+require "arvados/collection"
+
class ActionsController < ApplicationController
+ skip_filter :require_thread_api_token, only: [:report_issue_popup, :report_issue]
+ skip_filter :check_user_agreements, only: [:report_issue_popup, :report_issue]
+
@@exposed_actions = {}
def self.expose_action method, &block
@@exposed_actions[method] = true
def move_or_copy action
uuids_to_add = params["selection"]
- uuids_to_add.
+ uuids_to_add = [ uuids_to_add ] unless uuids_to_add.is_a? Array
+ resource_classes = uuids_to_add.
collect { |x| ArvadosBase::resource_class_for_uuid(x) }.
- uniq.
- each do |resource_class|
+ uniq
+ resource_classes.each do |resource_class|
resource_class.filter([['uuid','in',uuids_to_add]]).each do |src|
- if resource_class == Collection
+ if resource_class == Collection and not Collection.attribute_info.include?(:name)
dst = Link.new(owner_uuid: @object.uuid,
tail_uuid: @object.uuid,
head_uuid: src.uuid,
dst.name = "Copy of unnamed #{dst.class_for_display.downcase}"
end
end
+ if resource_class == Collection
+ dst.manifest_text = Collection.select([:manifest_text]).where(uuid: src.uuid).first.manifest_text
+ end
when :move
dst = src
else
end
end
end
- redirect_to @object
- end
-
- def arv_normalize mt, *opts
- r = ""
- IO.popen(['arv-normalize'] + opts, 'w+b') do |io|
- io.write mt
- io.close_write
- while buf = io.read(2**16)
- r += buf
- end
+ if (resource_classes == [Collection] and
+ @object.is_a? Group and
+ @object.group_class == 'project')
+ # In the common case where only collections are copied/moved
+ # into a project, it's polite to land on the collections tab on
+ # the destination project.
+ redirect_to project_url(@object.uuid, anchor: 'Data_collections')
+ else
+ # Otherwise just land on the default (Description) tab.
+ redirect_to @object
end
- r
end
expose_action :combine_selected_files_into_collection do
- lst = []
- files = []
- params["selection"].each do |s|
- a = ArvadosBase::resource_class_for_uuid s
- m = nil
- if a == Link
- begin
- m = CollectionsHelper.match(Link.find(s).head_uuid)
- rescue
+ link_uuids, coll_ids = params["selection"].partition do |sel_s|
+ ArvadosBase::resource_class_for_uuid(sel_s) == Link
+ end
+
+ unless link_uuids.empty?
+ Link.select([:head_uuid]).where(uuid: link_uuids).each do |link|
+ if ArvadosBase::resource_class_for_uuid(link.head_uuid) == Collection
+ coll_ids << link.head_uuid
end
- else
- m = CollectionsHelper.match(s)
end
+ end
- if m and m[1] and m[2]
- lst.append(m[1] + m[2])
- files.append(m)
+ uuids = []
+ pdhs = []
+ source_paths = Hash.new { |hash, key| hash[key] = [] }
+ coll_ids.each do |coll_id|
+ if m = CollectionsHelper.match(coll_id)
+ key = m[1] + m[2]
+ pdhs << key
+ source_paths[key] << m[4]
+ elsif m = CollectionsHelper.match_uuid_with_optional_filepath(coll_id)
+ key = m[1]
+ uuids << key
+ source_paths[key] << m[4]
end
end
- collections = Collection.where(uuid: lst)
-
- chash = {}
- collections.each do |c|
- c.reload()
- chash[c.uuid] = c
+ unless pdhs.empty?
+ Collection.where(portable_data_hash: pdhs.uniq).
+ select([:uuid, :portable_data_hash]).each do |coll|
+ unless source_paths[coll.portable_data_hash].empty?
+ uuids << coll.uuid
+ source_paths[coll.uuid] = source_paths.delete(coll.portable_data_hash)
+ end
+ end
end
- combined = ""
- files.each do |m|
- mt = chash[m[1]+m[2]].manifest_text
- if m[4]
- combined += arv_normalize mt, '--extract', m[4][1..-1]
+ new_coll = Arv::Collection.new
+ Collection.where(uuid: uuids.uniq).
+ select([:uuid, :manifest_text]).each do |coll|
+ src_coll = Arv::Collection.new(coll.manifest_text)
+ src_pathlist = source_paths[coll.uuid]
+ if src_pathlist.any?(&:blank?)
