GraphQL: Clone Samples and Transfer Samples mutations

app/graphql/mutations/clone_samples.rb

@@ -0,0 +1,109 @@
+# frozen_string_literal: true
+
+module Mutations
+  # Base Mutation
+  class CloneSamples < BaseMutation
+    null true
+    description 'Copy samples to another project.'
+    argument :new_project_id, ID,
+             required: false,
+             description: 'The Node ID of the project to copy to. For example, `gid://irida/Project/a84cd757-dedb-4c64-8b01-097020163077`.' # rubocop:disable Layout/LineLength
+    argument :new_project_puid, ID,
+             required: false,
+             description: 'Persistent Unique Identifier of the project to copy to. For example, `INXT_PRJ_AAAAAAAAAA`.'
+    argument :project_id, ID, # rubocop:disable GraphQL/ExtractInputType
+             required: false,
+             description: 'The Node ID of the project to copy to. For example, `gid://irida/Project/a84cd757-dedb-4c64-8b01-097020163077`.' # rubocop:disable Layout/LineLength
+    argument :project_puid, ID, # rubocop:disable GraphQL/ExtractInputType
+             required: false,
+             description: 'Persistent Unique Identifier of the project to copy to. For example, `INXT_PRJ_AAAAAAAAAA`.'
+
+    argument :sample_ids, [ID], required: true, description: 'List of samples to copy.' # rubocop:disable GraphQL/ExtractInputType
+    validates required: { one_of: %i[new_project_id new_project_puid] }
+    validates required: { one_of: %i[project_id project_puid] }
+
+    field :errors, [Types::UserErrorType], null: false, description: 'A list of errors that prevented the mutation.'
+    field :samples, GraphQL::Types::JSON, description: 'List of original and copied sample ids.'
+
+    def resolve(args) # rubocop:disable Metrics/MethodLength
+      project = get_project_from_id_or_puid_args(args)
+
+      if project.nil? || !project.persisted?
+        user_errors = [{
+          path: ['project'],
+          message: 'Project not found by provided ID or PUID'
+        }]
+        return {
+          samples: nil,
+          errors: user_errors
+        }
+      end
+
+      new_project_args = { project_id: args[:new_project_id], project_puid: args[:new_project_puid] }
+      new_project = get_project_from_id_or_puid_args(new_project_args)
+
+      if new_project.nil? || !new_project.persisted?
+        user_errors = [{
+          path: ['new_project'],
+          message: 'Project not found by provided ID or PUID'
+        }]
+        return {
+          samples: nil,
+          errors: user_errors
+        }
+      end
+
+      clone_samples(project, new_project.id, args[:sample_ids])
+    end
+
+    def ready?(**_args)
+      authorize!(to: :mutate?, with: GraphqlPolicy, context: { user: context[:current_user], token: context[:token] })
+    end
+
+    private
+
+    def clone_samples(project, new_project_id, sample_gids) # rubocop:disable Metrics/MethodLength,Metrics/AbcSize
+      user_errors = []
+      # remove prefix from sample_ids
+      sample_ids = sample_gids.map do |sample_gid|
+        IridaSchema.parse_gid(sample_gid, { expected_type: Sample }).model_id
+      rescue GraphQL::CoercionError => e
+        user_errors.append(
+          {
+            path: ['copySamples'],
+            message: e.message
+          }
+        )
+        next
+      end
+
+      samples = Samples::CloneService.new(
+        project, current_user
+      ).execute(new_project_id, sample_ids.compact)
+
+      prepended_samples = []
+      unless samples.empty?
+        # add the prefix to sample_ids
+        prepended_samples = samples.map do |key, value|
+          { original: URI::GID.build(app: GlobalID.app, model_name: Sample.name, model_id: key).to_s,
+            copy: URI::GID.build(app: GlobalID.app, model_name: Sample.name, model_id: value).to_s }
+        end
+      end
+
+      project_user_errors = []
+      if project.errors.count.positive?
+        project_user_errors = project.errors.map do |error|
+          {
+            path: ['samples', error.attribute.to_s.camelize(:lower)],
+            message: error.message
+          }
+        end
+      end
+
+      {
+        samples: prepended_samples,
+        errors: user_errors.concat(project_user_errors)
+      }
+    end
+  end
+end

