Merge pull request #82 from poseidon-framework/replaceArchiveExplorer

Replace archive explorer

Author: nevrome

_coverpage.md

@@ -2,6 +2,6 @@
 
 > A framework to work with human aDNA data and its archaeological context information.
 
-[Explore our Data <i class="fas fa-globe"></i>](archive_explorer.md)
+[Explore our Data <i class="fas fa-globe"></i>](https://server.poseidon-adna.org)
 [Read the Documentation <i class="fab fa-readme"></i>](home.md)
 [Join our Community <i class="fab fa-gitter"></i>](https://app.gitter.im/#/room/!TycQipeBdEPTHWqilU:gitter.im)

_sidebar.md

@@ -25,7 +25,7 @@
 	* [Developer notes](dev_notes.md)
 * **<i class="fas fa-download" aria-hidden="true"></i>&nbsp; The Poseidon Archives**
 	* [Public archives](archive_overview.md)
-	* [Archive explorer <i class="fas fa-globe-europe" aria-hidden="true"></i>](archive_explorer.md)
+	* [<i class="fas fa-globe-europe" aria-hidden="true"></i> Archive explorer](https://server.poseidon-adna.org)
 	* [Web API](web_api.md)
 	* [Submission guide](archive_submission_guide.md)
 	* [Minotaur workflow](minotaur.md)

archive_explorer.md archive_explorer_old.md

@@ -4,24 +4,26 @@ We, so the [Department of Archaeogenetics](https://www.eva.mpg.de/archaeogenetic
 
 At the moment there are three archives, which are described below:
 
-| Archive Name                                                          | Short | <i class="fab fa-github" aria-hidden="true"></i> GitHub Repository             |
-|-----------------------------------------------------------------------|-------|--------------------------------------------------------------------------------|
-| [The Poseidon Community Archive](#the-poseidon-community-archive-pca) | PCA   | [`community-archive`](https://github.com/poseidon-framework/community-archive) |
-| [The Poseidon Minotaur Archive](#the-poseidon-minotaur-archive-pma)   | PMA   | [`minotaur-archive`](https://github.com/poseidon-framework/minotaur-archive)   |
-| [The Poseidon AADR Archive](#the-poseidon-aadr-archive-paa)           | PAA   | [`aadr-archive`](https://github.com/poseidon-framework/aadr-archive)           |
+| Archive Name                   | Short | <i class="fab fa-github" aria-hidden="true"></i> GitHub Repository | <i class="fas fa-globe-europe" aria-hidden="true"></i> Archive Explorer    |
+|--------------------------------|-------|--------------------------------------------------------------------|----------------------------------------------------------------------------|
+| The Poseidon Community Archive | PCA   | [GitHub](https://github.com/poseidon-framework/community-archive)  | [Explorer](https://server.poseidon-adna.org/explorer/community-archive)    |
+| The Poseidon Minotaur Archive  | PMA   | [GitHub](https://github.com/poseidon-framework/minotaur-archive)   | [Explorer](http://server.poseidon-adna.org:3000/explorer/minotaur-archive) |
+| The Poseidon AADR Archive      | PAA   | [GitHub](https://github.com/poseidon-framework/aadr-archive)       | [Explorer](https://server.poseidon-adna.org/explorer/aadr-archive)         |
 
 We opted to maintain these archives with [Git](https://git-scm.com) on [GitHub](https://github.com/poseidon-framework) to ensure clean version management on the file level. The context data in a Poseidon package is text data that can be stored and maintained easily with line-wise version control. Unfortunately that does not hold true for the large genotype data files. They are not suitable to be handled in Git directly. Instead we rely on GitHub's [large file storage system](https://docs.github.com/en/repositories/working-with-files/managing-large-files/about-large-files-on-github), which comes with a number of technical drawbacks both for developers and users of the Poseidon archives.
 
 We therefore generally do **not** recommend to use the GitHub repositories for end-user-level access to the data. You can explore and download the packages through
 
-- a simple [archive viewer on this webpage](archive_explorer)
+- an [archive viewer](https://server.poseidon-adna.org) provided by our webserver
 - our [Web API](web_api)
 - the [`fetch`](trident#fetch-command) and [`list --remote`](trident#list-command) commands of trident, which use the API internally
 
 We do recommend that you work through GitHub, though, if you want to report an issue or suggest changes to the data (as described [here](archive_submission_guide.md)).
 
 ## The Poseidon Community Archive (PCA)
 
+<i class="fas fa-arrow-right"></i> [<i class="fab fa-github" aria-hidden="true"></i> GitHub](https://github.com/poseidon-framework/community-archive) | [<i class="fas fa-globe-europe" aria-hidden="true"></i> Explorer](https://server.poseidon-adna.org/explorer/community-archive)
+
 The Poseidon Community Archive is the oldest and arguably the most important public archive. It stores publication-wise packages, so one package for the genotype data released with one paper.
 
 **The PCA focusses on author submissions**, so Poseidon packages prepared by the authors of the packaged publication, containing exactly the genotype data used for the analysis in the paper. This ensures a high degree of computational reproducibility. Author submissions are also ideal for the context data in the .janno file, because the respective domain-experts are generally most knowledgable on the spatiotemporal origin of their samples.
@@ -30,10 +32,14 @@ For historical reasons the PCA does not only contain author submissions, though.
 
