Datasets:

kejian

/

codesearchnet-python-pep8-v1

like 3

def _results(self, product, path, cls=Results, **kwargs): """Returns _results for the specified API path with the specified **kwargs parameters""" if product != 'account-information' and self.rate_limit and not self.limits_set and not self.limits: self._rate_limit() uri = '/'.join(('{0}://api.domaintools.com'.format('https' if self.https else 'http'), path.lstrip('/'))) parameters = self.default_parameters.copy() parameters['api_username'] = self.username if self.https: parameters['api_key'] = self.key else: parameters['timestamp'] = datetime.utcnow().strftime('%Y-%m-%dT%H:%M:%SZ') parameters['signature'] = hmac(self.key.encode('utf8'), ''.join([self.username, parameters['timestamp'], path]).encode('utf8'), digestmod=sha1).hexdigest() parameters.update(dict((key, str(value).lower() if value in (True, False) else value) for key, value in kwargs.items() if value is not None)) return cls(self, product, uri, **parameters)

def get_file_properties( client, fileshare, prefix, timeout=None, snapshot=None): # type: (azure.storage.file.FileService, str, str, int, str) -> # azure.storage.file.models.File """Get file properties :param FileService client: blob client :param str fileshare: file share name :param str prefix: path prefix :param int timeout: timeout :param str snapshot: snapshot :rtype: azure.storage.file.models.File :return: file properties """ dirname, fname, ss = parse_file_path(prefix) if ss is not None: if snapshot is not None: raise RuntimeError( 'snapshot specified as {} but parsed {} from prefix {}'.format( snapshot, ss, prefix)) else: snapshot = ss try: return client.get_file_properties( share_name=fileshare, directory_name=dirname, file_name=fname, timeout=timeout, snapshot=snapshot, ) except azure.common.AzureMissingResourceHttpError: return None

def _get_ann_labels_data(self, order_ann, bins_ann): """Generate ColumnDataSource dictionary for annular labels. """ if self.yticks is None: return dict(x=[], y=[], text=[], angle=[]) mapping = self._compute_tick_mapping("radius", order_ann, bins_ann) values = [(label, radius[0]) for label, radius in mapping.items()] labels, radius = zip(*values) radius = np.array(radius) y_coord = np.sin(np.deg2rad(self.yrotation)) * radius + self.max_radius x_coord = np.cos(np.deg2rad(self.yrotation)) * radius + self.max_radius return dict(x=x_coord, y=y_coord, text=labels, angle=[0]*len(labels))

def is_valid_file(parser,arg): """verify the validity of the given file. Never trust the End-User""" if not os.path.exists(arg): parser.error("File %s not found"%arg) else: return arg

def _alpha_eff(self, r_eff, n_sersic, k_eff): """ deflection angle at r_eff :param r_eff: :param n_sersic: :param k_eff: :return: """ b = self.b_n(n_sersic) alpha_eff = n_sersic * r_eff * k_eff * b**(-2*n_sersic) * np.exp(b) * special.gamma(2*n_sersic) return -alpha_eff

def split_taf(txt: str) -> [str]: # type: ignore """ Splits a TAF report into each distinct time period """ lines = [] split = txt.split() last_index = 0 for i, item in enumerate(split): if starts_new_line(item) and i != 0 and not split[i - 1].startswith('PROB'): lines.append(' '.join(split[last_index:i])) last_index = i lines.append(' '.join(split[last_index:])) return lines

def intersect(self, other): """Constructs an unminimized DFA recognizing the intersection of the languages of two given DFAs. Args: other (DFA): The other DFA that will be used for the intersect operation Returns: Returns: DFA: The resulting DFA """ operation = bool.__and__ self.cross_product(other, operation) return self

def download(self, id, attid): # pylint: disable=invalid-name,redefined-builtin """Download a device's attachment. :param id: Device ID as an int. :param attid: Attachment ID as an int. :rtype: tuple `(io.BytesIO, 'filename')` """ resp = self.service.get_id(self._base(id), attid, params={'format': 'download'}, stream=True) b = io.BytesIO() stream.stream_response_to_file(resp, path=b) resp.close() b.seek(0) return (b, self.service.filename(resp))

def editProtocol(self, clusterProtocolObj): """ Updates the Cluster Protocol. This will cause the cluster to be restarted with updated protocol configuration. """ if isinstance(clusterProtocolObj, ClusterProtocol): pass else: raise AttributeError("Invalid Input, must be a ClusterProtocal Object") url = self._url + "/editProtocol" params = { "f" : "json", "tcpClusterPort" : str(clusterProtocolObj.value['tcpClusterPort']) } return self._post(url=url, param_dict=params, securityHandler=self._securityHandler, proxy_url=self._proxy_url, proxy_port=self._proxy_port)

def results_class_wise_metrics(self): """Class-wise metrics Returns ------- dict results in a dictionary format """ results = {} for scene_id, scene_label in enumerate(self.scene_label_list): if scene_label not in results: results[scene_label] = {} results[scene_label]['count'] = {} results[scene_label]['count']['Ncorr'] = self.scene_wise[scene_label]['Ncorr'] results[scene_label]['count']['Nref'] = self.scene_wise[scene_label]['Nref'] results[scene_label]['count']['Nsys'] = self.scene_wise[scene_label]['Nsys'] results[scene_label]['accuracy'] = { 'accuracy': metric.accuracy_corr( Ncorr=self.scene_wise[scene_label]['Ncorr'], N=self.scene_wise[scene_label]['Nref'] ) } return results

def get_objective_query_session(self, proxy): """Gets the ``OsidSession`` associated with the objective query service. :param proxy: a proxy :type proxy: ``osid.proxy.Proxy`` :return: an ``ObjectiveQuerySession`` :rtype: ``osid.learning.ObjectiveQuerySession`` :raise: ``NullArgument`` -- ``proxy`` is ``null`` :raise: ``OperationFailed`` -- unable to complete request :raise: ``Unimplemented`` -- ``supports_objective_query()`` is ``false`` *compliance: optional -- This method must be implemented if ``supports_objective_query()`` is ``true``.* """ if not self.supports_objective_query(): raise Unimplemented() try: from . import sessions except ImportError: raise OperationFailed() proxy = self._convert_proxy(proxy) try: session = sessions.ObjectiveQuerySession(proxy=proxy, runtime=self._runtime) except AttributeError: raise OperationFailed() return session

def get(self, reg, ty): """ Load a value from a machine register into a VEX temporary register. All values must be loaded out of registers before they can be used with operations, etc and stored back into them when the instruction is over. See Put(). :param reg: Register number as an integer, or register string name :param ty: The Type to use. :return: A VexValue of the gotten value. """ offset = self.lookup_register(self.irsb_c.irsb.arch, reg) if offset == self.irsb_c.irsb.arch.ip_offset: return self.constant(self.addr, ty) rdt = self.irsb_c.rdreg(offset, ty) return VexValue(self.irsb_c, rdt)

def random(length: int = 8, chars: str = digits + ascii_lowercase) -> Iterator[str]: """ A random string. Not unique, but has around 1 in a million chance of collision (with the default 8 character length). e.g. 'fubui5e6' Args: length: Length of the random string. chars: The characters to randomly choose from. """ while True: yield "".join([choice(chars) for _ in range(length)])

def aimport_module(self, module_name): """Import a module, and mark it reloadable Returns ------- top_module : module The imported module if it is top-level, or the top-level top_name : module Name of top_module """ self.mark_module_reloadable(module_name) import_module(module_name) top_name = module_name.split('.')[0] top_module = sys.modules[top_name] return top_module, top_name

def create_class(request): """Create new class POST parameters (JSON): name: Human readable name of class code (optional): unique code of class used for joining to class """ if request.method == 'GET': return render(request, 'classes_create.html', {}, help_text=create_class.__doc__) if request.method == 'POST': if not request.user.is_authenticated() or not hasattr(request.user, "userprofile"): return render_json(request, { 'error': _('User is not logged in.'), 'error_type': 'user_unauthorized' }, template='classes_create.html', status=401) data = json_body(request.body.decode("utf-8")) if 'code' in data and Class.objects.filter(code=data['code']).exists(): return render_json(request, { 'error': _('A class with this code already exists.'), 'error_type': 'class_with_code_exists' }, template='classes_create.html', status=400) if 'name' not in data or not data['name']: return render_json(request, {'error': _('Class name is missing.'), 'error_type': 'missing_class_name'}, template='classes_create.html', status=400) cls = Class(name=data['name'], owner=request.user.userprofile) if 'code' in data: cls.code = data['code'] cls.save() return render_json(request, cls.to_json(), template='classes_create.html', status=201) else: return HttpResponseBadRequest("method %s is not allowed".format(request.method))

def run(self, result): """Run tests in suite inside of suite fixtures. """ # proxy the result for myself log.debug("suite %s (%s) run called, tests: %s", id(self), self, self._tests) #import pdb #pdb.set_trace() if self.resultProxy: result, orig = self.resultProxy(result, self), result else: result, orig = result, result try: self.setUp() except KeyboardInterrupt: raise except: self.error_context = 'setup' result.addError(self, self._exc_info()) return try: for test in self._tests: if result.shouldStop: log.debug("stopping") break # each nose.case.Test will create its own result proxy # so the cases need the original result, to avoid proxy # chains test(orig) finally: self.has_run = True try: self.tearDown() except KeyboardInterrupt: raise except: self.error_context = 'teardown' result.addError(self, self._exc_info())

def update_email_asset(self, asset_id, name, asset_type): """ Updates a Email Asset Args: name: The name provided to the email asset asset_type: The type provided to the email asset asset_id: Returns: """ self.update_asset('EMAIL', asset_id, name, asset_type)

def parse_requests_response(response, **kwargs): """Build a ContentDisposition from a requests (PyPI) response. """ return parse_headers( response.headers.get('content-disposition'), response.url, **kwargs)

def delete_collection_namespaced_daemon_set(self, namespace, **kwargs): """ delete collection of DaemonSet This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.delete_collection_namespaced_daemon_set(namespace, async_req=True) >>> result = thread.get() :param async_req bool :param str namespace: object name and auth scope, such as for teams and projects (required) :param str pretty: If 'true', then the output is pretty printed. :param str _continue: The continue option should be set when retrieving more results from the server. Since this value is server defined, clients may only use the continue value from a previous query result with identical query parameters (except for the value of continue) and the server may reject a continue value it does not recognize. If the specified continue value is no longer valid whether due to expiration (generally five to fifteen minutes) or a configuration change on the server, the server will respond with a 410 ResourceExpired error together with a continue token. If the client needs a consistent list, it must restart their list without the continue field. Otherwise, the client may send another list request with the token received with the 410 error, the server will respond with a list starting from the next key, but from the latest snapshot, which is inconsistent from the previous list results - objects that are created, modified, or deleted after the first list request will be included in the response, as long as their keys are after the \"next key\". This field is not supported when watch is true. Clients may start a watch from the last resourceVersion value returned by the server and not miss any modifications. :param str field_selector: A selector to restrict the list of returned objects by their fields. Defaults to everything. :param str label_selector: A selector to restrict the list of returned objects by their labels. Defaults to everything. :param int limit: limit is a maximum number of responses to return for a list call. If more items exist, the server will set the `continue` field on the list metadata to a value that can be used with the same initial query to retrieve the next set of results. Setting a limit may return fewer than the requested amount of items (up to zero items) in the event all requested objects are filtered out and clients should only use the presence of the continue field to determine whether more results are available. Servers may choose not to support the limit argument and will return all of the available results. If limit is specified and the continue field is empty, clients may assume that no more results are available. This field is not supported if watch is true. The server guarantees that the objects returned when using continue will be identical to issuing a single list call without a limit - that is, no objects created, modified, or deleted after the first request is issued will be included in any subsequent continued requests. This is sometimes referred to as a consistent snapshot, and ensures that a client that is using limit to receive smaller chunks of a very large result can ensure they see all possible objects. If objects are updated during a chunked list the version of the object that was present at the time the first list result was calculated is returned. :param str resource_version: When specified with a watch call, shows changes that occur after that particular version of a resource. Defaults to changes from the beginning of history. When specified for list: - if unset, then the result is returned from remote storage based on quorum-read flag; - if it's 0, then we simply return what we currently have in cache, no guarantee; - if set to non zero, then the result is at least as fresh as given rv. :param int timeout_seconds: Timeout for the list/watch call. This limits the duration of the call, regardless of any activity or inactivity. :param bool watch: Watch for changes to the described resources and return them as a stream of add, update, and remove notifications. Specify resourceVersion. :return: V1Status If the method is called asynchronously, returns the request thread. """ kwargs['_return_http_data_only'] = True if kwargs.get('async_req'): return self.delete_collection_namespaced_daemon_set_with_http_info(namespace, **kwargs) else: (data) = self.delete_collection_namespaced_daemon_set_with_http_info(namespace, **kwargs) return data

