Merge pull request #1 from PatCapon39/Dev

Initial configuration

.github/workflows/jekyll.yml

@@ -12,6 +12,12 @@ permissions:
   id-token: write
 
 jobs:
+  fetch_references_update_tools:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: execute table conversion script
+        run: python scripts/table_conversion.py
   build:
     runs-on: ubuntu-latest
 
@@ -46,4 +52,4 @@ jobs:
           JEKYLL_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Upload artifact
-        uses: actions/upload-pages-artifact@v1
+        uses: actions/upload-pages-artifact@v1

README.md

@@ -1,11 +1,11 @@
 ## About
 
-Please see the [How-to Guide for the template](https://australianbiocommons.github.io/how-to-guide-template/) for more information on how to get started.  
+This is the Australian BioCommons Learning Library - a place for XXXX 
 
 
-## Acknowledgements for the guides
+## Acknowledgements
 
-This work is supported by the [Australian BioCommons](https://www.biocommons.org.au/) via funding from [Bioplatforms Australia](https://bioplatforms.com/), the Australian Research Data Commons (https://doi.org/10.47486/PL105) and the Queensland Government RICF programme. Bioplatforms Australia and the Australian Research Data Commons are funded by the National Collaborative Research Infrastructure Strategy (NCRIS).
+This work is supported by the [Australian BioCommons](https://www.biocommons.org.au/). BioCommons is enabled by the National Collaborative Research Infrastructure Strategy (NCRIS) via [Bioplatforms Australia](https://bioplatforms.com/) funding.
 
 This repository makes use of the ELIXIR toolkit theme: [![theme badge](https://img.shields.io/badge/ELIXIR%20toolkit%20theme-jekyll-blue?color=0d6efd)](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme)
 

_config.yml

@@ -1,10 +1,10 @@
-title: How-to Guide
+title: Learning Library
 # This appears in the html browser tab for the site title (seen mostly by search engines, not users)
 
-#topnav_title: Website title
+topnav_title: Learning Library
 # Optional: this appears on the top navigation bar next to the main_logo.svg icon
 
-description: "A bioinformatics focused How-to Guide"
+description: ""
 # Metadata description of the website
 
 remote_theme: ELIXIR-Belgium/[email protected]
@@ -13,7 +13,7 @@ theme_variables:
   # biocommons blue
   theme_color: 205a86
   topnav:
-    brand_logo: assets/img/Australian-Biocommons-Logo-Tagline-Community-RGB.png
+    brand_logo: images/main-logo.png
 
 exclude:
   - README.md
@@ -34,3 +34,4 @@ plugins:
   - jekyll-sitemap
   - jekyll-github-metadata
   - webrick
+  -jekyll-scholar

_data/CONTRIBUTORS.yml

@@ -12,11 +12,30 @@
 # an example contributor is included below
 # example roles include "lead", "first-author", "author", "editor", "workflow-tester"
 
-#Johan Gustafsson:
-#    git: supernord
-#    email: [email protected]
-#    orcid: 0000-0002-2977-5032
-#    role: author
-#    affiliation: Australian BioCommons / University of Melbourne
+Johan Gustafsson:
+    git: supernord
+    email: [email protected]
+    orcid: 0000-0002-2977-5032
+    role: author
+    affiliation: Australian BioCommons
 
+Patrick Capon:
+    git: PatCapon39
+    email: [email protected]
+    orcid: 0000-0002-7396-5757
+    role: author
+    affiliation: Australian BioCommons
 
+Farah Zaib Khan:
+    git: FarahZKhan
+    email: [email protected]
+    orcid: 0000-0002-6337-3037
+    role: author
+    affiliation: Australian BioCommons
+
+Melissa Burke:
+    git: burkemlou
+    email: [email protected]
+    orcid: 0000-0002-5571-8664
+    role: author
+    affiliation: Australian BioCommons

_data/footer.yml

@@ -1,11 +1,5 @@
-# see https://github.com/AustralianBioCommons/human-omics-data-sharing-field-guide/blob/main/_data/footer.yml
-copyright: Copyright notice
-extra_line: Add other relevant information here!
+copyright: 'This site uses Cookies. We use cookies to help the website run effectively. To find out more, read our [Privacy](https://www.biocommons.org.au/privacy) and [Cookies](https://www.biocommons.org.au/cookies) statements.'
+#extra_line: Add other relevant information here!
 columns:
   - type: links
     width: 3
-    children:
-      - url_text: Home
-        url: /
-      - url_text: Contributors
-        url: /contributors

contributors.md

@@ -3,6 +3,6 @@ title: Contributors
 toc: false
 ---
 
-This How-to Guide would not be possible without the following contributors.
+The Learning Library would not be possible without the following contributors.
 
-{% include contributor-tiles-all.html %}
+{% include contributor-tiles-all.html custom="Johan Gustafsson, Patrick Capon, Melissa Burke, Farah Zaib Khan %}

scripts/table_conversion.py

@@ -0,0 +1,38 @@
+"""
+Adapted from https://github.com/elixir-europe/rdmkit/blob/master/var/conversions.py
+"""
+
+import pandas as pd
+import yaml
+import os
+
+# --------- Variables ---------
+google_id = "1fkilWZmnh3P7VLEvM01I7g9shLkGGTHoT2pHsZmaCmc"
+gid = "0"
+url = f"https://docs.google.com/spreadsheets/d/1uIBItELephFZNjC4UPoegQpo1pIzY15IjOgX8q33slU/edit#gid=0"
+output_path = "_data/resource_list.yml"
+rootdir = '../pages'
+allowed_registries = ['biotools', 'fairsharing', 'tess', 'europmc']
+
+# --------- Converting the table ---------
+
+print(f"----> Converting google table to {output_path} started.")
+resource_table = pd.read_csv(url, dtype={'name': str, 'url': str, 'description': str, 'id': str, 'fairsharing': str,
+                                         'biotools': str, 'tess': str, 'europmc': pd.Int64Dtype()})
+resource_list = resource_table.to_dict("records")
+clean_resource_list = []
+for resource in resource_list:
+    registry_dict = {}
+    for registry in allowed_registries:
+        if not pd.isna(resource[registry]):
+            registry_dict[registry] = resource[registry]
+        del(resource[registry])
+    clean_resource = {k: resource[k] for k in resource if not pd.isna(resource[k])}
+    clean_resource_list.append(clean_resource)
+    clean_resource['registry'] = registry_dict
+
+print(os.getcwd())
+with open(output_path, 'w+') as yaml_file:
+    documents = yaml.dump(clean_resource_list, yaml_file)
+
+print("----> YAML is dumped successfully")