+require "arvados/collection"
+
class ActionsController < ApplicationController
skip_filter :require_thread_api_token, only: [:report_issue_popup, :report_issue]
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
+ expose_action :combine_selected_files_into_collection do
+ link_uuids, coll_ids = params["selection"].partition do |sel_s|
+ ArvadosBase::resource_class_for_uuid(sel_s) == Link
end
- r
- end
- expose_action :combine_selected_files_into_collection do
- uuids = []
- pdhs = []
- files = []
- params["selection"].each do |s|
- 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
+ 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
- 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
- pdhs = pdhs.uniq
- uuids = uuids.uniq
- chash = {}
-
- Collection.select([:uuid, :manifest_text]).where(uuid: uuids).each do |c|
- chash[c.uuid] = c
+ 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
- Collection.select([:portable_data_hash, :manifest_text]).where(portable_data_hash: pdhs).each do |c|
- chash[c.portable_data_hash] = 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_in_dirs = {}
- files.each do |m|
- 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
+ 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
- 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
-
- 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(' ')
+ destdir = "."
+ end
+ 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
- adjusted_streams.each do |stream|
- combined += (stream + "\n")
+ 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
- normalized = arv_normalize combined
- newc = Collection.new({:manifest_text => normalized})
- newc.name = newc.name || "Collection created at #{Time.now.localtime}"
+ 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
- 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
+ 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
- newc.save!
-
- chash.each do |k,v|
- l = Link.new({
- tail_uuid: k,
- head_uuid: newc.uuid,
- link_class: "provenance",
- name: "provided"
- })
- l.save!
+ 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
-
- 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}
+ redirect_to(newc, flash: flash)
end
def report_issue_popup
projects / arvados.git / commitdiff