dmyersturnbull /
mandos
| Total Complexity | 46 |
| Total Lines | 1174 |
| Duplicated Lines | 44.04 % |
| 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 import entry |
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| 16 | from mandos.entry.abstract_entries import Entry |
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| 17 | from mandos.entry.api_singletons import Apis |
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| 18 | from mandos.entry.tools.searchers import Searcher |
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| 19 | from mandos.entry.utils._arg_utils import ArgUtils |
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| 20 | from mandos.entry.utils._common_args import CommonArgs |
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| 21 | from mandos.entry.utils._entry_args import EntryArgs |
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| 22 | from mandos.model.apis.chembl_api import ChemblApi |
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| 23 | from mandos.model.apis.pubchem_support.pubchem_models import ( |
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| 24 | ClinicalTrialsGovUtils, |
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| 25 | CoOccurrenceType, |
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| 26 | DrugbankTargetType, |
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| 27 | ) |
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| 28 | from mandos.model.concrete_hits import GoType |
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| 29 | from mandos.model.utils.setup import logger |
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| 30 | from mandos.search.chembl.atc_search import AtcSearch |
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| 31 | from mandos.search.chembl.binding_search import BindingSearch |
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| 32 | from mandos.search.chembl.go_search import GoSearch |
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| 33 | from mandos.search.chembl.indication_search import IndicationSearch |
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| 34 | from mandos.search.chembl.mechanism_search import MechanismSearch |
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| 35 | from mandos.search.chembl.target_prediction_search import TargetPredictionSearch |
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| 36 | from mandos.search.g2p.g2p_interaction_search import G2pInteractionSearch |
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| 37 | from mandos.search.hmdb.tissue_concentration_search import TissueConcentrationSearch |
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| 38 | from mandos.search.meta.random_search import RandomSearch |
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| 39 | from mandos.search.pubchem.acute_effects_search import AcuteEffectSearch, Ld50Search |
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| 40 | from mandos.search.pubchem.bioactivity_search import BioactivitySearch |
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| 41 | from mandos.search.pubchem.computed_property_search import ComputedPropertySearch |
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| 42 | from mandos.search.pubchem.cooccurrence_search import ( |
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| 43 | ChemicalCoOccurrenceSearch, |
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| 44 | CoOccurrenceSearch, |
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| 45 | DiseaseCoOccurrenceSearch, |
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| 46 | GeneCoOccurrenceSearch, |
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| 47 | ) |
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| 48 | from mandos.search.pubchem.ctd_gene_search import CtdGeneSearch |
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| 49 | from mandos.search.pubchem.dgidb_search import DgiSearch |
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| 50 | from mandos.search.pubchem.disease_search import DiseaseSearch |
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| 51 | from mandos.search.pubchem.drugbank_ddi_search import DrugbankDdiSearch |
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| 52 | from mandos.search.pubchem.drugbank_interaction_search import ( |
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| 53 | DrugbankGeneralFunctionSearch, |
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| 54 | DrugbankTargetSearch, |
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| 55 | ) |
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| 56 | from mandos.search.pubchem.trials_search import TrialSearch |
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| 57 | |||
| 58 | U = TypeVar("U", covariant=True, bound=CoOccurrenceSearch) |
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| 59 | |||
| 60 | |||
| 61 | class EntryChemblBinding(Entry[BindingSearch]): |
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| 62 | @classmethod |
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| 63 | def run( |
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| 64 | cls, |
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| 65 | path: Path = CommonArgs.in_compound_table, |
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| 66 | key: str = EntryArgs.key("chembl:binding"), |
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| 67 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 68 | taxa: str = CommonArgs.taxa, |
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| 69 | traversal: str = EntryArgs.traversal, |
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| 70 | target_types: str = EntryArgs.target_types, |
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| 71 | confidence: int = EntryArgs.min_confidence, |
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| 72 | binding: float = EntryArgs.binds_cutoff, |
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| 73 | pchembl: float = EntryArgs.min_pchembl, |
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| 74 | as_of: Optional[str] = CommonArgs.as_of, |
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| 75 | replace: bool = CommonArgs.replace, |
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| 76 | proceed: bool = CommonArgs.proceed, |
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| 77 | check: bool = EntryArgs.check, |
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| 78 | log: Optional[Path] = CommonArgs.log, |
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| 79 | stderr: str = CommonArgs.stderr, |
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| 80 | ) -> Searcher: |
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| 81 | """ |
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| 82 | Binding data from ChEMBL. |
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| 83 | |||
| 84 | These are 'activity' annotations of the type 'B' that have a pCHEMBL value. |
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| 85 | https://mandos-chem.readthedocs.io/en/latest/binding.html |
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| 86 | |||
| 87 | OBJECT: The target name |
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| 88 | |||
| 89 | WEIGHT: The PCHEMBL value |
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| 90 | """ |
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| 91 | tax = ArgUtils.get_taxonomy(taxa) |
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| 92 | built = BindingSearch( |
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| 93 | key=key, |
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| 94 | api=Apis.Chembl, |
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| 95 | taxa=tax, |
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| 96 | traversal=traversal, |
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| 97 | target_types=ArgUtils.get_target_types(target_types), |
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| 98 | min_conf_score=confidence, |
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| 99 | relations={"<", "<=", "="}, # there are no others with pchembl |
