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""" |
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Command-line interface for mandos. |
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""" |
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from __future__ import annotations |
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from pathlib import Path |
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from typing import Optional |
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import typer |
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from mandos.model.taxonomy import TaxonomyDf |
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from mandos.entry._entry_utils import EntryUtils |
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from mandos.entry.docs import Documenter |
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from mandos import logger |
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from mandos.entry.searchers import InputFrame |
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from mandos.model.utils.setup import MANDOS_SETUP |
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from typeddfs.utils import Utils as TypedDfsUtils |
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from mandos.analysis.filtration import Filtration |
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from mandos.analysis.reification import Reifier |
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from mandos.entry._common_args import CommonArgs |
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from mandos.entry._arg_utils import Arg, Opt, ArgUtils |
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from mandos.entry._common_args import CommonArgs as Ca |
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from mandos.entry.multi_searches import MultiSearch, SearchExplainDf |
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from mandos.entry.fillers import CompoundIdFiller, IdMatchFrame |
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from mandos.model.utils.resources import MandosResources |
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from mandos.model.apis.g2p_api import CachingG2pApi |
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from mandos.model.hits import HitFrame |
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from mandos.model.settings import MANDOS_SETTINGS |
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from mandos.model.taxonomy_caches import TaxonomyFactories |
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DEF_SUFFIX = MANDOS_SETTINGS.default_table_suffix |
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class _InsertedCommandListSingleton: |
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commands = None |
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class MiscCommands: |
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@staticmethod |
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def list_default_settings( |
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log: Optional[Path] = CommonArgs.log, |
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stderr: str = CommonArgs.stderr, |
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): |
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""" |
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Write the default settings to stdout. |
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""" |
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MANDOS_SETUP(log, stderr) |
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for k, v in MANDOS_SETTINGS.defaults().items(): |
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typer.echo(f"{k} = {v}") |
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@staticmethod |
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def document( |
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to: Path = Opt.out_file( |
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r""" |
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The path to write command documentation to. |
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The filename can end with .txt with optional compression (e.g. .txt.gz) |
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for formatted text output alongside --format. |
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Can can also use any table format: .feather; .snappy/.parquet; |
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or .csv, .tsv, .tab, .json, .flexwf (with optional .gz/.bz2/.zip/.xz). |
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[default: "commands-level<level>.txt"] |
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""" |
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), |
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style: str = Opt.val( |
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rf""" |
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The format for formatted text output. |
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This is ignored if --to is not a .txt file (or .txt.gz, etc.). |
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The choices are: "table", "document", {", ".join(TypedDfsUtils.table_formats())}. |
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"table" is a special style that saves in any machine-readable table format, such |
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as Feather or Parquet (determined by --to). |
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"document" is a special style that emits non-table-like flat text. |
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""", |
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"--style", |
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default="table", |
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), |
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width: int = Opt.val( |
