Merge pull request seek4science#1907 from seek4science/github-app-sup…

…port

RO-Crate submission API

app/controllers/application_controller.rb

@@ -544,7 +544,8 @@ def json_api_errors(object)
     hash[:errors] = object.errors.map do |error|
       segments = error.attribute.to_s.split('.')
       attr = segments.first
-      if !['content_blobs', 'policy'].include?(attr) && object.class.reflect_on_association(attr)
+      if !['content_blobs', 'policy'].include?(attr) &&
+        object.class.respond_to?(:reflect_on_association) && object.class.reflect_on_association(attr)
         base = '/data/relationships'
       else
         base = '/data/attributes'

app/controllers/workflows_controller.rb

@@ -10,7 +10,8 @@ class WorkflowsController < ApplicationController
   before_action :find_display_asset, only: [:show, :download, :diagram, :ro_crate, :ro_crate_metadata, :edit_paths, :update_paths]
   before_action :login_required, only: [:create, :create_version, :new_version,
                                         :create_from_files, :create_from_ro_crate,
-                                        :create_metadata, :provide_metadata, :create_from_git, :create_version_from_git]
+                                        :create_metadata, :provide_metadata, :create_from_git, :create_version_from_git,
+                                        :submit]
   before_action :find_or_initialize_workflow, only: [:create_from_files, :create_from_ro_crate]
 
   include Seek::Publishing::PublishingCommon
@@ -307,6 +308,21 @@ def filter
     end
   end
 
+  def submit
+    @crate_extractor = WorkflowCrateExtractor.new(ro_crate: { data: params[:ro_crate] }, params: workflow_params, update_existing: true)
+
+    if @crate_extractor.valid?
+      @workflow = @crate_extractor.build
+      if @workflow.git_version.save && @workflow.save
+        render json: @workflow, include: json_api_include_param
+      else
+        render json: json_api_errors(@workflow), status: :unprocessable_entity
+      end
+    else
+      render json: json_api_errors(@crate_extractor), status: :unprocessable_entity
+    end
+  end
+
   private
 
   def handle_ro_crate_post(new_version = false)
@@ -321,7 +337,7 @@ def handle_ro_crate_post(new_version = false)
       else
         @crate_extractor.workflow = @workflow
         @workflow.latest_git_version.lock if @workflow.latest_git_version.mutable?
-        @crate_extractor.git_version = @workflow.latest_git_version.next_version(mutable: true).tap(&:save)
+        @crate_extractor.git_version = @workflow.latest_git_version.next_version(mutable: true)
       end
     end
     @workflow = @crate_extractor.build

app/models/workflow_crate_extractor.rb → app/forms/workflow_crate_extractor.rb

@@ -5,17 +5,29 @@
 class WorkflowCrateExtractor
   include ActiveModel::Model
 
-  attr_accessor :ro_crate, :workflow_class, :workflow, :git_version, :params
+  attr_accessor :ro_crate, :workflow_class, :workflow, :git_version, :params, :update_existing
 
   validate :resolve_crate
   validate :main_workflow_present?, if: -> { @crate.present? }
+  validate :source_url_and_version_present?, if: -> { update_existing }
+  validate :find_workflows_matching_id, if: -> { update_existing }
 
