diff --git a/.github/workflows/gh-pages.yml b/.github/workflows/gh-pages.yml index 19f9856771..b17842318e 100644 --- a/.github/workflows/gh-pages.yml +++ b/.github/workflows/gh-pages.yml @@ -58,7 +58,7 @@ jobs: run: find docsite/_site - name: Deploy to GitHub Pages - uses: JamesIves/github-pages-deploy-action@v4.6.3 + uses: JamesIves/github-pages-deploy-action@v4.6.4 with: branch: gh-pages folder: docsite/_site diff --git a/.semversioner/0.3.6.json b/.semversioner/0.3.6.json new file mode 100644 index 0000000000..69fe783b33 --- /dev/null +++ b/.semversioner/0.3.6.json @@ -0,0 +1,14 @@ +{ + "changes": [ + { + "description": "Collapse create_final_relationships.", + "type": "patch" + }, + { + "description": "Dependency update and cleanup", + "type": "patch" + } + ], + "created_at": "2024-09-20T00:09:13+00:00", + "version": "0.3.6" +} \ No newline at end of file diff --git a/.semversioner/next-release/patch-20240911201935470388.json b/.semversioner/next-release/patch-20240911201935470388.json new file mode 100644 index 0000000000..36b24ff432 --- /dev/null +++ b/.semversioner/next-release/patch-20240911201935470388.json @@ -0,0 +1,4 @@ +{ + "type": "patch", + "description": "Calculate new inputs and deleted inputs on update" +} diff --git a/.semversioner/next-release/patch-20240918221118566693.json b/.semversioner/next-release/patch-20240918221118566693.json new file mode 100644 index 0000000000..5e62e9bd9c --- /dev/null +++ b/.semversioner/next-release/patch-20240918221118566693.json @@ -0,0 +1,4 @@ +{ + "type": "patch", + "description": "Merge existing and new entities, updating values accordingly" +} diff --git a/.semversioner/next-release/patch-20240919003117336827.json b/.semversioner/next-release/patch-20240919003117336827.json new file mode 100644 index 0000000000..0d045034fe --- /dev/null +++ b/.semversioner/next-release/patch-20240919003117336827.json @@ -0,0 +1,4 @@ +{ + "type": "patch", + "description": "Collapse create_final_relationships." +} diff --git a/.semversioner/next-release/patch-20240919223518903171.json b/.semversioner/next-release/patch-20240919223518903171.json new file mode 100644 index 0000000000..1ccab463b7 --- /dev/null +++ b/.semversioner/next-release/patch-20240919223518903171.json @@ -0,0 +1,4 @@ +{ + "type": "patch", + "description": "remove redundant error-handling code from global-search" +} diff --git a/.semversioner/next-release/patch-20240920000120463201.json b/.semversioner/next-release/patch-20240920000120463201.json new file mode 100644 index 0000000000..d36c458201 --- /dev/null +++ b/.semversioner/next-release/patch-20240920000120463201.json @@ -0,0 +1,4 @@ +{ + "type": "patch", + "description": "Collapse create-final-nodes." +} diff --git a/CHANGELOG.md b/CHANGELOG.md index 87bbb82cde..bb42e56c4e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,26 @@ # Changelog Note: version releases in the 0.x.y range may introduce breaking changes. + +## 0.3.6 + +- patch: Collapse create_final_relationships. +- patch: Dependency update and cleanup + +## 0.3.5 + +- patch: Add compound verbs with tests infra. +- patch: Collapse create_final_communities. +- patch: Collapse create_final_text_units. +- patch: Covariate verb collapse. +- patch: Fix duplicates in community context builder +- patch: Fix prompt tune output path +- patch: Fix seed hardcoded init +- patch: Fix seeded random gen on clustering +- patch: Improve logging. +- patch: Set default values for cli parameters. +- patch: Use static output directories. + ## 0.3.4 - patch: Deep copy txt units on local search to avoid race conditions diff --git a/docsite/posts/config/env_vars.md b/docsite/posts/config/env_vars.md index 3c579d9411..406ed366d1 100644 --- a/docsite/posts/config/env_vars.md +++ b/docsite/posts/config/env_vars.md @@ -25,7 +25,7 @@ If the embedding target is `all`, and you want to only embed a subset of these f ## Input Data -Our pipeline can ingest .csv or .txt data from an input folder. These files can be nested within subfolders. To configure how input data is handled, what fields are mapped over, and how timestamps are parsed, look for configuration values starting with `GRAPHRAG_INPUT_` below. In general, CSV-based data provides the most customizeability. Each CSV should at least contain a `text` field (which can be mapped with environment variables), but it's helpful if