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r""" |
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Max number of characters for a cell. |
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After that, the text is wrapped. |
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Only applies when writing formatted text (.txt, etc.). |
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[default: 40 if level > 1; 100 otherwise] |
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""", |
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default=None, |
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show_default=False, |
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), |
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level: int = Opt.val( |
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r""" |
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The amount of detail to output. |
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- 1 : show a 1-line description |
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- 2 : Show a 1-line description, plus parameter names |
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- 3 : Show the full description, plus parameter names, types, and 1-line descriptions |
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- 4 : Show the full description, plus parameter names types, and full descriptions |
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- 5 : Same as 4, but enable --hidden and --common |
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""", |
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default=4, |
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min=1, |
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max=5, |
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), |
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main_only: bool = Opt.flag(r"Only include main commands."), |
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search_only: bool = Opt.flag(r"Only include search commands."), |
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hidden: bool = Opt.flag(r"Show hidden commands."), |
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common: bool = Opt.flag( |
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r""" |
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Show common arguments and options. |
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Normally --log, --quiet, and --verbose are excluded, |
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along with path, --key, --to, --as-of for searches, |
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and the hidden flags for searches --check and --no-setup. |
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""" |
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), |
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replace: bool = Ca.replace, |
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log: Optional[Path] = Ca.log, |
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stderr: str = CommonArgs.stderr, |
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): |
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r""" |
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Write documentation on commands to a file. |
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""" |
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MANDOS_SETUP(log, stderr) |
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if level == 5: |
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hidden = common = True |
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if width is None and level == 1: |
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width = 100 |
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elif width is None: |
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width = 40 |
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if width == 0: |
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width = 9223372036854775807 |
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default = f"commands-level{level}.txt" |
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to = EntryUtils.adjust_filename(to, default, replace) |
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doc = Documenter( |
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level=level, |
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main=main_only, |
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search=search_only, |
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hidden=hidden, |
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common=common, |
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width=width, |
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) |
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doc.document(_InsertedCommandListSingleton.commands, to, style) |
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@staticmethod |
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def search( |
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path: Path = Ca.in_compound_table, |
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config: Path = Arg.in_file( |
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r""" |
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TOML config file. See docs. |
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""" |
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), |
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out_dir: Path = Ca.out_misc_dir, |
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log: Optional[Path] = Ca.log, |
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stderr: str = CommonArgs.stderr, |
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) -> None: |
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r""" |
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Run multiple searches. |
