rafflesia 0.1.0

data/lib/rafflesia/objects.rb

@@ -0,0 +1,461 @@
+# frozen_string_literal: true
+
+# This file is auto-generated by oagen. Do not edit.
+
+require 'json'
+
+module Rafflesia
+  class Objects
+    def initialize(client)
+      @client = client
+    end
+
+    # POST /v1/objects/artifacts/import
+    # @param allow_incomplete [Boolean, nil] Allow import even when required material file sets are incomplete.
+    # @param archive_inventory_object_id [String, nil] Object id containing an archive inventory manifest whose extracted member objects become a collection. Mutually exclusive with path and archive_inventory_path.
+    # @param archive_inventory_path [String, nil] Archive inventory manifest whose extracted member objects become a collection without a local copy. Mutually exclusive with path and archive_inventory_object_id.
+    # @param archive_required_member_paths [Array<String>, nil] Archive member paths that must have extracted, hash-verified objects before marker files are created.
+    # @param dataset_name [String, nil] Optional dataset name carried into the manifest.
+    # @param dataset_version [String, nil] Optional dataset version carried into the manifest.
+    # @param dependency_manifest_ids [Array<String>, nil] Immutable manifest ids required by this collection.
+    # @param is_collection [Boolean, nil] Force directory input to use a shard-aware collection manifest even when it has no nested directories.
+    # @param kind [String] Immutable material kind: blast_db, blast_index, foldseek_index, mmseqs2_index, hmmer_index, model_weights, model_parameters, sequence_database, structure_database, annotation_database, or task_input.
+    # @param layout_prefix [String, nil] Optional portable path prefix prepended to archive member paths in the collection.
+    # @param license [String, nil] License identifier or source license label for this collection.
+    # @param marker_paths [Array<String>, nil] Optional portable marker-file paths created after every archive member object is validated.
+    # @param mount_path [String, nil] Expected absolute sandbox mount path for this collection.
+    # @param name [String, nil] Optional manifest name.
+    # @param output_dir [String, nil] Optional local directory where the stamped manifest JSON should be written.
+    # @param path [String, nil] Local material file, directory tree, or supported database/index prefix path. Mutually exclusive with archive_inventory_path and archive_inventory_object_id.
+    # @param shard_size_bytes [Integer, nil] Target collection shard size in bytes. Files are never split; zero defaults to 4 GiB.
+    # @param source_uri [String, nil] Source distribution URI recorded as provenance; no implicit download is performed.
+    # @param tool_name [String, nil] Optional external tool name. Defaults from kind.
+    # @param tool_version [String, nil] Optional external tool version string.
+    # @param version [String, nil] Optional manifest version.
+    # @param request_options [Hash] (see Rafflesia::Types::RequestOptions)
+    # @return [Rafflesia::EnvelopeObjectArtifactImportData]
+    def artifactsImport(
+      kind:,
+      allow_incomplete: nil,
+      archive_inventory_object_id: nil,
+      archive_inventory_path: nil,
+      archive_required_member_paths: nil,
+      dataset_name: nil,
+      dataset_version: nil,
+      dependency_manifest_ids: nil,
+      is_collection: nil,
+      layout_prefix: nil,
+      license: nil,
+      marker_paths: nil,
+      mount_path: nil,
+      name: nil,
+      output_dir: nil,
+      path: nil,
+      shard_size_bytes: nil,
+      source_uri: nil,
+      tool_name: nil,
+      tool_version: nil,
+      version: nil,
+      request_options: {}
+    )
+      body = {
+        'allow_incomplete' => allow_incomplete,
+        'archive_inventory_object_id' => archive_inventory_object_id,
+        'archive_inventory_path' => archive_inventory_path,
+        'archive_required_member_paths' => archive_required_member_paths,
+        'dataset_name' => dataset_name,
+        'dataset_version' => dataset_version,
+        'dependency_manifest_ids' => dependency_manifest_ids,
+        'is_collection' => is_collection,
+        'kind' => kind,
+        'layout_prefix' => layout_prefix,
