mandos.model.pubchem_support.pubchem_models.ClinicalTrial.known_phase() - Code Metrics - Inspection of "Bump sphinxcontrib-mermaid from 0.5.0 to 0.6.3" - dmyersturnbull/mandos - Measure and Improve Code Quality continuously with Scrutinizer

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created 2021-02-22 06:48 UTC

ClinicalTrial.known_phase() A

↳ Parent: mandos.model.pubchem_support.pubchem_models

Complexity

Conditions

Size

Total Lines	10
Code Lines	10

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	1
eloc	10
nop	1
dl	0
loc	10
rs	9.9
c	0
b	0
f	0

from __future__ import annotations

import enum
import re
from dataclasses import dataclass
from datetime import date
from typing import Union, Optional, FrozenSet, Sequence

from pocketutils.core.dot_dict import NestedDotDict


from mandos import MandosResources
from mandos.model.pubchem_support._nav_fns import Mapx

hazards = {
    d["code"]: d for d in NestedDotDict.read_toml(MandosResources.path("hazards.toml"))["signals"]
}


@dataclass(frozen=True, repr=True, eq=True, order=True)

class ComputedProperty:
    key: str
    value: Union[int, str, float, bool]
    unit: Optional[str]
    ref: str

    def req_is(self, type_) -> Union[int, str, float, bool]:

        if not isinstance(self.value, type_):
            raise TypeError(f"{self.key}->{self.value} has {type(self.value)}, not {type_}")
        return self.value

    @property
    def as_str(self) -> str:

        return f"{self.value} {self.unit}"


class Code(str):

    @property
    def type_name(self) -> str:

        return self.__class__.__name__.lower()

    @classmethod
    def of(cls, value: Union[str, int, float]):

        if isinstance(value, float):
            try:
                value = int(value)
            except ArithmeticError:
                value = str(value)
        value = str(value).strip()
        return cls(value)


class Codes:
    """
    These turn out to be extremely useful for documenting return types.
    For example, ``DrugbankInteraction`` might have a ``gene`` field,
    which can be described as a ``GenecardSymbol`` if known.
    """

    class EcNumber(Code):
        """
        e.g. 'EC:4.6.1.1'
        """

    class GeneId(Code):
        """
        GeneCard, UniProt gene name, etc.
        e.g. 'slc1a2'
        """

    class GenecardSymbol(GeneId):

        """"""

    class UniprotId(GeneId):

        """"""

    class PubchemCompoundId(Code):
        """
        e.g. 2352
        """

        @property
        def value(self) -> int:

            return int(self)

    class AtcCode(Code):

        """"""

    class PubmedId(Code):

        """"""

    class Doi(Code):

        """"""

    class MeshCode(Code):

        """"""

    class PdbId(Code):

        """"""

    class MeshHeading(Code):

        """"""

    class MeshSubheading(Code):

        """"""

    class DrugbankCompoundId(Code):

        """"""

    class DeaSchedule(Code):

        """"""

        @property
        def value(self) -> int:

            return Mapx.roman_to_arabic(1, 5)(self)

    class GhsCode(Code):

        """"""


class CoOccurrenceType(enum.Enum):

    chemical = enum.auto()
    gene = enum.auto()
    disease = enum.auto()

    @property
    def x_name(self) -> str:

        if self is CoOccurrenceType.chemical:

            return "ChemicalNeighbor"
        elif self is CoOccurrenceType.gene:
            return "ChemicalGeneSymbolNeighbor"
        elif self is CoOccurrenceType.disease:
            return "ChemicalDiseaseNeighbor"
        raise AssertionError(f"{self} not found!!")

    @property
    def id_name(self) -> str:

        if self is CoOccurrenceType.chemical:

            return "CID"
        elif self is CoOccurrenceType.gene:
            return "GeneSymbol"
        elif self is CoOccurrenceType.disease:
            return "MeSH"
        raise AssertionError(f"{self} not found!!")


