-7
        
        pass

class PackageZipBuilder(object):

    def __init__(self, namespace, version=None):
        self.namespace = namespace
        self.version = version

    def open_zip(self):
        self.zip_file = TemporaryFile()
        self.zip= ZipFile(self.zip_file, 'w')

    def install_package(self):
        self.open_zip()
        if not self.version:
            raise ValueError('You must provide a version to install a package')

        package_xml = PACKAGE_XML % self.namespace
        #package_xml = package_xml.encode('utf-8')
        self.zip.writestr('package.xml', package_xml)

        installed_package = INSTALLED_PACKAGE % self.version
        #installed_package.encode('utf-8')
        self.zip.writestr('installedPackages/%s.installedPackage' % self.namespace, installed_package)

        return self.encode_zip()

    def uninstall_package(self):
        self.open_zip()
        self.zip.writestr('package.xml', EMPTY_PACKAGE_XML)
        self.zip.writestr('destructiveChanges.xml', PACKAGE_XML % self.namespace)
        return self.encode_zip()
        
    def encode_zip(self):
        self.zip.close()
        self.zip_file.seek(0)
        return b64encode(self.zip_file.read())

    def test_read_several(self):
        """Read several stanzas from file"""
        tmpf = TemporaryFile()
        tmpf.write("""\
version_header: 1

name: foo
val: 123

name: quoted
address:   "Willowglen"
\t  42 Wallaby Way
\t  Sydney

name: bar
val: 129319
""")
        tmpf.seek(0)
        s = read_stanza(tmpf)
        self.assertEquals(s, Stanza(version_header='1'))
        s = read_stanza(tmpf)
        self.assertEquals(s, Stanza(name="foo", val='123'))
        s = read_stanza(tmpf)
        self.assertEqualDiff(s.get('name'), 'quoted')
        self.assertEqualDiff(s.get('address'), '  "Willowglen"\n  42 Wallaby Way\n  Sydney')
        s = read_stanza(tmpf)
        self.assertEquals(s, Stanza(name="bar", val='129319'))
        s = read_stanza(tmpf)
        self.assertEquals(s, None)
        self.check_rio_file(tmpf)

def set_sff_trimpoints_with_sfftools(
        sff_dir, technical_lengths, sffinfo_path='sffinfo', sfffile_path='sfffile',
        debug=False):
    """Set trimpoints to end of technical read for all SFF files in directory.

    This function essentially provides the reference implementation.
    It uses the official sfftools from Roche to process the SFF files.
    """
    if not (exists(sffinfo_path) or which(sffinfo_path)):
        raise ApplicationNotFoundError(
            'sffinfo executable not found. Is it installed and in your $PATH?')
    if not (exists(sfffile_path) or which(sfffile_path)):
        raise ApplicationNotFoundError(
            'sfffile executable not found. Is it installed and in your $PATH?')

    for lib_id, sff_fp in get_per_lib_sff_fps(sff_dir):
        try:
            readlength = technical_lengths[lib_id]
        except KeyError:
            continue

        sffinfo_args = [sffinfo_path, '-s', sff_fp]
        if debug:
            print "Running sffinfo command %s" % sffinfo_args
        sffinfo_output_file = TemporaryFile()
        check_call(sffinfo_args, stdout=sffinfo_output_file)
        sffinfo_output_file.seek(0)

        seqlengths = {}
        for line in sffinfo_output_file:
            if line.startswith('>'):
                fields = line[1:].split()
                seq_len = fields[1].split('=')[1]
                seqlengths[fields[0]] = seq_len

        trim_fp = sff_fp + '.trim'
        trim_file = open(trim_fp, 'w')
        for id_, length in seqlengths.items():
            curr_length = int(seqlengths[id_])
            # Sfftools use 1-based index
            left_trim = readlength + 1
            # Key sequence not included in FASTA length
            right_trim = curr_length + 4
            if curr_length > left_trim:
                trim_file.write(
                    "%s\t%s\t%s\n" % (id_, left_trim, right_trim))
            else:
                stderr.write(
                    'Rejected read %s with trim points %s and %s (orig '
                    'length %s)' % (id_, left_trim, curr_length, length))
        trim_file.close()

