dmyersturnbull /
mandos
| Total Complexity | 41 |
| Total Lines | 998 |
| Duplicated Lines | 33.57 % |
| Changes | 0 | ||
Duplicate code is one of the most pungent code smells. A rule that is often used is to re-structure code once it is duplicated in three or more places.
Common duplication problems, and corresponding solutions are:
Complex classes like mandos.entries.entries often do a lot of different things. To break such a class down, we need to identify a cohesive component within that class. A common approach to find such a component is to look for fields/methods that share the same prefixes, or suffixes.
Once you have determined the fields that belong together, you can apply the Extract Class refactoring. If the component makes sense as a sub-class, Extract Subclass is also a candidate, and is often faster.
| 1 | """ |
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| 2 | Run searches and write files. |
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| 3 | """ |
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| 4 | |||
| 5 | from __future__ import annotations |
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| 6 | |||
| 7 | import abc |
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| 8 | from pathlib import Path |
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| 9 | from typing import Optional, TypeVar |
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| 10 | |||
| 11 | from mandos import logger |
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| 12 | from mandos.entries._entry_args import EntryArgs |
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| 13 | from mandos.entries._entry_utils import EntryUtils |
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| 14 | from mandos.entries.abstract_entries import Entry |
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| 15 | from mandos.entries.api_singletons import Apis |
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| 16 | from mandos.entries.common_args import CommonArgs |
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| 17 | from mandos.entries.searcher import Searcher |
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| 18 | from mandos.model.utils import ReflectionUtils, InjectionError |
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| 19 | from mandos.model.apis.chembl_api import ChemblApi |
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| 20 | from mandos.model.apis.pubchem_support.pubchem_models import ( |
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| 21 | CoOccurrenceType, |
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| 22 | DrugbankTargetType, |
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| 23 | ) |
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| 24 | from mandos.model.searches import Search |
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| 25 | from mandos.search.chembl.atc_search import AtcSearch |
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| 26 | from mandos.search.chembl.binding_search import BindingSearch |
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| 27 | from mandos.search.chembl.go_search import GoSearch |
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| 28 | from mandos.model.concrete_hits import GoType |
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| 29 | from mandos.search.chembl.indication_search import IndicationSearch |
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| 30 | from mandos.search.chembl.mechanism_search import MechanismSearch |
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| 31 | from mandos.search.chembl.target_predictions import TargetPredictionSearch |
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| 32 | from mandos.search.g2p.g2p_interaction_search import G2pInteractionSearch |
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| 33 | from mandos.search.pubchem.acute_effects_search import AcuteEffectSearch, Ld50Search |
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| 34 | from mandos.search.pubchem.bioactivity_search import BioactivitySearch |
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| 35 | from mandos.search.pubchem.computed_property_search import ComputedPropertySearch |
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| 36 | from mandos.search.pubchem.cooccurrence_search import ( |
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| 37 | ChemicalCoOccurrenceSearch, |
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| 38 | CoOccurrenceSearch, |
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| 39 | DiseaseCoOccurrenceSearch, |
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| 40 | GeneCoOccurrenceSearch, |
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| 41 | ) |
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| 42 | from mandos.search.pubchem.ctd_gene_search import CtdGeneSearch |
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| 43 | from mandos.search.pubchem.dgidb_search import DgiSearch |
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| 44 | from mandos.search.pubchem.disease_search import DiseaseSearch |
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| 45 | from mandos.search.pubchem.drugbank_ddi_search import DrugbankDdiSearch |
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| 46 | from mandos.search.pubchem.drugbank_interaction_search import ( |
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| 47 | DrugbankGeneralFunctionSearch, |
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| 48 | DrugbankTargetSearch, |
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| 49 | ) |
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| 50 | |||
| 51 | S = TypeVar("S", bound=Search, covariant=True) |
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|
|
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| 52 | U = TypeVar("U", covariant=True, bound=CoOccurrenceSearch) |
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| 53 | |||
| 54 | |||
| 55 | class EntryChemblBinding(Entry[BindingSearch]): |
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| 56 | @classmethod |
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| 57 | def run( |
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| 58 | cls, |
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| 59 | path: Path = CommonArgs.compounds, |
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| 60 | key: str = EntryArgs.key("chembl:binding"), |
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| 61 | to: Optional[Path] = CommonArgs.to_single, |
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| 62 | taxa: str = CommonArgs.taxa, |
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| 63 | traversal: str = EntryArgs.traversal_strategy, |
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| 64 | target_types: str = EntryArgs.target_types, |
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| 65 | confidence: int = EntryArgs.min_confidence, |
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| 66 | binding: float = EntryArgs.binds_cutoff, |
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| 67 | nonbinding: float = EntryArgs.does_not_bind_cutoff, |
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| 68 | relations: str = EntryArgs.relations, |
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| 69 | min_pchembl: float = EntryArgs.min_pchembl, |
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| 70 | banned_flags: str = EntryArgs.banned_flags, |
