blast v1 added #65
blast v1 added #65
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| except Exception as e: | ||
| raise HTTPException(status_code=500, detail=str(e)) | ||
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| @app.post("/blastn") |
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Instead of many APIs I suggest to have 1 api with the type of blast that a user should use.
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Use a single endpoint /blast, pass type of blast to request model (as enum)
| return run_blast("blastx", query.sequence, query.descriptions, query.alignments, query.hitlist_size, query.expect) | ||
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| @app.post("/tblastn") | ||
| async def tblastn(query: SequenceQuery): |
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Add python typing for returns etc. everywhere
| @@ -0,0 +1,15 @@ | |||
| # FastAPI BLAST Service | |||
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Please also add the info to main readme about new microservice
| descriptions: int = 10 | ||
| alignments: int = 10 | ||
| hitlist_size: int = 10 | ||
| expect: float = 10.0 |
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| descriptions: int = 10 | |
| alignments: int = 10 | |
| hitlist_size: int = 10 | |
| expect: float = 10.0 | |
| descriptions: Optional[int] = 10 | |
| alignments: Optional[int] = 10 | |
| hitlist_size: Optional[int] = 10 | |
| expect: Optional[float] = 10.0 |
| @@ -0,0 +1,21 @@ | |||
| # Use a PyTorch base image with CUDA support | |||
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| # Use a PyTorch base image with CUDA support |
| else: | ||
| raise HTTPException(status_code=400, detail="Invalid program") | ||
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| def run_blast(program, query, descriptions=10, alignments=10, hitlist_size=10, expect=10.0): |
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| def run_blast(program, query, descriptions=10, alignments=10, hitlist_size=10, expect=10.0): | |
| def run_blast(program: some type, query: SearchQuery, descriptions: int=10, alignments: int =10, hitlist_size: int =10, expect: float =10.0): |
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Also please add the shell script to generate client and generate the client itself and add it to the changes. The script example can be found here: https://github.com/BasedLabs/NoLabs/blob/master/microservices/biobuddy/generate_client.sh And if everything successful the folder client/ should be generated (as in the example): https://github.com/BasedLabs/NoLabs/tree/master/microservices/biobuddy/client |
| title="BLAST Query" | ||
| ) | ||
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| def choose_dataset(program): |
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| def choose_dataset(program): | |
| def choose_dataset(program: str) -> str: |
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Program can be enum with predefined values
| else: | ||
| raise HTTPException(status_code=400, detail="Invalid program") |
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| else: | |
| raise HTTPException(status_code=400, detail="Invalid program") | |
| raise HTTPException(status_code=400, detail="Invalid program") |
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