   def build
-    self.workflow ||= Workflow.new(workflow_class: workflow_class)
     if valid?
+      if update_existing && @existing_workflows.length == 1
+        self.workflow = @existing_workflows.first
+        if self.workflow.git_versions.map(&:name).include?(@crate['version']&.to_s)
+          return self.workflow
+        else
+          self.workflow.latest_git_version.lock if self.workflow.latest_git_version.mutable?
+          self.git_version = self.workflow.latest_git_version.next_version(mutable: true)
+        end
+      end
+      self.workflow ||= default_workflow
       self.git_version ||= workflow.git_version.tap do |gv|
         gv.set_default_git_repository
       end
+      self.git_version.name = @crate['version'].to_s if @crate['version']
       git_version.main_workflow_path = URI.decode_www_form_component(@crate.main_workflow.id) if @crate.main_workflow && !@crate.main_workflow.remote?
       git_version.diagram_path = URI.decode_www_form_component(@crate.main_workflow.diagram.id) if @crate.main_workflow&.diagram && !@crate.main_workflow.diagram.remote?
       git_version.abstract_cwl_path = URI.decode_www_form_component(@crate.main_workflow.cwl_description.id) if @crate.main_workflow&.cwl_description && !@crate.main_workflow.cwl_description.remote?
@@ -30,19 +42,34 @@ def build
       workflow.provide_metadata(extractor.metadata)
       workflow.assign_attributes(params) if params.present?
       git_version.set_resource_attributes(workflow.attributes)
-
-      workflow
     end
 
-    workflow
+    workflow || default_workflow
   end
 
   private
 
+  def default_workflow
+    Workflow.new(workflow_class: workflow_class)
+  end
+
   def main_workflow_present?
     errors.add(:ro_crate, 'did not specify a main workflow.') unless @crate.main_workflow.present?
   end
 
+  def source_url_and_version_present?
+    errors.add(:ro_crate, 'source URL could not be determined.') unless @crate.source_url.present?
+    errors.add(:ro_crate, 'version could not be determined.') unless @crate['version'].present?
+  end
+
+  def find_workflows_matching_id
+    # Attempt to find existing workflow
+    @existing_workflows = Workflow.find_by_source_url(@crate.source_url)
+    if @existing_workflows.length > 1
+      errors.add(:ro_crate, "#{@existing_workflows.length} workflows found matching the given ID.")
+    end
+  end
+
   def extract_crate
     begin
       @crate = ROCrate::WorkflowCrateReader.read_zip(ro_crate[:data])

app/models/concerns/workflow_extraction.rb

@@ -273,7 +273,9 @@ def ro_crate_url(action = nil)
       end
 
       if exist
-        exist.update_attribute(:path, path)
+        exist.path = path
+        exist.save(validate: false) if exist.persisted?
+        exist
       else
         git_version.git_annotations.build(key: s_type, path: path)
       end

app/models/git/annotation.rb

@@ -6,6 +6,7 @@ class Annotation < ApplicationRecord
     before_validation :assign_contributor
 
     validates :key, uniqueness: { scope: [:git_version_id, :path, :value] }
+    validates :git_version, presence: true
     validate :check_valid_path
 
     def assign_contributor

app/models/workflow.rb

@@ -274,4 +274,7 @@ def execution_instance_url
       }
   )
 
+  def self.find_by_source_url(source_url)
+    joins(:source_link).where('asset_links.url' => source_url)
+  end
 end

config/routes.rb

@@ -528,6 +528,7 @@
       post :create_from_ro_crate
       post :create_from_files
       post :create_from_git
+      post :submit
       get :provide_metadata
       get :annotate_repository
       post :create_metadata

lib/ro_crate/workflow_crate.rb

@@ -56,5 +56,10 @@ def test_suites
     def find_entry(path)
       entries[path]
     end
+
+    def source_url
+      url = id if id.start_with?('http')
+      url || self['isBasedOn'] || self['url'] || self.main_workflow['url']
+    end
   end
 end

lib/seek/workflow_extractors/ro_crate.rb

@@ -103,11 +103,11 @@ def metadata_from_crate(crate, m)
           end
         end
 
-          source_url = crate['isBasedOn'] || crate['url'] || crate.main_workflow['url']
-          if source_url
-            m.merge!(extract_source_metadata(ContentBlob.remote_content_handler_for(source_url)))
-            m[:source_link_url] ||= source_url # Use plain source URL if handler doesn't have something more appropriate
-          end
+        source_url = crate.source_url
+        if source_url
+          m.merge!(extract_source_metadata(ContentBlob.remote_content_handler_for(source_url)))
+          m[:source_link_url] ||= source_url # Use plain source URL if handler doesn't have something more appropriate
+        end
 
         m
       end