#! /usr/bin/env python
"""
 Import sample properties from a text file.  
"""
print "########################################################"

import os
import glob
import re
import time
import shutil, sys

import xml.etree.ElementTree as ET
from xml.etree import ElementTree

from time import *
from datetime import datetime
import calendar

from ch.systemsx.cisd.openbis.generic.shared.managed_property.structured import ElementFactory
from ch.systemsx.cisd.openbis.generic.shared.managed_property.structured import XmlStructuredPropertyConverter

ATR_NAME='name'
ATR_CODE = "code"
ATR_CONC = "concentration"
DATE_ATTRIBUTE = 'date'
PERSON_ATTRIBUTE = 'person'
COMMENT_ENTRY_ELEMENT_LABEL = 'commentEntry'
LINK_LABEL = "link"
CODE_LABEL = "code"
CONC_LABEL = "concentration"
DATE_LABEL = 'Date'
PERSON_LABEL = 'Person'
COMMENT_TEXT_LABEL = 'Comment Text'
NAME_LABEL='name'

chemicals_list=[]
concentration_list=[]
buffers_list=[]
buffers_concentration_list =[]
date_list=[]
person_list=[]
comment_text_list=[]
antibodies_list=[]


def create_openbis_timestamp():
	tz=localtime()[3]-gmtime()[3]
	d=datetime.now().timetuple()
	timestamp = (calendar.timegm(d)*1000)
	return timestamp
   

def process(transaction):
	incomingPath = transaction.getIncoming().getAbsolutePath()

###PARSE XML FILE############################################################


	textfile = open(incomingPath, "r")
	tree = ET.parse(textfile)
	root = tree.getroot()

	
	
	for path in [ './Identifier']:
	  node = tree.find(path)
	  if node.text != "":
		sample_name = node.text
	  else:
		node.text = ""  
		
	  
	for path in [ './Experiment']:
	  node = tree.find(path)
	  if node.text != "":
		experiment_name = node.text
	  else:
		node.text = ""  
	
	
	   
	chemicals_found = False
	for child in root.getchildren():
		if child.tag == 'Chemicals':
			chemicals_found = True	  
			def Chemicals():
				for path in [ './Chemicals']:
					node = tree.find(path)
					if node.text is not None:
						chemicals = node.text
						tokens = chemicals.split(',')
						for token in tokens:
							if re.search(":", token): 
								token = token.split(':')
								chemical_name = token[0]
								chemical_concentration=token[1]
								chemicals_list.append(chemical_name)
								concentration_list.append(chemical_concentration)
							else:
								chemical_name=token  
								chemical_concentration = "n.a."
								chemicals_list.append(chemical_name)
								concentration_list.append(chemical_concentration)
					else:
						node.text = "n.a." 	  
				return chemicals_list, concentration_list	  
	
			Chemicals()
		if not chemicals_found:
			chemicals= None
			chemical_name = None
			chemical_concentration = None
			chemicals_list = None
			concentration_list = None


	buffers_found = False
	for child in root.getchildren():
		if child.tag == 'Solutions_Buffers':
			buffers_found = True
			def Buffers():
				  for path in [ './Solutions_Buffers']:
					node = tree.find(path)
					if node.text is not None:
					  buffers = node.text
					  tokens = buffers.split(',')
					  for token in tokens:
						if re.search(":", token): 
						  token = token.split(':')
						  buffer_name = token[0]
						  buffer_concentration=token[1]
						  buffers_list.append(buffer_name)
						  buffers_concentration_list.append(buffer_concentration)
						else:
						  buffer_name=token  
						  buffer_concentration = "n.a."
						  buffers_list.append(buffer_name)
						  buffers_concentration_list.append(buffer_concentration)
					else:
					  node.text = "n.a." 	  
				  return buffers_list, buffers_concentration_list
				  
			Buffers()	  
		if not chemicals_found:
			buffers= None
			buffer_name = None
			buffer_concentration = None
			buffers_list = None
			buffers_concentration_list = None
	


	antibodies_found = False
	for child in root.getchildren():
		if child.tag == 'Antibodies':
			antibodies_found = True
			def Antibodies():
				for path in [ './Antibodies']:
					node = tree.find(path)
					if node.text is not None:
						antibodies = node.text
						tokens = antibodies.split(',')
						for token in tokens:
							if re.search(":", token): 
								token = token.split(':')
								antibody_name = token[0]
								antibody_concentration=token[1]
								antibodies_list.append(antibody_name)
							else:
								antibody_name=token  
								antibody_concentration = "n.a."
								antibodies_list.append(antibody_name)
					else:
						node.text = "n.a." 	  
		  
