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Copy pathMSMDRParser.py
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MSMDRParser.py
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import pandas as pd
import numpy as np
# For regex
import re
import regex
import NumWords
import os
import json
from NumWords import text2int
import math
from sklearn import tree
from collections import Counter
from datetime import datetime
from lifelines import KaplanMeierFitter
import matplotlib.pyplot as plt
import seaborn as sns
from mlxtend.evaluate import mcnemar
# This first part should remain commented-out. I recieved the entire dump of narratives from the MSMDR, and parsed out the ones that contain
# path reports. Other ones appear to be medication notes? Worth looking into. Either way, I'm pulling out the narratives that have "Accession #" in them,
# as path reports seem to have. To avoid loading the 4gb and growing file of narratives, I'm just saving the panels. I'll re-open that.
# ndiData = pd.read_csv("/Users/bholmes/Desktop/DeleteMeSoon/MSMDR Narratives/FullNarratives.csv",low_memory=False)
# ndiDataWithReports = ndiData[ndiData['description'].str.contains("Accession #")]
# ndiDataWithReports.to_csv("~/Desktop/DeleteMeSoon/MSMDR Narratives/PathReports.csv", index=False)
# Now beginning the sorting out!
pathReports = pd.read_csv("/Users/bholmes/Desktop/DeleteMeSoon/MSMDR Narratives/PathReports.csv", low_memory=False)
accessions = ["hm19-2748", "pm19-1054", "hm19-2796", "hm19-2673", "pm19-625", "hm19-1526", "pm19-620", "pm19-628", "hm19-1533", "hm19-1543", "hm19-1548", "hm19-1537", "hm19-1551", "pm19-639",
"hm19-1348",
"hm19-1327", "pm19-640", "hm19-1546", "hm19-1570", "pm19-664", "hm19-1558", "pm19-647", "pm19-644", "hm19-1518", "hm19-1559", "hm19-1590", "pm19-650", "pm19-652", "hm19-1584",
"hm19-1596",
"hm19-1600", "hm19-1495", "hm19-1616", "hm19-1591", "hm19-1574", "hm19-1577", "pm19-661", "pm19-665", "pm19-589", "hm19-1568", "pm19-614", "hm19-1562", "pm19-666", "pm19-670",
"hm19-1588",
"pm19-663", "hm19-1607", "pm19-671", "hm19-1620", "hm19-1585", "hm19-1513", "hm19-1614", "hm19-1622", "hm19-1674", "hm19-1604", "hm19-2207", "hm19-2236", "pm19-934", "hm19-2250",
"hm19-2271", "hm19-2251", "pm19-935", "hm19-2262", "pm19-933", "hm19-2608", "hm19-2611", "hm19-2613", "hm19-2620", "hm19-2632", "hm19-2631", "hm19-2601", "hm19-2432", "hm19-2625",
"pm19-800",
"pm19-512", "pm19-534", "hm19-1366", "hm19-1364", "hs19-21822", "hm19-100013", "hs19-21218", "hm19-1415", "pm19-571", "hm19-1393", "pm19-566", "pm19-563", "pm19-550", "pm19-574",
"pm19-572",
"pm19-569", "hm19-1429", "hm19-1425", "hm19-1445", "hm19-1398", "hm19-1368", "pm19-584", "hm19-1418", "hm19-1384", "hm19-1386", "hm19-1385", "hm19-1403", "hm19-1413", "pm19-603",
"hs19-21744",
"hm19-1435", "hm19-1441", "hm19-1294", "pd19-335", "hm19-1840", "hm19-1829", "hm19-1838", "hm19-1834", "hm19-1847", "hm19-1871", "hm19-1865", "hm19-1864", "pm19-749", "hm19-1802",
"hm19-1792",
"hm19-1624", "hm19-1898", "pm19-680", "hm19-1676", "pm19-781", "hm19-1884", "pm19-760", "hm19-1912", "hm19-1868", "hm19-1869", "hm19-1922", "pm19-752", "pm19-753", "pm19-754",
"hm19-1878",
