text_csv

Strategy class for text/csv.

CSVDialect: Type[Enum] = Enum(value='CSVDialect', names={dialect.upper(): dialect for dialect in csv.list_dialects()}, module=__name__, type=str) module-attribute

CSV dialects.

All available dialects are retrieved through the csv.list_dialects() function, and will thus depend on the currently loaded and used Python interpreter.

CSVConfig

Bases: AttrDict

CSV parse-specific Configuration Data Model.

Source code in oteapi/strategies/parse/text_csv.py

class CSVConfig(AttrDict):
    """CSV parse-specific Configuration Data Model."""

    datacache_config: Optional[DataCacheConfig] = Field(
        None,
        description="Configurations for the data cache for storing the downloaded file content.",
    )
    dialect: DialectFormatting = Field(
        DialectFormatting(),
        description=(
            "Dialect and formatting parameters. See [the Python docs]"
            "(https://docs.python.org/3/library/csv.html#csv-fmt-params) for more "
            "information."
        ),
    )
    reader: ReaderConfig = Field(
        ReaderConfig(),
        description=(
            "CSV DictReader configuration parameters. See [the Python docs]"
            "(https://docs.python.org/3/library/csv.html#csv.DictReader) for more "
            "information."
        ),
    )

CSVParseStrategy

Parse strategy for CSV files.

Registers strategies:

• ("mediaType", "text/csv")

Source code in oteapi/strategies/parse/text_csv.py

@dataclass
class CSVParseStrategy:
    """Parse strategy for CSV files.

    **Registers strategies**:

    - `("mediaType", "text/csv")`

    """

    parse_config: CSVResourceConfig

    def initialize(self, session: "Optional[dict[str, Any]]" = None) -> SessionUpdate:
        """Initialize."""
        return SessionUpdate()

    def get(self, session: "Optional[dict[str, Any]]" = None) -> SessionUpdateCSVParse:
        """Parse CSV."""
        downloader = create_strategy("download", self.parse_config)
        output = downloader.get()
        cache = DataCache(self.parse_config.configuration.datacache_config)

        with cache.getfile(output["key"]) as csvfile_path:
            kwargs = self.parse_config.configuration.dialect.dict(
                exclude={"base", "quoting"}, exclude_unset=True
            )

            dialect = self.parse_config.configuration.dialect.base
            if dialect:
                kwargs["dialect"] = dialect.value
            quoting = self.parse_config.configuration.dialect.quoting
            if quoting:
                kwargs["quoting"] = quoting.csv_constant()

            kwargs.update(
                self.parse_config.configuration.reader.dict(exclude_unset=True)
            )

            with open(
                csvfile_path,
                newline="",
                encoding=self.parse_config.configuration.reader.encoding,
            ) as csvfile:
                csvreader = csv.DictReader(csvfile, **kwargs)
                content: dict[Union[str, None], list[Any]] = defaultdict(list)
                for row in csvreader:
                    for field, value in row.items():
                        if (
                            csvreader.reader.dialect.quoting == csv.QUOTE_NONNUMERIC
                            and isinstance(value, float)
                            and value.is_integer()
                        ):
                            value = int(value)
                        content[field].append(value)
            for key in list(content):
                if any(isinstance(value, float) for value in content[key]):
                    content[key] = [
                        float(value)
                        if (value or value == 0.0 or value == 0)
                        and value != csvreader.restval
                        else float("nan")
                        for value in content[key]
                    ]
                    continue
                if any(isinstance(value, int) for value in content[key]):
                    content[key] = [
                        int(value)
                        if (value or value == 0) and value != csvreader.restval
                        else csvreader.restval
                        for value in content[key]
                    ]

            return SessionUpdateCSVParse(content=content)

get(session=None)

Parse CSV.

Source code in oteapi/strategies/parse/text_csv.py

def get(self, session: "Optional[dict[str, Any]]" = None) -> SessionUpdateCSVParse:
    """Parse CSV."""
    downloader = create_strategy("download", self.parse_config)
    output = downloader.get()
    cache = DataCache(self.parse_config.configuration.datacache_config)

    with cache.getfile(output["key"]) as csvfile_path:
        kwargs = self.parse_config.configuration.dialect.dict(
            exclude={"base", "quoting"}, exclude_unset=True
        )

        dialect = self.parse_config.configuration.dialect.base
        if dialect:
            kwargs["dialect"] = dialect.value
        quoting = self.parse_config.configuration.dialect.quoting
        if quoting:
            kwargs["quoting"] = quoting.csv_constant()

        kwargs.update(
            self.parse_config.configuration.reader.dict(exclude_unset=True)
        )

        with open(
            csvfile_path,
            newline="",
            encoding=self.parse_config.configuration.reader.encoding,
        ) as csvfile:
            csvreader = csv.DictReader(csvfile, **kwargs)
            content: dict[Union[str, None], list[Any]] = defaultdict(list)
            for row in csvreader:
                for field, value in row.items():
                    if (
                        csvreader.reader.dialect.quoting == csv.QUOTE_NONNUMERIC
                        and isinstance(value, float)
                        and value.is_integer()
                    ):
                        value = int(value)
                    content[field].append(value)
        for key in list(content):
            if any(isinstance(value, float) for value in content[key]):
                content[key] = [
                    float(value)
                    if (value or value == 0.0 or value == 0)
                    and value != csvreader.restval
                    else float("nan")
                    for value in content[key]
                ]
                continue
            if any(isinstance(value, int) for value in content[key]):
                content[key] = [
                    int(value)
                    if (value or value == 0) and value != csvreader.restval
                    else csvreader.restval
                    for value in content[key]
                ]

        return SessionUpdateCSVParse(content=content)

initialize(session=None)

Initialize.

