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wip(agents-api): Add Doc sql queries #979

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@Vedantsahai18 Vedantsahai18 commented Dec 20, 2024

PR Type

Enhancement


Description

Added comprehensive document management system with the following features:

  • Core document operations:

    • Create, read, update, and delete (CRUD) operations
    • Owner association and validation
    • Metadata support
    • Error handling
  • Advanced search capabilities:

    • Full-text search with ranking
    • Vector-based embedding search
    • Hybrid search combining text and embeddings
    • Maximal Marginal Relevance (MMR) for result diversity
  • List and filtering:

    • Paginated document listing
    • Sorting options (created_at, updated_at)
    • Owner-based filtering
    • Support for user, agent, and org ownership types
  • Performance optimizations:

    • Parallel search execution
    • Optional simsimd support for faster similarity calculations
    • Efficient SQL queries with proper indexing

Changes walkthrough 📝

Relevant files
Enhancement
9 files
__init__.py
Initialize document management module with core operations

agents-api/agents_api/queries/docs/init.py

  • Added new module for document management operations
  • Defined core functionalities for document CRUD operations
  • Imported all document-related query functions
  • +25/-0   
    create_doc.py
    Document creation with ownership management                           

    agents-api/agents_api/queries/docs/create_doc.py

  • Implemented document creation with metadata support
  • Added owner association functionality
  • Included error handling for unique violations and foreign key
    constraints
  • +135/-0 
    delete_doc.py
    Document deletion with ownership validation                           

    agents-api/agents_api/queries/docs/delete_doc.py

  • Added document deletion functionality
  • Implemented ownership validation
  • Added cascade deletion for doc_owners
  • +77/-0   
    get_doc.py
    Single document retrieval functionality                                   

    agents-api/agents_api/queries/docs/get_doc.py

  • Implemented single document retrieval
  • Added owner-based filtering
  • +52/-0   
    list_docs.py
    Paginated document listing with filters                                   

    agents-api/agents_api/queries/docs/list_docs.py

  • Added paginated document listing
  • Implemented sorting and filtering options
  • Added owner-based filtering
  • +91/-0   
    mmr.py
    Maximal Marginal Relevance implementation for search         

    agents-api/agents_api/queries/docs/mmr.py

  • Implemented Maximal Marginal Relevance algorithm
  • Added cosine similarity calculation
  • Optimized with simsimd support
  • +109/-0 
    search_docs_by_embedding.py
    Vector-based document search implementation                           

    agents-api/agents_api/queries/docs/search_docs_by_embedding.py

  • Added vector-based document search
  • Implemented embedding similarity search
  • Added owner filtering support
  • +70/-0   
    search_docs_by_text.py
    Full-text document search implementation                                 

    agents-api/agents_api/queries/docs/search_docs_by_text.py

  • Implemented full-text search functionality
  • Added text ranking support
  • Included owner filtering
  • +65/-0   
    search_docs_hybrid.py
    Hybrid document search with score fusion                                 

    agents-api/agents_api/queries/docs/search_docs_hybrid.py

  • Implemented hybrid search combining text and embedding
  • Added score fusion algorithm
  • Implemented parallel search execution
  • +159/-0 

    💡 PR-Agent usage: Comment /help "your question" on any pull request to receive relevant information


    Important

    Add comprehensive document management system with CRUD, advanced search, and performance optimizations.

    • Document Management:
      • Added CRUD operations in create_doc.py, delete_doc.py, get_doc.py, and list_docs.py.
      • Owner association and validation, metadata support, and error handling.
    • Search Capabilities:
      • Full-text search in search_docs_by_text.py.
      • Vector-based search in search_docs_by_embedding.py.
      • Hybrid search in search_docs_hybrid.py.
      • MMR algorithm in mmr.py.
    • Performance:
      • Parallel search execution and simsimd support.
    • Models:
      • Updated Doc model in Docs.py with new fields like modality, language, index, embedding_model, and embedding_dimensions.
    • Tests:
      • Added tests in test_docs_queries.py for CRUD operations and listing.

    This description was created by Ellipsis for 831e950. It will automatically update as commits are pushed.