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| 100 | min_pchembl=pchembl, |
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| 101 | binds_cutoff=binding, |
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| 102 | ) |
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| 103 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
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| 104 | |||
| 105 | |||
| 106 | class EntryChemblMechanism(Entry[MechanismSearch]): |
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| 107 | View Code Duplication | @classmethod |
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| 108 | @entry() |
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| 109 | def run( |
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| 110 | cls, |
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| 111 | path: Path = CommonArgs.in_compound_table, |
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| 112 | key: str = EntryArgs.key("chembl:mechanism"), |
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| 113 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 114 | taxa: str = CommonArgs.taxa, |
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| 115 | traversal: str = EntryArgs.traversal, |
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| 116 | target_types: str = EntryArgs.target_types, |
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| 117 | min_confidence: Optional[int] = EntryArgs.min_confidence, |
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| 118 | as_of: Optional[str] = CommonArgs.as_of, |
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| 119 | replace: bool = CommonArgs.replace, |
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| 120 | proceed: bool = CommonArgs.proceed, |
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| 121 | check: bool = EntryArgs.check, |
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| 122 | log: Optional[Path] = CommonArgs.log, |
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| 123 | stderr: str = CommonArgs.stderr, |
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| 124 | ) -> Searcher: |
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| 125 | """ |
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| 126 | Mechanism of action (MOA) data from ChEMBL. |
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| 127 | |||
| 128 | OBJECT: The target name |
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| 129 | |||
| 130 | PREDICATE: The target action (e.g. "agonist") |
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| 131 | """ |
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| 132 | tax = ArgUtils.get_taxonomy(taxa) |
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| 133 | built = MechanismSearch( |
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| 134 | key=key, |
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| 135 | api=Apis.Chembl, |
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| 136 | taxa=tax, |
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| 137 | traversal=traversal, |
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| 138 | allowed_target_types=ArgUtils.get_target_types(target_types), |
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| 139 | min_confidence_score=min_confidence, |
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| 140 | ) |
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| 141 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
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| 142 | |||
| 143 | |||
| 144 | class ChemblQsarPredictions(Entry[TargetPredictionSearch]): |
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| 145 | View Code Duplication | @classmethod |
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| 146 | @entry() |
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| 147 | def run( |
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| 148 | cls, |
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| 149 | path: Path = CommonArgs.in_compound_table, |
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| 150 | key: str = EntryArgs.key("chembl:predictions"), |
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| 151 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 152 | taxa: str = CommonArgs.taxa, |
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| 153 | traversal: str = EntryArgs.traversal, |
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| 154 | target_types: str = EntryArgs.target_types, |
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| 155 | min_threshold: float = EntryArgs.min_threshold, |
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| 156 | as_of: Optional[str] = CommonArgs.as_of, |
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| 157 | replace: bool = CommonArgs.replace, |
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| 158 | proceed: bool = CommonArgs.proceed, |
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| 159 | check: bool = EntryArgs.check, |
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| 160 | log: Optional[Path] = CommonArgs.log, |
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| 161 | stderr: str = CommonArgs.stderr, |
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| 162 | ) -> Searcher: |
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| 163 | """ |
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| 164 | Predicted target binding from ChEMBL. |
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| 165 | |||
| 166 | https://mandos-chem.readthedocs.io/en/latest/binding.html |
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| 167 | These are from a QSAR model by ChEMBL. |
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| 168 | |||
| 169 | OBJECT: The target name |
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| 170 | |||
| 171 | WEIGHT: The square root of the PCHEMBL threshold |
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| 172 | multiplied by a prediction odds-ratio, normalized |
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| 173 | """ |
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| 174 | tax = ArgUtils.get_taxonomy(taxa) |
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| 175 | built = TargetPredictionSearch( |
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| 176 | key=key, |
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| 177 | api=Apis.Chembl, |
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| 178 | scrape=Apis.ChemblScrape, |
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| 179 | taxa=tax, |
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| 180 | traversal=traversal, |
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| 181 | target_types=ArgUtils.get_target_types(target_types), |
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| 182 | min_threshold=min_threshold, |
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| 183 | ) |
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| 184 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
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| 185 | |||
| 186 | |||
| 187 | class EntryChemblTrials(Entry[IndicationSearch]): |
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| 188 | @classmethod |
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| 189 | @entry() |
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| 190 | def run( |
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| 191 | cls, |
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| 192 | path: Path = CommonArgs.in_compound_table, |
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| 193 | key: str = EntryArgs.key("chembl:trial"), |
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| 194 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 195 | min_phase: Optional[int] = EntryArgs.chembl_trial, |
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| 196 | as_of: Optional[str] = CommonArgs.as_of, |
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| 197 | replace: bool = CommonArgs.replace, |
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| 198 | proceed: bool = CommonArgs.proceed, |
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| 199 | check: bool = EntryArgs.check, |