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""" |
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MANDOS_SETUP(log, stderr) |
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MultiSearch.build(path, out_dir, config).run() |
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@staticmethod |
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def detail_search( |
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config: Path = Arg.in_file( |
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r""" |
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TOML config file. See docs. |
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""" |
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), |
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to: Path = Opt.out_path( |
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rf""" |
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Write the table here. |
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{Ca.output_formats} |
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{ArgUtils.df_description(SearchExplainDf)} |
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[default: <config>-details{DEF_SUFFIX}] |
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""" |
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), |
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replace: bool = Ca.replace, |
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log: Optional[Path] = Ca.log, |
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stderr: str = CommonArgs.stderr, |
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) -> None: |
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r""" |
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Write details about a search (:search). |
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""" |
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MANDOS_SETUP(log, stderr) |
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to = EntryUtils.adjust_filename( |
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to, config.parent / (config.name + f"-details{DEF_SUFFIX}"), replace |
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) |
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search = MultiSearch.build(Path("."), Path("."), config) |
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df = search.to_table() |
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df.write_file(to) |
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logger.notice(f"Wrote search details to {to}") |
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@staticmethod |
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def serve( |
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port: int = Opt.val(r"Port to serve on", default=1540), |
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db: str = Opt.val("Name of the MySQL database", default="mandos"), |
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log: Optional[Path] = Ca.log, |
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stderr: str = CommonArgs.stderr, |
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) -> None: |
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r""" |
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Start a REST server. |
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215
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The connection information is stored in your global settings file. |
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""" |
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MANDOS_SETUP(log, stderr) |
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@staticmethod |
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def export_db( |
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path: Path = Ca.in_annotations_file, |
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db: str = Opt.val(r"Name of the MySQL database", default="mandos"), |
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host: str = Opt.val( |
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r"Database hostname (ignored if ``--socket`` is passed", default="127.0.0.1" |
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), |
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socket: Optional[str] = Opt.val("Path to a Unix socket (if set, ``--host`` is ignored)"), |
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user: Optional[str] = Opt.val("Database username (empty if not set)"), |
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password: Optional[str] = Opt.val("Database password (empty if not set)"), |
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as_of: Optional[str] = CommonArgs.as_of, |
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log: Optional[Path] = CommonArgs.log, |
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stderr: str = CommonArgs.stderr, |
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) -> None: |
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r""" |
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Export to a relational database. |
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236
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Saves data from Mandos search commands to a database for serving via REST. |
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238
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See also: ``:serve``. |
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""" |
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240
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MANDOS_SETUP(log, stderr) |
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241
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242
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@staticmethod |
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def init_db( |
