Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W A ABANDONED (protea.infrastructure.orm.models.experiment_run.ExperimentRunStatus attribute) absorption (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) accession (protea.infrastructure.orm.models.annotation.interpro_annotation.InterProAnnotation attribute) (protea.infrastructure.orm.models.protein.protein.Protein attribute) (protea.infrastructure.orm.models.query.query_set.QuerySetEntry attribute) accessions (protea.core.operations.run_interproscan_batch.RunInterProScanBatchPayload attribute) active_site (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) ACTIVE_STATUSES (in module protea.infrastructure.orm.models.job) activity_regulation (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) ADR after (protea.api.routers.jobs.JobListFilters attribute) alignment_length_nw (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) alignment_length_sw (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) alignment_score_nw (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) alignment_score_sw (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) allowed_origins (protea.infrastructure.settings.Settings attribute) AMQP amqp_heartbeat (protea.config.tuning.QueueTuning attribute) amqp_url (protea.infrastructure.settings.Settings attribute) anc2vec anc2vec_has_emb (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) anc2vec_neighbor_cos (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) anc2vec_neighbor_maxcos (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) anc2vec_path (protea.infrastructure.settings.Settings attribute) anc2vec_query_known_cos (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) anc2vec_query_known_count (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) anc2vec_query_known_maxcos (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) Ankh annotate() (in module protea.api.routers.annotate) AnnotateFormOptions (class in protea.api.routers.annotate) annotation_chunk_size (protea.config.tuning.OperationTuning attribute) annotation_date (protea.infrastructure.orm.models.annotation.protein_go_annotation.ProteinGOAnnotation attribute) annotation_set (protea.infrastructure.orm.models.annotation.protein_go_annotation.ProteinGOAnnotation attribute) (protea.infrastructure.orm.models.embedding.prediction_set.PredictionSet attribute) annotation_set_id (protea.core.operations.predict_go_terms_from_interpro.PredictGOTermsFromInterProPayload attribute) (protea.infrastructure.orm.models.annotation.protein_go_annotation.ProteinGOAnnotation attribute) (protea.infrastructure.orm.models.embedding.prediction_set.PredictionSet attribute) annotation_set_to_dict() (in module protea.services.annotations_service) annotation_sets (protea.infrastructure.orm.models.annotation.ontology_snapshot.OntologySnapshot attribute) annotation_source (protea.api.routers.datasets.CreateDatasetRequest attribute) (protea.api.routers.datasets.ImportDatasetByReferenceRequest attribute) (protea.infrastructure.orm.models.embedding.dataset.Dataset attribute) annotations (protea.infrastructure.orm.models.annotation.annotation_set.AnnotationSet attribute) (protea.infrastructure.orm.models.annotation.go_term.GOTerm attribute) AnnotationSet (class in protea.infrastructure.orm.models.annotation.annotation_set) AnnotationSetReferencedError AnnotationsServiceError anon_quota_per_day (protea.infrastructure.settings.Settings attribute) api (protea.config.tuning.TuningSettings attribute) api_cache_default_ttl_seconds (protea.config.tuning.WorkerTuning attribute) api_keys_limit() (in module protea.api.rate_limit) ApiKey (class in protea.infrastructure.orm.models.api_key) APILimits (class in protea.config.tuning) apply_baseline_scoring_default() (in module protea.services._annotations_evaluation_helpers) apply_canonical_bindings() (in module protea.core.features._bindings) arm() (protea.workers.shutdown.ShutdownGuard method) artifact store artifact_uri (protea.api.routers.reranker_models.ImportRerankerByReferenceRequest attribute) (protea.infrastructure.orm.models.embedding.reranker_model.RerankerModel attribute) artifacts_dir (protea.infrastructure.settings.Settings attribute) ArtifactStore (class in protea.infrastructure.storage) ArtifactStoreUnavailable Aspect (class in protea.core.domain.aspect) aspect (protea.infrastructure.orm.models.annotation.go_term.GOTerm attribute) (protea.infrastructure.orm.models.embedding.reranker_model.RerankerModel attribute) (protea.services._scoring_models.RerankerResponse attribute) aspect_knn_workers (protea.config.tuning.OperationTuning attribute) aspects (protea.infrastructure.benchmark_config.BenchmarkConfig attribute) assert_bearer_config() (in module protea.api.bearer) assert_evaluation_set_exists() (in module protea.services._annotations_evaluation_helpers) assigned_by (protea.infrastructure.orm.models.annotation.protein_go_annotation.ProteinGOAnnotation attribute) async job queue auc_pr (protea.core.metrics.CAFAMetrics attribute) audit trail AuPRC author (protea.api.routers.jobs.CreateJobCommentRequest attribute) (protea.api.routers.stack.PullRequest attribute) (protea.infrastructure.orm.models.job.JobComment attribute) axis_tuple_shortid (protea.infrastructure.orm.models.experiment_run.ExperimentRun attribute) axis_tuple_shortid() (in module protea.core.axis_tuple) B backoff_base_seconds (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataPayload attribute) (protea.core.operations.insert_proteins.InsertProteinsPayload attribute) backoff_max_seconds (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataPayload attribute) (protea.core.operations.insert_proteins.InsertProteinsPayload attribute) Base (class in protea.infrastructure.orm.base) base_delay (protea.core.retry.RetryPolicy attribute) baseline_scoring_name (protea.infrastructure.benchmark_config.BenchmarkConfig attribute) BaseWorker (class in protea.workers.base_worker) BatchSpanProcessor (protea.infrastructure.telemetry.SdkBundle attribute) BearerPrincipal (class in protea.api.bearer) bench-v1-K5-v226-lineage-prostt5 BenchmarkConfig (class in protea.infrastructure.benchmark_config) binary_path (protea.core.operations.run_interproscan_batch.RunInterProScanBatchPayload attribute) bind_compute() (protea.core.features.registry.CanonicalFeatureRegistry method) binding_site (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) BIOLOGICAL_PROCESS (protea.core.domain.aspect.Aspect attribute) BLASTP body (protea.api.routers.jobs.CreateJobCommentRequest attribute) (protea.infrastructure.orm.models.job.JobComment attribute) BPO build_engine() (in module protea.infrastructure.database.engine) build_feature_jsonb() (in module protea.infrastructure.orm.models.embedding.go_prediction_features) build_metric_registry() (in module protea.infrastructure.telemetry) build_pair_feature_dict() (in module protea.core._pair_feature_compute) build_predictions_for_protein() (in module protea.services._embeddings_predictions_helpers) build_relationships() (in module protea.core.operations._load_ontology_helpers) build_session_factory() (in module protea.infrastructure.session) build_training_gt_pairs() (in module protea.services._scoring_validation_helpers) C cached (protea.api.routers.stack.PullsResponse attribute) cached() (in module protea.api.cache) CAFA cafa (protea.core.domain.aspect.Aspect property) CAFAMetrics (class in protea.core.metrics) cancel() (protea.workers.shutdown.ShutdownGuard method) cancel_job() (in module protea.api.routers.jobs) CANCELLED (protea.infrastructure.orm.models.job.JobStatus attribute) canonical accession canonical_accession (protea.infrastructure.orm.models.protein.protein.Protein attribute) (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) CANONICAL_AXIS_KEYS (in module protea.core.axis_tuple) CanonicalFeatureRegistry (class in protea.core.features.registry) cascade_delete_embedding_config() (in module protea.services._embeddings_admin_helpers) catalytic_activity (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) categories (protea.infrastructure.benchmark_config.BenchmarkConfig attribute) category (protea.core.metrics.CAFAMetrics attribute) (protea.infrastructure.orm.models.embedding.reranker_model.RerankerModel attribute) (protea.services._scoring_models.RerankerResponse attribute) CCO CELLULAR_COMPONENT (protea.core.domain.aspect.Aspect attribute) child (protea.infrastructure.orm.models.annotation.go_term_relationship.GOTermRelationship attribute) child_go_term_id (protea.infrastructure.orm.models.annotation.go_term_relationship.GOTermRelationship attribute) chunk pooling chunk_index_e (protea.infrastructure.orm.models.embedding.sequence_embedding.SequenceEmbedding attribute) chunk_index_s (protea.infrastructure.orm.models.embedding.sequence_embedding.SequenceEmbedding attribute) chunk_overlap (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) chunk_size (protea.core.operations.load_interpro_go_mapping.LoadInterProGoMappingPayload attribute) (protea.core.operations.predict_go_terms_from_interpro.PredictGOTermsFromInterProPayload attribute) (protea.core.operations.run_interproscan_batch.RunInterProScanBatchPayload attribute) (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) chunks() (in module protea.core.utils) claims (protea.api.bearer.BearerPrincipal attribute) cls (protea.api.routers.registry.PluginInfo attribute) code (protea.core.domain.aspect.Aspect property) cofactor (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) column (protea.core._feature_enricher_helpers.LabelConfig attribute) comment (protea.api.routers.support.SupportCreate attribute) (protea.infrastructure.orm.models.support_entry.SupportEntry attribute) comment_within_limit() (protea.api.routers.support.SupportCreate class method) commit_every_chunk (protea.core.operations.run_interproscan_batch.RunInterProScanBatchPayload attribute) commit_every_page (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataPayload attribute) (protea.core.operations.load_goa_annotations.LoadGOAAnnotationsPayload attribute) (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsPayload attribute) compressed (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataPayload attribute) (protea.core.operations.insert_proteins.InsertProteinsPayload attribute) compute() (protea.core._pair_feature_compute.PairAlignmentComputer method) compute_alignment() (in module protea.core.feature_engineering) compute_alignments (protea.api.routers.datasets.CreateDatasetRequest attribute) compute_cafa_metrics() (in module protea.core.metrics) compute_dedup_key() (in module protea.services.jobs_service) compute_evaluation_data() (in module protea.core.evaluation) compute_evaluation_data_reconciled() (in module protea.core.evaluation) compute_go_term_distribution() (in module protea.services._embeddings_admin_helpers) compute_hash() (protea.infrastructure.orm.models.sequence.sequence.Sequence static method) compute_ia_weight() (in module protea.core._feature_enricher_helpers) compute_missing_signals() (in module protea.services._scoring_validation_helpers) compute_nw() (in module protea.core.feature_engineering) compute_prediction_metrics() (in module protea.services._scoring_prediction_metrics_helpers) compute_reranker_features (protea.api.routers.annotate.AnnotateFormOptions attribute) compute_score() (in module protea.core.scoring) compute_sw() (in module protea.core.feature_engineering) compute_taxonomy (protea.api.routers.datasets.CreateDatasetRequest attribute) compute_taxonomy() (in module protea.core.feature_engineering) config (protea.api.routers.experiment_runs.CreateExperimentRunRequest attribute) (protea.api.routers.experiment_runs.UpdateExperimentRunRequest attribute) (protea.infrastructure.orm.models.experiment_run.ExperimentRun attribute) configure_logging() (in module protea.infrastructure.logging) configure_telemetry() (in module protea.infrastructure.telemetry) ConsumerOptions (class in protea.infrastructure.queue.consumer) Coordinator create_api_key() (in module protea.api.routers.auth_api_keys) create_dataset() (in module protea.api.routers.datasets) create_embedding_config() (in module protea.api.routers.embeddings) create_experiment_run() (in module protea.api.routers.experiment_runs) create_job() (in module protea.api.routers.jobs) create_job_comment() (in module protea.api.routers.jobs) create_query_set() (in module protea.api.routers.query_sets) CreateApiKeyRequest (class in protea.api.routers.auth_api_keys) created_at (protea.api.routers.stack.PullRequest