def average_true_range_percent(close_data, period): """ Average True Range Percent. Formula: ATRP = (ATR / CLOSE) * 100 """ catch_errors.check_for_period_error(close_data, period) atrp = (atr(close_data, period) / np.array(close_data)) * 100 return atrp

def on_capacity(self, connection, command, query_kwargs, response, capacity): """ Hook that runs in response to a 'returned capacity' event """ now = time.time() args = (connection, command, query_kwargs, response, capacity) # Check total against the total_cap self._wait(args, now, self.total_cap, self._total_consumed, capacity.total) # Increment table consumed capacity & check it if capacity.tablename in self.table_caps: table_cap = self.table_caps[capacity.tablename] else: table_cap = self.default_cap consumed_history = self.get_consumed(capacity.tablename) if capacity.table_capacity is not None: self._wait(args, now, table_cap, consumed_history, capacity.table_capacity) # The local index consumed capacity also counts against the table if capacity.local_index_capacity is not None: for consumed in six.itervalues(capacity.local_index_capacity): self._wait(args, now, table_cap, consumed_history, consumed) # Increment global indexes # check global indexes against the table+index cap or default gic = capacity.global_index_capacity if gic is not None: for index_name, consumed in six.iteritems(gic): full_name = capacity.tablename + ':' + index_name if index_name in table_cap: index_cap = table_cap[index_name] elif full_name in self.table_caps: index_cap = self.table_caps[full_name] else: # If there's no specified capacity for the index, # use the cap on the table index_cap = table_cap consumed_history = self.get_consumed(full_name) self._wait(args, now, index_cap, consumed_history, consumed)

def get_structure_with_only_magnetic_atoms(self, make_primitive=True): """ Returns a Structure with only magnetic atoms present. :return: Structure """ sites = [site for site in self.structure if abs(site.properties["magmom"]) > 0] structure = Structure.from_sites(sites) if make_primitive: structure = structure.get_primitive_structure(use_site_props=True) return structure

def run(command, verbose=False): """ Run a shell command. Capture the stdout and stderr as a single stream. Capture the status code. If verbose=True, then print command and the output to the terminal as it comes in. """ def do_nothing(*args, **kwargs): return None v_print = print if verbose else do_nothing p = subprocess.Popen( command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, universal_newlines=True, ) v_print("run:", command) def log_and_yield(line): if six.PY2: # If not unicode, try to decode it first if isinstance(line, str): line = line.decode('utf8', 'replace') v_print(line) return line output = ''.join(map(log_and_yield, p.stdout)) status_code = p.wait() return CommandResult(command, output, status_code)

def main(argv=None): """script main. parses command line options in sys.argv, unless *argv* is given. """ if argv is None: argv = sys.argv # setup command line parser parser = U.OptionParser(version="%prog version: $Id$", usage=usage, description=globals()["__doc__"]) group = U.OptionGroup(parser, "dedup-specific options") group.add_option("--output-stats", dest="stats", type="string", default=False, help="Specify location to output stats") parser.add_option_group(group) # add common options (-h/--help, ...) and parse command line (options, args) = U.Start(parser, argv=argv) U.validateSamOptions(options, group=False) if options.random_seed: np.random.seed(options.random_seed) if options.stdin != sys.stdin: in_name = options.stdin.name options.stdin.close() else: raise ValueError("Input on standard in not currently supported") if options.stdout != sys.stdout: if options.no_sort_output: out_name = options.stdout.name else: out_name = U.getTempFilename(dir=options.tmpdir) sorted_out_name = options.stdout.name options.stdout.close() else: if options.no_sort_output: out_name = "-" else: out_name = U.getTempFilename(dir=options.tmpdir) sorted_out_name = "-" if not options.no_sort_output: # need to determine the output format for sort if options.out_sam: sort_format = "sam" else: sort_format = "bam" if options.in_sam: in_mode = "r" else: in_mode = "rb" if options.out_sam: out_mode = "wh" else: out_mode = "wb" if options.stats and options.ignore_umi: raise ValueError("'--output-stats' and '--ignore-umi' options" " cannot be used together") infile = pysam.Samfile(in_name, in_mode) outfile = pysam.Samfile(out_name, out_mode, template=infile) if options.paired: outfile = sam_methods.TwoPassPairWriter(infile, outfile) nInput, nOutput, input_reads, output_reads = 0, 0, 0, 0 if options.detection_method: bam_features = detect_bam_features(infile.filename) if not bam_features[options.detection_method]: if sum(bam_features.values()) == 0: raise ValueError( "There are no bam tags available to detect multimapping. " "Do not set --multimapping-detection-method") else: raise ValueError( "The chosen method of detection for multimapping (%s) " "will not work with this bam. Multimapping can be detected" " for this bam using any of the following: %s" % ( options.detection_method, ",".join( [x for x in bam_features if bam_features[x]]))) gene_tag = options.gene_tag metacontig2contig = None if options.chrom: inreads = infile.fetch(reference=options.chrom) else: if options.per_contig and options.gene_transcript_map: metacontig2contig = sam_methods.getMetaContig2contig( infile, options.gene_transcript_map) metatag = "MC" inreads = sam_methods.metafetcher(infile, metacontig2contig, metatag) gene_tag = metatag else: inreads = infile.fetch() # set up ReadCluster functor with methods specific to # specified options.method processor = network.ReadDeduplicator(options.method) bundle_iterator = sam_methods.get_bundles( options, metacontig_contig=metacontig2contig) if options.stats: # set up arrays to hold stats data stats_pre_df_dict = {"UMI": [], "counts": []} stats_post_df_dict = {"UMI": [], "counts": []} pre_cluster_stats = [] post_cluster_stats = [] pre_cluster_stats_null = [] post_cluster_stats_null = [] topology_counts = collections.Counter() node_counts = collections.Counter() read_gn = umi_methods.random_read_generator( infile.filename, chrom=options.chrom, barcode_getter=bundle_iterator.barcode_getter) for bundle, key, status in bundle_iterator(inreads): nInput += sum([bundle[umi]["count"] for umi in bundle]) while nOutput >= output_reads + 100000: output_reads += 100000 U.info("Written out %i reads" % output_reads) while nInput >= input_reads + 1000000: input_reads += 1000000 U.info("Parsed %i input reads" % input_reads) if options.stats: # generate pre-dudep stats average_distance = umi_methods.get_average_umi_distance(bundle.keys()) pre_cluster_stats.append(average_distance) cluster_size = len(bundle) random_umis = read_gn.getUmis(cluster_size) average_distance_null = umi_methods.get_average_umi_distance(random_umis) pre_cluster_stats_null.append(average_distance_null) if options.ignore_umi: for umi in bundle: nOutput += 1 outfile.write(bundle[umi]["read"]) else: # dedup using umis and write out deduped bam reads, umis, umi_counts = processor( bundle=bundle, threshold=options.threshold) for read in reads: outfile.write(read) nOutput += 1 if options.stats: # collect pre-dudupe stats stats_pre_df_dict['UMI'].extend(bundle) stats_pre_df_dict['counts'].extend( [bundle[UMI]['count'] for UMI in bundle]) # collect post-dudupe stats post_cluster_umis = [bundle_iterator.barcode_getter(x)[0] for x in reads] stats_post_df_dict['UMI'].extend(umis) stats_post_df_dict['counts'].extend(umi_counts) average_distance = umi_methods.get_average_umi_distance(post_cluster_umis) post_cluster_stats.append(average_distance) cluster_size = len(post_cluster_umis) random_umis = read_gn.getUmis(cluster_size) average_distance_null = umi_methods.get_average_umi_distance(random_umis) post_cluster_stats_null.append(average_distance_null) outfile.close() if not options.no_sort_output: # sort the output pysam.sort("-o", sorted_out_name, "-O", sort_format, out_name) os.unlink(out_name) # delete the tempfile if options.stats: # generate the stats dataframe stats_pre_df = pd.DataFrame(stats_pre_df_dict) stats_post_df = pd.DataFrame(stats_post_df_dict) # tally the counts per umi per position pre_counts = collections.Counter(stats_pre_df["counts"]) post_counts = collections.Counter(stats_post_df["counts"]) counts_index = list(set(pre_counts.keys()).union(set(post_counts.keys()))) counts_index.sort() with U.openFile(options.stats + "_per_umi_per_position.tsv", "w") as outf: outf.write("counts\tinstances_pre\tinstances_post\n") for count in counts_index: values = (count, pre_counts[count], post_counts[count]) outf.write("\t".join(map(str, values)) + "\n") # aggregate stats pre/post per UMI agg_pre_df = aggregateStatsDF(stats_pre_df) agg_post_df = aggregateStatsDF(stats_post_df) agg_df = pd.merge(agg_pre_df, agg_post_df, how='left', left_index=True, right_index=True, sort=True, suffixes=["_pre", "_post"]) # TS - if count value not observed either pre/post-dedup, # merge will leave an empty cell and the column will be cast as a float # see http://pandas.pydata.org/pandas-docs/dev/missing_data.html # --> Missing data casting rules and indexing # so, back fill with zeros and convert back to int agg_df = agg_df.fillna(0).astype(int) agg_df.index = [x.decode() for x in agg_df.index] agg_df.index.name = 'UMI' agg_df.to_csv(options.stats + "_per_umi.tsv", sep="\t") # bin distances into integer bins max_ed = int(max(map(max, [pre_cluster_stats, post_cluster_stats, pre_cluster_stats_null, post_cluster_stats_null]))) cluster_bins = range(-1, int(max_ed) + 2) def bin_clusters(cluster_list, bins=cluster_bins): ''' take list of floats and return bins''' return np.digitize(cluster_list, bins, right=True) def tallyCounts(binned_cluster, max_edit_distance): ''' tally counts per bin ''' return np.bincount(binned_cluster, minlength=max_edit_distance + 3) pre_cluster_binned = bin_clusters(pre_cluster_stats) post_cluster_binned = bin_clusters(post_cluster_stats) pre_cluster_null_binned = bin_clusters(pre_cluster_stats_null) post_cluster_null_binned = bin_clusters(post_cluster_stats_null) edit_distance_df = pd.DataFrame( {"unique": tallyCounts(pre_cluster_binned, max_ed), "unique_null": tallyCounts(pre_cluster_null_binned, max_ed), options.method: tallyCounts(post_cluster_binned, max_ed), "%s_null" % options.method: tallyCounts(post_cluster_null_binned, max_ed), "edit_distance": cluster_bins}, columns=["unique", "unique_null", options.method, "%s_null" % options.method, "edit_distance"]) # TS - set lowest bin (-1) to "Single_UMI" edit_distance_df['edit_distance'][0] = "Single_UMI" edit_distance_df.to_csv(options.stats + "_edit_distance.tsv", index=False, sep="\t") # write footer and output benchmark information. U.info( "Reads: %s" % ", ".join(["%s: %s" % (x[0], x[1]) for x in bundle_iterator.read_events.most_common()])) U.info("Number of reads out: %i" % nOutput) if not options.ignore_umi: # otherwise processor has not been used U.info("Total number of positions deduplicated: %i" % processor.UMIClusterer.positions) if processor.UMIClusterer.positions > 0: U.info("Mean number of unique UMIs per position: %.2f" % (float(processor.UMIClusterer.total_umis_per_position) / processor.UMIClusterer.positions)) U.info("Max. number of unique UMIs per position: %i" % processor.UMIClusterer.max_umis_per_position) else: U.warn("The BAM did not contain any valid " "reads/read pairs for deduplication") U.Stop()

