dmyersturnbull /
mandos
| Total Complexity | 46 |
| Total Lines | 1139 |
| Duplicated Lines | 35.12 % |
| 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 | import inspect |
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| 9 | from pathlib import Path |
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| 10 | from typing import Optional, TypeVar |
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| 11 | |||
| 12 | from pocketutils.core.exceptions import InjectionError |
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| 13 | from pocketutils.tools.reflection_tools import ReflectionTools |
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| 14 | |||
| 15 | from mandos.entry.abstract_entries import Entry |
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| 16 | from mandos.entry.api_singletons import Apis |
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| 17 | from mandos.entry.tools.searchers import Searcher |
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| 18 | from mandos.entry.utils._arg_utils import ArgUtils |
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| 19 | from mandos.entry.utils._common_args import CommonArgs |
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| 20 | from mandos.entry.utils._entry_args import EntryArgs |
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| 21 | from mandos.model.apis.chembl_api import ChemblApi |
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| 22 | from mandos.model.apis.pubchem_support.pubchem_models import ( |
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| 23 | ClinicalTrialsGovUtils, |
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| 24 | CoOccurrenceType, |
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| 25 | DrugbankTargetType, |
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| 26 | ) |
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| 27 | from mandos.model.concrete_hits import GoType |
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| 28 | from mandos.model.utils.setup import logger |
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| 29 | from mandos.search.chembl.atc_search import AtcSearch |
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| 30 | from mandos.search.chembl.binding_search import BindingSearch |
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| 31 | from mandos.search.chembl.go_search import GoSearch |
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| 32 | from mandos.search.chembl.indication_search import IndicationSearch |
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| 33 | from mandos.search.chembl.mechanism_search import MechanismSearch |
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| 34 | from mandos.search.chembl.target_prediction_search import TargetPredictionSearch |
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| 35 | from mandos.search.g2p.g2p_interaction_search import G2pInteractionSearch |
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| 36 | from mandos.search.hmdb.tissue_concentration_search import TissueConcentrationSearch |
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| 37 | from mandos.search.meta.random_search import RandomSearch |
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| 38 | from mandos.search.pubchem.acute_effects_search import AcuteEffectSearch, Ld50Search |
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| 39 | from mandos.search.pubchem.bioactivity_search import BioactivitySearch |
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| 40 | from mandos.search.pubchem.computed_property_search import ComputedPropertySearch |
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| 41 | from mandos.search.pubchem.cooccurrence_search import ( |
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| 42 | ChemicalCoOccurrenceSearch, |
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| 43 | CoOccurrenceSearch, |
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| 44 | DiseaseCoOccurrenceSearch, |
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| 45 | GeneCoOccurrenceSearch, |
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| 46 | ) |
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| 47 | from mandos.search.pubchem.ctd_gene_search import CtdGeneSearch |
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| 48 | from mandos.search.pubchem.dgidb_search import DgiSearch |
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| 49 | from mandos.search.pubchem.disease_search import DiseaseSearch |
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| 50 | from mandos.search.pubchem.drugbank_ddi_search import DrugbankDdiSearch |
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| 51 | from mandos.search.pubchem.drugbank_interaction_search import ( |
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| 52 | DrugbankGeneralFunctionSearch, |
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| 53 | DrugbankTargetSearch, |
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| 54 | ) |
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| 55 | from mandos.search.pubchem.trials_search import TrialSearch |
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| 56 | |||
| 57 | U = TypeVar("U", covariant=True, bound=CoOccurrenceSearch) |
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| 58 | |||
| 59 | |||
| 60 | class EntryChemblBinding(Entry[BindingSearch]): |
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| 61 | @classmethod |
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| 62 | def run( |
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| 63 | cls, |
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| 64 | path: Path = CommonArgs.in_compound_table, |
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| 65 | key: str = EntryArgs.key("chembl:binding"), |
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| 66 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 67 | taxa: str = CommonArgs.taxa, |
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| 68 | traversal: str = EntryArgs.traversal, |
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| 69 | target_types: str = EntryArgs.target_types, |
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| 70 | confidence: int = EntryArgs.min_confidence, |
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| 71 | binding: float = EntryArgs.binds_cutoff, |
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| 72 | pchembl: float = EntryArgs.min_pchembl, |
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| 73 | as_of: Optional[str] = CommonArgs.as_of, |
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| 74 | replace: bool = CommonArgs.replace, |
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| 75 | proceed: bool = CommonArgs.proceed, |
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| 76 | check: bool = EntryArgs.check, |
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| 77 | log: Optional[Path] = CommonArgs.log, |
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| 78 | stderr: str = CommonArgs.stderr, |
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| 79 | ) -> Searcher: |
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| 80 | """ |
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| 81 | Binding data from ChEMBL. |
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| 82 | |||
| 83 | These are 'activity' annotations of the type 'B' that have a pCHEMBL value. |
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| 84 | https://mandos-chem.readthedocs.io/en/latest/binding.html |
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| 85 | |||
| 86 | OBJECT: The target name |
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| 87 | |||
| 88 | WEIGHT: The PCHEMBL value |
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| 89 | """ |
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| 90 | tax = ArgUtils.get_taxonomy(taxa) |
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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=tax, |
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| 95 | traversal=traversal, |
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| 96 | target_types=ArgUtils.get_target_types(target_types), |