"hm19-1879", "pm19-738", "hm19-1911", "hm19-1927", "pm19-632", "hm19-1785", "hm19-1887", "pm19-748", "pm19-761", "hm19-1899", "hm19-1891", "hm19-1900", "hm19-1903", "pm19-769",
"hm19-1889",
"pm19-768", "hm19-1974", "hm19-1962", "hm19-1935", "pm19-780", "hm19-1929", "hm19-1800", "hm19-1953", "hm19-1939", "hm19-1850", "hm19-1931", "hm19-1943", "hm19-1950", "hm19-1936",
"pd19-557",
"hm19-1811", "hs19-29632", "pm19-448", "pm19-807", "hm19-1991", "hm19-1972", "hm19-1945", "pm19-789", "pm19-790", "pm19-810", "hm19-1925", "hm19-1967", "hm19-1982", "hm19-1940",
"hm19-1987",
"pm19-802", "pm19-826", "hm19-1892", "hm19-1986", "hm19-1949", "hm19-2019", "hm19-2003", "pm19-804", "hm19-1930", "hm19-1615", "hm19-2002", "gd19-1421", "hs19-30666", "hs19-31041",
"hm19-1979",
"pm19-817", "hs19-31627", "hm19-2006", "pm19-814", "hm19-2004", "hm19-2020", "hm19-2011", "hm19-2058", "pm19-799", "hm19-2036", "hm19-2041", "hm19-2043", "pm19-787", "pm19-759",
"hm19-100025",
"pm19-891", "hm19-2183", "hm19-2176", "hm19-2192", "pm19-904", "hm19-100027", "hm19-2142", "pm19-884", "hm19-1581", "hs19-34624", "hm19-2169", "hm19-2167", "hm19-2476", "hm19-2448",
"hm19-2485", "hm19-2496", "hm19-2493", "hm19-2497", "hm19-2901", "hm19-2891", "hm19-2906", "pm19-1086", "hs19-43285", "hs19-43157", "hm19-2859", "hm19-2879", "hm19-2908", "hm19-2838",
"hm19-2880", "pm19-1082", "pm19-1088", "hm19-2883", "hm19-2888", "pm19-1090", "ws19-9732", "hm19-2716", "pm19-1051", "hm19-2742", "hm19-2685", "pm19-1057", "hm19-2699", "hm19-2729",
"hm19-2709", "hm19-2731", "hm19-2714", "hm19-2781", "hm19-2907", "hm19-2821", "hm19-2820", "hm19-2328", "pm19-973", "hm19-2307", "hm19-2354", "hm19-2337", "hm19-2355", "hm19-2357",
"hm19-2358", "hm19-2365", "hm19-2367", "hm19-2373", "pm19-987", "hm19-2214", "hm19-2202", "pm19-898", "hm19-2188", "hm19-2210", "hm19-2238", "hm19-2239", "pm19-932", "pm19-931",
"pd19-530",
"pm19-955", "hm19-2721", "pm19-1006", "pm19-1005", "pm19-1077", "hm19-100015", "hm19-2798", "hm19-2869", "hm19-2817", "pm19-1075", "pm19-1076", "hm19-2754", "hm19-2793", "hm19-2812",
"hm19-2837", "hm19-2810", "pm19-1056", "hm19-2802", "hm19-2773", "hm19-2794", "hm19-2677", "hm19-2610", "hm19-2791", "hm19-2349", "hm19-1995", "hm19-2386", "hm19-2945", "pm19-1109",
"hm19-2918", "hm19-2923", "hm19-1438", "hm19-1420", "hm19-1462", "hm19-1452", "hm19-1439", "hs19-23316", "hm19-1484", "hm19-1453", "hm19-1401", "pm19-595", "hm19-1455", "hs19-22479",
"hm19-1481", "pm19-596", "hm19-1459", "hm19-1483", "hs19-23191", "hm19-1448", "hm19-1417", "hm19-1527", "hm19-1487", "pm19-600", "hm19-1497", "hm19-1389", "hm19-1470", "hm19-567",
"hm19-1501",
"hm19-1426", "hs19-23697", "hs19-21495", "hm19-1500", "hm19-1431", "pm19-618", "hm19-830", "hm19-1521", "hm19-1494", "hm19-1528", "pm19-559", "hs19-23229", "hm19-1465", "hs19-24441",
"hm19-1502", "hm19-1499", "pm19-616", "pm19-627", "hm19-1517", "hm19-1511", "hm19-1510", "pm19-611", "hm19-1535", "hs19-23263", "pm19-993", "hm19-2641", "hm19-2648", "hm19-2660",
"pm19-1050", "hm19-2569", "hm19-2253", "pm19-822", "pm19-967", "hm19-2291", "hm19-1613", "pm19-945", "pm19-941", "hm19-2268", "hm19-2769", "hm19-2719", "hm19-2778", "hm19-2782",
"hm19-2774",
