`<![CDATA[` not always recognized

[peterdesmet]

write_eml() will preserve text wrapped in <![CDATA[ and ]]> (expected), but the behaviour is not consistent:

library(EML)

text_1 <- "My text is <a href=\"https://example.com\">html</a>." # Does not work
text_2 <- "<em></em>My text is <a href=\"https://example.com\">html</a>." # Works
text_3 <- "My text is <em>html</em>." # Works

eml <- list(
  dataset = list(
    abstract = list(
      para = list(
        paste0("<![CDATA[", text_1, "]]>"),
        paste0("<![CDATA[", text_2, "]]>"),
        paste0("<![CDATA[", text_3, "]]>")
      )
    )
  )
)

EML::write_eml(eml, "test.xml")

Resulting XML:

<?xml version="1.0" encoding="UTF-8"?>
<eml:eml xmlns:eml="https://eml.ecoinformatics.org/eml-2.2.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:stmml="http://www.xml-cml.org/schema/stmml-1.2" packageId="ed7f9836-d2ae-4a04-9473-d377db387c54" system="uuid" xsi:schemaLocation="https://eml.ecoinformatics.org/eml-2.2.0 https://eml.ecoinformatics.org/eml-2.2.0/eml.xsd">
  <dataset>
    <abstract>
      <para>&lt;![CDATA[My text is &lt;a href="https://example.com"&gt;html&lt;/a&gt;.]]&gt;</para>
      <para><![CDATA[<em></em>My text is <a href="https://example.com">html</a>.]]></para>
      <para><![CDATA[My text is <em>html</em>.]]></para>
    </abstract>
  </dataset>
</eml:eml>

[mbjones]

My immediate guess is that this has the same root cause as #315 , and is a side-effect of the approach used to simplify docbook processing. There are some fundamental issues discussed in #315 that would need to be resolved to fix this.

[sannegovaert]

It seems that the problem only occurs for links when there is not other HMTL tag before the link.
It is unrelated to CDATA (see test 3).

