1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
|
from app import app as flask_app
#app.run(debug=True, host="0.0.0.0", port=8080)
from random import choice, shuffle
from string import digits, ascii_lowercase
from fastapi import Body,FastAPI
from fastapi.middleware.wsgi import WSGIMiddleware
from flask import Flask, escape, request
from pydantic import BaseModel
import os, subprocess
def gen_word(N, min_N_dig, min_N_low):
choose_from = [digits]*min_N_dig + [ascii_lowercase]*min_N_low
choose_from.extend([digits + ascii_lowercase] * (N-min_N_low-min_N_dig))
chars = [choice(bet) for bet in choose_from]
shuffle(chars)
return ''.join(chars)
dbFailing = False
import mysql.connector as con
from mysql.connector.errors import InterfaceError, DatabaseError
try:
mycon = con.connect(host=flask_app.config['DB_HOST'],user=flask_app.config['DB_USER'],password=flask_app.config['DB_PASSWORD'],port=flask_app.config['DB_PORT'],database=flask_app.config['DB_NAME'])
mycursor = mycon.cursor()
except InterfaceError:
print("Could not connect to the database!")
dbFailing = True
except DatabaseError:
print("Unknown Host")
dbFailing = True
"""
@flask_app.route("/")
def flask_main():
name = request.args.get("name", "World")
return f"Hello, {escape(name)} from Flask!"
"""
app = FastAPI(title="Curie-API",
description="API for accessing some of the features.",
version="0.1",)
@app.get("/v1")
async def API_Version():
return {"message":"Curie-API v1"}
@app.get("/v1/status/{job_id}")
async def get_status(job_id: str):
if dbFailing:
return {"message":"Could not connect to the database"}
sqlQuery = 'select id, protein_name, ligand_name, date, description, done from curieweb where id="%s"' % (job_id)
mycursor.execute(sqlQuery)
records = mycursor.fetchall()
if records == []:
return {"message":"Invalid Job ID"}
r = records[0]
return {"job_id":r[0],"Protein Name":r[1],"Ligand Name":r[2],"Submitted On":r[3],"Job Description":r[4],"Job Status":r[5]}
@app.get("/v1/3DModels/{job_id}")
async def get_models(job_id: str):
if dbFailing:
return {"message":"Could not connect to the database"}
sqlQuery = 'select done from curieweb where id="%s"' % (job_id)
mycursor.execute(sqlQuery)
records = mycursor.fetchall()
if records == []:
return {"message":"Invalid Job ID"}
if records[0][0] == 0:
return {"message": "The job is still qeued"}
return {"USDZ":"/static/uploads/3DModels/" + str(job_id) + ".usdz","glTF":"/static/uploads/3DModels/" + str(job_id) + ".gltf"}
@app.get("/v1/Report/{job_id}")
async def get_report(job_id:str):
if dbFailing:
return {"message":"Could not connect to the database"}
sqlQuery = 'select done from curieweb where id="%s"' % (job_id)
mycursor.execute(sqlQuery)
records = mycursor.fetchall()
if records == []:
return {"message":"Invalid Job ID"}
if records[0][0] == 0:
return {"message": "The job is still qeued"}
return {"PDF Report":"/static/uploads/reports/"+str(job_id)+".pdf"}
@app.post("/v1/docking/automatic")
async def docking_automatic(pdb: str, smiles:str,compound_name:str,email:str,description:str):
if dbFailing:
return {"message":"Could not connect to the database"}
if len(pdb) != 0:
return {"message": "Invalid PDB ID"}
sqlQuery = "insert into curieweb (id, email, pdb, ligand_smile, ligand_name, date, description) values (%s,%s,%s,%s,%s,CURDATE(),%s) "
jobID = gen_word(16, 1, 1)
insert_tuple = (jobID,email,pdb,smiles,compound_name,description)
"""
mycursor.execute(sqlQuery,insert_tuple)
mycon.commit()
if flask_app.config['INSTANT_EXEC']:
cwd = os.path.join(os.getcwd(),"app")
subprocess.Popen(['python3', 'dock-single.py'],cwd=cwd)
"""
return {"jobID":jobID,"message":"Sucessfuly Submitted","PDB ID":pdb,"SMILES":smiles,"email":email}
app.mount("/", WSGIMiddleware(flask_app))
|