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| 71 | as_of: Optional[str] = CommonArgs.as_of, |
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| 72 | check: bool = EntryArgs.check, |
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| 73 | log: Optional[Path] = CommonArgs.log_path, |
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| 74 | quiet: bool = CommonArgs.quiet, |
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| 75 | verbose: bool = CommonArgs.verbose, |
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| 76 | no_setup: bool = CommonArgs.no_setup, |
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| 77 | ) -> Searcher: |
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| 78 | """ |
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| 79 | Binding data from ChEMBL. |
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| 80 | These are 'activity' annotations of the type 'B' that have a pCHEMBL value. |
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| 81 | There is extended documentation on this search; see: |
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| 82 | |||
| 83 | https://mandos-chem.readthedocs.io/en/latest/binding.html |
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| 84 | |||
| 85 | OBJECT: ChEMBL preferred target name |
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| 86 | |||
| 87 | PREDICATE: "binding:yes" or "binding:no" |
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| 88 | |||
| 89 | WEIGHT: pchembl value |
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| 90 | """ |
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| 91 | built = BindingSearch( |
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| 92 | key=key, |
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| 93 | api=Apis.Chembl, |
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| 94 | taxa=EntryUtils.get_taxa(taxa), |
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| 95 | traversal=traversal, |
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| 96 | target_types=EntryUtils.get_target_types(target_types), |
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| 97 | min_conf_score=confidence, |
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| 98 | allowed_relations=EntryUtils.split(relations), |
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| 99 | min_pchembl=min_pchembl, |
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| 100 | banned_flags=EntryUtils.get_flags(banned_flags), |
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| 101 | binds_cutoff=binding, |
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| 102 | does_not_bind_cutoff=nonbinding, |
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| 103 | ) |
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| 104 | return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
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| 105 | |||
| 106 | |||
| 107 | View Code Duplication | class EntryChemblMechanism(Entry[MechanismSearch]): |
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| 108 | @classmethod |
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| 109 | def run( |
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| 110 | cls, |
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| 111 | path: Path = CommonArgs.compounds, |
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| 112 | key: str = EntryArgs.key("chembl:mechanism"), |
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| 113 | to: Optional[Path] = CommonArgs.to_single, |
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| 114 | taxa: Optional[str] = CommonArgs.taxa, |
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| 115 | traversal: str = EntryArgs.traversal_strategy, |
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| 116 | target_types: str = EntryArgs.target_types, |
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| 117 | min_confidence: Optional[int] = EntryArgs.min_confidence, |
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| 118 | as_of: Optional[str] = CommonArgs.as_of, |
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| 119 | check: bool = EntryArgs.check, |
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| 120 | log: Optional[Path] = CommonArgs.log_path, |
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| 121 | quiet: bool = CommonArgs.quiet, |
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| 122 | verbose: bool = CommonArgs.verbose, |
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| 123 | no_setup: bool = CommonArgs.no_setup, |
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| 124 | ) -> Searcher: |
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| 125 | """ |
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| 126 | Mechanism of action (MoA) data from ChEMBL. |
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| 127 | |||
| 128 | OBJECT: ChEMBL preferred target name |
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| 129 | |||
| 130 | PREDICATE: Target action; e.g. "agonist" or "positive allosteric modulator" |
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| 131 | |||
| 132 | WEIGHT: 1.0 |
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| 133 | """ |
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| 134 | built = MechanismSearch( |
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| 135 | key=key, |
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| 136 | api=Apis.Chembl, |
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| 137 | taxa=EntryUtils.get_taxa(taxa), |
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| 138 | traversal_strategy=traversal, |
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| 139 | allowed_target_types=EntryUtils.get_target_types(target_types), |
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| 140 | min_confidence_score=min_confidence, |
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| 141 | ) |
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| 142 | return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
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| 143 | |||
| 144 | |||
| 145 | View Code Duplication | class ChemblQsarPredictions(Entry[TargetPredictionSearch]): |
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| 146 | @classmethod |
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| 147 | def run( |
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| 148 | cls, |
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| 149 | path: Path = CommonArgs.compounds, |
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| 150 | key: str = EntryArgs.key("chembl:predictions"), |
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| 151 | to: Optional[Path] = CommonArgs.to_single, |
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| 152 | taxa: str = CommonArgs.taxa, |
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| 153 | traversal: str = EntryArgs.traversal_strategy, |
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| 154 | target_types: str = EntryArgs.target_types, |
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| 155 | min_threshold: float = EntryArgs.min_threshold, |
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| 156 | as_of: Optional[str] = CommonArgs.as_of, |
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| 157 | check: bool = EntryArgs.check, |
