Python : 如何有效地导航 XML 子节点？

Question

我正在尝试从 XML 中提取某些数据点并尝试了两个选项...

使用 ElementTree 处理 XML 格式
使用 xmltodict 处理字典

这是我目前得到的，

代码

# Packages
# --------------------------------------
import xml.etree.ElementTree as ET

# XML Data
# --------------------------------------
message_xml = \
'<ClinicalDocument> \
    <code code="34133-9" displayName="Summarization of Episode Note"/> \
    <title>Care Summary</title> \
    <recordTarget> \
        <patientRole> \
            <id assigningAuthorityName="LOCAL" extension="L123456"/> \
            <id assigningAuthorityName="SSN" extension="788889999"/> \
            <id assigningAuthorityName="GLOBAL" extension="G123456"/> \
            <addr use="HP"> \
                <streetAddressLine>1000 N SOME AVENUE</streetAddressLine> \
                <city>BIG CITY</city> \
                <state>NA</state> \
                <postalCode>12345-1010</postalCode> \
                <country>US</country> \
            </addr> \
            <telecom nullFlavor="NI"/> \
            <patient> \
                <name use="L"> \
                    <given>JANE</given> \
                    <given>JOE</given> \
                    <family>DOE</family> \
                </name> \
            </patient> \
        </patientRole> \
    </recordTarget> \
</ClinicalDocument>'

# Get Tree & Root
# --------------------------------------
tree = ET.ElementTree(ET.fromstring(message_xml))
root = tree.getroot()

# Iterate
# --------------------------------------
for node in root:

    tag = node.tag
    attribute = node.attrib

    # Get ClinicalDocument.code values
    if tag == 'code':
        document_code_code = attribute.get('code')
        document_code_name = attribute.get('displayName')

    else:
        pass

    # Get ClinicalDocument.recordTarget values
    if tag == 'recordTarget':

        for child in node.iter():

            # Multiple <id> tags
            record_target_local = ??
            record_target_ssn = ??
            record_target_global = ??

            # Multiple <given> tags
            record_target_name_first = ??
            record_target_name_middle = ??
            record_target_name_last = ??

    else:
        pass

预期输出

document_code,document_name,id_local,id_ssn,id_global,name_first, name_middle,name_last
34133-9,Summarization of Episode Note,L123456,788889999,G123456,JANE,JOE,DOE

可接受的输出

document_code,document_name,id_type,id,name_first,name_middle,name_last
34133-9,Summarization of Episode Note,LOCAL,L123456,JANE,JOE,DOE
34133-9,Summarization of Episode Note,SSN,788889999,JANE,JOE,DOE
34133-9,Summarization of Episode Note,GLOBAL,G123456,JANE,JOE,DOE

问题

如何有效地导航下有多个子节点的子节点？
如何处理重复标签（例如：<id>、<given>）？

Answer 1

How to efficiently navigate child-nodes with multiple child-nodes under them?

导航 XML 的一个好方法是使用 XPath. ElementTree has limited XPath support, but it appears good enough for what you need. If you end up needing to use more complicated XPath, I'd suggest using XPath in lxml。

How to handle duplicate tags (ex: <id>, <given>)?

这取决于您需要对这些元素做什么。例如，如果您希望每个 id 元素有单独的行，则需要遍历每个元素（在 ElementTree 中使用 findall() 或在 lxml 中使用 xpath()）。

如果您只需要一个值（文本或属性值），则需要将其缩小到 XPath 中的单个元素。

例如，assigningAuthorityName 属性值等于 LOCAL 的 id 元素将是 id[@assigningAuthorityName='LOCAL'].

given 元素有点棘手；你怎么知道一个是名字，一个是中间名？我能看到的唯一方法是位置；第一个 given (given[1]) 是名字，第二个 given (given[2]) 是第二个名字。你保证总是有两个 given 元素吗？如果没有，您可能需要做一些检查或 try/except 语句以获得所需的输出。

此外，由于您正在创建 csv 输出，我建议使用 csv module; specifically DictWriter。

这将允许您将 XML 中的值存储在字典中以写入行。您可以为新行创建字典的新副本，同时保持公共值（如 document_code 和 document_name）。

这是一个将为每个 recordTarget 创建新行的示例。

XML 输入 (input.xml)

