[Bug]: json.decoder.JSONDecodeError: Unterminated string starting at WHEN generate_text_embeddings

[gudehhh666]

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• I believe this is a legitimate bug, not just a question. If this is a question, please use the Discussions area.

Describe the bug

json.decoder.JSONDecodeError: Unterminated string starting at WHEN generate_text_embeddings

Could you tell me how toc cope with this?

Thank you so much!!

Steps to reproduce

graphrag index --root ./rag_book

Expected Behavior

No response

GraphRAG Config Used

# Paste your config here
### This config file contains required core defaults that must be set, along with a handful of common optional settings.
### For a full list of available settings, see https://microsoft.github.io/graphrag/config/yaml/

### LLM settings ###
## There are a number of settings to tune the threading and token limits for LLM calls - check the docs.

encoding_model: cl100k_base # this needs to be matched to your model!

llm:
  api_key: ${GRAPHRAG_API_KEY} # set this in the generated .env file
  type: openai_chat # or azure_openai_chat
  model: gpt-4o-mini
  model_supports_json: true # recommended if this is available for your model.
  # audience: "https://cognitiveservices.azure.com/.default"
  # api_base: https://<instance>.openai.azure.com
  # api_version: 2024-02-15-preview
  # organization: <organization_id>
  # deployment_name: <azure_model_deployment_name>

parallelization:
  stagger: 0.3
  # num_threads: 50

async_mode: threaded # or asyncio

embeddings:
  async_mode: threaded # or asyncio
  vector_store: 
    type: lancedb
    db_uri: 'output/lancedb'
    container_name: default
    overwrite: true
  llm:
    api_key: ${GRAPHRAG_API_KEY}
    type: openai_embedding # or azure_openai_embedding
    model: text-embedding-ada-002
    max_tokens: 8000

    api_base: https://platform.llmprovider.ai/v1
    # api_version: 2024-02-15-preview
    # audience: "https://cognitiveservices.azure.com/.default"
    # organization: <organization_id>
    # deployment_name: <azure_model_deployment_name>

### Input settings ###

input:
  type: file # or blob
  file_type: text # or csv
  base_dir: "input"
  file_encoding: utf-8
  file_pattern: ".*\\.txt$"

chunks:
  size: 1200
  overlap: 100
  group_by_columns: [id]

### Storage settings ###
## If blob storage is specified in the following four sections,
## connection_string and container_name must be provided

cache:
  type: file # or blob
  base_dir: "cache"

reporting:
  type: file # or console, blob
  base_dir: "logs"

storage:
  type: file # or blob
  base_dir: "output"

## only turn this on if running `graphrag index` with custom settings
## we normally use `graphrag update` with the defaults
update_index_storage:
  # type: file # or blob
  # base_dir: "update_output"

### Workflow settings ###

skip_workflows: []

entity_extraction:
  prompt: "prompts/entity_extraction.txt"
  entity_types: [organization,person,geo,event]
  max_gleanings: 1

summarize_descriptions:
  prompt: "prompts/summarize_descriptions.txt"
  max_length: 500

claim_extraction:
  enabled: false
  prompt: "prompts/claim_extraction.txt"
  description: "Any claims or facts that could be relevant to information discovery."
  max_gleanings: 1

community_reports:
  prompt: "prompts/community_report.txt"
  max_length: 2000
  max_input_length: 8000

cluster_graph:
  max_cluster_size: 10

embed_graph:
  enabled: false # if true, will generate node2vec embeddings for nodes

umap:
  enabled: false # if true, will generate UMAP embeddings for nodes

snapshots:
  graphml: false
  embeddings: false
  transient: false

### Query settings ###
## The prompt locations are required here, but each search method has a number of optional knobs that can be tuned.
## See the config docs: https://microsoft.github.io/graphrag/config/yaml/#query

local_search:
  prompt: "prompts/local_search_system_prompt.txt"

global_search:
  map_prompt: "prompts/global_search_map_system_prompt.txt"
  reduce_prompt: "prompts/global_search_reduce_system_prompt.txt"
  knowledge_prompt: "prompts/global_search_knowledge_system_prompt.txt"

drift_search:
  prompt: "prompts/drift_search_system_prompt.txt"

