dmyersturnbull /
mandos
| Total Complexity | 45 |
| Total Lines | 1148 |
| Duplicated Lines | 40.07 % |
| 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.entry.entry_commands 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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coding-style
introduced
by
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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.entry._entry_args import EntryArgs |
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| 13 | from mandos.entry._entry_utils import EntryUtils |
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| 14 | from mandos.entry.abstract_entries import Entry |
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| 15 | from mandos.entry.api_singletons import Apis |
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| 16 | from mandos.entry._common_args import CommonArgs |
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| 17 | from mandos.entry.searchers import Searcher |
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| 18 | from mandos.model.utils.reflection_utils import InjectionError |
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| 19 | from mandos.model.utils.reflection_utils import ReflectionUtils |
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| 20 | from mandos.model.apis.chembl_api import ChemblApi |
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| 21 | from mandos.model.apis.pubchem_support.pubchem_models import CoOccurrenceType, DrugbankTargetType |
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| 22 | from mandos.search.chembl.atc_search import AtcSearch |
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| 23 | from mandos.search.chembl.binding_search import BindingSearch |
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| 24 | from mandos.search.chembl.go_search import GoSearch |
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| 25 | from mandos.model.concrete_hits import GoType |
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| 26 | from mandos.search.chembl.indication_search import IndicationSearch |
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| 27 | from mandos.search.chembl.mechanism_search import MechanismSearch |
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| 28 | from mandos.search.chembl.target_prediction_search import TargetPredictionSearch |
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| 29 | from mandos.search.g2p.g2p_interaction_search import G2pInteractionSearch |
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| 30 | from mandos.search.pubchem.acute_effects_search import AcuteEffectSearch, Ld50Search |
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| 31 | from mandos.search.pubchem.bioactivity_search import BioactivitySearch |
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| 32 | from mandos.search.pubchem.computed_property_search import ComputedPropertySearch |
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| 33 | from mandos.search.pubchem.cooccurrence_search import ( |
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| 34 | ChemicalCoOccurrenceSearch, |
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| 35 | CoOccurrenceSearch, |
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| 36 | DiseaseCoOccurrenceSearch, |
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| 37 | GeneCoOccurrenceSearch, |
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| 38 | ) |
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| 39 | from mandos.search.pubchem.ctd_gene_search import CtdGeneSearch |
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| 40 | from mandos.search.pubchem.dgidb_search import DgiSearch |
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| 41 | from mandos.search.pubchem.disease_search import DiseaseSearch |
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| 42 | from mandos.search.pubchem.drugbank_ddi_search import DrugbankDdiSearch |
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| 43 | from mandos.search.pubchem.drugbank_interaction_search import ( |
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| 44 | DrugbankGeneralFunctionSearch, |
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| 45 | DrugbankTargetSearch, |
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| 46 | ) |
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| 47 | |||
| 48 | U = TypeVar("U", covariant=True, bound=CoOccurrenceSearch) |
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| 49 | |||
| 50 | |||
| 51 | class EntryChemblBinding(Entry[BindingSearch]): |
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| 52 | @classmethod |
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| 53 | def run( |
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| 54 | cls, |
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| 55 | path: Path = CommonArgs.in_compound_table, |
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| 56 | key: str = EntryArgs.key("chembl:binding"), |
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| 57 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 58 | taxa: str = CommonArgs.taxa, |
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| 59 | traversal: str = EntryArgs.traversal_strategy, |
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| 60 | target_types: str = EntryArgs.target_types, |
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| 61 | confidence: int = EntryArgs.min_confidence, |
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| 62 | binding: float = EntryArgs.binds_cutoff, |
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| 63 | nonbinding: float = EntryArgs.does_not_bind_cutoff, |
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| 64 | relations: str = EntryArgs.relations, |
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| 65 | min_pchembl: float = EntryArgs.min_pchembl, |
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| 66 | banned_flags: str = EntryArgs.banned_flags, |
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| 67 | as_of: Optional[str] = CommonArgs.as_of, |
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| 68 | check: bool = EntryArgs.check, |
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| 69 | log: Optional[Path] = CommonArgs.log, |
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| 70 | stderr: str = CommonArgs.stderr, |
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| 71 | no_setup: bool = CommonArgs.no_setup, |
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| 72 | ) -> Searcher: |
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| 73 | """ |
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| 74 | Binding data from ChEMBL. |
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| 75 | |||
| 76 | These are 'activity' annotations of the type 'B' that have a pCHEMBL value. |
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| 77 | https://mandos-chem.readthedocs.io/en/latest/binding.html |
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| 78 | |||
| 79 | OBJECT: The target name |
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| 80 | |||
| 81 | WEIGHT: The PCHEMBL value |
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| 82 | """ |
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| 83 | built = BindingSearch( |
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| 84 | key=key, |
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| 85 | api=Apis.Chembl, |
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| 86 | taxa=EntryUtils.get_taxa(taxa), |
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| 87 | traversal=traversal, |
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| 88 | target_types=EntryUtils.get_target_types(target_types), |
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| 89 | min_conf_score=confidence, |
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| 90 | allowed_relations=EntryUtils.split(relations), |
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| 91 | min_pchembl=min_pchembl, |
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| 92 | banned_flags=EntryUtils.get_flags(banned_flags), |
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| 93 | binds_cutoff=binding, |
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| 94 | does_not_bind_cutoff=nonbinding, |
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| 95 | ) |
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| 96 | return cls._run(built, path, to, check, log, stderr, no_setup) |
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| 97 | |||
| 98 | |||
| 99 | class EntryChemblMechanism(Entry[MechanismSearch]): |
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| 100 | @classmethod |
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| 101 | def run( |
