Package org.intermine.task

Class PrecomputeTask

  • public class PrecomputeTask
extends org.apache.tools.ant.Task
    A Task that reads a list of queries from a properties file (eg. testmodel_precompute.properties) and calls ObjectStoreInterMineImpl.precompute() using the Query.
    Author:
    Kim Rutherford

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected int minRows  
      protected java.lang.String objectStoreAlias  
      protected java.lang.String precomputePropertiesPath  
      protected static int THREAD_COUNT  

      • Fields inherited from class org.apache.tools.ant.Task

        description, location, target, taskName, taskType, wrapper

      • Fields inherited from class org.apache.tools.ant.ProjectComponent

        project

    • Constructor Summary

      Constructors 
      Constructor Description
      PrecomputeTask()  

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      protected static java.util.List<Query> constructQueries​(boolean createAllOrders, ObjectStore os, java.lang.String path, java.lang.String precomputeKey)
      Create queries for given path.
      void execute()
      protected ParallelPrecomputer getPrecomputer​(ObjectStoreInterMineImpl os)
      Create a ParallelPrecomputer.
      void precompute​(boolean createAllOrders, ObjectStore os, int minRows)
      Create precomputed tables for the given ObjectStore.
      void setMinRows​(java.lang.Integer minRows)
      Set the minimum row count for precomputed queries.
      void setObjectStoreAlias​(java.lang.String objectStoreAlias)  
      void setPrecomputePropertiesPath​(java.lang.String precomputePropertiesPath)  

      • Methods inherited from class org.apache.tools.ant.Task

        getDescription, getLocation, getOwningTarget, getRuntimeConfigurableWrapper, getTaskName, getTaskType, getWrapper, handleErrorFlush, handleErrorOutput, handleFlush, handleInput, handleOutput, init, isInvalid, log, log, maybeConfigure, perform, reconfigure, setDescription, setLocation, setOwningTarget, setRuntimeConfigurableWrapper, setTaskName, setTaskType

      • Methods inherited from class org.apache.tools.ant.ProjectComponent

        getProject, setProject

      • Methods inherited from class java.lang.Object

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

    • Field Detail

      • objectStoreAlias

        protected java.lang.String objectStoreAlias

      • precomputePropertiesPath

        protected java.lang.String precomputePropertiesPath

      • minRows

        protected int minRows

    • Constructor Detail

      • PrecomputeTask

        public PrecomputeTask()

    • Method Detail

      • setObjectStoreAlias

        public void setObjectStoreAlias​(java.lang.String objectStoreAlias)
        Parameters:
        objectStoreAlias - name of objectstore to use

      • setPrecomputePropertiesPath

        public void setPrecomputePropertiesPath​(java.lang.String precomputePropertiesPath)
        Parameters:
        precomputePropertiesPath - location of config file for precomputing

      • setMinRows

        public void setMinRows​(java.lang.Integer minRows)
        Set the minimum row count for precomputed queries. Queries that are estimated to have less than this number of rows will not be precomputed.
        Parameters:
        minRows - the minimum row count

      • execute

        public void execute()
        Overrides:
        execute in class org.apache.tools.ant.Task

      • precompute

        public void precompute​(boolean createAllOrders,
                       ObjectStore os,
                       int minRows)
        Create precomputed tables for the given ObjectStore.
        Parameters:
        createAllOrders - if true construct all permutations of order by for the QueryClass objects on the from list
        os - The ObjectStore to add precomputed tables to
        minRows - don't create any precomputed tables with less than this many rows
        Throws:
        org.apache.tools.ant.BuildException - if something goes wrong

      • getPrecomputer

        protected ParallelPrecomputer getPrecomputer​(ObjectStoreInterMineImpl os)
        Create a ParallelPrecomputer.
        Parameters:
        os - an ObjectStoreInterMineImpl
        Returns:
        a ParallelPrecomputer for the ObjectStore

      • constructQueries

        protected static java.util.List<Query> constructQueries​(boolean createAllOrders,
                                                        ObjectStore os,
                                                        java.lang.String path,
                                                        java.lang.String precomputeKey)
                                                 throws java.lang.ClassNotFoundException,
                                                        ObjectStoreException
        Create queries for given path. If path has a '+' next to any class then expand to include all subclasses.
        Parameters:
        createAllOrders - if true construct all permutations of order by for the QueryClass objects on the from list
        os - the ObjectStore
        path - the path to construct a query for
        precomputeKey - the key of the path in the config file, for logging
        Returns:
        a list of queries
        Throws:
        java.lang.ClassNotFoundException - if problem processing path
        java.lang.IllegalArgumentException - if problem processing path
        ObjectStoreException - if there is a problem running a query to process the path