+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
module ProvenanceHelper
class GenerateGraph
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
- else
- nil
- end
+ Keep::Locator.parse(uuid).andand.strip_hints.andand.to_s
end
def url_for u
end
def determine_fillcolor(n)
- fillcolor = %w(aaaaaa aaffaa aaaaff aaaaaa ffaaaa)[n || 0] || 'aaaaaa'
- "style=filled,fillcolor=\"##{fillcolor}\""
+ fillcolor = %w(666666 669966 666699 666666 996666)[n || 0] || '666666'
+ "style=\"filled\",color=\"#ffffff\",fillcolor=\"##{fillcolor}\",fontcolor=\"#ffffff\""
end
- def describe_node(uuid)
- uuid = uuid.to_sym
- bgcolor = determine_fillcolor @opts[:pips].andand[uuid]
-
- 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
- if Collection.is_empty_blob_locator? uuid.to_s
- # special case
- return "\"#{uuid}\" [label=\"(empty collection)\"];\n"
- end
- if @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
+ def describe_node(uuid, describe_opts={})
+ bgcolor = determine_fillcolor (describe_opts[:pip] || @opts[:pips].andand[uuid])
- 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
- extra_s = @node_extra[uuid].andand.map { |k,v|
- "#{k}=\"#{v}\""
- }.andand.join ","
- return "\"#{uuid}\" [label=\"#{label}\",href=\"#{href}\",shape=oval,#{bgcolor},#{extra_s}];\n"
- end
- end
- end
+ 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
+
+ if describe_opts[:col_uuid]
+ href = url_for ({:controller => Collection.to_s.tableize,
+ :action => :show,
+ :id => describe_opts[:col_uuid].to_s })
+ else
+ href = url_for ({:controller => Collection.to_s.tableize,
+ :action => :show,
+ :id => uuid.to_s })
+ end
+
+ 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=\"#{rsc}\",href=\"#{href}\",#{bgcolor}];\n"
+ return "\"#{uuid}\" [label=\"#{encode_quotes(describe_opts[:label] || uuid)}\",#{bgcolor},shape=#{describe_opts[:shape] || 'box'}#{href}];\n"
end
- "\"#{uuid}\" [#{bgcolor}];\n"
end
def job_uuid(job)
def edge(tail, head, extra)
if @opts[:direction] == :bottom_up
- gr = "\"#{tail}\" -> \"#{head}\""
+ gr = "\"#{encode_quotes head}\" -> \"#{encode_quotes tail}\""
else
- gr = "\"#{head}\" -> \"#{tail}\""
+ gr = "\"#{encode_quotes tail}\" -> \"#{encode_quotes head}\""
end
+
if extra.length > 0
gr += " ["
extra.each do |k, v|
- gr += "#{k}=\"#{v}\","
+ gr += "#{k}=\"#{encode_quotes v}\","
end
gr += "]"
end
gr
end
- def script_param_edges(job, prefix, sp)
+ def script_param_edges(uuid, sp)
gr = ""
- case sp
- when Hash
- sp.each do |k, v|
- if prefix.size > 0
- k = prefix + "::" + k.to_s
- end
- gr += script_param_edges(job, k.to_s, v)
- end
- when Array
- i = 0
- node = ""
- count = 0
- sp.each do |v|
- if GenerateGraph::collection_uuid(v)
- gr += script_param_edges(job, "#{prefix}[#{i}]", v)
- elsif @opts[:all_script_parameters]
- t = "#{v}"
- nl = (if (count+t.length) > 60 then "\\n" else " " end)
- count = 0 if (count+t.length) > 60
- node += "',#{nl}'" unless node == ""
- node = "['" if node == ""
- node += t
- count += t.length
+
+ 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
+ encv = v.to_json
end
- i += 1
- end
- unless node == ""
- node += "']"
- node_value = encode_quotes node
- gr += "\"#{node_value}\" [label=\"#{node_value}\"];\n"
- gr += edge(job_uuid(job), node_value, {:label => prefix})
+ gr += "\"#{encode_quotes encv}\" [shape=box];\n"
+ gr += edge(encv, uuid, {:label => k})
end
- when String
- return '' if sp.empty?
- m = GenerateGraph::collection_uuid(sp)
- 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]
- sp_value = encode_quotes sp
- gr += "\"#{sp_value}\" [label=\"#{sp_value}\"];\n"
- gr += edge(job_uuid(job), sp_value, {:label => prefix})
+ end
+ gr
+ end
+
+ def job_edges job, edge_opts={}
+ uuid = job_uuid(job)
+ gr = ""
+
+ 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 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
+
+ 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 job[:output] and !edge_opts[:no_output]
+ gr += describe_node(job[:output])
+ gr += edge(uuid, job[:output], {label: "output" })
+ end
+
+ if job[:log] and !edge_opts[:no_log]
+ gr += describe_node(job[:log])
+ gr += edge(uuid, job[:log], {label: "log"})
+ end
+
gr
end
m = GenerateGraph::collection_uuid(uuid)
uuid = m if m
- uuid = uuid.intern if uuid
-
- if (not uuid) or uuid.empty? or @visited[uuid]
+ if uuid.nil? or uuid.empty? or @visited[uuid]
return ""
end
- if not @pdata[uuid] then
- return describe_node(uuid)
+ if @pdata[uuid].nil?
