Index

_

__init__() (veupath_chatbot.ai.agents.executor.PathfinderAgent method) (veupath_chatbot.ai.agents.experiment.ExperimentAssistantAgent method) (veupath_chatbot.ai.agents.subtask.SubtaskAgent method) (veupath_chatbot.ai.agents.workbench.WorkbenchAgent method) (veupath_chatbot.ai.engines.mock.MockEngine method) (veupath_chatbot.ai.engines.responses_openai.ResponsesOpenAIEngine method) (veupath_chatbot.ai.models.catalog.ModelEntry method) (veupath_chatbot.ai.orchestration.delegation.DelegationPlan method) (veupath_chatbot.ai.orchestration.subkani.utils.SubKaniRoundResult method) (veupath_chatbot.ai.tools.catalog_rag_tools.CatalogRagTools method) (veupath_chatbot.ai.tools.conversation_tools.ConversationTools method) (veupath_chatbot.ai.tools.example_plans_rag_tools.ExamplePlansRagTools method) (veupath_chatbot.ai.tools.result_tools.ResultTools method) (veupath_chatbot.ai.tools.strategy_tools.graph_ops.CreateStepProtocol method) (veupath_chatbot.ai.tools.strategy_tools.operations.StrategyTools method) (veupath_chatbot.domain.parameters._value_helpers.ProcessedParam method) (veupath_chatbot.domain.parameters.canonicalize.ParameterCanonicalizer method) (veupath_chatbot.domain.parameters.normalize.ParameterNormalizer method) (veupath_chatbot.domain.parameters.specs.ParamSpecNormalized method) (veupath_chatbot.domain.research.citations.Citation method) (veupath_chatbot.domain.strategy.ast.PlanStepNode method) (veupath_chatbot.domain.strategy.ast.StepAnalysis method) (veupath_chatbot.domain.strategy.ast.StepFilter method) (veupath_chatbot.domain.strategy.ast.StepReport method) (veupath_chatbot.domain.strategy.ast.StepTreeNode method) (veupath_chatbot.domain.strategy.ast.StrategyAST method) (veupath_chatbot.domain.strategy.compile.CompilationResult method) (veupath_chatbot.domain.strategy.compile.CompiledStep method) (veupath_chatbot.domain.strategy.compile.StepDecoratorAPI method) (veupath_chatbot.domain.strategy.compile.StrategyCompiler method) (veupath_chatbot.domain.strategy.compile.StrategyCompilerAPI method) (veupath_chatbot.domain.strategy.ops.ColocationParams method) (veupath_chatbot.domain.strategy.session.StrategyGraph method) (veupath_chatbot.domain.strategy.session.StrategySession method) (veupath_chatbot.domain.strategy.validate.StepValidationIssue method) (veupath_chatbot.domain.strategy.validate.StrategyValidator method) (veupath_chatbot.domain.strategy.validate.ValidationResult method) (veupath_chatbot.integrations.embeddings.openai_embeddings.OpenAIEmbeddings method) (veupath_chatbot.integrations.vectorstore.qdrant_store.QdrantStore method) (veupath_chatbot.integrations.veupathdb.client.VEuPathDBClient method) (veupath_chatbot.integrations.veupathdb.discovery.DiscoveryService method) (veupath_chatbot.integrations.veupathdb.discovery.SearchCatalog method) (veupath_chatbot.integrations.veupathdb.factory.DiscoveryService method) (veupath_chatbot.integrations.veupathdb.factory.SiteInfo method) (veupath_chatbot.integrations.veupathdb.site_router.SiteInfo method) (veupath_chatbot.integrations.veupathdb.site_router.SiteRouter method) (veupath_chatbot.integrations.veupathdb.strategy_api.base.StrategyAPIBase method) (veupath_chatbot.integrations.veupathdb.strategy_api.helpers.StepTreeNode method) (veupath_chatbot.persistence.models.Base method) (veupath_chatbot.persistence.models.ControlSet method) (veupath_chatbot.persistence.models.ExperimentRow method) (veupath_chatbot.persistence.models.GeneSetRow method) (veupath_chatbot.persistence.models.Operation method) (veupath_chatbot.persistence.models.Stream method) (veupath_chatbot.persistence.models.StreamProjection method) (veupath_chatbot.persistence.models.User method) (veupath_chatbot.persistence.repositories.control_set.ControlSetRepository method) (veupath_chatbot.persistence.repositories.stream.StreamRepository method) (veupath_chatbot.persistence.repositories.user.UserRepository method) (veupath_chatbot.platform.config.TomlConfigSettingsSource method) (veupath_chatbot.platform.errors.AppError method) (veupath_chatbot.platform.errors.ForbiddenError method) (veupath_chatbot.platform.errors.InternalError method) (veupath_chatbot.platform.errors.NotFoundError method) (veupath_chatbot.platform.errors.UnauthorizedError method) (veupath_chatbot.platform.errors.ValidationError method) (veupath_chatbot.platform.errors.WDKError method) (veupath_chatbot.platform.store.Identifiable method) (veupath_chatbot.platform.store.WriteThruStore method) (veupath_chatbot.services.catalog.rag_search.RagSearchService method) (veupath_chatbot.services.chat.events.EventExtractor method) (veupath_chatbot.services.experiment.ai_analysis_tools.ExperimentAnalysisAgent method) (veupath_chatbot.services.experiment.seed.ControlSetDef method) (veupath_chatbot.services.experiment.seed.SeedDef method) (veupath_chatbot.services.experiment.seed.types.ControlSetDef method) (veupath_chatbot.services.experiment.seed.types.SeedDef method) (veupath_chatbot.services.experiment.types.BatchExperimentConfig method) (veupath_chatbot.services.experiment.types.BatchOrganismTarget method) (veupath_chatbot.services.experiment.types.BootstrapResult method) (veupath_chatbot.services.experiment.types.ConfidenceInterval method) (veupath_chatbot.services.experiment.types.ConfusionMatrix method) (veupath_chatbot.services.experiment.types.CrossValidationResult method) (veupath_chatbot.services.experiment.types.enrichment.EnrichmentResult method) (veupath_chatbot.services.experiment.types.enrichment.EnrichmentTerm method) (veupath_chatbot.services.experiment.types.EnrichmentResult method) (veupath_chatbot.services.experiment.types.EnrichmentTerm method) (veupath_chatbot.services.experiment.types.Experiment method) (veupath_chatbot.services.experiment.types.experiment.BatchExperimentConfig method) (veupath_chatbot.services.experiment.types.experiment.BatchOrganismTarget method) (veupath_chatbot.services.experiment.types.experiment.Experiment method) (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig method) (veupath_chatbot.services.experiment.types.ExperimentConfig method) (veupath_chatbot.services.experiment.types.ExperimentMetrics method) (veupath_chatbot.services.experiment.types.FoldMetrics method) (veupath_chatbot.services.experiment.types.GeneInfo method) (veupath_chatbot.services.experiment.types.metrics.ConfusionMatrix method) (veupath_chatbot.services.experiment.types.metrics.CrossValidationResult method) (veupath_chatbot.services.experiment.types.metrics.ExperimentMetrics method) (veupath_chatbot.services.experiment.types.metrics.FoldMetrics method) (veupath_chatbot.services.experiment.types.metrics.GeneInfo method) (veupath_chatbot.services.experiment.types.NegativeSetVariant method) (veupath_chatbot.services.experiment.types.OperatorComparison method) (veupath_chatbot.services.experiment.types.OperatorKnob method) (veupath_chatbot.services.experiment.types.OperatorVariant method) (veupath_chatbot.services.experiment.types.optimization.OperatorKnob method) (veupath_chatbot.services.experiment.types.optimization.OptimizationSpec method) (veupath_chatbot.services.experiment.types.optimization.ThresholdKnob method) (veupath_chatbot.services.experiment.types.optimization.TreeOptimizationResult method) (veupath_chatbot.services.experiment.types.optimization.TreeOptimizationTrial method) (veupath_chatbot.services.experiment.types.OptimizationSpec method) (veupath_chatbot.services.experiment.types.ParameterSensitivity method) (veupath_chatbot.services.experiment.types.ParameterSweepPoint method) (veupath_chatbot.services.experiment.types.rank.BootstrapResult method) (veupath_chatbot.services.experiment.types.rank.ConfidenceInterval method) (veupath_chatbot.services.experiment.types.rank.NegativeSetVariant method) (veupath_chatbot.services.experiment.types.rank.RankMetrics method) (veupath_chatbot.services.experiment.types.RankMetrics method) (veupath_chatbot.services.experiment.types.step_analysis.OperatorComparison method) (veupath_chatbot.services.experiment.types.step_analysis.OperatorVariant method) (veupath_chatbot.services.experiment.types.step_analysis.ParameterSensitivity method) (veupath_chatbot.services.experiment.types.step_analysis.ParameterSweepPoint method) (veupath_chatbot.services.experiment.types.step_analysis.StepAnalysisResult method) (veupath_chatbot.services.experiment.types.step_analysis.StepContribution method) (veupath_chatbot.services.experiment.types.step_analysis.StepEvaluation method) (veupath_chatbot.services.experiment.types.StepAnalysisResult method) (veupath_chatbot.services.experiment.types.StepContribution method) (veupath_chatbot.services.experiment.types.StepEvaluation method) (veupath_chatbot.services.experiment.types.ThresholdKnob method) (veupath_chatbot.services.experiment.types.TreeOptimizationResult method) (veupath_chatbot.services.experiment.types.TreeOptimizationTrial method) (veupath_chatbot.services.export.service.ExportResult method) (veupath_chatbot.services.export.service.ExportService method) (veupath_chatbot.services.gene_lookup.wdk.WdkTextResult method) (veupath_chatbot.services.gene_sets.confidence.GeneConfidenceScore method) (veupath_chatbot.services.gene_sets.operations.GeneSetService method) (veupath_chatbot.services.gene_sets.reverse_search.GeneSetCandidate method) (veupath_chatbot.services.gene_sets.reverse_search.RankedResult method) (veupath_chatbot.services.gene_sets.types.GeneSet method) (veupath_chatbot.services.parameter_optimization.OptimizationConfig method) (veupath_chatbot.services.parameter_optimization.OptimizationResult method) (veupath_chatbot.services.parameter_optimization.ParameterSpec method) (veupath_chatbot.services.parameter_optimization.TrialResult method) (veupath_chatbot.services.parameter_optimization.trials.TrialMetrics method) (veupath_chatbot.services.research.clients._base.BaseClient method) (veupath_chatbot.services.research.literature_search.LiteratureSearchService method) (veupath_chatbot.services.research.web_search.WebSearchService method) (veupath_chatbot.services.search_rerank.QueryIntent method) (veupath_chatbot.services.search_rerank.ScoredResult method) (veupath_chatbot.services.strategies.build.BuildResult method) (veupath_chatbot.services.strategies.build.RootResolutionError method) (veupath_chatbot.services.strategies.build.SiteInfoLike method) (veupath_chatbot.services.strategies.build.StepCountResult method) (veupath_chatbot.services.strategies.engine.base.StrategyToolsBase method) (veupath_chatbot.services.strategies.engine.graph_integrity.GraphIntegrityError method) (veupath_chatbot.services.strategies.step_creation.StepCreationResult method) (veupath_chatbot.services.wdk.step_results.StepResultsService method)

A

ablated_fpr (veupath_chatbot.services.experiment.types.step_analysis.StepContribution attribute) (veupath_chatbot.services.experiment.types.StepContribution attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepContributionResponse attribute) ablated_recall (veupath_chatbot.services.experiment.types.step_analysis.StepContribution attribute) (veupath_chatbot.services.experiment.types.StepContribution attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepContributionResponse attribute) accessed_at (veupath_chatbot.domain.research.citations.Citation attribute) (veupath_chatbot.transport.http.schemas.chat.CitationResponse attribute) action (veupath_chatbot.transport.http.schemas.experiments.RefineRequest attribute) adapt_param_specs() (in module veupath_chatbot.domain.parameters.specs) add_graph() (veupath_chatbot.domain.strategy.session.StrategySession method) add_request_id() (in module veupath_chatbot.platform.logging) add_step() (veupath_chatbot.domain.strategy.session.StrategyGraph method) add_step_analysis() (veupath_chatbot.ai.tools.strategy_tools.attachment_ops.StrategyAttachmentOps method) add_step_filter() (veupath_chatbot.ai.tools.strategy_tools.attachment_ops.StrategyAttachmentOps method) add_step_report() (veupath_chatbot.ai.tools.strategy_tools.attachment_ops.StrategyAttachmentOps method) adelete() (veupath_chatbot.platform.store.WriteThruStore method) AgentToolRegistryMixin (class in veupath_chatbot.ai.tools.registry) aget() (veupath_chatbot.platform.store.WriteThruStore method) AiAssistRequest (class in veupath_chatbot.transport.http.schemas.experiments) alist_all() (veupath_chatbot.services.experiment.store.ExperimentStore method) (veupath_chatbot.services.gene_sets.store.GeneSetStore method) alist_by_benchmark() (veupath_chatbot.services.experiment.store.ExperimentStore method) alist_for_user() (veupath_chatbot.services.gene_sets.store.GeneSetStore method) all_trials (veupath_chatbot.services.experiment.types.optimization.TreeOptimizationResult attribute) (veupath_chatbot.services.experiment.types.TreeOptimizationResult attribute) (veupath_chatbot.services.parameter_optimization.OptimizationResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OptimizationResultResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.TreeOptimizationResultResponse attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationProgressEventData attribute) allow_empty_value (veupath_chatbot.domain.parameters.specs.ParamSpecNormalized attribute) (veupath_chatbot.transport.http.schemas.sites.ParamSpecResponse attribute) allow_multiple_values (veupath_chatbot.transport.http.schemas.sites.ParamSpecResponse attribute) analyse_query() (in module veupath_chatbot.services.search_rerank) analyses (veupath_chatbot.domain.strategy.ast.PlanStepNode attribute) (veupath_chatbot.transport.http.schemas.plan.BasePlanNode attribute) (veupath_chatbot.transport.http.schemas.steps.StepResponse attribute) analysis (veupath_chatbot.transport.http.schemas.steps.StepAnalysisRunResponse attribute) analysis_name (veupath_chatbot.transport.http.schemas.experiments.RunAnalysisRequest attribute) (veupath_chatbot.transport.http.schemas.gene_sets.RunGeneSetAnalysisRequest attribute) analysis_type (veupath_chatbot.domain.strategy.ast.StepAnalysis attribute) (veupath_chatbot.services.experiment.types.enrichment.EnrichmentResult attribute) (veupath_chatbot.services.experiment.types.EnrichmentResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.EnrichmentResultResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.EnrichmentCompareRequest attribute) (veupath_chatbot.transport.http.schemas.steps.StepAnalysisRequest attribute) (veupath_chatbot.transport.http.schemas.steps.StepAnalysisResponse attribute)

AnalysisMixin (class in veupath_chatbot.integrations.veupathdb.strategy_api.analyses) analysisType (veupath_chatbot.services.experiment.enrichment_compare.EnrichmentRow attribute) (veupath_chatbot.transport.http.schemas.plan.StepAnalysisSpec attribute) analyze_contributions() (in module veupath_chatbot.services.experiment.step_analysis.phase_contribution) annotate_search() (in module veupath_chatbot.services.catalog.searches) anthropic (veupath_chatbot.transport.http.schemas.health.ProviderStatus attribute) anthropic_api_key (veupath_chatbot.platform.config.Settings attribute) anthropic_hyperparams (veupath_chatbot.platform.config.Settings attribute) anthropic_model (veupath_chatbot.platform.config.Settings attribute) anthropic_temperature (veupath_chatbot.platform.config.Settings attribute) anthropic_top_p (veupath_chatbot.platform.config.Settings attribute) api_debug (veupath_chatbot.platform.config.Settings attribute) api_docs_enabled (veupath_chatbot.platform.config.Settings attribute) api_env (veupath_chatbot.platform.config.Settings attribute) api_host (veupath_chatbot.platform.config.Settings attribute) api_key (veupath_chatbot.integrations.vectorstore.qdrant_store.QdrantStore attribute) api_port (veupath_chatbot.platform.config.Settings attribute) api_secret_key (veupath_chatbot.platform.config.Settings attribute) app_error_handler() (in module veupath_chatbot.platform.errors) AppError apply_step_decorations() (in module veupath_chatbot.domain.strategy.compile) arguments (veupath_chatbot.transport.http.schemas.chat.ToolCallResponse attribute) (veupath_chatbot.transport.http.schemas.sse.SubKaniToolCallStartEventData attribute) (veupath_chatbot.transport.http.schemas.sse.ToolCallStartEventData attribute) ArtifactToolsMixin (class in veupath_chatbot.ai.tools.planner.artifact_tools) ArxivClient (class in veupath_chatbot.services.research.clients.arxiv) as_json_array() (in module veupath_chatbot.platform.types) as_json_object() (in module veupath_chatbot.platform.types) assistant_delta (veupath_chatbot.transport.http.routers.internal.SSESchemaIndex attribute) assistant_message (veupath_chatbot.transport.http.routers.internal.SSESchemaIndex attribute) AssistantDeltaEventData (class in veupath_chatbot.transport.http.schemas.sse) AssistantMessageEventData (class in veupath_chatbot.transport.http.schemas.sse) assumptions (veupath_chatbot.transport.http.schemas.chat.PlanningArtifactResponse attribute) async_session_factory() (in module veupath_chatbot.persistence.session) auth_status() (in module veupath_chatbot.transport.http.routers.veupathdb_auth) authors (veupath_chatbot.domain.research.citations.Citation attribute) (veupath_chatbot.transport.http.schemas.chat.CitationResponse attribute) AuthStatusResponse (class in veupath_chatbot.transport.http.schemas.veupathdb_auth) AuthSuccessResponse (class in veupath_chatbot.transport.http.schemas.veupathdb_auth) auto_import_gene_sets() (in module veupath_chatbot.services.strategies.auto_import)

B

background_auto_import_gene_sets() (in module veupath_chatbot.services.strategies.auto_import) background_count (veupath_chatbot.services.experiment.types.enrichment.EnrichmentTerm attribute) (veupath_chatbot.services.experiment.types.EnrichmentTerm attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.EnrichmentTermResponse attribute) background_size (veupath_chatbot.services.experiment.types.enrichment.EnrichmentResult attribute) (veupath_chatbot.services.experiment.types.EnrichmentResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.EnrichmentResultResponse attribute) backgroundSize (veupath_chatbot.services.experiment.custom_enrichment.CustomEnrichmentResult attribute) backoff_delay_seconds() (in module veupath_chatbot.integrations.vectorstore.ingest.public_strategies_helpers) balanced_accuracy (veupath_chatbot.services.experiment.types.ExperimentMetrics attribute) (veupath_chatbot.services.experiment.types.metrics.ExperimentMetrics attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentMetricsResponse attribute) Base (class in veupath_chatbot.persistence.models) base (veupath_chatbot.transport.http.schemas.experiments.CreateBatchExperimentRequest attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateBenchmarkRequest attribute) base_config (veupath_chatbot.services.experiment.types.BatchExperimentConfig attribute) (veupath_chatbot.services.experiment.types.experiment.BatchExperimentConfig attribute) base_url (veupath_chatbot.integrations.embeddings.openai_embeddings.OpenAIEmbeddings attribute) (veupath_chatbot.integrations.veupathdb.site_router.SiteConfig attribute) (veupath_chatbot.transport.http.schemas.sites.SiteResponse attribute) BaseClient (class in veupath_chatbot.services.research.clients._base) baseline_fpr (veupath_chatbot.services.experiment.types.step_analysis.StepContribution attribute) (veupath_chatbot.services.experiment.types.StepContribution attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepContributionResponse attribute) baseline_recall (veupath_chatbot.services.experiment.types.step_analysis.StepContribution attribute) (veupath_chatbot.services.experiment.types.StepContribution attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepContributionResponse attribute) BasePlanNode (class in veupath_chatbot.transport.http.schemas.plan) batch_id (veupath_chatbot.persistence.models.ExperimentRow attribute) (veupath_chatbot.services.experiment.types.Experiment attribute) (veupath_chatbot.services.experiment.types.experiment.Experiment attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentSummaryResponse attribute) batch_size (veupath_chatbot.integrations.embeddings.openai_embeddings.OpenAIEmbeddings attribute) BatchExperimentConfig (class in veupath_chatbot.services.experiment.types) (class in veupath_chatbot.services.experiment.types.experiment) BatchOrganismTarget (class in veupath_chatbot.services.experiment.types) (class in veupath_chatbot.services.experiment.types.experiment) BatchOrganismTargetRequest (class in veupath_chatbot.transport.http.schemas.experiments) benchmark_id (veupath_chatbot.persistence.models.ExperimentRow attribute) (veupath_chatbot.services.experiment.types.Experiment attribute) (veupath_chatbot.services.experiment.types.experiment.Experiment attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentSummaryResponse attribute)

BenchmarkControlSet (class in veupath_chatbot.transport.http.schemas.experiments) best_trial (veupath_chatbot.services.experiment.types.optimization.TreeOptimizationResult attribute) (veupath_chatbot.services.experiment.types.TreeOptimizationResult attribute) (veupath_chatbot.services.parameter_optimization.OptimizationResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OptimizationResultResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.TreeOptimizationResultResponse attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationProgressEventData attribute) beta (veupath_chatbot.services.parameter_optimization.OptimizationConfig attribute) bonferroni (veupath_chatbot.services.experiment.types.enrichment.EnrichmentTerm attribute) (veupath_chatbot.services.experiment.types.EnrichmentTerm attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.EnrichmentTermResponse attribute) bootstrap_result (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) BootstrapResult (class in veupath_chatbot.services.experiment.types) (class in veupath_chatbot.services.experiment.types.rank) BootstrapResultResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) budget (veupath_chatbot.services.parameter_optimization.OptimizationConfig attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationProgressEventData attribute) build_agent_system_prompt() (in module veupath_chatbot.ai.prompts.executor_prompt) build_attribute_list() (in module veupath_chatbot.services.wdk.helpers) build_delegation_plan() (in module veupath_chatbot.ai.orchestration.delegation) build_gene_result() (in module veupath_chatbot.services.gene_lookup.result) build_mention_context() (in module veupath_chatbot.services.chat.mention_context) build_node_from_wdk() (in module veupath_chatbot.services.strategies.wdk_conversion) build_primary_key() (in module veupath_chatbot.services.experiment.ai_analysis_helpers) build_reasoning_hyperparams() (in module veupath_chatbot.ai.models.catalog) build_record_type_doc() (in module veupath_chatbot.integrations.vectorstore.ingest.wdk_transform) build_response() (in module veupath_chatbot.services.research.clients._base) build_search_doc() (in module veupath_chatbot.integrations.vectorstore.ingest.wdk_transform) build_snapshot_from_wdk() (in module veupath_chatbot.services.strategies.wdk_conversion) build_steps_data_from_ast() (in module veupath_chatbot.services.strategies.step_builders) build_strategy() (in module veupath_chatbot.services.strategies.build) build_strategy_for_site() (in module veupath_chatbot.services.strategies.build) build_strategy_session() (in module veupath_chatbot.services.strategies.session_factory) build_subkani_round_prompt() (in module veupath_chatbot.ai.orchestration.subkani.prompts) build_system_prompt() (in module veupath_chatbot.services.experiment.assistant) build_workbench_system_prompt() (in module veupath_chatbot.ai.prompts.workbench_chat) BuildResult (class in veupath_chatbot.services.strategies.build) by_key (veupath_chatbot.transport.http.schemas.sites.SearchValidationErrors attribute)

C

cache_ok (veupath_chatbot.persistence.models.GUID attribute) cached_input_price (veupath_chatbot.ai.models.catalog.ModelEntry attribute) (veupath_chatbot.transport.http.routers.models.ModelCatalogEntryResponse attribute) cached_tokens (veupath_chatbot.transport.http.schemas.chat.TokenUsageResponse attribute) (veupath_chatbot.transport.http.schemas.sse.MessageEndEventData attribute) CachedAnthropicEngine (class in veupath_chatbot.ai.engines.cached_anthropic) calls (veupath_chatbot.transport.http.schemas.chat.SubKaniActivityResponse attribute) cancel() (in module veupath_chatbot.transport.http.routers.operations) cancel_chat_operation() (in module veupath_chatbot.services.chat.orchestrator) cancel_operation() (veupath_chatbot.persistence.repositories.stream.StreamRepository method) cancel_workbench_chat_operation() (in module veupath_chatbot.services.workbench_chat.orchestrator) candidate_queries() (in module veupath_chatbot.services.research.utils) canonicalize() (veupath_chatbot.domain.parameters.canonicalize.ParameterCanonicalizer method) canonicalize_plan_parameters() (in module veupath_chatbot.services.strategies.plan_normalize) captured_negative_ids (veupath_chatbot.services.experiment.types.step_analysis.StepEvaluation attribute) (veupath_chatbot.services.experiment.types.StepEvaluation attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepEvaluationResponse attribute) captured_positive_ids (veupath_chatbot.services.experiment.types.step_analysis.StepEvaluation attribute) (veupath_chatbot.services.experiment.types.StepEvaluation attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepEvaluationResponse attribute) catalog_rag_tools (veupath_chatbot.ai.tools.catalog_registry.CatalogToolsMixin attribute) catalog_tools (veupath_chatbot.ai.tools.catalog_registry.CatalogToolsMixin attribute) CatalogRagTools (class in veupath_chatbot.ai.tools.catalog_rag_tools) CatalogTools (class in veupath_chatbot.ai.tools.catalog_tools) CatalogToolsMixin (class in veupath_chatbot.ai.tools.catalog_registry) chat() (in module veupath_chatbot.transport.http.routers.chat) chat_provider (veupath_chatbot.platform.config.Settings attribute) (veupath_chatbot.transport.http.schemas.health.SystemConfigResponse attribute) ChatMention (class in veupath_chatbot.transport.http.schemas.chat) ChatRequest (class in veupath_chatbot.transport.http.schemas.chat) check_database() (in module veupath_chatbot.platform.health) check_openapi_yaml() (in module veupath_chatbot.devtools.openapi) check_qdrant() (in module veupath_chatbot.platform.health) choices (veupath_chatbot.services.experiment.types.optimization.OptimizationSpec attribute) (veupath_chatbot.services.experiment.types.OptimizationSpec attribute) (veupath_chatbot.services.parameter_optimization.ParameterSpec attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OptimizationSpecResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.OptimizationSpecRequest attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationParameterSpecData attribute) Citation (class in veupath_chatbot.domain.research.citations) citation (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) CitationResponse (class in veupath_chatbot.transport.http.schemas.chat) citations (veupath_chatbot.transport.http.routers.internal.SSESchemaIndex attribute) (veupath_chatbot.transport.http.schemas.chat.MessageResponse attribute) (veupath_chatbot.transport.http.schemas.sse.CitationsEventData attribute) CitationsEventData (class in veupath_chatbot.transport.http.schemas.sse) classification_id_sets() (veupath_chatbot.services.experiment.types.Experiment method) (veupath_chatbot.services.experiment.types.experiment.Experiment method) classification_score (veupath_chatbot.services.gene_sets.confidence.GeneConfidenceScore attribute) (veupath_chatbot.transport.http.schemas.gene_sets.GeneConfidenceScoreResponse attribute) classify_gene() (in module veupath_chatbot.services.experiment.ai_analysis_helpers) classify_records() (in module veupath_chatbot.services.experiment.classification) cleanup_before_sweep() (in module veupath_chatbot.services.experiment.evaluation) cleanup_experiment_strategy() (in module veupath_chatbot.services.experiment.materialization) cleanup_internal_control_test_strategies() (in module veupath_chatbot.services.control_helpers) clear_strategy() (veupath_chatbot.ai.tools.conversation_tools.ConversationTools method) client (veupath_chatbot.domain.strategy.compile.StrategyCompilerAPI property) close() (veupath_chatbot.integrations.vectorstore.qdrant_store.QdrantStore method) (veupath_chatbot.integrations.veupathdb.client.VEuPathDBClient method) close_all() (veupath_chatbot.integrations.veupathdb.site_router.SiteRouter method) close_all_clients() (in module veupath_chatbot.integrations.veupathdb.factory) close_all_qdrant_stores() (in module veupath_chatbot.integrations.vectorstore.qdrant_store) close_db() (in module veupath_chatbot.persistence.session) close_redis() (in module veupath_chatbot.platform.redis) close_site_search_client() (in module veupath_chatbot.integrations.veupathdb.site_search) code (veupath_chatbot.domain.strategy.validate.StepValidationIssue attribute) (veupath_chatbot.platform.errors.ProblemDetail attribute) (veupath_chatbot.services.strategies.engine.graph_integrity.GraphIntegrityError attribute) coerce_step_id() (in module veupath_chatbot.services.experiment.helpers) coerce_wdk_boolean_question_params() (in module veupath_chatbot.services.strategies.step_creation) collect_all_result_ids() (in module veupath_chatbot.services.experiment.ai_analysis_helpers) collect_dict_combine_nodes() (in module veupath_chatbot.domain.strategy.tree) collect_dict_leaves() (in module veupath_chatbot.domain.strategy.tree) collect_dict_nodes() (in module veupath_chatbot.domain.strategy.tree) collect_leaf_terms() (in module veupath_chatbot.domain.parameters.vocab_utils) collect_plan_leaves() (in module veupath_chatbot.domain.strategy.tree) collect_plan_nodes() (in module veupath_chatbot.domain.strategy.tree) COLOCATE (veupath_chatbot.domain.strategy.ops.CombineOp attribute) colocation_params (veupath_chatbot.domain.strategy.ast.PlanStepNode attribute) (veupath_chatbot.transport.http.schemas.steps.StepResponse attribute) ColocationParams (class in veupath_chatbot.domain.strategy.ops) (class in veupath_chatbot.transport.http.schemas.plan) colocationParams (veupath_chatbot.transport.http.schemas.plan.PlanNode attribute) combine_node_id (veupath_chatbot.services.experiment.types.OperatorComparison attribute) (veupath_chatbot.services.experiment.types.OperatorKnob attribute) (veupath_chatbot.services.experiment.types.optimization.OperatorKnob attribute) (veupath_chatbot.services.experiment.types.step_analysis.OperatorComparison attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OperatorComparisonResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OperatorKnobResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.OperatorKnobRequest attribute) combined_result() (in module veupath_chatbot.ai.tools.combined_result) CombineOp (class in veupath_chatbot.domain.strategy.ops) combines (veupath_chatbot.ai.orchestration.delegation.DelegationPlan attribute) compare_enrichment() (in module veupath_chatbot.transport.http.routers.experiments.comparison) compare_enrichment_across() (in module veupath_chatbot.services.experiment.enrichment_compare) compare_operators() (in module veupath_chatbot.services.experiment.step_analysis.phase_operators) compilation (veupath_chatbot.services.strategies.build.BuildResult attribute) CompilationResult (class in veupath_chatbot.domain.strategy.compile) compile() (veupath_chatbot.domain.strategy.compile.StrategyCompiler method) compile_strategy() (in module veupath_chatbot.domain.strategy.compile) CompiledStep (class in veupath_chatbot.domain.strategy.compile) complete_operation() (veupath_chatbot.persistence.repositories.stream.StreamRepository method) completed_at (veupath_chatbot.persistence.models.Operation attribute) (veupath_chatbot.services.experiment.types.Experiment attribute) (veupath_chatbot.services.experiment.types.experiment.Experiment attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentResponse attribute) completion_tokens (veupath_chatbot.ai.orchestration.subkani.utils.SubKaniRoundResult attribute) (veupath_chatbot.transport.http.schemas.chat.SubKaniTokenUsageResponse attribute) (veupath_chatbot.transport.http.schemas.chat.TokenUsageResponse attribute) (veupath_chatbot.transport.http.schemas.sse.MessageEndEventData attribute) (veupath_chatbot.transport.http.schemas.sse.SubKaniTaskEndEventData attribute) component_timeout (veupath_chatbot.integrations.veupathdb.site_router.RoutingConfig attribute) composite_score (veupath_chatbot.services.gene_sets.confidence.GeneConfidenceScore attribute) (veupath_chatbot.transport.http.schemas.gene_sets.GeneConfidenceScoreResponse attribute) compute_confusion_matrix() (in module veupath_chatbot.services.experiment.metrics) compute_ensemble_scores() (in module veupath_chatbot.services.gene_sets.ensemble) compute_gene_confidence() (in module veupath_chatbot.services.gene_sets.confidence) compute_gene_set_overlap() (in module veupath_chatbot.services.experiment.overlap) compute_metrics() (in module veupath_chatbot.services.experiment.metrics) compute_overlap() (in module veupath_chatbot.transport.http.routers.experiments.comparison) compute_rank_metrics() (in module veupath_chatbot.services.experiment.rank_metrics) compute_robustness() (in module veupath_chatbot.services.experiment.robustness) compute_step_counts() (in module veupath_chatbot.transport.http.routers.strategies.counts) compute_step_counts_for_plan() (in module veupath_chatbot.services.strategies.wdk_counts) compute_sweep_values() (in module veupath_chatbot.services.experiment.evaluation) confidence_interval (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) ConfidenceInterval (class in veupath_chatbot.services.experiment.types) (class in veupath_chatbot.services.experiment.types.rank) ConfidenceIntervalResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) config (veupath_chatbot.domain.strategy.ast.StepReport attribute) (veupath_chatbot.services.experiment.types.Experiment attribute) (veupath_chatbot.services.experiment.types.experiment.Experiment attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentResponse attribute) (veupath_chatbot.transport.http.schemas.plan.StepReportSpec attribute) (veupath_chatbot.transport.http.schemas.steps.StepReportRequest attribute) (veupath_chatbot.transport.http.schemas.steps.StepReportResponse attribute) configure() (in module veupath_chatbot.services.chat.orchestrator) (in module veupath_chatbot.services.experiment.ai_analysis_tools) (in module veupath_chatbot.services.experiment.assistant) (in module veupath_chatbot.services.workbench_chat.orchestrator) confusion_matrix (veupath_chatbot.services.experiment.types.ExperimentMetrics attribute) (veupath_chatbot.services.experiment.types.metrics.ExperimentMetrics attribute) (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentMetricsResponse attribute)