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| 102 | cls, |
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| 103 | path: Path = CommonArgs.in_compound_table, |
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| 104 | key: str = EntryArgs.key("chembl:mechanism"), |
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| 105 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 106 | taxa: Optional[str] = CommonArgs.taxa, |
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| 107 | traversal: str = EntryArgs.traversal_strategy, |
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| 108 | target_types: str = EntryArgs.target_types, |
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| 109 | min_confidence: Optional[int] = EntryArgs.min_confidence, |
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| 110 | as_of: Optional[str] = CommonArgs.as_of, |
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| 111 | check: bool = EntryArgs.check, |
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| 112 | log: Optional[Path] = CommonArgs.log, |
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| 113 | stderr: str = CommonArgs.stderr, |
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| 114 | no_setup: bool = CommonArgs.no_setup, |
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| 115 | ) -> Searcher: |
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| 116 | """ |
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| 117 | Mechanism of action (MoA) data from ChEMBL. |
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| 118 | |||
| 119 | OBJECT: The target name |
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| 120 | |||
| 121 | PREDICATE: The target action (e.g. "agonist") |
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| 122 | """ |
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| 123 | built = MechanismSearch( |
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| 124 | key=key, |
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| 125 | api=Apis.Chembl, |
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| 126 | taxa=EntryUtils.get_taxa(taxa), |
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| 127 | traversal_strategy=traversal, |
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| 128 | allowed_target_types=EntryUtils.get_target_types(target_types), |
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| 129 | min_confidence_score=min_confidence, |
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| 130 | ) |
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| 131 | return cls._run(built, path, to, check, log, stderr, no_setup) |
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| 132 | |||
| 133 | |||
| 134 | class ChemblQsarPredictions(Entry[TargetPredictionSearch]): |
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| 135 | @classmethod |
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| 136 | def run( |
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| 137 | cls, |
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| 138 | path: Path = CommonArgs.in_compound_table, |
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| 139 | key: str = EntryArgs.key("chembl:predictions"), |
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| 140 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 141 | taxa: str = CommonArgs.taxa, |
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| 142 | traversal: str = EntryArgs.traversal_strategy, |
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| 143 | target_types: str = EntryArgs.target_types, |
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| 144 | min_threshold: float = EntryArgs.min_threshold, |
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| 145 | as_of: Optional[str] = CommonArgs.as_of, |
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| 146 | check: bool = EntryArgs.check, |
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| 147 | log: Optional[Path] = CommonArgs.log, |
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| 148 | stderr: str = CommonArgs.stderr, |
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| 149 | no_setup: bool = CommonArgs.no_setup, |
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| 150 | ) -> Searcher: |
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| 151 | """ |
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| 152 | Predicted target binding from ChEMBL. |
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| 153 | |||
| 154 | https://mandos-chem.readthedocs.io/en/latest/binding.html |
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| 155 | These are from a QSAR model by ChEMBL. |
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| 156 | |||
| 157 | OBJECT: The target name |
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| 158 | |||
| 159 | WEIGHT: The square root of the PCHEMBL threshold |
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| 160 | multiplied by a prediction odds-ratio, normalized |
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| 161 | """ |
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| 162 | built = TargetPredictionSearch( |
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| 163 | key=key, |
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| 164 | api=Apis.Chembl, |
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| 165 | scrape=Apis.ChemblScrape, |
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| 166 | taxa=EntryUtils.get_taxa(taxa), |
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| 167 | traversal=traversal, |
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| 168 | target_types=EntryUtils.get_target_types(target_types), |
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| 169 | min_threshold=min_threshold, |
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| 170 | ) |
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| 171 | return cls._run(built, path, to, check, log, stderr, no_setup) |
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| 172 | |||
| 173 | |||
| 174 | class EntryChemblTrials(Entry[IndicationSearch]): |
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| 175 | @classmethod |
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| 176 | def run( |
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| 177 | cls, |
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| 178 | path: Path = CommonArgs.in_compound_table, |
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| 179 | key: str = EntryArgs.key("chembl:trial"), |
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| 180 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 181 | min_phase: Optional[int] = EntryArgs.chembl_trial, |
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| 182 | as_of: Optional[str] = CommonArgs.as_of, |
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| 183 | check: bool = EntryArgs.check, |
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| 184 | log: Optional[Path] = CommonArgs.log, |
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| 185 | stderr: str = CommonArgs.stderr, |
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| 186 | no_setup: bool = CommonArgs.no_setup, |
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| 187 | ) -> Searcher: |
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| 188 | """ |
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| 189 | Diseases from clinical trials listed in ChEMBL. |
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| 190 | |||
| 191 | OBJECT: The name of the disease (in MeSH) |
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| 192 | """ |
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| 193 | built = IndicationSearch(key=key, api=Apis.Chembl, min_phase=min_phase) |
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| 194 | return cls._run(built, path, to, check, log, stderr, no_setup) |
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| 195 | |||
| 196 | |||
| 197 | class EntryChemblAtc(Entry[AtcSearch]): |
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| 198 | @classmethod |
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| 199 | def run( |
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| 200 | cls, |
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| 201 | path: Path = CommonArgs.in_compound_table, |
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| 202 | key: str = EntryArgs.key("chembl:atc"), |
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| 203 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 204 | levels: str = EntryArgs.atc_level, |
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| 205 | as_of: Optional[str] = CommonArgs.as_of, |