attribute) (protea.infrastructure.orm.models.annotation.annotation_set.AnnotationSet attribute) (protea.infrastructure.orm.models.annotation.evaluation_result.EvaluationResult attribute) (protea.infrastructure.orm.models.annotation.evaluation_set.EvaluationSet attribute) (protea.infrastructure.orm.models.annotation.interpro_annotation.InterProAnnotation attribute) (protea.infrastructure.orm.models.annotation.interpro_go_mapping.InterProGoMapping attribute) (protea.infrastructure.orm.models.api_key.ApiKey attribute) (protea.infrastructure.orm.models.embedding.dataset.Dataset attribute) (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) (protea.infrastructure.orm.models.embedding.prediction_set.PredictionSet attribute) (protea.infrastructure.orm.models.embedding.reranker_model.RerankerModel attribute) (protea.infrastructure.orm.models.embedding.scoring_config.ScoringConfig attribute) (protea.infrastructure.orm.models.embedding.sequence_embedding.SequenceEmbedding attribute) (protea.infrastructure.orm.models.experiment_run.ExperimentRun attribute) (protea.infrastructure.orm.models.job.Job attribute) (protea.infrastructure.orm.models.job.JobComment attribute) (protea.infrastructure.orm.models.protein.protein.Protein attribute) (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) (protea.infrastructure.orm.models.query.query_set.QuerySet attribute) (protea.infrastructure.orm.models.query.query_set.QuerySetEntry attribute) (protea.infrastructure.orm.models.sequence.sequence.Sequence attribute) (protea.infrastructure.orm.models.support_entry.SupportEntry attribute) (protea.infrastructure.orm.models.visitor_event.VisitorEvent attribute) (protea.services._scoring_models.RerankerResponse attribute) (protea.services._scoring_models.ScoringConfigResponse attribute) CreateDatasetRequest (class in protea.api.routers.datasets) CreateExperimentRunRequest (class in protea.api.routers.experiment_runs) CreateJobCommentRequest (class in protea.api.routers.jobs) CreateJobRequest (class in protea.api.routers.jobs) current_job_id (protea.workers.shutdown.ShutdownGuard property) curve (protea.core.metrics.CAFAMetrics attribute) D Dataset (class in protea.infrastructure.orm.models.embedding.dataset) dataset_id (protea.api.routers.reranker_models.ImportRerankerByReferenceRequest attribute) (protea.infrastructure.orm.models.embedding.reranker_model.RerankerModel attribute) (protea.services._scoring_models.RerankerResponse attribute) dataset_manifest_sha (protea.services._scoring_models.RerankerResponse attribute) dataset_name (protea.services._scoring_models.RerankerResponse attribute) dataset_schema_sha (protea.services._scoring_models.RerankerResponse attribute) datasets_limit() (in module protea.api.rate_limit) day (protea.infrastructure.orm.models.visitor_event.VisitorEvent attribute) db_pool_in_use (protea.infrastructure.telemetry.MetricRegistry attribute) db_pool_max_overflow (protea.config.tuning.WorkerTuning attribute) db_pool_recycle_seconds (protea.config.tuning.WorkerTuning attribute) db_pool_size (protea.config.tuning.WorkerTuning attribute) db_reference (protea.infrastructure.orm.models.annotation.protein_go_annotation.ProteinGOAnnotation attribute) db_url (protea.infrastructure.settings.Settings attribute) decode_bearer_token() (in module protea.api.bearer) dedup_key (protea.infrastructure.orm.models.job.Job attribute) DEFAULT_EVIDENCE_WEIGHT_FALLBACK (in module protea.infrastructure.orm.models.embedding.scoring_config) Deferred deferred (protea.core.contracts.operation.OperationResult attribute) definition (protea.infrastructure.orm.models.annotation.go_term.GOTerm attribute) delete() (protea.infrastructure.storage.ArtifactStore method) (protea.infrastructure.storage.local.LocalFsArtifactStore method) (protea.infrastructure.storage.LocalFsArtifactStore method) (protea.infrastructure.storage.minio_store.MinioArtifactStore method) delete_annotation_set_data() (in module protea.services.annotations_service) delete_embedding_config() (in module protea.api.routers.embeddings) delete_eval_result_collect_keys() (in module protea.services._annotations_evaluation_helpers) (in module protea.services.annotations_service) delete_evaluation_result() (in module protea.api.routers.annotations.evaluation_results) delete_evaluation_set_collect_keys() (in module protea.services._annotations_evaluation_helpers) (in module protea.services.annotations_service) delete_experiment_run() (in module protea.api.routers.experiment_runs) delete_job() (in module protea.api.routers.jobs) delete_prediction_set() (in module protea.api.routers.embeddings) delete_query_set() (in module protea.api.routers.query_sets) delta_proteins (protea.core.evaluation.EvaluationData property) deploy-keeper description (protea.api.routers.experiment_runs.CreateExperimentRunRequest attribute) (protea.api.routers.experiment_runs.UpdateExperimentRunRequest attribute) (protea.api.routers.jobs.CreateJobRequest attribute) (protea.core.contracts.operation.Operation attribute) (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataOperation attribute) (protea.core.operations.generate_evaluation_set.GenerateEvaluationSetOperation attribute) (protea.core.operations.insert_proteins.InsertProteinsOperation attribute) (protea.core.operations.load_goa_annotations.LoadGOAAnnotationsOperation attribute) (protea.core.operations.load_interpro_go_mapping.LoadInterProGoMappingOperation attribute) (protea.core.operations.load_ontology_snapshot.LoadOntologySnapshotOperation attribute) (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsOperation attribute) (protea.core.operations.ping.PingOperation attribute) (protea.core.operations.predict_go_terms_from_interpro.PredictGOTermsFromInterProOperation attribute) (protea.core.operations.run_interproscan_batch.RunInterProScanBatchOperation attribute) (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) (protea.infrastructure.orm.models.embedding.scoring_config.ScoringConfig attribute) (protea.infrastructure.orm.models.experiment_run.ExperimentRun attribute) (protea.infrastructure.orm.models.job.Job attribute) (protea.infrastructure.orm.models.query.query_set.QuerySet attribute) (protea.services._scoring_models.ScoringConfigCreate attribute) (protea.services._scoring_models.ScoringConfigResponse attribute) deserialize_evaluation_data_from_bytes() (in module protea.core.evaluation) detail (protea.api.problem_details.ProblemDetail attribute) DIAMOND discover_plugins() (in module protea.core.plugins) dispatch() (protea.api.middleware.visitor_counter.VisitorCounterMiddleware method) dispatch_validated_job() (in module protea.services.jobs_service) display_name (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) distance (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) distance_threshold (protea.infrastructure.orm.models.embedding.prediction_set.PredictionSet attribute) DLQ DlqPurgeRequest (class in protea.api.routers.admin) DlqReplayRequest (class in protea.api.routers.admin) DLX dna_binding (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) docs_url (protea.api.routers.stack.RepoEntry attribute) DONE (protea.infrastructure.orm.models.experiment_run.ExperimentRunStatus attribute) download_dataset_artifact() (in module protea.api.routers.datasets) download_evaluation_artifacts() (in module protea.api.routers.annotations.evaluation_results) download_evaluation_metrics() (in module protea.api.routers.annotations.evaluation_results) download_predictions_cafa() (in module protea.api.routers.embeddings) download_predictions_tsv() (in module protea.api.routers.embeddings) draft (protea.api.routers.stack.PullRequest attribute) dry_run (protea.api.routers.admin.DlqPurgeRequest attribute) (protea.api.routers.admin.DlqReplayRequest attribute) dual-write E ec_number (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) ECO eco_mapping_url (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsPayload attribute) emb_pca_query_0 (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) emb_pca_query_1 (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) emb_pca_query_10 (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) emb_pca_query_11 (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) emb_pca_query_12 (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) emb_pca_query_13 (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) emb_pca_query_14 (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) emb_pca_query_15 (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) emb_pca_query_2 (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) emb_pca_query_3 (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) emb_pca_query_4 (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) emb_pca_query_5 (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) emb_pca_query_6 (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) emb_pca_query_7 (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) emb_pca_query_8 (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) emb_pca_query_9 (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) embedding (protea.infrastructure.orm.models.embedding.sequence_embedding.SequenceEmbedding attribute) embedding backend embedding_config (protea.infrastructure.orm.models.embedding.prediction_set.PredictionSet attribute) (protea.infrastructure.orm.models.embedding.sequence_embedding.SequenceEmbedding attribute) embedding_config_id (protea.api.routers.datasets.CreateDatasetRequest attribute) (protea.api.routers.datasets.ImportDatasetByReferenceRequest attribute) (protea.core.operations.predict_go_terms_from_interpro.PredictGOTermsFromInterProPayload attribute) (protea.infrastructure.orm.models.embedding.dataset.Dataset attribute) (protea.infrastructure.orm.models.embedding.prediction_set.PredictionSet attribute) (protea.infrastructure.orm.models.embedding.reranker_model.RerankerModel attribute) (protea.infrastructure.orm.models.embedding.sequence_embedding.SequenceEmbedding attribute) embedding_dim (protea.infrastructure.orm.models.embedding.sequence_embedding.SequenceEmbedding attribute) EmbeddingConfig (class in protea.infrastructure.orm.models.embedding.embedding_config) embeddings_batch_seconds (protea.infrastructure.telemetry.MetricRegistry attribute) enabled (protea.infrastructure.telemetry.TelemetryConfig attribute) end (protea.infrastructure.orm.models.annotation.interpro_annotation.InterProAnnotation attribute) endpoint (protea.infrastructure.telemetry.TelemetryConfig attribute) enqueue_job() (in module protea.services.jobs_service) ensemble_spec (protea.infrastructure.orm.models.experiment_run.ExperimentRun attribute) EntityNotFoundError entries (protea.infrastructure.orm.models.query.query_set.QuerySet attribute) entry_name (protea.infrastructure.orm.models.protein.protein.Protein attribute) error_code (protea.infrastructure.orm.models.job.Job attribute) error_message (protea.infrastructure.orm.models.job.Job attribute) errors (protea.api.routers.stack.PullsResponse attribute) ESM-2 ESM-3 ESM-3c ESM-C eval_set_labels (protea.infrastructure.benchmark_config.BenchmarkConfig attribute) eval_set_manifest_sha (protea.infrastructure.orm.models.experiment_run.ExperimentRun attribute) eval_set_name (protea.infrastructure.orm.models.experiment_run.ExperimentRun attribute) eval_snapshot_pair (protea.api.routers.datasets.ImportDatasetByReferenceRequest attribute) (protea.infrastructure.orm.models.embedding.dataset.Dataset attribute) eval_uri (protea.api.routers.datasets.ImportDatasetByReferenceRequest attribute) (protea.infrastructure.orm.models.embedding.dataset.Dataset attribute) EvalContext (class in protea.core.evaluation) evaluation runner evaluation_result_to_dict() (in module protea.services._annotations_evaluation_helpers) (in module protea.services.annotations_service) evaluation_set (protea.infrastructure.orm.models.annotation.evaluation_result.EvaluationResult attribute) evaluation_set_id (protea.api.routers.reranker_models.ImportRerankerByReferenceRequest attribute) (protea.infrastructure.orm.models.annotation.evaluation_result.EvaluationResult attribute) (protea.infrastructure.orm.models.embedding.reranker_model.RerankerModel attribute) (protea.services._scoring_models.RerankerResponse attribute) evaluation_set_to_dict() (in module protea.services._annotations_evaluation_helpers) (in module protea.services.annotations_service) EvaluationData (class in protea.core.evaluation) EvaluationResult (class in