[ARVADOS] updated: b29ca38e4409fe0149aea28a0e26a84d56ccca17
Git user
git at public.curoverse.com
Mon May 8 10:53:41 EDT 2017
Summary of changes:
.../controllers/container_requests_controller.rb | 8 +-
apps/workbench/app/helpers/provenance_helper.rb | 150 +++++++++++++--------
2 files changed, 97 insertions(+), 61 deletions(-)
via b29ca38e4409fe0149aea28a0e26a84d56ccca17 (commit)
via b20770d7e5a4ba0a974a7b98fce87b81aead95d9 (commit)
from 4259263d270a5e377009d20835a463551c708d82 (commit)
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commit b29ca38e4409fe0149aea28a0e26a84d56ccca17
Author: Lucas Di Pentima <lucas at curoverse.com>
Date: Mon May 8 11:52:55 2017 -0300
10111: When dealing with output collection nodes, render the specific collection url instead of use its pdh
diff --git a/apps/workbench/app/helpers/provenance_helper.rb b/apps/workbench/app/helpers/provenance_helper.rb
index d65bc2b..3567cba 100644
--- a/apps/workbench/app/helpers/provenance_helper.rb
+++ b/apps/workbench/app/helpers/provenance_helper.rb
@@ -37,9 +37,15 @@ module ProvenanceHelper
return "\"#{uuid}\" [label=\"(empty collection)\"];\n"
end
- href = url_for ({:controller => Collection.to_s.tableize,
- :action => :show,
- :id => uuid.to_s })
+ 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
@@ -250,8 +256,14 @@ module ProvenanceHelper
if cr_node[:output_uuid] and output_cols[cr_node[:output_uuid]]
c = output_cols[cr_node[:output_uuid]]
visited_pdhs << c[:portable_data_hash]
- gr += describe_node(c[:portable_data_hash], {label: c[:name]})
- gr += edge(cr_node[:uuid], c[:portable_data_hash], {label: 'output'})
+ gr += describe_node(c[:portable_data_hash],
+ {
+ label: c[:name],
+ col_uuid: c[:uuid],
+ })
+ gr += edge(cr_node[:uuid],
+ c[:portable_data_hash],
+ {label: 'output'})
end
end
commit b20770d7e5a4ba0a974a7b98fce87b81aead95d9
Author: Lucas Di Pentima <lucas at curoverse.com>
Date: Mon May 8 11:31:06 2017 -0300
10111: Refactored the graph creation code to minimize the amount of API calls neeeded.
diff --git a/apps/workbench/app/controllers/container_requests_controller.rb b/apps/workbench/app/controllers/container_requests_controller.rb
index fd29cd3..d45e572 100644
--- a/apps/workbench/app/controllers/container_requests_controller.rb
+++ b/apps/workbench/app/controllers/container_requests_controller.rb
@@ -7,13 +7,7 @@ class ContainerRequestsController < ApplicationController
def generate_provenance(cr)
return if params['tab_pane'] != "Provenance"
- nodes = {}
- nodes[cr[:uuid]] = cr
- if cr[:container_uuid]
- ContainerRequest.where(requesting_container_uuid: cr[:container_uuid]).each do |child|
- nodes[child[:uuid]] = child
- end
- end
+ nodes = {cr[:uuid] => cr}
@svg = ProvenanceHelper::create_provenance_graph nodes,
"provenance_svg",
{
diff --git a/apps/workbench/app/helpers/provenance_helper.rb b/apps/workbench/app/helpers/provenance_helper.rb
index 3833243..d65bc2b 100644
--- a/apps/workbench/app/helpers/provenance_helper.rb
+++ b/apps/workbench/app/helpers/provenance_helper.rb
@@ -104,55 +104,17 @@ module ProvenanceHelper
gr
end
- def col_name_for_project(col_pdh, project_uuid)
- [
- # Search for collections within the same project first.
- {portable_data_hash: col_pdh, owner_uuid: project_uuid},
- # then, earch for collections in any project.
- {portable_data_hash: col_pdh},
- ].each do |query_args|
- col = Collection.where(query_args).limit(1)
- if col.results.any?
