为lxml xpath()中的空槽获取NA

Question

我有一个大型的xml (就是那个)：我在这里提供了一个示例：

    <?xml version="1.0" encoding="UTF-8"?>
    <hmdb xmlns="http://www.hmdb.ca">
        <metabolite>
            <normal_concentrations>
                <concentration>
                    <biospecimen>Blood</biospecimen>
                    <concentration_value>2.8 +/- 8.8</concentration_value>
                </concentration>
                <concentration>
                    <biospecimen>Feces</biospecimen>
                    <concentration_value/>
                </concentration>
                <concentration>
                    <biospecimen>Salvia</biospecimen>
                    <concentration_value>5.2</concentration_value>
                </concentration>
            </normal_concentrations>
        </metabolite>
        <metabolite>
            <normal_concentrations>
                <concentration>
                    <biospecimen>Blood</biospecimen>
                    <concentration_value>5</concentration_value>
                </concentration>
                <concentration>
                    <biospecimen>Feces</biospecimen>
                    <concentration_value/>
                </concentration>
                <concentration>
                    <biospecimen>Salvia</biospecimen>
                    <concentration_value>3-7</concentration_value>
                </concentration>
            </normal_concentrations>
        </metabolite>
    </hmdb>

我现在想拔出所有的生物果胶和concentration_value，并能够把它们联系在一起。我试着这样做：

from io import StringIO
from lxml import etree
import csv

def hmdbextract(name, file):
    ns = {'hmdb': 'http://www.hmdb.ca'}
    context = etree.iterparse(name, tag='{http://www.hmdb.ca}metabolite')
    csvfile = open(file, 'w')
    fieldnames = ['normal_concentration_spec',
                  'normal_concentration_conc']

    writer = csv.DictWriter(csvfile, fieldnames=fieldnames)
    writer.writeheader()
    for event, elem in context:
        try:
            tl = elem.xpath('hmdb:normal_concentrations/hmdb:concentration/hmdb:biospecimen/text()', namespaces=ns)
            normal_concentration_spec = '; '.join(str(e) for e in tl)
        except:
            normal_concentration_spec = 'NA'
        try:
            tl = elem.xpath('hmdb:normal_concentrations/hmdb:concentration/hmdb:concentration_value/text()', namespaces=ns)
            normal_concentration_conc = '; '.join(str(e) for e in tl)
        except:
            normal_concentration_conc = 'NA'


        writer.writerow({'normal_concentration_spec': normal_concentration_spec,
                        'normal_concentration_conc': normal_concentration_conc})

        elem.clear()
        for ancestor in elem.xpath('ancestor-or-self::*'):
            while ancestor.getprevious() is not None:
                del ancestor.getparent()[0]
        del context
        return;

hmdbextract('hmdb_file.xml', 'hmmdb_file.csv')

输出csv应该如下所示：

normal_concentration_spec,normal_concentration_conc
Blood; Feces; Salvia,2.8 +/- 8.8; NA; 5.2
Blood; Feces; Salvia,5; NA; 3-7

实际上，我还拿出了许多其他的东西，每个代谢物只有一个值，这就是为什么我更喜欢这种csv格式。但是，由于一些concentration_value插槽是空的，我只会得到不同数量的样本和值，并且无法分辨哪一个属于哪一个，

我如何才能得到像安娜一样的价值，为每一个缺失的concentration_value？(理想情况下，在保持代码和lxml包的一般结构的同时，我必须提取很多已经设置好的东西)

Answer 1

空元素将返回零长度列表。它可以用来显示NA。

>>> context = etree.iterparse('tmp.xml', tag='{http://www.hmdb.ca}concentration_value')
>>> for event, elem in context:
...     tlc = elem.xpath('text()', namespaces=ns)
...     print(len(tlc), tlc)
... 
1 ['2.8 +/- 8.8']
0 []
1 ['5.2']

使用OP代码

from lxml import etree

ns = {'hmdb': 'http://www.hmdb.ca'}
context = etree.iterparse('/home/luis/tmp/tmp.xml', tag='{http://www.hmdb.ca}metabolite')

for event, elem in context:
    try:
        tl = elem.xpath('hmdb:normal_concentrations/hmdb:concentration/hmdb:biospecimen', namespaces=ns)
        normal_concentration_spec = '; '.join(str(e.text) for e in tl)
    except Exception as ex:
        print(ex)
        normal_concentration_spec = 'NA'
    try:
        tl = elem.xpath('hmdb:normal_concentrations/hmdb:concentration/hmdb:concentration_value', namespaces=ns)
        normal_concentration_conc = '; '.join(str(e.text if e.text!=None else 'NA') for e in tl)
    except Exception as ex:
        normal_concentration_conc = 'NA'

    print(normal_concentration_spec, normal_concentration_conc)

结果

Blood; Feces; Salvia 2.8 +/- 8.8; NA; 5.2
Blood; Feces; Salvia 5; NA; 3-7