Add librsvg as dependency #489

miltondp · 2023-03-06T20:33:43Z

This PR is related to issue #488. It adds librsvg as a dependency so pandoc converts SVG images to a format supported by Word (.docx).

I think this was not introduced here, but when I build the rootstock manuscript with BUILD_DOCX=true, opening the docx file with OpenOffice Writer shows this error:

Clicking on "yes" allows to open the document. However, the SVG file (vector.svg) is not shown in the Word document. This is fixed if the file is downloaded and referenced locally. I thought it might be important to mention how to do this in the documentation, so I also added a note about this.

AppVeyorBot · 2023-03-06T20:37:26Z

AppVeyor build 1.0.320 for commit ee76e0f is now complete.

Found 51 potential spelling error(s). Preview:

content/02.delete-me.md:44:adipiscing
content/02.delete-me.md:44:aliqua
content/02.delete-me.md:44:amet
content/02.delete-me.md:44:consectetur
content/02.delete-me.md:44:dolore
content/02.delete-me.md:44:eiusmod
content/02.delete-me.md:44:elit
content/02.delete-me.md:44:incididunt
content/02.delete-me.md:44:ipsum
content/02.delete-me.md:44:labore
content/02.delete-me.md:44:Lorem
content/02.delete-me.md:44:magna
content/02...

The rendered manuscript from this build is temporarily available for download at:

AppVeyorBot · 2023-03-06T20:41:05Z

AppVeyor build 1.0.321 for commit 6071782 is now complete.

Found 51 potential spelling error(s). Preview:

content/02.delete-me.md:44:adipiscing
content/02.delete-me.md:44:aliqua
content/02.delete-me.md:44:amet
content/02.delete-me.md:44:consectetur
content/02.delete-me.md:44:dolore
content/02.delete-me.md:44:eiusmod
content/02.delete-me.md:44:elit
content/02.delete-me.md:44:incididunt
content/02.delete-me.md:44:ipsum
content/02.delete-me.md:44:labore
content/02.delete-me.md:44:Lorem
content/02.delete-me.md:44:magna
content/02...

The rendered manuscript from this build is temporarily available for download at:

dhimmel · 2023-03-07T13:04:10Z

Here's the text of the error message for searchability:

An error occurred during opening the file. This may be caused by incorrect file contents.
The error details are:
SAXException:
[word/document.xml line 1]: Opening and ending tag mismatch: t line 1 and p
./sax/source/fastparser/fastparser.cxx:619
Proceeding with import may cause data loss or corruption, and application may become unstable or crash.
Do you want to ignore the error and attempt to continue loading the file?

the SVG file (vector.svg) is not shown in the Word document. This is fixed if the file is downloaded and referenced locally.

Is the hypothesis here that Pandoc's SVG to raster conversion fails via rsvg-convert when the image is a URL as opposed to local file path? Is there anything in the Pandoc stderr log output that notes that the SVG conversion failed?

agitter · 2023-03-07T16:15:23Z

I can test the conda environment and local build on Windows but won't get to it immediately.

miltondp · 2023-03-10T20:02:18Z

Is the hypothesis here that Pandoc's SVG to raster conversion fails via rsvg-convert when the image is a URL as opposed to local file path? Is there anything in the Pandoc stderr log output that notes that the SVG conversion failed?

Yes, that's the hypothesis. I couldn't see anything in the output (see below) that helps support the hypothesis.

Also, if I remove the ?sanitize=true parameter from the image URL it does not work either.

$ BUILD_DOCX=true BUILD_PDF=true bash build/build.sh && manubot webpage 
Retrieving and processing reference metadata
## INFO
Manuscript content parts:
00.front-matter
01.abstract
02.delete-me
90.back-matter
## INFO
No explicit manuscript date provided. Dating manuscript based on the current datetime: 2023-03-10T19:58:00.571845+00:00 (in the UTC timezone)
## INFO
Generated manscript stats:
{
  "word_count": 1579
}
## WARNING
Template variable warning: 'dict object' has no attribute 'corresponding'
## WARNING
Template variable warning: 'dict object' has no attribute 'corresponding'
Exporting HTML manuscript
[INFO] Loaded build/themes/default.html from build/themes/default.html
[INFO] Loaded build/plugins/core.html from build/plugins/core.html
[INFO] Loaded build/plugins/accordion.html from build/plugins/accordion.html
[INFO] Loaded build/plugins/anchors.html from build/plugins/anchors.html
[INFO] Loaded build/plugins/attributes.html from build/plugins/attributes.html
[INFO] Loaded build/plugins/jump-to-first.html from build/plugins/jump-to-first.html
[INFO] Loaded build/plugins/lightbox.html from build/plugins/lightbox.html
[INFO] Loaded build/plugins/link-highlight.html from build/plugins/link-highlight.html
[INFO] Loaded build/plugins/table-of-contents.html from build/plugins/table-of-contents.html
[INFO] Loaded build/plugins/tooltips.html from build/plugins/tooltips.html
[INFO] Loaded build/plugins/analytics.html from build/plugins/analytics.html
[INFO] Loaded build/plugins/hypothesis.html from build/plugins/hypothesis.html
[INFO] Loaded build/plugins/mathjax.html from build/plugins/mathjax.html
[INFO] Running filter pandoc-fignos
[INFO] Completed filter pandoc-fignos in 20 ms
[INFO] Running filter pandoc-eqnos