app/graphql/mutations/transfer_samples.rb

@@ -0,0 +1,109 @@
+# frozen_string_literal: true
+
+module Mutations
+  # Base Mutation
+  class TransferSamples < BaseMutation
+    null true
+    description 'Transfer a list of sample to another project.'
+    argument :new_project_id, ID,
+             required: false,
+             description: 'The Node ID of the project to transfer to. For example, `gid://irida/Project/a84cd757-dedb-4c64-8b01-097020163077`.' # rubocop:disable Layout/LineLength
+    argument :new_project_puid, ID,
+             required: false,
+             description: 'Persistent Unique Identifier of the project to transfer to. For example, `INXT_PRJ_AAAAAAAAAA`.' # rubocop:disable Layout/LineLength
+    argument :project_id, ID, # rubocop:disable GraphQL/ExtractInputType
+             required: false,
+             description: 'The Node ID of the project to transfer to. For example, `gid://irida/Project/a84cd757-dedb-4c64-8b01-097020163077`.' # rubocop:disable Layout/LineLength
+    argument :project_puid, ID, # rubocop:disable GraphQL/ExtractInputType
+             required: false,
+             description: 'Persistent Unique Identifier of the project to transfer to. For example, `INXT_PRJ_AAAAAAAAAA`.' # rubocop:disable Layout/LineLength
+
+    argument :sample_ids, [ID], required: true, description: 'List of samples to transfer.' # rubocop:disable GraphQL/ExtractInputType
+    validates required: { one_of: %i[new_project_id new_project_puid] }
+    validates required: { one_of: %i[project_id project_puid] }
+
+    field :errors, [Types::UserErrorType], null: false, description: 'A list of errors that prevented the mutation.'
+    field :samples, [ID], description: 'List of transfered sample ids.'
+
+    def resolve(args) # rubocop:disable Metrics/MethodLength
+      project = get_project_from_id_or_puid_args(args)
+
+      if project.nil? || !project.persisted?
+        user_errors = [{
+          path: ['project'],
+          message: 'Project not found by provided ID or PUID'
+        }]
+        return {
+          samples: nil,
+          errors: user_errors
+        }
+      end
+
+      new_project_args = { project_id: args[:new_project_id], project_puid: args[:new_project_puid] }
+      new_project = get_project_from_id_or_puid_args(new_project_args)
+
+      if new_project.nil? || !new_project.persisted?
+        user_errors = [{
+          path: ['new_project'],
+          message: 'Project not found by provided ID or PUID'
+        }]
+        return {
+          samples: nil,
+          errors: user_errors
+        }
+      end
+
+      transfer_samples(project, new_project.id, args[:sample_ids])
+    end
+
+    def ready?(**_args)
+      authorize!(to: :mutate?, with: GraphqlPolicy, context: { user: context[:current_user], token: context[:token] })
+    end
+
+    private
+
+    def transfer_samples(project, new_project_id, sample_gids) # rubocop:disable Metrics/MethodLength,Metrics/AbcSize
+      user_errors = []
+      # remove prefix from sample_ids
+      sample_ids = sample_gids.map do |sample_gid|
+        IridaSchema.parse_gid(sample_gid, { expected_type: Sample }).model_id
+      rescue GraphQL::CoercionError => e
+        user_errors.append(
+          {
+            path: ['transferSamples'],
+            message: e.message
+          }
+        )
+        next
+      end
+
+      samples = Samples::TransferService.new(
+        project, current_user
+      ).execute(new_project_id, sample_ids.compact)
+
+      if samples.empty? # rubocop:disable Style/ConditionalAssignment
+        samples = nil
+      else
+        # add the prefix to sample_ids
+        samples = samples.map do |sample_id|
+          URI::GID.build(app: GlobalID.app, model_name: Sample.name, model_id: sample_id).to_s
+        end
+      end
+
+      project_user_errors = []
+      if project.errors.count.positive?
+        project_user_errors = project.errors.map do |error|
+          {
+            path: ['samples', error.attribute.to_s.camelize(:lower)],
+            message: error.message
+          }
+        end
+      end
+
+      {
+        samples:,
+        errors: user_errors.concat(project_user_errors)
+      }
+    end
+  end
+end

