Dev madina by madina1203 · Pull Request #169 · HolobiomicsLab/MetaboT

madina1203 · 2026-04-23T19:45:21Z

User description

Migrated deprecated langchain.pydantic_v1 imports to pydantic directly.

PR Type

enhancement, bug_fix, dependencies

Description

Migrate deprecated langchain.pydantic_v1 imports to pydantic
Update args_schema type annotations for tools
Add big_benchmark.csv for automated evaluation
Update dependencies in environment.yml

Diagram Walkthrough

flowchart LR
  A["langchain.pydantic_v1"] -- "migrate to" --> B["pydantic"]
  C["args_schema"] -- "update type" --> D["type[BaseModel]"]
  E["big_benchmark.csv"] -- "add for" --> F["automated evaluation"]
  G["environment.yml"] -- "update" --> H["dependencies"]

File Walkthrough

Relevant files

Enhancement

14 files

tool_chemicals.py `Migrate to Pydantic and update args_schema`	+2/-2
tool_smiles.py `Migrate to Pydantic and update args_schema`	+2/-2
tool_target.py `Migrate to Pydantic and update args_schema`	+2/-2
tool_taxon.py `Migrate to Pydantic and update args_schema`	+5/-5
tool_filesparser.py `Migrate to Pydantic and update args_schema`	+6/-2
tool_interpreter.py `Migrate to Pydantic and update args_schema`	+2/-2
tool_spectrum.py `Migrate to Pydantic and update args_schema`	+2/-2
tool_merge_result.py `Migrate to Pydantic and update args_schema`	+2/-2
tool_sparql.py `Migrate to Pydantic and update args_schema`	+5/-5
tool_wikidata_query.py `Migrate to Pydantic and update args_schema`	+5/-5
tool_validator.py `Migrate to Pydantic and update args_schema`	+2/-2
custom_sqlite_file.py `Add ClassVar typing for database path`	+3/-3
database_manager.py `Update memory database manager to use MemorySaver`	+40/-39
langraph_workflow.py `Improve error logging in process_workflow`	+1/-1

Tests

1 files

evaluation.py `Add big_benchmark.csv and improve evaluation script`	+74/-59

Dependencies

1 files

environment.yml `Update dependencies to newer versions`	+13/-13

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coderabbitai · 2026-04-23T19:45:29Z

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qodo-code-review · 2026-04-23T19:45:37Z

Review Summary by Qodo

Migrate to native Pydantic and update LangChain dependencies

✨ Enhancement 🐞 Bug fix

Walkthroughs

Description

• Migrated deprecated langchain.pydantic_v1 imports to native pydantic across all agent tools
• Added explicit type annotations for args_schema and class variables using ClassVar
• Updated dependencies to latest versions (langchain 0.3.27, pydantic 2.13.3, langgraph 0.3.34)
• Refactored evaluation script with dataset management and improved error handling
• Replaced custom SqliteCheckpointerSaver with langgraph's built-in MemorySaver

Diagram

flowchart LR
  A["Deprecated langchain.pydantic_v1"] -->|"Replace with"| B["Native pydantic imports"]
  C["Old type annotations"] -->|"Add explicit types"| D["ClassVar and type[BaseModel]"]
  E["Old dependencies"] -->|"Update to latest"| F["LangChain 0.3.27, Pydantic 2.13.3"]
  G["Custom SqliteCheckpointerSaver"] -->|"Replace with"| H["langgraph MemorySaver"]
  I["Basic evaluation script"] -->|"Enhance with"| J["Dataset management and error handling"]

File Changes

1. app/core/agents/enpkg/tool_chemicals.py ✨ Enhancement +2/-2

Replace pydantic_v1 import and add type annotation

app/core/agents/enpkg/tool_chemicals.py

2. app/core/agents/enpkg/tool_smiles.py ✨ Enhancement +2/-2

Replace pydantic_v1 import and add type annotation

app/core/agents/enpkg/tool_smiles.py

3. app/core/agents/enpkg/tool_target.py ✨ Enhancement +2/-2

Replace pydantic_v1 import and add type annotation

app/core/agents/enpkg/tool_target.py

View more (13)

