+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
require "arvados/keep"
+require "arvados/collection"
require "uri"
class CollectionsController < ApplicationController
RELATION_LIMIT = 5
def show_pane_list
- panes = %w(Files Upload Provenance_graph Used_by Advanced)
+ panes = %w(Files Upload Tags Provenance_graph Used_by Advanced)
panes = panes - %w(Upload) unless (@object.editable? rescue false)
panes
end
end
def show_file_links
- Thread.current[:reader_tokens] = [params[:reader_token]]
- return if false.equal?(find_object_by_uuid)
- render layout: false
+ return show_file
end
def show_file
- # We pipe from arv-get to send the file to the user. Before we start it,
- # we ask the API server if the file actually exists. This serves two
- # purposes: it lets us return a useful status code for common errors, and
- # helps us figure out which token to provide to arv-get.
# The order of searched tokens is important: because the anonymous user
# token is passed along with every API request, we have to check it first.
# Otherwise, it's impossible to know whether any other request succeeded
return
end
- # If we are configured to use a keep-web server, just redirect to
- # the appropriate URL.
- if Rails.configuration.keep_web_url or
- Rails.configuration.keep_web_download_url
- opts = {}
- if usable_token == params[:reader_token]
- opts[:path_token] = usable_token
- elsif usable_token == Rails.configuration.anonymous_user_token
- # Don't pass a token at all
- else
- # We pass the current user's real token only if it's necessary
- # to read the collection.
- opts[:query_token] = usable_token
- end
- opts[:disposition] = params[:disposition] if params[:disposition]
- return redirect_to keep_web_url(params[:uuid], params[:file], opts)
- end
-
- # No keep-web server available. Get the file data with arv-get,
- # and serve it through Rails.
-
- file_name = params[:file].andand.sub(/^(\.\/|\/|)/, './')
- if file_name.nil? or not coll.manifest.has_file?(file_name)
- return render_not_found
- end
-
- opts = params.merge(arvados_api_token: usable_token)
-
- # Handle Range requests. Currently we support only 'bytes=0-....'
- if request.headers.include? 'HTTP_RANGE'
- if m = /^bytes=0-(\d+)/.match(request.headers['HTTP_RANGE'])
- opts[:maxbytes] = m[1]
- size = params[:size] || '*'
- self.response.status = 206
- self.response.headers['Content-Range'] = "bytes 0-#{m[1]}/#{size}"
- end
- end
-
- ext = File.extname(params[:file])
- self.response.headers['Content-Type'] =
- Rack::Mime::MIME_TYPES[ext] || 'application/octet-stream'
- if params[:size]
- size = params[:size].to_i
- if opts[:maxbytes]
- size = [size, opts[:maxbytes].to_i].min
- end
- self.response.headers['Content-Length'] = size.to_s
- end
- self.response.headers['Content-Disposition'] = params[:disposition] if params[:disposition]
- begin
- file_enumerator(opts).each do |bytes|
- response.stream.write bytes
- end
- ensure
- response.stream.close
+ opts = {}
+ if usable_token == params[:reader_token]
+ opts[:path_token] = usable_token
+ elsif usable_token == Rails.configuration.anonymous_user_token
+ # Don't pass a token at all
+ else
+ # We pass the current user's real token only if it's necessary
+ # to read the collection.
+ opts[:query_token] = usable_token
end
+ opts[:disposition] = params[:disposition] if params[:disposition]
+ return redirect_to keep_web_url(params[:uuid], params[:file], opts)
end
def sharing_scopes
if params["tab_pane"] == "Provenance_graph"
@prov_svg = ProvenanceHelper::create_provenance_graph(@object.provenance, "provenance_svg",
{:request => request,
- :direction => :bottom_up,
+ :direction => :top_down,
:combine_jobs => :script_only}) rescue nil
end
render 'hash_matches'
return
else
- jobs_with = lambda do |conds|
- Job.limit(RELATION_LIMIT).where(conds)
- .results.sort_by { |j| j.finished_at || j.created_at }
+ if Job.api_exists?(:index)
+ jobs_with = lambda do |conds|
+ Job.limit(RELATION_LIMIT).where(conds)
+ .results.sort_by { |j| j.finished_at || j.created_at }
+ end
+ @output_of = jobs_with.call(output: @object.portable_data_hash)
+ @log_of = jobs_with.call(log: @object.portable_data_hash)
end
- @output_of = jobs_with.call(output: @object.portable_data_hash)
- @log_of = jobs_with.call(log: @object.portable_data_hash)
+
@project_links = Link.limit(RELATION_LIMIT).order("modified_at DESC")
.where(head_uuid: @object.uuid, link_class: 'name').results
project_hash = Group.where(uuid: @project_links.map(&:tail_uuid)).to_hash
@permissions = Link.limit(RELATION_LIMIT).order("modified_at DESC")
.where(head_uuid: @object.uuid, link_class: 'permission',
name: 'can_read').results
- @logs = Log.limit(RELATION_LIMIT).order("created_at DESC")
- .select(%w(uuid event_type object_uuid event_at summary))
- .where(object_uuid: @object.uuid).results
- @is_persistent = Link.limit(1)
- .where(head_uuid: @object.uuid, tail_uuid: current_user.uuid,
- link_class: 'resources', name: 'wants')
- .results.any?
