com.chemaxon.overlap.cli.util.pipeline

Interface PipelineStep

All Known Implementing Classes:

CloneCxnMolecule, CollectStorage, Connect, CxnFormatsMolExporter, CxnFormatsMolImporter, GetMoleculeName, GetSdfProperty, Mark, ProgressiveSerializeToFile, TextFileInput, TextFileOutput, ToLines, ToSdfs, TransformMolecule

public interface PipelineStep

Minimal life cycle of a MadFast import pipeline node.

Method Summary

Modifier and Type	Method and Description
void	addToPipeline(PipelineContext pipeline) Wire step into the pipeline.
default void	close() Close the step.
default void	init() Initialize the step.

Method Detail

addToPipeline

void addToPipeline(PipelineContext pipeline)

Wire step into the pipeline. Contracts:

• Introduce the step using PipelineContext.addStep(com.chemaxon.overlap.cli.util.pipeline.PipelineStep)
• Introduce inputs and outputs. The actual inputs, outputs and their types might depend on the parameterization.
• Invoked before init().
• Default parameterization is expected to be valid to invoke this method.
• Validity checks based on the parameterization might happen (consistency of the set parameters). Environment (other nodes, file system, etc) based verifications are expected to be executed in init().
• Apart from interacting with the passed PipelineContext reference this method is side effect free
• Parameterization is expected to be not changed after invoking this method.

Parameters:

pipeline - Target pipeline.

init

default void init()
           throws Exception

Initialize the step. Open required files, connections, etc. Be prepared to start stream data from now. Contracts:

• This method might not be invoked during the life cycle of an implementing instance.
• Method addToPipeline(com.chemaxon.overlap.cli.util.pipeline.PipelineContext) will be invoked before this method.
• File presence, possibly validity checking should be done here.
• Values for single inputs are all set from upstream nodes before invoking this method..
• Outputs are queried after this method returned.
• Method close() is expected to be invoked sometimes later, regardless of possible error(s) thrown.

Throws:

Exception - In case of initialization failure

close

default void close()
            throws Exception

Close the step. Close opened files, connections, etc. No further interaction is expected. Method init() is guaranteed to be invoked before. Note that it is possible that init() and close() methods are not invoked during the life cycle of an implementing instance.

Throws:

Exception - might be propagated from underlying IO