72 lines
3.1 KiB
Python
72 lines
3.1 KiB
Python
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#!/usr/bin/env python3
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import re
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import util
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import autoproc
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def parse_xml_rcrs(text, summary):
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summary = {row['uid']: row for row in summary}
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for patient in re.finditer(r'<Patient>(.+?)</Patient>', text, re.DOTALL):
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patient = patient.group(1)
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if (pos := patient.find('<Tumor>')) >= 0:
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data = parse_xml_items(patient[:pos])
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data['tumors'] = [parse_xml_items(tumor.group(1)) for tumor in re.finditer(r'<Tumor>(.+?)</Tumor>', patient[pos:], re.DOTALL)]
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for tumor in data['tumors']:
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acc = tumor['accessionNumberHosp']
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meta = tumor['meta'] = summary[acc[:4] + '-' + acc[4:] + '/' + tumor['sequenceNumberHospital']]
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data['name'] = meta.pop('name')
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data['last5'] = meta.pop('last5')
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else:
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data = parse_xml_items(patient)
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data['tumors'] = []
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yield data
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def parse_xml_items(text):
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return {item.group(1): item.group(2) for item in re.finditer(r'<Item naaccrId="([^"]+)">([^<]+)</Item>', text)}
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async def cmd_patients(proc, alpha, omega):
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"""Fetch patients from RCRS dump"""
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async with proc.sendline, autoproc.expect_async(proc) as expect:
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proc.sendline('^Create RCRS extract')
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async for prompt, response in expect.prompts_any({
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re.compile(r'^ Facility Identification Number \(FIN\): \d+// $'): None,
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' Select date field to be used for Start/End range: ': 'Date DX',
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re.compile(r'^ Start, Date DX: : \([^\)\r\n]+\): $'): util.vista_strftime(alpha),
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re.compile(r'^ End, Date DX: : \([^\)\r\n]+\): TODAY// $'): util.vista_strftime(omega),
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' Are these settings correct? YES// ': None,
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}, throw=True):
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proc.sendline(response)
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if prompt.index == 4:
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break
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assert await expect.endswith('\r\n --------------------------------------------------------------\r\n\r\n\r\n')
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proc.sendline() # skip delay
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assert (m := await expect.endswith('\r\n\x1a'))
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doc_rcrs = m.before
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assert await expect.endswith('\r\nDEVICE: ', timeout_settle=31)
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proc.sendline('HOME;80') # default HOME
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assert await expect.earliest('HOME(CRT)\r\n')
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summary = []
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async for prompt, response in expect.prompts_any({
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'\x07': None,
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'Type <Enter> to continue or \'^\' to exit: ': None,
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' Press \'RETURN\' to continue, \'^\' to stop: ': None,
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'Select *..Utility Options Option: ': None,
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'Select DHCP Tumor Registry Option: ': None,
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}, throw=True):
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proc.sendline(response)
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if prompt.index == 0 or prompt.index == 1:
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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))
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elif prompt.index == 4:
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break
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assert await expect.endswith('\r\nSelect Patient Information and OE/RR Option: ', '\r\nSelect Patient Information and OE/RR <TEST ACCOUNT> Option: ')
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expect.clear()
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for item in parse_xml_rcrs(doc_rcrs, summary):
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yield item
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async def cmd_tumors(proc, alpha, omega):
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async for patient in cmd_patients(proc, alpha, omega):
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tumors = patient.pop('tumors')
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for item in tumors:
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item['patient'] = patient
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yield item
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