mandos.entry.tools.multi_searches.CmdRunner.key() - Code Metrics - Inspection of "fix: misc" - dmyersturnbull/mandos - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Push — main ( 2e1b6b...3a0c28 )

by Douglas

created 2021-11-04 01:01 UTC

mandos.entry.tools.multi_searches.CmdRunner.key() A

↳ Parent: mandos.entry.tools.multi_searches

Complexity

Conditions

Size

Total Lines	3
Code Lines	3

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	1
eloc	3
nop	1
dl	0
loc	3
rs	10
c	0
b	0
f	0

"""
Runner.
"""

from __future__ import annotations

from dataclasses import dataclass
from datetime import datetime
from pathlib import Path
from typing import Any, Mapping, MutableMapping, Optional, Sequence, Type, Union

import pandas as pd

import typer

from pocketutils.core.exceptions import InjectionError, PathExistsError

from typeddfs import Checksums, TypedDfs

from typeddfs.abs_dfs import AbsDf


from mandos.entry.abstract_entries import Entry
from mandos.entry.api_singletons import Apis

from mandos.entry.entry_commands import Entries
from mandos.entry.utils._arg_utils import EntryUtils
from mandos.model.hit_dfs import HitDf
from mandos.model.settings import SETTINGS
from mandos.model.utils.setup import LOG_SETUP, logger

cli = typer.Typer()

EntriesByCmd: MutableMapping[str, Type[Entry]] = {e.cmd(): e for e in Entries}

# these are not permitted in individual searches
forbidden_keys = {"to", "stderr", "log", "replace", "proceed"}

SearchExplainDf = (
    TypedDfs.typed("SearchExplainDf")
    .require("key", "search", "source", dtype=str)
    .require("desc", "args", dtype=str)
    .strict()
    .secure()
).build()


def _no_duplicate_keys(self: AbsDf) -> Optional[str]:
    group = self[["key"]].groupby("key").count().to_dict()
    bad = {k for k, v in group.items() if v > 1}
    if len(bad) > 0:
        return f"Duplicate keys: {', '.join(bad)}"
    return None


def _no_illegal_cols(self: AbsDf) -> Optional[str]:
    illegal = {c for c in ["to", "path"] if c in self.columns}
    if len(illegal) > 0:
        return f"Illegal keys {', '.join(illegal)}"
    return None


SearchConfigDf = (
    TypedDfs.typed("SearchConfigDf")
    .require("key", "source", dtype=str)
    .verify(_no_duplicate_keys)
    .verify(_no_illegal_cols)
    .add_read_kwargs("toml", aot="search")
    .add_write_kwargs("toml", aot="search")
    .secure()
    .build()
)


@dataclass(frozen=True, repr=True)

class MultiSearch:
    config: SearchConfigDf
    input_path: Path
    out_dir: Path
    suffix: str
    restart: bool
    proceed: bool
    log_path: Optional[Path]

    @property
    def final_path(self) -> Path:

        name = "search_" + self.input_path.name + self.suffix
        return self.out_dir / name

    @property
    def is_complete(self):

        return Checksums().get_filesum_of_file(self.final_path).exists()

    @property
    def doc_path(self) -> Path:

        return Path(str(self.final_path.with_suffix("")) + ".doc.tsv")

    def test(self) -> None:

        self._build_and_test()

    def run(self) -> None:

        if self.final_path.exists():
            raise PathExistsError(f"{self.final_path} exists")
        commands = self._build_and_test()
        # start!
        for cmd in commands:
            cmd.run()
        logger.notice("Done with all searches!")
        self._write_final(commands)

    def _write_final(self, commands: Sequence[CmdRunner]):
        # write the final file
        df = HitDf(pd.concat([HitDf.read_file(cmd.output_path) for cmd in commands]))

        now = datetime.now().isoformat(timespec="milliseconds")
        docs = self.get_docs(commands)
        SearchExplainDf([pd.Series(x) for x in docs]).write_file(self.doc_path)
        df = df.set_attrs(commands=docs, written=now)

