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 set_persistent
+ case params[:value]
+ when 'persistent', 'cache'
+ persist_links = Link.filter([['owner_uuid', '=', current_user.uuid],
+ ['link_class', '=', 'resources'],
+ ['name', '=', 'wants'],
+ ['tail_uuid', '=', current_user.uuid],
+ ['head_uuid', '=', @object.uuid]])
+ logger.debug persist_links.inspect
+ else
+ return unprocessable "Invalid value #{value.inspect}"
+ end
+ if params[:value] == 'persistent'
+ if not persist_links.any?
+ Link.create(link_class: 'resources',
+ name: 'wants',
+ tail_uuid: current_user.uuid,
+ head_uuid: @object.uuid)
+ end
+ else
+ persist_links.each do |link|
+ link.destroy || raise
+ end
+ end
+
+ respond_to do |f|
+ f.json { render json: @object }
+ end
+ end
+
def index
if params[:search].andand.length.andand > 0
tags = Link.where(any: ['contains', params[:search]])
Collection.where(any: ['contains', params[:search]])).
uniq { |c| c.uuid }
else
- @collections = Collection.limit(100)
+ if params[:limit]
+ limit = params[:limit].to_i
+ else
+ limit = 100
+ end
+
+ if params[:offset]
+ offset = params[:offset].to_i
+ else
+ offset = 0
+ end
+
+ @collections = Collection.limit(limit).offset(offset)
end
@links = Link.limit(1000).
where(head_uuid: @collections.collect(&:uuid))
@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 describe_node(uuid)
- rsc = ArvadosBase::resource_class_for_uuid uuid
- if rsc
- "\"#{uuid}\" [label=\"#{rsc}\\n#{uuid}\",href=\"#{url_for rsc}/#{uuid}\"];"
- else
- ""
- end
- end
-
- def describe_script(job)
- #"""\"#{job.script_version}\" [label=\"#{job.script}: #{job.script_version}\"];
- # \"#{job.uuid}\" -> \"#{job.script_version}\" [label=\"script\"];"""
- "\"#{job.uuid}\" [label=\"#{job.script}\\n#{job.script_version}\"];"
- end
-
- def job_uuid(job)
- "#{job.script}\\n#{job.script_version}"
- end
-
- def collection_uuid(uuid)
- m = /([a-f0-9]{32}(\+[0-9]+)?)(\+.*)?/.match(uuid)
- if m
- m[1]
- else
- nil
- end
- end
-
- def script_param_edges(visited, job, prefix, sp)
- 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 += script_param_edges(visited, job, k.to_s, v)
- end
- when Array
- sp.each do |v|
- gr += script_param_edges(visited, job, prefix, v)
- end
- else
- m = collection_uuid(sp)
- if m
- gr += "\"#{job_uuid(job)}\" -> \"#{m}\" [label=\" #{prefix}\"];"
- gr += generate_provenance_edges(visited, m)
- end
- end
- end
- gr
- end
-
- def generate_provenance_edges(visited, uuid)
- gr = ""
- m = collection_uuid(uuid)
-
- if not uuid or uuid.empty? or visited[uuid] or visited[m]
- return ""
- end
-
- #puts "visiting #{uuid}"
-
- if m
- # uuid is a collection
- uuid = m
- visited[uuid] = true
-
- gr += describe_node(uuid)
-
- Job.where(output: uuid).each do |job|
- #gr += describe_node(job_uuid(job))
- gr += "\"#{uuid}\" -> \"#{job_uuid(job)}\" [label=\" output\"];"
- gr += generate_provenance_edges(visited, job.uuid)
- end
-
- Job.where(log: uuid).each do |job|
- #gr += describe_node(job_uuid(job))
- gr += "\"#{uuid}\" -> \"#{job_uuid(job)}\" [label=\" log\"];"
- gr += generate_provenance_edges(visited, job.uuid)
- end
-
- else
- visited[uuid] = true
-
- # uuid is something else
- rsc = ArvadosBase::resource_class_for_uuid uuid
-
- if rsc == Job
- Job.where(uuid: uuid).each do |job|
- gr += script_param_edges(visited, job, "", job.script_parameters)
- #gr += describe_script(job)
- end
- else
- gr += describe_node(uuid)
- end
- end
-
- Link.where(head_uuid: uuid, link_class: "provenance").each do |link|
- gr += describe_node(link.tail_uuid)
- gr += "\"#{link.head_uuid}\" -> \"#{link.tail_uuid}\" [label=\" #{link.name}\", href=\"/links/#{link.uuid}\"];"
- gr += generate_provenance_edges(visited, link.tail_uuid)
- end
-
- #puts "finished #{uuid}"
-
- gr
- end
-
- def create_provenance_graph(uuid)
- require 'open3'
-
- gr = """strict digraph {
-//rankdir=LR;
-node [fontsize=8,shape=box];
-edge [dir=back,fontsize=8];"""
-
- visited = {}
- gr += generate_provenance_edges(visited, uuid)
-
- 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
@provenance = []
Link.where(head_uuid: @sourcedata.keys | @output2job.keys).each do |link|
if link.link_class == 'resources' and link.name == 'wants'
@protected[link.head_uuid] = true
+ if link.tail_uuid == current_user.uuid
+ @is_persistent = true
+ end
end
end
Link.where(tail_uuid: @sourcedata.keys).each do |link|
if link.link_class == 'data_origin'
@sourcedata[link.tail_uuid][:data_origins] ||= []
- @sourcedata[link.tail_uuid][:data_origins] << [link.name, link.head_kind, link.head_uuid]
+ @sourcedata[link.tail_uuid][:data_origins] << [link.name, link.head_uuid]
end
end
Collection.where(uuid: @sourcedata.keys).each do |collection|
end
end
- @prov_svg = create_provenance_graph(@object.uuid)
+ Collection.where(uuid: @object.uuid).each do |u|
+ 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
protected
projects / arvados.git / blobdiff