they also have `title`, `timestamp`, and `source` fields. Additional fields can be included as well, which will land as extra fields on the `Document` table. +Our pipeline can ingest .csv or .txt data from an input folder. These files can be nested within subfolders. To configure how input data is handled, what fields are mapped over, and how timestamps are parsed, look for configuration values starting with `GRAPHRAG_INPUT_` below. In general, CSV-based data provides the most customizability. Each CSV should at least contain a `text` field (which can be mapped with environment variables), but it's helpful if they also have `title`, `timestamp`, and `source` fields. Additional fields can be included as well, which will land as extra fields on the `Document` table. ## Base LLM Settings diff --git a/docsite/yarn.lock b/docsite/yarn.lock index 0b44f6c362..40dc8bc13b 100644 --- a/docsite/yarn.lock +++ b/docsite/yarn.lock @@ -2033,9 +2033,9 @@ __metadata: linkType: hard "path-to-regexp@npm:^6.2.1": - version: 6.2.1 - resolution: "path-to-regexp@npm:6.2.1" - checksum: 1e266be712d1a08086ee77beab12a1804842ec635dfed44f9ee1ba960a0e01cec8063fb8c92561115cdc0ce73158cdc7766e353ffa039340b4a85b370084c4d4 + version: 6.3.0 + resolution: "path-to-regexp@npm:6.3.0" + checksum: 6822f686f01556d99538b350722ef761541ec0ce95ca40ce4c29e20a5b492fe8361961f57993c71b2418de12e604478dcf7c430de34b2c31a688363a7a944d9c languageName: node linkType: hard diff --git a/graphrag/index/run/run.py b/graphrag/index/run/run.py index 55ce71eac6..3d20f263f5 100644 --- a/graphrag/index/run/run.py +++ b/graphrag/index/run/run.py @@ -46,6 +46,7 @@ from graphrag.index.typing import PipelineRunResult # Register all verbs +from graphrag.index.update.dataframes import get_delta_docs, update_dataframe_outputs from graphrag.index.verbs import * # noqa from graphrag.index.workflows import ( VerbDefinitions, @@ -111,9 +112,6 @@ async def run_pipeline_with_config( else await _create_input(config.input, progress_reporter, root_dir) ) - if is_update_run: - # TODO: Filter dataset to only include new data (this should be done in the input module) - pass post_process_steps = input_post_process_steps or _create_postprocess_steps( config.input ) @@ -123,21 +121,47 @@ async def run_pipeline_with_config( msg = "No dataset provided!" raise ValueError(msg) - async for table in run_pipeline( - workflows=workflows, - dataset=dataset, - storage=storage, - cache=cache, - callbacks=callbacks, - input_post_process_steps=post_process_steps, - memory_profile=memory_profile, - additional_verbs=additional_verbs, - additional_workflows=additional_workflows, - progress_reporter=progress_reporter, - emit=emit, - is_resume_run=is_resume_run, - ): - yield table + if is_update_run: + delta_dataset = await get_delta_docs(dataset, storage) + + delta_storage = storage.child("delta") + + # Run the pipeline on the new documents + tables_dict = {} + async for table in run_pipeline( + workflows=workflows, + dataset=delta_dataset.new_inputs, + storage=delta_storage, + cache=cache, + callbacks=callbacks, + input_post_process_steps=post_process_steps, + memory_profile=memory_profile, + additional_verbs=additional_verbs, + additional_workflows=additional_workflows, + progress_reporter=progress_reporter, + emit=emit, + is_resume_run=False, + ): + tables_dict[table.workflow] = table.result + + await update_dataframe_outputs(tables_dict, storage) + + else: + async for table in run_pipeline( + workflows=workflows, + dataset=dataset, + storage=storage, + cache=cache, + callbacks=callbacks, + input_post_process_steps=post_process_steps, + memory_profile=memory_profile, + additional_verbs=additional_verbs, + additional_workflows=additional_workflows, + progress_reporter=progress_reporter, + emit=emit, + is_resume_run=is_resume_run, + ): + yield table async def run_pipeline( diff --git a/graphrag/index/update/__init__.py b/graphrag/index/update/__init__.py new file mode 100644 index 0000000000..e6966408fb --- /dev/null +++ b/graphrag/index/update/__init__.py @@ -0,0 +1,4 @@ +# Copyright (c) 2024 Microsoft Corporation. +# Licensed under the MIT License + +"""Incremental Indexing main module definition.""" diff --git a/graphrag/index/update/dataframes.py b/graphrag/index/update/dataframes.py new file mode 100644 index 0000000000..ee9ccf07f2 --- /dev/null +++ b/graphrag/index/update/dataframes.py @@ -0,0 +1,192 @@ +# Copyright (c) 2024 Microsoft Corporation. +# Licensed under the MIT License + +"""Dataframe operations and utils for Incremental Indexing.""" + +import os +from dataclasses import dataclass + +import numpy as np +import pandas as pd + +from graphrag.index.storage.typing import PipelineStorage +from graphrag.utils.storage import _load_table_from_storage + +mergeable_outputs = [ + "create_final_documents", + "create_final_entities", + "create_final_relationships", +] + + +@dataclass +class InputDelta: + """Dataclass to hold the input delta. + + Attributes + ---------- + new_inputs : pd.DataFrame + The new inputs. + deleted_inputs : pd.DataFrame + The deleted inputs. + """ + + new_inputs: pd.DataFrame + deleted_inputs: pd.DataFrame + + +async def get_delta_docs( + input_dataset: pd.DataFrame, storage: PipelineStorage +) -> InputDelta: + """Get the delta between the input dataset and the final documents. + + Parameters + ---------- + input_dataset : pd.DataFrame + The input dataset. + storage : PipelineStorage + The Pipeline storage. + + Returns + ------- + InputDelta + The input delta. With new inputs and deleted inputs. + """ + final_docs = await _load_table_from_storage( + "create_final_documents.parquet", storage + ) + + # Select distinct title from final docs and from dataset + previous_docs: list[str] = final_docs["title"].unique().tolist() + dataset_docs: list[str] = input_dataset["title"].unique().tolist() + + # Get the new documents (using loc to ensure DataFrame) + new_docs = input_dataset.loc[~input_dataset["title"].isin(previous_docs)] + + # Get the deleted documents (again using loc to ensure DataFrame) + deleted_docs = final_docs.loc[~final_docs["title"].isin(dataset_docs)] + + return InputDelta(new_docs, deleted_docs) + + +async def update_dataframe_outputs( + dataframe_dict: dict[str, pd.DataFrame], + storage: PipelineStorage, +) -> None: + """Update the mergeable outputs. + + Parameters + ---------- + dataframe_dict : dict[str, pd.DataFrame] + The dictionary of dataframes. + storage : PipelineStorage + The storage used to store the dataframes. + """ + await _concat_dataframes("create_base_text_units", dataframe_dict, storage) + await _concat_dataframes("create_final_documents", dataframe_dict, storage) + + old_entities = await _load_table_from_storage( + "create_final_entities.parquet", storage + ) + delta_entities = dataframe_dict["create_final_entities"] + + merged_entities_df, _ = _group_and_resolve_entities(old_entities, delta_entities) + # Save the updated entities back to storage + # TODO: Using _new in the mean time, to compare outputs without overwriting the original + await storage.set( + "create_final_entities_new.parquet", merged_entities_df.to_parquet() + ) + + +async def _concat_dataframes(name, dataframe_dict, storage): + """Concatenate the dataframes. + + Parameters + ---------- + name : str + The name of the dataframe to concatenate. + dataframe_dict : dict[str, pd.DataFrame] + The dictionary of dataframes from a pipeline run. + storage : PipelineStorage + The storage used to store the dataframes. + """ + old_df = await _load_table_from_storage(f"{name}.parquet", storage) + delta_df = dataframe_dict[name] + + # Merge the final documents + final_df = pd.concat([old_df, delta_df], copy=False) + + # TODO: Using _new in the mean time, to compare outputs without overwriting the original + await storage.set(f"{name}_new.parquet", final_df.to_parquet()) + + +def _group_and_resolve_entities( + df_a: pd.DataFrame, df_b: pd.DataFrame +) -> tuple[pd.DataFrame, dict]: + """Group and resolve entities. + + Parameters + ---------- + df_a : pd.DataFrame + The first dataframe. + df_b : pd.DataFrame + The second dataframe. + + Returns + ------- + pd.DataFrame + The resolved dataframe. + dict + The id mapping for existing entities. In the form of {df_b.id: df_a.id}. + """ + # If a name exists in A and B, make a dictionary for {B.id : A.id} + merged = df_b[["id", "name"]].merge( + df_a[["id", "name"]], + on="name", + suffixes=("_B", "_A"), + copy=False, + ) + id_mapping = dict(zip(merged["id_B"], merged["id_A"], strict=True)) + + # Concat A and B + combined = pd.concat([df_a, df_b], copy=False) + + # Group by name and resolve conflicts + aggregated = ( + combined.groupby("name") + .agg({ + "id": "first", + "type": "first", + "human_readable_id": "first", + "graph_embedding": "first", + "description": lambda x: os.linesep.join(x.astype(str)), # Ensure str + # Concatenate nd.array into a single list + "text_unit_ids": lambda x: ",".join(str(i) for j in x.tolist() for i in j), + # Keep only descriptions where the original value wasn't modified + "description_embedding": lambda x: x.iloc[0] if len(x) == 1 else np.nan, + }) + .reset_index() + ) + + # Force the result into a DataFrame + resolved: pd.DataFrame = pd.DataFrame(aggregated) + + # Recreate humand readable id with an autonumeric + resolved["human_readable_id"] = range(len(resolved)) + + # Modify column order to keep consistency + resolved = resolved.loc[ + :, + [ + "id", + "name", + "description", + "type", + "human_readable_id", + "graph_embedding", + "text_unit_ids", + "description_embedding", + ], + ] + + return resolved, id_mapping diff --git a/graphrag/index/verbs/graph/compute_edge_combined_degree.py b/graphrag/index/verbs/graph/compute_edge_combined_degree.py index 1f2dd71972..59101376dc 100644 --- a/graphrag/index/verbs/graph/compute_edge_combined_degree.py +++ b/graphrag/index/verbs/graph/compute_edge_combined_degree.py @@ -32,10 +32,34 @@ def compute_edge_combined_degree( - to: The name of the column to output the combined degree to. Default="rank" """ edge_df: pd.DataFrame = cast(pd.DataFrame, input.get_input()) - if to in edge_df.columns: - return TableContainer(table=edge_df) node_degree_df = _get_node_degree_table(input, node_name_column, node_degree_column) + output_df = compute_edge_combined_degree_df( + edge_df, + node_degree_df, + to, + node_name_column, + node_degree_column, + edge_source_column, + edge_target_column, + ) + + return TableContainer(table=output_df) + + +def compute_edge_combined_degree_df( + edge_df: pd.DataFrame, + node_degree_df: pd.DataFrame, + to: str, + node_name_column: str, + node_degree_column: str, + edge_source_column: str, + edge_target_column: str, +) -> pd.DataFrame: + """Compute the combined degree for each edge in a graph.""" + if to in edge_df.columns: + return edge_df + def join_to_degree(df: pd.DataFrame, column: str) -> pd.DataFrame: degree_column = _degree_colname(column) result = df.merge( @@ -48,14 +72,13 @@ def join_to_degree(df: pd.DataFrame, column: str) -> pd.DataFrame: result[degree_column] = result[degree_column].fillna(0) return result - edge_df = join_to_degree(edge_df, edge_source_column) - edge_df = join_to_degree(edge_df, edge_target_column) - edge_df[to] = ( - edge_df[_degree_colname(edge_source_column)] - + edge_df[_degree_colname(edge_target_column)] + output_df = join_to_degree(edge_df, edge_source_column) + output_df = join_to_degree(output_df, edge_target_column) + output_df[to] = ( + output_df[_degree_colname(edge_source_column)] + + output_df[_degree_colname(edge_target_column)] ) - - return TableContainer(table=edge_df) + return output_df def _degree_colname(column: str) -> str: diff --git a/graphrag/index/verbs/graph/layout/layout_graph.py b/graphrag/index/verbs/graph/layout/layout_graph.py index e1b55b1183..c952aab9c0 100644 --- a/graphrag/index/verbs/graph/layout/layout_graph.py +++ b/graphrag/index/verbs/graph/layout/layout_graph.py @@ -63,8 +63,25 @@ def layout_graph( min_dist: 0.75 # Optional, The min distance to use for the umap algorithm, default: 0.75 ``` """ - output_df = cast(pd.DataFrame, input.get_input()) + input_df = cast(pd.DataFrame, input.get_input()) + output_df = layout_graph_df( + input_df, callbacks, strategy, embeddings_column, graph_column, to, graph_to + ) + + return TableContainer(table=output_df) + +def layout_graph_df( + input_df: pd.DataFrame, + callbacks: VerbCallbacks, + strategy: dict[str, Any], + embeddings_column: str, + graph_column: str, + to: str, + graph_to: str | None = None, +): + """Apply a layout algorithm to a graph.""" + output_df = input_df num_items = len(output_df) strategy_type = strategy.get("type", LayoutGraphStrategyType.umap) strategy_args = {**strategy} @@ -93,7 +110,7 @@ def layout_graph( ), axis=1, ) - return TableContainer(table=output_df) + return output_df def _run_layout( diff --git a/graphrag/index/workflows/v1/create_final_nodes.py b/graphrag/index/workflows/v1/create_final_nodes.py index 31277e7bf0..65ab516d87 100644 --- a/graphrag/index/workflows/v1/create_final_nodes.py +++ b/graphrag/index/workflows/v1/create_final_nodes.py @@ -19,55 +19,6 @@ def build_steps( """ snapshot_top_level_nodes = config.get("snapshot_top_level_nodes", False) layout_graph_enabled = config.get("layout_graph_enabled", True) - _compute_top_level_node_positions = [ - { - "verb": "unpack_graph", - "args": {"column": "positioned_graph", "type": "nodes"}, - "input": {"source": "laid_out_entity_graph"}, - }, - { - "verb": "filter", - "args": { - "column": "level", - "criteria": [ - { - "type": "value", - "operator": "equals", - "value": config.get("level_for_node_positions", 0), - } - ], - }, - }, - { - "verb": "select", - "args": {"columns": ["id", "x", "y"]}, - }, - { - "verb": "snapshot", - "enabled": snapshot_top_level_nodes, - "args": { - "name": "top_level_nodes", - "formats": ["json"], - }, - }, - { - "id": "_compute_top_level_node_positions", - "verb": "rename", - "args": { - "columns": { - "id": "top_level_node_id", - } - }, - }, - { - "verb": "convert", - "args": { - "column": "top_level_node_id", - "to": "top_level_node_id", - "type": "string", - }, - }, - ] layout_graph_config = config.get( "layout_graph", { @@ -76,41 +27,17 @@ def build_steps( }, }, ) + level_for_node_positions = config.get("level_for_node_positions", 0) + return [ { "id": "laid_out_entity_graph", - "verb": "layout_graph", + "verb": "create_final_nodes", "args": { - "embeddings_column": "embeddings", - "graph_column": "clustered_graph", - "to": "node_positions", - "graph_to": "positioned_graph", **layout_graph_config, + "level_for_node_positions": level_for_node_positions, + "snapshot_top_level_nodes": snapshot_top_level_nodes, }, "input": {"source": "workflow:create_base_entity_graph"}, }, - { - "verb": "unpack_graph", - "args": {"column": "positioned_graph", "type": "nodes"}, - }, - { - "id": "nodes_without_positions", - "verb": "drop", - "args": {"columns": ["x", "y"]}, - }, - *_compute_top_level_node_positions, - { - "verb": "join", - "args": { - "on": ["id", "top_level_node_id"], - }, - "input": { - "source": "nodes_without_positions", - "others": ["_compute_top_level_node_positions"], - }, - }, - { - "verb": "rename", - "args": {"columns": {"label": "title", "cluster": "community"}}, - }, ] diff --git a/graphrag/index/workflows/v1/create_final_relationships.py b/graphrag/index/workflows/v1/create_final_relationships.py index a58c2a45b4..8e6396b253 100644 --- a/graphrag/index/workflows/v1/create_final_relationships.py +++ b/graphrag/index/workflows/v1/create_final_relationships.py @@ -16,6 +16,7 @@ def build_steps( ## Dependencies * `workflow:create_base_entity_graph` + * `workflow:create_final_nodes` """ base_text_embed = config.get("text_embed", {}) relationship_description_embed_config = config.get( @@ -25,25 +26,12 @@ def build_steps( return [ { - "verb": "unpack_graph", - "args": { - "column": "clustered_graph", - "type": "edges", - }, + "id": "pre_embedding", + "verb": "create_final_relationships_pre_embedding", "input": {"source": "workflow:create_base_entity_graph"}, }, { - "verb": "rename", - "args": {"columns": {"source_id": "text_unit_ids"}}, - }, - { - "verb": "filter", - "args": { - "column": "level", - "criteria": [{"type": "value", "operator": "equals", "value": 0}], - }, - }, - { + "id": "description_embedding", "verb": "text_embed", "enabled": not skip_description_embedding, "args": { @@ -54,41 +42,12 @@ def build_steps( }, }, { - "id": "pruned_edges", - "verb": "drop", - "args": {"columns": ["level"]}, - }, - { - "id": "filtered_nodes", - "verb": "filter", - "args": { - "column": "level", - "criteria": [{"type": "value", "operator": "equals", "value": 0}], - }, - "input": "workflow:create_final_nodes", - }, - { - "verb": "compute_edge_combined_degree", - "args": {"to": "rank"}, + "verb": "create_final_relationships_post_embedding", "input": { - "source": "pruned_edges", - "nodes": "filtered_nodes", - }, - }, - { - "verb": "convert", - "args": { - "column": "human_readable_id", - "type": "string", - "to": "human_readable_id", - }, - }, - { - "verb": "convert", - "args": { - "column": "text_unit_ids", - "type": "array", - "to": "text_unit_ids", + "source": "pre_embedding" + if skip_description_embedding + else "description_embedding", + "nodes": "workflow:create_final_nodes", }, }, ] diff --git a/graphrag/index/workflows/v1/subflows/__init__.py b/graphrag/index/workflows/v1/subflows/__init__.py new file mode 