        df.write_file(
            self.final_path.resolve(),
            dir_hash=True,
            file_hash=True,
            attrs=True,
            overwrite=self.restart,
        )
        logger.notice(f"Concatenated results to {self.final_path}")

    def _build_and_test(self) -> Sequence[CmdRunner]:
        # build up the list of Entry classes first, and run ``test`` on each one
        # that's to check that the parameters are correct before running anything
        logger.info("Building commands...")
        commands = self._build_commands()
        if len(commands) == 0:
            logger.warning(f"No searches — nothing to do")

            return []
        # build and test
        for cmd in commands:
            try:
                logger.info(f"Testing {cmd.key} ({cmd.cmd.__name__})")
                cmd.test()
            except Exception:
                logger.error(f"Bad search {cmd}")
                raise
        logger.success("Searches look ok")
        return commands

    def _build_commands(self) -> Sequence[CmdRunner]:
        commands = {}
        for i in range(len(self.config)):
            data = {
                k: v
                for k, v in self.config.iloc[i].to_dict().items()
                if v is not None and not pd.isna(v)
            }
            cmd = self._build_command(data)
            if cmd is not None:
                commands[cmd.key] = cmd
        return list(commands.values())

    def _build_command(self, data):
        key = data["key"]
        with logger.contextualize(key=key):
            default_to = self.out_dir / (key + SETTINGS.table_suffix)
            # not actually replacing -- we're just pretending so we can call adjust_filename
            data["to"] = EntryUtils.adjust_filename(
                None, default=default_to, replace=True, quiet=True
            )
            data["log"] = self._get_log_path(key)
            data["stderr"] = None  # MANDOS_SETUP.main.level
            cmd = CmdRunner.build(data, self.input_path, restart=self.restart, proceed=self.proceed)
        return cmd

    def get_docs(self, commands: Sequence[CmdRunner]) -> Sequence[Mapping[str, Any]]:
class Foo:
    def some_method(self, x, y):
        return x + y;
        rows = []
        for cmd in commands:
            st = cmd.cmd.get_search_type()

            name = st.search_name()
            src = st.primary_data_source()
            desc = cmd.cmd.describe()
            args = " ".join([f'{k}="{v}"' for k, v in cmd.params.items()])
            ser = dict(key=cmd.key, search=name, source=src, desc=desc, args=args)
            rows.append(ser)
        return rows

    def _get_log_path(self, key: str) -> Path:
        if self.log_path is None:

            suffix = SETTINGS.log_suffix
            return self.out_dir / (key + suffix)
        else:
            suffix = LOG_SETUP.guess_file_sink_info(self.log_path).suffix
            log_base = self.log_path.name[: -len(suffix)]
            return self.log_path.parent / (log_base + "_" + key + suffix)


@dataclass(frozen=True, repr=True)

class CmdRunner:
    cmd: Type[Entry]
    params: MutableMapping[str, Union[int, str, float]]
    input_path: Path

    @property
    def key(self) -> str:

        return self.params["key"]

    @property
    def output_path(self) -> Path:

        return Path(self.params["to"])

    def test(self) -> None:

        with logger.contextualize(key=self.key):
            self.cmd.test(self.input_path, **self.params)

    def run(self) -> None:

        with logger.contextualize(key=self.key):
            self.cmd.run(self.input_path, **self.params)

    @classmethod
    def build(

        cls, data: Mapping[str, Any], input_path: Path, *, restart: bool, proceed: bool

    ) -> CmdRunner:
        key, cmd = data["key"], data["source"]
        try:
            cmd = EntriesByCmd[cmd]
        except KeyError:
            raise InjectionError(f"Search command {cmd} (key {key}) does not exist") from None
        # we need to explicitly add the defaults from the OptionInfo instances
        # add our new stuff after that
        params = {
            **cmd.default_param_values(),
            **dict(replace=restart, proceed=proceed),
            **{k: v for k, v in data.items() if k != "source"},
        }
        return CmdRunner(cmd, params, input_path)


