skip_before_filter :find_object_by_uuid, :only => [:provenance]
skip_before_filter :check_user_agreements, :only => [:show_file]
+ def show_pane_list
+ %w(Files Attributes Metadata Provenance_graph Used_by JSON API)
+ end
def index
if params[:search].andand.length.andand > 0
tags = Link.where(any: ['contains', params[:search]])
@collection_info = {}
@collections.each do |c|
@collection_info[c.uuid] = {
- tags: [],
+ tag_links: [],
wanted: false,
wanted_by_me: false,
provenance: [],
info = @collection_info[link.head_uuid]
case link.link_class
when 'tag'
- info[:tags] << link.name
+ info[:tag_links] << link
when 'resources'
info[:wanted] = true
info[:wanted_by_me] ||= link.tail_uuid == current_user.uuid
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
end
Collection.where(uuid: @object.uuid).each do |u|
- @prov_svg = CollectionsController::create_provenance_graph u.provenance, u.uuid
+ puts request
+ @prov_svg = ProvenanceHelper::create_provenance_graph(u.provenance, "provenance_svg",
+ {:request => request,
+ :direction => :bottom_up,
+ :combine_jobs => :script_only}) rescue nil
+ @used_by_svg = ProvenanceHelper::create_provenance_graph(u.used_by, "used_by_svg",
+ {:request => request,
+ :direction => :top_down,
+ :combine_jobs => :script_only,
+ :pdata_only => true}) rescue nil
end
end
projects / arvados.git / blobdiff