Graphql: Submit Workflow Execution

app/controllers/workflow_executions_controller.rb

@@ -54,7 +54,7 @@ def workflow_execution_params_attributes
 
   def samples_workflow_execution_params_attributes
     [
-      :id,
+      :id, # index, increment for each one, not necissary for functionality
       :sample_id,
       { samplesheet_params: {} }
     ]

app/graphql/mutations/submit_workflow_execution.rb

@@ -0,0 +1,134 @@
+# frozen_string_literal: true
+
+module Mutations
+  # Base Mutation
+  class SubmitWorkflowExecution < BaseMutation # rubocop:disable Metrics/ClassLength
+    null true
+    description 'Create a new workflow execution..'
+
+    argument :email_notification,
+             Boolean,
+             required: false,
+             default_value: false,
+             description: 'Set to true to enable email notifications from this workflow execution'
+    argument :name, String, required: false, description: 'Name for the new workflow.'
+    argument :samples_workflow_executions_attributes, [GraphQL::Types::JSON], description: "A list of hashes containing a 'sample_id', and a hash of `samplesheet_params`." # rubocop:disable GraphQL/ExtractInputType,Layout/LineLength
+    argument :update_samples, # rubocop:disable GraphQL/ExtractInputType
+             Boolean,
+             required: false,
+             default_value: false,
+             description: 'Set true for samples to be updated from this workflow execution'
+    argument :workflow_engine, String, description: '' # rubocop:disable GraphQL/ExtractInputType
+    argument :workflow_engine_parameters, [GraphQL::Types::JSON], description: 'List of Hashes containing `key` and `value` to be passed to the workflow engine.' # rubocop:disable GraphQL/ExtractInputType,Layout/LineLength
+    argument :workflow_engine_version, String, description: 'Workflow Engine Version' # rubocop:disable GraphQL/ExtractInputType
+    argument :workflow_name, String, description: 'Name of the pipeline to be run on this workflow execution' # rubocop:disable GraphQL/ExtractInputType
+    argument :workflow_params, GraphQL::Types::JSON, description: 'Parameters to be passed to the pipeline.' # rubocop:disable GraphQL/ExtractInputType
+    argument :workflow_type, String, description: 'Type of pipelines workflow.' # rubocop:disable GraphQL/ExtractInputType
+    argument :workflow_type_version, String, description: 'Version of the pipelines workflow type.' # rubocop:disable GraphQL/ExtractInputType
+    argument :workflow_url, String, description: 'Url for the pipeline.' # rubocop:disable GraphQL/ExtractInputType
+    argument :workflow_version, String, description: 'Version of the pipeline to be run on this workflow execution' # rubocop:disable GraphQL/ExtractInputType
+
+    # one of project/group, to use as the namespace
+    argument :project_id, ID, # rubocop:disable GraphQL/ExtractInputType
+             required: false,
+             description: 'The Node ID of the project to run workflow in. For example, `gid://irida/Project/a84cd757-dedb-4c64-8b01-097020163077`.' # rubocop:disable Layout/LineLength
+    argument :group_id, ID, # rubocop:disable GraphQL/OrderedArguments,GraphQL/ExtractInputType
+             required: false,
+             description: 'The Node ID of the group to run workflow in. For example, `gid://irida/Group/a84cd757-dedb-4c64-8b01-097020163077`.' # rubocop:disable Layout/LineLength
+    validates required: { one_of: %i[project_id group_id] }
+
+    field :errors, [Types::UserErrorType], null: false, description: 'A list of errors that prevented the mutation.'
+    field :workflow_execution, Types::WorkflowExecutionType, description: 'The newly created workflow execution.'
+
+    def resolve(args)
+      create_workflow_execution(args)
+    end
+
+    def ready?(**_args)
+      authorize!(to: :mutate?, with: GraphqlPolicy, context: { user: context[:current_user], token: context[:token] })
+    end
+
+    private
+
+    def create_workflow_execution(args) # rubocop:disable Metrics/MethodLength,Metrics/AbcSize
+      workflow_engine_parameters = build_workflow_engine_parameters(args[:workflow_engine_parameters])
+
+      update_samples = args[:update_samples] ? '1' : '0'
+      email_notification = args[:email_notification] ? '1' : '0'
+
+      namespace_id = namespace(args[:project_id], args[:group_id])
+
+      samples_workflow_executions_attributes = build_samples_workflow_executions_attributes(args[:samples_workflow_executions_attributes]) # rubocop:disable Layout/LineLength
+
+      workflow_execution_params = {
+        name: args[:name],
+        metadata: { workflow_name: args[:workflow_name],
+                    workflow_version: args[:workflow_version] },
+        namespace_id:,
+        workflow_params: args[:workflow_params],
+        workflow_type: args[:workflow_type],
+        workflow_type_version: args[:workflow_type_version],
+        workflow_engine: args[:workflow_engine],
+        workflow_engine_version: args[:workflow_engine_version],
+        workflow_engine_parameters:,
+        workflow_url: args[:workflow_url],
+        update_samples:,
+        email_notification:,
+        samples_workflow_executions_attributes:
+      }
+
+      workflow_execution = WorkflowExecutions::CreateService.new(
+        current_user, workflow_execution_params
+      ).execute
+
+      if workflow_execution.persisted?
+        {
+          workflow_execution:,
+          errors: []
+        }
+      else
+        user_errors = workflow_execution.errors.map do |error|
+          {
+            path: ['workflow_execution', error.attribute.to_s.camelize(:lower)],
+            message: error.message
+          }
+        end
+        {
+          workflow_execution: nil,
+          errors: user_errors
+        }
+      end
+    end
+
+    def namespace(project_id, group_id)
+      if project_id
+        IridaSchema.object_from_id(project_id, { expected_type: Project }).namespace.id
+      else # group_id
+        IridaSchema.object_from_id(group_id, { expected_type: Group }).id
+      end
+    end
+
+    # workflow engine parameters can have keys that start with `-` which is not allowed in graphql,
+    # so we parse a list of key value pairs into a hash that can be used.
+    def build_workflow_engine_parameters(parameter_list)
+      result = {}
+      parameter_list.each do |params|
+        result[params['key']] = params['value']
+      end
+      result
+    end
+
+    def build_samples_workflow_executions_attributes(samples_workflow_executions_attributes)
+      result = {}
+      samples_workflow_executions_attributes.each_with_index do |data, index|
+        sample_id = IridaSchema.object_from_id(data['sample_id'], { expected_type: Sample }).id
+        result[index.to_s] = {
+          'sample_id' => sample_id,
+          'samplesheet_params' => data['samplesheet_params']
+        }
+      end
+
+      result
+    end
+  end
+end