@dataclass(frozen=True, repr=True, eq=True)

class ClinicalTrial:
    title: str
    conditions: FrozenSet[str]
    phase: str
    status: str
    interventions: FrozenSet[str]
    cids: FrozenSet[Codes.PubchemCompoundId]
    source: str

    @property
    def known_phase(self) -> int:

        return {
            "Phase 4": 4,
            "Phase 3": 3,
            "Phase 2": 2,
            "Phase 1": 1,
            "Early Phase 1": 1,
            "N/A": 0,
        }.get(self.status, 0)


@dataclass(frozen=True, repr=True, eq=True)

class GhsCode:
    code: Codes.GhsCode
    statement: str
    clazz: str
    categories: FrozenSet[str]
    signal_word: str
    type: str

    @classmethod
    def find(cls, code: str) -> GhsCode:

        h = hazards[code]

        cats = h["category"]  # TODO

        return GhsCode(
            code=Codes.GhsCode(code),
            statement=h["statement"],
            clazz=h["class"],
            categories=cats,
            signal_word=h["signal_word"],
            type=h["type"],
        )

    @property
    def level(self) -> int:

        return int(self.code[1])


@dataclass(frozen=True, repr=True, eq=True)

class AssociatedDisorder:
    disease: str
    evidence_type: str
    n_refs: int


@dataclass(frozen=True, repr=True, eq=True)

class AtcCode:
    code: str
    name: str

    @property
    def level(self) -> int:

        return len(self.parts)

    @property
    def parts(self) -> Sequence[str]:

        pat = re.compile(r"([A-Z])([0-9]{2})?([A-Z])?([A-Z])?([A-Z])?")
        match = pat.fullmatch(self.code)
        return [g for g in match.groups() if g is not None]


@dataclass(frozen=True, repr=True, eq=True)

class DrugbankInteraction:
    gene_symbol: Codes.GeneId
    action: str
    target_name: str
    general_function: Sequence[str]
    specific_function: str
    pmids: FrozenSet[Codes.PubmedId]
    dois: FrozenSet[Codes.Doi]


@dataclass(frozen=True, repr=True, eq=True)

class DrugbankDdi:
    drug_drugbank_id: Codes.DrugbankCompoundId
    drug_pubchem_id: Codes.PubchemCompoundId
    drug_drugbank_name: str
    description: str


class AssayType(enum.Enum):

    confirmatory = enum.auto()
    literature = enum.auto()


class Activity(enum.Enum):

    active = enum.auto()
    inactive = enum.auto()
    unspecified = enum.auto()


@dataclass(frozen=True, repr=True, eq=True)

class Bioactivity:
    assay_id: int
    assay_type: AssayType
    assay_ref: str
    assay_name: str
    assay_made_date: date
    gene_id: Optional[Codes.GeneId]
    tax_id: Optional[int]
    pmid: Optional[Codes.PubmedId]
    activity: Optional[Activity]
    activity_name: Optional[str]
    activity_value: float
    target_name: Optional[str]


@dataclass(frozen=True, repr=True, eq=True)

class PdbEntry:
    pdbid: Codes.PdbId
    title: str
    exp_method: str
    resolution: float
    lig_names: FrozenSet[str]
    cids: FrozenSet[Codes.PubchemCompoundId]
    uniprot_ids: FrozenSet[Codes.UniprotId]
    pmids: FrozenSet[Codes.PubmedId]
    dois: FrozenSet[Codes.Doi]


@dataclass(frozen=True, repr=True, eq=True)

class PubmedEntry:
    pmid: Codes.PubmedId
    article_type: str
    pmidsrcs: FrozenSet[str]
    mesh_headings: FrozenSet[Codes.MeshHeading]
    mesh_subheadings: FrozenSet[Codes.MeshSubheading]
    mesh_codes: FrozenSet[Codes.MeshCode]
    cids: FrozenSet[Codes.PubchemCompoundId]
    article_title: str
    article_abstract: str
    journal_name: str
    pub_date: date


@dataclass(frozen=True, repr=True, eq=True)

class Publication:
    pmid: Codes.PubmedId
    pub_date: date
    is_review: bool
    title: str
    journal: str
    relevance_score: int


