mandos.entries.args.EntryArgs.key() - Code Metrics - Inspection of "feat: much better entries and logging" - dmyersturnbull/mandos - Measure and Improve Code Quality continuously with Scrutinizer

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Push — main ( cdf0f7...3de8e8 )

by Douglas

created 2021-04-03 02:06 UTC

mandos.entries.args.EntryArgs.key() A

↳ Parent: mandos.entries.args

Complexity

Conditions

Size

Total Lines	7
Code Lines	7

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	1
eloc	7
nop	1
dl	0
loc	7
rs	10
c	0
b	0
f	0

from inspect import cleandoc as doc

from pathlib import Path
from typing import Mapping, Optional

import typer


from mandos.model.chembl_support import DataValidityComment
from mandos.model.chembl_support.chembl_targets import TargetType, ConfidenceLevel
from mandos.search.chembl.target_traversal import TargetTraversalStrategies


def _stringify(keys: Mapping[str, str]):
    return ", ".join((k if v is None else f"{k} ({v.lower()})" for k, v in keys.items()))



class EntryArgs:


    path = typer.Argument(
        ...,
        exists=True,
        dir_okay=False,
        readable=True,
        help=doc(
            """
            The path to the input file.
            One of:

              (A) *.txt, *.lines, or *.list (optionally with .gz/.zip/.xz/.bz2)), with one InChI Key per line;


              (B) A *.csv, *.tsv, *.tab file (or .gz/.zip/.xz/.bz2 variant) with a column called 'inchikey'; OR


              (C) An Arrow *.feather file or Parquet *.snappy file with a column called 'inchikey'
        """
        ),
    )

    to = typer.Option(
        None,
        show_default=False,
        help=doc(
            """
            The path to the output file.
            If not set, chooses <input-path>-<search>.csv.gz
            The filename extension should be one of: .csv, .tsv, .tab, .json (with optional .gz/.bz2/.zip/.xz);

            .feather; .snappy (or .parquet); or .h5.
            Feather (.feather), Parquet (.snappy), and tab-delimited (.tsv.gz) are recommended.
            If H5, will add a new dataset named <key> to any existing archive.
            Will fail if the file exists unless the `--overwrite` flag is set.

            If only the filename extension is provided (e.g. --to '.feather'), will only change the output format

            (and filename extension).
        """
        ),
    )

    replace: bool = typer.Option(False, help="Replace output file if they exist. See also: --skip")

    skip: bool = typer.Option(
        False, help="Skip any search if the output file exists (only warns). See also: --replace"
    )

    in_cache: bool = typer.Option(
        False,
        help="Do not download any data. Fails if the needed data is not cached.",
        hidden=True,
    )

    verbose: bool = typer.Option(
        False,
        "--verbose",
        help="Configure logger to output INFO (use ``--quiet`` for less info)",
    )

    quiet: bool = typer.Option(
        False,
        "--quiet",
        help="Configure logger to output only ERROR (use ``--verbose`` for more info)",
    )

    log_path: Optional[Path] = typer.Option(
        None,
        "--log",
        help="""
            Also log to a file.
            The suffix can be .log, .log.gz, .log.zip, or .json, .json.gz, or .json.gz.
            You can prefix the path with :LEVEL: to control the level. For example, :INFO:out.log
        """,
    )

    no_setup: bool = typer.Option(
        False,
        "--no-setup",
        hidden=True,
        help="Skip setup, such as configuring logging.",
    )

    @staticmethod
    def key(name: str) -> typer.Option:

        return typer.Option(
            name,
            min=1,
            max=120,
            help="""
            A free-text unique key for the search.
            Should be a short, <60-character name that describes the search and any parameters.
            The output file will be named according to a 'sanitized' variant of this value.
            """,
        )

    test = typer.Option(
        False,
        "--check",
        help="Do not run searches; just check that the parameters are ok.",
    )

    taxa = typer.Option(
        "7742",
        show_default=False,
        help=doc(
            """
        The IDs or names of UniProt taxa, comma-separated.
        Taxon names and common names can be used for vertebrate species (where available).

        This can have a significant effect on searches. See the docs for more info.