4. app/core/agents/enpkg/tool_taxon.py ✨ Enhancement +5/-5

Replace pydantic_v1 and add ClassVar annotations

app/core/agents/enpkg/tool_taxon.py

5. app/core/agents/entry/tool_filesparser.py ✨ Enhancement +6/-2

Replace pydantic_v1 and create FileAnalyzerInput schema

app/core/agents/entry/tool_filesparser.py

6. app/core/agents/interpreter/tool_interpreter.py ✨ Enhancement +2/-2

Replace pydantic_v1 import and add type annotation

app/core/agents/interpreter/tool_interpreter.py

7. app/core/agents/interpreter/tool_spectrum.py ✨ Enhancement +2/-2

Replace pydantic_v1 import and add type annotation

app/core/agents/interpreter/tool_spectrum.py

8. app/core/agents/sparql/tool_merge_result.py ✨ Enhancement +2/-2

Replace pydantic_v1 import and add type annotation

app/core/agents/sparql/tool_merge_result.py

9. app/core/agents/sparql/tool_sparql.py ✨ Enhancement +5/-5

Replace pydantic_v1 and add explicit type annotations

app/core/agents/sparql/tool_sparql.py

10. app/core/agents/sparql/tool_wikidata_query.py ✨ Enhancement +5/-5

Replace pydantic_v1 and add ClassVar annotations

app/core/agents/sparql/tool_wikidata_query.py

11. app/core/agents/validator/tool_validator.py ✨ Enhancement +2/-2

Replace pydantic_v1 import and add type annotation

app/core/agents/validator/tool_validator.py

12. app/core/memory/custom_sqlite_file.py ✨ Enhancement +3/-3

Remove pydantic_v1 Field import and add ClassVar

app/core/memory/custom_sqlite_file.py

13. app/core/memory/database_manager.py 🐞 Bug fix +40/-39

Replace custom SqliteCheckpointerSaver with MemorySaver

app/core/memory/database_manager.py

14. app/core/tests/evaluation.py ✨ Enhancement +74/-59

Refactor evaluation script with dataset management

app/core/tests/evaluation.py

15. app/core/workflow/langraph_workflow.py ✨ Enhancement +1/-1

Add exception info to error logging

app/core/workflow/langraph_workflow.py

16. environment.yml Dependencies +13/-13

Update all LangChain and dependency versions

environment.yml

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qodo-code-review · 2026-04-23T19:45:39Z

Code Review by Qodo

🐞 Bugs (3) 📘 Rule violations (0) 📎 Requirement gaps (0)

1. Eval runs at import 🐞 Bug ☼ Reliability

Description

app/core/tests/evaluation.py still executes LangSmith evaluation (run_on_dataset) at module import
time, so importing the module triggers network calls and long-running work. This can break
tooling/CI that imports the package and makes the module unsafe as a library import.

Code

app/core/tests/evaluation.py[R133-136]

+# Run evaluation
chain_results = run_on_dataset(
    dataset_name=dataset_name,
    llm_or_chain_factory=evaluate_result,

Evidence
The evaluation script runs substantial logic at top level (not under a main guard), including strict
env-var checks and an unconditional run_on_dataset() call.
app/core/tests/evaluation.py[22-35]
app/core/tests/evaluation.py[42-77]
app/core/tests/evaluation.py[131-146]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

### Issue description
`app/core/tests/evaluation.py` executes evaluation work (including LangSmith calls and `run_on_dataset`) at import time. This makes imports trigger network calls / long-running work and can fail in environments without required env vars.

### Issue Context
This file lives under `app/core/tests/`, which increases the chance it gets imported by IDE tooling, packaging checks, or test tooling.

### Fix Focus Areas
- Wrap all executable logic in a `main()` function and call it only under `if __name__ == "__main__":`.
- Keep only definitions (functions/classes/constants) at module scope.

- app/core/tests/evaluation.py[18-146]

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

2. Orphaned custom checkpointer 🐞 Bug ⚙ Maintainability

Description

SqliteCheckpointerSaver is no longer used after memory_database() switched to returning MemorySaver,
leaving app/core/memory/custom_sqlite_file.py as dead code with now-misleading rationale comments.
This increases maintenance burden and makes it unclear which checkpoint implementation is intended.

