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How to use none_of method in pyshould

Best Python code snippet using pyshould_python

test_query.py

Source:test_query.py

1import pytest2from ukbcc import query3def test_basic_query_creation(main_csv, gp_csv):4    cohort_criteria = {'all_of': [('6070', '1')], 'any_of': [], 'none_of': []}5    obs_query = query.create_queries(cohort_criteria,6                                   main_filename=main_csv,7                                   gpc_path=gp_csv)8    exp_query={'gp_clinical': {'all_of': '', 'any_of': '', 'none_of': ''}, 'main': {'all_of': "(t6070_0_0 == '1')", 'any_of': '', 'none_of': ''}}9    assert obs_query == exp_query10#Check all of with a single field works11def test_all_query_basic(main_csv, gp_csv):12    cohort_criteria = {'all_of': [('6070', "1")], 'any_of': [], 'none_of': []}13    gen_query = query.create_queries(cohort_criteria,14                                   main_filename=main_csv,15                                   gpc_path=gp_csv)16    ids = query.query_databases(cohort_criteria=cohort_criteria,17                                queries=gen_query, main_filename=main_csv,18                                write_dir=None, gpc_path=gp_csv,19                                out_filename=None, write=False)20    exp_ids = set(["1041796", "1037058", "1024938", "1016017", "1038882", "1030520", "1003670", "1027017"])21    assert exp_ids == set(ids)22#Check that "all of" works over fields with multiple columns23def test_all_multiple_columns(main_csv, gp_csv):24    cohort_criteria = {'all_of': [('6148', "4")], 'any_of': [], 'none_of': []}25    gen_query = query.create_queries(cohort_criteria,26                                   main_filename=main_csv,27                                   gpc_path=gp_csv)28    ids = query.query_databases(cohort_criteria=cohort_criteria,29                                queries=gen_query, main_filename=main_csv,30                                write_dir=None, gpc_path=gp_csv,31                                out_filename=None, write=False)32    exp_ids = set(["1037918",  "1033149",  "1016017",  "1033388",  "1030520",  "1003670"])33    assert exp_ids == set(ids)34#Check any of with a single field works35def test_any_singleton_query(main_csv, gp_csv):36    cohort_criteria = {'any_of': [('6070', "1")], 'all_of': [], 'none_of': []}37    gen_query = query.create_queries(cohort_criteria,38                                   main_filename=main_csv,39                                   gpc_path=gp_csv)40    ids = query.query_databases(cohort_criteria=cohort_criteria,41                                queries=gen_query, main_filename=main_csv,42                                write_dir=None, gpc_path=gp_csv,43                                out_filename=None, write=False)44    exp_ids = set(["1041796", "1037058", "1024938", "1016017", "1038882", "1030520", "1003670", "1027017"])45    assert exp_ids == set(ids)46#Check that any of works over fields with multiple columns47def test_any_multiple_columns(main_csv, gp_csv):48    cohort_criteria = {'any_of': [('6148', "4")], 'all_of': [], 'none_of': []}49    gen_query = query.create_queries(cohort_criteria,50                                   main_filename=main_csv,51                                   gpc_path=gp_csv)52    ids = query.query_databases(cohort_criteria=cohort_criteria,53                                queries=gen_query, main_filename=main_csv,54                                write_dir=None, gpc_path=gp_csv,55                                out_filename=None, write=False)56    exp_ids = set(["1037918",  "1033149",  "1016017",  "1033388",  "1030520",  "1003670"])57    assert exp_ids == set(ids)58#Check any of with two values for the same field returns their union59def test_any_pair_same_field_query(main_csv, gp_csv):60    cohort_criteria = {'any_of': [('6070', "1"), ('6070', "2")], 'all_of': [], 'none_of': []}61    gen_query = query.create_queries(cohort_criteria,62                                   main_filename=main_csv,63                                   gpc_path=gp_csv)64    ids = query.query_databases(cohort_criteria=cohort_criteria,65                                queries=gen_query, main_filename=main_csv,66                                write_dir=None, gpc_path=gp_csv,67                                out_filename=None, write=False)68    exp_ids = set(["1037918", "1041796", "1037058", "1024938", "1016017", "1038882", "1030520", "1003670", "1027017"])69    assert exp_ids == set(ids)70#Check any of with two fields returns their union71def test_any_pair_diff_field_query(main_csv, gp_csv):72    cohort_criteria = {'any_of': [('6070', "1"), ('6119', "1")], 'all_of': [], 'none_of': []}73    gen_query = query.create_queries(cohort_criteria,74                                   main_filename=main_csv,75                                   gpc_path=gp_csv)76    ids = query.query_databases(cohort_criteria=cohort_criteria,77                                queries=gen_query, main_filename=main_csv,78                                write_dir=None, gpc_path=gp_csv,79                                out_filename=None, write=False)80    exp_ids = set(["1041796", "1037058", "1024938", "1016017", "1038882", "1030520", "1003670", "1027017"])81    assert exp_ids == set(ids)82# Check if a none only query returns values83def test_none_basic(main_csv, gp_csv):84    cohort_criteria = {'none_of': [('6070', "1")], 'all_of': [], 'any_of': []}85    gen_query = query.create_queries(cohort_criteria,86                                   main_filename=main_csv,87                                   gpc_path=gp_csv)88    print(gen_query)89    ids = query.query_databases(cohort_criteria=cohort_criteria,90                                queries=gen_query, main_filename=main_csv,91                                write_dir=None, gpc_path=gp_csv,92                                out_filename=None, write=False)93    print(ids)94    exp_ids = set(["1037918",  "1033149",  "1033388",  "1031625",  "1031595",  "1008947"])95    assert exp_ids == set(ids)96#Check that "all of" and "none_of" works over fields with multiple columns97def test_all__none_multiple_columns(main_csv, gp_csv):98    cohort_criteria = {'all_of': [('6148', "4")], 'any_of': [], 'none_of': [("6070", "2")]}99    gen_query = query.create_queries(cohort_criteria,100                                   main_filename=main_csv,101                                   gpc_path=gp_csv)102    ids = query.query_databases(cohort_criteria=cohort_criteria,103                                queries=gen_query, main_filename=main_csv,104                                write_dir=None, gpc_path=gp_csv,105                                out_filename=None, write=False)106    exp_ids = set([ "1033149",  "1016017",  "1033388",  "1030520",  "1003670"])107    assert exp_ids == set(ids)108#Check that "none_of" returns empty fields.109def test_none_returns_empty(main_csv, gp_csv):110    cohort_criteria = {'all_of': [('6148', "4")], 'any_of': [], 'none_of': [("6070", "2"), ("6070", "1")]}111    gen_query = query.create_queries(cohort_criteria,112                                   main_filename=main_csv,113                                   gpc_path=gp_csv)114    ids = query.query_databases(cohort_criteria=cohort_criteria,115                                queries=gen_query, main_filename=main_csv,116                                write_dir=None, gpc_path=gp_csv,117                                out_filename=None, write=False)118    exp_ids = set(["1033149",  "1033388"])119    assert exp_ids == set(ids)120#Check fields with spaces121def test_fields_with_spaces(main_csv, gp_csv):122    cohort_criteria = {'all_of': [('41270', "Block H40-H42")], 'any_of': [], 'none_of': []}123    gen_query = query.create_queries(cohort_criteria,124                                   main_filename=main_csv,125                                   gpc_path=gp_csv)126    ids = query.query_databases(cohort_criteria=cohort_criteria,127                                queries=gen_query, main_filename=main_csv,128                                write_dir=None, gpc_path=gp_csv,129                                out_filename=None, write=False)130    exp_ids = set(["1033149",  "1041796"])131    assert exp_ids == set(ids)132#What do we do with fields that don't exist133def test_missing_fields(main_csv, gp_csv):134    cohort_criteria = {'all_of': [('DoesNotExist', "X")], 'any_of': [], 'none_of': []}135    gen_query = query.create_queries(cohort_criteria,136                                   main_filename=main_csv,137                                   gpc_path=gp_csv)138    ids = query.query_databases(cohort_criteria=cohort_criteria,139                                queries=gen_query, main_filename=main_csv,140                                