Started refactoring

diff --git a/apps/workbench/app/controllers/collections_controller.rb b/apps/workbench/app/controllers/collections_controller.rb
index 3a1013a32cb4f4b8e73447c7b96d3fc6556c5c18..ca176b4e10d2e4264000f4a84da37b91a410d95d 100644 (file)
--- a/apps/workbench/app/controllers/collections_controller.rb
+++ b/apps/workbench/app/controllers/collections_controller.rb
@@ -52,144 +52,6 @@ class CollectionsController < ApplicationController
     self.response_body = FileStreamer.new opts
   end
 
-  def self.describe_node(uuid)
-    uuid = uuid.to_s
-    rsc = ArvadosBase::resource_class_for_uuid uuid
-    if rsc
-      "\"#{uuid}\" [label=\"#{rsc}\\n#{uuid}\",href=\"/#{rsc.to_s.underscore.pluralize rsc}/#{uuid}\"];"
-    else
-      ""
-    end
-  end
-
-  def self.job_uuid(job)
-    # "#{job[:script]}\\n#{job[:script_version]}"
-    "#{job[:script]}"
-  end
-
-  def self.collection_uuid(uuid)
-    m = /([a-f0-9]{32}(\+[0-9]+)?)(\+.*)?/.match(uuid.to_s)
-    if m
-      m[1]
-    else
-      nil
-    end
-  end
-
-  def self.script_param_edges(visited, job, prefix, sp, opts)
-    gr = ""
-    if sp and not sp.empty?
-      case sp
-      when Hash
-        sp.each do |k, v|
-          if prefix.size > 0
-            k = prefix + "::" + k.to_s
-          end
-          gr += CollectionsController::script_param_edges(visited, job, k.to_s, v, opts)
-        end
-      when Array
-        sp.each do |v|
-          gr += CollectionsController::script_param_edges(visited, job, prefix, v, opts)
-        end
-      else
-        m = collection_uuid(sp)
-        if m
-          gr += "\"#{job_uuid(job)}\" -> \"#{m}\" [label=\" #{prefix}\"];"
-          gr += CollectionsController::generate_provenance_edges(visited, m, opts)
-        end
-      end
-    end
-    gr
-  end
-
-  def self.generate_provenance_edges(pdata, uuid, opts)
-    gr = ""
-    m = CollectionsController::collection_uuid(uuid)
-    uuid = m if m
-
-    uuid = uuid.intern if uuid
-
-    if (not uuid) or uuid.empty? \
-      or (pdata[uuid] and pdata[uuid][:_visited])
-
-      #puts "already visited #{uuid}"
-      return ""
-    end
-
-    if not pdata[uuid] then 
-      return CollectionsController::describe_node(uuid) 
-    else
-      pdata[uuid][:_visited] = true
-    end
-
-    #puts "visiting #{uuid}"
-
-    if m  
-      # uuid is a collection
-      gr += CollectionsController::describe_node(uuid)
-
-      pdata.each do |k, job|
-        if job[:output] == uuid.to_s
-          gr += "\"#{uuid}\" -> \"#{job_uuid(job)}\" [label=\"output\"];"
-          gr += CollectionsController::generate_provenance_edges(pdata, job[:uuid])
-        end
-        if job[:log] == uuid.to_s
-          gr += "\"#{uuid}\" -> \"#{job_uuid(job)}\" [label=\"log\"];"
-          gr += CollectionsController::generate_provenance_edges(pdata, job[:uuid])
-        end
-      end
-    else
-      # uuid is something else
-      rsc = ArvadosBase::resource_class_for_uuid uuid.to_s
-
-      if rsc == Job
-        job = pdata[uuid]
-        if job
-          gr += CollectionsController::script_param_edges(pdata, job, "", job[:script_parameters], opts)
-        end
-      else
-        gr += CollectionsController::describe_node(uuid)
-      end
-    end
-
-    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], opts)
-      end
-    end
-
-    #puts "finished #{uuid}"
-
-    gr
-  end
-
-  def self.create_provenance_graph(pdata, uuid, opts={})
-    require 'open3'
-    
-    gr = """strict digraph {
-node [fontsize=8,shape=box];
-edge [dir=back,fontsize=8];"""
-
-    #puts "pdata is #{pdata}"
-
-    gr += CollectionsController::generate_provenance_edges(pdata, uuid, opts)
-
-    gr += "}"
-    svg = ""
-
-    Open3.popen2("dot", "-Tsvg") do |stdin, stdout, wait_thr|
-      stdin.print(gr)
-      stdin.close
-      svg = stdout.read()
-      wait_thr.value
-      stdout.close()
-    end
-
-    svg = svg.sub(/<\?xml.*?\?>/m, "")
-    svg = svg.sub(/<!DOCTYPE.*?>/m, "")
-  end
 
   def show
     return super if !@object
@@ -237,7 +99,7 @@ edge [dir=back,fontsize=8];"""
     end
     
