r - 用R解析xml数据，代码很慢。如何让它更快？

Question

我有一个非常大的 xml 格式的数据集(大约 20 GB)，我需要将它解析成整洁的表格以进行一些统计。我要保存:
- 标签 controlfield
的属性 tag- 标签 datafield
的属性 tag- 标签子字段
的属性代码- 对应于所有这些属性/标签的值

以下来自此处的示例 (R XML - combining parent and child nodes into data frame) 我编写了自己的脚本。它工作正常，但非常非常慢......我有超过 100 万条记录，所以脚本不实用，但我不知道如何优化它。
有没有办法提高我的代码的性能，或者有另一种方法来解决这个问题。对我来说，使用什么包(xml2 或 xml 或其他)并不重要。我真正需要的是尽快将我的数据转换成整洁的表格。这是我的数据，对数据和代码的一些评论。

感谢您提供的所有可能的帮助。

数据

library(xml2)
library(tidyverse)
df <- read_xml(
'<collection>
<record>
  <controlfield tag="001">1</controlfield>
  <controlfield tag="005">20180109004353.0</controlfield>
  <datafield tag="020" ind1=" " ind2=" ">
    <subfield code="a">9780821812419</subfield>
    <subfield code="b">print</subfield>
  </datafield>
  <datafield tag="020" ind1=" " ind2=" ">
    <subfield code="a">9780821899854</subfield>
    <subfield code="b">online</subfield>
  </datafield>
  <datafield tag="024" ind1="7" ind2=" ">
    <subfield code="2">DOI</subfield>
    <subfield code="a">10.1090/memo/0041</subfield>
  </datafield>
  <datafield tag="035" ind1=" " ind2=" ">
    <subfield code="9">SPIRESTeX</subfield>
    <subfield code="a">Wong:1961af</subfield>
  </datafield>
  <datafield tag="035" ind1=" " ind2=" ">
    <subfield code="9">MSNET</subfield>
    <subfield code="a">0383311</subfield>
  </datafield>
  <datafield tag="035" ind1=" " ind2=" ">
    <subfield code="9">ZBLATT</subfield>
    <subfield code="a">0124.13401</subfield>
  </datafield>
  <datafield tag="650" ind1="1" ind2="7">
    <subfield code="2">INSPIRE</subfield>
    <subfield code="a">Math and Math Physics</subfield>
  </datafield>
  <datafield tag="773" ind1=" " ind2=" ">
    <subfield code="c">1-112</subfield>
    <subfield code="p">Mem.Am.Math.Soc.</subfield>
    <subfield code="v">41</subfield>
    <subfield code="y">1961</subfield>
    <subfield code="1">1214590</subfield>
  </datafield>
  <datafield tag="970" ind1=" " ind2=" ">
    <subfield code="a">SPIRES-60</subfield>
  </datafield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">Book</subfield>
  </datafield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">Citeable</subfield>
  </datafield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">HEP</subfield>
  </datafield>
  <datafield tag="999" ind1="C" ind2="5">
    <subfield code="9">CURATOR</subfield>
    <subfield code="o">1</subfield>
    <subfield code="s">Ann.Math.,43,161</subfield>
  </datafield>
  <datafield tag="999" ind1="C" ind2="5">
    <subfield code="9">CURATOR</subfield>
    <subfield code="o">2</subfield>
    <subfield code="s">Am.Math.Mon.,53,136</subfield>
  </datafield>
  <datafield tag="999" ind1="C" ind2="5">
    <subfield code="9">CURATOR</subfield>
    <subfield code="h">E. Cartan</subfield>
    <subfield code="m">Paris</subfield>
    <subfield code="o">3</subfield>
    <subfield code="t">Lecons sur la theorie des spineurs I</subfield>
    <subfield code="y">1938</subfield>
  </datafield>
  <datafield tag="999" ind1="C" ind2="5">
    <subfield code="9">CURATOR</subfield>
    <subfield code="o">4</subfield>
    <subfield code="s">Enseign.Math.,40,26</subfield>
  </datafield>
  <datafield tag="999" ind1="C" ind2="5">
    <subfield code="9">CURATOR</subfield>
    <subfield code="s">Annals Math.,47,510</subfield>
  </datafield>