				return antibodies_list
			Antibodies()
		if not antibodies_found:
			antibodies= None
			antibody_name = None
			antibody_concentration = None
			antibodies_list = None



	
	
	xmlcomments_found = False
	for child in root.getchildren():
		if child.tag == 'XMLCOMMENTS':
			xmlcomments_found = True
			for path in [ './XMLCOMMENTS']:
				node = tree.find(path)
				if node.text is not None:
					comment_text_list= node.text
				else:
					comment_text_list = None 
		if not xmlcomments_found:
			comment_text_list = None



	elementFactory = ElementFactory()
	
	propertyConverter = XmlStructuredPropertyConverter(elementFactory);
	


###IMPORT CHEMICALS####################################################################


	def _createChemicalsSampleLink(chemicals_list, concentration_list):
		"""
		   Creates sample link XML element for sample with specified 'code'. The element will contain
		   given code as 'code' attribute apart from standard 'permId' attribute.
		   
		   If the sample doesn't exist in DB a fake link will be created with the 'code' as permId.
		   
		   @return: sample link XML element as string, e.g.:
		   - '<Sample code="FRP1" permId="20110309154532868-4219"/>'
		   - '<Sample code="FAKE_SAMPLE_CODE" permId="FAKE_SAMPLE_CODE"/>
		"""
		if chemicals_list is not None:
		  chemicalPath= "/YEAST_LAB/" + chemicals_list
		  permId =transaction.getSample(chemicalPath).getSample().getPermId()
		  name = transaction.getSample(chemicalPath).getPropertyValue("NAME")
		  if not permId:
			permId = chemicals_list
		  sampleLink = elementFactory.createSampleLink(permId)
		
		  sampleLink.addAttribute(ATR_CODE, chemicals_list)
		  sampleLink.addAttribute(ATR_NAME, name)
		  sampleLink.addAttribute(ATR_CONC, concentration_list)
				 
		return sampleLink    
		
	
	"""
	Example input:
	
	FRC1: 2nM, FRC2, FRC3: 4nM, FRC4
	"""
	
	
	def updateChemicalsFromBatchInput(chemicals_list, concentration_list):
		elements = []
		input = chemicals_list
		input2 = concentration_list
		if input != "":
		   for i, j in zip(chemicals_list,concentration_list): #zip is used to iterate over two lists in parallel
				sampleLink = _createChemicalsSampleLink(i.strip(), j.strip())
				elements.append(sampleLink)
		return propertyConverter.convertToString(elements)


###IMPORT SOLUTION BUFFERS####################################################################


	def _createBuffersLink(buffers_list, buffers_concentration_list):
		"""
		   Creates sample link XML element for sample with specified 'code'. The element will contain
		   given code as 'code' attribute apart from standard 'permId' attribute.
		   
		   If the sample doesn't exist in DB a fake link will be created with the 'code' as permId.
		   
		   @return: sample link XML element as string, e.g.:
		   - '<Sample code="FRP1" permId="20110309154532868-4219"/>'
		   - '<Sample code="FAKE_SAMPLE_CODE" permId="FAKE_SAMPLE_CODE"/>
		"""
		if buffers_list is not None:
		  buffersPath= "/YEAST_LAB/" + buffers_list
		  permId =transaction.getSample(buffersPath).getSample().getPermId()
		  if not permId:
			permId = buffers_list
		  name = transaction.getSample(buffersPath).getPropertyValue("NAME")
		  sampleLink = elementFactory.createSampleLink(permId)
		
		  sampleLink.addAttribute(ATR_CODE, buffers_list)
		  sampleLink.addAttribute(ATR_NAME, name)
		  sampleLink.addAttribute(ATR_CONC, buffers_concentration_list)

		 
		return sampleLink    
		
	
	"""
	Example input:
	
	FRC1: 2nM, FRC2, FRC3: 4nM, FRC4
	"""
	
	
	def updateBuffersFromBatchInput(buffers_list, buffers_concentration_list):
		elements = []
		input = buffers_list
		input2 = buffers_concentration_list
		if input != "":
		   for i, j in zip(buffers_list,buffers_concentration_list): #zip is used to iterate over two lists in parallel
				sampleLink = _createBuffersLink(i.strip(), j.strip())
				elements.append(sampleLink)
		return propertyConverter.convertToString(elements)
		
###IMPORT MEDIA####################################################################


	def _createAntibodiesLink(antibodies_list):
		"""
		   Creates sample link XML element for sample with specified 'code'. The element will contain
		   given code as 'code' attribute apart from standard 'permId' attribute.
		   