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| 158 | log: Optional[Path] = CommonArgs.log_path, |
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| 159 | quiet: bool = CommonArgs.quiet, |
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| 160 | verbose: bool = CommonArgs.verbose, |
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| 161 | no_setup: bool = CommonArgs.no_setup, |
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| 162 | ) -> Searcher: |
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| 163 | """ |
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| 164 | Predicted target binding from ChEMBL. |
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| 165 | |||
| 166 | https://mandos-chem.readthedocs.io/en/latest/binding.html |
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| 167 | |||
| 168 | OBJECT: ChEMBL preferred target name |
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| 169 | |||
| 170 | PREDICATE: Either "binding:yes", "binding:no", or "binding:unknown". |
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| 171 | |||
| 172 | WEIGHT: The sqrt pchembl multiplied by a normalized odds ratio from the confidence set |
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| 173 | """ |
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| 174 | built = TargetPredictionSearch( |
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| 175 | key=key, |
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| 176 | api=Apis.Chembl, |
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| 177 | scrape=Apis.ChemblScrape, |
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| 178 | taxa=EntryUtils.get_taxa(taxa), |
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| 179 | traversal=traversal, |
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| 180 | target_types=EntryUtils.get_target_types(target_types), |
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| 181 | min_threshold=min_threshold, |
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| 182 | ) |
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| 183 | return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
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| 184 | |||
| 185 | |||
| 186 | class EntryChemblTrials(Entry[IndicationSearch]): |
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| 187 | @classmethod |
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| 188 | def run( |
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| 189 | cls, |
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| 190 | path: Path = CommonArgs.compounds, |
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| 191 | key: str = EntryArgs.key("chembl:trial"), |
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| 192 | to: Optional[Path] = CommonArgs.to_single, |
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| 193 | min_phase: Optional[int] = EntryArgs.chembl_trial, |
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| 194 | as_of: Optional[str] = CommonArgs.as_of, |
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| 195 | check: bool = EntryArgs.check, |
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| 196 | log: Optional[Path] = CommonArgs.log_path, |
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| 197 | quiet: bool = CommonArgs.quiet, |
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| 198 | verbose: bool = CommonArgs.verbose, |
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| 199 | no_setup: bool = CommonArgs.no_setup, |
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| 200 | ) -> Searcher: |
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| 201 | """ |
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| 202 | Diseases from clinical trials listed in ChEMBL. |
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| 203 | |||
| 204 | OBJECT: MeSH code |
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| 205 | |||
| 206 | PREDICATE: "trial" |
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| 207 | |||
| 208 | WEIGHT: phase (can be 1, 1.5, 2, etc.) |
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| 209 | """ |
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| 210 | built = IndicationSearch(key=key, api=Apis.Chembl, min_phase=min_phase) |
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| 211 | return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
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| 212 | |||
| 213 | |||
| 214 | class EntryChemblAtc(Entry[AtcSearch]): |
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| 215 | @classmethod |
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| 216 | def run( |
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| 217 | cls, |
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| 218 | path: Path = CommonArgs.compounds, |
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| 219 | key: str = EntryArgs.key("chembl:atc"), |
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| 220 | to: Optional[Path] = CommonArgs.to_single, |
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| 221 | levels: str = EntryArgs.atc_level, |
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| 222 | as_of: Optional[str] = CommonArgs.as_of, |
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| 223 | check: bool = EntryArgs.check, |
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| 224 | log: Optional[Path] = CommonArgs.log_path, |
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| 225 | quiet: bool = CommonArgs.quiet, |
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| 226 | verbose: bool = CommonArgs.verbose, |
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| 227 | no_setup: bool = CommonArgs.no_setup, |
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| 228 | ) -> Searcher: |
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| 229 | """ |
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| 230 | ATC codes from ChEMBL. |
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| 231 | |||
| 232 | OBJECT: ATC Code |
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| 233 | |||
| 234 | PREDICATE: "ATC L<leveL> code" |
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| 235 | |||
| 236 | WEIGHT: 1.0 |
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| 237 | """ |
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| 238 | built = AtcSearch( |
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| 239 | key=key, api=Apis.Chembl, levels={int(x.strip()) for x in levels.split(",")} |
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| 240 | ) |
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| 241 | return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
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| 242 | |||
| 243 | |||
| 244 | class _EntryChemblGo(Entry[GoSearch], metaclass=abc.ABCMeta): |
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| 245 | @classmethod |
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| 246 | def go_type(cls) -> GoType: |
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| 247 | raise NotImplementedError() |
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| 248 | |||
| 249 | @classmethod |
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| 250 | def cmd(cls) -> str: |
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| 251 | me = str(cls.go_type().name) |
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| 252 | return f"chembl:go.{me.lower()}" |