  <datafield tag="999" ind1="C" ind2="5">
    <subfield code="9">CURATOR</subfield>
    <subfield code="o">6</subfield>
    <subfield code="s">Comment.Math.Helv.,15,358</subfield>
  </datafield>
  <datafield tag="999" ind1="C" ind2="5">
    <subfield code="9">CURATOR</subfield>
    <subfield code="o">9</subfield>
    <subfield code="s">Trans.Am.Math.Soc.,61,193</subfield>
  </datafield>
  <datafield tag="999" ind1="C" ind2="5">
    <subfield code="9">CURATOR</subfield>
    <subfield code="o">10</subfield>
    <subfield code="s">Math.Ann.,88,1</subfield>
  </datafield>
  <datafield tag="999" ind1="C" ind2="5">
    <subfield code="9">CURATOR</subfield>
    <subfield code="o">12</subfield>
    <subfield code="s">Math.Ann.,60,546</subfield>
  </datafield>
  <datafield tag="999" ind1="C" ind2="5">
    <subfield code="9">CURATOR</subfield>
    <subfield code="o">14</subfield>
    <subfield code="s">Comment.Math.Helv.,21,261</subfield>
  </datafield>
  <datafield tag="999" ind1="C" ind2="5">
    <subfield code="9">CURATOR</subfield>
    <subfield code="o">17</subfield>
    <subfield code="s">Abh.Math.Sem.Univ.Hamburg,1,1</subfield>
  </datafield>
  <datafield tag="999" ind1="C" ind2="5">
    <subfield code="9">CURATOR</subfield>
    <subfield code="o">18</subfield>
    <subfield code="s">Am.J.Math.,67,472</subfield>
  </datafield>
  <datafield tag="999" ind1="C" ind2="5">
    <subfield code="9">CURATOR</subfield>
    <subfield code="o">20</subfield>
    <subfield code="s">Comment.Math.Helv.,8,3</subfield>
  </datafield>
  <datafield tag="999" ind1="C" ind2="5">
    <subfield code="9">CURATOR</subfield>
    <subfield code="o">21</subfield>
    <subfield code="s">Tohoku Math.J.,3,322</subfield>
  </datafield>
  <datafield tag="909" ind1="C" ind2="O">
    <subfield code="o">oai:inspirehep.net:1</subfield>
    <subfield code="p">INSPIRE:HEP</subfield>
  </datafield>
  <datafield tag="961" ind1=" " ind2=" ">
    <subfield code="x">2001-02-23</subfield>
    <subfield code="c">2018-01-09</subfield>
  </datafield>
  <datafield tag="245" ind1=" " ind2=" ">
    <subfield code="a">Isoclinic N planes in Euclidean 2N space, Clifford parallels in elliptic (2N-1) space, and the Hurwitz matrix equations</subfield>
  </datafield>
  <datafield tag="246" ind1=" " ind2=" ">
    <subfield code="9">arXiv</subfield>
    <subfield code="a">Isoclinic n-planes in Euclidean 2n-space, Clifford parallels in elliptic (2n-1)-space, and the Hurwitz matrix equations</subfield>
  </datafield>
  <datafield tag="100" ind1=" " ind2=" ">
    <subfield code="a">Wong, Yung-Chow</subfield>
    <subfield code="u">Hong Kong U.</subfield>
    <subfield code="w">Y.C.Wong.1</subfield>
    <subfield code="y">0</subfield>
    <subfield code="z">908370</subfield>
  </datafield>
  <datafield tag="269" ind1=" " ind2=" ">
    <subfield code="c">1961</subfield>
  </datafield>
  <datafield tag="300" ind1=" " ind2=" ">
    <subfield code="a">121</subfield>
  </datafield>
  <datafield tag="500" ind1=" " ind2=" ">
    <subfield code="a">Second printing with corrections 1971 (ISBN: 0-8218-1241-6).</subfield>
  </datafield>
  <datafield tag="520" ind1=" " ind2=" ">
    <subfield code="a">Introduction Part I. Isoclinic nn-planes in E2nE2n and Clifford parallel</subfield>
  </datafield>
</record>

