mandos.model.pubchem_support.ClinicalTrial.known_phase() - Code Metrics - dmyersturnbull/mandos - Measure and Improve Code Quality continuously with Scrutinizer

ClinicalTrial.known_phase() A
last analyzed 2021-01-25 23:07 UTC

↳ Parent: mandos.model.pubchem_support

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

import pandas as pd


from mandos import MandosResources
from mandos.model.query_utils import Fns

hazards = pd.read_csv(MandosResources.path("hazards.tab"), sep="\t")
hazards = dict(hazards.set_index("code").T.to_dict())


@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 Fns.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()


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

class PubchemAssay:
    type: AssayType
    ref: str  # e.g. "ChEMBL"
    name: str  # e.g. "Binding affinity towards human monoclonal antibody 2E2 using [3H]cocaine"
    made_date: date


class Activity(enum.Enum):

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


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

class Bioactivity:
    assay: PubchemAssay
    gene_id: Optional[Codes.GeneId]
    tax_id: Optional[int]
    pmid: Optional[Codes.PubmedId]
    activity: Activity
    activity_name: str
    activity_value: str
    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",
    "DrugbankInteraction",
    "DrugbankDdi",
    "Bioactivity",
    "PubchemAssay",
    "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			import pandas as pd
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9
10			from mandos import MandosResources
11			from mandos.model.query_utils import Fns
12
13			hazards = pd.read_csv(MandosResources.path("hazards.tab"), sep="\t")
14			hazards = dict(hazards.set_index("code").T.to_dict())
15
16
17			@dataclass(frozen=True, repr=True, eq=True, order=True)
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18			class ComputedProperty:
19			key: str
20			value: Union[int, str, float, bool]
21			unit: Optional[str]
22			ref: str
23
24			def req_is(self, type_) -> Union[int, str, float, bool]:
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25			if not isinstance(self.value, type_):
26			raise TypeError(f"{self.key}->{self.value} has {type(self.value)}, not {type_}")
27			return self.value
28
29			@property
30			def as_str(self) -> str:
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31			return f"{self.value} {self.unit}"
32
33
34			class Code(str):
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35			@property
36			def type_name(self) -> str:
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37			return self.__class__.__name__.lower()
38
39			@classmethod
40			def of(cls, value: Union[str, int, float]):
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41			if isinstance(value, float):
42			try:
43			value = int(value)
44			except ArithmeticError:
45			value = str(value)
46			value = str(value).strip()
47			return cls(value)
48
49
50			class Codes:
51			"""
52			These turn out to be extremely useful for documenting return types.
53			For example, ``DrugbankInteraction`` might have a ``gene`` field,
54			which can be described as a ``GenecardSymbol`` if known.
55			"""
56
57			class EcNumber(Code):
58			"""
59			e.g. 'EC:4.6.1.1'
60			"""
61
62			class GeneId(Code):
63			"""
64			GeneCard, UniProt gene name, etc.
65			e.g. 'slc1a2'
66			"""
67
68			class GenecardSymbol(GeneId):
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69			""""""
70
71			class UniprotId(GeneId):
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72			""""""
73
74			class PubchemCompoundId(Code):
75			"""
76			e.g. 2352
77			"""
78
79			@property
80			def value(self) -> int:
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81			return int(self)
82
83			class AtcCode(Code):
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84			""""""
85
86			class PubmedId(Code):
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87			""""""
88
89			class Doi(Code):
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90			""""""
91
92			class MeshCode(Code):
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93			""""""
94
95			class PdbId(Code):
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96			""""""
97
98			class MeshHeading(Code):
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99			""""""
100
101			class MeshSubheading(Code):
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102			""""""
