module ProvenanceHelper
- def self.describe_node(pdata, uuid)
- rsc = ArvadosBase::resource_class_for_uuid uuid.to_s
- if rsc
- href = "/#{rsc.to_s.underscore.pluralize rsc}/#{uuid}"
-
- #"\"#{uuid}\" [label=\"#{rsc}\\n#{uuid}\",href=\"#{href}\"];\n"
- if rsc == Collection
- if pdata[uuid]
- #puts pdata[uuid]
- if pdata[uuid][:name]
- return "\"#{uuid}\" [label=\"#{pdata[uuid][:name]}\",href=\"#{href}\",shape=oval];\n"
- else
- i = 0
- label = ""
- while i < 3 and i < pdata[uuid].files.length
- label += "\\n" unless label == ""
- label += pdata[uuid].files[i][1]
- i += 1
- end
- if i < pdata[uuid].files.length
- label += "\\n⋮"
- end
- return "\"#{uuid}\" [label=\"#{label}\",href=\"#{href}\",shape=oval];\n"
- end
+
+ class GenerateGraph
+ def initialize(pdata, opts)
+ @pdata = pdata
+ @opts = opts
+ @visited = {}
+ @jobs = {}
+ end
+
+ def self.collection_uuid(uuid)
+ m = CollectionsHelper.match(uuid)
+ if m
+ if m[2]
+ return m[1]+m[2]
+ else
+ return m[1]
end
- return "\"#{uuid}\" [label=\"#{rsc}\",href=\"#{href}\"];\n"
+ # Collection.where(uuid: ['contains', m[1]]).each do |u|
+ # puts "fixup #{uuid} to #{u.uuid}"
+ # return u.uuid
+ # end
+ #end
+ else
+ nil
end
end
- return ""
- end
- def self.job_uuid(job)
- # "#{job[:script]}\\n#{job[:script_version]}"
- "#{job[:script]}"
- end
+ def url_for u
+ p = { :host => @opts[:request].host,
+ :port => @opts[:request].port,
+ :protocol => @opts[:request].protocol }
+ p.merge! u
+ Rails.application.routes.url_helpers.url_for (p)
+ end
- def self.collection_uuid(uuid)
- m = /([a-f0-9]{32}(\+[0-9]+)?)(\+.*)?/.match(uuid.to_s)
- if m
- m[1]
- else
- nil
+ def determine_fillcolor(n)
+ fillcolor = %w(aaaaaa aaffaa aaaaff aaaaaa ffaaaa)[n || 0] || 'aaaaaa'
+ "style=filled,fillcolor=\"##{fillcolor}\""
end
- end
- def self.edge(tail, head, extra, opts)
- if opts[:direction] == :bottom_up
- gr = "\"#{tail}\" -> \"#{head}\""
- else
- gr = "\"#{head}\" -> \"#{tail}\""
+ def describe_node(uuid)
+ uuid = uuid.to_sym
+ bgcolor = determine_fillcolor @opts[:pips][uuid] if @opts[:pips]
+
+ rsc = ArvadosBase::resource_class_for_uuid uuid.to_s
+ if rsc
+ href = url_for ({:controller => rsc.to_s.tableize,
+ :action => :show,
+ :id => uuid.to_s })
+
+ #"\"#{uuid}\" [label=\"#{rsc}\\n#{uuid}\",href=\"#{href}\"];\n"
+ if rsc == Collection
+ #puts uuid
+ if uuid == :"d41d8cd98f00b204e9800998ecf8427e+0"
+ # special case
+ #puts "empty!"