Reproducible example

r code

``` r
library(EML)

text_1 <- "<div>text_1 - This is a division with some <b>bold text</b> inside</div>."
text_2 <- "<p>text_2 - This is a paragraph with a <a href=\"https://example.com\">link</a> and some <sup>superscript</sup> text.</p>"
text_3 <- "text_3 - <ul><li>First item</li><li>Second item with <sub>subscript</sub></li></ul>"
text_4 <- "text_4 - <ol><li>First ordered item</li><li>Second ordered item</li></ol>"
text_5 <- "<h1>text_5 - Main Title Here</h1>"
text_6 <- "text_6 - Only a <a href=\"https://example.com\">link</a>."
text_7 <- "<div>text_7 - This is a division with a <a href=\"https://example.com\">link</a> inside</div>."
text_8 <- "<p>text_8 - This is a paragraph with a <a href=\"https://example.com\">link</a> inside.</p>"


# Minimal valid EML
me <- list(individualName = list(givenName = "Sanne", surName = "Govaert"))
eml <- list(
  dataset = list(
    title = "A Minimal Valid EML Dataset",
    creator = me,
    contact = me
  )
)

dir.create(here::here("test"))
EML::write_eml(eml, here::here("test", "eml.xml"))
EML::eml_validate(here::here("test", "eml.xml"))
#> [1] TRUE
#> attr(,"errors")
#> character(0)

# Test 1: texts wrapped with CDATA
eml_1 <- eml
eml_1$dataset$abstract <- list(
  para = list(
    paste0("<![CDATA[", text_1, "]]>"),
    paste0("<![CDATA[", text_2, "]]>"),
    paste0("<![CDATA[", text_3, "]]>"),
    paste0("<![CDATA[", text_4, "]]>"),
    paste0("<![CDATA[", text_5, "]]>"),
    paste0("<![CDATA[", text_6, "]]>"),
    paste0("<![CDATA[", text_7, "]]>"),
    paste0("<![CDATA[", text_8, "]]>")
  )
)

EML::write_eml(eml_1, here::here("test", "eml_1.xml"))
EML::eml_validate(here::here("test", "eml_1.xml"))
#> [1] TRUE
#> attr(,"errors")
#> character(0)

# Test 2
eml_2 <- eml
eml_2$dataset$abstract <- list(
  para = list(
    paste0("<![CDATA[", text_1, "]]>"),
    paste0("<![CDATA[", text_2, "]]>"),
    paste0("<![CDATA[", text_3, "]]>"),
    paste0("<![CDATA[", text_4, "]]>"),
    paste0("<![CDATA[", text_5, "]]>"),
    paste0("<![CDATA[<div>", text_6, "</div>]]>"),
    paste0("<![CDATA[", text_7, "]]>"),
    paste0("<![CDATA[", text_8, "]]>")
  )
)

EML::write_eml(eml_2, here::here("test", "eml_2.xml"))
EML::eml_validate(here::here("test", "eml_2.xml"))
#> [1] TRUE
#> attr(,"errors")
#> character(0)

# Test 3: no CDATA wrap
eml_3 <- eml
eml_3$dataset$abstract <- list(
  para = list(
    text_1,
    text_2,
    text_3,
    text_4,
    text_5,
    text_6,
    text_7,
    text_8
  )
)

EML::write_eml(eml_3, here::here("test", "eml_3.xml"))
EML::eml_validate(here::here("test", "eml_3.xml"))
#> [1] FALSE
#> attr(,"errors")
#> [1] "Element 'div': This element is not expected."
#> [2] "Element 'p': This element is not expected."  
#> [3] "Element 'ul': This element is not expected." 
#> [4] "Element 'ol': This element is not expected." 
#> [5] "Element 'h1': This element is not expected." 
#> [6] "Element 'div': This element is not expected."
#> [7] "Element 'p': This element is not expected."

unlink(here::here("test"))

^{Created on 2025-06-23 with} reprex v2.1.1

eml_1.xml abstract

Text_6 is a problem.

    <abstract>
      <para><![CDATA[<div>text_1 - This is a division with some <b>bold text</b> inside</div>.]]></para>
      <para><![CDATA[<p>text_2 - This is a paragraph with a <a href="https://example.com">link</a> and some <sup>superscript</sup> text.</p>]]></para>
      <para><![CDATA[text_3 - <ul><li>First item</li><li>Second item with <sub>subscript</sub></li></ul>]]></para>
      <para><![CDATA[text_4 - <ol><li>First ordered item</li><li>Second ordered item</li></ol>]]></para>
      <para><![CDATA[<h1>text_5 - Main Title Here</h1>]]></para>
      <para>&lt;![CDATA[text_6 - Only a &lt;a href="https://example.com"&gt;link&lt;/a&gt;.]]&gt;</para>
      <para><![CDATA[<div>text_7 - This is a division with a <a href="https://example.com">link</a> inside</div>.]]></para>
      <para><![CDATA[<p>text_8 - This is a paragraph with a <a href="https://example.com">link</a> inside.</p>]]></para>
    </abstract>

eml_2.xml abstract

Bug in text_6 is fixed by introducing extra HTML tag before the link.

    <abstract>
      <para><![CDATA[<div>text_1 - This is a division with some <b>bold text</b> inside</div>.]]></para>
      <para><![CDATA[<p>text_2 - This is a paragraph with a <a href="https://example.com">link</a> and some <sup>superscript</sup> text.</p>]]></para>
      <para><![CDATA[text_3 - <ul><li>First item</li><li>Second item with <sub>subscript</sub></li></ul>]]></para>
      <para><![CDATA[text_4 - <ol><li>First ordered item</li><li>Second ordered item</li></ol>]]></para>
      <para><![CDATA[<h1>text_5 - Main Title Here</h1>]]></para>
      <para><![CDATA[<div>text_6 - Only a <a href="https://example.com">link</a>.</div>]]></para>
      <para><![CDATA[<div>text_7 - This is a division with a <a href="https://example.com">link</a> inside</div>.]]></para>
      <para><![CDATA[<p>text_8 - This is a paragraph with a <a href="https://example.com">link</a> inside.</p>]]></para>
    </abstract>

eml_3.xml abstract

(ignoring this is invalid EML)
Problem in text_6.

    <abstract>
      <para><div>text_1 - This is a division with some <b>bold text</b> inside</div>.</para>
      <para>
        <p>text_2 - This is a paragraph with a <a href="https://example.com">link</a> and some <sup>superscript</sup> text.</p>
      </para>
      <para>text_3 - <ul><li>First item</li><li>Second item with <sub>subscript</sub></li></ul></para>
      <para>text_4 - <ol><li>First ordered item</li><li>Second ordered item</li></ol></para>
      <para>
        <h1>text_5 - Main Title Here</h1>
      </para>
      <para>text_6 - Only a &lt;a href="https://example.com"&gt;link&lt;/a&gt;.</para>
      <para><div>text_7 - This is a division with a <a href="https://example.com">link</a> inside</div>.</para>
      <para>
        <p>text_8 - This is a paragraph with a <a href="https://example.com">link</a> inside.</p>
      </para>
    </abstract>