     Collection.where(uuid: @object.uuid).each do |u|
-      @prov_svg = CollectionsController::create_provenance_graph u.provenance, u.uuid
+      @prov_svg = ProvenanceHelper::create_provenance_graph u.provenance, u.uuid
     end
   end
 

diff --git a/apps/workbench/app/helpers/provenance_helper.rb b/apps/workbench/app/helpers/provenance_helper.rb
new file mode 100644 (file)
index 0000000..c393a1b
--- /dev/null
+++ b/apps/workbench/app/helpers/provenance_helper.rb
@@ -0,0 +1,140 @@
+class ProvenanceHelper
+  def self.describe_node(uuid)
+    uuid = uuid.to_s
+    rsc = ArvadosBase::resource_class_for_uuid uuid
+    if rsc
+      "\"#{uuid}\" [label=\"#{rsc}\\n#{uuid}\",href=\"/#{rsc.to_s.underscore.pluralize rsc}/#{uuid}\"];"
+    else
+      ""
+    end
+  end
+
+  def self.job_uuid(job)
+    # "#{job[:script]}\\n#{job[:script_version]}"
+    "#{job[:script]}"
+  end
+
+  def self.collection_uuid(uuid)
+    m = /([a-f0-9]{32}(\+[0-9]+)?)(\+.*)?/.match(uuid.to_s)
+    if m
+      m[1]
+    else
+      nil
+    end
+  end
+
+  def self.script_param_edges(visited, job, prefix, sp, opts)
+    gr = ""
+    if sp and not sp.empty?
+      case sp
+      when Hash
+        sp.each do |k, v|
+          if prefix.size > 0
+            k = prefix + "::" + k.to_s
+          end
+          gr += CollectionsController::script_param_edges(visited, job, k.to_s, v, opts)
+        end
+      when Array
+        sp.each do |v|
+          gr += CollectionsController::script_param_edges(visited, job, prefix, v, opts)
+        end
+      else
+        m = collection_uuid(sp)
+        if m
+          gr += "\"#{job_uuid(job)}\" -> \"#{m}\" [label=\" #{prefix}\"];"
+          gr += CollectionsController::generate_provenance_edges(visited, m, opts)
+        end
+      end
+    end
+    gr
+  end
+
+  def self.generate_provenance_edges(pdata, uuid, opts)
+    gr = ""
+    m = CollectionsController::collection_uuid(uuid)
+    uuid = m if m
+
+    uuid = uuid.intern if uuid
+
+    if (not uuid) or uuid.empty? \
+      or (pdata[uuid] and pdata[uuid][:_visited])
+
+      #puts "already visited #{uuid}"
+      return ""
+    end
+
+    if not pdata[uuid] then 
+      return CollectionsController::describe_node(uuid) 
+    else
+      pdata[uuid][:_visited] = true
+    end
+
+    #puts "visiting #{uuid}"
+
+    if m  
+      # uuid is a collection
+      gr += CollectionsController::describe_node(uuid)
+
+      pdata.each do |k, job|
+        if job[:output] == uuid.to_s
+          gr += "\"#{uuid}\" -> \"#{job_uuid(job)}\" [label=\"output\"];"
+          gr += CollectionsController::generate_provenance_edges(pdata, job[:uuid])
+        end
+        if job[:log] == uuid.to_s
+          gr += "\"#{uuid}\" -> \"#{job_uuid(job)}\" [label=\"log\"];"
+          gr += CollectionsController::generate_provenance_edges(pdata, job[:uuid])
+        end
+      end
+    else
+      # uuid is something else
+      rsc = ArvadosBase::resource_class_for_uuid uuid.to_s
+
+      if rsc == Job
+        job = pdata[uuid]
+        if job
+          gr += CollectionsController::script_param_edges(pdata, job, "", job[:script_parameters], opts)
+        end
+      else
+        gr += CollectionsController::describe_node(uuid)
+      end
+    end
+
+    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], opts)
+      end
+    end
+
+    #puts "finished #{uuid}"
+
+    gr
+  end
+
+  def self.create_provenance_graph(pdata, uuid, opts={})
+    require 'open3'
+    
+    gr = """strict digraph {
+node [fontsize=8,shape=box];
+edge [dir=back,fontsize=8];"""
+
+    #puts "pdata is #{pdata}"
+
+    gr += CollectionsController::generate_provenance_edges(pdata, uuid, opts)
+
+    gr += "}"
+    svg = ""
+
+    Open3.popen2("dot", "-Tsvg") do |stdin, stdout, wait_thr|
+      stdin.print(gr)
+      stdin.close
+      svg = stdout.read()
+      wait_thr.value
+      stdout.close()
+    end
+
+    svg = svg.sub(/<\?xml.*?\?>/m, "")
+    svg = svg.sub(/<!DOCTYPE.*?>/m, "")
+  end
+end