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Convert data from xml to R file

I am trying to convert an xml file to a dataframe, but the format seems to be off. I looked through various tutorials, and although I was moderately successful in getting the information I needed using the for loop and navigating through the analyzed file, I was told that this solution is not very effective.

I tried this code:

require(XML)
parsed<-xmlParse("SEWL.xml")
xmlToDataFrame(parsed)

But this gives an error: Error in [<-.data.frame( *tmp*, i, names (nodes [[i]]), value = c ("\" LL18179 \ "\" 2016/08 \ "0.32485. 43896.59801.2131 \" OK \ "", : duplicate indexes for columns

This other code works, but formatting is not what I need:

require(XML)
require(plyr)
pldf<-ldply(xmlToList("SEWL.xml"),data.frame)

The resulting data file is as follows:

          .id              X..i.. text  .attrs test.code test.validuntil test.meas.text test.meas..attrs test.meas.text.1
1  technician              "John" <NA>    <NA>      <NA>            <NA>           <NA>             <NA>             <NA>
2    location                "CO" <NA>    <NA>      <NA>            <NA>           <NA>             <NA>             <NA>
3        temp                <NA> 21.3 celsius      <NA>            <NA>           <NA>             <NA>             <NA>
4     runtype           "routine" <NA>    <NA>      <NA>            <NA>           <NA>             <NA>             <NA>
5      sample                <NA> <NA>    2323 "LL18179"       "2016/08"         0.3248         baseline           5.4389
6      sample                <NA> <NA>    2323 "LL18179"       "2016/08"         0.3248         baseline           5.4389
7      sample                <NA> <NA> 8979237 "AA09453"       "2016/03"         0.0117         baseline           5.6012
8      sample                <NA> <NA> 8979237 "AA09453"       "2016/03"         0.0117         baseline           5.6012
9      .attrs 2015_07_31_11_33_22 <NA>    <NA>      <NA>            <NA>           <NA>             <NA>             <NA>
10     .attrs            20150731 <NA>    <NA>      <NA>            <NA>           <NA>             <NA>             <NA>
11     .attrs              113322 <NA>    <NA>      <NA>            <NA>           <NA>             <NA>             <NA>
   test.meas..attrs.1 test.meas.text.2 test.meas..attrs.2 test.calc test.result test..attrs test.code.1 test.validuntil.1
1                <NA>             <NA>               <NA>      <NA>        <NA>        <NA>        <NA>              <NA>
2                <NA>             <NA>               <NA>      <NA>        <NA>        <NA>        <NA>              <NA>
3                <NA>             <NA>               <NA>      <NA>        <NA>        <NA>        <NA>              <NA>
4                <NA>             <NA>               <NA>      <NA>        <NA>        <NA>        <NA>              <NA>
5                 std           6.5980               data    1.2131        "OK"      laslum "ATR150607"         "2017/05"
6                 std           6.5980               data    1.2131        "OK"           3 "ATR150607"         "2017/05"
7                 std           1.1431               data    0.2041      "FAIL"       absat        <NA>              <NA>
8                 std           1.1431               data    0.2041      "FAIL"           2        <NA>              <NA>
9                <NA>             <NA>               <NA>      <NA>        <NA>        <NA>        <NA>              <NA>
10               <NA>             <NA>               <NA>      <NA>        <NA>        <NA>        <NA>              <NA>
11               <NA>             <NA>               <NA>      <NA>        <NA>        <NA>        <NA>              <NA>
   test.meas.text.3 test.meas..attrs.3 test.meas.text.4 test.meas..attrs.4 test.meas.text.5 test.meas..attrs.5
1              <NA>               <NA>             <NA>               <NA>             <NA>               <NA>
2              <NA>               <NA>             <NA>               <NA>             <NA>               <NA>
3              <NA>               <NA>             <NA>               <NA>             <NA>               <NA>
4              <NA>               <NA>             <NA>               <NA>             <NA>               <NA>
5            0.0673           baseline           4.9721                std          10.3851               data
6            0.0673           baseline           4.9721                std          10.3851               data
7              <NA>               <NA>             <NA>               <NA>             <NA>               <NA>
8              <NA>               <NA>             <NA>               <NA>             <NA>               <NA>
9              <NA>               <NA>             <NA>               <NA>             <NA>               <NA>
10             <NA>               <NA>             <NA>               <NA>             <NA>               <NA>
11             <NA>               <NA>             <NA>               <NA>             <NA>               <NA>
   test.calc.1 test.result.1 test..attrs.1
1         <NA>          <NA>          <NA>
2         <NA>          <NA>          <NA>
3         <NA>          <NA>          <NA>
4         <NA>          <NA>          <NA>
5       2.0886     "Warning"           atr
6       2.0886     "Warning"             1
7         <NA>          <NA>          <NA>
8         <NA>          <NA>          <NA>
9         <NA>          <NA>          <NA>
10        <NA>          <NA>          <NA>
11        <NA>          <NA>          <NA>