    PR Reviewer Guide 🔍

    Here are some key observations to aid the review process:

    ⏱️ Estimated effort to review: 4 🔵🔵🔵🔵⚪
    🧪 No relevant tests
    🔒 Security concerns

    SQL Injection:
    The code uses parameterized queries which is good, but the websearch_to_tsquery function in search_docs_by_text.py could potentially be vulnerable to injection if the input is not properly sanitized before being passed to the function.

    ⚡ Recommended focus areas for review

    Performance Issue
    The hybrid search implementation loads all results into memory before fusion. For large result sets this could cause memory issues.

    Input Validation
    Missing validation for embedding dimensions and model compatibility. Should validate that embedding dimensions match the specified model.

    Error Handling
    The maximal marginal relevance implementation lacks proper error handling for edge cases like zero vectors or NaN values.

    Copy link

    qodo-merge-pro-for-open-source bot commented Dec 20, 2024

    PR Code Suggestions ✨

    Explore these optional code suggestions:

    CategorySuggestion                                                                                                                                    Score
    Possible issue
    Add validation for vector embedding dimensions to prevent invalid configurations

    Add input validation for embedding_dimensions to ensure it's a positive integer when
    embedding_model is specified, preventing invalid vector dimensions.

    agents-api/agents_api/queries/docs/create_doc.py [122-123]

     data.embedding_model or "none",
    -data.embedding_dimensions or 0,
    +data.embedding_dimensions if data.embedding_model != "none" and data.embedding_dimensions > 0 else 0,
    • Apply this suggestion
    Suggestion importance[1-10]: 8

    Why: The suggestion adds crucial validation to prevent invalid vector dimensions when an embedding model is specified, which could cause serious issues in downstream vector operations.

    8
    Validate diversity-relevance tradeoff parameter to prevent invalid search results

    Add input validation for lambda_mult parameter to ensure it's between 0 and 1, as
    values outside this range would produce invalid diversity-relevance tradeoffs.

    agents-api/agents_api/queries/docs/mmr.py [64-69]

     def maximal_marginal_relevance(
         query_embedding: np.ndarray,
         embedding_list: list,
         lambda_mult: float = 0.5,
         k: int = 4,
     ) -> list[int]:
    +    if not 0 <= lambda_mult <= 1:
    +        raise ValueError("lambda_mult must be between 0 and 1")
    • Apply this suggestion
    Suggestion importance[1-10]: 7

    Why: Adding validation for lambda_mult is important as values outside [0,1] would produce invalid diversity-relevance tradeoffs, potentially breaking the MMR algorithm's functionality.

    7
    Validate hybrid search weight parameter to prevent invalid result ranking

    Add validation for alpha parameter to ensure it's between 0 and 1, as this weight
    controls the balance between text and embedding search results.

    agents-api/agents_api/queries/docs/search_docs_hybrid.py [107-114]

     async def search_docs_hybrid(
         developer_id: UUID,
         text_query: str = "",
         embedding: List[float] = None,
         k: int = 10,
         alpha: float = 0.5,
    +) -> List[Doc]:
    +    if not 0 <= alpha <= 1:
    +        raise ValueError("alpha must be between 0 and 1")
    • Apply this suggestion
    Suggestion importance[1-10]: 7

    Why: The validation ensures alpha stays within [0,1], preventing incorrect weighting between text and embedding search results that could lead to invalid rankings.

    7

    Copy link

    qodo-merge-pro-for-open-source bot commented Dec 20, 2024

    CI Failure Feedback 🧐

    (Checks updated until commit 74add36)

    Action: Typecheck

    Failed stage: Typecheck [❌]

    Failed test name: pytype

    Failure summary:

    The pytype static type checker failed with multiple errors:

  • Import error: Cannot find module pycozo in agents_api/common/utils/cozo.py
  • Bad return type in embed_snippets function in agents_api/queries/docs/embed_snippets.py
  • Attribute error in fuse_results function in agents_api/queries/docs/search_docs_hybrid.py: Trying to
    access model_copy on a None value
  • Type annotation mismatch in search_docs_hybrid.py
  • Stray type comments in test_workflow_routes.py

  • Relevant error logs:
    1:  ##[group]Operating System
    2:  Ubuntu
    ...
    