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| 97 | min_conf_score=confidence, |
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| 98 | relations={"<", "<=", "="}, # there are no others with pchembl |
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| 99 | min_pchembl=pchembl, |
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| 100 | binds_cutoff=binding, |
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| 101 | ) |
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| 102 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
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| 103 | |||
| 104 | |||
| 105 | class EntryChemblMechanism(Entry[MechanismSearch]): |
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| 106 | @classmethod |
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| 107 | def run( |
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| 108 | cls, |
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| 109 | path: Path = CommonArgs.in_compound_table, |
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| 110 | key: str = EntryArgs.key("chembl:mechanism"), |
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| 111 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 112 | taxa: str = CommonArgs.taxa, |
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| 113 | traversal: str = EntryArgs.traversal, |
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| 114 | target_types: str = EntryArgs.target_types, |
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| 115 | min_confidence: Optional[int] = EntryArgs.min_confidence, |
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| 116 | as_of: Optional[str] = CommonArgs.as_of, |
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| 117 | replace: bool = CommonArgs.replace, |
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| 118 | proceed: bool = CommonArgs.proceed, |
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| 119 | check: bool = EntryArgs.check, |
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| 120 | log: Optional[Path] = CommonArgs.log, |
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| 121 | stderr: str = CommonArgs.stderr, |
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| 122 | ) -> Searcher: |
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| 123 | """ |
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| 124 | Mechanism of action (MOA) data from ChEMBL. |
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| 125 | |||
| 126 | OBJECT: The target name |
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| 127 | |||
| 128 | PREDICATE: The target action (e.g. "agonist") |
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| 129 | """ |
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| 130 | tax = ArgUtils.get_taxonomy(taxa) |
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| 131 | built = MechanismSearch( |
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| 132 | key=key, |
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| 133 | api=Apis.Chembl, |
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| 134 | taxa=tax, |
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| 135 | traversal=traversal, |
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| 136 | allowed_target_types=ArgUtils.get_target_types(target_types), |
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| 137 | min_confidence_score=min_confidence, |
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| 138 | ) |
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| 139 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
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| 140 | |||
| 141 | |||
| 142 | class ChemblQsarPredictions(Entry[TargetPredictionSearch]): |
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| 143 | @classmethod |
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| 144 | def run( |
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| 145 | cls, |
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| 146 | path: Path = CommonArgs.in_compound_table, |
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| 147 | key: str = EntryArgs.key("chembl:predictions"), |
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| 148 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 149 | taxa: str = CommonArgs.taxa, |
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| 150 | traversal: str = EntryArgs.traversal, |
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| 151 | target_types: str = EntryArgs.target_types, |
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| 152 | min_threshold: float = EntryArgs.min_threshold, |
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| 153 | as_of: Optional[str] = CommonArgs.as_of, |
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| 154 | replace: bool = CommonArgs.replace, |
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| 155 | proceed: bool = CommonArgs.proceed, |
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| 156 | check: bool = EntryArgs.check, |
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| 157 | log: Optional[Path] = CommonArgs.log, |
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| 158 | stderr: str = CommonArgs.stderr, |
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| 159 | ) -> Searcher: |
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| 160 | """ |
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| 161 | Predicted target binding from ChEMBL. |
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| 162 | |||
| 163 | https://mandos-chem.readthedocs.io/en/latest/binding.html |
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| 164 | These are from a QSAR model by ChEMBL. |
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| 165 | |||
| 166 | OBJECT: The target name |
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| 167 | |||
| 168 | WEIGHT: The square root of the PCHEMBL threshold |
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| 169 | multiplied by a prediction odds-ratio, normalized |
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| 170 | """ |
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| 171 | tax = ArgUtils.get_taxonomy(taxa) |
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| 172 | built = TargetPredictionSearch( |
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| 173 | key=key, |
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| 174 | api=Apis.Chembl, |
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| 175 | scrape=Apis.ChemblScrape, |
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| 176 | taxa=tax, |
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| 177 | traversal=traversal, |
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| 178 | target_types=ArgUtils.get_target_types(target_types), |
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| 179 | min_threshold=min_threshold, |
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| 180 | ) |
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| 181 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
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| 182 | |||
| 183 | |||
| 184 | class EntryChemblTrials(Entry[IndicationSearch]): |
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| 185 | @classmethod |
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| 186 | def run( |
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| 187 | cls, |
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| 188 | path: Path = CommonArgs.in_compound_table, |
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| 189 | key: str = EntryArgs.key("chembl:trial"), |
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| 190 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 191 | min_phase: Optional[int] = EntryArgs.chembl_trial, |
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| 192 | as_of: Optional[str] = CommonArgs.as_of, |
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| 193 | replace: bool = CommonArgs.replace, |
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| 194 | proceed: bool = CommonArgs.proceed, |