<ClinicalDocument> 
    <code code="34133-9" displayName="Summarization of Episode Note"/> 
    <title>Care Summary</title> 
    <recordTarget> 
        <patientRole> 
            <id assigningAuthorityName="LOCAL" extension="L123456"/> 
            <id assigningAuthorityName="SSN" extension="788889999"/> 
            <id assigningAuthorityName="GLOBAL" extension="G123456"/> 
            <addr use="HP"> 
                <streetAddressLine>1000 N SOME AVENUE</streetAddressLine> 
                <city>BIG CITY</city> 
                <state>NA</state> 
                <postalCode>12345-1010</postalCode> 
                <country>US</country> 
            </addr> 
            <telecom nullFlavor="NI"/> 
            <patient> 
                <name use="L"> 
                    <given>JANE</given> 
                    <given>JOE</given> 
                    <family>DOE</family> 
                </name> 
            </patient> 
        </patientRole> 
    </recordTarget>
</ClinicalDocument>

Python

import csv
import xml.etree.ElementTree as ET
from copy import deepcopy

values_template = {"document_code": "", "document_name": "", "id_local": "", "id_ssn": "",
                   "id_global": "", "name_first": "", "name_middle": "", "name_last": ""}

with open("output.csv", "w", newline="") as csvfile:
    csvwriter = csv.DictWriter(csvfile, delimiter=",", quoting=csv.QUOTE_MINIMAL,
                               fieldnames=[name for name in values_template])
    csvwriter.writeheader()

    tree = ET.parse('input.xml')

    values_template["document_code"] = tree.find("code").get("code")
    values_template["document_name"] = tree.find("code").get("displayName")

    for target in tree.findall("recordTarget"):

        values = deepcopy(values_template)

        values["id_local"] = target.find("patientRole/id[@assigningAuthorityName='LOCAL']").get("extension")
        values["id_ssn"] = target.find("patientRole/id[@assigningAuthorityName='SSN']").get("extension")
        values["id_global"] = target.find("patientRole/id[@assigningAuthorityName='GLOBAL']").get("extension")
        values["name_first"] = target.find("patientRole/patient/name/given[1]").text
        values["name_middle"] = target.find("patientRole/patient/name/given[2]").text
        values["name_last"] = target.find("patientRole/patient/name/family").text

        csvwriter.writerow(values)

CSV 输出 (output.csv)

document_code,document_name,id_local,id_ssn,id_global,name_first,name_middle,name_last
34133-9,Summarization of Episode Note,L123456,788889999,G123456,JANE,JOE,DOE

这是另一个示例，将为每个 recordTarget/patientRole/id...

创建一个新行

Python

import csv
import xml.etree.ElementTree as ET
from copy import deepcopy

values_template = {"document_code": "", "document_name": "", "id": "",
                   "name_first": "", "name_middle": "", "name_last": ""}

with open("output.csv", "w", newline="") as csvfile:
    csvwriter = csv.DictWriter(csvfile, delimiter=",", quoting=csv.QUOTE_MINIMAL,
                               fieldnames=[name for name in values_template])
    csvwriter.writeheader()

    tree = ET.parse('input.xml')

    values_template["document_code"] = tree.find("code").get("code")
    values_template["document_name"] = tree.find("code").get("displayName")

    for target in tree.findall("recordTarget"):

        values = deepcopy(values_template)

        values["name_first"] = target.find("patientRole/patient/name/given[1]").text
        values["name_middle"] = target.find("patientRole/patient/name/given[2]").text
        values["name_last"] = target.find("patientRole/patient/name/family").text

        for role_id in target.findall("patientRole/id"):
            values["id"] = role_id.get("extension")
            csvwriter.writerow(values)

CSV 输出 (output.csv)

document_code,document_name,id,name_first,name_middle,name_last
34133-9,Summarization of Episode Note,L123456,JANE,JOE,DOE
34133-9,Summarization of Episode Note,788889999,JANE,JOE,DOE
34133-9,Summarization of Episode Note,G123456,JANE,JOE,DOE

Python : 如何有效地导航 XML 子节点？

Python : How to navigate XML sub-nodes efficiently?

python

xml

lxml

elementtree

xmltodict