    1185:  [17/370] check agents_api.autogen.Files
    1186:  [18/370] check agents_api.autogen.Executions
    1187:  [19/370] check agents_api.autogen.Entries
    1188:  [20/370] check agents_api.autogen.Agents
    1189:  [21/370] check agents_api.activities.sync_items_remote
    1190:  [22/370] check agents_api.clients.__init__
    1191:  [23/370] check agents_api.common.utils.datetime
    1192:  [24/370] check agents_api.common.utils.cozo
    1193:  FAILED: /home/runner/work/julep/julep/agents-api/.pytype/pyi/agents_api/common/utils/cozo.pyi 
    1194:  /home/runner/work/julep/julep/agents-api/.venv/bin/python -m pytype.main --disable pyi-error --imports_info /home/runner/work/julep/julep/agents-api/.pytype/imports/agents_api.common.utils.cozo.imports --module-name agents_api.common.utils.cozo --platform linux -V 3.12 -o /home/runner/work/julep/julep/agents-api/.pytype/pyi/agents_api/common/utils/cozo.pyi --analyze-annotated --nofail --none-is-not-bool --quick --strict-none-binding /home/runner/work/julep/julep/agents-api/agents_api/common/utils/cozo.py
    1195:  /home/runner/work/julep/julep/agents-api/agents_api/common/utils/cozo.py:9:1: error: in <module>: Can't find module 'pycozo'. [import-error]
    1196:  from pycozo import Client
    1197:  ~~~~~~~~~~~~~~~~~~~~~~~~~
    1198:  For more details, see https://google.github.io/pytype/errors.html#import-error
    ...
    
    1204:  [30/370] check agents_api.app
    1205:  [31/370] check agents_api.metrics.counters
    1206:  [32/370] check agents_api.common.utils.types
    1207:  [33/370] check agents_api.common.storage_handler
    1208:  [34/370] check agents_api.common.nlp
    1209:  [35/370] check agents_api.common.protocol.developers
    1210:  [36/370] check agents_api.common.exceptions.__init__
    1211:  [37/370] check agents_api.queries.utils
    1212:  ERROR:pytype.matcher Invalid type: <class 'pytype.abstract.function.ParamSpecMatch'>
    ...
    
    1304:  [129/370] check agents_api.rec_sum.trim
    1305:  [130/370] check agents_api.model_registry
    1306:  [131/370] check agents_api.common.exceptions.agents
    1307:  [132/370] check agents_api.common.exceptions.users
    1308:  [133/370] check agents_api.queries.docs.mmr
    1309:  [134/370] check agents_api.routers.sessions.exceptions
    1310:  [135/370] check agents_api.common.__init__
    1311:  [136/370] check agents_api.queries.docs.embed_snippets
    1312:  FAILED: /home/runner/work/julep/julep/agents-api/.pytype/pyi/agents_api/queries/docs/embed_snippets.pyi 
    1313:  /home/runner/work/julep/julep/agents-api/.venv/bin/python -m pytype.main --disable pyi-error --imports_info /home/runner/work/julep/julep/agents-api/.pytype/imports/agents_api.queries.docs.embed_snippets.imports --module-name agents_api.queries.docs.embed_snippets --platform linux -V 3.12 -o /home/runner/work/julep/julep/agents-api/.pytype/pyi/agents_api/queries/docs/embed_snippets.pyi --analyze-annotated --nofail --none-is-not-bool --quick --strict-none-binding /home/runner/work/julep/julep/agents-api/agents_api/queries/docs/embed_snippets.py
    1314:  /home/runner/work/julep/julep/agents-api/agents_api/queries/docs/embed_snippets.py:34:5: error: in embed_snippets: bad return type [bad-return-type]
    ...
    
    1317:  return (
    1318:  ~~~~~~~~
    1319:  vectorizer_query,
    1320:  ~~~~~~~~~~~~~~~~~~~~~~~~~
    1321:  [developer_id, doc_id, owner_type, owner_id],
    1322:  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    1323:  )
    1324:  ~~~~~
    1325:  For more details, see https://google.github.io/pytype/errors.html#bad-return-type
    ...
    