Source code in oteapi/strategies/parse/text_csv.py

def initialize(self, session: "Optional[dict[str, Any]]" = None) -> SessionUpdate:
    """Initialize."""
    return SessionUpdate()

CSVResourceConfig

Bases: ResourceConfig

CSV parse strategy filter config.

Source code in oteapi/strategies/parse/text_csv.py

class CSVResourceConfig(ResourceConfig):
    """CSV parse strategy filter config."""

    mediaType: str = Field(
        "text/csv",
        const=True,
        description=ResourceConfig.__fields__["mediaType"].field_info.description,
    )
    configuration: CSVConfig = Field(
        CSVConfig(), description="CSV parse strategy-specific configuration."
    )

DialectFormatting

Bases: BaseModel

Dialect and formatting parameters for CSV.

See the Python docs for more information.

Note

As Dialect.lineterminator is hardcoded in csv.reader, it is left out of this model.

Source code in oteapi/strategies/parse/text_csv.py

class DialectFormatting(BaseModel):
    """Dialect and formatting parameters for CSV.

    See [the Python docs](https://docs.python.org/3/library/csv.html#csv-fmt-params)
    for more information.

    Note:
        As `Dialect.lineterminator` is hardcoded in `csv.reader`, it is left out of
        this model.

    """

    base: Optional[CSVDialect] = Field(
        None,
        description=(
            "A specific CSV dialect, e.g., 'excel'. Any other parameters here will "
            "overwrite the preset dialect parameters for the specified dialect."
        ),
    )
    delimiter: Optional[str] = Field(
        None,
        description=(
            "A one-character string used to separate fields. "
            "See [the Python docs entry](https://docs.python.org/3/library/csv.html"
            "#csv.Dialect.delimiter) for more information."
        ),
        min_length=1,
        max_length=1,
    )
    doublequote: Optional[bool] = Field(
        None,
        description=(
            "Controls how instances of [`quotechar`]"
            "[oteapi.strategies.parse.text_csv.DialectFormatting.quotechar] "
            "appearing inside a field should themselves be quoted. When `True`, the "
            "character is doubled. When `False`, the [`escapechar`]"
            "[oteapi.strategies.parse.text_csv.DialectFormatting.escapechar] "
            "is used as a prefix to the [`quotechar`]"
            "[oteapi.strategies.parse.text_csv.DialectFormatting.quotechar]. "
            "See [the Python docs entry]"
            "(https://docs.python.org/3/library/csv.html#csv.Dialect.doublequote) "
            "for more information."
        ),
    )
    escapechar: Optional[str] = Field(
        None,
        description=(
            "A one-character string used by the writer to escape the [`delimiter`]"
            "[oteapi.strategies.parse.text_csv.DialectFormatting.delimiter] if "
            "[`quoting`][oteapi.strategies.parse.text_csv.DialectFormatting.quoting] "
            "is set to [`QUOTE_NONE`]"
            "[oteapi.strategies.parse.text_csv.QuoteConstants.QUOTE_NONE] and the "
            "[`quotechar`][oteapi.strategies.parse.text_csv.DialectFormatting."
            "quotechar] if [`doublequote`][oteapi.strategies.parse.text_csv."
            "DialectFormatting.doublequote] is `False`. On reading, the "
            "[`escapechar`][oteapi.strategies.parse.text_csv.DialectFormatting."
            "escapechar] removes any special meaning from the following character. "
            "See [the Python docs entry]"
            "(https://docs.python.org/3/library/csv.html#csv.Dialect.escapechar) "
            "for more information."
        ),
        min_length=1,
        max_length=1,
    )
    quotechar: Optional[str] = Field(
        None,
        description=(
            "A one-character string used to quote fields containing special "
            "characters, such as the [`delimiter`]"
            "[oteapi.strategies.parse.text_csv.DialectFormatting.delimiter] or "
            "[`quotechar`][oteapi.strategies.parse.text_csv.DialectFormatting."
            "quotechar], or which contain new-line characters. See "
            "[the Python docs entry](https://docs.python.org/3/library/csv.html"
            "#csv.Dialect.quotechar) for more information."
        ),
        min_length=1,
        max_length=1,
    )
    quoting: Optional[QuoteConstants] = Field(
        None,
        description=(
            "Controls when quotes should be generated by the writer and recognised by "
            "the reader. It can take on any of the `QUOTE_*` constants (see section "
            "[Module Contents](https://docs.python.org/3/library/csv.html"
            "#csv-contents)). See [the Python docs entry]"
            "(https://docs.python.org/3/library/csv.html#csv.Dialect.quoting) "
            "for more information."
        ),
    )
    skipinitialspace: Optional[bool] = Field(
        None,
        description=(
            "When `True`, whitespace immediately following the [`delimiter`]"
            "[oteapi.strategies.parse.text_csv.DialectFormatting.delimiter] is "
            "ignored. See [the Python docs entry]"
            "(https://docs.python.org/3/library/csv.html#csv.Dialect.skipinitialspace)"
            " for more information."
        ),
    )
    strict: Optional[bool] = Field(
        None,
        description=(
            "When `True`, raise exception [Error]"
            "(https://docs.python.org/3/library/csv.html#csv.Error) on bad CSV input. "
            "See [the Python docs entry](https://docs.python.org/3/library/csv.html"
            "#csv.Dialect.strict) for more information."
        ),
    )