This is an example of an XML file that I am using:

<?xml version="1.0" encoding="UTF-8"?>
<experiment name="abc123" date="20150731" time="113322">
    <technician>"John"</technician>
    <location>"CO"</location>
    <temp scale="celsius">21.3</temp>
    <runtype>"routine"</runtype>
    <sample id="2323">
        <test name="laslum" order="3">
            <code>"LL18179"</code>
            <validuntil>"2016/08"</validuntil>
            <meas name="baseline">0.3248</meas>
            <meas name="std">5.4389</meas>
            <meas name="data">6.5980</meas>
            <calc>1.2131</calc>
            <result>"OK"</result>
        </test>
        <test name="atr" order="1">
            <code>"ATR150607"</code>
            <validuntil>"2017/05"</validuntil>
            <meas name="baseline">0.0673</meas>
            <meas name="std">4.9721</meas>
            <meas name="data">10.3851</meas>
            <calc>2.0886</calc>
            <result>"Warning"</result>
        </test>
    </sample>
    <sample id="8979237">
        <test name="absat" order="2">
            <code>"AA09453"</code>
            <validuntil>"2016/03"</validuntil>
            <meas name="baseline">0.0117</meas>
            <meas name="std">5.6012</meas>
            <meas name="data">1.1431</meas>
            <calc>0.2041</calc>
            <result>"FAIL"</result>
        </test>
    </sample>
</experiment>

And the data block that I hope to get:

  experiment technician location temp runtype  sample   test order      code validuntil baseline    std    data   calc  result     date   time
1     abc123       John       CO 21.3 routine    2323 laslum     3   LL18179    2016/08   0.3248 5.4389  6.5980 1.2131      OK 20150731 113322
2     abc123       John       CO 21.3 routine    2323    atr     1 ATR150607    2017/05   0.0673 4.9721 10.3851 2.0886 Warning 20150731 113322
3     abc123       John       CO 21.3 routine 8979237  absat     2   AA09453    2016/03   0.0117 5.6012  1.1431 0.2041    FAIL 20150731 113322

, - , .

+4
1

XML. ( //) , ( node, ) .

1) Lines , xpathApply/xpathSApply // . e, s t , node, .

library(XML)
doc <- xmlTreeParse(Lines, asText = TRUE, useInternalNodes = TRUE)

do.call("rbind", xpathApply(doc, "//experiment", function(e) {
  data.frame(experiment = xmlAttrs(e)[["name"]],
       technician = xmlValue(e[["technician"]]),
       location = xmlValue(e[["location"]]),
       temp = xmlValue(e[["temp"]]),
       runtype = xmlValue(e[["runtype"]]),
       t(do.call(cbind, xpathApply(e, "sample", function(s) {
            sample <- xmlAttrs(s)[["id"]]
            xpathSApply(s, "test", function(t) {
                   c(sample = sample,
                        test = xmlAttrs(t)[["name"]],
                        order = xmlAttrs(t)[["order"]],
                        code = xmlValue(t[["code"]]),
                        validuntil = xmlValue(t[["validuntil"]]),
                        baseline = xmlValue(t["meas"][[1]]),
                        std = xmlValue(t["meas"][[2]]),
                        data = xmlValue(t["meas"][[3]]),
                        calc = xmlValue(t[["calc"]]),
                        result = xmlValue(t[["result"]])
             )})}))),
       date = xmlAttrs(e)[["date"]],
       time = xmlAttrs(e)[["time"]]
)}))