ConfusionMatrix (class in veupath_chatbot.services.experiment.types) (class in veupath_chatbot.services.experiment.types.metrics) ConfusionMatrixResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) connect() (veupath_chatbot.integrations.vectorstore.qdrant_store.QdrantStore method) consume_subkani_round() (in module veupath_chatbot.ai.orchestration.subkani.utils) content (veupath_chatbot.transport.http.schemas.chat.MessageResponse attribute) (veupath_chatbot.transport.http.schemas.sse.AssistantMessageEventData attribute) (veupath_chatbot.transport.http.schemas.sse.UserMessageEventData attribute) content_type (veupath_chatbot.services.export.service.ExportResult attribute) context (veupath_chatbot.transport.http.schemas.experiments.AiAssistRequest attribute) context_hash() (in module veupath_chatbot.integrations.vectorstore.qdrant_store) context_size (veupath_chatbot.ai.models.catalog.ModelEntry attribute) (veupath_chatbot.transport.http.routers.models.ModelCatalogEntryResponse attribute) (veupath_chatbot.transport.http.schemas.chat.ChatRequest attribute) context_values (veupath_chatbot.transport.http.schemas.sites.DependentParamsRequest attribute) (veupath_chatbot.transport.http.schemas.sites.ParamSpecsRequest attribute) (veupath_chatbot.transport.http.schemas.sites.SearchValidationRequest attribute) control_set (veupath_chatbot.services.experiment.seed.SeedDef attribute) (veupath_chatbot.services.experiment.seed.types.SeedDef attribute) control_set_id (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.BenchmarkControlSet attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) control_set_label (veupath_chatbot.services.experiment.types.Experiment attribute) (veupath_chatbot.services.experiment.types.experiment.Experiment attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentSummaryResponse attribute) control_set_summary (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) control_sets (veupath_chatbot.transport.http.schemas.experiments.CreateBenchmarkRequest attribute) controls_param_name (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) controls_search_name (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) controls_value_format (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) ControlSet (class in veupath_chatbot.persistence.models) ControlSetDef (class in veupath_chatbot.services.experiment.seed) (class in veupath_chatbot.services.experiment.seed.types) ControlSetRepository (class in veupath_chatbot.persistence.repositories.control_set) ControlSetResponse (class in veupath_chatbot.transport.http.routers.control_sets) ControlSetSummaryResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) CONVERSATION_NOT_FOUND (veupath_chatbot.platform.errors.ErrorCode attribute) conversation_tools (veupath_chatbot.ai.tools.strategy_registry.StrategyToolsMixin attribute) ConversationTools (class in veupath_chatbot.ai.tools.conversation_tools) cors_origin_regex (veupath_chatbot.platform.config.Settings attribute) cors_origins (veupath_chatbot.platform.config.Settings attribute) count (veupath_chatbot.services.gene_sets.ensemble.EnsembleScore attribute) (veupath_chatbot.services.strategies.build.StepCountResult attribute) count_dict_nodes() (in module veupath_chatbot.domain.strategy.tree) count_only_leaves (veupath_chatbot.domain.parameters.specs.ParamSpecNormalized attribute) (veupath_chatbot.transport.http.schemas.sites.ParamSpecResponse attribute) count_steps_in_tree() (in module veupath_chatbot.services.gene_sets.operations) counts (veupath_chatbot.services.strategies.build.BuildResult attribute) (veupath_chatbot.transport.http.schemas.strategies.StepCountsResponse attribute) create() (veupath_chatbot.persistence.repositories.control_set.ControlSetRepository method) (veupath_chatbot.persistence.repositories.stream.StreamRepository method) (veupath_chatbot.persistence.repositories.user.UserRepository method) (veupath_chatbot.services.gene_sets.operations.GeneSetService method) create_agent() (in module veupath_chatbot.ai.agents.factory) create_app() (in module veupath_chatbot.main) create_batch_experiment() (in module veupath_chatbot.transport.http.routers.experiments.execution) create_benchmark() (in module veupath_chatbot.transport.http.routers.experiments.execution) create_combined_step() (veupath_chatbot.domain.strategy.compile.StrategyCompilerAPI method) (veupath_chatbot.integrations.veupathdb.strategy_api.steps.StepsMixin method) create_control_set() (in module veupath_chatbot.transport.http.routers.control_sets) create_dataset() (veupath_chatbot.domain.strategy.compile.StrategyCompilerAPI method) (veupath_chatbot.integrations.veupathdb.strategy_api.steps.StepsMixin method) create_engine() (in module veupath_chatbot.ai.agents.factory) create_experiment() (in module veupath_chatbot.transport.http.routers.experiments.execution) create_gene_set() (in module veupath_chatbot.transport.http.routers.gene_sets) create_graph() (veupath_chatbot.domain.strategy.session.StrategySession method) create_or_update_wdk_strategy() (in module veupath_chatbot.services.strategies.build) create_step() (in module veupath_chatbot.services.strategies.step_creation) (veupath_chatbot.ai.tools.strategy_tools.graph_ops.CreateStepProtocol method) (veupath_chatbot.ai.tools.strategy_tools.step_ops.StrategyStepOps method) (veupath_chatbot.domain.strategy.compile.StrategyCompilerAPI method) (veupath_chatbot.integrations.veupathdb.strategy_api.steps.StepsMixin method) create_step_analysis() (veupath_chatbot.integrations.veupathdb.client.VEuPathDBClient method) create_strategy() (in module veupath_chatbot.transport.http.routers.strategies.crud) (veupath_chatbot.integrations.veupathdb.strategy_api.strategies.StrategiesMixin method) (veupath_chatbot.services.strategies.build.StrategyBuildAPI method) create_strategy_ast() (in module veupath_chatbot.services.strategies.build) create_temporary_result() (veupath_chatbot.integrations.veupathdb.temporary_results.TemporaryResultsAPI method) create_transform_step() (veupath_chatbot.domain.strategy.compile.StrategyCompilerAPI method) (veupath_chatbot.integrations.veupathdb.strategy_api.steps.StepsMixin method) create_user_token() (in module veupath_chatbot.platform.security) create_workbench_gene_set() (veupath_chatbot.ai.tools.planner.workbench_tools.WorkbenchToolsMixin method) CreateBatchExperimentRequest (class in veupath_chatbot.transport.http.schemas.experiments) CreateBenchmarkRequest (class in veupath_chatbot.transport.http.schemas.experiments) CreateControlSetRequest (class in veupath_chatbot.transport.http.routers.control_sets) created_at (veupath_chatbot.persistence.models.ControlSet attribute) (veupath_chatbot.persistence.models.ExperimentRow attribute) (veupath_chatbot.persistence.models.GeneSetRow attribute) (veupath_chatbot.persistence.models.Operation attribute) (veupath_chatbot.persistence.models.Stream attribute) (veupath_chatbot.persistence.models.User attribute) (veupath_chatbot.services.experiment.types.Experiment attribute) (veupath_chatbot.services.experiment.types.experiment.Experiment attribute) (veupath_chatbot.services.gene_sets.types.GeneSet attribute) (veupath_chatbot.transport.http.routers.control_sets.ControlSetResponse attribute) (veupath_chatbot.transport.http.schemas.chat.PlanningArtifactResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentSummaryResponse attribute) (veupath_chatbot.transport.http.schemas.gene_sets.GeneSetResponse attribute) (veupath_chatbot.transport.http.schemas.strategies.StrategyResponse attribute) created_steps (veupath_chatbot.ai.orchestration.subkani.utils.SubKaniRoundResult attribute) createdAt (veupath_chatbot.transport.http.schemas.plan.PlanMetadata attribute) CreateExperimentRequest (class in veupath_chatbot.transport.http.schemas.experiments) CreateGeneSetRequest (class in veupath_chatbot.transport.http.schemas.gene_sets) CreateStepProtocol (class in veupath_chatbot.ai.tools.strategy_tools.graph_ops) CreateStrategyRequest (class in veupath_chatbot.transport.http.schemas.strategies) cross_validation (veupath_chatbot.services.experiment.types.Experiment attribute) (veupath_chatbot.services.experiment.types.experiment.Experiment attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentResponse attribute) cross_validation_result (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) CrossrefClient (class in veupath_chatbot.services.research.clients.crossref) CrossValidationResult (class in veupath_chatbot.services.experiment.types) (class in veupath_chatbot.services.experiment.types.metrics) CrossValidationResultResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) current_operator (veupath_chatbot.services.experiment.types.OperatorComparison attribute) (veupath_chatbot.services.experiment.types.step_analysis.OperatorComparison attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OperatorComparisonResponse attribute) current_step (veupath_chatbot.transport.http.schemas.experiment_responses.StepAnalysisProgressDataResponse attribute) current_trial (veupath_chatbot.transport.http.schemas.optimization.OptimizationProgressEventData attribute) current_value (veupath_chatbot.services.experiment.types.ParameterSensitivity attribute) (veupath_chatbot.services.experiment.types.step_analysis.ParameterSensitivity attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ParameterSensitivityResponse attribute) custom_enrichment() (in module veupath_chatbot.transport.http.routers.experiments.enrichment) custom_name (veupath_chatbot.domain.strategy.ast.StepAnalysis attribute) (veupath_chatbot.transport.http.schemas.steps.StepAnalysisRequest attribute) (veupath_chatbot.transport.http.schemas.steps.StepAnalysisResponse attribute) CustomEnrichmentResult (class in veupath_chatbot.services.experiment.custom_enrichment) CustomEnrichRequest (class in veupath_chatbot.transport.http.schemas.experiments) customName (veupath_chatbot.transport.http.schemas.plan.StepAnalysisSpec attribute)

D

data (veupath_chatbot.persistence.models.ExperimentRow attribute) database_url (veupath_chatbot.platform.config.Settings attribute) decode_ddg_redirect() (in module veupath_chatbot.services.research.utils) decode_values() (in module veupath_chatbot.domain.parameters._decode_values) dedup_and_sort() (in module veupath_chatbot.services.search_rerank) dedupe_key() (in module veupath_chatbot.services.research.utils) default (veupath_chatbot.transport.http.routers.models.ModelListResponse attribute) default_model_id (veupath_chatbot.platform.config.Settings attribute) default_reasoning_budget (veupath_chatbot.ai.models.catalog.ModelEntry attribute) (veupath_chatbot.transport.http.routers.models.ModelCatalogEntryResponse attribute) default_reasoning_effort (veupath_chatbot.platform.config.Settings attribute) (veupath_chatbot.transport.http.routers.models.ModelListResponse attribute) default_site (veupath_chatbot.integrations.veupathdb.site_router.SitesConfig attribute) delegate_strategy_subtasks() (in module veupath_chatbot.ai.orchestration.subkani.orchestrator) (veupath_chatbot.ai.agents.executor.PathfinderAgent method) DelegationPlan (class in veupath_chatbot.ai.orchestration.delegation) delete() (veupath_chatbot.integrations.veupathdb.client.VEuPathDBClient method) (veupath_chatbot.persistence.repositories.control_set.ControlSetRepository method) (veupath_chatbot.persistence.repositories.stream.StreamRepository method) (veupath_chatbot.platform.store.WriteThruStore method) (veupath_chatbot.services.gene_sets.operations.GeneSetService method) delete_control_set() (in module veupath_chatbot.transport.http.routers.control_sets) delete_experiment() (in module veupath_chatbot.transport.http.routers.experiments.crud) delete_gene_set() (in module veupath_chatbot.transport.http.routers.gene_sets) delete_step() (veupath_chatbot.ai.tools.strategy_tools.edit_ops.StrategyEditOps method) delete_step_filter() (veupath_chatbot.integrations.veupathdb.strategy_api.filters.FilterMixin method) delete_strategy() (in module veupath_chatbot.transport.http.routers.strategies.crud) (veupath_chatbot.integrations.veupathdb.strategy_api.strategies.StrategiesMixin method) delete_temp_strategy() (in module veupath_chatbot.services.control_helpers) delta (veupath_chatbot.transport.http.schemas.sse.AssistantDeltaEventData attribute) dependent_params (veupath_chatbot.domain.parameters.specs.ParamSpecNormalized attribute) (veupath_chatbot.transport.http.schemas.sites.ParamSpecResponse attribute) DependentParamsRequest (class in veupath_chatbot.transport.http.schemas.sites) DependentParamsResponse (class in veupath_chatbot.transport.http.schemas.sites) dependents (veupath_chatbot.ai.orchestration.delegation.DelegationPlan attribute) derive_graph_metadata() (in module veupath_chatbot.domain.strategy.metadata) description (veupath_chatbot.ai.models.catalog.ModelEntry attribute) (veupath_chatbot.domain.strategy.ast.StrategyAST attribute) (veupath_chatbot.services.experiment.seed.SeedDef attribute) (veupath_chatbot.services.experiment.seed.types.SeedDef attribute) (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.transport.http.routers.models.ModelCatalogEntryResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) (veupath_chatbot.transport.http.schemas.plan.PlanMetadata attribute) (veupath_chatbot.transport.http.schemas.sites.RecordTypeResponse attribute) (veupath_chatbot.transport.http.schemas.sites.SearchResponse attribute) (veupath_chatbot.transport.http.schemas.sse.GraphPlanEventData attribute) (veupath_chatbot.transport.http.schemas.sse.StrategyLinkEventData attribute) (veupath_chatbot.transport.http.schemas.sse.StrategyMetaEventData attribute) (veupath_chatbot.transport.http.schemas.strategies.StrategyResponse attribute)

detail (veupath_chatbot.platform.errors.ProblemDetail attribute) DETAIL_ATTRIBUTE_LIMIT (in module veupath_chatbot.services.wdk.helpers) dev_login() (in module veupath_chatbot.transport.http.routers.dev) disable_rag (veupath_chatbot.transport.http.schemas.chat.ChatRequest attribute) disabled (veupath_chatbot.domain.strategy.ast.StepFilter attribute) (veupath_chatbot.transport.http.schemas.plan.StepFilterSpec attribute) (veupath_chatbot.transport.http.schemas.steps.StepFilterRequest attribute) (veupath_chatbot.transport.http.schemas.steps.StepFilterResponse attribute) disabled_tools (veupath_chatbot.transport.http.schemas.chat.ChatRequest attribute) DiscoveryService (class in veupath_chatbot.integrations.veupathdb.discovery) (class in veupath_chatbot.integrations.veupathdb.factory) dismiss() (veupath_chatbot.persistence.repositories.stream.StreamRepository method) dismissed_at (veupath_chatbot.persistence.models.StreamProjection attribute) (veupath_chatbot.transport.http.schemas.strategies.StrategyResponse attribute) display_name (veupath_chatbot.domain.strategy.ast.PlanStepNode attribute) (veupath_chatbot.domain.strategy.compile.CompiledStep attribute) (veupath_chatbot.integrations.veupathdb.site_router.SiteConfig attribute) (veupath_chatbot.services.experiment.types.step_analysis.StepEvaluation attribute) (veupath_chatbot.services.experiment.types.StepEvaluation attribute) (veupath_chatbot.transport.http.schemas.chat.ChatMention attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepEvaluationResponse attribute) (veupath_chatbot.transport.http.schemas.sites.ParamSpecResponse attribute) (veupath_chatbot.transport.http.schemas.sites.RecordTypeResponse attribute) (veupath_chatbot.transport.http.schemas.sites.SearchResponse attribute) (veupath_chatbot.transport.http.schemas.sites.SiteResponse attribute) (veupath_chatbot.transport.http.schemas.steps.StepResponse attribute) display_type (veupath_chatbot.domain.parameters.specs.ParamSpecNormalized attribute) (veupath_chatbot.transport.http.schemas.sites.ParamSpecResponse attribute) displayName (veupath_chatbot.transport.http.routers.sites.genes.GeneSearchResultResponse attribute) (veupath_chatbot.transport.http.routers.sites.genes.ResolvedGeneResponse attribute) (veupath_chatbot.transport.http.schemas.plan.BasePlanNode attribute) do_function_call() (veupath_chatbot.ai.agents.executor.PathfinderAgent method) doi (veupath_chatbot.domain.research.citations.Citation attribute) (veupath_chatbot.transport.http.schemas.chat.CitationResponse attribute) download_export() (in module veupath_chatbot.transport.http.routers.exports) downstream (veupath_chatbot.domain.strategy.ops.ColocationParams attribute) (veupath_chatbot.transport.http.schemas.plan.ColocationParams attribute)

E

EarlyStopReason (class in veupath_chatbot.services.parameter_optimization.trials) ec_search_params() (in module veupath_chatbot.services.experiment.seed.helpers) email (veupath_chatbot.transport.http.routers.veupathdb_auth.LoginPayload attribute) (veupath_chatbot.transport.http.schemas.veupathdb_auth.AuthStatusResponse attribute) embed_and_upsert() (in module veupath_chatbot.integrations.vectorstore.ingest.utils) embed_one() (in module veupath_chatbot.integrations.embeddings.openai_embeddings) embed_texts() (veupath_chatbot.integrations.embeddings.openai_embeddings.OpenAIEmbeddings method) embedding_text_for_example() (in module veupath_chatbot.integrations.vectorstore.ingest.public_strategies_helpers) embeddings_base_url (veupath_chatbot.platform.config.Settings attribute) embeddings_model (veupath_chatbot.platform.config.Settings attribute) emit() (in module veupath_chatbot.platform.events) emit_completed() (in module veupath_chatbot.services.parameter_optimization.callbacks) emit_error() (in module veupath_chatbot.services.parameter_optimization.callbacks) emit_started() (in module veupath_chatbot.services.parameter_optimization.callbacks) emit_trial_progress() (in module veupath_chatbot.services.parameter_optimization.callbacks) EMPTY (veupath_chatbot.domain.parameters._value_helpers.ParamKind attribute) enable_cross_validation (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) enable_step_analysis (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) enabled (veupath_chatbot.transport.http.routers.models.ModelCatalogEntryResponse attribute) encode_context_param_values_for_wdk() (in module veupath_chatbot.integrations.veupathdb.client) encode_vocab_params() (in module veupath_chatbot.services.experiment.enrichment) enrich_gene_set() (in module veupath_chatbot.transport.http.routers.gene_sets) enrich_sparse_gene_results() (in module veupath_chatbot.services.gene_lookup.enrich) enrichment_at_k (veupath_chatbot.services.experiment.types.rank.RankMetrics attribute) (veupath_chatbot.services.experiment.types.RankMetrics attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.RankMetricsResponse attribute) enrichment_delta (veupath_chatbot.services.experiment.types.step_analysis.StepContribution attribute) (veupath_chatbot.services.experiment.types.StepContribution attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepContributionResponse attribute) enrichment_gene_counts (veupath_chatbot.transport.http.schemas.gene_sets.GeneConfidenceRequest attribute) enrichment_result (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) enrichment_results (veupath_chatbot.services.experiment.types.Experiment attribute) (veupath_chatbot.services.experiment.types.experiment.Experiment attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentResponse attribute) enrichment_score (veupath_chatbot.services.gene_sets.confidence.GeneConfidenceScore attribute) (veupath_chatbot.transport.http.schemas.gene_sets.GeneConfidenceScoreResponse attribute) enrichment_term (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) enrichment_types (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) (veupath_chatbot.transport.http.schemas.experiments.RunEnrichmentRequest attribute) (veupath_chatbot.transport.http.schemas.gene_sets.GeneSetEnrichRequest attribute) EnrichmentCompareRequest (class in veupath_chatbot.transport.http.schemas.experiments) EnrichmentCompareResult (class in veupath_chatbot.services.experiment.enrichment_compare) EnrichmentResult (class in veupath_chatbot.services.experiment.types) (class in veupath_chatbot.services.experiment.types.enrichment) EnrichmentResultResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) EnrichmentRow (class in veupath_chatbot.services.experiment.enrichment_compare) EnrichmentService (class in veupath_chatbot.services.wdk.enrichment_service) EnrichmentTerm (class in veupath_chatbot.services.experiment.types) (class in veupath_chatbot.services.experiment.types.enrichment) EnrichmentTermResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) ensemble_score (veupath_chatbot.services.gene_sets.confidence.GeneConfidenceScore attribute) (veupath_chatbot.transport.http.schemas.gene_sets.GeneConfidenceScoreResponse attribute) ensemble_scores (veupath_chatbot.transport.http.schemas.gene_sets.GeneConfidenceRequest attribute) ensemble_scoring() (in module veupath_chatbot.transport.http.routers.gene_sets) EnsembleScore (class in veupath_chatbot.services.gene_sets.ensemble) EnsembleScoringRequest (class in veupath_chatbot.transport.http.schemas.gene_sets) ensure_collection() (veupath_chatbot.integrations.vectorstore.qdrant_store.QdrantStore method) ensure_dependent_vocab_collection() (in module veupath_chatbot.integrations.vectorstore.dependent_vocab_cache) ensure_rag_collections() (in module veupath_chatbot.integrations.vectorstore.bootstrap) ensure_single_output() (veupath_chatbot.ai.tools.strategy_tools.graph_ops.StrategyGraphOps method) ENSURE_SINGLE_OUTPUT_FAILED (veupath_chatbot.platform.errors.ErrorCode attribute) ensure_unique_citation_tags() (in module veupath_chatbot.domain.research.citations) error (veupath_chatbot.services.experiment.types.enrichment.EnrichmentResult attribute) (veupath_chatbot.services.experiment.types.EnrichmentResult attribute) (veupath_chatbot.services.experiment.types.Experiment attribute) (veupath_chatbot.services.experiment.types.experiment.Experiment attribute) (veupath_chatbot.services.strategies.step_creation.StepCreationResult attribute) (veupath_chatbot.transport.http.routers.internal.SSESchemaIndex attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.EnrichmentResultResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentResponse attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationProgressEventData attribute) (veupath_chatbot.transport.http.schemas.sse.ErrorEventData attribute) error_message (veupath_chatbot.services.parameter_optimization.OptimizationResult attribute) ErrorCode (class in veupath_chatbot.platform.errors) ErrorEventData (class in veupath_chatbot.transport.http.schemas.sse) errors (veupath_chatbot.ai.orchestration.subkani.utils.SubKaniRoundResult attribute) (veupath_chatbot.domain.strategy.validate.ValidationResult attribute) (veupath_chatbot.platform.errors.ProblemDetail attribute) (veupath_chatbot.transport.http.schemas.sites.SearchValidationPayload attribute)

estimate_cost() (in module veupath_chatbot.ai.models.pricing) estimated_cost_usd (veupath_chatbot.transport.http.schemas.chat.SubKaniTokenUsageResponse attribute) (veupath_chatbot.transport.http.schemas.chat.TokenUsageResponse attribute) (veupath_chatbot.transport.http.schemas.sse.MessageEndEventData attribute) (veupath_chatbot.transport.http.schemas.sse.SubKaniTaskEndEventData attribute) EuropePmcClient (class in veupath_chatbot.services.research.clients.europepmc) evaluate_gene_ids_against_controls() (in module veupath_chatbot.services.experiment.metrics) evaluate_steps() (in module veupath_chatbot.services.experiment.step_analysis.phase_step_eval) EventExtractor (class in veupath_chatbot.services.chat.events) example_plans_rag_tools (veupath_chatbot.ai.tools.catalog_registry.CatalogToolsMixin attribute) ExamplePlansRagTools (class in veupath_chatbot.ai.tools.example_plans_rag_tools) execution_tools (veupath_chatbot.ai.tools.strategy_registry.StrategyToolsMixin attribute) ExecutionTools (class in veupath_chatbot.ai.tools.execution_tools) executor_build_request (veupath_chatbot.transport.http.routers.internal.SSESchemaIndex attribute) (veupath_chatbot.transport.http.schemas.sse.ExecutorBuildRequestEventData attribute) ExecutorBuildRequestEventData (class in veupath_chatbot.transport.http.schemas.sse) existing_point_ids() (in module veupath_chatbot.integrations.vectorstore.ingest.utils) exon_count_params() (in module veupath_chatbot.services.experiment.seed.helpers) expand_search_details_with_params() (in module veupath_chatbot.services.catalog.param_resolution) (in module veupath_chatbot.services.catalog.parameters) Experiment (class in veupath_chatbot.services.experiment.types) (class in veupath_chatbot.services.experiment.types.experiment) experiment (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) experiment_config (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) experiment_from_json() (in module veupath_chatbot.services.experiment._deserialize) experiment_id (veupath_chatbot.ai.tools.workbench_read_tools.WorkbenchReadToolsMixin attribute) (veupath_chatbot.persistence.models.Stream attribute) experiment_ids (veupath_chatbot.transport.http.schemas.experiments.EnrichmentCompareRequest attribute) (veupath_chatbot.transport.http.schemas.experiments.OverlapRequest attribute) experiment_metrics (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) experiment_progress_data (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) experiment_schemas() (in module veupath_chatbot.transport.http.routers.internal) experiment_summary (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) experiment_summary_to_json() (in module veupath_chatbot.services.experiment.types) (in module veupath_chatbot.services.experiment.types.serialization) experiment_to_json() (in module veupath_chatbot.services.experiment.types) (in module veupath_chatbot.services.experiment.types.serialization) experimentA (veupath_chatbot.services.experiment.overlap.PairwiseOverlap attribute) ExperimentAnalysisAgent (class in veupath_chatbot.services.experiment.ai_analysis_tools) ExperimentAssistantAgent (class in veupath_chatbot.ai.agents.experiment) experimentB (veupath_chatbot.services.experiment.overlap.PairwiseOverlap attribute) ExperimentConfig (class in veupath_chatbot.services.experiment.types) (class in veupath_chatbot.services.experiment.types.experiment) ExperimentConfigResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) experimentCount (veupath_chatbot.services.experiment.enrichment_compare.EnrichmentRow attribute) experimentId (veupath_chatbot.services.experiment.overlap.PerExperimentSummary attribute) experimentIds (veupath_chatbot.services.experiment.enrichment_compare.EnrichmentCompareResult attribute) (veupath_chatbot.services.experiment.overlap.OverlapResult attribute) experimentLabels (veupath_chatbot.services.experiment.enrichment_compare.EnrichmentCompareResult attribute) (veupath_chatbot.services.experiment.overlap.OverlapResult attribute) ExperimentMetrics (class in veupath_chatbot.services.experiment.types) (class in veupath_chatbot.services.experiment.types.metrics) ExperimentMetricsResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) ExperimentProgressDataResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) ExperimentResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) ExperimentRow (class in veupath_chatbot.persistence.models) experiments (veupath_chatbot.services.experiment.overlap.GeneMembership attribute) ExperimentSchemaIndex (class in veupath_chatbot.transport.http.routers.internal) ExperimentStore (class in veupath_chatbot.services.experiment.store) ExperimentSummaryResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) ExperimentToolsMixin (class in veupath_chatbot.ai.tools.planner.experiment_tools) expires_in_seconds (veupath_chatbot.services.export.service.ExportResult attribute) explain_operation() (in module veupath_chatbot.domain.strategy.explain) explain_operator() (veupath_chatbot.ai.tools.strategy_tools.discovery_ops.StrategyDiscoveryOps method) export_enrichment() (veupath_chatbot.services.export.service.ExportService method) export_enrichment_json() (veupath_chatbot.services.export.service.ExportService method) export_enrichment_tsv() (veupath_chatbot.services.export.service.ExportService method) export_experiment_results() (veupath_chatbot.services.export.service.ExportService method) export_gene_set() (veupath_chatbot.ai.tools.export_tools.ExportToolsMixin method) (veupath_chatbot.services.export.service.ExportService method) export_id (veupath_chatbot.services.export.service.ExportResult attribute) export_json() (veupath_chatbot.services.export.service.ExportService method) ExportResult (class in veupath_chatbot.services.export.service) ExportService (class in veupath_chatbot.services.export.service) ExportToolsMixin (class in veupath_chatbot.ai.tools.export_tools) external_id (veupath_chatbot.persistence.models.User attribute) extract_and_enrich_genes() (in module veupath_chatbot.services.experiment.helpers) extract_detail_attributes() (in module veupath_chatbot.services.wdk.helpers) extract_estimated_size() (in module veupath_chatbot.services.strategies.wdk_conversion) extract_operator() (in module veupath_chatbot.services.strategies.wdk_conversion) extract_param_specs() (in module veupath_chatbot.domain.parameters.specs) extract_pk() (in module veupath_chatbot.services.wdk.helpers) extract_primary_step_id() (in module veupath_chatbot.ai.orchestration.subkani.utils) extract_record_ids() (in module veupath_chatbot.services.wdk.helpers) extract_record_type() (in module veupath_chatbot.services.strategies.wdk_conversion) extract_step_counts() (in module veupath_chatbot.services.strategies.build) extract_wdk_id() (in module veupath_chatbot.services.experiment.helpers) extract_wdk_is_saved() (in module veupath_chatbot.services.strategies.wdk_conversion)