Logs and screenshots

14:00:59,942 httpx INFO HTTP Request: POST https://platform.llmprovider.ai/v1/chat/completions "HTTP/1.1 200 OK"
15:52:48,215 graphrag.callbacks.file_workflow_callbacks INFO Error Invoking LLM details={'prompt': ['JOHN WILEY & SONS, INC.:John Wiley & Sons, Inc. is a publishing company known for its scientific and academic publications, including works on immunology.', 'AMERICAN JOURNAL OF EPIDEMIOLOGY:The American Journal of Epidemiology publishes research related to epidemiology and public health, featuring studies like the one on Guillain-Barre syndrome during the H1N1 vaccination campaign.', 'CURRENT PROTOCOLS IN IMMUNOLOGY:A publication that provides standardized procedures and protocols for immunology research, including vaccine studies.', 'PACKAGING REGULATIONS:Regulations concerning the development, safety, and distribution of vaccines and biological agents.', 'VACCINES AND ADJUVANTS SAFETY PROJECT COMMITTEE:A committee focusing on the safety evaluation of vaccines and their adjuvants.', 'M. THE EX VIVO IFN-G ENZYME-LINKED IMMUNOSPOT ASSAY:', 'YURASOV S:Yurasov S is an author who has contributed research in the field of rheumatology.', 'NUSSENZWEIG MC:Nussenzweig MC is a researcher noted for work on autoreactive antibodies and their regulation.', 'ZAITSEVA M:Zaitseva M is an author involved in research regarding the use of human MonoMac6 cells.', 'ROMANTSEVA T:Romantseva T is a collaborator on research surrounding vaccine safety.', 'BLINOVA K:Blanova K contributed to research on the in vitro assay predictive of adjuvant safety.', 'DRANE D:Drane D is an author associated with immunopotentiators in modern vaccines.', 'VACCINE 2012:Vaccine 2012 is a significant event or publication discussing advancements in vaccine research and safety.', 'CURRENTS OPINION RHEUMATOL:Current Opinion in Rheumatology is a journal that discusses contemporary issues in rheumatology.', 'MONOMAC6:', 'VERTEBRATE ADAPTIVE IMMUNE CELLS:The immune cells that possess two types of antigen receptors, immunoglobulins and T-cell receptors, crucial for adaptive immunity.'], 'kwargs': {}}
15:52:48,216 datashaper.workflow.workflow ERROR Error executing verb "generate_text_embeddings" in generate_text_embeddings: Unterminated string starting at: line 1 column 107183 (char 107182)
Traceback (most recent call last):
File "/root/miniconda3/lib/python3.12/site-packages/datashaper/workflow/workflow.py", line 415, in _execute_verb
result = await result
^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/graphrag/index/workflows/v1/generate_text_embeddings.py", line 96, in workflow
await generate_text_embeddings(
File "/root/miniconda3/lib/python3.12/site-packages/graphrag/index/flows/generate_text_embeddings.py", line 100, in generate_text_embeddings
await _run_and_snapshot_embeddings(
File "/root/miniconda3/lib/python3.12/site-packages/graphrag/index/flows/generate_text_embeddings.py", line 123, in _run_and_snapshot_embeddings
data["embedding"] = await embed_text(
^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/graphrag/index/operations/embed_text/embed_text.py", line 89, in embed_text
return await _text_embed_with_vector_store(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/graphrag/index/operations/embed_text/embed_text.py", line 179, in _text_embed_with_vector_store
result = await strategy_exec(
^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/graphrag/index/operations/embed_text/strategies/openai.py", line 62, in run
embeddings = await _execute(llm, text_batches, ticker, semaphore)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/graphrag/index/operations/embed_text/strategies/openai.py", line 102, in _execute
results = await asyncio.gather(*futures)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/graphrag/index/operations/embed_text/strategies/openai.py", line 96, in embed
chunk_embeddings = await llm(chunk)
^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/fnllm/base/base.py", line 112, in call
return await self._invoke(prompt, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/fnllm/base/base.py", line 128, in _invoke
return await self._decorated_target(prompt, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/fnllm/services/retryer.py", line 109, in invoke
result = await execute_with_retry()
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/fnllm/services/retryer.py", line 93, in execute_with_retry
async for a in AsyncRetrying(
File "/root/miniconda3/lib/python3.12/site-packages/tenacity/asyncio/init.py", line 166, in anext
do = await self.iter(retry_state=self._retry_state)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/tenacity/asyncio/init.py", line 153, in iter