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244
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db: str = Opt.val(r"Name of the MySQL database", default="mandos"), |
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245
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host: str = Opt.val( |
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246
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r"Database hostname (ignored if ``--socket`` is passed", default="127.0.0.1" |
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247
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), |
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248
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socket: Optional[str] = Opt.val("Path to a Unix socket (if set, ``--host`` is ignored)"), |
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249
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user: Optional[str] = Opt.val("Database username (empty if not set)"), |
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250
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password: Optional[str] = Opt.val("Database password (empty if not set)"), |
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251
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overwrite: bool = Opt.flag(r"Delete the database if it exists"), |
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252
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yes: bool = Ca.yes, |
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253
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log: Optional[Path] = CommonArgs.log, |
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254
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stderr: str = CommonArgs.stderr, |
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255
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) -> None: |
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256
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r""" |
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257
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Initialize an empty database. |
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258
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""" |
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259
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MANDOS_SETUP(log, stderr) |
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260
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261
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@staticmethod |
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262
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def fill( |
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263
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path: Path = Arg.in_file( |
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264
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rf""" |
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265
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The path to the file listing compounds by various IDs. |
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266
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|
267
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{Ca.input_formats} |
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268
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269
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Can use columns called 'inchikey', 'chembl_id', and 'pubchem_id'. |
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270
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Other columns are permitted but will not be used. |
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271
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272
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{ArgUtils.df_description(InputFrame)} |
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273
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""", |
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274
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), |
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275
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to: Path = Opt.out_path( |
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276
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rf""" |
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277
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|
A table of compounds and their database IDs will be written here. |
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278
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279
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{Ca.output_formats} |
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280
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281
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{ArgUtils.df_description(IdMatchFrame)} |
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282
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283
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[default: <path>-ids-<start-time>{DEF_SUFFIX}] |
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284
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""" |
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285
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), |
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286
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no_pubchem: bool = Opt.flag("Do not use PubChem.", "--no-pubchem"), |
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287
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no_chembl: bool = Opt.flag("Do not use ChEMBL.", "--no-chembl"), |
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288
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replace: bool = Ca.replace, |