103
104			class DrugbankCompoundId(Code):
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105			""""""
106
107			class DeaSchedule(Code):
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108			""""""
109
110			@property
111			def value(self) -> int:
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112			return Fns.roman_to_arabic(1, 5)(self)
113
114			class GhsCode(Code):
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115			""""""
116
117
118			class CoOccurrenceType(enum.Enum):
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119			chemical = enum.auto()
120			gene = enum.auto()
121			disease = enum.auto()
122
123			@property
124			def x_name(self) -> str:
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125			if self is CoOccurrenceType.chemical:
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126			return "ChemicalNeighbor"
127			elif self is CoOccurrenceType.gene:
128			return "ChemicalGeneSymbolNeighbor"
129			elif self is CoOccurrenceType.disease:
130			return "ChemicalDiseaseNeighbor"
131			raise AssertionError(f"{self} not found!!")
132
133			@property
134			def id_name(self) -> str:
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135			if self is CoOccurrenceType.chemical:
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136			return "CID"
137			elif self is CoOccurrenceType.gene:
138			return "GeneSymbol"
139			elif self is CoOccurrenceType.disease:
140			return "MeSH"
141			raise AssertionError(f"{self} not found!!")
142
143
144			@dataclass(frozen=True, repr=True, eq=True)
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145			class ClinicalTrial:
146			title: str
147			conditions: FrozenSet[str]
148			phase: str
149			status: str
150			interventions: FrozenSet[str]
151			cids: FrozenSet[Codes.PubchemCompoundId]
152			source: str
153
154			@property
155			def known_phase(self) -> int:
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156			return {
157			"Phase 4": 4,
158			"Phase 3": 3,
159			"Phase 2": 2,
160			"Phase 1": 1,
161			"Early Phase 1": 1,
162			"N/A": 0,
163			}.get(self.status, 0)
164
165
166			@dataclass(frozen=True, repr=True, eq=True)
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167			class GhsCode:
168			code: Codes.GhsCode
169			statement: str
170			clazz: str
171			categories: FrozenSet[str]
172			signal_word: str
173			type: str
174
175			@classmethod
176			def find(cls, code: str) -> GhsCode:
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177			h = hazards[code]
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178			cats = h["category"] # TODO
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179			return GhsCode(
180			code=Codes.GhsCode(code),
181			statement=h["statement"],
182			clazz=h["class"],
183			categories=cats,
184			signal_word=h["signal_word"],
185			type=h["type"],
186			)
187
188			@property
189			def level(self) -> int:
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190			return int(self.code[1])
191
192
193			@dataclass(frozen=True, repr=True, eq=True)
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194			class AssociatedDisorder:
195			disease: str
196			evidence_type: str
197			n_refs: int
198
199
200			@dataclass(frozen=True, repr=True, eq=True)
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201			class AtcCode:
202			code: str
203			name: str
204
205			@property
206			def level(self) -> int:
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207			return len(self.parts)
208
209			@property
210			def parts(self) -> Sequence[str]:
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211			pat = re.compile(r"([A-Z])([0-9]{2})?([A-Z])?([A-Z])?([A-Z])?")
212			match = pat.fullmatch(self.code)
213			return [g for g in match.groups() if g is not None]
214
215
216			@dataclass(frozen=True, repr=True, eq=True)
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217			class DrugbankInteraction:
218			gene_symbol: Codes.GeneId
219			action: str
220			target_name: str
221			general_function: Sequence[str]
222			specific_function: str
223			pmids: FrozenSet[Codes.PubmedId]
224			dois: FrozenSet[Codes.Doi]
225
226
227			@dataclass(frozen=True, repr=True, eq=True)
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228			class DrugbankDdi:
229			drug_drugbank_id: Codes.DrugbankCompoundId
230			drug_pubchem_id: Codes.PubchemCompoundId
231			drug_drugbank_name: str
232			description: str
233
234
