larkumlab
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Dealing_with_Gin


			
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<li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Dealing with Gin</a></li>
<li class="chapter" data-level="2" data-path="intro.html"><a href="intro.html"><i class="fa fa-check"></i><b>2</b> Intro</a><ul>
<li class="chapter" data-level="2.1" data-path="intro.html"><a href="intro.html#play-with-sandbox"><i class="fa fa-check"></i><b>2.1</b> Play with Sandbox</a></li>
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<li class="chapter" data-level="3" data-path="web-interface.html"><a href="web-interface.html"><i class="fa fa-check"></i><b>3</b> Web interface</a><ul>
<li class="chapter" data-level="3.1" data-path="web-interface.html"><a href="web-interface.html#cannot-see-a-repository"><i class="fa fa-check"></i><b>3.1</b> Cannot see a repository?</a><ul>
<li class="chapter" data-level="3.1.1" data-path="web-interface.html"><a href="web-interface.html#sign-in-to-gin"><i class="fa fa-check"></i><b>3.1.1</b> Sign in to Gin</a></li>
<li class="chapter" data-level="3.1.2" data-path="web-interface.html"><a href="web-interface.html#check-that-the-repository-exists"><i class="fa fa-check"></i><b>3.1.2</b> Check that the repository exists</a></li>
<li class="chapter" data-level="3.1.3" data-path="web-interface.html"><a href="web-interface.html#make-sure-you-have-access-to-the-repository"><i class="fa fa-check"></i><b>3.1.3</b> Make sure you have access to the repository</a></li>
</ul></li>
<li class="chapter" data-level="3.2" data-path="web-interface.html"><a href="web-interface.html#dashboard-how-to-use"><i class="fa fa-check"></i><b>3.2</b> Dashboard: how to use</a><ul>
<li class="chapter" data-level="3.2.1" data-path="web-interface.html"><a href="web-interface.html#activity"><i class="fa fa-check"></i><b>3.2.1</b> Activity</a></li>
<li class="chapter" data-level="3.2.2" data-path="web-interface.html"><a href="web-interface.html#collaborative-repositories"><i class="fa fa-check"></i><b>3.2.2</b> Collaborative repositories</a></li>
<li class="chapter" data-level="3.2.3" data-path="web-interface.html"><a href="web-interface.html#private-repositories"><i class="fa fa-check"></i><b>3.2.3</b> Private repositories</a></li>
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<li class="chapter" data-level="3.3" data-path="web-interface.html"><a href="web-interface.html#browsing-a-repository"><i class="fa fa-check"></i><b>3.3</b> Browsing a repository</a><ul>
<li class="chapter" data-level="3.3.1" data-path="web-interface.html"><a href="web-interface.html#overview-of-the-repository"><i class="fa fa-check"></i><b>3.3.1</b> Overview of the repository</a></li>
<li class="chapter" data-level="3.3.2" data-path="web-interface.html"><a href="web-interface.html#browsing-files"><i class="fa fa-check"></i><b>3.3.2</b> Browsing files</a></li>
</ul></li>
<li class="chapter" data-level="3.4" data-path="web-interface.html"><a href="web-interface.html#downloading-files"><i class="fa fa-check"></i><b>3.4</b> Downloading files</a><ul>
<li class="chapter" data-level="3.4.1" data-path="web-interface.html"><a href="web-interface.html#download-button"><i class="fa fa-check"></i><b>3.4.1</b> Download button</a></li>
</ul></li>
<li class="chapter" data-level="3.5" data-path="web-interface.html"><a href="web-interface.html#uploading-files"><i class="fa fa-check"></i><b>3.5</b> Uploading files</a><ul>
<li class="chapter" data-level="3.5.1" data-path="web-interface.html"><a href="web-interface.html#location-of-the-buttons"><i class="fa fa-check"></i><b>3.5.1</b> Location of the buttons</a></li>
<li class="chapter" data-level="3.5.2" data-path="web-interface.html"><a href="web-interface.html#common-features-for-file-upload"><i class="fa fa-check"></i><b>3.5.2</b> Common features for file-upload</a></li>
<li class="chapter" data-level="3.5.3" data-path="web-interface.html"><a href="web-interface.html#uploading-a-set-of-files"><i class="fa fa-check"></i><b>3.5.3</b> Uploading a set of files</a></li>
<li class="chapter" data-level="3.5.4" data-path="web-interface.html"><a href="web-interface.html#create-a-new-text-file"><i class="fa fa-check"></i><b>3.5.4</b> Create a new (text) file</a></li>
<li class="chapter" data-level="3.5.5" data-path="web-interface.html"><a href="web-interface.html#edit-a-text-file"><i class="fa fa-check"></i><b>3.5.5</b> Edit a (text) file</a></li>
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<li class="chapter" data-level="4" data-path="using-application-made-for-git.html"><a href="using-application-made-for-git.html"><i class="fa fa-check"></i><b>4</b> Using application made for git</a><ul>