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| 253 | |||
| 254 | @classmethod |
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| 255 | def run( |
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| 256 | cls, |
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| 257 | path: Path = CommonArgs.compounds, |
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| 258 | key: str = EntryArgs.key("<see above>"), |
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| 259 | to: Optional[Path] = CommonArgs.to_single, |
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| 260 | taxa: Optional[str] = CommonArgs.taxa, |
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| 261 | traversal_strategy: str = EntryArgs.traversal_strategy, |
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| 262 | target_types: str = EntryArgs.target_types, |
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| 263 | confidence: Optional[int] = EntryArgs.min_confidence, |
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| 264 | relations: str = EntryArgs.relations, |
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| 265 | min_pchembl: float = EntryArgs.min_pchembl, |
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| 266 | banned_flags: Optional[str] = EntryArgs.banned_flags, |
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| 267 | binding_search: Optional[str] = EntryArgs.binding_search_name, |
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| 268 | as_of: Optional[str] = CommonArgs.as_of, |
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| 269 | check: bool = EntryArgs.check, |
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| 270 | log: Optional[Path] = CommonArgs.log_path, |
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| 271 | quiet: bool = CommonArgs.quiet, |
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| 272 | verbose: bool = CommonArgs.verbose, |
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| 273 | no_setup: bool = CommonArgs.no_setup, |
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| 274 | ) -> Searcher: |
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| 275 | """ |
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| 276 | GO terms associated with ChEMBL binding targets. |
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| 277 | |||
| 278 | OBJECT: GO Term name |
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| 279 | |||
| 280 | PREDICATE: "go:<type>" |
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| 281 | |||
| 282 | WEIGHT: pchembl value |
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| 283 | |||
| 284 | Note: |
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| 285 | |||
| 286 | By default, the key is the "chembl:go.function", "chembl:go.process", or "chembl:go.component". |
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| 287 | """ |
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| 288 | if key is None or key == "<see above>": |
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| 289 | key = cls.cmd() |
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| 290 | api = ChemblApi.wrap(Apis.Chembl) |
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| 291 | if binding_search is None: |
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| 292 | binding_clazz = BindingSearch |
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| 293 | else: |
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| 294 | binding_clazz = ReflectionUtils.injection(binding_search, BindingSearch) |
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| 295 | logger.info(f"NOTICE: Passing parameters to {binding_clazz.__qualname__}") |
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| 296 | try: |
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| 297 | binding_search = binding_clazz( |
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| 298 | key=key, |
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| 299 | api=Apis.Chembl, |
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| 300 | taxa=EntryUtils.get_taxa(taxa), |
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| 301 | traversal=traversal_strategy, |
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| 302 | target_types=EntryUtils.get_target_types(target_types), |
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| 303 | min_conf_score=confidence, |
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| 304 | allowed_relations=EntryUtils.split(relations), |
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| 305 | min_pchembl=min_pchembl, |
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| 306 | banned_flags=EntryUtils.get_flags(banned_flags), |
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| 307 | ) |
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| 308 | except (TypeError, ValueError): |
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| 309 | raise InjectionError(f"Failed to build {binding_clazz.__qualname__}") |
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| 310 | built = GoSearch(key, api, cls.go_type(), binding_search) |
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| 311 | return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
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| 312 | |||
| 313 | |||
| 314 | class EntryGoFunction(_EntryChemblGo): |
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| 315 | @classmethod |
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| 316 | def go_type(cls) -> GoType: |
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| 317 | return GoType.function |
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| 318 | |||
| 319 | |||
| 320 | class EntryGoProcess(_EntryChemblGo): |
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| 321 | @classmethod |
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| 322 | def go_type(cls) -> GoType: |
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| 323 | return GoType.process |
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| 324 | |||
| 325 | |||
| 326 | class EntryGoComponent(_EntryChemblGo): |
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| 327 | @classmethod |
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| 328 | def go_type(cls) -> GoType: |
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| 329 | return GoType.component |
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| 330 | |||
| 331 | |||
| 332 | class EntryPubchemDisease(Entry[DiseaseSearch]): |
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| 333 | View Code Duplication | @classmethod |
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| 334 | def run( |
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| 335 | cls, |
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| 336 | path: Path = CommonArgs.compounds, |
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| 337 | key: str = EntryArgs.key("disease.ctd:mesh"), |
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| 338 | to: Optional[Path] = CommonArgs.to_single, |
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| 339 | as_of: Optional[str] = CommonArgs.as_of, |
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| 340 | check: bool = EntryArgs.check, |
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| 341 | log: Optional[Path] = CommonArgs.log_path, |
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| 342 | quiet: bool = CommonArgs.quiet, |
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| 343 | verbose: bool = CommonArgs.verbose, |
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| 344 | no_setup: bool = CommonArgs.no_setup, |
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| 345 | ) -> Searcher: |
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| 346 | """ |
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| 347 | Diseases in the CTD. |
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| 348 | |||
| 349 | Comparative Toxicogenomics Database. |
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| 350 | |||
| 351 | OBJECT: MeSH code of disease |
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| 352 | |||
| 353 | PREDICATE: "disease:marker/mechanism", etc. |
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| 354 | |||
| 355 | WEIGHT: depends on the evidence type |
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| 356 | """ |
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| 357 | built = DiseaseSearch(key, Apis.Pubchem) |
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| 358 | return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
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| 359 | |||
| 360 | |||
| 361 | class _EntryPubchemCoOccurrence(Entry[U], metaclass=abc.ABCMeta): |
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| 362 | @classmethod |
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| 363 | def cmd(cls) -> str: |
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| 364 | me = str(cls.get_cooccurrence_type().name) |
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| 365 | return f"lit.pubchem:{me.lower()}" |
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| 366 | |||
| 367 | @classmethod |
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| 368 | def get_cooccurrence_type(cls) -> CoOccurrenceType: |
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| 369 | s: CoOccurrenceSearch = cls.get_search_type() |
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| 370 | return s.cooccurrence_type() |
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| 371 | |||
| 372 | @classmethod |
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| 373 | def run( |
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| 374 | cls, |
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| 375 | path: Path = CommonArgs.compounds, |
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| 376 | key: str = EntryArgs.key("<see above>"), |
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| 377 | to: Optional[Path] = CommonArgs.to_single, |
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| 378 | min_score: float = EntryArgs.min_cooccurrence_score, |
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| 379 | min_articles: int = EntryArgs.min_cooccurring_articles, |
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| 380 | as_of: Optional[str] = CommonArgs.as_of, |
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| 381 | log: Optional[Path] = CommonArgs.log_path, |
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| 382 | check: bool = EntryArgs.check, |
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| 383 | quiet: bool = CommonArgs.quiet, |
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| 384 | verbose: bool = CommonArgs.verbose, |
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| 385 | no_setup: bool = CommonArgs.no_setup, |
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| 386 | ) -> Searcher: |
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| 387 | """ |
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| 388 | Co-occurrences from PubMed articles. |
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| 389 | There is extended documentation on this search. |
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| 390 | Also refer to https://pubchemdocs.ncbi.nlm.nih.gov/knowledge-panels |
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| 391 | |||
| 392 | OBJECT: Name of gene/chemical/disease |
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| 393 | |||
| 394 | PREDICATE: "co-occurrence:<gene/chemical/disease>" |
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| 395 | |||
| 396 | WEIGHT: enrichment score; see PubChem docs |
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| 397 | """ |
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| 398 | if key is None or key == "<see above>": |
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| 399 | key = cls.cmd() |
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| 400 | clazz = cls.get_search_type() |
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| 401 | built = clazz(key, Apis.Pubchem, min_score=min_score, min_articles=min_articles) |
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| 402 | return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
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| 403 | |||
| 404 | |||
| 405 | class EntryPubchemGeneCoOccurrence(_EntryPubchemCoOccurrence[GeneCoOccurrenceSearch]): |
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| 406 | """ """ |
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| 407 | |||
| 408 | |||
| 409 | class EntryPubchemDiseaseCoOccurrence(_EntryPubchemCoOccurrence[DiseaseCoOccurrenceSearch]): |
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| 410 | """ """ |
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| 411 | |||
| 412 | |||
| 413 | class EntryPubchemChemicalCoOccurrence(_EntryPubchemCoOccurrence[ChemicalCoOccurrenceSearch]): |
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| 414 | """ """ |
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| 415 | |||
| 416 | |||
| 417 | class EntryPubchemDgi(Entry[DgiSearch]): |
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| 418 | View Code Duplication | @classmethod |
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| 419 | def run( |
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| 420 | cls, |
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| 421 | path: Path = CommonArgs.compounds, |
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| 422 | key: str = EntryArgs.key("inter.dgidb:gene"), |
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| 423 | to: Optional[Path] = CommonArgs.to_single, |
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| 424 | as_of: Optional[str] = CommonArgs.as_of, |
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| 425 | log: Optional[Path] = CommonArgs.log_path, |
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| 426 | check: bool = EntryArgs.check, |
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| 427 | quiet: bool = CommonArgs.quiet, |
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| 428 | verbose: bool = CommonArgs.verbose, |
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| 429 | no_setup: bool = CommonArgs.no_setup, |
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| 430 | ) -> Searcher: |
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| 431 | """ |
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| 432 | Drug/gene interactions in the DGIDB. |
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| 433 | |||
| 434 | Drug Gene Interaction Database. |
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| 435 | Also see ``disease.dgidb:int``. |
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| 436 | |||
| 437 | OBJECT: Name of the gene |