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| 206 | check: bool = EntryArgs.check, |
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| 207 | log: Optional[Path] = CommonArgs.log, |
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| 208 | stderr: str = CommonArgs.stderr, |
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| 209 | no_setup: bool = CommonArgs.no_setup, |
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| 210 | ) -> Searcher: |
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| 211 | """ |
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| 212 | ATC codes from ChEMBL. |
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| 213 | |||
| 214 | OBJECT: The ATC code name |
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| 215 | """ |
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| 216 | built = AtcSearch( |
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| 217 | key=key, api=Apis.Chembl, levels={int(x.strip()) for x in levels.split(",")} |
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| 218 | ) |
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| 219 | return cls._run(built, path, to, check, log, stderr, no_setup) |
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| 220 | |||
| 221 | |||
| 222 | class _EntryChemblGo(Entry[GoSearch], metaclass=abc.ABCMeta): |
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| 223 | @classmethod |
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| 224 | def go_type(cls) -> GoType: |
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| 225 | raise NotImplementedError() |
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| 226 | |||
| 227 | @classmethod |
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| 228 | def cmd(cls) -> str: |
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| 229 | me = str(cls.go_type().name) |
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| 230 | return f"chembl:go.{me.lower()}" |
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| 231 | |||
| 232 | @classmethod |
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| 233 | def run( |
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| 234 | cls, |
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| 235 | path: Path = CommonArgs.in_compound_table, |
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| 236 | key: str = EntryArgs.key("<see above>"), |
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| 237 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 238 | taxa: Optional[str] = CommonArgs.taxa, |
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| 239 | traversal_strategy: str = EntryArgs.traversal_strategy, |
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| 240 | target_types: str = EntryArgs.target_types, |
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| 241 | confidence: Optional[int] = EntryArgs.min_confidence, |
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| 242 | relations: str = EntryArgs.relations, |
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| 243 | min_pchembl: float = EntryArgs.min_pchembl, |
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| 244 | banned_flags: Optional[str] = EntryArgs.banned_flags, |
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| 245 | binding_search: Optional[str] = EntryArgs.binding_search_name, |
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| 246 | as_of: Optional[str] = CommonArgs.as_of, |
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| 247 | check: bool = EntryArgs.check, |
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| 248 | log: Optional[Path] = CommonArgs.log, |
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| 249 | stderr: str = CommonArgs.stderr, |
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| 250 | no_setup: bool = CommonArgs.no_setup, |
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| 251 | ) -> Searcher: |
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| 252 | """ |
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| 253 | See the docs for the specific entries. |
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| 254 | """ |
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| 255 | if key is None or key == "<see above>": |
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| 256 | key = cls.cmd() |
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| 257 | api = ChemblApi.wrap(Apis.Chembl) |
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| 258 | if binding_search is None: |
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| 259 | binding_clazz = BindingSearch |
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| 260 | else: |
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| 261 | binding_clazz = ReflectionUtils.injection(binding_search, BindingSearch) |
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| 262 | logger.info(f"Passing parameters to {binding_clazz.__qualname__}") |
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| 263 | try: |
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| 264 | binding_search = binding_clazz( |
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| 265 | key=key, |
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| 266 | api=Apis.Chembl, |
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| 267 | taxa=EntryUtils.get_taxa(taxa), |
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| 268 | traversal=traversal_strategy, |
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| 269 | target_types=EntryUtils.get_target_types(target_types), |
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| 270 | min_conf_score=confidence, |
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| 271 | allowed_relations=EntryUtils.split(relations), |
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| 272 | min_pchembl=min_pchembl, |
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| 273 | banned_flags=EntryUtils.get_flags(banned_flags), |
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| 274 | ) |
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| 275 | except (TypeError, ValueError): |
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| 276 | raise InjectionError(f"Failed to build {binding_clazz.__qualname__}") |
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| 277 | built = GoSearch(key, api, cls.go_type(), binding_search) |
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| 278 | return cls._run(built, path, to, check, log, stderr, no_setup) |
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| 279 | |||
| 280 | |||
| 281 | View Code Duplication | class EntryGoFunction(_EntryChemblGo): |
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| 282 | @classmethod |
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| 283 | def go_type(cls) -> GoType: |
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| 284 | return GoType.function |
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| 285 | |||
| 286 | @classmethod |
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| 287 | def run( |
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| 288 | cls, |
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| 289 | path: Path = CommonArgs.in_compound_table, |
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| 290 | key: str = EntryArgs.key("chembl:go.function"), |
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| 291 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 292 | taxa: Optional[str] = CommonArgs.taxa, |
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| 293 | traversal_strategy: str = EntryArgs.traversal_strategy, |
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| 294 | target_types: str = EntryArgs.target_types, |
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| 295 | confidence: Optional[int] = EntryArgs.min_confidence, |
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| 296 | relations: str = EntryArgs.relations, |
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| 297 | min_pchembl: float = EntryArgs.min_pchembl, |
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| 298 | banned_flags: Optional[str] = EntryArgs.banned_flags, |
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| 299 | binding_search: Optional[str] = EntryArgs.binding_search_name, |
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| 300 | as_of: Optional[str] = CommonArgs.as_of, |
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| 301 | check: bool = EntryArgs.check, |
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| 302 | log: Optional[Path] = CommonArgs.log, |
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| 303 | stderr: str = CommonArgs.stderr, |
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| 304 | no_setup: bool = CommonArgs.no_setup, |
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| 305 | ) -> Searcher: |