"pm19-1067", "pm19-1068", "hm19-2797", "hm19-2767", "hm19-2786", "pm19-1064", "hm19-2301", "hm19-2304", "pm19-966", "hm19-2197", "pm19-971", "pm19-963", "pm19-1031", "hm19-2552",
"hs19-38440",
"hm19-2576", "hm19-2582", "hm19-2561", "pm19-902", "hm19-2588", "hm19-2592", "pm19-1029", "hm19-2600", "hm19-2605", "hm19-2579", "hm19-2573", "hm19-2483", "hs19-39756", "pm19-890",
"hm19-2174", "hm19-2261", "hm19-2323", "hm19-2327", "hm19-2315", "hm19-2317", "pm19-990", "hm19-2340", "hm19-2377", "hm19-2379", "hm19-2387", "hm19-2361", "pm19-937", "hm19-2376",
"hm19-2394",
"hm19-2401", "hm19-2398", "pm19-996", "hm19-2415", "hs19-30768", "pm19-939", "hm19-2233", "pm19-951", "pm19-952", "ms19-9293", "hm19-2284", "pm19-1022", "hm19-2474", "hm19-2392",
"hm19-2362",
"hm19-2893", "pm19-1093", "hm19-2739", "hm19-2745", "hm19-2596", "hm19-2955", "pm19-1053", "hm19-2818", "hm19-2949", "hm19-2453", "pm19-956", "as19-14142", "hm19-2502", "hm19-2321",
"hm19-2396", "hm19-2306", "hm19-2469", "hm19-2501", "hm19-2503", "hm19-2507", "hm19-2509", "hm19-2517", "pm19-1026", "hm19-2513", "hm19-2515", "hm19-2479", "hm19-2471", "pm19-1025",
"pm19-1017", "hm19-2531", "hm19-2522", "pd19-669", "hm19-2372", "hm19-2443", "hs19-38010", "pm19-1009", "hm19-2417", "hm19-2433", "hs19-38174", "pm19-1011", "hm19-2297", "hm19-2437",
"hm19-2442",
"hm19-2445", "hm19-2439", "hm19-2289", "hm19-2278", "hm19-2285", "hm19-2280", "pm19-948", "hm19-2277", "hm19-2266", "hm19-2422", "hm19-2462", "hm19-2724", "hm19-2759",
"hm19-2762", "hm19-2768", "hm19-2779", "hm19-2763", "hm19-2948", "hm19-2836", "pm19-1108", "hm19-2904", "hm19-2912", "hs19-37101", "hs19-36645", "hm19-2329", "hm19-2359", "hm19-2313",
"pm19-974", "pm19-980", "pm19-984", "hs19-35739", "hm19-2303", "hm19-100035", "lm19-100002", "hm19-2828", "pm19-1079", "hm19-2826", "hm19-2854", "hm19-2850", "hm19-2858", "hm19-2842",
"hm19-2890", "hm19-2921", "hm19-2808", "hm19-1738", "hm19-1750", "hm19-1682", "hm19-1743", "hm19-1822", "hm19-1716", "hm19-1729", "pm19-624", "hm19-1741", "hm19-1760", "pm19-723",
"hm19-1765",
"pm19-722", "hm19-1723", "hm19-1824", "pm19-682", "pm19-709", "pm19-690", "hm19-1689", "hm19-1712", "hm19-1745", "hm19-1713", "hm19-1764", "hm19-1823", "hm19-1749",
"hm19-100023", "hm19-1799", "pm19-700", "hm19-1795", "hm19-1821", "hm19-1815", "hm19-1816", "hm19-1740", "hm19-1673", "hm19-1778", "hm19-1791", "hm19-1737", "hm19-1718", "hm19-1710",
"hm19-1773", "hm19-1786", "hm19-1789", "pm19-733", "hm19-1768", "hm19-1746", "hm19-1814", "pm19-716", "hm19-1835", "pm19-741", "pm19-743", "hm19-1857", "hm19-1858", "hm19-1836",
"hm19-1841",
"hm19-1976", "hm19-2008", "hm19-2025", "hm19-2052", "hm19-2048", "pm19-833", "hm19-2018", "hm19-1715", "ls19-100010", "hm19-100030", "hm19-1861", "pm19-843", "hm19-2066", "hm19-2065",
"pm19-846", "hm19-2072", "pm19-852", "hm19-2081", "hm19-2084", "pm19-832", "pm19-845", "pm19-812", "hm19-2015", "hm19-1827", "hm19-2068", "pm19-838", "hm19-2097", "hm19-2109",
"hm19-2088",
"hm19-2086", "pm19-857", "hm19-2095", "hm19-2089", "hs19-32061", "pm19-851", "hm19-2077", "hm19-2090", "hm19-1422", "hm19-2112", "hm19-2111", "hm19-2107", "hs19-33222", "hm19-2106",
