Merge pull request #4 from PyEED/blast_graph_db

Blast graph db

blast/Dockerfile

@@ -10,8 +10,5 @@ COPY app.py /usr/local/bin/app.py
 # Set the working directory
 WORKDIR /usr/local/bin
 
-# Expose the port the server will run on
-EXPOSE 6001
-
 # Run the Python server script
 CMD ["python3", "app.py"]

blast/app.py

@@ -1,71 +1,129 @@
-from fastapi import FastAPI, HTTPException, Request
-from pydantic import BaseModel
+from fastapi import FastAPI, HTTPException, Request, UploadFile
 import subprocess
 import os
-import uuid
-from typing import Optional
-import logging
 
 app = FastAPI()
-logger = logging.getLogger(__name__)
 
-class BlastRequest(BaseModel):
-    tool: str
-    query: str
-    db: str
-    evalue: str
-    outfmt: str
-
-
-## ENDPOINTS --------------------------
-
-def create_fastas_file_from_seq(seq, filename):
-    with open(filename, 'w') as file:
+def create_fasta_files_from_seq(seq, filename):
+    with open(filename, 'w') as file: 
         file.write(f">seq\n{seq}\n")
 
 @app.get("/")
-async def read_root():
-    return {"message": "Welcome to the BLAST API!"}
+async def read_root(): 
+    return {"message": "Welcome to the BLAST API"}
+
+@app.get("/blastp_help")
+def blastp_help():
+    try:
+        result = subprocess.run(
+            ["blastp", "--help"],
+            capture_output=True,
+            text=True,
+        )
+        return {"help": result.stdout}
+    except subprocess.CalledProcessError as e:
+        raise HTTPException(status_code=400, detail=f"Command failed: {e.stderr}")
 
-# this get json params
-@app.post("/run_blast")
-async def run_blast(request: Request):
-    request = await request.json()
+@app.get("/blastn_help")
+def blastn_help():
+    try:
+        result = subprocess.run(
+            ["blastn", "--help"],
+            capture_output=True,
+            text=True,
+        )
+        return {"help": result.stdout}
+    except subprocess.CalledProcessError as e:
+        raise HTTPException(status_code=400, detail=f"Command failed: {e.stderr}")
 
+@app.post("/blastp")
+async def run_blastp(request: Request):
+    data = await request.json()
+
+    print(f" Received request to run blastp with data: {data}")
+
     query_filename = f"in.fasta"
     result_filename = f"out.out"
-    # create empty file
+
+    # Clear or create result file
     open(result_filename, 'w').close()
-
-    # Create the FASTA file
-    create_fastas_file_from_seq(request['query'], query_filename)
-
-    # Run the BLAST command
-    command = [
-        request['tool'],
-        '-query', query_filename,
-        '-db', request['db'],
-        '-evalue', request['evalue'],
-        '-outfmt', request['outfmt'],
-        '-num_threads', request['num_threads'],
-        '-out', result_filename,
-        '-max_target_seqs', '10000'
-    ]
-
+
+    # Create the fasta file from the query string
+    create_fasta_files_from_seq(data['query'], query_filename)
+
     try:
-        subprocess.run(command, check=True)
+        command = [
+            "blastp",
+            '-query', query_filename,
+            '-db', data['db'],
+            '-evalue', str(data['evalue']),
+            '-outfmt', str(data['outfmt']),
+            '-num_threads', str(data['num_threads']),
+            '-out', result_filename,
+            '-max_target_seqs', str(data['max_target_seqs'])
+        ]
+
+        result = subprocess.run(
+            command, 
+            capture_output=True, 
+            check=True,
+            text=True
+        )
+
+        with open(result_filename, 'r') as file:
+            result_data = file.read()
+
+        return {"result": result_data}
+
     except subprocess.CalledProcessError as e:
-        raise HTTPException(status_code=500, detail=str(e))
-
-
-    with open(result_filename, 'r') as file:
-        result = file.read()
-
-    return result
-
-
+        raise HTTPException(status_code=400, detail=f"Command failed: {e.stderr}")
+
 
-if __name__ == '__main__':
-    import uvicorn
+@app.post("/blastn")
+async def run_blastn(request: Request):
+    data = await request.json()
+
+    print(f" Received request to run blastn with data: {data}")
+
+    query_filename = f"in.fasta"
+    result_filename = f"out.out"
+
+    # Clear or create result file
+    open(result_filename, 'w').close()
 
+    # Create the fasta file from the query string
+    create_fasta_files_from_seq(data['query'], query_filename)
+
+    try:
+        command = [
+            "blastn",
+            '-query', query_filename,
+            '-db', data['db'],
+            '-evalue', str(data['evalue']),
+            '-outfmt', str(data['outfmt']),
+            '-num_threads', str(data['num_threads']),
+            '-out', result_filename,
+            '-max_target_seqs', str(data['max_target_seqs'])
+        ]
+
+        result = subprocess.run(
+            command, 
+            capture_output=True, 
+            check=True,
+            text=True
+        )
+
+        with open(result_filename, 'r') as file:
+            result_data = file.read()
+
+        return {"result": result_data}
+
+    except subprocess.CalledProcessError as e:
+        raise HTTPException(status_code=400, detail=f"Command failed: {e.stderr}")
+
+
+if __name__ == "__main__":
+    import uvicorn
+
     uvicorn.run("app:app", host="0.0.0.0", port=6001, reload=True)
+

blast/reload_development.sh

@@ -1,4 +1,4 @@
-sudo docker stop blast_docker
-sudo docker remove blast_docker
-sudo docker build --no-cache -t blast_docker .
-sudo docker run --name blast_docker --volume /mnt/databases:/blast/blastdb -p 6001:6001 blast_docker
+sudo docker stop blast
+sudo docker remove blast
+sudo docker build --no-cache -t blast_image .
+sudo docker run --name blast --volume /home/ala/BA/mydb:/blast/db --volume /mnt/databases:/blast/db/custom -p 6001:6001 blast_image