Pyparsing：提取可变长度、可变内容、可变空白子字符串

Question

我需要从前列腺切除术的最终诊断报告中提取格里森评分。这些分数总是有Gleason这个词和两个数相加后得到另一个数。人类在20多年的时间里就把这些打印出来了。包括各种空格和修饰符的约定。下面是到目前为止我的巴克斯诺尔表，和两个例子记录。就前列腺切除术而言，我们正在研究上千个病例。在

我之所以使用pyparsing，是因为我在学习python，而且对我有限的regex编写经验没有什么好感。在

我的问题是：如果不解析这些最终诊断中可能存在或不存在的每一个可选数据片段，我如何提取出这些格里森评分？在

num = Word(nums)
record ::= accessionDate + accessionNumber + patMedicalRecordNum + finalDxText
accessionDate ::= num + "/" + num + "/" num
accessionNumber ::= "S" + num + "-" + num
patMedicalRecordNum ::= num + "/" + num + "-" + num + "-" + num
finalDxText ::= listOfParts + optionalComment + optionalpTNMStage
listOfParts ::= OneOrMore(part)
part ::= <multiline idiosyncratic freetext which may contain a Gleason score I want> + optionalpTNMStage
optionalComment ::= <multiline idiosyncratic freetext which may contain a Gleason score I don't want>
optionalpTNMStage ::= <multiline idiosyncratic freetext which may contain a Gleason score I don't want>


01/01/11  S11-55555 20/444-55-6666 A.  PROSTATE AND SEMINAL VESICLES, PROSTATECTOMY:                           
                                   -  ADENOCARCINOMA.                                                      

                                   TOTAL GLEASON SCORE:  GLEASON 5+4=9                                     
                                   TUMOR LOCATION:  BILATERAL                                              
                                   TUMOR QUANTITATION:  15% OF PROSTATE INVOLVED BY TUMOR                  
                                   EXTRAPROSTATIC EXTENSION:  PRESENT AT RIGHT POSTERIOR                   
                                   SEMINAL VESICLE INVASION:  PRESENT                                      
                                   MARGINS:  UNINVOLVED                                                    
                                   LYMPHOVASCULAR INVASION:  PRESENT                                       
                                   PERINEURAL INVASION:  PRESENT                                           
                                   LYMPH NODES (SPECIMENS B AND C):                                        
                                      NUMBER EXAMINED:  25                                                 
                                      NUMBER INVOLVED:  1                                                  
                                      DIAMETER OF LARGEST METASTASIS:  1.7 mm                              
                                   ADDITIONAL FINDINGS:  HIGH-GRADE PROSTATIC INTRAEPITHELIAL NEOPLASIA,   
                                      ACUTE AND CHRONIC INFLAMMATION, INTRADUCTAL EXTENSION OF INVASIVE    
                                      CARCINOMA                                                            

                                   PATHOLOGIC STAGE:  pT3b N1 MX                                           

                               B.  LYMPH NODES, RIGHT PELVIC, EXCISION:                                    
                                   -  ONE OF SEVENTEEN LYMPH NODES POSITIVE FOR METASTASIS (1/17).         

                               C.  LYMPH NODES, LEFT PELVIC, EXCISION:                                     
                                   -  EIGHT LYMPH NODES NEGATIVE FOR METASTASIS (0/8).                     
01/02/11  S11-4444 20/111-22-3333 PROSTATE AND SEMINAL VESICLES, PROSTATECTOMY:                               
                                  - ADENOCARCINOMA.                                                        
                                    GLEASON SCORE:  3 + 3 = 6 WITH TERTIARY PATTERN OF 5.                                             
                                    TUMOR QUANTITATION:  APPROXIMATELY 10% BY VOLUME.                      
                                    TUMOR LOCATION:  BILATERAL.                                            
                                    EXTRAPROSTATIC EXTENSION:  NOT IDENTIFIED.                             
                                    MARGINS:  NEGATIVE.                                                    
                                    PERINEURAL INVASION:  IDENTIFIED.                                      
                                    LYMPH-VASCULAR INVASION:  NOT IDENTIFIED.                              
                                    SEMINAL VESICLE/VASA DEFERENTIA INVASION: NOT IDENTIFIED.              
                                    LYMPH NODES:  NONE SUBMITTED.                                          
                                    OTHER:  HIGH GRADE PROSTATIC INTRAEPITHELIAL NEOPLASIA.                
                               PATHOLOGIC STAGE (pTNM):  pT2c NX.                                       

完全披露：我是一名从事研究的医生；这是我第一次真正使用python。我读过Lutz的《学习Python》，Shaw的《用艰苦的方式学习Python》，并完成了各种问题集。我在这个论坛pyparsing wiki上回顾了许多与pyparsing相关的问题，我购买并阅读了McGuire先生的《pyparsing入门》。也许我在问一个问题，当我真的应该被告知我正站在“frustation的死亡螺旋，当你不得不编写解析器时，这是如此常见”（McGuire，17）？我不知道。到目前为止，我很高兴能在一个真正的项目上工作。在

Answer 1

看看pyparsing中的SkipTo parse元素。如果为num+num=num部分定义一个pyparsing结构，那么应该能够使用SkipTo跳过“Gleason”和那个之间的任何内容。大致如下（未经测试的pseuo pyparsing）：

score = num + "+" + num + "=" num
Gleason = "Gleason" + SkipTo(score) + score

PyParsing在默认情况下会跳过空白，使用SkipTo，您可以跳过任何与所需格式不匹配的内容。在

Answer 2

gleason = re.compile("gleason\d+\d=\d")
scores = set()
for record in records:
    for line in record.lower().split("\n"):
        if "gleason" in line:
            scores.add(gleason.match(line.replace(" ", "")).group(0)[7:])

或者别的什么

Answer 3

下面是一个示例，用于提取患者数据和任何匹配的Gleason数据。在

from pyparsing import *
num = Word(nums)
accessionDate = Combine(num + "/" + num + "/" + num)("accDate")
accessionNumber = Combine("S" + num + "-" + num)("accNum")
patMedicalRecordNum = Combine(num + "/" + num + "-" + num + "-" + num)("patientNum")
gleason = Group("GLEASON" + Optional("SCORE:") + num("left") + "+" + num("right") + "=" + num("total"))
assert 'GLEASON 5+4=9' == gleason
assert 'GLEASON SCORE:  3 + 3 = 6' == gleason

patientData = Group(accessionDate + accessionNumber + patMedicalRecordNum)
assert '01/02/11  S11-4444 20/111-22-3333' == patientData

partMatch = patientData("patientData") | gleason("gleason")

lastPatientData = None
for match in partMatch.searchString(data):
    if match.patientData:
        lastPatientData = match
    elif match.gleason:
        if lastPatientData is None:
            print "bad!"
            continue
        print "{0.accDate}: {0.accNum} {0.patientNum} Gleason({1.left}+{1.right}={1.total})".format(
                        lastPatientData.patientData, match.gleason
                        )

印刷品：

^{pr2}$