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README.md

An R Package for Building Books or Documents using pandoc

Travis CI Build Status

  1. Introduction
  2. Features via Extented Markdown
  3. Running the Tool Chain Locally
  4. Running the Tool Chain in the Cloud / via GitHub + Travis CI
  5. Related Projects and Building Blocks
  6. License
  7. Contact

1. Introduction

This is an R package intended for building electronic books from pandoc's markdown flavor by using, well, pandoc and R. You can see it in action in our project An Introduction to Optimization Algorithms, which is written in Markdown and automatically converted to pdf, html, epub, and azw3 by using this package. Our package aims at making it easier to dynamically write books and even publish them online by reducing most of the work to the invocation of a single command. It therefore extends the standard tools provided by pandoc with a set of additional commands.

The package is the basis for our docker container "thomasweise/docker-bookbuilder" at Docker Hub. The sources of this container are provided in the GitHub repository thomasWeise/docker-bookbuilder. The container includes all necessary software components needed to run and build electronic books by using the scripts here, such as complete installations of pandoc, R, and TeX Live.

It is suitable for the integration into a CI environment, which can be used to completely automate the development of electronic books.

2. Features via Extented Markdown

If you use this tool chain, you will write the book in pandoc flavored markdown flavor. However, we introduce some additional features to make life easier. For instance, pandoc traditionally processes a list of files sequentially. If you write a larger book, however, you may sometimes want to insert a section as a new file into a chapter. Thus, we add commands so that you can structure your book as a hierarchy of files where each file can "include" other files, making it unnecessary to maintain a global file order in a single location. Also, you may want to include the current date or repository commit into the book – and there are now commands for that as well. Thus, we provide several additional commands to ease the work on books, especially for the fields of computer science and mathematics.

2.1. Added Functionality

The core facility is the hierarchical inclusion and referencing of files, which allows for a more 'decentralized' working method, where the global book structure results from the locally included files and does not need to be known in the root document. You can easily modify the book structure by including files and nesting folders in your current working directory without going back and forth to the main document. We also add commands also allow you to define and reference proof/definition/...-like environments.

Furthermore, the added commands allow for dynamically linking to a "source code repository". Let's say you write a book about Java. You would then probably want to have a lot of programming examples. You can keep these in a separate source code repository, e.g., on GitHub. This repository could also feature build and test scripts, etc., and could be a fully functional application or library. The book's sources then can reside in a different repository and are thus separate from the programming code examples. You can specify this repository as codeRepo in the book's YAML metadata. The source code repository is automatically cloned during the book building process and all of its files are accessible. You even have access to the commit id of the source code repository, so that you can print it in the book and thus allow the readers to go back to exactly the right version of the code even if you further improve the code in the future.

The scripts of our package are to be used from the command line. The functions are is designed to hard-fail on any error, so you can directly see if there is a problem instead of having some garbage output somewhere in your compiled book.

This package, together with a complete installation of pandoc, R, TeX Live, calibre, and all other necessary tools is available as a Docker image at http://hub.docker.com/r/thomasweise/docker-bookbuilder. Thus, you can use it as tool for all your book-writing purposes. You may even integrate it with Travis CI and GitHub, as described here to achieve a fully-automated book writing and publishing tool chain.

2.2. Provided Commands

You can now use the following commands in your markdown:

  • \relative.path{path} is a path expression relative to the currently processed file's directory which will be resolved to be relative to the root folder of the document. This is intended to allow you to place chapters and sections in a hierarchical folder structure and their contained images in sub-folders, while referencing them relatively from the current path.
  • \relative.input{file} is a command similar to \relativel.path. If this command is used, it must be the only text/command on the current line. It will resolve the path to file relative to the directory of the current file and recursively include that file. This is another tool to allow for building documents structured in chapters, sections, and folders without needed to specify the overall, global structure anywhere and instead specify the inclusion of files where they are actually needed.
  • \meta.time prints the current date and time.
  • \meta.date prints the current date.
  • \meta.year prints the current year.
  • \text.block{type}{label}{body} creates a text block by putting the title-cased type together with the block number in front in double-emphasis (the blocks of each type are numbered separately) and then the body. \text.block{definition}{d1}{blabla} \text.block{definition}{d2}{blubblub} will render to **Defininition 1:** blabla**Defininition 2:** blubblub in the Markdown to be processed by pandoc. Blocks can be referenced in the text via their label in \text.ref{label}. The goal is to achieve theorem-style environments, but on top of markdown.
  • \text.ref{label} references a text block with the same label (see command above). In the example given above, \text.ref{d2} would render to Definition 2 in the Markdown.
  • \relative.code{path}{lines}{tags} inserts the content of a file identified by the path path which is interpreted relative to the current file. Different from \relative.input, this is intented for reading code and this command therefore provides two content selection mechanisms: lines allows you to specify lines to insert, e.g., 20:22,1:4,7 would insert the lines 1 to 4, 7, and 20 to 22 (in that order). tags allows you to specify a comma-separated list of tags. A tag is a string, say "example1", and then everything between a line containing "start example1" and a line "end example1" is included. The idea is that you would put these start and end markers into line comments (in R starting with "#", in Java with "//"). If you specify multiple tags, the corresponding bodies are merged. If you specify both \code{lines} and \code{tags}, we first apply the line selection and then the tag selection only on the selected lines.
  • \repo.code{path}{lines}{tags} if and only if you specify a codeRepo url in your YAML metadata of the book, you can use this command, which allows you to download and access a repository with source code. This way, you can have a book project in one repository and a repository with separate, working, executable examples somewhere else. This second repository, identified by codeRepo, will be cloned once. Then, the path path is interpreted relative to the root path of the repository and you can include code from that repository in the same fashion as with \relative.code.
  • \repo.listing{label}{caption}{language}{path}{lines}{tags} puts the result of \repo.code{path}{lines}{tags} into a markdown/pandoc-crossref compatible listing environment that can be referenced via [@label] (where label should start with lst:), has caption caption, and is formatted for programming language language. Furthermore, this method also automatically removes meta-comments, such as /** ... */ in Java or #' .. in R, a feature currently only implemented for Java and R. If the source code repository resides on GitHub, this method will also append a link of the form (src) to the caption which goes to the file in the repository.
  • \repo.name is replaced with the source code repository name provided as codeRepo in the YAML metadata, without a trailing .git, if any.
  • \repo.commit is replaced with the commit of the source code repository that was downloaded an during the book building procedure.
  • \direct.r{rcode} directly executes a piece rcode of R code. If the code writes any output via, e.g., cat(..), then this output is pasted into the file. If the code does not produce such output, the its return value is transformed to a string and pasted.
  • \relative.r{path} similar to \direct.r, but instead execute the file refered by path, which is relative to the current directory.

The following commands will only work within Travis CI builds and (intentionally) crash otherwise:

  • \meta.repository get the repository in format owner/repository, taken from the environment variable TRAVIS_REPO_SLUG or, if that is not defined, REPOSITORY
  • \meta.commit get the commit id, taken from the environment variable TRAVIS_COMMIT, or, if that not exists, COMMIT

2.3. Graphics

Generally, we suggest to use only vector graphics in your books, as opposed to raster graphics like jpg or png. Don't use jpg or png for anything different from photos. Vector graphics can scale well and have a higher quality when being printed or when being zoomed in. Raster graphics often get blurry or even display artifacts.

In my opinion, the best graphics format to use in conjunction with our tool is svg (and, in particular, its compressed variant svgz). You can create svg graphics using the open-source editor Inkscape or software such as Adobe Illustrator or Corel DRAW.

We provide the small tool ultraSvgz, which runs under Linux and can create very small, minified and compressd svgz files from svgs. Our tool suite supports svgz fully and such files tend to actually be smaller than pdf or eps graphics.

3. Automated Local Book Compilation based on pandoc, calibre, and docker

You can apply this package locally to a book or document you write on your computer. In order to avoid installing all required software and even to avoid messing with R, you can use the docker container we have developed for this purpose. Docker is something like a light-weight virtual machine, and our container is basically a copy of a complete Linux installation with all required components that you can run on your local computer.

By using our container, the following output formats will automatically be generated:

  • PDF for reading on the computer and/or printing,
  • EPUB3 for reading on most mobile phones or other hand-held devices,
  • AZW3 for reading on Kindle and similar devices, and
  • stand-alone HTML5 for reading in a web browser on any device.

Additionally, a file named index.html will be created, which is a rundimentary directory index listing the above four generated files with their sizes and description.