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| 195 | check: bool = EntryArgs.check, |
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| 196 | log: Optional[Path] = CommonArgs.log, |
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| 197 | stderr: str = CommonArgs.stderr, |
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| 198 | ) -> Searcher: |
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| 199 | """ |
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| 200 | Diseases from clinical trials listed in ChEMBL. |
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| 201 | |||
| 202 | OBJECT: The name of the disease (in MeSH) |
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| 203 | """ |
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| 204 | built = IndicationSearch(key=key, api=Apis.Chembl, min_phase=min_phase) |
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| 205 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
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| 206 | |||
| 207 | |||
| 208 | class EntryChemblAtc(Entry[AtcSearch]): |
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| 209 | @classmethod |
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| 210 | def run( |
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| 211 | cls, |
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| 212 | path: Path = CommonArgs.in_compound_table, |
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| 213 | key: str = EntryArgs.key("chembl:atc"), |
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| 214 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 215 | levels: str = EntryArgs.atc_level, |
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| 216 | as_of: Optional[str] = CommonArgs.as_of, |
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| 217 | replace: bool = CommonArgs.replace, |
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| 218 | proceed: bool = CommonArgs.proceed, |
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| 219 | check: bool = EntryArgs.check, |
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| 220 | log: Optional[Path] = CommonArgs.log, |
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| 221 | stderr: str = CommonArgs.stderr, |
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| 222 | ) -> Searcher: |
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| 223 | """ |
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| 224 | ATC codes from ChEMBL. |
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| 225 | |||
| 226 | OBJECT: The ATC code name |
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| 227 | """ |
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| 228 | built = AtcSearch( |
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| 229 | key=key, api=Apis.Chembl, levels={int(x.strip()) for x in levels.split(",")} |
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| 230 | ) |
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| 231 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
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| 232 | |||
| 233 | |||
| 234 | class _EntryChemblGo(Entry[GoSearch], metaclass=abc.ABCMeta): |
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| 235 | @classmethod |
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| 236 | def go_type(cls) -> GoType: |
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| 237 | raise NotImplementedError() |
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| 238 | |||
| 239 | @classmethod |
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| 240 | def cmd(cls) -> str: |
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| 241 | me = str(cls.go_type().name) |
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| 242 | return f"chembl:go.{me.lower()}" |
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| 243 | |||
| 244 | @classmethod |
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| 245 | def run( |
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| 246 | cls, |
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| 247 | path: Path = CommonArgs.in_compound_table, |
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| 248 | key: str = EntryArgs.key("<see above>"), |
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| 249 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 250 | taxa: str = CommonArgs.taxa, |
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| 251 | traversal: str = EntryArgs.traversal, |
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| 252 | target_types: str = EntryArgs.target_types, |
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| 253 | confidence: Optional[int] = EntryArgs.min_confidence, |
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| 254 | pchembl: float = EntryArgs.min_pchembl, |
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| 255 | binding_search: Optional[str] = EntryArgs.binding_search_name, |
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| 256 | as_of: Optional[str] = CommonArgs.as_of, |
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| 257 | replace: bool = CommonArgs.replace, |
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| 258 | proceed: bool = CommonArgs.proceed, |
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| 259 | check: bool = EntryArgs.check, |
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| 260 | log: Optional[Path] = CommonArgs.log, |
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| 261 | stderr: str = CommonArgs.stderr, |
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| 262 | ) -> Searcher: |
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| 263 | """ |
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| 264 | See the docs for the specific entries. |
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| 265 | """ |
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| 266 | if key is None or key == "<see above>": |
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| 267 | key = cls.cmd() |
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| 268 | api = ChemblApi.wrap(Apis.Chembl) |
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| 269 | if binding_search is None: |
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| 270 | binding_clazz = BindingSearch |
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| 271 | else: |
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| 272 | binding_clazz = ReflectionTools.injection(binding_search, BindingSearch) |
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| 273 | logger.info(f"Passing parameters to {binding_clazz.__qualname__}") |
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| 274 | try: |
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| 275 | tax = ArgUtils.get_taxonomy(taxa) |
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| 276 | binding_search = binding_clazz( |
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| 277 | key=key, |
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| 278 | api=Apis.Chembl, |
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| 279 | taxa=tax, |
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| 280 | traversal=traversal, |
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| 281 | target_types=ArgUtils.get_target_types(target_types), |
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| 282 | min_conf_score=confidence, |
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| 283 | relations={"<", "<=", "="}, |
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| 284 | min_pchembl=pchembl, |
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| 285 | ) |
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| 286 | except (TypeError, ValueError): |
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| 287 | raise InjectionError(f"Failed to build {binding_clazz.__qualname__}") |
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| 288 | built = GoSearch(key, api, cls.go_type(), binding_search) |
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| 289 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
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| 290 | |||