<record>
  <controlfield tag="001">17</controlfield>
  <controlfield tag="005">20190325225547.0</controlfield>
  <datafield tag="035" ind1=" " ind2=" ">
    <subfield code="9">SPIRESTeX</subfield>
    <subfield code="a">Breymayer:1963bh</subfield>
  </datafield>
  <datafield tag="037" ind1=" " ind2=" ">
    <subfield code="a">SLAC-TN-63-023</subfield>
  </datafield>
  <datafield tag="100" ind1=" " ind2=" ">
    <subfield code="a">Breymayer, K.E.</subfield>
    <subfield code="u">SLAC</subfield>
    <subfield code="w">K.E.Breymayer.1</subfield>
    <subfield code="y">0</subfield>
    <subfield code="z">903206</subfield>
  </datafield>
  <datafield tag="245" ind1=" " ind2=" ">
    <subfield code="a">SYSTEM INTERCONNECTION AND PROTECTION OF THE MODULATOR</subfield>
  </datafield>
  <datafield tag="269" ind1=" " ind2=" ">
    <subfield code="c">1963-03</subfield>
  </datafield>
  <datafield tag="300" ind1=" " ind2=" ">
    <subfield code="a">21</subfield>
  </datafield>
  <datafield tag="650" ind1="1" ind2="7">
    <subfield code="2">INSPIRE</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="a">Mallory, Kenneth B.</subfield>
    <subfield code="u">SLAC</subfield>
    <subfield code="w">K.B.Mallory.1</subfield>
    <subfield code="y">0</subfield>
    <subfield code="z">903206</subfield>
  </datafield>
  <datafield tag="710" ind1=" " ind2=" ">
    <subfield code="a">SLAC</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="u">http://www-public.slac.stanford.edu/sciDoc/docMeta.aspx?slacPubNumber=slac-tn-63-023</subfield>
    <subfield code="w">slac-tn-63-023</subfield>
    <subfield code="y">SLAC</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">1903536</subfield>
    <subfield code="u">http://inspirehep.net/record/17/files/slac-tn-63-023.pdf</subfield>
  </datafield>
  <datafield tag="909" ind1="C" ind2="O">
    <subfield code="o">oai:inspirehep.net:17</subfield>
    <subfield code="p">INSPIRE:HEP</subfield>
  </datafield>
  <datafield tag="961" ind1=" " ind2=" ">
    <subfield code="x">1963-03-01</subfield>
    <subfield code="c">2019-03-25</subfield>
  </datafield>
  <datafield tag="970" ind1=" " ind2=" ">
    <subfield code="a">SPIRES-329</subfield>
  </datafield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">HEP</subfield>
  </datafield>
  <datafield tag="999" ind1="C" ind2="6">
    <subfield code="a">0-0-0-0-0-0-1</subfield>
    <subfield code="t">2014-08-13 15:34:53</subfield>
    <subfield code="v">Invenio/1.1.2.1260-aa76f refextract/1.5.44</subfield>
    <subfield code="v">content.pdf;1</subfield>
  </datafield>
  <datafield tag="999" ind1="C" ind2="5">
    <subfield code="m">will open, thus o~nlng the ac cQxuit to the -</subfield>
    <subfield code="o">1</subfield>
  </datafield>
  <datafield tag="999" ind1="C" ind2="5">
    <subfield code="m">2</subfield>
  </datafield>
  <datafield tag="999" ind1="C" ind2="5">
    <subfield code="m">Apply the trigger. If the high voltage is present, the klystron is pulsed and draws average current</subfield>
    <subfield code="o">3</subfield>
    <subfield code="t">relay comes on. In addI.tion, a light at the modulator comes on, indicating Klystron Current</subfield>
  </datafield>
  <datafield tag="999" ind1="C" ind2="5">
    <subfield code="m">no recycling</subfield>
    <subfield code="o">3</subfield>
  </datafield>
  <datafield tag="999" ind1="C" ind2="5">
    <subfield code="m">removes the 260-6~0 vous l (2) Resetting: close circuit breaker only, no further action necessary if fault is cleared.</subfield>
    <subfield code="o">3</subfield>
  </datafield>
  <datafield tag="999" ind1="C" ind2="5">
    <subfield code="m">% u --L--_ I ‘2 Q-4 -r---.‘-i-’I ___----_.--_.-_. -.L.-</subfield>
    <subfield code="o">4</subfield>
  </datafield>
</record>