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289
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log: Optional[Path] = Ca.log, |
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290
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stderr: str = CommonArgs.stderr, |
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291
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) -> None: |
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292
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r""" |
|
293
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|
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Fill in missing IDs from existing compound data. |
|
294
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295
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The idea is to find a ChEMBL ID, a PubChem ID, and parent-compound InChI/InChI Key. |
|
296
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Useful to check compound/ID associations before running a search. |
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297
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298
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To be filled, each row must should have a non-null value for |
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299
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"inchikey", "chembl_id", and/or "pubchem_id". |
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300
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"inchi" will be used but not to match to PubChem and ChEMBL. |
|
301
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302
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No existing columns will be dropped or modified. |
|
303
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Any conflicting column will be renamed to 'origin_<column>'. |
|
304
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E.g. 'inchikey' will be renamed to 'origin_inchikey'. |
|
305
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(Do not include a column beginning with 'origin_'). |
|
306
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|
307
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Final columns (assuming --no-chembl and --no-pubchem) will include: |
|
308
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|
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inchikey, inchi, pubchem_id, chembl_id, pubchem_inch, chembl_inchi, |
|
309
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pubchem_inchikey, and chembl_inchikey. |
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310
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The "inchikey" and "inchikey" columns will be the "best" available: |
|
311
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|
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chembl (preferred), then pubchem, then your source inchikey column. |
|
312
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|
In cases where PubChem and ChEMBL differ, an error will be logged. |
|
313
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|
You can always check the columns "origin_inchikey" (yours), |
|
314
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|
|
chembl_inchikey, and pubchem_inchikey. |
|
315
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|
316
|
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|
The steps are: |
|
317
|
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|
318
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|
|
- If "chembl_id" or "pubchem_id" is non-null, uses that to find an InChI Key (for each). |
|
319
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|
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|
320
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|
|
- Otherwise, if only "inchikey" is non-null, uses it to find ChEMBL and PubChem records. |
|
321
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|
322
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|
|
- Log an error if the inchikeys or inchis differ between PubChem and ChEMBL. |
|
323
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|
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|
324
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|
|
- Set the final "inchi" and "inchikey" to the best choice, |
|
325
|
|
|
falling back to the input inchi and inchikey if they are missing. |
|
326
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|
|
""" |
|
327
|
|
|
MANDOS_SETUP(log, stderr) |
|
328
|
|
|
default = str(Path(path).with_suffix("")) + "-filled" + "".join(path.suffixes) |
|
329
|
|
|
to = EntryUtils.adjust_filename(to, default, replace) |
|
330
|
|
|
df = IdMatchFrame.read_file(path) |
|
|
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|
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|
331
|
|
|
df = CompoundIdFiller(chembl=not no_chembl, pubchem=not no_pubchem).fill(df) |
|
|
|
|
|
|
332
|
|
|
df.write_file(to) |
|
333
|
|
|
|
|
334
|
|
|
@staticmethod |
|
335
|
|
|
def cache_data( |
|
336
|
|
|
path: Path = Ca.in_compound_table, |
|
|
|
|
|
|
337
|
|
|
no_pubchem: bool = Opt.flag(r"Do not download data from PubChem", "--no-pubchem"), |
|
|
|
|
|
|
338
|
|
|
no_chembl: bool = Opt.flag(r"Do not fetch IDs from ChEMBL", "--no_chembl"), |
|
|
|
|
|
|
339
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
340
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
341
|
|
|
) -> None: |
|
342
|
|
|
r""" |
|
343
|
|
|
Fetch and cache compound data. |
|
344
|
|
|
|
|
345
|
|
|
Useful to freeze data before running a search. |
|
346
|
|
|
""" |
|
347
|
|
|
MANDOS_SETUP(log, stderr) |
|
348
|
|
|
logger.error(f"Not implemented fully yet.") |
|
|
|
|
|
|
349
|
|
|
df = IdMatchFrame.read_file(path) |
|
|
|
|
|
|
350
|
|
|
df = CompoundIdFiller(chembl=not no_chembl, pubchem=not no_pubchem).fill(df) |
|
|
|
|
|
|
351
|
|
|
