### What problem does this PR solve?
## Problem
During the REST API refactoring (#13690), the
`/api/v2/kb/check_embedding` endpoint was removed and never migrated to
the new RESTful structure. The frontend was pointed to the
`/api/v1/datasets/{id}/embedding` endpoint (which is `run_embedding` — a
completely different function). Additionally, a hard guard was
introduced that rejects any `embd_id` change when `chunk_num > 0`,
making it impossible to switch embedding models on datasets with
existing chunks.
## Root Cause
1. **Missing endpoint**: The old `check_embedding` logic (sample random
chunks, re-embed with the new model, compare cosine similarity) was not
carried over to the new REST API service layer.
2. **Wrong frontend URL**: `checkEmbedding` in `api.ts` pointed to
`/datasets/{id}/embedding` (`run_embedding`) instead of a dedicated
check endpoint.
3. **Overly restrictive guard**: `dataset_api_service.py` line 310
blocked all `embd_id` updates when `chunk_num > 0`. This check did not
exist in the pre-refactor code — it was incorrectly introduced during
the refactor.
## Changes
### Backend
- **`api/apps/services/dataset_api_service.py`**
- Remove the `chunk_num > 0` hard guard on `embd_id` updates
- Add `check_embedding()` service function: samples random chunks,
re-embeds them with the candidate model, computes cosine similarity,
returns compatibility result (avg ≥ 0.9 = compatible)
- Add `import re` for the `_clean()` helper
- **`api/apps/restful_apis/dataset_api.py`**
- Add `POST /datasets/<dataset_id>/embedding/check` endpoint following
the new REST API conventions
- Clean up unused top-level imports (`random`, `re`, `numpy`)
### Frontend
- **`web/src/utils/api.ts`**
- Fix `checkEmbedding` URL from `/datasets/${datasetId}/embedding` →
`/datasets/${datasetId}/embedding/check`
### Tests
-
**`test/testcases/test_http_api/test_dataset_management/test_update_dataset.py`**
- Update `test_embedding_model_with_existing_chunks` to assert success
(`code == 0`) instead of expecting the old `102` error
-
**`test/testcases/test_web_api/test_dataset_management/test_dataset_sdk_routes_unit.py`**
- Update `test_update_route_branch_matrix_unit` to assert
`RetCode.SUCCESS` when updating `embd_id` on a chunked dataset,
replacing the old `chunk_num` error assertion
### Type of change
- [x] Bug Fix (non-breaking change which fixes an issue)
---------
Signed-off-by: noob <yixiao121314@outlook.com>
This PR addresses three related GraphRAG reliability issues that
together allow long-running GraphRAG tasks (10+ hours of LLM extraction)
to be resumed after a crash or pause without re-doing completed work. It
builds on #14096 (per-doc subgraph cache) and extends the same idea to
the resolution and community-detection phases.
Fixes#14236.
## 1. Fix concurrent merge crash
Long GraphRAG runs would crash near the end of entity resolution with:
```
RuntimeError: dictionary keys changed during iteration
```
in `Extractor._merge_graph_nodes`. Two changes:
- `rag/graphrag/general/extractor.py`: snapshot `graph.neighbors(node1)`
via `list(...)` before iterating, so concurrent `add_edge` /
`remove_node` mutations on the shared `nx.Graph` cannot invalidate the
iterator. Also tracks each redirected neighbour in `node0_neighbors` so
a later merged node sharing the same external neighbour takes the
edge-merge branch instead of overwriting via `add_edge`.
- `rag/graphrag/entity_resolution.py`: serialize the merge step with a
dedicated `asyncio.Semaphore(1)`. `nx.Graph` is not thread-safe and
concurrent merges on overlapping neighbourhoods can produce incorrect
results even with the snapshot fix.
## 2. Don't wipe partial graph on pause
Previously the pause / cancel UI path called
`settings.docStoreConn.delete({"knowledge_graph_kwd": [...]}, ...)`,
destroying every subgraph, entity, relation, and graph row.
Re-triggering then started GraphRAG from scratch even though #14096 had
already added `load_subgraph_from_store`.
After main was merged in (which deleted `api/apps/kb_app.py` per
#14394), the pause path now lives on the new REST surface `DELETE
/v1/datasets/<id>/<index_type>`:
- `api/apps/services/dataset_api_service.py`: `delete_index` accepts a
`wipe: bool = True` parameter. When `False` the doc-store rows and
GraphRAG phase markers are left intact and only the running task is
cancelled. Default preserves historical behaviour.
- `api/apps/restful_apis/dataset_api.py`: parses `?wipe=false|0|no|off`
from the query string and forwards it.
- `web/src/utils/api.ts` + `web/src/services/knowledge-service.ts`:
`unbindPipelineTask` appends `?wipe=false` when explicitly false.
- The GraphRAG pause action in
`web/src/pages/dataset/dataset/generate-button/hook.ts` passes `wipe:
false` for `KnowledgeGraph`; raptor is unchanged.
**UX impact:** the pause icon next to a running GraphRAG task no longer
wipes graph data. The only path that still wipes is the explicit Delete
action in `GenerateLogButton` (trash icon behind a confirmation modal).
