Feat/sdk modulector - #104
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Replaced direct Modulector HTTP calls with modulector-sdk wrappers in `MRNAService` and updated all related consumers (`api_service`, `biomarkers`, `molecules_details`, and assistant tools). Added dedicated SDK-backed methods for miRNA/methylation lookup, interactions, diseases, drugs, and code/site search, plus paginated response normalization and safer fallbacks. Also introduced `MODULECTOR_BASE_URL` settings, added `modulector-sdk` dependency, updated MCP server command args for BioMCP, and fixed a null-response edge case in biomarker gene lookup.
Enable a dedicated `modulector` MCP server in `mcp_servers.json` and remove the in-process miRNA helper tools from `tools.py` (search/details/targets/diseases/drugs), along with their registration. This centralizes miRNA and related biological lookups through the external Modulector MCP integration instead of local assistant wrappers.
Genarito
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Aug 1, 2026
| @@ -168,6 +168,8 @@ def find_genes_from_request(request: Request) -> List[Dict]: | |||
| """ | |||
| genes_found = global_mrna_service.get_bioapi_service_content('gene-symbols-finder', | |||
| return '&'.join([f'{key}={value}' for (key, value) in get_request.items()]) | ||
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| def __get_service_content( | ||
| def __get_bioapi_content( |
| return self.__get_service_content(service_name, request_params, is_paginated, self.url_modulector_prefix, | ||
| method, append_slash=True) | ||
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| def get_bioapi_service_content( |
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Borrar, no debería usarse más ahora que tenemos la SDK
| def find_methylation_sites(self, query: str, limit: Optional[int] = None) -> List[str]: | ||
| """Search methylation site identifiers via Modulector SDK.""" | ||
| try: | ||
| kwargs: Dict[str, Any] = {'query': query, 'base_url': self._modulector_base_url} |
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Simplificar, en vez de hacer un diccionario y después desconstruir:
return modulector.find_methylation_sites(query=query, limit=limit)Aplica esta mejora a todas las funciones de este archivo
| 'port': os.getenv('MODULECTOR_PORT', 443), | ||
| 'protocol': os.getenv('BIOAPI_PROTOCOL', 'https') | ||
| } | ||
| _modulector_protocol = os.getenv('MODULECTOR_PROTOCOL', os.getenv('BIOAPI_PROTOCOL', 'https')) |
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Tipar, en caso el caso del puerto, hacer un int() para que, en caso de configurarlo mal, salte el error
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