def _get_xk(self, yk): '''Compute approximate solution from initial guess and approximate solution of the preconditioned linear system.''' if yk is not None: return self.x0 + self.linear_system.Mr * yk return self.x0

def copy_to_clipboard(self): """ Copies selected items to clipboard. """ tree = self.treeview # get the selected item: selection = tree.selection() if selection: self.filter_remove(remember=True) root = ET.Element('selection') for item in selection: node = self.tree_node_to_xml('', item) root.append(node) # python2 issue try: text = ET.tostring(root, encoding='unicode') except LookupError: text = ET.tostring(root, encoding='UTF-8') tree.clipboard_clear() tree.clipboard_append(text) self.filter_restore()

def create_307_response(self): """ Creates a 307 "Temporary Redirect" response including a HTTP Warning header with code 299 that contains the user message received during processing the request. """ request = get_current_request() msg_mb = UserMessageMember(self.message) coll = request.root['_messages'] coll.add(msg_mb) # Figure out the new location URL. qs = self.__get_new_query_string(request.query_string, self.message.slug) resubmit_url = "%s?%s" % (request.path_url, qs) headers = [('Warning', '299 %s' % self.message.text), # ('Content-Type', cnt_type), ] http_exc = HttpWarningResubmit(location=resubmit_url, detail=self.message.text, headers=headers) return request.get_response(http_exc)

def image_function(f='sin(5*x)*cos(5*y)', xmin=-1, xmax=1, ymin=-1, ymax=1, xsteps=100, ysteps=100, p='x,y', g=None, **kwargs): """ Plots a 2-d function over the specified range Parameters ---------- f='sin(5*x)*cos(5*y)' Takes two inputs and returns one value. Can also be a string function such as sin(x*y) xmin=-1, xmax=1, ymin=-1, ymax=1 Range over which to generate/plot the data xsteps=100, ysteps=100 How many points to plot on the specified range p='x,y' If using strings for functions, this is a string of parameters. g=None Optional additional globals. Try g=globals()! See spinmob.plot.image.data() for additional optional keyword arguments. """ default_kwargs = dict(clabel=str(f), xlabel='x', ylabel='y') default_kwargs.update(kwargs) # aggregate globals if not g: g = {} for k in list(globals().keys()): if k not in g: g[k] = globals()[k] if type(f) == str: f = eval('lambda ' + p + ': ' + f, g) # generate the grid x and y coordinates xones = _n.linspace(1,1,ysteps) x = _n.linspace(xmin, xmax, xsteps) xgrid = _n.outer(xones, x) yones = _n.linspace(1,1,xsteps) y = _n.linspace(ymin, ymax, ysteps) ygrid = _n.outer(y, yones) # now get the z-grid try: # try it the fast numpy way. Add 0 to assure dimensions zgrid = f(xgrid, ygrid) + xgrid*0.0 except: print("Notice: function is not rocking hardcore. Generating grid the slow way...") # manually loop over the data to generate the z-grid zgrid = [] for ny in range(0, len(y)): zgrid.append([]) for nx in range(0, len(x)): zgrid[ny].append(f(x[nx], y[ny])) zgrid = _n.array(zgrid) # now plot! image_data(zgrid.transpose(), x, y, **default_kwargs)

def scan_in_memory(node, env, path=()): """ "Scans" a Node.FS.Dir for its in-memory entries. """ try: entries = node.entries except AttributeError: # It's not a Node.FS.Dir (or doesn't look enough like one for # our purposes), which can happen if a target list containing # mixed Node types (Dirs and Files, for example) has a Dir as # the first entry. return [] entry_list = sorted(filter(do_not_scan, list(entries.keys()))) return [entries[n] for n in entry_list]

def cell_normalize(data): """ Returns the data where the expression is normalized so that the total count per cell is equal. """ if sparse.issparse(data): data = sparse.csc_matrix(data.astype(float)) # normalize in-place sparse_cell_normalize(data.data, data.indices, data.indptr, data.shape[1], data.shape[0]) return data data_norm = data.astype(float) total_umis = [] for i in range(data.shape[1]): di = data_norm[:,i] total_umis.append(di.sum()) di /= total_umis[i] med = np.median(total_umis) data_norm *= med return data_norm

def move_item(self, token, item_id, src_folder_id, dest_folder_id): """ Move an item from the source folder to the destination folder. :param token: A valid token for the user in question. :type token: string :param item_id: The id of the item to be moved :type item_id: int | long :param src_folder_id: The id of source folder where the item is located :type src_folder_id: int | long :param dest_folder_id: The id of destination folder where the item is moved to :type dest_folder_id: int | long :returns: Dictionary containing the details of the moved item :rtype: dict """ parameters = dict() parameters['token'] = token parameters['id'] = item_id parameters['srcfolderid'] = src_folder_id parameters['dstfolderid'] = dest_folder_id response = self.request('midas.item.move', parameters) return response

def find_by_id(self, team, params={}, **options): """Returns the full record for a single team. Parameters ---------- team : {Id} Globally unique identifier for the team. [params] : {Object} Parameters for the request """ path = "/teams/%s" % (team) return self.client.get(path, params, **options)

def get_watchlist_ttl(self, item: str) -> int: """ Get the amount of time a specific item will remain on the watchlist. :param str item: The item to get the TTL for on the watchlist :return: Time in seconds. Returns None for a non-existing element :rtype: int """ assert item is not None item = self._encode_item(item) return self.__get_ttl(self.__redis_conf['watchlist_template'].format(item))

def _clean_key_type(key_name, escape_char=ESCAPE_SEQ): """Removes type specifier returning detected type and a key name without type specifier. :param str key_name: A key name containing type postfix. :rtype: tuple[type|None, str] :returns: Type definition and cleaned key name. """ for i in (2, 1): if len(key_name) < i: return None, key_name type_v = key_name[-i:] if type_v in _KEY_SPLIT: if len(key_name) <= i: return _KEY_SPLIT[type_v], '' esc_cnt = 0 for pos in range(-i - 1, -len(key_name) - 1, -1): if key_name[pos] == escape_char: esc_cnt += 1 else: break if esc_cnt % 2 == 0: return _KEY_SPLIT[type_v], key_name[:-i] else: return None, key_name return None, key_name

def fill_auth_list(self, auth_provider, name, groups, auth_list=None, permissive=None): ''' Returns a list of authorisation matchers that a user is eligible for. This list is a combination of the provided personal matchers plus the matchers of any group the user is in. ''' if auth_list is None: auth_list = [] if permissive is None: permissive = self.opts.get('permissive_acl') name_matched = False for match in auth_provider: if match == '*' and not permissive: continue if match.endswith('%'): if match.rstrip('%') in groups: auth_list.extend(auth_provider[match]) else: if salt.utils.stringutils.expr_match(match, name): name_matched = True auth_list.extend(auth_provider[match]) if not permissive and not name_matched and '*' in auth_provider: auth_list.extend(auth_provider['*']) return auth_list

def randomizer_bin_und(R, alpha, seed=None): ''' This function randomizes a binary undirected network, while preserving the degree distribution. The function directly searches for rewirable edge pairs (rather than trying to rewire edge pairs at random), and hence avoids long loops and works especially well in dense matrices. Parameters ---------- A : NxN np.ndarray binary undirected connection matrix alpha : float fraction of edges to rewire seed : hashable, optional If None (default), use the np.random's global random state to generate random numbers. Otherwise, use a new np.random.RandomState instance seeded with the given value. Returns ------- R : NxN np.ndarray randomized network ''' rng = get_rng(seed) R = binarize(R, copy=True) # binarize if not np.all(R == R.T): raise BCTParamError( 'randomizer_bin_und only takes undirected matrices') ax = len(R) nr_poss_edges = (np.dot(ax, ax) - ax) / 2 # find maximum possible edges savediag = np.diag(R) np.fill_diagonal(R, np.inf) # replace diagonal with high value # if there are more edges than non-edges, invert the matrix to reduce # computation time. "invert" means swap meaning of 0 and 1, not matrix # inversion i, j = np.where(np.triu(R, 1)) k = len(i) if k > nr_poss_edges / 2: swap = True R = np.logical_not(R) np.fill_diagonal(R, np.inf) i, j = np.where(np.triu(R, 1)) k = len(i) else: swap = False # exclude fully connected nodes fullnodes = np.where((np.sum(np.triu(R, 1), axis=0) + np.sum(np.triu(R, 1), axis=1).T) == (ax - 1)) if np.size(fullnodes): R[fullnodes, :] = 0 R[:, fullnodes] = 0 np.fill_diagonal(R, np.inf) i, j = np.where(np.triu(R, 1)) k = len(i) if k == 0 or k >= (nr_poss_edges - 1): raise BCTParamError("No possible randomization") for it in range(k): if rng.random_sample() > alpha: continue # rewire alpha% of edges a = i[it] b = j[it] # it is the chosen edge from a<->b alliholes, = np.where(R[:, a] == 0) # find where each end can connect alljholes, = np.where(R[:, b] == 0) # we can only use edges with connection to neither node i_intersect = np.intersect1d(alliholes, alljholes) # find which of these nodes are connected ii, jj = np.where(R[np.ix_(i_intersect, i_intersect)]) # if there is an edge to switch if np.size(ii): # choose one randomly nummates = np.size(ii) mate = rng.randint(nummates) # randomly orient the second edge if rng.random_sample() > .5: c = i_intersect[ii[mate]] d = i_intersect[jj[mate]] else: d = i_intersect[ii[mate]] c = i_intersect[jj[mate]] # swap the edges R[a, b] = 0 R[c, d] = 0 R[b, a] = 0 R[d, c] = 0 R[a, c] = 1 R[b, d] = 1 R[c, a] = 1 R[d, b] = 1 # update the edge index (this is inefficient) for m in range(k): if i[m] == d and j[m] == c: i.setflags(write=True) j.setflags(write=True) i[it] = c j[m] = b elif i[m] == c and j[m] == d: i.setflags(write=True) j.setflags(write=True) j[it] = c i[m] = b # restore fullnodes if np.size(fullnodes): R[fullnodes, :] = 1 R[:, fullnodes] = 1 # restore inversion if swap: R = np.logical_not(R) # restore diagonal np.fill_diagonal(R, 0) R += savediag return np.array(R, dtype=int)

def single(self, trigger_id, full=False): """ Get an existing (full) trigger definition. :param trigger_id: Trigger definition id to be retrieved. :param full: Fetch the full definition, default is False. :return: Trigger of FullTrigger depending on the full parameter value. """ if full: returned_dict = self._get(self._service_url(['triggers', 'trigger', trigger_id])) return FullTrigger(returned_dict) else: returned_dict = self._get(self._service_url(['triggers', trigger_id])) return Trigger(returned_dict)

def _check_infinite_flows(self, steps, flows=None): """ Recursively loop through the flow_config and check if there are any cycles. :param steps: Set of step definitions to loop through :param flows: Flows already visited. :return: None """ if flows is None: flows = [] for step in steps.values(): if "flow" in step: flow = step["flow"] if flow == "None": continue if flow in flows: raise FlowInfiniteLoopError( "Infinite flows detected with flow {}".format(flow) ) flows.append(flow) flow_config = self.project_config.get_flow(flow) self._check_infinite_flows(flow_config.steps, flows)