        trimmed_sff_fp = sff_fp + '.trimmed'
        sfffile_args = [
            sfffile_path, '-t', trim_fp, '-o', trimmed_sff_fp, sff_fp]
        if debug:
            print "Running sfffile command:", sfffile_args
        check_call(sfffile_args, stdout=open(devnull, 'w'))
        remove(sff_fp)
        rename(trimmed_sff_fp, sff_fp)

def test_get_xml_iter():
    #1 file object
    #2 stream (file-like)
    #3 string
    #4 zipfile
    from openpyxl.reader.worksheet import _get_xml_iter
    from tempfile import TemporaryFile
    FUT = _get_xml_iter
    s = ""
    stream = FUT(s)
    assert isinstance(stream, BytesIO), type(stream)

    u = unicode(s)
    stream = FUT(u)
    assert isinstance(stream, BytesIO), type(stream)

    f = TemporaryFile(mode='rb+', prefix='openpyxl.', suffix='.unpack.temp')
    stream = FUT(f)
    assert isinstance(stream, tempfile), type(stream)
    f.close()

    from zipfile import ZipFile
    t = TemporaryFile()
    z = ZipFile(t, mode="w")
    z.writestr("test", "whatever")
    stream = FUT(z.open("test"))
    assert hasattr(stream, "read")
    z.close()

def sort_diskbased(stream, field, nsize=100000):
    buf = []
    files = []
    count = 0
    t = None

    def iter_on_file(f):
        try:
            while True:
                (key, v) = cPickle.load(f)
                yield (key, t._make(v))
        except EOFError:
            f.close()
    for elt in stream:
        if isinstance(elt, StreamHeader):
            t = elt.t
            yield elt
        elif isinstance(elt, StreamFooter):
            buf.sort()
            iterables = [iter_on_file(f) for f in files] + [itertools.imap(lambda obj: (getattr(obj, field), obj), buf)]
            for (k, row) in heapq.merge(*iterables):
                yield row
            yield elt
        else:
            buf.append(elt)
            count = count + 1
            if count % nsize == 0:
                buf.sort(key=lambda obj: getattr(obj, field))
                f = TemporaryFile()
                for item in buf:
                    cPickle.dump((getattr(item, field), list(item)), f, cPickle.HIGHEST_PROTOCOL)
                f.flush()
                files.append(f)
                del buf[:]

    def process_response(self, response):
        # Parse the metadata zip file from the response
        zipstr = parseString(response.content).getElementsByTagName('zipFile')
        if zipstr:
            zipstr = zipstr[0].firstChild.nodeValue
        else:
            return self.packages
        zipfp = TemporaryFile()
        zipfp.write(base64.b64decode(zipstr))
        zipfile = ZipFile(zipfp, 'r')
    
        packages = {}
    
        # Loop through all files in the zip skipping anything other than InstalledPackages
        for path in zipfile.namelist():
            if not path.endswith('.installedPackage'):
                continue
            namespace = path.split('/')[-1].split('.')[0]
            version = parseString(zipfile.open(path).read()).getElementsByTagName('versionNumber')
            if version:
                version = version[0].firstChild.nodeValue
    
            packages[namespace] = version

        self.packages = packages
        return self.packages

def main(argv):
    args = docopt(__doc__, argv=argv)

    headers = get_args_dict(args['--header'])
    if args['--size-hint']:
        headers['x-archive-size-hint'] = args['--size-hint']

