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How to use _parse_structure method in localstack

Best Python code snippet using localstack_python

app.py

Source:app.py

...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))...

parse_course.py

Source:parse_course.py

...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'))...

pdb_parse.py

Source:pdb_parse.py

...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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