"pm19-868", "hm19-2102", "pm19-864", "hm19-2076", "pd19-584", "hm19-2225", "pm19-1111", "hm19-1638", "hm19-1645", "hm19-1629", "hm19-1648", "hm19-1632", "hm19-100021", "pm19-693",
"pm19-597",
"pm19-708", "hm19-1680", "hm19-1647", "pm19-683", "hm19-1677", "hm19-1686", "hm19-1704", "pm19-691", "pm19-687", "pm19-703", "hm19-1681", "hm19-1685", "hm19-1734", "hm19-1612",
"hm19-1751",
"hm19-1690", "hm19-1790", "hm19-1691", "hm19-1720", "hm19-1759", "pm19-721", "pm19-714", "hm19-1728", "hm19-1594", "pm19-711", "hm19-1669", "pm19-697", "hm19-2350", "hm19-2679",
"hm19-2678",
"hm19-2694", "hm19-2675", "hm19-2680", "hm19-2639", "pm19-1052", "pm19-1045", "hm19-2692", "hm19-2671", "hm19-2690", "hm19-2684", "hm19-2286", "pm19-1021", "hm19-2717", "hm19-2630",
"hm19-2662", "hm19-2563", "hm19-2383", "as19-14533", "pd19-725", "hm19-2461", "hm19-2451", "hm19-2425", "hm19-2446", "hm19-2310", "hm19-2452", "hm19-2534", "hm19-2528", "hm19-2546",
"hm19-2529",
"hm19-2530", "hm19-2536", "hm19-2548", "pm19-672", "hm19-1626", "hm19-1635", "hm19-1634", "pm19-675", "hm19-1561", "hs19-25198", "hs19-25412", "hs19-25536", "hm19-100051",
"hm19-1394", "hm19-1504", "hm19-1671", "hs19-24870", "hm19-1659", "hm19-1665", "hs19-26793", "hm19-1675", "hm19-1655", "hm19-2635", "hm19-2638", "hm19-2651", "pm19-1048", "hm19-2667",
"hm19-2668", "hm19-2672", "hm19-2467", "pm19-1040", "hm19-2516", "hm19-2597", "hm19-2598", "hm19-2542", "pm19-1060", "hm19-2839", "hm19-2166", "hm19-2135", "hs19-33554", "hm19-2061",
"hm19-2151", "hm19-2127", "hm19-2136", "hm19-2139", "hm19-2138", "ls19-6874", "hm19-2128", "pm19-871", "hm19-2645", "pm19-927", "pm19-926", "pm19-917", "pm19-916", "pm19-915",
"pm19-914",
"hm19-2205", "hm19-2103", "hm19-2231", "hm19-2224", "hm19-2228", "hm19-2200", "hm19-2221", "hm19-2185", "pm19-764", "pm19-922", "hm19-2219", "ps19-4587", "hm19-1705", "hm18-2587",
"pm19-918",
"pm19-860", "hm19-2177", "hm19-1490", "hm19-2218", "pm19-887", "pm19-962", "hm19-2299", "hm19-2290", "hm19-2300", "hm19-2302", "hs19-33826", "hm18-1613", "hm18-1733", "hm18-1910",
"hm18-1833",
"hm18-1644", "hm18-1754", "hm18-1804", "pm18-619", "hm18-1658", "hm18-1665", "hm18-1678", "pm18-626", "hm18-1873", "pm18-556", "pm18-605", "hm18-1755", "pm18-560", "pm18-536",
"pm18-614", "pm18-617",
"hm18-1640", "hm18-1650", "hm18-1805", "pd18-638", "hm18-1682", "hm18-1880", "hm18-1745", "pm18-596", "hm18-1674", "pm18-592", "hm18-1751", "pm18-588", "pm18-632", "hm18-1701",
"pm18-628",
"hm18-1803", "hm18-1839", "hm18-1633", "hm18-1802", "hm18-1886", "hm18-1706", "hm18-1857", "pd18-703", "hm18-1868", "hm18-1749", "pm18-621", "hm18-1734", "pm18-587", "pm18-538",
"hm18-1629",
"hm18-1631", "hm18-1793", "pm18-557", "hm18-1750", "hm18-1843", "hm18-1822", "hm18-1680", "pm18-634", "hm18-1595", "hm18-1579", "pm18-561", "hm18-1854", "pm18-488", "hm18-1675",
"pm18-597",
"hm18-1699", "hm18-1661", "hm18-1835", "pm18-585", "hm18-1630", "hm18-1643", "hm18-1304", "hm18-1729", "hm18-1782", "hm18-1559", "hs18-26051", "hm18-1627", "hm18-1700", "pd18-640",
"hm18-1829",
"hm18-1716", "hm18-1846", "pm18-618", "hm18-1847", "gd18-1916", "hm18-1636", "pm18-608", "hm18-1818", "hm18-1791", "hm18-1679", "hm18-1764", "hm18-1684", "hm18-1897", "pm18-574",
"hs18-24899",