F

f1 (veupath_chatbot.services.experiment.types.ParameterSweepPoint attribute) (veupath_chatbot.services.experiment.types.step_analysis.ParameterSweepPoint attribute) (veupath_chatbot.services.gene_sets.reverse_search.RankedResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ParameterSweepPointResponse attribute) (veupath_chatbot.transport.http.schemas.gene_sets.ReverseSearchResultItem attribute) f1_score (veupath_chatbot.services.experiment.types.ExperimentMetrics attribute) (veupath_chatbot.services.experiment.types.metrics.ExperimentMetrics attribute) (veupath_chatbot.services.experiment.types.OperatorVariant attribute) (veupath_chatbot.services.experiment.types.step_analysis.OperatorVariant attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentMetricsResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentSummaryResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OperatorVariantResponse attribute) fail_operation() (veupath_chatbot.persistence.repositories.stream.StreamRepository method) failure() (veupath_chatbot.domain.strategy.validate.ValidationResult class method) fallback_ratio() (in module veupath_chatbot.services.research.utils) false_negative_genes (veupath_chatbot.services.experiment.types.Experiment attribute) (veupath_chatbot.services.experiment.types.experiment.Experiment attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentResponse attribute) false_negative_rate (veupath_chatbot.services.experiment.types.ExperimentMetrics attribute) (veupath_chatbot.services.experiment.types.metrics.ExperimentMetrics attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentMetricsResponse attribute) false_negatives (veupath_chatbot.services.experiment.types.ConfusionMatrix attribute) (veupath_chatbot.services.experiment.types.metrics.ConfusionMatrix attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ConfusionMatrixResponse attribute) false_positive_genes (veupath_chatbot.services.experiment.types.Experiment attribute) (veupath_chatbot.services.experiment.types.experiment.Experiment attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentResponse attribute) false_positive_rate (veupath_chatbot.services.experiment.types.ExperimentMetrics attribute) (veupath_chatbot.services.experiment.types.metrics.ExperimentMetrics attribute) (veupath_chatbot.services.experiment.types.OperatorVariant attribute) (veupath_chatbot.services.experiment.types.step_analysis.OperatorVariant attribute) (veupath_chatbot.services.experiment.types.step_analysis.StepEvaluation attribute) (veupath_chatbot.services.experiment.types.StepEvaluation attribute) (veupath_chatbot.services.parameter_optimization.TrialResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentMetricsResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OperatorVariantResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepEvaluationResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.TrialProgressDataResponse attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationTrialData attribute) false_positives (veupath_chatbot.services.experiment.types.ConfusionMatrix attribute) (veupath_chatbot.services.experiment.types.metrics.ConfusionMatrix attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ConfusionMatrixResponse attribute) fdr (veupath_chatbot.services.experiment.types.enrichment.EnrichmentTerm attribute) (veupath_chatbot.services.experiment.types.EnrichmentTerm attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.EnrichmentTermResponse attribute) fetch_and_convert() (in module veupath_chatbot.services.strategies.wdk_sync) fetch_gene_ids_from_step() (in module veupath_chatbot.services.gene_sets.operations) fetch_group_records() (in module veupath_chatbot.services.experiment.ai_analysis_helpers) fetch_ordered_result_ids() (in module veupath_chatbot.services.experiment.rank_metrics) fetch_page_summary() (in module veupath_chatbot.services.research.utils) fetch_record_types_and_searches() (in module veupath_chatbot.integrations.vectorstore.ingest.wdk_fetch) fetch_search_details() (in module veupath_chatbot.integrations.vectorstore.ingest.wdk_fetch) fetch_site_search_genes() (in module veupath_chatbot.services.gene_lookup.site_search) fetch_wdk_text_genes() (in module veupath_chatbot.services.gene_lookup.wdk) filename (veupath_chatbot.services.export.service.ExportResult attribute) FILTER (veupath_chatbot.domain.parameters._value_helpers.ParamKind attribute) filter_existing_record_types() (in module veupath_chatbot.integrations.vectorstore.ingest.wdk_index) filter_existing_searches() (in module veupath_chatbot.integrations.vectorstore.ingest.wdk_index) FilterMixin (class in veupath_chatbot.integrations.veupathdb.strategy_api.filters) filters (veupath_chatbot.domain.strategy.ast.PlanStepNode attribute) (veupath_chatbot.transport.http.schemas.plan.BasePlanNode attribute) (veupath_chatbot.transport.http.schemas.steps.StepFiltersResponse attribute) (veupath_chatbot.transport.http.schemas.steps.StepResponse attribute)

find_by_experiment() (veupath_chatbot.persistence.repositories.stream.StreamRepository method) find_by_wdk_strategy() (veupath_chatbot.services.gene_sets.operations.GeneSetService method) find_input_step_param() (in module veupath_chatbot.domain.parameters.specs) find_missing_required_params() (in module veupath_chatbot.domain.parameters.specs) find_record_type_for_search() (in module veupath_chatbot.services.catalog.searches) (veupath_chatbot.integrations.veupathdb.discovery.SearchCatalog method) find_root_step_ids() (in module veupath_chatbot.services.strategies.engine.graph_integrity) find_search() (veupath_chatbot.integrations.veupathdb.discovery.SearchCatalog method) find_vocab_node() (in module veupath_chatbot.domain.parameters.vocab_utils) flatten_vocab() (in module veupath_chatbot.domain.parameters.vocab_utils) flush() (veupath_chatbot.services.gene_sets.operations.GeneSetService method) fn_ids (veupath_chatbot.transport.http.schemas.gene_sets.GeneConfidenceRequest attribute) fn_movement (veupath_chatbot.services.experiment.types.step_analysis.StepEvaluation attribute) (veupath_chatbot.services.experiment.types.StepEvaluation attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepEvaluationResponse attribute) fold_enrichment (veupath_chatbot.services.experiment.types.enrichment.EnrichmentTerm attribute) (veupath_chatbot.services.experiment.types.EnrichmentTerm attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.EnrichmentTermResponse attribute) fold_index (veupath_chatbot.services.experiment.types.FoldMetrics attribute) (veupath_chatbot.services.experiment.types.metrics.FoldMetrics attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.FoldMetricsResponse attribute) fold_metrics (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) foldEnrichment (veupath_chatbot.services.experiment.custom_enrichment.CustomEnrichmentResult attribute) FoldEvaluator (in module veupath_chatbot.services.experiment.cross_validation) FoldMetrics (class in veupath_chatbot.services.experiment.types) (class in veupath_chatbot.services.experiment.types.metrics) FoldMetricsResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) folds (veupath_chatbot.services.experiment.types.CrossValidationResult attribute) (veupath_chatbot.services.experiment.types.metrics.CrossValidationResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.CrossValidationResultResponse attribute) FORBIDDEN (veupath_chatbot.platform.errors.ErrorCode attribute) ForbiddenError format_dependency_context() (in module veupath_chatbot.ai.orchestration.subkani.utils) format_metrics_dict() (in module veupath_chatbot.services.experiment.evaluation) format_task_context() (in module veupath_chatbot.ai.orchestration.subkani.utils) foundIn (veupath_chatbot.services.experiment.overlap.GeneMembership attribute) fp_ids (veupath_chatbot.transport.http.schemas.gene_sets.GeneConfidenceRequest attribute) fp_movement (veupath_chatbot.services.experiment.types.step_analysis.StepEvaluation attribute) (veupath_chatbot.services.experiment.types.StepEvaluation attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepEvaluationResponse attribute) fpr (veupath_chatbot.services.experiment.types.ParameterSweepPoint attribute) (veupath_chatbot.services.experiment.types.step_analysis.ParameterSweepPoint attribute) (veupath_chatbot.services.parameter_optimization.trials.TrialMetrics attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ParameterSweepPointResponse attribute) fpr_delta (veupath_chatbot.services.experiment.types.step_analysis.StepContribution attribute) (veupath_chatbot.services.experiment.types.StepContribution attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepContributionResponse attribute) frequency (veupath_chatbot.services.gene_sets.ensemble.EnsembleScore attribute) from_config() (veupath_chatbot.integrations.veupathdb.factory.SiteInfo class method) (veupath_chatbot.integrations.veupathdb.site_router.SiteInfo class method) from_dict() (in module veupath_chatbot.domain.strategy.ast) from_json() (in module veupath_chatbot.services.experiment.types) (in module veupath_chatbot.services.experiment.types.json_codec) from_settings() (veupath_chatbot.integrations.vectorstore.qdrant_store.QdrantStore class method) full_strategy_payload() (in module veupath_chatbot.integrations.vectorstore.ingest.public_strategies_helpers) functions (veupath_chatbot.ai.agents.executor.PathfinderAgent attribute) fuzzy_score() (in module veupath_chatbot.services.research.utils)

G

gemini_api_key (veupath_chatbot.platform.config.Settings attribute) gemini_hyperparams (veupath_chatbot.platform.config.Settings attribute) gemini_model (veupath_chatbot.platform.config.Settings attribute) gemini_temperature (veupath_chatbot.platform.config.Settings attribute) gemini_top_p (veupath_chatbot.platform.config.Settings attribute) gene_confidence() (in module veupath_chatbot.transport.http.routers.gene_sets) gene_count (veupath_chatbot.services.experiment.types.enrichment.EnrichmentTerm attribute) (veupath_chatbot.services.experiment.types.EnrichmentTerm attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.EnrichmentTermResponse attribute) (veupath_chatbot.transport.http.schemas.gene_sets.GeneSetResponse attribute) (veupath_chatbot.transport.http.schemas.sse.GeneSetSummary attribute) gene_id (veupath_chatbot.services.gene_sets.confidence.GeneConfidenceScore attribute) (veupath_chatbot.transport.http.schemas.gene_sets.GeneConfidenceScoreResponse attribute) gene_ids (veupath_chatbot.persistence.models.GeneSetRow attribute) (veupath_chatbot.services.gene_sets.reverse_search.GeneSetCandidate attribute) (veupath_chatbot.services.gene_sets.types.GeneSet attribute) (veupath_chatbot.transport.http.schemas.experiments.CustomEnrichRequest attribute) (veupath_chatbot.transport.http.schemas.gene_sets.CreateGeneSetRequest attribute) (veupath_chatbot.transport.http.schemas.gene_sets.GeneSetResponse attribute) gene_info (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) gene_set (veupath_chatbot.transport.http.schemas.sse.WorkbenchGeneSetEventData attribute) gene_set_auto_imported (veupath_chatbot.persistence.models.StreamProjection attribute) gene_set_id (veupath_chatbot.persistence.models.StreamProjection attribute) (veupath_chatbot.services.gene_sets.reverse_search.RankedResult attribute) (veupath_chatbot.transport.http.schemas.gene_sets.ReverseSearchResultItem attribute) (veupath_chatbot.transport.http.schemas.strategies.StrategyResponse attribute) gene_set_ids (veupath_chatbot.transport.http.schemas.gene_sets.EnsembleScoringRequest attribute) gene_set_name (veupath_chatbot.transport.http.schemas.experiments.CustomEnrichRequest attribute) gene_set_summary (veupath_chatbot.transport.http.routers.internal.SSESchemaIndex attribute) gene_type_params() (in module veupath_chatbot.services.experiment.seed.helpers) GeneConfidenceRequest (class in veupath_chatbot.transport.http.schemas.gene_sets) GeneConfidenceScore (class in veupath_chatbot.services.gene_sets.confidence) GeneConfidenceScoreResponse (class in veupath_chatbot.transport.http.schemas.gene_sets) geneId (veupath_chatbot.services.experiment.overlap.GeneMembership attribute) (veupath_chatbot.services.gene_sets.ensemble.EnsembleScore attribute) (veupath_chatbot.transport.http.routers.sites.genes.GeneSearchResultResponse attribute) (veupath_chatbot.transport.http.routers.sites.genes.ResolvedGeneResponse attribute) geneIds (veupath_chatbot.transport.http.routers.sites.genes.GeneResolveRequest attribute) GeneInfo (class in veupath_chatbot.services.experiment.types) (class in veupath_chatbot.services.experiment.types.metrics) GeneInfoResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) GeneMembership (class in veupath_chatbot.services.experiment.overlap) geneMembership (veupath_chatbot.services.experiment.overlap.OverlapResult attribute) geneName (veupath_chatbot.transport.http.routers.sites.genes.GeneSearchResultResponse attribute) (veupath_chatbot.transport.http.routers.sites.genes.ResolvedGeneResponse attribute) general (veupath_chatbot.transport.http.schemas.sites.SearchValidationErrors attribute) generate_experiment_report() (in module veupath_chatbot.services.experiment.report) generate_openapi_yaml() (in module veupath_chatbot.devtools.openapi) generate_step_id() (in module veupath_chatbot.domain.strategy.ast) generate_sweep_events() (in module veupath_chatbot.services.experiment.evaluation) GeneResolveRequest (class in veupath_chatbot.transport.http.routers.sites.genes) GeneResolveResponse (class in veupath_chatbot.transport.http.routers.sites.genes) genes (veupath_chatbot.services.experiment.types.enrichment.EnrichmentTerm attribute) (veupath_chatbot.services.experiment.types.EnrichmentTerm attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.EnrichmentTermResponse attribute) GeneSearchResponse (class in veupath_chatbot.transport.http.routers.sites.genes) GeneSearchResultResponse (class in veupath_chatbot.transport.http.routers.sites.genes) GeneSet (class in veupath_chatbot.services.gene_sets.types) GeneSetCandidate (class in veupath_chatbot.services.gene_sets.reverse_search) GeneSetEnrichRequest (class in veupath_chatbot.transport.http.schemas.gene_sets) geneSetName (veupath_chatbot.services.experiment.custom_enrichment.CustomEnrichmentResult attribute) GeneSetResponse (class in veupath_chatbot.transport.http.schemas.gene_sets) GeneSetRow (class in veupath_chatbot.persistence.models) GeneSetService (class in veupath_chatbot.services.gene_sets.operations) geneSetSize (veupath_chatbot.services.experiment.custom_enrichment.CustomEnrichmentResult attribute) GeneSetStore (class in veupath_chatbot.services.gene_sets.store) GeneSetSummary (class in veupath_chatbot.transport.http.schemas.sse) GeneToolsMixin (class in veupath_chatbot.ai.tools.planner.gene_tools) geneType (veupath_chatbot.transport.http.routers.sites.genes.GeneSearchResultResponse attribute) (veupath_chatbot.transport.http.routers.sites.genes.ResolvedGeneResponse attribute) get() (veupath_chatbot.integrations.vectorstore.qdrant_store.QdrantStore method) (veupath_chatbot.integrations.veupathdb.client.VEuPathDBClient method) (veupath_chatbot.platform.store.WriteThruStore method) get_active_operations() (veupath_chatbot.persistence.repositories.stream.StreamRepository method) get_all_seeds() (in module veupath_chatbot.services.experiment.seed) get_all_steps() (veupath_chatbot.domain.strategy.ast.StrategyAST method) get_analysis_result() (veupath_chatbot.integrations.veupathdb.client.VEuPathDBClient method) get_analysis_status() (veupath_chatbot.integrations.veupathdb.client.VEuPathDBClient method) get_analysis_type() (veupath_chatbot.integrations.veupathdb.client.VEuPathDBClient method) (veupath_chatbot.integrations.veupathdb.strategy_api.analyses.AnalysisMixin method) get_attributes() (veupath_chatbot.services.wdk.step_results.StepResultsService method) get_by_id() (veupath_chatbot.persistence.repositories.control_set.ControlSetRepository method) (veupath_chatbot.persistence.repositories.stream.StreamRepository method) (veupath_chatbot.persistence.repositories.user.UserRepository method) get_by_wdk_strategy_id() (veupath_chatbot.persistence.repositories.stream.StreamRepository method) get_catalog() (veupath_chatbot.integrations.veupathdb.discovery.DiscoveryService method) (veupath_chatbot.integrations.veupathdb.factory.DiscoveryService method) get_client() (veupath_chatbot.integrations.veupathdb.site_router.SiteRouter method) get_column_distribution() (veupath_chatbot.integrations.veupathdb.strategy_api.records.RecordsMixin method) get_confidence_scores() (veupath_chatbot.ai.tools.workbench_read_tools.WorkbenchReadToolsMixin method) get_control_set() (in module veupath_chatbot.transport.http.routers.control_sets) get_control_set_repo() (in module veupath_chatbot.transport.http.deps) get_current_user() (in module veupath_chatbot.platform.security) get_current_user_with_db_row() (in module veupath_chatbot.transport.http.deps) get_db_session() (in module veupath_chatbot.persistence.session) get_default_site() (veupath_chatbot.integrations.veupathdb.site_router.SiteRouter method) get_dependent_vocab() (veupath_chatbot.ai.tools.catalog_registry.CatalogToolsMixin method) (veupath_chatbot.services.catalog.rag_search.RagSearchService method) get_dependent_vocab_authoritative_cached() (in module veupath_chatbot.integrations.vectorstore.dependent_vocab_cache) get_discovery_service() (in module veupath_chatbot.integrations.veupathdb.discovery) (in module veupath_chatbot.integrations.veupathdb.factory) get_distribution() (veupath_chatbot.services.wdk.step_results.StepResultsService method) get_download_url() (veupath_chatbot.ai.tools.result_tools.ResultTools method) (veupath_chatbot.integrations.veupathdb.temporary_results.TemporaryResultsAPI method) get_embedding_dim() (in module veupath_chatbot.integrations.vectorstore.bootstrap) get_engine() (in module veupath_chatbot.persistence.session) get_enrichment_results() (veupath_chatbot.ai.tools.workbench_read_tools.WorkbenchReadToolsMixin method) get_ensemble_analysis() (veupath_chatbot.ai.tools.workbench_read_tools.WorkbenchReadToolsMixin method) get_evaluation_summary() (veupath_chatbot.ai.tools.workbench_read_tools.WorkbenchReadToolsMixin method) get_experiment() (in module veupath_chatbot.transport.http.routers.experiments.crud) get_experiment_attributes() (in module veupath_chatbot.transport.http.routers.experiments.results) get_experiment_config() (veupath_chatbot.ai.tools.workbench_read_tools.WorkbenchReadToolsMixin method) get_experiment_distribution() (in module veupath_chatbot.transport.http.routers.experiments.results) get_experiment_owned_by_user() (in module veupath_chatbot.transport.http.deps) get_experiment_record_detail() (in module veupath_chatbot.transport.http.routers.experiments.results) get_experiment_records() (in module veupath_chatbot.transport.http.routers.experiments.results) get_experiment_report() (in module veupath_chatbot.transport.http.routers.experiments.evaluation) get_experiment_store() (in module veupath_chatbot.services.experiment.store) get_experiments_owned_by_user() (in module veupath_chatbot.transport.http.deps)

get_export() (veupath_chatbot.services.export.service.ExportService method) get_field_value() (veupath_chatbot.platform.config.TomlConfigSettingsSource method) get_for_user() (veupath_chatbot.services.gene_sets.operations.GeneSetService method) get_gene_set() (in module veupath_chatbot.transport.http.routers.gene_sets) get_gene_set_attributes() (in module veupath_chatbot.transport.http.routers.gene_sets) get_gene_set_distribution() (in module veupath_chatbot.transport.http.routers.gene_sets) get_gene_set_record_detail() (in module veupath_chatbot.transport.http.routers.gene_sets) get_gene_set_records() (in module veupath_chatbot.transport.http.routers.gene_sets) get_gene_set_store() (in module veupath_chatbot.services.gene_sets.store) get_graph() (veupath_chatbot.domain.strategy.session.StrategySession method) get_logger() (in module veupath_chatbot.platform.logging) get_model_catalog() (in module veupath_chatbot.ai.models.catalog) get_model_entry() (in module veupath_chatbot.ai.models.catalog) get_node_term() (in module veupath_chatbot.domain.parameters.vocab_utils) get_optional_user() (in module veupath_chatbot.platform.security) get_or_create() (veupath_chatbot.persistence.repositories.user.UserRepository method) get_or_create_by_external_id() (veupath_chatbot.persistence.repositories.user.UserRepository method) get_param_specs_with_context() (in module veupath_chatbot.transport.http.routers.sites.params) get_portal_client() (veupath_chatbot.integrations.veupathdb.site_router.SiteRouter method) get_projection() (veupath_chatbot.persistence.repositories.stream.StreamRepository method) get_raw_record_types() (in module veupath_chatbot.services.catalog.searches) get_raw_searches() (in module veupath_chatbot.services.catalog.searches) get_record_detail() (veupath_chatbot.services.wdk.step_results.StepResultsService method) get_record_type_details() (veupath_chatbot.ai.tools.catalog_registry.CatalogToolsMixin method) (veupath_chatbot.services.catalog.rag_search.RagSearchService method) get_record_type_info() (veupath_chatbot.integrations.veupathdb.strategy_api.records.RecordsMixin method) get_record_types() (in module veupath_chatbot.services.catalog.sites) (in module veupath_chatbot.transport.http.routers.sites.catalog) (veupath_chatbot.ai.agents.experiment.ExperimentAssistantAgent method) (veupath_chatbot.ai.tools.catalog_registry.CatalogToolsMixin method) (veupath_chatbot.ai.tools.catalog_tools.CatalogTools method) (veupath_chatbot.integrations.veupathdb.client.VEuPathDBClient method) (veupath_chatbot.integrations.veupathdb.discovery.DiscoveryService method) (veupath_chatbot.integrations.veupathdb.discovery.SearchCatalog method) (veupath_chatbot.integrations.veupathdb.factory.DiscoveryService method) get_records() (veupath_chatbot.services.wdk.step_results.StepResultsService method) get_redis() (in module veupath_chatbot.platform.redis) get_refreshed_dependent_params() (in module veupath_chatbot.services.catalog.param_resolution) (in module veupath_chatbot.services.catalog.parameters) (veupath_chatbot.integrations.veupathdb.client.VEuPathDBClient method) get_result_count() (in module veupath_chatbot.services.strategies.build) (veupath_chatbot.ai.tools.execution_tools.ExecutionTools method) get_result_count_for_site() (in module veupath_chatbot.services.strategies.build) get_result_gene_lists() (veupath_chatbot.ai.tools.workbench_read_tools.WorkbenchReadToolsMixin method) get_results_api() (in module veupath_chatbot.integrations.veupathdb.factory) get_round_result() (in module veupath_chatbot.ai.orchestration.subkani.utils) get_sample_records() (veupath_chatbot.ai.tools.result_tools.ResultTools method) get_search_details() (veupath_chatbot.integrations.veupathdb.client.VEuPathDBClient method) (veupath_chatbot.integrations.veupathdb.discovery.DiscoveryService method) (veupath_chatbot.integrations.veupathdb.discovery.SearchCatalog method) (veupath_chatbot.integrations.veupathdb.factory.DiscoveryService method) (veupath_chatbot.services.catalog.rag_search.RagSearchService method) get_search_details_with_params() (veupath_chatbot.integrations.veupathdb.client.VEuPathDBClient method) get_search_metadata() (veupath_chatbot.services.catalog.rag_search.RagSearchService method) get_search_parameters() (in module veupath_chatbot.services.catalog.param_resolution) (in module veupath_chatbot.services.catalog.parameters) (veupath_chatbot.ai.agents.experiment.ExperimentAssistantAgent method) (veupath_chatbot.ai.tools.catalog_registry.CatalogToolsMixin method) (veupath_chatbot.ai.tools.catalog_tools.CatalogTools method) get_search_parameters_tool() (in module veupath_chatbot.services.catalog.param_resolution) (in module veupath_chatbot.services.catalog.parameters) get_searches() (in module veupath_chatbot.transport.http.routers.sites.catalog) (veupath_chatbot.integrations.veupathdb.client.VEuPathDBClient method) (veupath_chatbot.integrations.veupathdb.discovery.DiscoveryService method) (veupath_chatbot.integrations.veupathdb.discovery.SearchCatalog method) (veupath_chatbot.integrations.veupathdb.factory.DiscoveryService method) get_seeds_for_site() (in module veupath_chatbot.services.experiment.seed) get_settings() (in module veupath_chatbot.platform.config) get_single_record() (veupath_chatbot.integrations.veupathdb.strategy_api.records.RecordsMixin method) get_site() (in module veupath_chatbot.integrations.veupathdb.factory) (veupath_chatbot.integrations.veupathdb.site_router.SiteRouter method) get_site_router() (in module veupath_chatbot.integrations.veupathdb.site_router) get_step() (veupath_chatbot.domain.strategy.session.StrategyGraph method) get_step_answer() (veupath_chatbot.integrations.veupathdb.strategy_api.reports.ReportsMixin method) get_step_by_id() (veupath_chatbot.domain.strategy.ast.StrategyAST method) get_step_contributions() (veupath_chatbot.ai.tools.workbench_read_tools.WorkbenchReadToolsMixin method) get_step_count() (veupath_chatbot.integrations.veupathdb.strategy_api.reports.ReportsMixin method) (veupath_chatbot.services.strategies.build.StrategyBuildAPI method) get_step_info() (in module veupath_chatbot.services.strategies.wdk_conversion) get_step_preview() (veupath_chatbot.integrations.veupathdb.temporary_results.TemporaryResultsAPI method) get_step_records() (veupath_chatbot.integrations.veupathdb.strategy_api.reports.ReportsMixin method) get_step_results_service() (veupath_chatbot.services.gene_sets.operations.GeneSetService method) get_step_view_filters() (veupath_chatbot.integrations.veupathdb.client.VEuPathDBClient method) get_strategy() (in module veupath_chatbot.transport.http.routers.strategies.crud) (veupath_chatbot.integrations.veupathdb.strategy_api.strategies.StrategiesMixin method) (veupath_chatbot.services.strategies.build.StrategyBuildAPI method) (veupath_chatbot.services.wdk.step_results.StepResultsService method) get_strategy_api() (in module veupath_chatbot.integrations.veupathdb.factory) get_strategy_ast() (in module veupath_chatbot.transport.http.routers.strategies.crud) get_strategy_summary() (veupath_chatbot.ai.tools.conversation_tools.ConversationTools method) get_strategy_tree() (veupath_chatbot.services.gene_sets.operations.GeneSetService method) get_stream_repo() (in module veupath_chatbot.transport.http.deps) get_temporary_result() (veupath_chatbot.integrations.veupathdb.temporary_results.TemporaryResultsAPI method) get_user_repo() (in module veupath_chatbot.transport.http.deps) get_vocab_children() (in module veupath_chatbot.domain.parameters.vocab_utils) get_wdk_client() (in module veupath_chatbot.integrations.veupathdb.factory) get_wdk_operator() (in module veupath_chatbot.domain.strategy.ops) get_workbench_chat_messages() (in module veupath_chatbot.transport.http.routers.experiments.chat) GetGraphFn (in module veupath_chatbot.services.chat.events) go_search_params() (in module veupath_chatbot.services.experiment.seed.helpers) goal (veupath_chatbot.ai.orchestration.delegation.DelegationPlan attribute) google (veupath_chatbot.transport.http.schemas.health.ProviderStatus attribute) graph_cleared (veupath_chatbot.transport.http.routers.internal.SSESchemaIndex attribute) graph_id (veupath_chatbot.transport.http.schemas.sse.GraphClearedEventData attribute) (veupath_chatbot.transport.http.schemas.sse.GraphPlanEventData attribute) (veupath_chatbot.transport.http.schemas.sse.StrategyLinkEventData attribute) (veupath_chatbot.transport.http.schemas.sse.StrategyMetaEventData attribute) (veupath_chatbot.transport.http.schemas.sse.StrategyUpdateEventData attribute) graph_name (veupath_chatbot.transport.http.schemas.sse.StrategyMetaEventData attribute) graph_plan (veupath_chatbot.transport.http.routers.internal.SSESchemaIndex attribute) graph_snapshot (veupath_chatbot.transport.http.routers.internal.SSESchemaIndex attribute) (veupath_chatbot.transport.http.schemas.sse.GraphSnapshotEventData attribute) GraphClearedEventData (class in veupath_chatbot.transport.http.schemas.sse) GraphIntegrityError (class in veupath_chatbot.services.strategies.engine.graph_integrity) GraphOpsMixin (class in veupath_chatbot.services.strategies.engine.graph_ops) GraphPlanEventData (class in veupath_chatbot.transport.http.schemas.sse) GraphSnapshotEventData (class in veupath_chatbot.transport.http.schemas.sse) group (veupath_chatbot.domain.parameters.specs.ParamSpecNormalized attribute) (veupath_chatbot.transport.http.schemas.sites.ParamSpecResponse attribute) GUID (class in veupath_chatbot.persistence.models)

H

handle_wdk_step_error() (in module veupath_chatbot.ai.tools.wdk_error_handler) health_check() (in module veupath_chatbot.transport.http.routers.health) HealthResponse (class in veupath_chatbot.transport.http.schemas.health) help (veupath_chatbot.domain.parameters.specs.ParamSpecNormalized attribute) (veupath_chatbot.transport.http.schemas.sites.ParamSpecResponse attribute)

history (veupath_chatbot.transport.http.schemas.experiments.AiAssistRequest attribute) http_exception_handler() (in module veupath_chatbot.platform.errors) hydrate_graph_from_steps_data() (in module veupath_chatbot.domain.strategy.session) hypergeometric_log_sf() (in module veupath_chatbot.services.experiment.stats)

I

id (veupath_chatbot.ai.models.catalog.ModelEntry attribute) (veupath_chatbot.domain.research.citations.Citation attribute) (veupath_chatbot.domain.strategy.ast.PlanStepNode attribute) (veupath_chatbot.persistence.models.ControlSet attribute) (veupath_chatbot.persistence.models.ExperimentRow attribute) (veupath_chatbot.persistence.models.GeneSetRow attribute) (veupath_chatbot.persistence.models.Stream attribute) (veupath_chatbot.persistence.models.User attribute) (veupath_chatbot.platform.store.Identifiable property) (veupath_chatbot.services.experiment.types.Experiment attribute) (veupath_chatbot.services.experiment.types.experiment.Experiment attribute) (veupath_chatbot.services.experiment.types.GeneInfo attribute) (veupath_chatbot.services.experiment.types.metrics.GeneInfo attribute) (veupath_chatbot.services.gene_sets.reverse_search.GeneSetCandidate attribute) (veupath_chatbot.services.gene_sets.types.GeneSet attribute) (veupath_chatbot.transport.http.routers.control_sets.ControlSetResponse attribute) (veupath_chatbot.transport.http.routers.models.ModelCatalogEntryResponse attribute) (veupath_chatbot.transport.http.schemas.chat.ChatMention attribute) (veupath_chatbot.transport.http.schemas.chat.CitationResponse attribute) (veupath_chatbot.transport.http.schemas.chat.PlanningArtifactResponse attribute) (veupath_chatbot.transport.http.schemas.chat.ToolCallResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ControlSetSummaryResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentSummaryResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.GeneInfoResponse attribute) (veupath_chatbot.transport.http.schemas.gene_sets.GeneSetResponse attribute) (veupath_chatbot.transport.http.schemas.plan.BasePlanNode attribute) (veupath_chatbot.transport.http.schemas.sites.SiteResponse attribute) (veupath_chatbot.transport.http.schemas.sse.GeneSetSummary attribute) (veupath_chatbot.transport.http.schemas.sse.SubKaniToolCallEndEventData attribute) (veupath_chatbot.transport.http.schemas.sse.SubKaniToolCallStartEventData attribute) (veupath_chatbot.transport.http.schemas.sse.ToolCallEndEventData attribute) (veupath_chatbot.transport.http.schemas.sse.ToolCallStartEventData attribute) (veupath_chatbot.transport.http.schemas.steps.StepResponse attribute) (veupath_chatbot.transport.http.schemas.strategies.StrategyResponse attribute) Identifiable (class in veupath_chatbot.platform.store) IdMappingMixin (class in veupath_chatbot.services.strategies.engine.id_mapping) impl (veupath_chatbot.persistence.models.GUID attribute) implied_organism (veupath_chatbot.services.search_rerank.QueryIntent attribute) implied_organism_score (veupath_chatbot.services.search_rerank.QueryIntent attribute) INCOMPATIBLE_STEPS (veupath_chatbot.platform.errors.ErrorCode attribute) increment (veupath_chatbot.domain.parameters.specs.ParamSpecNormalized attribute) (veupath_chatbot.transport.http.schemas.sites.ParamSpecResponse attribute) infer_enrichment_type() (in module veupath_chatbot.services.experiment.enrichment) infer_kind() (veupath_chatbot.domain.strategy.ast.PlanStepNode method) ingest_public_strategies() (in module veupath_chatbot.integrations.vectorstore.ingest.public_strategies) ingest_site() (in module veupath_chatbot.integrations.vectorstore.ingest.public_strategies) (in module veupath_chatbot.integrations.vectorstore.ingest.wdk_catalog) ingest_wdk_catalog() (in module veupath_chatbot.integrations.vectorstore.ingest.wdk_catalog)

init_db() (in module veupath_chatbot.persistence.session) init_redis() (in module veupath_chatbot.platform.redis) initial_display_value (veupath_chatbot.transport.http.schemas.sites.ParamSpecResponse attribute) inPositives (veupath_chatbot.services.gene_sets.ensemble.EnsembleScore attribute) INPUT_DATASET (veupath_chatbot.domain.parameters._value_helpers.ParamKind attribute) input_price (veupath_chatbot.ai.models.catalog.ModelEntry attribute) (veupath_chatbot.transport.http.routers.models.ModelCatalogEntryResponse attribute) input_step_id (veupath_chatbot.services.strategies.engine.graph_integrity.GraphIntegrityError attribute) instance (veupath_chatbot.platform.errors.ProblemDetail attribute) INTERNAL_ERROR (veupath_chatbot.platform.errors.ErrorCode attribute) InternalError interpro_params() (in module veupath_chatbot.services.experiment.seed.helpers) INTERSECT (veupath_chatbot.domain.strategy.ops.CombineOp attribute) intersection (veupath_chatbot.services.experiment.overlap.PairwiseOverlap attribute) INVALID_PARAMETERS (veupath_chatbot.platform.errors.ErrorCode attribute) INVALID_STRATEGY (veupath_chatbot.platform.errors.ErrorCode attribute) invalidate_build() (veupath_chatbot.domain.strategy.session.StrategyGraph method) is_chooser_search() (in module veupath_chatbot.services.catalog.searches) is_development (veupath_chatbot.platform.config.Settings property) is_enrichment_analysis() (in module veupath_chatbot.services.experiment.enrichment) is_gene_id_like (veupath_chatbot.services.search_rerank.QueryIntent attribute) is_internal (veupath_chatbot.transport.http.schemas.strategies.WdkStrategySummaryResponse attribute) is_internal_wdk_strategy_name() (in module veupath_chatbot.integrations.veupathdb.strategy_api.helpers) is_leaf_only_strategy() (in module veupath_chatbot.services.strategies.wdk_counts) is_number (veupath_chatbot.domain.parameters.specs.ParamSpecNormalized attribute) (veupath_chatbot.transport.http.schemas.sites.ParamSpecResponse attribute) is_portal (veupath_chatbot.integrations.veupathdb.site_router.SiteConfig attribute) (veupath_chatbot.transport.http.schemas.sites.SiteResponse attribute) is_primary (veupath_chatbot.transport.http.schemas.experiments.BenchmarkControlSet attribute) is_primary_benchmark (veupath_chatbot.services.experiment.types.Experiment attribute) (veupath_chatbot.services.experiment.types.experiment.Experiment attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentSummaryResponse attribute) is_production (veupath_chatbot.platform.config.Settings property) is_public (veupath_chatbot.persistence.models.ControlSet attribute) (veupath_chatbot.transport.http.routers.control_sets.ControlSetResponse attribute) (veupath_chatbot.transport.http.routers.control_sets.CreateControlSetRequest attribute) is_saved (veupath_chatbot.persistence.models.StreamProjection attribute) (veupath_chatbot.transport.http.schemas.sse.StrategyLinkEventData attribute) (veupath_chatbot.transport.http.schemas.strategies.StrategyResponse attribute) (veupath_chatbot.transport.http.schemas.strategies.UpdateStrategyRequest attribute) (veupath_chatbot.transport.http.schemas.strategies.WdkStrategySummaryResponse attribute) is_sortable() (in module veupath_chatbot.services.wdk.helpers) is_suggested_score() (in module veupath_chatbot.services.wdk.helpers) is_tree_mode (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig property) (veupath_chatbot.services.experiment.types.ExperimentConfig property) is_valid (veupath_chatbot.transport.http.schemas.sites.SearchValidationPayload attribute) is_visible (veupath_chatbot.domain.parameters.specs.ParamSpecNormalized attribute) (veupath_chatbot.transport.http.schemas.sites.ParamSpecResponse attribute) iter_compact_steps() (in module veupath_chatbot.integrations.vectorstore.ingest.public_strategies_helpers)