def get_is_authorized(request, pid): """MNAuthorization.isAuthorized(did, action) -> Boolean.""" if 'action' not in request.GET: raise d1_common.types.exceptions.InvalidRequest( 0, 'Missing required parameter. required="action"' ) # Convert action string to action level. Raises InvalidRequest if the # action string is not valid. level = d1_gmn.app.auth.action_to_level(request.GET['action']) d1_gmn.app.auth.assert_allowed(request, level, pid) return d1_gmn.app.views.util.http_response_with_boolean_true_type()

def refresh(self, id_or_uri, timeout=-1): """ The Refresh action reclaims the top-of-rack switches in a logical switch. Args: id_or_uri: Can be either the Logical Switch ID or URI timeout: Timeout in seconds. Wait for task completion by default. The timeout does not abort the operation in OneView, just stop waiting for its completion. Returns: dict: The Logical Switch """ uri = self._client.build_uri(id_or_uri) + "/refresh" return self._client.update_with_zero_body(uri, timeout=timeout)

def _rgetattr(obj, key): """Recursive getattr for handling dots in keys.""" for k in key.split("."): obj = getattr(obj, k) return obj

def dt_from_rfc8601(date_str): """Convert 8601 (ISO) date string to datetime object. Handles "Z" and milliseconds transparently. :param date_str: Date string. :type date_str: ``string`` :return: Date time. :rtype: :class:`datetime.datetime` """ # Normalize string and adjust for milliseconds. Note that Python 2.6+ has # ".%f" format, but we're going for Python 2.5, so truncate the portion. date_str = date_str.rstrip('Z').split('.')[0] # Format string. (2010-04-13T14:02:48.000Z) fmt = "%Y-%m-%dT%H:%M:%S" # Python 2.6+: Could format and handle milliseconds. # if date_str.find('.') >= 0: # fmt += ".%f" return datetime.strptime(date_str, fmt)

def _complete_values(self, symbol = ""): """Compiles a list of possible symbols that can hold a value in place. These consist of local vars, global vars, and functions.""" result = {} #Also add the subroutines from the module and its dependencies. moddict = self._generic_filter_execs(self.context.module) self._cond_update(result, moddict, symbol) self._cond_update(result, self.context.module.interfaces, symbol) for depend in self.context.module.dependencies: if depend in self.context.module.parent.modules: #We don't want to display executables that are part of an interface, or that are embedded in #a derived type, since those will be called through the type or interface filtdict = self._generic_filter_execs(self.context.module.parent.modules[depend]) self._cond_update(result, filtdict, symbol) self._cond_update(result, self.context.module.parent.modules[depend].interfaces, symbol) #Add all the local vars if we are in an executable if (isinstance(self.context.element, Function) or isinstance(self.context.element, Subroutine)): self._cond_update(result, self.element.members, symbol) #Next add the global variables from the module if self.context.module is not None: self._cond_update(result, self.context.module.members, symbol) #Next add user defined functions to the mix for execkey in self.context.module.executables: iexec = self.context.module.executables[execkey] if isinstance(iexec, Function) and self._symbol_in(symbol, iexec.name): result[iexec.name] = iexec #Finally add the builtin functions to the mix. We need to add support #for these in a separate file so we have their call signatures. if symbol == "": #Use the abbreviated list of most common fortran builtins self._cond_update(result, cache.common_builtin, symbol) else: #we can use the full list as there will probably not be that #many left over. self._cond_update(result, cache.builtin, symbol) return result

def number_to_string(n, alphabet): """ Given an non-negative integer ``n``, convert it to a string composed of the given ``alphabet`` mapping, where the position of each element in ``alphabet`` is its radix value. Examples:: >>> number_to_string(12345678, '01') '101111000110000101001110' >>> number_to_string(12345678, 'ab') 'babbbbaaabbaaaababaabbba' >>> number_to_string(12345678, string.ascii_letters + string.digits) 'ZXP0' >>> number_to_string(12345, ['zero ', 'one ', 'two ', 'three ', 'four ', 'five ', 'six ', 'seven ', 'eight ', 'nine ']) 'one two three four five ' """ result = '' base = len(alphabet) current = int(n) if current < 0: raise ValueError("invalid n (must be non-negative): %s", n) while current: result = alphabet[current % base] + result current = current // base return result

def list_from_json(source_list_json): """ Deserialise all the items in source_list from json """ result = [] if source_list_json == [] or source_list_json == None: return result for list_item in source_list_json: item = json.loads(list_item) try: if item['class_name'] == 'Departure': temp = Departure() elif item['class_name'] == 'Disruption': temp = Disruption() elif item['class_name'] == 'Station': temp = Station() elif item['class_name'] == 'Trip': temp = Trip() elif item['class_name'] == 'TripRemark': temp = TripRemark() elif item['class_name'] == 'TripStop': temp = TripStop() elif item['class_name'] == 'TripSubpart': temp = TripSubpart() else: print('Unrecognised Class ' + item['class_name'] + ', skipping') continue temp.from_json(list_item) result.append(temp) except KeyError: print('Unrecognised item with no class_name, skipping') continue return result

def install_handler(self, app): """Install logging handler.""" # Configure python logging if app.config['LOGGING_CONSOLE_PYWARNINGS']: self.capture_pywarnings(logging.StreamHandler()) if app.config['LOGGING_CONSOLE_LEVEL'] is not None: for h in app.logger.handlers: h.setLevel(app.config['LOGGING_CONSOLE_LEVEL']) # Add request_id to log record app.logger.addFilter(add_request_id_filter)

def t(root, children=None, debug=False, root_id=None): "Create (DGParented)Tree from a root (str) and a list of (str, list) tuples." if isinstance(root, Tree): if children is None: return root return root.__class__(root, children, root_id) elif isinstance(root, basestring): root = debug_root_label(root, debug, root_id) # Beware: (DGParented)Tree is a subclass of list! if isinstance(children, Tree): child_trees = [children] elif isinstance(children, list): child_trees = [] for child in children: if isinstance(child, Tree): child_trees.append(child) elif isinstance(child, list): child_trees.extend(child) elif isinstance(child, tuple): child_trees.append(t(*child)) elif isinstance(child, basestring): child_trees.append(child) else: raise NotImplementedError elif isinstance(children, basestring): # this tree does only have one child, a leaf node # TODO: this is a workaround for the following problem: # Tree('foo', [Tree('bar', [])]) != Tree('foo', ['bar']) child_trees = [Tree(children, [])] else: # this tree only consists of one leaf node assert children is None child_trees = [] return DGParentedTree(root, child_trees, root_id) else: raise NotImplementedError

def get_cf_files(path, queue): """Get rule files in a directory and put them in a queue""" for root, _, files in os.walk(os.path.abspath(path)): if not files: continue for filename in files: fullname = os.path.join(root, filename) if os.path.isfile(fullname) and fullname.endswith('.cf') or \ fullname.endswith('.post'): queue.put(fullname)

def get_image(self): """Get the image currently being displayed. Returns ------- image : `~ginga.AstroImage.AstroImage` or `~ginga.RGBImage.RGBImage` Image object. """ if self._imgobj is not None: # quick optomization return self._imgobj.get_image() canvas_img = self.get_canvas_image() return canvas_img.get_image()

def img2img_transformer_tiny(): """Tiny params.""" hparams = img2img_transformer2d_base() hparams.num_hidden_layers = 2 hparams.hidden_size = 128 hparams.batch_size = 4 hparams.max_length = 128 hparams.attention_key_channels = hparams.attention_value_channels = 0 hparams.filter_size = 128 hparams.num_heads = 1 hparams.pos = "timing" return hparams

def rpcproxy(spec): """Decorator to enable this class to proxy RPC client calls The decorated class constructor takes two additional arguments, `context=` is required to be a :class:`~p4p.client.thread.Context`. `format`= can be a string, tuple, or dictionary and is applied to PV name strings given to :py:func:`rpcall`. Other arguments are passed to the user class constructor. :: @rpcproxy class MyProxy(object): @rpccall("%s:add") def add(lhs='d', rhs='d'): pass ctxt = Context('pva') proxy = MyProxy(context=ctxt, format="tst:") # evaluates "%s:add"%"tst:" The decorated class will be a sub-class of the provided class and :class:`RPCProxyBase`. """ # inject our ctor first so we don't have to worry about super() non-sense. def _proxyinit(self, context=None, format={}, **kws): assert context is not None, context self.context = context self.format = format spec.__init__(self, **kws) obj = {'__init__': _proxyinit} for K, V in inspect.getmembers(spec, lambda M: hasattr(M, '_call_PV')): obj[K] = _wrapMethod(K, V) return type(spec.__name__, (RPCProxyBase, spec), obj)

def resolve_weak_types(storage, debug=False): """Reslove weak type rules W1 - W3. See: http://unicode.org/reports/tr9/#Resolving_Weak_Types """ for run in storage['runs']: prev_strong = prev_type = run['sor'] start, length = run['start'], run['length'] chars = storage['chars'][start:start+length] for _ch in chars: # W1. Examine each nonspacing mark (NSM) in the level run, and # change the type of the NSM to the type of the previous character. # If the NSM is at the start of the level run, it will get the type # of sor. bidi_type = _ch['type'] if bidi_type == 'NSM': _ch['type'] = bidi_type = prev_type # W2. Search backward from each instance of a European number until # the first strong type (R, L, AL, or sor) is found. If an AL is # found, change the type of the European number to Arabic number. if bidi_type == 'EN' and prev_strong == 'AL': _ch['type'] = 'AN' # update prev_strong if needed if bidi_type in ('R', 'L', 'AL'): prev_strong = bidi_type prev_type = _ch['type'] # W3. Change all ALs to R for _ch in chars: if _ch['type'] == 'AL': _ch['type'] = 'R' # W4. A single European separator between two European numbers changes # to a European number. A single common separator between two numbers of # the same type changes to that type. for idx in range(1, len(chars) - 1): bidi_type = chars[idx]['type'] prev_type = chars[idx-1]['type'] next_type = chars[idx+1]['type'] if bidi_type == 'ES' and (prev_type == next_type == 'EN'): chars[idx]['type'] = 'EN' if bidi_type == 'CS' and prev_type == next_type and \ prev_type in ('AN', 'EN'): chars[idx]['type'] = prev_type # W5. A sequence of European terminators adjacent to European numbers # changes to all European numbers. for idx in range(len(chars)): if chars[idx]['type'] == 'EN': for et_idx in range(idx-1, -1, -1): if chars[et_idx]['type'] == 'ET': chars[et_idx]['type'] = 'EN' else: break for et_idx in range(idx+1, len(chars)): if chars[et_idx]['type'] == 'ET': chars[et_idx]['type'] = 'EN' else: break # W6. Otherwise, separators and terminators change to Other Neutral. for _ch in chars: if _ch['type'] in ('ET', 'ES', 'CS'): _ch['type'] = 'ON' # W7. Search backward from each instance of a European number until the # first strong type (R, L, or sor) is found. If an L is found, then # change the type of the European number to L. prev_strong = run['sor'] for _ch in chars: if _ch['type'] == 'EN' and prev_strong == 'L': _ch['type'] = 'L' if _ch['type'] in ('L', 'R'): prev_strong = _ch['type'] if debug: debug_storage(storage, runs=True)

def verify_upload(self): """ Confirm that the last upload was sucessful. Raises TusUploadFailed exception if the upload was not sucessful. """ if self.request.status_code == 204: return True else: raise TusUploadFailed('', self.request.status_code, self.request.response_content)

def copy_artifact(src_path: str, artifact_hash: str, conf: Config): """Copy the artifact at `src_path` with hash `artifact_hash` to artifacts cache dir. If an artifact already exists at that location, it is assumed to be identical (since it's based on hash), and the copy is skipped. TODO: pruning policy to limit cache size. """ cache_dir = conf.get_artifacts_cache_dir() if not isdir(cache_dir): makedirs(cache_dir) cached_artifact_path = join(cache_dir, artifact_hash) if isfile(cached_artifact_path) or isdir(cached_artifact_path): logger.debug('Skipping copy of existing cached artifact {} -> {}', src_path, cached_artifact_path) return abs_src_path = join(conf.project_root, src_path) logger.debug('Caching artifact {} under {}', abs_src_path, cached_artifact_path) shutil.copy(abs_src_path, cached_artifact_path)