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| 306 | """ |
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| 307 | GO Function terms associated with ChEMBL binding targets. |
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| 308 | |||
| 309 | OBJECT: The GO Function term name |
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| 310 | |||
| 311 | WEIGHT: The sum of the PCHEMBL values |
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| 312 | """ |
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| 313 | return super().run( |
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| 314 | path=path, |
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| 315 | key=key, |
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| 316 | to=to, |
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| 317 | taxa=taxa, |
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| 318 | traversal_strategy=traversal_strategy, |
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| 319 | target_types=target_types, |
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| 320 | confidence=confidence, |
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| 321 | relations=relations, |
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| 322 | min_pchembl=min_pchembl, |
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| 323 | banned_flags=banned_flags, |
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| 324 | binding_search=binding_search, |
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| 325 | as_of=as_of, |
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| 326 | check=check, |
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| 327 | log=log, |
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| 328 | stderr=stderr, |
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| 329 | ) |
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| 330 | |||
| 331 | |||
| 332 | View Code Duplication | class EntryGoProcess(_EntryChemblGo): |
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| 333 | @classmethod |
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| 334 | def go_type(cls) -> GoType: |
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| 335 | return GoType.process |
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| 336 | |||
| 337 | @classmethod |
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| 338 | def run( |
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| 339 | cls, |
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| 340 | path: Path = CommonArgs.in_compound_table, |
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| 341 | key: str = EntryArgs.key("chembl:go.process"), |
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| 342 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 343 | taxa: Optional[str] = CommonArgs.taxa, |
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| 344 | traversal_strategy: str = EntryArgs.traversal_strategy, |
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| 345 | target_types: str = EntryArgs.target_types, |
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| 346 | confidence: Optional[int] = EntryArgs.min_confidence, |
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| 347 | relations: str = EntryArgs.relations, |
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| 348 | min_pchembl: float = EntryArgs.min_pchembl, |
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| 349 | banned_flags: Optional[str] = EntryArgs.banned_flags, |
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| 350 | binding_search: Optional[str] = EntryArgs.binding_search_name, |
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| 351 | as_of: Optional[str] = CommonArgs.as_of, |
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| 352 | check: bool = EntryArgs.check, |
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| 353 | log: Optional[Path] = CommonArgs.log, |
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| 354 | stderr: str = CommonArgs.stderr, |
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| 355 | no_setup: bool = CommonArgs.no_setup, |
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| 356 | ) -> Searcher: |
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| 357 | """ |
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| 358 | GO Process terms associated with ChEMBL binding targets. |
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| 359 | |||
| 360 | OBJECT: The GO Process term name |
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| 361 | |||
| 362 | WEIGHT: The sum of the PCHEMBL values |
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| 363 | """ |
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| 364 | return super().run( |
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| 365 | path=path, |
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| 366 | key=key, |
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| 367 | to=to, |
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| 368 | taxa=taxa, |
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| 369 | traversal_strategy=traversal_strategy, |
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| 370 | target_types=target_types, |
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| 371 | confidence=confidence, |
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| 372 | relations=relations, |
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| 373 | min_pchembl=min_pchembl, |
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| 374 | banned_flags=banned_flags, |
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| 375 | binding_search=binding_search, |
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| 376 | as_of=as_of, |
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| 377 | check=check, |
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| 378 | log=log, |
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| 379 | stderr=stderr, |
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| 380 | ) |
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| 381 | |||
| 382 | |||
| 383 | View Code Duplication | class EntryGoComponent(_EntryChemblGo): |
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| 384 | @classmethod |
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| 385 | def go_type(cls) -> GoType: |
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| 386 | return GoType.component |
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| 387 | |||
| 388 | @classmethod |
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| 389 | def run( |
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| 390 | cls, |
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| 391 | path: Path = CommonArgs.in_compound_table, |
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| 392 | key: str = EntryArgs.key("chembl:go.component"), |
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| 393 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 394 | taxa: Optional[str] = CommonArgs.taxa, |
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| 395 | traversal_strategy: str = EntryArgs.traversal_strategy, |
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| 396 | target_types: str = EntryArgs.target_types, |
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| 397 | confidence: Optional[int] = EntryArgs.min_confidence, |
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| 398 | relations: str = EntryArgs.relations, |
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| 399 | min_pchembl: float = EntryArgs.min_pchembl, |
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| 400 | banned_flags: Optional[str] = EntryArgs.banned_flags, |
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| 401 | binding_search: Optional[str] = EntryArgs.binding_search_name, |
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| 402 | as_of: Optional[str] = CommonArgs.as_of, |
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| 403 | check: bool = EntryArgs.check, |
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| 404 | log: Optional[Path] = CommonArgs.log, |
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| 405 | stderr: str = CommonArgs.stderr, |
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| 406 | no_setup: bool = CommonArgs.no_setup, |
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| 407 | ) -> Searcher: |
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| 408 | """ |
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| 409 | GO Component terms associated with ChEMBL binding targets. |
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| 410 | |||
| 411 | OBJECT: The GO Component term name |
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| 412 | |||
