+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
+require "arvados/keep"
+require "trashable"
+
class Arvados::V1::CollectionsController < ApplicationController
- def create
- if !resource_attrs[:manifest_text]
- return send_error("'manifest_text' attribute must be specified",
- status: :unprocessable_entity)
- end
+ include DbCurrentTime
+ include TrashableController
- # Check permissions on the collection manifest.
- # If any signature cannot be verified, return 403 Permission denied.
- api_token = current_api_client_authorization.andand.api_token
- signing_opts = {
- key: Rails.configuration.blob_signing_key,
- api_token: api_token,
- ttl: Rails.configuration.blob_signing_ttl,
- }
- resource_attrs[:manifest_text].lines.each do |entry|
- entry.split[1..-1].each do |tok|
- if /^[[:digit:]]+:[[:digit:]]+:/.match tok
- # This is a filename token, not a blob locator. Note that we
- # keep checking tokens after this, even though manifest
- # format dictates that all subsequent tokens will also be
- # filenames. Safety first!
- elsif Blob.verify_signature tok, signing_opts
- # OK.
- elsif Locator.parse(tok).andand.signature
- # Signature provided, but verify_signature did not like it.
- logger.warn "Invalid signature on locator #{tok}"
- raise ArvadosModel::PermissionDeniedError
- elsif Rails.configuration.permit_create_collection_with_unsigned_manifest
- # No signature provided, but we are running in insecure mode.
- logger.debug "Missing signature on locator #{tok} ignored"
- elsif Blob.new(tok).empty?
- # No signature provided -- but no data to protect, either.
- else
- logger.warn "Missing signature on locator #{tok}"
- raise ArvadosModel::PermissionDeniedError
- end
- end
+ def self._index_requires_parameters
+ (super rescue {}).
+ merge({
+ include_trash: {
+ type: 'boolean', required: false, default: false, description: "Include collections whose is_trashed attribute is true.",
+ },
+ include_old_versions: {
+ type: 'boolean', required: false, default: false, description: "Include past collection versions.",
+ },
+ })
+ end
+
+ def self._show_requires_parameters
+ (super rescue {}).
+ merge({
+ include_trash: {
+ type: 'boolean', required: false, default: false, description: "Show collection even if its is_trashed attribute is true.",
+ },
+ include_old_versions: {
+ type: 'boolean', required: false, default: true, description: "Include past collection versions.",
+ },
+ })
+ end
+
+ def create
+ 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
+ resource_attrs.delete :version
+ resource_attrs.delete :current_version_uuid
+ super
+ end
- # Remove any permission signatures from the manifest.
- munge_manifest_locators(resource_attrs[:manifest_text]) do |loc|
- loc.without_signature.to_s
+ def update
+ # preserve_version should be disabled unless explicitly asked otherwise.
+ if !resource_attrs[:preserve_version]
+ resource_attrs[:preserve_version] = false
end
+ super
+ end
+ def find_objects_for_index
+ opts = {
+ include_trash: params[:include_trash] || ['destroy', 'trash', 'untrash'].include?(action_name),
+ include_old_versions: params[:include_old_versions] || false,
+ }
+ @objects = Collection.readable_by(*@read_users, opts) if !opts.empty?
super
end
- def find_object_by_uuid
- if loc = Locator.parse(params[:id])
+ def find_object_by_uuid(with_lock: false)
+ 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
+
+ opts = {
+ include_trash: params[:include_trash],
+ include_old_versions: params[:include_old_versions],
+ }
+
+ # It matters which Collection object we pick because blob
+ # signatures depend on the value of trash_at.
+ #
+ # From postgres doc: "By default, null values sort as if larger
+ # than any non-null value; that is, NULLS FIRST is the default
+ # for DESC order, and NULLS LAST otherwise."
+ #
+ # "trash_at desc" sorts null first, then latest to earliest, so
+ # it will select the Collection object with the longest
+ # available lifetime.
+
+ select_attrs = (@select || ["manifest_text"]) | ["portable_data_hash", "trash_at"]
+ model = Collection
+ if with_lock && Rails.configuration.API.LockBeforeUpdate
+ model = model.lock
+ end
+ if c = model.
+ readable_by(*@read_users, opts).