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| 200 | log: Optional[Path] = CommonArgs.log, |
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| 201 | stderr: str = CommonArgs.stderr, |
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| 202 | ) -> Searcher: |
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| 203 | """ |
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| 204 | Diseases from clinical trials listed in ChEMBL. |
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| 205 | |||
| 206 | OBJECT: The name of the disease (in MeSH) |
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| 207 | """ |
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| 208 | built = IndicationSearch(key=key, api=Apis.Chembl, min_phase=min_phase) |
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| 209 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
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| 210 | |||
| 211 | |||
| 212 | class EntryChemblAtc(Entry[AtcSearch]): |
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| 213 | @classmethod |
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| 214 | @entry() |
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| 215 | def run( |
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| 216 | cls, |
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| 217 | path: Path = CommonArgs.in_compound_table, |
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| 218 | key: str = EntryArgs.key("chembl:atc"), |
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| 219 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 220 | levels: str = EntryArgs.atc_level, |
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| 221 | as_of: Optional[str] = CommonArgs.as_of, |
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| 222 | replace: bool = CommonArgs.replace, |
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| 223 | proceed: bool = CommonArgs.proceed, |
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| 224 | check: bool = EntryArgs.check, |
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| 225 | log: Optional[Path] = CommonArgs.log, |
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| 226 | stderr: str = CommonArgs.stderr, |
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| 227 | ) -> Searcher: |
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| 228 | """ |
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| 229 | ATC codes from ChEMBL. |
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| 230 | |||
| 231 | OBJECT: The ATC code name |
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| 232 | """ |
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| 233 | built = AtcSearch( |
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| 234 | key=key, api=Apis.Chembl, levels={int(x.strip()) for x in levels.split(",")} |
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| 235 | ) |
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| 236 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
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| 237 | |||
| 238 | |||
| 239 | class _EntryChemblGo(Entry[GoSearch], metaclass=abc.ABCMeta): |
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| 240 | @classmethod |
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| 241 | def go_type(cls) -> GoType: |
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| 242 | raise NotImplementedError() |
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| 243 | |||
| 244 | @classmethod |
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| 245 | def cmd(cls) -> str: |
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| 246 | me = str(cls.go_type().name) |
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| 247 | return f"chembl:go.{me.lower()}" |
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| 248 | |||
| 249 | @classmethod |
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| 250 | @entry() |
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| 251 | def run( |
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| 252 | cls, |
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| 253 | path: Path = CommonArgs.in_compound_table, |
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| 254 | key: str = EntryArgs.key("<see above>"), |
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| 255 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 256 | taxa: str = CommonArgs.taxa, |
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| 257 | traversal: str = EntryArgs.traversal, |
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| 258 | target_types: str = EntryArgs.target_types, |
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| 259 | confidence: Optional[int] = EntryArgs.min_confidence, |
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| 260 | pchembl: float = EntryArgs.min_pchembl, |
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| 261 | binding_search: Optional[str] = EntryArgs.binding_search_name, |
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| 262 | as_of: Optional[str] = CommonArgs.as_of, |
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| 263 | replace: bool = CommonArgs.replace, |
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| 264 | proceed: bool = CommonArgs.proceed, |
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| 265 | check: bool = EntryArgs.check, |
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| 266 | log: Optional[Path] = CommonArgs.log, |
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| 267 | stderr: str = CommonArgs.stderr, |
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| 268 | ) -> Searcher: |
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| 269 | """ |
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| 270 | See the docs for the specific entries. |
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| 271 | """ |
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| 272 | if key is None or key == "<see above>": |
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| 273 | key = cls.cmd() |
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| 274 | api = ChemblApi.wrap(Apis.Chembl) |
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| 275 | if binding_search is None: |
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| 276 | binding_clazz = BindingSearch |
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| 277 | else: |
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| 278 | binding_clazz = ReflectionTools.injection(binding_search, BindingSearch) |
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| 279 | logger.info(f"Passing parameters to {binding_clazz.__qualname__}") |
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| 280 | try: |
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| 281 | tax = ArgUtils.get_taxonomy(taxa) |
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| 282 | binding_search = binding_clazz( |
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| 283 | key=key, |
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| 284 | api=Apis.Chembl, |
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| 285 | taxa=tax, |
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| 286 | traversal=traversal, |
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| 287 | target_types=ArgUtils.get_target_types(target_types), |
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| 288 | min_conf_score=confidence, |
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| 289 | relations={"<", "<=", "="}, |
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| 290 | min_pchembl=pchembl, |
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| 291 | ) |
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| 292 | except (TypeError, ValueError): |
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| 293 | raise InjectionError(f"Failed to build {binding_clazz.__qualname__}") |
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| 294 | built = GoSearch(key, api, cls.go_type(), binding_search) |
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| 295 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
