How to use _parse_structure method in localstack

Best Python code snippet using localstack_python

app.py

Source: app.py Github

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...75 # we don't have anomalies in the conf76 anomalies = [lambda x: x for i in range(structure.W.shape[0])]77 logging.debug(anomalies)78 return structure, anomalies, m079def _parse_structure(conf):80 structures = []81 m0 = []82 anomalies = []83 for structure in conf:84 _structure, _anomalies, _m0 = _parse_component(structure)85 m0.extend(_m0)86 anomalies.extend(_anomalies)87 structures.append(_structure)88 m0 = np.array(m0)89 C0 = np.eye(len(m0))90 return reduce((lambda x, y: x + y), structures), m0, C0, anomalies91def _parse_composite(conf):92 models = []93 prior_mean = []94 anomaly_vector = []95 for element in conf:96 if 'replicate' in element:97 structure, m0, C0, anomalies = _parse_structure(98 element['structure'])99 prior_mean.extend([m0] * element['replicate'])100 anomaly_vector.extend(anomalies * element['replicate'])101 model = _parse_observations(element['observations'], structure)102 models.extend([model] * element['replicate'])103 else:104 structure, m0, C0, anomalies = _parse_structure(105 element['structure'])106 prior_mean.extend(m0)107 anomaly_vector.extend(anomalies)108 model = _parse_observations(element['observations'], structure)109 models.append(model)110 print(models)111 model = CompositeTransformer(*models)112 m0 = np.array(prior_mean)113 C0 = np.eye(len(m0))114 return model, m0, C0, anomaly_vector115def _parse_observations(obs, structure):116 if obs['type'] == 'continuous':117 model = NormalDLM(structure=structure, V=obs['noise'])118 elif obs['type'] == 'discrete':119 model = PoissonDLM(structure=structure)120 elif obs['type'] == 'categorical':121 if 'values' in obs:122 values = obs['values'].split(',')123 model = BinomialTransformer(structure=structure, source=values)124 elif 'categories' in obs:125 model = BinomialDLM(structure=structure,126 categories=obs['categories'])127 else:128 raise ValueError("Categorical models must have either 'values' "129 "or 'categories'")130 else:131 raise ValueError("Model type {} is not valid".format(obs['type']))132 return model133def parse_configuration(conf):134 """135 Parse a YAML configuration string into an state-space model136 :param conf:137 :return: A state-space model138 """139 if 'compose' in conf:140 model, m0, C0, anomalies = _parse_composite(conf['compose'])141 else:142 structure, m0, C0, anomalies = _parse_structure(conf['structure'])143 model = _parse_observations(conf['observations'], structure)144 state = mvn(m0, C0).rvs()145 period = float(conf['period'])146 name = conf['name']147 return model, state, period, name, anomalies148def build_message(name, value):149 return json.dumps({150 'name': name,151 'value': value152 }).encode()153def main(args):154 logging.basicConfig(level=args.logging)155 logging.info('brokers={}'.format(args.brokers))156 logging.info('topic={}'.format(args.topic))...