| 291 | |||
| 292 | View Code Duplication | class EntryGoFunction(_EntryChemblGo): |
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| 293 | @classmethod |
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| 294 | def go_type(cls) -> GoType: |
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| 295 | return GoType.function |
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| 296 | |||
| 297 | @classmethod |
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| 298 | def run( |
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| 299 | cls, |
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| 300 | path: Path = CommonArgs.in_compound_table, |
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| 301 | key: str = EntryArgs.key("chembl:go.function"), |
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| 302 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 303 | taxa: str = CommonArgs.taxa, |
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| 304 | traversal: str = EntryArgs.traversal, |
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| 305 | target_types: str = EntryArgs.target_types, |
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| 306 | confidence: Optional[int] = EntryArgs.min_confidence, |
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| 307 | pchembl: float = EntryArgs.min_pchembl, |
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| 308 | binding_search: Optional[str] = EntryArgs.binding_search_name, |
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| 309 | as_of: Optional[str] = CommonArgs.as_of, |
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| 310 | replace: bool = CommonArgs.replace, |
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| 311 | proceed: bool = CommonArgs.proceed, |
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| 312 | check: bool = EntryArgs.check, |
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| 313 | log: Optional[Path] = CommonArgs.log, |
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| 314 | stderr: str = CommonArgs.stderr, |
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| 315 | ) -> Searcher: |
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| 316 | """ |
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| 317 | GO Function terms associated with ChEMBL binding targets. |
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| 318 | |||
| 319 | OBJECT: The GO Function term name |
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| 320 | |||
| 321 | WEIGHT: The sum of the PCHEMBL values |
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| 322 | """ |
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| 323 | args, _, _, locs = inspect.getargvalues(inspect.currentframe()) |
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| 324 | return super().run(**{a: locs[a] for a in args if a != "cls"}) |
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| 325 | |||
| 326 | |||
| 327 | View Code Duplication | class EntryGoProcess(_EntryChemblGo): |
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| 328 | @classmethod |
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| 329 | def go_type(cls) -> GoType: |
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| 330 | return GoType.process |
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| 331 | |||
| 332 | @classmethod |
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| 333 | def run( |
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| 334 | cls, |
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| 335 | path: Path = CommonArgs.in_compound_table, |
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| 336 | key: str = EntryArgs.key("chembl:go.process"), |
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| 337 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 338 | taxa: str = CommonArgs.taxa, |
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| 339 | traversal: str = EntryArgs.traversal, |
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| 340 | target_types: str = EntryArgs.target_types, |
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| 341 | confidence: Optional[int] = EntryArgs.min_confidence, |
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| 342 | pchembl: float = EntryArgs.min_pchembl, |
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| 343 | binding_search: Optional[str] = EntryArgs.binding_search_name, |
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| 344 | as_of: Optional[str] = CommonArgs.as_of, |
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| 345 | replace: bool = CommonArgs.replace, |
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| 346 | proceed: bool = CommonArgs.proceed, |
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| 347 | check: bool = EntryArgs.check, |
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| 348 | log: Optional[Path] = CommonArgs.log, |
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| 349 | stderr: str = CommonArgs.stderr, |
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| 350 | ) -> Searcher: |
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| 351 | """ |
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| 352 | GO Process terms associated with ChEMBL binding targets. |
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| 353 | |||
| 354 | OBJECT: The GO Process term name |
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| 355 | |||
| 356 | WEIGHT: The sum of the PCHEMBL values |
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| 357 | """ |
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| 358 | args, _, _, locs = inspect.getargvalues(inspect.currentframe()) |
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| 359 | return super().run(**{a: locs[a] for a in args if a != "cls"}) |
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| 360 | |||
| 361 | |||
| 362 | View Code Duplication | class EntryGoComponent(_EntryChemblGo): |
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| 363 | @classmethod |
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| 364 | def go_type(cls) -> GoType: |
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| 365 | return GoType.component |
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| 366 | |||
| 367 | @classmethod |
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| 368 | def run( |
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| 369 | cls, |
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| 370 | path: Path = CommonArgs.in_compound_table, |
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| 371 | key: str = EntryArgs.key("chembl:go.component"), |
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| 372 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 373 | taxa: str = CommonArgs.taxa, |
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| 374 | traversal: str = EntryArgs.traversal, |
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| 375 | target_types: str = EntryArgs.target_types, |
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| 376 | confidence: Optional[int] = EntryArgs.min_confidence, |
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| 377 | pchembl: float = EntryArgs.min_pchembl, |
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| 378 | binding_search: Optional[str] = EntryArgs.binding_search_name, |
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| 379 | as_of: Optional[str] = CommonArgs.as_of, |
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| 380 | replace: bool = CommonArgs.replace, |
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| 381 | proceed: bool = CommonArgs.proceed, |
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| 382 | check: bool = EntryArgs.check, |
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| 383 | log: Optional[Path] = CommonArgs.log, |
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| 384 | stderr: str = CommonArgs.stderr, |
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| 385 | ) -> Searcher: |
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| 386 | """ |
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| 387 | GO Component terms associated with ChEMBL binding targets. |