+        'license' => license,
+        'marker_paths' => marker_paths,
+        'mount_path' => mount_path,
+        'name' => name,
+        'output_dir' => output_dir,
+        'path' => path,
+        'shard_size_bytes' => shard_size_bytes,
+        'source_uri' => source_uri,
+        'tool_name' => tool_name,
+        'tool_version' => tool_version,
+        'version' => version
+      }.compact
+      response = @client.request(
+        method: :post,
+        path: '/v1/objects/artifacts/import',
+        auth: true,
+        body: body,
+        request_options: request_options
+      )
+      result = Rafflesia::EnvelopeObjectArtifactImportData.new(response.body)
+      result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
+      result
+    end
+
+    # POST /v1/objects/artifacts/materialize
+    # @param manifest_object_id [String, nil] Neutral object-artifact manifest object id
+    # @param manifest_path [String, nil] Local neutral object-artifact manifest path
+    # @param shards [Array<String>, nil] Optional shard ids to materialize; empty materializes every shard
+    # @param target_dir [String, nil] Local object-artifact cache root
+    # @param verify [Boolean, nil] Verify materialized files by SHA-256
+    # @param request_options [Hash] (see Rafflesia::Types::RequestOptions)
+    # @return [Rafflesia::EnvelopeObjectArtifactMaterializeData]
+    def artifactsMaterialize(
+      manifest_object_id: nil,
+      manifest_path: nil,
+      shards: nil,
+      target_dir: nil,
+      verify: nil,
+      request_options: {}
+    )
+      body = {
+        'manifest_object_id' => manifest_object_id,
+        'manifest_path' => manifest_path,
+        'shards' => shards,
+        'target_dir' => target_dir,
+        'verify' => verify
+      }.compact
+      response = @client.request(
+        method: :post,
+        path: '/v1/objects/artifacts/materialize',
+        auth: true,
+        body: body,
+        request_options: request_options
+      )
+      result = Rafflesia::EnvelopeObjectArtifactMaterializeData.new(response.body)
+      result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
+      result
+    end
+
+    # Return raw content-addressed object bytes.
+    # @param object_id [String]
+    # @param filename [String, nil]
+    # @param request_options [Hash] (see Rafflesia::Types::RequestOptions)
+    # @return [String]
+    def contentGet(
+      object_id:,
+      filename: nil,
+      request_options: {}
+    )
+      params = {
+        'object_id' => object_id,
+        'filename' => filename
+      }.compact
+      response = @client.request(
+        method: :get,
+        path: '/v1/objects/content/get',
+        auth: true,
+        params: params,
+        request_options: request_options
+      )
+      response.body
+    end
+
+    # POST /v1/objects/download
+    # @param allow_network [Boolean, nil]
+    # @param content_type [String, nil]
+    # @param file_name [String, nil]
+    # @param kind [String, nil]
+    # @param max_download_bytes [Integer, nil]
+    # @param url [String]
+    # @param request_options [Hash] (see Rafflesia::Types::RequestOptions)
+    # @return [Rafflesia::EnvelopeObjectDownloadData]
+    def download(
+      url:,
+      allow_network: nil,
+      content_type: nil,
+      file_name: nil,
+      kind: nil,
+      max_download_bytes: nil,
+      request_options: {}
+    )
+      body = {
+        'allow_network' => allow_network,
+        'content_type' => content_type,
+        'file_name' => file_name,
+        'kind' => kind,
+        'max_download_bytes' => max_download_bytes,
+        'url' => url
+      }.compact
+      response = @client.request(
+        method: :post,
+        path: '/v1/objects/download',
+        auth: true,
+        body: body,
+        request_options: request_options
+      )
+      result = Rafflesia::EnvelopeObjectDownloadData.new(response.body)
+      result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
+      result
+    end
+
+    # POST /v1/objects/gc
+    # @param candidate_object_ids [Array<String>, nil] Optional object ids to evaluate instead of every local CAS object.
+    # @param delete [Boolean, nil] Delete eligible unreferenced local CAS files when dry_run is false.