J

jaccard (veupath_chatbot.services.experiment.overlap.PairwiseOverlap attribute) JSONArray (in module veupath_chatbot.platform.types)

JSONObject (in module veupath_chatbot.platform.types) JSONValue (in module veupath_chatbot.platform.types)

K

k (veupath_chatbot.services.experiment.types.CrossValidationResult attribute) (veupath_chatbot.services.experiment.types.metrics.CrossValidationResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.CrossValidationResultResponse attribute) k_folds (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) (veupath_chatbot.transport.http.schemas.experiments.RunCrossValidationRequest attribute)

kind (veupath_chatbot.domain.parameters._value_helpers.ProcessedParam attribute) (veupath_chatbot.services.strategies.engine.graph_integrity.GraphIntegrityError attribute) (veupath_chatbot.transport.http.schemas.steps.StepResponse attribute)

L

label (veupath_chatbot.services.experiment.overlap.PerExperimentSummary attribute) (veupath_chatbot.services.experiment.types.NegativeSetVariant attribute) (veupath_chatbot.services.experiment.types.rank.NegativeSetVariant attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.NegativeSetVariantResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.BenchmarkControlSet attribute) labelA (veupath_chatbot.services.experiment.overlap.PairwiseOverlap attribute) labelB (veupath_chatbot.services.experiment.overlap.PairwiseOverlap attribute) last_event_id (veupath_chatbot.persistence.models.StreamProjection attribute) last_tool_calls (veupath_chatbot.transport.http.schemas.chat.ThinkingResponse attribute) lazy_fetch_wdk_detail() (in module veupath_chatbot.services.strategies.wdk_sync) lifespan() (in module veupath_chatbot.main) limit_authors() (in module veupath_chatbot.services.research.utils) list_active() (in module veupath_chatbot.transport.http.routers.operations) list_active_operations() (veupath_chatbot.persistence.repositories.stream.StreamRepository method) list_all() (veupath_chatbot.services.experiment.store.ExperimentStore method) (veupath_chatbot.services.gene_sets.store.GeneSetStore method) list_analysis_types() (veupath_chatbot.integrations.veupathdb.client.VEuPathDBClient method) (veupath_chatbot.integrations.veupathdb.strategy_api.analyses.AnalysisMixin method) (veupath_chatbot.services.wdk.step_results.StepResultsService method) list_by_benchmark() (veupath_chatbot.services.experiment.store.ExperimentStore method) list_by_site() (veupath_chatbot.persistence.repositories.control_set.ControlSetRepository method) list_control_sets() (in module veupath_chatbot.transport.http.routers.control_sets) list_current_steps() (veupath_chatbot.ai.tools.strategy_tools.graph_ops.StrategyGraphOps method) list_dismissed_projections() (veupath_chatbot.persistence.repositories.stream.StreamRepository method) list_dismissed_strategies() (in module veupath_chatbot.transport.http.routers.strategies.crud) list_experiments() (in module veupath_chatbot.transport.http.routers.experiments.crud) list_for_user() (veupath_chatbot.services.gene_sets.operations.GeneSetService method) (veupath_chatbot.services.gene_sets.store.GeneSetStore method) list_gene_sets() (in module veupath_chatbot.transport.http.routers.gene_sets) list_models() (in module veupath_chatbot.transport.http.routers.models) list_organisms() (in module veupath_chatbot.transport.http.routers.sites.genes) list_projections() (veupath_chatbot.persistence.repositories.stream.StreamRepository method) list_searches() (in module veupath_chatbot.services.catalog.searches) (veupath_chatbot.ai.agents.experiment.ExperimentAssistantAgent method) (veupath_chatbot.ai.tools.catalog_registry.CatalogToolsMixin method) (veupath_chatbot.ai.tools.catalog_tools.CatalogTools method) list_sites() (in module veupath_chatbot.integrations.veupathdb.factory) (in module veupath_chatbot.services.catalog.sites) (in module veupath_chatbot.transport.http.routers.sites.catalog) (veupath_chatbot.ai.tools.catalog_registry.CatalogToolsMixin method) (veupath_chatbot.ai.tools.catalog_tools.CatalogTools method) (veupath_chatbot.integrations.veupathdb.site_router.SiteRouter method) list_size (veupath_chatbot.services.experiment.types.optimization.TreeOptimizationTrial attribute) (veupath_chatbot.services.experiment.types.TreeOptimizationTrial attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.TreeOptimizationTrialResponse attribute) list_size_vs_recall (veupath_chatbot.services.experiment.types.rank.RankMetrics attribute) (veupath_chatbot.services.experiment.types.RankMetrics attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.RankMetricsResponse attribute)

list_step_analyses() (veupath_chatbot.integrations.veupathdb.client.VEuPathDBClient method) (veupath_chatbot.integrations.veupathdb.strategy_api.analyses.AnalysisMixin method) list_step_filters() (veupath_chatbot.integrations.veupathdb.strategy_api.filters.FilterMixin method) list_str() (in module veupath_chatbot.services.research.utils) list_strategies() (in module veupath_chatbot.transport.http.routers.strategies.crud) (veupath_chatbot.integrations.veupathdb.strategy_api.strategies.StrategiesMixin method) list_tools() (in module veupath_chatbot.transport.http.routers.tools) list_transforms() (in module veupath_chatbot.services.catalog.searches) (veupath_chatbot.ai.tools.catalog_tools.CatalogTools method) list_workbench_gene_sets() (veupath_chatbot.ai.tools.planner.workbench_tools.WorkbenchToolsMixin method) literature_search() (veupath_chatbot.ai.tools.research_registry.ResearchToolsMixin method) literature_search_service (veupath_chatbot.ai.tools.research_registry.ResearchToolsMixin attribute) LiteratureSearchService (class in veupath_chatbot.services.research.literature_search) llm_call_count (veupath_chatbot.ai.orchestration.subkani.utils.SubKaniRoundResult attribute) (veupath_chatbot.transport.http.schemas.chat.SubKaniTokenUsageResponse attribute) (veupath_chatbot.transport.http.schemas.chat.TokenUsageResponse attribute) (veupath_chatbot.transport.http.schemas.sse.MessageEndEventData attribute) (veupath_chatbot.transport.http.schemas.sse.SubKaniTaskEndEventData attribute) llm_configured (veupath_chatbot.transport.http.schemas.health.SystemConfigResponse attribute) load() (veupath_chatbot.integrations.veupathdb.discovery.SearchCatalog method) load_dialect_impl() (veupath_chatbot.persistence.models.GUID method) load_sites_config() (in module veupath_chatbot.integrations.veupathdb.site_router) load_system_prompt() (in module veupath_chatbot.ai.prompts.loader) local_id (veupath_chatbot.domain.strategy.compile.CompiledStep attribute) location (veupath_chatbot.transport.http.routers.sites.genes.GeneSearchResultResponse attribute) (veupath_chatbot.transport.http.routers.sites.genes.ResolvedGeneResponse attribute) location_params() (in module veupath_chatbot.services.experiment.seed.helpers) log_format (veupath_chatbot.platform.config.Settings attribute) log_level (veupath_chatbot.platform.config.Settings attribute) log_scale (veupath_chatbot.services.parameter_optimization.ParameterSpec attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationParameterSpecData attribute) login_with_password() (in module veupath_chatbot.transport.http.routers.veupathdb_auth) LoginPayload (class in veupath_chatbot.transport.http.routers.veupathdb_auth) logout() (in module veupath_chatbot.transport.http.routers.veupathdb_auth) LONLY (veupath_chatbot.domain.strategy.ops.CombineOp attribute) looks_blocked() (in module veupath_chatbot.services.research.utils) lookup_gene_records() (veupath_chatbot.ai.tools.planner.gene_tools.GeneToolsMixin method) lookup_genes() (veupath_chatbot.ai.agents.experiment.ExperimentAssistantAgent method) lookup_genes_by_text() (in module veupath_chatbot.services.gene_lookup) (in module veupath_chatbot.services.gene_lookup.lookup) lookup_phyletic_codes() (in module veupath_chatbot.services.catalog.param_resolution) (in module veupath_chatbot.services.catalog.parameters) (veupath_chatbot.ai.tools.catalog_registry.CatalogToolsMixin method) (veupath_chatbot.ai.tools.catalog_tools.CatalogTools method) lower (veupath_chatbot.services.experiment.types.ConfidenceInterval attribute) (veupath_chatbot.services.experiment.types.rank.ConfidenceInterval attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ConfidenceIntervalResponse attribute)

M

main() (in module veupath_chatbot.devtools.openapi) (in module veupath_chatbot.integrations.vectorstore.ingest.public_strategies) (in module veupath_chatbot.integrations.vectorstore.ingest.wdk_catalog) make_citation() (in module veupath_chatbot.services.research.clients._base) make_record_type_resolver() (in module veupath_chatbot.services.catalog.searches) map_dict_tree() (in module veupath_chatbot.domain.strategy.tree) match_vocab_value() (in module veupath_chatbot.domain.parameters.vocab_utils) matchedFields (veupath_chatbot.transport.http.routers.sites.genes.GeneSearchResultResponse attribute) max (veupath_chatbot.services.experiment.types.optimization.OptimizationSpec attribute) (veupath_chatbot.services.experiment.types.OptimizationSpec attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OptimizationSpecResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.OptimizationSpecRequest attribute) max_context_size (veupath_chatbot.ai.engines.mock.MockEngine attribute) max_enrichment_terms (veupath_chatbot.transport.http.schemas.gene_sets.GeneConfidenceRequest attribute) max_length (veupath_chatbot.domain.parameters.specs.ParamSpecNormalized attribute) max_list_size (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) max_selected_count (veupath_chatbot.domain.parameters.specs.ParamSpecNormalized attribute) (veupath_chatbot.transport.http.schemas.sites.ParamSpecResponse attribute) max_val (veupath_chatbot.services.experiment.types.optimization.ThresholdKnob attribute) (veupath_chatbot.services.experiment.types.ThresholdKnob attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ThresholdKnobResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.ThresholdKnobRequest attribute) max_value (veupath_chatbot.domain.parameters.specs.ParamSpecNormalized attribute) (veupath_chatbot.services.parameter_optimization.ParameterSpec attribute) (veupath_chatbot.transport.http.schemas.experiments.ThresholdSweepRequest attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationParameterSpecData attribute) (veupath_chatbot.transport.http.schemas.sites.ParamSpecResponse attribute) maxScore (veupath_chatbot.services.experiment.enrichment_compare.EnrichmentRow attribute) mcc (veupath_chatbot.services.experiment.types.ExperimentMetrics attribute) (veupath_chatbot.services.experiment.types.metrics.ExperimentMetrics attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentMetricsResponse attribute) mean (veupath_chatbot.services.experiment.types.ConfidenceInterval attribute) (veupath_chatbot.services.experiment.types.rank.ConfidenceInterval attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ConfidenceIntervalResponse attribute) mean_metrics (veupath_chatbot.services.experiment.types.CrossValidationResult attribute) (veupath_chatbot.services.experiment.types.metrics.CrossValidationResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.CrossValidationResultResponse attribute) mentions (veupath_chatbot.transport.http.schemas.chat.ChatRequest attribute) merge_analysis_params() (in module veupath_chatbot.services.wdk.helpers) message (veupath_chatbot.domain.strategy.validate.StepValidationIssue attribute) (veupath_chatbot.services.strategies.engine.graph_integrity.GraphIntegrityError attribute) (veupath_chatbot.transport.http.schemas.chat.ChatRequest attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentProgressDataResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepAnalysisProgressDataResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.AiAssistRequest attribute) (veupath_chatbot.transport.http.schemas.workbench_chat.WorkbenchChatRequest attribute) message_count (veupath_chatbot.persistence.models.StreamProjection attribute) message_end (veupath_chatbot.transport.http.routers.internal.SSESchemaIndex attribute) message_id (veupath_chatbot.transport.http.schemas.sse.AssistantDeltaEventData attribute) (veupath_chatbot.transport.http.schemas.sse.AssistantMessageEventData attribute) (veupath_chatbot.transport.http.schemas.sse.UserMessageEventData attribute) message_start (veupath_chatbot.transport.http.routers.internal.SSESchemaIndex attribute) MessageEndEventData (class in veupath_chatbot.transport.http.schemas.sse) MessageResponse (class in veupath_chatbot.transport.http.schemas.chat) messages (veupath_chatbot.transport.http.schemas.strategies.StrategyResponse attribute) MessageStartEventData (class in veupath_chatbot.transport.http.schemas.sse) metadata (veupath_chatbot.domain.strategy.ast.StrategyAST attribute) (veupath_chatbot.persistence.models.Base attribute) (veupath_chatbot.transport.http.schemas.plan.StrategyPlan attribute) method (veupath_chatbot.services.parameter_optimization.OptimizationConfig attribute) metric_cis (veupath_chatbot.services.experiment.types.BootstrapResult attribute) (veupath_chatbot.services.experiment.types.rank.BootstrapResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.BootstrapResultResponse attribute) metrics (veupath_chatbot.services.experiment.types.Experiment attribute) (veupath_chatbot.services.experiment.types.experiment.Experiment attribute) (veupath_chatbot.services.experiment.types.FoldMetrics attribute) (veupath_chatbot.services.experiment.types.metrics.FoldMetrics attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.FoldMetricsResponse attribute) metrics_from_control_result() (in module veupath_chatbot.services.experiment.metrics) min (veupath_chatbot.services.experiment.types.optimization.OptimizationSpec attribute) (veupath_chatbot.services.experiment.types.OptimizationSpec attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OptimizationSpecResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.OptimizationSpecRequest attribute) min_selected_count (veupath_chatbot.domain.parameters.specs.ParamSpecNormalized attribute) (veupath_chatbot.transport.http.schemas.sites.ParamSpecResponse attribute) min_val (veupath_chatbot.services.experiment.types.optimization.ThresholdKnob attribute) (veupath_chatbot.services.experiment.types.ThresholdKnob attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ThresholdKnobResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.ThresholdKnobRequest attribute) min_value (veupath_chatbot.domain.parameters.specs.ParamSpecNormalized attribute) (veupath_chatbot.services.parameter_optimization.ParameterSpec attribute) (veupath_chatbot.transport.http.schemas.experiments.ThresholdSweepRequest attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationParameterSpecData attribute) (veupath_chatbot.transport.http.schemas.sites.ParamSpecResponse attribute) MINUS (veupath_chatbot.domain.strategy.ops.CombineOp attribute) MockEngine (class in veupath_chatbot.ai.engines.mock) mode (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentSummaryResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) model (veupath_chatbot.ai.models.catalog.ModelEntry attribute) (veupath_chatbot.integrations.embeddings.openai_embeddings.OpenAIEmbeddings attribute) (veupath_chatbot.transport.http.routers.models.ModelCatalogEntryResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.AiAssistRequest attribute) model_config (veupath_chatbot.integrations.veupathdb.site_router.RoutingConfig attribute) (veupath_chatbot.integrations.veupathdb.site_router.SiteConfig attribute) (veupath_chatbot.integrations.veupathdb.site_router.SitesConfig attribute) (veupath_chatbot.platform.config.Settings attribute) (veupath_chatbot.platform.errors.ProblemDetail attribute) (veupath_chatbot.transport.http.routers.control_sets.ControlSetResponse attribute) (veupath_chatbot.transport.http.routers.control_sets.CreateControlSetRequest attribute) (veupath_chatbot.transport.http.routers.experiments.crud.PatchExperimentRequest attribute) (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) (veupath_chatbot.transport.http.routers.internal.SSESchemaIndex attribute) (veupath_chatbot.transport.http.routers.models.ModelCatalogEntryResponse attribute) (veupath_chatbot.transport.http.routers.models.ModelListResponse attribute) (veupath_chatbot.transport.http.routers.sites.genes.GeneResolveRequest attribute) (veupath_chatbot.transport.http.routers.sites.genes.GeneResolveResponse attribute) (veupath_chatbot.transport.http.routers.sites.genes.GeneSearchResponse attribute) (veupath_chatbot.transport.http.routers.sites.genes.GeneSearchResultResponse attribute) (veupath_chatbot.transport.http.routers.sites.genes.OrganismsResponse attribute) (veupath_chatbot.transport.http.routers.sites.genes.ResolvedGeneResponse attribute) (veupath_chatbot.transport.http.routers.veupathdb_auth.LoginPayload attribute) (veupath_chatbot.transport.http.schemas.chat.ChatMention attribute) (veupath_chatbot.transport.http.schemas.chat.ChatRequest attribute) (veupath_chatbot.transport.http.schemas.chat.CitationResponse attribute) (veupath_chatbot.transport.http.schemas.chat.MessageResponse attribute) (veupath_chatbot.transport.http.schemas.chat.PlanningArtifactResponse attribute) (veupath_chatbot.transport.http.schemas.chat.SubKaniActivityResponse attribute) (veupath_chatbot.transport.http.schemas.chat.SubKaniTokenUsageResponse attribute) (veupath_chatbot.transport.http.schemas.chat.ThinkingResponse attribute) (veupath_chatbot.transport.http.schemas.chat.TokenUsageResponse attribute) (veupath_chatbot.transport.http.schemas.chat.ToolCallResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.BootstrapResultResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ConfidenceIntervalResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ConfusionMatrixResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ControlSetSummaryResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.CrossValidationResultResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.EnrichmentResultResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.EnrichmentTermResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentMetricsResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentProgressDataResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentSummaryResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.FoldMetricsResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.GeneInfoResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.NegativeSetVariantResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OperatorComparisonResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OperatorKnobResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OperatorVariantResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OptimizationResultResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OptimizationSpecResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ParameterSensitivityResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ParameterSweepPointResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.RankMetricsResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepAnalysisProgressDataResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepAnalysisResultResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepContributionResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepEvaluationResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ThresholdKnobResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.TreeOptimizationResultResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.TreeOptimizationTrialResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.TrialProgressDataResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.AiAssistRequest attribute) (veupath_chatbot.transport.http.schemas.experiments.BatchOrganismTargetRequest attribute) (veupath_chatbot.transport.http.schemas.experiments.BenchmarkControlSet attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateBatchExperimentRequest attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateBenchmarkRequest attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) (veupath_chatbot.transport.http.schemas.experiments.CustomEnrichRequest attribute) (veupath_chatbot.transport.http.schemas.experiments.EnrichmentCompareRequest attribute) (veupath_chatbot.transport.http.schemas.experiments.OperatorKnobRequest attribute) (veupath_chatbot.transport.http.schemas.experiments.OptimizationSpecRequest attribute) (veupath_chatbot.transport.http.schemas.experiments.OverlapRequest attribute) (veupath_chatbot.transport.http.schemas.experiments.RefineRequest attribute) (veupath_chatbot.transport.http.schemas.experiments.RunAnalysisRequest attribute) (veupath_chatbot.transport.http.schemas.experiments.RunCrossValidationRequest attribute) (veupath_chatbot.transport.http.schemas.experiments.RunEnrichmentRequest attribute) (veupath_chatbot.transport.http.schemas.experiments.ThresholdKnobRequest attribute) (veupath_chatbot.transport.http.schemas.experiments.ThresholdSweepRequest attribute) (veupath_chatbot.transport.http.schemas.gene_sets.CreateGeneSetRequest attribute) (veupath_chatbot.transport.http.schemas.gene_sets.EnsembleScoringRequest attribute) (veupath_chatbot.transport.http.schemas.gene_sets.GeneConfidenceRequest attribute) (veupath_chatbot.transport.http.schemas.gene_sets.GeneConfidenceScoreResponse attribute) (veupath_chatbot.transport.http.schemas.gene_sets.GeneSetEnrichRequest attribute) (veupath_chatbot.transport.http.schemas.gene_sets.GeneSetResponse attribute) (veupath_chatbot.transport.http.schemas.gene_sets.ReverseSearchRequest attribute) (veupath_chatbot.transport.http.schemas.gene_sets.ReverseSearchResultItem attribute) (veupath_chatbot.transport.http.schemas.gene_sets.RunGeneSetAnalysisRequest attribute) (veupath_chatbot.transport.http.schemas.gene_sets.SetOperationRequest attribute) (veupath_chatbot.transport.http.schemas.health.HealthResponse attribute) (veupath_chatbot.transport.http.schemas.health.ProviderStatus attribute) (veupath_chatbot.transport.http.schemas.health.SystemConfigResponse attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationParameterSpecData attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationProgressEventData attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationTrialData attribute) (veupath_chatbot.transport.http.schemas.plan.BasePlanNode attribute) (veupath_chatbot.transport.http.schemas.plan.ColocationParams attribute) (veupath_chatbot.transport.http.schemas.plan.PlanMetadata attribute) (veupath_chatbot.transport.http.schemas.plan.PlanNode attribute) (veupath_chatbot.transport.http.schemas.plan.PlanNormalizeRequest attribute) (veupath_chatbot.transport.http.schemas.plan.PlanNormalizeResponse attribute) (veupath_chatbot.transport.http.schemas.plan.StepAnalysisSpec attribute) (veupath_chatbot.transport.http.schemas.plan.StepFilterSpec attribute) (veupath_chatbot.transport.http.schemas.plan.StepReportSpec attribute) (veupath_chatbot.transport.http.schemas.plan.StrategyPlan attribute) (veupath_chatbot.transport.http.schemas.sites.DependentParamsRequest attribute) (veupath_chatbot.transport.http.schemas.sites.DependentParamsResponse attribute) (veupath_chatbot.transport.http.schemas.sites.ParamSpecResponse attribute) (veupath_chatbot.transport.http.schemas.sites.ParamSpecsRequest attribute) (veupath_chatbot.transport.http.schemas.sites.RecordTypeResponse attribute) (veupath_chatbot.transport.http.schemas.sites.SearchDetailsResponse attribute) (veupath_chatbot.transport.http.schemas.sites.SearchResponse attribute) (veupath_chatbot.transport.http.schemas.sites.SearchValidationErrors attribute) (veupath_chatbot.transport.http.schemas.sites.SearchValidationPayload attribute) (veupath_chatbot.transport.http.schemas.sites.SearchValidationRequest attribute) (veupath_chatbot.transport.http.schemas.sites.SearchValidationResponse attribute) (veupath_chatbot.transport.http.schemas.sites.SiteResponse attribute) (veupath_chatbot.transport.http.schemas.sse.AssistantDeltaEventData attribute) (veupath_chatbot.transport.http.schemas.sse.AssistantMessageEventData attribute) (veupath_chatbot.transport.http.schemas.sse.CitationsEventData attribute) (veupath_chatbot.transport.http.schemas.sse.ErrorEventData attribute) (veupath_chatbot.transport.http.schemas.sse.ExecutorBuildRequestEventData attribute) (veupath_chatbot.transport.http.schemas.sse.GeneSetSummary attribute) (veupath_chatbot.transport.http.schemas.sse.GraphClearedEventData attribute) (veupath_chatbot.transport.http.schemas.sse.GraphPlanEventData attribute) (veupath_chatbot.transport.http.schemas.sse.GraphSnapshotEventData attribute) (veupath_chatbot.transport.http.schemas.sse.MessageEndEventData attribute) (veupath_chatbot.transport.http.schemas.sse.MessageStartEventData attribute) (veupath_chatbot.transport.http.schemas.sse.ModelSelectedEventData attribute) (veupath_chatbot.transport.http.schemas.sse.PlanningArtifactEventData attribute) (veupath_chatbot.transport.http.schemas.sse.ReasoningEventData attribute) (veupath_chatbot.transport.http.schemas.sse.StrategyLinkEventData attribute) (veupath_chatbot.transport.http.schemas.sse.StrategyMetaEventData attribute) (veupath_chatbot.transport.http.schemas.sse.StrategyUpdateEventData attribute) (veupath_chatbot.transport.http.schemas.sse.SubKaniTaskEndEventData attribute) (veupath_chatbot.transport.http.schemas.sse.SubKaniTaskStartEventData attribute) (veupath_chatbot.transport.http.schemas.sse.SubKaniToolCallEndEventData attribute) (veupath_chatbot.transport.http.schemas.sse.SubKaniToolCallStartEventData attribute) (veupath_chatbot.transport.http.schemas.sse.TokenUsagePartialEventData attribute) (veupath_chatbot.transport.http.schemas.sse.ToolCallEndEventData attribute) (veupath_chatbot.transport.http.schemas.sse.ToolCallStartEventData attribute) (veupath_chatbot.transport.http.schemas.sse.UserMessageEventData attribute) (veupath_chatbot.transport.http.schemas.sse.WorkbenchGeneSetEventData attribute) (veupath_chatbot.transport.http.schemas.steps.PrimaryKeyPart attribute) (veupath_chatbot.transport.http.schemas.steps.RecordDetailRequest attribute) (veupath_chatbot.transport.http.schemas.steps.StepAnalysisRequest attribute) (veupath_chatbot.transport.http.schemas.steps.StepAnalysisResponse attribute) (veupath_chatbot.transport.http.schemas.steps.StepAnalysisRunResponse attribute) (veupath_chatbot.transport.http.schemas.steps.StepFilterRequest attribute) (veupath_chatbot.transport.http.schemas.steps.StepFilterResponse attribute) (veupath_chatbot.transport.http.schemas.steps.StepFiltersResponse attribute) (veupath_chatbot.transport.http.schemas.steps.StepReportRequest attribute) (veupath_chatbot.transport.http.schemas.steps.StepReportResponse attribute) (veupath_chatbot.transport.http.schemas.steps.StepReportRunResponse attribute) (veupath_chatbot.transport.http.schemas.steps.StepResponse attribute) (veupath_chatbot.transport.http.schemas.strategies.CreateStrategyRequest attribute) (veupath_chatbot.transport.http.schemas.strategies.OpenStrategyRequest attribute) (veupath_chatbot.transport.http.schemas.strategies.OpenStrategyResponse attribute) (veupath_chatbot.transport.http.schemas.strategies.StepCountsRequest attribute) (veupath_chatbot.transport.http.schemas.strategies.StepCountsResponse attribute) (veupath_chatbot.transport.http.schemas.strategies.StrategyResponse attribute) (veupath_chatbot.transport.http.schemas.strategies.UpdateStrategyRequest attribute) (veupath_chatbot.transport.http.schemas.strategies.WdkStrategySummaryResponse attribute) (veupath_chatbot.transport.http.schemas.veupathdb_auth.AuthStatusResponse attribute) (veupath_chatbot.transport.http.schemas.veupathdb_auth.AuthSuccessResponse attribute) (veupath_chatbot.transport.http.schemas.workbench_chat.WorkbenchChatRequest attribute) (veupath_chatbot.transport.http.schemas.workbench_chat.WorkbenchChatResponse attribute) model_id (veupath_chatbot.persistence.models.StreamProjection attribute) (veupath_chatbot.transport.http.schemas.chat.ChatRequest attribute) (veupath_chatbot.transport.http.schemas.chat.MessageResponse attribute) (veupath_chatbot.transport.http.schemas.chat.TokenUsageResponse attribute) (veupath_chatbot.transport.http.schemas.sse.MessageEndEventData attribute) (veupath_chatbot.transport.http.schemas.sse.ModelSelectedEventData attribute) (veupath_chatbot.transport.http.schemas.sse.SubKaniTaskEndEventData attribute) (veupath_chatbot.transport.http.schemas.sse.SubKaniTaskStartEventData attribute) (veupath_chatbot.transport.http.schemas.strategies.StrategyResponse attribute) (veupath_chatbot.transport.http.schemas.workbench_chat.WorkbenchChatRequest attribute) model_post_init() (veupath_chatbot.platform.config.Settings method) model_selected (veupath_chatbot.transport.http.routers.internal.SSESchemaIndex attribute) ModelCatalogEntryResponse (class in veupath_chatbot.transport.http.routers.models) ModelEntry (class in veupath_chatbot.ai.models.catalog) ModelListResponse (class in veupath_chatbot.transport.http.routers.models)

