jku-vds-lab · sSwerk · Feb 1, 2022 · Dec 16, 2021 · Dec 16, 2021 · Dec 16, 2021
diff --git a/.env b/.env
@@ -0,0 +1,3 @@
+LC_ALL: "C.UTF-8"
+LANG: "en_US.UTF-8"
+LANGUAGE: "en_US.UTF-8"
diff --git a/.github/workflows/htmlproofer.yml b/.github/workflows/htmlproofer.yml
@@ -0,0 +1,43 @@
+name: htmlproofer
+
+on:
+  push:
+    branches:
+      - htmlproofer
+
+  workflow_dispatch:
+    inputs:
+      branchname:
+        description: 'Run htmlproofer on branch'
+        default: 'htmlproofer'
+        required: true
+
+
+jobs:
+  htmlproofer1:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+    steps:
+      - name: Checkout ${{ github.event.inputs.branchname }}
+        uses: actions/checkout@v2
+        with:
+          ref: ${{ github.event.inputs.branchname }}
+      - name: Setup Ruby
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: '2.7'
+      - name: Build jekyll site
+        run: |
+          bundle install
+          bundle update github-pages
+          bundle exec jekyll build
+
+      - name: Run HTMLProofer action
+        run: |
+          bundle exec htmlproofer --empty_alt_ignore --checks-to-ignore ImageCheck --only_4xx  --url-ignore "https://fonts.gstatic.com,https://fonts.gstatic.com/,https://www.linkedin.com,https://github.com/jku-vds-lab/rubiks-cube-demonstrator,https://www.amd.com/en/support,https://support.amd.com/us/gpudownload/Pages/index.aspx,dx.doi.org/10.33313/380/218" --assume-extension  ./_site
+
+          #branding:
+          #icon: "check"
+          #color: "green"
+
diff --git a/.gitignore b/.gitignore
@@ -10,6 +10,8 @@ css/site.css
 .jekyll-metadata
 _data/repos-expected.yml
 *.swp
+workflow/
+workflow/*
 
 /Gemfile.lock
 # Ignoring Gemfile.lock is generally a mistake, but here the deployment that matters

diff --git a/README.md b/README.md
@@ -1,4 +1,5 @@
 # JKU Visual Data Science Lab Website
+[![htmlproofer](https://github.com/jku-vds-lab/jku-vds-lab.github.io/actions/workflows/htmlproofer.yml/badge.svg?branch=htmlproofer&event=push)](https://github.com/jku-vds-lab/jku-vds-lab.github.io/actions/workflows/htmlproofer.yml)
 
 The new Visual Data Science Lab Website built with [Jekyll](https://jekyllrb.com),
 [SASS](https://www.sass-lang.com),

diff --git a/_layouts/release_caleydo.html b/_layouts/release_caleydo.html
@@ -206,7 +206,7 @@ <h3>Graphics Cards</h3>
     graphics card better of the NVidia Geforce 8 series or better should be
     fine). Also make sure that you have the <b>latest drivers</b>
     installed. Download <a href="https://www.nvidia.com/Drivers">NVidia</a>
-    or <a href="https://support.amd.com/us/gpudownload/Pages/index.aspx">AMD</a>
+    or <a href="https://www.amd.com/en/support">AMD</a>
     drivers.
   </p>
   <br/>
@@ -230,4 +230,4 @@ <h2>Source Code</h2>
 
 </article>
 
-</div>
+</div>
diff --git a/_layouts/release_domino.html b/_layouts/release_domino.html
@@ -203,7 +203,7 @@ <h3>Graphics Cards</h3>
     graphics card better of the NVidia Geforce 8 series or better should be
     fine). Also make sure that you have the <b>latest drivers</b>
     installed. Download <a href="https://www.nvidia.com/Drivers">NVidia</a>
-    or <a href="https://support.amd.com/us/gpudownload/Pages/index.aspx">AMD</a>
+    or <a href="https://www.amd.com/en/support">AMD</a>
     drivers.
   </p>
   <br/>
@@ -227,4 +227,4 @@ <h2>Source Code</h2>
 
 </article>
 
-</div>
+</div>
diff --git a/_persons/kawan.md b/_persons/kawan.md
@@ -7,7 +7,6 @@ key: kawan
 permalink: /persons/kawan/
 role: alumni
 # email: bikram.kawan@jku.at
-# image: /assets/images/team_colored/placeholder.png
 organization: Johannes Kepler University Linz
 position: PhD Student
 website:

diff --git a/_persons/schoefl.md b/_persons/schoefl.md
@@ -3,7 +3,6 @@ layout: team-member
 first_name: Moritz
 last_name: Heckmann
 title: "Moritz Heckmann"
-# cg_website: "https://www.jku.at/en/institute-of-computer-graphics/about-us/team/moritz-schoefl/" #remove to show person directly on data-vis page
 key: heckmann
 permalink: /persons/heckmann/
 role: undergrad
@@ -13,4 +12,4 @@ organization: Johannes Kepler University Linz
 position: Technical Support
 website: 
 ---
-o
+o
diff --git a/_publications/2013_infovis_lineup.md b/_publications/2013_infovis_lineup.md
@@ -57,7 +57,7 @@ abstract: "
 In the examples and demos we have used three datasets:
 