def set_user_agent_component(self, key, value, sanitize=True): """Add or replace new user-agent component strings. Given strings are formatted along the format agreed upon by Mollie and implementers: - key and values are separated by a forward slash ("/"). - multiple key/values are separated by a space. - keys are camel-cased, and cannot contain spaces. - values cannot contain spaces. Note: When you set sanitize=false yuu need to make sure the formatting is correct yourself. """ if sanitize: key = ''.join(_x.capitalize() for _x in re.findall(r'\S+', key)) if re.search(r'\s+', value): value = '_'.join(re.findall(r'\S+', value)) self.user_agent_components[key] = value

def split_url(url): """ Split the given URL ``base#anchor`` into ``(base, anchor)``, or ``(base, None)`` if no anchor is present. In case there are two or more ``#`` characters, return only the first two tokens: ``a#b#c => (a, b)``. :param string url: the url :rtype: list of str """ if url is None: return (None, None) array = url.split("#") if len(array) == 1: array.append(None) return tuple(array[0:2])

def get_logging_level(debug): """Returns logging level based on boolean""" level = logging.INFO if debug: level = logging.DEBUG return level

def done(self, result, noraise=False): """This method is called when a task has finished executing. Subclass can override this method if desired, but should call superclass method at the end. """ # [??] Should this be in a critical section? # Has done() already been called on this task? if self.ev_done.is_set(): # ?? if isinstance(self.result, Exception) and (not noraise): raise self.result return self.result # calculate running time and other finalization self.endtime = time.time() try: self.totaltime = self.endtime - self.starttime except AttributeError: # task was not initialized properly self.totaltime = 0.0 self.result = result # Release thread waiters self.ev_done.set() # Perform callbacks for event-style waiters self.make_callback('resolved', self.result) # If the result is an exception, then our final act is to raise # it in the caller, unless the caller explicitly supressed that if isinstance(result, Exception) and (not noraise): raise result return result

def quote_value(value): """ convert values to mysql code for the same mostly delegate directly to the mysql lib, but some exceptions exist """ try: if value == None: return SQL_NULL elif isinstance(value, SQL): return quote_sql(value.template, value.param) elif is_text(value): return SQL("'" + "".join(ESCAPE_DCT.get(c, c) for c in value) + "'") elif is_data(value): return quote_value(json_encode(value)) elif is_number(value): return SQL(text_type(value)) elif isinstance(value, datetime): return SQL("str_to_date('" + value.strftime("%Y%m%d%H%M%S.%f") + "', '%Y%m%d%H%i%s.%f')") elif isinstance(value, Date): return SQL("str_to_date('" + value.format("%Y%m%d%H%M%S.%f") + "', '%Y%m%d%H%i%s.%f')") elif hasattr(value, '__iter__'): return quote_value(json_encode(value)) else: return quote_value(text_type(value)) except Exception as e: Log.error("problem quoting SQL {{value}}", value=repr(value), cause=e)

def recall_score(gold, pred, pos_label=1, ignore_in_gold=[], ignore_in_pred=[]): """ Calculate recall for a single class. Args: gold: A 1d array-like of gold labels pred: A 1d array-like of predicted labels (assuming abstain = 0) ignore_in_gold: A list of labels for which elements having that gold label will be ignored. ignore_in_pred: A list of labels for which elements having that pred label will be ignored. pos_label: The class label to treat as positive for recall Returns: rec: The (float) recall score """ gold, pred = _preprocess(gold, pred, ignore_in_gold, ignore_in_pred) positives = np.where(pred == pos_label, 1, 0).astype(bool) trues = np.where(gold == pos_label, 1, 0).astype(bool) TP = np.sum(positives * trues) FN = np.sum(np.logical_not(positives) * trues) if TP or FN: rec = TP / (TP + FN) else: rec = 0 return rec

def view_decorator(function_decorator): """Convert a function based decorator into a class based decorator usable on class based Views. Can't subclass the `View` as it breaks inheritance (super in particular), so we monkey-patch instead. Based on http://stackoverflow.com/a/8429311 """ def simple_decorator(View): View.dispatch = method_decorator(function_decorator)(View.dispatch) return View return simple_decorator

def send_request(self, request): """ Add itself to the observing list :param request: the request :return: the request unmodified """ if request.observe == 0: # Observe request host, port = request.destination key_token = hash(str(host) + str(port) + str(request.token)) self._relations[key_token] = ObserveItem(time.time(), None, True, None) return request

def tomorrow(hour=None, minute=None): """ Gives the ``datetime.datetime`` object corresponding to tomorrow. The default value for optional parameters is the current value of hour and minute. I.e: when called without specifying values for parameters, the resulting object will refer to the time = now + 24 hours; when called with only hour specified, the resulting object will refer to tomorrow at the specified hour and at the current minute. :param hour: the hour for tomorrow, in the format *0-23* (defaults to ``None``) :type hour: int :param minute: the minute for tomorrow, in the format *0-59* (defaults to ``None``) :type minute: int :returns: a ``datetime.datetime`` object :raises: *ValueError* when hour or minute have bad values """ if hour is None: hour = datetime.now().hour if minute is None: minute = datetime.now().minute tomorrow_date = date.today() + timedelta(days=1) return datetime(tomorrow_date.year, tomorrow_date.month, tomorrow_date.day, hour, minute, 0)

def splitlines(self, keepends=False): """ B.splitlines([keepends]) -> list of lines Return a list of the lines in B, breaking at line boundaries. Line breaks are not included in the resulting list unless keepends is given and true. """ # Py2 str.splitlines() takes keepends as an optional parameter, # not as a keyword argument as in Python 3 bytes. parts = super(newbytes, self).splitlines(keepends) return [newbytes(part) for part in parts]

def distance(self, y, measure=None): """ Compute a pairwise distance measure between all rows of two numeric H2OFrames. :param H2OFrame y: Frame containing queries (small) :param str use: A string indicating what distance measure to use. Must be one of: - ``"l1"``: Absolute distance (L1-norm, >=0) - ``"l2"``: Euclidean distance (L2-norm, >=0) - ``"cosine"``: Cosine similarity (-1...1) - ``"cosine_sq"``: Squared Cosine similarity (0...1) :examples: >>> >>> iris_h2o = h2o.import_file(path=pyunit_utils.locate("smalldata/iris/iris.csv")) >>> references = iris_h2o[10:150,0:4 >>> queries = iris_h2o[0:10,0:4] >>> A = references.distance(queries, "l1") >>> B = references.distance(queries, "l2") >>> C = references.distance(queries, "cosine") >>> D = references.distance(queries, "cosine_sq") >>> E = queries.distance(references, "l1") >>> (E.transpose() == A).all() :returns: An H2OFrame of the matrix containing pairwise distance / similarity between the rows of this frame (N x p) and ``y`` (M x p), with dimensions (N x M). """ assert_is_type(y, H2OFrame) if measure is None: measure = "l2" return H2OFrame._expr(expr=ExprNode("distance", self, y, measure))._frame()

def correct_peaks(sig, peak_inds, search_radius, smooth_window_size, peak_dir='compare'): """ Adjust a set of detected peaks to coincide with local signal maxima, and Parameters ---------- sig : numpy array The 1d signal array peak_inds : np array Array of the original peak indices max_gap : int The radius within which the original peaks may be shifted. smooth_window_size : int The window size of the moving average filter applied on the signal. Peak distance is calculated on the difference between the original and smoothed signal. peak_dir : str, optional The expected peak direction: 'up' or 'down', 'both', or 'compare'. - If 'up', the peaks will be shifted to local maxima - If 'down', the peaks will be shifted to local minima - If 'both', the peaks will be shifted to local maxima of the rectified signal - If 'compare', the function will try both 'up' and 'down' options, and choose the direction that gives the largest mean distance from the smoothed signal. Returns ------- corrected_peak_inds : numpy array Array of the corrected peak indices Examples -------- """ sig_len = sig.shape[0] n_peaks = len(peak_inds) # Subtract the smoothed signal from the original sig = sig - smooth(sig=sig, window_size=smooth_window_size) # Shift peaks to local maxima if peak_dir == 'up': shifted_peak_inds = shift_peaks(sig=sig, peak_inds=peak_inds, search_radius=search_radius, peak_up=True) elif peak_dir == 'down': shifted_peak_inds = shift_peaks(sig=sig, peak_inds=peak_inds, search_radius=search_radius, peak_up=False) elif peak_dir == 'both': shifted_peak_inds = shift_peaks(sig=np.abs(sig), peak_inds=peak_inds, search_radius=search_radius, peak_up=True) else: shifted_peak_inds_up = shift_peaks(sig=sig, peak_inds=peak_inds, search_radius=search_radius, peak_up=True) shifted_peak_inds_down = shift_peaks(sig=sig, peak_inds=peak_inds, search_radius=search_radius, peak_up=False) # Choose the direction with the biggest deviation up_dist = np.mean(np.abs(sig[shifted_peak_inds_up])) down_dist = np.mean(np.abs(sig[shifted_peak_inds_down])) if up_dist >= down_dist: shifted_peak_inds = shifted_peak_inds_up else: shifted_peak_inds = shifted_peak_inds_down return shifted_peak_inds

def call(self, name, options=None, o=None): """ Call another command. :param name: The command name :type name: str :param options: The options :type options: list or None :param o: The output :type o: cleo.outputs.output.Output """ if options is None: options = [] command = self.get_application().find(name) options = [('command', command.get_name())] + options return command.run(ListInput(options), o)

def handle(self, t_input: inference.TranslatorInput, t_output: inference.TranslatorOutput, t_walltime: float = 0.): """ :param t_input: Translator input. :param t_output: Translator output. :param t_walltime: Total walltime for translation. """ self.stream.write("input=%s\toutput=%s\tinput_tokens=%d\toutput_tokens=%d\ttranslation_time=%0.4f\n" % (" ".join(t_input.tokens), t_output.translation, len(t_input.tokens), len(t_output.tokens), t_walltime)) self.stream.flush()

def __calculate_score(self, index_point, index_cluster): """! @brief Calculates Silhouette score for the specific object defined by index_point. @param[in] index_point (uint): Index point from input data for which Silhouette score should be calculated. @param[in] index_cluster (uint): Index cluster to which the point belongs to. @return (float) Silhouette score for the object. """ difference = self.__calculate_dataset_difference(index_point) a_score = self.__calculate_within_cluster_score(index_cluster, difference) b_score = self.__caclulate_optimal_neighbor_cluster_score(index_cluster, difference) return (b_score - a_score) / max(a_score, b_score)

def pos(self, p_x=None, y=None, z=None): """Set/Get actor position.""" if p_x is None: return np.array(self.GetPosition()) if z is None: # assume p_x is of the form (x,y,z) self.SetPosition(p_x) else: self.SetPosition(p_x, y, z) if self.trail: self.updateTrail() return self