| 413 | WEIGHT: The sum of the PCHEMBL values |
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| 414 | """ |
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| 415 | return super().run( |
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| 416 | path=path, |
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| 417 | key=key, |
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| 418 | to=to, |
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| 419 | taxa=taxa, |
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| 420 | traversal_strategy=traversal_strategy, |
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| 421 | target_types=target_types, |
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| 422 | confidence=confidence, |
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| 423 | relations=relations, |
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| 424 | min_pchembl=min_pchembl, |
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| 425 | banned_flags=banned_flags, |
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| 426 | binding_search=binding_search, |
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| 427 | as_of=as_of, |
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| 428 | check=check, |
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| 429 | log=log, |
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| 430 | stderr=stderr, |
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| 431 | ) |
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| 432 | |||
| 433 | |||
| 434 | class EntryPubchemDisease(Entry[DiseaseSearch]): |
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| 435 | View Code Duplication | @classmethod |
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| 436 | def run( |
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| 437 | cls, |
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| 438 | path: Path = CommonArgs.in_compound_table, |
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| 439 | key: str = EntryArgs.key("disease.ctd:mesh"), |
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| 440 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 441 | as_of: Optional[str] = CommonArgs.as_of, |
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| 442 | check: bool = EntryArgs.check, |
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| 443 | log: Optional[Path] = CommonArgs.log, |
||
| 444 | stderr: str = CommonArgs.stderr, |
||
| 445 | no_setup: bool = CommonArgs.no_setup, |
||
| 446 | ) -> Searcher: |
||
| 447 | """ |
||
| 448 | Diseases in the CTD. |
||
| 449 | |||
| 450 | (Comparative Toxicogenomics Database.) |
||
| 451 | |||
| 452 | OBJECT: The MeSH code of the disease |
||
| 453 | |||
| 454 | """ |
||
| 455 | built = DiseaseSearch(key, Apis.Pubchem) |
||
| 456 | return cls._run(built, path, to, check, log, stderr, no_setup) |
||
| 457 | |||
| 458 | |||
| 459 | class _EntryPubchemCoOccurrence(Entry[U], metaclass=abc.ABCMeta): |
||
| 460 | @classmethod |
||
| 461 | def cmd(cls) -> str: |
||
| 462 | me = str(cls.get_cooccurrence_type().name) |
||
| 463 | return f"lit.pubchem:{me.lower()}" |
||
| 464 | |||
| 465 | @classmethod |
||
| 466 | def get_cooccurrence_type(cls) -> CoOccurrenceType: |
||
| 467 | s: CoOccurrenceSearch = cls.get_search_type() |
||
| 468 | return s.cooccurrence_type() |
||
| 469 | |||
| 470 | @classmethod |
||
| 471 | def run( |
||
| 472 | cls, |
||
| 473 | path: Path = CommonArgs.in_compound_table, |
||
| 474 | key: str = EntryArgs.key("<see above>"), |
||
| 475 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 476 | min_score: float = EntryArgs.min_cooccurrence_score, |
||
| 477 | min_articles: int = EntryArgs.min_cooccurring_articles, |
||
| 478 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 479 | log: Optional[Path] = CommonArgs.log, |
||
| 480 | check: bool = EntryArgs.check, |
||
| 481 | stderr: str = CommonArgs.stderr, |
||
| 482 | no_setup: bool = CommonArgs.no_setup, |
||
| 483 | ) -> Searcher: |
||
| 484 | """See the docstrings for the individual entries.""" |
||
| 485 | clazz = cls.get_search_type() |
||
| 486 | built = clazz(key, Apis.Pubchem, min_score=min_score, min_articles=min_articles) |
||
| 487 | return cls._run(built, path, to, check, log, stderr, no_setup) |
||
| 488 | |||
| 489 | |||
| 490 | View Code Duplication | class EntryPubchemGeneCoOccurrence(_EntryPubchemCoOccurrence[GeneCoOccurrenceSearch]): |
|
| 491 | @classmethod |
||
| 492 | def run( |
||
| 493 | cls, |
||
| 494 | path: Path = CommonArgs.in_compound_table, |
||
| 495 | key: str = EntryArgs.key(f"lit.pubchem:{CoOccurrenceType.gene.name.lower()}"), |
||
| 496 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 497 | min_score: float = EntryArgs.min_cooccurrence_score, |
||
| 498 | min_articles: int = EntryArgs.min_cooccurring_articles, |
||
| 499 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 500 | log: Optional[Path] = CommonArgs.log, |
||
| 501 | check: bool = EntryArgs.check, |
||
| 502 | stderr: str = CommonArgs.stderr, |
||
| 503 | no_setup: bool = CommonArgs.no_setup, |
||
| 504 | ) -> Searcher: |
||
| 505 | """ |
||
| 506 | Co-occurrences of genes from PubMed articles. |
||
| 507 | |||
| 508 | https://mandos-chem.readthedocs.io/en/latest/co-occurrences.html |
||
| 509 | |||
| 510 | OBJECT: The name of the gene |
||
| 511 | |||
| 512 | WEIGHT: The co-occurrence score (refer to the docs) |
||
| 513 | """ |
||
| 514 | return super().run( |
||
| 515 | path=path, |
||
| 516 | key=key, |
||
| 517 | to=to, |
||
| 518 | min_score=min_score, |
||
| 519 | min_articles=min_articles, |
||
| 520 | as_of=as_of, |
||
| 521 | log=log, |
||
| 522 | check=check, |
||
| 523 | stderr=stderr, |
||
| 524 | no_setup=no_setup, |
||
| 525 | ) |
||
| 526 | |||
| 527 | |||
| 528 | View Code Duplication | class EntryPubchemDiseaseCoOccurrence(_EntryPubchemCoOccurrence[DiseaseCoOccurrenceSearch]): |
|
| 529 | @classmethod |
||
| 530 | def run( |
||
| 531 | cls, |
||
| 532 | path: Path = CommonArgs.in_compound_table, |
||
| 533 | key: str = EntryArgs.key(f"lit.pubchem:{CoOccurrenceType.disease.name.lower()}"), |
||
| 534 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 535 | min_score: float = EntryArgs.min_cooccurrence_score, |
||
| 536 | min_articles: int = EntryArgs.min_cooccurring_articles, |
||
| 537 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 538 | log: Optional[Path] = CommonArgs.log, |
||
| 539 | check: bool = EntryArgs.check, |
||
| 540 | stderr: str = CommonArgs.stderr, |
||
| 541 | no_setup: bool = CommonArgs.no_setup, |
||
| 542 | ) -> Searcher: |
||
| 543 | """ |
||
| 544 | Co-occurrences of diseases from PubMed articles. |
||
| 545 | |||
| 546 | https://mandos-chem.readthedocs.io/en/latest/co-occurrences.html |
||
| 547 | |||
| 548 | OBJECT: The name of the disease |
||
| 549 | |||
| 550 | WEIGHT: The co-occurrence score (refer to the docs) |
||
| 551 | """ |
||
| 552 | return super().run( |
||
| 553 | path=path, |
||
| 554 | key=key, |
||
| 555 | to=to, |
||
| 556 | min_score=min_score, |
||
| 557 | min_articles=min_articles, |
||
| 558 | as_of=as_of, |
||
| 559 | log=log, |
||
| 560 | check=check, |
||
| 561 | stderr=stderr, |
||
| 562 | no_setup=no_setup, |
||
| 563 | ) |
||
| 564 | |||
| 565 | |||
| 566 | View Code Duplication | class EntryPubchemChemicalCoOccurrence(_EntryPubchemCoOccurrence[ChemicalCoOccurrenceSearch]): |
|
| 567 | @classmethod |
||
| 568 | def run( |
||
| 569 | cls, |
||
| 570 | path: Path = CommonArgs.in_compound_table, |
||
| 571 | key: str = EntryArgs.key(f"lit.pubchem:{CoOccurrenceType.chemical.name.lower()}"), |
||
| 572 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 573 | min_score: float = EntryArgs.min_cooccurrence_score, |
||
| 574 | min_articles: int = EntryArgs.min_cooccurring_articles, |
||
| 575 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 576 | log: Optional[Path] = CommonArgs.log, |
||
| 577 | check: bool = EntryArgs.check, |
||
| 578 | stderr: str = CommonArgs.stderr, |
||
| 579 | no_setup: bool = CommonArgs.no_setup, |
||
| 580 | ) -> Searcher: |
||
| 581 | """ |
||
| 582 | Co-occurrences of chemicals from PubMed articles. |
||
| 583 | |||
| 584 | https://mandos-chem.readthedocs.io/en/latest/co-occurrences.html |
||
| 585 | |||
| 586 | OBJECT: The name of the chemical (e.g. "cocaine") |
||
| 587 | |||
| 588 | WEIGHT: The co-occurrence score (refer to the docs) |
||
| 589 | """ |
||
| 590 | return super().run( |
||
| 591 | path=path, |
||
| 592 | key=key, |
||
| 593 | to=to, |
||
| 594 | min_score=min_score, |
||
| 595 | min_articles=min_articles, |
||
| 596 | as_of=as_of, |
||
| 597 | log=log, |
||
| 598 | check=check, |
||
| 599 | stderr=stderr, |
||
| 600 | no_setup=no_setup, |
||
| 601 | ) |
||
| 602 | |||
| 603 | |||
| 604 | class EntryPubchemDgi(Entry[DgiSearch]): |
