Merge branch 'master' into 3036-collection-uuids

Conflicts:
	services/api/app/controllers/arvados/v1/collections_controller.rb
	services/api/app/models/collection.rb

diff --cc services/api/app/controllers/application_controller.rb
Simple merge

diff --cc services/api/app/controllers/arvados/v1/collections_controller.rb
index 443bbb46a520873fb3e38ae37bd19df4c01e5f8c,b65fa5b962ab76b9c26e52a0443cb4586f90a043..6b2bd64be93d1211100fd44d5767b16ac5631ea5
--- 1/services/api/app/controllers/arvados/v1/collections_controller.rb
--- 2/services/api/app/controllers/arvados/v1/collections_controller.rb
+++ b/services/api/app/controllers/arvados/v1/collections_controller.rb
@@@ -39,62 -45,63 +39,40 @@@ class Arvados::V1::CollectionsControlle
      end
  
      # Remove any permission signatures from the manifest.
-     resource_attrs[:manifest_text]
-       .gsub!(/ [[:xdigit:]]{32}(\+[[:digit:]]+)?(\+\S+)/) { |word|
-       word.strip!
-       loc = Locator.parse(word)
-       if loc
-         " " + loc.without_signature.to_s
-       else
-         " " + word
-       end
-     }
+     munge_manifest_locators(resource_attrs[:manifest_text]) do |loc|
+       loc.without_signature.to_s
+     end
  
 -    # Save the collection with the stripped manifest.
 -    act_as_system_user do
 -      @object = model_class.new resource_attrs.reject { |k,v| k == :owner_uuid }
 -      begin
 -        @object.save!
 -      rescue ActiveRecord::RecordNotUnique
 -        logger.debug resource_attrs.inspect
 -        if @object.manifest_text and @object.uuid
 -          @existing_object = model_class.
 -            where('uuid=? and manifest_text=?',
 -                  @object.uuid,
 -                  @object.manifest_text).
 -            first
 -          @object = @existing_object || @object
 -        end
 -      end
 -      if @object
 -        link_attrs = {
 -          owner_uuid: owner_uuid,
 -          link_class: 'permission',
 -          name: 'can_read',
 -          head_uuid: @object.uuid,
 -          tail_uuid: owner_uuid
 +    super
 +  end
 +
 +  def find_object_by_uuid
 +    if loc = Locator.parse(params[:id])
 +      loc.strip_hints!
 +      if c = Collection.readable_by(*@read_users).where({ portable_data_hash: loc.to_s }).limit(1).first
 +        @object = {
 +          portable_data_hash: c.portable_data_hash,
 +          manifest_text: c.manifest_text,
 +          files: c.files,
 +          data_size: c.data_size
          }
 -        ActiveRecord::Base.transaction do
 -          if Link.where(link_attrs).empty?
 -            Link.create! link_attrs
 -          end
 -        end
        end
 +    else
 +      super
      end
 -    show
 +    true
    end
  
    def show
-     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,
-       }
-       @object[:manifest_text]
-         .gsub!(/ [[:xdigit:]]{32}(\+[[:digit:]]+)?(\+\S+)/) { |word|
-         word.strip!
-         loc = Locator.parse(word)
-         if loc
-           " " + Blob.sign_locator(word, signing_opts)
-         else
-           " " + word
-         end
-       }
-     end
-     if @object.is_a? Collection
-       render json: @object.as_api_response(:with_data)
-     else
-       render json: @object
-     end
+     sign_manifests(@object[:manifest_text])
+     super
+   end
+ 
+   def index
+     sign_manifests(*@objects.map { |c| c[:manifest_text] })
+     super
    end
  
 -  def collection_uuid(uuid)
 -    m = /([a-f0-9]{32}(\+[0-9]+)?)(\+.*)?/.match(uuid)
 -    if m
 -      m[1]
 -    else
 -      nil
 -    end
 -  end
 -
    def script_param_edges(visited, sp)
      case sp
      when Hash

diff --cc services/api/app/controllers/arvados/v1/jobs_controller.rb
Simple merge

diff --cc services/api/app/models/arvados_model.rb
Simple merge

diff --cc services/api/app/models/collection.rb
index 2bf781013bce167ae1a376740ad100cb1c73abf9,ac845f50adc71e5e95d4eded09779be72ffdca46..c0c2b7ef7d3af5c21e67fb51bebde066907d7276
--- 1/services/api/app/models/collection.rb
--- 2/services/api/app/models/collection.rb
+++ b/services/api/app/models/collection.rb
@@@ -9,44 -6,15 +9,47 @@@ class Collection < ArvadosMode
    api_accessible :user, extend: :common do |t|
      t.add :data_size
      t.add :files
 +    t.add :name
 +    t.add :description
 +    t.add :properties
 +    t.add :portable_data_hash
+     t.add :manifest_text
    end
  
-   api_accessible :with_data, extend: :user do |t|
-     t.add :manifest_text
+   def self.attributes_required_columns
+     super.merge({ "data_size" => ["manifest_text"],
+                   "files" => ["manifest_text"],
+                 })
    end
  
 +  def set_portable_data_hash
 +    if (self.portable_data_hash.nil? or (self.portable_data_hash == "") or (manifest_text_changed? and !portable_data_hash_changed?))
 +      self.portable_data_hash = "#{Digest::MD5.hexdigest(manifest_text)}+#{manifest_text.length}"
 +    elsif portable_data_hash_changed?
 +      begin
 +        loc = Locator.parse!(self.portable_data_hash)
 +        loc.strip_hints!
 +        self.portable_data_hash = loc.to_s
 +      rescue ArgumentError => e
 +        errors.add(:portable_data_hash, "#{e}")
 +        return false
 +      end
 +    end
 +    true
 +  end
 +
 +  def ensure_hash_matches_manifest_text
 +    if manifest_text_changed? or portable_data_hash_changed?
 +      computed_hash = "#{Digest::MD5.hexdigest(manifest_text)}+#{manifest_text.length}"
 +      unless computed_hash == portable_data_hash
 +        logger.debug "(computed) '#{computed_hash}' != '#{portable_data_hash}' (provided)"
 +        errors.add(:portable_data_hash, "does not match hash of manifest_text")
 +        return false
 +      end
 +    end
 +    true
 +  end
 +
    def redundancy_status
      if redundancy_confirmed_as.nil?
        'unconfirmed'

diff --cc services/api/app/models/job.rb
Simple merge

diff --cc services/api/test/functional/arvados/v1/collections_controller_test.rb
Simple merge