@dataclass(frozen=True, repr=True, eq=True)

class CoOccurrence:
    neighbor_id: str
    neighbor_name: str
    kind: CoOccurrenceType
    # https://pubchemdocs.ncbi.nlm.nih.gov/knowledge-panels
    article_count: int
    query_article_count: int
    neighbor_article_count: int
    score: int
    publications: FrozenSet[Publication]

    def strip_pubs(self) -> CoOccurrence:

        return CoOccurrence(
            self.neighbor_id,
            self.neighbor_name,
            self.kind,
            self.article_count,
            self.query_article_count,
            self.neighbor_article_count,
            self.score,
            frozenset({}),
        )


@dataclass(frozen=True, repr=True, eq=True)

class DrugGeneInteraction:
    """"""

    gene_name: Optional[str]
    gene_claim_id: Optional[str]
    source: str
    interactions: FrozenSet[str]
    pmids: FrozenSet[Codes.PubmedId]
    dois: FrozenSet[Codes.Doi]


@dataclass(frozen=True, repr=True, eq=True)

class CompoundGeneInteraction:
    gene_name: Optional[Codes.GeneId]
    interactions: FrozenSet[str]
    tax_name: Optional[str]
    pmids: FrozenSet[Codes.PubmedId]


__all__ = [
    "ClinicalTrial",
    "AssociatedDisorder",
    "AtcCode",
    "AssayType",
    "DrugbankInteraction",
    "DrugbankDdi",
    "Bioactivity",
    "Activity",
    "DrugGeneInteraction",
    "CompoundGeneInteraction",
    "GhsCode",
    "PubmedEntry",
    "Code",
    "Codes",
    "CoOccurrenceType",
    "CoOccurrence",
    "Publication",
    "ComputedProperty",
]