+ return "\"#{uuid}\" [label=\"(empty collection)\"];\n"
+ end
+ puts "#{uuid.class} #{@pdata[uuid]}"
+ if @pdata[uuid]
+ #puts @pdata[uuid]
+ if @pdata[uuid][:name]
+ return "\"#{uuid}\" [label=\"#{@pdata[uuid][:name]}\",href=\"#{href}\",shape=oval,#{bgcolor}];\n"
+ else
+ files = nil
+ if @pdata[uuid].respond_to? :files
+ files = @pdata[uuid].files
+ elsif @pdata[uuid][:files]
+ files = @pdata[uuid][:files]
+ end
+
+ if files
+ i = 0
+ label = ""
+ while i < 3 and i < files.length
+ label += "\\n" unless label == ""
+ label += files[i][1]
+ i += 1
+ end
+ if i < files.length
+ label += "\\n⋮"
+ end
+ #puts "#{uuid} #{label} #{files}"
+ return "\"#{uuid}\" [label=\"#{label}\",href=\"#{href}\",shape=oval,#{bgcolor}];\n"
+ end
+ end
+ end
+ end
+ return "\"#{uuid}\" [label=\"#{rsc}\",href=\"#{href}\",#{bgcolor}];\n"
+ end
+ "\"#{uuid}\" [#{bgcolor}];\n"
+ end
+
+ def job_uuid(job)
+ if @opts[:combine_jobs] == :script_only
+ uuid = "#{job[:script]}"
+ elsif @opts[:combine_jobs] == :script_and_version
+ uuid = "#{job[:script]}_#{job[:script_version]}"
+ else
+ uuid = "#{job[:uuid]}"
+ end
+
+ @jobs[uuid] = [] unless @jobs[uuid]
+ @jobs[uuid] << job unless @jobs[uuid].include? job
+
+ uuid
end
- if extra.length > 0
- gr += "["
- extra.each do |k, v|
- gr += "#{k}=\"#{v}\","
+
+ def edge(tail, head, extra)
+ if @opts[:direction] == :bottom_up
+ gr = "\"#{tail}\" -> \"#{head}\""
+ else
+ gr = "\"#{head}\" -> \"#{tail}\""
+ end
+ if extra.length > 0
+ gr += " ["
+ extra.each do |k, v|
+ gr += "#{k}=\"#{v}\","
+ end
+ gr += "]"
end
- gr += "]"
+ gr += ";\n"
+ gr
end
- gr += ";\n"
- gr
- end
- def self.script_param_edges(pdata, visited, job, prefix, sp, opts)
- gr = ""
- if sp and not sp.empty?
+ def script_param_edges(job, prefix, sp)
+ gr = ""
case sp
when Hash
sp.each do |k, v|
if prefix.size > 0
k = prefix + "::" + k.to_s
end
- gr += ProvenanceHelper::script_param_edges(pdata, visited, job, k.to_s, v, opts)
+ gr += script_param_edges(job, k.to_s, v)
end
when Array
i = 0
node = ""
sp.each do |v|
- if collection_uuid(v)
- gr += ProvenanceHelper::script_param_edges(pdata, visited, job, "#{prefix}[#{i}]", v, opts)
- else
+ if GenerateGraph::collection_uuid(v)
+ gr += script_param_edges(job, "#{prefix}[#{i}]", v)
+ elsif @opts[:all_script_parameters]
node += "', '" unless node == ""
node = "['" if node == ""
node += "#{v}"
unless node == ""
node += "']"
#puts node
- id = "#{job[:uuid]}_#{prefix}"
- gr += "\"#{id}\" [label=\"#{node}\"];\n"
- gr += edge(job_uuid(job), id, {:label => prefix}, opts)
+ #id = "#{job[:uuid]}_#{prefix}"
+ gr += "\"#{node}\" [label=\"#{node}\"];\n"
+ gr += edge(job_uuid(job), node, {:label => prefix})
end
- else
- m = collection_uuid(sp)
- if m
- gr += edge(job_uuid(job), m, {:label => prefix}, opts)
- gr += ProvenanceHelper::generate_provenance_edges(pdata, visited, m, opts)
- elsif opts[:all_script_parameters]
- id = "#{job[:uuid]}_#{prefix}"
- gr += "\"#{id}\" [label=\"#{sp}\"];\n"
- gr += edge(job_uuid(job), id, {:label => prefix}, opts)
+ when String
+ return '' if sp.empty?