protea.infrastructure.orm.models.annotation.evaluation_result) EvaluationSet (class in protea.infrastructure.orm.models.annotation.evaluation_set) event (protea.infrastructure.orm.models.job.JobEvent attribute) events (protea.infrastructure.orm.models.job.Job attribute) evidence (protea.core.operations.load_interpro_go_mapping.LoadInterProGoMappingPayload attribute) (protea.infrastructure.orm.models.annotation.interpro_annotation.InterProAnnotation attribute) (protea.infrastructure.orm.models.annotation.interpro_go_mapping.InterProGoMapping attribute) evidence code evidence_code (protea.infrastructure.orm.models.annotation.protein_go_annotation.ProteinGOAnnotation attribute) (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) EVIDENCE_CODE_GROUPS (in module protea.infrastructure.orm.models.embedding.scoring_config) evidence_weight() (in module protea.core.scoring) evidence_weights (protea.infrastructure.orm.models.embedding.scoring_config.ScoringConfig attribute) (protea.services._scoring_models.ScoringConfigCreate attribute) (protea.services._scoring_models.ScoringConfigResponse attribute) EvidenceFilter exactly_one_input() (protea.core.operations.run_interproscan_batch.RunInterProScanBatchPayload method) execute() (protea.core.contracts.operation.Operation method) (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataOperation method) (protea.core.operations.generate_evaluation_set.GenerateEvaluationSetOperation method) (protea.core.operations.insert_proteins.InsertProteinsOperation method) (protea.core.operations.load_goa_annotations.LoadGOAAnnotationsOperation method) (protea.core.operations.load_interpro_go_mapping.LoadInterProGoMappingOperation method) (protea.core.operations.load_ontology_snapshot.LoadOntologySnapshotOperation method) (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsOperation method) (protea.core.operations.ping.PingOperation method) (protea.core.operations.predict_go_terms_from_interpro.PredictGOTermsFromInterProOperation method) (protea.core.operations.run_interproscan_batch.RunInterProScanBatchOperation method) exists() (protea.infrastructure.storage.ArtifactStore method) (protea.infrastructure.storage.local.LocalFsArtifactStore method) (protea.infrastructure.storage.LocalFsArtifactStore method) (protea.infrastructure.storage.minio_store.MinioArtifactStore method) expand_votes_to_ancestors (protea.api.routers.datasets.CreateDatasetRequest attribute) ExperimentRun (class in protea.infrastructure.orm.models.experiment_run) ExperimentRunStatus (class in protea.infrastructure.orm.models.experiment_run) extend_lease() (protea.workers.base_worker.BaseWorker method) external_source (protea.api.routers.datasets.ImportDatasetByReferenceRequest attribute) (protea.api.routers.reranker_models.ImportRerankerByReferenceRequest attribute) (protea.infrastructure.orm.models.embedding.reranker_model.RerankerModel attribute) (protea.services._scoring_models.RerankerResponse attribute) extra (protea.api.routers.registry.PluginInfo attribute) extra_args (protea.core.operations.run_interproscan_batch.RunInterProScanBatchPayload attribute) extract_bearer_token() (in module protea.api.bearer) extract_trace_context() (in module protea.infrastructure.telemetry) extract_uniprot_header_metadata() (in module protea.api.routers.query_sets) F f1 (protea.core.metrics.PRPoint attribute) FAILED (protea.infrastructure.orm.models.job.JobStatus attribute) FAISS families() (protea.core.features.registry.CanonicalFeatureRegistry method) family (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) FASTA feature_importance (protea.infrastructure.orm.models.embedding.reranker_model.RerankerModel attribute) (protea.services._scoring_models.RerankerResponse attribute) FEATURE_JSONB_KEYS (in module protea.infrastructure.orm.models.embedding.go_prediction_features) feature_schema_sha (protea.infrastructure.orm.models.embedding.reranker_model.RerankerModel attribute) (protea.infrastructure.orm.models.experiment_run.ExperimentRun attribute) (protea.services._scoring_models.RerankerResponse attribute) feature_selection (protea.services._scoring_models.RerankerResponse attribute) FeatureRegistry features (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) fetched_at (protea.api.routers.stack.PullsResponse attribute) FetchUniProtMetadataOperation (class in protea.core.operations.fetch_uniprot_metadata) FetchUniProtMetadataPayload (class in protea.core.operations.fetch_uniprot_metadata) FIELD_MAP (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataOperation attribute) fields (protea.infrastructure.orm.models.job.JobEvent attribute) findings (protea.api.routers.experiment_runs.UpdateExperimentRunRequest attribute) (protea.infrastructure.orm.models.experiment_run.ExperimentRun attribute) (protea.infrastructure.orm.models.job.Job attribute) finished_at (protea.infrastructure.orm.models.experiment_run.ExperimentRun attribute) (protea.infrastructure.orm.models.job.Job attribute) first_death_queue (protea.api.routers.admin.DlqPurgeRequest attribute) (protea.api.routers.admin.DlqReplayRequest attribute) Fmax fmax (protea.core.metrics.CAFAMetrics attribute) force (protea.api.routers.datasets.ImportDatasetByReferenceRequest attribute) (protea.api.routers.reranker_models.ImportRerankerByReferenceRequest attribute) force_relationships (protea.core.operations.load_ontology_snapshot.LoadOntologySnapshotPayload attribute) format() (protea.infrastructure.logging.JSONFormatter method) format_training_row() (in module protea.services._scoring_training_helpers) formula (protea.infrastructure.orm.models.embedding.scoring_config.ScoringConfig attribute) (protea.services._scoring_models.ScoringConfigCreate attribute) (protea.services._scoring_models.ScoringConfigResponse attribute) from_cafa() (protea.core.domain.aspect.Aspect class method) from_code() (protea.core.domain.aspect.Aspect class method) from_json() (in module protea.infrastructure.orm.models.embedding.go_prediction_features) function_cc (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) G GAF gaf_url (protea.core.operations.load_goa_annotations.LoadGOAAnnotationsPayload attribute) gaps_pct_nw (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) gaps_pct_sw (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) gene_name (protea.infrastructure.orm.models.protein.protein.Protein attribute) gene_product_batch_size (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsPayload attribute) gene_product_ids (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsPayload attribute) generate_raw_key() (in module protea.api.auth) GenerateEvaluationSetOperation (class in protea.core.operations.generate_evaluation_set) GenerateEvaluationSetPayload (class in protea.core.operations.generate_evaluation_set) get() (protea.core.contracts.registry.OperationRegistry method) (protea.core.features.registry.CanonicalFeatureRegistry method) (protea.infrastructure.storage.ArtifactStore method) (protea.infrastructure.storage.local.LocalFsArtifactStore method) (protea.infrastructure.storage.LocalFsArtifactStore method) (protea.infrastructure.storage.minio_store.MinioArtifactStore method) get_amqp_url() (in module protea.api.deps) get_annotation_set_data() (in module protea.services.annotations_service) get_artifact_store() (in module protea.infrastructure.storage) (in module protea.infrastructure.storage.factory) get_artifacts_dir() (in module protea.api.deps) get_benchmark_config() (in module protea.api.deps) get_benchmark_matrix() (in module protea.api.routers.benchmark) get_canonical_registry() (in module protea.core.features.registry) get_dataset() (in module protea.api.routers.datasets) get_dataset_stats() (in module protea.api.routers.datasets) get_dlq_summary() (in module protea.api.routers.admin) get_embedding_config() (in module protea.api.routers.embeddings) get_eval_result_with_keys() (in module protea.services._annotations_evaluation_helpers) (in module protea.services.annotations_service) get_evaluation_set_data() (in module protea.services._annotations_evaluation_helpers) (in module protea.services.annotations_service) get_experiment_run() (in module protea.api.routers.experiment_runs) get_go_subgraph_data() (in module protea.services._annotations_method_helpers) (in module protea.services.annotations_service) get_go_term_distribution() (in module protea.api.routers.embeddings) get_job() (in module protea.api.routers.jobs) get_job_events() (in module protea.api.routers.jobs) get_last_known() (in module protea.api.cache) get_metrics() (in module protea.api.routers.metrics) get_operation_registry() (in module protea.api.deps) get_prediction_set() (in module protea.api.routers.embeddings) get_protein() (in module protea.api.routers.proteins) get_protein_annotations() (in module protea.api.routers.proteins) get_protein_predictions() (in module protea.api.routers.embeddings) get_protein_stats() (in module protea.api.routers.proteins) get_query_set() (in module protea.api.routers.query_sets) get_runner_plugins() (in module protea.core.runners) get_session_factory() (in module protea.api.deps) get_settings() (in module protea.api.deps) get_showcase() (in module protea.api.routers.showcase) get_snapshot_data() (in module protea.services.annotations_service) get_stack() (in module protea.api.routers.stack) get_support() (in module protea.api.routers.support) get_tracer() (in module protea.infrastructure.telemetry) get_tuning() (in module protea.config.tuning) get_user_quota_per_day() (in module protea.api.deps) github_url (protea.api.routers.stack.RepoEntry attribute) GO GO term go_id (protea.infrastructure.orm.models.annotation.go_term.GOTerm attribute) (protea.infrastructure.orm.models.annotation.interpro_go_mapping.InterProGoMapping attribute) go_term (protea.infrastructure.orm.models.annotation.protein_go_annotation.ProteinGOAnnotation attribute) (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) go_term_frequency (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) go_term_id (protea.infrastructure.orm.models.annotation.protein_go_annotation.ProteinGOAnnotation attribute) (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) go_terms (protea.infrastructure.orm.models.annotation.ontology_snapshot.OntologySnapshot attribute) GOA golden parquet gate GOPrediction (class in protea.infrastructure.orm.models.embedding.go_prediction) GOTerm (class in protea.infrastructure.orm.models.annotation.go_term) GOTermRelationship (class in protea.infrastructure.orm.models.annotation.go_term_relationship) groundtruth_key_for() (in module protea.core.evaluation) groundtruth_uri (protea.infrastructure.orm.models.annotation.evaluation_set.EvaluationSet attribute) group (protea.api.routers.registry.PluginListResponse attribute) gt_pairs (protea.core._feature_enricher_helpers.LabelConfig attribute) H handle_existing_snapshot() (in module protea.core.operations._load_ontology_helpers) handle_job() (protea.workers.base_worker.BaseWorker method) hash_key() (in module protea.api.auth) HeartbeatLoop (class in protea.workers.shutdown) hidden_embeddings (protea.infrastructure.benchmark_config.BenchmarkConfig attribute) hidden_stages (protea.infrastructure.benchmark_config.BenchmarkConfig attribute) http_request_duration_seconds (protea.infrastructure.telemetry.MetricRegistry attribute) http_requests_in_flight (protea.infrastructure.telemetry.MetricRegistry attribute) http_requests_total (protea.infrastructure.telemetry.MetricRegistry attribute) hypothesis (protea.api.routers.experiment_runs.CreateExperimentRunRequest attribute) (protea.api.routers.experiment_runs.UpdateExperimentRunRequest attribute) (protea.infrastructure.orm.models.experiment_run.ExperimentRun attribute) I IA ia_url (protea.infrastructure.orm.models.annotation.ontology_snapshot.OntologySnapshot attribute) IC id (protea.infrastructure.orm.models.annotation.annotation_set.AnnotationSet attribute) (protea.infrastructure.orm.models.annotation.evaluation_result.EvaluationResult attribute) (protea.infrastructure.orm.models.annotation.evaluation_set.EvaluationSet attribute) (protea.infrastructure.orm.models.annotation.go_term.GOTerm attribute) (protea.infrastructure.orm.models.annotation.go_term_relationship.GOTermRelationship attribute) (protea.infrastructure.orm.models.annotation.interpro_annotation.InterProAnnotation attribute) (protea.infrastructure.orm.models.annotation.interpro_go_mapping.InterProGoMapping attribute) (protea.infrastructure.orm.models.annotation.ontology_snapshot.OntologySnapshot