Merge pull request #167 from NFDI4Microbiota/elhossary

minor fixes
NFDI4Microbiota · Feb 16, 2024 · 05ebcbf · 05ebcbf
2 parents f142484 + 130b1c8
commit 05ebcbf
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diff --git a/Gemfile b/Gemfile
@@ -7,3 +7,5 @@ gemspec
 gem 'jemoji'
 gem 'jekyll-scholar', group: :jekyll_plugins
 gem 'jekyll-redirect-from'
+
+gem "liquid", "~> 4.0.4"
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -84,7 +84,7 @@ GEM
     kramdown-parser-gfm (1.1.0)
       kramdown (~> 2.0)
     latex-decode (0.4.0)
-    liquid (4.0.3)
+    liquid (4.0.4)
     listen (3.7.1)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
@@ -130,6 +130,7 @@ DEPENDENCIES
   jekyll-redirect-from
   jekyll-scholar
   jemoji
+  liquid (~> 4.0.4)
   nokogiri (~> 1.14, >= 1.14.2)
   webrick (~> 1.7)
 

diff --git a/_config.yml b/_config.yml
@@ -6,7 +6,7 @@ description: >- # this means to ignore newlines until "baseurl:"
   Write an awesome description for your new site here. You can edit this
   line in _config.yml. It will appear in your document head meta (for
   Google search results) and in your feed.xml site description.
-baseurl: /nfdi4microbiota-knowledge-base
+#baseurl: /nfdi4microbiota-knowledge-base
 
 excerpts:
   # Displays or hides post excerpts from home layout post listing.
@@ -86,5 +86,5 @@ collections:
 
 # Plugin settings
 scholar:
-  style: american-medical-association
+  #style: american-medical-association # causes duplication in numbering of the references when enabled
   source: ./docs/_bibliography
diff --git a/_includes/navbar.html b/_includes/navbar.html
@@ -14,7 +14,7 @@
     </div>
 
     <a class="navbar-brand p-0 me-0 me-lg-2" href="https://nfdi4microbiota.de/" aria-label="Bootstrap">
-      <img height="45" width="70" src="/nfdi4microbiota-knowledge-base/assets/img/nfdi4microbiota_Logo_new.png"></img>
+      <img height="45" width="70" src="{{ '/assets/img/nfdi4microbiota_Logo_new.png' | relative_url }}"></img>
       <!-- <svg xmlns="http://www.w3.org/2000/svg" width="40" height="32" class="d-block my-1" viewBox="0 0 118 94"
         role="img">
         <title>NFDI4Microbiota</title>
@@ -48,7 +48,7 @@ <h5 class="offcanvas-title text-white" id="bdNavbarOffcanvasLabel">NFDI4Microbio
         <ul class="navbar-nav flex-row flex-wrap bd-navbar-nav">
           <li class="nav-item col-6 col-lg-auto">
             <a class="nav-link py-2 px-0 px-lg-2 active" aria-current="true"
-              href="/nfdi4microbiota-knowledge-base/">KNOWLEDGE BASE</a>
+              href="{{ '/' | relative_url }}">KNOWLEDGE BASE</a>
           </li>
         </ul>
 

diff --git a/_layouts/default.html b/_layouts/default.html
@@ -4,22 +4,22 @@
 <head>
     <meta charset="utf-8">
     <meta name="viewport" content="width=device-width, initial-scale=1">    
-    <link rel="icon" type="image/x-icon" href={{ '/assets/img/favicon.ico' | relative_url }}>
+    <link rel="icon" type="image/x-icon" href="{{ '/assets/img/favicon.ico' | relative_url }}">
     <meta name="docsearch:language" content="en">
 
     <title>The NFDI4Microbiota Knowledge Base</title>
 
-    <script src="/nfdi4microbiota-knowledge-base/assets/js/color-modes.js"></script>
+    <script src="{{ '/assets/js/color-modes.js' | relative_url }}"></script>
 
-    <link rel="stylesheet" href="/nfdi4microbiota-knowledge-base/assets/css/docsearch.css">
+    <link rel="stylesheet" href="{{ '/assets/css/docsearch.css' | relative_url }}">
 
-    <link href="/nfdi4microbiota-knowledge-base/assets/css/bootstrap53..min.css" rel="stylesheet">
+    <link href="{{ '/assets/css/bootstrap53..min.css' | relative_url }}" rel="stylesheet">
 
-    <link href="/nfdi4microbiota-knowledge-base/assets/css/docs53.css" rel="stylesheet">
+    <link href="{{ '/assets/css/docs53.css' | relative_url }}" rel="stylesheet">
 
 
 
-    <script defer src="/nfdi4microbiota-knowledge-base/assets/js/usefathom.js" data-site="ITUSEYJG"></script>
+    <script defer src="{{ '/assets/js/usefathom.js' | relative_url }}" data-site="ITUSEYJG"></script>
     <script>
         window.ga = window.ga || function () { (ga.q = ga.q || []).push(arguments) }; ga.l = +new Date;
         ga('create', 'UA-146052-10', 'getbootstrap.com');
@@ -230,17 +230,17 @@ <h1 class="bd-title mb-0" id="content">{{ page.title }}</h1>
 
