Codido.py

#!/usr/bin/env python

import argparse
from pathlib import Path
import os
import boto3
import zipfile
import shutil
import openslide
import logging
from logging import FileHandler
import time
import sys
import tifffile

class Codido:
	
	def __init__(self,arguments,root):
		
		self.root=root
		self.parser = argparse.ArgumentParser()
		self.parser.add_argument("--input", help="input")
		self.parser.add_argument("--output", help="output")
		self.parser.add_argument("--codido", help="running on codido")
		for arg,help in arguments:
			self.parser.add_argument("--"+arg, help=help)
		self.args = self.parser.parse_args()
		self.file=None
		

		
			
		#self.input_folder="."
		
		
		
		
		
		if self.args.codido == 'False' or  self.args.codido is None:
			cwd = os.getcwd()
			print(cwd)
			if cwd=="/app":
				self.root=cwd+"/"

			self.input_folder_path=self.root+"inputs/"
			self.output_folder_path =self.root+"outputs"
			
		else:
			self.root="./"
			#os.chdir("./app/")
			#self.input_folder_path=os.path.join(os.sep, 'app', 'inputs/')
			#self.output_folder_path = os.path.join(os.sep, 'app', 'outputs')
			self.input_folder_path="/app/inputs/"
			self.output_folder_path = "/app/outputs"
			self.input_file_path = os.path.join(self.input_folder_path, self.args.input.split('_SPLIT_')[-1])
			print(self.input_file_path)
			
			s3 = boto3.client('s3')
			s3.download_file(os.environ['S3_BUCKET'], self.args.input,  self.input_file_path)
			
	def logging(self,logfilefolder=None):
		if logfilefolder is not None:
			timestr = time.strftime("%Y%m%d-%H%M%S")
			self.logfilefolder=logfilefolder+"/log-"+timestr+".txt"
			self.file = open(self.logfilefolder, "w")
		else:
			self.logfilefolder=None
			self.file = None
			
	def write(self, data):
		if data is not None:
			if self.file is not None:
				self.file.write(str(data))
			print(data)	
					
	def copylocalinputs(self):
		file=self.getinputfile()
		if file is None:
			for folder_name, subfolders, filenames in os.walk(self.root+'localinputs/'):
				for filename in filenames:
					file_path=folder_name+"/" + filename 
					basename=os.path.basename(file_path)
					self.input_file_path=self.input_folder_path+"/"+basename
					print(file_path)
					print(self.input_file_path)
					shutil.copyfile(file_path,self.input_file_path)
					return
		
				
		
	def svstopng(self,file_name):
		img=openslide.OpenSlide(file_name)
		print('img read')
		print(img.dimensions)
		img=img.read_region((0,0),level=0,size=img.dimensions)
		print('img read done')	
		basename=Path(file_name).stem
		out_image_path=self.input_folder_path + basename+'.png'
		os.remove(file_name)
		img.save(out_image_path) #create png file
		#os.remove(file_name) #remove svs file
		file_name = out_image_path
		return file_name
		
	def svstotiff(self,file_name):
		#img=openslide.OpenSlide(file_name)
		img=tifffile.imread(file_name)
		print('img read')
		#print(img.dimensions)
		#img=img.read_region((0,0),level=0,size=img.dimensions)
		print('img read done')	
		basename=Path(file_name).stem
		out_image_path=self.input_folder_path + basename+'.tif'
		#os.remove(file_name)
		#img.save(out_image_path) #create png file
		tifffile.imwrite(out_image_path, img, photometric='rgb',bigtiff=True)
		#os.remove(file_name) #remove svs file
		file_name = out_image_path
		return file_name
		
	def getinputfile(self):#return first file found in inputs folder
		for folder_name, subfolders, filenames in os.walk(self.input_folder_path):
			for filename in filenames:
				file_path=folder_name+"/" + filename 
				return file_path
			
		return None
	
	def getinputfiles(self):#return first file found in inputs folder
		filelist=[]
		for folder_name, subfolders, filenames in os.walk(self.input_folder_path):
			for filename in filenames:
				file_path=filename 
				filelist.append(file_path)
		return filelist
		
	def unzip(self,filepath=None,dst=None):
		
		
		if filepath is None:
			filepath=self.input_file_path
		print("zip filepath "+ filepath)
		if dst is None:
			dst=self.input_folder_path
		
		f=Path(filepath)
		if f.suffix==".zip":
			print("unzip "+filepath+" to "+dst)	
			with zipfile.ZipFile(filepath, 'r') as zip_ref:
				zip_ref.extractall(dst)
			os.remove(filepath)
	
	def uploadfiles(self):
		zip_name = self.output_folder_path + '.zip'
		print(zip_name)
		with zipfile.ZipFile(zip_name, 'w', zipfile.ZIP_DEFLATED) as zip_ref:
			for folder_name, subfolders, filenames in os.walk(self.output_folder_path):
				for filename in filenames:
					file_path = os.path.join(folder_name, filename)
					zip_ref.write(file_path, arcname=os.path.relpath(file_path, self.output_folder_path))
		print('zip file created')

		file_stats = os.stat(zip_name)
		
	

		if self.args.codido == 'True':
			
			#config = TransferConfig(multipart_chunksize=200000)
			s3 = boto3.client('s3')
			#s3.upload_file(zip_name, os.environ['S3_BUCKET'], args.output, Config=config)
			s3.upload_file(zip_name, os.environ['S3_BUCKET'], self.args.output)		
	
	def cleanupimages(self,path=None):
		if path is None:
			path=self.input_folder_path
			
		# delete files moved from input folder to test folder
		for folder_name, subfolders, filenames in os.walk(path):
			for filename in filenames:
				file_path=folder_name+"/" + filename 
				os.unlink(file_path)