+    # @param dry_run [Boolean, nil] When true, compute candidates without deleting. Defaults to true.
+    # @param max_candidates [Integer, nil] Maximum candidate rows to return. 0 returns every candidate.
+    # @param max_delete [Integer, nil] Maximum candidate files to delete when delete is enabled. 0 deletes every eligible returned candidate.
+    # @param max_scan_object_bytes [Integer, nil] Maximum size of live JSON objects to scan transitively for object refs. Defaults to 16777216.
+    # @param older_than_seconds [Integer, nil] Only local CAS files with mtime older than this age are eligible. Defaults to 604800 seconds.
+    # @param protect_object_ids [Array<String>, nil] Additional object ids to force-retain.
+    # @param scan_object_contents [Boolean, nil] Scan reachable JSON objects for transitive object refs. Defaults to true.
+    # @param scan_records [Boolean, nil] Scan local record JSON files for live object refs. Defaults to true.
+    # @param request_options [Hash] (see Rafflesia::Types::RequestOptions)
+    # @return [Rafflesia::EnvelopeObjectGcData]
+    def gc(
+      candidate_object_ids: nil,
+      delete: nil,
+      dry_run: nil,
+      max_candidates: nil,
+      max_delete: nil,
+      max_scan_object_bytes: nil,
+      older_than_seconds: nil,
+      protect_object_ids: nil,
+      scan_object_contents: nil,
+      scan_records: nil,
+      request_options: {}
+    )
+      body = {
+        'candidate_object_ids' => candidate_object_ids,
+        'delete' => delete,
+        'dry_run' => dry_run,
+        'max_candidates' => max_candidates,
+        'max_delete' => max_delete,
+        'max_scan_object_bytes' => max_scan_object_bytes,
+        'older_than_seconds' => older_than_seconds,
+        'protect_object_ids' => protect_object_ids,
+        'scan_object_contents' => scan_object_contents,
+        'scan_records' => scan_records
+      }.compact
+      response = @client.request(
+        method: :post,
+        path: '/v1/objects/gc',
+        auth: true,
+        body: body,
+        request_options: request_options
+      )
+      result = Rafflesia::EnvelopeObjectGcData.new(response.body)
+      result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
+      result
+    end
+
+    # Return raw content-addressed object bytes.
+    # @param object_id [String]
+    # @param filename [String, nil]
+    # @param request_options [Hash] (see Rafflesia::Types::RequestOptions)
+    # @return [String]
+    def get(
+      object_id:,
+      filename: nil,
+      request_options: {}
+    )
+      params = {
+        'object_id' => object_id,
+        'filename' => filename
+      }.compact
+      response = @client.request(
+        method: :get,
+        path: '/v1/objects/get',
+        auth: true,
+        params: params,
+        request_options: request_options
+      )
+      response.body
+    end
+
+    # POST /v1/objects/hash
+    # @param content_type [String, nil]
+    # @param kind [String, nil]
+    # @param path [String]
+    # @param request_options [Hash] (see Rafflesia::Types::RequestOptions)
+    # @return [Rafflesia::EnvelopeObjectHashData]
+    def hash(
+      path:,
+      content_type: nil,
+      kind: nil,
+      request_options: {}
+    )
+      body = {
+        'content_type' => content_type,
+        'kind' => kind,
+        'path' => path
+      }.compact
+      response = @client.request(
+        method: :post,
+        path: '/v1/objects/hash',
+        auth: true,
+        body: body,
+        request_options: request_options
+      )
+      result = Rafflesia::EnvelopeObjectHashData.new(response.body)
+      result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
+      result
+    end
+
+    # POST /v1/objects/head
+    # @param encoding [Rafflesia::Types::ObjectHeadRequestEncoding, nil]
+    # @param limit [Integer, nil]
+    # @param object_id [String]
+    # @param request_options [Hash] (see Rafflesia::Types::RequestOptions)
+    # @return [Rafflesia::EnvelopeObjectHeadData]
+    def head(
+      object_id:,
+      encoding: nil,
+      limit: nil,
+      request_options: {}
+    )
+      body = {
+        'encoding' => encoding,
+        'limit' => limit,
+        'object_id' => object_id
+      }.compact
+      response = @client.request(
+        method: :post,
+        path: '/v1/objects/head',