1			from __future__ import annotations
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2			import enum
3			import re
4			from dataclasses import dataclass
5			from datetime import date
6			from typing import Union, Optional, FrozenSet, Sequence
7
8			from pocketutils.core.dot_dict import NestedDotDict
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9
10			from mandos import MandosResources
11			from mandos.model.pubchem_support._nav_fns import Mapx
12
13			hazards = {
14			d["code"]: d for d in NestedDotDict.read_toml(MandosResources.path("hazards.toml"))["signals"]
15			}
16
17
18			@dataclass(frozen=True, repr=True, eq=True, order=True)
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19			class ComputedProperty:
20			key: str
21			value: Union[int, str, float, bool]
22			unit: Optional[str]
23			ref: str
24
25			def req_is(self, type_) -> Union[int, str, float, bool]:
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26			if not isinstance(self.value, type_):
27			raise TypeError(f"{self.key}->{self.value} has {type(self.value)}, not {type_}")
28			return self.value
29
30			@property
31			def as_str(self) -> str:
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32			return f"{self.value} {self.unit}"
33
34
35			class Code(str):
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36			@property
37			def type_name(self) -> str:
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38			return self.__class__.__name__.lower()
39
40			@classmethod
41			def of(cls, value: Union[str, int, float]):
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42			if isinstance(value, float):
43			try:
44			value = int(value)
45			except ArithmeticError:
46			value = str(value)
47			value = str(value).strip()
48			return cls(value)
49
50
51			class Codes:
52			"""
53			These turn out to be extremely useful for documenting return types.
54			For example, ``DrugbankInteraction`` might have a ``gene`` field,
55			which can be described as a ``GenecardSymbol`` if known.
56			"""
57
58			class EcNumber(Code):
59			"""
60			e.g. 'EC:4.6.1.1'
61			"""
62
63			class GeneId(Code):
64			"""
65			GeneCard, UniProt gene name, etc.
66			e.g. 'slc1a2'
67			"""
68
69			class GenecardSymbol(GeneId):
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70			""""""
71
72			class UniprotId(GeneId):
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73			""""""
74
75			class PubchemCompoundId(Code):
76			"""
77			e.g. 2352
78			"""
79
80			@property
81			def value(self) -> int:
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82			return int(self)
83
84			class AtcCode(Code):
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85			""""""
86
87			class PubmedId(Code):
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88			""""""
89
90			class Doi(Code):
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91			""""""
92
93			class MeshCode(Code):
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94			""""""
95
96			class PdbId(Code):
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97			""""""
98
99			class MeshHeading(Code):
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100			""""""
101
102			class MeshSubheading(Code):
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103			""""""
104
105			class DrugbankCompoundId(Code):
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106			""""""
107
108			class DeaSchedule(Code):
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109			""""""
110
111			@property
112			def value(self) -> int:
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113			return Mapx.roman_to_arabic(1, 5)(self)
114
115			class GhsCode(Code):
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116			""""""
117
118
119			class CoOccurrenceType(enum.Enum):
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120			chemical = enum.auto()
121			gene = enum.auto()
122			disease = enum.auto()
123
124			@property
125			def x_name(self) -> str:
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126			if self is CoOccurrenceType.chemical:
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127			return "ChemicalNeighbor"
128			elif self is CoOccurrenceType.gene:
129			return "ChemicalGeneSymbolNeighbor"
130			elif self is CoOccurrenceType.disease:
131			return "ChemicalDiseaseNeighbor"
132			raise AssertionError(f"{self} not found!!")
133
134			@property
135			def id_name(self) -> str:
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136			if self is CoOccurrenceType.chemical:
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137			return "CID"
138			elif self is CoOccurrenceType.gene:
139			return "GeneSymbol"
140			elif self is CoOccurrenceType.disease:
141			return "MeSH"
142			raise AssertionError(f"{self} not found!!")
143
144
145			@dataclass(frozen=True, repr=True, eq=True)
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146			class ClinicalTrial:
147			title: str
148			conditions: FrozenSet[str]
149			phase: str
150			status: str
151			interventions: FrozenSet[str]
152			cids: FrozenSet[Codes.PubchemCompoundId]
153			source: str
154
155			@property
156			def known_phase(self) -> int:
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157			return {
158			"Phase 4": 4,
159			"Phase 3": 3,
160			"Phase 2": 2,
161			"Phase 1": 1,
162			"Early Phase 1": 1,
163			"N/A": 0,
164			}.get(self.status, 0)
165
166
167			@dataclass(frozen=True, repr=True, eq=True)
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168			class GhsCode:
169			code: Codes.GhsCode
170			statement: str
171			clazz: str
172			categories: FrozenSet[str]
173			signal_word: str
174			type: str
175
176			@classmethod
177			def find(cls, code: str) -> GhsCode:
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178			h = hazards[code]
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179			cats = h["category"] # TODO
