Package ca.corefacility.bioinformatics.irida.model.workflow.submission

Class AbstractAnalysisSubmission

    • Field Detail

      • id

        protected java.lang.Long id

      • name

        @NotNull
@Size(min=3)
protected @NotNull @Size(min=3) java.lang.String name

      • submitter

        protected User submitter

      • workflowId

        @NotNull
protected @NotNull java.util.UUID workflowId
        Defines the id of an installed workflow in IRIDA for performing this analysis.

      • inputParameters

        protected java.util.Map<java.lang.String,​java.lang.String> inputParameters

      • createdDate

        @NotNull
protected @NotNull java.util.Date createdDate

      • modifiedDate

        protected java.util.Date modifiedDate

      • updateSamples

        @NotNull
protected @javax.validation.constraints.NotNull boolean updateSamples

      • analysisDescription

        protected java.lang.String analysisDescription

      • emailPipelineResultCompleted

        @NotNull
protected @javax.validation.constraints.NotNull boolean emailPipelineResultCompleted

      • emailPipelineResultError

        @NotNull
protected @javax.validation.constraints.NotNull boolean emailPipelineResultError

    • Constructor Detail

      • AbstractAnalysisSubmission

        protected AbstractAnalysisSubmission()

    • Method Detail

      • setReferenceFile

        public void setReferenceFile​(ReferenceFile referenceFile)
        Sets the reference file.
        Parameters:
        referenceFile - The reference file.

      • getReferenceFile

        public java.util.Optional<ReferenceFile> getReferenceFile()
        Gets the ReferenceFile.
        Returns:
        The ReferenceFile.

      • getCreatedDate

        public java.util.Date getCreatedDate()
        Description copied from interface: Timestamped
        Get the created date of the object
        Specified by:
        getCreatedDate in interface Timestamped<java.lang.Long>
        Returns:
        A Date object of the created date

      • getModifiedDate

        public java.util.Date getModifiedDate()
        Description copied from interface: MutableIridaThing
        Get the date that this object was last modified
        Specified by:
        getModifiedDate in interface MutableIridaThing
        Returns:
        Date object of the modified date

      • setModifiedDate

        public void setModifiedDate​(java.util.Date modifiedDate)
        Description copied from interface: MutableIridaThing
        Set the modification time of this object
        Specified by:
        setModifiedDate in interface MutableIridaThing
        Parameters:
        modifiedDate - The date where this object was modified

      • getLabel

        public java.lang.String getLabel()
        Description copied from interface: IridaThing
        Get a human readable label for this object.
        Specified by:
        getLabel in interface IridaThing
        Returns:
        a human-readable label for the object.

      • getId

        public java.lang.Long getId()
        Description copied from interface: IridaThing
        Get the numerical identifier for this object
        Specified by:
        getId in interface IridaThing
        Specified by:
        getId in interface Timestamped<java.lang.Long>
        Returns:
        the numerical identifier for the object

      • setId

        public void setId​(java.lang.Long id)
        Description copied from interface: MutableIridaThing
        Set the numerical identifier for this object
        Specified by:
        setId in interface MutableIridaThing
        Parameters:
        id - The ID to set

      • getSubmitter

        public User getSubmitter()

      • setSubmitter

        public void setSubmitter​(User submitter)
        Sets the User who is submitting this analysis.
        Parameters:
        submitter - The User who is submitting this analysis.

      • getName

        public java.lang.String getName()
        Returns:
        the name

      • setName

        public void setName​(java.lang.String name)
        Parameters:
        name - the name to set

      • getWorkflowId

        public java.util.UUID getWorkflowId()
        Gets the id of the implementing workflow for this analysis.
        Returns:
        The id of the implementing workflow for this analysis.

      • setWorkflowId

        public void setWorkflowId​(java.util.UUID workflowId)
        Sets the id of the workflow for this analysis.
        Parameters:
        workflowId - The id of the workflow for this analysis.

      • getInputParameters

        public java.util.Map<java.lang.String,​java.lang.String> getInputParameters()
        Gets the input parameters for this submission.
        Returns:
        The input parameters for this submission.

      • getAnalysisDescription

        public java.lang.String getAnalysisDescription()
        Get the description of the analysis
        Returns:
        The description of the analysis

      • setAnalysisDescription

        public void setAnalysisDescription​(java.lang.String description)
        Set the description of the analysis for this submission
        Parameters:
        description - The description of the analysis

      • setUpdateSamples

        public void setUpdateSamples​(boolean updateSamples)
        Sets flag to indicate whether or not samples in the submission should be updated with analysis results following completion.
        Parameters:
        updateSamples - If true, updates samples from results on completion.

      • getUpdateSamples

        public boolean getUpdateSamples()
        Whether or not to update samples from results on completion.
        Returns:
        Update samples from results on completion.

      • setEmailPipelineResultCompleted

        public void setEmailPipelineResultCompleted​(boolean emailPipelineResultCompleted)
        Sets flag to indicate whether or not user should be emailed upon pipeline completion.
        Parameters:
        emailPipelineResultCompleted - If true, email pipeline result to user.

      • getEmailPipelineResultCompleted

        public boolean getEmailPipelineResultCompleted()
        Whether or not to send an email upon pipeline completion.
        Returns:
        Email pipeline result on completion or error.

      • setEmailPipelineResultError

        public void setEmailPipelineResultError​(boolean emailPipelineResultError)
        Sets flag to indicate whether or not user should be emailed upon pipeline error.
        Parameters:
        emailPipelineResultError - If true, email pipeline result to user.

      • getEmailPipelineResultError

        public boolean getEmailPipelineResultError()
        Whether or not to send an email upon pipeline error.
        Returns:
        Email pipeline result on completion or error.