<record>
  <controlfield tag="001">18</controlfield>
  <controlfield tag="005">20140813111316.0</controlfield>
  <datafield tag="035" ind1=" " ind2=" ">
    <subfield code="a">Johnston:1977saa</subfield>
    <subfield code="9">INSPIRETeX</subfield>
  </datafield>
  <datafield tag="037" ind1=" " ind2=" ">
    <subfield code="a">SLAC-PUB-0341</subfield>
  </datafield>
  <datafield tag="100" ind1=" " ind2=" ">
    <subfield code="a">Johnston, Lawrence II.</subfield>
    <subfield code="u">SLAC</subfield>
    <subfield code="w">L.H.Johnston.1</subfield>
    <subfield code="y">0</subfield>
    <subfield code="z">903206</subfield>
  </datafield>
  <datafield tag="245" ind1=" " ind2=" ">
    <subfield code="a">A target beam monitor using secondary electron emission</subfield>
  </datafield>
  <datafield tag="269" ind1=" " ind2=" ">
    <subfield code="c">1977-08</subfield>
  </datafield>
  <datafield tag="300" ind1=" " ind2=" ">
    <subfield code="a">17</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="a">Murray, Joseph J.</subfield>
    <subfield code="u">SLAC</subfield>
    <subfield code="w">J.J.Murray.1</subfield>
    <subfield code="y">0</subfield>
    <subfield code="z">903206</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="a">Gearhart, Roger A.</subfield>
    <subfield code="u">LBL, Berkeley</subfield>
    <subfield code="w">R.Gearhart.1</subfield>
    <subfield code="y">0</subfield>
    <subfield code="z">902953</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="a">Hauser, Todd</subfield>
    <subfield code="u">LBL, Berkeley</subfield>
    <subfield code="w">T.Hauser.2</subfield>
    <subfield code="y">0</subfield>
    <subfield code="z">902953</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="a">Klein, Paul R.</subfield>
    <subfield code="u">Purdue U.</subfield>
    <subfield code="w">P.Klein.2</subfield>
    <subfield code="y">0</subfield>
    <subfield code="z">903142</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="w">0341</subfield>
    <subfield code="y">SLACPUB</subfield>
    <subfield code="u">http://www-public.slac.stanford.edu/sciDoc/docMeta.aspx?slacPubNumber=SLAC-PUB-0341</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">1110230</subfield>
    <subfield code="u">http://inspirehep.net/record/18/files/slac-pub-0341.pdf</subfield>
  </datafield>
  <datafield tag="909" ind1="C" ind2="O">
    <subfield code="o">oai:inspirehep.net:18</subfield>
    <subfield code="p">INSPIRE:HEP</subfield>
  </datafield>
  <datafield tag="961" ind1=" " ind2=" ">
    <subfield code="x">1977-01-01</subfield>
    <subfield code="c">2014-08-13</subfield>
  </datafield>
  <datafield tag="970" ind1=" " ind2=" ">
    <subfield code="a">SPIRES-337</subfield>
  </datafield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">HEP</subfield>
  </datafield>
  <datafield tag="999" ind1="C" ind2="5">
    <subfield code="s">Rev.Sci.Instrum.,26,229</subfield>
  </datafield>
  <datafield tag="999" ind1="C" ind2="5">
    <subfield code="s">IEEE Trans.Nucl.Sci.,12,935</subfield>
    <subfield code="0">48647</subfield>
  </datafield>
  <datafield tag="999" ind1="C" ind2="5">
    <subfield code="s">Nucl.Instrum.Meth.,15,63</subfield>
  </datafield>
  <datafield tag="999" ind1="C" ind2="5">
    <subfield code="s">Phys.Rev.Lett.,18,366</subfield>
  </datafield>
</record>
</collection>')

对标签的评论:
<controlfield tag="001">This is identifier of the record</controlfield>
<controlfield tag="005">This is time of last record update</controlfield>

我的代码

start_t <- Sys.time()
x1 <- df %>% xml_find_all('.//record')

x2 <- x1 %>% 
    xml_find_all('.//datafield') %>% 
    map_df(~list(rec      = list(map(xml_find_all(.x, './/preceding-sibling::controlfield'), xml_text)),
                 attrs    = list(xml_attr(.x, attr = 'tag')), 
                 variable = list(map(xml_children(.x), xml_attrs)), 
                 value    = list(map(xml_children(.x), xml_text))
                 ))

x2_tidy <- x2 %>% unnest(c(variable, value)) %>% mutate(rec = as.character(rec))
Sys.time() - start_t

