class Arvados::V1::CollectionsController < ApplicationController
def create
- # Collections are owned by system_user. Creating a collection has
- # two effects: The collection is added if it doesn't already
- # exist, and a "permission" Link is added (if one doesn't already
- # exist) giving the current user (or specified owner_uuid)
- # permission to read it.
- owner_uuid = resource_attrs.delete(:owner_uuid) || current_user.uuid
- unless current_user.can? write: owner_uuid
- logger.warn "User #{current_user.andand.uuid} tried to set collection owner_uuid to #{owner_uuid}"
- raise ArvadosModel::PermissionDeniedError
+ if !resource_attrs[:manifest_text]
+ return send_error("'manifest_text' attribute must be specified",
+ status: :unprocessable_entity)
end
# Check permissions on the collection manifest.
loc.without_signature.to_s
end
- # Save the collection with the stripped manifest.
- act_as_system_user do
- @object = model_class.new resource_attrs.reject { |k,v| k == :owner_uuid }
- begin
- @object.save!
- rescue ActiveRecord::RecordNotUnique
- logger.debug resource_attrs.inspect
- if @object.manifest_text and @object.uuid
- @existing_object = model_class.
- where('uuid=? and manifest_text=?',
- @object.uuid,
- @object.manifest_text).
- first
- @object = @existing_object || @object
- end
- end
- if @object
- link_attrs = {
- owner_uuid: owner_uuid,
- link_class: 'permission',
- name: 'can_read',
- head_uuid: @object.uuid,
- tail_uuid: owner_uuid
+ super
+ end
+
+ def find_object_by_uuid
+ if loc = Locator.parse(params[:id])
+ loc.strip_hints!
+ if c = Collection.readable_by(*@read_users).where({ portable_data_hash: loc.to_s }).limit(1).first
+ @object = {
+ portable_data_hash: c.portable_data_hash,
+ manifest_text: c.manifest_text,
+ files: c.files,
+ data_size: c.data_size
}
- ActiveRecord::Base.transaction do
- if Link.where(link_attrs).empty?
- Link.create! link_attrs
- end
- end
end
+ else
+ super
end
- show
+ true
end
def show
super
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, sp)
case sp
when Hash
end
when String
return if sp.empty?
- m = collection_uuid(sp)
- if m
- generate_provenance_edges(visited, m)
+ if loc = Locator.parse(sp)
+ search_edges(visited, loc.to_s, :search_up)
end
end
end
- def generate_provenance_edges(visited, uuid)
- m = collection_uuid(uuid)
- uuid = m if m
+ def search_edges(visited, uuid, direction)
+ if uuid.nil? or uuid.empty? or visited[uuid]
+ return
+ end
- if not uuid or uuid.empty? or visited[uuid]
- return ""
+ if loc = Locator.parse(uuid)
+ loc.strip_hints!
+ return if visited[loc.to_s]
end
logger.debug "visiting #{uuid}"
- if m
- # uuid is a collection
- Collection.readable_by(current_user).where(uuid: uuid).each do |c|
- visited[uuid] = c.as_api_response
- visited[uuid][:files] = []
- c.files.each do |f|
- visited[uuid][:files] << f
- end
- end
-
- Job.readable_by(current_user).where(output: uuid).each do |job|
- generate_provenance_edges(visited, job.uuid)
+ if loc
+ # uuid is a portable_data_hash
+ if c = Collection.readable_by(*@read_users).where(portable_data_hash: loc.to_s).limit(1).first
+ visited[loc.to_s] = {
+ portable_data_hash: c.portable_data_hash,
+ files: c.files,
+ data_size: c.data_size
+ }
end
- Job.readable_by(current_user).where(log: uuid).each do |job|
- generate_provenance_edges(visited, job.uuid)
- end
+ if direction == :search_up
+ # Search upstream for jobs where this locator is the output of some job
+ Job.readable_by(*@read_users).where(output: loc.to_s).each do |job|
+ search_edges(visited, job.uuid, :search_up)
+ end
- else
- # uuid is something else
- rsc = ArvadosModel::resource_class_for_uuid uuid
- if rsc == Job
- Job.readable_by(current_user).where(uuid: uuid).each do |job|
- visited[uuid] = job.as_api_response
- script_param_edges(visited, job.script_parameters)
+ Job.readable_by(*@read_users).where(log: loc.to_s).each do |job|
+ search_edges(visited, job.uuid, :search_up)
end
- elsif rsc != nil
- rsc.where(uuid: uuid).each do |r|
- visited[uuid] = r.as_api_response
+ elsif direction == :search_down
+ if loc.to_s == "d41d8cd98f00b204e9800998ecf8427e+0"
+ # Special case, don't follow the empty collection.