+ where({ portable_data_hash: loc.to_s }).
+ order("trash_at desc").
+ select(select_attrs.join(", ")).
+ limit(1).
+ first
@object = {
+ uuid: c.portable_data_hash,
portable_data_hash: c.portable_data_hash,
- manifest_text: c.manifest_text,
- files: c.files,
- data_size: c.data_size
+ trash_at: c.trash_at,
}
+ if select_attrs.index("manifest_text")
+ @object[:manifest_text] = c.manifest_text
+ end
end
else
- super
+ super(with_lock: with_lock)
end
- true
end
def show
- sign_manifests(@object[:manifest_text])
- super
+ if @object.is_a? Collection
+ # Omit unsigned_manifest_text
+ @select ||= model_class.selectable_attributes - ["unsigned_manifest_text"]
+ super
+ else
+ send_json @object
+ end
end
- def index
- sign_manifests(*@objects.map { |c| c[:manifest_text] })
- super
- end
- def script_param_edges(visited, sp)
+ def find_collections(visited, sp, ignore_columns=[], &b)
case sp
+ when ArvadosModel
+ sp.class.columns.each do |c|
+ find_collections(visited, sp[c.name.to_sym], &b) if !ignore_columns.include?(c.name)
+ end
when Hash
sp.each do |k, v|
- script_param_edges(visited, v)
+ find_collections(visited, v, &b)
end
when Array
sp.each do |v|
- script_param_edges(visited, v)
+ find_collections(visited, v, &b)
end
when String
- return if sp.empty?
- if loc = Locator.parse(sp)
- search_edges(visited, loc.to_s, :search_up)
+ 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
return
end
- if loc = Locator.parse(uuid)
+ if loc = Keep::Locator.parse(uuid)
loc.strip_hints!
return if visited[loc.to_s]
end
- logger.debug "visiting #{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
- }
+ 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
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)
+ if !Rails.configuration.API.DisabledAPIs["jobs.list"]
+ Job.readable_by(*@read_users).where(output: loc.to_s).each do |job|
+ search_edges(visited, job.uuid, :search_up)
+ end
+
+ Job.readable_by(*@read_users).where(log: loc.to_s).each do |job|
+ search_edges(visited, job.uuid, :search_up)
+ end
+ end
+
+ Container.readable_by(*@read_users).where(output: loc.to_s).pluck(:uuid).each do |c_uuid|
+ search_edges(visited, c_uuid, :search_up)
end
- Job.readable_by(*@read_users).where(log: loc.to_s).each do |job|
- search_edges(visited, job.uuid, :search_up)
+ Container.readable_by(*@read_users).where(log: loc.to_s).pluck(:uuid).each do |c_uuid|
+ search_edges(visited, c_uuid, :search_up)
end
elsif direction == :search_down
if loc.to_s == "d41d8cd98f00b204e9800998ecf8427e+0"
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)
+ if !Rails.configuration.API.DisabledAPIs["jobs.list"]
+ 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
+
+ Container.readable_by(*@read_users).where([Container.full_text_trgm + " like ?", "%#{loc.to_s}%"]).select("output, log, uuid").each do |c|
+ if c.output != loc.to_s && c.log != loc.to_s
+ search_edges(visited, c.uuid, :search_down)
+ end
end
end
else
visited[uuid] = job.as_api_response
if direction == :search_up
# Follow upstream collections referenced in the script parameters
- script_param_edges(visited, job.script_parameters)
+ find_collections(visited, job) do |hash, col_uuid|
+ search_edges(visited, hash, :search_up) if hash
+ search_edges(visited, col_uuid, :search_up) if col_uuid
+ end
elsif direction == :search_down
# Follow downstream job output
search_edges(visited, job.output, direction)
end
end
+ elsif rsc == Container
+ c = Container.readable_by(*@read_users).where(uuid: uuid).limit(1).first
+ if c
+ visited[uuid] = c.as_api_response
+ if direction == :search_up
+ # Follow upstream collections referenced in the script parameters
+ find_collections(visited, c, ignore_columns=["log", "output"]) do |hash, col_uuid|
+ search_edges(visited, hash, :search_up) if hash