def Ntubes_Phadkeb(DBundle, Do, pitch, Ntp, angle=30): r'''Using tabulated values and correction factors for number of passes, the highly accurate method of [1]_ is used to obtain the tube count of a given tube bundle outer diameter for a given tube size and pitch. Parameters ---------- DBundle : float Outer diameter of tube bundle, [m] Do : float Tube outer diameter, [m] pitch : float Pitch; distance between two orthogonal tube centers, [m] Ntp : int Number of tube passes, [-] angle : float, optional The angle the tubes are positioned; 30, 45, 60 or 90, [degrees] Returns ------- Nt : int Total number of tubes that fit in the heat exchanger, [-] Notes ----- For single-pass cases, the result is exact, and no tubes need to be removed for any reason. For 4, 6, 8 pass arrangements, a number of tubes must be removed to accomodate pass partition plates. The following assumptions are involved with that: * The pass partition plate is where a row of tubes would have been. Only one or two rows are assumed affected. * The thickness of partition plate is < 70% of the tube outer diameter. * The distance between the centerline of the partition plate and the centerline of the nearest row of tubes is equal to the pitch. This function will fail when there are more than 100,000 tubes. [1]_ tabulated values up to approximately 3,000 tubes derived with number theory. The sequesnces of integers were identified in the On-Line Encyclopedia of Integer Sequences (OEIS), and formulas listed in it were used to generate more coefficient to allow up to 100,000 tubes. The integer sequences are A003136, A038590, A001481, and A057961. The generation of coefficients for A038590 is very slow, but the rest are reasonably fast. The number of tubes that fit generally does not increase one-by-one, but by several. >>> Ntubes_Phadkeb(DBundle=1.007, Do=.028, pitch=.036, Ntp=2, angle=45.) 558 >>> Ntubes_Phadkeb(DBundle=1.008, Do=.028, pitch=.036, Ntp=2, angle=45.) 574 Because a pass partition needs to be installed in multiple tube pass shells, more tubes fit in an exchanger the fewer passes are used. >>> Ntubes_Phadkeb(DBundle=1.008, Do=.028, pitch=.036, Ntp=1, angle=45.) 593 Examples -------- >>> Ntubes_Phadkeb(DBundle=1.200-.008*2, Do=.028, pitch=.036, Ntp=2, angle=45.) 782 References ---------- .. [1] Phadke, P. S., Determining tube counts for shell and tube exchangers, Chem. Eng., September, 91, 65-68 (1984). ''' if DBundle <= Do*Ntp: return 0 if Ntp == 6: e = 0.265 elif Ntp == 8: e = 0.404 else: e = 0. r = 0.5*(DBundle - Do)/pitch s = r*r Ns, Nr = floor(s), floor(r) # If Ns is between two numbers, take the smaller one # C1 is the number of tubes for a single pass arrangement. if angle == 30 or angle == 60: i = np.searchsorted(triangular_Ns, Ns, side='right') C1 = int(triangular_C1s[i-1]) elif angle == 45 or angle == 90: i = np.searchsorted(square_Ns, Ns, side='right') C1 = int(square_C1s[i-1]) Cx = 2*Nr + 1. # triangular and rotated triangular if (angle == 30 or angle == 60): w = 2*r/3**0.5 Nw = floor(w) if Nw % 2 == 0: Cy = 3*Nw else: Cy = 3*Nw + 1 if Ntp == 2: if angle == 30 : C2 = C1 - Cx else: C2 = C1 - Cy - 1 else: # 4 passes, or 8; this value is needed C4 = C1 - Cx - Cy if (angle == 30 or angle == 60) and (Ntp == 6 or Ntp == 8): if angle == 30: # triangular v = 2*e*r/3**0.5 + 0.5 Nv = floor(v) u = 3**0.5*Nv/2. if Nv % 2 == 0: z = (s-u*u)**0.5 else: z = (s-u*u)**0.5 - 0.5 Nz = floor(z) if Ntp == 6: C6 = C1 - Cy - 4*Nz - 1 else: C8 = C4 - 4*Nz else: # rotated triangular v = 2.*e*r Nv = floor(v) u1 = 0.5*Nv z = (s - u1*u1)**0.5 w1 = 2*z/2**0.5 # w1 = 2**2**0.5 # WRONG u2 = 0.5*(Nv + 1) zs = (s-u2*u2)**0.5 w2 = 2.*zs/3**0.5 if Nv%2 == 0: z1 = 0.5*w1 z2 = 0.5*(w2+1) else: z1 = 0.5*(w1+1) z2 = 0.5*w2 Nz1 = floor(z1) Nz2 = floor(z2) if Ntp == 6: C6 = C1 - Cx - 4.*(Nz1 + Nz2) else: # 8 C8 = C4 - 4.*(Nz1 + Nz2) if (angle == 45 or angle == 90): if angle == 90: Cy = Cx - 1. # eq 6 or 8 for c2 or c4 if Ntp == 2: C2 = C1 - Cx else: # 4 passes, or 8; this value is needed C4 = C1 - Cx - Cy else: # rotated square w = r/2**0.5 Nw = floor(w) Cx = 2.*Nw + 1 Cy = Cx - 1 if Ntp == 2: C2 = C1 - Cx else: # 4 passes, or 8; this value is needed C4 = C1 - Cx - Cy if (angle == 45 or angle == 90) and (Ntp == 6 or Ntp == 8): if angle == 90: v = e*r + 0.5 Nv = floor(v) z = (s - Nv*Nv)**0.5 Nz = floor(z) if Ntp == 6: C6 = C1 - Cy - 4*Nz - 1 else: C8 = C4 - 4*Nz else: w = r/2**0.5 Nw = floor(w) Cx = 2*Nw + 1 v = 2**0.5*e*r Nv = floor(v) u1 = Nv/2**0.5 z = (s-u1*u1)**0.5 w1 = 2**0.5*z u2 = (Nv + 1)/2**0.5 zs = (s-u2*u2)**0.5 w2 = 2**0.5*zs # if Nv is odd, 21a and 22a. If even, 21b and 22b. Nz1, Nz2 if Nv %2 == 0: z1 = 0.5*w1 z2 = 0.5*(w2 + 1) else: z1 = 0.5*(w1 + 1) z2 = 0.5*w2 Nz1 = floor(z1) Nz2 = floor(z2) if Ntp == 6: C6 = C1 - Cx - 4*(Nz1 + Nz2) else: # 8 C8 = C4 - 4*(Nz1 + Nz2) if Ntp == 1: ans = C1 elif Ntp == 2: ans = C2 elif Ntp == 4: ans = C4 elif Ntp == 6: ans = C6 elif Ntp == 8: ans = C8 else: raise Exception('Only 1, 2, 4, 6, or 8 tube passes are supported') ans = int(ans) # In some cases, a negative number would be returned by these formulas if ans < 0: ans = 0 # pragma: no cover return ans

def binarize_percent(netin, level, sign='pos', axis='time'): """ Binarizes a network proprtionally. When axis='time' (only one available at the moment) then the top values for each edge time series are considered. Parameters ---------- netin : array or dict network (graphlet or contact representation), level : float Percent to keep (expressed as decimal, e.g. 0.1 = top 10%) sign : str, default='pos' States the sign of the thresholding. Can be 'pos', 'neg' or 'both'. If "neg", only negative values are thresholded and vice versa. axis : str, default='time' Specify which dimension thresholding is applied against. Can be 'time' (takes top % for each edge time-series) or 'graphlet' (takes top % for each graphlet) Returns ------- netout : array or dict (depending on input) Binarized network """ netin, netinfo = process_input(netin, ['C', 'G', 'TO']) # Set diagonal to 0 netin = set_diagonal(netin, 0) if axis == 'graphlet' and netinfo['nettype'][-1] == 'u': triu = np.triu_indices(netinfo['netshape'][0], k=1) netin = netin[triu[0], triu[1], :] netin = netin.transpose() if sign == 'both': net_sorted = np.argsort(np.abs(netin), axis=-1) elif sign == 'pos': net_sorted = np.argsort(netin, axis=-1) elif sign == 'neg': net_sorted = np.argsort(-1*netin, axis=-1) else: raise ValueError('Unknown value for parameter: sign') # Predefine netout = np.zeros(netinfo['netshape']) if axis == 'time': # These for loops can probabaly be removed for speed for i in range(netinfo['netshape'][0]): for j in range(netinfo['netshape'][1]): netout[i, j, net_sorted[i, j, - int(round(net_sorted.shape[-1])*level):]] = 1 elif axis == 'graphlet': netout_tmp = np.zeros(netin.shape) for i in range(netout_tmp.shape[0]): netout_tmp[i, net_sorted[i, - int(round(net_sorted.shape[-1])*level):]] = 1 netout_tmp = netout_tmp.transpose() netout[triu[0], triu[1], :] = netout_tmp netout[triu[1], triu[0], :] = netout_tmp netout = set_diagonal(netout, 0) # If input is contact, output contact if netinfo['inputtype'] == 'C': netinfo['nettype'] = 'b' + netinfo['nettype'][1] netout = graphlet2contact(netout, netinfo) netout.pop('inputtype') netout.pop('values') netout['diagonal'] = 0 return netout

def begin(self, service_endpoint): """Create an AuthRequest object for the specified service_endpoint. This method will create an association if necessary.""" if self.store is None: assoc = None else: assoc = self._getAssociation(service_endpoint) request = AuthRequest(service_endpoint, assoc) request.return_to_args[self.openid1_nonce_query_arg_name] = mkNonce() if request.message.isOpenID1(): request.return_to_args[self.openid1_return_to_identifier_name] = \ request.endpoint.claimed_id return request

def scan_videopath(videopath, callback, recursive=False): """ Scan the videopath string for video files. :param videopath: Path object :param callback: Instance of ProgressCallback :param recursive: True if the scanning should happen recursive :return: tuple with list of videos and list of subtitles (videos have matched subtitles) """ log.debug('scan_videopath(videopath="{videopath}", recursive={recursive})'.format( videopath=videopath, recursive=recursive)) if not videopath.exists(): log.debug('"{videopath}" does not exist'.format(videopath=videopath)) raise IllegalPathException(path=videopath) if videopath.is_dir(): log.debug('"{videopath}" is a directory'.format(videopath=videopath)) return __scan_folder(videopath, callback=callback, recursive=recursive) elif videopath.is_file(): log.debug('"{videopath}" is a file'.format(videopath=videopath)) videopath_dir = videopath.parent [all_subs, _] = filter_files_extensions(videopath_dir.iterdir(), [SUBTITLES_EXT, VIDEOS_EXT]) [_, video] = filter_files_extensions([videopath], [SUBTITLES_EXT, VIDEOS_EXT]) sub_videos = [all_subs, video] path_subvideos = {videopath_dir: sub_videos} return merge_path_subvideo(path_subvideos, callback) else: log.debug('"{videopath}" is of unknown type'.format(videopath=videopath)) return [], []

def striptags(self): r"""Unescape markup into an unicode string and strip all tags. This also resolves known HTML4 and XHTML entities. Whitespace is normalized to one: >>> Markup("Main &raquo; <em>About</em>").striptags() u'Main \xbb About' """ stripped = u' '.join(_striptags_re.sub('', self).split()) return Markup(stripped).unescape()

def _set_siteinfo(self): """ capture API sitematrix data in data attribute """ data = self._load_response('siteinfo').get('query') mostviewed = data.get('mostviewed') self.data['mostviewed'] = [] for item in mostviewed[1:]: if item['ns'] == 0: self.data['mostviewed'].append(item) general = data.get('general') self.params.update({'title': general.get('sitename')}) self.params.update({'lang': general.get('lang')}) self.data['site'] = general.get('wikiid') info = {} for item in general: ginfo = general.get(item) if ginfo: info[item] = ginfo self.data['info'] = info siteviews = data.get('siteviews') if siteviews: values = [x for x in siteviews.values() if x] if values: self.data['siteviews'] = int(sum(values) / len(values)) else: self.data['siteviews'] = 0 stats = data.get('statistics') for item in stats: self.data[item] = stats[item]

def compose(self, to, subject, text): """Login required. Sends POST to send a message to a user. Returns True or raises :class:`exceptions.UnexpectedResponse` if non-"truthy" value in response. URL: ``http://www.reddit.com/api/compose/`` :param to: username or :class`things.Account` of user to send to :param subject: subject of message :param text: message body text """ if isinstance(to, Account): to = to.name data = dict(to=to, subject=subject, text=text) j = self.post('api', 'compose', data=data) return assert_truthy(j)

def list(self, request, *args, **kwargs): """ To get a list of price list items, run **GET** against */api/merged-price-list-items/* as authenticated user. If service is not specified default price list items are displayed. Otherwise service specific price list items are displayed. In this case rendered object contains {"is_manually_input": true} In order to specify service pass query parameters: - service_type (Azure, OpenStack etc.) - service_uuid Example URL: http://example.com/api/merged-price-list-items/?service_type=Azure&service_uuid=cb658b491f3644a092dd223e894319be """ return super(MergedPriceListItemViewSet, self).list(request, *args, **kwargs)