    1334:  [145/370] check tests.test_chat_routes
    1335:  [146/370] check agents_api.clients.worker.__init__
    1336:  [147/370] check agents_api.common.protocol.__init__
    1337:  [148/370] check tests.test_messages_truncation
    1338:  [149/370] check agents_api.queries.agents.__init__
    1339:  [150/370] check agents_api.autogen.__init__
    1340:  [151/370] check agents_api.workflows.__init__
    1341:  [152/370] check agents_api.queries.docs.search_docs_hybrid
    1342:  FAILED: /home/runner/work/julep/julep/agents-api/.pytype/pyi/agents_api/queries/docs/search_docs_hybrid.pyi 
    1343:  /home/runner/work/julep/julep/agents-api/.venv/bin/python -m pytype.main --disable pyi-error --imports_info /home/runner/work/julep/julep/agents-api/.pytype/imports/agents_api.queries.docs.search_docs_hybrid.imports --module-name agents_api.queries.docs.search_docs_hybrid --platform linux -V 3.12 -o /home/runner/work/julep/julep/agents-api/.pytype/pyi/agents_api/queries/docs/search_docs_hybrid.pyi --analyze-annotated --nofail --none-is-not-bool --quick --strict-none-binding /home/runner/work/julep/julep/agents-api/agents_api/queries/docs/search_docs_hybrid.py
    1344:  /home/runner/work/julep/julep/agents-api/agents_api/queries/docs/search_docs_hybrid.py:103:15: error: in fuse_results: No attribute 'model_copy' on None [attribute-error]
    1345:  In Optional[agents_api.autogen.Docs.Doc]
    1346:  doc = doc.model_copy()  # or copy if you are using Pydantic
    1347:  ~~~~~~~~~~~~~~
    1348:  /home/runner/work/julep/julep/agents-api/agents_api/queries/docs/search_docs_hybrid.py:110:1: error: in <module>: Type annotation for embedding does not match type of assignment [annotation-type-mismatch]
    ...
    
    1443:  # fuse them
    1444:  ~~~~~~~~~~~~~~~
    1445:  fused = fuse_results(text_results, embed_results, alpha)
    1446:  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    1447:  # Then pick top K overall
    1448:  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    1449:  return fused[:k]
    1450:  ~~~~~~~~~~~~~~~~~~~~
    1451:  For more details, see https://google.github.io/pytype/errors.html
    1452:  [153/370] check tests.test_workflow_routes
    1453:  /home/runner/work/julep/julep/agents-api/tests/test_workflow_routes.py:65:1: error: : Stray type comment: object [ignored-type-comment]
    1454:  #   type: object~~~~~~~~~~~~~~~
    1455:  #   type: object
    1456:  /home/runner/work/julep/julep/agents-api/tests/test_workflow_routes.py:114:1: error: : Stray type comment: object [ignored-type-comment]
    1457:  #   type: object~~~~~~~~~~~~~~~
    1458:  #   type: object
    1459:  For more details, see https://google.github.io/pytype/errors.html#ignored-type-comment
    ...
    
    1469:  [163/370] check tests.test_agent_routes
    1470:  [164/370] check tests.test_tool_queries
    1471:  [165/370] check agents_api.queries.sessions.__init__
    1472:  [166/370] check tests.test_docs_routes
    1473:  [167/370] check tests.test_execution_workflow
    1474:  [168/370] check agents_api.queries.files.__init__
    1475:  [169/370] check agents_api.activities.logger
    1476:  [170/370] check agents_api.queries.users.__init__
    1477:  ninja: build stopped: cannot make progress due to previous errors.
    1478:  Computing dependencies
    1479:  Generated API key since not set in the environment: 30387414966998362232017619243305
    1480:  Sentry DSN not found. Sentry will not be enabled.
    1481:  Analyzing 342 sources with 0 local dependencies
    1482:  Leaving directory '.pytype'
    1483:  ##[error]Process completed with exit code 1.
    