"pm18-604", "hm18-1743", "hm18-1667", "hm18-1628", "hm18-1625", "hm18-1730", "hm18-1815", "hm18-1717", "hm18-1720", "pm18-624", "pm18-589", "hm18-1759", "hm18-1864", "pm18-565",
"pm18-639",
"pm18-564", "hm18-1774", "hm18-1617", "hm18-1753", "hm18-1849", "pm18-573", "hm18-1688", "hm18-1639", "hm18-1881", "hm18-1827", "hm18-1861", "hm18-1856", "hm18-1748", "hm18-1760",
"hm18-1419",
"hm18-1660", "pm18-563", "pm18-572", "hm18-1762", "hm18-1776", "hm18-1612", "hm18-1600", "hm18-1761", "hm18-1832", "hm18-1798", "hm18-1654", "hm18-1599", "hm18-1692", "hm18-1844",
"hm18-1792",
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"hm18-729", "hm18-940", "pm18-230", "hm18-987", "hm18-857", "hm18-781", "hm18-964", "hm18-825", "hm18-956", "hm18-961", "hm18-915", "hm18-974", "pm18-233", "hm18-737", "hm18-782",
"hm18-772",
"hm18-835", "hm18-874", "hm18-935", "hm18-862", "hs18-9003", "hm18-732", "hm18-901", "pm18-263", "hs18-9454", "hm18-823", "hm18-830", "pd18-282", "hm18-798", "hm18-683", "hm18-728",
"hm18-893",
"hm18-769", "hm18-900", "pm18-271", "hm18-733", "hm18-887", "hm18-930", "pm18-212", "hm18-617", "hm18-807", "hm18-927", "hm18-790", "hm18-899", "hm18-783", "hm18-973", "hm18-839",
"hm18-929",
"hm18-872", "hs18-11111", "hm18-678", "hm18-883", "hm18-928", "pm18-207", "hm18-906", "hm18-882", "pm18-226", "hm18-306", "hm18-908", "pm18-394", "pm18-389", "hm17-2026", "hm18-1125",
"hm18-1121",
"hm18-1205", "hm18-1176", "hm18-975", "hm18-1171", "pm18-260", "pm18-335", "hm18-1046", "hm18-1198", "hm18-1021", "hm18-1057", "pm18-283", "pm18-342", "hm18-1025", "hm18-1199",
"hm18-1094",
"hm18-1202", "hm18-1104", "pd18-357", "hm18-1127", "pm18-292", "hm18-1058", "hm18-1246", "hm18-1022", "hm18-1064", "pm18-361", "hm18-1088", "hm18-1150", "hm18-1092", "hm18-1003",
"hm18-1099",
"hm18-1188", "pm18-276", "hm18-1017", "hm18-1036", "pm18-390", "hm18-1013", "pm18-267", "hm18-993", "pm18-330", "pm18-324", "hm18-1081", "hm18-1235", "pm18-299", "pm18-346", "hm18-1091",
"hm18-1147",
"pm18-379", "hm18-1238", "pm18-364", "pm18-287", "hm18-1182", "hm18-1050", "pm18-317", "pm18-288", "hm18-1031", "hm18-1044", "hm18-1060", "hm18-1070", "hm18-1113", "hm18-1100",
"pm18-331",
"hm18-1096", "pm18-358", "pm18-401", "pm18-274", "hm18-1236", "pm18-306", "hm18-1172", "hm18-1249", "pm18-297", "hm18-1080", "pm18-301", "hm18-1203", "hm18-1052", "pm18-347", "hm18-925",
"pm18-338",
"pd18-274", "pm18-308", "hm18-1153", "hm18-1023", "hm18-774", "hm18-1001", "hm18-1119", "hm18-1019", "hm18-1117", "hm18-1252", "pm18-332", "hm18-1116", "hm18-1093", "pm18-286",
"hm18-963",
"pm18-258", "hm18-1005", "hm18-1059", "hm18-991", "hm18-1224", "hm18-1072", "hm18-1006", "hm18-1095", "pm18-303", "hm18-914", "hm18-1128", "hm18-1161", "hm18-1053", "hm18-1257",
"hm18-1056",
"hm18-1014", "hm18-1163", "hm18-1108", "pm18-318", "hm18-1111", "hm18-1038", "pm18-354", "pm18-310", "hm18-1137", "hm18-100010", "hm18-1112", "hm18-954", "pm18-285", "hm18-972",
"pm18-312",
"hm18-1120", "pd18-366", "hm18-962", "hm18-1041", "hs18-16189", "hm18-944", "pm18-305", "hm18-1144", "hm18-949", "pm18-392", "hm18-1009", "hm18-913", "pm18-126", "pm18-323", "hm18-1156",
"pm18-295",