+ src_pathlist = src_coll.each_file_path
+ destdir = nil
else
- combined += chash[m[1]+m[2]].manifest_text
+ destdir = "."
end
- end
-
- normalized = arv_normalize combined
- normalized_stripped = arv_normalize combined, '--strip'
-
- require 'digest/md5'
-
- d = Digest::MD5.new()
- d << normalized_stripped
- newuuid = "#{d.hexdigest}+#{normalized_stripped.length}"
-
- env = Hash[ENV].
- merge({
- 'ARVADOS_API_HOST' =>
- arvados_api_client.arvados_v1_base.
- sub(/\/arvados\/v1/, '').
- sub(/^https?:\/\//, ''),
- 'ARVADOS_API_TOKEN' => Thread.current[:arvados_api_token],
- 'ARVADOS_API_HOST_INSECURE' =>
- Rails.configuration.arvados_insecure_https ? 'true' : 'false'
- })
-
- IO.popen([env, 'arv-put', '--raw'], 'w+b') do |io|
- io.write normalized_stripped
- io.close_write
- while buf = io.read(2**16)
+ src_pathlist.each do |src_path|
+ src_path = src_path.sub(/^(\.\/|\/|)/, "./")
+ src_stream, _, basename = src_path.rpartition("/")
+ dst_stream = destdir || src_stream
+ # Generate a unique name by adding (1), (2), etc. to it.
+ # If the filename has a dot that's not at the beginning, insert the
+ # number just before that. Otherwise, append the number to the name.
+ if match = basename.match(/[^\.]\./)
+ suffix_start = match.begin(0) + 1
+ else
+ suffix_start = basename.size
+ end
+ suffix_size = 0
+ dst_path = nil
+ loop.each_with_index do |_, try_count|
+ dst_path = "#{dst_stream}/#{basename}"
+ break unless new_coll.exist?(dst_path)
+ uniq_suffix = "(#{try_count + 1})"
+ basename[suffix_start, suffix_size] = uniq_suffix
+ suffix_size = uniq_suffix.size
+ end
+ new_coll.cp_r(src_path, dst_path, src_coll)
end
end
- newc = Collection.new({:uuid => newuuid, :manifest_text => normalized})
- newc.save!
-
- chash.each do |k,v|
- l = Link.new({
- tail_uuid: k,
- head_uuid: newuuid,
- link_class: "provenance",
- name: "provided"
- })
- l.save!
+ coll_attrs = {
+ manifest_text: new_coll.manifest_text,
+ name: "Collection created at #{Time.now.localtime}",
+ }
+ flash = {}
+
+ # set owner_uuid to current project, provided it is writable
+ action_data = Oj.load(params['action_data'] || "{}")
+ if action_data['current_project_uuid'] and
+ current_project = Group.find?(action_data['current_project_uuid']) and
+ current_project.writable_by.andand.include?(current_user.uuid)
+ coll_attrs[:owner_uuid] = current_project.uuid
+ flash[:message] =
+ "Created new collection in the project #{current_project.name}."
+ else
+ flash[:message] = "Created new collection in your Home project."
end
- redirect_to controller: 'collections', action: :show, id: newc.uuid
+ newc = Collection.create!(coll_attrs)
+ source_paths.each_key do |src_uuid|
+ unless Link.create({
+ tail_uuid: src_uuid,
+ head_uuid: newc.uuid,
+ link_class: "provenance",
+ name: "provided",
+ })
+ flash[:error] = "
+An error occurred when saving provenance information for this collection.
+You can try recreating the collection to get a copy with full provenance data."
+ break
+ end
+ end
+ redirect_to(newc, flash: flash)
end
def report_issue_popup
- @popup_params = params
respond_to do |format|
format.js
format.html
end
def report_issue
+ logger.warn "report_issue: #{params.inspect}"
+
respond_to do |format|
IssueReporter.send_report(current_user, params).deliver
- format.js
+ format.js {render nothing: true}
+ end
+ end
+
+ protected
+
+ def derive_unique_filename filename, manifest_files
+ filename_parts = filename.split('.')
+ filename_part = filename_parts[0]
+ counter = 1
+ while true
+ return filename if !manifest_files.include? filename
+ filename_parts[0] = filename_part + "(" + counter.to_s + ")"
+ filename = filename_parts.join('.')
+ counter += 1
end
end
projects / arvados.git / blobdiff