100644 index 0000000000..7ea0346f86 --- /dev/null +++ b/graphrag/index/workflows/v1/subflows/__init__.py @@ -0,0 +1,22 @@ +# Copyright (c) 2024 Microsoft Corporation. +# Licensed under the MIT License + +"""The Indexing Engine workflows -> subflows package root.""" + +from .create_final_communities import create_final_communities +from .create_final_nodes import create_final_nodes +from .create_final_relationships_post_embedding import ( + create_final_relationships_post_embedding, +) +from .create_final_relationships_pre_embedding import ( + create_final_relationships_pre_embedding, +) +from .create_final_text_units_pre_embedding import create_final_text_units_pre_embedding + +__all__ = [ + "create_final_communities", + "create_final_nodes", + "create_final_relationships_post_embedding", + "create_final_relationships_pre_embedding", + "create_final_text_units_pre_embedding", +] diff --git a/graphrag/index/workflows/v1/subflows/create_final_nodes.py b/graphrag/index/workflows/v1/subflows/create_final_nodes.py new file mode 100644 index 0000000000..4bdbb6f154 --- /dev/null +++ b/graphrag/index/workflows/v1/subflows/create_final_nodes.py @@ -0,0 +1,78 @@ +# Copyright (c) 2024 Microsoft Corporation. +# Licensed under the MIT License + +"""All the steps to transform final nodes.""" + +from typing import Any, cast + +import pandas as pd +from datashaper import ( + Table, + VerbCallbacks, + VerbInput, + verb, +) +from datashaper.table_store.types import VerbResult, create_verb_result + +from graphrag.index.verbs.graph.layout.layout_graph import layout_graph_df +from graphrag.index.verbs.graph.unpack import unpack_graph_df + + +@verb(name="create_final_nodes", treats_input_tables_as_immutable=True) +def create_final_nodes( + input: VerbInput, + callbacks: VerbCallbacks, + strategy: dict[str, Any], + level_for_node_positions: int, + **_kwargs: dict, +) -> VerbResult: + """All the steps to transform final nodes.""" + table = cast(pd.DataFrame, input.get_input()) + + laid_out_entity_graph = cast( + pd.DataFrame, + layout_graph_df( + table, + callbacks, + strategy, + embeddings_column="embeddings", + graph_column="clustered_graph", + to="node_positions", + graph_to="positioned_graph", + ), + ) + + nodes = cast( + pd.DataFrame, + unpack_graph_df( + laid_out_entity_graph, callbacks, column="positioned_graph", type="nodes" + ), + ) + + nodes_without_positions = nodes.drop(columns=["x", "y"]) + + nodes = nodes[nodes["level"] == level_for_node_positions].reset_index(drop=True) + nodes = cast(pd.DataFrame, nodes[["id", "x", "y"]]) + + # TODO: original workflow saved an optional snapshot of top level nodes + # Combining the verbs loses the `storage` injection, so it would fail + # verb arg: snapshot_top_level_nodes: bool, + # (name: "top_level_nodes", formats: ["json"]) + + nodes.rename(columns={"id": "top_level_node_id"}, inplace=True) + nodes["top_level_node_id"] = nodes["top_level_node_id"].astype(str) + + joined = nodes_without_positions.merge( + nodes, + left_on="id", + right_on="top_level_node_id", + how="inner", + ) + joined.rename(columns={"label": "title", "cluster": "community"}, inplace=True) + + return create_verb_result( + cast( + Table, + joined, + ) + ) diff --git a/graphrag/index/workflows/v1/subflows/create_final_relationships_post_embedding.py b/graphrag/index/workflows/v1/subflows/create_final_relationships_post_embedding.py new file mode 100644 index 0000000000..0e29e70104 --- /dev/null +++ b/graphrag/index/workflows/v1/subflows/create_final_relationships_post_embedding.py @@ -0,0 +1,72 @@ +# Copyright (c) 2024 Microsoft Corporation. +# Licensed under the MIT License + +"""All the steps to transform final relationships after they are embedded.""" + +from typing import Any, cast + +import pandas as pd +from datashaper import ( + Table, + VerbInput, + verb, +) +from datashaper.table_store.types import VerbResult, create_verb_result + +from graphrag.index.utils.ds_util import get_required_input_table +from graphrag.index.verbs.graph.compute_edge_combined_degree import ( + compute_edge_combined_degree_df, +) + + +@verb( + name="create_final_relationships_post_embedding", + treats_input_tables_as_immutable=True, +) +def create_final_relationships_post_embedding( + input: VerbInput, + **_kwargs: dict, +) -> VerbResult: + """All the steps to transform final relationships after