#!/usr/bin/env python3

import re
import util
import autoproc

def parse_xml_rcrs(text, summary):
	summary = {row['uid']: row for row in summary}
	for patient in re.finditer(r'<Patient>(.+?)</Patient>', text, re.DOTALL):
		patient = patient.group(1)
		if (pos := patient.find('<Tumor>')) >= 0:
			data = parse_xml_items(patient[:pos])
			data['tumors'] = [parse_xml_items(tumor.group(1)) for tumor in re.finditer(r'<Tumor>(.+?)</Tumor>', patient[pos:], re.DOTALL)]
			for tumor in data['tumors']:
				acc = tumor['accessionNumberHosp']
				meta = tumor['meta'] = summary[acc[:4] + '-' + acc[4:] + '/' + tumor['sequenceNumberHospital']]
			data['name'] = meta.pop('name')
			data['last5'] = meta.pop('last5')
		else:
			data = parse_xml_items(patient)
			data['tumors'] = []
		yield data

def parse_xml_items(text):
	return {item.group(1): item.group(2) for item in re.finditer(r'<Item naaccrId="([^"]+)">([^<]+)</Item>', text)}

async def cmd_patients(proc, alpha, omega):
	"""Fetch patients from RCRS dump"""
	async with proc.sendline, autoproc.expect_async(proc) as expect:
		proc.sendline('^Create RCRS extract')
		async for prompt, response in expect.prompts_any({
				re.compile(r'^ Facility Identification Number \(FIN\): \d+// $'):	None,
				' Select date field to be used for Start/End range: ':				'Date DX',
				re.compile(r'^ Start, Date DX: :  \([^\)\r\n]+\): $'):				util.vista_strftime(alpha),
				re.compile(r'^   End, Date DX: :  \([^\)\r\n]+\): TODAY// $'):		util.vista_strftime(omega),
				' Are these settings correct? YES// ':								None,
			}, throw=True):
			proc.sendline(response)
			if prompt.index == 4:
				break
		assert await expect.endswith('\r\n      --------------------------------------------------------------\r\n\r\n\r\n')
		proc.sendline()	# skip delay
		assert (m := await expect.endswith('\r\n\x1a'))
		doc_rcrs = m.before
		assert await expect.endswith('\r\nDEVICE: ', timeout_settle=31)
		proc.sendline('HOME;80')	# default HOME
		assert await expect.earliest('HOME(CRT)\r\n')
		summary = []
		async for prompt, response in expect.prompts_any({
				'\x07':															None,
				'Type <Enter> to continue or \'^\' to exit: ':					None,
				'               Press \'RETURN\' to continue, \'^\' to stop: ':	None,
				'Select *..Utility Options Option: ':							None,
				'Select DHCP Tumor Registry Option: ':							None,
			}, throw=True):
			proc.sendline(response)
			if prompt.index == 0 or prompt.index == 1:
				summary.extend({k.strip(): v.strip() for k, v in row.groupdict().items()} for row in re.finditer(r'(?P<last5>[A-Z]\d{4}) (?P<name>[^\r\n]{30}) (?P<uid>[^ \r\n]+) (?P<primarySite>[^ \r\n]+) (?P<dateOfDiagnosis>\d{2}/\d{2}/\d{4})  (?P<dateCaseLastChanged>\d{2}/\d{2}/\d{4})', prompt.before))
			elif prompt.index == 4:
				break
		assert await expect.endswith('\r\nSelect Patient Information and OE/RR Option: ', '\r\nSelect Patient Information and OE/RR  <TEST ACCOUNT> Option: ')
		expect.clear()
		for item in parse_xml_rcrs(doc_rcrs, summary):
			yield item

async def cmd_tumors(proc, alpha, omega):
	async for patient in cmd_patients(proc, alpha, omega):
		tumors = patient.pop('tumors')
		for item in tumors:
			item['patient'] = patient
			yield item