235			class AssayType(enum.Enum):
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236			confirmatory = enum.auto()
237			literature = enum.auto()
238
239
240			@dataclass(frozen=True, repr=True, eq=True)
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241			class PubchemAssay:
242			type: AssayType
243			ref: str # e.g. "ChEMBL"
244			name: str # e.g. "Binding affinity towards human monoclonal antibody 2E2 using [3H]cocaine"
245			made_date: date
246
247
248			class Activity(enum.Enum):
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249			active = enum.auto()
250			inactive = enum.auto()
251			unspecified = enum.auto()
252
253
254			@dataclass(frozen=True, repr=True, eq=True)
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255			class Bioactivity:
256			assay: PubchemAssay
257			gene_id: Optional[Codes.GeneId]
258			tax_id: Optional[int]
259			pmid: Optional[Codes.PubmedId]
260			activity: Activity
261			activity_name: str
262			activity_value: str
263			target_name: Optional[str]
264
265
266			@dataclass(frozen=True, repr=True, eq=True)
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267			class PdbEntry:
268			pdbid: Codes.PdbId
269			title: str
270			exp_method: str
271			resolution: float
272			lig_names: FrozenSet[str]
273			cids: FrozenSet[Codes.PubchemCompoundId]
274			uniprot_ids: FrozenSet[Codes.UniprotId]
275			pmids: FrozenSet[Codes.PubmedId]
276			dois: FrozenSet[Codes.Doi]
277
278
279			@dataclass(frozen=True, repr=True, eq=True)
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280			class PubmedEntry:
281			pmid: Codes.PubmedId
282			article_type: str
283			pmidsrcs: FrozenSet[str]
284			mesh_headings: FrozenSet[Codes.MeshHeading]
285			mesh_subheadings: FrozenSet[Codes.MeshSubheading]
286			mesh_codes: FrozenSet[Codes.MeshCode]
287			cids: FrozenSet[Codes.PubchemCompoundId]
288			article_title: str
289			article_abstract: str
290			journal_name: str
291			pub_date: date
292
293
294			@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...
295			class Publication:
296			pmid: Codes.PubmedId
297			pub_date: date
298			is_review: bool
299			title: str
300			journal: str
301			relevance_score: int
302
303
304			@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... best-practice introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Too many instance attributes (8/7) Loading history...
305			class CoOccurrence:
306			neighbor_id: str
307			neighbor_name: str
308			kind: CoOccurrenceType
309			# https://pubchemdocs.ncbi.nlm.nih.gov/knowledge-panels
310			article_count: int
311			query_article_count: int
312			neighbor_article_count: int
313			score: int
314			publications: FrozenSet[Publication]
315
316			def strip_pubs(self) -> CoOccurrence:
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317			return CoOccurrence(
318			self.neighbor_id,
319			self.neighbor_name,
320			self.kind,
321			self.article_count,
322			self.query_article_count,
323			self.neighbor_article_count,
324			self.score,
325			frozenset({}),
326			)
327
328
329			@dataclass(frozen=True, repr=True, eq=True)
			0 ignored issues – show Documentation introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Empty class docstring Loading history...
330			class DrugGeneInteraction:
331			""""""
332
333			gene_name: Optional[str]
334			gene_claim_id: Optional[str]
335			source: str
336			interactions: FrozenSet[str]
337			pmids: FrozenSet[Codes.PubmedId]
338			dois: FrozenSet[Codes.Doi]
339
340
341			@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...
342			class CompoundGeneInteraction:
343			gene_name: Optional[Codes.GeneId]
344			interactions: FrozenSet[str]
345			tax_name: Optional[str]
346			pmids: FrozenSet[Codes.PubmedId]
347
348
349			__all__ = [
350			"ClinicalTrial",
351			"AssociatedDisorder",
352			"AtcCode",
353			"DrugbankInteraction",
354			"DrugbankDdi",
355			"Bioactivity",
356			"PubchemAssay",
357			"DrugGeneInteraction",
358			"CompoundGeneInteraction",
359			"GhsCode",
360			"PubmedEntry",
361			"Code",
362			"Codes",
363			"CoOccurrenceType",
364			"CoOccurrence",
365			"Publication",
366			"ComputedProperty",
367			]
368

dmyersturnbull / mandos

ClinicalTrial.known_phase() A last analyzed 2021-01-25 23:07 UTC

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Duplication

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ClinicalTrial.known_phase() A
last analyzed 2021-01-25 23:07 UTC