app/graphql/schema.graphql

@@ -578,6 +578,61 @@ enum AttachmentOrderField {
   updated_at
 }
 
+"""
+Autogenerated input type of CloneSamples
+"""
+input CloneSamplesInput {
+  """
+  A unique identifier for the client performing the mutation.
+  """
+  clientMutationId: String
+
+  """
+  The Node ID of the project to copy to. For example, `gid://irida/Project/a84cd757-dedb-4c64-8b01-097020163077`.
+  """
+  newProjectId: ID
+
+  """
+  Persistent Unique Identifier of the project to copy to. For example, `INXT_PRJ_AAAAAAAAAA`.
+  """
+  newProjectPuid: ID
+
+  """
+  The Node ID of the project to copy to. For example, `gid://irida/Project/a84cd757-dedb-4c64-8b01-097020163077`.
+  """
+  projectId: ID
+
+  """
+  Persistent Unique Identifier of the project to copy to. For example, `INXT_PRJ_AAAAAAAAAA`.
+  """
+  projectPuid: ID
+
+  """
+  List of samples to copy.
+  """
+  sampleIds: [ID!]!
+}
+
+"""
+Autogenerated return type of CloneSamples.
+"""
+type CloneSamplesPayload {
+  """
+  A unique identifier for the client performing the mutation.
+  """
+  clientMutationId: String
+
+  """
+  A list of errors that prevented the mutation.
+  """
+  errors: [UserError!]!
+
+  """
+  List of original and copied sample ids.
+  """
+  samples: JSON
+}
+
 """
 Autogenerated input type of CreateDirectUpload
 """
@@ -1311,6 +1366,16 @@ type Mutation {
     input: AttachFilesToSampleInput!
   ): AttachFilesToSamplePayload
 
+  """
+  Copy samples to another project.
+  """
+  copySamples(
+    """
+    Parameters for CloneSamples
+    """
+    input: CloneSamplesInput!
+  ): CloneSamplesPayload
+
   """
   Create blob to upload data to.
   """
@@ -1351,6 +1416,16 @@ type Mutation {
     input: CreateSampleInput!
   ): CreateSamplePayload
 
+  """
+  Transfer a list of sample to another project.
+  """
+  transferSamples(
+    """
+    Parameters for TransferSamples
+    """
+    input: TransferSamplesInput!
+  ): TransferSamplesPayload
+
   """
   Update metadata for a sample.
   """
@@ -2630,6 +2705,61 @@ enum SampleOrderField {
   updated_at
 }
 
+"""
+Autogenerated input type of TransferSamples
+"""
+input TransferSamplesInput {
+  """
+  A unique identifier for the client performing the mutation.
+  """
+  clientMutationId: String
+
+  """
+  The Node ID of the project to transfer to. For example, `gid://irida/Project/a84cd757-dedb-4c64-8b01-097020163077`.
+  """
+  newProjectId: ID
+
+  """
+  Persistent Unique Identifier of the project to transfer to. For example, `INXT_PRJ_AAAAAAAAAA`.
+  """
+  newProjectPuid: ID
+
+  """
+  The Node ID of the project to transfer to. For example, `gid://irida/Project/a84cd757-dedb-4c64-8b01-097020163077`.
+  """
+  projectId: ID
+
+  """
+  Persistent Unique Identifier of the project to transfer to. For example, `INXT_PRJ_AAAAAAAAAA`.
+  """
+  projectPuid: ID
+
+  """
+  List of samples to transfer.
+  """
+  sampleIds: [ID!]!
+}
+
+"""
+Autogenerated return type of TransferSamples.
+"""
+type TransferSamplesPayload {
+  """
+  A unique identifier for the client performing the mutation.
+  """
+  clientMutationId: String
+
+  """
+  A list of errors that prevented the mutation.
+  """
+  errors: [UserError!]!
+
+  """
+  List of transfered sample ids.
+  """
+  samples: [ID!]
+}
+
 """
 Autogenerated input type of UpdateSampleMetadata
 """

app/graphql/types/mutation_type.rb

@@ -8,10 +8,12 @@ class MutationType < Types::BaseObject
     field :attach_files_to_group, mutation: Mutations::AttachFilesToGroup # rubocop:disable GraphQL/FieldDescription
     field :attach_files_to_project, mutation: Mutations::AttachFilesToProject # rubocop:disable GraphQL/FieldDescription
     field :attach_files_to_sample, mutation: Mutations::AttachFilesToSample # rubocop:disable GraphQL/FieldDescription, GraphQL/ExtractType
+    field :copy_samples, mutation: Mutations::CloneSamples # rubocop:disable GraphQL/FieldDescription
     field :create_direct_upload, mutation: Mutations::CreateDirectUpload # rubocop:disable GraphQL/FieldDescription
     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 :transfer_samples, mutation: Mutations::TransferSamples # rubocop:disable GraphQL/FieldDescription
     field :update_sample_metadata, mutation: Mutations::UpdateSampleMetadata # rubocop:disable GraphQL/FieldDescription
   end
 end