ModelProvider (in module veupath_chatbot.platform.types) models (veupath_chatbot.transport.http.routers.models.ModelListResponse attribute) (veupath_chatbot.transport.http.schemas.chat.SubKaniActivityResponse attribute) ModelSelectedEventData (class in veupath_chatbot.transport.http.schemas.sse) module veupath_chatbot.ai.agents.executor veupath_chatbot.ai.agents.experiment veupath_chatbot.ai.agents.factory veupath_chatbot.ai.agents.subtask veupath_chatbot.ai.agents.workbench veupath_chatbot.ai.engines.cached_anthropic veupath_chatbot.ai.engines.mock veupath_chatbot.ai.engines.responses_openai veupath_chatbot.ai.models.catalog veupath_chatbot.ai.models.pricing veupath_chatbot.ai.orchestration.delegation veupath_chatbot.ai.orchestration.scheduler veupath_chatbot.ai.orchestration.subkani.orchestrator veupath_chatbot.ai.orchestration.subkani.prompts veupath_chatbot.ai.orchestration.subkani.utils veupath_chatbot.ai.prompts.executor_prompt veupath_chatbot.ai.prompts.loader veupath_chatbot.ai.prompts.workbench_chat veupath_chatbot.ai.tools.catalog_rag_tools veupath_chatbot.ai.tools.catalog_registry veupath_chatbot.ai.tools.catalog_tools veupath_chatbot.ai.tools.combined_result veupath_chatbot.ai.tools.conversation_tools veupath_chatbot.ai.tools.example_plans_rag_tools veupath_chatbot.ai.tools.execution_tools veupath_chatbot.ai.tools.export_tools veupath_chatbot.ai.tools.planner.artifact_tools veupath_chatbot.ai.tools.planner.experiment_tools veupath_chatbot.ai.tools.planner.gene_tools veupath_chatbot.ai.tools.planner.optimization_tools veupath_chatbot.ai.tools.planner.workbench_tools veupath_chatbot.ai.tools.query_validation veupath_chatbot.ai.tools.registry veupath_chatbot.ai.tools.research_registry veupath_chatbot.ai.tools.result_tools veupath_chatbot.ai.tools.strategy_registry veupath_chatbot.ai.tools.strategy_tools.attachment_ops veupath_chatbot.ai.tools.strategy_tools.discovery_ops veupath_chatbot.ai.tools.strategy_tools.edit_ops veupath_chatbot.ai.tools.strategy_tools.graph_ops veupath_chatbot.ai.tools.strategy_tools.operations veupath_chatbot.ai.tools.strategy_tools.step_ops veupath_chatbot.ai.tools.unified_registry veupath_chatbot.ai.tools.wdk_error_handler veupath_chatbot.ai.tools.workbench_read_tools veupath_chatbot.devtools.openapi veupath_chatbot.domain.parameters._decode_values veupath_chatbot.domain.parameters._value_helpers veupath_chatbot.domain.parameters.canonicalize veupath_chatbot.domain.parameters.normalize veupath_chatbot.domain.parameters.specs veupath_chatbot.domain.parameters.vocab_utils veupath_chatbot.domain.research.citations veupath_chatbot.domain.strategy.ast veupath_chatbot.domain.strategy.compile veupath_chatbot.domain.strategy.explain veupath_chatbot.domain.strategy.metadata veupath_chatbot.domain.strategy.ops veupath_chatbot.domain.strategy.session veupath_chatbot.domain.strategy.tree veupath_chatbot.domain.strategy.validate veupath_chatbot.integrations.embeddings.openai_embeddings veupath_chatbot.integrations.vectorstore.bootstrap veupath_chatbot.integrations.vectorstore.collections veupath_chatbot.integrations.vectorstore.dependent_vocab_cache veupath_chatbot.integrations.vectorstore.ingest.pipeline veupath_chatbot.integrations.vectorstore.ingest.public_fetch veupath_chatbot.integrations.vectorstore.ingest.public_index veupath_chatbot.integrations.vectorstore.ingest.public_strategies veupath_chatbot.integrations.vectorstore.ingest.public_strategies_helpers veupath_chatbot.integrations.vectorstore.ingest.public_transform veupath_chatbot.integrations.vectorstore.ingest.utils veupath_chatbot.integrations.vectorstore.ingest.wdk_catalog veupath_chatbot.integrations.vectorstore.ingest.wdk_fetch veupath_chatbot.integrations.vectorstore.ingest.wdk_index veupath_chatbot.integrations.vectorstore.ingest.wdk_transform veupath_chatbot.integrations.vectorstore.qdrant_store veupath_chatbot.integrations.veupathdb.client veupath_chatbot.integrations.veupathdb.discovery veupath_chatbot.integrations.veupathdb.factory veupath_chatbot.integrations.veupathdb.param_utils veupath_chatbot.integrations.veupathdb.site_router veupath_chatbot.integrations.veupathdb.site_search veupath_chatbot.integrations.veupathdb.strategy_api.analyses veupath_chatbot.integrations.veupathdb.strategy_api.api veupath_chatbot.integrations.veupathdb.strategy_api.base veupath_chatbot.integrations.veupathdb.strategy_api.filters veupath_chatbot.integrations.veupathdb.strategy_api.helpers veupath_chatbot.integrations.veupathdb.strategy_api.records veupath_chatbot.integrations.veupathdb.strategy_api.reports veupath_chatbot.integrations.veupathdb.strategy_api.steps veupath_chatbot.integrations.veupathdb.strategy_api.strategies veupath_chatbot.integrations.veupathdb.temporary_results veupath_chatbot.jobs.rag_startup veupath_chatbot.main veupath_chatbot.persistence.models veupath_chatbot.persistence.repositories.control_set veupath_chatbot.persistence.repositories.stream veupath_chatbot.persistence.repositories.user veupath_chatbot.persistence.session veupath_chatbot.platform.config veupath_chatbot.platform.context veupath_chatbot.platform.errors veupath_chatbot.platform.events veupath_chatbot.platform.health veupath_chatbot.platform.logging veupath_chatbot.platform.parsing veupath_chatbot.platform.pydantic_validation veupath_chatbot.platform.redis veupath_chatbot.platform.security veupath_chatbot.platform.store veupath_chatbot.platform.tasks veupath_chatbot.platform.tool_errors veupath_chatbot.platform.types veupath_chatbot.services.catalog.param_resolution veupath_chatbot.services.catalog.param_validation veupath_chatbot.services.catalog.parameters veupath_chatbot.services.catalog.rag_search veupath_chatbot.services.catalog.searches veupath_chatbot.services.catalog.sites veupath_chatbot.services.chat.events veupath_chatbot.services.chat.mention_context veupath_chatbot.services.chat.orchestrator veupath_chatbot.services.chat.streaming veupath_chatbot.services.chat.utils veupath_chatbot.services.control_helpers veupath_chatbot.services.control_tests veupath_chatbot.services.experiment._deserialize veupath_chatbot.services.experiment.ai_analysis_helpers veupath_chatbot.services.experiment.ai_analysis_tools veupath_chatbot.services.experiment.ai_refinement_tools veupath_chatbot.services.experiment.assistant veupath_chatbot.services.experiment.classification veupath_chatbot.services.experiment.core.streaming veupath_chatbot.services.experiment.cross_validation veupath_chatbot.services.experiment.custom_enrichment veupath_chatbot.services.experiment.enrichment veupath_chatbot.services.experiment.enrichment_compare veupath_chatbot.services.experiment.evaluation veupath_chatbot.services.experiment.helpers veupath_chatbot.services.experiment.materialization veupath_chatbot.services.experiment.metrics veupath_chatbot.services.experiment.overlap veupath_chatbot.services.experiment.rank_metrics veupath_chatbot.services.experiment.report veupath_chatbot.services.experiment.robustness veupath_chatbot.services.experiment.seed veupath_chatbot.services.experiment.seed.helpers veupath_chatbot.services.experiment.seed.runner veupath_chatbot.services.experiment.seed.types veupath_chatbot.services.experiment.service veupath_chatbot.services.experiment.stats veupath_chatbot.services.experiment.step_analysis veupath_chatbot.services.experiment.step_analysis._evaluation veupath_chatbot.services.experiment.step_analysis._tree_utils veupath_chatbot.services.experiment.step_analysis.orchestrator veupath_chatbot.services.experiment.step_analysis.phase_contribution veupath_chatbot.services.experiment.step_analysis.phase_operators veupath_chatbot.services.experiment.step_analysis.phase_sensitivity veupath_chatbot.services.experiment.step_analysis.phase_step_eval veupath_chatbot.services.experiment.store veupath_chatbot.services.experiment.tree_knobs veupath_chatbot.services.experiment.types veupath_chatbot.services.experiment.types.core veupath_chatbot.services.experiment.types.enrichment veupath_chatbot.services.experiment.types.experiment veupath_chatbot.services.experiment.types.json_codec veupath_chatbot.services.experiment.types.metrics veupath_chatbot.services.experiment.types.optimization veupath_chatbot.services.experiment.types.rank veupath_chatbot.services.experiment.types.serialization veupath_chatbot.services.experiment.types.step_analysis veupath_chatbot.services.export.service veupath_chatbot.services.gene_lookup veupath_chatbot.services.gene_lookup.enrich veupath_chatbot.services.gene_lookup.lookup veupath_chatbot.services.gene_lookup.organism veupath_chatbot.services.gene_lookup.result veupath_chatbot.services.gene_lookup.scoring veupath_chatbot.services.gene_lookup.site_search veupath_chatbot.services.gene_lookup.wdk veupath_chatbot.services.gene_sets.confidence veupath_chatbot.services.gene_sets.ensemble veupath_chatbot.services.gene_sets.operations veupath_chatbot.services.gene_sets.reverse_search veupath_chatbot.services.gene_sets.store veupath_chatbot.services.gene_sets.types veupath_chatbot.services.parameter_optimization veupath_chatbot.services.parameter_optimization.callbacks veupath_chatbot.services.parameter_optimization.config veupath_chatbot.services.parameter_optimization.core veupath_chatbot.services.parameter_optimization.scoring veupath_chatbot.services.parameter_optimization.trials veupath_chatbot.services.research.clients._base veupath_chatbot.services.research.clients.arxiv veupath_chatbot.services.research.clients.crossref veupath_chatbot.services.research.clients.europepmc veupath_chatbot.services.research.clients.openalex veupath_chatbot.services.research.clients.preprint veupath_chatbot.services.research.clients.pubmed veupath_chatbot.services.research.clients.semanticscholar veupath_chatbot.services.research.literature_search veupath_chatbot.services.research.utils veupath_chatbot.services.research.web_search veupath_chatbot.services.search_rerank veupath_chatbot.services.strategies.auto_import veupath_chatbot.services.strategies.auto_push veupath_chatbot.services.strategies.build veupath_chatbot.services.strategies.engine.base veupath_chatbot.services.strategies.engine.graph_integrity veupath_chatbot.services.strategies.engine.graph_ops veupath_chatbot.services.strategies.engine.helpers veupath_chatbot.services.strategies.engine.id_mapping veupath_chatbot.services.strategies.engine.step_builder veupath_chatbot.services.strategies.engine.validation veupath_chatbot.services.strategies.plan_normalize veupath_chatbot.services.strategies.plan_validation veupath_chatbot.services.strategies.session_factory veupath_chatbot.services.strategies.step_builders veupath_chatbot.services.strategies.step_creation veupath_chatbot.services.strategies.wdk_conversion veupath_chatbot.services.strategies.wdk_counts veupath_chatbot.services.strategies.wdk_sync veupath_chatbot.services.wdk.enrichment_service veupath_chatbot.services.wdk.helpers veupath_chatbot.services.wdk.record_types veupath_chatbot.services.wdk.step_results veupath_chatbot.services.workbench_chat.orchestrator veupath_chatbot.transport.http.deps veupath_chatbot.transport.http.routers.chat veupath_chatbot.transport.http.routers.control_sets veupath_chatbot.transport.http.routers.dev veupath_chatbot.transport.http.routers.experiments.analysis veupath_chatbot.transport.http.routers.experiments.chat veupath_chatbot.transport.http.routers.experiments.comparison veupath_chatbot.transport.http.routers.experiments.cross_validation veupath_chatbot.transport.http.routers.experiments.crud veupath_chatbot.transport.http.routers.experiments.enrichment veupath_chatbot.transport.http.routers.experiments.evaluation veupath_chatbot.transport.http.routers.experiments.execution veupath_chatbot.transport.http.routers.experiments.results veupath_chatbot.transport.http.routers.exports veupath_chatbot.transport.http.routers.gene_sets veupath_chatbot.transport.http.routers.health veupath_chatbot.transport.http.routers.internal veupath_chatbot.transport.http.routers.models veupath_chatbot.transport.http.routers.operations veupath_chatbot.transport.http.routers.sites.catalog veupath_chatbot.transport.http.routers.sites.genes veupath_chatbot.transport.http.routers.sites.params veupath_chatbot.transport.http.routers.strategies.counts veupath_chatbot.transport.http.routers.strategies.crud veupath_chatbot.transport.http.routers.strategies.plan veupath_chatbot.transport.http.routers.strategies.wdk_import veupath_chatbot.transport.http.routers.tools veupath_chatbot.transport.http.routers.user_data veupath_chatbot.transport.http.routers.veupathdb_auth veupath_chatbot.transport.http.schemas.chat veupath_chatbot.transport.http.schemas.experiment_responses veupath_chatbot.transport.http.schemas.experiments veupath_chatbot.transport.http.schemas.gene_sets veupath_chatbot.transport.http.schemas.health veupath_chatbot.transport.http.schemas.optimization veupath_chatbot.transport.http.schemas.plan veupath_chatbot.transport.http.schemas.sites veupath_chatbot.transport.http.schemas.sse veupath_chatbot.transport.http.schemas.steps veupath_chatbot.transport.http.schemas.strategies veupath_chatbot.transport.http.schemas.veupathdb_auth veupath_chatbot.transport.http.schemas.workbench_chat veupath_chatbot.transport.http.sse mol_weight_params() (in module veupath_chatbot.services.experiment.seed.helpers) MULTI_PICK (veupath_chatbot.domain.parameters._value_helpers.ParamKind attribute) multi_pick (veupath_chatbot.transport.http.schemas.sites.ParamSpecResponse attribute)

N

n_iterations (veupath_chatbot.services.experiment.types.BootstrapResult attribute) (veupath_chatbot.services.experiment.types.rank.BootstrapResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.BootstrapResultResponse attribute) name (veupath_chatbot.ai.models.catalog.ModelEntry attribute) (veupath_chatbot.domain.parameters.specs.ParamSpecNormalized attribute) (veupath_chatbot.domain.strategy.ast.StepFilter attribute) (veupath_chatbot.domain.strategy.ast.StrategyAST attribute) (veupath_chatbot.integrations.veupathdb.site_router.SiteConfig attribute) (veupath_chatbot.persistence.models.ControlSet attribute) (veupath_chatbot.persistence.models.ExperimentRow attribute) (veupath_chatbot.persistence.models.GeneSetRow attribute) (veupath_chatbot.persistence.models.StreamProjection attribute) (veupath_chatbot.services.experiment.seed.ControlSetDef attribute) (veupath_chatbot.services.experiment.seed.SeedDef attribute) (veupath_chatbot.services.experiment.seed.types.ControlSetDef attribute) (veupath_chatbot.services.experiment.seed.types.SeedDef attribute) (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.GeneInfo attribute) (veupath_chatbot.services.experiment.types.metrics.GeneInfo attribute) (veupath_chatbot.services.experiment.types.optimization.OptimizationSpec attribute) (veupath_chatbot.services.experiment.types.OptimizationSpec attribute) (veupath_chatbot.services.gene_sets.reverse_search.GeneSetCandidate attribute) (veupath_chatbot.services.gene_sets.reverse_search.RankedResult attribute) (veupath_chatbot.services.gene_sets.types.GeneSet attribute) (veupath_chatbot.services.parameter_optimization.ParameterSpec attribute) (veupath_chatbot.transport.http.routers.control_sets.ControlSetResponse attribute) (veupath_chatbot.transport.http.routers.control_sets.CreateControlSetRequest attribute) (veupath_chatbot.transport.http.routers.models.ModelCatalogEntryResponse attribute) (veupath_chatbot.transport.http.schemas.chat.ToolCallResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ControlSetSummaryResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentSummaryResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.GeneInfoResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OptimizationSpecResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) (veupath_chatbot.transport.http.schemas.experiments.OptimizationSpecRequest attribute) (veupath_chatbot.transport.http.schemas.gene_sets.CreateGeneSetRequest attribute) (veupath_chatbot.transport.http.schemas.gene_sets.GeneSetResponse attribute) (veupath_chatbot.transport.http.schemas.gene_sets.ReverseSearchResultItem attribute) (veupath_chatbot.transport.http.schemas.gene_sets.SetOperationRequest attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationParameterSpecData attribute) (veupath_chatbot.transport.http.schemas.plan.PlanMetadata attribute) (veupath_chatbot.transport.http.schemas.plan.StepFilterSpec attribute) (veupath_chatbot.transport.http.schemas.sites.ParamSpecResponse attribute) (veupath_chatbot.transport.http.schemas.sites.RecordTypeResponse attribute) (veupath_chatbot.transport.http.schemas.sites.SearchResponse attribute) (veupath_chatbot.transport.http.schemas.sites.SiteResponse attribute) (veupath_chatbot.transport.http.schemas.sse.GeneSetSummary attribute) (veupath_chatbot.transport.http.schemas.sse.GraphPlanEventData attribute) (veupath_chatbot.transport.http.schemas.sse.StrategyLinkEventData attribute) (veupath_chatbot.transport.http.schemas.sse.StrategyMetaEventData attribute) (veupath_chatbot.transport.http.schemas.sse.SubKaniToolCallStartEventData attribute) (veupath_chatbot.transport.http.schemas.sse.ToolCallStartEventData attribute) (veupath_chatbot.transport.http.schemas.steps.PrimaryKeyPart attribute) (veupath_chatbot.transport.http.schemas.steps.StepFilterResponse attribute) (veupath_chatbot.transport.http.schemas.strategies.CreateStrategyRequest attribute) (veupath_chatbot.transport.http.schemas.strategies.StrategyResponse attribute) (veupath_chatbot.transport.http.schemas.strategies.UpdateStrategyRequest attribute) (veupath_chatbot.transport.http.schemas.strategies.WdkStrategySummaryResponse attribute) (veupath_chatbot.transport.http.schemas.veupathdb_auth.AuthStatusResponse attribute) narrative (veupath_chatbot.services.experiment.types.step_analysis.StepContribution attribute) (veupath_chatbot.services.experiment.types.StepContribution attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepContributionResponse attribute)

negative_control_ids (veupath_chatbot.services.experiment.types.FoldMetrics attribute) (veupath_chatbot.services.experiment.types.metrics.FoldMetrics attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.FoldMetricsResponse attribute) negative_controls (veupath_chatbot.services.experiment.types.BatchOrganismTarget attribute) (veupath_chatbot.services.experiment.types.experiment.BatchOrganismTarget attribute) (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.BatchOrganismTargetRequest attribute) (veupath_chatbot.transport.http.schemas.experiments.BenchmarkControlSet attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) negative_count (veupath_chatbot.services.experiment.types.NegativeSetVariant attribute) (veupath_chatbot.services.experiment.types.rank.NegativeSetVariant attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ControlSetSummaryResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.NegativeSetVariantResponse attribute) negative_gene_ids (veupath_chatbot.transport.http.schemas.gene_sets.ReverseSearchRequest attribute) negative_hits (veupath_chatbot.services.experiment.types.OperatorVariant attribute) (veupath_chatbot.services.experiment.types.ParameterSweepPoint attribute) (veupath_chatbot.services.experiment.types.step_analysis.OperatorVariant attribute) (veupath_chatbot.services.experiment.types.step_analysis.ParameterSweepPoint attribute) (veupath_chatbot.services.experiment.types.step_analysis.StepEvaluation attribute) (veupath_chatbot.services.experiment.types.StepEvaluation attribute) (veupath_chatbot.services.parameter_optimization.TrialResult attribute) (veupath_chatbot.services.parameter_optimization.trials.TrialMetrics attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OperatorVariantResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ParameterSweepPointResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepEvaluationResponse attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationTrialData attribute) negative_ids (veupath_chatbot.persistence.models.ControlSet attribute) (veupath_chatbot.services.experiment.seed.ControlSetDef attribute) (veupath_chatbot.services.experiment.seed.types.ControlSetDef attribute) (veupath_chatbot.transport.http.routers.control_sets.ControlSetResponse attribute) (veupath_chatbot.transport.http.routers.control_sets.CreateControlSetRequest attribute) negative_predictive_value (veupath_chatbot.services.experiment.types.ExperimentMetrics attribute) (veupath_chatbot.services.experiment.types.metrics.ExperimentMetrics attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentMetricsResponse attribute) negative_set_sensitivity (veupath_chatbot.services.experiment.types.BootstrapResult attribute) (veupath_chatbot.services.experiment.types.rank.BootstrapResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.BootstrapResultResponse attribute) negative_set_variant (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) negative_total (veupath_chatbot.services.experiment.types.step_analysis.StepEvaluation attribute) (veupath_chatbot.services.experiment.types.StepEvaluation attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepEvaluationResponse attribute) NegativeSetVariant (class in veupath_chatbot.services.experiment.types) (class in veupath_chatbot.services.experiment.types.rank) NegativeSetVariantResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) nodes_by_id (veupath_chatbot.ai.orchestration.delegation.DelegationPlan attribute) norm_for_match() (in module veupath_chatbot.services.research.utils) norm_text() (in module veupath_chatbot.services.research.utils) normalize() (veupath_chatbot.domain.parameters.normalize.ParameterNormalizer method) normalize_organism() (in module veupath_chatbot.services.gene_lookup.organism) normalize_param_value() (in module veupath_chatbot.integrations.veupathdb.param_utils) normalize_plan() (in module veupath_chatbot.transport.http.routers.strategies.plan) normalize_synced_parameters() (in module veupath_chatbot.services.strategies.wdk_conversion) normalize_vocab_key() (in module veupath_chatbot.domain.parameters.vocab_utils) normalized_context_values (veupath_chatbot.transport.http.schemas.sites.SearchValidationPayload attribute) NOT_FOUND (veupath_chatbot.platform.errors.ErrorCode attribute) notes (veupath_chatbot.services.experiment.types.Experiment attribute) (veupath_chatbot.services.experiment.types.experiment.Experiment attribute) (veupath_chatbot.transport.http.routers.experiments.crud.PatchExperimentRequest attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentResponse attribute) NotFoundError numeric_equivalent() (in module veupath_chatbot.domain.parameters.vocab_utils)

O

objective (veupath_chatbot.services.experiment.types.optimization.TreeOptimizationResult attribute) (veupath_chatbot.services.experiment.types.TreeOptimizationResult attribute) (veupath_chatbot.services.parameter_optimization.OptimizationConfig attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.TreeOptimizationResultResponse attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationProgressEventData attribute) odds_ratio (veupath_chatbot.services.experiment.types.enrichment.EnrichmentTerm attribute) (veupath_chatbot.services.experiment.types.EnrichmentTerm attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.EnrichmentTermResponse attribute) oddsRatio (veupath_chatbot.services.experiment.custom_enrichment.CustomEnrichmentResult attribute) ollama (veupath_chatbot.transport.http.schemas.health.ProviderStatus attribute) ollama_base_url (veupath_chatbot.platform.config.Settings attribute) open_strategy() (in module veupath_chatbot.transport.http.routers.strategies.wdk_import) openai (veupath_chatbot.transport.http.schemas.health.ProviderStatus attribute) openai_api_key (veupath_chatbot.platform.config.Settings attribute) openai_hyperparams (veupath_chatbot.platform.config.Settings attribute) openai_model (veupath_chatbot.platform.config.Settings attribute) openai_temperature (veupath_chatbot.platform.config.Settings attribute) openai_top_p (veupath_chatbot.platform.config.Settings attribute) OpenAIEmbeddings (class in veupath_chatbot.integrations.embeddings.openai_embeddings) OpenAlexClient (class in veupath_chatbot.services.research.clients.openalex) OpenStrategyRequest (class in veupath_chatbot.transport.http.schemas.strategies) OpenStrategyResponse (class in veupath_chatbot.transport.http.schemas.strategies) Operation (class in veupath_chatbot.persistence.models) operation (veupath_chatbot.persistence.models.GeneSetRow attribute) (veupath_chatbot.services.gene_sets.types.GeneSet attribute) (veupath_chatbot.transport.http.schemas.gene_sets.GeneSetResponse attribute) (veupath_chatbot.transport.http.schemas.gene_sets.SetOperationRequest attribute) operation_id (veupath_chatbot.persistence.models.Operation attribute) (veupath_chatbot.transport.http.schemas.workbench_chat.WorkbenchChatResponse attribute) operator (veupath_chatbot.domain.strategy.ast.PlanStepNode attribute) (veupath_chatbot.services.experiment.types.OperatorVariant attribute) (veupath_chatbot.services.experiment.types.step_analysis.OperatorVariant attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OperatorVariantResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.RefineRequest attribute) (veupath_chatbot.transport.http.schemas.plan.PlanNode attribute) (veupath_chatbot.transport.http.schemas.steps.StepResponse attribute) operator_comparison (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) operator_comparisons (veupath_chatbot.services.experiment.types.step_analysis.StepAnalysisResult attribute) (veupath_chatbot.services.experiment.types.StepAnalysisResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepAnalysisResultResponse attribute) operator_knob (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) operator_knobs (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) operator_variant (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) OperatorComparison (class in veupath_chatbot.services.experiment.types) (class in veupath_chatbot.services.experiment.types.step_analysis) OperatorComparisonResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) OperatorKnob (class in veupath_chatbot.services.experiment.types) (class in veupath_chatbot.services.experiment.types.optimization) OperatorKnobRequest (class in veupath_chatbot.transport.http.schemas.experiments) OperatorKnobResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) OperatorVariant (class in veupath_chatbot.services.experiment.types) (class in veupath_chatbot.services.experiment.types.step_analysis) OperatorVariantResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) optimization_budget (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) optimization_id (veupath_chatbot.services.parameter_optimization.OptimizationResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OptimizationResultResponse attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationProgressEventData attribute) optimization_objective (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute)

optimization_parameter_spec (veupath_chatbot.transport.http.routers.internal.SSESchemaIndex attribute) optimization_progress (veupath_chatbot.transport.http.routers.internal.SSESchemaIndex attribute) (veupath_chatbot.transport.http.schemas.chat.MessageResponse attribute) optimization_result (veupath_chatbot.services.experiment.types.Experiment attribute) (veupath_chatbot.services.experiment.types.experiment.Experiment attribute) (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentResponse attribute) optimization_spec (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) optimization_specs (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) optimization_target_step (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) optimization_trial (veupath_chatbot.transport.http.routers.internal.SSESchemaIndex attribute) OptimizationConfig (class in veupath_chatbot.services.parameter_optimization) OptimizationParameterSpecData (class in veupath_chatbot.transport.http.schemas.optimization) OptimizationProgressEventData (class in veupath_chatbot.transport.http.schemas.optimization) OptimizationResult (class in veupath_chatbot.services.parameter_optimization) OptimizationResultResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) OptimizationSpec (class in veupath_chatbot.services.experiment.types) (class in veupath_chatbot.services.experiment.types.optimization) OptimizationSpecRequest (class in veupath_chatbot.transport.http.schemas.experiments) OptimizationSpecResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) OptimizationToolsMixin (class in veupath_chatbot.ai.tools.planner.optimization_tools) OptimizationTrialData (class in veupath_chatbot.transport.http.schemas.optimization) optimize_search_parameters() (in module veupath_chatbot.services.parameter_optimization) (in module veupath_chatbot.services.parameter_optimization.core) (veupath_chatbot.ai.tools.planner.optimization_tools.OptimizationToolsMixin method) optimize_tree_knobs() (in module veupath_chatbot.services.experiment.tree_knobs) options (veupath_chatbot.services.experiment.types.OperatorKnob attribute) (veupath_chatbot.services.experiment.types.optimization.OperatorKnob attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OperatorKnobResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.OperatorKnobRequest attribute) order_primary_key() (in module veupath_chatbot.services.wdk.helpers) org() (in module veupath_chatbot.services.experiment.seed.helpers) organism (veupath_chatbot.services.experiment.types.BatchOrganismTarget attribute) (veupath_chatbot.services.experiment.types.experiment.BatchOrganismTarget attribute) (veupath_chatbot.services.experiment.types.GeneInfo attribute) (veupath_chatbot.services.experiment.types.metrics.GeneInfo attribute) (veupath_chatbot.transport.http.routers.sites.genes.GeneSearchResultResponse attribute) (veupath_chatbot.transport.http.routers.sites.genes.ResolvedGeneResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ControlSetSummaryResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.GeneInfoResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.BatchOrganismTargetRequest attribute) organism_param_name (veupath_chatbot.services.experiment.types.BatchExperimentConfig attribute) (veupath_chatbot.services.experiment.types.experiment.BatchExperimentConfig attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateBatchExperimentRequest attribute) organisms (veupath_chatbot.transport.http.routers.sites.genes.OrganismsResponse attribute) OrganismsResponse (class in veupath_chatbot.transport.http.routers.sites.genes) output_price (veupath_chatbot.ai.models.catalog.ModelEntry attribute) (veupath_chatbot.transport.http.routers.models.ModelCatalogEntryResponse attribute) overfitting_level (veupath_chatbot.services.experiment.types.CrossValidationResult attribute) (veupath_chatbot.services.experiment.types.metrics.CrossValidationResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.CrossValidationResultResponse attribute) overfitting_score (veupath_chatbot.services.experiment.types.CrossValidationResult attribute) (veupath_chatbot.services.experiment.types.metrics.CrossValidationResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.CrossValidationResultResponse attribute) overlap_count (veupath_chatbot.services.gene_sets.reverse_search.RankedResult attribute) (veupath_chatbot.transport.http.schemas.gene_sets.ReverseSearchResultItem attribute) overlapCount (veupath_chatbot.services.experiment.custom_enrichment.CustomEnrichmentResult attribute) overlapGenes (veupath_chatbot.services.experiment.custom_enrichment.CustomEnrichmentResult attribute) OverlapRequest (class in veupath_chatbot.transport.http.schemas.experiments) OverlapResult (class in veupath_chatbot.services.experiment.overlap)

P

p_value (veupath_chatbot.services.experiment.types.enrichment.EnrichmentTerm attribute) (veupath_chatbot.services.experiment.types.EnrichmentTerm attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.EnrichmentTermResponse attribute) pairwise (veupath_chatbot.services.experiment.overlap.OverlapResult attribute) PairwiseOverlap (class in veupath_chatbot.services.experiment.overlap) paralog_count_params() (in module veupath_chatbot.services.experiment.seed.helpers) param_map (veupath_chatbot.transport.http.schemas.sites.SearchDetailsResponse attribute) param_name (veupath_chatbot.services.experiment.types.optimization.ThresholdKnob attribute) (veupath_chatbot.services.experiment.types.ParameterSensitivity attribute) (veupath_chatbot.services.experiment.types.step_analysis.ParameterSensitivity attribute) (veupath_chatbot.services.experiment.types.ThresholdKnob attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ParameterSensitivityResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ThresholdKnobResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.ThresholdKnobRequest attribute) param_type (veupath_chatbot.domain.parameters.specs.ParamSpecNormalized attribute) (veupath_chatbot.services.parameter_optimization.ParameterSpec attribute) parameter_display_values (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) parameter_name (veupath_chatbot.transport.http.schemas.experiments.ThresholdSweepRequest attribute) (veupath_chatbot.transport.http.schemas.sites.DependentParamsRequest attribute) parameter_sensitivities (veupath_chatbot.services.experiment.types.step_analysis.StepAnalysisResult attribute) (veupath_chatbot.services.experiment.types.StepAnalysisResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepAnalysisResultResponse attribute) parameter_sensitivity (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) parameter_specs (veupath_chatbot.transport.http.schemas.optimization.OptimizationProgressEventData attribute) parameter_sweep_point (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) ParameterCanonicalizer (class in veupath_chatbot.domain.parameters.canonicalize) ParameterNormalizer (class in veupath_chatbot.domain.parameters.normalize) parameters (veupath_chatbot.domain.strategy.ast.PlanStepNode attribute) (veupath_chatbot.domain.strategy.ast.StepAnalysis attribute) (veupath_chatbot.persistence.models.GeneSetRow attribute) (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.optimization.TreeOptimizationTrial attribute) (veupath_chatbot.services.experiment.types.TreeOptimizationTrial attribute) (veupath_chatbot.services.gene_sets.types.GeneSet attribute) (veupath_chatbot.services.parameter_optimization.TrialResult attribute) (veupath_chatbot.transport.http.schemas.chat.PlanningArtifactResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.TreeOptimizationTrialResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.TrialProgressDataResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) (veupath_chatbot.transport.http.schemas.experiments.RefineRequest attribute) (veupath_chatbot.transport.http.schemas.experiments.RunAnalysisRequest attribute) (veupath_chatbot.transport.http.schemas.gene_sets.CreateGeneSetRequest attribute) (veupath_chatbot.transport.http.schemas.gene_sets.GeneSetResponse attribute) (veupath_chatbot.transport.http.schemas.gene_sets.RunGeneSetAnalysisRequest attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationTrialData attribute) (veupath_chatbot.transport.http.schemas.plan.PlanNode attribute) (veupath_chatbot.transport.http.schemas.plan.StepAnalysisSpec attribute) (veupath_chatbot.transport.http.schemas.sites.SearchDetailsResponse attribute) (veupath_chatbot.transport.http.schemas.steps.StepAnalysisRequest attribute) (veupath_chatbot.transport.http.schemas.steps.StepAnalysisResponse attribute) (veupath_chatbot.transport.http.schemas.steps.StepResponse attribute) ParameterSensitivity (class in veupath_chatbot.services.experiment.types) (class in veupath_chatbot.services.experiment.types.step_analysis) ParameterSensitivityResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) ParameterSpec (class in veupath_chatbot.services.parameter_optimization) ParameterSweepPoint (class in veupath_chatbot.services.experiment.types) (class in veupath_chatbot.services.experiment.types.step_analysis) ParameterSweepPointResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) ParameterValueMixin (class in veupath_chatbot.domain.parameters._value_helpers) ParamKind (class in veupath_chatbot.domain.parameters._value_helpers) ParamSpecNormalized (class in veupath_chatbot.domain.parameters.specs) ParamSpecResponse (class in veupath_chatbot.transport.http.schemas.sites) ParamSpecsRequest (class in veupath_chatbot.transport.http.schemas.sites) parent_experiment_id (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) parent_set_ids (veupath_chatbot.persistence.models.GeneSetRow attribute) (veupath_chatbot.services.gene_sets.types.GeneSet attribute) (veupath_chatbot.transport.http.schemas.gene_sets.GeneSetResponse attribute) pareto_frontier (veupath_chatbot.services.parameter_optimization.OptimizationResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OptimizationResultResponse attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationProgressEventData attribute) parse_analyses() (in module veupath_chatbot.domain.strategy.ast) parse_colocation_params() (in module veupath_chatbot.domain.strategy.ast) parse_enrichment_from_raw() (in module veupath_chatbot.services.experiment.enrichment) parse_filters() (in module veupath_chatbot.domain.strategy.ast) parse_json5_value() (in module veupath_chatbot.domain.parameters._decode_values) parse_jsonish() (in module veupath_chatbot.platform.parsing) parse_op() (in module veupath_chatbot.domain.strategy.ops) parse_pydantic_validation_error_text() (in module veupath_chatbot.platform.pydantic_validation) parse_reports() (in module veupath_chatbot.domain.strategy.ast) parse_selected_nodes() (in module veupath_chatbot.services.chat.utils) parse_site_search_docs() (in module veupath_chatbot.services.gene_lookup.site_search) parse_sites() (in module veupath_chatbot.integrations.vectorstore.ingest.utils) parse_wdk_strategy_id() (in module veupath_chatbot.services.strategies.wdk_conversion) partition_task_results() (in module veupath_chatbot.ai.orchestration.scheduler) passes_filters() (in module veupath_chatbot.services.research.utils) password (veupath_chatbot.transport.http.routers.veupathdb_auth.LoginPayload attribute) patch() (veupath_chatbot.integrations.veupathdb.client.VEuPathDBClient method) PatchExperimentRequest (class in veupath_chatbot.transport.http.routers.experiments.crud) path (veupath_chatbot.domain.strategy.validate.StepValidationIssue attribute) PathfinderAgent (class in veupath_chatbot.ai.agents.executor) perExperiment (veupath_chatbot.services.experiment.overlap.OverlapResult attribute) PerExperimentSummary (class in veupath_chatbot.services.experiment.overlap) PERFECT_SCORE (veupath_chatbot.services.parameter_optimization.trials.EarlyStopReason attribute) perform_set_operation() (veupath_chatbot.services.gene_sets.operations.GeneSetService method) phase (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentProgressDataResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepAnalysisProgressDataResponse attribute) plan (veupath_chatbot.persistence.models.StreamProjection attribute) (veupath_chatbot.transport.http.schemas.plan.PlanNormalizeRequest attribute) (veupath_chatbot.transport.http.schemas.plan.PlanNormalizeResponse attribute) (veupath_chatbot.transport.http.schemas.sse.GraphPlanEventData attribute) (veupath_chatbot.transport.http.schemas.strategies.CreateStrategyRequest attribute) (veupath_chatbot.transport.http.schemas.strategies.StepCountsRequest attribute) (veupath_chatbot.transport.http.schemas.strategies.UpdateStrategyRequest attribute) plan_cache_key() (in module veupath_chatbot.services.strategies.wdk_counts)