result = await action(retry_state)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/tenacity/_utils.py", line 99, in inner
return call(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/tenacity/init.py", line 398, in
self._add_action_func(lambda rs: rs.outcome.result())
^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/concurrent/futures/_base.py", line 449, in result
return self.__get_result()
^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/concurrent/futures/_base.py", line 401, in __get_result
raise self._exception
File "/root/miniconda3/lib/python3.12/site-packages/fnllm/services/retryer.py", line 101, in execute_with_retry
return await attempt()
^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/fnllm/services/retryer.py", line 78, in attempt
return await delegate(prompt, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/fnllm/services/rate_limiter.py", line 70, in invoke
result = await delegate(prompt, **args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/fnllm/base/base.py", line 152, in _decorator_target
output = await self._execute_llm(prompt, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/fnllm/openai/llm/embeddings.py", line 133, in _execute_llm
response = await self._call_embeddings_or_cache(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/fnllm/openai/llm/embeddings.py", line 110, in _call_embeddings_or_cache
return await self._cache.get_or_insert(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/fnllm/services/cache_interactor.py", line 50, in get_or_insert
entry = await func()
^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/openai/resources/embeddings.py", line 236, in create
return await self._post(
^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/openai/_base_client.py", line 1843, in post
return await self.request(cast_to, opts, stream=stream, stream_cls=stream_cls)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/openai/_base_client.py", line 1537, in request
return await self._request(
^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/openai/_base_client.py", line 1640, in _request
return await self._process_response(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/openai/_base_client.py", line 1737, in _process_response
return await api_response.parse()
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/openai/_response.py", line 431, in parse
await self.read()
^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/openai/_response.py", line 266, in _parse
data = response.json()
^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/httpx/_models.py", line 832, in json
return jsonlib.loads(self.content, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/json/init.py", line 346, in loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/json/decoder.py", line 353, in raw_decode
obj, end = self.scan_once(s, idx)
^^^^^^^^^^^^^^^^^^^^^^
json.decoder.JSONDecodeError: Unterminated string starting at: line 1 column 107183 (char 107182)
15:52:48,218 graphrag.callbacks.file_workflow_callbacks INFO Error executing verb "generate_text_embeddings" in generate_text_embeddings: Unterminated string starting at: line 1 column 107183 (char 107182) details=None
15:52:48,225 graphrag.index.run.run ERROR error running workflow generate_text_embeddings
Traceback (most recent call last):
File "/root/miniconda3/lib/python3.12/site-packages/graphrag/index/run/run.py", line 262, in run_pipeline
result = await _process_workflow(
^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/graphrag/index/run/workflow.py", line 103, in _process_workflow
result = await workflow.run(context, callbacks)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/datashaper/workflow/workflow.py", line 369, in run
timing = await self._execute_verb(node, context, callbacks)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/datashaper/workflow/workflow.py", line 415, in _execute_verb
result = await result
^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/graphrag/index/workflows/v1/generate_text_embeddings.py", line 96, in workflow
await generate_text_embeddings(
File "/root/miniconda3/lib/python3.12/site-packages/graphrag/index/flows/generate_text_embeddings.py", line 100, in generate_text_embeddings
await _run_and_snapshot_embeddings(
File "/root/miniconda3/lib/python3.12/site-packages/graphrag/index/flows/generate_text_embeddings.py", line 123, in _run_and_snapshot_embeddings
data["embedding"] = await embed_text(
^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/graphrag/index/operations/embed_text/embed_text.py", line 89, in embed_text
return await _text_embed_with_vector_store(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/graphrag/index/operations/embed_text/embed_text.py", line 179, in _text_embed_with_vector_store
