schrodinger.application.models.execution.transforms module

class schrodinger.application.models.execution.transforms.GenerateRowsDoFn(row_source)

Bases: DoFn

__init__(row_source)
process(_)

Method to use for processing elements.

This is invoked by DoFnRunner for each element of a input PCollection.

The following parameters can be used as default values on process arguments to indicate that a DoFn accepts the corresponding parameters. For example, a DoFn might accept the element and its timestamp with the following signature:

def process(element=DoFn.ElementParam, timestamp=DoFn.TimestampParam):
  ...

The full set of parameters is:

  • DoFn.ElementParam: element to be processed, should not be mutated.

  • DoFn.SideInputParam: a side input that may be used when processing.

  • DoFn.TimestampParam: timestamp of the input element.

  • DoFn.WindowParam: Window the input element belongs to.

  • DoFn.TimerParam: a userstate.RuntimeTimer object defined by the spec of the parameter.

  • DoFn.StateParam: a userstate.RuntimeState object defined by the spec of the parameter.

  • DoFn.KeyParam: key associated with the element.

  • DoFn.RestrictionParam: an iobase.RestrictionTracker will be provided here to allow treatment as a Splittable DoFn. The restriction tracker will be derived from the restriction provider in the parameter.

  • DoFn.WatermarkEstimatorParam: a function that can be used to track output watermark of Splittable DoFn implementations.

  • DoFn.BundleContextParam: allows a shared context manager to be used per bundle

  • DoFn.SetupContextParam: allows a shared context manager to be used per DoFn

Args:

element: The element to be processed *args: side inputs **kwargs: other keyword arguments.

Returns:

An Iterable of output elements or None.

class schrodinger.application.models.execution.transforms.ReadFromRowSource(label: Optional[str] = None)

Bases: _LocalOnlyPTransform, ReadFromRowSource

class schrodinger.application.models.execution.transforms.WriteRowDoFn(row_sink)

Bases: DoFn

__init__(row_sink)
process(row: Row)

Method to use for processing elements.

This is invoked by DoFnRunner for each element of a input PCollection.

The following parameters can be used as default values on process arguments to indicate that a DoFn accepts the corresponding parameters. For example, a DoFn might accept the element and its timestamp with the following signature:

def process(element=DoFn.ElementParam, timestamp=DoFn.TimestampParam):
  ...

The full set of parameters is:

  • DoFn.ElementParam: element to be processed, should not be mutated.

  • DoFn.SideInputParam: a side input that may be used when processing.

  • DoFn.TimestampParam: timestamp of the input element.

  • DoFn.WindowParam: Window the input element belongs to.

  • DoFn.TimerParam: a userstate.RuntimeTimer object defined by the spec of the parameter.

  • DoFn.StateParam: a userstate.RuntimeState object defined by the spec of the parameter.

  • DoFn.KeyParam: key associated with the element.

  • DoFn.RestrictionParam: an iobase.RestrictionTracker will be provided here to allow treatment as a Splittable DoFn. The restriction tracker will be derived from the restriction provider in the parameter.

  • DoFn.WatermarkEstimatorParam: a function that can be used to track output watermark of Splittable DoFn implementations.

  • DoFn.BundleContextParam: allows a shared context manager to be used per bundle

  • DoFn.SetupContextParam: allows a shared context manager to be used per DoFn

Args:

element: The element to be processed *args: side inputs **kwargs: other keyword arguments.

Returns:

An Iterable of output elements or None.

class schrodinger.application.models.execution.transforms.WriteToRowSink(label: Optional[str] = None)

Bases: _LocalOnlyPTransform, WriteToRowSink

class schrodinger.application.models.execution.transforms.ExtractStructure(field: str = 'structure')

Bases: PTransform

Extract a Structure-valued field from a Row.

__init__(field: str = 'structure')
expand(pcoll)
class schrodinger.application.models.execution.transforms.StructureToRow(properties: list[str | dict[str, str]] | None = None, strict: bool = False)

Bases: PTransform

Convert Structures to Rows for an LD-model row sink.

Parameters:

  • properties – List of property keys / built-in attribute names to extract from each structure. Each element is either a plain string (when the key is a valid field name) or a {output_name: property_key} dict to alias properties with non-identifier keys.

  • strict – If True, raise when a requested property is missing. If False, missing properties yield empty cells in the LD output.

__init__(properties: list[str | dict[str, str]] | None = None, strict: bool = False)
expand(pcoll)