更新我的结果是这样的。抱歉，我不知道如何在此处添加文本表格，所以我将其添加为图像。 Image with resulting table

Answer 1

好吧，只是因为我跳进了兔子洞……下面是工作代码。不过，我不知道您为什么要以这种方式构建输出数据，以防万一您以后决定采用另一种格式，我为记录(行/行)关联的节点的名称添加了一个 col 不记录节点

• 请注意，我正在使用 library(xml2) 来完成所有这些:

这里有一个函数来处理我们需要的属性:

.attrs_targeted <- function(x){
  ats <- xml_attrs(x)
  ats_array <- unlist(ats)
  hits <- grepl("tag|code", names(ats_array), ignore.case = TRUE, perl = TRUE)
  ats <- ats_array[hits]
  data.frame(
    attrs = names(ats),
    variable = ats,
    row.names = NULL,
    stringsAsFactors = FALSE
  )
}

记录节点如下:

records <- xml_find_all(df, ".//record")
> records
{xml_nodeset (3)}
[1] <record>\n  <controlfield tag="001">1</controlfield>\n  <controlfield tag="005">20180109004353.0</controlfield>\n  <datafield tag="020" ind1=" " ind2=" ">\n    <subfield code="a">9780821812419</subfiel ...
[2] <record>\n  <controlfield tag="001">17</controlfield>\n  <controlfield tag="005">20190325225547.0</controlfield>\n  <datafield tag="035" ind1=" " ind2=" ">\n    <subfield code="9">SPIRESTeX</subfield>\ ...
[3] <record>\n  <controlfield tag="001">18</controlfield>\n  <controlfield tag="005">20140813111316.0</controlfield>\n  <datafield tag="035" ind1=" " ind2=" ">\n    <subfield code="a">Johnston:1977saa</sub ...
> 

这是我们的迭代器:

library(dplyr)
library(jsonlite)

results <- rbind_pages(lapply(records, function(i){
  # Controlfield nodes
  controls <- xml_find_all(i, ".//controlfield")
  # control attributes
  ats <- .attrs_targeted(controls)
  # control values
  c_vals <- xml_text(controls)
  # store on a data frame
  d <- data.frame(
    node_name = xml_name(controls),
    record_id = c_vals[[1]], 
    edit_time = c_vals[[2]],
    ats, 
    value = c_vals
  )
  # now to the datafields
  dfields <- xml_find_all(i, ".//datafield")
  # loop through the datafield nodes, and then the subfield nodes, which have code/values we want, but build and 
  # bind data.frames along the way
  d_loop <- rbind_pages(lapply(dfields, function(j){
    d_ats <- .attrs_targeted(j)
    d2 <- data.frame(
      node_name = xml_name(j),
      d_ats,
      value = NA
    )
    # Now target the subfields
    sfields <- xml_find_all(j, ".//subfield")
    d3 <- rbind_pages(Map(function(k){
      data.frame(
        node_name = xml_name(k),
        .attrs_targeted(k),
        value = xml_text(k)
      )
    }, sfields))
    rbind_pages(list(d2, d3))
  })) %>% mutate(record_id = c_vals[[1]], edit_time = c_vals[[2]]) # add the records back in

  rbind_pages(list(d, d_loop))
}))

> head(results)
     node_name record_id        edit_time attrs variable            value
1 controlfield         1 20180109004353.0   tag      001                1
2 controlfield         1 20180109004353.0   tag      005 20180109004353.0
3    datafield         1 20180109004353.0   tag      020             <NA>
4     subfield         1 20180109004353.0  code        a    9780821812419
5     subfield         1 20180109004353.0  code        b            print
6    datafield         1 20180109004353.0   tag      020             <NA>

查看数据:

 results %>% filter(attrs == "code") %>% data.table::dcast(record_id ~ variable)
  record_id 0 1 2  9  a b c h m  o p  s t u v w x y z
1         1 0 1 2 18 17 2 3 1 1 14 2 13 1 1 1 1 1 3 1
2        17 0 0 1  1 10 0 2 0 6  6 1  1 2 4 2 3 1 3 2
3        18 1 0 0  1 11 0 2 0 0  1 1  5 0 7 0 6 1 6 5