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| 296 | |||
| 297 | |||
| 298 | View Code Duplication | class EntryGoFunction(_EntryChemblGo): |
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| 299 | @classmethod |
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| 300 | def go_type(cls) -> GoType: |
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| 301 | return GoType.function |
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| 302 | |||
| 303 | @classmethod |
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| 304 | @entry() |
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| 305 | def run( |
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| 306 | cls, |
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| 307 | path: Path = CommonArgs.in_compound_table, |
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| 308 | key: str = EntryArgs.key("chembl:go.function"), |
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| 309 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 310 | taxa: str = CommonArgs.taxa, |
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| 311 | traversal: str = EntryArgs.traversal, |
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| 312 | target_types: str = EntryArgs.target_types, |
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| 313 | confidence: Optional[int] = EntryArgs.min_confidence, |
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| 314 | pchembl: float = EntryArgs.min_pchembl, |
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| 315 | binding_search: Optional[str] = EntryArgs.binding_search_name, |
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| 316 | as_of: Optional[str] = CommonArgs.as_of, |
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| 317 | replace: bool = CommonArgs.replace, |
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| 318 | proceed: bool = CommonArgs.proceed, |
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| 319 | check: bool = EntryArgs.check, |
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| 320 | log: Optional[Path] = CommonArgs.log, |
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| 321 | stderr: str = CommonArgs.stderr, |
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| 322 | ) -> Searcher: |
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| 323 | """ |
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| 324 | GO Function terms associated with ChEMBL binding targets. |
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| 325 | |||
| 326 | OBJECT: The GO Function term name |
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| 327 | |||
| 328 | WEIGHT: The sum of the PCHEMBL values |
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| 329 | """ |
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| 330 | args, _, _, locs = inspect.getargvalues(inspect.currentframe()) |
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| 331 | return super().run(**{a: locs[a] for a in args if a != "cls"}) |
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| 332 | |||
| 333 | |||
| 334 | View Code Duplication | class EntryGoProcess(_EntryChemblGo): |
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| 335 | @classmethod |
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| 336 | def go_type(cls) -> GoType: |
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| 337 | return GoType.process |
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| 338 | |||
| 339 | @classmethod |
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| 340 | @entry() |
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| 341 | def run( |
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| 342 | cls, |
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| 343 | path: Path = CommonArgs.in_compound_table, |
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| 344 | key: str = EntryArgs.key("chembl:go.process"), |
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| 345 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 346 | taxa: str = CommonArgs.taxa, |
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| 347 | traversal: str = EntryArgs.traversal, |
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| 348 | target_types: str = EntryArgs.target_types, |
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| 349 | confidence: Optional[int] = EntryArgs.min_confidence, |
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| 350 | pchembl: float = EntryArgs.min_pchembl, |
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| 351 | binding_search: Optional[str] = EntryArgs.binding_search_name, |
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| 352 | as_of: Optional[str] = CommonArgs.as_of, |
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| 353 | replace: bool = CommonArgs.replace, |
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| 354 | proceed: bool = CommonArgs.proceed, |
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| 355 | check: bool = EntryArgs.check, |
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| 356 | log: Optional[Path] = CommonArgs.log, |
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| 357 | stderr: str = CommonArgs.stderr, |
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| 358 | ) -> Searcher: |
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| 359 | """ |
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| 360 | GO Process terms associated with ChEMBL binding targets. |
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| 361 | |||
| 362 | OBJECT: The GO Process term name |
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| 363 | |||
| 364 | WEIGHT: The sum of the PCHEMBL values |
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| 365 | """ |
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| 366 | args, _, _, locs = inspect.getargvalues(inspect.currentframe()) |
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| 367 | return super().run(**{a: locs[a] for a in args if a != "cls"}) |
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| 368 | |||
| 369 | |||
| 370 | View Code Duplication | class EntryGoComponent(_EntryChemblGo): |
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| 371 | @classmethod |
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| 372 | def go_type(cls) -> GoType: |
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| 373 | return GoType.component |
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| 374 | |||
| 375 | @classmethod |
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| 376 | @entry() |
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| 377 | def run( |
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| 378 | cls, |
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| 379 | path: Path = CommonArgs.in_compound_table, |
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| 380 | key: str = EntryArgs.key("chembl:go.component"), |
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| 381 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 382 | taxa: str = CommonArgs.taxa, |
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| 383 | traversal: str = EntryArgs.traversal, |
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| 384 | target_types: str = EntryArgs.target_types, |
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| 385 | confidence: Optional[int] = EntryArgs.min_confidence, |
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| 386 | pchembl: float = EntryArgs.min_pchembl, |
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| 387 | binding_search: Optional[str] = EntryArgs.binding_search_name, |
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| 388 | as_of: Optional[str] = CommonArgs.as_of, |
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| 389 | replace: bool = CommonArgs.replace, |
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| 390 | proceed: bool = CommonArgs.proceed, |
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| 391 | check: bool = EntryArgs.check, |
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| 392 | log: Optional[Path] = CommonArgs.log, |
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| 393 | stderr: str = CommonArgs.stderr, |
