skip_before_filter :find_object_by_uuid, only: :compare
before_filter :find_objects_by_uuid, only: :compare
include PipelineInstancesHelper
+ include PipelineComponentsHelper
def copy
- @object = @object.dup
+ template = PipelineTemplate.find?(@object.pipeline_template_uuid)
+
+ source = @object
+ @object = PipelineInstance.new
+ @object.pipeline_template_uuid = source.pipeline_template_uuid
+
+ if params['components'] == 'use_latest' and template
+ @object.components = template.components.deep_dup
+ @object.components.each do |cname, component|
+ # Go through the script parameters of each component
+ # that are marked as user input and copy them over.
+ # Skip any components that are not present in the
+ # source instance (there's nothing to copy)
+ if source.components.include? cname
+ component[:script_parameters].each do |pname, val|
+ if val.is_a? Hash and val[:dataclass]
+ # this is user-inputtable, so check the value from the source pipeline
+ srcvalue = source.components[cname][:script_parameters][pname]
+ if not srcvalue.nil?
+ component[:script_parameters][pname] = srcvalue
+ end
+ end
+ end
+ end
+ end
+ else
+ @object.components = source.components.deep_dup
+ end
+
+ if params['script'] == 'use_same'
+ # Go through each component and copy the script_version from each job.
+ @object.components.each do |cname, component|
+ if source.components.include? cname and source.components[cname][:job]
+ component[:script_version] = source.components[cname][:job][:script_version]
+ end
+ end
+ end
+
@object.components.each do |cname, component|
component.delete :job
end
@object.state = 'New'
+
+ # set owner_uuid to that of source, provided it is a project and wriable by current user
+ current_project = Group.find(source.owner_uuid) rescue nil
+ if (current_project && current_project.writable_by.andand.include?(current_user.uuid))
+ @object.owner_uuid = source.owner_uuid
+ end
+
super
end
if component[:script_parameters]
component[:script_parameters].each do |param, value_info|
if value_info.is_a? Hash
- if resource_class_for_uuid(value_info[:value]) == Link
+ value_info_partitioned = value_info[:value].partition('/') if value_info[:value].andand.class.eql?(String)
+ value_info_value = value_info_partitioned ? value_info_partitioned[0] : value_info[:value]
+ value_info_class = resource_class_for_uuid value_info_value
+ if value_info_class == Link
# Use the link target, not the link itself, as script
# parameter; but keep the link info around as well.
link = Link.find value_info[:value]
value_info[:link_uuid] = nil
value_info[:link_name] = nil
end
+ if value_info_class == Collection
+ # to ensure reproducibility, the script_parameter for a
+ # collection should be the portable_data_hash
+ # keep the collection name and uuid for human-readability
+ obj = Collection.find value_info_value
+ if value_info_partitioned
+ value_info[:value] = obj.portable_data_hash + value_info_partitioned[1] + value_info_partitioned[2]
+ value_info[:selection_name] = obj.name + value_info_partitioned[1] + value_info_partitioned[2]
+ else
+ value_info[:value] = obj.portable_data_hash
+ value_info[:selection_name] = obj.name
+ end
+ value_info[:selection_uuid] = obj.uuid
+ end
end
end
end
def graph(pipelines)
return nil, nil if params['tab_pane'] != "Graph"
- count = {}
provenance = {}
pips = {}
n = 1
+ # When comparing more than one pipeline, "pips" stores bit fields that
+ # indicates which objects are part of which pipelines.
+
pipelines.each do |p|
collections = []
+ hashes = []
+ jobs = []
+
+ p[:components].each do |k, v|
+ provenance["component_#{p[:uuid]}_#{k}"] = v
+
+ collections << v[:output_uuid] if v[:output_uuid]
+ jobs << v[:job][:uuid] if v[:job]
+ end
- p.components.each do |k, v|
- j = v[:job] || next
+ jobs = jobs.compact.uniq
+ if jobs.any?
+ Job.where(uuid: jobs).each do |j|
+ job_uuid = j.uuid
- # The graph is interested in whether the component is
- # indicated as persistent, more than whether the job
- # satisfying it (which could have been reused, or someone
- # else's) is.
- j[:output_is_persistent] = v[:output_is_persistent]
+ provenance[job_uuid] = j
+ pips[job_uuid] = 0 unless pips[job_uuid] != nil
+ pips[job_uuid] |= n
- uuid = j[:uuid].intern
- provenance[uuid] = j
- pips[uuid] = 0 unless pips[uuid] != nil
- pips[uuid] |= n
+ hashes << j[:output] if j[:output]
+ ProvenanceHelper::find_collections(j) do |hash, uuid|
+ collections << uuid if uuid
+ hashes << hash if hash
+ end
- collections << j[:output]
- ProvenanceHelper::find_collections(j[:script_parameters]).each do |k|
- collections << k
+ if j[:script_version]
+ script_uuid = j[:script_version]
+ provenance[script_uuid] = {:uuid => script_uuid}
+ pips[script_uuid] = 0 unless pips[script_uuid] != nil
+ pips[script_uuid] |= n
+ end
end
+ end
- uuid = j[:script_version].intern
- provenance[uuid] = {:uuid => uuid}
- pips[uuid] = 0 unless pips[uuid] != nil
- pips[uuid] |= n
+ hashes = hashes.compact.uniq
+ if hashes.any?