		   If the sample doesn't exist in DB a fake link will be created with the 'code' as permId.
		   
		   @return: sample link XML element as string, e.g.:
		   - '<Sample code="FRP1" permId="20110309154532868-4219"/>'
		   - '<Sample code="FAKE_SAMPLE_CODE" permId="FAKE_SAMPLE_CODE"/>
		"""
		if antibodies_list is not None:
		  antibodiesPath= "/YEAST_LAB/" + antibodies_list
		  permId =transaction.getSample(antibodiesPath).getSample().getPermId()
		  if not permId:
			permId = antibodies_list
		  name = transaction.getSample(antibodiesPath).getPropertyValue("NAME")
		  sampleLink = elementFactory.createSampleLink(permId)
		
		  sampleLink.addAttribute(ATR_CODE, antibodies_list)
		  sampleLink.addAttribute(ATR_NAME, name)
				 
		return sampleLink    
		
	
	"""
	Example input:
	
	FRC1: 2nM, FRC2, FRC3: 4nM, FRC4
	"""
	
	
	def updateAntibodiesFromBatchInput(antibodies_list):
		elements = []
		input = antibodies_list
		if input != "":
		   for i in antibodies_list: 
				sampleLink = _createAntibodiesLink(i.strip())
				elements.append(sampleLink)
		return propertyConverter.convertToString(elements)			
		
		
###IMPORT COMMENTS####################################################################
	
	

	def _createCommentsSampleLink(comment_text_list):
		#if comment_text_list is not None:
		commentEntry = elementFactory.createElement(COMMENT_ENTRY_ELEMENT_LABEL)
				
		user = transaction.getUserId()
		commentEntry.addAttribute(PERSON_ATTRIBUTE, user)
		commentEntry.addAttribute(DATE_ATTRIBUTE,str(create_openbis_timestamp()))
		commentEntry.setData(comment_text_list)
		print "comments", comment_text_list  
		return commentEntry   
	
	def updateCommentsFromBatchInput(comment_text_list):
		elements = []
		input = comment_text_list
		#if input is not None:
		commentEntry = _createCommentsSampleLink(comment_text_list)
		elements.append(commentEntry)
		return propertyConverter.convertToString(elements)
	
	_createCommentsSampleLink(comment_text_list)
	
	
	

###CREATE New sample with related properties#################################################

	newSampleIdentifier="/YEAST_LAB/" + sample_name
	newSample=transaction.createNewSample(newSampleIdentifier,'WESTERN_BLOTTING')
	
	
	exp = transaction.getExperiment(experiment_name)
	newSample.setExperiment(exp)

	""" Set antibodies, chemicals, buffers as parents for the sample"""	

	antibodyId_list =[]
	if antibodies_list != None:
		for antibody in antibodies_list:
			antibodyIdentifier = "/YEAST_LAB/" + antibody.strip()
			antibodyId_list.append(antibodyIdentifier)

	chemicalId_list =[]
	if chemicals_list != None:
		for chemical in chemicals_list:
			chemicalIdentifier = "/YEAST_LAB/" + chemical.strip()
			chemicalId_list.append(chemicalIdentifier)
		
	bufferId_list =[]
	if buffers_list != None:
		for buffer in buffers_list:
			bufferIdentifier = "/YEAST_LAB/" + buffer.strip()
			bufferId_list.append(bufferIdentifier)
		
	parents_list = antibodyId_list + chemicalId_list + bufferId_list
	newSample.setParentSampleIdentifiers(parents_list)	
	
	
	for child in root:
		if child.tag == "Chemicals":
			newSample.setPropertyValue("CHEMICALS",updateChemicalsFromBatchInput(chemicals_list,concentration_list))
		if child.tag == "Solutions_Buffers":
			newSample.setPropertyValue("SOLUTIONS_BUFFERS",updateBuffersFromBatchInput(buffers_list,buffers_concentration_list))
		if child.tag == "Antibodies":
			newSample.setPropertyValue("ANTIBODIES",updateAntibodiesFromBatchInput(antibodies_list))
		if child.tag == "XMLCOMMENTS":
			newSample.setPropertyValue("XMLCOMMENTS", updateCommentsFromBatchInput(comment_text_list))
		if child.tag != "Identifier" and child.tag !="Experiment" and child.tag != "Chemicals" and child.tag != "XMLCOMMENTS" and child.tag != "Solutions_Buffers" and child.tag != "Antibodies":
			if child.text != None:
				newSample.setPropertyValue(child.tag, child.text)
			else:
				child.text= ""
				newSample.setPropertyValue(child.tag, child.text)