bash - Shell script to parse CSV to an XML query?

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bash - Shell script to parse CSV to an XML query?

asked Oct 24, 2021 in Technique[技术] by 深蓝 (71.8m points)

bash - Shell script to parse CSV to an XML query?

I have a list of citations in a csv file that I would like to use to fill out the XML based query form at CrossRef

CrossRef provides an XML template (below, with unused fields removed), and I would like to parse the columns of the csv file to fill out repeated fields within the query tag :

 <?xml version = "1.0" encoding="UTF-8"?>
<query_batch xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="2.0" xmlns="http://www.crossref.org/qschema/2.0"
  xsi:schemaLocation="http://www.crossref.org/qschema/2.0 http://www.crossref.org/qschema/crossref_query_input2.0.xsd">
<head>
   <email_address>[email protected]</email_address>
   <doi_batch_id>test</doi_batch_id>
</head>
<body>
  <query enable-multiple-hits="true"
            list-components="false"
            expanded-results="false" key="key">
    <article_title match="fuzzy"></article_title>
    <author search-all-authors="false"></author>
    <volume></volume>
    <year></year>
    <first_page></first_page>
    <journal_title></journal_title>
  </query>
</body>
</query_batch>

How can this be done in a shell script?

sample input:

author,year,article_title,journal_title,volume,first_page
Adler,2006,"Biomass yield and biofuel quality of switchgrass harvested in fall or spring","Agronomy Journal",98,1518
Alexopolou,2008,"Biomass yields for upland and lowland switchgrass varieties grown in the Mediterranean region","Biomass and Bioenergy",32,926
Balasko,1984,"Yield and Quality of Switchgrass Grown without Soil Amendments.","Agronomy Journal",76,204

desired output:

<?xml version = "1.0" encoding="UTF-8"?>
<query_batch xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="2.0" xmlns="http://www.crossref.org/qschema/2.0"
  xsi:schemaLocation="http://www.crossref.org/qschema/2.0 http://www.crossref.org/qschema/crossref_query_input2.0.xsd">
<head>
   <email_address>[email protected]</email_address>
   <doi_batch_id>test</doi_batch_id>
</head>
<body>
 <query>
  <author>Adler</author >
  <year>2006</year >
  <article_title>Biomass yield and biofuel quality of switchgrass harvested in fall or spring</article_title >
  <journal_title>Agronomy Journal</journal_title >
  <volume>98</volume >
  <first_page>1518</first_page >
 </query>
 <query>
  <author>Alexopolou</author >
  <year>2008</year >
  <article_title>Biomass yields for upland and lowland switchgrass varieties grown in the Mediterranean region</article_title >
  <journal_title>Biomass and Bioenergy</journal_title >
  <volume>32</volume >
  <first_page>926</first_page >
 </query>
 <query>
  <author>Balasko</author >
  <year>1984</year >
  <article_title>Yield and Quality of Switchgrass Grown without Soil Amendments.</article_title >
  <journal_title>Agronomy Journal</journal_title >
  <volume>76</volume >
  <first_page>204</first_page >
 </query>
</body>

Other questions provide some help on doing this in C# and Java

See Question&Answers more detail:os

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1 Answer

深蓝 · Answer 1 · 2021-10-23T18:25:56+0000

#!/usr/bin/awk -f
# XML Attributes Must be Quoted. Attribute values must always be quoted. Either single or double quotes can be used.

BEGIN{
    FS=","
    print "<?xml version = '1.0' encoding='UTF-8'?>"
    print "<query_batch xmlns:xsi='http://www.w3.org/2001/XMLSchema-instance' version='2.0' xmlns='http://www.crossref.org/qschema/2.0'"
    print "  xsi:schemaLocation='http://www.crossref.org/qschema/2.0 http://www.crossref.org/qschema/crossref_query_input2.0.xsd'>"
    print "<head>"
    print "   <email_address>[email protected]</email_address>"
    print "   <doi_batch_id>test</doi_batch_id>"
    print "</head>"
    print "<body>"
}

NR>1{
    print "  <query enable-multiple-hits='true'"
    print "            list-components='false'"
    print "            expanded-results='false' key='key'>"
    print "    <article_title match='fuzzy'>" $3 "</article_title>"
    print "    <author search-all-authors='false'>" $1 "</author>"
    print "    <volume>" $5 "</volume>"
    print "    <year>" $2 "</year>"
    print "    <first_page>" $6 "</first_page>"
    print "    <journal_title>" $4 "</journal_title>"
    print "  </query>"
}

END{
    print "</body>"
    print "</query_batch>"
}

$ awk -f script.awk input.csv

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bash - Shell script to parse CSV to an XML query?

bash - Shell script to parse CSV to an XML query?

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