pandoc-eqnos: Wrote the following blocks to header-includes.  If you
use pandoc's --include-in-header option then you will need to manually
include these yourself.

    <!-- pandoc-eqnos: equation style -->
    <style>
      .eqnos { display: inline-block; position: relative; width: 100%; }
      .eqnos br { display: none; }
      .eqnos-number { position: absolute; right: 0em; top: 50%; line-height: 0; }
    </style>
[INFO] Completed filter pandoc-eqnos in 6 ms
[INFO] Running filter pandoc-tablenos
[INFO] Completed filter pandoc-tablenos in 6 ms
[INFO] Running filter pandoc-manubot-cite
[INFO] Completed filter pandoc-manubot-cite in 19 ms
[INFO] Loaded build/assets/style.csl from build/assets/style.csl
Exporting PDF manuscript using Docker + Athena
ATTENTION: default value of option force_s3tc_enable overridden by environment.
Converted 'file:///converted/manuscript.html' to PDF: 'manuscript.pdf'
PDF Conversion: 2253.848ms
Exporting Word Docx manuscript
[INFO] Running filter pandoc-fignos
[INFO] Completed filter pandoc-fignos in 9 ms
[INFO] Running filter pandoc-eqnos
[INFO] Completed filter pandoc-eqnos in 6 ms
[INFO] Running filter pandoc-tablenos
[INFO] Completed filter pandoc-tablenos in 7 ms
[INFO] Running filter pandoc-manubot-cite
[INFO] Completed filter pandoc-manubot-cite in 17 ms
[INFO] Loaded build/assets/style.csl from build/assets/style.csl
[INFO] Loaded images/orcid.svg from content/images/orcid.svg
[INFO] Loaded images/github.svg from content/images/github.svg
[INFO] Loaded images/twitter.svg from content/images/twitter.svg
[INFO] Loaded images/mastodon.svg from content/images/mastodon.svg
[INFO] Fetching https://github.com/manubot/resources/raw/15493970f8882fce22bef829619d3fb37a613ba5/test/square.png...
[INFO] Fetching https://github.com/manubot/resources/raw/15493970f8882fce22bef829619d3fb37a613ba5/test/wide.png...
[INFO] Fetching https://github.com/manubot/resources/raw/15493970f8882fce22bef829619d3fb37a613ba5/test/tall.png...
[INFO] Fetching https://raw.githubusercontent.com/manubot/resources/main/test/vector.svg?sanitize=true...
[INFO] Not rendering RawInline (Format "html") "<small>"
[INFO] Not rendering RawInline (Format "html") "<em>"
[INFO] Not rendering RawInline (Format "html") "</em>"
[INFO] Not rendering RawInline (Format "html") "</small>"
[INFO] Not rendering RawInline (Format "html") "<br>"
[INFO] Not rendering RawInline (Format "html") "<br>"
[INFO] Not rendering RawInline (Format "html") "<small>"
[INFO] Not rendering RawInline (Format "html") "</small>"
[INFO] Not rendering RawInline (Format "html") "<br>"
[INFO] Not rendering RawInline (Format "html") "<br>"
[INFO] Not rendering RawInline (Format "html") "<small>"
[INFO] Not rendering RawInline (Format "html") "</small>"
[INFO] Not rendering RawInline (Format "html") "<!-- $colspan=\"2\" -->"
[INFO] Not rendering RawInline (Format "html") "<i class=\"fas fa-exclamation-triangle\">"
[INFO] Not rendering RawInline (Format "html") "</i>"
[INFO] Not rendering RawInline (Format "html") "<!-- $id=\"element_id\" class=\"some_class\" $style=\"color: #ad1457; margin-left: 40px;\" $disabled=\"true\" $title=\"a paragraph of text\" $data-color=\"red\" -->"
[INFO] Not rendering RawInline (Format "html") "<link rel=\"stylesheet\" href=\"https://use.fontawesome.com/releases/v5.7.2/css/all.css\">"
[INFO] Not rendering RawInline (Format "html") "<i class=\"fas fa-check\">"
[INFO] Not rendering RawInline (Format "html") "</i>"
[INFO] Not rendering RawInline (Format "html") "<i class=\"fas fa-question\">"
[INFO] Not rendering RawInline (Format "html") "</i>"
[INFO] Not rendering RawInline (Format "html") "<i class=\"fas fa-star\">"
[INFO] Not rendering RawInline (Format "html") "</i>"
[INFO] Not rendering RawInline (Format "html") "<i class=\"fas fa-bell\">"
[INFO] Not rendering RawInline (Format "html") "</i>"
[INFO] Not rendering RawInline (Format "html") "<i class=\"fas fa-times-circle\">"
[INFO] Not rendering RawInline (Format "html") "</i>"
[INFO] Not rendering RawInline (Format "html") "<i class=\"fas fa-ellipsis-h\">"
[INFO] Not rendering RawInline (Format "html") "</i>"
[INFO] Not rendering RawInline (Format "html") "<i class=\"fas fa-scroll fa-lg\">"
[INFO] Not rendering RawInline (Format "html") "</i>"
[INFO] Not rendering RawInline (Format "html") "<br>"
[INFO] Not rendering RawInline (Format "html") "<i class=\"fas fa-info-circle fa-lg\">"
[INFO] Not rendering RawInline (Format "html") "</i>"
[INFO] Not rendering RawInline (Format "html") "<br>"
[INFO] Not rendering RawInline (Format "html") "<i class=\"fas fa-ban fa-lg\">"
[INFO] Not rendering RawInline (Format "html") "</i>"
[INFO] Not rendering RawInline (Format "html") "<br>"
Build complete
## WARNING
webpage/v/local exists: replacing it with an empty directory