attribute) (protea.infrastructure.orm.models.annotation.protein_go_annotation.ProteinGOAnnotation attribute) (protea.infrastructure.orm.models.api_key.ApiKey attribute) (protea.infrastructure.orm.models.embedding.dataset.Dataset attribute) (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) (protea.infrastructure.orm.models.embedding.prediction_set.PredictionSet attribute) (protea.infrastructure.orm.models.embedding.reranker_model.RerankerModel attribute) (protea.infrastructure.orm.models.embedding.scoring_config.ScoringConfig attribute) (protea.infrastructure.orm.models.embedding.sequence_embedding.SequenceEmbedding attribute) (protea.infrastructure.orm.models.experiment_run.ExperimentRun attribute) (protea.infrastructure.orm.models.job.Job attribute) (protea.infrastructure.orm.models.job.JobComment attribute) (protea.infrastructure.orm.models.job.JobEvent attribute) (protea.infrastructure.orm.models.query.query_set.QuerySet attribute) (protea.infrastructure.orm.models.query.query_set.QuerySetEntry attribute) (protea.infrastructure.orm.models.sequence.sequence.Sequence attribute) (protea.infrastructure.orm.models.support_entry.SupportEntry attribute) (protea.infrastructure.orm.models.visitor_event.VisitorEvent attribute) (protea.services._scoring_models.RerankerResponse attribute) (protea.services._scoring_models.ScoringConfigResponse attribute) identity_nw (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) identity_sw (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) IEA import_dataset_by_reference() (in module protea.api.routers.datasets) import_reranker_model_by_reference() (in module protea.api.routers.reranker_models) import_reranker_model_multipart() (in module protea.api.routers.reranker_models) ImportDatasetByReferenceRequest (class in protea.api.routers.datasets) ImportRerankerByReferenceRequest (class in protea.api.routers.reranker_models) include_children (protea.api.routers.jobs.JobListFilters attribute) include_isoforms (protea.core.operations.insert_proteins.InsertProteinsPayload attribute) inject_trace_context() (in module protea.infrastructure.telemetry) insert_new_snapshot() (in module protea.core.operations._load_ontology_helpers) InsertProteinsOperation (class in protea.core.operations.insert_proteins) InsertProteinsPayload (class in protea.core.operations.insert_proteins) install_problem_openapi_schema() (in module protea.api.problem_details) install_rate_limiter() (in module protea.api.rate_limit) instance (protea.api.problem_details.ProblemDetail attribute) instrument_sqlalchemy_engine() (in module protea.infrastructure.telemetry) integration runner intern_string() (in module protea.core.annotation_intern) InterProAnnotation (class in protea.infrastructure.orm.models.annotation.interpro_annotation) InterProGoMapping (class in protea.infrastructure.orm.models.annotation.interpro_go_mapping) invalidate() (in module protea.api.cache) InvalidJobPayloadError ipr_accession (protea.infrastructure.orm.models.annotation.interpro_go_mapping.InterProGoMapping attribute) ipr_release (protea.infrastructure.orm.models.annotation.interpro_annotation.InterProAnnotation attribute) ipr_release_floor (protea.core.operations.predict_go_terms_from_interpro.PredictGOTermsFromInterProPayload attribute) (protea.core.operations.run_interproscan_batch.RunInterProScanBatchPayload attribute) is_canonical (protea.infrastructure.orm.models.protein.protein.Protein attribute) is_dual_write_enabled() (in module protea.core.schema_sha_v2) is_experimental() (in module protea.core.evidence_codes) is_jsonb_dual_write_enabled() (in module protea.core.jsonb_dual_write) is_obsolete (protea.infrastructure.orm.models.annotation.go_term.GOTerm attribute) is_retryable() (in module protea.core.retry) is_retryable_connection_error() (in module protea.core.retry) is_retryable_db_error() (in module protea.core.retry) isoform isoform_index (protea.infrastructure.orm.models.protein.protein.Protein attribute) iter_delta_proteins_fasta() (in module protea.services._annotations_method_helpers) (in module protea.services.annotations_service) iter_evaluation_artifacts_zip() (in module protea.services._annotations_streaming_helpers) iter_groundtruth_tsv() (in module protea.services.annotations_service) iter_predictions_cafa_tsv() (in module protea.services._embeddings_cafa_helpers) iter_predictions_tsv() (in module protea.services._embeddings_predictions_helpers) iter_reranked_predictions_tsv() (in module protea.services._scoring_streaming_helpers) iter_scored_predictions() (in module protea.services._scoring_streaming_helpers) iter_training_data() (in module protea.services._scoring_streaming_helpers) J jitter_ratio (protea.core.retry.RetryPolicy attribute) jitter_seconds (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataPayload attribute) (protea.core.operations.insert_proteins.InsertProteinsPayload attribute) Job (class in protea.infrastructure.orm.models.job) job (protea.infrastructure.orm.models.annotation.annotation_set.AnnotationSet attribute) (protea.infrastructure.orm.models.annotation.evaluation_result.EvaluationResult attribute) (protea.infrastructure.orm.models.annotation.evaluation_set.EvaluationSet attribute) (protea.infrastructure.orm.models.job.JobEvent attribute) job_duration_seconds (protea.infrastructure.telemetry.MetricRegistry attribute) job_heartbeat_interval_seconds (protea.config.tuning.WorkerTuning attribute) job_id (protea.infrastructure.orm.models.annotation.annotation_set.AnnotationSet attribute) (protea.infrastructure.orm.models.annotation.evaluation_result.EvaluationResult attribute) (protea.infrastructure.orm.models.annotation.evaluation_set.EvaluationSet attribute) (protea.infrastructure.orm.models.embedding.dataset.Dataset attribute) (protea.infrastructure.orm.models.job.JobComment attribute) (protea.infrastructure.orm.models.job.JobEvent attribute) JobComment (class in protea.infrastructure.orm.models.job) JobEvent (class in protea.infrastructure.orm.models.job) JobListFilters (class in protea.api.routers.jobs) jobs_limit() (in module protea.api.rate_limit) jobs_total (protea.infrastructure.telemetry.MetricRegistry attribute) JobStatus (class in protea.infrastructure.orm.models.job) JSONB JSONB_DUAL_WRITE_ENV (in module protea.core.jsonb_dual_write) JSONFormatter (class in protea.infrastructure.logging) JWT K k (protea.api.routers.datasets.CreateDatasetRequest attribute) (protea.api.routers.datasets.ImportDatasetByReferenceRequest attribute) (protea.infrastructure.orm.models.embedding.dataset.Dataset attribute) (protea.infrastructure.orm.models.experiment_run.ExperimentRun attribute) k_position (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) key_hash (protea.infrastructure.orm.models.api_key.ApiKey attribute) key_prefix (protea.api.routers.datasets.ImportDatasetByReferenceRequest attribute) (protea.infrastructure.orm.models.embedding.dataset.Dataset attribute) keywords (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) kinetics (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) KNN known (protea.core.evaluation.EvaluationData attribute) known_terms_count (protea.core.evaluation.EvaluationData property) L label_for_stage() (protea.infrastructure.benchmark_config.BenchmarkConfig method) LabelConfig (class in protea.core._feature_enricher_helpers) labels (protea.api.routers.stack.PullRequest attribute) LAFA last_used_at (protea.infrastructure.orm.models.api_key.ApiKey attribute) layer_agg (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) layer_indices (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) LCP leakage-free temporal holdout LEASE_EXPIRED_FAILED_EVENT (in module protea.workers.stale_job_reaper) LEASE_REQUEUE_EVENT (in module protea.workers.stale_job_reaper) leased_until (protea.infrastructure.orm.models.job.Job attribute) length (protea.infrastructure.orm.models.protein.protein.Protein attribute) length_query (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) length_ref (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) level (protea.infrastructure.orm.models.job.JobEvent attribute) limit (protea.api.routers.jobs.JobListFilters attribute) limit_per_entry (protea.infrastructure.orm.models.embedding.prediction_set.PredictionSet attribute) list_annotation_sets_data() (in module protea.services.annotations_service) list_api_keys() (in module protea.api.routers.auth_api_keys) list_backends() (in module protea.api.routers.registry) list_benchmark_embeddings() (in module protea.api.routers.benchmark) list_datasets() (in module protea.api.routers.datasets) list_embedding_configs() (in module protea.api.routers.embeddings) list_evaluation_results() (in module protea.api.routers.annotations.evaluation_results) list_evaluation_results_data() (in module protea.services._annotations_evaluation_helpers) (in module protea.services.annotations_service) list_evaluation_sets_data() (in module protea.services._annotations_evaluation_helpers) (in module protea.services.annotations_service) list_experiment_runs() (in module protea.api.routers.experiment_runs) list_job_comments() (in module protea.api.routers.jobs) list_jobs() (in module protea.api.routers.jobs) list_open_pulls() (in module protea.api.routers.stack) list_prediction_set_proteins() (in module protea.api.routers.embeddings) list_prediction_sets() (in module protea.api.routers.embeddings) list_proteins() (in module protea.api.routers.proteins) list_proteins_in_prediction_set() (in module protea.services._embeddings_proteins_helpers) list_query_sets() (in module protea.api.routers.query_sets) list_runners() (in module protea.api.routers.registry) list_snapshots_data() (in module protea.services.annotations_service) list_sources() (in module protea.api.routers.registry) LK lk (protea.core.evaluation.EvaluationData attribute) lk_annotations (protea.core.evaluation.EvaluationData property) lk_proteins (protea.core.evaluation.EvaluationData property) load_benchmark_config() (in module protea.infrastructure.benchmark_config) load_evaluation_data_for_set() (in module protea.core.evaluation) load_settings() (in module protea.infrastructure.settings) loaded_at (protea.infrastructure.orm.models.annotation.ontology_snapshot.OntologySnapshot attribute) LoadGOAAnnotationsOperation (class in protea.core.operations.load_goa_annotations) LoadGOAAnnotationsPayload (class in protea.core.operations.load_goa_annotations) LoadInterProGoMappingOperation (class in protea.core.operations.load_interpro_go_mapping) LoadInterProGoMappingPayload (class in protea.core.operations.load_interpro_go_mapping) LoadOntologySnapshotOperation (class in protea.core.operations.load_ontology_snapshot) LoadOntologySnapshotPayload (class in protea.core.operations.load_ontology_snapshot) LoadQuickGOAnnotationsOperation (class in protea.core.operations.load_quickgo_annotations) LoadQuickGOAnnotationsPayload (class in protea.core.operations.load_quickgo_annotations) local_docs_path (protea.api.routers.stack.RepoEntry attribute) LocalFsArtifactStore (class in protea.infrastructure.storage) (class in protea.infrastructure.storage.local) M make_ancestor_closure() (in module protea.core._feature_enricher_helpers) make_safe_emit() (in module protea.core.contracts.operation) manage.sh manifest_sha (protea.api.routers.datasets.ImportDatasetByReferenceRequest attribute) (protea.infrastructure.orm.models.embedding.dataset.Dataset attribute) manifest_uri (protea.api.routers.datasets.ImportDatasetByReferenceRequest attribute) (protea.infrastructure.orm.models.embedding.dataset.Dataset attribute) mapping_url (protea.core.operations.load_interpro_go_mapping.LoadInterProGoMappingPayload attribute) max_attempts (protea.core.retry.RetryPolicy attribute) max_comment_length (protea.config.tuning.APILimits attribute) max_delay (protea.core.retry.RetryPolicy attribute) max_fasta_bytes (protea.config.tuning.APILimits attribute) max_lease_requeues (protea.config.tuning.WorkerTuning attribute) max_length (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) max_messages (protea.api.routers.admin.DlqPurgeRequest attribute) (protea.api.routers.admin.DlqReplayRequest attribute) max_retries (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataPayload attribute) (protea.core.operations.insert_proteins.InsertProteinsPayload attribute) maybe_jsonb() (in module protea.core.jsonb_dual_write) maybe_v2() (in module protea.core.schema_sha_v2) MD5 merge_into_existing_leaf() (in module protea.core._feature_enricher_helpers) message (protea.infrastructure.orm.models.job.JobEvent attribute) meta (protea.api.routers.datasets.ImportDatasetByReferenceRequest attribute) (protea.api.routers.jobs.CreateJobRequest attribute) (protea.infrastructure.orm.models.annotation.annotation_set.AnnotationSet attribute) (protea.infrastructure.orm.models.embedding.dataset.Dataset attribute) (protea.infrastructure.orm.models.embedding.prediction_set.PredictionSet attribute) (protea.infrastructure.orm.models.job.Job attribute) method (protea.infrastructure.orm.models.visitor_event.VisitorEvent attribute) Method Object MetricRegistry (class in protea.infrastructure.telemetry) metrics (protea.infrastructure.orm.models.embedding.reranker_model.RerankerModel attribute) (protea.services._scoring_models.RerankerResponse attribute) MFO MIL MinIO minio_access_key (protea.infrastructure.settings.Settings attribute) minio_bucket (protea.infrastructure.settings.Settings attribute) minio_endpoint (protea.infrastructure.settings.Settings attribute) minio_secret_key (protea.infrastructure.settings.Settings attribute) minio_secure (protea.infrastructure.settings.Settings attribute) MinioArtifactStore (class in protea.infrastructure.storage.minio_store) model_backend (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) model_cache_max (protea.config.tuning.WorkerTuning attribute) model_config (protea.api.problem_details.ProblemDetail attribute) (protea.api.routers.admin.DlqPurgeRequest attribute) (protea.api.routers.admin.DlqReplayRequest attribute) (protea.api.routers.annotate.AnnotateFormOptions attribute) (protea.api.routers.auth_api_keys.CreateApiKeyRequest attribute) (protea.api.routers.datasets.CreateDatasetRequest attribute) (protea.api.routers.datasets.ImportDatasetByReferenceRequest attribute) (protea.api.routers.experiment_runs.CreateExperimentRunRequest attribute) (protea.api.routers.experiment_runs.UpdateExperimentRunRequest attribute) (protea.api.routers.jobs.CreateJobCommentRequest attribute) (protea.api.routers.jobs.CreateJobRequest attribute) (protea.api.routers.registry.PluginInfo attribute) (protea.api.routers.registry.PluginListResponse attribute) (protea.api.routers.reranker_models.ImportRerankerByReferenceRequest attribute) (protea.api.routers.stack.PullRequest attribute) (protea.api.routers.stack.PullsResponse attribute) (protea.api.routers.stack.RepoEntry attribute) (protea.api.routers.stack.StackResponse attribute) (protea.api.routers.support.SupportCreate attribute) (protea.config.tuning.APILimits attribute) (protea.config.tuning.OperationTuning attribute) (protea.config.tuning.QueueTuning attribute) (protea.config.tuning.TuningSettings attribute) (protea.config.tuning.WorkerTuning attribute) (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataPayload attribute) (protea.core.operations.generate_evaluation_set.GenerateEvaluationSetPayload attribute) (protea.core.operations.insert_proteins.InsertProteinsPayload attribute) (protea.core.operations.load_goa_annotations.LoadGOAAnnotationsPayload attribute) (protea.core.operations.load_interpro_go_mapping.LoadInterProGoMappingPayload attribute) (protea.core.operations.load_ontology_snapshot.LoadOntologySnapshotPayload attribute) (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsPayload attribute) (protea.core.operations.predict_go_terms_from_interpro.PredictGOTermsFromInterProPayload attribute) (protea.core.operations.run_interproscan_batch.RunInterProScanBatchPayload attribute) (protea.services._scoring_models.RerankerResponse attribute) (protea.services._scoring_models.ScoringConfigCreate attribute) (protea.services._scoring_models.ScoringConfigResponse attribute) model_data (protea.infrastructure.orm.models.embedding.reranker_model.RerankerModel attribute) model_name (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) module protea.api.auth protea.api.bearer protea.api.cache protea.api.deps protea.api.middleware.visitor_counter protea.api.problem_details protea.api.rate_limit protea.api.routers.admin protea.api.routers.annotate protea.api.routers.annotations.evaluation_results protea.api.routers.auth_api_keys protea.api.routers.benchmark protea.api.routers.datasets protea.api.routers.embeddings protea.api.routers.experiment_runs protea.api.routers.jobs protea.api.routers.maintenance protea.api.routers.metrics protea.api.routers.proteins protea.api.routers.query_sets protea.api.routers.registry protea.api.routers.reranker_models protea.api.routers.showcase protea.api.routers.stack protea.api.routers.support protea.api.stages protea.config.tuning protea.core._feature_enricher_helpers protea.core._pair_feature_compute protea.core._training_dump_loaders protea.core.annotation_intern protea.core.axis_tuple protea.core.contracts.operation protea.core.contracts.parent_progress protea.core.contracts.registry protea.core.disk_cache protea.core.domain.aspect protea.core.evaluation protea.core.evidence_codes protea.core.feature_engineering protea.core.features._bindings protea.core.features.registry protea.core.jsonb_dual_write protea.core.metrics protea.core.operations._load_ontology_helpers protea.core.operations._run_cafa_data_helpers protea.core.operations._run_cafa_setup protea.core.operations._run_cafa_summary protea.core.operations.fetch_uniprot_metadata protea.core.operations.generate_evaluation_set protea.core.operations.insert_proteins protea.core.operations.load_goa_annotations protea.core.operations.load_interpro_go_mapping protea.core.operations.load_ontology_snapshot protea.core.operations.load_quickgo_annotations protea.core.operations.ping protea.core.operations.predict_go_terms_from_interpro protea.core.operations.run_interproscan_batch protea.core.plugins protea.core.retry protea.core.runners protea.core.schema_sha_v2 protea.core.scoring protea.core.utils protea.infrastructure.benchmark_config protea.infrastructure.database.engine protea.infrastructure.logging protea.infrastructure.orm.base protea.infrastructure.orm.models.annotation.annotation_set protea.infrastructure.orm.models.annotation.evaluation_result protea.infrastructure.orm.models.annotation.evaluation_set protea.infrastructure.orm.models.annotation.go_term protea.infrastructure.orm.models.annotation.go_term_relationship protea.infrastructure.orm.models.annotation.interpro_annotation protea.infrastructure.orm.models.annotation.interpro_go_mapping protea.infrastructure.orm.models.annotation.ontology_snapshot protea.infrastructure.orm.models.annotation.protein_go_annotation protea.infrastructure.orm.models.api_key protea.infrastructure.orm.models.embedding.dataset protea.infrastructure.orm.models.embedding.embedding_config protea.infrastructure.orm.models.embedding.go_prediction protea.infrastructure.orm.models.embedding.go_prediction_features protea.infrastructure.orm.models.embedding.prediction_set protea.infrastructure.orm.models.embedding.reranker_model protea.infrastructure.orm.models.embedding.scoring_config protea.infrastructure.orm.models.embedding.sequence_embedding protea.infrastructure.orm.models.experiment_run protea.infrastructure.orm.models.job protea.infrastructure.orm.models.protein.protein protea.infrastructure.orm.models.protein.protein_metadata protea.infrastructure.orm.models.query.query_set protea.infrastructure.orm.models.sequence.sequence protea.infrastructure.orm.models.support_entry protea.infrastructure.orm.models.visitor_event protea.infrastructure.queue.consumer protea.infrastructure.queue.publisher protea.infrastructure.session protea.infrastructure.settings protea.infrastructure.storage protea.infrastructure.storage.factory protea.infrastructure.storage.local protea.infrastructure.storage.minio_store protea.infrastructure.telemetry protea.services._annotations_evaluation_helpers protea.services._annotations_method_helpers protea.services._annotations_streaming_helpers protea.services._embeddings_admin_helpers protea.services._embeddings_cafa_helpers protea.services._embeddings_predictions_helpers protea.services._embeddings_proteins_helpers protea.services._embeddings_validation_helpers protea.services._scoring_models protea.services._scoring_prediction_metrics_helpers protea.services._scoring_streaming_helpers protea.services._scoring_training_helpers protea.services._scoring_validation_helpers protea.services.annotations_service protea.services.jobs_service protea.workers.base_worker protea.workers.shutdown protea.workers.stale_job_reaper module (protea.api.routers.registry.PluginInfo attribute) MOLECULAR_FUNCTION (protea.core.domain.aspect.Aspect attribute) must_be_non_empty() (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataPayload class method) (protea.core.operations.generate_evaluation_set.GenerateEvaluationSetPayload class method) (protea.core.operations.insert_proteins.InsertProteinsPayload class method) (protea.core.operations.load_goa_annotations.LoadGOAAnnotationsPayload class method) (protea.core.operations.load_ontology_snapshot.LoadOntologySnapshotPayload class method) (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsPayload class method) (protea.core.operations.run_interproscan_batch.RunInterProScanBatchPayload class method) must_be_non_empty_list() (protea.core.operations.run_interproscan_batch.RunInterProScanBatchPayload class method) N n_eval_rows (protea.api.routers.datasets.ImportDatasetByReferenceRequest attribute) (protea.infrastructure.orm.models.embedding.dataset.Dataset attribute) n_ground_truth_proteins (protea.core.metrics.CAFAMetrics attribute) n_predicted_proteins (protea.core.metrics.CAFAMetrics attribute) n_predictions (protea.core.metrics.CAFAMetrics attribute) n_train_rows (protea.api.routers.datasets.ImportDatasetByReferenceRequest attribute) (protea.infrastructure.orm.models.embedding.dataset.Dataset attribute) name (protea.api.routers.auth_api_keys.CreateApiKeyRequest attribute) (protea.api.routers.datasets.ImportDatasetByReferenceRequest attribute) (protea.api.routers.experiment_runs.CreateExperimentRunRequest attribute) (protea.api.routers.registry.PluginInfo attribute) (protea.api.routers.reranker_models.ImportRerankerByReferenceRequest attribute) (protea.api.routers.stack.RepoEntry attribute) (protea.core.contracts.operation.Operation attribute) (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataOperation attribute) (protea.core.operations.generate_evaluation_set.GenerateEvaluationSetOperation attribute) (protea.core.operations.insert_proteins.InsertProteinsOperation attribute) (protea.core.operations.load_goa_annotations.LoadGOAAnnotationsOperation attribute) (protea.core.operations.load_interpro_go_mapping.LoadInterProGoMappingOperation attribute) (protea.core.operations.load_ontology_snapshot.LoadOntologySnapshotOperation attribute) (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsOperation attribute) (protea.core.operations.ping.PingOperation attribute) (protea.core.operations.predict_go_terms_from_interpro.PredictGOTermsFromInterProOperation attribute) (protea.core.operations.run_interproscan_batch.RunInterProScanBatchOperation attribute) (protea.infrastructure.orm.models.annotation.go_term.GOTerm attribute) (protea.infrastructure.orm.models.api_key.ApiKey attribute) (protea.infrastructure.orm.models.embedding.dataset.Dataset attribute) (protea.infrastructure.orm.models.embedding.reranker_model.RerankerModel attribute) (protea.infrastructure.orm.models.embedding.scoring_config.ScoringConfig attribute) (protea.infrastructure.orm.models.experiment_run.ExperimentRun attribute) (protea.infrastructure.orm.models.query.query_set.QuerySet attribute) (protea.services._scoring_models.RerankerResponse attribute) (protea.services._scoring_models.ScoringConfigCreate attribute) (protea.services._scoring_models.ScoringConfigResponse attribute) names() (protea.core.features.registry.CanonicalFeatureRegistry method) neighbor_distance_std (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) neighbor_mean_distance (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) neighbor_min_distance (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) neighbor_vote_fraction (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) NetGO new_annotation_set (protea.infrastructure.orm.models.annotation.evaluation_set.EvaluationSet attribute) new_annotation_set_id (protea.core.evaluation.EvalContext attribute) (protea.core.operations.generate_evaluation_set.GenerateEvaluationSetPayload attribute) (protea.infrastructure.orm.models.annotation.evaluation_set.EvaluationSet attribute) ngrok tunnel NK nk (protea.core.evaluation.EvaluationData attribute) nk_annotations (protea.core.evaluation.EvaluationData