||
| 605 | View Code Duplication | @classmethod |
|
| 606 | def run( |
||
| 607 | cls, |
||
| 608 | path: Path = CommonArgs.in_compound_table, |
||
| 609 | key: str = EntryArgs.key("inter.dgidb:gene"), |
||
| 610 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 611 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 612 | log: Optional[Path] = CommonArgs.log, |
||
| 613 | check: bool = EntryArgs.check, |
||
| 614 | stderr: str = CommonArgs.stderr, |
||
| 615 | no_setup: bool = CommonArgs.no_setup, |
||
| 616 | ) -> Searcher: |
||
| 617 | """ |
||
| 618 | Drug/gene interactions in the DGIDB. |
||
| 619 | |||
| 620 | Drug Gene Interaction Database. |
||
| 621 | Also see disease.dgidb:int. |
||
| 622 | |||
| 623 | OBJECT: The name of the gene |
||
| 624 | |||
| 625 | PREDICATE: "interaction:generic" or "interaction:<type>" |
||
| 626 | """ |
||
| 627 | built = DgiSearch(key, Apis.Pubchem) |
||
| 628 | return cls._run(built, path, to, check, log, stderr, no_setup) |
||
| 629 | |||
| 630 | |||
| 631 | class EntryPubchemCgi(Entry[CtdGeneSearch]): |
||
| 632 | View Code Duplication | @classmethod |
|
| 633 | def run( |
||
| 634 | cls, |
||
| 635 | path: Path = CommonArgs.in_compound_table, |
||
| 636 | key: str = EntryArgs.key("inter.ctd:gene"), |
||
| 637 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 638 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 639 | log: Optional[Path] = CommonArgs.log, |
||
| 640 | check: bool = EntryArgs.check, |
||
| 641 | stderr: str = CommonArgs.stderr, |
||
| 642 | no_setup: bool = CommonArgs.no_setup, |
||
| 643 | ) -> Searcher: |
||
| 644 | """ |
||
| 645 | Compound/gene interactions in the DGIDB. |
||
| 646 | |||
| 647 | Drug Gene Interaction Database. |
||
| 648 | Also see ``interact.dgidb:int``. |
||
| 649 | |||
| 650 | OBJECT: The name of the gene |
||
| 651 | |||
| 652 | PREDICATE: derived from the interaction type (e.g. "downregulation") |
||
| 653 | """ |
||
| 654 | built = CtdGeneSearch(key, Apis.Pubchem) |
||
| 655 | return cls._run(built, path, to, check, log, stderr, no_setup) |
||
| 656 | |||
| 657 | |||
| 658 | class EntryDrugbankTarget(Entry[DrugbankTargetSearch]): |
||
| 659 | View Code Duplication | @classmethod |
|
| 660 | def run( |
||
| 661 | cls, |
||
| 662 | path: Path = CommonArgs.in_compound_table, |
||
| 663 | key: str = EntryArgs.key("inter.drugbank:targ"), |
||
| 664 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 665 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 666 | check: bool = EntryArgs.check, |
||
| 667 | log: Optional[Path] = CommonArgs.log, |
||
| 668 | stderr: str = CommonArgs.stderr, |
||
| 669 | no_setup: bool = CommonArgs.no_setup, |
||
| 670 | ) -> Searcher: |
||
| 671 | """ |
||
| 672 | Protein targets from DrugBank. |
||
| 673 | |||
| 674 | OBJECT: The target name (e.g. "Solute carrier family 22 member 11") |
||
| 675 | |||
| 676 | PREDICATE: "<target_type>:<action>" |
||
| 677 | """ |
||
| 678 | built = DrugbankTargetSearch(key, Apis.Pubchem, {DrugbankTargetType.target}) |
||
| 679 | return cls._run(built, path, to, check, log, stderr, no_setup) |
||
| 680 | |||
| 681 | |||
| 682 | class EntryGeneralFunction(Entry[DrugbankGeneralFunctionSearch]): |
||
| 683 | View Code Duplication | @classmethod |
|
| 684 | def run( |
||
| 685 | cls, |
||
| 686 | path: Path = CommonArgs.in_compound_table, |
||
| 687 | key: str = EntryArgs.key("inter.drugbank:targ-fn"), |
||
| 688 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 689 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 690 | check: bool = EntryArgs.check, |
||
| 691 | log: Optional[Path] = CommonArgs.log, |
||
| 692 | stderr: str = CommonArgs.stderr, |
||
| 693 | no_setup: bool = CommonArgs.no_setup, |
||
| 694 | ) -> Searcher: |
||
| 695 | """ |
||
| 696 | General functions from DrugBank targets. |
||
| 697 | |||
| 698 | OBJECT: The name of the "general function" (e.g. "Toxic substance binding") |
||
| 699 | |||
| 700 | PREDICATE: "<target_type>:<action>" |
||
| 701 | """ |
||
| 702 | built = DrugbankGeneralFunctionSearch(key, Apis.Pubchem, {DrugbankTargetType.target}) |
||
| 703 | return cls._run(built, path, to, check, log, stderr, no_setup) |
||
| 704 | |||
| 705 | |||
| 706 | View Code Duplication | class EntryDrugbankTransporter(Entry[DrugbankTargetSearch]): |
|
| 707 | @classmethod |
||
| 708 | def run( |
||
| 709 | cls, |
||
| 710 | path: Path = CommonArgs.in_compound_table, |
||
| 711 | key: str = EntryArgs.key("inter.drugbank:pk"), |
||
| 712 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 713 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 714 | check: bool = EntryArgs.check, |
||
| 715 | log: Optional[Path] = CommonArgs.log, |
||
| 716 | stderr: str = CommonArgs.stderr, |
||
| 717 | no_setup: bool = CommonArgs.no_setup, |
||
| 718 | ) -> Searcher: |
||
| 719 | """ |
||
| 720 | PK-related proteins from DrugBank. |
||
| 721 | |||
| 722 | OBJECT: The transporter name (e.g. "Solute carrier family 22 member 11") |
||
| 723 | |||
| 724 | PREDICATE: "<target_type>:<action>" (e.g. metabolized, transported, etc.) |
||
| 725 | """ |
||
| 726 | target_types = { |
||
| 727 | DrugbankTargetType.transporter, |
||
| 728 | DrugbankTargetType.carrier, |
||
| 729 | DrugbankTargetType.enzyme, |
||
| 730 | } |
||
| 731 | built = DrugbankTargetSearch(key, Apis.Pubchem, target_types) |
||
| 732 | return cls._run(built, path, to, check, log, stderr, no_setup) |
||
| 733 | |||
| 734 | |||
| 735 | View Code Duplication | class EntryTransporterGeneralFunction(Entry[DrugbankGeneralFunctionSearch]): |
|
| 736 | @classmethod |
||
| 737 | def run( |
||
| 738 | cls, |
||
| 739 | path: Path = CommonArgs.in_compound_table, |
||
| 740 | key: str = EntryArgs.key("inter.drugbank:pk-fn"), |
||
| 741 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 742 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 743 | check: bool = EntryArgs.check, |
||
| 744 | log: Optional[Path] = CommonArgs.log, |
||
| 745 | stderr: str = CommonArgs.stderr, |
||
| 746 | no_setup: bool = CommonArgs.no_setup, |
||
| 747 | ) -> Searcher: |
||
| 748 | """ |
||
| 749 | DrugBank PK-related protein functions. |
||
| 750 | |||
| 751 | OBJECT: The name of the general function (e.g. "Toxic substance binding") |
||
| 752 | |||
| 753 | PREDICATE: "<target_type>:<action>" (e.g. metabolized, transported, etc.) |
||
| 754 | """ |
||
| 755 | target_types = { |
||
| 756 | DrugbankTargetType.transporter, |
||
| 757 | DrugbankTargetType.carrier, |
||
| 758 | DrugbankTargetType.enzyme, |
||
| 759 | } |
||
| 760 | built = DrugbankGeneralFunctionSearch(key, Apis.Pubchem, target_types) |
||
| 761 | return cls._run(built, path, to, check, log, stderr, no_setup) |
||
| 762 | |||
| 763 | |||
| 764 | class EntryDrugbankDdi(Entry[DrugbankDdiSearch]): |
||
| 765 | View Code Duplication | @classmethod |
|
| 766 | def run( |
||
| 767 | cls, |
||
| 768 | path: Path = CommonArgs.in_compound_table, |
||
| 769 | key: str = EntryArgs.key("inter.drugbank:ddi"), |
||
| 770 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 771 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 772 | check: bool = EntryArgs.check, |
||
| 773 | log: Optional[Path] = CommonArgs.log, |
||
| 774 | stderr: str = CommonArgs.stderr, |
||
| 775 | no_setup: bool = CommonArgs.no_setup, |
||
| 776 | ) -> Searcher: |
||
| 777 | """ |
||
| 778 | Drug/drug interactions listed by DrugBank. |
||
| 779 | |||
| 780 | The "description" column includes useful information about the interaction, |
||
| 781 | such as diseases and whether a risk is increased or decreased. |
||
| 782 | |||
| 783 | OBJECT: The name of the drug (e.g. "ibuprofen") |
||
| 784 | |||
| 785 | PREDICATE: typically increase/decrease/change followed by risk/activity/etc. |
||
| 786 | """ |
||
| 787 | built = DrugbankDdiSearch(key, Apis.Pubchem) |
||
| 788 | return cls._run(built, path, to, check, log, stderr, no_setup) |
||
| 789 | |||
| 790 | |||
| 791 | class EntryPubchemAssay(Entry[BioactivitySearch]): |
||
| 792 | @classmethod |
||
| 793 | def run( |
||
| 794 | cls, |
||
| 795 | path: Path = CommonArgs.in_compound_table, |
||
| 796 | key: str = EntryArgs.key("assay.pubchem:act"), |
||
| 797 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 798 | name_must_match: bool = EntryArgs.name_must_match, |
||
| 799 | ban_sources: Optional[str] = EntryArgs.banned_sources, |
||
| 800 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 801 | check: bool = EntryArgs.check, |
||
| 802 | log: Optional[Path] = CommonArgs.log, |
||
| 803 | stderr: str = CommonArgs.stderr, |
||
| 804 | no_setup: bool = CommonArgs.no_setup, |
||
| 805 | ) -> Searcher: |
||
| 806 | """ |
||
| 807 | PubChem bioactivity results. |
||
| 808 | |||
| 809 | Note: The species name, if present, is taken from the target name. |
||
| 810 | The taxon ID is what was curated in PubChem. |