+        auth: true,
+        body: body,
+        request_options: request_options
+      )
+      result = Rafflesia::EnvelopeObjectHeadData.new(response.body)
+      result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
+      result
+    end
+
+    # POST /v1/objects/json/get
+    # @param limit [Integer, nil]
+    # @param max_bytes [Integer, nil]
+    # @param object_id [String]
+    # @param path [String, nil]
+    # @param request_options [Hash] (see Rafflesia::Types::RequestOptions)
+    # @return [Rafflesia::EnvelopeObjectJsonGetData]
+    def jsonGet(
+      object_id:,
+      limit: nil,
+      max_bytes: nil,
+      path: nil,
+      request_options: {}
+    )
+      body = {
+        'limit' => limit,
+        'max_bytes' => max_bytes,
+        'object_id' => object_id,
+        'path' => path
+      }.compact
+      response = @client.request(
+        method: :post,
+        path: '/v1/objects/json/get',
+        auth: true,
+        body: body,
+        request_options: request_options
+      )
+      result = Rafflesia::EnvelopeObjectJsonGetData.new(response.body)
+      result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
+      result
+    end
+
+    # POST /v1/objects/json/inspect
+    # @param max_bytes [Integer, nil]
+    # @param max_children [Integer, nil]
+    # @param object_id [String]
+    # @param request_options [Hash] (see Rafflesia::Types::RequestOptions)
+    # @return [Rafflesia::EnvelopeObjectJsonInspectData]
+    def jsonInspect(
+      object_id:,
+      max_bytes: nil,
+      max_children: nil,
+      request_options: {}
+    )
+      body = {
+        'max_bytes' => max_bytes,
+        'max_children' => max_children,
+        'object_id' => object_id
+      }.compact
+      response = @client.request(
+        method: :post,
+        path: '/v1/objects/json/inspect',
+        auth: true,
+        body: body,
+        request_options: request_options
+      )
+      result = Rafflesia::EnvelopeObjectJsonInspectData.new(response.body)
+      result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
+      result
+    end
+
+    # POST /v1/objects/lineage
+    # @param object_id [String]
+    # @param request_options [Hash] (see Rafflesia::Types::RequestOptions)
+    # @return [Rafflesia::EnvelopeObjectLineageData]
+    def lineage(
+      object_id:,
+      request_options: {}
+    )
+      body = {
+        'object_id' => object_id
+      }
+      response = @client.request(
+        method: :post,
+        path: '/v1/objects/lineage',
+        auth: true,
+        body: body,
+        request_options: request_options
+      )
+      result = Rafflesia::EnvelopeObjectLineageData.new(response.body)
+      result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
+      result
+    end
+
+    # POST /v1/objects/metadata
+    # @param object_id [String]
+    # @param request_options [Hash] (see Rafflesia::Types::RequestOptions)
+    # @return [Rafflesia::EnvelopeObjectMetadataData]
+    def metadata(
+      object_id:,
+      request_options: {}
+    )
+      body = {
+        'object_id' => object_id
+      }
+      response = @client.request(
+        method: :post,
+        path: '/v1/objects/metadata',
+        auth: true,
+        body: body,
+        request_options: request_options
+      )
+      result = Rafflesia::EnvelopeObjectMetadataData.new(response.body)
+      result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
+      result
+    end
+
+    # POST /v1/objects/put
+    # @param content_type [String, nil]
+    # @param kind [String, nil]
+    # @param path [String]
+    # @param request_options [Hash] (see Rafflesia::Types::RequestOptions)
+    # @return [Rafflesia::EnvelopeObjectPutData]
+    def put(
+      path:,
+      content_type: nil,
+      kind: nil,
+      request_options: {}
+    )
+      body = {
+        'content_type' => content_type,
+        'kind' => kind,
+        'path' => path
+      }.compact
+      response = @client.request(
+        method: :post,
+        path: '/v1/objects/put',
+        auth: true,
+        body: body,
+        request_options: request_options
+      )
+      result = Rafflesia::EnvelopeObjectPutData.new(response.body)
+      result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
+      result
+    end
+  end
+end