     {% include footer.html %}
 
-    <script src="/nfdi4microbiota-knowledge-base/assets/js/boostrap53.bundle.min.js"></script>
+    <script src="{{ '/assets/js/boostrap53.bundle.min.js' | relative_url }}"></script>
 
 
-    <script src="/nfdi4microbiota-knowledge-base/assets/js/docsearch.js"></script>
+    <script src="{{ '/assets/js/docsearch.js' | relative_url }}"></script>
 
-    <script src="/nfdi4microbiota-knowledge-base/assets/js/bundle.sdk.js"></script>
+    <script src="{{ '/assets/js/bundle.sdk.js' | relative_url }}"></script>
 
-    <script src="/nfdi4microbiota-knowledge-base/assets/js/doc53.js"></script>
+    <script src="{{ '/assets/js/doc53.js' | relative_url }}"></script>
     <script src="https://code.jquery.com/jquery-3.6.0.js" integrity="sha256-H+K7U5CnXl1h5ywQfKtSj8PCmoN9aaq30gDh27Xc0jk="
     crossorigin="anonymous"></script>
-    <script src="/nfdi4microbiota-knowledge-base/assets/js/main.js"></script>
+    <script src="{{ '/assets/js/main.js' | relative_url }}"></script>
 
     <script>
 

diff --git a/docs/_Research-Data-Management/02-rdm.md b/docs/_Research-Data-Management/02-rdm.md
@@ -19,7 +19,7 @@ With the growing application of machine learning in microbiology, such as predic
 ## Research data life cycle
 The research data life cycle is a model that illustrates the steps of RDM and describes how data should ideally flow through a research project to ensure successful data curation and preservation {% cite NTU_LibGuides_RD_life_cycle bobrov_2021 %}. The research data life cycle can be illustrated as follow: 
 
-![Research data life cycle](/nfdi4microbiota-knowledge-base/assets/img/research_data_life_cycle.png)
+![Research data life cycle]({{ '/assets/img/research_data_life_cycle.png' | relative_url }})
 
 ## Benefits of RDM
 

diff --git a/docs/_Research-Data-Management/04-fair.md b/docs/_Research-Data-Management/04-fair.md
@@ -12,7 +12,7 @@ The FAIR data principles are a concise and measurable set of principles that may
 * Enhancing the ability of machines to automatically find and use data.
 * Supporting the reuse of data by individuals, which “is essential to the advancement of research and clinical practice”.
 
-![FAIR Data Principles](/nfdi4microbiota-knowledge-base/assets/img/fair_principles_cropped.png)
+![FAIR Data Principles]({{ '/assets/img/fair_principles_cropped.png' | relative_url }})
 
 The principles {% cite wilkinson_2016 go_fair_2022 %} are reproduced below:
 

diff --git a/docs/_Research-Data-Management/23-research-data-commons.md b/docs/_Research-Data-Management/23-research-data-commons.md
@@ -19,7 +19,7 @@ A brief overview of the RDC architecture is outlined in the attached figure. In
 * Management and Governance
 * External Data Interfaces
 
-![Architecture of the Research Data Commons](/nfdi4microbiota-knowledge-base/assets/img/rdc.png "Architecture of the Research Data Commons"){:width="70%"}
+![Architecture of the Research Data Commons]({{ '/assets/img/rdc.png' | relative_url }} "Architecture of the Research Data Commons"){:width="70%"}
 
 The lower layers contain more technical functionality whereas the upper layers are primarily designed to end-users with domain knowledge. Each of the three lower layers consists of a few different technical components.
 

diff --git a/docs/_Research-Data-Management/24-aruna-object-storage.md b/docs/_Research-Data-Management/24-aruna-object-storage.md
@@ -9,14 +9,14 @@ docs_css: markdown
 Aruna Object Storage (AOS) is a modern distributed storage platform designed to meet the increasing demand for effective data management and storage of scientific data. It is the central storage of the [Research Data Commons (RDC)](02-research-data-commons) cloud layer and the data foundation for the upper layers. It is a cloud-native, scalable system with an API and a S3-compatible interface. It allows resource organization into Objects, Datasets, Collections and Projects. Additionally, it provides an event-driven architecture which enables automation, data validation and improves accessibility and reproducibility of scientific results. AOS is open-source and available at [https://aruna-storage.org](https://aruna-storage.org).
 
