Workbench is able to put together a graph from the provenance document served by...

diff --git a/apps/workbench/app/controllers/collections_controller.rb b/apps/workbench/app/controllers/collections_controller.rb
index 2508d3d49a7c28404800a31ddb8c2b9a5b76b648..57b9bab413b92f734bfecd8c5f964e371c6e1fdf 100644 (file)
--- a/apps/workbench/app/controllers/collections_controller.rb
+++ b/apps/workbench/app/controllers/collections_controller.rb
@@ -52,27 +52,28 @@ class CollectionsController < ApplicationController
     self.response_body = FileStreamer.new opts
   end
 
-  def describe_node(uuid)
+  def self.describe_node(uuid)
+    uuid = uuid.to_s
     rsc = ArvadosBase::resource_class_for_uuid uuid
     if rsc
-      "\"#{uuid}\" [label=\"#{rsc}\\n#{uuid}\",href=\"#{url_for rsc}/#{uuid}\"];"
+      "\"#{uuid}\" [label=\"#{rsc}\\n#{uuid}\",href=\"/#{rsc.to_s.underscore.pluralize rsc}/#{uuid}\"];"
     else
       ""
     end
   end
 
-  def describe_script(job)
-    #"""\"#{job.script_version}\" [label=\"#{job.script}: #{job.script_version}\"];
+  def self.describe_script(job)
+    # """\"#{job.script_version}\" [label=\"#{job.script}: #{job.script_version}\"];
     #   \"#{job.uuid}\" -> \"#{job.script_version}\" [label=\"script\"];"""
     "\"#{job.uuid}\" [label=\"#{job.script}\\n#{job.script_version}\"];"
   end
 
-  def job_uuid(job)
+  def self.job_uuid(job)
     "#{job.script}\\n#{job.script_version}"
   end
 
-  def collection_uuid(uuid)
-    m = /([a-f0-9]{32}(\+[0-9]+)?)(\+.*)?/.match(uuid)
+  def self.collection_uuid(uuid)
+    m = /([a-f0-9]{32}(\+[0-9]+)?)(\+.*)?/.match(uuid.to_s)
     if m
       m[1]
     else
@@ -80,7 +81,7 @@ class CollectionsController < ApplicationController
     end
   end
 
-  def script_param_edges(visited, job, prefix, sp)
+  def self.script_param_edges(visited, job, prefix, sp)
     gr = ""
     if sp and not sp.empty?
       case sp
@@ -89,89 +90,93 @@ class CollectionsController < ApplicationController
           if prefix.size > 0
             k = prefix + "::" + k.to_s
           end
-          gr += script_param_edges(visited, job, k.to_s, v)
+          gr += CollectionsController::script_param_edges(visited, job, k.to_s, v)
         end
       when Array
         sp.each do |v|
-          gr += script_param_edges(visited, job, prefix, v)
+          gr += CollectionsController::script_param_edges(visited, job, prefix, v)
         end
       else
         m = collection_uuid(sp)
         if m
           gr += "\"#{job_uuid(job)}\" -> \"#{m}\" [label=\" #{prefix}\"];"
-          gr += generate_provenance_edges(visited, m)
+          gr += CollectionsController::generate_provenance_edges(visited, m)
         end
       end
     end
     gr
   end
 
-  def generate_provenance_edges(visited, uuid)
+  def self.generate_provenance_edges(pdata, uuid)
     gr = ""
-    m = collection_uuid(uuid)
+    m = CollectionsController::collection_uuid(uuid)
+    uuid = m if m
 
-    if not uuid or uuid.empty? or visited[uuid] or visited[m]
+    uuid = uuid.intern if uuid
+
+    if (not uuid) or uuid.empty? \
+      or (pdata[uuid] and pdata[uuid][:_visited]) \
+      or (not pdata[uuid])
+
+      puts "already visited #{uuid}"
       return ""
     end
 
-    #puts "visiting #{uuid}"
+    puts "visiting #{uuid}"
+
+    pdata[uuid][:_visited] = true
 
     if m  
       # uuid is a collection
-      uuid = m
-      visited[uuid] = true
-
-      gr += describe_node(uuid)
+      gr += CollectionsController::describe_node(uuid)
 
-      Job.where(output: uuid).each do |job|
-        #gr += describe_node(job_uuid(job)) 
-        gr += "\"#{uuid}\" -> \"#{job_uuid(job)}\" [label=\" output\"];"
-        gr += generate_provenance_edges(visited, job.uuid)
-      end
-
-      Job.where(log: uuid).each do |job|
-        #gr += describe_node(job_uuid(job))
-        gr += "\"#{uuid}\" -> \"#{job_uuid(job)}\" [label=\" log\"];"
-        gr += generate_provenance_edges(visited, job.uuid)
+      pdata.each do |k, job|
+        if job[:output] == uuid
+          gr += "\"#{uuid}\" -> \"#{job_uuid(job)}\" [label=\"output\"];"
+          gr += CollectionsController::generate_provenance_edges(pdata, job[:uuid])
+        end
+        if job[:log] == uuid
+          gr += "\"#{uuid}\" -> \"#{job_uuid(job)}\" [label=\"log\"];"
+          gr += CollectionsController::generate_provenance_edges(pdata, job[:uuid])
+        end
       end
-      
     else
-      visited[uuid] = true
-
       # uuid is something else
       rsc = ArvadosBase::resource_class_for_uuid uuid
 
       if rsc == Job
-        Job.where(uuid: uuid).each do |job|
-          gr += script_param_edges(visited, job, "", job.script_parameters)
-          #gr += describe_script(job)
+        job = pdata[uuid]
+        if job
+          gr += CollectionsController::script_param_edges(pdata, job, "", job.script_parameters)
         end
       else
-        gr += describe_node(uuid)
+        gr += CollectionsController::describe_node(uuid)
       end
     end
 
-    Link.where(head_uuid: uuid, link_class: "provenance").each do |link|
-      gr += describe_node(link.tail_uuid)
-      gr += "\"#{link.head_uuid}\" -> \"#{link.tail_uuid}\" [label=\" #{link.name}\", href=\"/links/#{link.uuid}\"];"
-      gr += generate_provenance_edges(visited, link.tail_uuid)
+    pdata.each do |k, link|
+      if link[:head_uuid] == uuid.to_s and link[:link_class] == "provenance"
+        gr += CollectionsController::describe_node(link[:tail_uuid])
+        gr += "\"#{link[:head_uuid]}\" -> \"#{link[:tail_uuid]}\" [label=\" #{link[:name]}\", href=\"/links/#{link[:uuid]}\"];"
+        gr += CollectionsController::generate_provenance_edges(pdata, link[:tail_uuid])
+      end
     end
 
-    #puts "finished #{uuid}"
+    puts "finished #{uuid}"
 
     gr
   end
 
-  def create_provenance_graph(uuid)
+  def self.create_provenance_graph(pdata, uuid)
     require 'open3'
     
     gr = """strict digraph {
-//rankdir=LR;
 node [fontsize=8,shape=box];
 edge [dir=back,fontsize=8];"""
 
-    visited = {}
-    gr += generate_provenance_edges(visited, uuid)
+    puts "pdata is #{pdata}"
+
+    gr += CollectionsController::generate_provenance_edges(pdata, uuid)
 
     gr += "}"
     svg = ""
@@ -232,8 +237,10 @@ edge [dir=back,fontsize=8];"""
         @sourcedata[collection.uuid][:collection] = collection
       end
     end
-
-    @prov_svg = create_provenance_graph(@object.uuid)
+    
+    Collection.where(uuid: @object.uuid).each do |u|
+      @prov_svg = CollectionsController::create_provenance_graph u.provenance, u.uuid
+    end
   end
 
   protected

diff --git a/apps/workbench/app/models/collection.rb b/apps/workbench/app/models/collection.rb
index cfbb6405041a41f5efb0de50f11ab6dbbf179835..94a2b959164200e874869a8f15b6e9724e04b7c3 100644 (file)
--- a/apps/workbench/app/models/collection.rb
+++ b/apps/workbench/app/models/collection.rb
@@ -12,4 +12,8 @@ class Collection < ArvadosBase
   def attribute_editable?(attr)
     false
   end
+
+  def provenance
+    $arvados_api_client.api "collections/#{self.uuid}/", "provenance"
+  end
 end