app/graphql/schema.graphql

@@ -1416,6 +1416,16 @@ type Mutation {
     input: CreateSampleInput!
   ): CreateSamplePayload
 
+  """
+  Create a new workflow execution..
+  """
+  submitWorkflowExecution(
+    """
+    Parameters for SubmitWorkflowExecution
+    """
+    input: SubmitWorkflowExecutionInput!
+  ): SubmitWorkflowExecutionPayload
+
   """
   Transfer a list of sample to another project.
   """
@@ -2857,6 +2867,111 @@ type SamplesWorkflowExecution implements Node {
   workflowExecution: WorkflowExecution
 }
 
+"""
+Autogenerated input type of SubmitWorkflowExecution
+"""
+input SubmitWorkflowExecutionInput {
+  """
+  A unique identifier for the client performing the mutation.
+  """
+  clientMutationId: String
+
+  """
+  Set to true to enable email notifications from this workflow execution
+  """
+  emailNotification: Boolean = false
+
+  """
+  The Node ID of the group to run workflow in. For example, `gid://irida/Group/a84cd757-dedb-4c64-8b01-097020163077`.
+  """
+  groupId: ID
+
+  """
+  Name for the new workflow.
+  """
+  name: String
+
+  """
+  The Node ID of the project to run workflow in. For example, `gid://irida/Project/a84cd757-dedb-4c64-8b01-097020163077`.
+  """
+  projectId: ID
+
+  """
+  A list of hashes containing a 'sample_id', and a hash of `samplesheet_params`.
+  """
+  samplesWorkflowExecutionsAttributes: [JSON!]!
+
+  """
+  Set true for samples to be updated from this workflow execution
+  """
+  updateSamples: Boolean = false
+
+  """
+
+  """
+  workflowEngine: String!
+
+  """
+  List of Hashes containing `key` and `value` to be passed to the workflow engine.
+  """
+  workflowEngineParameters: [JSON!]!
+
+  """
+  Workflow Engine Version
+  """
+  workflowEngineVersion: String!
+
+  """
+  Name of the pipeline to be run on this workflow execution
+  """
+  workflowName: String!
+
+  """
+  Parameters to be passed to the pipeline.
+  """
+  workflowParams: JSON!
+
+  """
+  Type of pipelines workflow.
+  """
+  workflowType: String!
+
+  """
+  Version of the pipelines workflow type.
+  """
+  workflowTypeVersion: String!
+
+  """
+  Url for the pipeline.
+  """
+  workflowUrl: String!
+
+  """
+  Version of the pipeline to be run on this workflow execution
+  """
+  workflowVersion: String!
+}
+
+"""
+Autogenerated return type of SubmitWorkflowExecution.
+"""
+type SubmitWorkflowExecutionPayload {
+  """
+  A unique identifier for the client performing the mutation.
+  """
+  clientMutationId: String
+
+  """
+  A list of errors that prevented the mutation.
+  """
+  errors: [UserError!]!
+
+  """
+  The newly created workflow execution.
+  """
+  workflowExecution: WorkflowExecution
+}
+
 """
 Autogenerated input type of TransferSamples
 """