property) nk_proteins (protea.core.evaluation.EvaluationData property) normalize (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) normalize() (in module protea.core.evidence_codes) normalize_residues (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) number (protea.api.routers.stack.PullRequest attribute) numpy_query_chunk (protea.config.tuning.OperationTuning attribute) O OBO obo_url (protea.core.operations.load_ontology_snapshot.LoadOntologySnapshotPayload attribute) (protea.infrastructure.orm.models.annotation.ontology_snapshot.OntologySnapshot attribute) obo_version (protea.infrastructure.orm.models.annotation.ontology_snapshot.OntologySnapshot attribute) old_annotation_set (protea.infrastructure.orm.models.annotation.evaluation_set.EvaluationSet attribute) old_annotation_set_id (protea.core.evaluation.EvalContext attribute) (protea.core.operations.generate_evaluation_set.GenerateEvaluationSetPayload attribute) (protea.infrastructure.orm.models.annotation.evaluation_set.EvaluationSet attribute) on_retry (protea.core.retry.RetryPolicy attribute) ontology_snapshot (protea.infrastructure.orm.models.annotation.annotation_set.AnnotationSet attribute) (protea.infrastructure.orm.models.annotation.go_term.GOTerm attribute) (protea.infrastructure.orm.models.annotation.go_term_relationship.GOTermRelationship attribute) (protea.infrastructure.orm.models.embedding.prediction_set.PredictionSet attribute) ontology_snapshot_id (protea.api.routers.datasets.CreateDatasetRequest attribute) (protea.api.routers.datasets.ImportDatasetByReferenceRequest attribute) (protea.core.evaluation.EvalContext attribute) (protea.core.operations.load_goa_annotations.LoadGOAAnnotationsPayload attribute) (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsPayload attribute) (protea.core.operations.predict_go_terms_from_interpro.PredictGOTermsFromInterProPayload attribute) (protea.infrastructure.orm.models.annotation.annotation_set.AnnotationSet attribute) (protea.infrastructure.orm.models.annotation.go_term.GOTerm attribute) (protea.infrastructure.orm.models.annotation.go_term_relationship.GOTermRelationship attribute) (protea.infrastructure.orm.models.embedding.dataset.Dataset attribute) (protea.infrastructure.orm.models.embedding.prediction_set.PredictionSet attribute) (protea.infrastructure.orm.models.embedding.reranker_model.RerankerModel attribute) OntologySnapshot (class in protea.infrastructure.orm.models.annotation.ontology_snapshot) OOM oom_base_delay (protea.config.tuning.QueueTuning attribute) oom_max_delay (protea.config.tuning.QueueTuning attribute) oom_max_retries (protea.config.tuning.QueueTuning attribute) Operation (class in protea.core.contracts.operation) operation (protea.api.routers.admin.DlqPurgeRequest attribute) (protea.api.routers.admin.DlqReplayRequest attribute) (protea.api.routers.jobs.CreateJobRequest attribute) (protea.api.routers.jobs.JobListFilters attribute) (protea.config.tuning.TuningSettings attribute) (protea.infrastructure.orm.models.embedding.dataset.Dataset attribute) (protea.infrastructure.orm.models.job.Job attribute) OperationConsumer (class in protea.infrastructure.queue.consumer) OperationRegistry (class in protea.core.contracts.registry) OperationResult (class in protea.core.contracts.operation) OperationTuning (class in protea.config.tuning) organism (protea.infrastructure.orm.models.protein.protein.Protein attribute) ORM OTel OTLPSpanExporter (protea.infrastructure.telemetry.SdkBundle attribute) output_name (protea.api.routers.datasets.CreateDatasetRequest attribute) P package_url (protea.api.routers.stack.RepoEntry attribute) page_limit (protea.config.tuning.APILimits attribute) page_size (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataPayload attribute) (protea.core.operations.insert_proteins.InsertProteinsPayload attribute) (protea.core.operations.load_goa_annotations.LoadGOAAnnotationsPayload attribute) (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsPayload attribute) PairAlignmentComputer (class in protea.core._pair_feature_compute) param_count (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) Parameter Object parent (protea.infrastructure.orm.models.annotation.go_term_relationship.GOTermRelationship attribute) parent_go_term_id (protea.infrastructure.orm.models.annotation.go_term_relationship.GOTermRelationship attribute) parent_job_id (protea.api.routers.jobs.JobListFilters attribute) (protea.infrastructure.orm.models.job.Job attribute) ParentBased (protea.infrastructure.telemetry.SdkBundle attribute) parse_isoform() (protea.infrastructure.orm.models.protein.protein.Protein static method) path (protea.infrastructure.orm.models.visitor_event.VisitorEvent attribute) pathway (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) payload (protea.api.routers.jobs.CreateJobRequest attribute) (protea.infrastructure.orm.models.job.Job attribute) pgvector ph_dependence (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) PingOperation (class in protea.core.operations.ping) pivot_ontology_snapshot_id (protea.core.operations.generate_evaluation_set.GenerateEvaluationSetPayload attribute) pivot_opt_non_empty() (protea.core.operations.generate_evaluation_set.GenerateEvaluationSetPayload class method) PK pk (protea.core.evaluation.EvaluationData attribute) pk_annotations (protea.core.evaluation.EvaluationData property) pk_known (protea.core.evaluation.EvaluationData attribute) pk_proteins (protea.core.evaluation.EvaluationData property) PLANNED (protea.infrastructure.orm.models.experiment_run.ExperimentRunStatus attribute) PLM plm (protea.infrastructure.orm.models.experiment_run.ExperimentRun attribute) plugin registry dispatch PluginInfo (class in protea.api.routers.registry) PluginListResponse (class in protea.api.routers.registry) plugins (protea.api.routers.registry.PluginListResponse attribute) pool_size() (in module protea.core.annotation_intern) pooling (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) post_support() (in module protea.api.routers.support) precision (protea.core.metrics.PRPoint attribute) precompute_alignment_features() (in module protea.core._pair_feature_compute) predicate() (protea.core.retry.RetryPolicy method) predict_go_terms() (in module protea.api.routers.embeddings) PredictGOTermsFromInterProOperation (class in protea.core.operations.predict_go_terms_from_interpro) PredictGOTermsFromInterProPayload (class in protea.core.operations.predict_go_terms_from_interpro) prediction_set (protea.infrastructure.orm.models.annotation.evaluation_result.EvaluationResult attribute) (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) prediction_set_id (protea.api.routers.reranker_models.ImportRerankerByReferenceRequest attribute) (protea.infrastructure.orm.models.annotation.evaluation_result.EvaluationResult attribute) (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) (protea.infrastructure.orm.models.embedding.reranker_model.RerankerModel attribute) (protea.services._scoring_models.RerankerResponse attribute) predictions (protea.infrastructure.orm.models.embedding.prediction_set.PredictionSet attribute) predictions_batch_seconds (protea.infrastructure.telemetry.MetricRegistry attribute) predictions_jsonb (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) PredictionSet (class in protea.infrastructure.orm.models.embedding.prediction_set) preferred_default_stages (protea.infrastructure.benchmark_config.BenchmarkConfig attribute) prefetch_count (protea.infrastructure.queue.consumer.ConsumerOptions attribute) prefix (protea.infrastructure.orm.models.api_key.ApiKey attribute) prefix_of() (in module protea.api.auth) prepare_cafa_export() (in module protea.services._embeddings_cafa_helpers) present (protea.core._feature_enricher_helpers.LabelConfig attribute) PRESET_CONFIGS (in module protea.services._scoring_models) preview_orphan_sequences() (in module protea.api.routers.maintenance) preview_unindexed_embeddings() (in module protea.api.routers.maintenance) prewarm_benchmark_embeddings() (in module protea.api.routers.benchmark) prewarm_benchmark_matrix() (in module protea.api.routers.benchmark) prewarm_embedding_configs() (in module protea.api.routers.embeddings) prewarm_prediction_sets() (in module protea.api.routers.embeddings) prewarm_protein_stats() (in module protea.api.routers.proteins) ProblemDetail (class in protea.api.problem_details) producer_git_sha (protea.api.routers.datasets.ImportDatasetByReferenceRequest attribute) (protea.infrastructure.orm.models.embedding.dataset.Dataset attribute) (protea.infrastructure.orm.models.embedding.reranker_model.RerankerModel attribute) (protea.services._scoring_models.RerankerResponse attribute) producer_version (protea.api.routers.datasets.ImportDatasetByReferenceRequest attribute) (protea.infrastructure.orm.models.embedding.dataset.Dataset attribute) (protea.infrastructure.orm.models.embedding.reranker_model.RerankerModel attribute) (protea.services._scoring_models.RerankerResponse attribute) progress_current (protea.core.contracts.operation.OperationResult attribute) (protea.infrastructure.orm.models.job.Job attribute) progress_total (protea.core.contracts.operation.OperationResult attribute) (protea.infrastructure.orm.models.job.Job attribute) propagate_ground_truth_to_ancestors() (in module protea.core.scoring) propagate_scores_to_ancestors() (in module protea.core.scoring) propagation (protea.infrastructure.orm.models.experiment_run.ExperimentRun attribute) ProstT5 PROTEA protea.api.auth module protea.api.bearer module protea.api.cache module protea.api.deps module protea.api.middleware.visitor_counter module protea.api.problem_details module protea.api.rate_limit module protea.api.routers.admin module protea.api.routers.annotate module protea.api.routers.annotations.evaluation_results module protea.api.routers.auth_api_keys module protea.api.routers.benchmark module protea.api.routers.datasets module protea.api.routers.embeddings module protea.api.routers.experiment_runs module protea.api.routers.jobs module protea.api.routers.maintenance module protea.api.routers.metrics module protea.api.routers.proteins module protea.api.routers.query_sets module protea.api.routers.registry module protea.api.routers.reranker_models module protea.api.routers.showcase module protea.api.routers.stack module protea.api.routers.support module protea.api.stages module protea.config.tuning module protea.core._feature_enricher_helpers module protea.core._pair_feature_compute module protea.core._training_dump_loaders module protea.core.annotation_intern module protea.core.axis_tuple module protea.core.contracts.operation module protea.core.contracts.parent_progress module protea.core.contracts.registry module protea.core.disk_cache module protea.core.domain.aspect module protea.core.evaluation module protea.core.evidence_codes module protea.core.feature_engineering module protea.core.features._bindings module protea.core.features.registry module protea.core.jsonb_dual_write module protea.core.metrics module protea.core.operations._load_ontology_helpers module protea.core.operations._run_cafa_data_helpers module protea.core.operations._run_cafa_setup module protea.core.operations._run_cafa_summary module protea.core.operations.fetch_uniprot_metadata module protea.core.operations.generate_evaluation_set module protea.core.operations.insert_proteins module protea.core.operations.load_goa_annotations module protea.core.operations.load_interpro_go_mapping module protea.core.operations.load_ontology_snapshot module protea.core.operations.load_quickgo_annotations module protea.core.operations.ping module protea.core.operations.predict_go_terms_from_interpro module protea.core.operations.run_interproscan_batch module protea.core.plugins module protea.core.retry module protea.core.runners module protea.core.schema_sha_v2 module protea.core.scoring module protea.core.utils module protea.infrastructure.benchmark_config module protea.infrastructure.database.engine module protea.infrastructure.logging module protea.infrastructure.orm.base module protea.infrastructure.orm.models.annotation.annotation_set module protea.infrastructure.orm.models.annotation.evaluation_result module protea.infrastructure.orm.models.annotation.evaluation_set module protea.infrastructure.orm.models.annotation.go_term module protea.infrastructure.orm.models.annotation.go_term_relationship module protea.infrastructure.orm.models.annotation.interpro_annotation module protea.infrastructure.orm.models.annotation.interpro_go_mapping