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Patricia Grubel edited this page Mar 23, 2020 · 8 revisions

DRAFT: Preliminary Design

Basics

A Neo4j graph consists of nodes and relationships. Nodes can have labels (e.g. :Label) and properties (name value pairs like name = "Pat"). Relationships have a type (e.g. :DEPENDS_ON) and properties. Property values can be number, string, boolean, spatial (only Point), temporal (e.g. Time, Date, Duration), or composite types of the previous types (e.g. lists and maps).

BEE Workflow Graph Entities

A BEE workflow is a DAG (currently implemented in Neo4j) that represents a workflow originally specified in a CWL (Common Workflow Language) file. The fundamental structure of the workflow is based on Task nodes and DEPENDS_ON relationships. There are other nodes and relationships that are used to represent other properties of the workflow such as Metadata, Requirements, Hints, REQUIRES, etc. BEE's nodes, relationships, and properties are documented below.

:Task

  • task_id: unique ID for every task in workflow
  • name: name of task as a string
  • command: command (and parameters) to be executed
  • inputs: array of inputs to task
  • outputs: array of outputs of task
  • state: state of task during execution of workflow
    • Still designing, but may be one of:
      • WAITING: These tasks are in the database and are waiting for the tasks that they are dependent on to COMPLETE
      • READY: These tasks are ready to be executed (sent to the task manager). The tasks they depend on are COMPLETE so al their inputs are available.
      • SUBMITTED: These tasks have been sent to to the task manager but we don't know that they're actually RUNNING until we hear that from the task manager.
      • SUBMIT_FAIL: The task manager attempted to submit a job for this task but there was a failure.
      • PENDING: The task has been submitted and the ensuing job is pending execution on the machine, message via task manager.
      • RUNNING: The task is actively executing on the machine. The task manager told us that this is true.
      • ABORTED: The task has stopped because it was told to by the user or other entity. The task is not COMPLETE and tasks that depend on it can not be run (we can't assume all of its outputs were successfully created). The task manager tells us that the task was ABORTED.
      • CRASHED: An abnormal termination. In other respects it's the same as ABORTED.
      • ZOMBIE: We may use this to indicate an unknown state after a system crash or loss of connection to the task manager. Maybe.
      • COMPLETE: The task has successfully completed execution and all of its outputs have been produced. Its dependent tasks may now be set to READY.
  • :DEPENDS_ON: relationship(s) to :Tasks that must complete before this task can run
    • This relationship has no properties
  • :HAS_METADATA: relationship to :TaskMetadata for this task
    • This relationship has no properties
  • :HAS_REQUIREMENTS: relationship to :TaskRequirements (must have) for this task
    • This relationship has no properties
  • :HAS_HINTS: relationship to :TaskHints (may have) for this task
    • This relationship has no properties

:TaskMedatata, :Metadata

:TaskMetadata is also labelled as :Metadata. This is so that we can easily search the database for all metadata nodes (e.g. :TaskMetadata, :WorkflowMetadata).

:TaskRequirements, :Requirements

:TaskRequirements is also labelled as :Requirements. This is so that we can easily search the database for all requirements nodes (e.g. :TaskRequirements, :WorkflowRequirements).

:TaskHints, :Hints

:TaskHints is also labelled as :Hints. This is so that we can easily search the database for all hint nodes (e.g. :TaskHints, :WorkflowHints).

:Workflow

  • workflow_id: unique ID for the single workflow in this database
  • name: name of workflow as a string
  • inputs: array of inputs to workflow
  • outputs: array of outputs of workflow
  • :HAS_METADATA: relationship to :WorkflowMetadata for this workflow
    • This relationship has no properties
  • :HAS_REQUIREMENTS: relationship to :WorkflowRequirements (must have) for this workflow
    • This relationship has no properties
  • :HAS_HINTS: relationship to :WorkflowHints (may have) for this workflow
    • This relationship has no properties

:WorkflowMedatata, :Metadata

:WorkflowMetadata is also labelled as :Metadata. This is so that we can easily search the database for all metadata nodes (e.g. :TaskMetadata, :WorkflowMetadata).

:WorkflowRequirements, :Requirements

:WorkflowRequirements is also labelled as :Requirements. This is so that we can easily search the database for all requirements nodes (e.g. :TaskRequirements, :WorkflowRequirements).

:WorkflowHints, :Hints

:WorkflowHints is also labelled as :Hints. This is so that we can easily search the database for all hint nodes (e.g. :TaskHints, :WorkflowHints).

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