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| 388 | |||
| 389 | OBJECT: The GO Component term name |
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| 390 | |||
| 391 | WEIGHT: The sum of the PCHEMBL values |
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| 392 | """ |
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| 393 | args, _, _, locs = inspect.getargvalues(inspect.currentframe()) |
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| 394 | return super().run(**{a: locs[a] for a in args if a != "cls"}) |
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| 395 | |||
| 396 | |||
| 397 | class EntryPubchemTrials(Entry[TrialSearch]): |
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| 398 | @classmethod |
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| 399 | def run( |
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| 400 | cls, |
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| 401 | path: Path = CommonArgs.in_compound_table, |
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| 402 | key: str = EntryArgs.key("pubchem:trial"), |
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| 403 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 404 | min_phase: Optional[int] = EntryArgs.pubchem_trial_phase, |
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| 405 | statuses: str = EntryArgs.pubchem_trial_statuses, |
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| 406 | req_explicit: bool = EntryArgs.req_explicit, |
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| 407 | as_of: Optional[str] = CommonArgs.as_of, |
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| 408 | replace: bool = CommonArgs.replace, |
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| 409 | proceed: bool = CommonArgs.proceed, |
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| 410 | check: bool = EntryArgs.check, |
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| 411 | log: Optional[Path] = CommonArgs.log, |
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| 412 | stderr: str = CommonArgs.stderr, |
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| 413 | ) -> Searcher: |
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| 414 | """ |
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| 415 | Diseases from clinical trials listed in clinicaltrials.gov. |
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| 416 | |||
| 417 | OBJECT: The name of the disease (in MeSH) |
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| 418 | """ |
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| 419 | statuses = ClinicalTrialsGovUtils.resolve_statuses(statuses) |
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| 420 | built = TrialSearch( |
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| 421 | key=key, api=Apis.Pubchem, min_phase=min_phase, statuses=statuses, explicit=req_explicit |
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| 422 | ) |
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| 423 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
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| 424 | |||
| 425 | |||
| 426 | class EntryPubchemDisease(Entry[DiseaseSearch]): |
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| 427 | View Code Duplication | @classmethod |
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| 428 | def run( |
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| 429 | cls, |
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| 430 | path: Path = CommonArgs.in_compound_table, |
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| 431 | key: str = EntryArgs.key("disease.ctd:mesh"), |
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| 432 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 433 | as_of: Optional[str] = CommonArgs.as_of, |
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| 434 | replace: bool = CommonArgs.replace, |
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| 435 | proceed: bool = CommonArgs.proceed, |
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| 436 | check: bool = EntryArgs.check, |
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| 437 | log: Optional[Path] = CommonArgs.log, |
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| 438 | stderr: str = CommonArgs.stderr, |
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| 439 | ) -> Searcher: |
||
| 440 | """ |
||
| 441 | Diseases in the CTD. |
||
| 442 | |||
| 443 | (Comparative Toxicogenomics Database.) |
||
| 444 | |||
| 445 | OBJECT: The MeSH code of the disease |
||
| 446 | |||
| 447 | """ |
||
| 448 | built = DiseaseSearch(key, Apis.Pubchem) |
||
| 449 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 450 | |||
| 451 | |||
| 452 | class _EntryPubchemCoOccurrence(Entry[U], metaclass=abc.ABCMeta): |
||
| 453 | @classmethod |
||
| 454 | def cmd(cls) -> str: |
||
| 455 | me = str(cls.get_cooccurrence_type().name) |
||
| 456 | return f"lit.pubchem:{me.lower()}" |
||
| 457 | |||
| 458 | @classmethod |
||
| 459 | def get_cooccurrence_type(cls) -> CoOccurrenceType: |
||
| 460 | s: CoOccurrenceSearch = cls.get_search_type() |
||
| 461 | return s.cooccurrence_type() |
||
| 462 | |||
| 463 | @classmethod |
||
| 464 | def run( |
||
| 465 | cls, |
||
| 466 | path: Path = CommonArgs.in_compound_table, |
||
| 467 | key: str = EntryArgs.key("<see above>"), |
||
| 468 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 469 | min_score: float = EntryArgs.min_cooccurrence_score, |
||
| 470 | min_articles: int = EntryArgs.min_cooccurring_articles, |
||
| 471 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 472 | replace: bool = CommonArgs.replace, |
||
| 473 | proceed: bool = CommonArgs.proceed, |
||
| 474 | check: bool = EntryArgs.check, |
||
| 475 | log: Optional[Path] = CommonArgs.log, |
||
| 476 | stderr: str = CommonArgs.stderr, |
||
| 477 | ) -> Searcher: |
||
| 478 | """See the docstrings for the individual entries.""" |
||
| 479 | clazz = cls.get_search_type() |
||
| 480 | built = clazz(key, Apis.Pubchem, min_score=min_score, min_articles=min_articles) |
||
| 481 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 482 | |||
| 483 | |||
| 484 | View Code Duplication | class EntryPubchemGeneCoOccurrence(_EntryPubchemCoOccurrence[GeneCoOccurrenceSearch]): |
|
| 485 | @classmethod |
||
| 486 | def run( |
||
| 487 | cls, |
||
| 488 | path: Path = CommonArgs.in_compound_table, |
||
| 489 | key: str = EntryArgs.key(f"lit.pubchem:{CoOccurrenceType.gene.name.lower()}"), |
||
| 490 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 491 | min_score: float = EntryArgs.min_cooccurrence_score, |
||
| 492 | min_articles: int = EntryArgs.min_cooccurring_articles, |
||
| 493 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 494 | replace: bool = CommonArgs.replace, |
||
| 495 | proceed: bool = CommonArgs.proceed, |
||
| 496 | check: bool = EntryArgs.check, |
||
| 497 | log: Optional[Path] = CommonArgs.log, |
||
| 498 | stderr: str = CommonArgs.stderr, |
||
| 499 | ) -> Searcher: |
||
| 500 | """ |
||
| 501 | Co-occurrences of genes from PubMed articles. |
||
| 502 | |||
| 503 | https://mandos-chem.readthedocs.io/en/latest/co-occurrences.html |
||
| 504 | |||
| 505 | OBJECT: The name of the gene |
||
| 506 | |||
| 507 | WEIGHT: The co-occurrence score (refer to the docs) |
||
| 508 | """ |
||
| 509 | args, _, _, locs = inspect.getargvalues(inspect.currentframe()) |
||
| 510 | return super().run(**{a: locs[a] for a in args if a != "cls"}) |
||
| 511 | |||
| 512 | |||
| 513 | View Code Duplication | class EntryPubchemDiseaseCoOccurrence(_EntryPubchemCoOccurrence[DiseaseCoOccurrenceSearch]): |
|
| 514 | @classmethod |
||
| 515 | def run( |
||
| 516 | cls, |
||
| 517 | path: Path = CommonArgs.in_compound_table, |
||
| 518 | key: str = EntryArgs.key(f"lit.pubchem:{CoOccurrenceType.disease.name.lower()}"), |
||
| 519 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 520 | min_score: float = EntryArgs.min_cooccurrence_score, |
||
| 521 | min_articles: int = EntryArgs.min_cooccurring_articles, |
||
| 522 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 523 | replace: bool = CommonArgs.replace, |
||
| 524 | proceed: bool = CommonArgs.proceed, |