app/graphql/types/mutation_type.rb

@@ -13,6 +13,7 @@ class MutationType < Types::BaseObject
     field :create_group, mutation: Mutations::CreateGroup # rubocop:disable GraphQL/FieldDescription
     field :create_project, mutation: Mutations::CreateProject # rubocop:disable GraphQL/FieldDescription
     field :create_sample, mutation: Mutations::CreateSample # rubocop:disable GraphQL/FieldDescription,GraphQL/ExtractType
+    field :submit_workflow_execution, mutation: Mutations::SubmitWorkflowExecution # rubocop:disable GraphQL/FieldDescription
     field :transfer_samples, mutation: Mutations::TransferSamples # rubocop:disable GraphQL/FieldDescription
     field :update_sample_metadata, mutation: Mutations::UpdateSampleMetadata # rubocop:disable GraphQL/FieldDescription
   end

app/models/samples_workflow_execution.rb

@@ -9,4 +9,6 @@ class SamplesWorkflowExecution < ApplicationRecord
   belongs_to :sample
   has_many_attached :inputs
   has_many :outputs, dependent: :destroy, class_name: 'Attachment', as: :attachable
+
+  validates_with WorkflowExecutionSamplesheetParamsValidator
 end

app/models/workflow_execution.rb

@@ -40,7 +40,7 @@ def send_email
   end
 
   def cancellable?
-    %w[submitted running prepared initial].include?(state) 
+    %w[submitted running prepared initial].include?(state)
   end
 
   def deletable?

app/validators/workflow_execution_samplesheet_params_validator.rb

@@ -0,0 +1,39 @@
+# frozen_string_literal: true
+
+# Validator for Workflow Execution Samplesheet Params
+# This will cause the validation to fail if any of the attachment ids cannot be resolved
+class WorkflowExecutionSamplesheetParamsValidator < ActiveModel::Validator
+  def validate(record) # rubocop:disable Metrics/MethodLength,Metrics/AbcSize,Metrics/CyclomaticComplexity,Metrics/PerceivedComplexity
+    record.samplesheet_params.each do |key, value| # rubocop:disable Metrics/BlockLength
+      if key == 'sample'
+        if value.nil? || value == ''
+          error_message = 'No Sample PUID provided'
+          record.errors.add :sample, error_message
+          record.workflow_execution.errors.add :sample, error_message
+        elsif value != (record.sample.puid)
+          error_message = "Provided Sample PUID #{value} does not match SampleWorkflowExecution Sample PUID #{record.sample.puid}" # rubocop:disable Layout/LineLength
+          record.errors.add :sample, error_message
+          record.workflow_execution.errors.add :sample, error_message
+        end
+        next
+      end
+
+      next if value == ''
+
+      begin
+        # Attempt to parse an object from the id provided
+        attachment = IridaSchema.object_from_id(value, { expected_type: Attachment })
+        unless attachment.attachable == record.sample
+          error_message = "Attachment does not belong to Sample #{record.sample.puid}."
+          record.errors.add :attachment, error_message
+          record.workflow_execution.errors.add :attachment, error_message
+        end
+      rescue StandardError => e
+        error_message = e.message
+        record.errors.add :attachment, error_message
+        record.workflow_execution.errors.add :attachment, error_message
+        next
+      end
+    end
+  end
+end

db/seeds.rb

@@ -166,7 +166,15 @@ def seed_workflow_executions # rubocop:disable Metrics/MethodLength, Metrics/Abc
     workflow_engine_version: '23.10.0',
     workflow_engine_parameters: { '-r': 'dev' },
     workflow_url: 'https://github.com/phac-nml/iridanextexample',
-    submitter: User.find_by(email: '[email protected]')
+    submitter: User.find_by(email: '[email protected]'),
+    samples_workflow_executions_attributes: {
+      '0': {
+        sample_id: Sample.first.id,
+        samplesheet_params: {
+          sample: Sample.first.puid
+        }
+      }
+    }
   )
 
   SamplesWorkflowExecution.create(
@@ -188,7 +196,15 @@ def seed_workflow_executions # rubocop:disable Metrics/MethodLength, Metrics/Abc
     workflow_url: 'https://github.com/phac-nml/iridanextexample',
     submitter: User.find_by(email: '[email protected]'),
     blob_run_directory: 'this should be a generated key',
-    state: :completed
+    state: :completed,
+    samples_workflow_executions_attributes: {
+      '0': {
+        sample_id: Sample.first.id,
+        samplesheet_params: {
+          sample: Sample.first.puid
+        }
+      }
+    }
   )
 
   filename = 'summary.txt'
@@ -197,7 +213,6 @@ def seed_workflow_executions # rubocop:disable Metrics/MethodLength, Metrics/Abc
   attachment.save!
 
   SamplesWorkflowExecution.create(
-    samplesheet_params: { my_key1: 'my_value_2', my_key2: 'my_value_3' },
     sample: Sample.first,
     workflow_execution: workflow_execution_completed
   )

test/controllers/workflow_executions_controller_test.rb

@@ -30,7 +30,7 @@ class WorkflowExecutionsControllerTest < ActionDispatch::IntegrationTest
                  {
                    sample_id: @sample1.id,
                    samplesheet_params: {
-                     sample: "Sample_#{@sample1.id}",
+                     sample: @sample1.puid,
                      'fastq_1' => @attachment1.to_global_id,
                      'fastq_2' => ''
                    }