@search_sharing = search_scopes
if params["tab_pane"] == "Used_by"
@used_by_svg = ProvenanceHelper::create_provenance_graph(@object.used_by, "used_by_svg",
{:request => request,
- :direction => :top_down,
- :combine_jobs => :script_only,
- :pdata_only => true}) rescue nil
+ :direction => :top_down,
+ :combine_jobs => :script_only,
+ :pdata_only => true}) rescue nil
end
end
end
helper_method :download_link
def download_link
- collections_url + "/download/#{@object.uuid}/#{@search_sharing.first.api_token}/"
+ token = @search_sharing.first.api_token
+ keep_web_url(@object.uuid, nil, {path_token: token})
end
def share
sharing_popup
end
+ def remove_selected_files
+ uuids, source_paths = selected_collection_files params
+
+ arv_coll = Arv::Collection.new(@object.manifest_text)
+ source_paths[uuids[0]].each do |p|
+ arv_coll.rm "."+p
+ end
+
+ if @object.update_attributes manifest_text: arv_coll.manifest_text
+ show
+ else
+ self.render_error status: 422
+ end
+ end
+
+ def update
+ updated_attr = params[:collection].each.select {|a| a[0].andand.start_with? 'rename-file-path:'}
+
+ if updated_attr.size > 0
+ # Is it file rename?
+ file_path = updated_attr[0][0].split('rename-file-path:')[-1]
+
+ new_file_path = updated_attr[0][1]
+ if new_file_path.start_with?('./')
+ # looks good
+ elsif new_file_path.start_with?('/')
+ new_file_path = '.' + new_file_path
+ else
+ new_file_path = './' + new_file_path
+ end
+
+ arv_coll = Arv::Collection.new(@object.manifest_text)
+
+ if arv_coll.exist?(new_file_path)
+ @errors = 'Duplicate file path. Please use a different name.'
+ self.render_error status: 422
+ else
+ arv_coll.rename "./"+file_path, new_file_path
+
+ if @object.update_attributes manifest_text: arv_coll.manifest_text
+ show
+ else
+ self.render_error status: 422
+ end
+ end
+ else
+ # Not a file rename; use default
+ super
+ end
+ end
+
+ def tags
+ render
+ end
+
+ def save_tags
+ tags_param = params['tag_data']
+ if tags_param
+ if tags_param.is_a?(String) && tags_param == "empty"
+ tags = {}
+ else
+ tags = tags_param
+ end
+ end
+
+ if tags
+ if @object.update_attributes properties: tags
+ @saved_tags = true
+ render
+ else
+ self.render_error status: 422
+ end
+ end
+ end
+
protected
def find_usable_token(token_list)
# Prefer the attachment-only-host when we want an attachment
# (and when there is no preview link configured)
tmpl = Rails.configuration.keep_web_download_url
- else
+ elsif not Rails.configuration.trust_all_content
check_uri = URI.parse(tmpl % fmt)
if opts[:query_token] and
not check_uri.host.start_with?(munged_id + "--") and
uri.path += 't=' + opts[:path_token] + '/'
end
uri.path += '_/'
- uri.path += URI.escape(file)
+ uri.path += URI.escape(file) if file
query = Hash[URI.decode_www_form(uri.query || '')]
{ query_token: 'api_token',
uri.to_s
end
-
- # Note: several controller and integration tests rely on stubbing
- # file_enumerator to return fake file content.
- def file_enumerator opts
- FileStreamer.new opts
- end
-
- class FileStreamer
- include ArvadosApiClientHelper
- def initialize(opts={})
- @opts = opts
- end
- def each
- return unless @opts[:uuid] && @opts[:file]
-
- env = Hash[ENV].dup
-
- require 'uri'
- u = URI.parse(arvados_api_client.arvados_v1_base)
- env['ARVADOS_API_HOST'] = "#{u.host}:#{u.port}"
- env['ARVADOS_API_TOKEN'] = @opts[:arvados_api_token]
- env['ARVADOS_API_HOST_INSECURE'] = "true" if Rails.configuration.arvados_insecure_https
-
- bytesleft = @opts[:maxbytes].andand.to_i || 2**16
- io = IO.popen([env, 'arv-get', "#{@opts[:uuid]}/#{@opts[:file]}"], 'rb')
- while bytesleft > 0 && (buf = io.read([bytesleft, 2**16].min)) != nil
- # shrink the bytesleft count, if we were given a maximum byte
- # count to read
- if @opts.include? :maxbytes
- bytesleft = bytesleft - buf.length
- end
- yield buf
- end
- io.close
- # "If ios is opened by IO.popen, close sets $?."
- # http://www.ruby-doc.org/core-2.1.3/IO.html#method-i-close
- Rails.logger.warn("#{@opts[:uuid]}/#{@opts[:file]}: #{$?}") if $? != 0
- end
- end
end
projects / arvados.git / blobdiff