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
- 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
- return "\"#{uuid}\" [label=\"#{label}\",href=\"#{href}\",shape=oval];\n"
- end
- end
- end
- return "\"#{uuid}\" [label=\"#{rsc}\",href=\"#{href}\"];\n"
- end
+
+ class GenerateGraph
+ def initialize(pdata, opts)
+ @pdata = pdata
+ @opts = opts
+ @visited = {}
+ @jobs = {}
+ @node_extra = {}
end
- return ""
- end
- def self.job_uuid(job)
- # "#{job[:script]}\\n#{job[:script_version]}"
- "#{job[:script]}"
- end
+ def self.collection_uuid(uuid)
+ Keep::Locator.parse(uuid).andand.strip_hints.andand.to_s
+ end
- def self.collection_uuid(uuid)
- m = /([a-f0-9]{32}(\+[0-9]+)?)(\+.*)?/.match(uuid.to_s)
- if m
- m[1]
- else
- nil
+ 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
- end
- def self.edge(tail, head, extra, opts)
- if opts[:direction] == :bottom_up
- gr = "\"#{tail}\" -> \"#{head}\""
- else
- gr = "\"#{head}\" -> \"#{tail}\""
+ def determine_fillcolor(n)
+ fillcolor = %w(666666 669966 666699 666666 996666)[n || 0] || '666666'
+ "style=\"filled\",color=\"#ffffff\",fillcolor=\"##{fillcolor}\",fontcolor=\"#ffffff\""
end
- if extra.length > 0
- gr += "["
- extra.each do |k, v|
- gr += "#{k}=\"#{v}\","
+
+ def describe_node(uuid, describe_opts={})
+ bgcolor = determine_fillcolor (describe_opts[:pip] || @opts[:pips].andand[uuid])
+
+ rsc = ArvadosBase::resource_class_for_uuid uuid
+
+ if GenerateGraph::collection_uuid(uuid) || rsc == Collection
+ if Collection.is_empty_blob_locator? uuid.to_s
+ # special case
+ return "\"#{uuid}\" [label=\"(empty collection)\"];\n"
+ end
+
+ href = url_for ({:controller => Collection.to_s.tableize,
+ :action => :show,
+ :id => uuid.to_s })
+
+ return "\"#{uuid}\" [label=\"#{encode_quotes(describe_opts[:label] || (@pdata[uuid] and @pdata[uuid][:name]) || uuid)}\",shape=box,href=\"#{href}\",#{bgcolor}];\n"
+ else
+ href = ""
+ if describe_opts[:href]
+ href = ",href=\"#{url_for ({:controller => describe_opts[:href][:controller],
+ :action => :show,
+ :id => describe_opts[:href][:id] })}\""
+ end
+ return "\"#{uuid}\" [label=\"#{encode_quotes(describe_opts[:label] || uuid)}\",#{bgcolor},shape=#{describe_opts[:shape] || 'box'}#{href}];\n"
end
- gr += "]"
end
- gr += ";\n"
- gr
- end
- def self.script_param_edges(pdata, 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 += ProvenanceHelper::script_param_edges(pdata, visited, job, k.to_s, v, opts)
+ def job_uuid(job)
+ d = Digest::MD5.hexdigest(job[:script_parameters].to_json)
+ if @opts[:combine_jobs] == :script_only
+ uuid = "#{job[:script]}_#{d}"
+ elsif @opts[:combine_jobs] == :script_and_version
+ uuid = "#{job[:script]}_#{job[:script_version]}_#{d}"
+ else
+ uuid = "#{job[:uuid]}"
+ end
+
+ @jobs[uuid] = [] unless @jobs[uuid]
+ @jobs[uuid] << job unless @jobs[uuid].include? job
+
+ uuid
+ end
+
+ def edge(tail, head, extra)
+ if @opts[:direction] == :bottom_up