If you have Linux and docker installed on your system, all what it takes is the following command:

  docker run -v "INPUT_DIR":/input/ \
             -v "OUTPUT_DIR":/output/ \
             -e COMMIT=MY_COMMIT \
             -e REPOSITORY=MY_REPOSITORY_NAME \
             -t -i thomasweise/docker-bookbuilder BOOK_ROOT_MD_FILE YOUR_BOOK_OUTPUT_BASENAME

Here, it is assumed that

  • INPUT_DIR is the directory where your book sources reside, let's say /home/my/book/sources/.
  • BOOK_ROOT_MD_FILE is the root file of your book, say book.md (in which case, the full path of book.md would be /home/my/book/sources/book.md). Notice that you can specify only a single file, but this file can reference other files in sub-directories of INPUT_DIR by using commands such as \relative.input.
  • OUTPUT_DIR is the output directory where the compiled files should be placed, e.g., /home/my/book/compiled/. This is where the resulting files will be placed.
  • YOUR_BOOK_OUTPUT_BASENAME is the basis for the names of the compiled files, e.g., coolBook, which would lead to the creation of coolBook.pdf, coolBook.html, and coolBook.epub in the folder references by OUTPUT_DIR.
  • If you make use of the command \meta.commit, you need to tell the container a commit-id. Only in this case, you need to specify the parameter "-e COMMIT=MY_COMMIT", where MY_COMMIT must be replaced with that id. Otherwise, you can leave this parameter away.
  • If you make use of the command \meta.repository, you need to tell the container a commit-id. Only in this case, you need to specify the parameter "-e REPOSITORY=MY_REPOSITORY_NAME", where MY_REPOSITORY_NAME must be replaced with that id. Otherwise, you can leave this parameter away.

And that's it. No software installation, besides docker, is required. The container brings all required tools, scripts, packages, and what not. Additionally, in the section below you can see how the whole build process can be automated by using continuous integration tool chains.

4. An Automatic Online-Book Building Approach by Using GitHub and Travis-CI

With out package and associated docker container, you can conveniently build your electronic book on your computer with a single command. However, you can also integrate the whole process with a version control software like Git and a continuous integration framework. Then, you can automate the compilation of your book to run every time you change your book sources. Actually, there are several open source and free environments that you can use to that for you for free – in exchange for you making your book free for everyone to read.

First, both for writing and hosting the book, we suggest to use a GitHub repository, very much like the one for the book I just began working on here. The book should be written in Pandoc's markdown syntax, which allows us to include most of the stuff we need, such as equations and citation references, with the additional comments listed above. For building the book, we will use Travis CI, which offers a free integration with GitHub to build open source software - triggered by repository commits.

Every time you push a commit to your book repository, Travis CI will be notified, and check out the repository. But we have to tell Travis CI what to do with out book's sources, namely to compile them with Pandoc, which we have packaged with all necessary tools and filters into a docker container. Once Travis has finished downloading the container and building the book with it, it can "deploy" the produced files.

For this purpose, we make use of GitHub Pages, a feature of GitHub which allows you to have a website for a repository. So we simply let Travis deploy the compiled book, in PDF and EPUB, to the book's repository website. Once the repository, website, and Travis build procedure are all set up, we can concentrate on working on our book and whenever some section or text is finished, commit, and enjoy the automatically new versions.

Having your book sources on GitHub brings several additional advantages, for instance:

  • Since the book's sources are available as GitHub repository, our readers can file issues to the repository, with change suggestions, discovered typos, or with questions to add clarification.
  • They may even file pull requests with content to include.
  • You could also write a book collaboratively – like a software project. This might also be interesting for students who write course notes together.

4.1. The Repository

In order to use our workflow, you need to first have an account at GitHub and then create an open repository for your book. GitHub is built around the distributed version control system git, for which a variety of graphical user interfaces exist - see, e.g., of here. If you have a Debian-based Linux system, you can install the basic git client with command line interface as follows: sudo apt-get install git. You can use either this client or such a GUI to work with your repository.

We suggest that in your main branch of the repository, you put a folder book where all the raw sources and graphics for your book go. In the repository root folder, you can then leave the non-book-related things, like README.md, .travis.yml, and LICENSE.md. At this step, you should choose a license for your project, maybe a creative commons one, if you want.

You should now put a file named "book.md" into the "book" folder of your repository, it could just contain some random text for now, the real book comes later.

4.2. The gh-pages Branch

Since we want the book to be automatically be built and published to the internet, we should have a gh-pages branch in our repository as well. I assume that you have a Unix/Linux system with git installed. In that case, you can do this as follows (based on here and here), by replacing YOUR_USER_NAME with your user name and YOUR_REPOSITORY with your repository name:

git clone --depth=50 --branch=master https://github.com/YOUR_USER_NAME/YOUR_REPOSITORY.git YOUR_USER_NAME/YOUR_REPOSITORY
cd YOUR_USER_NAME/YOUR_REPOSITORY
git checkout --orphan gh-pages
ls -la |awk '{print $9}' |grep -v git |xargs -I _ rm -rf ./_ 
git rm -rf .
git commit --allow-empty -m "root commit"
git push origin gh-pages

You can now safely delete the folder YOUR_USER_NAME/YOUR_REPOSITORY that was created during this procedure. If you go to the settings page of your repository, it should now display something like " Your site is published at https://YOUR_USER_NAME.github.io/YOUR_REPOSITORY/" under point "GitHub Pages". This is where your book will later go.

