workflow.py

import subprocess 
import sys 
import glob 
import os 
import shutil
from datetime import datetime
     
class magpie_workflow:
    def __init__(self):
        self.outdir='./OUTDIR/'
        self.poscars_dir = './input_poscars/'
        self.poscars_ext = '*'
        self.prop_dir    = './Magpie/lookup-data/'
        self.magpie_exec = ['java', '-jar', './Magpie/Magpie.jar']

    def OWrite(self,s,pr=True,wr=True):
        s = '\n'+str(datetime.now())+' ::  '+s
        if pr:  
            print(s)
            sys.stdout.flush()
        if wr:
            with open(os.path.join(self.outdir,'out.workflow.txt'),'a') as fout:  
                fout.write(s)

     
    def run_magpie(self): 
        self.runfile_ext = [self.mag_ip_file+'.in','|', 'tee', self.mag_ip_file+'.out'] 

        self.OWrite('May check out.workflow.txt for Magpie messages')

        with open(os.path.join(self.outdir,'out.workflow.txt'),'a') as fout: 
            with open(os.path.join(self.outdir,'err.worksflow.txt'),'a') as ferr: 
                out=subprocess.call(self.magpie_exec+self.runfile_ext, stdout=fout, stderr=ferr) 
     
     
    def input_gen(self): 
        self.mag_feats_file  = os.path.join(self.outdir,'features_generated_magpie.csv')
        magpie_comms = ['data = new data.materials.CrystalStructureDataset', \
                        'timer start', 'data import '+self.poscars_dir, 'timer elapsed', \
                        'data attributes properties directory '+self.prop_dir, \
                        'data attributes properties add set general', \
                        'data target local_reference', \
                        'attr = new utility.tools.BatchAttributeGenerator 1000 DelimitedOutput ,', \
                        'timer start', 'attr write '+self.mag_feats_file+' $data', \
                        'timer elapsed', 'exit'] 
     
        self.mag_ip_file = os.path.join(self.outdir,'generate-attributes')
        with open(self.mag_ip_file+'.in','w') as fout: 
            fout.write('\n'.join(magpie_comms)) 
        self.OWrite('Magpie input file created as '+self.mag_ip_file+'.in')
     
    def reference_gen(self):
        if os.path.isfile(self.poscars_dir+'properties.txt'):
            os.remove(self.poscars_dir+'properties.txt') 
        if not self.poscars_ext.startswith('*'): 
            self.poscars_ext = '*'+self.poscars_ext 
     
        files_list = glob.glob(os.path.join(self.poscars_dir,self.poscars_ext)) 
        files_list = [' '.join([item.split('/')[-1],str(i)]) for i,item in enumerate(files_list)]
        title      = [' '.join(['filename','local_reference'])]
        with open(os.path.join(self.poscars_dir+'properties.txt'),'w') as fout:
            fout.write('\n'.join(title+files_list))


    def post_process(self):
        if not os.path.isfile(self.mag_feats_file):
            print('magpie output file not found. Run Magpie first')
            return
        data  = open(self.mag_feats_file,'r').read().strip().split('\n')
        data  = [item.strip().split(',') for item in data]
        title = ','.join(['filename']+data[0][:-1])
        data  = data[1:] 
        self.processed_feats_file = os.path.join(self.outdir,'features_processed_final.csv')

        ref_data = open(os.path.join(self.poscars_dir+'properties.txt'),'r').read().strip().split('\n')[1:]
        for i,item in enumerate(data):
            out_index = int(round(float(item[-1])))
            data[i]   = ','.join([ref_data[out_index].strip().split(' ')[0]] + item[:-1])

        with open(self.processed_feats_file,'w') as fout:
            data = '\n'.join([title]+data)
            fout.write(data)
         
     
     
def main():
    print ('Initializing the workflow class')
    workflow = magpie_workflow()

    if os.path.isdir('./OUTDIR'):
        shutil.rmtree('./OUTDIR')
    os.mkdir('./OUTDIR')

    workflow.OWrite('Generating property.txt file')
    workflow.reference_gen()

    workflow.OWrite('Generating Magpie input commands file ')
    workflow.input_gen()

    workflow.OWrite('Calling Magpie with the input script.. ')
    workflow.run_magpie()

    workflow.OWrite('Finished Magpie generation. Now post-processing')
    workflow.post_process()

    workflow.OWrite('Done')

main()