Module org.cruk.clarity.api
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

    • processType

      protected ProcessTypeLink processType

    • permittedContainerTypes

      protected List<GenericTypeLink> permittedContainerTypes

    • permittedReagentCategories

      protected List<GenericTypeLink> permittedReagentCategories

    • requiredReagentKits

      protected List<ReagentKitLink> requiredReagentKits
      Since:
      2.18

    • permittedControlTypes

      protected List<ControlTypeLink> permittedControlTypes

    • permittedInstrumentTypes

      protected List<GenericTypeLink> permittedInstrumentTypes
      Since:
      2.25

    • transitions

      protected List<NextStep> transitions

    • defaultGrouping

      @Deprecated protected GenericTypeLink defaultGrouping
      Deprecated.
      Since:
      2.18

    • queueFields

      protected List<QueueField> queueFields

    • iceBucketFields

      protected List<IceBucketField> iceBucketFields
      Since:
      2.25

    • stepFields

      protected List<Field> stepFields

    • sampleFields

      protected List<Field> sampleFields

    • stepProperties

      protected List<StepProperty> stepProperties

    • stepSetup

      protected StepSetup stepSetup

    • eppTriggers

      protected List<EppTrigger> eppTriggers

    • name

      protected String name

    • uri

      protected URI uri

    • protocolUri

      protected URI protocolUri

  • Constructor Details

    • ProtocolStep

      public ProtocolStep()

    • ProtocolStep

      public ProtocolStep(URI uri)

    • ProtocolStep

      public ProtocolStep(URI uri, String name)

  • 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()

    • setProtocolStepIndex

      public void setProtocolStepIndex(Integer protocolStepIndex)

    • getProcessType

      public ProcessTypeLink getProcessType()

    • setProcessType

      public void setProcessType(Linkable<ProcessType> processType)

    • getPermittedContainerTypes

      public List<GenericTypeLink> getPermittedContainerTypes()

    • addPermittedContainer

      public String addPermittedContainer(String containerType)

    • addPermittedContainer

      public String addPermittedContainer(ContainerType type)

    • getPermittedReagentCategories

      public List<GenericTypeLink> getPermittedReagentCategories()

    • addPermittedReagentCategory

      public String addPermittedReagentCategory(String category)

    • addPermittedReagentCategory

      public String addPermittedReagentCategory(ReagentType reagentType)

    • getRequiredReagentKits

      public List<ReagentKitLink> getRequiredReagentKits()

    • addRequiredReagentKit

      public ReagentKitLink addRequiredReagentKit(Linkable<ReagentKit> kit)

    • getPermittedControlTypes

      public List<ControlTypeLink> getPermittedControlTypes()

    • addPermittedControlType

      public ControlTypeLink addPermittedControlType(Linkable<ControlType> controlType)

    • getPermittedInstrumentTypes

      public List<GenericTypeLink> getPermittedInstrumentTypes()

    • getTransitions

      public List<NextStep> getTransitions()

    • addTransition

      public NextStep addTransition(NextStep 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.

    • getQueueFields

      public List<QueueField> getQueueFields()

    • addQueueField

      public QueueField addQueueField(QueueField field)

    • getIceBucketFields

      public List<IceBucketField> getIceBucketFields()

    • addIceBucketField

      public IceBucketField addIceBucketField(IceBucketField field)

    • getStepFields

      public List<Field> getStepFields()

    • addStepField

      public Field addStepField(Field field)

    • getSampleFields

      public List<Field> getSampleFields()

    • setSampleFields

      public Field setSampleFields(Field field)

    • getStepProperties

      public List<StepProperty> getStepProperties()

    • addStepProperty

      public StepProperty addStepProperty(StepProperty property)

    • addStepProperty

      public StepProperty addStepProperty(String name, String value)

    • getStepSetup

      public StepSetup getStepSetup()

    • setStepSetup

      public void setStepSetup(StepSetup stepSetup)

    • getEppTriggers

      public List<EppTrigger> getEppTriggers()

    • addEppTriggers

      public EppTrigger addEppTriggers(EppTrigger trigger)

    • getName

      public String getName()

    • setName

      public void setName(String name)

    • getUri

      public URI getUri()
      Description copied from interface: Locatable
      Get the URI of this object.
      Specified by:
      getUri in interface Locatable
      Returns:
      The URI.

    • setUri

      public void setUri(URI uri)
      Description copied from interface: Locatable
      Set the URI of this object.
      Specified by:
      setUri in interface Locatable
      Parameters:
      uri - The new URI.

    • getProtocolUri

      public URI getProtocolUri()

    • setProtocolUri

      public void setProtocolUri(URI protocolUri)