"pm18-356", "hm18-948", "hm18-1077", "pm18-316", "ls18-2573", "hm18-1179", "hm18-1174", "hm18-1216", "hm18-978", "hm18-1115", "hm18-981", "hm18-1237", "hm18-1045", "lm18-100008",
"pm18-328",
"hm18-1063", "hm18-1033", "pm18-294", "hm18-1020", "hm18-992", "pm18-340", "hm18-1008", "pm18-404", "hm18-934", "hm18-1016", "hm18-1051", "hm18-986", "pm18-375", "hm18-918", "hm18-1181",
"pm18-391",
"hm18-1054", "hm18-1015", "hs18-15970", "pm18-296", "pm18-253", "hm18-1177", "hm18-1097", "hm18-1206", "hm18-1043", "hm18-1129", "hm18-968", "pm18-290", "hm18-1106", "hm18-2344",
"pm18-792",
"hm18-2450", "hm18-2349", "pm18-857", "hm18-2424", "hm18-2463", "hm18-2353", "pm18-818", "pm18-850", "hm18-2457", "pm18-829", "pm18-819", "hm18-2360", "hm18-2422", "hm18-2453",
"hm18-2405",
"hm18-2396", "hm18-2254", "hs18-37603", "hm18-2342", "hm18-2515", "pm18-782", "hm17-2489", "hm18-2426", "pm18-830", "hm18-2365", "hm18-2433", "hm18-2403", "pm18-827", "pm18-821",
"pm18-799",
"hm18-2341", "pm18-811", "pm18-855", "hm18-2260", "hm18-2443", "hm18-2534", "hm17-2601", "pm18-803", "pm18-843", "hm18-2295", "hm18-2268", "hm18-2356", "pm18-816", "pm18-844",
"hm18-2435",
"hm18-2215", "pm18-831", "pm18-801", "pm18-806", "hm18-2418", "hm18-2472", "hm18-2408", "hm18-2331", "hm18-2441", "hm18-2266", "hm18-2326", "hm18-2381", "hm18-2398", "hm18-2437",
"hs18-37063",
"hm18-2310", "lm18-100002", "hm18-2466", "pm18-840", "hm18-2364", "pm18-832", "hm18-2494", "hm18-2291", "hm18-2391", "hm18-2461", "hm18-2277", "hm18-2467", "hm18-2400", "hm18-2417",
"hm18-2385",
"hm18-2357", "hm18-2328", "hm18-2445", "hm18-2384", "pm18-838", "hm18-2174", "hm18-2476", "hm18-2399", "hm18-2401", "hm18-2413", "hm18-2375", "hm18-2434", "pm18-824", "pm18-777",
"pm18-793",
"hm18-2334", "hm18-2308", "hm18-2289", "hm18-1000503", "pm18-822", "pm18-848", "pm18-847", "hm18-2414", "pm18-876", "hm18-2498", "hm18-2429", "hm18-2325", "hm18-2460", "pm18-872",
"pm18-784",
"hm18-2347", "pm18-858", "hm18-2479", "pm18-796", "hm18-2313", "pm18-865", "pm18-837", "hm18-2354", "hm18-2488", "pm18-791", "hm18-2351", "hm18-2447", "hm18-2449", "hm18-2321",
"pm18-853",
"hm18-2502", "pm18-813", "hm18-2352", "hm18-2478", "hm18-2420", "hm18-2439", "hs18-36217", "hm18-2432", "hm18-2371", "hm18-2410", "hm18-2297", "pm18-860", "hs18-36539", "hm18-2446",
"hm18-2474",
"hm18-2335", "hm18-2299", "hm18-2392", "hm18-2513", "hm18-2311", "hm18-2455", "hm18-2292", "pm18-786", "pm18-808", "ms18-9523", "hm18-2389", "hm18-2290", "pm18-863", "pm18-861",
"pm18-879",
"hm18-2258", "pd18-867", "hm18-2329", "hm18-1543", "hm18-1596", "hm18-1488", "hm18-1309", "pm18-452", "pm18-532", "hm18-1439", "hm18-1371", "hm18-1378", "pm18-528", "hm18-1496",
"hm18-1469",
"hm18-1570", "hm18-1535", "hm18-1169", "pm18-537", "pm18-482", "hm18-1422", "hm18-1614", "hm18-1545", "hm18-1490", "hm18-1494", "pm18-505", "pm18-530", "pm18-483", "hm18-1555",
"hm18-1531",
"hm18-1430", "pm18-492", "hm18-1479", "hm18-1526", "hm18-1413", "pd18-556", "hm18-1606", "hm18-1460", "pm18-479", "hm18-1424", "pm18-164", "hm18-1471", "hm18-1593", "pm18-507",
"hm18-1414",
"hm18-1317", "pm18-525", "pm18-468", "hm18-1576", "pm18-493", "hm18-1431", "hm18-1428", "hm18-1468", "pm18-476", "hm18-1618", "hm18-1556", "hm18-1456", "hm18-1394", "hm18-1503",
"hm18-1557",