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| 438 | |||
| 439 | PREDICATE: "interaction:generic" or "interaction:<type>" |
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| 440 | |||
| 441 | WEIGHT: 1.0 |
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| 442 | """ |
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| 443 | built = DgiSearch(key, Apis.Pubchem) |
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| 444 | return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
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| 445 | |||
| 446 | |||
| 447 | class EntryPubchemCgi(Entry[CtdGeneSearch]): |
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| 448 | View Code Duplication | @classmethod |
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| 449 | def run( |
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| 450 | cls, |
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| 451 | path: Path = CommonArgs.compounds, |
||
| 452 | key: str = EntryArgs.key("inter.ctd:gene"), |
||
| 453 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 454 | to: Optional[Path] = CommonArgs.to_single, |
||
| 455 | log: Optional[Path] = CommonArgs.log_path, |
||
| 456 | check: bool = EntryArgs.check, |
||
| 457 | quiet: bool = CommonArgs.quiet, |
||
| 458 | verbose: bool = CommonArgs.verbose, |
||
| 459 | no_setup: bool = CommonArgs.no_setup, |
||
| 460 | ) -> Searcher: |
||
| 461 | """ |
||
| 462 | Compound/gene interactions in the DGIDB. |
||
| 463 | |||
| 464 | Drug Gene Interaction Database. |
||
| 465 | Also see ``interact.dgidb:int``. |
||
| 466 | |||
| 467 | OBJECT: Name of the gene |
||
| 468 | |||
| 469 | PREDICATE: derived from the interaction type (e.g. downregulation) |
||
| 470 | |||
| 471 | WEIGHT: 1.0 |
||
| 472 | """ |
||
| 473 | built = CtdGeneSearch(key, Apis.Pubchem) |
||
| 474 | return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
||
| 475 | |||
| 476 | |||
| 477 | View Code Duplication | class EntryDrugbankTarget(Entry[DrugbankTargetSearch]): |
|
| 478 | @classmethod |
||
| 479 | def run( |
||
| 480 | cls, |
||
| 481 | path: Path = CommonArgs.compounds, |
||
| 482 | key: str = EntryArgs.key("inter.drugbank:targ"), |
||
| 483 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 484 | to: Optional[Path] = CommonArgs.to_single, |
||
| 485 | check: bool = EntryArgs.check, |
||
| 486 | log: Optional[Path] = CommonArgs.log_path, |
||
| 487 | quiet: bool = CommonArgs.quiet, |
||
| 488 | verbose: bool = CommonArgs.verbose, |
||
| 489 | no_setup: bool = CommonArgs.no_setup, |
||
| 490 | ) -> Searcher: |
||
| 491 | """ |
||
| 492 | Protein targets from DrugBank. |
||
| 493 | |||
| 494 | OBJECT: Target name (e.g. "Solute carrier family 22 member 11") from DrugBank |
||
| 495 | |||
| 496 | PREDICATE: "<target_type>:<action>" |
||
| 497 | """ |
||
| 498 | built = DrugbankTargetSearch(key, Apis.Pubchem, {DrugbankTargetType.target}) |
||
| 499 | return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
||
| 500 | |||
| 501 | |||
| 502 | View Code Duplication | class EntryGeneralFunction(Entry[DrugbankGeneralFunctionSearch]): |
|
| 503 | @classmethod |
||
| 504 | def run( |
||
| 505 | cls, |
||
| 506 | path: Path = CommonArgs.compounds, |
||
| 507 | key: str = EntryArgs.key("inter.drugbank:targ-fn"), |
||
| 508 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 509 | to: Optional[Path] = CommonArgs.to_single, |
||
| 510 | check: bool = EntryArgs.check, |
||
| 511 | log: Optional[Path] = CommonArgs.log_path, |
||
| 512 | quiet: bool = CommonArgs.quiet, |
||
| 513 | verbose: bool = CommonArgs.verbose, |
||
| 514 | no_setup: bool = CommonArgs.no_setup, |
||
| 515 | ) -> Searcher: |
||
| 516 | """ |
||
| 517 | General functions from DrugBank targets. |
||
| 518 | |||
| 519 | OBJECT: Name of the general function (e.g. "Toxic substance binding") |
||
| 520 | |||
| 521 | PREDICATE: "<target_type>:<action>" |
||
| 522 | """ |
||
| 523 | built = DrugbankGeneralFunctionSearch(key, Apis.Pubchem, {DrugbankTargetType.target}) |
||
| 524 | return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
||
| 525 | |||
| 526 | |||
| 527 | View Code Duplication | class EntryDrugbankTransporter(Entry[DrugbankTargetSearch]): |
|
| 528 | @classmethod |
||
| 529 | def run( |
||
| 530 | cls, |
||
| 531 | path: Path = CommonArgs.compounds, |
||
| 532 | key: str = EntryArgs.key("inter.drugbank:pk"), |
||
| 533 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 534 | to: Optional[Path] = CommonArgs.to_single, |
||
| 535 | check: bool = EntryArgs.check, |
||
| 536 | log: Optional[Path] = CommonArgs.log_path, |
||
| 537 | quiet: bool = CommonArgs.quiet, |
||
| 538 | verbose: bool = CommonArgs.verbose, |
||
| 539 | no_setup: bool = CommonArgs.no_setup, |
||
| 540 | ) -> Searcher: |
||
| 541 | """ |
||
| 542 | PK-related proteins from DrugBank. |
||
| 543 | |||
| 544 | OBJECT: Transporter name (e.g. "Solute carrier family 22 member 11") from DrugBank |
||
| 545 | |||
| 546 | PREDICATE: "<target_type>:<action>" (e.g. metabolized, transported, etc.) |
||
| 547 | """ |
||
| 548 | target_types = { |
||
| 549 | DrugbankTargetType.transporter, |
||
| 550 | DrugbankTargetType.carrier, |
||
| 551 | DrugbankTargetType.enzyme, |
||
| 552 | } |
||
| 553 | built = DrugbankTargetSearch(key, Apis.Pubchem, target_types) |
||
| 554 | return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
||
| 555 | |||
| 556 | |||
| 557 | View Code Duplication | class EntryTransporterGeneralFunction(Entry[DrugbankGeneralFunctionSearch]): |
|
| 558 | @classmethod |
||
| 559 | def run( |
||
| 560 | cls, |
||
| 561 | path: Path = CommonArgs.compounds, |
||
| 562 | key: str = EntryArgs.key("inter.drugbank:pk-fn"), |
||
| 563 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 564 | to: Optional[Path] = CommonArgs.to_single, |
||
| 565 | check: bool = EntryArgs.check, |
||
| 566 | log: Optional[Path] = CommonArgs.log_path, |
||
| 567 | quiet: bool = CommonArgs.quiet, |
||
| 568 | verbose: bool = CommonArgs.verbose, |
||
| 569 | no_setup: bool = CommonArgs.no_setup, |
||
| 570 | ) -> Searcher: |
||
| 571 | """ |
||
| 572 | DrugBank PK-related protein functions. |
||
| 573 | |||
| 574 | OBJECT: Name of the general function (e.g. "Toxic substance binding") |
||
| 575 | |||
| 576 | PREDICATE: "<target_type>:<action>" (e.g. metabolized, transported, etc.) |
||
| 577 | """ |
||
| 578 | target_types = { |
||
| 579 | DrugbankTargetType.transporter, |
||
| 580 | DrugbankTargetType.carrier, |
||
| 581 | DrugbankTargetType.enzyme, |
||
| 582 | } |
||
| 583 | built = DrugbankGeneralFunctionSearch(key, Apis.Pubchem, target_types) |
||
| 584 | return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
||
| 585 | |||
| 586 | |||
| 587 | class EntryDrugbankDdi(Entry[DrugbankDdiSearch]): |
||
| 588 | View Code Duplication | @classmethod |
|
| 589 | def run( |
||
| 590 | cls, |
||
| 591 | path: Path = CommonArgs.compounds, |
||
| 592 | key: str = EntryArgs.key("inter.drugbank:ddi"), |
||
| 593 | to: Optional[Path] = CommonArgs.to_single, |
||
| 594 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 595 | check: bool = EntryArgs.check, |
||
| 596 | log: Optional[Path] = CommonArgs.log_path, |
||
| 597 | quiet: bool = CommonArgs.quiet, |
||
| 598 | verbose: bool = CommonArgs.verbose, |
||
| 599 | no_setup: bool = CommonArgs.no_setup, |
||
| 600 | ) -> Searcher: |
||
| 601 | """ |
||
| 602 | Drug/drug interactions listed by DrugBank. |
||
| 603 | |||
| 604 | The 'description' column includes useful information about the interaction, |
