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Error with xml_serialize()/xml_unserialize() roundtrip: Opening and ending tag mismatch [PATCH] #407

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HenrikBengtsson opened this issue Oct 3, 2023 · 3 comments
Closed

Error with xml_serialize()/xml_unserialize() roundtrip: Opening and ending tag mismatch [PATCH] #407

HenrikBengtsson opened this issue Oct 3, 2023 · 3 comments
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bug an unexpected problem or unintended behavior

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@HenrikBengtsson
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Issue

xml_serialize()-xml_unserialize() roundtrip failes with: "Opening and ending tag mismatch: link line 12 and head [76]"

I'd expect a roundtrip to always work.

Reproducible Example

doc <- xml2::read_html("https://www.r-project.org")
doc
#> {html_document}
#> <html lang="en">
#> [1] <head>\n<meta http-equiv="Content-Type" content="text/html; charset=UTF-8 ...
#> [2] <body>\n    <div class="container page">\n      <div class="row">\n       ...

raw <- xml2::xml_serialize(doc, connection = NULL)
doc2 <- xml2::xml_unserialize(raw)
#> Error in read_xml.raw(charToRaw(enc2utf8(x)), "UTF-8", ..., as_html = as_html,  : 
#>   Opening and ending tag mismatch: link line 12 and head [76]

Traceback:

> traceback()
4: read_xml.raw(charToRaw(enc2utf8(x)), "UTF-8", ..., as_html = as_html, 
       options = options)
3: read_xml.character(unclass(object), ...)
2: read_xml(unclass(object), ...)
1: xml2::xml_unserialize(raw)
Session Info 
> devtools::session_info() # Paste output below
─ Session info ─────────────────────
 setting  value
 version  R version 4.3.1 (2023-06-16)
 os       Ubuntu 22.04.3 LTS
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/Los_Angeles
 date     2023-10-03
 pandoc   3.1.7 @ /home/henrik/shared/software/CBI/pandoc-3.1.7/bin/pandoc

─ Packages ──────────────────────
 package     * version date (UTC) lib source
 cachem        1.0.8   2023-05-01 [1] CRAN (R 4.3.0)
 callr         3.7.3   2022-11-02 [1] CRAN (R 4.3.0)
 cli           3.6.1   2023-03-23 [1] CRAN (R 4.3.0)
 crayon        1.5.2   2022-09-29 [1] RSPM (R 4.3.0)
 devtools      2.4.5   2022-10-11 [1] RSPM (R 4.3.0)
 digest        0.6.33  2023-07-07 [1] CRAN (R 4.3.1)
 ellipsis      0.3.2   2021-04-29 [1] CRAN (R 4.3.0)
 fastmap       1.1.1   2023-02-24 [1] CRAN (R 4.3.0)
 fs            1.6.3   2023-07-20 [1] RSPM (R 4.3.0)
 glue          1.6.2   2022-02-24 [1] CRAN (R 4.3.0)
 htmltools     0.5.6   2023-08-10 [1] CRAN (R 4.3.1)
 htmlwidgets   1.6.2   2023-03-17 [1] RSPM (R 4.3.0)
 httpuv        1.6.11  2023-05-11 [1] RSPM (R 4.3.0)
 later         1.3.1   2023-05-02 [1] CRAN (R 4.3.0)
 lifecycle     1.0.3   2022-10-07 [1] CRAN (R 4.3.0)
 magrittr      2.0.3   2022-03-30 [1] RSPM (R 4.3.0)
 memoise       2.0.1   2021-11-26 [1] CRAN (R 4.3.0)
 mime          0.12    2021-09-28 [1] CRAN (R 4.3.0)
 miniUI        0.1.1.1 2018-05-18 [1] RSPM (R 4.3.0)
 pkgbuild      1.4.2   2023-06-26 [1] CRAN (R 4.3.1)
 pkgload       1.3.3   2023-09-22 [1] CRAN (R 4.3.1)
 prettyunits   1.2.0   2023-09-24 [1] RSPM (R 4.3.0)
 processx      3.8.2   2023-06-30 [1] CRAN (R 4.3.1)
 profvis       0.3.8   2023-05-02 [1] RSPM (R 4.3.0)
 promises      1.2.1   2023-08-10 [1] CRAN (R 4.3.1)
 ps            1.7.5   2023-04-18 [1] RSPM (R 4.3.0)
 purrr         1.0.2   2023-08-10 [1] CRAN (R 4.3.1)
 R6            2.5.1   2021-08-19 [1] CRAN (R 4.3.0)
 Rcpp          1.0.11  2023-07-06 [1] CRAN (R 4.3.1)
 remotes       2.4.2.1 2023-07-18 [1] CRAN (R 4.3.1)
 rlang         1.1.1   2023-04-28 [1] CRAN (R 4.3.0)
 sessioninfo   1.2.2   2021-12-06 [1] RSPM (R 4.3.0)
 shiny         1.7.5   2023-08-12 [1] RSPM (R 4.3.0)
 stringi       1.7.12  2023-01-11 [1] CRAN (R 4.3.0)
 stringr       1.5.0   2022-12-02 [1] CRAN (R 4.3.0)
 urlchecker    1.0.1   2021-11-30 [1] RSPM (R 4.3.0)
 usethis       2.2.2   2023-07-06 [1] CRAN (R 4.3.1)
 vctrs         0.6.3   2023-06-14 [1] CRAN (R 4.3.0)
 xtable        1.8-4   2019-04-21 [1] RSPM (R 4.3.0)