||
| 525 | check: bool = EntryArgs.check, |
||
| 526 | log: Optional[Path] = CommonArgs.log, |
||
| 527 | stderr: str = CommonArgs.stderr, |
||
| 528 | ) -> Searcher: |
||
| 529 | """ |
||
| 530 | Co-occurrences of diseases from PubMed articles. |
||
| 531 | |||
| 532 | https://mandos-chem.readthedocs.io/en/latest/co-occurrences.html |
||
| 533 | |||
| 534 | OBJECT: The name of the disease |
||
| 535 | |||
| 536 | WEIGHT: The co-occurrence score (refer to the docs) |
||
| 537 | """ |
||
| 538 | args, _, _, locs = inspect.getargvalues(inspect.currentframe()) |
||
| 539 | return super().run(**{a: locs[a] for a in args if a != "cls"}) |
||
| 540 | |||
| 541 | |||
| 542 | View Code Duplication | class EntryPubchemChemicalCoOccurrence(_EntryPubchemCoOccurrence[ChemicalCoOccurrenceSearch]): |
|
| 543 | @classmethod |
||
| 544 | def run( |
||
| 545 | cls, |
||
| 546 | path: Path = CommonArgs.in_compound_table, |
||
| 547 | key: str = EntryArgs.key(f"lit.pubchem:{CoOccurrenceType.chemical.name.lower()}"), |
||
| 548 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 549 | min_score: float = EntryArgs.min_cooccurrence_score, |
||
| 550 | min_articles: int = EntryArgs.min_cooccurring_articles, |
||
| 551 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 552 | replace: bool = CommonArgs.replace, |
||
| 553 | proceed: bool = CommonArgs.proceed, |
||
| 554 | check: bool = EntryArgs.check, |
||
| 555 | log: Optional[Path] = CommonArgs.log, |
||
| 556 | stderr: str = CommonArgs.stderr, |
||
| 557 | ) -> Searcher: |
||
| 558 | """ |
||
| 559 | Co-occurrences of chemicals from PubMed articles. |
||
| 560 | |||
| 561 | https://mandos-chem.readthedocs.io/en/latest/co-occurrences.html |
||
| 562 | |||
| 563 | OBJECT: The name of the chemical (e.g. "cocaine") |
||
| 564 | |||
| 565 | WEIGHT: The co-occurrence score (refer to the docs) |
||
| 566 | """ |
||
| 567 | args, _, _, locs = inspect.getargvalues(inspect.currentframe()) |
||
| 568 | return super().run(**{a: locs[a] for a in args if a != "cls"}) |
||
| 569 | |||
| 570 | |||
| 571 | class EntryPubchemDgi(Entry[DgiSearch]): |
||
| 572 | View Code Duplication | @classmethod |
|
| 573 | def run( |
||
| 574 | cls, |
||
| 575 | path: Path = CommonArgs.in_compound_table, |
||
| 576 | key: str = EntryArgs.key("inter.dgidb:gene"), |
||
| 577 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 578 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 579 | replace: bool = CommonArgs.replace, |
||
| 580 | proceed: bool = CommonArgs.proceed, |
||
| 581 | check: bool = EntryArgs.check, |
||
| 582 | log: Optional[Path] = CommonArgs.log, |
||
| 583 | stderr: str = CommonArgs.stderr, |
||
| 584 | ) -> Searcher: |
||
| 585 | """ |
||
| 586 | Drug/gene interactions in the DGIDB. |
||
| 587 | |||
| 588 | Drug Gene Interaction Database. |
||
| 589 | Also see disease.dgidb:int. |
||
| 590 | |||
| 591 | OBJECT: The name of the gene |
||
| 592 | |||
| 593 | PREDICATE: "interaction:generic" or "interaction:<type>" |
||
| 594 | """ |
||
| 595 | built = DgiSearch(key, Apis.Pubchem) |
||
| 596 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 597 | |||
| 598 | |||
| 599 | class EntryPubchemCgi(Entry[CtdGeneSearch]): |
||
| 600 | View Code Duplication | @classmethod |
|
| 601 | def run( |
||
| 602 | cls, |
||
| 603 | path: Path = CommonArgs.in_compound_table, |
||
| 604 | key: str = EntryArgs.key("inter.ctd:gene"), |
||
| 605 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 606 | replace: bool = CommonArgs.replace, |
||
| 607 | proceed: bool = CommonArgs.proceed, |
||
| 608 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 609 | check: bool = EntryArgs.check, |
||
| 610 | log: Optional[Path] = CommonArgs.log, |
||
| 611 | stderr: str = CommonArgs.stderr, |
||
| 612 | ) -> Searcher: |
||
| 613 | """ |
||
| 614 | Compound/gene interactions in the DGIDB. |
||
| 615 | |||
| 616 | Drug Gene Interaction Database. |
||
| 617 | Also see ``interact.dgidb:int``. |
||
| 618 | |||
| 619 | OBJECT: The name of the gene |
||
| 620 | |||
| 621 | PREDICATE: derived from the interaction type (e.g. "downregulation") |
||
| 622 | """ |
||
| 623 | built = CtdGeneSearch(key, Apis.Pubchem) |
||
| 624 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 625 | |||
| 626 | |||
| 627 | class EntryDrugbankTarget(Entry[DrugbankTargetSearch]): |
||
| 628 | View Code Duplication | @classmethod |
|
| 629 | def run( |
||
| 630 | cls, |
||
| 631 | path: Path = CommonArgs.in_compound_table, |
||
| 632 | key: str = EntryArgs.key("inter.drugbank:targ"), |
||
| 633 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 634 | replace: bool = CommonArgs.replace, |
||
| 635 | proceed: bool = CommonArgs.proceed, |
||
| 636 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 637 | check: bool = EntryArgs.check, |
||
| 638 | log: Optional[Path] = CommonArgs.log, |
||
| 639 | stderr: str = CommonArgs.stderr, |
||
| 640 | ) -> Searcher: |
||
| 641 | """ |
||
| 642 | Protein targets from DrugBank. |
||
| 643 | |||
| 644 | OBJECT: The target name (e.g. "Solute carrier family 22 member 11") |
||
| 645 | |||
| 646 | PREDICATE: "<target_type>:<action>" |
||
| 647 | """ |
||
| 648 | built = DrugbankTargetSearch(key, Apis.Pubchem, {DrugbankTargetType.target}) |
||
| 649 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 650 | |||
| 651 | |||
| 652 | class EntryGeneralFunction(Entry[DrugbankGeneralFunctionSearch]): |
||
| 653 | View Code Duplication | @classmethod |
|
| 654 | def run( |
||
| 655 | cls, |
||
| 656 | path: Path = CommonArgs.in_compound_table, |
||
| 657 | key: str = EntryArgs.key("inter.drugbank:targ-fn"), |
||
| 658 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 659 | replace: bool = CommonArgs.replace, |
||
| 660 | proceed: bool = CommonArgs.proceed, |
||
| 661 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 662 | check: bool = EntryArgs.check, |
||
| 663 | log: Optional[Path] = CommonArgs.log, |
||
| 664 | stderr: str = CommonArgs.stderr, |
||
| 665 | ) -> Searcher: |
||
| 666 | """ |
||
| 667 | General functions from DrugBank targets. |
||
| 668 | |||
| 669 | OBJECT: The name of the "general function" (e.g. "Toxic substance binding") |
||
| 670 | |||
| 671 | PREDICATE: "<target_type>:<action>" |
||
| 672 | """ |
||
| 673 | built = DrugbankGeneralFunctionSearch(key, Apis.Pubchem, {DrugbankTargetType.target}) |
||
| 674 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 675 | |||
| 676 | |||
| 677 | View Code Duplication | class EntryDrugbankTransporter(Entry[DrugbankTargetSearch]): |
|
| 678 | @classmethod |
||
| 679 | def run( |
||
| 680 | cls, |
||
| 681 | path: Path = CommonArgs.in_compound_table, |
||
| 682 | key: str = EntryArgs.key("inter.drugbank:pk"), |
||
| 683 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 684 | replace: bool = CommonArgs.replace, |
||
| 685 | proceed: bool = CommonArgs.proceed, |
||
| 686 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 687 | check: bool = EntryArgs.check, |
||
| 688 | log: Optional[Path] = CommonArgs.log, |
||
| 689 | stderr: str = CommonArgs.stderr, |
||
| 690 | ) -> Searcher: |
||
| 691 | """ |
||
| 692 | PK-related proteins from DrugBank. |
||
| 693 | |||
| 694 | OBJECT: The transporter name (e.g. "Solute carrier family 22 member 11") |
||
| 695 | |||
| 696 | PREDICATE: "<target_type>:<action>" (e.g. metabolized, transported, etc.) |
||
| 697 | """ |
||
| 698 | target_types = { |
||
| 699 | DrugbankTargetType.transporter, |
||
| 700 | DrugbankTargetType.carrier, |
||
| 701 | DrugbankTargetType.enzyme, |
||
| 702 | } |
||
| 703 | built = DrugbankTargetSearch(key, Apis.Pubchem, target_types) |
||
| 704 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 705 | |||
| 706 | |||
| 707 | View Code Duplication | class EntryTransporterGeneralFunction(Entry[DrugbankGeneralFunctionSearch]): |
|
| 708 | @classmethod |
||
| 709 | def run( |
||
| 710 | cls, |
||
| 711 | path: Path = CommonArgs.in_compound_table, |
||
| 712 | key: str = EntryArgs.key("inter.drugbank:pk-fn"), |
||
| 713 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 714 | replace: bool = CommonArgs.replace, |
||
| 715 | proceed: bool = CommonArgs.proceed, |
||
| 716 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 717 | check: bool = EntryArgs.check, |