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180			return GhsCode(
181			code=Codes.GhsCode(code),
182			statement=h["statement"],
183			clazz=h["class"],
184			categories=cats,
185			signal_word=h["signal_word"],
186			type=h["type"],
187			)
188
189			@property
190			def level(self) -> int:
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191			return int(self.code[1])
192
193
194			@dataclass(frozen=True, repr=True, eq=True)
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195			class AssociatedDisorder:
196			disease: str
197			evidence_type: str
198			n_refs: int
199
200
201			@dataclass(frozen=True, repr=True, eq=True)
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202			class AtcCode:
203			code: str
204			name: str
205
206			@property
207			def level(self) -> int:
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208			return len(self.parts)
209
210			@property
211			def parts(self) -> Sequence[str]:
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212			pat = re.compile(r"([A-Z])([0-9]{2})?([A-Z])?([A-Z])?([A-Z])?")
213			match = pat.fullmatch(self.code)
214			return [g for g in match.groups() if g is not None]
215
216
217			@dataclass(frozen=True, repr=True, eq=True)
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218			class DrugbankInteraction:
219			gene_symbol: Codes.GeneId
220			action: str
221			target_name: str
222			general_function: Sequence[str]
223			specific_function: str
224			pmids: FrozenSet[Codes.PubmedId]
225			dois: FrozenSet[Codes.Doi]
226
227
228			@dataclass(frozen=True, repr=True, eq=True)
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229			class DrugbankDdi:
230			drug_drugbank_id: Codes.DrugbankCompoundId
231			drug_pubchem_id: Codes.PubchemCompoundId
232			drug_drugbank_name: str
233			description: str
234
235
236			class AssayType(enum.Enum):
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237			confirmatory = enum.auto()
238			literature = enum.auto()
239
240
241			class Activity(enum.Enum):
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242			active = enum.auto()
243			inactive = enum.auto()
244			unspecified = enum.auto()
245
246
247			@dataclass(frozen=True, repr=True, eq=True)
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248			class Bioactivity:
249			assay_id: int
250			assay_type: AssayType
251			assay_ref: str
252			assay_name: str
253			assay_made_date: date
254			gene_id: Optional[Codes.GeneId]
255			tax_id: Optional[int]
256			pmid: Optional[Codes.PubmedId]
257			activity: Optional[Activity]
258			activity_name: Optional[str]
259			activity_value: float
260			target_name: Optional[str]
261
262
263			@dataclass(frozen=True, repr=True, eq=True)
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264			class PdbEntry:
265			pdbid: Codes.PdbId
266			title: str
267			exp_method: str
268			resolution: float
269			lig_names: FrozenSet[str]
270			cids: FrozenSet[Codes.PubchemCompoundId]
271			uniprot_ids: FrozenSet[Codes.UniprotId]
272			pmids: FrozenSet[Codes.PubmedId]
273			dois: FrozenSet[Codes.Doi]
274
275
276			@dataclass(frozen=True, repr=True, eq=True)
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277			class PubmedEntry:
278			pmid: Codes.PubmedId
279			article_type: str
280			pmidsrcs: FrozenSet[str]
281			mesh_headings: FrozenSet[Codes.MeshHeading]
282			mesh_subheadings: FrozenSet[Codes.MeshSubheading]
283			mesh_codes: FrozenSet[Codes.MeshCode]
284			cids: FrozenSet[Codes.PubchemCompoundId]
285			article_title: str
286			article_abstract: str
287			journal_name: str
288			pub_date: date
289
290
291			@dataclass(frozen=True, repr=True, eq=True)
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292			class Publication:
293			pmid: Codes.PubmedId
294			pub_date: date
295			is_review: bool
296			title: str
297			journal: str
298			relevance_score: int
299
300
301			@dataclass(frozen=True, repr=True, eq=True)
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302			class CoOccurrence:
303			neighbor_id: str
304			neighbor_name: str
305			kind: CoOccurrenceType
306			# https://pubchemdocs.ncbi.nlm.nih.gov/knowledge-panels
307			article_count: int
308			query_article_count: int
309			neighbor_article_count: int
310			score: int
311			publications: FrozenSet[Publication]
312
313			def strip_pubs(self) -> CoOccurrence:
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314			return CoOccurrence(
315			self.neighbor_id,
316			self.neighbor_name,
317			self.kind,
318			self.article_count,
319			self.query_article_count,
320			self.neighbor_article_count,
321			self.score,
322			frozenset({}),
323			)
324
325
326			@dataclass(frozen=True, repr=True, eq=True)
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327			class DrugGeneInteraction:
328			""""""
329
330			gene_name: Optional[str]
331			gene_claim_id: Optional[str]
332			source: str
333			interactions: FrozenSet[str]
334			pmids: FrozenSet[Codes.PubmedId]
335			dois: FrozenSet[Codes.Doi]
336
337
338			@dataclass(frozen=True, repr=True, eq=True)
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
339			class CompoundGeneInteraction:
340			gene_name: Optional[Codes.GeneId]
341			interactions: FrozenSet[str]
342			tax_name: Optional[str]
343			pmids: FrozenSet[Codes.PubmedId]
344
345
346			__all__ = [
347			"ClinicalTrial",
348			"AssociatedDisorder",
349			"AtcCode",
350			"AssayType",
351			"DrugbankInteraction",
352			"DrugbankDdi",
353			"Bioactivity",
354			"Activity",
355			"DrugGeneInteraction",
356			"CompoundGeneInteraction",
357			"GhsCode",
358			"PubmedEntry",
359			"Code",
360			"Codes",
361			"CoOccurrenceType",
362			"CoOccurrence",
363			"Publication",
364			"ComputedProperty",
365			]
366

dmyersturnbull / mandos

Push — dependabot/pip/sphinxcontrib-m... ( bd5eb4 )

ClinicalTrial.known_phase() A

Complexity

Size

Duplication

Importance

Duplication Side-by-Side

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