    # Upload keyword arguments.
    upload_kwargs = dict(
        metadata=get_args_dict(args['--metadata']),
        headers=headers,
        debug=args['--debug'],
        queue_derive=True if args['--no-derive'] is False else False,
        ignore_preexisting_bucket=args['--ignore-bucket'],
        checksum=args['--checksum'],
        verbose=True if args['--quiet'] is False else False,
        retries=int(args['--retries']) if args['--retries'] else 0,
        retries_sleep=int(args['--sleep']),
        delete=args['--delete'],
    )

    if args['<file>'] == ['-'] and not args['-']:
        sys.stderr.write('--remote-name is required when uploading from stdin.\n')
        call(['ia', 'upload', '--help'])
        sys.exit(1)

    # Upload from stdin.
    if args['-']:
        local_file = TemporaryFile()
        local_file.write(sys.stdin.read())
        local_file.seek(0)
        _upload_files(args, args['<identifier>'], local_file, upload_kwargs)

    # Bulk upload using spreadsheet.
    elif args['--spreadsheet']:
        # Use the same session for each upload request.
        session = ArchiveSession()

        spreadsheet = csv.DictReader(open(args['--spreadsheet'], 'rU'))
        prev_identifier = None
        for row in spreadsheet:
            local_file = row['file']
            identifier = row['identifier']
            del row['file']
            del row['identifier']
            if (not identifier) and (prev_identifier):
                identifier = prev_identifier
            # TODO: Clean up how indexed metadata items are coerced
            # into metadata.
            md_args = ['{0}:{1}'.format(k.lower(), v) for (k, v) in row.items() if v]
            metadata = get_args_dict(md_args)
            upload_kwargs['metadata'].update(metadata)
            _upload_files(args, identifier, local_file, upload_kwargs, prev_identifier,
                          session)
            prev_identifier = identifier

    # Upload files.
    else:
        local_file = args['<file>']
        _upload_files(args, args['<identifier>'], local_file, upload_kwargs)

def run_cmd(options, jenkins):
    """Run the jshint command using options.

    Run the jshint command using options and return the output.

    :param options: Options received by the code_analysis_jshint funciton.
    :param jenkins: It is true when the jenkins output is turned on.

    """
    # cmd is a sequence of program arguments
    # first argument is child program
    paths = options['directory'].split('\n')
    cmd = [
        options['jshint-bin'],
        '--verbose',
        '--exclude={0}'.format(options['jshint-exclude'] or ' ')] + paths
    try:
        if jenkins:
            cmd.append('--reporter=jslint')
            output_file_name = os.path.join(options['location'], 'jshint.xml')
            output_file = open(output_file_name, 'w+')
        else:
            output_file = TemporaryFile('w+')

        # Wrapper to subprocess.Popen
        try:
            # Return code is not used for jshint.
            output = read_subprocess_output(cmd, output_file)[0]
            return output
        except OSError:
            log('skip')
            message = 'Command: {0}. Outputfile: {1}'.format(cmd, output_file)
            raise CmdError(message)
    finally:
        output_file.close()

    def read_file(self, data):
        temp_file = TemporaryFile(mode="w+b")

        if "content-length" in self.current_headers:
            temp_file.write(data.read(self.current_headers["content-length"]))
        else:
            bytes = data.readline()

            while not bytes[-2:] == "\r\n":
                temp_file.write(bytes)
                bytes = data.readline()
            
            temp_file.write(bytes.rstrip())
        
        filesize     = temp_file.tell()

        if filesize == 0:
            self.read_boundry(data)
            return

        key          = self.current_headers["content-disposition"]["name"]
        filename     = self.current_headers["content-disposition"].get("filename", "")
        content_type = self.current_headers["content-type"]
        
        if key not in self.files:
            self.files[key] = []

        temp_file.seek(0)
        self.files[key].append({"filename":filename, "filesize":filesize, "content-type":content_type, "data":temp_file})
        
        self.read_boundry(data)

    def build (self):
        data = []
        datapath = self.home.joinpath('data.xml')
        dom = minidom.parse(datapath.absolute().as_posix())
        index = 0
        for page in dom.getElementsByTagName('page'):
            page_data = self.parse_page(page)
            page_data['page.index'] = index
            data.append(page_data)
            index += 1

        data_loader = """
(function initData(w){{
w.Sectioner = new Object();
w.Sectioner.pages = {};
Object.freeze(w.Sectioner.pages);
}})(window);
        """.format(json.dumps(data, indent=2)).encode('UTF-8')

        data_js = TemporaryFile()
        data_js.write(data_loader)
        self.compiler.add_file(data_js, 'data.js')

        for asset in dom.getElementsByTagName('asset'):
            self.parse_asset(asset)

        return data

	def string_to_numpy(string):
		"""Convert human-readable string into numpy array.
		