agitter · 2023-03-11T04:40:12Z

I'm testing the environment in Windows and couldn't install the current environment from f99263d. I received incompatible package conflicts until I unpinned the Python version and let conda choose Python 3.10.6. I also removed Weasyprint in case that was causing problems as it has in the past (#448).

I also got the warning from Word when opening a docx built in the current environment. That is due to the known problems with equations (#435). When I delete equations from the content, the warning disappears.

My document in the current environment looks like this:

manuscript.docx

In the new environment with librsvg it looks like this:

manuscript.docx

So librsvg works on Windows. I didn't attempt to investigate the problems with svg images referenced by URL. Even if we don't fix those in this pull request, this is an improvement. Do we want to explore that problem further or merge this?

dhimmel · 2023-03-11T18:38:47Z

I didn't attempt to investigate the problems with svg images referenced by URL. Even if we don't fix those in this pull request, this is an improvement. Do we want to explore that problem further or merge this?

I'm in favor of merging now. We probably should update all the conda versions including weasyprint if possible and this issue might resolve itself since its an upstream problem.

miltondp · 2023-03-11T22:41:05Z

I also agree with merging now. The URL issue with images should probably be addressed in a separate issue, and could probably be low priority since there is an easy workaround.

merges manubot/rootstock#489 closes manubot/rootstock#488 * environment: add librsvg * add note about using SVG files from URL and exporting to docx

miltondp added 2 commits March 6, 2023 15:14

environment: add librsvg

ee76e0f

add note about using SVG files and exporting to docx

6071782

miltondp marked this pull request as ready for review March 6, 2023 20:41

dhimmel approved these changes Mar 11, 2023

View reviewed changes

agitter approved these changes Mar 12, 2023

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agitter merged commit f3e0520 into manubot:main Mar 12, 2023

danich1 pushed a commit to danich1/word_lapse_manuscript that referenced this pull request Apr 5, 2023

Add librsvg as dependency

6b66718

merges manubot/rootstock#489 closes manubot/rootstock#488 * environment: add librsvg * add note about using SVG files from URL and exporting to docx

miltondp deleted the docx-svg branch June 1, 2023 19:13

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Add librsvg as dependency #489

Add librsvg as dependency #489

miltondp commented Mar 6, 2023

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miltondp commented Mar 11, 2023

Add librsvg as dependency #489

Add librsvg as dependency #489

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