 ## The Poseidon Minotaur Archive (PMA)
 
+<i class="fas fa-arrow-right"></i> [<i class="fab fa-github" aria-hidden="true"></i> GitHub](https://github.com/poseidon-framework/minotaur-archive) | [<i class="fas fa-globe-europe" aria-hidden="true"></i> Explorer](https://server.poseidon-adna.org/explorer/minotaur-archive)
+
 The Poseidon Minotaur Archive mirrors the PCA in that it features publication-wise packages, sometimes even the very same as the PCA. To distinguish them clearly, package titles and sample-wise Poseidon_IDs in the PMA carry the suffix `_MNT` (for "MiNoTaur").
 
 **Packages in the PMA include consistently reprocessed genotype data**, run through the [Minotaur workflow](minotaur). Consitent bioinformatic processing across publications is an important quality for meta-analysis. So while the context information in the .janno file between PCA and PMA overlaps, the PMA packages are adjusted for data reuse beyond paper-wise reproducibility.
 
 ## The Poseidon AADR Archive (PAA)
 
+<i class="fas fa-arrow-right"></i> [<i class="fab fa-github" aria-hidden="true"></i> GitHub](https://github.com/poseidon-framework/aadr-archive) | [<i class="fas fa-globe-europe" aria-hidden="true"></i> Explorer](https://server.poseidon-adna.org/explorer/aadr-archive)
+
 The Poseidon AADR Archive is the conceptionally most simple archive. It features **"poseidonized" versions of releases of the [Allen Ancient DNA Resource (AADR)](https://reich.hms.harvard.edu/allen-ancient-dna-resource-aadr-downloadable-genotypes-present-day-and-ancient-dna-data)**. The code and decisions for the cleaning and packaging process are documented [here](https://github.com/poseidon-framework/aadr2poseidon). Due to file size limitations of GitHub's LFS system each AADR dataset is split into smaller sub-packages by data type and geographic origin.

archive_overview.md

@@ -128,7 +128,7 @@ An article about Poseidon has been published in <a href="https://elifesciences.o
       <li>A <a href="#archive_overview">guide</a> explains the repositories</li>
       <li>And how to <a href="#archive_submission_guide">contribute data</a></li>
       <li>Our server software provides an open <a href="#web_api">Web-API</a> to access packages</li>
-      <li style="color: #7CFC00">Which enables an <a href="#archive_explorer">overview and download</a> page to browse the archives</li>
+      <li style="color: #7CFC00">Which enables an <a href="https://server.poseidon-adna.org">overview and download</a> page to browse the archives</li>
     </ul>
   </div>
 </div>

home.md

@@ -135,7 +135,7 @@
           var footer = [
             '<hr/>',
             '<footer>',
-            '&copy;2023 Poseidon is an initiative of the <a href="https://www.eva.mpg.de/archaeogenetics/index.html">Department of Archaeogenetics</a> at the Max Planck Institute for Evolutionary Anthropology in Leipzig. The main contact is <a href="https://www.eva.mpg.de/archaeogenetics/staff/stephan-schiffels/">Stephan Schiffels</a>. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement number 851511). This website was built with <a href="https://github.com/docsifyjs/docsify" target="_blank">docsify</a>.',
+            '&copy;2025 Poseidon is an initiative of the <a href="https://www.eva.mpg.de/archaeogenetics/index.html">Department of Archaeogenetics</a> at the Max Planck Institute for Evolutionary Anthropology in Leipzig. The main contact is <a href="https://www.eva.mpg.de/archaeogenetics/staff/stephan-schiffels/">Stephan Schiffels</a>. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement number 851511). This website was built with <a href="https://github.com/docsifyjs/docsify" target="_blank">docsify</a>.',
             '</footer>'
           ].join('');
           hook.afterEach(function(html) {
@@ -187,16 +187,16 @@
   <!-- <script src="https://unpkg.com/browse/[email protected]/src/plugins/external-script.js"></script> -->
 
   <!-- leaflet map -->
-  <link rel="stylesheet" href="https://unpkg.com/[email protected]/dist/leaflet.css"
+  <!-- <link rel="stylesheet" href="https://unpkg.com/[email protected]/dist/leaflet.css"
    integrity="sha256-p4NxAoJBhIIN+hmNHrzRCf9tD/miZyoHS5obTRR9BMY="
-   crossorigin=""/>
+   crossorigin=""/> -->
   <!-- Make sure you put this AFTER Leaflet's CSS -->
-  <script src="https://unpkg.com/[email protected]/dist/leaflet.js"
+  <!-- <script src="https://unpkg.com/[email protected]/dist/leaflet.js"
    integrity="sha256-20nQCchB9co0qIjJZRGuk2/Z9VM+kNiyxNV1lvTlZBo="
    crossorigin=""></script>
   <script src="https://unpkg.com/[email protected]/dist/leaflet.markercluster.js"></script>
   <link rel="stylesheet" href="https://unpkg.com/[email protected]/dist/MarkerCluster.css"></script>
-  <link rel="stylesheet" href="https://unpkg.com/[email protected]/dist/MarkerCluster.Default.css"></script>
+  <link rel="stylesheet" href="https://unpkg.com/[email protected]/dist/MarkerCluster.Default.css"></script> -->
 
   <!-- diagrams with mermaid: https://github.com/Leward/mermaid-docsify -->
   <script type="module">