Code

app/core/memory/database_manager.py[R1-40]

+import os
+from app.core.memory.tools_database import SqliteToolsDatabaseManager
+import importlib
+
+def tools_database():
+    """
+    Get the database manager based on the environment variables
+
+    :return: The database manager
+    """
+    if os.getenv('DATABASE_URL') and os.getenv("TOOLS_DATABASE_MANAGER_CLASS"):
+        class_path = os.getenv('TOOLS_DATABASE_MANAGER_CLASS')
+        if class_path:
+            # Dynamically import the module and class based on the environment variable
+            module_name, class_name = class_path.rsplit('.', 1)
+            module = importlib.import_module(module_name)
+            manager_class = getattr(module, class_name)
+            return manager_class()
+    else:
+        return SqliteToolsDatabaseManager()
+
+def memory_database():
+    """
+    Get the database manager based on the environment variables
+
+    :return: The database manager
+    """
+
+    if os.getenv('DATABASE_URL') and os.getenv("MEMORY_DATABASE_MANAGER_CLASS"):
+        class_path = os.getenv('MEMORY_DATABASE_MANAGER_CLASS')
+        if class_path:
+            # Dynamically import the module and class based on the environment variable
+            module_name, class_name = class_path.rsplit('.', 1)
+            module = importlib.import_module(module_name)
+            manager_class = getattr(module, class_name)
+            return manager_class()
+    else:
+        # Use langgraph's built-in MemorySaver which implements the current checkpoint API
+        from langgraph.checkpoint.memory import MemorySaver
+        return MemorySaver()

Evidence
database_manager.memory_database() no longer imports/returns SqliteCheckpointerSaver, while the
custom implementation remains in the repo and documents itself as necessary for Streamlit
multithreading.
app/core/memory/database_manager.py[1-40]
app/core/memory/custom_sqlite_file.py[1-29]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

### Issue description
`SqliteCheckpointerSaver` remains in the repo but is no longer wired in as the default checkpointer. This leaves dead code and misleading comments.

### Issue Context
The fallback in `memory_database()` now returns `MemorySaver()`, and the import of `SqliteCheckpointerSaver` was removed.

### Fix Focus Areas
- Decide whether the custom sqlite saver is still needed:
 - If not needed: delete `custom_sqlite_file.py` (and any references), or clearly mark it deprecated.
 - If needed for some modes: reintroduce it behind a config/env toggle and document when it should be used.

- app/core/memory/database_manager.py[1-40]
- app/core/memory/custom_sqlite_file.py[1-29]

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

3. Duplicate Optional import 🐞 Bug ⚙ Maintainability

Description

tool_taxon.py now imports Optional twice, which is redundant and adds avoidable noise. This makes
the file harder to maintain and review.

Code

app/core/agents/enpkg/tool_taxon.py[R1-9]

+from typing import ClassVar, Optional

from SPARQLWrapper import JSON, SPARQLWrapper


-from langchain.pydantic_v1 import BaseModel, Field
+from pydantic import BaseModel, Field

from typing import Optional

Evidence
The file imports Optional in the combined import and again later as a standalone import.
app/core/agents/enpkg/tool_taxon.py[1-9]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

### Issue description
`Optional` is imported twice in `tool_taxon.py`.

### Issue Context
The PR added `ClassVar` to the first typing import, but left the previous `from typing import Optional` line in place.

### Fix Focus Areas
- Remove the second `from typing import Optional`.

- app/core/agents/enpkg/tool_taxon.py[1-9]

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

github-actions · 2026-04-23T19:46:38Z

PR Reviewer Guide 🔍

Here are some key observations to aid the review process:

⏱️ Estimated effort to review: 3 🔵🔵🔵⚪⚪
🔒 No security concerns identified
⚡ Recommended focus areas for review Docstring Format The newly added FileAnalyzerInput class has a minimal docstring. To meet the requirement of using Google Docstring format for key classes, please update it with a short summary line followed by detailed sections (e.g. Args, Returns). This will improve consistency and clarity for users of the tool. class FileAnalyzerInput(BaseModel): """Input schema for FileAnalyzer - no input fields required.""" pass

github-actions · 2026-04-23T19:46:57Z

PR Code Suggestions ✨

No code suggestions found for the PR.

madina1203 added 3 commits April 23, 2026 18:51

Add big_benchmark.csv for automated evaluation

f9bf608

Fix deprecated pydantic imports and update requirements

69ec4a5

Update the order of questions to be consistent with automated evaluation

2dd5135

dosubot Bot added the size:L This PR changes 100-499 lines, ignoring generated files. label Apr 23, 2026

dosubot Bot added the Dependencies label Apr 23, 2026

github-actions Bot added the Review effort 3/5 label Apr 23, 2026

madina1203 added 2 commits April 24, 2026 10:27

Update installation_test

3aa9458

Clean the evaluation dateset (remove redundant column)

5384796

lfnothias merged commit 085c973 into dev Apr 24, 2026
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