:

  experiment technician location temp   runtype  sample   test order
1     abc123     "John"     "CO" 21.3 "routine"    2323 laslum     3
2     abc123     "John"     "CO" 21.3 "routine"    2323    atr     1
3     abc123     "John"     "CO" 21.3 "routine" 8979237  absat     2
         code validuntil baseline    std    data   calc    result     date
1   "LL18179"  "2016/08"   0.3248 5.4389  6.5980 1.2131      "OK" 20150731
2 "ATR150607"  "2017/05"   0.0673 4.9721 10.3851 2.0886 "Warning" 20150731
3   "AA09453"  "2016/03"   0.0117 5.6012  1.1431 0.2041    "FAIL" 20150731
    time
1 113322
2 113322
3 113322

2). , , , .

library(XML)
doc <- xmlTreeParse(Lines, asText = TRUE, useInternalNodes = TRUE)

do.call("rbind", xpathApply(doc, "//test", function(t) { # t is test node
        s <- xmlParent(t) # s is sample node
        e <- xmlParent(s) # e is experiment node
        data.frame(experiment = xmlAttrs(e)[["name"]],
          technician = xmlValue(e[["technician"]]),
          location = xmlValue(e[["location"]]),
          temp = xmlValue(e[["temp"]]),
          runtype = xmlValue(e[["runtype"]]),
          sample = xmlAttrs(s)[["id"]],
          test = xmlAttrs(t)[["name"]],
          order = xmlAttrs(t)[["order"]],
          code = xmlValue(t[["code"]]),
          validuntil = xmlValue(t[["validuntil"]]),
          baseline = xmlValue(t["meas"][[1]]),
          std = xmlValue(t["meas"][[2]]),
          data = xmlValue(t["meas"][[3]]),
          calc = xmlValue(t[["calc"]]),
          result = xmlValue(t[["result"]]),
          date = xmlAttrs(e)[["date"]],
          time = xmlAttrs(e)[["time"]]
       )
}))

:

  experiment technician location temp   runtype  sample   test order
1     abc123     "John"     "CO" 21.3 "routine"    2323 laslum     3
2     abc123     "John"     "CO" 21.3 "routine"    2323    atr     1
3     abc123     "John"     "CO" 21.3 "routine" 8979237  absat     2
         code validuntil baseline    std    data   calc    result     date
1   "LL18179"  "2016/08"   0.3248 5.4389  6.5980 1.2131      "OK" 20150731
2 "ATR150607"  "2017/05"   0.0673 4.9721 10.3851 2.0886 "Warning" 20150731
3   "AA09453"  "2016/03"   0.0117 5.6012  1.1431 0.2041    "FAIL" 20150731
    time
1 113322
2 113322
3 113322

1:

, XML, SEWL.xml, Excel, , , .

2:

Lines R:

Lines <- '<?xml version="1.0" encoding="UTF-8"?>
<experiment name="abc123" date="20150731" time="113322">
    <technician>"John"</technician>
    <location>"CO"</location>
    <temp scale="celsius">21.3</temp>
    <runtype>"routine"</runtype>
    <sample id="2323">
        <test name="laslum" order="3">
            <code>"LL18179"</code>
            <validuntil>"2016/08"</validuntil>
            <meas name="baseline">0.3248</meas>
            <meas name="std">5.4389</meas>
            <meas name="data">6.5980</meas>
            <calc>1.2131</calc>
            <result>"OK"</result>
        </test>
        <test name="atr" order="1">
            <code>"ATR150607"</code>
            <validuntil>"2017/05"</validuntil>
            <meas name="baseline">0.0673</meas>
            <meas name="std">4.9721</meas>
            <meas name="data">10.3851</meas>
            <calc>2.0886</calc>
            <result>"Warning"</result>
        </test>
    </sample>
    <sample id="8979237">
        <test name="absat" order="2">
            <code>"AA09453"</code>
            <validuntil>"2016/03"</validuntil>
            <meas name="baseline">0.0117</meas>
            <meas name="std">5.6012</meas>
            <meas name="data">1.1431</meas>
            <calc>0.2041</calc>
            <result>"FAIL"</result>
        </test>
    </sample>
</experiment>'
+6

Source: https://habr.com/ru/post/1661847/

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