"hm18-1482", "hm18-1477", "hm18-1580", "hm18-1542", "hm18-1500", "hm18-1511", "pm18-539", "hm18-1567", "pm18-509", "hm18-1352", "hm18-1499", "hm18-308", "hm18-1426", "hm18-1635",
"pm18-498",
"hm18-1467", "hm18-1504", "hm18-1506", "hm18-1498", "hm18-1551", "hm18-1429", "hm18-1323", "hm18-1395", "hm18-1432", "hm18-1461", "hm18-1473", "hm18-1546", "pm18-519", "hm18-1291",
"hm18-1569",
"hm18-1566", "pd18-535", "hm18-1459", "hm18-1434", "hm18-1451", "hm18-1320", "hm18-1547", "hm18-1474", "hm18-1328", "pm18-531", "hm18-1515", "pm18-529", "pm18-499", "hm18-1444",
"pm18-474",
"hm18-1558", "pm18-466", "pm18-475", "pm18-510", "pm18-521", "pm18-535", "pm18-490", "pm18-517", "hm18-1548", "hm18-1392", "hm18-1560", "hm18-1611", "hm18-1538", "pm18-435", "hm18-1544",
"hm18-1508",
"hm18-1472", "pm18-552", "pm18-511", "pd18-525", "pm18-485", "hm18-1470", "hm18-1568", "pm18-534", "hm18-1484", "hm18-1590", "hm18-1446", "hm18-1452", "hm18-1289", "pd18-511",
"hm18-1437",
"hs18-23540", "hm18-1520", "hm18-1539", "pm18-549", "hm18-1415", "pm18-459", "hm18-1550", "hm18-1457", "hm18-1501", "hm18-1440", "pm18-523", "hm18-1292", "hm18-1399", "hm18-1463",
"hm18-1487",
"hm18-1502", "hs18-21166", "hm18-1390", "hm18-1376", "hm18-1442", "hm18-1464", "hs18-21534", "hm18-1510", "hm18-1433", "hm18-1509", "hm18-1619", "hm18-1497", "hm18-983", "hm18-1492",
"hm18-1462",
"hm18-1530", "hs18-19170", "pm18-467", "hm18-1541", "pm18-533", "ls18-4061", "pm18-501", "hm18-2614", "hm18-2505", "hm18-2615", "pm18-903", "pm18-886", "pm18-890", "hs18-37860",
"hm18-2657",
"hm18-2597", "hm18-2703", "hm18-2589", "pm18-921", "pm18-941", "pm18-887", "hm18-2578", "hm18-2633", "hm18-2725", "hm18-2580", "hm18-2692", "hm18-2641", "hm18-2720", "pm18-874",
"hm18-2672",
"pm18-900", "hm18-2716", "pm18-945", "hm18-2440", "pm18-907", "hm18-2508", "pm18-935", "hm18-2510", "hm18-2727", "pm18-962", "hm18-2386", "hm18-2711", "hm18-1642", "hm18-2512",
"pm18-939",
"hm18-2537", "hm18-2516", "hs18-41615", "hm18-2624", "hm18-2656", "hm18-100021", "hm18-2609", "hm18-2501", "hm18-2601", "pm18-877", "pm18-944", "hm18-2665", "hm18-2525", "hm18-2629",
"pm18-927",
"hm18-2556", "hm18-2707", "hm18-2640", "pm18-937", "lm18-100003", "hm18-2648", "pm18-933", "ms18-9254", "hm18-2593", "hm18-2518", "hm18-2575", "hm18-2676", "pm18-946", "hm18-2487",
"hm18-2605",
"hm18-2613", "hm18-2619", "hm18-2710", "hm18-2636", "hm18-2557", "hm18-1178", "hm17-2188", "hm18-2709", "pm18-885", "hm18-2591", "hm18-2520", "hm18-2704", "hs18-42653", "hm18-2632",
"pm18-947",
"hm18-2740", "hm18-2653", "hm18-2687", "pm18-749", "hm18-2628", "hm18-2506", "hm18-2671", "hm18-2547", "hm18-2714", "hm18-2754", "hm18-2607", "pd18-990", "hm18-2554", "hm18-2532",
"hs18-39595",
"pm18-969", "hm18-2599", "hm18-2553", "hm18-2483", "pm18-878", "hm18-2675", "pm18-931", "pm18-870", "hm18-2695", "pm18-911", "hm18-2113", "hm18-2550", "hm18-2533", "hm18-1505",
"hm18-2705",
"pm18-949", "hm18-2594", "hm18-2585", "hm18-1970", "hm18-2555", "pm18-901", "pm18-920", "hm18-2680", "hm18-2618", "hm18-2500", "lm18-100005", "hm18-2560", "pm18-867", "hm18-2522",
"hm18-2529",
"hm18-2611", "hm18-2616", "hm18-2577", "hm18-2635", "pm18-859", "hm18-2592", "hs18-39371", "hm18-2495", "hm18-2542", "hm18-2562", "hm18-2701", "pm18-913", "pm18-942", "hs18-41717",