+ search_edges(visited, col_uuid, :search_up) if col_uuid
+ end
+ elsif direction == :search_down
+ # Follow downstream job output
+ search_edges(visited, c.output, :search_down)
+ end
+ end
+ elsif rsc == ContainerRequest
+ c = ContainerRequest.readable_by(*@read_users).where(uuid: uuid).limit(1).first
+ if c
+ visited[uuid] = c.as_api_response
+ if direction == :search_up
+ # Follow upstream collections
+ find_collections(visited, c, ignore_columns=["log_uuid", "output_uuid"]) do |hash, col_uuid|
+ search_edges(visited, hash, :search_up) if hash
+ search_edges(visited, col_uuid, :search_up) if col_uuid
+ end
+ elsif direction == :search_down
+ # Follow downstream job output
+ search_edges(visited, c.output_uuid, :search_down)
+ 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
+ c = Collection.readable_by(*@read_users).where(uuid: uuid).limit(1).first
+ if c
+ if direction == :search_up
+ visited[c.uuid] = c.as_api_response
+
+ if !Rails.configuration.API.DisabledAPIs["jobs.list"]
+ Job.readable_by(*@read_users).where(output: c.portable_data_hash).each do |job|
+ search_edges(visited, job.uuid, :search_up)
+ end
+
+ Job.readable_by(*@read_users).where(log: c.portable_data_hash).each do |job|
+ search_edges(visited, job.uuid, :search_up)
+ end
+ end
+
+ ContainerRequest.readable_by(*@read_users).where(output_uuid: uuid).pluck(:uuid).each do |cr_uuid|
+ search_edges(visited, cr_uuid, :search_up)
+ end
+
+ ContainerRequest.readable_by(*@read_users).where(log_uuid: uuid).pluck(:uuid).each do |cr_uuid|
+ search_edges(visited, cr_uuid, :search_up)
+ end
+ elsif direction == :search_down
+ search_edges(visited, c.portable_data_hash, :search_down)
+ end
end
elsif rsc != nil
rsc.where(uuid: uuid).each do |r|
def provenance
visited = {}
- search_edges(visited, @object[:uuid] || @object[:portable_data_hash], :search_up)
- render json: visited
+ if @object[:uuid]
+ search_edges(visited, @object[:uuid], :search_up)
+ else
+ search_edges(visited, @object[:portable_data_hash], :search_up)
+ end
+ send_json visited
end
def used_by
visited = {}
- search_edges(visited, @object[:uuid] || @object[:portable_data_hash], :search_down)
- render json: visited
- end
-
- def self.munge_manifest_locators(manifest)
- # Given a manifest text and a block, yield each locator,
- # and replace it with whatever the block returns.
- manifest.andand.gsub!(/ [[:xdigit:]]{32}(\+[[:digit:]]+)?(\+\S+)/) do |word|
- if loc = Locator.parse(word.strip)
- " " + yield(loc)
- else
- " " + word
- end
+ if @object[:uuid]
+ search_edges(visited, @object[:uuid], :search_down)
+ else
+ search_edges(visited, @object[:portable_data_hash], :search_down)
end
+ send_json visited
end
protected
- def find_objects_for_index
- # Omit manifest_text from index results unless expressly selected.
- @select ||= model_class.api_accessible_attributes(:user).
- map { |attr_spec| attr_spec.first.to_s } - ["manifest_text"]
+ def load_select_param *args
super
- end
-
- def find_object_by_uuid
- 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
- end
- end
-
- def munge_manifest_locators(manifest, &block)
- self.class.munge_manifest_locators(manifest, &block)
- end
-
- def sign_manifests(*manifests)
- if current_api_client_authorization
- signing_opts = {
- key: Rails.configuration.blob_signing_key,
- api_token: current_api_client_authorization.api_token,
- ttl: Rails.configuration.blob_signing_ttl,
- }
- manifests.each do |text|
- munge_manifest_locators(text) do |loc|
- Blob.sign_locator(loc.to_s, signing_opts)
- end
- end
+ if action_name == 'index'
+ # Omit manifest_text and unsigned_manifest_text from index results unless expressly selected.
+ @select ||= model_class.selectable_attributes - ["manifest_text", "unsigned_manifest_text"]
end
end
end
projects / arvados.git / blobdiff