<li class="chapter" data-level="4.1" data-path="using-application-made-for-git.html"><a href="using-application-made-for-git.html#generalities"><i class="fa fa-check"></i><b>4.1</b> generalities</a></li>
<li class="chapter" data-level="4.2" data-path="using-application-made-for-git.html"><a href="using-application-made-for-git.html#git-gui"><i class="fa fa-check"></i><b>4.2</b> Git GUI</a></li>
<li class="chapter" data-level="4.3" data-path="using-application-made-for-git.html"><a href="using-application-made-for-git.html#using-rstudio-with-gin"><i class="fa fa-check"></i><b>4.3</b> Using Rstudio with GIN</a></li>
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<div id="web-interface" class="section level1">
<h1><span class="header-section-number">3</span> Web interface</h1>
<div id="cannot-see-a-repository" class="section level2">
<h2><span class="header-section-number">3.1</span> Cannot see a repository?</h2>
<p>So often, you try to visit a repository, and find something like below:</p>
<div class="figure">
<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/norepository.png" alt="404 page" />
<p class="caption">404 page</p>
</div>
<p>The solutions are:</p>
<ol style="list-style-type: decimal">
<li>Sign in to Gin</li>
<li>Check that the repository exists</li>
<li>Make sure you have access to the repository</li>
</ol>
<div id="sign-in-to-gin" class="section level3">
<h3><span class="header-section-number">3.1.1</span> Sign in to Gin</h3>
<p>It happens when you are not signed in to Gin.</p>
<p>Click on the “Sign in” button at the top-right corner of the page:</p>
<div class="figure">
<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/signin.png" alt="Sign-in button" />
<p class="caption">Sign-in button</p>
</div>
<p>(If you have not yet got registered to Gin, then do it first from the “Register” button on the right.</p>
</div>
<div id="check-that-the-repository-exists" class="section level3">
<h3><span class="header-section-number">3.1.2</span> Check that the repository exists</h3>
<p>If the situation persists, go visit your <a href="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/Dashboard.md">dashboard</a>,
and find the name of the repository from the list.
If you click on it, the repository page should show up.</p>
</div>
<div id="make-sure-you-have-access-to-the-repository" class="section level3">
<h3><span class="header-section-number">3.1.3</span> Make sure you have access to the repository</h3>
<p>If you don’t find the repository in your dashboard, then
it is possible that you don’t have access to the repository at all.</p>
<p>Ask somebody who has access rights to the repository <a href="collaboration.md">for adding you as a Collaborator</a>.</p>

</div>
</div>
<div id="dashboard-how-to-use" class="section level2">
<h2><span class="header-section-number">3.2</span> Dashboard: how to use</h2>
<p>When you simply sign in to Gin, without selecting any specific repository,
you fill find a page like below (note that this is just an example):</p>
<div class="figure">
<img src="images/dashboard.png" alt="Dashboard overview" />
<p class="caption">Dashboard overview</p>
</div>
<p>This is called the “dashboard”, and here you can see most of your activity on Gin.</p>
<p>The dashboard may be divided into several areas:</p>
<ol style="list-style-type: decimal">
<li><a href="web-interface.html#activity"><strong>Activity</strong></a> area: shows what you did with your repositories</li>
<li><a href="web-interface.html#collaborative-repositories"><strong>Collaborative repository</strong></a> area: lists up the shared repositories you have access to</li>
<li><a href="web-interface.html#private-repositories"><strong>Private repository</strong></a> area: lists up your <em>own</em> repositories</li>
</ol>
<div id="activity" class="section level3">
<h3><span class="header-section-number">3.2.1</span> Activity</h3>
<div class="figure">
<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/activity-area.png" alt="Activity area" />
<p class="caption">Activity area</p>
</div>
<p>This shows your recent activity on Gin, e.g.</p>
<ul>
<li>your recent commits to your repositories</li>
<li>issues and comments reported to your repositories</li>
</ul>
</div>
<div id="collaborative-repositories" class="section level3">
<h3><span class="header-section-number">3.2.2</span> Collaborative repositories</h3>
<div class="figure">
<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/collaboration-area.png" alt="Collaborative repository area" />