||
| 718 | log: Optional[Path] = CommonArgs.log, |
||
| 719 | stderr: str = CommonArgs.stderr, |
||
| 720 | ) -> Searcher: |
||
| 721 | """ |
||
| 722 | DrugBank PK-related protein functions. |
||
| 723 | |||
| 724 | OBJECT: The name of the general function (e.g. "Toxic substance binding") |
||
| 725 | |||
| 726 | PREDICATE: "<target_type>:<action>" (e.g. metabolized, transported, etc.) |
||
| 727 | """ |
||
| 728 | target_types = { |
||
| 729 | DrugbankTargetType.transporter, |
||
| 730 | DrugbankTargetType.carrier, |
||
| 731 | DrugbankTargetType.enzyme, |
||
| 732 | } |
||
| 733 | built = DrugbankGeneralFunctionSearch(key, Apis.Pubchem, target_types) |
||
| 734 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 735 | |||
| 736 | |||
| 737 | class EntryDrugbankDdi(Entry[DrugbankDdiSearch]): |
||
| 738 | View Code Duplication | @classmethod |
|
| 739 | def run( |
||
| 740 | cls, |
||
| 741 | path: Path = CommonArgs.in_compound_table, |
||
| 742 | key: str = EntryArgs.key("inter.drugbank:ddi"), |
||
| 743 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 744 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 745 | replace: bool = CommonArgs.replace, |
||
| 746 | proceed: bool = CommonArgs.proceed, |
||
| 747 | check: bool = EntryArgs.check, |
||
| 748 | log: Optional[Path] = CommonArgs.log, |
||
| 749 | stderr: str = CommonArgs.stderr, |
||
| 750 | ) -> Searcher: |
||
| 751 | """ |
||
| 752 | Drug/drug interactions listed by DrugBank. |
||
| 753 | |||
| 754 | The "description" column includes useful information about the interaction, |
||
| 755 | such as diseases and whether a risk is increased or decreased. |
||
| 756 | |||
| 757 | OBJECT: The name of the drug (e.g. "ibuprofen") |
||
| 758 | |||
| 759 | PREDICATE: typically increase/decrease/change followed by risk/activity/etc. |
||
| 760 | """ |
||
| 761 | built = DrugbankDdiSearch(key, Apis.Pubchem) |
||
| 762 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 763 | |||
| 764 | |||
| 765 | class EntryPubchemAssay(Entry[BioactivitySearch]): |
||
| 766 | @classmethod |
||
| 767 | def run( |
||
| 768 | cls, |
||
| 769 | path: Path = CommonArgs.in_compound_table, |
||
| 770 | key: str = EntryArgs.key("assay.pubchem:act"), |
||
| 771 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 772 | match_name: bool = EntryArgs.match_name, |
||
| 773 | ban_sources: Optional[str] = EntryArgs.banned_sources, |
||
| 774 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 775 | replace: bool = CommonArgs.replace, |
||
| 776 | proceed: bool = CommonArgs.proceed, |
||
| 777 | check: bool = EntryArgs.check, |
||
| 778 | log: Optional[Path] = CommonArgs.log, |
||
| 779 | stderr: str = CommonArgs.stderr, |
||
| 780 | ) -> Searcher: |
||
| 781 | """ |
||
| 782 | PubChem bioactivity results. |
||
| 783 | |||
| 784 | Note: The species name, if present, is taken from the target name. |
||
| 785 | The taxon ID is what was curated in PubChem. |
||
| 786 | |||
| 787 | OBJECT: The name of the target without species suffix |
||
| 788 | (e.g. "Slc6a3 - solute carrier family 6 member 3") |
||
| 789 | |||
| 790 | PREDICATE: "active", "inactive", "inconclusive", or "undetermined" |
||
| 791 | |||
| 792 | WEIGHT: 2 for confirmatory; 1 otherwise |
||
| 793 | """ |
||
| 794 | built = BioactivitySearch(key, Apis.Pubchem, compound_name_must_match=match_name) |
||
| 795 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 796 | |||
| 797 | |||
| 798 | class EntryDeaSchedule(Entry[BioactivitySearch]): |
||
| 799 | @classmethod |
||
| 800 | def run( |
||
| 801 | cls, |
||
| 802 | path: Path = CommonArgs.in_compound_table, |
||
| 803 | key: str = EntryArgs.key("drug.dea:schedule"), |
||
| 804 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 805 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 806 | replace: bool = CommonArgs.replace, |
||
| 807 | proceed: bool = CommonArgs.proceed, |
||
| 808 | check: bool = EntryArgs.check, |
||
| 809 | log: Optional[Path] = CommonArgs.log, |
||
| 810 | stderr: str = CommonArgs.stderr, |
||
| 811 | ) -> Searcher: |
||
| 812 | """ |
||
| 813 | DEA schedules (PENDING). |
||
| 814 | |||
| 815 | OBJECT: The DEA schedule (1 to 4, or "unscheduled") |
||
| 816 | """ |
||
| 817 | pass |
||
| 818 | |||
| 819 | |||
| 820 | class EntryDeaClass(Entry[BioactivitySearch]): |
||
| 821 | @classmethod |
||
| 822 | def run( |
||
| 823 | cls, |
||
| 824 | path: Path = CommonArgs.in_compound_table, |
||
| 825 | key: str = EntryArgs.key("drug.dea:class"), |
||
| 826 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 827 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 828 | replace: bool = CommonArgs.replace, |
||
| 829 | proceed: bool = CommonArgs.proceed, |
||
| 830 | check: bool = EntryArgs.check, |
||
| 831 | log: Optional[Path] = CommonArgs.log, |
||
| 832 | stderr: str = CommonArgs.stderr, |
||
| 833 | ) -> Searcher: |
||
| 834 | """ |
||
| 835 | DEA classes (PENDING). |
||
| 836 | |||
| 837 | OBJECT: The DEA class name (e.g. "hallucinogen") |
||
| 838 | """ |
||
| 839 | pass |
||
| 840 | |||
| 841 | |||
| 842 | class EntryChemidPlusAcute(Entry[AcuteEffectSearch]): |
||
| 843 | @classmethod |
||
| 844 | def run( |
||
| 845 | cls, |
||
| 846 | path: Path = CommonArgs.in_compound_table, |
||
| 847 | key: str = EntryArgs.key("tox.chemidplus:acute"), |
||
| 848 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 849 | level: int = EntryArgs.acute_effect_level, |
||
| 850 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 851 | replace: bool = CommonArgs.replace, |
||
| 852 | proceed: bool = CommonArgs.proceed, |
||
| 853 | check: bool = EntryArgs.check, |
||
| 854 | log: Optional[Path] = CommonArgs.log, |
||
| 855 | stderr: str = CommonArgs.stderr, |
||
| 856 | ) -> Searcher: |
||
| 857 | """ |
||
| 858 | Acute effect codes from ChemIDPlus. |
||
| 859 | |||
| 860 | OBJECT: The code name (e.g. "behavioral: excitement") |
||
| 861 | """ |
||
| 862 | built = AcuteEffectSearch( |
||
| 863 | key, |
||
| 864 | Apis.Pubchem, |
||
| 865 | top_level=level == 1, |
||
| 866 | ) |
||
| 867 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 868 | |||
| 869 | |||
| 870 | class EntryChemidPlusLd50(Entry[Ld50Search]): |
||
| 871 | View Code Duplication | @classmethod |
|
| 872 | def run( |
||
| 873 | cls, |
||
| 874 | path: Path = CommonArgs.in_compound_table, |
||
| 875 | key: str = EntryArgs.key("tox.chemidplus:ld50"), |
||
| 876 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 877 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 878 | replace: bool = CommonArgs.replace, |
||
| 879 | proceed: bool = CommonArgs.proceed, |
||
| 880 | check: bool = EntryArgs.check, |
||
| 881 | log: Optional[Path] = CommonArgs.log, |
||
| 882 | stderr: str = CommonArgs.stderr, |
||
| 883 | ) -> Searcher: |
||
| 884 | """ |
||
| 885 | LD50 acute effects from ChemIDPlus. |
||
| 886 | |||
| 887 | OBJECT: The negative of the dose in mg/kg |
||
| 888 | |||
| 889 | PREDICATE: "LD50:<route>" (e.g. "LD50:intravenous") |
||
| 890 | """ |
||
| 891 | built = Ld50Search(key, Apis.Pubchem) |
||
| 892 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 893 | |||
| 894 | |||
| 895 | class EntryPubchemComputed(Entry[ComputedPropertySearch]): |
||
| 896 | @classmethod |
||
| 897 | def run( |
||
| 898 | cls, |
||
| 899 | path: Path = CommonArgs.in_compound_table, |
||
| 900 | key: str = EntryArgs.key("chem.pubchem:computed"), |
||
| 901 | keys: str = EntryArgs.pubchem_computed_keys, |
||
| 902 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 903 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 904 | replace: bool = CommonArgs.replace, |
||
| 905 | proceed: bool = CommonArgs.proceed, |
||
| 906 | check: bool = EntryArgs.check, |
||
| 907 | log: Optional[Path] = CommonArgs.log, |
||
| 908 | stderr: str = CommonArgs.stderr, |
||
| 909 | ) -> Searcher: |
||
| 910 | """ |
||
| 911 | Computed properties from PubChem. |
||
| 912 | |||
| 913 | OBJECT: Number |
||
| 914 | |||
| 915 | PREDICATE: e.g. "complexity" |
||
| 916 | """ |
||
| 917 | # replace acronyms, etc. |
||
| 918 | # ComputedPropertySearch standardizes punctuation and casing |
||
| 919 | known = { |
||
| 920 | k: v |
||
| 921 | for k, v in { |