data/lib/rafflesia/ontology/database_join_evidence_requirement.rb

@@ -0,0 +1,36 @@
+# frozen_string_literal: true
+
+# This file is auto-generated by oagen. Do not edit.
+
+module Rafflesia
+  class DatabaseJoinEvidenceRequirement < Rafflesia::Types::BaseModel
+
+    HASH_ATTRS = {
+      evidence_digest: :evidence_digest,
+      key_variant: :key_variant,
+      left_source: :left_source,
+      relationship_id: :relationship_id,
+      requirement: :requirement,
+      right_source: :right_source
+    }.freeze
+
+    attr_accessor \
+      :evidence_digest,
+      :key_variant,
+      :left_source,
+      :relationship_id,
+      :requirement,
+      :right_source
+
+    def initialize(json)
+      super()
+      hash = self.class.normalize(json)
+      @evidence_digest = hash[:evidence_digest]
+      @key_variant = hash[:key_variant]
+      @left_source = hash[:left_source]
+      @relationship_id = hash[:relationship_id]
+      @requirement = hash[:requirement]
+      @right_source = hash[:right_source]
+    end
+  end
+end

data/lib/rafflesia/ontology/database_release_selector.rb

@@ -0,0 +1,33 @@
+# frozen_string_literal: true
+
+# This file is auto-generated by oagen. Do not edit.
+
+module Rafflesia
+  class DatabaseReleaseSelector < Rafflesia::Types::BaseModel
+
+    HASH_ATTRS = {
+      database: :database,
+      digest: :digest,
+      release: :release,
+      resolution: :resolution,
+      selector: :selector
+    }.freeze
+
+    attr_accessor \
+      :database,
+      :digest,
+      :release,
+      :resolution,
+      :selector
+
+    def initialize(json)
+      super()
+      hash = self.class.normalize(json)
+      @database = hash[:database]
+      @digest = hash[:digest]
+      @release = hash[:release]
+      @resolution = hash[:resolution]
+      @selector = hash[:selector]
+    end
+  end
+end

data/lib/rafflesia/ontology/dataset_binding_artifact.rb

@@ -0,0 +1,39 @@
+# frozen_string_literal: true
+
+# This file is auto-generated by oagen. Do not edit.
+
+module Rafflesia
+  class DatasetBindingArtifact < Rafflesia::Types::BaseModel
+
+    HASH_ATTRS = {
+      format: :format,
+      id: :id,
+      object_id: :object_id,
+      row_count: :row_count,
+      sha256: :sha_256,
+      size_bytes: :size_bytes,
+      status: :status
+    }.freeze
+
+    attr_accessor \
+      :format,
+      :id,
+      :object_id,
+      :row_count,
+      :sha_256,
+      :size_bytes,
+      :status
+
+    def initialize(json)
+      super()
+      hash = self.class.normalize(json)
+      @format = hash[:format]
+      @id = hash[:id]
+      @object_id = hash[:object_id]
+      @row_count = hash[:row_count]
+      @sha_256 = hash[:sha256]
+      @size_bytes = hash[:size_bytes]
+      @status = hash[:status]
+    end
+  end
+end