plan_needs_detail_fetch() (in module veupath_chatbot.services.strategies.wdk_sync) PlanMetadata (class in veupath_chatbot.transport.http.schemas.plan) planning_artifact (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) (veupath_chatbot.transport.http.routers.internal.SSESchemaIndex attribute) (veupath_chatbot.transport.http.schemas.sse.PlanningArtifactEventData attribute) planning_artifacts (veupath_chatbot.transport.http.schemas.chat.MessageResponse attribute) PlanningArtifactEventData (class in veupath_chatbot.transport.http.schemas.sse) PlanningArtifactResponse (class in veupath_chatbot.transport.http.schemas.chat) PlanNode (class in veupath_chatbot.transport.http.schemas.plan) PlanNormalizeRequest (class in veupath_chatbot.transport.http.schemas.plan) PlanNormalizeResponse (class in veupath_chatbot.transport.http.schemas.plan) PlanStepNode (class in veupath_chatbot.domain.strategy.ast) PLATEAU (veupath_chatbot.services.parameter_optimization.trials.EarlyStopReason attribute) pmid (veupath_chatbot.domain.research.citations.Citation attribute) (veupath_chatbot.transport.http.schemas.chat.CitationResponse attribute) point_uuid() (in module veupath_chatbot.integrations.vectorstore.qdrant_store) portal_timeout (veupath_chatbot.integrations.veupathdb.site_router.RoutingConfig attribute) positive_control_ids (veupath_chatbot.services.experiment.types.FoldMetrics attribute) (veupath_chatbot.services.experiment.types.metrics.FoldMetrics attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.FoldMetricsResponse attribute) positive_controls (veupath_chatbot.services.experiment.types.BatchOrganismTarget attribute) (veupath_chatbot.services.experiment.types.experiment.BatchOrganismTarget attribute) (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.BatchOrganismTargetRequest attribute) (veupath_chatbot.transport.http.schemas.experiments.BenchmarkControlSet attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) (veupath_chatbot.transport.http.schemas.gene_sets.EnsembleScoringRequest attribute) positive_count (veupath_chatbot.transport.http.schemas.experiment_responses.ControlSetSummaryResponse attribute) positive_gene_ids (veupath_chatbot.transport.http.schemas.gene_sets.ReverseSearchRequest attribute) positive_hits (veupath_chatbot.services.experiment.types.OperatorVariant attribute) (veupath_chatbot.services.experiment.types.ParameterSweepPoint attribute) (veupath_chatbot.services.experiment.types.step_analysis.OperatorVariant attribute) (veupath_chatbot.services.experiment.types.step_analysis.ParameterSweepPoint attribute) (veupath_chatbot.services.experiment.types.step_analysis.StepEvaluation attribute) (veupath_chatbot.services.experiment.types.StepEvaluation attribute) (veupath_chatbot.services.parameter_optimization.TrialResult attribute) (veupath_chatbot.services.parameter_optimization.trials.TrialMetrics attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OperatorVariantResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ParameterSweepPointResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepEvaluationResponse attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationTrialData attribute) positive_ids (veupath_chatbot.persistence.models.ControlSet attribute) (veupath_chatbot.services.experiment.seed.ControlSetDef attribute) (veupath_chatbot.services.experiment.seed.types.ControlSetDef attribute) (veupath_chatbot.transport.http.routers.control_sets.ControlSetResponse attribute) (veupath_chatbot.transport.http.routers.control_sets.CreateControlSetRequest attribute) positive_total (veupath_chatbot.services.experiment.types.step_analysis.StepEvaluation attribute) (veupath_chatbot.services.experiment.types.StepEvaluation attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepEvaluationResponse attribute) post() (veupath_chatbot.integrations.veupathdb.client.VEuPathDBClient method) pr_curve (veupath_chatbot.services.experiment.types.rank.RankMetrics attribute) (veupath_chatbot.services.experiment.types.RankMetrics attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.RankMetricsResponse attribute) precision (veupath_chatbot.services.experiment.types.ExperimentMetrics attribute) (veupath_chatbot.services.experiment.types.metrics.ExperimentMetrics attribute) (veupath_chatbot.services.gene_sets.reverse_search.RankedResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentMetricsResponse attribute) (veupath_chatbot.transport.http.schemas.gene_sets.ReverseSearchResultItem attribute) precision_at_k (veupath_chatbot.services.experiment.types.rank.RankMetrics attribute) (veupath_chatbot.services.experiment.types.RankMetrics attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.RankMetricsResponse attribute) precision_at_k_delta (veupath_chatbot.services.experiment.types.OperatorComparison attribute) (veupath_chatbot.services.experiment.types.step_analysis.OperatorComparison attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OperatorComparisonResponse attribute) precision_weight (veupath_chatbot.services.parameter_optimization.OptimizationConfig attribute) predict() (veupath_chatbot.ai.engines.mock.MockEngine method) preload_all() (veupath_chatbot.integrations.veupathdb.discovery.DiscoveryService method) (veupath_chatbot.integrations.veupathdb.factory.DiscoveryService method) PreprintClient (class in veupath_chatbot.services.research.clients.preprint) primary_input (veupath_chatbot.domain.strategy.ast.PlanStepNode attribute) primary_input_step_id (veupath_chatbot.transport.http.schemas.steps.StepResponse attribute) primary_key (veupath_chatbot.transport.http.schemas.steps.RecordDetailRequest attribute) primaryInput (veupath_chatbot.transport.http.schemas.plan.PlanNode attribute) PrimaryKeyPart (class in veupath_chatbot.transport.http.schemas.steps) ProblemDetail (class in veupath_chatbot.platform.errors) process_bind_param() (veupath_chatbot.persistence.models.GUID method) process_result_value() (veupath_chatbot.persistence.models.GUID method) ProcessedParam (class in veupath_chatbot.domain.parameters._value_helpers) product (veupath_chatbot.services.experiment.types.GeneInfo attribute) (veupath_chatbot.services.experiment.types.metrics.GeneInfo attribute) (veupath_chatbot.transport.http.routers.sites.genes.GeneSearchResultResponse attribute) (veupath_chatbot.transport.http.routers.sites.genes.ResolvedGeneResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.GeneInfoResponse attribute) ProgressCallback (in module veupath_chatbot.services.experiment.cross_validation) (in module veupath_chatbot.services.experiment.helpers) project_id (veupath_chatbot.integrations.veupathdb.site_router.SiteConfig attribute) (veupath_chatbot.transport.http.schemas.sites.SiteResponse attribute) prompt_len() (veupath_chatbot.ai.engines.mock.MockEngine method) prompt_tokens (veupath_chatbot.ai.orchestration.subkani.utils.SubKaniRoundResult attribute) (veupath_chatbot.transport.http.schemas.chat.SubKaniTokenUsageResponse attribute) (veupath_chatbot.transport.http.schemas.chat.TokenUsageResponse attribute) (veupath_chatbot.transport.http.schemas.sse.MessageEndEventData attribute) (veupath_chatbot.transport.http.schemas.sse.SubKaniTaskEndEventData attribute) (veupath_chatbot.transport.http.schemas.sse.TokenUsagePartialEventData attribute) proposed_strategy_plan (veupath_chatbot.transport.http.schemas.chat.PlanningArtifactResponse attribute) provenance_notes (veupath_chatbot.persistence.models.ControlSet attribute) (veupath_chatbot.services.experiment.seed.ControlSetDef attribute) (veupath_chatbot.services.experiment.seed.types.ControlSetDef attribute) (veupath_chatbot.transport.http.routers.control_sets.ControlSetResponse attribute) (veupath_chatbot.transport.http.routers.control_sets.CreateControlSetRequest attribute) provider (veupath_chatbot.ai.models.catalog.ModelEntry attribute) (veupath_chatbot.transport.http.routers.models.ModelCatalogEntryResponse attribute) (veupath_chatbot.transport.http.schemas.chat.ChatRequest attribute) (veupath_chatbot.transport.http.schemas.workbench_chat.WorkbenchChatRequest attribute) providers (veupath_chatbot.transport.http.schemas.health.SystemConfigResponse attribute) ProviderStatus (class in veupath_chatbot.transport.http.schemas.health) prune_wdk_orphans() (veupath_chatbot.persistence.repositories.stream.StreamRepository method) PubmedClient (class in veupath_chatbot.services.research.clients.pubmed) purge_user_data() (in module veupath_chatbot.transport.http.routers.user_data) put() (veupath_chatbot.integrations.veupathdb.client.VEuPathDBClient method) pValue (veupath_chatbot.services.experiment.custom_enrichment.CustomEnrichmentResult attribute)

Q

qdrant_api_key (veupath_chatbot.platform.config.Settings attribute) qdrant_timeout_seconds (veupath_chatbot.platform.config.Settings attribute) qdrant_url (veupath_chatbot.platform.config.Settings attribute)

QdrantStore (class in veupath_chatbot.integrations.vectorstore.qdrant_store) query_site_search() (in module veupath_chatbot.integrations.veupathdb.site_search) QueryIntent (class in veupath_chatbot.services.search_rerank) question (veupath_chatbot.transport.http.schemas.sites.SearchDetailsResponse attribute)

R

rag_enabled (veupath_chatbot.platform.config.Settings attribute) rag_get_dependent_vocab() (veupath_chatbot.ai.tools.catalog_rag_tools.CatalogRagTools method) rag_get_record_type_details() (veupath_chatbot.ai.tools.catalog_rag_tools.CatalogRagTools method) rag_get_record_types() (veupath_chatbot.ai.tools.catalog_rag_tools.CatalogRagTools method) rag_get_search_metadata() (veupath_chatbot.ai.tools.catalog_rag_tools.CatalogRagTools method) rag_search_example_plans() (veupath_chatbot.ai.tools.example_plans_rag_tools.ExamplePlansRagTools method) rag_search_for_searches() (veupath_chatbot.ai.tools.catalog_rag_tools.CatalogRagTools method) rag_startup_max_strategies_per_site (veupath_chatbot.platform.config.Settings attribute) rag_startup_public_strategies_concurrency (veupath_chatbot.platform.config.Settings attribute) rag_startup_public_strategies_llm_model (veupath_chatbot.platform.config.Settings attribute) rag_startup_public_strategies_report_path (veupath_chatbot.platform.config.Settings attribute) RagSearchService (class in veupath_chatbot.services.catalog.rag_search) RANGE (veupath_chatbot.domain.parameters._value_helpers.ParamKind attribute) rank_gene_sets_by_recall() (in module veupath_chatbot.services.gene_sets.reverse_search) rank_metric_cis (veupath_chatbot.services.experiment.types.BootstrapResult attribute) (veupath_chatbot.services.experiment.types.rank.BootstrapResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.BootstrapResultResponse attribute) rank_metrics (veupath_chatbot.services.experiment.types.Experiment attribute) (veupath_chatbot.services.experiment.types.experiment.Experiment attribute) (veupath_chatbot.services.experiment.types.NegativeSetVariant attribute) (veupath_chatbot.services.experiment.types.optimization.TreeOptimizationTrial attribute) (veupath_chatbot.services.experiment.types.rank.NegativeSetVariant attribute) (veupath_chatbot.services.experiment.types.TreeOptimizationTrial attribute) (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.NegativeSetVariantResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.TreeOptimizationTrialResponse attribute) RankedResult (class in veupath_chatbot.services.gene_sets.reverse_search) RankMetrics (class in veupath_chatbot.services.experiment.types) (class in veupath_chatbot.services.experiment.types.rank) RankMetricsResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) RATE_LIMITED (veupath_chatbot.platform.errors.ErrorCode attribute) raw (veupath_chatbot.services.search_rerank.QueryIntent attribute) re_evaluate() (in module veupath_chatbot.services.experiment.evaluation) re_evaluate_controls() (veupath_chatbot.services.experiment.ai_refinement_tools.RefinementToolsMixin method) re_evaluate_experiment() (in module veupath_chatbot.transport.http.routers.experiments.evaluation) read_stream_messages() (in module veupath_chatbot.platform.events) read_stream_thinking() (in module veupath_chatbot.platform.events) readiness_check() (in module veupath_chatbot.transport.http.routers.health) reasoning (veupath_chatbot.transport.http.routers.internal.SSESchemaIndex attribute) (veupath_chatbot.transport.http.schemas.chat.MessageResponse attribute) (veupath_chatbot.transport.http.schemas.chat.ThinkingResponse attribute) (veupath_chatbot.transport.http.schemas.sse.ReasoningEventData attribute) reasoning_budget (veupath_chatbot.transport.http.schemas.chat.ChatRequest attribute) reasoning_effort (veupath_chatbot.transport.http.schemas.chat.ChatRequest attribute) (veupath_chatbot.transport.http.schemas.workbench_chat.WorkbenchChatRequest attribute) ReasoningEffort (in module veupath_chatbot.platform.types) ReasoningEventData (class in veupath_chatbot.transport.http.schemas.sse) recall (veupath_chatbot.services.experiment.types.OperatorVariant attribute) (veupath_chatbot.services.experiment.types.ParameterSweepPoint attribute) (veupath_chatbot.services.experiment.types.step_analysis.OperatorVariant attribute) (veupath_chatbot.services.experiment.types.step_analysis.ParameterSweepPoint attribute) (veupath_chatbot.services.experiment.types.step_analysis.StepEvaluation attribute) (veupath_chatbot.services.experiment.types.StepEvaluation attribute) (veupath_chatbot.services.gene_sets.reverse_search.RankedResult attribute) (veupath_chatbot.services.parameter_optimization.TrialResult attribute) (veupath_chatbot.services.parameter_optimization.trials.TrialMetrics attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OperatorVariantResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ParameterSweepPointResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepEvaluationResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.TrialProgressDataResponse attribute) (veupath_chatbot.transport.http.schemas.gene_sets.ReverseSearchResultItem attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationTrialData attribute) recall_at_k (veupath_chatbot.services.experiment.types.rank.RankMetrics attribute) (veupath_chatbot.services.experiment.types.RankMetrics attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.RankMetricsResponse attribute) recall_delta (veupath_chatbot.services.experiment.types.step_analysis.StepContribution attribute) (veupath_chatbot.services.experiment.types.StepContribution attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepContributionResponse attribute) recall_weight (veupath_chatbot.services.parameter_optimization.OptimizationConfig attribute) recent_trials (veupath_chatbot.transport.http.schemas.optimization.OptimizationProgressEventData attribute) recommendation (veupath_chatbot.services.experiment.types.OperatorComparison attribute) (veupath_chatbot.services.experiment.types.ParameterSensitivity attribute) (veupath_chatbot.services.experiment.types.step_analysis.OperatorComparison attribute) (veupath_chatbot.services.experiment.types.step_analysis.ParameterSensitivity attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OperatorComparisonResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ParameterSensitivityResponse attribute) recommended_operator (veupath_chatbot.services.experiment.types.OperatorComparison attribute) (veupath_chatbot.services.experiment.types.step_analysis.OperatorComparison attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OperatorComparisonResponse attribute) recommended_value (veupath_chatbot.services.experiment.types.ParameterSensitivity attribute) (veupath_chatbot.services.experiment.types.step_analysis.ParameterSensitivity attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ParameterSensitivityResponse attribute) recompute_roots() (veupath_chatbot.domain.strategy.session.StrategyGraph method) record_matches() (in module veupath_chatbot.services.experiment.ai_analysis_helpers) record_type (veupath_chatbot.domain.strategy.ast.StrategyAST attribute) (veupath_chatbot.persistence.models.ControlSet attribute) (veupath_chatbot.persistence.models.GeneSetRow attribute) (veupath_chatbot.persistence.models.StreamProjection attribute) (veupath_chatbot.services.experiment.seed.SeedDef attribute) (veupath_chatbot.services.experiment.seed.types.SeedDef attribute) (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.services.gene_sets.types.GeneSet attribute) (veupath_chatbot.transport.http.routers.control_sets.ControlSetResponse attribute) (veupath_chatbot.transport.http.routers.control_sets.CreateControlSetRequest attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentSummaryResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) (veupath_chatbot.transport.http.schemas.gene_sets.CreateGeneSetRequest attribute) (veupath_chatbot.transport.http.schemas.gene_sets.GeneSetResponse attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationProgressEventData attribute) (veupath_chatbot.transport.http.schemas.sites.SearchResponse attribute) (veupath_chatbot.transport.http.schemas.sse.GraphPlanEventData attribute) (veupath_chatbot.transport.http.schemas.sse.StrategyMetaEventData attribute) (veupath_chatbot.transport.http.schemas.steps.StepResponse attribute) (veupath_chatbot.transport.http.schemas.strategies.StrategyResponse attribute) record_type_query_error() (in module veupath_chatbot.ai.tools.query_validation) RecordDetailRequest (class in veupath_chatbot.transport.http.schemas.steps) records (veupath_chatbot.services.gene_lookup.wdk.WdkTextResult attribute) RecordsMixin (class in veupath_chatbot.integrations.veupathdb.strategy_api.records) recordType (veupath_chatbot.transport.http.schemas.plan.StrategyPlan attribute) RecordTypeResponse (class in veupath_chatbot.transport.http.schemas.sites) redis_url (veupath_chatbot.platform.config.Settings attribute) refine_experiment() (in module veupath_chatbot.transport.http.routers.experiments.results) refine_with_gene_ids() (veupath_chatbot.services.experiment.ai_refinement_tools.RefinementToolsMixin method) refine_with_search() (veupath_chatbot.services.experiment.ai_refinement_tools.RefinementToolsMixin method) RefinementToolsMixin (class in veupath_chatbot.services.experiment.ai_refinement_tools) RefineRequest (class in veupath_chatbot.transport.http.schemas.experiments) refresh_internal_auth() (in module veupath_chatbot.transport.http.routers.veupathdb_auth) register_operation() (veupath_chatbot.persistence.repositories.stream.StreamRepository method)

registered_tool_count (veupath_chatbot.transport.http.schemas.chat.TokenUsageResponse attribute) (veupath_chatbot.transport.http.schemas.sse.MessageEndEventData attribute) (veupath_chatbot.transport.http.schemas.sse.TokenUsagePartialEventData attribute) registry (veupath_chatbot.persistence.models.Base attribute) rename_step() (veupath_chatbot.ai.tools.strategy_tools.edit_ops.StrategyEditOps method) rename_strategy() (veupath_chatbot.ai.tools.conversation_tools.ConversationTools method) report (veupath_chatbot.transport.http.schemas.steps.StepReportRunResponse attribute) report_name (veupath_chatbot.domain.strategy.ast.StepReport attribute) (veupath_chatbot.transport.http.schemas.steps.StepReportRequest attribute) (veupath_chatbot.transport.http.schemas.steps.StepReportResponse attribute) report_reasoning() (veupath_chatbot.ai.tools.planner.artifact_tools.ArtifactToolsMixin method) reportName (veupath_chatbot.transport.http.schemas.plan.StepReportSpec attribute) reports (veupath_chatbot.domain.strategy.ast.PlanStepNode attribute) (veupath_chatbot.transport.http.schemas.plan.BasePlanNode attribute) (veupath_chatbot.transport.http.schemas.steps.StepResponse attribute) ReportsMixin (class in veupath_chatbot.integrations.veupathdb.strategy_api.reports) rerank_score() (in module veupath_chatbot.services.research.utils) ResearchToolsMixin (class in veupath_chatbot.ai.tools.research_registry) reset_collections() (veupath_chatbot.integrations.vectorstore.qdrant_store.QdrantStore method) resolve_controls_param_type() (in module veupath_chatbot.services.control_tests) resolve_effective_model_id() (in module veupath_chatbot.ai.agents.factory) resolve_gene_ids() (in module veupath_chatbot.services.gene_lookup) (in module veupath_chatbot.services.gene_lookup.wdk) resolve_gene_ids_to_records() (veupath_chatbot.ai.tools.planner.gene_tools.GeneToolsMixin method) resolve_genes() (in module veupath_chatbot.transport.http.routers.sites.genes) resolve_record_type() (in module veupath_chatbot.services.wdk.record_types) resolve_record_type_from_steps() (in module veupath_chatbot.services.catalog.searches) resolve_root_step() (in module veupath_chatbot.services.strategies.build) resolve_root_step_id() (in module veupath_chatbot.services.gene_sets.operations) resolve_wdk_user_id() (in module veupath_chatbot.integrations.veupathdb.strategy_api.helpers) resolved (veupath_chatbot.transport.http.routers.sites.genes.GeneResolveResponse attribute) ResolvedGeneResponse (class in veupath_chatbot.transport.http.routers.sites.genes) response_text (veupath_chatbot.ai.orchestration.subkani.utils.SubKaniRoundResult attribute) response_tokens (veupath_chatbot.transport.http.schemas.chat.ChatRequest attribute) ResponsesOpenAIEngine (class in veupath_chatbot.ai.engines.responses_openai) restore() (veupath_chatbot.persistence.repositories.stream.StreamRepository method) restore_strategy() (in module veupath_chatbot.transport.http.routers.strategies.crud) result (veupath_chatbot.services.search_rerank.ScoredResult attribute) (veupath_chatbot.transport.http.schemas.chat.ToolCallResponse attribute) (veupath_chatbot.transport.http.schemas.sse.SubKaniToolCallEndEventData attribute) (veupath_chatbot.transport.http.schemas.sse.ToolCallEndEventData attribute) result_count (veupath_chatbot.persistence.models.StreamProjection attribute) (veupath_chatbot.services.experiment.types.step_analysis.StepEvaluation attribute) (veupath_chatbot.services.experiment.types.StepEvaluation attribute) (veupath_chatbot.services.gene_sets.reverse_search.RankedResult attribute) (veupath_chatbot.services.parameter_optimization.TrialResult attribute) (veupath_chatbot.services.parameter_optimization.trials.TrialMetrics attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepEvaluationResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.TrialProgressDataResponse attribute) (veupath_chatbot.transport.http.schemas.gene_sets.ReverseSearchResultItem attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationTrialData attribute) (veupath_chatbot.transport.http.schemas.steps.StepResponse attribute) (veupath_chatbot.transport.http.schemas.strategies.StrategyResponse attribute) result_count_penalty (veupath_chatbot.services.parameter_optimization.OptimizationConfig attribute) result_gene_ids() (veupath_chatbot.services.experiment.types.Experiment method) (veupath_chatbot.services.experiment.types.experiment.Experiment method) result_to_json() (in module veupath_chatbot.services.parameter_optimization) (in module veupath_chatbot.services.parameter_optimization.scoring) result_tools (veupath_chatbot.ai.tools.strategy_registry.StrategyToolsMixin attribute) results (veupath_chatbot.transport.http.routers.sites.genes.GeneSearchResponse attribute) ResultTools (class in veupath_chatbot.ai.tools.result_tools) reverse_search() (in module veupath_chatbot.transport.http.routers.gene_sets) ReverseSearchRequest (class in veupath_chatbot.transport.http.schemas.gene_sets) ReverseSearchResultItem (class in veupath_chatbot.transport.http.schemas.gene_sets) RMINUS (veupath_chatbot.domain.strategy.ops.CombineOp attribute) rnaseq_fc_params() (in module veupath_chatbot.services.experiment.seed.helpers) robustness (veupath_chatbot.services.experiment.types.Experiment attribute) (veupath_chatbot.services.experiment.types.experiment.Experiment attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentResponse attribute) role (veupath_chatbot.transport.http.schemas.chat.MessageResponse attribute) RONLY (veupath_chatbot.domain.strategy.ops.CombineOp attribute) root (veupath_chatbot.domain.strategy.ast.StrategyAST attribute) (veupath_chatbot.transport.http.schemas.plan.StrategyPlan attribute) root_count (veupath_chatbot.services.strategies.build.BuildResult attribute) root_step_id (veupath_chatbot.domain.strategy.compile.CompilationResult attribute) (veupath_chatbot.persistence.models.StreamProjection attribute) (veupath_chatbot.services.strategies.build.BuildResult attribute) (veupath_chatbot.transport.http.schemas.strategies.StrategyResponse attribute) (veupath_chatbot.transport.http.schemas.strategies.WdkStrategySummaryResponse attribute) RootResolutionError routing (veupath_chatbot.integrations.veupathdb.site_router.SitesConfig attribute) RoutingConfig (class in veupath_chatbot.integrations.veupathdb.site_router) rows (veupath_chatbot.services.experiment.enrichment_compare.EnrichmentCompareResult attribute) run() (veupath_chatbot.services.wdk.enrichment_service.EnrichmentService method) run_analysis() (veupath_chatbot.services.wdk.step_results.StepResultsService method) run_analysis_instance() (veupath_chatbot.integrations.veupathdb.client.VEuPathDBClient method) run_analysis_raw() (veupath_chatbot.services.wdk.step_results.StepResultsService method) run_assistant() (in module veupath_chatbot.services.experiment.assistant) run_batch() (veupath_chatbot.services.wdk.enrichment_service.EnrichmentService method) run_concurrent_pipeline() (in module veupath_chatbot.integrations.vectorstore.ingest.pipeline) run_control_tests() (veupath_chatbot.ai.tools.planner.experiment_tools.ExperimentToolsMixin method) run_controls_against_tree() (in module veupath_chatbot.services.experiment.step_analysis) (in module veupath_chatbot.services.experiment.step_analysis._evaluation) run_cross_validation() (in module veupath_chatbot.services.experiment.cross_validation) run_custom_enrichment() (in module veupath_chatbot.services.experiment.custom_enrichment) run_cv() (in module veupath_chatbot.transport.http.routers.experiments.cross_validation) run_enrichment() (in module veupath_chatbot.transport.http.routers.experiments.enrichment) (veupath_chatbot.services.gene_sets.operations.GeneSetService method) run_enrichment_analysis() (in module veupath_chatbot.services.experiment.enrichment) run_enrichment_on_step() (in module veupath_chatbot.services.experiment.enrichment) run_experiment() (in module veupath_chatbot.services.experiment.service) run_gene_set_enrichment() (veupath_chatbot.ai.tools.planner.workbench_tools.WorkbenchToolsMixin method) run_nodes_with_dependencies() (in module veupath_chatbot.ai.orchestration.scheduler) run_positive_negative_controls() (in module veupath_chatbot.services.control_tests) run_search_indexing_pipeline() (in module veupath_chatbot.integrations.vectorstore.ingest.wdk_index) run_search_report() (veupath_chatbot.integrations.veupathdb.client.VEuPathDBClient method) run_seed() (in module veupath_chatbot.services.experiment.seed) (in module veupath_chatbot.services.experiment.seed.runner) run_step_analysis() (in module veupath_chatbot.services.experiment.step_analysis) (in module veupath_chatbot.services.experiment.step_analysis.orchestrator) (veupath_chatbot.domain.strategy.compile.StepDecoratorAPI method) (veupath_chatbot.integrations.veupathdb.strategy_api.analyses.AnalysisMixin method) run_step_report() (veupath_chatbot.domain.strategy.compile.StepDecoratorAPI method) (veupath_chatbot.integrations.veupathdb.client.VEuPathDBClient method) (veupath_chatbot.integrations.veupathdb.strategy_api.reports.ReportsMixin method) run_subkani_task() (in module veupath_chatbot.ai.orchestration.subkani.orchestrator) run_sweep_point() (in module veupath_chatbot.services.experiment.evaluation) run_trial_loop() (in module veupath_chatbot.services.parameter_optimization.trials) RunAnalysisRequest (class in veupath_chatbot.transport.http.schemas.experiments) RunCrossValidationRequest (class in veupath_chatbot.transport.http.schemas.experiments) RunEnrichmentRequest (class in veupath_chatbot.transport.http.schemas.experiments) RunGeneSetAnalysisRequest (class in veupath_chatbot.transport.http.schemas.gene_sets)

