roboliq-processor

Module: roboliq

Roboliq's top module with functions for processing protocols.

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Methods

<inner> _run(opts [, userProtocol])

Process the protocol(s) given by the command line options and an optional userProtocol passed in separately to the API (currently this is just for testing).

Parameters:
Name Type Argument Description
opts object

command line arguments as processed by nomnom.
userProtocol Protocol <optional>

an optional protocol that can be directly passed into the function rather than supplied via argv; currently this is only for testing purposes.
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Returns:

Processing results with properties output (the final processed protocol) and protocol (same as output, but without tables).

Type
object

<inner> createStateItems(name, o, stateList)

This function recurively iterates through all objects, and for each object whose type has an entry in protocol.objectToPredicateConverters, it generates the logical predicates and appends them to stateList.

Mutates stateList.

Parameters:
Name Type Description
name string

name of current object
o object

current object
stateList array

array of logical predicates
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<inner> expandProtocol(The)

Expand the protocol's steps. This means that commands are passed to command handlers to possibly be expanded to lower-level sub-commands.

Mutates protocol.

Parameters:
Name Type Description
The Protocol

protocol.
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Returns:

The final state of objects.

Type
object

<inner> expandStep(protocol, prefix, step, objects)

Expand the given step by passing a command to its command handler and recursively expanding sub-steps.

Mutates protocol. However, since protocol.objects should still hold the initial objects after processing, rather than mutating protocol.objects during processing, a separate objects variable is mutated, which starts out as a deep copy of protocol.objects.

Parameters:
Name Type Description
protocol Protocol

the protocol
prefix array

array of string representing the current step ID (initially []).
step object

the current step (initially protocol.steps).
objects object

a mutable copy of the protocol's objects.
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<inner> loadProtocol(a, b [, url])

Finishing loading/processing an unprocessed protocol: handle imports, directives, and file nodes

Parameters:
Name Type Argument Description
a Object

Previously loaded protocol data
b Object

The protocol to pre-process
url String <optional>

The url of the protocol
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Returns:

protocol with

Type
Object

<inner> loadUrlContent(url, filecache)

Loads the raw content at the given URL. Supported formats are: JSON, YAML, JavaScript, and pre-cached file data.

Parameters:
Name Type Description
url string

URL to load.
filecache object

map of cached file data, map from URL to data.
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Returns:

content at URL.

<inner> mergeProtocolList(protocols)

Merge a list of protocols.

Parameters:
Name Type Description
protocols array

list of protocols.
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Returns:

merged protocol.

Type
Protocol

<inner> mergeProtocols(a, b)

Merge protocols A & B, returning a new protocol.

Parameters:
Name Type Description
a Object

protocol representing the result of all previous mergeProtocols
b Object

newly loaded protocol to merge into previous protocols
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Returns:

result of merging protocol B into A.

Type
Object

<inner> postProcessProtocol(protocol)

Post-process protocol: flatten predicate list, parse wells strings for Liquid objects.

Mutates the passed protocol.

Parameters:
Name Type Description
protocol Object

A protocol.
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<inner> postProcessProtocol_variables(protocol)

For all variables that have a calculate property, handle the calculation and put the result in the value property. For 'Data' objects: if it doesn't have a value, call Design.flattenDesign; if its value is a filename, load the file into the value

Mutates protocol.

Parameters:
Name Type Description
protocol Protocol

The protocol to inspect.
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<inner> preProcessExclamationMarks(protocol, obj, path)

Any properties that have a "!" suffix are renamed to not have that suffix, overwritting an already existing property if necessary. Mutates the object.

Parameters:
Name Type Description
protocol Protocol
obj any
path array
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<inner> preProcessQuestionMarks(protocol, obj, path)

Remove properties with '?'-suffix. If the propery value has a 'value!' property, add a new property to the object without the '?'-suffix and with the given value. Mutates the object. Also add the path to the property to the protocol's fillIns

Parameters:
Name Type Description
protocol Protocol
obj any
path array
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<inner> runWithOpts(argv [, userProtocol])

Process a roboliq protocol.

Parameters:
Name Type Argument Description
argv array

command line options.
userProtocol Protocol <optional>

an optional protocol that can be directly passed into the function rather than supplied via argv; currently this is only for testing purposes.
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Returns:

Processing results with properties output (the final processed protocol) and protocol (the result of merging all input protocols).

Type
object

<inner> validateProtocol1(protocol)

Perorms a schema check, makes sure that all objects are valid.

Throws an error if the protocol isn't valid.

Parameters:
Name Type Description
protocol Protocol

The protocol to validate.
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Type Definitions

CommandHandlerResult

Command handler result.

Type:
  • Object
Properties:
Name Type Description
errors Array

array of error strings
warnings Array

array of warning strings
expansion Object | Array

an array or map of sub-steps
effects Object

a map of object property effects
alternatives Object

???
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Protocol

Protocol specification.

Type:
  • Object
Properties:
Name Type Description
objects Object
steps Object
effects Object
predicates Array
directiveHandlers Object
objectToPredicateConverters Object
commandHandlers Object
planHandlers Object
files Object
errors Object
warnings Object
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WellContents

Well contents.

Well contents are encoded as an array. The first element always holds the volume in the well. If the array has exactly one element, the volume should be 0l. If the array has exactly two elements, the second element is the name of the substance. If the array has more than two elements, each element after the volume has the same structure as the top array and they represent the mixture originally dispensed in the well.

     objects:
         plate1:
             contents:
                 A01: ["30ul", ["25ul", "water"], ["5ul", "reagent1"]]
Type:
  • array
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