result = await strategy_exec(
^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/graphrag/index/operations/embed_text/strategies/openai.py", line 62, in run
embeddings = await _execute(llm, text_batches, ticker, semaphore)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/graphrag/index/operations/embed_text/strategies/openai.py", line 102, in _execute
results = await asyncio.gather(*futures)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/graphrag/index/operations/embed_text/strategies/openai.py", line 96, in embed
chunk_embeddings = await llm(chunk)
^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/fnllm/base/base.py", line 112, in call
return await self._invoke(prompt, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/fnllm/base/base.py", line 128, in _invoke
return await self._decorated_target(prompt, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/fnllm/services/retryer.py", line 109, in invoke
result = await execute_with_retry()
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/fnllm/services/retryer.py", line 93, in execute_with_retry
async for a in AsyncRetrying(
File "/root/miniconda3/lib/python3.12/site-packages/tenacity/asyncio/init.py", line 166, in anext
do = await self.iter(retry_state=self._retry_state)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/tenacity/asyncio/init.py", line 153, in iter
result = await action(retry_state)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/tenacity/_utils.py", line 99, in inner
return call(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/tenacity/init.py", line 398, in
self._add_action_func(lambda rs: rs.outcome.result())
^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/concurrent/futures/_base.py", line 449, in result
return self.__get_result()
^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/concurrent/futures/_base.py", line 401, in __get_result
raise self._exception
File "/root/miniconda3/lib/python3.12/site-packages/fnllm/services/retryer.py", line 101, in execute_with_retry
return await attempt()
^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/fnllm/services/retryer.py", line 78, in attempt
return await delegate(prompt, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/fnllm/services/rate_limiter.py", line 70, in invoke
result = await delegate(prompt, **args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/fnllm/base/base.py", line 152, in _decorator_target
output = await self._execute_llm(prompt, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/fnllm/openai/llm/embeddings.py", line 133, in _execute_llm
response = await self._call_embeddings_or_cache(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/fnllm/openai/llm/embeddings.py", line 110, in _call_embeddings_or_cache
return await self._cache.get_or_insert(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/fnllm/services/cache_interactor.py", line 50, in get_or_insert
entry = await func()
^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/openai/resources/embeddings.py", line 236, in create
return await self._post(
^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/openai/_base_client.py", line 1843, in post
return await self.request(cast_to, opts, stream=stream, stream_cls=stream_cls)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/openai/_base_client.py", line 1537, in request
return await self._request(
^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/openai/_base_client.py", line 1640, in _request
return await self._process_response(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/openai/_base_client.py", line 1737, in _process_response
return await api_response.parse()
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/openai/_response.py", line 431, in parse
await self.read()
^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/openai/_response.py", line 266, in _parse
data = response.json()
^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/site-packages/httpx/_models.py", line 832, in json
return jsonlib.loads(self.content, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/json/init.py", line 346, in loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/lib/python3.12/json/decoder.py", line 353, in raw_decode
obj, end = self.scan_once(s, idx)
^^^^^^^^^^^^^^^^^^^^^^
json.decoder.JSONDecodeError: Unterminated string starting at: line 1 column 107183 (char 107182)
15:52:48,229 graphrag.callbacks.file_workflow_callbacks INFO Error running pipeline! details=None
15:52:48,254 graphrag.cli.index ERROR Errors occurred during the pipeline run, see logs for more details.

Additional Information

• GraphRAG Version:1.0.1
• Operating System:ubuntu 20.04
• Python Version:3.12
• Related Issues: