From cb3700132bf3b23f631e180d505699113307e803 Mon Sep 17 00:00:00 2001 From: Patrick Capon <137233925+PatCapon39@users.noreply.github.com> Date: Thu, 11 Apr 2024 13:35:03 +0930 Subject: [PATCH 1/8] Update README.md --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 0800d6b..345f9c5 100644 --- a/README.md +++ b/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) From b831f8782c72f0257950a27f4c4b13e9fb56361b Mon Sep 17 00:00:00 2001 From: Patrick Capon <137233925+PatCapon39@users.noreply.github.com> Date: Thu, 11 Apr 2024 13:37:23 +0930 Subject: [PATCH 2/8] Update contributors.md --- contributors.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/contributors.md b/contributors.md index 71f3d44..f7a4892 100644 --- a/contributors.md +++ b/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 %} \ No newline at end of file +{% include contributor-tiles-all.html custom="Johan Gustafsson, Patrick Capon, Melissa Burke, Farah Zaib Khan %} From 781e92407195663f665592539ba722304677d70f Mon Sep 17 00:00:00 2001 From: Patrick Capon <137233925+PatCapon39@users.noreply.github.com> Date: Thu, 11 Apr 2024 13:41:33 +0930 Subject: [PATCH 3/8] Add action for table conversion --- .github/workflows/jekyll.yml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/.github/workflows/jekyll.yml b/.github/workflows/jekyll.yml index e844f14..53d7291 100644 --- a/.github/workflows/jekyll.yml +++ b/.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 \ No newline at end of file + uses: actions/upload-pages-artifact@v1 From 836408359d9e3203d8900b6aad6133bacb0f65be Mon Sep 17 00:00:00 2001 From: Patrick Capon <137233925+PatCapon39@users.noreply.github.com> Date: Thu, 11 Apr 2024 13:45:18 +0930 Subject: [PATCH 4/8] Create table_conversion.py as per Marion's code --- scripts/table_conversion.py | 38 +++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 scripts/table_conversion.py diff --git a/scripts/table_conversion.py b/scripts/table_conversion.py new file mode 100644 index 0000000..9e0b725 --- /dev/null +++ b/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/{google_id}/export?format=csv&gid={gid}" +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") From 80a00c7beb9f29555e7c5374b741db3d8d2d65d7 Mon Sep 17 00:00:00 2001 From: Patrick Capon <137233925+PatCapon39@users.noreply.github.com> Date: Thu, 11 Apr 2024 13:49:54 +0930 Subject: [PATCH 5/8] Update CONTRIBUTORS.yml --- _data/CONTRIBUTORS.yml | 31 +++++++++++++++++++++++++------ 1 file changed, 25 insertions(+), 6 deletions(-) diff --git a/_data/CONTRIBUTORS.yml b/_data/CONTRIBUTORS.yml index 931299a..32d7711 100644 --- a/_data/CONTRIBUTORS.yml +++ b/_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: johan@biocommons.org.au -# orcid: 0000-0002-2977-5032 -# role: author -# affiliation: Australian BioCommons / University of Melbourne +Johan Gustafsson: + git: supernord + email: johan@biocommons.org.au + orcid: 0000-0002-2977-5032 + role: author + affiliation: Australian BioCommons +Patrick Capon: + git: PatCapon39 + email: patrick@biocommons.org.au + orcid: 0000-0002-7396-5757 + role: author + affiliation: Australian BioCommons +Farah Zaib Khan: + git: FarahZKhan + email: farah@biocommons.org.au + orcid: 0000-0002-6337-3037 + role: author + affiliation: Australian BioCommons + +Melissa Burke: + git: burkemlou + email: melissa@biocommons.org.au + orcid: 0000-0002-5571-8664 + role: author + affiliation: Australian BioCommons From 61d6cce7011e375195002c0e19649d0f4619f174 Mon Sep 17 00:00:00 2001 From: Patrick Capon <137233925+PatCapon39@users.noreply.github.com> Date: Thu, 11 Apr 2024 13:51:18 +0930 Subject: [PATCH 6/8] Update footer.yml --- _data/footer.yml | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/_data/footer.yml b/_data/footer.yml index 44ac3e9..a328f4e 100644 --- a/_data/footer.yml +++ b/_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 \ No newline at end of file From 2ce302e44b0503693024f406f7a45e554a72f910 Mon Sep 17 00:00:00 2001 From: Patrick Capon <137233925+PatCapon39@users.noreply.github.com> Date: Thu, 11 Apr 2024 13:54:39 +0930 Subject: [PATCH 7/8] Switch to Melissa's draft table --- scripts/table_conversion.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/table_conversion.py b/scripts/table_conversion.py index 9e0b725..d406266 100644 --- a/scripts/table_conversion.py +++ b/scripts/table_conversion.py @@ -9,7 +9,7 @@ # --------- Variables --------- google_id = "1fkilWZmnh3P7VLEvM01I7g9shLkGGTHoT2pHsZmaCmc" gid = "0" -url = f"https://docs.google.com/spreadsheets/d/{google_id}/export?format=csv&gid={gid}" +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'] From 56d64260eff6521d6eca0c7299ba74f9012e8a68 Mon Sep 17 00:00:00 2001 From: Patrick Capon <137233925+PatCapon39@users.noreply.github.com> Date: Thu, 11 Apr 2024 13:57:11 +0930 Subject: [PATCH 8/8] Update _config.yml --- _config.yml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/_config.yml b/_config.yml index f315fd4..e70dcd7 100644 --- a/_config.yml +++ b/_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/elixir-toolkit-theme@2.3.0 @@ -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