+require "arvados/keep"
+
class Arvados::V1::CollectionsController < ApplicationController
+ def self.limit_index_columns_read
+ ["manifest_text"]
+ end
+
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
- owner_kind = if owner_uuid.match(/-(\w+)-/)[1] == User.uuid_prefix
- 'arvados#user'
- else
- 'arvados#group'
- end
- 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[:uuid] and (loc = Keep::Locator.parse(resource_attrs[:uuid]))
+ resource_attrs[:portable_data_hash] = loc.to_s
+ resource_attrs.delete :uuid
end
- 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 resource_attrs[:manifest_text] and resource_attrs[:uuid]
- @existing_object = model_class.
- where('uuid=? and manifest_text=?',
- resource_attrs[:uuid],
- resource_attrs[:manifest_text]).
- first
- @object = @existing_object || @object
- end
- end
+ super
+ end
- if @object
- link_attrs = {
- owner_uuid: owner_uuid,
- link_class: 'permission',
- name: 'can_read',
- head_kind: 'arvados#collection',
- head_uuid: @object.uuid,
- tail_kind: owner_kind,
- tail_uuid: owner_uuid
+ def find_object_by_uuid
+ if loc = Keep::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 = {
+ uuid: c.portable_data_hash,
+ portable_data_hash: c.portable_data_hash,
+ manifest_text: c.signed_manifest_text,
}
- ActiveRecord::Base.transaction do
- if Link.where(link_attrs).empty?
- Link.create! link_attrs
- end
- end
end
+ else
+ super
end
- show
+ true
end
- def collection_uuid(uuid)
- m = /([a-f0-9]{32}(\+[0-9]+)?)(\+.*)?/.match(uuid)
- if m
- m[1]
+ def show
+ if @object.is_a? Collection
+ super
else
- nil
+ send_json @object
end
end
- def script_param_edges(visited, sp)
- if sp and not sp.empty?
- case sp
- when Hash
- sp.each do |k, v|
- script_param_edges(visited, v)
- end
- when Array
- sp.each do |v|
- script_param_edges(visited, v)
- end
- else
- m = collection_uuid(sp)
- if m
- generate_provenance_edges(visited, m)
- end
+ def find_collections(visited, sp, &b)
+ case sp
+ when ArvadosModel
+ sp.class.columns.each do |c|
+ find_collections(visited, sp[c.name.to_sym], &b) if c.name != "log"
+ end
+ when Hash
+ sp.each do |k, v|
+ find_collections(visited, v, &b)
+ end
+ when Array
+ sp.each do |v|
+ find_collections(visited, v, &b)
+ end
+ when String
+ if m = /[a-f0-9]{32}\+\d+/.match(sp)
+ yield m[0], nil
+ elsif m = Collection.uuid_regex.match(sp)
+ yield nil, m[0]
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 = Keep::Locator.parse(uuid)
+ loc.strip_hints!
+ return if visited[loc.to_s]
end
- #puts "visiting #{uuid}"
+ logger.debug "visiting #{uuid}"
- if m
- # uuid is a collection
- Collection.where(uuid: uuid).each do |c|
- visited[uuid] = c.as_api_response
- visited[uuid][:files] = []
- c.files.each do |f|
- visited[uuid][:files] << f
+ if loc
+ # uuid is a portable_data_hash
+ collections = Collection.readable_by(*@read_users).where(portable_data_hash: loc.to_s)
+ c = collections.limit(2).all
+ if c.size == 1
+ visited[loc.to_s] = c[0]
+ elsif c.size > 1
+ name = collections.limit(1).where("name <> ''").first
+ if name
+ visited[loc.to_s] = {
+ portable_data_hash: c[0].portable_data_hash,
+ name: "#{name.name} + #{collections.count-1} more"
+ }
+ else
+ visited[loc.to_s] = {
+ portable_data_hash: c[0].portable_data_hash,
+ name: loc.to_s
+ }
end
end
- Job.where(output: 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
- Job.where(log: uuid).each do |job|
- generate_provenance_edges(visited, job.uuid)
+ Job.readable_by(*@read_users).where(log: loc.to_s).each do |job|
+ search_edges(visited, job.uuid, :search_up)
+ end
+ elsif direction == :search_down
+ if loc.to_s == "d41d8cd98f00b204e9800998ecf8427e+0"
+ # Special case, don't follow the empty collection.
+ return
+ end
+
+ # 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
+
+ Job.readable_by(*@read_users).where(["jobs.docker_image_locator = ?", "#{loc.to_s}"]).each do |job|
+ search_edges(visited, job.uuid, :search_down)
+ end
end
-
else
- # uuid is something else
+ # uuid is a regular Arvados UUID
rsc = ArvadosModel::resource_class_for_uuid uuid
if rsc == Job
- Job.where(uuid: uuid).each do |job|
+ Job.readable_by(*@read_users).where(uuid: uuid).each do |job|
visited[uuid] = job.as_api_response
- script_param_edges(visited, job.script_parameters)
+ if direction == :search_up
+ # Follow upstream collections referenced in the script parameters
+ find_collections(visited, job) do |hash, uuid|
+ search_edges(visited, hash, :search_up) if hash
+ search_edges(visited, uuid, :search_up) if uuid
+ end
+ 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.where(head_uuid: uuid, link_class: "provenance").each do |link|
- visited[link.uuid] = link.as_api_response
- generate_provenance_edges(visited, link.tail_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
-
- #puts "finished #{uuid}"
end
def provenance
visited = {}
- generate_provenance_edges(visited, @object[:uuid])
- render json: visited
+ search_edges(visited, @object[:portable_data_hash], :search_up)
+ search_edges(visited, @object[:uuid], :search_up)
+ send_json visited
end
+ def used_by
+ visited = {}
+ search_edges(visited, @object[:uuid], :search_down)
+ search_edges(visited, @object[:portable_data_hash], :search_down)
+ send_json visited
+ end
protected
- def find_object_by_uuid
+
+ def load_limit_offset_order_params *args
super
- if !@object and !params[:uuid].match(/^[0-9a-f]+\+\d+$/)
- # Normalize the given uuid and search again.
- hash_part = params[:uuid].match(/^([0-9a-f]*)/)[1]
- collection = Collection.where('uuid like ?', hash_part + '+%').first
- if collection
- # We know the collection exists, and what its real uuid is in
- # the database. Now, throw out @objects and repeat the usual
- # lookup procedure. (Returning the collection at this point
- # would bypass permission checks.)
- @objects = nil
- @where = { uuid: collection.uuid }
- find_objects_for_index
- @object = @objects.first
- end
+ if action_name == 'index'
+ # Omit manifest_text from index results unless expressly selected.
+ @select ||= model_class.selectable_attributes - ["manifest_text"]
end
end
-
end
projects / arvados.git / blobdiff