write_dir=None, gpc_path=gp_csv,141                                out_filename=None, write=False)142    exp_ids = set([])143    assert exp_ids == set(ids)144#What do we do when we query nan?145def test_missing_fields(main_csv, gp_csv):146    cohort_criteria = {'all_of': [('6070', "nan")], 'any_of': [], 'none_of': []}147    gen_query = query.create_queries(cohort_criteria,148                                   main_filename=main_csv,149                                   gpc_path=gp_csv)150    ids = query.query_databases(cohort_criteria=cohort_criteria,151                                queries=gen_query, main_filename=main_csv,152                                write_dir=None, gpc_path=gp_csv,153                                out_filename=None, write=False)154    exp_ids = set([])155    assert exp_ids == set(ids)156#Can we do a query on read2 at all?157def test_all_gp_clinical_read2(main_csv, gp_csv):158    cohort_criteria = {'all_of': [('read_2', "4662.")], 'any_of': [], 'none_of': []}159    gen_query = query.create_queries(cohort_criteria,160                                   main_filename=main_csv,161                                   gpc_path=gp_csv)162    ids = query.query_databases(cohort_criteria=cohort_criteria,163                                queries=gen_query, main_filename=main_csv,164                                write_dir=None, gpc_path=gp_csv,165                                out_filename=None, write=False)166    exp_ids = set(["1041796"])167    assert exp_ids == set(ids)168#Can we read read2 when multiple entries per person169def test_all_gp_clinical_read_2_multiple(main_csv, gp_csv):170    cohort_criteria = {'all_of': [('read_2', "XE0of")], 'any_of': [], 'none_of': []}171    gen_query = query.create_queries(cohort_criteria,172                                   main_filename=main_csv,173                                   gpc_path=gp_csv)174    ids = query.query_databases(cohort_criteria=cohort_criteria,175                                queries=gen_query, main_filename=main_csv,176                                write_dir=None, gpc_path=gp_csv,177                                out_filename=None, write=False)178    exp_ids = set(["1016017"])179    assert exp_ids == set(ids)180#Can we read read3181def test_all_gp_clinical_read_3(main_csv, gp_csv):182    cohort_criteria = {'all_of': [('read_3', "XE0Gu")], 'any_of': [], 'none_of': []}183    gen_query = query.create_queries(cohort_criteria,184                                   main_filename=main_csv,185                                   gpc_path=gp_csv)186    ids = query.query_databases(cohort_criteria=cohort_criteria,187                                queries=gen_query, main_filename=main_csv,188                                write_dir=None, gpc_path=gp_csv,189                                out_filename=None, write=False)190    exp_ids = set(["1037918"])191    assert exp_ids == set(ids)192#Can we query 2 and 3?193def test_all_gp_clinical_read2and3(main_csv, gp_csv):194    cohort_criteria = {'all_of': [], 'any_of': [('read_2', "XE0of"), ('read_3', 'XE0Gu')],  'none_of': []}195    gen_query = query.create_queries(cohort_criteria,196                                   main_filename=main_csv,197                                   gpc_path=gp_csv)198    ids = query.query_databases(cohort_criteria=cohort_criteria,199                                queries=gen_query, main_filename=main_csv,200                                write_dir=None, gpc_path=gp_csv,201                                out_filename=None, write=False)202    exp_ids = set(["1016017", "1037918"])203    assert exp_ids == set(ids)204#Complex query, use gp_clinical and main, and use all, not and any205def test_any_pair_same_field_query(main_csv, gp_csv):206    cohort_criteria = {'any_of': [('41270', "Block H40-H42"), ('6119', "3"), ('6148','4')], 'all_of': [(('6070', "1"))], 'none_of': [('read_2', "XE0of")]}207    gen_query = query.create_queries(cohort_criteria,208                                   main_filename=main_csv,209                                   gpc_path=gp_csv)210    ids = query.query_databases(cohort_criteria=cohort_criteria,211                                queries=gen_query, main_filename=main_csv,212                                write_dir=None, gpc_path=gp_csv,213                                out_filename=None, write=False)214    exp_ids = set(["1041796", "1037058",  "1030520",  "1003670"])...