 [1] /home/henrik/R/ubuntu22_04-x86_64-pc-linux-gnu-library/4.3-CBI-gcc11
 [2] /home/henrik/shared/software/CBI/_ubuntu22_04/R-4.3.1-gcc11/lib/R/library
@HenrikBengtsson
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Same example using the example HTML file that comes with the package:

library(xml2)
file <- system.file("extdata", "r-project.html", package = "xml2")
doc <- read_html(file)
class(doc)
#> [1] "xml_document" "xml_node"

raw <- xml2::xml_serialize(doc, connection = NULL)
doc2 <- xml2::xml_unserialize(raw)
#> Error in read_xml.raw(charToRaw(enc2utf8(x)), "UTF-8", ..., as_html = as_html,  : 
#>  Opening and ending tag mismatch: link line 12 and head [76]

Now, the problem seems to be with the xml_document class; it works with the xml_nodeset class:

children <- xml_children(doc)
class(children)
#> [1] "xml_nodeset"

raw <- xml2::xml_serialize(children, connection = NULL)
children2 <- xml2::xml_unserialize(raw)
#> {xml_nodeset (2)}
#> [1] <head>\n  <meta http-equiv="Content-Type" content="text/html; charset=UTF ...
#> [2] <body>\n  <div class="container page">\n    <div class="row">\n      <div ...

all.equal(children2, children)
#> [1] TRUE

@HenrikBengtsson
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I think it's because xml_unserialize() attempts to read it as an XML file and not as an HTML file in:

xml2/R/xml_serialize.R

Lines 66 to 67 in ef2310b

} else if (inherits(object, "xml_serialized_document")) {
res <- read_xml(unclass(object), ...)

We get the same error message if we try:

file <- system.file("extdata", "r-project.html", package = "xml2")
doc <- xml2::read_xml(file)
#> Error in read_xml.character(file) : 
#>   Opening and ending tag mismatch: link line 14 and head [76]

HenrikBengtsson added a commit to futureverse/marshal that referenced this issue Oct 6, 2023
@HenrikBengtsson
xml2: Workaround bug for HTML documents (r-lib/xml2#407)
13caa3d
HenrikBengtsson added a commit to HenrikBengtsson/xml2 that referenced this issue Oct 7, 2023
@HenrikBengtsson
Make xml_serialize()/xml_unserialize() work also for HTML documents (fix
7ae7ad0 
 r-lib#407)
@HenrikBengtsson HenrikBengtsson mentioned this issue Oct 7, 2023
Merged
@HenrikBengtsson
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HenrikBengtsson commented Oct 7, 2023 •
edited
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One solution for this it to have xml_serialize.xml_document() record also the document type and then have xml_unserialize() set as_html accordingly. Here's a working patch:

$ git diff -u R/xml_serialize.R
diff --git a/R/xml_serialize.R b/R/xml_serialize.R
index 3f7357f..74e1608 100644
--- a/R/xml_serialize.R
+++ b/R/xml_serialize.R
@@ -22,7 +22,7 @@ xml_serialize.xml_document <- function(object, connection, ...) {
     connection <- file(connection, "w", raw = TRUE)
     on.exit(close(connection))
   }
-  serialize(structure(as.character(object, ...), class = "xml_serialized_document"), connection)
+  serialize(structure(as.character(object, ...), doc_type = doc_type(object), class = "xml_serialized_document"), connection)
 }
 
 #' @export
@@ -64,7 +64,13 @@ xml_unserialize <- function(connection, ...) {
     # Select only the root
     res <- xml_find_first(x, "/node()")
   } else if (inherits(object, "xml_serialized_document")) {
-    res <- read_xml(unclass(object), ...)
+    read_xml_int <- function(object, as_html = FALSE, ...) {
+      if (missing(as_html)) {
+        as_html <- identical(attr(object, "doc_type", exact = TRUE), "html")
+      }
+      read_xml(unclass(object), as_html = as_html, ...)
+    }
+    res <- read_xml_int(unclass(object), ...)
   } else {
     stop("Not a serialized xml2 object", call. = FALSE)
   }

I've submitted this patch in PR #408.

@HenrikBengtsson HenrikBengtsson changed the title Error with xml_serialize()/xml_unserialize() roundtrip: Opening and ending tag mismatch: link line 12 and head [76] Error with xml_serialize()/xml_unserialize() roundtrip: Opening and ending tag mismatch [PATCH] Oct 8, 2023
@hadley hadley added the bug an unexpected problem or unintended behavior label Oct 30, 2023
HenrikBengtsson added a commit to HenrikBengtsson/xml2 that referenced this issue Nov 8, 2023
@HenrikBengtsson
Add xml_serialize()/xml_unserialize() tests for HTML-based documents …
ffb1426 
…+ NEWS entry [r-lib#407]
HenrikBengtsson added a commit to HenrikBengtsson/xml2 that referenced this issue Nov 8, 2023
@HenrikBengtsson
Add xml_serialize()/xml_unserialize() tests for HTML-based documents …
a355327 
…+ NEWS entry [r-lib#407]
@hadley hadley closed this as completed in b9f65ba Nov 10, 2023
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