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    ❌ Changes requested. Reviewed everything up to 6c77490 in 1 minute and 30 seconds

    More details
    • Looked at 848 lines of code in 10 files
    • Skipped 0 files when reviewing.
    • Skipped posting 8 drafted comments based on config settings.
    1. agents-api/agents_api/queries/docs/search_docs_hybrid.py:13
    • Draft comment:
      The import statement for run_concurrently is unnecessary since it's not used in the code. Consider removing it to clean up the imports.
    • Reason this comment was not posted:
      Confidence changes required: 10%
      The import statement for run_concurrently is unnecessary since it's not used in the code.
    2. agents-api/agents_api/queries/docs/search_docs_hybrid.py:134
    • Draft comment:
      Appending an empty list to tasks is incorrect. You should append a coroutine or task. Consider using None or a similar placeholder if you intend to skip adding a task.
    • Reason this comment was not posted:
      Confidence changes required: 50%
      The code uses tasks.append([]) which is incorrect for appending tasks. It should append a coroutine instead.
    3. agents-api/agents_api/queries/docs/search_docs_hybrid.py:147
    • Draft comment:
      Appending an empty list to tasks is incorrect. You should append a coroutine or task. Consider using None or a similar placeholder if you intend to skip adding a task.
    • Reason this comment was not posted:
      Confidence changes required: 50%
      The code uses tasks.append([]) which is incorrect for appending tasks. It should append a coroutine instead.
    4. agents-api/agents_api/queries/docs/search_docs_hybrid.py:154
    • Draft comment:
      Ensure that at least one valid task is added to tasks before calling gather. If both text_query and embedding are empty, tasks will contain only empty lists, leading to an error.
    • Reason this comment was not posted:
      Confidence changes required: 50%
      The code does not handle the case where both text_query and embedding are empty, which could lead to an error when calling gather.
    5. agents-api/agents_api/queries/docs/search_docs_hybrid.py:110
    • Draft comment:
      The embedding parameter should have a default value of an empty list [] instead of None to avoid type issues and simplify checks.
    • Reason this comment was not posted:
      Confidence changes required: 50%
      The embedding parameter should have a default value of an empty list instead of None to avoid type issues.
    6. agents-api/agents_api/queries/docs/create_doc.py:69
    • Draft comment:
      Consider adding more exception handling for other potential database errors, such as asyncpg.DataError or asyncpg.SyntaxOrAccessError, to make the function more robust.
    • Reason this comment was not posted:
      Confidence changes required: 50%
      The rewrap_exceptions decorator is used to handle exceptions, but it doesn't cover all possible exceptions that might occur during database operations.
    7. agents-api/agents_api/queries/docs/delete_doc.py:43
    • Draft comment:
      Consider adding more exception handling for other potential database errors, such as asyncpg.DataError or asyncpg.SyntaxOrAccessError, to make the function more robust.
    • Reason this comment was not posted:
      Confidence changes required: 50%
      The rewrap_exceptions decorator is used to handle exceptions, but it doesn't cover all possible exceptions that might occur during database operations.
    8. agents-api/agents_api/queries/docs/get_doc.py:29
    • Draft comment:
      Consider adding exception handling for potential database errors, such as asyncpg.DataError or asyncpg.SyntaxOrAccessError, to make the function more robust.
    • Reason this comment was not posted:
      Confidence changes required: 50%
      The rewrap_exceptions decorator is used to handle exceptions, but it doesn't cover all possible exceptions that might occur during database operations.

    Workflow ID: wflow_0SgPnESfFL0Scwfr


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    return similarity


    def maximal_marginal_relevance(
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    This is an exact duplicate of the existing implementation.

    • function maximal_marginal_relevance (mmr.py)

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    👍 Looks good to me! Incremental review on 93673b7 in 1 minute and 3 seconds