||
| 811 | |||
| 812 | OBJECT: The name of the target without species suffix |
||
| 813 | (e.g. "Slc6a3 - solute carrier family 6 member 3") |
||
| 814 | |||
| 815 | PREDICATE: "active", "inactive", "inconclusive", or "undetermined" |
||
| 816 | |||
| 817 | WEIGHT: 2 for confirmatory; 1 otherwise |
||
| 818 | """ |
||
| 819 | built = BioactivitySearch(key, Apis.Pubchem, compound_name_must_match=name_must_match) |
||
| 820 | return cls._run(built, path, to, check, log, stderr, no_setup) |
||
| 821 | |||
| 822 | |||
| 823 | class EntryDeaSchedule(Entry[BioactivitySearch]): |
||
| 824 | @classmethod |
||
| 825 | def run( |
||
| 826 | cls, |
||
| 827 | path: Path = CommonArgs.in_compound_table, |
||
| 828 | key: str = EntryArgs.key("drug.dea:schedule"), |
||
| 829 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 830 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 831 | check: bool = EntryArgs.check, |
||
| 832 | log: Optional[Path] = CommonArgs.log, |
||
| 833 | stderr: str = CommonArgs.stderr, |
||
| 834 | no_setup: bool = CommonArgs.no_setup, |
||
| 835 | ) -> Searcher: |
||
| 836 | """ |
||
| 837 | DEA schedules (PENDING). |
||
| 838 | |||
| 839 | OBJECT: The DEA schedule (1 to 4, or "unscheduled") |
||
| 840 | """ |
||
| 841 | pass |
||
| 842 | |||
| 843 | |||
| 844 | class EntryDeaClass(Entry[BioactivitySearch]): |
||
| 845 | @classmethod |
||
| 846 | def run( |
||
| 847 | cls, |
||
| 848 | path: Path = CommonArgs.in_compound_table, |
||
| 849 | key: str = EntryArgs.key("drug.dea:class"), |
||
| 850 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 851 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 852 | check: bool = EntryArgs.check, |
||
| 853 | log: Optional[Path] = CommonArgs.log, |
||
| 854 | stderr: str = CommonArgs.stderr, |
||
| 855 | no_setup: bool = CommonArgs.no_setup, |
||
| 856 | ) -> Searcher: |
||
| 857 | """ |
||
| 858 | DEA classes (PENDING). |
||
| 859 | |||
| 860 | OBJECT: The DEA class name (e.g. "hallucinogen") |
||
| 861 | """ |
||
| 862 | pass |
||
| 863 | |||
| 864 | |||
| 865 | class EntryChemidPlusAcute(Entry[AcuteEffectSearch]): |
||
| 866 | @classmethod |
||
| 867 | def run( |
||
| 868 | cls, |
||
| 869 | path: Path = CommonArgs.in_compound_table, |
||
| 870 | key: str = EntryArgs.key("tox.chemidplus:acute"), |
||
| 871 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 872 | level: int = EntryArgs.acute_effect_level, |
||
| 873 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 874 | check: bool = EntryArgs.check, |
||
| 875 | log: Optional[Path] = CommonArgs.log, |
||
| 876 | stderr: str = CommonArgs.stderr, |
||
| 877 | no_setup: bool = CommonArgs.no_setup, |
||
| 878 | ) -> Searcher: |
||
| 879 | """ |
||
| 880 | Acute effect codes from ChemIDPlus. |
||
| 881 | |||
| 882 | OBJECT: The code name (e.g. "behavioral: excitement") |
||
| 883 | """ |
||
| 884 | built = AcuteEffectSearch( |
||
| 885 | key, |
||
| 886 | Apis.Pubchem, |
||
| 887 | top_level=level == 1, |
||
| 888 | ) |
||
| 889 | return cls._run(built, path, to, check, log, stderr, no_setup) |
||
| 890 | |||
| 891 | |||
| 892 | class EntryChemidPlusLd50(Entry[Ld50Search]): |
||
| 893 | View Code Duplication | @classmethod |
|
| 894 | def run( |
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| 895 | cls, |
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| 896 | path: Path = CommonArgs.in_compound_table, |
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| 897 | key: str = EntryArgs.key("tox.chemidplus:ld50"), |
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| 898 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 899 | as_of: Optional[str] = CommonArgs.as_of, |
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| 900 | check: bool = EntryArgs.check, |
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| 901 | log: Optional[Path] = CommonArgs.log, |
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| 902 | stderr: str = CommonArgs.stderr, |
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| 903 | no_setup: bool = CommonArgs.no_setup, |
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| 904 | ) -> Searcher: |
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| 905 | """ |
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| 906 | LD50 acute effects from ChemIDPlus. |
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| 907 | |||
| 908 | OBJECT: The negative log10 of the dose in mg/kg |
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| 909 | |||
| 910 | PREDICATE: "LD50:<route>" (e.g. "LD50:intravenous") |
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| 911 | """ |
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| 912 | built = Ld50Search(key, Apis.Pubchem) |
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| 913 | return cls._run(built, path, to, check, log, stderr, no_setup) |
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| 914 | |||
| 915 | |||
| 916 | class EntryG2pInteractions(Entry[G2pInteractionSearch]): |
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| 917 | @classmethod |
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| 918 | def run( |
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| 919 | cls, |
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| 920 | path: Path = CommonArgs.in_compound_table, |
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| 921 | key: str = EntryArgs.key("g2p:interactions"), |
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| 922 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 923 | as_of: Optional[str] = CommonArgs.as_of, |
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| 924 | check: bool = EntryArgs.check, |
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| 925 | log: Optional[Path] = CommonArgs.log, |
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| 926 | stderr: str = CommonArgs.stderr, |
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| 927 | no_setup: bool = CommonArgs.no_setup, |
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| 928 | ) -> Searcher: |
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| 929 | """ |
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| 930 | Target interactions with affinities from Guide to Pharmacology. |
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| 931 | |||
| 932 | OBJECT: A molecular target |
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| 933 | |||
| 934 | PREDICATE: "interaction:agonism", etc. |
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| 935 | |||
| 936 | WEIGHT: 1.0 |
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| 937 | """ |
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| 938 | built = G2pInteractionSearch(key, Apis.G2p) |
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| 939 | return cls._run(built, path, to, check, log, stderr, no_setup) |
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| 940 | |||
| 941 | |||
| 942 | class EntryHmdbTissue(Entry[BioactivitySearch]): |
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| 943 | @classmethod |
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| 944 | def run( |
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| 945 | cls, |
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| 946 | path: Path = CommonArgs.in_compound_table, |
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| 947 | key: str = EntryArgs.key("hmdb:tissue"), |
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| 948 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 949 | min_nanomolar: Optional[float] = EntryArgs.min_nanomolar, |
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| 950 | as_of: Optional[str] = CommonArgs.as_of, |
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| 951 | check: bool = EntryArgs.check, |
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| 952 | log: Optional[Path] = CommonArgs.log, |
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| 953 | stderr: str = CommonArgs.stderr, |
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| 954 | no_setup: bool = CommonArgs.no_setup, |
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| 955 | ) -> Searcher: |
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| 956 | """ |
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| 957 | Tissue concentrations from HMDB (PENDING). |
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| 958 | |||
| 959 | OBJECT: |
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| 960 | |||
| 961 | PREDICATE: "tissue:..." |
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| 962 | """ |
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| 963 | pass |
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| 964 | |||
| 965 | |||
| 966 | class EntryHmdbComputed(Entry[BioactivitySearch]): |