"pm18-891",
"hm18-2625", "hm18-2645", "pm18-948", "pm18-909", "hm18-2623", "hm18-2756", "hm18-2503", "hm18-2428", "hm18-2561", "pm18-889", "hm18-2684", "hm18-2670", "hm18-2345", "pm18-928",
"hm18-2646",
"hm18-2603", "pm18-902", "hm18-2664", "hm18-2685", "pm18-896", "hm18-2493", "pm18-943", "hm18-2642", "hm18-2667", "pm18-839", "hm18-2582", "pm18-964", "pm18-888", "hm18-2566",
"hm18-2486",
"pm18-881", "hm18-2647", "hm18-2683", "hm18-2559", "hm18-2749", "hm18-100090", "hm18-2729", "hm18-2620", "hm18-2373", "hm18-2643", "hm18-2528", "hm18-2721", "pm18-926", "hm18-2650",
"pm18-919",
"pm18-841", "hs18-41871", "hm18-2327", "hm18-2568", "hm18-2651", "hm18-2524", "hm18-2491", "hm18-1277", "pm18-434", "hm18-1242", "pm18-372", "hm18-1149", "pm18-403", "hm18-1410",
"pm18-463",
"pm18-472", "hm18-1357", "hm18-1364", "hm18-1258", "pm18-416", "hm18-1374", "hm18-1148", "hm18-1337", "hm18-1241", "hm18-1253", "hm18-1322", "pm18-441", "hm18-100012", "pm18-471",
"pm18-430",
"hm18-1195", "hm18-1298", "hm18-1363", "hm18-1272", "pm18-447", "pm18-427", "hm18-1302", "hm18-1190", "hm18-1281", "pm18-429", "hs18-21171", "pm18-357", "hm18-1367", "hs18-18641",
"hm18-1284",
"hm18-1165", "hm18-1369", "hm18-1226", "pm18-408", "hm18-1307", "pm18-449", "pm18-425", "pm18-439", "pm18-419", "hm18-1209", "hm18-1221", "hm18-1167", "pm18-374", "hm18-1361",
"hm18-1285",
"pm18-455", "hm18-1308", "hm18-1315", "hm18-1244", "hm18-1286", "hm18-1287", "pm18-431", "hm18-1409", "hm18-1354", "pm18-460", "hm18-1280", "hm18-1274", "hm18-1314", "pm18-426",
"pm18-418",
"hm18-1343", "hm18-1295", "pm18-377", "hm18-1389", "pm18-453", "hm18-1251", "pm18-424", "hm18-1360", "hs18-16045", "hm18-1194", "hm18-1276", "hm18-1250", "hm18-1297", "hm18-1261",
"hm18-1387",
"hm18-1316", "hm18-1213",
"hm18-1229", "hm18-1275", "pm18-451", "hm18-1381", "pm18-409", "hm18-1310", "hm18-1273", "hm18-1301", "pm18-355", "hm18-1330", "pm18-407", "pm18-397", "hm18-1398", "hm18-1255",
"hm18-1411",
"hm18-1260",
"hm18-1154", "hm18-1346", "hm18-1265", "pm18-442", "hm18-1391", "pm18-360", "hm18-1396", "hm18-1222", "hm18-1313", "pm18-473", "hm18-1269", "hm18-1402", "pm18-410", "hs18-15656",
"pm18-448",
"hm18-1248",
"pm18-353", "hm18-1162", "hm18-1350", "hm18-1348", "hm18-1356", "pm18-469", "hm18-1151", "hm18-1254", "hm18-1232", "hm18-1225", "hm18-1270", "hm18-1341", "hm18-1370", "ls18-3638",
"pm18-378",
"pm18-420"]
testTypes = []
for x in range(0, len(pathReports['description'])):
print(x, ' of ', len(pathReports['description']))
lower = pathReports['description'][x].lower()
lower = re.sub(' +', ' ', lower)
splitReport = lower.split('\n')
if 'patient name:' not in lower:
print(lower)
continue
index = [idx for idx, s in enumerate(splitReport) if 'patient name:' in s][0]
indexTT = index-1
testType = splitReport[indexTT]
# Pull out test type
while testType == '' or 'amended' in testType.lower():
indexTT = indexTT-1
testType = splitReport[indexTT].strip()
if testType.endswith('.'):
testType = testType[:-1]
if 'her2' in lower or 'her-2' in lower or 'her 2' in lower:
testTypes.append(testType)
testTypes = list(set(testTypes))
print(testTypes)