logger.notice(f"Done caching.") |
|
|
|
|
|
|
352
|
|
|
|
|
353
|
|
|
@staticmethod |
|
354
|
|
|
def export_taxa( |
|
|
|
|
|
|
355
|
|
|
taxa: str = Ca.taxa, |
|
|
|
|
|
|
356
|
|
|
forbid: str = Opt.val( |
|
|
|
|
|
|
357
|
|
|
r"""Exclude descendents of these taxa IDs or names (comma-separated).""", default="" |
|
358
|
|
|
), |
|
359
|
|
|
to: Path = typer.Option( |
|
|
|
|
|
|
360
|
|
|
None, |
|
361
|
|
|
help=rf""" |
|
362
|
|
|
Where to export. |
|
363
|
|
|
|
|
364
|
|
|
{Ca.output_formats} |
|
365
|
|
|
|
|
366
|
|
|
{ArgUtils.df_description(TaxonomyDf)} |
|
367
|
|
|
|
|
368
|
|
|
[default: ./<taxa>-<datetime>{DEF_SUFFIX}] |
|
369
|
|
|
""", |
|
370
|
|
|
), |
|
371
|
|
|
replace: bool = Ca.replace, |
|
|
|
|
|
|
372
|
|
|
in_cache: bool = CommonArgs.in_cache, |
|
|
|
|
|
|
373
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
374
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
375
|
|
|
): |
|
376
|
|
|
""" |
|
377
|
|
|
Export a taxonomic tree to a table. |
|
378
|
|
|
|
|
379
|
|
|
Writes a taxonomy of given taxa and their descendants to a table. |
|
380
|
|
|
""" |
|
381
|
|
|
MANDOS_SETUP(log, stderr) |
|
382
|
|
|
concat = taxa + "-" + forbid |
|
383
|
|
|
taxa = ArgUtils.parse_taxa(taxa) |
|
384
|
|
|
forbid = ArgUtils.parse_taxa(forbid) |
|
385
|
|
|
default = concat + "-" + MandosResources.start_timestamp_filesys + DEF_SUFFIX |
|
386
|
|
|
to = EntryUtils.adjust_filename(to, default, replace) |
|
387
|
|
|
my_tax = TaxonomyFactories.get_smart_taxonomy(taxa, forbid) |
|
388
|
|
|
my_tax = my_tax.to_df() |
|
389
|
|
|
my_tax.write_file(to, mkdirs=True) |
|
390
|
|
|
|
|
391
|
|
|
@staticmethod |
|
392
|
|
|
def cache_taxa( |
|
393
|
|
|
taxa: str = Opt.val( |
|
|
|
|
|
|
394
|
|
|
r""" |
|
395
|
|
|
Either "vertebrata", "all", or a comma-separated list of UniProt taxon IDs. |
|
396
|
|
|
|
|
397
|
|
|
"all" is only valid when --replace is passed; |
|
398
|
|
|
this will regenerate all taxonomy files that are found in the cache. |
|
399
|
|
|
""", |
|
400
|
|
|
default="", |
|
401
|
|
|
), |
|
402
|
|
|
replace: bool = Ca.replace, |
|
|
|
|
|
|
403
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
404
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
405
|
|
|
) -> None: |
|
406
|
|
|
""" |
|
407
|
|
|
Prep a new taxonomy file for use in mandos. |
|
408
|
|
|
|
|
409
|
|
|
With --replace set, will delete any existing file. |
|
410
|
|
|
This can be useful to make sure your cached taxonomy is up-to-date before running. |
|
411
|
|
|
|
|
412
|
|
|
Downloads and converts a tab-separated file from UniProt. |
|
413
|
|
|
(To find manually, follow the ``All lower taxonomy nodes`` link and click ``Download``.) |
|
414
|
|
|
Then applies fixes and reduces the file size, creating a new file alongside. |
|
415
|
|
|
Puts both the raw data and fixed data in the cache under ``~/.mandos/taxonomy/``. |
|
416
|
|
|
""" |
|
417
|
|
|
if taxa == "": |
|
418
|
|
|
logger.info("No taxa were specified. No data downloaded.") |
|
419
|
|
|
return |
|
420
|
|
|
if ( |
|
421
|
|
|
taxa not in ["all", "vertebrata"] |
|
|
|
|
|
|
422
|
|
|
and not taxa.replace(",", "").replace(" ", "").isdigit() |
|
|
|
|
|
|
423
|
|
|
): |
|
424
|
|
|
raise ValueError(f"Use either 'all', 'vertebrata', or a UniProt taxon ID") |
|
|
|
|
|
|
425
|
|
|
if taxa == "all" and not replace: |
|
426
|
|
|
raise ValueError(f"Use --replace with taxon 'all'") |
|
|
|
|
|
|
427
|
|
|
MANDOS_SETUP(log, stderr) |
|
428
|
|
|
factory = TaxonomyFactories.from_uniprot() |
|
429
|
|
|
if taxa == "all" and replace: |
|
430
|
|
|
listed = TaxonomyFactories.list_cached_files() |
|
431
|
|
|
for p in listed.values(): |
|
|
|
|
|
|
432
|
|
|
p.unlink() |
|
433
|
|
|
factory.rebuild_vertebrata() |
|
434
|
|
|
for t in listed.keys(): |
|
|
|
|
|
|
435
|
|
|
factory.load_dl(t) |
|
436
|
|
|
elif taxa == "vertebrata" and (replace or not factory.resolve_path(7742).exists()): |
|
437
|
|
|
factory.rebuild_vertebrata() |
|
438
|
|
|
elif taxa == "vertebrata": |
|
439
|
|
|
factory.load_vertebrate(7742) # should usually do nothing |
|
440
|
|
|
else: |
|
441
|
|
|
for taxon in [int(t.strip()) for t in taxa.split(",")]: |
|
442
|
|
|
factory.delete_exact(taxon) |
|
443
|
|
|
|
|
444
|
|
|
@staticmethod |
|
445
|
|
|
def cache_g2p( |
|
446
|
|
|
replace: bool = Ca.replace, |
|
|
|
|
|
|
447
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
448
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
449
|
|
|
) -> None: |
|
450
|
|
|
""" |
|
451
|
|
|
Caches GuideToPharmacology data. |
|
452
|
|
|
|
|
453
|
|
|
With --replace set, will overwrite existing cached data. |
|
454
|
|
|
Data will generally be stored under``~/.mandos/g2p/``. |
|
455
|
|
|
""" |
|
456
|
|
|
MANDOS_SETUP(log, stderr) |
|
457
|
|
|
api = CachingG2pApi(MANDOS_SETTINGS.g2p_cache_path) |
|
458
|
|
|
api.download(force=replace) |
|
459
|
|
|
|
|
460
|
|
|
@staticmethod |
|
461
|
|
|
def cache_clear( |
|
462
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
463
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
464
|
|
|
yes: bool = CommonArgs.yes, |
|
|
|
|
|
|
465
|
|
|
) -> None: |
|
466
|
|
|
""" |
|
467
|
|
|
Deletes all cached data. |
|
468
|
|
|
""" |
|
469
|
|
|
MANDOS_SETUP(log, stderr) |
|
470
|
|
|
typer.echo(f"Will recursively delete all of these paths:") |
|
|
|
|
|
|
471
|
|
|
for p in MANDOS_SETTINGS.all_cache_paths: |
|
|
|
|
|
|
472
|
|
|
typer.echo(f" {p}") |
|
473
|
|
|
if not yes: |
|
474
|
|
|
typer.confirm("Delete?", abort=True) |
|
475
|
|
|
for p in MANDOS_SETTINGS.all_cache_paths: |
|
|
|
|
|
|
476
|
|
|
p.unlink(missing_ok=True) |
|
477
|
|
|
logger.notice("Deleted all cached data") |
|
478
|
|
|
|
|
479
|
|
|
@staticmethod |
|
480
|
|
|
def concat( |
|
|
|
|
|
|
481
|
|
|
path: Path = Arg.in_dir( |
|
|
|
|
|
|
482
|
|
|
rf""" |
|
483
|
|
|
Directory containing results from a mandos search. |
|
484
|
|
|
|
|
485
|
|
|
{Ca.input_formats} |
|
486
|
|
|
""" |
|
487
|
|
|
), |