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parse_course.py

Source: parse_course.py Github

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...65 content['parent'] = parent_id66 for attr in root.attrib:67 content[attr] = root.attrib.get(attr)68 return content69 def _parse_structure(self, label, instance_id, usage_id, parent_id=None):70 file_name = "{}/​{}/​{}.xml".format(self.directory, label, instance_id)71 root = ElementTree.parse(file_name).getroot()72 content = self._populate_attributes(root, parent_id)73 if instance_id:74 content['id'] = instance_id75 content['usage_id'] = usage_id76 for child in root:77 try:78 child_parser = getattr(EdXMLParser, '_parse_' + child.tag)79 except AttributeError:80 child_parser = getattr(EdXMLParser, '_parse_leaf')81 content['children'] = content.get('children', [])82 child = child_parser(self, child, instance_id, child.tag)83 content['children'].append(child)84 content['score'] = content['score'] + child['score']85 return content86 def _calculate_usage_id(self, instance_id, label):87 # This method returns a usage ID for a split-mongo installation. For88 # the mongo DB in the Devstack or Full Stack installations, use:89 # return "i4x:;_;_{};_{};_{}".format(self.usage_prefix.replace('/​', ';_'), label, instance_id)90 return "block-v1:{}+{}+{}+type@{}+block@{}".format(91 self.org,92 self.course,93 self.url_name,94 label,95 instance_id96 )97 def _parse_course_xml(self):98 file_name = "{}/​course.xml".format(self.directory)99 root = ElementTree.parse(file_name).getroot()100 self.url_name = root.attrib.get('url_name')101 self.course = root.attrib.get('course')102 self.org = root.attrib.get('org')103 def _parse_course(self):104 self._parse_course_xml()105 usage_id = self._calculate_usage_id(self.url_name, 'course')106 self.parsed_course = self._parse_structure('course', self.url_name, usage_id)107 def _parse_chapter(self, element, parent_id, tag):108 instance_id = self._get_instance_id(element)109 usage_id = self._calculate_usage_id(element.attrib.get('url_name'), tag)110 return self._parse_structure(tag, instance_id=instance_id, usage_id=usage_id, parent_id=parent_id)111 def _parse_sequential(self, element, parent_id, tag):112 instance_id = self._get_instance_id(element)113 usage_id = self._calculate_usage_id(element.attrib.get('url_name'), tag)114 return self._parse_structure(tag, instance_id=instance_id, usage_id=usage_id, parent_id=parent_id)115 def _parse_vertical(self, element, parent_id, tag):116 instance_id = self._get_instance_id(element)117 usage_id = self._calculate_usage_id(element.attrib.get('url_name'), tag)118 return self._parse_structure(tag, instance_id=instance_id, usage_id=usage_id, parent_id=parent_id)119 def _parse_problem(self, element, parent_id, tag):120 if element.attrib.get('display_name'):121 content = self._populate_attributes(element, parent_id)122 content['score'] = 1123 else:124 instance_id = self._get_instance_id(element)125 # instance_id = element.attrib.get('url_name')126 file_name = "{}/​problem/​{}.xml".format(self.directory, instance_id)127 root = ElementTree.parse(file_name).getroot()128 content = self._populate_attributes(root, parent_id)129 content['id'] = instance_id130 content['usage_id'] = self._calculate_usage_id(content['id'], tag)131 score = 0132 score += len(root.findall('./​/​coderesponse'))...

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pdb_parse.py

Source: pdb_parse.py Github

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...19 for line in f:20 content.append(line.decode("utf-8"))21 temp_fp = StringIO("".join(content))22 return temp_fp23def _parse_structure(24 parser: Union[PDBParser, MMCIFParser], name: str, file_path: str25) -> Structure:26 """Parse a .pdb or .cif file into a structure object.27 The file can be gzipped."""28 if pd.isnull(file_path):29 return None30 if file_path.endswith(".gz"):31 structure = parser.get_structure(name, gunzip_to_ram(file_path))32 else: # not gzipped33 structure = parser.get_structure(name, file_path)34 return structure35parse_pdb_structure = _parse_structure # for backward compatiblity36def parse_structure(37 pdb_parser: PDBParser, cif_parser: MMCIFParser, name: str, file_path: str38) -> Structure:39 """Parse a .pdb file or .cif file into a structure object.40 The file can be gzipped."""41 if file_path.rstrip(".gz").endswith("pdb"):42 return _parse_structure(pdb_parser, name, file_path)43 else:44 return _parse_structure(cif_parser, name, file_path)45def three_to_one_standard(res: Residue) -> str:46 """Encode non-standard AA to X."""47 if not is_aa(res, standard=True):48 return "X"49 return three_to_one(res)50def is_aa_by_target_atoms(res: Residue) -> bool:51 """Tell if a Residue object is AA"""52 target_atoms = ["N", "CA", "C", "O"]53 for atom in target_atoms:54 try:55 res[atom]56 except KeyError:57 return False58 return True...

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