prim.py

Source:prim.py

...59    return PrimitiveParser(f, pattern)60# def char() -> Parser:61#     """Char function."""62#     return regex(r"\S")63def none_of(s: str) -> Parser:64    """none_of function.65    As the dual of oneOf, none_of(cs) succeeds if the current character66    not in the supplied list of characters cs. Returns the parsed character.67    Example68    -------69    >>> from simpleparser import none_of, choice, token, many, transform, seq70    >>> p = none_of("abcdefg")71    >>> p.exec("hello")72    ['h']73    >>> chars = choice(token('""'), none_of('",'))74    >>> p = transform(many(chars), lambda x: ["".join(x)])75    >>> text = r'Shirt with ""Haskell"" text'76    >>> p.exec(text)77    ['Shirt with ""Haskell"" text']78    >>> dq = token('"')79    >>> p2 = transform(seq(dq, p, dq), lambda x: ["".join(x)])80    >>> text = r'"Shirt with ""Haskell"" text"'81    >>> p2.exec(text)82    ['"Shirt with ""Haskell"" text"']83    """  # noqa: E50184    name: str = f"none_of {s}"85    def f(target: str, position: int = 0) -> ParseResult:86        exists: bool = False87        targetChar: str = target[position:position + 1]...

query.py

Source:query.py

1from __future__ import annotations2from typing import *3from ecstremity.bit_util import *4from functools import reduce5if TYPE_CHECKING:6    from ecstremity.component import Component7    from ecstremity.world import World8def from_name(world: World, component_name: str) -> Component:9    return world.engine.components[component_name]10class Query:11    _cache = []12    def __init__(13            self,14            world: World,15            any_of: Optional[List[Union[Component, str]]] = None,16            all_of: Optional[List[Union[Component, str]]] = None,17            none_of: Optional[List[Union[Component, str]]] = None18    ) -> None:19        self._cache = []20        self.world = world21        self.any_of = any_of if any_of is not None else []22        self.all_of = all_of if all_of is not None else []23        self.none_of = none_of if none_of is not None else []24        self._any = reduce(lambda a, b: add_bit(a, b.cbit), self.any_of, 0)25        self._all = reduce(lambda a, b: add_bit(a, b.cbit), self.all_of, 0)26        self._none = reduce(lambda a, b: add_bit(a, b.cbit), self.none_of, 0)27        self.refresh()28    def idx(self, entity):29        try:30            return self._cache.index(entity)31        except ValueError:32            return -133    def matches(self, entity):34        bits = entity.cbits35        any_of = self._any == 0 or bit_intersection(bits, self._any) > 036        all_of = bit_intersection(bits, self._all) == self._all37        none_of = bit_intersection(bits, self._none) == 038        return any_of & all_of & none_of39    def candidate(self, entity):40        idx = self.idx(entity)41        is_tracking = idx >= 042        if self.matches(entity):43            if not is_tracking:44                self._cache.append(entity)45            return True46        if is_tracking:47            del self._cache[idx]48        return False49    def refresh(self):50        self._cache = []51        for entity in self.world.entities:52            self.candidate(entity)53    @property54    def result(self):...

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