		Note:
			loads as floats even if stored as ints. 
			
			human-readable string example:
				1 2 3
				4 5 6
			is a string for the following array:
				[[1,2,3]
				 [4,5,6]]
		
		Args:
			string (string): human-readable string to convert to numpy array

		Returns:
			numpy array

		"""
		f = TemporaryFile()
		f.write(string)
		f.seek(0)
		array = np.loadtxt(f)
		return array

    def generate_pdf_ticket(registration=None, context=None, encoding='utf-8'):
        import ho.pisa as pisa
        import cStringIO as StringIO
        from django.utils.six import BytesIO

        if not registration and not context:
            raise Http404(_("Invalid arguments"))

        if not context:
            d = ConfirmationEmailView.get_extra_context(registration)
            context = Context(d)
        template = loader.get_template('registration/ticket.html')
        html  = template.render(context)

        if not registration:
            registration = context['r']

        result = StringIO.StringIO()
        pdf = pisa.pisaDocument(StringIO.StringIO(html.encode("ISO-8859-1")), result)
        result = result.getvalue()

        try:
            file = TemporaryFile()
            file.write(result)
            registration.ticket_file = File(file)
            registration.save()
            file.close()
        except Exception, e:
            charge = registration.charge
            if charge:
                charge.save_server_message(
                    ['Failed while saving ticket file'], exception=e)

    def write_lines(self, key, lines):
        self._verify_key_format(key)
        storage = self.bucket.new_key(key + ".json.gz")

        buff = TemporaryFile()
        archive = gzip.GzipFile(fileobj=buff, mode='w')
        count = 0
        for l in lines:
            if hasattr(l, "__iter__"):
                for ll in l:
                    archive.write(ll.encode("utf8"))
                    archive.write(b"\n")
                    count += 1
            else:
                archive.write(l.encode("utf8"))
                archive.write(b"\n")
                count += 1
        archive.close()
        file_length = buff.tell()

        retry = 3
        while retry:
            try:
                with Timer("Sending {{count}} lines in {{file_length|comma}} bytes", {"file_length": file_length, "count": count}, debug=self.settings.debug):
                    buff.seek(0)
                    storage.set_contents_from_file(buff)
                break
            except Exception, e:
                Log.warning("could not push data to s3", cause=e)
                retry -= 1

 def run_reduce(self):
     self.stopped_received = 0
     self.merged_files = []
     merged_iterator = None
     while True:
         # Iterate and merge files until all jobs are processed
         get_next = self.get_next_file()
         files = get_next
         # itertools.islice(get_next, self.reduce_max_files)
         all_files = [file for file in files]
         iterables = [self.iter_on_file(file) for file in all_files]
         merged_iterator = heapq.merge(*iterables)
         if self.stopped_received < self.numprocs:
             if self.debug:
                 debug_print("Performing intermediate merge on %u  files" % len(iterables))
             f = TemporaryFile()
             self.merged_files.append(f)
             for m in merged_iterator:
                 cPickle.dump(m, f, cPickle.HIGHEST_PROTOCOL)
             f.seek(0)
             f.flush()
         else:
             break
     if len(self.merged_files) > 0:
         if self.debug:
             debug_print("Final merge")
         # Final merge if required
         merged_iterator = heapq.merge(
             *([self.iter_on_file(stream) for stream in self.merged_files] + [merged_iterator])
         )
     if self.debug:
         debug_print("Reduce loop")
     result = self.reduce_loop(merged_iterator)
     return result