Package ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy

Class GalaxyWorkflowService

  • public class GalaxyWorkflowService
extends java.lang.Object
    Handles operating with workflows in Galaxy.

    • Constructor Summary

      Constructors 
      Constructor Description
      GalaxyWorkflowService​(com.github.jmchilton.blend4j.galaxy.WorkflowsClient workflowsClient, java.nio.charset.Charset workflowCharset)
      Constructs a new GalaxyWorkflowSubmitter with the given information.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void deleteWorkflow​(java.lang.String workflowId)
      Deletes a workflow with the given id.
      com.github.jmchilton.blend4j.galaxy.beans.WorkflowDetails getWorkflowDetails​(java.lang.String workflowId)
      Gets details about a given workflow.
      java.lang.String getWorkflowInputId​(com.github.jmchilton.blend4j.galaxy.beans.WorkflowDetails workflowDetails, java.lang.String workflowInputLabel)
      Given a WorkflowDetails an a workflowInputLabel find the corresponding id for this input.
      com.github.jmchilton.blend4j.galaxy.beans.WorkflowInvocationOutputs runWorkflow​(WorkflowInputsGalaxy inputs)
      Attempts to run the workflow definined by the given WorkflowInputs object.
      java.lang.String uploadGalaxyWorkflow​(java.nio.file.Path workflowFile)
      Uploads a workflow definined in the given file to Galaxy.

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • GalaxyWorkflowService

        public GalaxyWorkflowService​(com.github.jmchilton.blend4j.galaxy.WorkflowsClient workflowsClient,
                             java.nio.charset.Charset workflowCharset)
        Constructs a new GalaxyWorkflowSubmitter with the given information.
        Parameters:
        workflowsClient - The WorkflowsClient used to connect to Galaxy workflows.
        workflowCharset - The Charset to use for reading in workflows from files.

    • Method Detail

      • uploadGalaxyWorkflow

        public java.lang.String uploadGalaxyWorkflow​(java.nio.file.Path workflowFile)
                                      throws java.io.IOException,
                                             WorkflowUploadException
        Uploads a workflow definined in the given file to Galaxy.
        Parameters:
        workflowFile - The file to upload.
        Returns:
        The id of the workflow in Galaxy.
        Throws:
        java.io.IOException - If there was an issue reading the file.
        WorkflowUploadException - If there was an issue uploading the workflow to Galaxy.

      • getWorkflowInputId

        public java.lang.String getWorkflowInputId​(com.github.jmchilton.blend4j.galaxy.beans.WorkflowDetails workflowDetails,
                                           java.lang.String workflowInputLabel)
                                    throws WorkflowException
        Given a WorkflowDetails an a workflowInputLabel find the corresponding id for this input.
        Parameters:
        workflowDetails - The WorkflowDetails describing the workflow.
        workflowInputLabel - The label defining the input to search for.
        Returns:
        The id of the input corresponding to the passed label.
        Throws:
        WorkflowException - If no such input id could be found.

      • getWorkflowDetails

        public com.github.jmchilton.blend4j.galaxy.beans.WorkflowDetails getWorkflowDetails​(java.lang.String workflowId)
                                                                             throws WorkflowException
        Gets details about a given workflow.
        Parameters:
        workflowId - The id of the workflow.
        Returns:
        A details object for this workflow.
        Throws:
        WorkflowException - If there was an issue getting the details of the workflow.

      • runWorkflow

        public com.github.jmchilton.blend4j.galaxy.beans.WorkflowInvocationOutputs runWorkflow​(WorkflowInputsGalaxy inputs)
                                                                                throws WorkflowException
        Attempts to run the workflow definined by the given WorkflowInputs object.
        Parameters:
        inputs - The inputs to the workflow.
        Returns:
        A WorkflowOutputs object with information on output files in the workflow.
        Throws:
        WorkflowException - If there was an issue running the workflow.