def parse_theta2_report (self, fh): """ Parse the final THetA2 log file. """ parsed_data = {} for l in fh: if l.startswith('#'): continue else: s = l.split("\t") purities = s[1].split(',') parsed_data['proportion_germline'] = float(purities[0]) * 100.0 for i, v in enumerate(purities[1:]): if i <= 5: parsed_data['proportion_tumour_{}'.format(i+1)] = float(v) * 100.0 else: parsed_data['proportion_tumour_gt5'] = (float(v) * 100.0) + parsed_data.get('proportion_tumour_gt5', 0) break return parsed_data

def get_login_button_url(self, button_color=None, caption_color=None, button_size=None): """Return URL for image used for RunKeeper Login button. @param button_color: Button color. Either 'blue', 'grey' or 'black'. Default: 'blue'. @param caption_color: Button text color. Either 'white' or 'black'. Default: 'white' @param button_size: Button width in pixels. Either 200, 300 or 600. Default: 200 @return: URL for Login Button Image. """ if not button_color in settings.LOGIN_BUTTON_COLORS: button_color = settings.LOGIN_BUTTON_COLORS[0] if not caption_color in settings.LOGIN_BUTTON_CAPTION_COLORS: caption_color = settings.LOGIN_BUTTON_CAPTION_COLORS[0] if settings.LOGIN_BUTTON_SIZES.has_key(button_size): button_size = settings.LOGIN_BUTTON_SIZES[button_size] else: button_size = settings.LOGIN_BUTTON_SIZES['None'] return settings.LOGIN_BUTTON_URL % (button_color, caption_color, button_size)

def get_annotations(self, min_rho=None): ''' Get the list of annotations found. :param min_rho: if set, only get entities with a rho-score (confidence) higher than this. ''' return (a for a in self.annotations if min_rho is None or a.score > min_rho)

def stationary_coefficients(self, j, coeff_type='ma'): """ Wold representation moving average or VAR coefficients for the steady state Kalman filter. Parameters ---------- j : int The lag length coeff_type : string, either 'ma' or 'var' (default='ma') The type of coefficent sequence to compute. Either 'ma' for moving average or 'var' for VAR. """ # == simplify notation == # A, G = self.ss.A, self.ss.G K_infinity = self.K_infinity # == compute and return coefficients == # coeffs = [] i = 1 if coeff_type == 'ma': coeffs.append(np.identity(self.ss.k)) P_mat = A P = np.identity(self.ss.n) # Create a copy elif coeff_type == 'var': coeffs.append(dot(G, K_infinity)) P_mat = A - dot(K_infinity, G) P = np.copy(P_mat) # Create a copy else: raise ValueError("Unknown coefficient type") while i <= j: coeffs.append(dot(dot(G, P), K_infinity)) P = dot(P, P_mat) i += 1 return coeffs

def notifyPop(self, queue, length = 1): ''' Internal notify for sub-queues been poped :returns: List of any events generated by this pop ''' self.totalSize = self.totalSize - length ret1 = [] ret2 = [] if self.isWaited and self.canAppend(): self.isWaited = False ret1.append(QueueCanWriteEvent(self)) if self.isWaitEmpty and not self: self.isWaitEmpty = False ret2.append(QueueIsEmptyEvent(self)) if self.parent is not None: pr = self.parent.notifyPop(self, length) ret1 += pr[0] ret2 += pr[1] newblocked = not self.canPop() if newblocked != self.blocked: self.blocked = newblocked if self.parent is not None: self.parent.notifyBlock(self, newblocked) return (ret1, ret2)

def actuator_on(self, service_location_id, actuator_id, duration=None): """ Turn actuator on Parameters ---------- service_location_id : int actuator_id : int duration : int, optional 300,900,1800 or 3600 , specifying the time in seconds the actuator should be turned on. Any other value results in turning on for an undetermined period of time. Returns ------- requests.Response """ return self._actuator_on_off( on_off='on', service_location_id=service_location_id, actuator_id=actuator_id, duration=duration)

def overfit(self, tau=None, plot=True, clobber=False, w=9, **kwargs): r""" Compute the masked & unmasked overfitting metrics for the light curve. This routine injects a transit model given by `tau` at every cadence in the light curve and recovers the transit depth when (1) leaving the transit unmasked and (2) masking the transit prior to performing regression. :param tau: A function or callable that accepts two arguments, \ `time` and `t0`, and returns an array corresponding to a \ zero-mean, unit depth transit model centered at \ `t0` and evaluated at `time`. \ The easiest way to provide this is to use an instance of \ :py:class:`everest.transit.TransitShape`. Default is \ :py:class:`everest.transit.TransitShape(dur=0.1)`, a transit \ with solar-like limb darkening and a duratio of 0.1 days. :param bool plot: Plot the results as a PDF? Default :py:obj:`True` :param bool clobber: Overwrite the results if present? Default \ :py:obj:`False` :param int w: The size of the masking window in cadences for \ computing the masked overfitting metric. Default `9` \ (about 4.5 hours for `K2` long cadence). :returns: An instance of `everest.basecamp.Overfitting`. """ fname = os.path.join(self.dir, self.name + '_overfit.npz') figname = os.path.join(self.dir, self.name) # Compute if not os.path.exists(fname) or clobber: # Baseline med = np.nanmedian(self.fraw) # Default transit model if tau is None: tau = TransitShape(dur=0.1) # The overfitting metrics O1 = [None for brkpt in self.breakpoints] O2 = [None for brkpt in self.breakpoints] O3 = [None for brkpt in self.breakpoints] O4 = [None for brkpt in self.breakpoints] O5 = [None for brkpt in self.breakpoints] # Loop over all chunks for b, brkpt in enumerate(self.breakpoints): # Masks for current chunk m = self.get_masked_chunk(b, pad=False) time = self.time[m] ferr = self.fraw_err[m] / med y = self.fraw[m] / med - 1 # The metrics we're computing here O1[b] = np.zeros(len(y)) * np.nan O2[b] = np.zeros(len(y)) * np.nan O3[b] = np.zeros(len(y)) * np.nan O4[b] = np.zeros(len(y)) * np.nan O5[b] = np.zeros(len(y)) * np.nan # Compute the astrophysical covariance and its inverse log.info("Computing the covariance...") if self.kernel == 'Basic': wh, am, ta = self.kernel_params wh /= med am /= med kernel_params = [wh, am, ta] elif self.kernel == 'QuasiPeriodic': wh, am, ga, pe = self.kernel_params wh /= med am /= med kernel_params = [wh, am, ga, pe] K = GetCovariance(self.kernel, kernel_params, time, ferr) Kinv = cho_solve((cholesky(K), False), np.eye(len(time))) # Loop over all orders log.info("Computing some large matrices...") X = [None for n in range(self.pld_order)] XL = [None for n in range(self.pld_order)] XLX = [None for n in range(self.pld_order)] for n in range(self.pld_order): if (self.lam_idx >= n) and (self.lam[b][n] is not None): X[n] = self.X(n, m, **kwargs) XL[n] = (self.lam[b][n] / med ** 2) * X[n] XLX[n] = np.dot(XL[n], X[n].T) X = np.hstack(X) XL = np.hstack(XL) XLX = np.sum(XLX, axis=0) # The full covariance C = XLX + K # The unmasked linear problem log.info("Solving the unmasked linear problem...") m = np.dot(XLX, np.linalg.solve(C, y)) m -= np.nanmedian(m) f = y - m R = np.linalg.solve(C, XLX.T).T # The masked linear problem log.info("Solving the masked linear problem...") A = MaskSolve(C, y, w=w) # Now loop through and compute the metric log.info("Computing the overfitting metrics...") for n in prange(len(y)): # # *** Unmasked overfitting metric *** # # Evaluate the sparse transit model TAU = tau(time, t0=time[n]) i = np.where(TAU < 0)[0] TAU = TAU.reshape(-1, 1) # Fast sparse algebra AA = np.dot(np.dot(TAU[i].T, Kinv[i, :][:, i]), TAU[i]) BB = np.dot(TAU[i].T, Kinv[i, :]) CC = TAU - np.dot(R[:, i], TAU[i]) O1[b][n] = AA O2[b][n] = np.dot(BB, CC) O3[b][n] = np.dot(BB, f) O4[b][n] = np.dot(BB, y) # # *** Masked overfitting metric *** # # The current mask and mask centerpoint mask = np.arange(n, n + w) j = n + (w + 1) // 2 - 1 if j >= len(y) - w: continue # The regularized design matrix # This is the same as # XLmX[:, n - 1] = \ # np.dot(XL, np.delete(X, mask, axis=0).T)[:, n - 1] if n == 0: XLmX = np.dot(XL, np.delete(X, mask, axis=0).T) else: XLmX[:, n - 1] = np.dot(XL, X[n - 1, :].T) # The linear solution to this step m = np.dot(XLmX, A[n]) # Evaluate the sparse transit model TAU = tau(time, t0=time[j]) i = np.where(TAU < 0)[0] TAU = TAU[i].reshape(-1, 1) # Dot the transit model in den = np.dot(np.dot(TAU.T, Kinv[i, :][:, i]), TAU) num = np.dot(TAU.T, Kinv[i, :]) # Compute the overfitting metric # Divide this number by a depth # to get the overfitting for that # particular depth. O5[b][j] = -np.dot(num, y - m) / den # Save! np.savez(fname, O1=O1, O2=O2, O3=O3, O4=O4, O5=O5) else: data = np.load(fname) O1 = data['O1'] O2 = data['O2'] O3 = data['O3'] O4 = data['O4'] O5 = data['O5'] # Plot if plot and (clobber or not os.path.exists(figname + '_overfit.pdf')): log.info("Plotting the overfitting metrics...") # Masked time array time = self.apply_mask(self.time) # Plot the final corrected light curve ovr = OVERFIT() self.plot_info(ovr) # Loop over the two metrics for kind, axes, axesh in zip(['unmasked', 'masked'], [ovr.axes1, ovr.axes2], [ovr.axes1h, ovr.axes2h]): # Loop over three depths for depth, ax, axh in zip([0.01, 0.001, 0.0001], axes, axesh): # Get the metric if kind == 'unmasked': metric = 1 - (np.hstack(O2) + np.hstack(O3) / depth) / np.hstack(O1) color = 'r' elif kind == 'masked': metric = np.hstack(O5) / depth color = 'b' else: raise ValueError("Invalid metric.") # Median and median absolute deviation med = np.nanmedian(metric) mad = np.nanmedian(np.abs(metric - med)) # Plot the metric as a function of time ax.plot(time, metric, 'k.', alpha=0.5, ms=2) ax.plot(time, metric, 'k-', alpha=0.1, lw=0.5) ylim = (-0.2, 1.0) ax.margins(0, None) ax.axhline(0, color='k', lw=1, alpha=0.5) ax.set_ylim(*ylim) if kind == 'masked' and depth == 0.0001: ax.set_xlabel('Time (days)', fontsize=14) else: ax.set_xticklabels([]) # Plot the histogram rng = (max(ylim[0], np.nanmin(metric)), min(ylim[1], np.nanmax(metric))) axh.hist(metric, bins=30, range=rng, orientation="horizontal", histtype="step", fill=False, color='k') axh.axhline(med, color=color, ls='-', lw=1) axh.axhspan(med - mad, med + mad, color=color, alpha=0.1) axh.axhline(0, color='k', lw=1, alpha=0.5) axh.yaxis.tick_right() axh.set_ylim(*ax.get_ylim()) axh.set_xticklabels([]) bbox = dict(fc="w", ec="1", alpha=0.5) info = r"$\mathrm{med}=%.3f$" % med + \ "\n" + r"$\mathrm{mad}=%.3f$" % mad axh.annotate(info, xy=(0.1, 0.925), xycoords='axes fraction', ha="left", va="top", bbox=bbox, color=color) bbox = dict(fc="w", ec="1", alpha=0.95) ax.annotate("%s overfitting metric" % kind, xy=(1-0.035, 0.92), xycoords='axes fraction', ha='right', va='top', bbox=bbox, color=color) pl.figtext(0.025, 0.77, "depth = 0.01", rotation=90, ha='left', va='center', fontsize=18) pl.figtext(0.025, 0.48, "depth = 0.001", rotation=90, ha='left', va='center', fontsize=18) pl.figtext(0.025, 0.19, "depth = 0.0001", rotation=90, ha='left', va='center', fontsize=18) ovr.fig.savefig(figname + '_overfit.pdf') log.info("Saved plot to %s_overfit.pdf" % figname) pl.close() return Overfitting(O1, O2, O3, O4, O5, figname + '_overfit.pdf')

