Remove dependency on task graph branch

Signed-off-by: Ben Sherman <[email protected]>

docs/config.md

@@ -483,9 +483,6 @@ The following settings are available:
 `dag.overwrite`
 : When `true` overwrites any existing DAG file with the same name.
 
-`dag.type`
-: Can be `abstract` to render the abstract (process) DAG or `concrete` to render the concrete (task) DAG (default: `abstract`).
-
 Read the {ref}`dag-visualisation` page to learn more about the execution graph that can be generated by Nextflow.
 
 (config-docker)=

modules/nextflow/src/main/groovy/nextflow/Session.groovy

@@ -39,7 +39,6 @@ import nextflow.conda.CondaConfig
 import nextflow.config.Manifest
 import nextflow.container.ContainerConfig
 import nextflow.dag.DAG
-import nextflow.dag.ConcreteDAG
 import nextflow.exception.AbortOperationException
 import nextflow.exception.AbortSignalException
 import nextflow.exception.IllegalConfigException
@@ -194,8 +193,6 @@ class Session implements ISession {
 
     private DAG dag
 
-    private ConcreteDAG concreteDag
-
     private CacheDB cache
 
     private Barrier processesBarrier = new Barrier()
@@ -348,7 +345,6 @@ class Session implements ISession {
 
         // -- DAG object
         this.dag = new DAG()
-        this.concreteDag = new ConcreteDAG()
 
         // -- init work dir
         this.workDir = ((config.workDir ?: 'work') as Path).complete()
@@ -803,8 +799,6 @@ class Session implements ISession {
 
     DAG getDag() { this.dag }
 
-    ConcreteDAG getConcreteDAG() { this.concreteDag }
-
     ExecutorService getExecService() { execService }
 
     /**
@@ -1024,9 +1018,6 @@ class Session implements ISession {
         final trace = handler.safeTraceRecord()
         cache.putTaskAsync(handler, trace)
 
-        // save the task meta file to the task directory
-        handler.writeMetaFile()
-
         // notify the event to the observers
         for( int i=0; i<observers.size(); i++ ) {
             final observer = observers.get(i)

modules/nextflow/src/main/groovy/nextflow/dag/CytoscapeHtmlRenderer.groovy

@@ -28,7 +28,7 @@ import java.nio.file.Path
 class CytoscapeHtmlRenderer implements DagRenderer {
 
     @Override
-    void renderAbstractGraph(DAG dag, Path file) {
+    void renderDocument(DAG dag, Path file) {
         String tmplPage = readTemplate()
         String network = CytoscapeJsRenderer.renderNetwork(dag)
         file.text = tmplPage.replaceAll(~/\/\* REPLACE_WITH_NETWORK_DATA \*\//, network)

modules/nextflow/src/main/groovy/nextflow/dag/CytoscapeJsRenderer.groovy

@@ -28,7 +28,7 @@ import java.nio.file.Path
 class CytoscapeJsRenderer implements DagRenderer {
 
     @Override
-    void renderAbstractGraph(DAG dag, Path file) {
+    void renderDocument(DAG dag, Path file) {
         file.text = renderNetwork(dag)
     }
 

modules/nextflow/src/main/groovy/nextflow/dag/DAG.groovy

@@ -43,7 +43,7 @@ import nextflow.script.params.TupleOutParam
 import java.util.concurrent.atomic.AtomicLong
 
 /**
- * Model the abstract graph of a pipeline execution.
+ * Model a direct acyclic graph of the pipeline execution.
  *
  * @author Paolo Di Tommaso <[email protected]>
  */

modules/nextflow/src/main/groovy/nextflow/dag/DagRenderer.groovy

@@ -23,19 +23,10 @@ import java.nio.file.Path
  * @author Paolo Di Tommaso <[email protected]>
  * @author Mike Smoot <[email protected]>
  */
-trait DagRenderer {
+interface DagRenderer {
 
     /**
-     * Render an abstract (process) DAG.
+     * Render the dag to the specified file.
      */
-    void renderAbstractGraph(DAG dag, Path file) {
-        throw new UnsupportedOperationException("Abstract graph rendering is not supported for this file format")
-    }
-
-    /**
-     * Render a concrete (task) DAG.
-     */
-    void renderConcreteGraph(ConcreteDAG dag, Path file) {
-        throw new UnsupportedOperationException("Concrete graph rendering is not supported for this file format")
-    }
+    void renderDocument(DAG dag, Path file);
 }

modules/nextflow/src/main/groovy/nextflow/dag/DotRenderer.groovy

@@ -45,7 +45,7 @@ class DotRenderer implements DagRenderer {
     static String normalise(String str) { str.replaceAll(/[^0-9_A-Za-z]/,'') }
 