+ return ""
else
@visited[uuid] = true
end
- if m
- # uuid is a collection
- if not Collection.is_empty_blob_locator? uuid.to_s
- @pdata.each do |k, job|
- if job[:output] == uuid.to_s
- extra = { label: 'output' }
- gr += edge(uuid, job_uuid(job), extra)
- 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
+ if uuid.start_with? "component_"
+ # Pipeline component inputs
+ job = @pdata[@pdata[uuid][:job].andand[:uuid]]
+
+ if job
+ 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
- gr += describe_node(uuid)
else
- # uuid is something else
- rsc = ArvadosBase::resource_class_for_uuid uuid.to_s
+ rsc = ArvadosBase::resource_class_for_uuid uuid
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"})
+ gr += job_edges job if job
+ elsif rsc == ContainerRequest
+ cr = @pdata[uuid]
+ if cr
+ gr += describe_node(cr[:uuid], {href: {controller: 'container_requests',
+ id: cr[:uuid]},
+ label: cr[:name],
+ shape: 'oval'})
+ # Connect child CRs
+ children = @opts[:cr_children_of].andand[cr[:uuid]]
+ if children
+ children.each do |child|
+ gr += edge(child[:uuid], cr[:uuid], {label: 'child'})
+ end
+ end
+ # Output collection node
+ if cr[:output_uuid] and @opts[:output_collections][cr[:output_uuid]]
+ c = @opts[:output_collections][cr[:output_uuid]]
+ gr += describe_node(c[:portable_data_hash],
+ {
+ label: c[:name],
+ col_uuid: c[:uuid],
+ })
+ gr += edge(cr[:uuid],
+ c[:portable_data_hash],
+ {label: 'output'})
+ end
+ # Input collection nodes
+ output_pdhs = @opts[:output_collections].values.collect{|c|
+ c[:portable_data_hash]}
+ ProvenanceHelper::cr_input_pdhs(cr).each do |pdh|
+ if not output_pdhs.include?(pdh)
+ # Search for collections on the same project first
+ cols = @opts[:input_collections][pdh].andand.select{|c|
+ c[:owner_uuid] == cr[:owner_uuid]}
+ if not cols or cols.empty?
+ # Search for any collection with this PDH
+ cols = @opts[:input_collections][pdh]
+ end
+ names = cols.collect{|x| x[:name]}.uniq
+ input_name = names.first
+ if names.length > 1
+ input_name += " + #{names.length - 1} more"
+ end
+ gr += describe_node(pdh, {label: input_name})
+ end
+ gr += edge(pdh, cr[:uuid], {label: 'input'})
end
end
- elsif rsc == Link
- # do nothing
- else
- gr += describe_node(uuid)
end
end
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]
+ 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=\""
- 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]}"
+ 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.andand.gsub("\"", "\\\"")
+ value.to_s.gsub("\"", "\\\"").gsub("\n", "\\n")
end
end
if pdata.is_a? Array or pdata.is_a? ArvadosResourceList
p2 = {}
pdata.each do |k|
- p2[k[:uuid].intern] = k if k[:uuid]
+ p2[k[:uuid]] = k if k[:uuid]
end
pdata = p2
end
end
gr = """strict digraph {
-node [fontsize=10,shape=box];
-edge [fontsize=10];
+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
- g = GenerateGraph.new(pdata, opts)
+ begin
+ pdata = pdata.stringify_keys
- pdata.each do |k, v|
- gr += g.generate_provenance_edges(k)
- end
+ g = GenerateGraph.new(pdata, opts)
- gr += g.describe_jobs
+ 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
+
+ if !opts[:only_components]
+ gr += g.describe_jobs
+ end
+
+ rescue => e
+ Rails.logger.warn "#{e.inspect}"
+ Rails.logger.warn "#{e.backtrace.join("\n\t")}"
+ raise
+ end
gr += "}"
svg = ""
svg = svg.sub(/<svg /, "<svg id=\"#{svgId}\" ")
end
- def self.find_collections(sp)
- c = []
+ # 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|
- c.concat(find_collections(v))
+ find_collections(v, key || k, &b)
end
when Array
sp.each do |v|
- c.concat(find_collections(v))
+ find_collections(v, key, &b)
end
when String
- if !sp.empty?
- m = GenerateGraph::collection_uuid(sp)
- if m
- c << m
+ 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
+
+ def self.cr_input_pdhs cr
+ pdhs = []
+ input_obj = cr[:mounts].andand[:"/var/lib/cwl/cwl.input.json"].andand[:content] || cr[:mounts]
+ if input_obj
+ find_collections input_obj do |col_hash, col_uuid, key|
+ if col_hash
+ pdhs << col_hash
end
end
end
- c
+ pdhs
end
end
projects / arvados.git / blobdiff