__all__ = ["MultiSearch", "SearchExplainDf", "SearchConfigDf"]


1			"""
2			Runner.
3			"""
4
5			from __future__ import annotations
6
7			from dataclasses import dataclass
8			from datetime import datetime
9			from pathlib import Path
10			from typing import Any, Mapping, MutableMapping, Optional, Sequence, Type, Union
11
12			import pandas as pd
			0 ignored issues – show introduced 2021-10-12 03:37 UTC by Report Bug Copy Issue Report Unable to import 'pandas' Loading history...
13			import typer
			0 ignored issues – show introduced 2021-03-21 02:08 UTC by Report Bug Copy Issue Report Unable to import 'typer' Loading history...
14			from pocketutils.core.exceptions import InjectionError, PathExistsError
			0 ignored issues – show introduced 2021-10-12 03:37 UTC by Report Bug Copy Issue Report Unable to import 'pocketutils.core.exceptions' Loading history...
15			from typeddfs import Checksums, TypedDfs
			0 ignored issues – show introduced 2021-07-05 18:49 UTC by Report Bug Copy Issue Report Unable to import 'typeddfs' Loading history...
16			from typeddfs.abs_dfs import AbsDf
			0 ignored issues – show introduced 2021-09-29 03:10 UTC by Report Bug Copy Issue Report Unable to import 'typeddfs.abs_dfs' Loading history...
17
18			from mandos.entry.abstract_entries import Entry
19			from mandos.entry.api_singletons import Apis
			0 ignored issues – show Unused Code introduced 2021-10-28 02:14 UTC by Report Bug Copy Issue Report Unused Apis imported from mandos.entry.api_singletons Loading history...
20			from mandos.entry.entry_commands import Entries
21			from mandos.entry.utils._arg_utils import EntryUtils
22			from mandos.model.hit_dfs import HitDf
23			from mandos.model.settings import SETTINGS
24			from mandos.model.utils.setup import LOG_SETUP, logger
25
26			cli = typer.Typer()
27
28			EntriesByCmd: MutableMapping[str, Type[Entry]] = {e.cmd(): e for e in Entries}
29
30			# these are not permitted in individual searches
31			forbidden_keys = {"to", "stderr", "log", "replace", "proceed"}
32
33			SearchExplainDf = (
34			TypedDfs.typed("SearchExplainDf")
35			.require("key", "search", "source", dtype=str)
36			.require("desc", "args", dtype=str)
37			.strict()
38			.secure()
39			).build()
40
41
42			def _no_duplicate_keys(self: AbsDf) -> Optional[str]:
43			group = self[["key"]].groupby("key").count().to_dict()
44			bad = {k for k, v in group.items() if v > 1}
45			if len(bad) > 0:
46			return f"Duplicate keys: {', '.join(bad)}"
47			return None
48
49
50			def _no_illegal_cols(self: AbsDf) -> Optional[str]:
51			illegal = {c for c in ["to", "path"] if c in self.columns}
52			if len(illegal) > 0:
53			return f"Illegal keys {', '.join(illegal)}"
54			return None
55
56
57			SearchConfigDf = (
58			TypedDfs.typed("SearchConfigDf")
59			.require("key", "source", dtype=str)
60			.verify(_no_duplicate_keys)
61			.verify(_no_illegal_cols)
62			.add_read_kwargs("toml", aot="search")
63			.add_write_kwargs("toml", aot="search")
64			.secure()
65			.build()
66			)
67
68
69			@dataclass(frozen=True, repr=True)
			0 ignored issues – show introduced 2021-07-05 18:49 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
70			class MultiSearch:
71			config: SearchConfigDf
72			input_path: Path
73			out_dir: Path
74			suffix: str
75			restart: bool
76			proceed: bool
77			log_path: Optional[Path]
78
79			@property
80			def final_path(self) -> Path:
			0 ignored issues – show introduced 2021-07-05 18:49 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
81			name = "search_" + self.input_path.name + self.suffix
82			return self.out_dir / name
83
84			@property
85			def is_complete(self):
			0 ignored issues – show introduced 2021-07-05 18:49 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
86			return Checksums().get_filesum_of_file(self.final_path).exists()
87
88			@property
89			def doc_path(self) -> Path:
			0 ignored issues – show introduced 2021-03-21 02:08 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
90			return Path(str(self.final_path.with_suffix("")) + ".doc.tsv")
91
92			def test(self) -> None:
			0 ignored issues – show introduced 2021-07-05 18:49 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
93			self._build_and_test()
94
95			def run(self) -> None:
			0 ignored issues – show introduced 2021-07-05 18:49 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
96			if self.final_path.exists():
97			raise PathExistsError(f"{self.final_path} exists")
98			commands = self._build_and_test()
99			# start!
100			for cmd in commands:
101			cmd.run()
102			logger.notice("Done with all searches!")
103			self._write_final(commands)
104
105			def _write_final(self, commands: Sequence[CmdRunner]):
106			# write the final file
107			df = HitDf(pd.concat([HitDf.read_file(cmd.output_path) for cmd in commands]))
			0 ignored issues – show Coding Style Naming introduced 2021-09-29 03:10 UTC by Report Bug Copy Issue Report Variable name "df" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
108			now = datetime.now().isoformat(timespec="milliseconds")
109			docs = self.get_docs(commands)
110			SearchExplainDf([pd.Series(x) for x in docs]).write_file(self.doc_path)
111			df = df.set_attrs(commands=docs, written=now)
			0 ignored issues – show Coding Style Naming introduced 2021-07-05 18:49 UTC by Report Bug Copy Issue Report Variable name "df" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
112			df.write_file(
113			self.final_path.resolve(),
114			dir_hash=True,
115			file_hash=True,
116			attrs=True,
117			overwrite=self.restart,
118			)
119			logger.notice(f"Concatenated results to {self.final_path}")
120
121			def _build_and_test(self) -> Sequence[CmdRunner]:
122			# build up the list of Entry classes first, and run ``test`` on each one
123			# that's to check that the parameters are correct before running anything
124			logger.info("Building commands...")
125			commands = self._build_commands()
126			if len(commands) == 0:
127			logger.warning(f"No searches — nothing to do")
			0 ignored issues – show introduced 2021-09-23 03:01 UTC by Report Bug Copy Issue Report Using an f-string that does not have any interpolated variables Loading history...
128			return []
129			# build and test
130			for cmd in commands:
131			try:
132			logger.info(f"Testing {cmd.key} ({cmd.cmd.__name__})")
133			cmd.test()
134			except Exception:
135			logger.error(f"Bad search {cmd}")
136			raise
137			logger.success("Searches look ok")
138			return commands
139
140			def _build_commands(self) -> Sequence[CmdRunner]:
141			commands = {}
142			for i in range(len(self.config)):
143			data = {
144			k: v
145			for k, v in self.config.iloc[i].to_dict().items()
146			if v is not None and not pd.isna(v)
147			}
148			cmd = self._build_command(data)
149			if cmd is not None:
150			commands[cmd.key] = cmd
151			return list(commands.values())
152
153			def _build_command(self, data):
154			key = data["key"]
155			with logger.contextualize(key=key):
156			default_to = self.out_dir / (key + SETTINGS.table_suffix)
157			# not actually replacing -- we're just pretending so we can call adjust_filename
158			data["to"] = EntryUtils.adjust_filename(
159			None, default=default_to, replace=True, quiet=True
160			)
161			data["log"] = self._get_log_path(key)
162			data["stderr"] = None # MANDOS_SETUP.main.level
163			cmd = CmdRunner.build(data, self.input_path, restart=self.restart, proceed=self.proceed)
164			return cmd
165
166			def get_docs(self, commands: Sequence[CmdRunner]) -> Sequence[Mapping[str, Any]]:
			0 ignored issues – show introduced 2021-07-05 18:49 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history... Coding Style introduced 2021-11-04 01:02 UTC by Report Bug Copy Issue Report This method could be written as a function/class method. If a method does not access any attributes of the class, it could also be implemented as a function or static method. This can help improve readability. For example class Foo: def some_method(self, x, y): return x + y; could be written as class Foo: @classmethod def some_method(cls, x, y): return x + y; Loading history...
167			rows = []
168			for cmd in commands:
169			st = cmd.cmd.get_search_type()
			0 ignored issues – show Coding Style Naming introduced 2021-10-28 02:14 UTC by Report Bug Copy Issue Report Variable name "st" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
170			name = st.search_name()
171			src = st.primary_data_source()
172			desc = cmd.cmd.describe()
173			args = " ".join([f'{k}="{v}"' for k, v in cmd.params.items()])
174			ser = dict(key=cmd.key, search=name, source=src, desc=desc, args=args)
175			rows.append(ser)
176			return rows
177
178			def _get_log_path(self, key: str) -> Path:
179			if self.log_path is None:
			0 ignored issues – show unused-code introduced 2021-10-28 02:14 UTC by Report Bug Copy Issue Report Unnecessary "else" after "return" Loading history...
180			suffix = SETTINGS.log_suffix
181			return self.out_dir / (key + suffix)
182			else:
183			suffix = LOG_SETUP.guess_file_sink_info(self.log_path).suffix
184			log_base = self.log_path.name[: -len(suffix)]
185			return self.log_path.parent / (log_base + "_" + key + suffix)
186
187
188			@dataclass(frozen=True, repr=True)
			0 ignored issues – show introduced 2021-07-05 18:49 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
189			class CmdRunner:
190			cmd: Type[Entry]
191			params: MutableMapping[str, Union[int, str, float]]
192			input_path: Path
193
194			@property
195			def key(self) -> str:
			0 ignored issues – show introduced 2021-07-05 18:49 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
196			return self.params["key"]
197
198			@property
199			def output_path(self) -> Path:
			0 ignored issues – show introduced 2021-07-05 18:49 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
200			return Path(self.params["to"])
201
202			def test(self) -> None:
			0 ignored issues – show introduced 2021-07-05 18:49 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
203			with logger.contextualize(key=self.key):
204			self.cmd.test(self.input_path, **self.params)
205
206			def run(self) -> None:
			0 ignored issues – show introduced 2021-07-05 18:49 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
207			with logger.contextualize(key=self.key):
208			self.cmd.run(self.input_path, **self.params)
209
210			@classmethod
211			def build(
			0 ignored issues – show introduced 2021-07-05 19:05 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
212			cls, data: Mapping[str, Any], input_path: Path, *, restart: bool, proceed: bool
			0 ignored issues – show Coding Style introduced 2021-10-28 02:14 UTC by Report Bug Copy Issue Report Wrong hanging indentation before block (add 4 spaces). Loading history...
213			) -> CmdRunner:
214			key, cmd = data["key"], data["source"]
215			try:
216			cmd = EntriesByCmd[cmd]
217			except KeyError:
218			raise InjectionError(f"Search command {cmd} (key {key}) does not exist") from None
219			# we need to explicitly add the defaults from the OptionInfo instances
220			# add our new stuff after that
221			params = {
222			**cmd.default_param_values(),
223			**dict(replace=restart, proceed=proceed),
224			**{k: v for k, v in data.items() if k != "source"},
225			}
226			return CmdRunner(cmd, params, input_path)
227
228
229			__all__ = ["MultiSearch", "SearchExplainDf", "SearchConfigDf"]
230

dmyersturnbull / mandos

Push — main ( 2e1b6b...3a0c28 )

mandos.entry.tools.multi_searches.CmdRunner.key() A

Complexity

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Duplication

Importance

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