||
| 605 | such as diseases and whether a risk is increased or decreased. |
||
| 606 | |||
| 607 | OBJECT: name of the drug (e.g. "ibuprofen") |
||
| 608 | |||
| 609 | PREDICATE: typically increase/decrease/change followed by risk/activity/etc. |
||
| 610 | """ |
||
| 611 | built = DrugbankDdiSearch(key, Apis.Pubchem) |
||
| 612 | return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
||
| 613 | |||
| 614 | |||
| 615 | class EntryPubchemAssay(Entry[BioactivitySearch]): |
||
| 616 | @classmethod |
||
| 617 | def run( |
||
| 618 | cls, |
||
| 619 | path: Path = CommonArgs.compounds, |
||
| 620 | key: str = EntryArgs.key("assay.pubchem:act"), |
||
| 621 | to: Optional[Path] = CommonArgs.to_single, |
||
| 622 | name_must_match: bool = EntryArgs.name_must_match, |
||
| 623 | ban_sources: Optional[str] = None, |
||
| 624 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 625 | check: bool = EntryArgs.check, |
||
| 626 | log: Optional[Path] = CommonArgs.log_path, |
||
| 627 | quiet: bool = CommonArgs.quiet, |
||
| 628 | verbose: bool = CommonArgs.verbose, |
||
| 629 | no_setup: bool = CommonArgs.no_setup, |
||
| 630 | ) -> Searcher: |
||
| 631 | """ |
||
| 632 | PubChem bioactivity results. |
||
| 633 | |||
| 634 | Note: The species name, if present, is taken from the target name. |
||
| 635 | The taxon ID is what was curated in PubChem. |
||
| 636 | |||
| 637 | OBJECT: Name of the target without species suffix (e.g. "Slc6a3 - solute carrier family 6 member 3") |
||
| 638 | |||
| 639 | PREDICATE: "active"|"inactive"|"inconclusive"|"undetermined" |
||
| 640 | |||
| 641 | WEIGHT: 2 for confirmatory; 1 otherwise |
||
| 642 | """ |
||
| 643 | built = BioactivitySearch(key, Apis.Pubchem, compound_name_must_match=name_must_match) |
||
| 644 | return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
||
| 645 | |||
| 646 | |||
| 647 | class EntryDeaSchedule(Entry[BioactivitySearch]): |
||
| 648 | @classmethod |
||
| 649 | def run( |
||
| 650 | cls, |
||
| 651 | path: Path = CommonArgs.compounds, |
||
| 652 | key: str = EntryArgs.key("drug.dea:schedule"), |
||
| 653 | to: Optional[Path] = CommonArgs.to_single, |
||
| 654 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 655 | check: bool = EntryArgs.check, |
||
| 656 | log: Optional[Path] = CommonArgs.log_path, |
||
| 657 | quiet: bool = CommonArgs.quiet, |
||
| 658 | verbose: bool = CommonArgs.verbose, |
||
| 659 | no_setup: bool = CommonArgs.no_setup, |
||
| 660 | ) -> Searcher: |
||
| 661 | """ |
||
| 662 | DEA schedules (PENDING). |
||
| 663 | |||
| 664 | OBJECT: (1 to 4, or "unscheduled") |
||
| 665 | |||
| 666 | PREDICATE: "dea:schedule" |
||
| 667 | |||
| 668 | WEIGHT: 1.0 |
||
| 669 | """ |
||
| 670 | pass |
||
| 671 | |||
| 672 | |||
| 673 | class EntryDeaClass(Entry[BioactivitySearch]): |
||
| 674 | @classmethod |
||
| 675 | def run( |
||
| 676 | cls, |
||
| 677 | path: Path = CommonArgs.compounds, |
||
| 678 | key: str = EntryArgs.key("drug.dea:class"), |
||
| 679 | to: Optional[Path] = CommonArgs.to_single, |
||
| 680 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 681 | check: bool = EntryArgs.check, |
||
| 682 | log: Optional[Path] = CommonArgs.log_path, |
||
| 683 | quiet: bool = CommonArgs.quiet, |
||
| 684 | verbose: bool = CommonArgs.verbose, |
||
| 685 | no_setup: bool = CommonArgs.no_setup, |
||
| 686 | ) -> Searcher: |
||
| 687 | """ |
||
| 688 | DEA classes (PENDING). |
||
| 689 | |||
| 690 | OBJECT: e.g. "hallucinogen" |
||
| 691 | |||
| 692 | PREDICATE: "dea:class" |
||
| 693 | |||
| 694 | WEIGHT: 1.0 |
||
| 695 | """ |
||
| 696 | pass |
||
| 697 | |||
| 698 | |||
| 699 | class EntryChemidPlusAcute(Entry[AcuteEffectSearch]): |
||
| 700 | @classmethod |
||
| 701 | def run( |
||
| 702 | cls, |
||
| 703 | path: Path = CommonArgs.compounds, |
||
| 704 | key: str = EntryArgs.key("tox.chemidplus:acute"), |
||
| 705 | to: Optional[Path] = CommonArgs.to_single, |
||
| 706 | level: int = EntryArgs.acute_effect_level, |
||
| 707 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 708 | check: bool = EntryArgs.check, |
||
| 709 | log: Optional[Path] = CommonArgs.log_path, |
||
| 710 | quiet: bool = CommonArgs.quiet, |
||
| 711 | verbose: bool = CommonArgs.verbose, |
||
| 712 | no_setup: bool = CommonArgs.no_setup, |
||
| 713 | ) -> Searcher: |
||
| 714 | """ |
||
| 715 | Acute effect codes from ChemIDPlus. |
||
| 716 | |||
| 717 | OBJECT: E.g. "behavioral: excitement" |
||
| 718 | |||
| 719 | PREDICATE: "effect:acute" |
||
| 720 | |||
| 721 | WEIGHT: 1.0 |
||
| 722 | """ |
||
| 723 | built = AcuteEffectSearch( |
||
| 724 | key, |
||
| 725 | Apis.Pubchem, |
||
| 726 | top_level=level == 1, |
||
| 727 | ) |
||
| 728 | return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
||
| 729 | |||
| 730 | |||
| 731 | class EntryChemidPlusLd50(Entry[Ld50Search]): |
||
| 732 | View Code Duplication | @classmethod |
|
| 733 | def run( |
||
| 734 | cls, |
||
| 735 | path: Path = CommonArgs.compounds, |
||
| 736 | key: str = EntryArgs.key("tox.chemidplus:ld50"), |
||
| 737 | to: Optional[Path] = CommonArgs.to_single, |
||
| 738 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 739 | check: bool = EntryArgs.check, |
||
| 740 | log: Optional[Path] = CommonArgs.log_path, |
||
| 741 | quiet: bool = CommonArgs.quiet, |
||
| 742 | verbose: bool = CommonArgs.verbose, |
||
| 743 | no_setup: bool = CommonArgs.no_setup, |
||
| 744 | ) -> Searcher: |
||
| 745 | """ |
||
| 746 | LD50 acute effects from ChemIDPlus. |
||
| 747 | |||
| 748 | OBJECT: A dose in mg/kg (e.g. 3100) |
||
| 749 | |||
| 750 | PREDICATE: "LD50::<route>" (e.g. "LD50::intravenous) |
||
| 751 | |||
| 752 | WEIGHT: 1.0 |
||
| 753 | """ |
||
| 754 | built = Ld50Search(key, Apis.Pubchem) |
||
| 755 | return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
||
| 756 | |||
| 757 | |||
| 758 | class EntryG2pInteractions(Entry[G2pInteractionSearch]): |
||
| 759 | View Code Duplication | @classmethod |
|
| 760 | def run( |
||
| 761 | cls, |
||
| 762 | path: Path = CommonArgs.compounds, |
||
| 763 | key: str = EntryArgs.key("g2p:interactions"), |
||
| 764 | to: Optional[Path] = CommonArgs.to_single, |
||
| 765 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 766 | check: bool = EntryArgs.check, |
||
| 767 | log: Optional[Path] = CommonArgs.log_path, |
||
| 768 | quiet: bool = CommonArgs.quiet, |
||
| 769 | verbose: bool = CommonArgs.verbose, |
||
| 770 | no_setup: bool = CommonArgs.no_setup, |
||
| 771 | ) -> Searcher: |
||
| 772 | """ |
||
| 773 | Target interactions with affinities from Guide to Pharmacology. |
||
| 774 | |||
| 775 | OBJECT: A molecular target |
||
| 776 | |||
| 777 | PREDICATE: "interaction:agonism", etc. |
||
| 778 | |||
| 779 | WEIGHT: 1.0 |
||
| 780 | """ |
||
| 781 | built = G2pInteractionSearch(key, Apis.G2p) |
||
| 782 | return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
||
| 783 | |||
| 784 | |||
| 785 | class EntryHmdbTissue(Entry[BioactivitySearch]): |
||
| 786 | @classmethod |
||
| 787 | def run( |
||
| 788 | cls, |
||
| 789 | path: Path = CommonArgs.compounds, |
||
| 790 | key: str = EntryArgs.key("hmdb:tissue"), |
||
| 791 | to: Optional[Path] = CommonArgs.to_single, |
||
| 792 | min_nanomolar: Optional[float] = None, |
||
| 793 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 794 | check: bool = EntryArgs.check, |
||
| 795 | log: Optional[Path] = CommonArgs.log_path, |
||
| 796 | quiet: bool = CommonArgs.quiet, |
||
| 797 | verbose: bool = CommonArgs.verbose, |
||