||
| 922 | **EntryArgs.KNOWN_USEFUL_KEYS, |
||
| 923 | **EntryArgs.KNOWN_USELESS_KEYS, |
||
| 924 | }.items() |
||
| 925 | if v is not None |
||
| 926 | } |
||
| 927 | keys = {known.get(s.strip(), s) for s in keys.split(",")} |
||
| 928 | built = ComputedPropertySearch(key, Apis.Pubchem, descriptors=keys) |
||
| 929 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 930 | |||
| 931 | |||
| 932 | class EntryG2pInteractions(Entry[G2pInteractionSearch]): |
||
| 933 | @classmethod |
||
| 934 | def run( |
||
| 935 | cls, |
||
| 936 | path: Path = CommonArgs.in_compound_table, |
||
| 937 | key: str = EntryArgs.key("g2p:interactions"), |
||
| 938 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 939 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 940 | replace: bool = CommonArgs.replace, |
||
| 941 | proceed: bool = CommonArgs.proceed, |
||
| 942 | check: bool = EntryArgs.check, |
||
| 943 | log: Optional[Path] = CommonArgs.log, |
||
| 944 | stderr: str = CommonArgs.stderr, |
||
| 945 | ) -> Searcher: |
||
| 946 | """ |
||
| 947 | Target interactions with affinities from Guide to Pharmacology. |
||
| 948 | |||
| 949 | OBJECT: A molecular target |
||
| 950 | |||
| 951 | PREDICATE: "interaction:agonism", etc. |
||
| 952 | |||
| 953 | WEIGHT: 1.0 |
||
| 954 | """ |
||
| 955 | built = G2pInteractionSearch(key, Apis.G2p) |
||
| 956 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 957 | |||
| 958 | |||
| 959 | class EntryHmdbTissue(Entry[TissueConcentrationSearch]): |
||
| 960 | @classmethod |
||
| 961 | def run( |
||
| 962 | cls, |
||
| 963 | path: Path = CommonArgs.in_compound_table, |
||
| 964 | key: str = EntryArgs.key("hmdb:tissue"), |
||
| 965 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 966 | min_nm: Optional[float] = EntryArgs.min_nanomolar, |
||
| 967 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 968 | replace: bool = CommonArgs.replace, |
||
| 969 | proceed: bool = CommonArgs.proceed, |
||
| 970 | check: bool = EntryArgs.check, |
||
| 971 | log: Optional[Path] = CommonArgs.log, |
||
| 972 | stderr: str = CommonArgs.stderr, |
||
| 973 | ) -> Searcher: |
||
| 974 | """ |
||
| 975 | Tissue concentrations from HMDB. |
||
| 976 | |||
| 977 | OBJECT: |
||
| 978 | |||
| 979 | PREDICATE: "tissue:..." |
||
| 980 | """ |
||
| 981 | built = TissueConcentrationSearch(key, Apis.Hmdb) |
||
| 982 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 983 | |||
| 984 | |||
| 985 | class EntryHmdbComputed(Entry[BioactivitySearch]): |
||
| 986 | @classmethod |
||
| 987 | def run( |
||
| 988 | cls, |
||
| 989 | path: Path = CommonArgs.in_compound_table, |
||
| 990 | key: str = EntryArgs.key("hmdb:computed"), |
||
| 991 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 992 | min_nm: Optional[float] = None, |
||
| 993 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 994 | replace: bool = CommonArgs.replace, |
||
| 995 | proceed: bool = CommonArgs.proceed, |
||
| 996 | check: bool = EntryArgs.check, |
||
| 997 | log: Optional[Path] = CommonArgs.log, |
||
| 998 | stderr: str = CommonArgs.stderr, |
||
| 999 | ) -> Searcher: |
||
| 1000 | """ |
||
| 1001 | Computed properties from HMDB (PENDING). |
||
| 1002 | |||
| 1003 | Keys include pKa, logP, logS, etc. |
||
| 1004 | |||
| 1005 | OBJECT: A number; booleans are converted to 0/1 |
||
| 1006 | |||
| 1007 | PREDICATE: The name of the property |
||
| 1008 | """ |
||
| 1009 | pass |
||
| 1010 | |||
| 1011 | |||
| 1012 | class EntryDrugbankAdmet(Entry[DrugbankTargetSearch]): |
||
| 1013 | @classmethod |
||
| 1014 | def run( |
||
| 1015 | cls, |
||
| 1016 | path: Path = CommonArgs.in_compound_table, |
||
| 1017 | key: str = EntryArgs.key("drugbank.admet:properties"), |
||
| 1018 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 1019 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 1020 | replace: bool = CommonArgs.replace, |
||
| 1021 | proceed: bool = CommonArgs.proceed, |
||
| 1022 | check: bool = EntryArgs.check, |
||
| 1023 | log: Optional[Path] = CommonArgs.log, |
||
| 1024 | stderr: str = CommonArgs.stderr, |
||
| 1025 | ) -> Searcher: |
||
| 1026 | """ |
||
| 1027 | Enzyme predictions from DrugBank (PENDING). |
||
| 1028 | |||
| 1029 | OBJECT: Enzyme name |
||
| 1030 | |||
| 1031 | PREDICATE: Action |
||
| 1032 | """ |
||
| 1033 | |||
| 1034 | |||
| 1035 | class EntryDrugbankMetabolites(Entry[DrugbankTargetSearch]): |
||
| 1036 | @classmethod |
||
| 1037 | def run( |
||
| 1038 | cls, |
||
| 1039 | path: Path = CommonArgs.in_compound_table, |
||
| 1040 | key: str = EntryArgs.key("drugbank.admet:metabolites"), |
||
| 1041 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 1042 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 1043 | replace: bool = CommonArgs.replace, |
||
| 1044 | proceed: bool = CommonArgs.proceed, |
||
| 1045 | check: bool = EntryArgs.check, |
||
| 1046 | log: Optional[Path] = CommonArgs.log, |
||
| 1047 | stderr: str = CommonArgs.stderr, |
||
| 1048 | ) -> Searcher: |
||
| 1049 | """ |
||
| 1050 | Metabolites from DrugBank (PENDING). |
||
| 1051 | |||
| 1052 | OBJECT: Compound name (e.g. "norcocaine"). |
||
| 1053 | |||
| 1054 | PREDICATE: "metabolized to" |
||
| 1055 | """ |
||
| 1056 | |||
| 1057 | |||
| 1058 | class EntryDrugbankDosage(Entry[DrugbankTargetSearch]): |
||
| 1059 | @classmethod |
||
| 1060 | def run( |
||
| 1061 | cls, |
||
| 1062 | path: Path = CommonArgs.in_compound_table, |
||
| 1063 | key: str = EntryArgs.key("drugbank.admet:dosage"), |
||
| 1064 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 1065 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 1066 | replace: bool = CommonArgs.replace, |
||
| 1067 | proceed: bool = CommonArgs.proceed, |
||
| 1068 | check: bool = EntryArgs.check, |
||
| 1069 | log: Optional[Path] = CommonArgs.log, |
||
| 1070 | stderr: str = CommonArgs.stderr, |
||
| 1071 | ) -> Searcher: |
||
| 1072 | """ |
||
| 1073 | Dosage from DrugBank (PENDING). |
||
| 1074 | |||
| 1075 | OBJECT: concentration in mg/mL |
||
| 1076 | |||
| 1077 | PREDICATE: "dosage :: <route>" |
||
| 1078 | |||
| 1079 | OTHER COLUMNS: |
||
| 1080 | |||
| 1081 | - form (e.g. liquid) |
||
| 1082 | """ |
||
| 1083 | |||
| 1084 | |||
| 1085 | class EntryMetaRandom(Entry[RandomSearch]): |
||
| 1086 | @classmethod |
||
| 1087 | def run( |
||
| 1088 | cls, |
||
| 1089 | path: Path = CommonArgs.in_compound_table, |
||
| 1090 | key: str = EntryArgs.key("meta:random"), |
||
| 1091 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 1092 | n: int = EntryArgs.random_n, |
||
| 1093 | seed: int = CommonArgs.seed, |
||
| 1094 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 1095 | replace: bool = CommonArgs.replace, |
||
| 1096 | proceed: bool = CommonArgs.proceed, |
||
| 1097 | check: bool = EntryArgs.check, |
||
| 1098 | log: Optional[Path] = CommonArgs.log, |
||
| 1099 | stderr: str = CommonArgs.stderr, |
||
| 1100 | ) -> Searcher: |
||
| 1101 | r""" |
||
| 1102 | Random class assignment. |
||
| 1103 | |||
| 1104 | OBJECT: 0 thru n (inclusive-exclusive). |
||
| 1105 | |||
| 1106 | PREDICATE: "random" |
||
| 1107 | """ |
||
| 1108 | built = RandomSearch(key, seed, n) |
||
| 1109 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 1110 | |||
| 1111 | |||
| 1112 | Entries = [ |
||
| 1113 | EntryChemblBinding, |
||
| 1114 | EntryChemblMechanism, |
||
| 1115 | EntryChemblAtc, |
||
| 1116 | EntryChemblTrials, |
||
| 1117 | EntryGoFunction, |
||
| 1118 | EntryGoProcess, |
||
| 1119 | EntryGoComponent, |
||
| 1120 | EntryPubchemComputed, |
||
| 1121 | EntryPubchemDisease, |
||
| 1122 | EntryPubchemGeneCoOccurrence, |
||
| 1123 | EntryPubchemDiseaseCoOccurrence, |
||
| 1124 | EntryPubchemChemicalCoOccurrence, |
||
| 1125 | EntryPubchemDgi, |
||
| 1126 | EntryPubchemCgi, |
||
| 1127 | EntryDrugbankTarget, |
||
| 1128 | EntryGeneralFunction, |
||
| 1129 | EntryDrugbankTransporter, |
||
| 1130 | EntryTransporterGeneralFunction, |
||
| 1131 | EntryDrugbankDdi, |
||
| 1132 | EntryPubchemAssay, |
||
| 1133 | EntryDeaSchedule, |
||
| 1134 | EntryDeaClass, |
||
| 1135 | EntryChemidPlusAcute, |
||
| 1136 | EntryChemidPlusLd50, |
||
| 1137 | EntryHmdbTissue, |
||
| 1138 | EntryMetaRandom, |
||
| 1139 | ] |
||
| 1140 |
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