From e3e224295f2a3aa53ee82ebfc3982b90e85cfc08 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Wed, 29 Jan 2014 14:58:11 -0500 Subject: [PATCH] Started refactoring --- .../app/controllers/collections_controller.rb | 140 +----------------- .../app/helpers/provenance_helper.rb | 140 ++++++++++++++++++ 2 files changed, 141 insertions(+), 139 deletions(-) create mode 100644 apps/workbench/app/helpers/provenance_helper.rb diff --git a/apps/workbench/app/controllers/collections_controller.rb b/apps/workbench/app/controllers/collections_controller.rb index 3a1013a32c..ca176b4e10 100644 --- 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(//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 index 0000000000..c393a1b86f --- /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(//m, "") + end +end -- 2.30.2