        [default: 7742] (Euteleostomi)
        """
        ),
    )

    atc_level = typer.Option(
        "1,2,3,4", min=1, max=4, help="""List of ATC levels, comma-separated."""
    )

    min_cooccurrence_score = typer.Option(
        0.0,
        help="Minimum enrichment score, inclusive. See docs for more info.",
        min=0.0,
    )

    min_cooccurring_articles = typer.Option(
        0,
        help="Minimum number of articles for both the compound and object, inclusive.",
        min=0,
    )

    name_must_match = typer.Option(
        False,
        help=doc(
            """
        Require that the name of the compound(s) exactly matches the compound name on PubChem (case-insensitive)

        """
        ),
    )

    acute_effect_level = typer.Option(
        2,
        min=1,
        max=2,
        help="""
      The level in the ChemIDPlus hierarchy of effect names.
      Level 1: e.g. 'behavioral'
      Level 2: 'behavioral: excitement'
      """,
    )

    traversal_strategy = typer.Option(
        "@null",
        "--traversal",
        show_default=False,
        help=doc(
            """
        Target traversal strategy name, file, or class.
        Dictates the way the network of ChEMBL targets is traversed (from the annotated target as a source).

        Specifies the network links that are followed and which targets are 'accepted' for final annotations.

        This option has a dramatic effect on the search. See the docs for more info.

        Can be one of:
        (A) A standard strategy name, starting with @;
        (B) The path to a ``*.strat`` file; OR
        (C) The fully qualified name of a ``TargetTraversal``

        The standard traversal strategies are: {}

        [default: @null] (No traversal; targets as-is)
        """.format(
                "; ".join(TargetTraversalStrategies.standard_strategies())

            )
        ),
    )

    target_types = typer.Option(
        "@molecular",
        "--targets",
        show_default=False,
        help=doc(
            """
        The accepted target types, comma-separated.

        NOTE: This affects only the types are are accepted after traversal,
        and the types must be included in the traversal.
        This means that this must be AT LEAST as restrictive as the traversal strategy.

        The ChEMBL-defined types are:

          {}

        These special names are also accepted:

          - {}

        [default: @molecular]
        """.format(
                "; ".join([s.name for s in TargetType.all_types()]),

                "\n\n          - ".join(

                    [f"{k} ({v})" for k, v in TargetType.special_type_names().items()]
                ),
            )
        ),
    )

    min_confidence = typer.Option(
        3,
        "--confidence",
        min=0,
        max=9,
        show_default=False,
        help=doc(
            """
        Minimum target confidence score, inclusive.
        This is useful to modify in only some cases. More important options are min_pchembl and taxa.


        Values are: {}

        [default: 3]
        """.format(
                "; ".join([f"{s.value} ({s.name})" for s in ConfidenceLevel])

            )
        ),
    )

    relations = typer.Option(
        "<,<=,=",
        "--relations",
        show_default=False,
        help=doc(
            """
        Assay activity relations allowed, comma-separated.
        If post-processing yourself, consider including all.
        Values are: <, <=, =, >, >=, ~.
        [default: <,<=,=]
        """
        ),
    )

    min_pchembl = typer.Option(
        6.0,
        "--pchembl",
        min=0.0,
        show_default=False,
        help=doc(
            """
        Minimum pCHEMBL value, inclusive.
        If post-processing yourself, consider setting to 0.0.
        [default: 6.0]
        """
        ),
    )

    banned_flags = typer.Option(
        "@negative",
        show_default=False,
        help=doc(
            """
        Exclude activity annotations with data validity flags, comma-separated.
        It is rare to need to change this.

        Values are: {}.

        Special sets are:

          - @all (all flags are banned)

          - @negative ({})

          - @positive ({})

        [default: @negative]
        """.format(
                "; ".join([s.name for s in DataValidityComment]),

                ", ".join([s.name for s in DataValidityComment.negative_comments()]),

                ", ".join([s.name for s in DataValidityComment.positive_comments()]),

            ),
        ),
    )

    binding_search_name = typer.Option(
        None,
        help="""
        The fully qualified name of a class inheriting ``BindingSearch``.
        If specified, all parameters above are passed to its constructor.
        """,
    )

    chembl_trial = typer.Option(
        0,
        "--phase",
        show_default=False,
        help=doc(
            """
        Minimum phase of a clinical trial, inclusive.
        Values are: 0, 1, 2, 3.
        [default: 0]
        """
        ),
        min=0,
        max=3,
    )