<p class="caption">Collaborative repository area</p>
</div>
<p>This area lists up the repositories <strong>owned by others</strong> and those you have access to.</p>
<p>Normally, most of your repositories will show up here, as they are owned and managed by <span class="citation">@larkumlab</span>.</p>
</div>
<div id="private-repositories" class="section level3">
<h3><span class="header-section-number">3.2.3</span> Private repositories</h3>
<div class="figure">
<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/private-repositories.png" alt="Private repository area" />
<p class="caption">Private repository area</p>
</div>
<p>This area lists up the repositories owned by yourself.</p>
<p>In many cases, these are visible only to you unless you add a <a href="collaboration.md">Collaborator</a> to one of them.</p>

</div>
</div>
<div id="browsing-a-repository" class="section level2">
<h2><span class="header-section-number">3.3</span> Browsing a repository</h2>
<p>If you visit the repository page, it looks like below:</p>
<div class="figure">
<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/repository-top.png" alt="A typical repository page" />
<p class="caption">A typical repository page</p>
</div>
<p>From here, you can browse what is in the repository including:</p>
<ol style="list-style-type: decimal">
<li><a href="web-interface.html#overview-of-the-repository">overview of the repository</a></li>
<li><a href="web-interface.html#browsing-files">file contents</a></li>
</ol>
<div id="overview-of-the-repository" class="section level3">
<h3><span class="header-section-number">3.3.1</span> Overview of the repository</h3>
<p>On top of the page, you will find the header consisting of <code>&lt;owner name&gt;/&lt;repository name&gt;</code>:</p>
<div class="figure">
<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/repository-title.png" alt="Repository name" />
<p class="caption">Repository name</p>
</div>
<p>This represents the <em>identifier</em> of the repository so that
you can specify a single repository inside <code>https://gin.g-node.org</code>.</p>
<p>Down to the bottom, you may find some document:</p>
<div class="figure">
<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/readme.png" alt="README file" />
<p class="caption">README file</p>
</div>
<p>This represents the (hopefully) detailed description of the repository about what it is
or what it contains.</p>
<blockquote>
<p>In fact, this description comes from the <code>README.md</code> file in the root directory of the repository.
The name of the file comes from a tradition of programmers community to contain the “read-me-first”
file in the top directory of any code.</p>
<p>You can add or edit it by adding / editing the <code>README.md</code> file.</p>
<p>Even inside the sub-directories of the repositories, the description will automatically show up
if you add and edit a <code>README.md</code> file in it.</p>
</blockquote>
</div>
<div id="browsing-files" class="section level3">
<h3><span class="header-section-number">3.3.2</span> Browsing files</h3>
<p>In the middle, you can find a list of files and directories in the repository:</p>
<div class="figure">
<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/files.png" alt="File list" />
<p class="caption">File list</p>
</div>
<p>By clicking on individual file/directory entry, you can browse its contents.</p>
<p>For example, you can see the contents of a sub-directory by clicking on it:</p>
<div class="figure">
<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/directory-view.png" alt="Directory view" />
<p class="caption">Directory view</p>
</div>
<p>Contents of normal files may be visible, as long as your browser supports it.</p>
<ul>
<li><p>For example, you can browse to <a href="images/dashboard.png">web-interface/images/dashboard.png</a>,
and you can have a glimpse of the original image file:
<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/image-view.png" alt="Image-file view" /></p></li>
<li><p>If you write the documents in the <a href="https://www.markdownguide.org/getting-started">Markdown</a> format
(and I recommend to do so whenever possible), you can see the formatted-view of the document:
<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/markdown-view.png" alt="Markdown view" /></p></li>
<li>Other text-based files (CSV, TSV etc.) may be seen in its raw format.</li>
<li><p>Binary files (Excel, Word, Spike2 etc.) will not be visible, so you must <a href="downloading.md">download it</a> to see the contents.</p></li>