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| 394 | ) -> Searcher: |
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| 395 | """ |
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| 396 | GO Component terms associated with ChEMBL binding targets. |
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| 397 | |||
| 398 | OBJECT: The GO Component term name |
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| 399 | |||
| 400 | WEIGHT: The sum of the PCHEMBL values |
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| 401 | """ |
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| 402 | args, _, _, locs = inspect.getargvalues(inspect.currentframe()) |
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| 403 | return super().run(**{a: locs[a] for a in args if a != "cls"}) |
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| 404 | |||
| 405 | |||
| 406 | class EntryPubchemTrials(Entry[TrialSearch]): |
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| 407 | @classmethod |
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| 408 | @entry() |
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| 409 | def run( |
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| 410 | cls, |
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| 411 | path: Path = CommonArgs.in_compound_table, |
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| 412 | key: str = EntryArgs.key("pubchem:trial"), |
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| 413 | to: Optional[Path] = CommonArgs.out_annotations_file, |
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| 414 | min_phase: Optional[int] = EntryArgs.pubchem_trial_phase, |
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| 415 | statuses: str = EntryArgs.pubchem_trial_statuses, |
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| 416 | req_explicit: bool = EntryArgs.req_explicit, |
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| 417 | as_of: Optional[str] = CommonArgs.as_of, |
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| 418 | replace: bool = CommonArgs.replace, |
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| 419 | proceed: bool = CommonArgs.proceed, |
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| 420 | check: bool = EntryArgs.check, |
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| 421 | log: Optional[Path] = CommonArgs.log, |
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| 422 | stderr: str = CommonArgs.stderr, |
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| 423 | ) -> Searcher: |
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| 424 | """ |
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| 425 | Diseases from clinical trials listed in clinicaltrials.gov. |
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| 426 | |||
| 427 | OBJECT: The name of the disease (in MeSH) |
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| 428 | """ |
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| 429 | statuses = ClinicalTrialsGovUtils.resolve_statuses(statuses) |
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| 430 | built = TrialSearch( |
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| 431 | key=key, api=Apis.Pubchem, min_phase=min_phase, statuses=statuses, explicit=req_explicit |
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| 432 | ) |
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| 433 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
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| 434 | |||
| 435 | |||
| 436 | class EntryPubchemDisease(Entry[DiseaseSearch]): |
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| 437 | View Code Duplication | @classmethod |
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| 438 | @entry() |
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| 439 | def run( |
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| 440 | cls, |
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| 441 | path: Path = CommonArgs.in_compound_table, |
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| 442 | key: str = EntryArgs.key("disease.ctd:mesh"), |
||
| 443 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 444 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 445 | replace: bool = CommonArgs.replace, |
||
| 446 | proceed: bool = CommonArgs.proceed, |
||
| 447 | check: bool = EntryArgs.check, |
||
| 448 | log: Optional[Path] = CommonArgs.log, |
||
| 449 | stderr: str = CommonArgs.stderr, |
||
| 450 | ) -> Searcher: |
||
| 451 | """ |
||
| 452 | Diseases in the CTD. |
||
| 453 | |||
| 454 | (Comparative Toxicogenomics Database.) |
||
| 455 | |||
| 456 | OBJECT: The MeSH code of the disease |
||
| 457 | |||
| 458 | """ |
||
| 459 | built = DiseaseSearch(key, Apis.Pubchem) |
||
| 460 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 461 | |||
| 462 | |||
| 463 | class _EntryPubchemCoOccurrence(Entry[U], metaclass=abc.ABCMeta): |
||
| 464 | @classmethod |
||
| 465 | def cmd(cls) -> str: |
||
| 466 | me = str(cls.get_cooccurrence_type().name) |
||
| 467 | return f"lit.pubchem:{me.lower()}" |
||
| 468 | |||
| 469 | @classmethod |
||
| 470 | def get_cooccurrence_type(cls) -> CoOccurrenceType: |
||
| 471 | s: CoOccurrenceSearch = cls.get_search_type() |
||
| 472 | return s.cooccurrence_type() |
||
| 473 | |||
| 474 | @classmethod |
||
| 475 | @entry() |
||
| 476 | def run( |
||
| 477 | cls, |
||
| 478 | path: Path = CommonArgs.in_compound_table, |
||
| 479 | key: str = EntryArgs.key("<see above>"), |
||
| 480 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 481 | min_score: float = EntryArgs.min_cooccurrence_score, |
||
| 482 | min_articles: int = EntryArgs.min_cooccurring_articles, |
||
| 483 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 484 | replace: bool = CommonArgs.replace, |
||
| 485 | proceed: bool = CommonArgs.proceed, |
||
| 486 | check: bool = EntryArgs.check, |
||
| 487 | log: Optional[Path] = CommonArgs.log, |
||
| 488 | stderr: str = CommonArgs.stderr, |
||
| 489 | ) -> Searcher: |
||
| 490 | """See the docstrings for the individual entries.""" |
||
| 491 | clazz = cls.get_search_type() |
||
| 492 | built = clazz(key, Apis.Pubchem, min_score=min_score, min_articles=min_articles) |
||
| 493 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 494 | |||
| 495 | |||
| 496 | View Code Duplication | class EntryPubchemGeneCoOccurrence(_EntryPubchemCoOccurrence[GeneCoOccurrenceSearch]): |
|
| 497 | @classmethod |
||
| 498 | @entry() |
||
| 499 | def run( |
||
| 500 | cls, |
||
| 501 | path: Path = CommonArgs.in_compound_table, |
||
| 502 | key: str = EntryArgs.key(f"lit.pubchem:{CoOccurrenceType.gene.name.lower()}"), |
||
| 503 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 504 | min_score: float = EntryArgs.min_cooccurrence_score, |
||
| 505 | min_articles: int = EntryArgs.min_cooccurring_articles, |
||
| 506 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 507 | replace: bool = CommonArgs.replace, |
||
| 508 | proceed: bool = CommonArgs.proceed, |
||
| 509 | check: bool = EntryArgs.check, |
||
| 510 | log: Optional[Path] = CommonArgs.log, |
||
| 511 | stderr: str = CommonArgs.stderr, |
||
| 512 | ) -> Searcher: |
||
| 513 | """ |
||
| 514 | Co-occurrences of genes from PubMed articles. |
||
| 515 | |||
| 516 | https://mandos-chem.readthedocs.io/en/latest/co-occurrences.html |
||
| 517 | |||
| 518 | OBJECT: The name of the gene |
||
| 519 | |||
| 520 | WEIGHT: The co-occurrence score (refer to the docs) |
||
| 521 | """ |
||
| 522 | args, _, _, locs = inspect.getargvalues(inspect.currentframe()) |
||
| 523 | return super().run(**{a: locs[a] for a in args if a != "cls"}) |
||
| 524 | |||
| 525 | |||
| 526 | View Code Duplication | class EntryPubchemDiseaseCoOccurrence(_EntryPubchemCoOccurrence[DiseaseCoOccurrenceSearch]): |
|
| 527 | @classmethod |
||
| 528 | @entry() |
||
| 529 | def run( |
||
| 530 | cls, |
||
| 531 | path: Path = CommonArgs.in_compound_table, |
||
| 532 | key: str = EntryArgs.key(f"lit.pubchem:{CoOccurrenceType.disease.name.lower()}"), |
||
| 533 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 534 | min_score: float = EntryArgs.min_cooccurrence_score, |
||
| 535 | min_articles: int = EntryArgs.min_cooccurring_articles, |
||