    More details
    • Looked at 1195 lines of code in 21 files
    • Skipped 0 files when reviewing.
    • Skipped posting 5 drafted comments based on config settings.
    1. agents-api/agents_api/queries/docs/get_doc.py:5
    • Draft comment:
      The import statement for 'asyncpg' is unnecessary and can be removed to clean up the code. This is also applicable in other files like 'list_docs.py', 'search_docs_by_embedding.py', and 'search_docs_by_text.py'.
    • Reason this comment was not posted:
      Confidence changes required: 50%
      The import statement for 'asyncpg' is unnecessary in multiple files as it is not used anywhere in the code. Removing it will clean up the code.
    2. agents-api/agents_api/queries/docs/list_docs.py:5
    • Draft comment:
      The import statement for 'asyncpg' is unnecessary and can be removed to clean up the code. This is also applicable in other files like 'search_docs_by_embedding.py', and 'search_docs_by_text.py'.
    • Reason this comment was not posted:
      Confidence changes required: 50%
      The import statement for 'asyncpg' is unnecessary in multiple files as it is not used anywhere in the code. Removing it will clean up the code.
    3. agents-api/agents_api/queries/docs/search_docs_by_embedding.py:6
    • Draft comment:
      The import statement for 'asyncpg' is unnecessary and can be removed to clean up the code. This is also applicable in 'search_docs_by_text.py'.
    • Reason this comment was not posted:
      Confidence changes required: 50%
      The import statement for 'asyncpg' is unnecessary in multiple files as it is not used anywhere in the code. Removing it will clean up the code.
    4. agents-api/agents_api/queries/docs/search_docs_by_text.py:6
    • Draft comment:
      The import statement for 'asyncpg' is unnecessary and can be removed to clean up the code.
    • Reason this comment was not posted:
      Confidence changes required: 50%
      The import statement for 'asyncpg' is unnecessary in multiple files as it is not used anywhere in the code. Removing it will clean up the code.
    5. agents-api/agents_api/queries/docs/create_doc.py:98
    • Draft comment:
      The 'org' option is removed from the owner_type Literal, but this change is not reflected in the PR description. This should be documented for clarity. This change is also applicable in 'delete_doc.py', 'get_doc.py', and 'list_docs.py'.
    • Reason this comment was not posted:
      Confidence changes required: 50%
      The 'org' option is removed from the owner_type Literal in multiple files, but this change is not reflected in the PR description. This should be documented for clarity.

    Workflow ID: wflow_pnbwiXEmTCJVnbrw


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    ❌ Changes requested. Incremental review on dc0ec36 in 48 seconds

    More details
    • Looked at 939 lines of code in 28 files
    • Skipped 0 files when reviewing.
    • Skipped posting 1 drafted comments based on config settings.
    1. agents-api/agents_api/queries/users/delete_user.py:59
    • Draft comment:
      The asyncpg.exceptions.UniqueViolationError should not be handled here as it is not relevant to delete operations. Consider removing this exception handling.
    • Reason this comment was not posted:
      Marked as duplicate.

    Workflow ID: wflow_WUrKdAU41fxw9Cd0


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    status_code=404,
    detail="The specified developer does not exist.",
    ),
    asyncpg.exceptions.UniqueViolationError: partialclass(
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    The asyncpg.exceptions.UniqueViolationError should not be handled here as it is not relevant to delete operations. Consider removing this exception handling.

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    👍 Looks good to me! Incremental review on 831e950 in 51 seconds

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    • Looked at 440 lines of code in 11 files
    • Skipped 0 files when reviewing.
    • Skipped posting 3 drafted comments based on config settings.
    1. agents-api/agents_api/queries/docs/get_doc.py:36
    • Draft comment:
      Using ast.literal_eval on d["content"] can be unsafe if the content is not guaranteed to be a valid Python literal. Consider using a safer method to parse or handle the content.
    • Reason this comment was not posted:
      Comment was on unchanged code.
    2. agents-api/agents_api/queries/docs/embed_snippets.py:10
    • Draft comment:
      vectorizer_query is set to None. This is a placeholder and should be replaced with an actual query before deployment.
    • Reason this comment was not posted:
      Decided after close inspection that this draft comment was likely wrong and/or not actionable:
      The comment is essentially repeating information that's already explicitly stated in a TODO comment one line above. The TODO comment is more visible and serves the same purpose. This makes the PR comment redundant and not adding any new information or value.
      Perhaps the comment is trying to emphasize the importance of not deploying with a None query, which could be a critical issue.
      While deployment concerns are valid, the existing TODO comment already makes it clear this needs to be replaced, and deployment issues would be caught by basic testing since the function would fail immediately.
      Delete the comment as it's redundant with the existing TODO comment and doesn't provide additional actionable value.
    3. agents-api/agents_api/queries/entries/list_entries.py:88
    • Draft comment:
      Ensure sort_by and direction are validated and sanitized to prevent SQL injection, as they are used in string interpolation for SQL queries.
    • Reason this comment was not posted:
      Comment did not seem useful.

    Workflow ID: wflow_TPwdOI1YwvBHnQ9P


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