+ m = GenerateGraph::collection_uuid(sp)
+ #puts "#{m} pdata is #{@pdata[m.intern]}"
+ if m and (@pdata[m.intern] or (not @opts[:pdata_only]))
+ gr += edge(job_uuid(job), m, {:label => prefix})
+ gr += generate_provenance_edges(m)
+ elsif @opts[:all_script_parameters]
+ #id = "#{job[:uuid]}_#{prefix}"
+ gr += "\"#{sp}\" [label=\"#{sp}\"];\n"
+ gr += edge(job_uuid(job), sp, {:label => prefix})
end
end
+ gr
end
- gr
- end
- def self.generate_provenance_edges(pdata, visited, uuid, opts)
- gr = ""
- m = ProvenanceHelper::collection_uuid(uuid)
- uuid = m if m
+ def generate_provenance_edges(uuid)
+ gr = ""
+ m = GenerateGraph::collection_uuid(uuid)
+ uuid = m if m
- uuid = uuid.intern if uuid
+ uuid = uuid.intern if uuid
- if (not uuid) or uuid.empty? or visited[uuid]
+ if (not uuid) or uuid.empty? or @visited[uuid]
- #puts "already visited #{uuid}"
- return ""
- end
+ #puts "already @visited #{uuid}"
+ return ""
+ end
- if not pdata[uuid] then
- return ProvenanceHelper::describe_node(pdata, uuid)
- else
- visited[uuid] = true
- end
+ if not @pdata[uuid] then
+ return describe_node(uuid)
+ else
+ @visited[uuid] = true
+ end
+
+ #puts "visiting #{uuid}"
- #puts "visiting #{uuid}"
+ if m
+ # uuid is a collection
+ gr += describe_node(uuid)
- if m
- # uuid is a collection
- gr += ProvenanceHelper::describe_node(pdata, uuid)
+ if m == :"d41d8cd98f00b204e9800998ecf8427e+0"
+ # empty collection, don't follow any further
+ return gr
+ end
- pdata.each do |k, job|
- if job[:output] == uuid.to_s
- gr += self.edge(uuid, job_uuid(job), {:label => "output"}, opts)
- gr += ProvenanceHelper::generate_provenance_edges(pdata, visited, job[:uuid], opts)
+ @pdata.each do |k, job|
+ if job[:output] == uuid.to_s
+ gr += edge(uuid, job_uuid(job), {:label => "output"})
+ gr += generate_provenance_edges(job[:uuid])
+ end
+ if job[:log] == uuid.to_s
+ gr += edge(uuid, job_uuid(job), {:label => "log"})
+ gr += generate_provenance_edges(job[:uuid])
+ end
end
- if job[:log] == uuid.to_s
- gr += edge(uuid, job_uuid(job), {:label => "log"}, opts)
- gr += ProvenanceHelper::generate_provenance_edges(pdata, visited, job[:uuid], opts)
+ else
+ # uuid is something else
+ rsc = ArvadosBase::resource_class_for_uuid uuid.to_s
+
+ if rsc == Job
+ job = @pdata[uuid]
+ if job
+ gr += script_param_edges(job, "", job[:script_parameters])
+
+ if @opts[:script_version_nodes]
+ gr += describe_node(job[:script_version])
+ gr += edge(job_uuid(job), job[:script_version], {:label => "script_version"})
+ end
+ end
+ elsif rsc == Link
+ # do nothing
+ else
+ gr += describe_node(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 += ProvenanceHelper::script_param_edges(pdata, visited, job, "", job[:script_parameters], opts)
+ @pdata.each do |k, link|
+ if link[:head_uuid] == uuid.to_s and link[:link_class] == "provenance"
+ href = url_for ({:controller => Link.to_s.tableize,
+ :action => :show,
+ :id => link[:uuid] })
+
+ gr += describe_node(link[:tail_uuid])
+ gr += edge(link[:head_uuid], link[:tail_uuid], {:label => link[:name], :href => href})
+ gr += generate_provenance_edges(link[:tail_uuid])
end
- else
- gr += ProvenanceHelper::describe_node(pdata, uuid)
end
+
+ #puts "finished #{uuid}"
+
+ gr
end
- pdata.each do |k, link|
- if link[:head_uuid] == uuid.to_s and link[:link_class] == "provenance"
- gr += ProvenanceHelper::describe_node(pdata, link[:tail_uuid])
- gr += edge(link[:head_uuid], link[:tail_uuid], {:label => link[:name], :href => "/links/#{link[:uuid]}"}, opts)
- gr += ProvenanceHelper::generate_provenance_edges(pdata, visited, link[:tail_uuid], opts)
+ def describe_jobs
+ gr = ""
+ @jobs.each do |k, v|
+ href = url_for ({:controller => Job.to_s.tableize,
+ :action => :index })
+
+ gr += "\"#{k}\" [href=\"#{href}?"