</ul>
<div id="a-small-side-note" class="section level4">
<h4><span class="header-section-number">3.3.2.1</span> A small side note</h4>
<p>On the left columns of the files list, you can see some information like below:</p>
<div class="figure">
<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/commit-description.png" alt="Commit description" />
<p class="caption">Commit description</p>
</div>
<p>Sadly <strong>it is <em>not</em> about the description to the file itself</strong> but describes the commit
that updated this file most recently.</p>
<p>In the case of the image above, the directory “web-interface” was updated by the commit
with the commit ID being <code>b42b7633f7</code>, and with the commit message <code>update dashboard.md</code>.</p>

</div>
</div>
</div>
<div id="downloading-files" class="section level2">
<h2><span class="header-section-number">3.4</span> Downloading files</h2>
<p>Although the files may be browsable on the web interface, you might want to interact with them on your desktop, using one of your favorite programs.</p>
<p>It is possible to download files individually from the web interface.</p>
<blockquote>
<p>Note that this “individual download” feature differs from what Git-people call “cloning of the repository”. Git-clone involves downloading of the whole repository, whereas this individual download concerns only with the current single file.</p>
</blockquote>
<div id="download-button" class="section level3">
<h3><span class="header-section-number">3.4.1</span> Download button</h3>
<p>When you open a single file, you will see buttons on the top-right of the file:</p>
<div class="figure">
<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/file-actions.png" alt="Location of buttons" />
<p class="caption">Location of buttons</p>
</div>
<p>These buttons represent the actions that you can execute on this specific file, including:</p>
<ul>
<li>Obtaining the link to this specific version of the file (<strong>Permalink</strong>)</li>
<li>Browsing different versions of this file (<strong>History</strong>)</li>
<li>Downloading the file (<strong>Download</strong>)</li>
<li>Editing the file (<strong>the pencil symbol</strong>; it may not be available in the case of read-only repositories, or Gin does not have a way to edit the file e.g. PDF)</li>
<li>Deleting the file from the repository (<strong>the trash-can simbol</strong>; may not be available)</li>
</ul>
<p>For downloading the file, click on the “download” button:</p>
<div class="figure">
<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/download-button.png" alt="Download button" />
<p class="caption">Download button</p>
</div>
<p>Then your browser will start downloading the file.</p>

</div>
</div>
<div id="uploading-files" class="section level2">
<h2><span class="header-section-number">3.5</span> Uploading files</h2>
<p>The Gin web-interface allows you to:</p>
<ul>
<li><a href="web-interface.html#create-a-new-text-file">create</a> a new text-based file,</li>
<li><a href="web-interface.html#edit-a-text-file">edit</a> a text-based file, or</li>
<li><a href="web-interface.html#uploading-a-set-of-files">upload</a> a new set of files.</li>
</ul>
<p>All of the above procedures share some features in common:</p>
<ul>
<li>You can start both of the procedures easily by <a href="web-interface.html#location-of-the-buttons">a click of a button</a>.</li>
<li>You can <a href="web-interface.html#specifying-the-directory-to-be-uploaded">specify the sub-directory in the repository</a> for the file(s) to be uploaded.</li>
<li>You can <a href="web-interface.html#committing-new-files">specify the commit options</a>.</li>
</ul>
<div id="location-of-the-buttons" class="section level3">
<h3><span class="header-section-number">3.5.1</span> Location of the buttons</h3>
<p>When the web interface shows a list of files in a repository, you can see blue buttons in the middle, above the file list.</p>
<blockquote>
<p>Note that, if you don’t have the “write” permission to the repository, these buttons will not appear. If you still want to create or upload files, contact the person responsible for the repository to <a href="collaboration.md">add you as a Collaborator</a>.</p>
</blockquote>
<div class="figure">
<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/upload-actions.png" alt="Where you can find the buttons for file-creation / upload" />
<p class="caption">Where you can find the buttons for file-creation / upload</p>
</div>
<p>There, you have two types of buttons:</p>
<ul>