+ gr = "\"#{encode_quotes head}\" -> \"#{encode_quotes tail}\""
+ else
+ gr = "\"#{encode_quotes tail}\" -> \"#{encode_quotes head}\""
+ end
+
+ if extra.length > 0
+ gr += " ["
+ extra.each do |k, v|
+ gr += "#{k}=\"#{encode_quotes 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)
+ gr += "]"
+ end
+ gr += ";\n"
+ gr
+ end
+
+ def script_param_edges(uuid, sp)
+ gr = ""
+
+ sp.each do |k, v|
+ if @opts[:all_script_parameters]
+ if v.is_a? Array or v.is_a? Hash
+ encv = JSON.pretty_generate(v).gsub("\n", "\\l") + "\\l"
else
- node += "', '" unless node == ""
- node = "['" if node == ""
- node += "#{v}"
+ encv = v.to_json
end
- i += 1
- end
- unless node == ""
- node += "']"
- #puts node
- #id = "#{job[:uuid]}_#{prefix}"
- gr += "\"#{node}\" [label=\"#{node}\"];\n"
- gr += edge(job_uuid(job), node, {:label => prefix}, opts)
- 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 += "\"#{sp}\" [label=\"#{sp}\"];\n"
- gr += edge(job_uuid(job), sp, {:label => prefix}, opts)
+ gr += "\"#{encode_quotes encv}\" [shape=box];\n"
+ gr += edge(encv, uuid, {:label => k})
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 job_edges job, edge_opts={}
+ uuid = job_uuid(job)
+ gr = ""
- uuid = uuid.intern if uuid
+ ProvenanceHelper::find_collections job[:script_parameters] do |collection_hash, collection_uuid, key|
+ if collection_uuid
+ gr += describe_node(collection_uuid)
+ gr += edge(collection_uuid, uuid, {:label => key})
+ else
+ gr += describe_node(collection_hash)
+ gr += edge(collection_hash, uuid, {:label => key})
+ end
+ end
- if (not uuid) or uuid.empty? or visited[uuid]
+ if job[:docker_image_locator] and !@opts[:no_docker]
+ gr += describe_node(job[:docker_image_locator], {label: (job[:runtime_constraints].andand[:docker_image] || job[:docker_image_locator])})
+ gr += edge(job[:docker_image_locator], uuid, {label: "docker_image"})
+ end
- #puts "already visited #{uuid}"
- return ""
- end
+ if @opts[:script_version_nodes]
+ gr += describe_node(job[:script_version], {:label => "git:#{job[:script_version]}"})
+ gr += edge(job[:script_version], uuid, {:label => "script_version"})
+ end
- if not pdata[uuid] then
- return ProvenanceHelper::describe_node(pdata, uuid)
- else
- visited[uuid] = true
+ if job[:output] and !edge_opts[:no_output]
+ gr += describe_node(job[:output])
+ gr += edge(uuid, job[:output], {label: "output" })
+ end
+
+ gr += edge(uuid, job[:log], {label: "log"}) if job[:log] and !edge_opts[:no_log]
+
+ gr
end
- #puts "visiting #{uuid}"
+ def generate_provenance_edges(uuid)
+ gr = ""
+ m = GenerateGraph::collection_uuid(uuid)
+ uuid = m if m
- if m
- # uuid is a collection
- gr += ProvenanceHelper::describe_node(pdata, uuid)
+ if uuid.nil? or uuid.empty? or @visited[uuid]
+ return ""
+ 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)
- 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)
- end
+ if @pdata[uuid].nil?