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| 967 | @classmethod |
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| 968 | def run( |
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| 969 | cls, |
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| 970 | path: Path = CommonArgs.in_compound_table, |
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| 971 | key: str = EntryArgs.key("hmdb:computed"), |
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| 972 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 973 | min_nanomolar: Optional[float] = None, |
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| 974 | as_of: Optional[str] = CommonArgs.as_of, |
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| 975 | check: bool = EntryArgs.check, |
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| 976 | log: Optional[Path] = CommonArgs.log, |
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| 977 | stderr: str = CommonArgs.stderr, |
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| 978 | no_setup: bool = CommonArgs.no_setup, |
||
| 979 | ) -> Searcher: |
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| 980 | """ |
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| 981 | Computed properties from HMDB (PENDING). |
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| 982 | |||
| 983 | Keys include pKa, logP, logS, etc. |
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| 984 | |||
| 985 | OBJECT: A number; booleans are converted to 0/1 |
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| 986 | |||
| 987 | PREDICATE: The name of the property |
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| 988 | """ |
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| 989 | pass |
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| 990 | |||
| 991 | |||
| 992 | class EntryPubchemComputed(Entry[ComputedPropertySearch]): |
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| 993 | @classmethod |
||
| 994 | def run( |
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| 995 | cls, |
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| 996 | path: Path = CommonArgs.in_compound_table, |
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| 997 | key: str = EntryArgs.key("chem.pubchem:computed"), |
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| 998 | keys: str = EntryArgs.pubchem_computed_keys, |
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| 999 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 1000 | as_of: Optional[str] = CommonArgs.as_of, |
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| 1001 | check: bool = EntryArgs.check, |
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| 1002 | log: Optional[Path] = CommonArgs.log, |
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| 1003 | stderr: str = CommonArgs.stderr, |
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| 1004 | no_setup: bool = CommonArgs.no_setup, |
||
| 1005 | ) -> Searcher: |
||
| 1006 | """ |
||
| 1007 | Computed properties from PubChem. |
||
| 1008 | |||
| 1009 | OBJECT: Number |
||
| 1010 | |||
| 1011 | PREDICATE: e.g. "complexity" |
||
| 1012 | """ |
||
| 1013 | # replace acronyms, etc. |
||
| 1014 | # ComputedPropertySearch standardizes punctuation and casing |
||
| 1015 | known = { |
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| 1016 | k: v |
||
| 1017 | for k, v in { |
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| 1018 | **EntryArgs.KNOWN_USEFUL_KEYS, |
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| 1019 | **EntryArgs.KNOWN_USELESS_KEYS, |
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| 1020 | }.items() |
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| 1021 | if v is not None |
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| 1022 | } |
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| 1023 | keys = {known.get(s.strip(), s) for s in keys.split(",")} |
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| 1024 | built = ComputedPropertySearch(key, Apis.Pubchem, descriptors=keys) |
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| 1025 | return cls._run(built, path, to, check, log, stderr, no_setup) |
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| 1026 | |||
| 1027 | |||
| 1028 | class EntryDrugbankAdmet(Entry[DrugbankTargetSearch]): |
||
| 1029 | @classmethod |
||
| 1030 | def run( |
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| 1031 | cls, |
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| 1032 | path: Path = CommonArgs.in_compound_table, |
||
| 1033 | key: str = EntryArgs.key("drugbank.admet:properties"), |
||
| 1034 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 1035 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 1036 | check: bool = EntryArgs.check, |
||
| 1037 | log: Optional[Path] = CommonArgs.log, |
||
| 1038 | stderr: str = CommonArgs.stderr, |
||
| 1039 | no_setup: bool = CommonArgs.no_setup, |
||
| 1040 | ) -> Searcher: |
||
| 1041 | """ |
||
| 1042 | Enzyme predictions from DrugBank (PENDING). |
||
| 1043 | |||
| 1044 | OBJECT: Enzyme name |
||
| 1045 | |||
| 1046 | PREDICATE: Action |
||
| 1047 | """ |
||
| 1048 | |||
| 1049 | |||
| 1050 | class EntryDrugbankMetabolites(Entry[DrugbankTargetSearch]): |
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| 1051 | @classmethod |
||
| 1052 | def run( |
||
| 1053 | cls, |
||
| 1054 | path: Path = CommonArgs.in_compound_table, |
||
| 1055 | key: str = EntryArgs.key("drugbank.admet:metabolites"), |
||
| 1056 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 1057 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 1058 | check: bool = EntryArgs.check, |
||
| 1059 | log: Optional[Path] = CommonArgs.log, |
||
| 1060 | stderr: str = CommonArgs.stderr, |
||
| 1061 | no_setup: bool = CommonArgs.no_setup, |
||
| 1062 | ) -> Searcher: |
||
| 1063 | """ |
||
| 1064 | Metabolites from DrugBank (PENDING). |
||
| 1065 | |||
| 1066 | OBJECT: Compound name (e.g. "norcocaine"). |
||
| 1067 | |||
| 1068 | PREDICATE: "metabolized to" |
||
| 1069 | """ |
||
| 1070 | |||
| 1071 | |||
| 1072 | class EntryDrugbankDosage(Entry[DrugbankTargetSearch]): |
||
| 1073 | @classmethod |
||
| 1074 | def run( |
||
| 1075 | cls, |
||
| 1076 | path: Path = CommonArgs.in_compound_table, |
||
| 1077 | key: str = EntryArgs.key("drugbank.admet:dosage"), |
||
| 1078 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 1079 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 1080 | check: bool = EntryArgs.check, |
||
| 1081 | log: Optional[Path] = CommonArgs.log, |
||
| 1082 | stderr: str = CommonArgs.stderr, |
||
| 1083 | no_setup: bool = CommonArgs.no_setup, |
||
| 1084 | ) -> Searcher: |
||
| 1085 | """ |
||
| 1086 | Dosage from DrugBank (PENDING). |
||
| 1087 | |||
| 1088 | OBJECT: concentration in mg/mL |
||
| 1089 | |||
| 1090 | PREDICATE: "dosage :: <route>" |
||
| 1091 | |||
| 1092 | OTHER COLUMNS: |
||
| 1093 | |||
| 1094 | - form (e.g. liquid) |
||
| 1095 | """ |
||
| 1096 | |||
| 1097 | |||
| 1098 | class EntryMetaRandom(Entry[BioactivitySearch]): |
||
| 1099 | @classmethod |
||
| 1100 | def run( |
||
| 1101 | cls, |
||
| 1102 | path: Path = CommonArgs.in_compound_table, |
||
| 1103 | key: str = EntryArgs.key("meta:random"), |
||
| 1104 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 1105 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 1106 | check: bool = EntryArgs.check, |
||
| 1107 | log: Optional[Path] = CommonArgs.log, |
||
| 1108 | stderr: str = CommonArgs.stderr, |
||
| 1109 | no_setup: bool = CommonArgs.no_setup, |
||
| 1110 | ) -> Searcher: |
||
| 1111 | """ |
||
| 1112 | Random class assignment (PENDING). |
||
| 1113 | |||
| 1114 | OBJECT: 1 thru n-compounds |
||
| 1115 | |||
| 1116 | PREDICATE: "random" |
||
| 1117 | """ |
||
| 1118 | pass |
||
| 1119 | |||
| 1120 | |||
| 1121 | Entries = [ |
||
| 1122 | EntryChemblBinding, |
||
| 1123 | EntryChemblMechanism, |
||
| 1124 | EntryChemblAtc, |
||
| 1125 | EntryChemblTrials, |
||
| 1126 | EntryGoFunction, |
||
| 1127 | EntryGoProcess, |
||
| 1128 | EntryGoComponent, |
||
| 1129 | EntryPubchemComputed, |
||
| 1130 | EntryPubchemDisease, |
||
| 1131 | EntryPubchemGeneCoOccurrence, |
||
| 1132 | EntryPubchemDiseaseCoOccurrence, |
||
| 1133 | EntryPubchemChemicalCoOccurrence, |
||
| 1134 | EntryPubchemDgi, |
||
| 1135 | EntryPubchemCgi, |
||
| 1136 | EntryDrugbankTarget, |
||
| 1137 | EntryGeneralFunction, |
||
| 1138 | EntryDrugbankTransporter, |
||
| 1139 | EntryTransporterGeneralFunction, |
||
| 1140 | EntryDrugbankDdi, |
||
| 1141 | EntryPubchemAssay, |
||
| 1142 | EntryDeaSchedule, |
||
| 1143 | EntryDeaClass, |
||
| 1144 | EntryChemidPlusAcute, |
||
| 1145 | EntryChemidPlusLd50, |
||
| 1146 | EntryHmdbTissue, |
||
| 1147 | EntryMetaRandom, |
||
| 1148 | ] |
||
| 1149 |
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