| 536 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 537 | replace: bool = CommonArgs.replace, |
||
| 538 | proceed: bool = CommonArgs.proceed, |
||
| 539 | check: bool = EntryArgs.check, |
||
| 540 | log: Optional[Path] = CommonArgs.log, |
||
| 541 | stderr: str = CommonArgs.stderr, |
||
| 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 | args, _, _, locs = inspect.getargvalues(inspect.currentframe()) |
||
| 553 | return super().run(**{a: locs[a] for a in args if a != "cls"}) |
||
| 554 | |||
| 555 | |||
| 556 | View Code Duplication | class EntryPubchemChemicalCoOccurrence(_EntryPubchemCoOccurrence[ChemicalCoOccurrenceSearch]): |
|
| 557 | @classmethod |
||
| 558 | @entry() |
||
| 559 | def run( |
||
| 560 | cls, |
||
| 561 | path: Path = CommonArgs.in_compound_table, |
||
| 562 | key: str = EntryArgs.key(f"lit.pubchem:{CoOccurrenceType.chemical.name.lower()}"), |
||
| 563 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 564 | min_score: float = EntryArgs.min_cooccurrence_score, |
||
| 565 | min_articles: int = EntryArgs.min_cooccurring_articles, |
||
| 566 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 567 | replace: bool = CommonArgs.replace, |
||
| 568 | proceed: bool = CommonArgs.proceed, |
||
| 569 | check: bool = EntryArgs.check, |
||
| 570 | log: Optional[Path] = CommonArgs.log, |
||
| 571 | stderr: str = CommonArgs.stderr, |
||
| 572 | ) -> Searcher: |
||
| 573 | """ |
||
| 574 | Co-occurrences of chemicals from PubMed articles. |
||
| 575 | |||
| 576 | https://mandos-chem.readthedocs.io/en/latest/co-occurrences.html |
||
| 577 | |||
| 578 | OBJECT: The name of the chemical (e.g. "cocaine") |
||
| 579 | |||
| 580 | WEIGHT: The co-occurrence score (refer to the docs) |
||
| 581 | """ |
||
| 582 | args, _, _, locs = inspect.getargvalues(inspect.currentframe()) |
||
| 583 | return super().run(**{a: locs[a] for a in args if a != "cls"}) |
||
| 584 | |||
| 585 | |||
| 586 | class EntryPubchemDgi(Entry[DgiSearch]): |
||
| 587 | View Code Duplication | @classmethod |
|
| 588 | @entry() |
||
| 589 | def run( |
||
| 590 | cls, |
||
| 591 | path: Path = CommonArgs.in_compound_table, |
||
| 592 | key: str = EntryArgs.key("inter.dgidb:gene"), |
||
| 593 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 594 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 595 | replace: bool = CommonArgs.replace, |
||
| 596 | proceed: bool = CommonArgs.proceed, |
||
| 597 | check: bool = EntryArgs.check, |
||
| 598 | log: Optional[Path] = CommonArgs.log, |
||
| 599 | stderr: str = CommonArgs.stderr, |
||
| 600 | ) -> Searcher: |
||
| 601 | """ |
||
| 602 | Drug/gene interactions in the DGIDB. |
||
| 603 | |||
| 604 | Drug Gene Interaction Database. |
||
| 605 | Also see disease.dgidb:int. |
||
| 606 | |||
| 607 | OBJECT: The name of the gene |
||
| 608 | |||
| 609 | PREDICATE: "interaction:generic" or "interaction:<type>" |
||
| 610 | """ |
||
| 611 | built = DgiSearch(key, Apis.Pubchem) |
||
| 612 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 613 | |||
| 614 | |||
| 615 | class EntryPubchemCgi(Entry[CtdGeneSearch]): |
||
| 616 | View Code Duplication | @classmethod |
|
| 617 | @entry() |
||
| 618 | def run( |
||
| 619 | cls, |
||
| 620 | path: Path = CommonArgs.in_compound_table, |
||
| 621 | key: str = EntryArgs.key("inter.ctd:gene"), |
||
| 622 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 623 | replace: bool = CommonArgs.replace, |
||
| 624 | proceed: bool = CommonArgs.proceed, |
||
| 625 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 626 | check: bool = EntryArgs.check, |
||
| 627 | log: Optional[Path] = CommonArgs.log, |
||
| 628 | stderr: str = CommonArgs.stderr, |
||
| 629 | ) -> Searcher: |
||
| 630 | """ |
||
| 631 | Compound/gene interactions in the DGIDB. |
||
| 632 | |||
| 633 | Drug Gene Interaction Database. |
||
| 634 | Also see ``interact.dgidb:int``. |
||
| 635 | |||
| 636 | OBJECT: The name of the gene |
||
| 637 | |||
| 638 | PREDICATE: derived from the interaction type (e.g. "downregulation") |
||
| 639 | """ |
||
| 640 | built = CtdGeneSearch(key, Apis.Pubchem) |
||
| 641 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 642 | |||
| 643 | |||
| 644 | View Code Duplication | class EntryDrugbankTarget(Entry[DrugbankTargetSearch]): |
|
| 645 | @classmethod |
||
| 646 | @entry() |
||
| 647 | def run( |
||
| 648 | cls, |
||
| 649 | path: Path = CommonArgs.in_compound_table, |
||
| 650 | key: str = EntryArgs.key("inter.drugbank:targ"), |
||
| 651 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 652 | replace: bool = CommonArgs.replace, |
||
| 653 | proceed: bool = CommonArgs.proceed, |
||
| 654 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 655 | check: bool = EntryArgs.check, |
||
| 656 | log: Optional[Path] = CommonArgs.log, |
||
| 657 | stderr: str = CommonArgs.stderr, |
||
| 658 | ) -> Searcher: |
||
| 659 | """ |
||
| 660 | Protein targets from DrugBank. |
||
| 661 | |||
| 662 | OBJECT: The target name (e.g. "Solute carrier family 22 member 11") |
||
| 663 | |||
| 664 | PREDICATE: "<target_type>:<action>" |
||
| 665 | """ |
||
| 666 | built = DrugbankTargetSearch(key, Apis.Pubchem, {DrugbankTargetType.target}) |
||
| 667 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 668 | |||
| 669 | |||
| 670 | View Code Duplication | class EntryGeneralFunction(Entry[DrugbankGeneralFunctionSearch]): |
|
| 671 | @classmethod |
||
| 672 | @entry() |
||
| 673 | def run( |
||
| 674 | cls, |
||
| 675 | path: Path = CommonArgs.in_compound_table, |
||
| 676 | key: str = EntryArgs.key("inter.drugbank:targ-fn"), |
||
| 677 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 678 | replace: bool = CommonArgs.replace, |
||
| 679 | proceed: bool = CommonArgs.proceed, |
||
| 680 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 681 | check: bool = EntryArgs.check, |
||
| 682 | log: Optional[Path] = CommonArgs.log, |
||
| 683 | stderr: str = CommonArgs.stderr, |
||
| 684 | ) -> Searcher: |
||
| 685 | """ |
||
| 686 | General functions from DrugBank targets. |
||
| 687 | |||
| 688 | OBJECT: The name of the "general function" (e.g. "Toxic substance binding") |
||
| 689 | |||
| 690 | PREDICATE: "<target_type>:<action>" |
||
| 691 | """ |
||
| 692 | built = DrugbankGeneralFunctionSearch(key, Apis.Pubchem, {DrugbankTargetType.target}) |
||
| 693 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 694 | |||
| 695 | |||
| 696 | View Code Duplication | class EntryDrugbankTransporter(Entry[DrugbankTargetSearch]): |
|
| 697 | @classmethod |
||
| 698 | @entry() |
||
| 699 | def run( |
||
| 700 | cls, |
||
| 701 | path: Path = CommonArgs.in_compound_table, |
||
| 702 | key: str = EntryArgs.key("inter.drugbank:pk"), |
||
| 703 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 704 | replace: bool = CommonArgs.replace, |
||
| 705 | proceed: bool = CommonArgs.proceed, |
||
| 706 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 707 | check: bool = EntryArgs.check, |
||
| 708 | log: Optional[Path] = CommonArgs.log, |
||
| 709 | stderr: str = CommonArgs.stderr, |
||
| 710 | ) -> Searcher: |
||
| 711 | """ |
||
| 712 | PK-related proteins from DrugBank. |
||
| 713 | |||
| 714 | OBJECT: The transporter name (e.g. "Solute carrier family 22 member 11") |
||
| 715 | |||
| 716 | PREDICATE: "<target_type>:<action>" (e.g. metabolized, transported, etc.) |
||
| 717 | """ |
||
| 718 | target_types = { |
||
| 719 | DrugbankTargetType.transporter, |
||
| 720 | DrugbankTargetType.carrier, |
||
| 721 | DrugbankTargetType.enzyme, |
||
| 722 | } |
||
| 723 | built = DrugbankTargetSearch(key, Apis.Pubchem, target_types) |
||
| 724 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 725 | |||
| 726 | |||
| 727 | View Code Duplication | class EntryTransporterGeneralFunction(Entry[DrugbankGeneralFunctionSearch]): |
|
| 728 | @classmethod |
||
| 729 | @entry() |
||
| 730 | def run( |
||
| 731 | cls, |
||
| 732 | path: Path = CommonArgs.in_compound_table, |
||
| 733 | key: str = EntryArgs.key("inter.drugbank:pk-fn"), |
||
| 734 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 735 | replace: bool = CommonArgs.replace, |
||
| 736 | proceed: bool = CommonArgs.proceed, |
||
| 737 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 738 | check: bool = EntryArgs.check, |
||
| 739 | log: Optional[Path] = CommonArgs.log, |