they are embedded.""" + table = cast(pd.DataFrame, input.get_input()) + nodes = cast(pd.DataFrame, get_required_input_table(input, "nodes").table) + + pruned_edges = table.drop(columns=["level"]) + + filtered_nodes = cast( + pd.DataFrame, + nodes[nodes["level"] == 0].reset_index(drop=True)[["title", "degree"]], + ) + + edge_combined_degree = compute_edge_combined_degree_df( + pruned_edges, + filtered_nodes, + to="rank", + node_name_column="title", + node_degree_column="degree", + edge_source_column="source", + edge_target_column="target", + ) + + edge_combined_degree["human_readable_id"] = edge_combined_degree[ + "human_readable_id" + ].astype(str) + edge_combined_degree["text_unit_ids"] = _to_array( + edge_combined_degree["text_unit_ids"], "," + ) + + return create_verb_result(cast(Table, edge_combined_degree)) + + +# from datashaper, we should be able to inline this +def _to_array(column, delimiter: str): + def convert_value(value: Any) -> list: + if pd.isna(value): + return [] + if isinstance(value, list): + return value + if isinstance(value, str): + return value.split(delimiter) + return [value] + + return column.apply(convert_value) diff --git a/graphrag/index/workflows/v1/subflows/create_final_relationships_pre_embedding.py b/graphrag/index/workflows/v1/subflows/create_final_relationships_pre_embedding.py new file mode 100644 index 0000000000..bcc0f762b8 --- /dev/null +++ b/graphrag/index/workflows/v1/subflows/create_final_relationships_pre_embedding.py @@ -0,0 +1,38 @@ +# Copyright (c) 2024 Microsoft Corporation. +# Licensed under the MIT License + +"""All the steps to transform final relationships before they are embedded.""" + +from typing import cast + +import pandas as pd +from datashaper import ( + Table, + VerbCallbacks, + VerbInput, + verb, +) +from datashaper.table_store.types import VerbResult, create_verb_result + +from graphrag.index.verbs.graph.unpack import unpack_graph_df + + +@verb( + name="create_final_relationships_pre_embedding", + treats_input_tables_as_immutable=True, +) +def create_final_relationships_pre_embedding( + input: VerbInput, + callbacks: VerbCallbacks, + **_kwargs: dict, +) -> VerbResult: + """All the steps to transform final relationships before they are embedded.""" + table = cast(pd.DataFrame, input.get_input()) + + graph_edges = unpack_graph_df(table, callbacks, "clustered_graph", "edges") + + graph_edges.rename(columns={"source_id": "text_unit_ids"}, inplace=True) + + filtered = graph_edges[graph_edges["level"] == 0].reset_index(drop=True) + + return create_verb_result(cast(Table, filtered)) diff --git a/graphrag/query/structured_search/global_search/search.py b/graphrag/query/structured_search/global_search/search.py index 4079141aba..7e34162f81 100644 --- a/graphrag/query/structured_search/global_search/search.py +++ b/graphrag/query/structured_search/global_search/search.py @@ -221,15 +221,10 @@ async def _map_response_single_batch( # parse search response json processed_response = self.parse_search_response(search_response) except ValueError: - # Clean up and retry parse - try: - # parse search response json - processed_response = self.parse_search_response(search_response) - except ValueError: - log.warning( - "Warning: Error parsing search response json - skipping this batch" - ) - processed_response = [] + log.warning( + "Warning: Error parsing search response json - skipping this batch" + ) + processed_response = [] return SearchResult( response=processed_response, diff --git a/poetry.lock b/poetry.lock index 58b765eacc..350e3ff39e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -35,13 +35,13 @@ files = [ [[package]] name = "anyio" -version = "4.4.0" +version = "4.6.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false -python-versions = ">=3.8" +python-versions = ">=3.9" files = [ - {file = "anyio-4.4.0-py3-none-any.whl", hash = "sha256:c1b2d8f46a8a812513012e1107cb0e68c17159a7a594208005a57dc776e1bdc7"}, - {file = "anyio-4.4.0.tar.gz", hash = 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azure-search-documents = "^11.4.0" -lancedb = "^0.12.0" - -# Event Loops -uvloop = { version = "^0.20.0", markers = "platform_system != 'Windows'" } -nest-asyncio = { version = "^1.6.0", markers = "platform_system == 'Windows'" } +lancedb = "^0.13.0" # Async IO aiolimiter = "^1.1.0" aiofiles = "^24.1.0" # LLM -openai = "^1.37.1" +openai = "^1.46.1" nltk = "3.9.1" tiktoken = "^0.7.0" # Data-Sci -numba = "0.60.0" numpy = "^1.25.2" graspologic = "^3.4.1" networkx = "^3" -fastparquet = "^2024.2.0" -# 1.13.0 was a footgun -scipy = "1.12.0" +pandas = "^2.2.2" +matplotlib = "^3.9.0" +pyarrow = "^15.0.0" +umap-learn = "^0.5.6" # Configuration pyyaml = "^6.0.2" @@ -80,12 +76,9 @@ python-dotenv = "^1.0.0" # Network tenacity = "^9.0.0" -swifter = "^1.4.0" -pydantic = "^2" +pydantic = "^2.9.2" rich = "^13.6.0" -textual = "^0.78.0" devtools = "^0.12.2" - typing-extensions = "^4.12.2" #Azure @@ -93,21 +86,22 @@ azure-storage-blob = "^12.22.0" azure-identity = "^1.17.1" json-repair = "^0.28.4" -future = "^1.0.0" +future = "^1.0.0" # Needed until graspologic fixes their dependency + [tool.poetry.group.dev.dependencies] coverage = "^7.6.0" ipykernel = "^6.29.4" -jupyter = "^1.0.0" +jupyter = "^1.1.1" nbconvert = "^7.16.3" -poethepoet = "^0.27.0" +poethepoet = "^0.28.0" pyright = "^1.1.371" pytest = "^8.3.2" pytest-asyncio = "^0.24.0" pytest-timeout = "^2.3.1" -ruff = "^0.6.2" +ruff = "^0.6.5" semversioner = "^2.0.3" - update-toml = "^0.2.1" +deptry = "^0.16.1" [build-system] requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning>=1.0.0,<2.0.0"] diff --git a/tests/fixtures/min-csv/config.json b/tests/fixtures/min-csv/config.json index fb15f5d4c8..e1d55c4974 100644 --- a/tests/fixtures/min-csv/config.json +++ b/tests/fixtures/min-csv/config.json @@ -52,7 +52,7 @@ 1, 2000 ], - "subworkflows": 8, + "subworkflows": 2, "max_runtime": 100 }, "create_final_nodes": { @@ -67,7 +67,7 @@ "community", "level" ], - "subworkflows": 10, + "subworkflows": 1, "max_runtime": 10 }, "create_final_communities": { diff --git a/tests/fixtures/text/config.json b/tests/fixtures/text/config.json index 809ca0f624..f71215b241 100644 --- a/tests/fixtures/text/config.json +++ b/tests/fixtures/text/config.json @@ -79,7 +79,7 @@ 1, 2000 ], - "subworkflows": 8, + "subworkflows": 2, "max_runtime": 100 }, "create_final_nodes": { @@ -94,7 +94,7 @@ "community", "level" ], - "subworkflows": 10, + "subworkflows": 1, "max_runtime": 10 }, "create_final_communities": { diff --git a/tests/verbs/test_create_final_nodes.py b/tests/verbs/test_create_final_nodes.py new file mode 100644 index 0000000000..7f0e20428a --- /dev/null +++ b/tests/verbs/test_create_final_nodes.py @@ -0,0 +1,40 @@ +# Copyright (c) 2024 Microsoft Corporation. +# Licensed under the MIT License + +from graphrag.index.workflows.v1.create_final_nodes import ( + build_steps, + workflow_name, +) + +from .util import ( + compare_outputs, + get_config_for_workflow, + get_workflow_output, + load_expected, + load_input_tables, + remove_disabled_steps, +) + + +async def test_create_final_nodes(): + input_tables = load_input_tables([ + "workflow:create_base_entity_graph", + ]) + expected = load_expected(workflow_name) + + config = get_config_for_workflow(workflow_name) + + # default config turns UMAP off, which translates into false for layout + # we don't have graph embeddings in the test data, so this will fail if True + config["layout_graph_enabled"] = False + + steps = remove_disabled_steps(build_steps(config)) + + actual = await get_workflow_output( + input_tables, + { + "steps": steps, + }, + ) + + compare_outputs(actual, expected) diff --git a/tests/verbs/test_create_final_relationships.py b/tests/verbs/test_create_final_relationships.py new file mode 100644 index 0000000000..6e86836874 --- /dev/null +++ b/tests/verbs/test_create_final_relationships.py @@ -0,0 +1,39 @@ +# Copyright (c) 2024 Microsoft Corporation. +# Licensed under the MIT License + +from graphrag.index.workflows.v1.create_final_relationships import ( + build_steps, + workflow_name, +) + +from .util import ( + compare_outputs, + get_config_for_workflow, + get_workflow_output, + load_expected, + load_input_tables, + remove_disabled_steps, +) + + +async def test_create_final_relationships(): + input_tables = load_input_tables([ + "workflow:create_base_entity_graph", + "workflow:create_final_nodes", + ]) + expected = load_expected(workflow_name) + + config = get_config_for_workflow(workflow_name) + + config["skip_description_embedding"] = True + + steps = remove_disabled_steps(build_steps(config)) + + actual = await get_workflow_output( + input_tables, + { + "steps": steps, + }, + ) + + compare_outputs(actual, expected)