Module com.genologics.ri
Package com.genologics.ri.stepconfiguration

Class ProtocolStep

java.lang.Object
com.genologics.ri.stepconfiguration.ProtocolStep
All Implemented Interfaces:
Linkable<ProtocolStep>, Locatable, Serializable
public class ProtocolStep extends Object implements Linkable<ProtocolStep>, Serializable

Detailed representation of a Step

Steps are the elements that compose protocols. They have various properties regarding different UDFs contained on each view of the step as well as configuration option and filters

See Also:

  • Field Details

    • ID_EXTRACTOR_PATTERN

      public static final Pattern ID_EXTRACTOR_PATTERN
      Regular expression to extract protocol id and protocol step id from a protocol step URI.
      Since:
      2.22

    • protocolStepIndex

      protected Integer protocolStepIndex
      The index of this step within the protocol.

    • processType

      protected ProcessTypeLink processType
      The process type associated with this step.

    • permittedContainerTypes

      protected List<GenericTypeLink> permittedContainerTypes
      List of permitted container types for this step.

    • permittedReagentCategories

      protected List<GenericTypeLink> permittedReagentCategories
      List of permitted reagent categories for this step.

    • requiredReagentKits

      protected List<ReagentKitLink> requiredReagentKits
      List of required reagent kits for this step.
      Since:
      2.18

    • permittedControlTypes

      protected List<ControlTypeLink> permittedControlTypes
      List of permitted control types for this step.

    • permittedInstrumentTypes

      protected List<GenericTypeLink> permittedInstrumentTypes
      List of permitted instrument types for this step.
      Since:
      2.25

    • transitions

      protected List<NextStep> transitions
      List of transitions to next steps in the protocol.

    • defaultGrouping

      @Deprecated protected GenericTypeLink defaultGrouping
      Deprecated.
      Please use "<milestone>DefaultGrouping" in a StepProperty field instead.
      Default field for grouping samples in the queue view.
      Since:
      2.18

    • queueFields

      protected List<QueueField> queueFields
      List of fields to display in the queue view.

    • iceBucketFields

      protected List<IceBucketField> iceBucketFields
      List of fields to display in the ice bucket view.
      Since:
      2.25

    • stepFields

      protected List<Field> stepFields
      List of fields to display on the step.

    • sampleFields

      protected List<Field> sampleFields
      List of fields to display for samples.

    • stepProperties

      protected List<StepProperty> stepProperties
      List of step properties.

    • stepSetup

      protected StepSetup stepSetup
      Configuration for the step setup view.

    • eppTriggers

      protected List<EppTrigger> eppTriggers
      List of EPP triggers for this step.

    • name

      protected String name
      The name of the protocol step.

    • uri

      protected URI uri
      The URI of the protocol step.

    • protocolUri

      protected URI protocolUri
      The URI of the protocol this step belongs to.

  • Constructor Details

    • ProtocolStep

      public ProtocolStep()
      Default constructor.

    • ProtocolStep

      public ProtocolStep(URI uri)
      Constructor with URI.
      Parameters:
      uri - The URI of the protocol step.

    • ProtocolStep

      public ProtocolStep(URI uri, String name)
      Constructor with URI and name.
      Parameters:
      uri - The URI of the protocol step.
      name - The name of the protocol step.

  • Method Details

    • getId

      public Integer getId()
      Get the numeric identifier for this protocol step from its URI.
      Returns:
      The protocol step id, or null if either the URI is not set or it doesn't match the form expected for a protocol step URI.
      Since:
      2.22

    • getProtocolId

      public Integer getProtocolId()
      Get the numeric identifier for this step's protocol from its URI.
      Returns:
      The protocol id, or null if either the URI is not set or it doesn't match the form expected for a protocol step URI.
      Since:
      2.22

    • getProtocolStepIndex

      public Integer getProtocolStepIndex()
      Gets the protocol step index.
      Returns:
      The protocol step index.

    • setProtocolStepIndex

      public void setProtocolStepIndex(Integer protocolStepIndex)
      Sets the protocol step index.
      Parameters:
      protocolStepIndex - The protocol step index.

    • getProcessType

      public ProcessTypeLink getProcessType()
      Gets the process type for this step.
      Returns:
      The process type link.

    • setProcessType

      public void setProcessType(Linkable<ProcessType> processType)
      Sets the process type for this step.
      Parameters:
      processType - The linkable process type.

    • getPermittedContainerTypes

      public List<GenericTypeLink> getPermittedContainerTypes()
      Gets the list of permitted container types for this step.
      Returns:
      The list of permitted container types.

    • addPermittedContainer

      public String addPermittedContainer(String containerType)
      Adds a permitted container type by name.
      Parameters:
      containerType - The container type name.
      Returns:
      The container type name.

    • addPermittedContainer

      public String addPermittedContainer(ContainerType type)
      Adds a permitted container type from a ContainerType entity.
      Parameters:
      type - The container type entity.
      Returns:
      The container type name.

    • getPermittedReagentCategories

      public List<GenericTypeLink> getPermittedReagentCategories()
      Gets the list of permitted reagent categories for this step.
      Returns:
      The list of permitted reagent categories.

    • addPermittedReagentCategory

      public String addPermittedReagentCategory(String category)
      Adds a permitted reagent category by name.
      Parameters:
      category - The reagent category name.
      Returns:
      The reagent category name.

    • addPermittedReagentCategory

      public String addPermittedReagentCategory(ReagentType reagentType)
      Adds a permitted reagent category from a ReagentType entity.
      Parameters:
      reagentType - The reagent type entity.
      Returns:
      The reagent category name, or null if not available.