||
| 740 | stderr: str = CommonArgs.stderr, |
||
| 741 | ) -> Searcher: |
||
| 742 | """ |
||
| 743 | DrugBank PK-related protein functions. |
||
| 744 | |||
| 745 | OBJECT: The name of the general function (e.g. "Toxic substance binding") |
||
| 746 | |||
| 747 | PREDICATE: "<target_type>:<action>" (e.g. metabolized, transported, etc.) |
||
| 748 | """ |
||
| 749 | target_types = { |
||
| 750 | DrugbankTargetType.transporter, |
||
| 751 | DrugbankTargetType.carrier, |
||
| 752 | DrugbankTargetType.enzyme, |
||
| 753 | } |
||
| 754 | built = DrugbankGeneralFunctionSearch(key, Apis.Pubchem, target_types) |
||
| 755 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 756 | |||
| 757 | |||
| 758 | class EntryDrugbankDdi(Entry[DrugbankDdiSearch]): |
||
| 759 | View Code Duplication | @classmethod |
|
| 760 | @entry() |
||
| 761 | def run( |
||
| 762 | cls, |
||
| 763 | path: Path = CommonArgs.in_compound_table, |
||
| 764 | key: str = EntryArgs.key("inter.drugbank:ddi"), |
||
| 765 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 766 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 767 | replace: bool = CommonArgs.replace, |
||
| 768 | proceed: bool = CommonArgs.proceed, |
||
| 769 | check: bool = EntryArgs.check, |
||
| 770 | log: Optional[Path] = CommonArgs.log, |
||
| 771 | stderr: str = CommonArgs.stderr, |
||
| 772 | ) -> Searcher: |
||
| 773 | """ |
||
| 774 | Drug/drug interactions listed by DrugBank. |
||
| 775 | |||
| 776 | The "description" column includes useful information about the interaction, |
||
| 777 | such as diseases and whether a risk is increased or decreased. |
||
| 778 | |||
| 779 | OBJECT: The name of the drug (e.g. "ibuprofen") |
||
| 780 | |||
| 781 | PREDICATE: typically increase/decrease/change followed by risk/activity/etc. |
||
| 782 | """ |
||
| 783 | built = DrugbankDdiSearch(key, Apis.Pubchem) |
||
| 784 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 785 | |||
| 786 | |||
| 787 | class EntryPubchemAssay(Entry[BioactivitySearch]): |
||
| 788 | @classmethod |
||
| 789 | @entry() |
||
| 790 | def run( |
||
| 791 | cls, |
||
| 792 | path: Path = CommonArgs.in_compound_table, |
||
| 793 | key: str = EntryArgs.key("assay.pubchem:act"), |
||
| 794 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 795 | match_name: bool = EntryArgs.match_name, |
||
| 796 | ban_sources: Optional[str] = EntryArgs.banned_sources, |
||
| 797 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 798 | replace: bool = CommonArgs.replace, |
||
| 799 | proceed: bool = CommonArgs.proceed, |
||
| 800 | check: bool = EntryArgs.check, |
||
| 801 | log: Optional[Path] = CommonArgs.log, |
||
| 802 | stderr: str = CommonArgs.stderr, |
||
| 803 | ) -> Searcher: |
||
| 804 | """ |
||
| 805 | PubChem bioactivity results. |
||
| 806 | |||
| 807 | Note: The species name, if present, is taken from the target name. |
||
| 808 | The taxon ID is what was curated in PubChem. |
||
| 809 | |||
| 810 | OBJECT: The name of the target without species suffix |
||
| 811 | (e.g. "Slc6a3 - solute carrier family 6 member 3") |
||
| 812 | |||
| 813 | PREDICATE: "active", "inactive", "inconclusive", or "undetermined" |
||
| 814 | |||
| 815 | WEIGHT: 2 for confirmatory; 1 otherwise |
||
| 816 | """ |
||
| 817 | built = BioactivitySearch(key, Apis.Pubchem, compound_name_must_match=match_name) |
||
| 818 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 819 | |||
| 820 | |||
| 821 | class EntryDeaSchedule(Entry[BioactivitySearch]): |
||
| 822 | @classmethod |
||
| 823 | @entry() |
||
| 824 | def run( |
||
| 825 | cls, |
||
| 826 | path: Path = CommonArgs.in_compound_table, |
||
| 827 | key: str = EntryArgs.key("drug.dea:schedule"), |
||
| 828 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 829 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 830 | replace: bool = CommonArgs.replace, |
||
| 831 | proceed: bool = CommonArgs.proceed, |
||
| 832 | check: bool = EntryArgs.check, |
||
| 833 | log: Optional[Path] = CommonArgs.log, |
||
| 834 | stderr: str = CommonArgs.stderr, |
||
| 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 | @entry() |
||
| 847 | def run( |
||
| 848 | cls, |
||
| 849 | path: Path = CommonArgs.in_compound_table, |
||
| 850 | key: str = EntryArgs.key("drug.dea:class"), |
||
| 851 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 852 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 853 | replace: bool = CommonArgs.replace, |
||
| 854 | proceed: bool = CommonArgs.proceed, |
||
| 855 | check: bool = EntryArgs.check, |
||
| 856 | log: Optional[Path] = CommonArgs.log, |
||
| 857 | stderr: str = CommonArgs.stderr, |
||
| 858 | ) -> Searcher: |
||
| 859 | """ |
||
| 860 | DEA classes (PENDING). |
||
| 861 | |||
| 862 | OBJECT: The DEA class name (e.g. "hallucinogen") |
||
| 863 | """ |
||
| 864 | pass |
||
| 865 | |||
| 866 | |||
| 867 | class EntryChemidPlusAcute(Entry[AcuteEffectSearch]): |
||
| 868 | @classmethod |
||
| 869 | @entry() |
||
| 870 | def run( |
||
| 871 | cls, |
||
| 872 | path: Path = CommonArgs.in_compound_table, |
||
| 873 | key: str = EntryArgs.key("tox.chemidplus:acute"), |
||
| 874 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 875 | level: int = EntryArgs.acute_effect_level, |
||
| 876 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 877 | replace: bool = CommonArgs.replace, |
||
| 878 | proceed: bool = CommonArgs.proceed, |
||
| 879 | check: bool = EntryArgs.check, |
||
| 880 | log: Optional[Path] = CommonArgs.log, |
||
| 881 | stderr: str = CommonArgs.stderr, |
||
| 882 | ) -> Searcher: |
||
| 883 | """ |
||
| 884 | Acute effect codes from ChemIDPlus. |
||
| 885 | |||
| 886 | OBJECT: The code name (e.g. "behavioral: excitement") |
||
| 887 | """ |
||
| 888 | built = AcuteEffectSearch( |
||
| 889 | key, |
||
| 890 | Apis.Pubchem, |
||
| 891 | top_level=level == 1, |
||
| 892 | ) |
||
| 893 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 894 | |||
| 895 | |||
| 896 | class EntryChemidPlusLd50(Entry[Ld50Search]): |
||
| 897 | View Code Duplication | @classmethod |
|
| 898 | @entry() |
||
| 899 | def run( |
||
| 900 | cls, |
||
| 901 | path: Path = CommonArgs.in_compound_table, |
||
| 902 | key: str = EntryArgs.key("tox.chemidplus:ld50"), |
||
| 903 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 904 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 905 | replace: bool = CommonArgs.replace, |
||
| 906 | proceed: bool = CommonArgs.proceed, |
||
| 907 | check: bool = EntryArgs.check, |
||
| 908 | log: Optional[Path] = CommonArgs.log, |
||
| 909 | stderr: str = CommonArgs.stderr, |
||
| 910 | ) -> Searcher: |
||
| 911 | """ |
||
| 912 | LD50 acute effects from ChemIDPlus. |
||
| 913 | |||
| 914 | OBJECT: The negative of the dose in mg/kg |
||
| 915 | |||
| 916 | PREDICATE: "LD50:<route>" (e.g. "LD50:intravenous") |
||
| 917 | """ |
||
| 918 | built = Ld50Search(key, Apis.Pubchem) |
||
| 919 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 920 | |||
| 921 | |||
| 922 | class EntryPubchemComputed(Entry[ComputedPropertySearch]): |
||
| 923 | @classmethod |
||
| 924 | @entry() |
||
| 925 | def run( |
||
| 926 | cls, |
||
| 927 | path: Path = CommonArgs.in_compound_table, |
||
| 928 | key: str = EntryArgs.key("chem.pubchem:computed"), |
||
| 929 | keys: str = EntryArgs.pubchem_computed_keys, |
||
| 930 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 931 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 932 | replace: bool = CommonArgs.replace, |
||
| 933 | proceed: bool = CommonArgs.proceed, |
||
| 934 | check: bool = EntryArgs.check, |
||
| 935 | log: Optional[Path] = CommonArgs.log, |
||
| 936 | stderr: str = CommonArgs.stderr, |
||
| 937 | ) -> Searcher: |
||
| 938 | """ |
||
| 939 | Computed properties from PubChem. |
||
| 940 | |||
| 941 | OBJECT: Number |
||
| 942 | |||
| 943 | PREDICATE: e.g. "complexity" |
||
| 944 | """ |
||
| 945 | # replace acronyms, etc. |
||
| 946 | # ComputedPropertySearch standardizes punctuation and casing |
||
| 947 | known = { |
||
| 948 | k: v |
||
| 949 | for k, v in { |
||
| 950 | **EntryArgs.KNOWN_USEFUL_KEYS, |
||
| 951 | **EntryArgs.KNOWN_USELESS_KEYS, |
||
| 952 | }.items() |
||
| 953 | if v is not None |
||
| 954 | } |
||
| 955 | keys = {known.get(s.strip(), s) for s in keys.split(",")} |