module protea.infrastructure.orm.models.annotation.ontology_snapshot module protea.infrastructure.orm.models.annotation.protein_go_annotation module protea.infrastructure.orm.models.api_key module protea.infrastructure.orm.models.embedding.dataset module protea.infrastructure.orm.models.embedding.embedding_config module protea.infrastructure.orm.models.embedding.go_prediction module protea.infrastructure.orm.models.embedding.go_prediction_features module protea.infrastructure.orm.models.embedding.prediction_set module protea.infrastructure.orm.models.embedding.reranker_model module protea.infrastructure.orm.models.embedding.scoring_config module protea.infrastructure.orm.models.embedding.sequence_embedding module protea.infrastructure.orm.models.experiment_run module protea.infrastructure.orm.models.job module protea.infrastructure.orm.models.protein.protein module protea.infrastructure.orm.models.protein.protein_metadata module protea.infrastructure.orm.models.query.query_set module protea.infrastructure.orm.models.sequence.sequence module protea.infrastructure.orm.models.support_entry module protea.infrastructure.orm.models.visitor_event module protea.infrastructure.queue.consumer module protea.infrastructure.queue.publisher module protea.infrastructure.session module protea.infrastructure.settings module protea.infrastructure.storage module protea.infrastructure.storage.factory module protea.infrastructure.storage.local module protea.infrastructure.storage.minio_store module protea.infrastructure.telemetry module protea.services._annotations_evaluation_helpers module protea.services._annotations_method_helpers module protea.services._annotations_streaming_helpers module protea.services._embeddings_admin_helpers module protea.services._embeddings_cafa_helpers module protea.services._embeddings_predictions_helpers module protea.services._embeddings_proteins_helpers module protea.services._embeddings_validation_helpers module protea.services._scoring_models module protea.services._scoring_prediction_metrics_helpers module protea.services._scoring_streaming_helpers module protea.services._scoring_training_helpers module protea.services._scoring_validation_helpers module protea.services.annotations_service module protea.services.jobs_service module protea.workers.base_worker module protea.workers.shutdown module protea.workers.stale_job_reaper module Protein (class in protea.infrastructure.orm.models.protein.protein) protein (protea.infrastructure.orm.models.annotation.interpro_annotation.InterProAnnotation attribute) (protea.infrastructure.orm.models.annotation.protein_go_annotation.ProteinGOAnnotation attribute) protein_accession (protea.infrastructure.orm.models.annotation.interpro_annotation.InterProAnnotation attribute) (protea.infrastructure.orm.models.annotation.protein_go_annotation.ProteinGOAnnotation attribute) (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) ProteinGOAnnotation (class in protea.infrastructure.orm.models.annotation.protein_go_annotation) proteins (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) (protea.infrastructure.orm.models.sequence.sequence.Sequence attribute) ProteinUniProtMetadata (class in protea.infrastructure.orm.models.protein.protein_metadata) ProtT5 provenance (protea.api.routers.experiment_runs.CreateExperimentRunRequest attribute) (protea.api.routers.experiment_runs.UpdateExperimentRunRequest attribute) (protea.infrastructure.orm.models.experiment_run.ExperimentRun attribute) PRPoint (class in protea.core.metrics) publish_after_commit (protea.core.contracts.operation.OperationResult attribute) publish_job() (in module protea.infrastructure.queue.publisher) publish_operation() (in module protea.infrastructure.queue.publisher) publish_operations (protea.core.contracts.operation.OperationResult attribute) publisher_base_delay (protea.config.tuning.QueueTuning attribute) publisher_max_attempts (protea.config.tuning.QueueTuning attribute) PullRequest (class in protea.api.routers.stack) pulls (protea.api.routers.stack.PullsResponse attribute) PullsResponse (class in protea.api.routers.stack) purge_dlq() (in module protea.api.routers.admin) put() (protea.infrastructure.storage.ArtifactStore method) (protea.infrastructure.storage.local.LocalFsArtifactStore method) (protea.infrastructure.storage.LocalFsArtifactStore method) (protea.infrastructure.storage.minio_store.MinioArtifactStore method) Q q_acc (protea.core._feature_enricher_helpers.LabelConfig attribute) qualifier (protea.infrastructure.orm.models.annotation.protein_go_annotation.ProteinGOAnnotation attribute) (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) query_accessions (protea.core.operations.predict_go_terms_from_interpro.PredictGOTermsFromInterProPayload attribute) query_set (protea.infrastructure.orm.models.embedding.prediction_set.PredictionSet attribute) (protea.infrastructure.orm.models.query.query_set.QuerySetEntry attribute) query_set_id (protea.core.operations.predict_go_terms_from_interpro.PredictGOTermsFromInterProPayload attribute) (protea.core.operations.run_interproscan_batch.RunInterProScanBatchPayload attribute) (protea.infrastructure.orm.models.embedding.prediction_set.PredictionSet attribute) (protea.infrastructure.orm.models.query.query_set.QuerySetEntry attribute) query_taxonomy_id (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) QuerySet (class in protea.infrastructure.orm.models.query.query_set) QuerySetEntry (class in protea.infrastructure.orm.models.query.query_set) queue (protea.config.tuning.TuningSettings attribute) queue_name (protea.api.routers.jobs.CreateJobRequest attribute) (protea.infrastructure.orm.models.job.Job attribute) QueueConsumer (class in protea.infrastructure.queue.consumer) QUEUED (protea.infrastructure.orm.models.job.JobStatus attribute) QueueTuning (class in protea.config.tuning) quickgo_base_url (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsPayload attribute) R RabbitMQ rate_limit_remaining (protea.api.routers.stack.PullsResponse attribute) reaper_default_timeout_seconds (protea.config.tuning.WorkerTuning attribute) reaper_main_timeout_seconds (protea.config.tuning.WorkerTuning attribute) reaper_stall_seconds (protea.config.tuning.WorkerTuning attribute) recall (protea.core.metrics.PRPoint attribute) recent_limit (protea.config.tuning.APILimits attribute) Redis redox_potential (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) ref_annotation_density (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) ref_cache_freshness_seconds (protea.config.tuning.OperationTuning attribute) ref_cache_max (protea.config.tuning.WorkerTuning attribute) ref_protein_accession (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) ref_taxonomy_id (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) refresh_db_pool_gauge() (in module protea.infrastructure.telemetry) register() (protea.core.contracts.registry.OperationRegistry method) (protea.core.features.registry.CanonicalFeatureRegistry method) register_problem_handlers() (in module protea.api.problem_details) REGISTRY (in module protea.core.features.registry) registry (protea.infrastructure.orm.base.Base attribute) (protea.infrastructure.telemetry.MetricRegistry attribute) relation_type (protea.infrastructure.orm.models.annotation.go_term_relationship.GOTermRelationship attribute) release-please render_evaluation_metrics_tsv() (in module protea.services._annotations_streaming_helpers) (in module protea.services.annotations_service) render_metrics() (in module protea.infrastructure.telemetry) replay_dlq() (in module protea.api.routers.admin) repo (protea.api.routers.stack.PullRequest attribute) RepoEntry (class in protea.api.routers.stack) repos (protea.api.routers.stack.StackResponse attribute) repos_queried (protea.api.routers.stack.PullsResponse attribute) requeue_on_failure (protea.infrastructure.queue.consumer.ConsumerOptions attribute) requeue_on_shutdown() (protea.workers.base_worker.BaseWorker method) require_api_key() (in module protea.api.auth) require_api_key_or_bearer() (in module protea.api.auth) require_bearer() (in module protea.api.bearer) reranker_cache reranker_config (protea.infrastructure.orm.models.annotation.evaluation_result.EvaluationResult attribute) reranker_model (protea.infrastructure.orm.models.annotation.evaluation_result.EvaluationResult attribute) reranker_model_id (protea.infrastructure.orm.models.annotation.evaluation_result.EvaluationResult attribute) reranker_spec_id (protea.infrastructure.orm.models.experiment_run.ExperimentRun attribute) RerankerModel (class in protea.infrastructure.orm.models.embedding.reranker_model) RerankerResponse (class in protea.services._scoring_models) reset_canonical_registry() (in module protea.core.features.registry) reset_db() (in module protea.api.routers.admin) reset_plugin_cache() (in module protea.core.plugins) resolve_runner() (in module protea.core.runners) resolve_telemetry_config() (in module protea.infrastructure.telemetry) resolve_workers() (in module protea.core._pair_feature_compute) Resource (protea.infrastructure.telemetry.SdkBundle attribute) restrict_data_to_predicted() (in module protea.core.operations._run_cafa_data_helpers) result (protea.core.contracts.operation.OperationResult attribute) results (protea.infrastructure.orm.models.annotation.evaluation_result.EvaluationResult attribute) RetryLaterError, [1] RetryPolicy (class in protea.core.retry) reviewed (protea.infrastructure.orm.models.protein.protein.Protein attribute) revoke_api_key() (in module protea.api.routers.auth_api_keys) revoked_at (protea.infrastructure.orm.models.api_key.ApiKey attribute) rhea_id (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) role (protea.api.routers.stack.RepoEntry attribute) (protea.infrastructure.orm.models.api_key.ApiKey attribute) role_label (protea.api.routers.stack.RepoEntry attribute) run (protea.api.routers.reranker_models.ImportRerankerByReferenceRequest attribute) run() (protea.infrastructure.queue.consumer.OperationConsumer method) (protea.infrastructure.queue.consumer.QueueConsumer method) (protea.workers.stale_job_reaper.StaleJobReaper method) RunInterProScanBatchOperation (class in protea.core.operations.run_interproscan_batch) RunInterProScanBatchPayload (class in protea.core.operations.run_interproscan_batch) RUNNING (protea.infrastructure.orm.models.experiment_run.ExperimentRunStatus attribute) (protea.infrastructure.orm.models.job.JobStatus attribute) S safe_republish_job() (in module protea.infrastructure.queue.publisher) sample_ratio (protea.infrastructure.telemetry.TelemetryConfig attribute) schema_sha (protea.api.routers.datasets.ImportDatasetByReferenceRequest attribute) (protea.infrastructure.orm.models.embedding.dataset.Dataset attribute) schema_sha_v2 (protea.infrastructure.orm.models.embedding.dataset.Dataset attribute) (protea.infrastructure.orm.models.embedding.reranker_model.RerankerModel attribute) (protea.infrastructure.orm.models.experiment_run.ExperimentRun attribute) score_predictions() (in module protea.core.scoring) scoring_config (protea.infrastructure.orm.models.annotation.evaluation_result.EvaluationResult attribute) scoring_config_id (protea.infrastructure.orm.models.annotation.evaluation_result.EvaluationResult attribute) ScoringConfig (class in protea.infrastructure.orm.models.embedding.scoring_config) ScoringConfigCreate (class in protea.services._scoring_models) ScoringConfigResponse (class in protea.services._scoring_models) SdkBundle (class in protea.infrastructure.telemetry) search_backend (protea.api.routers.datasets.CreateDatasetRequest attribute) search_criteria (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataPayload attribute) (protea.core.operations.insert_proteins.InsertProteinsPayload attribute) selected() (protea.core.features.registry.CanonicalFeatureRegistry method) SemVer Sequence (class in protea.infrastructure.orm.models.sequence.sequence) sequence (protea.infrastructure.orm.models.embedding.sequence_embedding.SequenceEmbedding attribute) (protea.infrastructure.orm.models.protein.protein.Protein attribute) (protea.infrastructure.orm.models.query.query_set.QuerySetEntry attribute) (protea.infrastructure.orm.models.sequence.sequence.Sequence attribute) sequence_hash (protea.infrastructure.orm.models.sequence.sequence.Sequence attribute) sequence_id (protea.infrastructure.orm.models.embedding.sequence_embedding.SequenceEmbedding attribute) (protea.infrastructure.orm.models.protein.protein.Protein