execute

package
v0.0.0-...-040724e Latest Latest
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 Go to latest Published: Jun 6, 2019 License: BSD-3-Clause, GPL-2.0 Imports: 22 Imported by: 4

Documentation

Overview

Package execute connects Antha elements to the trace execution infrastructure.

Index

Constants

This section is empty.

Variables

This section is empty.

Functions

func Errorf 

func Errorf(ctx context.Context, format string, args ...interface{})

Errorf reports an execution error. Does not return

func ExecuteMixes 

func ExecuteMixes(ctx context.Context, liquids ...*wtype.LHComponent) []*wtype.Liquid

ExecuteMixes will ensure that all mix activities in a workflow prior to this point must be completed before Mix instructions after this point.

func Incubate 

func Incubate(ctx context.Context, in *wtype.Liquid, opt IncubateOpt) *wtype.Liquid

Incubate incubates a component

func Issue 

func Issue(ctx context.Context, instruction *commandInst)

Issue an instruction - this records the instruction into the trace.

func Mix 

func Mix(ctx context.Context, components ...*wtype.Liquid) *wtype.Liquid

Mix mixes components

func MixInto 

func MixInto(ctx context.Context, outplate *wtype.Plate, address string, components ...*wtype.Liquid) *wtype.Liquid

MixInto mixes components

func MixNamed 

func MixNamed(ctx context.Context, outplatetype, address string, platename string, components ...*wtype.Liquid) *wtype.Liquid

MixNamed mixes components

func MixTo 

func MixTo(ctx context.Context, outplatetype, address string, platenum int, components ...*wtype.Liquid) *wtype.Liquid

MixTo mixes components

TODO: Addresses break dependence information. Deprecated.

func MixerPrompt 

func MixerPrompt(ctx context.Context, message string, in ...*wtype.Liquid) []*wtype.Liquid

MixerPrompt prompts user with a message during mixer execution

func MixerWait 

func MixerWait(ctx context.Context, time wunit.Time, message string, in ...*wtype.Liquid) []*wtype.Liquid

MixerWait prompts user with a message during mixer execution and waits for the specifed time before resuming.

func NewComponent 

func NewComponent(ctx context.Context, typ string) *wtype.Liquid

NewComponent returns a new component given a component type

func NewPlate 

func NewPlate(ctx context.Context, typ string) *wtype.Plate

NewPlate returns a new plate given a plate type

func PlateRead 

func PlateRead(ctx context.Context, opt PlateReadOpts) *wtype.Liquid

PlateRead reads absorbance of a component

func Prompt 

func Prompt(ctx context.Context, in *wtype.Liquid, message string) *wtype.Liquid

Prompt prompts user with a message

func RunQPCRExperiment 

func RunQPCRExperiment(ctx context.Context, opt QPCROptions) []*wtype.Liquid

RunQPCRExperiment starts a new QPCR experiment, using an experiment input file.

func RunQPCRFromTemplate 

func RunQPCRFromTemplate(ctx context.Context, opt QPCROptions) []*wtype.Liquid

RunQPCRFromTemplate starts a new QPCR experiment, using a template input file.

func Sample 

func Sample(ctx context.Context, liquid *wtype.Liquid, v wunit.Volume) *wtype.Liquid

Sample takes a sample of volume v from this liquid

func SetInputPlate 

func SetInputPlate(ctx context.Context, plate *wtype.Plate)

SetInputPlate Indicate to the scheduler the the contents of the plate is user supplied. This modifies the argument to mark each well as such.

func SplitSample 

func SplitSample(ctx context.Context, component *wtype.Liquid, volume wunit.Volume) (removed, remaining *wtype.Liquid)

SplitSample is essentially an inverse mix: takes one component and a volume and returns two the question is then over what happens subsequently.. unlike mix this does not have a destination as it's intrinsically a source operation

func WithElementName 

func WithElementName(parent context.Context, name string) context.Context

WithElementName returns a new context that stores the current element name

Types

type Annotatable 

type Annotatable interface {
	GetData(key string) ([]byte, error)
	SetData(key string, data []byte) error
}

An Annotatable is an object that can data attached to it

type IncubateOpt 

type IncubateOpt struct {
	// Time for which to incubate component
	Time wunit.Time
	// Temperature at which to incubate component
	Temp wunit.Temperature
	// Rate at which to shake incubator (force is device dependent)
	ShakeRate wunit.Rate
	// Radius at which ShakeRate is defined
	ShakeRadius wunit.Length

	// Time for which to pre-heat incubator
	PreTemp wunit.Temperature
	// Temperature at which to pre-heat incubator
	PreTime wunit.Time
	// Rate at which to pre-heat incubator
	PreShakeRate wunit.Rate
	// Radius at which PreShakeRate is defined
	PreShakeRadius wunit.Length
}

An IncubateOpt are options to an incubate command

type Opt 

type Opt struct {
	// Target machine configuration
	Target *target.Target
	// Deprecated for separate assignment of values to workflow. Raw workflow.
	Workflow *workflow.Desc
	// Deprecated for separate assignment of values to workflow. Raw parameters.
	Params *RawParams
	// Job ID.
	ID string
	// Deprecated for separate assignment of values to workflow. If true, read
	// content for each wtype.File from file of the same name in the current
	// directory.
	TransitionalReadLocalFiles bool
}

An Opt are options for Run.

type Params 

type Params struct {
	Parameters map[string]map[string]interface{} `json:"Parameters"`
	Config     *mixer.Opt                        `json:"Config"`
}

Params is the structure of parameter data for marshalling.

Deprecated for github.com/antha-lang/antha/api/v1/WorkflowParameters.

type PlateReadOpts 

type PlateReadOpts struct {
	Sample  *wtype.Liquid
	Options string
}

PlateReadOpts defines plate-reader absorbance options

type QPCROptions 

type QPCROptions struct {
	Reactions  []*wtype.Liquid
	Definition string
	Barcode    string
	TagAs      string
}

QPCROptions are the options for a QPCR request.

type RawParams 

type RawParams struct {
	Parameters map[string]map[string]json.RawMessage `json:"Parameters"`
	Config     *mixer.Opt                            `json:"Config"`
}

RawParams is the structure of parameter data for unmarshalling.

Deprecated for github.com/antha-lang/antha/api/v1/WorkflowParameters.

type Result 

type Result struct {
	Workflow *workflow.Workflow
	Input    []ast.Node
	Insts    []ast.Inst
}

Result of executing a workflow.

func Run 

func Run(parent context.Context, opt Opt) (res *Result, err error)

Run is a simple entrypoint for one-shot execution of workflows.

type Trace 

type Trace struct {
	// contains filtered or unexported fields
}

func WithTrace 

func WithTrace(parent context.Context) (context.Context, *Trace)

func (*Trace) Instructions 

func (tr *Trace) Instructions() []*commandInst

Returns a (shallow) copy (to avoid data races) of the issued instructions.

func (*Trace) Issue 

func (tr *Trace) Issue(instruction *commandInst)

Issue an instruction - this records the instruction into the trace.

type UserError 

type UserError struct {
	// contains filtered or unexported fields
}

An UserError reported by user code

func (UserError) Error 

func (err UserError) Error() string

Error satisfies the error interface

Source Files

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