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Merged
Genarito merged 4 commits into from
Sep 25, 2026
Merged

Feat/sdk modulector #104

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1d8b283
Migrate Modulector integration to SDK
TheSinnerAR Jul 24, 2026
83094ad
Move miRNA tools to Modulector MCP server
TheSinnerAR Jul 30, 2026
3b5efd6
Replace direct BioAPI HTTP calls with bioapi-sdk integration
TheSinnerAR Sep 17, 2026
a03fdd1
Replace direct BioAPI HTTP calls with bioapi-sdk integration
TheSinnerAR Sep 17, 2026
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14 changes: 12 additions & 2 deletions config/mcp_servers.json
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Original file line number Diff line number Diff line change
Expand Up @@ -5,9 +5,19 @@
"enabled": true,
"description": "Biomedical research: PubMed papers, bioRxiv, ClinicalTrials.gov, NCI, variants, OncoKB",
"transport": "stdio",
"command": "biomcp",
"args": ["run", "--mode", "stdio"],
"command": "biomcp-cli",
"args": ["mcp"],
"env": {}
},
"modulector": {
"enabled": true,
"description": "miRNA target interactions, aliases, methylation sites, disease and drug associations",
"transport": "stdio",
"command": "modulector-mcp",
"args": [],
"env": {
"MODULECTOR_API_BASE_URL": "https://modulector.multiomix.org"
}
}
}
}
4 changes: 3 additions & 1 deletion config/requirements.txt
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Expand Up @@ -38,4 +38,6 @@ langchain-mcp-adapters==0.2.2
pgvector==0.4.2
sentence-transformers==3.0.0
openai==2.38.0
biomcp-cli==0.8.22
biomcp-cli==0.8.22
modulector-sdk==2.6.1
bioapi-sdk==0.1.0
15 changes: 3 additions & 12 deletions src/api_service/mongo_service.py
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Expand Up @@ -214,20 +214,11 @@ def __get_standard_ids(file_type: FileType, molecules: List[str]) -> Optional[Di
elif file_type == FileType.MIRNA:
logging.warning('Retrieving data from Modulector')

data: Optional[Dict]
if is_for_bioapi:
data = global_mrna_service.get_bioapi_service_content(
'gene-symbols',
request_params={'gene_ids': molecules},
is_paginated=False,
method='post'
)
data = global_mrna_service.get_gene_symbols(gene_ids=molecules)
elif file_type == FileType.MIRNA:
data = global_mrna_service.get_modulector_service_content(
'mirna-codes',
request_params={'mirna_codes': molecules},
is_paginated=False,
method='post'
)
data = global_mrna_service.get_mirna_codes(mirna_codes=molecules)
else:
# In case of methylation, cBioPortal don't manage the methylation sites, so we don't need to use Modulector.
# Generates a dummy dict with the same keys and values as the molecules list
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