+
+ n = 0
+ v.each do |u|
+ gr += "uuid%5b%5d=#{u[:uuid]}&"
+ n |= @opts[:pips][u[:uuid].intern] if @opts[:pips] and @opts[:pips][u[:uuid].intern]
+ end
+
+ gr += "\",label=\""
+
+ if @opts[:combine_jobs] == :script_only
+ gr += "#{v[0][:script]}"
+ elsif @opts[:combine_jobs] == :script_and_version
+ gr += "#{v[0][:script]}" # Just show the name but the nodes will be distinct
+ else
+ gr += "#{v[0][:script]}\\n#{v[0][:finished_at]}"
+ end
+ gr += "\",#{determine_fillcolor n}];\n"
end
+ gr
end
- #puts "finished #{uuid}"
-
- gr
end
- def self.create_provenance_graph(pdata, uuid, opts={})
- require 'open3'
+ def self.create_provenance_graph(pdata, svgId, opts={})
+ if pdata.is_a? Array or pdata.is_a? ArvadosResourceList
+ p2 = {}
+ pdata.each do |k|
+ p2[k[:uuid].intern] = k if k[:uuid]
+ end
+ pdata = p2
+ end
+
+ unless pdata.is_a? Hash
+ raise "create_provenance_graph accepts Array or Hash for pdata only, pdata is #{pdata.class}"
+ end
gr = """strict digraph {
-node [fontsize=8,shape=box];
-edge [fontsize=8];"""
+node [fontsize=10,shape=box];
+edge [fontsize=10];
+"""
if opts[:direction] == :bottom_up
gr += "edge [dir=back];"
end
- #puts "pdata is #{pdata}"
+ #puts "@pdata is #{pdata}"
- visited = {}
- if uuid.respond_to? :each
- uuid.each do |u|
- gr += ProvenanceHelper::generate_provenance_edges(pdata, visited, u, opts)
- end
- else
- gr += ProvenanceHelper::generate_provenance_edges(pdata, visited, uuid, opts)
+ g = GenerateGraph.new(pdata, opts)
+
+ pdata.each do |k, v|
+ gr += g.generate_provenance_edges(k)
end
+ gr += g.describe_jobs
+
gr += "}"
svg = ""
- #puts gr
+ puts gr
+
+ require 'open3'
Open3.popen2("dot", "-Tsvg") do |stdin, stdout, wait_thr|
stdin.print(gr)
svg = svg.sub(/<\?xml.*?\?>/m, "")
svg = svg.sub(/<!DOCTYPE.*?>/m, "")
+ svg = svg.sub(/<svg /, "<svg id=\"#{svgId}\" ")
+ end
+
+ def self.find_collections(sp)
+ c = []
+ case sp
+ when Hash
+ sp.each do |k, v|
+ c.concat(find_collections(v))
+ end
+ when Array
+ sp.each do |v|
+ c.concat(find_collections(v))
+ end
+ when String
+ if !sp.empty?
+ m = GenerateGraph::collection_uuid(sp)
+ if m
+ c << m
+ end
+ end
+ end
+ c
end
end
projects / arvados.git / blobdiff