| 798 | no_setup: bool = CommonArgs.no_setup, |
||
| 799 | ) -> Searcher: |
||
| 800 | """ |
||
| 801 | Tissue concentrations from HMDB (PENDING). |
||
| 802 | |||
| 803 | OBJECT: |
||
| 804 | |||
| 805 | PREDICATE: "tissue:..." |
||
| 806 | """ |
||
| 807 | pass |
||
| 808 | |||
| 809 | |||
| 810 | class EntryHmdbComputed(Entry[BioactivitySearch]): |
||
| 811 | @classmethod |
||
| 812 | def run( |
||
| 813 | cls, |
||
| 814 | path: Path = CommonArgs.compounds, |
||
| 815 | key: str = EntryArgs.key("hmdb:computed"), |
||
| 816 | to: Optional[Path] = CommonArgs.to_single, |
||
| 817 | min_nanomolar: Optional[float] = None, |
||
| 818 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 819 | check: bool = EntryArgs.check, |
||
| 820 | log: Optional[Path] = CommonArgs.log_path, |
||
| 821 | quiet: bool = CommonArgs.quiet, |
||
| 822 | verbose: bool = CommonArgs.verbose, |
||
| 823 | no_setup: bool = CommonArgs.no_setup, |
||
| 824 | ) -> Searcher: |
||
| 825 | """ |
||
| 826 | Computed properties from HMDB (PENDING). |
||
| 827 | |||
| 828 | Keys include pKa, logP, logS, etc. |
||
| 829 | |||
| 830 | OBJECT: A number; booleans are converted to 0/1 |
||
| 831 | |||
| 832 | PREDICATE: The name of the property |
||
| 833 | """ |
||
| 834 | pass |
||
| 835 | |||
| 836 | |||
| 837 | class EntryPubchemComputed(Entry[ComputedPropertySearch]): |
||
| 838 | @classmethod |
||
| 839 | def run( |
||
| 840 | cls, |
||
| 841 | path: Path = CommonArgs.compounds, |
||
| 842 | key: str = EntryArgs.key("chem.pubchem:computed"), |
||
| 843 | keys: str = EntryArgs.pubchem_computed_keys, |
||
| 844 | to: Optional[Path] = CommonArgs.to_single, |
||
| 845 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 846 | check: bool = EntryArgs.check, |
||
| 847 | log: Optional[Path] = CommonArgs.log_path, |
||
| 848 | quiet: bool = CommonArgs.quiet, |
||
| 849 | verbose: bool = CommonArgs.verbose, |
||
| 850 | no_setup: bool = CommonArgs.no_setup, |
||
| 851 | ) -> Searcher: |
||
| 852 | """ |
||
| 853 | Computed properties from PubChem. |
||
| 854 | |||
| 855 | OBJECT: Number |
||
| 856 | |||
| 857 | PREDICATE: e.g. "complexity" |
||
| 858 | """ |
||
| 859 | # replace acronyms, etc. |
||
| 860 | # ComputedPropertySearch standardizes punctuation and casing |
||
| 861 | known = { |
||
| 862 | k: v |
||
| 863 | for k, v in { |
||
| 864 | **EntryArgs.KNOWN_USEFUL_KEYS, |
||
| 865 | **EntryArgs.KNOWN_USELESS_KEYS, |
||
| 866 | }.items() |
||
| 867 | if v is not None |
||
| 868 | } |
||
| 869 | keys = {known.get(s.strip(), s) for s in keys.split(",")} |
||
| 870 | built = ComputedPropertySearch(key, Apis.Pubchem, descriptors=keys) |
||
| 871 | return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
||
| 872 | |||
| 873 | |||
| 874 | class EntryDrugbankAdmet(Entry[DrugbankTargetSearch]): |
||
| 875 | @classmethod |
||
| 876 | def run( |
||
| 877 | cls, |
||
| 878 | path: Path = CommonArgs.compounds, |
||
| 879 | key: str = EntryArgs.key("drugbank.admet:properties"), |
||
| 880 | to: Optional[Path] = CommonArgs.to_single, |
||
| 881 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 882 | check: bool = EntryArgs.check, |
||
| 883 | log: Optional[Path] = CommonArgs.log_path, |
||
| 884 | quiet: bool = CommonArgs.quiet, |
||
| 885 | verbose: bool = CommonArgs.verbose, |
||
| 886 | no_setup: bool = CommonArgs.no_setup, |
||
| 887 | ) -> Searcher: |
||
| 888 | """ |
||
| 889 | Enzyme predictions from DrugBank (PENDING). |
||
| 890 | |||
| 891 | OBJECT: Enzyme name |
||
| 892 | |||
| 893 | PREDICATE: Action |
||
| 894 | """ |
||
| 895 | |||
| 896 | |||
| 897 | class EntryDrugbankMetabolites(Entry[DrugbankTargetSearch]): |
||
| 898 | @classmethod |
||
| 899 | def run( |
||
| 900 | cls, |
||
| 901 | path: Path = CommonArgs.compounds, |
||
| 902 | key: str = EntryArgs.key("drugbank.admet:metabolites"), |
||
| 903 | to: Optional[Path] = CommonArgs.to_single, |
||
| 904 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 905 | check: bool = EntryArgs.check, |
||
| 906 | log: Optional[Path] = CommonArgs.log_path, |
||
| 907 | quiet: bool = CommonArgs.quiet, |
||
| 908 | verbose: bool = CommonArgs.verbose, |
||
| 909 | no_setup: bool = CommonArgs.no_setup, |
||
| 910 | ) -> Searcher: |
||
| 911 | """ |
||
| 912 | Metabolites from DrugBank (PENDING). |
||
| 913 | |||
| 914 | OBJECT: Compound name (e.g. "norcocaine"). |
||
| 915 | |||
| 916 | PREDICATE: "metabolized to" |
||
| 917 | """ |
||
| 918 | |||
| 919 | |||
| 920 | class EntryDrugbankDosage(Entry[DrugbankTargetSearch]): |
||
| 921 | @classmethod |
||
| 922 | def run( |
||
| 923 | cls, |
||
| 924 | path: Path = CommonArgs.compounds, |
||
| 925 | key: str = EntryArgs.key("drugbank.admet:dosage"), |
||
| 926 | to: Optional[Path] = CommonArgs.to_single, |
||
| 927 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 928 | check: bool = EntryArgs.check, |
||
| 929 | log: Optional[Path] = CommonArgs.log_path, |
||
| 930 | quiet: bool = CommonArgs.quiet, |
||
| 931 | verbose: bool = CommonArgs.verbose, |
||
| 932 | no_setup: bool = CommonArgs.no_setup, |
||
| 933 | ) -> Searcher: |
||
| 934 | """ |
||
| 935 | Dosage from DrugBank (PENDING). |
||
| 936 | |||
| 937 | OBJECT: concentration in mg/mL |
||
| 938 | |||
| 939 | PREDICATE: "dosage :: <route>" |
||
| 940 | |||
| 941 | OTHER COLUMNS: |
||
| 942 | |||
| 943 | - form (e.g. liquid) |
||
| 944 | """ |
||
| 945 | |||
| 946 | |||
| 947 | class EntryMetaRandom(Entry[BioactivitySearch]): |
||
| 948 | @classmethod |
||
| 949 | def run( |
||
| 950 | cls, |
||
| 951 | path: Path = CommonArgs.compounds, |
||
| 952 | key: str = EntryArgs.key("meta:random"), |
||
| 953 | to: Optional[Path] = CommonArgs.to_single, |
||
| 954 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 955 | check: bool = EntryArgs.check, |
||
| 956 | log: Optional[Path] = CommonArgs.log_path, |
||
| 957 | quiet: bool = CommonArgs.quiet, |
||
| 958 | verbose: bool = CommonArgs.verbose, |
||
| 959 | no_setup: bool = CommonArgs.no_setup, |
||
| 960 | ) -> Searcher: |
||
| 961 | """ |
||
| 962 | Random class assignment (PENDING). |
||
| 963 | |||
| 964 | OBJECT: 1 thru n-compounds |
||
| 965 | |||
| 966 | PREDICATE: "random" |
||
| 967 | """ |
||
| 968 | pass |
||
| 969 | |||
| 970 | |||
| 971 | Entries = [ |
||
| 972 | EntryChemblBinding, |
||
| 973 | EntryChemblMechanism, |
||
| 974 | EntryChemblAtc, |
||
| 975 | EntryChemblTrials, |
||
| 976 | EntryGoFunction, |
||
| 977 | EntryGoProcess, |
||
| 978 | EntryGoComponent, |
||
| 979 | EntryPubchemComputed, |
||
| 980 | EntryPubchemDisease, |
||
| 981 | EntryPubchemGeneCoOccurrence, |
||
| 982 | EntryPubchemDiseaseCoOccurrence, |
||
| 983 | EntryPubchemChemicalCoOccurrence, |
||
| 984 | EntryPubchemDgi, |
||
| 985 | EntryPubchemCgi, |
||
| 986 | EntryDrugbankTarget, |
||
| 987 | EntryGeneralFunction, |
||
| 988 | EntryDrugbankTransporter, |
||
| 989 | EntryTransporterGeneralFunction, |
||
| 990 | EntryDrugbankDdi, |
||
| 991 | EntryPubchemAssay, |
||
| 992 | EntryDeaSchedule, |
||
| 993 | EntryDeaClass, |
||
| 994 | EntryChemidPlusAcute, |
||
| 995 | EntryChemidPlusLd50, |
||
| 996 | EntryHmdbTissue, |
||
| 997 | EntryMetaRandom, |
||
| 998 | ] |
||
| 999 |
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This check looks for invalid names for a range of different identifiers.
You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements.
If your project includes a Pylint configuration file, the settings contained in that file take precedence.
To find out more about Pylint, please refer to their site.