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core/src/main/scala/dagr/core/execsystem2/DependencyGraph.scala
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,144 @@ | ||
| /* | ||
| * The MIT License | ||
| * | ||
| * Copyright (c) 2017 Fulcrum Genomics LLC | ||
| * | ||
| * Permission is hereby granted, free of charge, to any person obtaining a copy | ||
| * of this software and associated documentation files (the "Software"), to deal | ||
| * in the Software without restriction, including without limitation the rights | ||
| * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| * copies of the Software, and to permit persons to whom the Software is | ||
| * furnished to do so, subject to the following conditions: | ||
| * | ||
| * The above copyright notice and this permission notice shall be included in | ||
| * all copies or substantial portions of the Software. | ||
| * | ||
| * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
| * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
| * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | ||
| * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | ||
| * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | ||
| * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | ||
| * THE SOFTWARE. | ||
| * | ||
| */ | ||
|
|
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| package dagr.core.execsystem2 | ||
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| import java.util.concurrent.CountDownLatch | ||
| import java.util.concurrent.atomic.AtomicInteger | ||
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| import com.fulcrumgenomics.commons.util.LazyLogging | ||
| import dagr.core.tasksystem.Task | ||
|
|
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| /** | ||
| * A trait that classes that track and update dependencies on tasks should implement. | ||
| */ | ||
| trait DependencyGraph { | ||
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| /** Add a task to the dependency graph and returns true if the task has no dependencies, false otherwise. */ | ||
| def add(task: Task): Boolean | ||
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| /** None if the task was already added, true if the task was added and has no dependencies, false otherwise. */ | ||
| def maybeAdd(task: Task): Option[Boolean] | ||
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| /** Removes this task as a dependency for all other tasks in this dependency graph. The task should not depend on | ||
| * any tasks, and all tasks that depend on it will have their dependency on this task removed. | ||
| */ | ||
| def remove(task: Task): Seq[Task] | ||
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| /** Returns None if the task is not in the graph, true if it has dependencies, false otherwise. | ||
| */ | ||
| def hasDependencies(task: Task): Option[Boolean] | ||
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| /** Returns true if the task is in the graph, false otherwise. */ | ||
| def contains(task: Task): Boolean | ||
|
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| /** The number of tasks in the dependency graph. */ | ||
| def size: Int | ||
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| /** Throws an exception if there is a cycle in the dependency graph. The exception may have relevant debug | ||
| * information. | ||
| * @param task | ||
| */ | ||
| def exceptIfCyclicalDependency(task: Task): Unit | ||
| } | ||
|
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| object DependencyGraph { | ||
| /** Returns a default implementation of a dependency graph (i.e. a [[SimpleDependencyGraph]])*/ | ||
| def apply(): DependencyGraph = new SimpleDependencyGraph | ||
| } | ||
|
|
||
| /** | ||
| * A very simple dependency graph that uses a [[CountDownLatch]] on the number of dependencies for a [[Task]] to | ||
| * block until a task has no dependencies. | ||
| */ | ||
| private class SimpleDependencyGraph extends DependencyGraph with LazyLogging { | ||
| import scala.collection.mutable | ||
|
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| /** The map of tasks to the number of remaining unsatisfied dependencies. */ | ||
| private val graph: mutable.Map[Task, AtomicInteger] = ExecDef.concurrentMap() | ||
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| /** Adds the task to the dependency graph. Returns None if the task has already been added, true if the task | ||
| * has no dependencies, and false if it has dependencies. */ | ||
| def maybeAdd(task: Task): Option[Boolean] = this.synchronized { if (contains(task)) None else Some(add(task)) } | ||
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| /** Adds the task to the dependency graph. The task should not already be part of the graph. Returns true if the task | ||
| * has no dependencies, and false if it has dependencies */ | ||
| def add(task: Task): Boolean = this.synchronized { | ||
| require(!this.graph.contains(task), s"Task '${task.name}' is already part of the dependency graph") | ||