def run(self, scenario): """Run the algorithm, utilizing a classifier set to choose the most appropriate action for each situation produced by the scenario. Improve the situation/action mapping on each reward cycle to maximize reward. Return the classifier set that was created. Usage: scenario = MUXProblem() model = algorithm.run(scenario) Arguments: scenario: A Scenario instance. Return: A new classifier set, trained on the given scenario. """ assert isinstance(scenario, scenarios.Scenario) model = self.new_model(scenario) model.run(scenario, learn=True) return model

def __presence_unavailable(self,stanza): """Process an unavailable presence from a MUC room. :Parameters: - `stanza`: the stanza received. :Types: - `stanza`: `Presence` :return: `True` if the stanza was properly recognized as generated by one of the managed rooms, `False` otherwise. :returntype: `bool`""" fr=stanza.get_from() key=fr.bare().as_unicode() rs=self.rooms.get(key) if not rs: return False rs.process_unavailable_presence(MucPresence(stanza)) return True

async def create( cls, fabric: Union[Fabric, int], vid: int, *, name: str = None, description: str = None, mtu: int = None, relay_vlan: Union[Vlan, int] = None, dhcp_on: bool = False, primary_rack: Union[RackController, str] = None, secondary_rack: Union[RackController, str] = None, space: Union[Space, int] = None): """ Create a `Vlan` in MAAS. :param fabric: Fabric to create the VLAN on. :type fabric: `Fabric` or `int` :param vid: VID for the VLAN. :type vid: `int` :param name: The name of the VLAN (optional). :type name: `str` :param description: A description of the VLAN (optional). :type description: `str` :param mtu: The MTU for VLAN (optional, default of 1500 will be used). :type mtu: `int` :param relay_vlan: VLAN to relay this VLAN through. :type relay_vlan: `Vlan` or `int` :param dhcp_on: True turns the DHCP on, false keeps the DHCP off. True requires that `primary_rack` is also set. :type dhcp_on: `bool` :param primary_rack: Primary rack controller to run the DCHP service on. :type primary_rack: `RackController` or `int` :parma secondary_rack: Secondary rack controller to run the DHCP service on. This will enable HA operation of the DHCP service. :type secondary_rack: `RackController` or `int` :returns: The created VLAN. :rtype: `Vlan` """ params = {} if isinstance(fabric, int): params['fabric_id'] = fabric elif isinstance(fabric, Fabric): params['fabric_id'] = fabric.id else: raise TypeError( "fabric must be Fabric or int, not %s" % ( type(fabric).__class__)) params['vid'] = vid if name is not None: params['name'] = name if description is not None: params['description'] = description if mtu is not None: params['mtu'] = mtu if relay_vlan is not None: if isinstance(relay_vlan, int): params['relay_vlan'] = relay_vlan elif isinstance(relay_vlan, Vlan): params['relay_vlan'] = relay_vlan.id else: raise TypeError( "relay_vlan must be Vlan or int, not %s" % ( type(relay_vlan).__class__)) params['dhcp_on'] = dhcp_on if primary_rack is not None: if isinstance(primary_rack, str): params['primary_rack'] = primary_rack elif isinstance(primary_rack, RackController): params['primary_rack'] = primary_rack.system_id else: raise TypeError( "primary_rack must be RackController or str, not %s" % ( type(primary_rack).__class__)) if secondary_rack is not None: if isinstance(secondary_rack, str): params['secondary_rack'] = secondary_rack elif isinstance(secondary_rack, RackController): params['secondary_rack'] = secondary_rack.system_id else: raise TypeError( "secondary_rack must be RackController or str, not %s" % ( type(secondary_rack).__class__)) if space is not None: if isinstance(space, int): params['space'] = space elif isinstance(space, Space): params['space'] = space.id else: raise TypeError( "space must be Space or int, not %s" % ( type(space).__class__)) return cls._object(await cls._handler.create(**params))

def assert_no_text(self, *args, **kwargs): """ Asserts that the page or current node doesn't have the given text content, ignoring any HTML tags. Args: *args: Variable length argument list for :class:`TextQuery`. **kwargs: Arbitrary keyword arguments for :class:`TextQuery`. Returns: True Raises: ExpectationNotMet: If the assertion hasn't succeeded during the wait time. """ query = TextQuery(*args, **kwargs) @self.synchronize(wait=query.wait) def assert_no_text(): count = query.resolve_for(self) if matches_count(count, query.options) and ( count > 0 or expects_none(query.options)): raise ExpectationNotMet(query.negative_failure_message) return True return assert_no_text()

def _get_password(params): """Get the password for a database connection from :mod:`keyring` Args: params (dict): database configuration, as defined in :mod:`ozelot.config` Returns: str: password """ user_name = params['user'] service_name = params['host'] + ':' + params['driver'] return keyring.get_password(service_name=service_name, username=user_name)

def create_organisation(self, organisation_json): ''' Create an Organisation object from a JSON object Returns: Organisation: The organisation from the given `organisation_json`. ''' return trolly.organisation.Organisation( trello_client=self, organisation_id=organisation_json['id'], name=organisation_json['name'], data=organisation_json, )

def free_parameter(self, name, par, free=True): """Free/Fix a parameter of a source by name. Parameters ---------- name : str Source name. par : str Parameter name. """ name = self.get_source_name(name) if par in self._lck_params.get(name, []): return idx = self.like.par_index(name, par) self.like[idx].setFree(free) self._sync_params(name)

def get_task_cache(self, username, courseid, taskid): """ Shorthand for get_task_caches([username], courseid, taskid)[username] """ return self.get_task_caches([username], courseid, taskid)[username]

def set_cursor(self, col, row): """Move the cursor to an explicit column and row position.""" # Clamp row to the last row of the display. if row > self._lines: row = self._lines - 1 # Set location. self.write8(LCD_SETDDRAMADDR | (col + LCD_ROW_OFFSETS[row]))

def get(self): """ get method """ try: cluster = self.get_argument_cluster() role = self.get_argument_role() environ = self.get_argument_environ() topology_name = self.get_argument_topology() component = self.get_argument_component() metric_names = self.get_required_arguments_metricnames() start_time = self.get_argument_starttime() end_time = self.get_argument_endtime() self.validateInterval(start_time, end_time) instances = self.get_arguments(constants.PARAM_INSTANCE) topology = self.tracker.getTopologyByClusterRoleEnvironAndName( cluster, role, environ, topology_name) metrics = yield tornado.gen.Task(metricstimeline.getMetricsTimeline, topology.tmaster, component, metric_names, instances, int(start_time), int(end_time)) self.write_success_response(metrics) except Exception as e: Log.debug(traceback.format_exc()) self.write_error_response(e)

def evaluate(data_loader): """Evaluate given the data loader Parameters ---------- data_loader : DataLoader Returns ------- avg_loss : float Average loss real_translation_out : list of list of str The translation output """ translation_out = [] all_inst_ids = [] avg_loss_denom = 0 avg_loss = 0.0 for _, (src_seq, tgt_seq, src_valid_length, tgt_valid_length, inst_ids) \ in enumerate(data_loader): src_seq = src_seq.as_in_context(ctx) tgt_seq = tgt_seq.as_in_context(ctx) src_valid_length = src_valid_length.as_in_context(ctx) tgt_valid_length = tgt_valid_length.as_in_context(ctx) # Calculating Loss out, _ = model(src_seq, tgt_seq[:, :-1], src_valid_length, tgt_valid_length - 1) loss = loss_function(out, tgt_seq[:, 1:], tgt_valid_length - 1).mean().asscalar() all_inst_ids.extend(inst_ids.asnumpy().astype(np.int32).tolist()) avg_loss += loss * (tgt_seq.shape[1] - 1) avg_loss_denom += (tgt_seq.shape[1] - 1) # Translate samples, _, sample_valid_length =\ translator.translate(src_seq=src_seq, src_valid_length=src_valid_length) max_score_sample = samples[:, 0, :].asnumpy() sample_valid_length = sample_valid_length[:, 0].asnumpy() for i in range(max_score_sample.shape[0]): translation_out.append( [tgt_vocab.idx_to_token[ele] for ele in max_score_sample[i][1:(sample_valid_length[i] - 1)]]) avg_loss = avg_loss / avg_loss_denom real_translation_out = [None for _ in range(len(all_inst_ids))] for ind, sentence in zip(all_inst_ids, translation_out): real_translation_out[ind] = sentence return avg_loss, real_translation_out

def indices2one_hot(indices, nb_classes): """ Convert an iterable of indices to one-hot encoded list. You might also be interested in sklearn.preprocessing.OneHotEncoder Parameters ---------- indices : iterable iterable of indices nb_classes : int Number of classes dtype : type Returns ------- one_hot : list Examples -------- >>> indices2one_hot([0, 1, 1], 3) [[1, 0, 0], [0, 1, 0], [0, 1, 0]] >>> indices2one_hot([0, 1, 1], 2) [[1, 0], [0, 1], [0, 1]] """ if nb_classes < 1: raise ValueError('nb_classes={}, but positive number expected' .format(nb_classes)) one_hot = [] for index in indices: one_hot.append([0] * nb_classes) one_hot[-1][index] = 1 return one_hot

def get_unique_constraint_declaration_sql(self, name, index): """ Obtains DBMS specific SQL code portion needed to set a unique constraint declaration to be used in statements like CREATE TABLE. :param name: The name of the unique constraint. :type name: str :param index: The index definition :type index: Index :return: DBMS specific SQL code portion needed to set a constraint. :rtype: str """ columns = index.get_quoted_columns(self) name = Identifier(name) if not columns: raise DBALException('Incomplete definition. "columns" required.') return "CONSTRAINT %s UNIQUE (%s)%s" % ( name.get_quoted_name(self), self.get_index_field_declaration_list_sql(columns), self.get_partial_index_sql(index), )

def confidence_intervals(self, X, width=.95, quantiles=None): """estimate confidence intervals for the model. Parameters ---------- X : array-like of shape (n_samples, m_features) Input data matrix width : float on [0,1], optional quantiles : array-like of floats in (0, 1), optional Instead of specifying the prediciton width, one can specify the quantiles. So ``width=.95`` is equivalent to ``quantiles=[.025, .975]`` Returns ------- intervals: np.array of shape (n_samples, 2 or len(quantiles)) Notes ----- Wood 2006, section 4.9 Confidence intervals based on section 4.8 rely on large sample results to deal with non-Gaussian distributions, and treat the smoothing parameters as fixed, when in reality they are estimated from the data. """ if not self._is_fitted: raise AttributeError('GAM has not been fitted. Call fit first.') X = check_X(X, n_feats=self.statistics_['m_features'], edge_knots=self.edge_knots_, dtypes=self.dtype, features=self.feature, verbose=self.verbose) return self._get_quantiles(X, width, quantiles, prediction=False)

def get_draft_page_by_id(self, page_id, status='draft'): """ Provide content by id with status = draft :param page_id: :param status: :return: """ url = 'rest/api/content/{page_id}?status={status}'.format(page_id=page_id, status=status) return self.get(url)