Module signals_notebook.entities.biological_sequence

Expand source code 
import logging
from enum import Enum
from typing import ClassVar, Literal

from pydantic import Field

from signals_notebook.common_types import EntityType, File
from signals_notebook.entities import Entity
from signals_notebook.entities.container import Container
from signals_notebook.entities.contentful_entity import ContentfulEntity
from signals_notebook.jinja_env import env

log = logging.getLogger(__name__)


class BiologicalSequence(ContentfulEntity):
    class ContentType(str, Enum):
        FASTA = 'biosequence/fasta'
        GB = 'biosequence/genbank'
        GBK = 'biosequence/genpept'
        SW = 'chemical/x-swissprot'
        DNA = 'application/vnd.snapgene.dna'
        PROT = 'application/vnd.snapgene.protein'

    type: Literal[EntityType.BIO_SEQUENCE] = Field(allow_mutation=False)
    _template_name: ClassVar = 'bio_sequence.html'

    @classmethod
    def _get_entity_type(cls) -> EntityType:
        return EntityType.BIO_SEQUENCE

    @classmethod
    def create(
        cls,
        *,
        container: Container,
        name: str,
        content: bytes = b'',
        content_type: str = ContentType.GB,
        force: bool = True,
    ) -> Entity:
        """Create BiologicalSequence Entity

        Args:
            container: Container where create new BiologicalSequence
            name: file name
            content_type: content type of BiologicalSequence entity
            content: BiologicalSequence content
            force: Force to post attachment

        Returns:
            BiologicalSequence
        """
        cls.ContentType(content_type)
        log.debug('Create entity: %s with name: %s in Container: %s', cls.__name__, name, container.eid)
        return container.add_child(
            name=name,
            content=content,
            content_type=content_type,
            force=force,
        )

    def get_content(self) -> File:
        """Get BiologicalSequence content

        Returns:
            File
        """
        return super()._get_content()

    def get_html(self) -> str:
        """Get in HTML format

        Returns:
            Rendered template as a string
        """
        data = {'name': self.name}
        file = self.get_content()
        data['bio_sequence'] = 'data:{};base64,{}'.format(file.content_type, file.base64.decode('ascii'))

        template = env.get_template(self._template_name)
        log.info('Html template for %s:%s has been rendered.', self.__class__.__name__, self.eid)

        return template.render(data=data)

Classes

class BiologicalSequence (**data: Any)

Create a new model by parsing and validating input data from keyword arguments.

Raises ValidationError if the input data cannot be parsed to form a valid model.

Expand source code 
class BiologicalSequence(ContentfulEntity):
    class ContentType(str, Enum):
        FASTA = 'biosequence/fasta'
        GB = 'biosequence/genbank'
        GBK = 'biosequence/genpept'
        SW = 'chemical/x-swissprot'
        DNA = 'application/vnd.snapgene.dna'
        PROT = 'application/vnd.snapgene.protein'

    type: Literal[EntityType.BIO_SEQUENCE] = Field(allow_mutation=False)
    _template_name: ClassVar = 'bio_sequence.html'

    @classmethod
    def _get_entity_type(cls) -> EntityType:
        return EntityType.BIO_SEQUENCE

    @classmethod
    def create(
        cls,
        *,
        container: Container,
        name: str,
        content: bytes = b'',
        content_type: str = ContentType.GB,
        force: bool = True,
    ) -> Entity:
        """Create BiologicalSequence Entity

        Args:
            container: Container where create new BiologicalSequence
            name: file name
            content_type: content type of BiologicalSequence entity
            content: BiologicalSequence content
            force: Force to post attachment

        Returns:
            BiologicalSequence
        """
        cls.ContentType(content_type)
        log.debug('Create entity: %s with name: %s in Container: %s', cls.__name__, name, container.eid)
        return container.add_child(
            name=name,
            content=content,
            content_type=content_type,
            force=force,
        )

    def get_content(self) -> File:
        """Get BiologicalSequence content

        Returns:
            File
        """
        return super()._get_content()

    def get_html(self) -> str:
        """Get in HTML format

        Returns:
            Rendered template as a string
        """
        data = {'name': self.name}
        file = self.get_content()
        data['bio_sequence'] = 'data:{};base64,{}'.format(file.content_type, file.base64.decode('ascii'))

        template = env.get_template(self._template_name)
        log.info('Html template for %s:%s has been rendered.', self.__class__.__name__, self.eid)

        return template.render(data=data)

Ancestors

Class variables

var type : Literal[]

Static methods

def create(*, container: Container, name: str, content: bytes = b'', content_type: str = ContentType.GB, force: bool = True) ‑> Entity

Create BiologicalSequence Entity

Args

container
Container where create new BiologicalSequence
name
file name
content_type
content type of BiologicalSequence entity
content
BiologicalSequence content
force
Force to post attachment

Returns

BiologicalSequence

Expand source code 
@classmethod
def create(
    cls,
    *,
    container: Container,
    name: str,
    content: bytes = b'',
    content_type: str = ContentType.GB,
    force: bool = True,
) -> Entity:
    """Create BiologicalSequence Entity

    Args:
        container: Container where create new BiologicalSequence
        name: file name
        content_type: content type of BiologicalSequence entity
        content: BiologicalSequence content
        force: Force to post attachment

    Returns:
        BiologicalSequence
    """
    cls.ContentType(content_type)
    log.debug('Create entity: %s with name: %s in Container: %s', cls.__name__, name, container.eid)
    return container.add_child(
        name=name,
        content=content,
        content_type=content_type,
        force=force,
    )

Methods

def get_content(self) ‑> File

Get BiologicalSequence content

Returns

File

Expand source code 
def get_content(self) -> File:
    """Get BiologicalSequence content

    Returns:
        File
    """
    return super()._get_content()

Inherited members