text_csv

Strategy class for parser/csv.

CSVDialect: type[Enum] = Enum(value='CSVDialect', names={dialect.upper(): dialectfor 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."""

    # Resource config
    downloadUrl: Optional[HostlessAnyUrl] = Field(
        None,
        description=ResourceConfig.model_fields["downloadUrl"].description,
    )
    mediaType: Literal["text/csv"] = Field(
        "text/csv",
        description=ResourceConfig.model_fields["mediaType"].description,
    )

    # CSV parse strategy-specific configuration
    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."
        ),
    )

datacache_config: Optional[DataCacheConfig] = Field(None, description='Configurations for the data cache for storing the downloaded file content.') class-attribute instance-attribute

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.') class-attribute instance-attribute

downloadUrl: Optional[HostlessAnyUrl] = Field(None, description=ResourceConfig.model_fields['downloadUrl'].description) class-attribute instance-attribute

mediaType: Literal['text/csv'] = Field('text/csv', description=ResourceConfig.model_fields['mediaType'].description) class-attribute instance-attribute

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.') class-attribute instance-attribute

CSVParseContent

Bases: AttrDict

Class for returning values from CSV Parse.

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

class CSVParseContent(AttrDict):
    """Class for returning values from CSV Parse."""

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

content: dict[Union[str, None], list[Any]] = Field(..., description='Content of the CSV document.') class-attribute instance-attribute

CSVParseStrategy

Parse strategy for CSV files.

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

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

    parse_config: CSVParserConfig

    def initialize(self) -> AttrDict:
        """Initialize."""
        return AttrDict()

    def get(self) -> CSVParseContent:
        """Parse CSV."""
        config = self.parse_config.configuration

        # Download the file
        download_config = config.model_dump()
        download_config["configuration"] = config.model_dump()
        output = create_strategy("download", download_config).get()

        if config.datacache_config and config.datacache_config.accessKey:
            cache_key = config.datacache_config.accessKey
        elif "key" in output:
            cache_key = output["key"]
        else:
            raise RuntimeError("No data cache key provided to the downloaded content")

        cache = DataCache(config.datacache_config)

        with cache.getfile(cache_key) as csvfile_path:
            kwargs = config.dialect.model_dump(
                exclude={"base", "quoting"}, exclude_unset=True
            )

            dialect = config.dialect.base
            if dialect:
                kwargs["dialect"] = dialect.value
            quoting = config.dialect.quoting
            if quoting:
                kwargs["quoting"] = quoting.csv_constant()

            kwargs.update(config.reader.model_dump(exclude_unset=True))

            with csvfile_path.open(
                newline="",
                encoding=config.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()
                        ):
                            content[field].append(int(value))
                        else:
                            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 CSVParseContent(content=content)

parse_config: CSVParserConfig instance-attribute

get()

Parse CSV.

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

def get(self) -> CSVParseContent:
    """Parse CSV."""
    config = self.parse_config.configuration

    # Download the file
    download_config = config.model_dump()
    download_config["configuration"] = config.model_dump()
    output = create_strategy("download", download_config).get()

    if config.datacache_config and config.datacache_config.accessKey:
        cache_key = config.datacache_config.accessKey
    elif "key" in output:
        cache_key = output["key"]
    else:
        raise RuntimeError("No data cache key provided to the downloaded content")

    cache = DataCache(config.datacache_config)

    with cache.getfile(cache_key) as csvfile_path:
        kwargs = config.dialect.model_dump(
            exclude={"base", "quoting"}, exclude_unset=True
        )

        dialect = config.dialect.base
        if dialect:
            kwargs["dialect"] = dialect.value
        quoting = config.dialect.quoting
        if quoting:
            kwargs["quoting"] = quoting.csv_constant()

        kwargs.update(config.reader.model_dump(exclude_unset=True))

        with csvfile_path.open(
            newline="",
            encoding=config.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()
                    ):
                        content[field].append(int(value))
                    else:
                        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 CSVParseContent(content=content)

initialize()

Initialize.

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

def initialize(self) -> AttrDict:
    """Initialize."""
    return AttrDict()

CSVParserConfig

Bases: ParserConfig

CSV parse strategy filter config.

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

class CSVParserConfig(ParserConfig):
    """CSV parse strategy filter config."""

    parserType: Literal["parser/csv"] = Field(
        "parser/csv",
        description=ParserConfig.model_fields["parserType"].description,
    )
    configuration: CSVConfig = Field(
        ..., description="CSV parse strategy-specific configuration."
    )

configuration: CSVConfig = Field(..., description='CSV parse strategy-specific configuration.') class-attribute instance-attribute

parserType: Literal['parser/csv'] = Field('parser/csv', description=ParserConfig.model_fields['parserType'].description) class-attribute instance-attribute

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."
        ),
    )

    @field_validator("base")
    @classmethod
    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

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.") class-attribute instance-attribute

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) class-attribute instance-attribute

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.') class-attribute instance-attribute

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) class-attribute instance-attribute

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) class-attribute instance-attribute

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.') class-attribute instance-attribute

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.') class-attribute instance-attribute

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.') class-attribute instance-attribute

validate_dialect_base(value) classmethod

Ensure the given base dialect is registered locally.

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

@field_validator("base")
@classmethod
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]

QUOTE_ALL = 'QUOTE_ALL' class-attribute instance-attribute

QUOTE_MINIMAL = 'QUOTE_MINIMAL' class-attribute instance-attribute

QUOTE_NONE = 'QUOTE_NONE' class-attribute instance-attribute

QUOTE_NONUMERIC = 'QUOTE_NONNUMERIC' class-attribute instance-attribute

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.",
    )

encoding: str = Field('utf8', description='The file encoding.') class-attribute instance-attribute

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.') class-attribute instance-attribute

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].') class-attribute instance-attribute

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].') class-attribute instance-attribute