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setup_class.py
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from __future__ import print_function
import os
import shutil
from os.path import dirname,join
from ase.io import read,write
import argparse
import sys
from ase.io import read,write
class isv():
def __init__(self,appname='myapp',apptype='stand_alone'):
import os
import sys
currentdir=os.getcwd()
self.appname=appname
self.apptype=apptype
self.approot=os.path.dirname(__file__)
if (currentdir==self.approot) and (apptype=='server'):
print ("It seems you are running the code from source code directory.")
sys.exit("Please run it from another directory.")
print("Initializing: ", appname)
if apptype=='stand_alone':
rmdir_list=[appname]
# destdir={'static':os.path.join(appname,'static'),}
static_path=os.path.join(appname,'static')
else:
rmdir_list=[appname,'templates']
static_path='static'
self.rmdir_list=rmdir_list
self.static=static_path
print("The following Directory will be overwritten if you continue:")
print (self.rmdir_list)
# if self.confirm_overwrite() :
for dir in self.rmdir_list :
if os.path.exists(dir): shutil.rmtree(dir,ignore_errors=True)
# os.makedirs(dir)
def setup(self,datafile,structure_file):
try:
self.setup_base()
self.setup_static()
self.setup_templates()
self.add_data(datafile)
except:
sys.exit("There was a problem in setting up directory structure.\nTry Running from a clean directory.")
try:
self.add_structures(structure_file)
except:
print("There was problem handling the Trajectory file. You will not have atomic structures in server")
pass
try:self.setup_offline_arxiv()
except:
print("There was a problem setting up the static archive. You will not be able to use static html download option")
pass
if self.apptype =="server" :
try: self.setup_cover()
except:print("Problem creating cover image. Your website will not look good but it will work !" )
shutil.copy2(os.path.join(self.approot,'server.py'),'server.py')
def setup_cover(self):
from create_cover import cover
print ("Creating Cover")
cover(self.appname)
def setup_offline_arxiv(self):
zname=self.appname+'-static-offline'
print("Setting up archive template:",zname)
if not os.path.exists('.isv'):os.mkdir('.isv')
rmpath=os.path.join('.isv','static')
if os.path.exists(rmpath):
shutil.rmtree(rmpath)
os.mkdir(rmpath)
os.mkdir(os.path.join('.isv','static','css'))
shutil.copy2(os.path.join(self.static,'css','w3.css'),os.path.join('.isv','static','css'))
shutil.copytree(os.path.join(self.static,self.appname+'-structures'),os.path.join('.isv','static',self.appname+'-structures'))
shutil.copytree(os.path.join(self.static,'jmol'),os.path.join('.isv','static','jmol'))
shutil.copy2(os.path.join(self.static,'pop.html'),os.path.join('.isv','static'))
shutil.copy2(os.path.join(self.static,'compare.html'),os.path.join('.isv','static'))
shutil.copy2(os.path.join(self.static,'loading.gif'),os.path.join('.isv','static'))
# rmpath=os.path.join('.isv','static','js')
# if os.path.exists(rmpath): shutil.rmtree(rmpath)
shutil.copy2(os.path.join(self.approot,'static','README'),os.path.join('.isv','README'))
shutil.make_archive(os.path.join(self.static,zname),'zip','.isv')
try: shutil.rmtree('.isv')
except: pass
def add_data(self,datafile):
appname=self.appname
os.mkdir(os.path.join(appname,'data'))
shutil.copy2(datafile,os.path.join(appname,'data','COLVAR'))
def add_structures(self,structure_file):
from ase.atoms import Atoms
# Split trajectory file separate xyz files
static_path=self.static
appname=self.appname
frames = read(structure_file,index=':')
dest=os.path.join(static_path,appname+'-structures')
if os.path.exists(dest): shutil.rmtree(dest)
os.mkdir(dest)
print ("Read ",len(frames)," frames from ", structure_file)
print ("Splitting frames into xyz files...")
for it,frame in enumerate(frames):
sys.stderr.write("Writing frame no %d \r: " %(it))
fn = open(os.path.join(dest,'set.{:06d}.xyz'.format(it)),'w')
symbols = Atoms(frame).get_chemical_symbols()
natoms = len(symbols)
comment=appname+' frame: '+str(it)
fn.write('%d\n%s\n' % (natoms, comment))
for s, (x, y, z) in zip(symbols, frame.positions):
fn.write('%-2s %12.2f %12.2f %12.2f\n' % (s, x, y, z))
print("\nDone !")
def setup_base(self):
print("Setting up app-base: ", self.appname)
approot=self.approot
appname=self.appname
os.makedirs(appname)
for file in ['main.py','smaplib.py','theme.yaml']:
src=os.path.join(approot,'app-base',file)
dest=os.path.join(appname,file)
if not os.path.exists(dest):
shutil.copy2(src,dest)
def setup_static(self):
print("Setting up static:", self.static)
# copy folder and file from app-base/static folder to static folder
ref_static_path=os.path.join(self.approot,'static')
static_path=self.static
if not os.path.exists(static_path):os.mkdir(static_path)
for dir in ['css','jmol']:
src=os.path.join(ref_static_path,dir)
dest=os.path.join(static_path,dir)
if not os.path.exists(dest):
shutil.copytree(src,dest)
for file in ['loading.gif','pop.html','compare.html']:
src=os.path.join(ref_static_path,file)
dest=os.path.join(static_path,file)
if not os.path.exists(dest):
shutil.copy2(src,dest)
if self.apptype=='server':
for dir in ['js']:
src=os.path.join(self.approot,'static',dir)
dest=os.path.join(static_path,dir)
if not os.path.exists(dest):
shutil.copytree(src,dest)
# src=os.path.join(self.approot,'static','css')
# src_files = os.listdir(src)
# for file_name in src_files:
# full_file_name = os.path.join(src, file_name)
# dest=os.path.join(static_path,'css')
# if (os.path.isfile(full_file_name)):
# shutil.copy2(full_file_name, dest)
def setup_templates(self):
print("Setting up templates")
approot=self.approot
appname=self.appname
src=os.path.join(approot,'app-base','templates')
dest=os.path.join(appname,'templates')
if not os.path.exists(dest):
shutil.copytree(src,dest)
if self.apptype=='server':
src=os.path.join(approot,'templates')
dest='templates'
if not os.path.exists(dest):
shutil.copytree(src,dest)
def confirm_overwrite(self):
yes = {'yes','y', 'ye', ''}
no = {'no','n'}
while True:
try:
choice = raw_input("Continue ? [y/n]").lower()
except:
choice = input().lower()
if choice in yes:
return True
elif choice in no:
return False
else:
sys.stdout.write("Please respond with 'yes' or 'no'")