S

safe_float() (in module veupath_chatbot.services.experiment.helpers) safe_int() (in module veupath_chatbot.services.experiment.helpers) save() (veupath_chatbot.platform.store.WriteThruStore method) save_history() (veupath_chatbot.domain.strategy.session.StrategyGraph method) save_planning_artifact() (veupath_chatbot.ai.tools.planner.artifact_tools.ArtifactToolsMixin method) save_strategy() (veupath_chatbot.ai.tools.conversation_tools.ConversationTools method) SCALAR (veupath_chatbot.domain.parameters._value_helpers.ParamKind attribute) score (veupath_chatbot.services.experiment.types.optimization.TreeOptimizationTrial attribute) (veupath_chatbot.services.experiment.types.TreeOptimizationTrial attribute) (veupath_chatbot.services.parameter_optimization.TrialResult attribute) (veupath_chatbot.services.search_rerank.ScoredResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.TreeOptimizationTrialResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.TrialProgressDataResponse attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationTrialData attribute) score_field_quality() (in module veupath_chatbot.services.search_rerank) score_gene_relevance() (in module veupath_chatbot.services.gene_lookup.scoring) score_organism_match() (in module veupath_chatbot.services.gene_lookup.organism) score_search() (in module veupath_chatbot.services.catalog.searches) score_text_match() (in module veupath_chatbot.services.search_rerank) ScoredResult (class in veupath_chatbot.services.search_rerank) scores (veupath_chatbot.services.experiment.enrichment_compare.EnrichmentRow attribute) search() (veupath_chatbot.integrations.vectorstore.qdrant_store.QdrantStore method) (veupath_chatbot.services.research.clients._base.StandardClient method) (veupath_chatbot.services.research.clients.preprint.PreprintClient method) (veupath_chatbot.services.research.clients.pubmed.PubmedClient method) (veupath_chatbot.services.research.literature_search.LiteratureSearchService method) (veupath_chatbot.services.research.web_search.WebSearchService method) search_config (veupath_chatbot.transport.http.schemas.sites.SearchDetailsResponse attribute) search_data (veupath_chatbot.transport.http.schemas.sites.SearchDetailsResponse attribute) search_example_plans() (veupath_chatbot.ai.tools.catalog_registry.CatalogToolsMixin method) (veupath_chatbot.services.catalog.rag_search.RagSearchService method) search_for_searches() (in module veupath_chatbot.services.catalog.searches) (veupath_chatbot.ai.agents.experiment.ExperimentAssistantAgent method) (veupath_chatbot.ai.tools.catalog_registry.CatalogToolsMixin method) (veupath_chatbot.ai.tools.catalog_tools.CatalogTools method) (veupath_chatbot.services.catalog.rag_search.RagSearchService method) search_genes() (in module veupath_chatbot.transport.http.routers.sites.genes) search_name (veupath_chatbot.domain.strategy.ast.PlanStepNode attribute) (veupath_chatbot.persistence.models.GeneSetRow attribute) (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.step_analysis.StepContribution attribute) (veupath_chatbot.services.experiment.types.step_analysis.StepEvaluation attribute) (veupath_chatbot.services.experiment.types.StepContribution attribute) (veupath_chatbot.services.experiment.types.StepEvaluation attribute) (veupath_chatbot.services.gene_sets.reverse_search.GeneSetCandidate attribute) (veupath_chatbot.services.gene_sets.reverse_search.RankedResult attribute) (veupath_chatbot.services.gene_sets.types.GeneSet attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentSummaryResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepAnalysisProgressDataResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepContributionResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepEvaluationResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) (veupath_chatbot.transport.http.schemas.experiments.RefineRequest attribute) (veupath_chatbot.transport.http.schemas.gene_sets.CreateGeneSetRequest attribute) (veupath_chatbot.transport.http.schemas.gene_sets.GeneSetResponse attribute) (veupath_chatbot.transport.http.schemas.gene_sets.ReverseSearchResultItem attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationProgressEventData attribute) (veupath_chatbot.transport.http.schemas.steps.StepResponse attribute) SEARCH_NOT_FOUND (veupath_chatbot.platform.errors.ErrorCode attribute) search_query_error() (in module veupath_chatbot.ai.tools.query_validation) search_record_types() (veupath_chatbot.services.catalog.rag_search.RagSearchService method) search_searches_by_keywords() (veupath_chatbot.ai.tools.strategy_tools.discovery_ops.StrategyDiscoveryOps method) SearchCatalog (class in veupath_chatbot.integrations.veupathdb.discovery) SearchDetailsResponse (class in veupath_chatbot.transport.http.schemas.sites) searchName (veupath_chatbot.transport.http.schemas.plan.PlanNode attribute) SearchResponse (class in veupath_chatbot.transport.http.schemas.sites) SearchValidationErrors (class in veupath_chatbot.transport.http.schemas.sites) SearchValidationPayload (class in veupath_chatbot.transport.http.schemas.sites) SearchValidationRequest (class in veupath_chatbot.transport.http.schemas.sites) SearchValidationResponse (class in veupath_chatbot.transport.http.schemas.sites) secondary_input (veupath_chatbot.domain.strategy.ast.PlanStepNode attribute) secondary_input_step_id (veupath_chatbot.transport.http.schemas.steps.StepResponse attribute) secondaryInput (veupath_chatbot.transport.http.schemas.plan.PlanNode attribute) seed (veupath_chatbot.transport.http.schemas.chat.ChatRequest attribute) seed_strategies() (in module veupath_chatbot.transport.http.routers.experiments.execution) SeedDef (class in veupath_chatbot.services.experiment.seed) (class in veupath_chatbot.services.experiment.seed.types) SemanticScholarClient (class in veupath_chatbot.services.research.clients.semanticscholar) sensitivity (veupath_chatbot.services.experiment.types.ExperimentMetrics attribute) (veupath_chatbot.services.experiment.types.metrics.ExperimentMetrics attribute) (veupath_chatbot.services.parameter_optimization.OptimizationResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentMetricsResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentSummaryResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OptimizationResultResponse attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationProgressEventData attribute) service_url (veupath_chatbot.integrations.veupathdb.factory.SiteInfo property) (veupath_chatbot.integrations.veupathdb.site_router.SiteInfo property) set_a_id (veupath_chatbot.transport.http.schemas.gene_sets.SetOperationRequest attribute) set_b_id (veupath_chatbot.transport.http.schemas.gene_sets.SetOperationRequest attribute) set_conversation_title() (veupath_chatbot.ai.tools.planner.artifact_tools.ArtifactToolsMixin method) set_operations() (in module veupath_chatbot.transport.http.routers.gene_sets) set_saved() (veupath_chatbot.integrations.veupathdb.strategy_api.strategies.StrategiesMixin method) set_step_filter() (veupath_chatbot.domain.strategy.compile.StepDecoratorAPI method) (veupath_chatbot.integrations.veupathdb.strategy_api.filters.FilterMixin method) SetOperationRequest (class in veupath_chatbot.transport.http.schemas.gene_sets) Settings (class in veupath_chatbot.platform.config) settings_customise_sources() (veupath_chatbot.platform.config.Settings class method) setup_logging() (in module veupath_chatbot.platform.logging) sha256_hex() (in module veupath_chatbot.integrations.vectorstore.qdrant_store) sharedGenes (veupath_chatbot.services.experiment.overlap.PairwiseOverlap attribute) (veupath_chatbot.services.experiment.overlap.PerExperimentSummary attribute) signal_peptide_params() (in module veupath_chatbot.services.experiment.seed.helpers) signedIn (veupath_chatbot.transport.http.schemas.veupathdb_auth.AuthStatusResponse attribute) simplify_strategy_details() (in module veupath_chatbot.integrations.vectorstore.ingest.public_strategies_helpers) SINGLE_PICK (veupath_chatbot.domain.parameters._value_helpers.ParamKind attribute) site_id (veupath_chatbot.ai.tools.catalog_registry.CatalogToolsMixin attribute) (veupath_chatbot.ai.tools.export_tools.ExportToolsMixin attribute) (veupath_chatbot.ai.tools.planner.experiment_tools.ExperimentToolsMixin attribute) (veupath_chatbot.ai.tools.planner.gene_tools.GeneToolsMixin attribute) (veupath_chatbot.ai.tools.planner.optimization_tools.OptimizationToolsMixin attribute) (veupath_chatbot.ai.tools.planner.workbench_tools.WorkbenchToolsMixin attribute) (veupath_chatbot.ai.tools.workbench_read_tools.WorkbenchReadToolsMixin attribute) (veupath_chatbot.persistence.models.ControlSet attribute) (veupath_chatbot.persistence.models.ExperimentRow attribute) (veupath_chatbot.persistence.models.GeneSetRow attribute) (veupath_chatbot.persistence.models.Stream attribute) (veupath_chatbot.persistence.models.StreamProjection attribute) (veupath_chatbot.services.experiment.ai_refinement_tools.RefinementToolsMixin attribute) (veupath_chatbot.services.experiment.seed.SeedDef attribute) (veupath_chatbot.services.experiment.seed.types.SeedDef attribute) (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.services.gene_sets.types.GeneSet attribute) (veupath_chatbot.transport.http.routers.control_sets.ControlSetResponse attribute) (veupath_chatbot.transport.http.routers.control_sets.CreateControlSetRequest attribute) (veupath_chatbot.transport.http.schemas.chat.ChatRequest attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentSummaryResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.AiAssistRequest attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) (veupath_chatbot.transport.http.schemas.gene_sets.CreateGeneSetRequest attribute) (veupath_chatbot.transport.http.schemas.gene_sets.GeneSetResponse attribute) (veupath_chatbot.transport.http.schemas.gene_sets.ReverseSearchRequest attribute) (veupath_chatbot.transport.http.schemas.sse.GeneSetSummary attribute) (veupath_chatbot.transport.http.schemas.strategies.CreateStrategyRequest attribute) (veupath_chatbot.transport.http.schemas.strategies.OpenStrategyRequest attribute) (veupath_chatbot.transport.http.schemas.strategies.StepCountsRequest attribute) (veupath_chatbot.transport.http.schemas.strategies.StrategyResponse attribute) (veupath_chatbot.transport.http.schemas.strategies.WdkStrategySummaryResponse attribute) (veupath_chatbot.transport.http.schemas.workbench_chat.WorkbenchChatRequest attribute) SITE_NOT_FOUND (veupath_chatbot.platform.errors.ErrorCode attribute) SiteConfig (class in veupath_chatbot.integrations.veupathdb.site_router) siteId (veupath_chatbot.transport.http.schemas.plan.PlanMetadata attribute) (veupath_chatbot.transport.http.schemas.plan.PlanNormalizeRequest attribute) SiteInfo (class in veupath_chatbot.integrations.veupathdb.factory) (class in veupath_chatbot.integrations.veupathdb.site_router) SiteInfoLike (class in veupath_chatbot.services.strategies.build) SiteResponse (class in veupath_chatbot.transport.http.schemas.sites) SiteRouter (class in veupath_chatbot.integrations.veupathdb.site_router) sites (veupath_chatbot.integrations.veupathdb.site_router.SitesConfig attribute) SitesConfig (class in veupath_chatbot.integrations.veupathdb.site_router) size_bytes (veupath_chatbot.services.export.service.ExportResult attribute) sizeA (veupath_chatbot.services.experiment.overlap.PairwiseOverlap attribute) sizeB (veupath_chatbot.services.experiment.overlap.PairwiseOverlap attribute) snippet (veupath_chatbot.domain.research.citations.Citation attribute) (veupath_chatbot.transport.http.schemas.chat.CitationResponse attribute) sort_attribute (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) sort_direction (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) source (veupath_chatbot.domain.research.citations.Citation attribute) (veupath_chatbot.persistence.models.ControlSet attribute) (veupath_chatbot.persistence.models.GeneSetRow attribute) (veupath_chatbot.services.gene_sets.types.GeneSet attribute) (veupath_chatbot.services.search_rerank.ScoredResult attribute) (veupath_chatbot.transport.http.routers.control_sets.ControlSetResponse attribute) (veupath_chatbot.transport.http.routers.control_sets.CreateControlSetRequest attribute) (veupath_chatbot.transport.http.schemas.chat.CitationResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ControlSetSummaryResponse attribute) (veupath_chatbot.transport.http.schemas.gene_sets.CreateGeneSetRequest attribute) (veupath_chatbot.transport.http.schemas.gene_sets.GeneSetResponse attribute) (veupath_chatbot.transport.http.schemas.sse.GeneSetSummary attribute) source_strategy_id (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) spawn() (in module veupath_chatbot.platform.tasks) specificity (veupath_chatbot.services.experiment.types.ExperimentMetrics attribute) (veupath_chatbot.services.experiment.types.metrics.ExperimentMetrics attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentMetricsResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentSummaryResponse attribute) specs (veupath_chatbot.domain.parameters.canonicalize.ParameterCanonicalizer attribute) (veupath_chatbot.domain.parameters.normalize.ParameterNormalizer attribute) sse_schemas() (in module veupath_chatbot.transport.http.routers.internal) sse_stream() (in module veupath_chatbot.transport.http.sse) SSESchemaIndex (class in veupath_chatbot.transport.http.routers.internal) stable_json_dumps() (in module veupath_chatbot.integrations.vectorstore.qdrant_store) StandardClient (class in veupath_chatbot.services.research.clients._base) start_batch_experiment() (in module veupath_chatbot.services.experiment.core.streaming) start_benchmark() (in module veupath_chatbot.services.experiment.core.streaming) start_chat_stream() (in module veupath_chatbot.services.chat.orchestrator) start_experiment() (in module veupath_chatbot.services.experiment.core.streaming) start_rag_startup_ingestion_background() (in module veupath_chatbot.jobs.rag_startup) start_workbench_chat_stream() (in module veupath_chatbot.services.workbench_chat.orchestrator) status (veupath_chatbot.persistence.models.ExperimentRow attribute) (veupath_chatbot.persistence.models.Operation attribute) (veupath_chatbot.platform.errors.ProblemDetail attribute) (veupath_chatbot.services.experiment.types.Experiment attribute) (veupath_chatbot.services.experiment.types.experiment.Experiment attribute) (veupath_chatbot.services.parameter_optimization.OptimizationResult attribute) (veupath_chatbot.transport.http.schemas.chat.SubKaniActivityResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentSummaryResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OptimizationResultResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.TrialProgressDataResponse attribute) (veupath_chatbot.transport.http.schemas.health.HealthResponse attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationProgressEventData attribute) (veupath_chatbot.transport.http.schemas.sse.SubKaniTaskEndEventData attribute)

std (veupath_chatbot.services.experiment.types.ConfidenceInterval attribute) (veupath_chatbot.services.experiment.types.rank.ConfidenceInterval attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ConfidenceIntervalResponse attribute) std_metrics (veupath_chatbot.services.experiment.types.CrossValidationResult attribute) (veupath_chatbot.services.experiment.types.metrics.CrossValidationResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.CrossValidationResultResponse attribute) step (veupath_chatbot.services.experiment.types.optimization.OptimizationSpec attribute) (veupath_chatbot.services.experiment.types.OptimizationSpec attribute) (veupath_chatbot.services.parameter_optimization.ParameterSpec attribute) (veupath_chatbot.services.strategies.step_creation.StepCreationResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OptimizationSpecResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.AiAssistRequest attribute) (veupath_chatbot.transport.http.schemas.experiments.OptimizationSpecRequest attribute) (veupath_chatbot.transport.http.schemas.sse.StrategyUpdateEventData attribute) step_analysis (veupath_chatbot.services.experiment.types.Experiment attribute) (veupath_chatbot.services.experiment.types.experiment.Experiment attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentResponse attribute) step_analysis_phases (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) step_analysis_progress (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentProgressDataResponse attribute) step_analysis_progress_data (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) step_analysis_result (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) step_contribution (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) step_contributions (veupath_chatbot.services.experiment.types.step_analysis.StepAnalysisResult attribute) (veupath_chatbot.services.experiment.types.StepAnalysisResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepAnalysisResultResponse attribute) step_count (veupath_chatbot.persistence.models.GeneSetRow attribute) (veupath_chatbot.persistence.models.StreamProjection attribute) (veupath_chatbot.services.gene_sets.types.GeneSet attribute) (veupath_chatbot.services.strategies.build.BuildResult attribute) (veupath_chatbot.transport.http.schemas.gene_sets.GeneSetResponse attribute) (veupath_chatbot.transport.http.schemas.strategies.StrategyResponse attribute) step_evaluation (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) step_evaluations (veupath_chatbot.services.experiment.types.step_analysis.StepAnalysisResult attribute) (veupath_chatbot.services.experiment.types.StepAnalysisResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepAnalysisResultResponse attribute) step_id (veupath_chatbot.services.experiment.types.optimization.ThresholdKnob attribute) (veupath_chatbot.services.experiment.types.ParameterSensitivity attribute) (veupath_chatbot.services.experiment.types.step_analysis.ParameterSensitivity attribute) (veupath_chatbot.services.experiment.types.step_analysis.StepContribution attribute) (veupath_chatbot.services.experiment.types.step_analysis.StepEvaluation attribute) (veupath_chatbot.services.experiment.types.StepContribution attribute) (veupath_chatbot.services.experiment.types.StepEvaluation attribute) (veupath_chatbot.services.experiment.types.ThresholdKnob attribute) (veupath_chatbot.services.strategies.build.StepCountResult attribute) (veupath_chatbot.services.strategies.engine.graph_integrity.GraphIntegrityError attribute) (veupath_chatbot.services.strategies.step_creation.StepCreationResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ParameterSensitivityResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepAnalysisProgressDataResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepContributionResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepEvaluationResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ThresholdKnobResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.ThresholdKnobRequest attribute) STEP_NOT_FOUND (veupath_chatbot.platform.errors.ErrorCode attribute) step_size (veupath_chatbot.services.experiment.types.optimization.ThresholdKnob attribute) (veupath_chatbot.services.experiment.types.ThresholdKnob attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ThresholdKnobResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.ThresholdKnobRequest attribute) step_tree (veupath_chatbot.domain.strategy.compile.CompilationResult attribute) (veupath_chatbot.services.experiment.seed.SeedDef attribute) (veupath_chatbot.services.experiment.seed.types.SeedDef attribute) (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) step_type (veupath_chatbot.domain.strategy.compile.CompiledStep attribute) StepAnalysis (class in veupath_chatbot.domain.strategy.ast) StepAnalysisProgressDataResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) StepAnalysisRequest (class in veupath_chatbot.transport.http.schemas.steps) StepAnalysisResponse (class in veupath_chatbot.transport.http.schemas.steps) StepAnalysisResult (class in veupath_chatbot.services.experiment.types) (class in veupath_chatbot.services.experiment.types.step_analysis) StepAnalysisResultResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) StepAnalysisRunResponse (class in veupath_chatbot.transport.http.schemas.steps) StepAnalysisSpec (class in veupath_chatbot.transport.http.schemas.plan) StepBuilderMixin (class in veupath_chatbot.services.strategies.engine.step_builder) StepContribution (class in veupath_chatbot.services.experiment.types) (class in veupath_chatbot.services.experiment.types.step_analysis) StepContributionResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) StepCountResult (class in veupath_chatbot.services.strategies.build) StepCountsRequest (class in veupath_chatbot.transport.http.schemas.strategies) StepCountsResponse (class in veupath_chatbot.transport.http.schemas.strategies) StepCreationResult (class in veupath_chatbot.services.strategies.step_creation) StepDecoratorAPI (class in veupath_chatbot.domain.strategy.compile) StepEvaluation (class in veupath_chatbot.services.experiment.types) (class in veupath_chatbot.services.experiment.types.step_analysis) StepEvaluationResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) StepFilter (class in veupath_chatbot.domain.strategy.ast) StepFilterRequest (class in veupath_chatbot.transport.http.schemas.steps) StepFilterResponse (class in veupath_chatbot.transport.http.schemas.steps) StepFilterSpec (class in veupath_chatbot.transport.http.schemas.plan) StepFiltersResponse (class in veupath_chatbot.transport.http.schemas.steps) StepReport (class in veupath_chatbot.domain.strategy.ast) StepReportRequest (class in veupath_chatbot.transport.http.schemas.steps) StepReportResponse (class in veupath_chatbot.transport.http.schemas.steps) StepReportRunResponse (class in veupath_chatbot.transport.http.schemas.steps) StepReportSpec (class in veupath_chatbot.transport.http.schemas.plan) StepResponse (class in veupath_chatbot.transport.http.schemas.steps) StepResultsService (class in veupath_chatbot.services.wdk.step_results) steps (veupath_chatbot.domain.strategy.compile.CompilationResult attribute) (veupath_chatbot.persistence.models.StreamProjection attribute) (veupath_chatbot.transport.http.schemas.experiments.ThresholdSweepRequest attribute) (veupath_chatbot.transport.http.schemas.strategies.StrategyResponse attribute) StepsMixin (class in veupath_chatbot.integrations.veupathdb.strategy_api.steps) StepTreeNode (class in veupath_chatbot.domain.strategy.ast) (class in veupath_chatbot.integrations.veupathdb.strategy_api.helpers) StepValidationIssue (class in veupath_chatbot.domain.strategy.validate) strand (veupath_chatbot.domain.strategy.ops.ColocationParams attribute) (veupath_chatbot.transport.http.schemas.plan.ColocationParams attribute) StrategiesMixin (class in veupath_chatbot.integrations.veupathdb.strategy_api.strategies) strategy (veupath_chatbot.transport.http.schemas.sse.MessageStartEventData attribute) strategy_id (veupath_chatbot.transport.http.schemas.chat.ChatRequest attribute) (veupath_chatbot.transport.http.schemas.sse.MessageStartEventData attribute) (veupath_chatbot.transport.http.schemas.strategies.OpenStrategyRequest attribute) (veupath_chatbot.transport.http.schemas.strategies.OpenStrategyResponse attribute) strategy_link (veupath_chatbot.transport.http.routers.internal.SSESchemaIndex attribute) strategy_meta (veupath_chatbot.transport.http.routers.internal.SSESchemaIndex attribute) STRATEGY_NOT_FOUND (veupath_chatbot.platform.errors.ErrorCode attribute) strategy_tools (veupath_chatbot.ai.tools.strategy_registry.StrategyToolsMixin attribute) strategy_update (veupath_chatbot.transport.http.routers.internal.SSESchemaIndex attribute) strategy_url() (veupath_chatbot.integrations.veupathdb.factory.SiteInfo method) (veupath_chatbot.integrations.veupathdb.site_router.SiteInfo method) (veupath_chatbot.services.strategies.build.SiteInfoLike method) StrategyAPI (class in veupath_chatbot.integrations.veupathdb.strategy_api.api) StrategyAPIBase (class in veupath_chatbot.integrations.veupathdb.strategy_api.base) StrategyAST (class in veupath_chatbot.domain.strategy.ast) StrategyAttachmentOps (class in veupath_chatbot.ai.tools.strategy_tools.attachment_ops) StrategyBuildAPI (class in veupath_chatbot.services.strategies.build) StrategyCompiler (class in veupath_chatbot.domain.strategy.compile) StrategyCompilerAPI (class in veupath_chatbot.domain.strategy.compile) StrategyDiscoveryOps (class in veupath_chatbot.ai.tools.strategy_tools.discovery_ops) StrategyEditOps (class in veupath_chatbot.ai.tools.strategy_tools.edit_ops) StrategyGraph (class in veupath_chatbot.domain.strategy.session) StrategyGraphOps (class in veupath_chatbot.ai.tools.strategy_tools.graph_ops) StrategyLinkEventData (class in veupath_chatbot.transport.http.schemas.sse) StrategyMetaEventData (class in veupath_chatbot.transport.http.schemas.sse) StrategyPlan (class in veupath_chatbot.transport.http.schemas.plan) StrategyResponse (class in veupath_chatbot.transport.http.schemas.strategies) StrategySession (class in veupath_chatbot.domain.strategy.session) StrategyStepOps (class in veupath_chatbot.ai.tools.strategy_tools.step_ops) StrategyTools (class in veupath_chatbot.ai.tools.strategy_tools.operations) StrategyToolsBase (class in veupath_chatbot.services.strategies.engine.base) StrategyToolsHelpers (class in veupath_chatbot.services.strategies.engine.helpers) StrategyToolsMixin (class in veupath_chatbot.ai.tools.strategy_registry) StrategyUpdateEventData (class in veupath_chatbot.transport.http.schemas.sse) StrategyValidator (class in veupath_chatbot.domain.strategy.validate) Stream (class in veupath_chatbot.persistence.models) stream (veupath_chatbot.persistence.models.Operation attribute) (veupath_chatbot.persistence.models.StreamProjection attribute) stream() (veupath_chatbot.ai.engines.mock.MockEngine method) stream_chat() (in module veupath_chatbot.services.chat.streaming) stream_id (veupath_chatbot.persistence.models.Operation attribute) (veupath_chatbot.persistence.models.StreamProjection attribute) (veupath_chatbot.transport.http.schemas.workbench_chat.WorkbenchChatResponse attribute) StreamProjection (class in veupath_chatbot.persistence.models) StreamRepository (class in veupath_chatbot.persistence.repositories.stream) streams (veupath_chatbot.persistence.models.User attribute) strip_html_tags() (in module veupath_chatbot.integrations.veupathdb.site_search) strip_internal_wdk_strategy_name() (in module veupath_chatbot.integrations.veupathdb.strategy_api.helpers) strip_tags() (in module veupath_chatbot.services.research.utils) sub_kani_activity (veupath_chatbot.transport.http.schemas.chat.MessageResponse attribute) sub_kani_call_count (veupath_chatbot.transport.http.schemas.chat.TokenUsageResponse attribute) (veupath_chatbot.transport.http.schemas.sse.MessageEndEventData attribute) sub_kani_calls (veupath_chatbot.transport.http.schemas.chat.ThinkingResponse attribute) sub_kani_completion_tokens (veupath_chatbot.transport.http.schemas.chat.TokenUsageResponse attribute) (veupath_chatbot.transport.http.schemas.sse.MessageEndEventData attribute) sub_kani_prompt_tokens (veupath_chatbot.transport.http.schemas.chat.TokenUsageResponse attribute) (veupath_chatbot.transport.http.schemas.sse.MessageEndEventData attribute) sub_kani_status (veupath_chatbot.transport.http.schemas.chat.ThinkingResponse attribute) subkani_max_concurrency (veupath_chatbot.platform.config.Settings attribute) subkani_model (veupath_chatbot.platform.config.Settings attribute) subkani_task_end (veupath_chatbot.transport.http.routers.internal.SSESchemaIndex attribute) subkani_task_start (veupath_chatbot.transport.http.routers.internal.SSESchemaIndex attribute) subkani_temperature (veupath_chatbot.platform.config.Settings attribute) subkani_timeout_seconds (veupath_chatbot.platform.config.Settings attribute) subkani_tool_call_end (veupath_chatbot.transport.http.routers.internal.SSESchemaIndex attribute) subkani_tool_call_start (veupath_chatbot.transport.http.routers.internal.SSESchemaIndex attribute) subkani_top_p (veupath_chatbot.platform.config.Settings attribute) SubKaniActivityResponse (class in veupath_chatbot.transport.http.schemas.chat) SubKaniRoundResult (class in veupath_chatbot.ai.orchestration.subkani.utils) SubKaniTaskEndEventData (class in veupath_chatbot.transport.http.schemas.sse) SubKaniTaskStartEventData (class in veupath_chatbot.transport.http.schemas.sse) SubKaniTokenUsageResponse (class in veupath_chatbot.transport.http.schemas.chat) SubKaniToolCallEndEventData (class in veupath_chatbot.transport.http.schemas.sse) SubKaniToolCallStartEventData (class in veupath_chatbot.transport.http.schemas.sse) subscribe() (in module veupath_chatbot.transport.http.routers.operations) SubtaskAgent (class in veupath_chatbot.ai.agents.subtask) success (veupath_chatbot.transport.http.schemas.veupathdb_auth.AuthSuccessResponse attribute) success() (veupath_chatbot.domain.strategy.validate.ValidationResult class method) suggest_organisms() (in module veupath_chatbot.services.gene_lookup.organism) suggestedOrganisms (veupath_chatbot.transport.http.routers.sites.genes.GeneSearchResponse attribute) summary_markdown (veupath_chatbot.transport.http.schemas.chat.PlanningArtifactResponse attribute) supports_reasoning (veupath_chatbot.ai.models.catalog.ModelEntry attribute) (veupath_chatbot.transport.http.routers.models.ModelCatalogEntryResponse attribute) SWEEP_CONCURRENCY (in module veupath_chatbot.services.experiment.evaluation) sweep_parameters() (in module veupath_chatbot.services.experiment.step_analysis.phase_sensitivity) SWEEP_POINT_TIMEOUT_S (in module veupath_chatbot.services.experiment.evaluation) sweep_points (veupath_chatbot.services.experiment.types.ParameterSensitivity attribute) (veupath_chatbot.services.experiment.types.step_analysis.ParameterSensitivity attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ParameterSensitivityResponse attribute) SWEEP_TIMEOUT_S (in module veupath_chatbot.services.experiment.evaluation) sweep_type (veupath_chatbot.transport.http.schemas.experiments.ThresholdSweepRequest attribute) sync_all_wdk_strategies() (in module veupath_chatbot.transport.http.routers.strategies.wdk_import) sync_is_saved_to_wdk() (in module veupath_chatbot.services.strategies.wdk_sync) sync_to_projection() (in module veupath_chatbot.services.strategies.wdk_sync) system_config() (in module veupath_chatbot.transport.http.routers.health) SystemConfigResponse (class in veupath_chatbot.transport.http.schemas.health)

T

tag (veupath_chatbot.transport.http.schemas.chat.CitationResponse attribute) tag_internal_wdk_strategy_name() (in module veupath_chatbot.integrations.veupathdb.strategy_api.helpers) tags (veupath_chatbot.persistence.models.ControlSet attribute) (veupath_chatbot.services.experiment.seed.ControlSetDef attribute) (veupath_chatbot.services.experiment.seed.types.ControlSetDef attribute) (veupath_chatbot.transport.http.routers.control_sets.ControlSetResponse attribute) (veupath_chatbot.transport.http.routers.control_sets.CreateControlSetRequest attribute) target_gene_ids (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) target_organisms (veupath_chatbot.services.experiment.types.BatchExperimentConfig attribute) (veupath_chatbot.services.experiment.types.experiment.BatchExperimentConfig attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateBatchExperimentRequest attribute) task (veupath_chatbot.transport.http.schemas.sse.SubKaniTaskEndEventData attribute) (veupath_chatbot.transport.http.schemas.sse.SubKaniTaskStartEventData attribute) (veupath_chatbot.transport.http.schemas.sse.SubKaniToolCallEndEventData attribute) (veupath_chatbot.transport.http.schemas.sse.SubKaniToolCallStartEventData attribute) tasks (veupath_chatbot.ai.orchestration.delegation.DelegationPlan attribute) taxon_params() (in module veupath_chatbot.services.experiment.seed.helpers) temperature (veupath_chatbot.transport.http.schemas.chat.ChatRequest attribute) TemporaryResultsAPI (class in veupath_chatbot.integrations.veupathdb.temporary_results) term_id (veupath_chatbot.services.experiment.types.enrichment.EnrichmentTerm attribute) (veupath_chatbot.services.experiment.types.EnrichmentTerm attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.EnrichmentTermResponse attribute) term_name (veupath_chatbot.services.experiment.types.enrichment.EnrichmentTerm attribute) (veupath_chatbot.services.experiment.types.EnrichmentTerm attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.EnrichmentTermResponse attribute) termKey (veupath_chatbot.services.experiment.enrichment_compare.EnrichmentRow attribute) termName (veupath_chatbot.services.experiment.enrichment_compare.EnrichmentRow attribute) terms (veupath_chatbot.services.experiment.types.enrichment.EnrichmentResult attribute) (veupath_chatbot.services.experiment.types.EnrichmentResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.EnrichmentResultResponse attribute) text_search_params() (in module veupath_chatbot.services.experiment.seed.helpers) thinking (veupath_chatbot.transport.http.schemas.strategies.StrategyResponse attribute) ThinkingResponse (class in veupath_chatbot.transport.http.schemas.chat) threshold_knob (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) threshold_knobs (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) threshold_sweep() (in module veupath_chatbot.transport.http.routers.experiments.evaluation) ThresholdKnob (class in veupath_chatbot.services.experiment.types) (class in veupath_chatbot.services.experiment.types.optimization) ThresholdKnobRequest (class in veupath_chatbot.transport.http.schemas.experiments) ThresholdKnobResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) ThresholdSweepRequest (class in veupath_chatbot.transport.http.schemas.experiments) timeout_seconds (veupath_chatbot.integrations.vectorstore.qdrant_store.QdrantStore attribute) timestamp (veupath_chatbot.transport.http.schemas.chat.MessageResponse attribute) (veupath_chatbot.transport.http.schemas.health.HealthResponse attribute) title (veupath_chatbot.domain.research.citations.Citation attribute) (veupath_chatbot.platform.errors.ProblemDetail attribute) (veupath_chatbot.transport.http.schemas.chat.CitationResponse attribute) (veupath_chatbot.transport.http.schemas.chat.PlanningArtifactResponse attribute) (veupath_chatbot.transport.http.schemas.strategies.StrategyResponse attribute) tn_ids (veupath_chatbot.transport.http.schemas.gene_sets.GeneConfidenceRequest attribute) to_dict() (veupath_chatbot.domain.research.citations.Citation method) (veupath_chatbot.domain.strategy.ast.PlanStepNode method) (veupath_chatbot.domain.strategy.ast.StepAnalysis method) (veupath_chatbot.domain.strategy.ast.StepFilter method) (veupath_chatbot.domain.strategy.ast.StepReport method) (veupath_chatbot.domain.strategy.ast.StepTreeNode method) (veupath_chatbot.domain.strategy.ast.StrategyAST method) (veupath_chatbot.domain.strategy.compile.CompilationResult method) (veupath_chatbot.integrations.veupathdb.factory.SiteInfo method) (veupath_chatbot.integrations.veupathdb.site_router.SiteInfo method) (veupath_chatbot.integrations.veupathdb.strategy_api.helpers.StepTreeNode method) (veupath_chatbot.services.strategies.engine.graph_integrity.GraphIntegrityError method) to_json() (in module veupath_chatbot.services.experiment.types) (in module veupath_chatbot.services.experiment.types.json_codec) token_usage (veupath_chatbot.transport.http.schemas.chat.MessageResponse attribute) (veupath_chatbot.transport.http.schemas.chat.SubKaniActivityResponse attribute) token_usage_partial (veupath_chatbot.transport.http.routers.internal.SSESchemaIndex attribute) tokenize_query() (in module veupath_chatbot.ai.tools.query_validation) TokenUsagePartialEventData (class in veupath_chatbot.transport.http.schemas.sse) TokenUsageResponse (class in veupath_chatbot.transport.http.schemas.chat) TomlConfigSettingsSource (class in veupath_chatbot.platform.config) tool_call_count (veupath_chatbot.transport.http.schemas.chat.TokenUsageResponse attribute) (veupath_chatbot.transport.http.schemas.sse.MessageEndEventData attribute) tool_call_end (veupath_chatbot.transport.http.routers.internal.SSESchemaIndex attribute) tool_call_start (veupath_chatbot.transport.http.routers.internal.SSESchemaIndex attribute) tool_calls (veupath_chatbot.transport.http.schemas.chat.MessageResponse attribute) (veupath_chatbot.transport.http.schemas.chat.ThinkingResponse attribute) tool_error() (in module veupath_chatbot.platform.tool_errors) tool_result_to_events() (in module veupath_chatbot.services.chat.events) ToolCallEndEventData (class in veupath_chatbot.transport.http.schemas.sse) ToolCallResponse (class in veupath_chatbot.transport.http.schemas.chat) ToolCallStartEventData (class in veupath_chatbot.transport.http.schemas.sse) ToolListResponse (class in veupath_chatbot.transport.http.routers.tools) tools (veupath_chatbot.transport.http.routers.tools.ToolListResponse attribute) top_k_stability (veupath_chatbot.services.experiment.types.BootstrapResult attribute) (veupath_chatbot.services.experiment.types.rank.BootstrapResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.BootstrapResultResponse attribute) total (veupath_chatbot.services.gene_sets.ensemble.EnsembleScore attribute) total_count (veupath_chatbot.services.gene_lookup.wdk.WdkTextResult attribute) total_genes_analyzed (veupath_chatbot.services.experiment.types.enrichment.EnrichmentResult attribute) (veupath_chatbot.services.experiment.types.EnrichmentResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.EnrichmentResultResponse attribute) total_negatives (veupath_chatbot.services.experiment.types.ExperimentMetrics attribute) (veupath_chatbot.services.experiment.types.metrics.ExperimentMetrics attribute) (veupath_chatbot.services.parameter_optimization.TrialResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentMetricsResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentSummaryResponse attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationTrialData attribute)

