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""" |
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Run searches and write files. |
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""" |
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from __future__ import annotations |
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import gzip |
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import logging |
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from pathlib import Path |
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from typing import Sequence, Optional, Dict |
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import pandas as pd |
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from pocketutils.core.dot_dict import NestedDotDict |
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from pocketutils.tools.path_tools import PathTools |
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from typeddfs import TypedDfs |
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from mandos.model import CompoundNotFoundError |
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from mandos.model.chembl_support.chembl_utils import ChemblUtils |
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from mandos.model.searches import Search |
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from mandos.model.settings import MANDOS_SETTINGS |
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from mandos.search.chembl import ChemblSearch |
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from mandos.search.pubchem import PubchemSearch |
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from mandos.entries.api_singletons import Apis |
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Chembl, Pubchem = Apis.Chembl, Apis.Pubchem |
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logger = logging.getLogger(__package__) |
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IdMatchFrame = ( |
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TypedDfs.typed("IdMatchFrame") |
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.require("inchikey") |
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.require("chembl_id") |
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.require("pubchem_id") |
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.strict() |
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).build() |
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class SearcherUtils: |
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@classmethod |
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def dl( |
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cls, inchikeys: Sequence[str], pubchem: bool = True, chembl: bool = True |
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) -> IdMatchFrame: |
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# we actually cache the results, even though the underlying APIs cache |
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# the reasons for this are a little obscure -- |
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# when running a Searcher, we want to run before the FIRST search |
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# for the typer commands to be replicas of the ``Entry.run`` methods, Searcher fetches before running a search |
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# but if we have multiple searches (as in ``mandos search --config``), we only want that at the beginning |
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# the alternative was having ``mandos search`` dynamically subclass each ``Entry`` -- which was really hard |
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# this is much cleaner, even though it's redundant |
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# if the cached results under /pubchem and /chembl are deleted, we unfortunately won't cache the results |
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# when running this command |
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# to fix that, we need to delete the cached /match dataframes |
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# now that I'm writing this down, I realize this is pretty bad |
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# TODO |
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key = hash(",".join(inchikeys)) |
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cached_path = (MANDOS_SETTINGS.match_cache_path / str(key)).with_suffix(".feather") |
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if cached_path.exists(): |
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logger.info(f"Found ID matching results at {cached_path}") |
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return IdMatchFrame.read_feather(cached_path) |
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found_chembl: Dict[str, str] = {} |
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found_pubchem: Dict[str, str] = {} |
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if pubchem: |
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for inchikey in inchikeys: |
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try: |
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found_pubchem[inchikey] = str(Pubchem.fetch_data(inchikey).cid) |
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except CompoundNotFoundError: |
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logger.error(f"Did not find compound {inchikey}") |
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logger.debug(f"Did not find compound {inchikey}", exc_info=True) |
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if chembl: |
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for inchikey in inchikeys: |
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try: |
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found_chembl[inchikey] = ChemblUtils(Chembl).get_compound(inchikey).chid |
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except CompoundNotFoundError: |
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logger.error(f"Did not find compound {inchikey}") |
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logger.debug(f"Did not find compound {inchikey}", exc_info=True) |
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df = pd.DataFrame([pd.Series(dict(inchikey=c)) for c in inchikeys]) |
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df["chembl_id"] = df["inchikey"].map(found_chembl.get) |
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df["pubchem_id"] = df["inchikey"].map(found_pubchem.get) |
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df = IdMatchFrame(df) |
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df.to_feather(cached_path) |
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@classmethod |
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def read(cls, input_path: Path) -> Sequence[str]: |
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sep = cls._get_sep(input_path) |
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if sep in {"\t", ","}: |
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df = pd.read_csv(input_path, sep=sep) |
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return cls._from_df(df) |
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elif sep == "feather": |
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df = pd.read_feather(input_path) |
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return cls._from_df(df) |
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elif sep == "gz": |
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with gzip.open(input_path, "rt") as f: |
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return cls._from_txt(f.read()) |
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elif sep == "txt": |
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return cls._from_txt(input_path.read_text(encoding="utf8")) |
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else: |
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raise AssertionError(sep) |
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@classmethod |
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def _from_df(cls, df: pd.DataFrame) -> Sequence[str]: |
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df.columns = [c.lower() if isinstance(c, str) else c for c in df.columns] |
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if "inchikey" not in df.columns: |
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raise KeyError("For a CSV or TSV file, include a column called 'inchikey'") |
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return df["inchikey"].values.tolist() |
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@classmethod |
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def _from_txt(cls, text: str) -> Sequence[str]: |
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return [line.strip() for line in text.splitlines() if len(line.strip()) > 0] |
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@classmethod |
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def _get_sep(cls, input_path: Path) -> str: |
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if any((str(input_path).endswith(z) for z in {".tab", ".tsv", ".tab.gz", ".tsv.gz"})): |
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return "\t" |
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elif any((str(input_path).endswith(z) for z in {".csv", ".csv.gz"})): |
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return "," |
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elif any((str(input_path).endswith(z) for z in {".feather"})): |
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return "feather" |
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elif any((str(input_path).endswith(z) for z in {".txt.gz", ".lines.gz"})): |
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return "gz" |
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elif any((str(input_path).endswith(z) for z in {".txt", ".lines"})): |
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return "txt" |
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else: |
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raise ValueError(f"{input_path} should end in .tab, .tsv, .csv, .txt, .lines, or .gz") |
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class Searcher: |
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""" |
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Executes one or more searches and saves the results to CSV files. |
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Create and use once. |
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""" |
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def __init__(self, searches: Sequence[Search], input_path: Path): |
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""" |
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Constructor. |
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Args: |
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searches: |
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input_path: Path to the input file of one of the formats: |
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- .txt containing one InChI Key per line |
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- .csv, .tsv, .tab, csv.gz, .tsv.gz, .tab.gz, or .feather containing a column called inchikey |
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""" |
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self.what = searches |
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self.input_path: Optional[Path] = input_path |
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self.inchikeys: Optional[Sequence[str]] = [] |
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def search(self) -> Searcher: |
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""" |
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Performs the search, and writes data. |
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""" |
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if self.inchikeys is not None: |
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raise ValueError(f"Already ran a search") |
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self.inchikeys = SearcherUtils.read(self.input_path) |
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has_pubchem = any((isinstance(what, PubchemSearch) for what in self.what)) |
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has_chembl = any((isinstance(what, ChemblSearch) for what in self.what)) |
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# find the compounds first so the user knows what's missing before proceeding |
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SearcherUtils.dl(self.inchikeys, pubchem=has_pubchem, chembl=has_chembl) |
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for what in self.what: |
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output_path = self.output_path_of(what) |
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df = what.find_to_df(self.inchikeys) |
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df.to_csv(output_path) |
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metadata = NestedDotDict( |
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dict(key=what.key, search=what.search_class, params=what.get_params()) |
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) |
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metadata.write_json(output_path.with_suffix(".json")) |
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return self |
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def paths(self) -> Sequence[Path]: |
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return [self.output_path_of(what) for what in self.what] |
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def output_path_of(self, what: Search) -> Path: |
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parent = self.input_path.parent |
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child = self.input_path.stem + what.key + ".tab" |
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node = PathTools.sanitize_path_node(child) |
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if (parent / node).resolve() != (parent / child).resolve(): |
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logger.debug(f"Path {child} sanitized to {node}") |
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return parent / node |
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__all__ = ["Searcher", "IdMatchFrame", "SearcherUtils"] |
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dmyersturnbull /
mandos
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