     @Override
-    void renderAbstractGraph(DAG dag, Path file) {
+    void renderDocument(DAG dag, Path file) {
         file.text = renderNetwork(dag)
     }
 

modules/nextflow/src/main/groovy/nextflow/dag/GexfRenderer.groovy

@@ -41,7 +41,7 @@ class GexfRenderer implements DagRenderer {
     }
 
     @Override
-    void renderAbstractGraph(DAG dag, Path file) {
+    void renderDocument(DAG dag, Path file) {
         final Charset charset = Charset.defaultCharset()
         Writer bw = Files.newBufferedWriter(file, charset) 
         final XMLOutputFactory xof = XMLOutputFactory.newFactory()

modules/nextflow/src/main/groovy/nextflow/dag/GraphVizRenderer.groovy

@@ -41,7 +41,7 @@ class GraphvizRenderer implements DagRenderer {
      * See http://www.graphviz.org for more info.
      */
     @Override
-    void renderAbstractGraph(DAG dag, Path target) {
+    void renderDocument(DAG dag, Path target) {
         def result = Files.createTempFile('nxf-',".$format")
         def temp = Files.createTempFile('nxf-','.dot')
         // save the DAG as `dot` to a temp file

modules/nextflow/src/main/groovy/nextflow/dag/MermaidRenderer.groovy

@@ -26,7 +26,11 @@ import java.nio.file.Path
 class MermaidRenderer implements DagRenderer {
 
     @Override
-    void renderAbstractGraph(DAG dag, Path file) {
+    void renderDocument(DAG dag, Path file) {
+        file.text = renderNetwork(dag)
+    }
+
+    String renderNetwork(DAG dag) {
         def lines = []
         lines << "flowchart TD"
 
@@ -40,7 +44,7 @@ class MermaidRenderer implements DagRenderer {
 
         lines << ""
 
-        file.text = lines.join('\n')
+        return lines.join('\n')
     }
 
     private String renderVertex(DAG.Vertex vertex) {
@@ -71,49 +75,4 @@ class MermaidRenderer implements DagRenderer {
 
         return "${edge.from.name} -->${label} ${edge.to.name}"
     }
-
-    @Override
-    void renderConcreteGraph(ConcreteDAG graph, Path file) {
-        def renderedOutputs = [] as Set<Path>
-        def numInputs = 0
-        def numOutputs = 0
-
-        def lines = []
-        lines << "flowchart TD"
-
-        // render tasks and task inputs
-        graph.nodes.values().each { task ->
-            // render task node
-            lines << "    ${task.getSlug()}[\"${task.label}\"]"
-
-            task.inputs.each { input ->
-                // render task input from predecessor
-                if( input.predecessor != null ) {
-                    final pred = graph.nodes[input.predecessor]
-                    lines << "    ${pred.getSlug()} -->|${input.name}| ${task.getSlug()}"
-                    renderedOutputs << input.path
-                }
-
-                // render task input from source node
-                else {
-                    numInputs += 1
-                    lines << "    i${numInputs}(( )) -->|${input.name}| ${task.getSlug()}"
-                }
-            }
-        }
-
-        // render task outputs with sink nodes
-        graph.nodes.values().each { task ->
-            task.outputs.each { output ->
-                if( output.path !in renderedOutputs ) {
-                    numOutputs += 1
-                    lines << "    ${task.getSlug()} -->|${output.name}| o${numOutputs}(( ))"
-                }
-            }
-        }
-
-        lines << ""
-
-        file.text = lines.join('\n')
-    }
 }

modules/nextflow/src/main/groovy/nextflow/dag/NodeMarker.groovy

@@ -40,7 +40,7 @@ class NodeMarker {
     static private Session getSession() { Global.session as Session }
 
     /**
-     * Creates a vertex in the abstract DAG representing a computing `process`
+     *  Creates a new vertex in the DAG representing a computing `process`
      *
      * @param label The label associated to the process
      * @param inputs The list of inputs entering in the process
@@ -52,7 +52,7 @@ class NodeMarker {
     }
 
     /**
-     * Creates a vertex in the abstract DAG representing a dataflow operator
+     * Creates a new DAG vertex representing a dataflow operator
      *
      * @param label The operator label
      * @param inputs The operator input(s). It can be either a single channel or a list of channels.
@@ -66,7 +66,7 @@ class NodeMarker {
     }
 
     /**
-     * Creates a vertex in the abstract DAG representing a dataflow channel source.
+     * Creates a vertex in the DAG representing a dataflow channel source.
      *
      * @param label The node description
      * @param source Either a dataflow channel or a list of channel.