total_positives (veupath_chatbot.services.experiment.types.ExperimentMetrics attribute) (veupath_chatbot.services.experiment.types.metrics.ExperimentMetrics attribute) (veupath_chatbot.services.parameter_optimization.TrialResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentMetricsResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentSummaryResponse attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationTrialData attribute) total_results (veupath_chatbot.services.experiment.types.ExperimentMetrics attribute) (veupath_chatbot.services.experiment.types.metrics.ExperimentMetrics attribute) (veupath_chatbot.services.experiment.types.OperatorVariant attribute) (veupath_chatbot.services.experiment.types.ParameterSweepPoint attribute) (veupath_chatbot.services.experiment.types.rank.RankMetrics attribute) (veupath_chatbot.services.experiment.types.RankMetrics attribute) (veupath_chatbot.services.experiment.types.step_analysis.OperatorVariant attribute) (veupath_chatbot.services.experiment.types.step_analysis.ParameterSweepPoint attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentMetricsResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OperatorVariantResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ParameterSweepPointResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.RankMetricsResponse attribute) total_steps (veupath_chatbot.transport.http.schemas.experiment_responses.StepAnalysisProgressDataResponse attribute) total_time_seconds (veupath_chatbot.services.experiment.types.Experiment attribute) (veupath_chatbot.services.experiment.types.experiment.Experiment attribute) (veupath_chatbot.services.experiment.types.optimization.TreeOptimizationResult attribute) (veupath_chatbot.services.experiment.types.TreeOptimizationResult attribute) (veupath_chatbot.services.parameter_optimization.OptimizationResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OptimizationResultResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.TreeOptimizationResultResponse attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationProgressEventData attribute) total_tokens (veupath_chatbot.transport.http.schemas.chat.TokenUsageResponse attribute) (veupath_chatbot.transport.http.schemas.sse.MessageEndEventData attribute) total_trials (veupath_chatbot.transport.http.schemas.experiment_responses.OptimizationResultResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.TrialProgressDataResponse attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationProgressEventData attribute) totalCount (veupath_chatbot.transport.http.routers.sites.genes.GeneSearchResponse attribute) totalExperiments (veupath_chatbot.services.experiment.overlap.GeneMembership attribute) totalGenes (veupath_chatbot.services.experiment.overlap.PerExperimentSummary attribute) totalTerms (veupath_chatbot.services.experiment.enrichment_compare.EnrichmentCompareResult attribute) totalUniqueGenes (veupath_chatbot.services.experiment.overlap.OverlapResult attribute) tp_ids (veupath_chatbot.transport.http.schemas.gene_sets.GeneConfidenceRequest attribute) tp_movement (veupath_chatbot.services.experiment.types.step_analysis.StepEvaluation attribute) (veupath_chatbot.services.experiment.types.StepEvaluation attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepEvaluationResponse attribute) tpCount (veupath_chatbot.services.experiment.custom_enrichment.CustomEnrichmentResult attribute) transform_name (veupath_chatbot.transport.http.schemas.experiments.RefineRequest attribute) transmembrane_params() (in module veupath_chatbot.services.experiment.seed.helpers) tree_optimization (veupath_chatbot.services.experiment.types.Experiment attribute) (veupath_chatbot.services.experiment.types.experiment.Experiment attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentResponse attribute) tree_optimization_budget (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) tree_optimization_objective (veupath_chatbot.services.experiment.types.experiment.ExperimentConfig attribute) (veupath_chatbot.services.experiment.types.ExperimentConfig attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentConfigResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.CreateExperimentRequest attribute) tree_optimization_result (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) tree_optimization_trial (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) TreeOptimizationResult (class in veupath_chatbot.services.experiment.types) (class in veupath_chatbot.services.experiment.types.optimization) TreeOptimizationResultResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) TreeOptimizationTrial (class in veupath_chatbot.services.experiment.types) (class in veupath_chatbot.services.experiment.types.optimization) TreeOptimizationTrialResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) trial (veupath_chatbot.transport.http.schemas.optimization.OptimizationProgressEventData attribute) trial_number (veupath_chatbot.services.experiment.types.optimization.TreeOptimizationTrial attribute) (veupath_chatbot.services.experiment.types.TreeOptimizationTrial attribute) (veupath_chatbot.services.parameter_optimization.TrialResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.TreeOptimizationTrialResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.TrialProgressDataResponse attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationTrialData attribute) trial_progress (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentProgressDataResponse attribute) trial_progress_data (veupath_chatbot.transport.http.routers.internal.ExperimentSchemaIndex attribute) TrialMetrics (class in veupath_chatbot.services.parameter_optimization.trials) TrialProgressDataResponse (class in veupath_chatbot.transport.http.schemas.experiment_responses) TrialResult (class in veupath_chatbot.services.parameter_optimization) true_negative_genes (veupath_chatbot.services.experiment.types.Experiment attribute) (veupath_chatbot.services.experiment.types.experiment.Experiment attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentResponse attribute) true_negatives (veupath_chatbot.services.experiment.types.ConfusionMatrix attribute) (veupath_chatbot.services.experiment.types.metrics.ConfusionMatrix attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ConfusionMatrixResponse attribute) true_positive_genes (veupath_chatbot.services.experiment.types.Experiment attribute) (veupath_chatbot.services.experiment.types.experiment.Experiment attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentResponse attribute) true_positives (veupath_chatbot.services.experiment.types.ConfusionMatrix attribute) (veupath_chatbot.services.experiment.types.metrics.ConfusionMatrix attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ConfusionMatrixResponse attribute) truncate() (in module veupath_chatbot.integrations.vectorstore.ingest.public_strategies_helpers) truncate_text() (in module veupath_chatbot.services.research.utils) try_auto_push_to_wdk() (in module veupath_chatbot.services.strategies.auto_push) type (veupath_chatbot.persistence.models.Operation attribute) (veupath_chatbot.platform.errors.ProblemDetail attribute) (veupath_chatbot.services.experiment.types.optimization.OptimizationSpec attribute) (veupath_chatbot.services.experiment.types.OptimizationSpec attribute) (veupath_chatbot.transport.http.schemas.chat.ChatMention attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OptimizationSpecResponse attribute) (veupath_chatbot.transport.http.schemas.experiments.OptimizationSpecRequest attribute) (veupath_chatbot.transport.http.schemas.optimization.OptimizationParameterSpecData attribute) (veupath_chatbot.transport.http.schemas.sites.ParamSpecResponse attribute) type_annotation_map (veupath_chatbot.persistence.models.Base attribute)

U

UNAUTHORIZED (veupath_chatbot.platform.errors.ErrorCode attribute) UnauthorizedError undo() (veupath_chatbot.domain.strategy.session.StrategyGraph method) undo_last_change() (veupath_chatbot.ai.tools.strategy_tools.edit_ops.StrategyEditOps method) UnifiedToolRegistryMixin (class in veupath_chatbot.ai.tools.unified_registry) UNION (veupath_chatbot.domain.strategy.ops.CombineOp attribute) union (veupath_chatbot.services.experiment.overlap.PairwiseOverlap attribute) uniqueA (veupath_chatbot.services.experiment.overlap.PairwiseOverlap attribute) uniqueB (veupath_chatbot.services.experiment.overlap.PairwiseOverlap attribute) uniqueGenes (veupath_chatbot.services.experiment.overlap.PerExperimentSummary attribute) universalGenes (veupath_chatbot.services.experiment.overlap.OverlapResult attribute) UNKNOWN (veupath_chatbot.domain.parameters._value_helpers.ParamKind attribute) unresolved (veupath_chatbot.transport.http.routers.sites.genes.GeneResolveResponse attribute) unwrap_search_data() (in module veupath_chatbot.domain.parameters.specs) update_experiment() (in module veupath_chatbot.transport.http.routers.experiments.crud) update_projection() (veupath_chatbot.persistence.repositories.stream.StreamRepository method) update_step() (veupath_chatbot.ai.tools.strategy_tools.edit_ops.StrategyEditOps method) update_step_view_filters() (veupath_chatbot.integrations.veupathdb.client.VEuPathDBClient method) update_strategy() (in module veupath_chatbot.transport.http.routers.strategies.crud) (veupath_chatbot.integrations.veupathdb.strategy_api.strategies.StrategiesMixin method) (veupath_chatbot.services.strategies.build.StrategyBuildAPI method) updated_at (veupath_chatbot.persistence.models.ExperimentRow attribute) (veupath_chatbot.persistence.models.StreamProjection attribute) (veupath_chatbot.transport.http.schemas.chat.ThinkingResponse attribute) (veupath_chatbot.transport.http.schemas.strategies.StrategyResponse attribute) UpdateStrategyRequest (class in veupath_chatbot.transport.http.schemas.strategies) upper (veupath_chatbot.services.experiment.types.ConfidenceInterval attribute) (veupath_chatbot.services.experiment.types.rank.ConfidenceInterval attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ConfidenceIntervalResponse attribute)

upsert() (veupath_chatbot.integrations.vectorstore.qdrant_store.QdrantStore method) upsert_enrichment_result() (in module veupath_chatbot.services.experiment.enrichment) upsert_projection() (in module veupath_chatbot.services.strategies.wdk_sync) upsert_record_type_docs() (in module veupath_chatbot.integrations.vectorstore.ingest.wdk_index) upsert_search_docs_batch() (in module veupath_chatbot.integrations.vectorstore.ingest.wdk_index) upsert_summary_projection() (in module veupath_chatbot.services.strategies.wdk_sync) upstream (veupath_chatbot.domain.strategy.ops.ColocationParams attribute) (veupath_chatbot.transport.http.schemas.plan.ColocationParams attribute) url (veupath_chatbot.domain.research.citations.Citation attribute) (veupath_chatbot.integrations.vectorstore.qdrant_store.QdrantStore attribute) (veupath_chatbot.services.export.service.ExportResult attribute) (veupath_chatbot.transport.http.schemas.chat.CitationResponse attribute) User (class in veupath_chatbot.persistence.models) user (veupath_chatbot.persistence.models.Stream attribute) user_id (veupath_chatbot.ai.tools.export_tools.ExportToolsMixin attribute) (veupath_chatbot.ai.tools.planner.workbench_tools.WorkbenchToolsMixin attribute) (veupath_chatbot.persistence.models.ControlSet attribute) (veupath_chatbot.persistence.models.ExperimentRow attribute) (veupath_chatbot.persistence.models.GeneSetRow attribute) (veupath_chatbot.persistence.models.Stream attribute) (veupath_chatbot.services.experiment.types.Experiment attribute) (veupath_chatbot.services.experiment.types.experiment.Experiment attribute) (veupath_chatbot.services.gene_sets.types.GeneSet attribute) (veupath_chatbot.transport.http.routers.control_sets.ControlSetResponse attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentResponse attribute) user_message (veupath_chatbot.transport.http.routers.internal.SSESchemaIndex attribute) UserMessageEventData (class in veupath_chatbot.transport.http.schemas.sse) UserRepository (class in veupath_chatbot.persistence.repositories.user)

V

valid (veupath_chatbot.domain.strategy.validate.ValidationResult attribute) validate() (veupath_chatbot.domain.strategy.ops.ColocationParams method) (veupath_chatbot.domain.strategy.validate.StrategyValidator method) validate_graph_integrity() (in module veupath_chatbot.services.strategies.engine.graph_integrity) validate_graph_structure() (veupath_chatbot.ai.tools.strategy_tools.graph_ops.StrategyGraphOps method) validate_parameters() (in module veupath_chatbot.services.catalog.param_validation) validate_plan_or_raise() (in module veupath_chatbot.services.strategies.plan_validation) validate_search_params() (in module veupath_chatbot.services.catalog.param_validation) (in module veupath_chatbot.services.catalog.parameters) (in module veupath_chatbot.transport.http.routers.sites.params) validate_strategy() (in module veupath_chatbot.domain.strategy.validate) validate_sweep_parameter() (in module veupath_chatbot.services.experiment.evaluation) validation (veupath_chatbot.transport.http.schemas.sites.SearchDetailsResponse attribute) (veupath_chatbot.transport.http.schemas.sites.SearchValidationResponse attribute) VALIDATION_ERROR (veupath_chatbot.platform.errors.ErrorCode attribute) validation_error (veupath_chatbot.transport.http.schemas.steps.StepResponse attribute) ValidationError ValidationMixin (class in veupath_chatbot.services.strategies.engine.validation) ValidationResult (class in veupath_chatbot.domain.strategy.validate) value (veupath_chatbot.domain.parameters._value_helpers.ProcessedParam attribute) (veupath_chatbot.domain.strategy.ast.StepFilter attribute) (veupath_chatbot.services.experiment.types.ParameterSweepPoint attribute) (veupath_chatbot.services.experiment.types.step_analysis.ParameterSweepPoint attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ParameterSweepPointResponse attribute) (veupath_chatbot.transport.http.schemas.plan.StepFilterSpec attribute) (veupath_chatbot.transport.http.schemas.steps.PrimaryKeyPart attribute) (veupath_chatbot.transport.http.schemas.steps.StepFilterRequest attribute) (veupath_chatbot.transport.http.schemas.steps.StepFilterResponse attribute) values (veupath_chatbot.transport.http.schemas.experiments.ThresholdSweepRequest attribute) variants (veupath_chatbot.services.experiment.types.OperatorComparison attribute) (veupath_chatbot.services.experiment.types.step_analysis.OperatorComparison attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.OperatorComparisonResponse attribute) verdict (veupath_chatbot.services.experiment.types.step_analysis.StepContribution attribute) (veupath_chatbot.services.experiment.types.StepContribution attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.StepContributionResponse attribute) version (veupath_chatbot.persistence.models.ControlSet attribute) (veupath_chatbot.transport.http.routers.control_sets.ControlSetResponse attribute) (veupath_chatbot.transport.http.schemas.health.HealthResponse attribute) veupath_chatbot.ai.agents.executor module veupath_chatbot.ai.agents.experiment module veupath_chatbot.ai.agents.factory module veupath_chatbot.ai.agents.subtask module veupath_chatbot.ai.agents.workbench module veupath_chatbot.ai.engines.cached_anthropic module veupath_chatbot.ai.engines.mock module veupath_chatbot.ai.engines.responses_openai module veupath_chatbot.ai.models.catalog module veupath_chatbot.ai.models.pricing module veupath_chatbot.ai.orchestration.delegation module veupath_chatbot.ai.orchestration.scheduler module veupath_chatbot.ai.orchestration.subkani.orchestrator module veupath_chatbot.ai.orchestration.subkani.prompts module veupath_chatbot.ai.orchestration.subkani.utils module veupath_chatbot.ai.prompts.executor_prompt module veupath_chatbot.ai.prompts.loader module veupath_chatbot.ai.prompts.workbench_chat module veupath_chatbot.ai.tools.catalog_rag_tools module veupath_chatbot.ai.tools.catalog_registry module veupath_chatbot.ai.tools.catalog_tools module veupath_chatbot.ai.tools.combined_result module veupath_chatbot.ai.tools.conversation_tools module veupath_chatbot.ai.tools.example_plans_rag_tools module veupath_chatbot.ai.tools.execution_tools module veupath_chatbot.ai.tools.export_tools module veupath_chatbot.ai.tools.planner.artifact_tools module veupath_chatbot.ai.tools.planner.experiment_tools module veupath_chatbot.ai.tools.planner.gene_tools module veupath_chatbot.ai.tools.planner.optimization_tools module veupath_chatbot.ai.tools.planner.workbench_tools module veupath_chatbot.ai.tools.query_validation module veupath_chatbot.ai.tools.registry module veupath_chatbot.ai.tools.research_registry module veupath_chatbot.ai.tools.result_tools module veupath_chatbot.ai.tools.strategy_registry module veupath_chatbot.ai.tools.strategy_tools.attachment_ops module veupath_chatbot.ai.tools.strategy_tools.discovery_ops module veupath_chatbot.ai.tools.strategy_tools.edit_ops module veupath_chatbot.ai.tools.strategy_tools.graph_ops module veupath_chatbot.ai.tools.strategy_tools.operations module veupath_chatbot.ai.tools.strategy_tools.step_ops module veupath_chatbot.ai.tools.unified_registry module veupath_chatbot.ai.tools.wdk_error_handler module veupath_chatbot.ai.tools.workbench_read_tools module veupath_chatbot.devtools.openapi module veupath_chatbot.domain.parameters._decode_values module veupath_chatbot.domain.parameters._value_helpers module veupath_chatbot.domain.parameters.canonicalize module veupath_chatbot.domain.parameters.normalize module veupath_chatbot.domain.parameters.specs module veupath_chatbot.domain.parameters.vocab_utils module veupath_chatbot.domain.research.citations module veupath_chatbot.domain.strategy.ast module veupath_chatbot.domain.strategy.compile module veupath_chatbot.domain.strategy.explain module veupath_chatbot.domain.strategy.metadata module veupath_chatbot.domain.strategy.ops module veupath_chatbot.domain.strategy.session module veupath_chatbot.domain.strategy.tree module veupath_chatbot.domain.strategy.validate module veupath_chatbot.integrations.embeddings.openai_embeddings module veupath_chatbot.integrations.vectorstore.bootstrap module veupath_chatbot.integrations.vectorstore.collections module veupath_chatbot.integrations.vectorstore.dependent_vocab_cache module veupath_chatbot.integrations.vectorstore.ingest.pipeline module veupath_chatbot.integrations.vectorstore.ingest.public_fetch module veupath_chatbot.integrations.vectorstore.ingest.public_index module veupath_chatbot.integrations.vectorstore.ingest.public_strategies module veupath_chatbot.integrations.vectorstore.ingest.public_strategies_helpers module veupath_chatbot.integrations.vectorstore.ingest.public_transform module veupath_chatbot.integrations.vectorstore.ingest.utils module veupath_chatbot.integrations.vectorstore.ingest.wdk_catalog module veupath_chatbot.integrations.vectorstore.ingest.wdk_fetch module veupath_chatbot.integrations.vectorstore.ingest.wdk_index module veupath_chatbot.integrations.vectorstore.ingest.wdk_transform module veupath_chatbot.integrations.vectorstore.qdrant_store module veupath_chatbot.integrations.veupathdb.client module veupath_chatbot.integrations.veupathdb.discovery module veupath_chatbot.integrations.veupathdb.factory module veupath_chatbot.integrations.veupathdb.param_utils module veupath_chatbot.integrations.veupathdb.site_router module veupath_chatbot.integrations.veupathdb.site_search module veupath_chatbot.integrations.veupathdb.strategy_api.analyses module veupath_chatbot.integrations.veupathdb.strategy_api.api module veupath_chatbot.integrations.veupathdb.strategy_api.base module veupath_chatbot.integrations.veupathdb.strategy_api.filters module veupath_chatbot.integrations.veupathdb.strategy_api.helpers module veupath_chatbot.integrations.veupathdb.strategy_api.records module veupath_chatbot.integrations.veupathdb.strategy_api.reports module veupath_chatbot.integrations.veupathdb.strategy_api.steps module veupath_chatbot.integrations.veupathdb.strategy_api.strategies module veupath_chatbot.integrations.veupathdb.temporary_results module veupath_chatbot.jobs.rag_startup module veupath_chatbot.main module veupath_chatbot.persistence.models module veupath_chatbot.persistence.repositories.control_set module veupath_chatbot.persistence.repositories.stream module veupath_chatbot.persistence.repositories.user module veupath_chatbot.persistence.session module veupath_chatbot.platform.config module veupath_chatbot.platform.context module veupath_chatbot.platform.errors module veupath_chatbot.platform.events module veupath_chatbot.platform.health module veupath_chatbot.platform.logging module veupath_chatbot.platform.parsing module veupath_chatbot.platform.pydantic_validation module veupath_chatbot.platform.redis module veupath_chatbot.platform.security module veupath_chatbot.platform.store module veupath_chatbot.platform.tasks module veupath_chatbot.platform.tool_errors module veupath_chatbot.platform.types module veupath_chatbot.services.catalog.param_resolution module veupath_chatbot.services.catalog.param_validation module veupath_chatbot.services.catalog.parameters module veupath_chatbot.services.catalog.rag_search module veupath_chatbot.services.catalog.searches module veupath_chatbot.services.catalog.sites module veupath_chatbot.services.chat.events module veupath_chatbot.services.chat.mention_context module veupath_chatbot.services.chat.orchestrator module veupath_chatbot.services.chat.streaming module veupath_chatbot.services.chat.utils module veupath_chatbot.services.control_helpers module veupath_chatbot.services.control_tests module veupath_chatbot.services.experiment._deserialize module

veupath_chatbot.services.experiment.ai_analysis_helpers module veupath_chatbot.services.experiment.ai_analysis_tools module veupath_chatbot.services.experiment.ai_refinement_tools module veupath_chatbot.services.experiment.assistant module veupath_chatbot.services.experiment.classification module veupath_chatbot.services.experiment.core.streaming module veupath_chatbot.services.experiment.cross_validation module veupath_chatbot.services.experiment.custom_enrichment module veupath_chatbot.services.experiment.enrichment module veupath_chatbot.services.experiment.enrichment_compare module veupath_chatbot.services.experiment.evaluation module veupath_chatbot.services.experiment.helpers module veupath_chatbot.services.experiment.materialization module veupath_chatbot.services.experiment.metrics module veupath_chatbot.services.experiment.overlap module veupath_chatbot.services.experiment.rank_metrics module veupath_chatbot.services.experiment.report module veupath_chatbot.services.experiment.robustness module veupath_chatbot.services.experiment.seed module veupath_chatbot.services.experiment.seed.helpers module veupath_chatbot.services.experiment.seed.runner module veupath_chatbot.services.experiment.seed.types module veupath_chatbot.services.experiment.service module veupath_chatbot.services.experiment.stats module veupath_chatbot.services.experiment.step_analysis module veupath_chatbot.services.experiment.step_analysis._evaluation module veupath_chatbot.services.experiment.step_analysis._tree_utils module veupath_chatbot.services.experiment.step_analysis.orchestrator module veupath_chatbot.services.experiment.step_analysis.phase_contribution module veupath_chatbot.services.experiment.step_analysis.phase_operators module veupath_chatbot.services.experiment.step_analysis.phase_sensitivity module veupath_chatbot.services.experiment.step_analysis.phase_step_eval module veupath_chatbot.services.experiment.store module veupath_chatbot.services.experiment.tree_knobs module veupath_chatbot.services.experiment.types module veupath_chatbot.services.experiment.types.core module veupath_chatbot.services.experiment.types.enrichment module veupath_chatbot.services.experiment.types.experiment module veupath_chatbot.services.experiment.types.json_codec module veupath_chatbot.services.experiment.types.metrics module veupath_chatbot.services.experiment.types.optimization module veupath_chatbot.services.experiment.types.rank module veupath_chatbot.services.experiment.types.serialization module veupath_chatbot.services.experiment.types.step_analysis module veupath_chatbot.services.export.service module veupath_chatbot.services.gene_lookup module veupath_chatbot.services.gene_lookup.enrich module veupath_chatbot.services.gene_lookup.lookup module veupath_chatbot.services.gene_lookup.organism module veupath_chatbot.services.gene_lookup.result module veupath_chatbot.services.gene_lookup.scoring module veupath_chatbot.services.gene_lookup.site_search module veupath_chatbot.services.gene_lookup.wdk module veupath_chatbot.services.gene_sets.confidence module veupath_chatbot.services.gene_sets.ensemble module veupath_chatbot.services.gene_sets.operations module veupath_chatbot.services.gene_sets.reverse_search module veupath_chatbot.services.gene_sets.store module veupath_chatbot.services.gene_sets.types module veupath_chatbot.services.parameter_optimization module veupath_chatbot.services.parameter_optimization.callbacks module veupath_chatbot.services.parameter_optimization.config module veupath_chatbot.services.parameter_optimization.core module veupath_chatbot.services.parameter_optimization.scoring module veupath_chatbot.services.parameter_optimization.trials module veupath_chatbot.services.research.clients._base module veupath_chatbot.services.research.clients.arxiv module veupath_chatbot.services.research.clients.crossref module veupath_chatbot.services.research.clients.europepmc module veupath_chatbot.services.research.clients.openalex module veupath_chatbot.services.research.clients.preprint module veupath_chatbot.services.research.clients.pubmed module veupath_chatbot.services.research.clients.semanticscholar module veupath_chatbot.services.research.literature_search module veupath_chatbot.services.research.utils module veupath_chatbot.services.research.web_search module veupath_chatbot.services.search_rerank module veupath_chatbot.services.strategies.auto_import module veupath_chatbot.services.strategies.auto_push module veupath_chatbot.services.strategies.build module veupath_chatbot.services.strategies.engine.base module veupath_chatbot.services.strategies.engine.graph_integrity module veupath_chatbot.services.strategies.engine.graph_ops module veupath_chatbot.services.strategies.engine.helpers module veupath_chatbot.services.strategies.engine.id_mapping module veupath_chatbot.services.strategies.engine.step_builder module veupath_chatbot.services.strategies.engine.validation module veupath_chatbot.services.strategies.plan_normalize module veupath_chatbot.services.strategies.plan_validation module veupath_chatbot.services.strategies.session_factory module veupath_chatbot.services.strategies.step_builders module veupath_chatbot.services.strategies.step_creation module veupath_chatbot.services.strategies.wdk_conversion module veupath_chatbot.services.strategies.wdk_counts module veupath_chatbot.services.strategies.wdk_sync module veupath_chatbot.services.wdk.enrichment_service module veupath_chatbot.services.wdk.helpers module veupath_chatbot.services.wdk.record_types module veupath_chatbot.services.wdk.step_results module veupath_chatbot.services.workbench_chat.orchestrator module veupath_chatbot.transport.http.deps module veupath_chatbot.transport.http.routers.chat module veupath_chatbot.transport.http.routers.control_sets module veupath_chatbot.transport.http.routers.dev module veupath_chatbot.transport.http.routers.experiments.analysis module veupath_chatbot.transport.http.routers.experiments.chat module veupath_chatbot.transport.http.routers.experiments.comparison module veupath_chatbot.transport.http.routers.experiments.cross_validation module veupath_chatbot.transport.http.routers.experiments.crud module veupath_chatbot.transport.http.routers.experiments.enrichment module veupath_chatbot.transport.http.routers.experiments.evaluation module veupath_chatbot.transport.http.routers.experiments.execution module veupath_chatbot.transport.http.routers.experiments.results module veupath_chatbot.transport.http.routers.exports module veupath_chatbot.transport.http.routers.gene_sets module veupath_chatbot.transport.http.routers.health module veupath_chatbot.transport.http.routers.internal module veupath_chatbot.transport.http.routers.models module veupath_chatbot.transport.http.routers.operations module veupath_chatbot.transport.http.routers.sites.catalog module veupath_chatbot.transport.http.routers.sites.genes module veupath_chatbot.transport.http.routers.sites.params module veupath_chatbot.transport.http.routers.strategies.counts module veupath_chatbot.transport.http.routers.strategies.crud module veupath_chatbot.transport.http.routers.strategies.plan module veupath_chatbot.transport.http.routers.strategies.wdk_import module veupath_chatbot.transport.http.routers.tools module veupath_chatbot.transport.http.routers.user_data module veupath_chatbot.transport.http.routers.veupathdb_auth module veupath_chatbot.transport.http.schemas.chat module veupath_chatbot.transport.http.schemas.experiment_responses module veupath_chatbot.transport.http.schemas.experiments module veupath_chatbot.transport.http.schemas.gene_sets module veupath_chatbot.transport.http.schemas.health module veupath_chatbot.transport.http.schemas.optimization module veupath_chatbot.transport.http.schemas.plan module veupath_chatbot.transport.http.schemas.sites module veupath_chatbot.transport.http.schemas.sse module veupath_chatbot.transport.http.schemas.steps module veupath_chatbot.transport.http.schemas.strategies module veupath_chatbot.transport.http.schemas.veupathdb_auth module veupath_chatbot.transport.http.schemas.workbench_chat module veupath_chatbot.transport.http.sse module veupathdb_auth_token (veupath_chatbot.platform.config.Settings attribute) veupathdb_cache_ttl (veupath_chatbot.platform.config.Settings attribute) veupathdb_default_site (veupath_chatbot.platform.config.Settings attribute) veupathdb_oauth_client_id (veupath_chatbot.platform.config.Settings attribute) veupathdb_oauth_url (veupath_chatbot.platform.config.Settings attribute) veupathdb_sites_config (veupath_chatbot.platform.config.Settings attribute) VEuPathDBClient (class in veupath_chatbot.integrations.veupathdb.client) vocabulary (veupath_chatbot.domain.parameters.specs.ParamSpecNormalized attribute) (veupath_chatbot.transport.http.schemas.sites.ParamSpecResponse attribute)

W

walk_dict_tree() (in module veupath_chatbot.domain.strategy.tree) walk_plan_tree() (in module veupath_chatbot.domain.strategy.tree) warnings (veupath_chatbot.transport.http.schemas.plan.PlanNormalizeResponse attribute) wdk (veupath_chatbot.transport.http.schemas.steps.StepAnalysisRunResponse attribute) (veupath_chatbot.transport.http.schemas.steps.StepReportRunResponse attribute) wdk_entity_name() (in module veupath_chatbot.integrations.veupathdb.param_utils) WDK_ERROR (veupath_chatbot.platform.errors.ErrorCode attribute) wdk_search_matches() (in module veupath_chatbot.integrations.veupathdb.param_utils) wdk_step_id (veupath_chatbot.domain.strategy.compile.CompiledStep attribute) (veupath_chatbot.persistence.models.GeneSetRow attribute) (veupath_chatbot.services.experiment.types.Experiment attribute) (veupath_chatbot.services.experiment.types.experiment.Experiment attribute) (veupath_chatbot.services.gene_sets.types.GeneSet attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentResponse attribute) (veupath_chatbot.transport.http.schemas.gene_sets.CreateGeneSetRequest attribute) (veupath_chatbot.transport.http.schemas.gene_sets.GeneSetResponse attribute) (veupath_chatbot.transport.http.schemas.steps.StepResponse attribute) wdk_strategy_id (veupath_chatbot.persistence.models.GeneSetRow attribute) (veupath_chatbot.persistence.models.StreamProjection attribute) (veupath_chatbot.services.experiment.types.Experiment attribute) (veupath_chatbot.services.experiment.types.experiment.Experiment attribute) (veupath_chatbot.services.gene_sets.types.GeneSet attribute) (veupath_chatbot.services.strategies.build.BuildResult attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentResponse attribute) (veupath_chatbot.transport.http.schemas.gene_sets.CreateGeneSetRequest attribute) (veupath_chatbot.transport.http.schemas.gene_sets.GeneSetResponse attribute) (veupath_chatbot.transport.http.schemas.sse.StrategyLinkEventData attribute) (veupath_chatbot.transport.http.schemas.strategies.OpenStrategyRequest attribute) (veupath_chatbot.transport.http.schemas.strategies.StrategyResponse attribute) (veupath_chatbot.transport.http.schemas.strategies.UpdateStrategyRequest attribute) (veupath_chatbot.transport.http.schemas.strategies.WdkStrategySummaryResponse attribute)

wdk_url (veupath_chatbot.services.strategies.build.BuildResult attribute) (veupath_chatbot.transport.http.schemas.sse.StrategyLinkEventData attribute) (veupath_chatbot.transport.http.schemas.strategies.StrategyResponse attribute) (veupath_chatbot.transport.http.schemas.strategies.WdkStrategySummaryResponse attribute) wdk_weight (veupath_chatbot.domain.strategy.ast.PlanStepNode attribute) WDKError WdkStrategySummaryResponse (class in veupath_chatbot.transport.http.schemas.strategies) WdkTextResult (class in veupath_chatbot.services.gene_lookup.wdk) web_base_url (veupath_chatbot.integrations.veupathdb.factory.SiteInfo property) (veupath_chatbot.integrations.veupathdb.site_router.SiteInfo property) web_search() (veupath_chatbot.ai.tools.research_registry.ResearchToolsMixin method) web_search_service (veupath_chatbot.ai.tools.research_registry.ResearchToolsMixin attribute) WebSearchService (class in veupath_chatbot.services.research.web_search) wildcard_ids (veupath_chatbot.services.search_rerank.QueryIntent attribute) workbench_chat() (in module veupath_chatbot.transport.http.routers.experiments.chat) workbench_gene_set (veupath_chatbot.transport.http.routers.internal.SSESchemaIndex attribute) WorkbenchAgent (class in veupath_chatbot.ai.agents.workbench) WorkbenchChatRequest (class in veupath_chatbot.transport.http.schemas.workbench_chat) WorkbenchChatResponse (class in veupath_chatbot.transport.http.schemas.workbench_chat) WorkbenchGeneSetEventData (class in veupath_chatbot.transport.http.schemas.sse) WorkbenchReadToolsMixin (class in veupath_chatbot.ai.tools.workbench_read_tools) WorkbenchToolsMixin (class in veupath_chatbot.ai.tools.planner.workbench_tools) WriteThruStore (class in veupath_chatbot.platform.store)

Y

year (veupath_chatbot.domain.research.citations.Citation attribute) (veupath_chatbot.transport.http.schemas.chat.CitationResponse attribute)

youdens_j (veupath_chatbot.services.experiment.types.ExperimentMetrics attribute) (veupath_chatbot.services.experiment.types.metrics.ExperimentMetrics attribute) (veupath_chatbot.transport.http.schemas.experiment_responses.ExperimentMetricsResponse attribute)

Z

zero_step_ids (veupath_chatbot.services.strategies.build.BuildResult attribute)