## 3. Phase-completion markers (`rag/graphrag/phase_markers.py`)
A small Redis-backed marker layer at
`graphrag:phase:{kb_id}:{resolution_done|community_done}` (7-day TTL).
`run_graphrag_for_kb` consults the markers on entry and skips phases
that already completed in a prior run. Markers are cleared automatically
when:
- new docs are merged into the graph (which invalidates prior resolution
and community results),
- `delete_index` wipes the graph, or
- `delete_knowledge_graph` is called.
Redis failures never block a run -- markers are an optimization, not a
gate.
## 4. Idempotent community detection
`extract_community` previously did `delete-then-insert` on
`community_report` rows; a crash mid-insert left the dataset with no
reports. Now report IDs are derived deterministically from `(kb_id,
community.title)`, the existing report IDs are snapshotted before
insert, new rows are written, then only stale rows are pruned. A failure
at any step leaves either the prior or the new report set intact --
never a partial mix.
## 5. Tunable doc-store insert pipeline
The GraphRAG insert loop in `rag/graphrag/utils.py` and the
`community_report` insert in `rag/graphrag/general/index.py` were both
hardcoded to `es_bulk_size = 4` and ran strictly sequentially. On a real
KB this meant 1077 chunks took ~21 minutes for a 100-chunk slice -- pure
round-trip overhead.
- New `insert_chunks_bounded()` helper in `rag/graphrag/utils.py`
batches inserts via a bounded `asyncio.Semaphore`. Same retry / timeout
semantics as the prior loop.
- Defaults: 64 docs per batch, 4 batches in flight (matches the regular
ingest pipeline in `document_service.py`). Tunable per-deployment via
`GRAPHRAG_INSERT_BULK_SIZE` and `GRAPHRAG_INSERT_CONCURRENCY`.
- Both `set_graph` and `extract_community` now use the helper.
This dropped the same 1077-chunk insert from minutes to seconds in local
testing without measurable extra pressure on Infinity (total in-flight
docs ≤ `BULK_SIZE × CONCURRENCY` = 256 by default).
## Tests
- `test/unit_test/rag/graphrag/test_merge_graph_nodes.py` (3 tests):
dense neighbourhood merge, neighbour-snapshot regression, concurrent
serialized merges.
- `test/unit_test/rag/graphrag/test_phase_markers.py` (4 tests): set/has
round-trip, kb-scoped clear, no-op on empty input, graceful Redis
failure.
-
`test/testcases/test_web_api/test_dataset_management/test_dataset_sdk_routes_unit.py`:
new `test_delete_index_wipe_flag_unit` covers `wipe=false` for both
GraphRAG and raptor on the new REST route, and confirms the default
still wipes and clears phase markers.
## Compatibility
- Backward compatible: tasks queued before this change behave
identically (default `wipe=true`, no markers expected).
- No schema/migration changes; all new state lives in Redis.
- New optional REST query param `wipe` on `DELETE
/v1/datasets/<id>/<index_type>`.
- New optional env vars `GRAPHRAG_INSERT_BULK_SIZE` and
`GRAPHRAG_INSERT_CONCURRENCY`; defaults preserve safe behaviour.
## Example of resume
Screenshot below shows a test resuming knowledge graph generation after
applying the concurrency fix and re-deploying.
<img width="521" height="677" alt="image"
src="https://github.com/user-attachments/assets/9ef0d405-cbb3-420d-a1a1-e51f3e7e9b7a"
/>
### Type of change
- [X] Bug Fix (non-breaking change which fixes an issue)
- [ ] New Feature (non-breaking change which adds functionality)
- [ ] Documentation Update
- [ ] Refactoring
- [ ] Performance Improvement
- [ ] Other (please describe):
### What problem does this PR solve?
1. Split dataset api to gateway and service, and modify web UI to use
restful http api.
2. Old KB releated APIs are commented.
### Type of change
- [x] Refactoring
---------
Co-authored-by: Yingfeng <yingfeng.zhang@gmail.com>
### What problem does this PR solve?
1. Split dataset api to gateway and service, and modify web UI to use
restful http api.
2. Old KB releated APIs are commented.
### Type of change
- [x] Refactoring
### What problem does this PR solve?
1. Split dataset api to gateway and service, and modify web UI to use
restful http api.
2. Old KB releated APIs are commented.
### Type of change
- [x] Refactoring
### What problem does this PR solve?
Empty ids means no-op operation.
### Type of change
- [x] Bug Fix (non-breaking change which fixes an issue)
- [x] Documentation Update
- [x] Refactoring
---------
Co-authored-by: writinwaters <cai.keith@gmail.com>
### What problem does this PR solve?
Codecov’s coverage report shows that several RAGFlow code paths are
currently untested or under-tested. This makes it easier for regressions
to slip in during refactors and feature work.
This PR adds targeted automated tests to cover the files and branches
highlighted by Codecov, improving confidence in core behavior while
keeping runtime functionality unchanged.
### Type of change
- [x] Other (please describe): Test coverage improvement (adds/extends
unit and integration tests to address Codecov-reported gaps)
