import_facs.py

#! /usr/bin/env python
"""
  Script for uploading FACS data for the YeastLab.

  FACS data are organized in one main folder which contains a folder with the username. Inside this folder there are folders and subfolders that correspond 
  to different FACS experiments. Inside the username folder there is a file called data_structure.ois which contains the structure of the FACS experiments.
  This script creates a sample in openBIS for each FACS experiment and uploads the corresponding data in one dataset connected to the samples.
  The space where the sample should go is detected from the username. The project and experiment are detected from the name of the folders given by the user.
  The FACS experiment should be named by the users as PROJECT-EXPERIMENT-SAMPLE.  
  The script also automatically assign teh FREEFORM_TABLE_STATE property, which creates tables in the ELN UI. If there are plates in the directories (these are directories named "96 Wells") 
  it creates 96-well plates table (8x12); if there are .fcs files it creates a table with one row and as many columns as there are .fcs files. Multiple tables for one sample can be created.

  
"""

import os, glob, re, csv, time, shutil
from java.io import File
from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1 import SimpleImageDataConfig, ImageMetadata, Location
from ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto import Geometry
from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1 import SimpleImageContainerDataConfig, ChannelColor
from loci.formats import ImageReader
from time import *
from datetime import *

print "##############################################################"

def process(transaction):
	incoming = transaction.getIncoming()
	
	projectNameList=[]
	experimentNameList=[]
	sampleNameList=[]
	directoryToImportList=[]
	userNameList=[]


	# read the data_structure.ois file to get the structure of the FACS experiment. The name of the FACS experiment contains project, experiment, sample info for openBIS.
	def getProjExpSample(incoming):
		for userName in os.listdir(incoming):
			if not userName.startswith('.'):
				dataStructure = incoming + "/" + userName + "/data_structure.ois" 
				f = open(dataStructure)
				lines=f.readlines()
				for line in lines:
					path = re.split("/", line)
					directoryToImport= incoming +"/"+ "/".join(path[:-1])
					projectName = re.split("-",path[-1])[0]
					if len(re.split("-",path[-1])) == 3: #in some cases the user specifies the sample name in the file name
						experimentName = re.split("-",path[-1])[1]
						sampleNameFile = re.split("-",path[-1])[2]
						sampleName = re.split("_properties.oix", sampleNameFile)[0]
					elif len(re.split("-",path[-1]))==2: #in some cases the sample name is not in the file name, and it will be generated by openBIS
						experimentNameProp = re.split("-",path[-1])[1]
						experimentName = re.split("_properties.oix", experimentNameProp)[0]
						sampleName = "na" 
					

					projectNameList.append(projectName)
					experimentNameList.append(experimentName)
					sampleNameList.append(sampleName)
					directoryToImportList.append(directoryToImport)
					userNameList.append(userName)

		return userNameList, projectNameList, experimentNameList, sampleNameList, directoryToImportList
					

	getProjExpSample(incoming.getPath()) 


	#get the space according to the user	
	for user in set (userNameList):
		if user == "pontia":
			space = "AARON"
		elif user == "ottozd":
			space = "DIANA"
		elif user == "elfstrok":
			space = "KRISTINA"

	#get or create the project
	for proj in set(projectNameList):
		project = transaction.getProject("/" + space + "/" + proj)
		if not project:
	 		project = transaction.createNewProject("/" + space + "/" + proj)

	#get or create the experiment
	for exp in set(experimentNameList):
		experiment = transaction.getExperiment("/" + space  + "/" + proj + "/" + exp)
		if not experiment:
  			experiment = transaction.createNewExperiment("/" + space  + "/" + proj + "/" + exp, "ANALYSIS")	

  	#create te samples, upload the datasets for the sample, create the tables for the ELN UI
  	for sample, directory in zip(sampleNameList,directoryToImportList):
		
		fcs_number = len(glob.glob1(directory, '*.fcs'))
		plate_number= len(glob.glob1(directory, '96 Well*'))  		
		table =[]
  		ilist=[]
  		
  		for i in range(1,fcs_number+1):
  			ilist.append(i)

  		s = "[\"" + "\",\"".join(str(x) for x in ilist) + "\"]"
 		t = "{\"name\":\"\",\"modelDetailed\":[" + s  + "],\"modelMini\":{\"rows\":[\"\"],\"columns\":" + s + "}}"
 		table.append(t)

  		
  		for p in range(1,plate_number+1):
  			t = "{\"name\":\"\",\"modelDetailed\":[[null,null,null,null,null,null,null,null,null,null,null,null],[null,null,null,null,null,null,null,null,null,null,null,null],[null,null,null,null,null,null,null,null,null,null,null,null],[null,null,null,null,null,null,null,null,null,null,null,null],[null,null,null,null,null,null,null,null,null,null,null,null],[null,null,null,null,null,null,null,null,null,null,null,null],[null,null,null,null,null,null,null,null,null,null,null,null],[null,null,null,null,null,null,null,null,null,null,null,null]],\"modelMini\":{\"rows\":[null,null,null,null,null,null,null,null],\"columns\":[null,null,null,null,null,null,null,null,null,null,null,null]}}"
  			table.append(t)
  			
  		freeform_table = "[" +','.join(map(str,table)) +"]"
  		
  		if sample == "na":
  			sampleNew = transaction.createNewSampleWithGeneratedCode(space, "RESULT")
  			sampleNew.setExperiment(experiment)
  			sampleNew.setPropertyValue("FREEFORM_TABLE_STATE", freeform_table)
  		else:
  			sampleNew = transaction.createNewSample("/" + space + "/" + sample, "RESULT" )
			sampleNew.setExperiment(experiment)
			sampleNew.setPropertyValue("FREEFORM_TABLE_STATE", freeform_table)


		dataSet = transaction.createNewDataSet()
		dataSet.setDataSetType("FACS_DATA_RAW")
		dataSet.setSample(sampleNew)
		transaction.moveFile(directory, dataSet)