    KNOWN_USEFUL_KEYS: Mapping[str, str] = {
        "weight": "Molecular Weight",
        "xlogp3": None,
        "hydrogen-bond-donors": "Hydrogen Bond Donor Count",
        "hydrogen-bond-acceptors": "Hydrogen Bond Acceptor Count",
        "rotatable-bonds": "Rotatable Bond Count",
        "exact-mass": None,
        "monoisotopic-mass": None,
        "tpsa": "Topological Polar Surface Area",
        "heavy-atoms": "Heavy Atom Count",
        "charge": "Formal Charge",
        "complexity": None,
    }
    KNOWN_USELESS_KEYS: Mapping[str, str] = {
        "components": "Covalently-Bonded Unit Count",
        "isotope-atoms": "Isotope Atom Count",
        "defined-atom-stereocenter-count": None,
        "undefined-atom-stereocenter-count": None,
        "defined-bond-stereocenter-count": None,
        "undefined-bond-stereocenter-count": None,
        "compound-is-canonicalized": None,
    }

    pubchem_computed_keys = typer.Option(
        "weight,xlogp3,tpsa,complexity,exact-mass,heavy-atom-count,charge",
        help="""
            The keys of the computed properties, comma-separated.
            Key names are case-insensitive and ignore punctuation like underscores and hyphens.

            Known keys are: {}

            Known, less-useful (metadata-like) keys are: {}
        """.format(
            _stringify(KNOWN_USEFUL_KEYS), _stringify(KNOWN_USELESS_KEYS)
        ),
    )