+ return ""
+ else
+ @visited[uuid] = true
end
- else
- # uuid is something else
- rsc = ArvadosBase::resource_class_for_uuid uuid.to_s
- if rsc == Job
- job = pdata[uuid]
+ if uuid.start_with? "component_"
+ # Pipeline component inputs
+ job = @pdata[@pdata[uuid][:job].andand[:uuid]]
+
if job
- gr += ProvenanceHelper::script_param_edges(pdata, visited, job, "", job[:script_parameters], opts)
+ gr += describe_node(job_uuid(job), {label: uuid[38..-1], pip: @opts[:pips].andand[job[:uuid]], shape: "oval",
+ href: {controller: 'jobs', id: job[:uuid]}})
+ gr += job_edges job, {no_output: true, no_log: true}
+ end
+
+ # Pipeline component output
+ outuuid = @pdata[uuid][:output_uuid]
+ if outuuid
+ outcollection = @pdata[outuuid]
+ if outcollection
+ gr += edge(job_uuid(job), outcollection[:portable_data_hash], {label: "output"})
+ gr += describe_node(outcollection[:portable_data_hash], {label: outcollection[:name]})
+ end
+ elsif job and job[:output]
+ gr += describe_node(job[:output])
+ gr += edge(job_uuid(job), job[:output], {label: "output" })
end
else
- gr += ProvenanceHelper::describe_node(pdata, uuid)
+ rsc = ArvadosBase::resource_class_for_uuid uuid
+
+ if rsc == Job
+ job = @pdata[uuid]
+ gr += job_edges job if job
+ end
end
- 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)
+ @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
end
+
+ gr
end
- #puts "finished #{uuid}"
+ def describe_jobs
+ gr = ""
+ @jobs.each do |k, v|
+ href = url_for ({:controller => Job.to_s.tableize,
+ :action => :index })
- gr
+ gr += "\"#{k}\" [href=\"#{href}?"
+
+ n = 0
+ v.each do |u|
+ gr += ";" unless gr.end_with? "?"
+ gr += "uuid%5b%5d=#{u[:uuid]}"
+ n |= @opts[:pips][u[:uuid]] if @opts[:pips] and @opts[:pips][u[:uuid]]
+ end
+
+ gr += "\",label=\""
+
+ label = "#{v[0][:script]}"
+
+ if label == "run-command" and v[0][:script_parameters][:command].is_a? Array
+ label = v[0][:script_parameters][:command].join(' ')
+ end
+
+ if not @opts[:combine_jobs]
+ label += "\\n#{v[0][:finished_at]}"
+ end
+
+ gr += encode_quotes label
+
+ gr += "\",#{determine_fillcolor n}];\n"
+ end
+ gr
+ end
+
+ def encode_quotes value
+ value.to_s.gsub("\"", "\\\"").gsub("\n", "\\n")
+ end
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]] = 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,fontname=\"Helvetica,Arial,sans-serif\"];
+edge [fontsize=10,fontname=\"Helvetica,Arial,sans-serif\"];
+"""
if opts[:direction] == :bottom_up
gr += "edge [dir=back];"
end
- #puts "pdata is #{pdata}"
+ begin
+ pdata = pdata.stringify_keys
+
+ g = GenerateGraph.new(pdata, opts)
+
+ pdata.each do |k, v|
+ if !opts[:only_components] or k.start_with? "component_"
+ gr += g.generate_provenance_edges(k)
+ else
+ #gr += describe_node(k)
+ end
+ end
- visited = {}
- if uuid.respond_to? :each
- uuid.each do |u|
- gr += ProvenanceHelper::generate_provenance_edges(pdata, visited, u, opts)
+ if !opts[:only_components]
+ gr += g.describe_jobs
end
- else
- gr += ProvenanceHelper::generate_provenance_edges(pdata, visited, uuid, opts)
+
+ rescue => e
+ Rails.logger.warn "#{e.inspect}"
+ Rails.logger.warn "#{e.backtrace.join("\n\t")}"
+ raise
end
gr += "}"
svg = ""
- #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
+
+ # yields hash, uuid
+ # Position indicates whether it is a content hash or arvados uuid.
+ # One will hold a value, the other will always be nil.
+ def self.find_collections(sp, key=nil, &b)
+ case sp
+ when ArvadosBase
+ sp.class.columns.each do |c|
+ find_collections(sp[c.name.to_sym], nil, &b)
+ end
+ when Hash
+ sp.each do |k, v|
+ find_collections(v, key || k, &b)
+ end
+ when Array
+ sp.each do |v|
+ find_collections(v, key, &b)
+ end
+ when String
+ if m = /[a-f0-9]{32}\+\d+/.match(sp)
+ yield m[0], nil, key
+ elsif m = /[0-9a-z]{5}-4zz18-[0-9a-z]{15}/.match(sp)
+ yield nil, m[0], key
+ end
+ end
end
end
projects / arvados.git / blobdiff