| this.graph.put(task, new AtomicInteger(task.tasksDependedOn.size)) | ||
| !this.hasDependencies(task).get | ||
| } | ||
|
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| /** Removes this task from the dependency graph. It should not depend on any tasks itself, and all tasks that depend | ||
| * on it will have their dependency on this task removed. Returns any dependent task that now has no more | ||
| * dependencies. | ||
| */ | ||
| def remove(task: Task): Seq[Task] = { | ||
| require(task.tasksDependedOn.isEmpty, | ||
| s"Removing a task '${task.name}' from the dependency graph that has dependencies: " | ||
| + task.tasksDependedOn.map(_.name).mkString(", ")) | ||
| // remove this as a dependency for all other tasks that depend on this task | ||
| task.tasksDependingOnThisTask.flatMap { dependent => | ||
| dependent.synchronized { | ||
| require(this.graph.contains(dependent), s"Dependent '${dependent.name}' not in the dependency graph") | ||
| task !=> dependent | ||
| val latch = this.graph(dependent) | ||
| if (latch.decrementAndGet() == 0) Some(dependent) else None | ||
| } | ||
| }.toSeq | ||
| } | ||
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| /** Returns None if the task is not part of the graph, true if the task has dependencies, false otherwise. */ | ||
| def hasDependencies(task: Task): Option[Boolean] = { | ||
| this.graph.get(task).map { e => e.get() > 0 } | ||
| } | ||
|
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| /** Returns true if the task is part of the graph, false otherwise. */ | ||
| def contains(task: Task): Boolean = this.graph.contains(task) | ||
|
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| /** Returns the number of tasks in the graph. */ | ||
| def size: Int = this.graph.size | ||
|
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| // NB: I think that the dependents in Task could be updated while were are doing this! How do we synchronize? Do we | ||
| // have a global lock in the Task object? | ||
| /** Throws an exception if there is a cycle in the dependency graph. The exception may have relevant debug | ||
| * information. | ||
| * @param task | ||
| */ | ||
| def exceptIfCyclicalDependency(task: Task): Unit = this.synchronized { | ||
| // check for cycles | ||
| if (Task.hasCycle(task)) { | ||
| logger.error("Task was part of a graph that had a cycle") | ||
| for (component <- Task.findStronglyConnectedComponents(task = task)) { | ||
| if (Task.isComponentACycle(component = component)) { | ||
| logger.error("Tasks were part of a strongly connected component with a cycle: " | ||
| + component.map(t => s"'${t.name}'").mkString(", ")) | ||
| } | ||
| } | ||
| throw new IllegalArgumentException(s"Task was part of a graph that had a cycle '${task.name}'") | ||
| } | ||
| } | ||
| } | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| /* | ||
| * The MIT License | ||
| * | ||
| * Copyright (c) 2017 Fulcrum Genomics LLC | ||
| * | ||
| * Permission is hereby granted, free of charge, to any person obtaining a copy | ||
| * of this software and associated documentation files (the "Software"), to deal | ||
| * in the Software without restriction, including without limitation the rights | ||
| * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| * copies of the Software, and to permit persons to whom the Software is | ||
| * furnished to do so, subject to the following conditions: | ||
| * | ||
| * The above copyright notice and this permission notice shall be included in | ||
| * all copies or substantial portions of the Software. | ||
| * | ||
| * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
| * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
| * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | ||
| * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | ||
| * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | ||
| * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | ||
| * THE SOFTWARE. | ||
| * | ||
| */ | ||
|
|
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| package dagr.core.execsystem2 | ||
|
|
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| import scala.collection.mutable | ||
|
|
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| private[execsystem2] object ExecDef { | ||
| /** Create a thread-safe mutable map. */ | ||
| def concurrentMap[A,B](): mutable.Map[A,B] = { | ||
| import scala.collection.convert.decorateAsScala._ | ||
| new java.util.concurrent.ConcurrentHashMap[A, B]().asScala | ||
| } | ||
|
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| /** Create a thread-safe mutable set. */ | ||
| def concurrentSet[A](): mutable.Set[A] = { | ||
| import scala.collection.convert.decorateAsScala._ | ||
| val map: java.util.Map[A, java.lang.Boolean] = new java.util.concurrent.ConcurrentHashMap[A, java.lang.Boolean]() | ||
| val set: java.util.Set[A] = java.util.Collections.newSetFromMap[A](map) | ||
| set.asScala | ||
| } | ||
| } |
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