    • getRequiredReagentKits

      public List<ReagentKitLink> getRequiredReagentKits()
      Gets the list of required reagent kits for this step.
      Returns:
      The list of required reagent kits.

    • addRequiredReagentKit

      public ReagentKitLink addRequiredReagentKit(Linkable<ReagentKit> kit)
      Adds a required reagent kit.
      Parameters:
      kit - The linkable reagent kit.
      Returns:
      The reagent kit link.

    • getPermittedControlTypes

      public List<ControlTypeLink> getPermittedControlTypes()
      Gets the list of permitted control types for this step.
      Returns:
      The list of permitted control types.

    • addPermittedControlType

      public ControlTypeLink addPermittedControlType(Linkable<ControlType> controlType)
      Adds a permitted control type.
      Parameters:
      controlType - The linkable control type.
      Returns:
      The control type link.

    • getPermittedInstrumentTypes

      public List<GenericTypeLink> getPermittedInstrumentTypes()
      Gets the list of permitted instrument types for this step.
      Returns:
      The list of permitted instrument types.

    • getTransitions

      public List<NextStep> getTransitions()
      Gets the list of transitions to next steps.
      Returns:
      The list of transitions.

    • addTransition

      public NextStep addTransition(NextStep transition)
      Adds a transition to a next step.
      Parameters:
      transition - The next step transition.
      Returns:
      The next step transition.

    • getDefaultGrouping

      @Deprecated public GenericTypeLink getDefaultGrouping()
      Deprecated.
      Please use "<milestone>DefaultGrouping" (for example, "queueDefaultGrouping") in a StepProperty field instead.
      Field by which the queue view samples will be grouped by default.
      Returns:
      Grouping field.

    • setDefaultGrouping

      @Deprecated public void setDefaultGrouping(GenericTypeLink defaultGrouping)
      Deprecated.
      Please use "<milestone>DefaultGrouping" (for example, "queueDefaultGrouping") in a StepProperty field instead.
      Sets the field by which the queue view samples will be grouped by default.
      Parameters:
      defaultGrouping - The grouping field.

    • getQueueFields

      public List<QueueField> getQueueFields()
      Gets the list of queue fields for this step.
      Returns:
      The list of queue fields.

    • addQueueField

      public QueueField addQueueField(QueueField field)
      Adds a queue field.
      Parameters:
      field - The queue field.
      Returns:
      The queue field.

    • getIceBucketFields

      public List<IceBucketField> getIceBucketFields()
      Gets the list of ice bucket fields for this step.
      Returns:
      The list of ice bucket fields.

    • addIceBucketField

      public IceBucketField addIceBucketField(IceBucketField field)
      Adds an ice bucket field.
      Parameters:
      field - The ice bucket field.
      Returns:
      The ice bucket field.

    • getStepFields

      public List<Field> getStepFields()
      Gets the list of step fields.
      Returns:
      The list of step fields.

    • addStepField

      public Field addStepField(Field field)
      Adds a step field.
      Parameters:
      field - The step field.
      Returns:
      The step field.

    • getSampleFields

      public List<Field> getSampleFields()
      Gets the list of sample fields.
      Returns:
      The list of sample fields.

    • setSampleFields

      public Field setSampleFields(Field field)
      Adds a sample field.
      Parameters:
      field - The sample field.
      Returns:
      The sample field.

    • getStepProperties

      public List<StepProperty> getStepProperties()
      Gets the list of step properties.
      Returns:
      The list of step properties.

    • addStepProperty

      public StepProperty addStepProperty(StepProperty property)
      Adds a step property.
      Parameters:
      property - The step property.
      Returns:
      The step property.

    • addStepProperty

      public StepProperty addStepProperty(String name, String value)
      Adds a step property with name and value.
      Parameters:
      name - The property name.
      value - The property value.
      Returns:
      The step property.

    • getStepSetup

      public StepSetup getStepSetup()
      Gets the step setup configuration.
      Returns:
      The step setup.

    • setStepSetup

      public void setStepSetup(StepSetup stepSetup)
      Sets the step setup configuration.
      Parameters:
      stepSetup - The step setup.

    • getEppTriggers

      public List<EppTrigger> getEppTriggers()
      Gets the list of EPP triggers for this step.
      Returns:
      The list of EPP triggers.

    • addEppTriggers

      public EppTrigger addEppTriggers(EppTrigger trigger)
      Adds an EPP trigger.
      Parameters:
      trigger - The EPP trigger.
      Returns:
      The EPP trigger.

    • getName

      public String getName()
      Gets the name of the protocol step.
      Returns:
      The step name.

    • setName

      public void setName(String name)
      Sets the name of the protocol step.
      Parameters:
      name - The step name.

    • getUri

      public URI getUri()
      Gets the URI of the protocol step.
      Specified by:
      getUri in interface Locatable
      Returns:
      The step URI.

    • setUri

      public void setUri(URI uri)
      Sets the URI of the protocol step.
      Specified by:
      setUri in interface Locatable
      Parameters:
      uri - The step URI.

    • getProtocolUri

      public URI getProtocolUri()
      Gets the URI of the protocol this step belongs to.
      Returns:
      The protocol URI.

    • setProtocolUri

      public void setProtocolUri(URI protocolUri)
      Sets the URI of the protocol this step belongs to.
      Parameters:
      protocolUri - The protocol URI.

    • getLink

      public LimsLink<ProtocolStep> getLink()
      Get a concrete link object to this Linkable thing.
      Specified by:
      getLink in interface Linkable<ProtocolStep>
      Returns:
      A LimsLink to this object.