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import mysql . connector as con
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from misc . common import get3DModel , CopyContentOfFolder , RemoveAllFilesMatching
from misc . email import email
import os
import sys
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from misc . config import iniConfig
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mycon = con . connect ( host = iniConfig [ ' DATABASE ' ] [ ' HOST ' ] , user = iniConfig [ ' DATABASE ' ] [ ' USER ' ] , password = iniConfig [ ' DATABASE ' ] [ ' PASSWORD ' ] , port = iniConfig [ ' DATABASE ' ] [ ' PORT ' ] , database = iniConfig [ ' DATABASE ' ] [ ' NAME ' ] )
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mycursor = mycon . cursor ( )
sql_select_Query = " select * from curieweb where done=0 LIMIT 1 "
mycursor . execute ( sql_select_Query )
records = mycursor . fetchall ( )
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if records == [ ] :
print ( " Empty Set 😳 " )
print ( " No active task, exitting gracefully " )
exit ( 0 )
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receptor_name = " protein.pdbqt "
ligand_name = " ligand.pdbqt "
description = " Curie Web Task "
#print(records[0])
r = records [ 0 ]
jobID = r [ 0 ]
toEmail = r [ 1 ]
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toaddr = toEmail
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targetB = r [ 2 ]
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if r [ 3 ] is not None :
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receptor_name = str ( r [ 3 ] )
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if r [ 6 ] is not None :
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ligand_name = str ( r [ 6 ] )
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ligandB = r [ 4 ]
configB = r [ 7 ]
date = r [ 8 ]
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if r [ 9 ] is not None :
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description = r [ 9 ]
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else :
description = " not specified "
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cd = os . getcwd ( )
f = os . path . join ( cd , " static/uploads " )
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reportDirectory = os . path . join ( f , " reports " )
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scripts = os . path . join ( cd , " scripts " )
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modelDirectory = os . path . join ( f , " 3DModels " )
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import tempfile
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from shutil import make_archive , copyfile , copy
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with tempfile . TemporaryDirectory ( ) as directory :
print ( ' The created temporary directory is %s ' % directory )
os . chdir ( directory )
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with open ( receptor_name , " wb " ) as file :
file . write ( targetB )
with open ( ligand_name , " wb " ) as file :
file . write ( ligandB )
with open ( " config.txt " , " wb " ) as file :
file . write ( configB )
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# Legacy Docker Curie-Cli Run
#os.system("docker run --rm -v ${PWD}:/results -w /results -u $(id -u ${USER}):$(id -g ${USER}) navanchauhan/curie-cli -r %s -l %s -c config.txt -dpi" % (receptor_name,ligand_name))
CopyContentOfFolder ( scripts , directory )
os . system ( " ./main.sh -r %s -l %s -c config.txt -dpi " % ( receptor_name , ligand_name ) )
RemoveAllFilesMatching ( directory , " .py " )
RemoveAllFilesMatching ( directory , " .sh " )
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z = " Curie_Web_Result_ " + str ( jobID )
zi = os . path . join ( f , z )
make_archive ( zi , ' zip ' , directory )
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try :
copyfile ( " report.pdf " , os . path . join ( reportDirectory , ( str ( jobID ) + " .pdf " ) ) )
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except FileNotFoundError :
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reason = " Could not generate the report, this could be because of a failed docking job. Please check the ZIP archive for the configuration and converted PDBQTs and try submitting manually. "
email ( toaddr , jobID , date , description , zipArchive = zi , reason = reason )
mycursor . execute ( ' UPDATE curieweb set done=1 where id= " %s " ' % ( jobID ) )
mycon . commit ( )
sys . exit ( 0 )
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"""
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res = get3DModel ( receptor_name , ligand_name . replace ( " .pdbqt " , " _out.pdbqt " ) )
if res == None :
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reason = " Could not generate the 3D models. "
email ( toaddr , jobID , date , description , zipArchive = zi )
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mycursor . execute ( ' UPDATE curieweb set done=1 where id= " %s " ' % ( jobID ) )
mycon . commit ( )
sys . exit ( 0 )
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os . system ( " collada2gltf -i model.dae -o model.gltf " )
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try :
copyfile ( " model.gltf " , os . path . join ( modelDirectory , ( str ( jobID ) + " .gltf " ) ) )
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except FileNotFoundError :
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print ( " Does not have Collada2GLTF Installed " )
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email ( toaddr , jobID , date , description , zipArchive = zi )
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mycursor . execute ( ' UPDATE curieweb set done=1 where id= " %s " ' % ( jobID ) )
mycon . commit ( )
exit ( 0 )
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arch = os . popen ( " uname -m " ) . read ( )
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print ( " Generating 3D Model " )
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if " x86 " in arch :
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os . system ( " docker run --rm -v $(pwd):/usr/app leon/usd-from-gltf:latest model.gltf model.usdz " )
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elif " aarch64 " in arch :
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os . system ( " docker run --rm -v $(pwd):/usr/app navanchauhan/usd-from-gltf:latest model.gltf model.usdz " )
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try :
copyfile ( " model.usdz " , os . path . join ( modelDirectory , ( str ( jobID ) + " .usdz " ) ) )
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except FileNotFoundError :
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print ( " Could not generate USDZ file " )
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"""
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email ( toaddr , jobID , date , description , zipArchive = zi )
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mycursor . execute ( ' UPDATE curieweb set done=1 where id= " %s " ' % ( jobID ) )
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mycon . commit ( )