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
ArvadosBase::resource_class_for_uuid(params[:uuid])
end
+ def show
+ @object = model_class.andand.find(params[:uuid])
+ if @object.is_a? Link and
+ @object.link_class == 'name' and
+ ArvadosBase::resource_class_for_uuid(@object.head_uuid) == Collection
+ redirect_to collection_path(id: @object.uuid)
+ elsif @object
+ redirect_to @object
+ else
+ raise ActiveRecord::RecordNotFound
+ end
+ end
+
def post
params.keys.collect(&:to_sym).each do |param|
if @@exposed_actions[param]
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
+ 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
+ end
+
+ def arv_normalize mt, *opts
+ r = ""
+ env = Hash[ENV].
+ merge({'ARVADOS_API_HOST' =>
+ arvados_api_client.arvados_v1_base.
+ sub(/\/arvados\/v1/, '').
+ sub(/^https?:\/\//, ''),
+ 'ARVADOS_API_TOKEN' => 'x',
+ 'ARVADOS_API_HOST_INSECURE' =>
+ Rails.configuration.arvados_insecure_https ? 'true' : 'false'
+ })
+ IO.popen([env, 'arv-normalize'] + opts, 'w+b') do |io|
+ io.write mt
+ io.close_write
+ while buf = io.read(2**16)
+ r += buf
+ end
+ end
+ r
end
expose_action :combine_selected_files_into_collection do
- lst = []
+ uuids = []
+ pdhs = []
files = []
params["selection"].each do |s|
- m = CollectionsHelper.match(s)
- if m and m[1] and m[2]
- lst.append(m[1] + m[2])
+ a = ArvadosBase::resource_class_for_uuid s
+ if a == Link
+ begin
+ if (m = CollectionsHelper.match(Link.find(s).head_uuid))
+ pdhs.append(m[1] + m[2])
+ files.append(m)
+ end
+ rescue
+ end
+ elsif (m = CollectionsHelper.match(s))
+ pdhs.append(m[1] + m[2])
+ files.append(m)
+ elsif (m = CollectionsHelper.match_uuid_with_optional_filepath(s))
+ uuids.append(m[1])
files.append(m)
end
end
- collections = Collection.where(uuid: lst)
-
+ pdhs = pdhs.uniq
+ uuids = uuids.uniq
chash = {}
- collections.each do |c|
- c.reload()
+
+ Collection.select([:uuid, :manifest_text]).where(uuid: uuids).each do |c|
chash[c.uuid] = c
end
+ Collection.select([:portable_data_hash, :manifest_text]).where(portable_data_hash: pdhs).each do |c|
+ chash[c.portable_data_hash] = c
+ end
+
combined = ""
+ files_in_dirs = {}
files.each do |m|
- mt = chash[m[1]+m[2]].manifest_text
- if m[4]
- IO.popen(['arv-normalize', '--extract', m[4][1..-1]], 'w+b') do |io|
- io.write mt
- io.close_write
- while buf = io.read(2**20)
- combined += buf
- end
+ mt = chash[m[1]+m[2]].andand.manifest_text
+ if not m[4].nil? and m[4].size > 1
+ manifest_files = files_in_dirs['.']
+ if !manifest_files
+ manifest_files = []
+ files_in_dirs['.'] = manifest_files
end
+ manifest_file = m[4].split('/')[-1]
+ uniq_file = derive_unique_filename(manifest_file, manifest_files)
+ normalized = arv_normalize mt, '--extract', ".#{m[4]}"
+ normalized = normalized.gsub(/(\d+:\d+:)(#{Regexp.quote manifest_file})/) {|s| "#{$1}#{uniq_file}" }
+ combined += normalized
+ manifest_files << uniq_file
else
- combined += chash[m[1]+m[2]].manifest_text
- end
- end
+ mt = arv_normalize mt
+ manifest_streams = mt.split "\n"
+ adjusted_streams = []
+ manifest_streams.each do |stream|
+ manifest_parts = stream.split
+ adjusted_parts = []
+ manifest_files = files_in_dirs[manifest_parts[0]]
+ if !manifest_files
+ manifest_files = []
+ files_in_dirs[manifest_parts[0]] = manifest_files
+ end
- normalized = ''
- IO.popen(['arv-normalize'], 'w+b') do |io|
- io.write combined
- io.close_write
- while buf = io.read(2**20)
- normalized += buf
+ manifest_parts.each do |part|
+ part_match = /(\d+:\d+:)(\S+)/.match(part)
+ if part_match
+ uniq_file = derive_unique_filename(part_match[2], manifest_files)
+ adjusted_parts << "#{part_match[1]}#{uniq_file}"
+ manifest_files << uniq_file
+ else
+ adjusted_parts << part
+ end
+ end
+ adjusted_streams << adjusted_parts.join(' ')
+ end
+ adjusted_streams.each do |stream|
+ combined += (stream + "\n")
+ end
end
end
- require 'digest/md5'
-
- d = Digest::MD5.new()
- d << normalized
- newuuid = "#{d.hexdigest}+#{normalized.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
- io.close_write
- while buf = io.read(2**20)
+ normalized = arv_normalize combined
+ newc = Collection.new({:manifest_text => normalized})
+ newc.name = newc.name || "Collection created at #{Time.now.localtime}"
+ # set owner_uuid to current project, provided it is writable
+ current_project_writable = false
+ action_data = JSON.parse(params['action_data']) if params['action_data']
+ if action_data && action_data['current_project_uuid']
+ current_project = Group.find(action_data['current_project_uuid']) rescue nil
+ if (current_project && current_project.writable_by.andand.include?(current_user.uuid))
+ newc.owner_uuid = action_data['current_project_uuid']
+ current_project_writable = true
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,
+ head_uuid: newc.uuid,
link_class: "provenance",
name: "provided"
})
l.save!
end
- redirect_to controller: 'collections', action: :show, id: newc.uuid
+ msg = current_project_writable ?
+ "Created new collection in the project #{current_project.name}." :
+ "Created new collection in your Home project."
+
+ redirect_to newc, flash: {'message' => msg}
+ end
+
+ def report_issue_popup
+ respond_to do |format|
+ format.js
+ format.html
+ end
+ end
+
+ def report_issue
+ logger.warn "report_issue: #{params.inspect}"
+
+ respond_to do |format|
+ IssueReporter.send_report(current_user, params).deliver
+ 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
end
projects / arvados.git / blobdiff