|
488
|
|
|
to: Optional[Path] = Ca.out_annotations_file, |
|
|
|
|
|
|
489
|
|
|
replace: bool = Ca.replace, |
|
|
|
|
|
|
490
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
491
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
492
|
|
|
) -> None: |
|
493
|
|
|
r""" |
|
494
|
|
|
Concatenate Mandos annotation files into one. |
|
495
|
|
|
|
|
496
|
|
|
Note that ``:search`` automatically performs this; |
|
497
|
|
|
this is needed only if you want to combine results from multiple independent searches. |
|
498
|
|
|
""" |
|
499
|
|
|
MANDOS_SETUP(log, stderr) |
|
500
|
|
|
default = path / ("concat" + DEF_SUFFIX) |
|
501
|
|
|
to = EntryUtils.adjust_filename(to, default, replace) |
|
502
|
|
|
for found in path.iterdir(): |
|
|
|
|
|
|
503
|
|
|
pass |
|
504
|
|
|
|
|
505
|
|
|
@staticmethod |
|
506
|
|
|
def filter( |
|
|
|
|
|
|
507
|
|
|
path: Path = Ca.out_annotations_file, |
|
|
|
|
|
|
508
|
|
|
by: Optional[Path] = Arg.in_file( |
|
|
|
|
|
|
509
|
|
|
r""" |
|
510
|
|
|
Path to a file containing filters. |
|
511
|
|
|
|
|
512
|
|
|
See the docs for more info. |
|
513
|
|
|
""" |
|
514
|
|
|
), |
|
515
|
|
|
to: Optional[Path] = Ca.out_annotations_file, |
|
|
|
|
|
|
516
|
|
|
replace: bool = Ca.replace, |
|
|
|
|
|
|
517
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
518
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
519
|
|
|
) -> None: |
|
520
|
|
|
""" |
|
521
|
|
|
Filters by simple expressions. |
|
522
|
|
|
""" |
|
523
|
|
|
MANDOS_SETUP(log, stderr) |
|
524
|
|
|
default = str(path) + "-filter-" + by.stem + DEF_SUFFIX |
|
525
|
|
|
to = EntryUtils.adjust_filename(to, default, replace) |
|
526
|
|
|
df = HitFrame.read_file(path) |
|
|
|
|
|
|
527
|
|
|
Filtration.from_file(by).apply(df).write_file(to) |
|
528
|
|
|
|
|
529
|
|
|
@staticmethod |
|
530
|
|
|
def export_state( |
|
|
|
|
|
|
531
|
|
|
path: Path = Ca.in_annotations_file, |
|
|
|
|
|
|
532
|
|
|
to: Optional[Path] = Opt.out_path( |
|
|
|
|
|
|
533
|
|
|
""" |
|
534
|
|
|
Path to the output file. |
|
535
|
|
|
|
|
536
|
|
|
Valid formats and filename suffixes are .nt and .txt with an optional .gz, .zip, or .xz. |
|
537
|
|
|
If only a filename suffix is provided, will use that suffix with the default directory. |
|
538
|
|
|
If no suffix is provided, will interpret the path as a directory and use the default filename. |
|
|
|
|
|
|
539
|
|
|
Will fail if the file exists and ``--replace`` is not set. |
|
540
|
|
|
|
|
541
|
|
|
[default: <path>-statements.nt] |
|
542
|
|
|
""" |
|
543
|
|
|
), |
|
544
|
|
|
replace: bool = Ca.replace, |
|
|
|
|
|
|
545
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
546
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
547
|
|
|
) -> None: |
|
548
|
|
|
""" |
|
549
|
|
|
Output simple N-triples statements. |
|
550
|
|
|
|
|
551
|
|
|
Each statement is of this form, where the InChI Key refers to the input data: |
|
552
|
|
|
|
|
553
|
|
|
`"InChI Key" "predicate" "object" .` |
|
554
|
|
|
""" |
|
555
|
|
|
MANDOS_SETUP(log, stderr) |
|
556
|
|
|
default = f"{path}-statements.nt" |
|
557
|
|
|
to = EntryUtils.adjust_filename(to, default, replace) |
|
558
|
|
|
hits = HitFrame.read_file(path).to_hits() |
|
559
|
|
|
with to.open() as f: |
|
|
|
|
|
|
560
|
|
|
for hit in hits: |
|
561
|
|
|
f.write(hit.to_triple.n_triples) |
|
562
|
|
|
|
|
563
|
|
|
@staticmethod |
|
564
|
|
|
def export_reify( |
|
|
|
|
|
|
565
|
|
|
path: Path = Ca.in_annotations_file, |
|
|
|
|
|
|
566
|
|
|
to: Optional[Path] = Opt.out_path( |
|
|
|
|
|
|
567
|
|
|
r""" |
|
568
|
|
|
Path to the output file. |
|
569
|
|
|
|
|
570
|
|
|
The filename suffix should be either .nt (N-triples) or .ttl (Turtle), |
|
571
|
|
|
with an optional .gz, .zip, or .xz. |
|
572
|
|
|
If only a filename suffix is provided, will use that suffix with the default directory. |
|
573
|
|
|
If no suffix is provided, will interpret the path as a directory but use the default filename. |
|
|
|
|
|
|
574
|
|
|
Will fail if the file exists and ``--replace`` is not set. |
|
575
|
|
|
|
|
576
|
|
|
[default: <path>-reified.nt] |
|
577
|
|
|
""" |
|
578
|
|
|
), |
|
579
|
|
|
replace: bool = Ca.replace, |
|
|
|
|
|
|
580
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
581
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
582
|
|
|
) -> None: |
|
583
|
|
|
""" |
|
584
|
|
|
Outputs reified semantic triples. |
|
585
|
|
|
""" |
|
586
|
|
|
MANDOS_SETUP(log, stderr) |
|
587
|
|
|
default = f"{path}-reified.nt" |
|
588
|
|
|
to = EntryUtils.adjust_filename(to, default, replace) |
|
589
|
|
|
hits = HitFrame.read_file(path).to_hits() |
|
590
|
|
|
with to.open() as f: |
|
|
|
|
|
|
591
|
|
|
for triple in Reifier().reify(hits): |
|
592
|
|
|
f.write(triple.n_triples) |
|
593
|
|
|
|
|
594
|
|
|
@staticmethod |
|
595
|
|
|
def export_copy( |
|
|
|
|
|
|
596
|
|
|
path: Path = Ca.in_annotations_file, |
|
|
|
|
|
|
597
|
|
|
to: Optional[Path] = Opt.out_path( |
|
|
|
|
|
|
598
|
|
|
rf""" |
|
599
|
|
|
Path to the output file. |
|
600
|
|
|
|
|
601
|
|
|
{Ca.output_formats} |
|
602
|
|
|
|
|
603
|
|
|
[default: <path.parent>/export{DEF_SUFFIX}] |
|
604
|
|
|
""" |
|
605
|
|
|
), |
|
606
|
|
|
replace: bool = Ca.replace, |
|
|
|
|
|
|
607
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
608
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
609
|
|
|
) -> None: |
|
610
|
|
|
""" |
|
611
|
|
|
Copies and/or converts annotation files. |
|
612
|
|
|
|
|
613
|
|
|
Example: ``:export:copy --to .snappy`` to highly compress a data set. |
|
614
|
|
|
""" |
|
615
|
|
|
MANDOS_SETUP(log, stderr) |
|
616
|
|
|
default = path.parent / DEF_SUFFIX |
|
617
|
|
|
to = EntryUtils.adjust_filename(to, default, replace) |
|
618
|
|
|
df = HitFrame.read_file(path) |
|
|
|
|
|
|
619
|
|
|
df.write_file(to) |
|
620
|
|
|
|
|
621
|
|
|
|
|
622
|
|
|
__all__ = ["MiscCommands"] |
|
623
|
|
|
|
dmyersturnbull /
mandos
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