 # Factsheet
-* ![Aruna Object Storage Logo](/nfdi4microbiota-knowledge-base/assets/img/aruna_dark_font.png "Aruna Object Storage Logo"){:width="20%"}
+* ![Aruna Object Storage Logo]({{ '/assets/img/aruna_dark_font.png' | relative_url }} "Aruna Object Storage Logo"){:width="20%"}
 * Status: V2.x BETA, V1.x deprecated
 * Current Version: V2.0.x beta
 * Weblink: [https://aruna-storage.org](https://aruna-storage.org)
 * Keywords:  data management, storage, FAIR, multi-cloud, cloud-native, data mesh
 * RDC Integration: integrated or connected
 
-![AOS inside RDC](/nfdi4microbiota-knowledge-base/assets/img/rdc_aruna.png "AOS inside RDC"){:width="70%"}
+![AOS inside RDC]({{ '/assets/img/rdc_aruna.png' | relative_url }} "AOS inside RDC"){:width="70%"}
 
 # Overview
 AOS is a fast, secure and geo-redundant data storage. It offers a sophisticated metadata management according to the FAIR principles. It builds the foundation for RDCs mediation and semantic layer and and handles all stored data objects secure, and data-agnostically.
@@ -31,12 +31,12 @@ AOS key features are:
 
 Storing data in localized, domain-specific data silos has limited use for collaboration, reuse and data analysis. AOS offers significant benefits for research data in NFDI4Biodiversity. These benefits include improved collaboration, compliance with FAIR principles, scalability, robust data security and seamless integration with existing systems and workflow tools. Ultimately, this facilitates scientific progress and enhances the quality of our research.
 
-![Aruna Object Storage Concept](/nfdi4microbiota-knowledge-base/assets/img/concept_aruna.png "Aruna Object Storage Concept"){:width="40%"}
+![Aruna Object Storage Concept]({{ '/assets/img/concept_aruna.png' | relative_url }} "Aruna Object Storage Concept"){:width="40%"}
 
 # Getting started
 AOS is located at [https://aruna-storage.org](https://aruna-storage.org). Users can log in there. Currently, the AAI of the GWDG is used for this purpose, which requires a user account at the GWDG, the DFN or at LifeScience AAI. Nevertheless, additional identity providers are possible. Thus, login via an SSO of NFDI4Biodiversity (and other NFDIs) will be supported when the service is established. After the AOS account has been activated, the user can create a project. Further users can then be activated for this project to enable data exchange and joint processing. The project can then be filled with data either via the API or via the S3 interface.
 
-![Aruna Object Storage Start Page](/nfdi4microbiota-knowledge-base/assets/img/aruna-startpage-2023-7-28_8-24-10.png "Aruna Object Storage Start Page"){:width="60%"}
+![Aruna Object Storage Start Page]({{ '/assets/img/aruna-startpage-2023-7-28_8-24-10.png' | relative_url }} "Aruna Object Storage Start Page"){:width="60%"}
 
 # User Guide
 Basically, AOS is intended as a data backend for the RDC. For this reason, very few end users will use AOS directly. Data import, verification, transformation and processing is basically possible via the services in the mediation layer. This also ensures the consistency of the data. Users and services can be informed about changes to individual data objects or even entire projects via the AOS notification service and can thus react to these changes.
@@ -50,11 +50,11 @@ The main component of AOS is a distributed database system. It synchronizes all
 ## AOS data structure
 AOS organizes data in Version 1.x into Projects, Collections, Object Groups, and Objects, starting with version 2.x the data structure will be even more flexible and are organized into Projects, Collections, Datasets, and Objects with a more flexible relation model.
 
-|![Aruna Object Storage Structure V1](/nfdi4microbiota-knowledge-base/assets/img/aruna-1-structure.png "Aruna Object Storage Structure V1"){:width="50%"} |
+|![Aruna Object Storage Structure V1]({{ '/assets/img/aruna-1-structure.png' | relative_url }} "Aruna Object Storage Structure V1"){:width="50%"} |
 |-|
 | UML diagram of the Aruna Object Storage data structure in Version v1.0.x |
 
- | ![Aruna Object Storage Structure V2](/nfdi4microbiota-knowledge-base/assets/img/aruna-2-structure.png "Aruna Object Storage Structure V2"){:width="50%"} |
+ | ![Aruna Object Storage Structure V2]({{ '/assets/img/aruna-2-structure.png' | relative_url }} "Aruna Object Storage Structure V2"){:width="50%"} |
 |-|
 | UML diagram of the Aruna Object Storage data structure starting in Version v2.0. All resources form a directed acyclic graph of belongs to relationships (blue) with Projects as roots and Objects as leaves. Resources can also describe horizontal version relationships (orange), data/metadata relationships (yellow) or even custom user-defined relationships (green). |
 

diff --git a/docs/_Research-Data-Management/26-licenses.md b/docs/_Research-Data-Management/26-licenses.md
@@ -43,7 +43,7 @@ There are different versions of CC that consist of the core license with further
 - **Non-derivative (ND):** No derivatives or adaptations of the work are permitted (not compatible with share-alike).
 
 
-![ccsprectrum](/nfdi4microbiota-knowledge-base/assets/img/Creative_commons_license_spectrum.svg)
+![ccsprectrum]({{ '/assets/img/Creative_commons_license_spectrum.svg' | relative_url }})
 
 ([Source](https://commons.wikimedia.org/wiki/File:Creative_commons_license_spectrum.svg), CC-BY Shaddim; original CC license symbols by Creative Commons)