    @validator("base")
    def validate_dialect_base(cls, value: str) -> str:
        """Ensure the given `base` dialect is registered locally."""
        if value not in csv.list_dialects():
            raise ValueError(
                f"{value!r} is not a known registered CSV dialect. "
                f"Registered dialects: {', '.join(csv.list_dialects())}."
            )
        return value

validate_dialect_base(value)

Ensure the given base dialect is registered locally.

Source code in oteapi/strategies/parse/text_csv.py

@validator("base")
def validate_dialect_base(cls, value: str) -> str:
    """Ensure the given `base` dialect is registered locally."""
    if value not in csv.list_dialects():
        raise ValueError(
            f"{value!r} is not a known registered CSV dialect. "
            f"Registered dialects: {', '.join(csv.list_dialects())}."
        )
    return value

QuoteConstants

Bases: str, Enum

CSV module QUOTE_* constants.

Source code in oteapi/strategies/parse/text_csv.py

class QuoteConstants(str, Enum):
    """CSV module `QUOTE_*` constants."""

    QUOTE_ALL = "QUOTE_ALL"
    QUOTE_MINIMAL = "QUOTE_MINIMAL"
    QUOTE_NONUMERIC = "QUOTE_NONNUMERIC"
    QUOTE_NONE = "QUOTE_NONE"

    def csv_constant(self) -> int:
        """Return the CSV lib equivalent constant."""
        return {
            self.QUOTE_ALL: csv.QUOTE_ALL,
            self.QUOTE_MINIMAL: csv.QUOTE_MINIMAL,
            self.QUOTE_NONUMERIC: csv.QUOTE_NONNUMERIC,
            self.QUOTE_NONE: csv.QUOTE_NONE,
        }[self]

csv_constant()

Return the CSV lib equivalent constant.

Source code in oteapi/strategies/parse/text_csv.py

def csv_constant(self) -> int:
    """Return the CSV lib equivalent constant."""
    return {
        self.QUOTE_ALL: csv.QUOTE_ALL,
        self.QUOTE_MINIMAL: csv.QUOTE_MINIMAL,
        self.QUOTE_NONUMERIC: csv.QUOTE_NONNUMERIC,
        self.QUOTE_NONE: csv.QUOTE_NONE,
    }[self]

ReaderConfig

Bases: BaseModel

CSV DictReader configuration parameters.

See the Python docs for more information.

Source code in oteapi/strategies/parse/text_csv.py

class ReaderConfig(BaseModel):
    """CSV DictReader configuration parameters.

    See [the Python docs](https://docs.python.org/3/library/csv.html#csv.DictReader)
    for more information.
    """

    fieldnames: Optional[list[str]] = Field(
        None,
        description=(
            "List of headers. If not set, the values in the first row of the CSV file "
            "will be used as the field names."
        ),
    )
    restkey: Optional[Hashable] = Field(
        None,
        description=(
            "If a row has more fields than [`fieldnames`]"
            "[oteapi.strategies.parse.text_csv.ReaderConfig.fieldnames], the "
            "remaining data is put in a list and stored with the field name specified "
            "by [`restkey`][oteapi.strategies.parse.text_csv.ReaderConfig.restkey]."
        ),
    )
    restval: Optional[Any] = Field(
        None,
        description=(
            "If a non-blank row has fewer fields than the length of [`fieldnames`]"
            "[oteapi.strategies.parse.text_csv.ReaderConfig.fieldnames], the missing "
            "values are filled-in with the value of [`restval`]"
            "[oteapi.strategies.parse.text_csv.ReaderConfig.restval]."
        ),
    )
    encoding: str = Field(
        "utf8",
        description="The file encoding.",
    )

SessionUpdateCSVParse

Bases: SessionUpdate

Class for returning values from CSV Parse.

Source code in oteapi/strategies/parse/text_csv.py

class SessionUpdateCSVParse(SessionUpdate):
    """Class for returning values from CSV Parse."""

    content: dict[Union[str, None], list[Any]] = Field(
        ..., description="Content of the CSV document."
    )