||
| 956 | built = ComputedPropertySearch(key, Apis.Pubchem, descriptors=keys) |
||
| 957 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 958 | |||
| 959 | |||
| 960 | class EntryG2pInteractions(Entry[G2pInteractionSearch]): |
||
| 961 | View Code Duplication | @classmethod |
|
| 962 | @entry() |
||
| 963 | def run( |
||
| 964 | cls, |
||
| 965 | path: Path = CommonArgs.in_compound_table, |
||
| 966 | key: str = EntryArgs.key("g2p:interactions"), |
||
| 967 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 968 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 969 | replace: bool = CommonArgs.replace, |
||
| 970 | proceed: bool = CommonArgs.proceed, |
||
| 971 | check: bool = EntryArgs.check, |
||
| 972 | log: Optional[Path] = CommonArgs.log, |
||
| 973 | stderr: str = CommonArgs.stderr, |
||
| 974 | ) -> Searcher: |
||
| 975 | """ |
||
| 976 | Target interactions with affinities from Guide to Pharmacology. |
||
| 977 | |||
| 978 | OBJECT: A molecular target |
||
| 979 | |||
| 980 | PREDICATE: "interaction:agonism", etc. |
||
| 981 | |||
| 982 | WEIGHT: 1.0 |
||
| 983 | """ |
||
| 984 | built = G2pInteractionSearch(key, Apis.G2p) |
||
| 985 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 986 | |||
| 987 | |||
| 988 | class EntryHmdbTissue(Entry[TissueConcentrationSearch]): |
||
| 989 | @classmethod |
||
| 990 | @entry() |
||
| 991 | def run( |
||
| 992 | cls, |
||
| 993 | path: Path = CommonArgs.in_compound_table, |
||
| 994 | key: str = EntryArgs.key("hmdb:tissue"), |
||
| 995 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 996 | min_nm: Optional[float] = EntryArgs.min_nanomolar, |
||
| 997 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 998 | replace: bool = CommonArgs.replace, |
||
| 999 | proceed: bool = CommonArgs.proceed, |
||
| 1000 | check: bool = EntryArgs.check, |
||
| 1001 | log: Optional[Path] = CommonArgs.log, |
||
| 1002 | stderr: str = CommonArgs.stderr, |
||
| 1003 | ) -> Searcher: |
||
| 1004 | """ |
||
| 1005 | Tissue concentrations from HMDB. |
||
| 1006 | |||
| 1007 | OBJECT: |
||
| 1008 | |||
| 1009 | PREDICATE: "tissue:..." |
||
| 1010 | """ |
||
| 1011 | built = TissueConcentrationSearch(key, Apis.Hmdb) |
||
| 1012 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 1013 | |||
| 1014 | |||
| 1015 | class EntryHmdbComputed(Entry[BioactivitySearch]): |
||
| 1016 | @classmethod |
||
| 1017 | @entry() |
||
| 1018 | def run( |
||
| 1019 | cls, |
||
| 1020 | path: Path = CommonArgs.in_compound_table, |
||
| 1021 | key: str = EntryArgs.key("hmdb:computed"), |
||
| 1022 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 1023 | min_nm: Optional[float] = None, |
||
| 1024 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 1025 | replace: bool = CommonArgs.replace, |
||
| 1026 | proceed: bool = CommonArgs.proceed, |
||
| 1027 | check: bool = EntryArgs.check, |
||
| 1028 | log: Optional[Path] = CommonArgs.log, |
||
| 1029 | stderr: str = CommonArgs.stderr, |
||
| 1030 | ) -> Searcher: |
||
| 1031 | """ |
||
| 1032 | Computed properties from HMDB (PENDING). |
||
| 1033 | |||
| 1034 | Keys include pKa, logP, logS, etc. |
||
| 1035 | |||
| 1036 | OBJECT: A number; booleans are converted to 0/1 |
||
| 1037 | |||
| 1038 | PREDICATE: The name of the property |
||
| 1039 | """ |
||
| 1040 | pass |
||
| 1041 | |||
| 1042 | |||
| 1043 | class EntryDrugbankAdmet(Entry[DrugbankTargetSearch]): |
||
| 1044 | @classmethod |
||
| 1045 | @entry() |
||
| 1046 | def run( |
||
| 1047 | cls, |
||
| 1048 | path: Path = CommonArgs.in_compound_table, |
||
| 1049 | key: str = EntryArgs.key("drugbank.admet:properties"), |
||
| 1050 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 1051 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 1052 | replace: bool = CommonArgs.replace, |
||
| 1053 | proceed: bool = CommonArgs.proceed, |
||
| 1054 | check: bool = EntryArgs.check, |
||
| 1055 | log: Optional[Path] = CommonArgs.log, |
||
| 1056 | stderr: str = CommonArgs.stderr, |
||
| 1057 | ) -> Searcher: |
||
| 1058 | """ |
||
| 1059 | Enzyme predictions from DrugBank (PENDING). |
||
| 1060 | |||
| 1061 | OBJECT: Enzyme name |
||
| 1062 | |||
| 1063 | PREDICATE: Action |
||
| 1064 | """ |
||
| 1065 | |||
| 1066 | |||
| 1067 | class EntryDrugbankMetabolites(Entry[DrugbankTargetSearch]): |
||
| 1068 | @classmethod |
||
| 1069 | @entry() |
||
| 1070 | def run( |
||
| 1071 | cls, |
||
| 1072 | path: Path = CommonArgs.in_compound_table, |
||
| 1073 | key: str = EntryArgs.key("drugbank.admet:metabolites"), |
||
| 1074 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 1075 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 1076 | replace: bool = CommonArgs.replace, |
||
| 1077 | proceed: bool = CommonArgs.proceed, |
||
| 1078 | check: bool = EntryArgs.check, |
||
| 1079 | log: Optional[Path] = CommonArgs.log, |
||
| 1080 | stderr: str = CommonArgs.stderr, |
||
| 1081 | ) -> Searcher: |
||
| 1082 | """ |
||
| 1083 | Metabolites from DrugBank (PENDING). |
||
| 1084 | |||
| 1085 | OBJECT: Compound name (e.g. "norcocaine"). |
||
| 1086 | |||
| 1087 | PREDICATE: "metabolized to" |
||
| 1088 | """ |
||
| 1089 | |||
| 1090 | |||
| 1091 | class EntryDrugbankDosage(Entry[DrugbankTargetSearch]): |
||
| 1092 | @classmethod |
||
| 1093 | @entry() |
||
| 1094 | def run( |
||
| 1095 | cls, |
||
| 1096 | path: Path = CommonArgs.in_compound_table, |
||
| 1097 | key: str = EntryArgs.key("drugbank.admet:dosage"), |
||
| 1098 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 1099 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 1100 | replace: bool = CommonArgs.replace, |
||
| 1101 | proceed: bool = CommonArgs.proceed, |
||
| 1102 | check: bool = EntryArgs.check, |
||
| 1103 | log: Optional[Path] = CommonArgs.log, |
||
| 1104 | stderr: str = CommonArgs.stderr, |
||
| 1105 | ) -> Searcher: |
||
| 1106 | """ |
||
| 1107 | Dosage from DrugBank (PENDING). |
||
| 1108 | |||
| 1109 | OBJECT: concentration in mg/mL |
||
| 1110 | |||
| 1111 | PREDICATE: "dosage :: <route>" |
||
| 1112 | |||
| 1113 | OTHER COLUMNS: |
||
| 1114 | |||
| 1115 | - form (e.g. liquid) |
||
| 1116 | """ |
||
| 1117 | |||
| 1118 | |||
| 1119 | class EntryMetaRandom(Entry[RandomSearch]): |
||
| 1120 | @classmethod |
||
| 1121 | @entry() |
||
| 1122 | def run( |
||
| 1123 | cls, |
||
| 1124 | path: Path = CommonArgs.in_compound_table, |
||
| 1125 | key: str = EntryArgs.key("meta:random"), |
||
| 1126 | to: Optional[Path] = CommonArgs.out_annotations_file, |
||
| 1127 | n: int = EntryArgs.random_n, |
||
| 1128 | seed: int = CommonArgs.seed, |
||
| 1129 | as_of: Optional[str] = CommonArgs.as_of, |
||
| 1130 | replace: bool = CommonArgs.replace, |
||
| 1131 | proceed: bool = CommonArgs.proceed, |
||
| 1132 | check: bool = EntryArgs.check, |
||
| 1133 | log: Optional[Path] = CommonArgs.log, |
||
| 1134 | stderr: str = CommonArgs.stderr, |
||
| 1135 | ) -> Searcher: |
||
| 1136 | r""" |
||
| 1137 | Random class assignment. |
||
| 1138 | |||
| 1139 | OBJECT: 0 thru n (inclusive-exclusive). |
||
| 1140 | |||
| 1141 | PREDICATE: "random" |
||
| 1142 | """ |
||
| 1143 | built = RandomSearch(key, seed, n) |
||
| 1144 | return cls._run(built, path, to, replace, proceed, check, log, stderr) |
||
| 1145 | |||
| 1146 | |||
| 1147 | Entries = [ |
||
| 1148 | EntryChemblBinding, |
||
| 1149 | EntryChemblMechanism, |
||
| 1150 | EntryChemblAtc, |
||
| 1151 | EntryChemblTrials, |
||
| 1152 | EntryGoFunction, |
||
| 1153 | EntryGoProcess, |
||
| 1154 | EntryGoComponent, |
||
| 1155 | EntryPubchemComputed, |
||
| 1156 | EntryPubchemDisease, |
||
| 1157 | EntryPubchemGeneCoOccurrence, |
||
| 1158 | EntryPubchemDiseaseCoOccurrence, |
||
| 1159 | EntryPubchemChemicalCoOccurrence, |
||
| 1160 | EntryPubchemDgi, |
||
| 1161 | EntryPubchemCgi, |
||
| 1162 | EntryDrugbankTarget, |
||
| 1163 | EntryGeneralFunction, |
||
| 1164 | EntryDrugbankTransporter, |
||
| 1165 | EntryTransporterGeneralFunction, |
||
| 1166 | EntryDrugbankDdi, |
||
| 1167 | EntryPubchemAssay, |
||
| 1168 | EntryDeaSchedule, |
||
| 1169 | EntryDeaClass, |
||
| 1170 | EntryChemidPlusAcute, |
||
| 1171 | EntryChemidPlusLd50, |
||
| 1172 | EntryHmdbTissue, |
||
| 1173 | EntryMetaRandom, |
||
| 1174 | ] |
||
| 1175 |
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