data/lib/rafflesia/ontology/dataset_ontology_binding.rb

@@ -0,0 +1,72 @@
+# frozen_string_literal: true
+
+# This file is auto-generated by oagen. Do not edit.
+
+module Rafflesia
+  class DatasetOntologyBinding < Rafflesia::Types::BaseModel
+
+    HASH_ATTRS = {
+      conformance_status: :conformance_status,
+      dataset_name: :dataset_name,
+      dataset_relation: :dataset_relation,
+      dataset_relation_digest: :dataset_relation_digest,
+      dataset_release_id: :dataset_release_id,
+      dataset_repository_id: :dataset_repository_id,
+      dataset_version: :dataset_version,
+      id: :id,
+      is_queryable: :is_queryable,
+      object: :object,
+      observed_schema_hash: :observed_schema_hash,
+      ontology_digest: :ontology_digest,
+      ontology_relation: :ontology_relation,
+      ontology_release_id: :ontology_release_id,
+      ontology_repository_id: :ontology_repository_id,
+      ontology_schema_hash: :ontology_schema_hash,
+      ontology_version: :ontology_version,
+      table_artifacts: :table_artifacts
+    }.freeze
+
+    attr_accessor \
+      :conformance_status,
+      :dataset_name,
+      :dataset_relation,
+      :dataset_relation_digest,
+      :dataset_release_id,
+      :dataset_repository_id,
+      :dataset_version,
+      :id,
+      :is_queryable,
+      :object,
+      :observed_schema_hash,
+      :ontology_digest,
+      :ontology_relation,
+      :ontology_release_id,
+      :ontology_repository_id,
+      :ontology_schema_hash,
+      :ontology_version,
+      :table_artifacts
+
+    def initialize(json)
+      super()
+      hash = self.class.normalize(json)
+      @conformance_status = hash[:conformance_status]
+      @dataset_name = hash[:dataset_name]
+      @dataset_relation = hash[:dataset_relation]
+      @dataset_relation_digest = hash[:dataset_relation_digest]
+      @dataset_release_id = hash[:dataset_release_id]
+      @dataset_repository_id = hash[:dataset_repository_id]
+      @dataset_version = hash[:dataset_version]
+      @id = hash[:id]
+      @is_queryable = hash[:is_queryable]
+      @object = hash[:object]
+      @observed_schema_hash = hash[:observed_schema_hash]
+      @ontology_digest = hash[:ontology_digest]
+      @ontology_relation = hash[:ontology_relation]
+      @ontology_release_id = hash[:ontology_release_id]
+      @ontology_repository_id = hash[:ontology_repository_id]
+      @ontology_schema_hash = hash[:ontology_schema_hash]
+      @ontology_version = hash[:ontology_version]
+      @table_artifacts = (hash[:table_artifacts] || []).map { |item| item ? Rafflesia::DatasetBindingArtifact.new(item) : nil }
+    end
+  end
+end

data/lib/rafflesia/ontology/dataset_ontology_binding_list_data.rb

@@ -0,0 +1,33 @@
+# frozen_string_literal: true
+
+# This file is auto-generated by oagen. Do not edit.
+
+module Rafflesia
+  class DatasetOntologyBindingListData < Rafflesia::Types::BaseModel
+
+    HASH_ATTRS = {
+      data: :data,
+      has_more: :has_more,
+      object: :object,
+      ontology_digest: :ontology_digest,
+      ontology_version: :ontology_version
+    }.freeze
+
+    attr_accessor \
+      :data,
+      :has_more,
+      :object,
+      :ontology_digest,
+      :ontology_version
+
+    def initialize(json)
+      super()
+      hash = self.class.normalize(json)
+      @data = (hash[:data] || []).map { |item| item ? Rafflesia::DatasetOntologyBinding.new(item) : nil }
+      @has_more = hash[:has_more]
+      @object = hash[:object]
+      @ontology_digest = hash[:ontology_digest]
+      @ontology_version = hash[:ontology_version]
+    end
+  end
+end