__all__ = ["EntryArgs"]


1			from inspect import cleandoc as doc
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2			from pathlib import Path
3			from typing import Mapping, Optional
4
5			import typer
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6
7			from mandos.model.chembl_support import DataValidityComment
8			from mandos.model.chembl_support.chembl_targets import TargetType, ConfidenceLevel
9			from mandos.search.chembl.target_traversal import TargetTraversalStrategies
10
11
12			def _stringify(keys: Mapping[str, str]):
13			return ", ".join((k if v is None else f"{k} ({v.lower()})" for k, v in keys.items()))
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14
15
16			class EntryArgs:
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17
18			path = typer.Argument(
19			...,
20			exists=True,
21			dir_okay=False,
22			readable=True,
23			help=doc(
24			"""
25			The path to the input file.
26			One of:
27
28			(A) .txt, .lines, or *.list (optionally with .gz/.zip/.xz/.bz2)), with one InChI Key per line;
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29
30			(B) A .csv, .tsv, *.tab file (or .gz/.zip/.xz/.bz2 variant) with a column called 'inchikey'; OR
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31
32			(C) An Arrow .feather file or Parquet .snappy file with a column called 'inchikey'
33			"""
34			),
35			)
36
37			to = typer.Option(
38			None,
39			show_default=False,
40			help=doc(
41			"""
42			The path to the output file.
43			If not set, chooses <input-path>-<search>.csv.gz
44			The filename extension should be one of: .csv, .tsv, .tab, .json (with optional .gz/.bz2/.zip/.xz);
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45			.feather; .snappy (or .parquet); or .h5.
46			Feather (.feather), Parquet (.snappy), and tab-delimited (.tsv.gz) are recommended.
47			If H5, will add a new dataset named <key> to any existing archive.
48			Will fail if the file exists unless the `--overwrite` flag is set.
49
50			If only the filename extension is provided (e.g. --to '.feather'), will only change the output format
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51			(and filename extension).
52			"""
53			),
54			)
55
56			replace: bool = typer.Option(False, help="Replace output file if they exist. See also: --skip")
57
58			skip: bool = typer.Option(
59			False, help="Skip any search if the output file exists (only warns). See also: --replace"
60			)
61
62			in_cache: bool = typer.Option(
63			False,
64			help="Do not download any data. Fails if the needed data is not cached.",
65			hidden=True,
66			)
67
68			verbose: bool = typer.Option(
69			False,
70			"--verbose",
71			help="Configure logger to output INFO (use ``--quiet`` for less info)",
72			)
73
74			quiet: bool = typer.Option(
75			False,
76			"--quiet",
77			help="Configure logger to output only ERROR (use ``--verbose`` for more info)",
78			)
79
80			log_path: Optional[Path] = typer.Option(
81			None,
82			"--log",
83			help="""
84			Also log to a file.
85			The suffix can be .log, .log.gz, .log.zip, or .json, .json.gz, or .json.gz.
86			You can prefix the path with :LEVEL: to control the level. For example, :INFO:out.log
87			""",
88			)
89
90			no_setup: bool = typer.Option(
91			False,
92			"--no-setup",
93			hidden=True,
94			help="Skip setup, such as configuring logging.",
95			)
96
97			@staticmethod
98			def key(name: str) -> typer.Option:
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99			return typer.Option(
100			name,
101			min=1,
102			max=120,
103			help="""
104			A free-text unique key for the search.
105			Should be a short, <60-character name that describes the search and any parameters.
106			The output file will be named according to a 'sanitized' variant of this value.
107			""",
108			)
109
110			test = typer.Option(
111			False,
112			"--check",
113			help="Do not run searches; just check that the parameters are ok.",
114			)
115
116			taxa = typer.Option(
117			"7742",
118			show_default=False,
119			help=doc(
120			"""
121			The IDs or names of UniProt taxa, comma-separated.
122			Taxon names and common names can be used for vertebrate species (where available).
123
124			This can have a significant effect on searches. See the docs for more info.
125
126			[default: 7742] (Euteleostomi)
127			"""
128			),
129			)
130
131			atc_level = typer.Option(
132			"1,2,3,4", min=1, max=4, help="""List of ATC levels, comma-separated."""
133			)
134
135			min_cooccurrence_score = typer.Option(
136			0.0,
137			help="Minimum enrichment score, inclusive. See docs for more info.",
138			min=0.0,
139			)
140
141			min_cooccurring_articles = typer.Option(
142			0,
143			help="Minimum number of articles for both the compound and object, inclusive.",
144			min=0,
145			)
146
147			name_must_match = typer.Option(
148			False,
149			help=doc(
150			"""
151			Require that the name of the compound(s) exactly matches the compound name on PubChem (case-insensitive)
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152			"""
153			),
154			)
155
156			acute_effect_level = typer.Option(
157			2,
158			min=1,
159			max=2,
160			help="""
161			The level in the ChemIDPlus hierarchy of effect names.
162			Level 1: e.g. 'behavioral'
163			Level 2: 'behavioral: excitement'
164			""",
165			)
166
167			traversal_strategy = typer.Option(
168			"@null",
169			"--traversal",
170			show_default=False,
171			help=doc(
172			"""
173			Target traversal strategy name, file, or class.
174			Dictates the way the network of ChEMBL targets is traversed (from the annotated target as a source).