attribute) (protea.infrastructure.orm.models.query.query_set.QuerySetEntry attribute) SequenceEmbedding (class in protea.infrastructure.orm.models.embedding.sequence_embedding) serialize_evaluation_data_to_parquet() (in module protea.core.evaluation) service_name (protea.infrastructure.telemetry.TelemetryConfig attribute) session_scope() (in module protea.infrastructure.session) set_snapshot_ia_url() (in module protea.services.annotations_service) Settings (class in protea.infrastructure.settings) SHORTID_HEX_LEN (in module protea.core.axis_tuple) ShutdownGuard (class in protea.workers.shutdown) similarity_nw (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) similarity_sw (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) site (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) slug (protea.api.routers.stack.RepoEntry attribute) smell budget Smin smtp_enabled (protea.infrastructure.settings.Settings attribute) smtp_from_addr (protea.infrastructure.settings.Settings attribute) smtp_host (protea.infrastructure.settings.Settings attribute) smtp_password (protea.infrastructure.settings.Settings attribute) smtp_port (protea.infrastructure.settings.Settings attribute) smtp_user (protea.infrastructure.settings.Settings attribute) snapshot_to_dict() (in module protea.services.annotations_service) source (protea.infrastructure.orm.models.annotation.annotation_set.AnnotationSet attribute) source_db (protea.infrastructure.orm.models.annotation.interpro_annotation.InterProAnnotation attribute) source_published_at (protea.infrastructure.orm.models.annotation.annotation_set.AnnotationSet attribute) source_version (protea.core.operations.load_goa_annotations.LoadGOAAnnotationsPayload attribute) (protea.core.operations.load_interpro_go_mapping.LoadInterProGoMappingPayload attribute) (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsPayload attribute) (protea.core.operations.predict_go_terms_from_interpro.PredictGOTermsFromInterProPayload attribute) (protea.infrastructure.orm.models.annotation.annotation_set.AnnotationSet attribute) (protea.infrastructure.orm.models.annotation.interpro_go_mapping.InterProGoMapping attribute) spec_yaml (protea.api.routers.reranker_models.ImportRerankerByReferenceRequest attribute) (protea.infrastructure.orm.models.embedding.reranker_model.RerankerModel attribute) (protea.services._scoring_models.RerankerResponse attribute) species (protea.infrastructure.orm.models.query.query_set.QuerySetEntry attribute) StackResponse (class in protea.api.routers.stack) stage_kind() (in module protea.api.stages) stage_labels (protea.infrastructure.benchmark_config.BenchmarkConfig attribute) stage_of() (in module protea.api.stages) StaleJobReaper (class in protea.workers.stale_job_reaper) start (protea.infrastructure.orm.models.annotation.interpro_annotation.InterProAnnotation attribute) start() (protea.workers.shutdown.HeartbeatLoop method) started_at (protea.infrastructure.orm.models.experiment_run.ExperimentRun attribute) (protea.infrastructure.orm.models.job.Job attribute) state (protea.api.routers.stack.PullRequest attribute) stats (protea.infrastructure.orm.models.annotation.evaluation_set.EvaluationSet attribute) stats() (protea.core.evaluation.EvaluationData method) status (protea.api.problem_details.ProblemDetail attribute) (protea.api.routers.experiment_runs.UpdateExperimentRunRequest attribute) (protea.api.routers.jobs.JobListFilters attribute) (protea.api.routers.stack.RepoEntry attribute) (protea.infrastructure.orm.models.experiment_run.ExperimentRun attribute) (protea.infrastructure.orm.models.job.Job attribute) (protea.infrastructure.orm.models.visitor_event.VisitorEvent attribute) stop() (protea.workers.shutdown.HeartbeatLoop method) storage_backend (protea.api.routers.datasets.ImportDatasetByReferenceRequest attribute) (protea.infrastructure.orm.models.embedding.dataset.Dataset attribute) (protea.infrastructure.settings.Settings attribute) storage_root (protea.infrastructure.settings.Settings attribute) store_chunk_size (protea.config.tuning.OperationTuning attribute) stream_chunk_size (protea.config.tuning.OperationTuning attribute) strip_and_require() (protea.api.routers.jobs.CreateJobRequest class method) strip_body() (protea.api.routers.jobs.CreateJobCommentRequest class method) strip_name() (protea.api.routers.experiment_runs.CreateExperimentRunRequest class method) study_v9 sub (protea.api.bearer.BearerPrincipal attribute) SUCCEEDED (protea.infrastructure.orm.models.job.JobStatus attribute) summarize_payload() (in module protea.core.operations._run_cafa_summary) (protea.core.contracts.operation.Operation method) (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataOperation method) (protea.core.operations.generate_evaluation_set.GenerateEvaluationSetOperation method) (protea.core.operations.insert_proteins.InsertProteinsOperation method) (protea.core.operations.load_goa_annotations.LoadGOAAnnotationsOperation method) (protea.core.operations.load_interpro_go_mapping.LoadInterProGoMappingOperation method) (protea.core.operations.load_ontology_snapshot.LoadOntologySnapshotOperation method) (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsOperation method) (protea.core.operations.ping.PingOperation method) (protea.core.operations.predict_go_terms_from_interpro.PredictGOTermsFromInterProOperation method) (protea.core.operations.run_interproscan_batch.RunInterProScanBatchOperation method) summary (protea.api.routers.stack.RepoEntry attribute) summary() (protea.core.metrics.CAFAMetrics method) SupportCreate (class in protea.api.routers.support) SupportEntry (class in protea.infrastructure.orm.models.support_entry) T t0 t1 tags (protea.api.routers.experiment_runs.CreateExperimentRunRequest attribute) (protea.api.routers.experiment_runs.UpdateExperimentRunRequest attribute) (protea.api.routers.jobs.CreateJobRequest attribute) (protea.infrastructure.orm.models.experiment_run.ExperimentRun attribute) (protea.infrastructure.orm.models.job.Job attribute) target_queue (protea.api.routers.admin.DlqReplayRequest attribute) tax_voters_close_frac (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) tax_voters_mean_common_ancestors (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) tax_voters_same_frac (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) taxonomic_common_ancestors (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) taxonomic_distance (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) taxonomic_lca (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) taxonomic_relation (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) taxonomy_id (protea.infrastructure.orm.models.protein.protein.Protein attribute) (protea.infrastructure.orm.models.query.query_set.QuerySetEntry attribute) TelemetryConfig (class in protea.infrastructure.telemetry) temperature_dependence (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) test_versions (protea.api.routers.datasets.CreateDatasetRequest attribute) thesis_pdf_url (protea.api.routers.stack.StackResponse attribute) threshold (protea.core.metrics.PRPoint attribute) threshold_at_fmax (protea.core.metrics.CAFAMetrics attribute) timeout_seconds (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataPayload attribute) (protea.core.operations.insert_proteins.InsertProteinsPayload attribute) (protea.core.operations.load_goa_annotations.LoadGOAAnnotationsPayload attribute) (protea.core.operations.load_interpro_go_mapping.LoadInterProGoMappingPayload attribute) (protea.core.operations.load_ontology_snapshot.LoadOntologySnapshotPayload attribute) (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsPayload attribute) (protea.core.operations.run_interproscan_batch.RunInterProScanBatchPayload attribute) timer (protea.workers.shutdown.ShutdownGuard property) title (protea.api.problem_details.ProblemDetail attribute) (protea.api.routers.stack.PullRequest attribute) to_reranker_response() (in module protea.services._scoring_models) to_response() (in module protea.services._scoring_models) total_limit (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataPayload attribute) (protea.core.operations.insert_proteins.InsertProteinsPayload attribute) (protea.core.operations.load_goa_annotations.LoadGOAAnnotationsPayload attribute) (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsPayload attribute) TraceIdRatioBased (protea.infrastructure.telemetry.SdkBundle attribute) TracerProvider (protea.infrastructure.telemetry.SdkBundle attribute) track() (protea.workers.shutdown.ShutdownGuard method) train_snapshot_pairs (protea.api.routers.datasets.ImportDatasetByReferenceRequest attribute) (protea.infrastructure.orm.models.embedding.dataset.Dataset attribute) train_uri (protea.api.routers.datasets.ImportDatasetByReferenceRequest attribute) (protea.infrastructure.orm.models.embedding.dataset.Dataset attribute) train_versions (protea.api.routers.datasets.CreateDatasetRequest attribute) ts (protea.infrastructure.orm.models.job.JobEvent attribute) TSV TTFB TuningSettings (class in protea.config.tuning) two-session worker pattern type (protea.api.problem_details.ProblemDetail attribute) U UNIPROT_FIELDS (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataOperation attribute) uniprot_metadata (protea.infrastructure.orm.models.protein.protein.Protein attribute) untrack() (protea.workers.shutdown.ShutdownGuard method) update_experiment_run() (in module protea.api.routers.experiment_runs) update_parent_progress() (in module protea.core.contracts.parent_progress) update_protein_core (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataPayload attribute) update_synth_entry() (in module protea.core._feature_enricher_helpers) updated_at (protea.api.routers.stack.PullRequest attribute) (protea.infrastructure.orm.models.protein.protein.Protein attribute) (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) (protea.infrastructure.orm.models.sequence.sequence.Sequence attribute) UpdateExperimentRunRequest (class in protea.api.routers.experiment_runs) url (protea.api.routers.stack.PullRequest attribute) url() (protea.infrastructure.storage.ArtifactStore method) (protea.infrastructure.storage.local.LocalFsArtifactStore method) (protea.infrastructure.storage.LocalFsArtifactStore method) (protea.infrastructure.storage.minio_store.MinioArtifactStore method) use_chunking (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) use_db_accessions (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsPayload attribute) use_embedding_pca (protea.api.routers.datasets.CreateDatasetRequest attribute) user_agent (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataPayload attribute) (protea.core.operations.insert_proteins.InsertProteinsPayload attribute) user_quota_per_day (protea.infrastructure.settings.Settings attribute) utcnow() (in module protea.core.utils) V vacuum_embeddings() (in module protea.api.routers.maintenance) vacuum_sequences() (in module protea.api.routers.maintenance) validate_embedding_config_body() (in module protea.services._embeddings_validation_helpers) validate_evidence_weights() (protea.services._scoring_models.ScoringConfigCreate class method) validate_formula() (protea.services._scoring_models.ScoringConfigCreate class method) validate_weights() (protea.services._scoring_models.ScoringConfigCreate class method) visitor_hash (protea.infrastructure.orm.models.visitor_event.VisitorEvent attribute) VisitorCounterMiddleware (class in protea.api.middleware.visitor_counter) VisitorEvent (class in protea.infrastructure.orm.models.visitor_event) vote_count (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) W warmup_taxonomy_db() (in module protea.core.feature_engineering) weights (protea.infrastructure.orm.models.embedding.scoring_config.ScoringConfig attribute) (protea.services._scoring_models.ScoringConfigCreate attribute) (protea.services._scoring_models.ScoringConfigResponse attribute) with_from (protea.infrastructure.orm.models.annotation.protein_go_annotation.ProteinGOAnnotation attribute) with_retry() (in module protea.core.retry) worker (protea.config.tuning.TuningSettings attribute) worker_name (protea.workers.base_worker.WorkerConfig attribute) worker_shutdown_grace_seconds (protea.config.tuning.WorkerTuning attribute) WorkerConfig (class in protea.workers.base_worker) WorkerShutdown WorkerTuning (class in protea.config.tuning) write_ground_truth_files() (in module protea.core.operations._run_cafa_data_helpers) write_terms_of_interest() (in module protea.core.operations._run_cafa_data_helpers)