4.3. Personal Access Token

Later, we will use Travis CI to automatically build your book and to automatically deploy it the GitHub pages branch of your repository. For the latter, Travis will need a so-called personal access token, as described here. You need to create such a token following the steps detailed here. Basically, you go to your personal settings page for your GitHub account, click "Developer Settings" and then "Personal Access Tokens". You click "Generate new token" and confirm your password. Then you need to choose public_repo and click "Generate token". Make sure you store the token as text somewhere safe, we need this token text later on.

4.4. Travis CI: Building and Deployment

With that in place, we can now setup Travis CI for automated building and deployment. You can get a Travis account easily and even sign in with GitHub. When you sign into Travis, it should show you a list with your public GitHub repositories. You need to should enable your book repository for automated build.

Click on the now-activated repository in Travis and click "More Settings". Scroll down to "Environment Variables" and then add a variable named "GITHUB_TOKEN". As value, copy the text of the personal access token that we have created in the previous step.

4.5. .travis.yml

Now we need to finally tell Travis how to build our book, and this can be done by placing a file called .travis.yml into the root folder of your GitHub repository. This file should have the following contents, where YOUR_BOOK_OUTPUT_BASENAME should be replaced with the base name of the files to be generated (e.g., "myBook" will result in "myBook.pdf" and "myBook.epub" later):

sudo: required

language: generic

services:
  - docker

script:
- |
  baseDir="$(pwd)" &&\
  inputDir="${baseDir}/book" &&\
  outputDir="${baseDir}/output" &&\
  mkdir -p "${outputDir}" &&\
  docker run -v "${inputDir}/":/input/ \
             -v "${outputDir}/":/output/ \
             -e TRAVIS_COMMIT=$TRAVIS_COMMIT \
             -e TRAVIS_REPO_SLUG=$TRAVIS_REPO_SLUG \
             -t -i thomasweise/docker-bookbuilder book.md YOUR_BOOK_OUTPUT_BASENAME &&\
  cd "${outputDir}"

deploy:
  provider: pages
  skip-cleanup: true
  github-token: $GITHUB_TOKEN
  keep-history: false
  on:
    branch: master
  target-branch: gh-pages
  local-dir: output

After adding this file, commit the changes and push the commit to the repository. Shortly thereafter, a new Travis build should start. If it goes well, it will produce three files, namely "http://YOUR_USER_NAME.github.io/YOUR_REPOSITORY/YOUR_BOOK_OUTPUT_BASENAME.pdf", "http://YOUR_USER_NAME.github.io/YOUR_REPOSITORY/YOUR_BOOK_OUTPUT_BASENAME.html", "http://YOUR_USER_NAME.github.io/YOUR_REPOSITORY/YOUR_BOOK_OUTPUT_BASENAME.epub", and "http://YOUR_USER_NAME.github.io/YOUR_REPOSITORY/YOUR_BOOK_OUTPUT_BASENAME.azw3", as well as "http://YOUR_USER_NAME.github.io/YOUR_REPOSITORY/index.html" (where YOUR_USER_NAME will be the lower-case version of your user name). You can link them from the README.md file that you probably have in your project's root folder.

4.6. Interaction with Source Code Repository

As discussed above, there are several commands for inte racting with a source code repository. The idea is as follows: You can write your book online, by keeping the book sources in a GitHub repository. Whenever you make a commit to the repository, the book's pdf and epub files will be rebuilt, so the newest book version is always online.

If you write a book related to, e.g., computer science, you may have lots of example codes in some programming language in your book. I think that it is often nice to not just have examples on some "meta-level," but to have real, executable programs as examples. Of course, you may choose to print snippets of them in the book only, but they should be available "in full" somewhere.

For this purpose, the code repository exists. It can be a second GitHub repository, where you keep your programming examples. This second repository may have an independent build cycle, e.g., be a Maven build with unit tests executed on Travis CI, as well. You can specify the URL of this repository as codeRepo in the YAML meta data of your book and then use commands such as \repo.code{path}{lines}{tags}, \repo.listing{label}{caption}{language}{path}{lines}{tags}, \repo.name, and \repo.commit to directly access files in the meta information of this repository.

If you do that, you may choose to follow the approach given in plume-lib/trigger-travis to automatically trigger a build of your book when a commit to your source code repository happens. This is a good idea, because this way your book will stay up-to-date when you, e.g., fix bugs in your example codes or refactor them. Each time your example code repository passes the automatic build process, your book's build process will be triggered and the book will be compiled and published anew.