- if col.items_available == 1
- return col.results.first.name
- else
- return "#{col.results.first.name} + #{col.items_available - 1} more"
- end
- end
- end
-
- # No collections found with this pdh
- col_pdh
- end
-
- def cr_edges cr
- uuid = cr[:uuid]
- gr = ""
-
- # Search for input mounts
- input_obj = cr[:mounts].andand[:"/var/lib/cwl/cwl.input.json"].andand[:content] || cr[:mounts] || {}
+ def cr_input_pdhs cr
+ pdhs = []
+ input_obj = cr[:mounts].andand[:"/var/lib/cwl/cwl.input.json"].andand[:content] || cr[:mounts]
if input_obj
- ProvenanceHelper::find_collections input_obj, 'input' do |col_hash, col_uuid, key|
- # Only include input PDHs
+ ProvenanceHelper::find_collections input_obj do |col_hash, col_uuid, key|
if col_hash
- gr += describe_node(col_hash,
- {label: col_name_for_project(col_hash, cr[:owner_uuid])})
- gr += edge(col_hash, uuid, {:label => key})
+ pdhs << col_hash
end
end
end
-
- # Add CR outputs by PDH so they connect with the child CR's inputs.
- if cr[:output_uuid]
- output_col = Collection.find(cr[:output_uuid])
- if output_col
- gr += describe_node(output_col[:portable_data_hash],
- {label: output_col[:name]})
- gr += edge(uuid, output_col[:portable_data_hash], {label: 'output'})
- end
- end
-
- gr
+ pdhs
end
def job_edges job, edge_opts={}
@@ -238,17 +200,85 @@ module ProvenanceHelper
elsif rsc == ContainerRequest
cr = @pdata[uuid]
if cr
- gr += cr_edges cr
- gr += describe_node(uuid, {href: {controller: 'container_requests',
- id: uuid},
- label: @pdata[uuid][:name],
- shape: 'oval'})
+ child_crs = []
+ col_uuids = []
+ col_pdhs = []
+ col_uuids << cr[:output_uuid] if cr[:output_uuid]
+ col_pdhs += cr_input_pdhs(cr)
# Search for child CRs
if cr[:container_uuid]
child_crs = ContainerRequest.where(requesting_container_uuid: cr[:container_uuid])
child_crs.each do |child|
- gr += generate_provenance_edges(child[:uuid])
- gr += edge(child[:uuid], uuid, {label: 'child'})
+ col_uuids << child[:output_uuid] if child[:output_uuid]
+ col_pdhs += cr_input_pdhs(child)
+ end
+ end
+
+ output_cols = {} # Indexed by UUID
+ input_cols = {} # Indexed by PDH
+
+ # Batch requests to get all related collections
+ Collection.filter([['uuid', 'in', col_uuids.uniq]]).each do |c|
+ output_cols[c[:uuid]] = c
+ end
+ output_pdhs = output_cols.values.map{|c| c[:portable_data_hash]}.uniq
+ Collection.filter([['portable_data_hash', 'in', col_pdhs - output_pdhs]]).each do |c|
+ if input_cols[c[:portable_data_hash]]
+ input_cols[c[:portable_data_hash]] << c
+ else
+ input_cols[c[:portable_data_hash]] = [c]
+ end
+ end
+
+ # Make the graph
+ visited_pdhs = []
+ all_cr_nodes = [cr] + child_crs.results
+
+ # First pass: add the CR nodes with their outputs, because they're
+ # referenced by UUID.
+ all_cr_nodes.each do |cr_node|
+ # CR node
+ gr += describe_node(cr_node[:uuid], {href: {controller: 'container_requests',
+ id: cr_node[:uuid]},
+ label: cr_node[:name],
+ shape: 'oval'})
+ # Connect child CRs with the main one
+ if cr_node != cr
+ gr += edge(cr_node[:uuid], cr[:uuid], {label: 'child'})
+ end
+ # Output collection node
+ if cr_node[:output_uuid] and output_cols[cr_node[:output_uuid]]
+ c = output_cols[cr_node[:output_uuid]]
+ visited_pdhs << c[:portable_data_hash]
+ gr += describe_node(c[:portable_data_hash], {label: c[:name]})
+ gr += edge(cr_node[:uuid], c[:portable_data_hash], {label: 'output'})
+ end
+ end
+
+ # Second pass: add the input collection nodes.
+ all_cr_nodes.each do |cr_node|
+ cr_input_pdhs(cr_node).each do |pdh|
+ if not visited_pdhs.include?(pdh)
+ visited_pdhs << pdh
+ if input_cols[pdh]
+ # First search for collections within the CR project
+ cols = input_cols[pdh].select{|x| x[:owner_uuid] == cr_node[:owner_uuid]}
+ if cols.empty?
+ # Search for any collection with this PDH
+ cols = input_cols[pdh]
+ end
+ names = cols.collect{|x| x[:name]}.uniq
+ input_name = names.first
+ if names.length > 1
+ input_name += " + #{names.length - 1} others"
+ end
+ else
+ # No collection found by this PDH
+ input_name = pdh
+ end
+ gr += describe_node(pdh, {label: input_name})
+ end
+ gr += edge(pdh, cr_node[:uuid], {label: 'input'})
end
end
end
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