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175			Specifies the network links that are followed and which targets are 'accepted' for final annotations.
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176			This option has a dramatic effect on the search. See the docs for more info.
177
178			Can be one of:
179			(A) A standard strategy name, starting with @;
180			(B) The path to a ``*.strat`` file; OR
181			(C) The fully qualified name of a ``TargetTraversal``
182
183			The standard traversal strategies are: {}
184
185			[default: @null] (No traversal; targets as-is)
186			""".format(
187			"; ".join(TargetTraversalStrategies.standard_strategies())
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188			)
189			),
190			)
191
192			target_types = typer.Option(
193			"@molecular",
194			"--targets",
195			show_default=False,
196			help=doc(
197			"""
198			The accepted target types, comma-separated.
199
200			NOTE: This affects only the types are are accepted after traversal,
201			and the types must be included in the traversal.
202			This means that this must be AT LEAST as restrictive as the traversal strategy.
203
204			The ChEMBL-defined types are:
205
206			{}
207
208			These special names are also accepted:
209
210			- {}
211
212			[default: @molecular]
213			""".format(
214			"; ".join([s.name for s in TargetType.all_types()]),
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215			"\n\n - ".join(
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216			[f"{k} ({v})" for k, v in TargetType.special_type_names().items()]
217			),
218			)
219			),
220			)
221
222			min_confidence = typer.Option(
223			3,
224			"--confidence",
225			min=0,
226			max=9,
227			show_default=False,
228			help=doc(
229			"""
230			Minimum target confidence score, inclusive.
231			This is useful to modify in only some cases. More important options are min_pchembl and taxa.
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232
233			Values are: {}
234
235			[default: 3]
236			""".format(
237			"; ".join([f"{s.value} ({s.name})" for s in ConfidenceLevel])
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238			)
239			),
240			)
241
242			relations = typer.Option(
243			"<,<=,=",
244			"--relations",
245			show_default=False,
246			help=doc(
247			"""
248			Assay activity relations allowed, comma-separated.
249			If post-processing yourself, consider including all.
250			Values are: <, <=, =, >, >=, ~.
251			[default: <,<=,=]
252			"""
253			),
254			)
255
256			min_pchembl = typer.Option(
257			6.0,
258			"--pchembl",
259			min=0.0,
260			show_default=False,
261			help=doc(
262			"""
263			Minimum pCHEMBL value, inclusive.
264			If post-processing yourself, consider setting to 0.0.
265			[default: 6.0]
266			"""
267			),
268			)
269
270			banned_flags = typer.Option(
271			"@negative",
272			show_default=False,
273			help=doc(
274			"""
275			Exclude activity annotations with data validity flags, comma-separated.
276			It is rare to need to change this.
277
278			Values are: {}.
279
280			Special sets are:
281
282			- @all (all flags are banned)
283
284			- @negative ({})
285
286			- @positive ({})
287
288			[default: @negative]
289			""".format(
290			"; ".join([s.name for s in DataValidityComment]),
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291			", ".join([s.name for s in DataValidityComment.negative_comments()]),
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292			", ".join([s.name for s in DataValidityComment.positive_comments()]),
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293			),
294			),
295			)
296
297			binding_search_name = typer.Option(
298			None,
299			help="""
300			The fully qualified name of a class inheriting ``BindingSearch``.
301			If specified, all parameters above are passed to its constructor.
302			""",
303			)
304
305			chembl_trial = typer.Option(
306			0,
307			"--phase",
308			show_default=False,
309			help=doc(
310			"""
311			Minimum phase of a clinical trial, inclusive.
312			Values are: 0, 1, 2, 3.
313			[default: 0]
314			"""
315			),
316			min=0,
317			max=3,
318			)
319
320			KNOWN_USEFUL_KEYS: Mapping[str, str] = {
321			"weight": "Molecular Weight",
322			"xlogp3": None,
323			"hydrogen-bond-donors": "Hydrogen Bond Donor Count",
324			"hydrogen-bond-acceptors": "Hydrogen Bond Acceptor Count",
325			"rotatable-bonds": "Rotatable Bond Count",
326			"exact-mass": None,
327			"monoisotopic-mass": None,
328			"tpsa": "Topological Polar Surface Area",
329			"heavy-atoms": "Heavy Atom Count",
330			"charge": "Formal Charge",
331			"complexity": None,
332			}
333			KNOWN_USELESS_KEYS: Mapping[str, str] = {
334			"components": "Covalently-Bonded Unit Count",
335			"isotope-atoms": "Isotope Atom Count",
336			"defined-atom-stereocenter-count": None,
337			"undefined-atom-stereocenter-count": None,
338			"defined-bond-stereocenter-count": None,
339			"undefined-bond-stereocenter-count": None,
340			"compound-is-canonicalized": None,
341			}
342
343			pubchem_computed_keys = typer.Option(
344			"weight,xlogp3,tpsa,complexity,exact-mass,heavy-atom-count,charge",
345			help="""
346			The keys of the computed properties, comma-separated.
347			Key names are case-insensitive and ignore punctuation like underscores and hyphens.
348
349			Known keys are: {}
350
351			Known, less-useful (metadata-like) keys are: {}
352			""".format(
353			_stringify(KNOWN_USEFUL_KEYS), _stringify(KNOWN_USELESS_KEYS)
354			),
355			)
356
357
358			__all__ = ["EntryArgs"]
359

dmyersturnbull / mandos

Push — main ( cdf0f7...3de8e8 )

mandos.entries.args.EntryArgs.key() A

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