<li><strong><a href="web-interface.html#uploading-a-set-of-files">“Upload file” button</a></strong>: used to upload a set of files.</li>
<li><strong><a href="#create-new-files">“New file” button</a></strong>: used to create a new file in the repository.</li>
</ul>
<div class="figure">
<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/upload-actions-buttons.png" alt="Two buttons for new files" />
<p class="caption">Two buttons for new files</p>
</div>
</div>
<div id="common-features-for-file-upload" class="section level3">
<h3><span class="header-section-number">3.5.2</span> Common features for file-upload</h3>
<p>No matter which button you use, there are some features shared in common.</p>
<div id="specifying-the-directory-to-be-uploaded" class="section level4">
<h4><span class="header-section-number">3.5.2.1</span> Specifying the directory to be uploaded</h4>
<p>On top of the view, an empty text field will show up:</p>
<div class="figure">
<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/directory-selector-empty.png" alt="Directory selector" />
<p class="caption">Directory selector</p>
</div>
<p>This is for specifying the directory to upload the file(s).</p>
<p>For instance:</p>
<ul>
<li>Enter the name of the subdirectory (within the repository) in this field:</li>
</ul>
<div class="figure">
<img src="images/directory-selector-subdir.png" alt="A subdirectory is specified" />
<p class="caption">A subdirectory is specified</p>
</div>
<ul>
<li>Gin will automatically create a new directory with the given name (in case it does not exist) as you <a href="web-interface.html#committing-new-files">commit uploads (see the section below)</a>:</li>
</ul>
<div class="figure">
<img src="images/created-subdir.png" alt="Created subdirectory" />
<p class="caption">Created subdirectory</p>
</div>
<ul>
<li>Inside the subdirectory, you will find the uploaded file(s):</li>
</ul>
<div class="figure">
<img src="images/subdir-content.png" alt="The uploaded file in the sub-directory" />
<p class="caption">The uploaded file in the sub-directory</p>
</div>
<p>You can also specify the <em>path</em> to the directory of interest, by connecting a hierarchy of directories by a <code>/</code> (slash):</p>
<p>TODO</p>
</div>
<div id="committing-new-files" class="section level4">
<h4><span class="header-section-number">3.5.2.2</span> Committing new files</h4>
<p>TODO</p>
</div>
</div>
<div id="uploading-a-set-of-files" class="section level3">
<h3><span class="header-section-number">3.5.3</span> Uploading a set of files</h3>
<p>When you click on the “Upload file” button, the file upload view will appear:</p>
<div class="figure">
<img src="images/upload-view.png" alt="File-upload view" />
<p class="caption">File-upload view</p>
</div>
<p>The dotted region in the middle of the page is the <em>upload area</em>:</p>
<div class="figure">
<img src="images/upload-view-upload-area.png" alt="The upload area" />
<p class="caption">The upload area</p>
</div>
<p>You can add the files to be uploaded by either:</p>
<ul>
<li><strong>Clicking on the area</strong>: the file chooser dialog will appear so that you can select files from it.</li>
<li><strong>Drag and drop</strong> individual files or a directory containing a set of files. In the latter case, you can upload the whole directory structure easily.</li>
</ul>
<p>In either case, the upload process will start immediately, and you will see the progress on the area:</p>
<div class="figure">
<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/upload-progress.png" alt="Progress of upload" />
<p class="caption">Progress of upload</p>
</div>
<p>You can specify the directory to be uploaded from the <a href="web-interface.html#specifying-the-directory-to-be-uploaded">directory selector (see the section above)</a>.</p>
<p>After completion of the upload processes for all files, you can proceed to finish the <a href="web-interface.html#committing-new-files">commit process (see the section above)</a>.</p>
<blockquote>
<p>Note, by using this upload view, you can only upload 100 files at once, with each file being less than 10 GB in size. If you want to upload more files at once, or upload larger files, you will have to use the command-line interface or WinGIN.</p>
</blockquote>
</div>
<div id="create-a-new-text-file" class="section level3">
<h3><span class="header-section-number">3.5.4</span> Create a new (text) file</h3>
<p>TODO</p>
</div>
<div id="edit-a-text-file" class="section level3">
<h3><span class="header-section-number">3.5.5</span> Edit a (text) file</h3>
<p>TODO</p>

</div>
</div>
</div>
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