+ Collection.where(portable_data_hash: hashes).each do |c|
+ hash_uuid = c.portable_data_hash
+ provenance[hash_uuid] = c
+ pips[hash_uuid] = 0 unless pips[hash_uuid] != nil
+ pips[hash_uuid] |= n
+ end
end
- Collection.where(uuid: collections.compact).each do |c|
- uuid = c.uuid.intern
- provenance[uuid] = c
- pips[uuid] = 0 unless pips[uuid] != nil
- pips[uuid] |= n
+ collections = collections.compact.uniq
+ if collections.any?
+ Collection.where(uuid: collections).each do |c|
+ collection_uuid = c.uuid
+ provenance[collection_uuid] = c
+ pips[collection_uuid] = 0 unless pips[collection_uuid] != nil
+ pips[collection_uuid] |= n
+ end
end
n = n << 1
:request => request,
:all_script_parameters => true,
:combine_jobs => :script_and_version,
- :script_version_nodes => true,
- :pips => pips }
+ :pips => pips,
+ :only_components => true,
+ :no_docker => true,
+ :no_log => true}
end
super
@rows = [] # each is {name: S, components: [...]}
- # Build a table: x=pipeline y=component
- @objects.each_with_index do |pi, pi_index|
- pipeline_jobs(pi).each do |component|
- # Find a cell with the same name as this component but no
- # entry for this pipeline
- target_row = nil
- @rows.each_with_index do |row, row_index|
- if row[:name] == component[:name] and !row[:components][pi_index]
- target_row = row
+ if params['tab_pane'] == "Compare" or params['tab_pane'].nil?
+ # Build a table: x=pipeline y=component
+ @objects.each_with_index do |pi, pi_index|
+ pipeline_jobs(pi).each do |component|
+ # Find a cell with the same name as this component but no
+ # entry for this pipeline
+ target_row = nil
+ @rows.each_with_index do |row, row_index|
+ if row[:name] == component[:name] and !row[:components][pi_index]
+ target_row = row
+ end
end
+ if !target_row
+ target_row = {name: component[:name], components: []}
+ @rows << target_row
+ end
+ target_row[:components][pi_index] = component
end
- if !target_row
- target_row = {name: component[:name], components: []}
- @rows << target_row
- end
- target_row[:components][pi_index] = component
end
- end
- @rows.each do |row|
- # Build a "normal" pseudo-component for this row by picking the
- # most common value for each attribute. If all values are
- # equally common, there is no "normal".
- normal = {} # attr => most common value
- highscore = {} # attr => how common "normal" is
- score = {} # attr => { value => how common }
- row[:components].each do |pj|
- next if pj.nil?
- pj.each do |k,v|
- vstr = for_comparison v
- score[k] ||= {}
- score[k][vstr] = (score[k][vstr] || 0) + 1
- highscore[k] ||= 0
- if score[k][vstr] == highscore[k]
- # tie for first place = no "normal"
- normal.delete k
- elsif score[k][vstr] == highscore[k] + 1
- # more pipelines have v than anything else
- highscore[k] = score[k][vstr]
- normal[k] = vstr
+ @rows.each do |row|
+ # Build a "normal" pseudo-component for this row by picking the
+ # most common value for each attribute. If all values are
+ # equally common, there is no "normal".
+ normal = {} # attr => most common value
+ highscore = {} # attr => how common "normal" is
+ score = {} # attr => { value => how common }
+ row[:components].each do |pj|
+ next if pj.nil?
+ pj.each do |k,v|
+ vstr = for_comparison v
+ score[k] ||= {}
+ score[k][vstr] = (score[k][vstr] || 0) + 1
+ highscore[k] ||= 0
+ if score[k][vstr] == highscore[k]
+ # tie for first place = no "normal"
+ normal.delete k
+ elsif score[k][vstr] == highscore[k] + 1
+ # more pipelines have v than anything else
+ highscore[k] = score[k][vstr]
+ normal[k] = vstr
+ end
end
end
- end
- # Add a hash in component[:is_normal]: { attr => is_the_value_normal? }
- row[:components].each do |pj|
- next if pj.nil?
- pj[:is_normal] = {}
- pj.each do |k,v|
- pj[:is_normal][k] = (normal.has_key?(k) && normal[k] == for_comparison(v))
+ # Add a hash in component[:is_normal]: { attr => is_the_value_normal? }
+ row[:components].each do |pj|
+ next if pj.nil?
+ pj[:is_normal] = {}
+ pj.each do |k,v|
+ pj[:is_normal][k] = (normal.has_key?(k) && normal[k] == for_comparison(v))
+ end
end
end
end
- provenance, pips = graph(@objects)
+ if params['tab_pane'] == "Graph"
+ provenance, pips = graph(@objects)
- @pipelines = @objects
+ @pipelines = @objects
- if provenance
- @prov_svg = ProvenanceHelper::create_provenance_graph provenance, "provenance_svg", {
- :request => request,
- :all_script_parameters => true,
- :combine_jobs => :script_and_version,
- :script_version_nodes => true,
- :pips => pips }
+ if provenance
+ @prov_svg = ProvenanceHelper::create_provenance_graph provenance, "provenance_svg", {
+ :request => request,
+ :all_script_parameters => true,
+ :combine_jobs => :script_and_version,
+ :script_version_nodes => true,
+ :pips => pips }
+ end
end
+
@object = @objects.first
+
+ show
end
def show_pane_list
- panes = %w(Components Graph Advanced)
+ panes = %w(Components Log Graph Advanced)
if @object and @object.state.in? ['New', 'Ready']
- panes = %w(Inputs) + panes
+ panes = %w(Inputs) + panes - %w(Log)
end
- if not @object.components.values.collect { |x| x[:job] }.compact.any?
+ if not @object.components.values.any? { |x| x[:job] rescue false }
panes -= ['Graph']
end
panes
projects / arvados.git / blobdiff