This concept means that you can edit your source code examples completely independently from the book. You could even write a book about an application you develop on GitHub and cite its sources wherever you want. By using the trigger-travis approach, you will get a new version of the book whenever you change the book and whenever you change the source code.

4.7. Infrastructure

While we have already discussed the interplay of GitHub and Travis CI to get your book compiled, we have omitted one more element of our infrastructure: Docker. Docker allows us to build something like very light-weight virtual machines (I know, they are not strictly virtual machines). For this purpose, we can build images, which are basically states of a file system. Our Travis builds load such an image, namely thomasweise/docker-bookbuilder, which provides my bookbuildeR R package on top of an R installation (thomasweise/docker-pandoc-r) on top of a Pandoc installation (thomasweise/docker-pandoc) on top of a TeX Live installation (thomasweise/docker-texlive-full). Of course, you could also use any of these containers locally or extend them in any way you want, in order to use different tools or book building procedures.

5. Related Projects and Components

5.1. Own Contributed Projects and Components

The following components have been contributed by us to provide this tool chain. They are all open source and available on GitHub.

  • The R package bookbuildeR providing the commands wrapping around pandoc and extending Markdown to automatically build electronic books.
  • "An Introduction to Optimization Algorithms," is a book we are currently working on. It is work in progress, but can serve as an example on how to use this tool chain.
    • aitoa the repository for the sources of the book,
    • aitoa-code the repository for the sources of the example programs used in and referenced by the book,
    • aitoa.pdf the pdf version of the book, generated automatically by this tool chain,
    • aitoa.html the html version of the book, generated automatically by this tool chain,
    • aitoa.epub the epub version of the book, and
    • aitoa.awz3 the awz3 version of the book. generated automatically by this tool chain (the epub format is not yet working well).
  • A hierarchy of docker containers forms the infrastructure for the automated builds:
  • The R package utilizeR holds some utility methods used by bookbuildeR.

5.2. Related Projects and Components Used

6. License

The copyright holder of this package is Prof. Dr. Thomas Weise (see Contact). The package is licensed under the GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007. This package also contains third-party components which are under the following licenses;

6.1. Wandmalfarbe/pandoc-latex-template

We include the pandoc LaTeX template from Wandmalfarbe/pandoc-latex-template by Pascal Wagler and John MacFarlane, which is under the BSD 3 license. For this, the following terms hold:

% Copyright (c) 2018, Pascal Wagler;  
% Copyright (c) 2014--2018, John MacFarlane
% 
% All rights reserved.
% 
% Redistribution and use in source and binary forms, with or without 
% modification, are permitted provided that the following conditions 
% are met:
% 
% - Redistributions of source code must retain the above copyright 
% notice, this list of conditions and the following disclaimer.
% 
% - Redistributions in binary form must reproduce the above copyright 
% notice, this list of conditions and the following disclaimer in the 
% documentation and/or other materials provided with the distribution.
% 
% - Neither the name of John MacFarlane nor the names of other 
% contributors may be used to endorse or promote products derived 
% from this software without specific prior written permission.
% 
% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS 
% "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT 
% LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS 
% FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE 
% COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, 
% INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
% BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 
% LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 
% CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT 
% LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN 
% ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
% POSSIBILITY OF SUCH DAMAGE.
%%

%%
% For usage information and examples visit the GitHub page of this template:
% http://github.com/Wandmalfarbe/pandoc-latex-template
%%

6.2 tajmone/pandoc-goodies HTML Template

We include the pandoc HTML-5 template from tajmone/pandoc-goodies by Tristano Ajmone, Sindre Sorhus, and GitHub Inc., which is under the MIT license. For this, the following terms hold:

MIT License

Copyright (c) Tristano Ajmone, 2017 (github.com/tajmone/pandoc-goodies)
Copyright (c) Sindre Sorhus <sindresorhus@gmail.com> (sindresorhus.com)
Copyright (c) 2017 GitHub Inc.

"GitHub Pandoc HTML5 Template" is Copyright (c) Tristano Ajmone, 2017, released
under the MIT License (MIT); it contains readaptations of substantial portions
of the following third party softwares:

(1) "GitHub Markdown CSS", Copyright (c) Sindre Sorhus, MIT License (MIT).
(2) "Primer CSS", Copyright (c) 2016 GitHub Inc., MIT License (MIT).

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

7. Contact

If you have any questions or suggestions, please contact Prof. Dr. Thomas Weise of the Institute of Applied Optimization at Hefei University in Hefei, Anhui, China via email to tweise@hfuu.edu.cn and tweise@gmx.de.

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