+ return
end
- end
- end
-
- Link.readable_by(current_user).
- where(head_uuid: uuid, link_class: "provenance").
- each do |link|
- visited[link.uuid] = link.as_api_response
- generate_provenance_edges(visited, link.tail_uuid)
- end
-
- #puts "finished #{uuid}"
- end
-
- def provenance
- visited = {}
- generate_provenance_edges(visited, @object[:uuid])
- render json: visited
- end
-
- def generate_used_by_edges(visited, uuid)
- m = collection_uuid(uuid)
- uuid = m if m
- if not uuid or uuid.empty? or visited[uuid]
- return ""
- end
-
- logger.debug "visiting #{uuid}"
-
- if m
- # uuid is a collection
- Collection.readable_by(current_user).where(uuid: uuid).each do |c|
- visited[uuid] = c.as_api_response
- visited[uuid][:files] = []
- c.files.each do |f|
- visited[uuid][:files] << f
+ # Search downstream for jobs where this locator is in script_parameters
+ Job.readable_by(*@read_users).where(["jobs.script_parameters like ?", "%#{loc.to_s}%"]).each do |job|
+ search_edges(visited, job.uuid, :search_down)
end
end
-
- if uuid == "d41d8cd98f00b204e9800998ecf8427e+0"
- # special case for empty collection
- return
- end
-
- Job.readable_by(current_user).where(["jobs.script_parameters like ?", "%#{uuid}%"]).each do |job|
- generate_used_by_edges(visited, job.uuid)
- end
-
else
- # uuid is something else
+ # uuid is a regular Arvados UUID
rsc = ArvadosModel::resource_class_for_uuid uuid
if rsc == Job
- Job.readable_by(current_user).where(uuid: uuid).each do |job|
+ Job.readable_by(*@read_users).where(uuid: uuid).each do |job|
visited[uuid] = job.as_api_response
- generate_used_by_edges(visited, job.output)
+ if direction == :search_up
+ # Follow upstream collections referenced in the script parameters
+ script_param_edges(visited, job.script_parameters)
+ elsif direction == :search_down
+ # Follow downstream job output
+ search_edges(visited, job.output, direction)
+ end
+ end
+ elsif rsc == Collection
+ if c = Collection.readable_by(*@read_users).where(uuid: uuid).limit(1).first
+ search_edges(visited, c.portable_data_hash, direction)
+ visited[c.portable_data_hash] = c.as_api_response
end
elsif rsc != nil
rsc.where(uuid: uuid).each do |r|
end
end
- Link.readable_by(current_user).
- where(tail_uuid: uuid, link_class: "provenance").
- each do |link|
- visited[link.uuid] = link.as_api_response
- generate_used_by_edges(visited, link.head_uuid)
+ if direction == :search_up
+ # Search for provenance links pointing to the current uuid
+ Link.readable_by(*@read_users).
+ where(head_uuid: uuid, link_class: "provenance").
+ each do |link|
+ visited[link.uuid] = link.as_api_response
+ search_edges(visited, link.tail_uuid, direction)
+ end
+ elsif direction == :search_down
+ # Search for provenance links emanating from the current uuid
+ Link.readable_by(current_user).
+ where(tail_uuid: uuid, link_class: "provenance").
+ each do |link|
+ visited[link.uuid] = link.as_api_response
+ search_edges(visited, link.head_uuid, direction)
+ end
end
+ end
- #puts "finished #{uuid}"
+ def provenance
+ visited = {}
+ search_edges(visited, @object[:uuid] || @object[:portable_data_hash], :search_up)
+ render json: visited
end
def used_by
visited = {}
- generate_used_by_edges(visited, @object[:uuid])
+ search_edges(visited, @object[:uuid] || @object[:portable_data_hash], :search_down)
render json: visited
end
projects / arvados.git / blobdiff