 * [Times Higher Education 100 Under 50 University Ranking](https://www.timeshighereducation.co.uk/world-university-rankings/2012/one-hundred-under-fifty)
-* [QS World University Ranking](https://www.iu.qs.com/university-rankings/world-university-rankings/)
+* [QS World University Ranking](https://www.topuniversities.com/university-rankings)
 * [USDA National Nutrient Database](https://www.ars.usda.gov/ba/bhnrc/ndl)
 
 # Related Work

diff --git a/_publications/2014_bmc_furby.md b/_publications/2014_bmc_furby.md
@@ -76,12 +76,12 @@ Datasets
 
 The following projects contain public demo data, which can be used to test Furby. But everyone is welcome to load his/her own data, via the `Load BiCluster Results` tab within the Caleydo Startup-Wizard.
 
-* <i class="fa fa-download"></i>&nbsp;[Caleydo-Project (CAL)]({{site.paper_content_url}}2014_bmc_furby_multi_tissue_fabia20.cal) containing Microarray data from Broad Institute "Cancer Program Data Sets" which was produced by [Su et al. 2002](https://www.broadinstitute.org/cgi-bin/cancer/datasets.cgi). It consists of 102 samples and 5565 genes as was clustered using the FABIA algorithm.
+* <i class="fa fa-download"></i>&nbsp;[Caleydo-Project (CAL)]({{site.paper_content_url}}2014_bmc_furby_multi_tissue_fabia20.cal) containing Microarray data from Broad Institute "Cancer Program Data Sets" which was produced by [Su et al. 2002](https://www.broadinstitute.org/cancer/cancer-program-scientific-tools-and-resources). It consists of 102 samples and 5565 genes as was clustered using the FABIA algorithm.
 * <i class="fa fa-download"></i>&nbsp;[Zip package (ZIP)]({{site.paper_content_url}}2014_bmc_furby_multi_tissue_fabia20.zip) containing the exported CSV-files using to create the previous Caleydo-Project
 
 Utilities
 =========
 We provide two helper R-Scripts, which simplify exporting R bicluster results in the correct format.
 
 * <i class="fa fa-download"></i>&nbsp;[R-Script]({{site.paper_content_url}}2014_bmc_furby_export_fabia.R) for exporting FABIA results, generated via the [fabia](https://www.bioconductor.org/packages/2.12/bioc/html/fabia.html) bioconductor package.
-* <i class="fa fa-download"></i>&nbsp;[R-Script]({{site.paper_content_url}}2014_bmc_furby_export_biclust.R) for exporting result from the [biclust](https://cran.r-project.org/web/packages/biclust/index.html) CRAN package.
+* <i class="fa fa-download"></i>&nbsp;[R-Script]({{site.paper_content_url}}2014_bmc_furby_export_biclust.R) for exporting result from the [biclust](https://cran.r-project.org/web/packages/biclust/index.html) CRAN package.
diff --git a/_publications/2019_eurova_rubik.md b/_publications/2019_eurova_rubik.md
@@ -81,7 +81,7 @@ supplements:
 #  linksym: true
 
 # Link to the repository where the code is hosted
-code: https://github.com/JKU-ICG/rubiks-cube-demonstrator
+code: https://github.com/jku-vds-lab/rubiks-cube-demonstrator
 
 
 abstract: "

diff --git a/_publications/2020_imimic_projective-latent-space-deculttering.md b/_publications/2020_imimic_projective-latent-space-deculttering.md
@@ -33,7 +33,7 @@ bib:
   editor: Cardoso, Jaime and others
   series: Lecture Notes in Computer Science
   doi: 10.1007/978-3-030-61166-8_2
-  url: 
+  url: https://link.springer.com/chapter/10.1007%2F978-3-030-61166-8_2
   volume: 12446
   number: 
   pages: 13--22

diff --git a/_publications/2021_forecasting_model_sinter.md b/_publications/2021_forecasting_model_sinter.md
@@ -15,7 +15,7 @@ abstract: "Sintering is a complex production process where the process stability
 
 
 # set this url, if your paper is on another server; defaults to data.jku-vds-lab.at
-paper_content_url: https://www.scopus.com/record/display.uri?eid=2-s2.0-85092267170&origin=inward&txGid=5f94bfde7a78639aa60327d0e70e1a23
+paper_content_url: https://dx.doi.org/10.33313/380/218
 # uncomment the "hide" property, if you do not want the publication to be displayed on the website (usually you don't need this)
 # hide: True
 # uncomment the "hide" property, if you only want the publication to be displayed on your personal page (i.e. publications where you contributed, but does not have anything to do with the Vis Group e.g. Master Thesis,...)
@@ -67,7 +67,7 @@ bib:
   pages:
   month: 
 
-preprint:	https://www.scopus.com/record/display.uri?eid=2-s2.0-85092267170&origin=inward&txGid=5f94bfde7a78639aa60327d0e70e1a23 # here you can put the preprint link (arxiv.org, osf.io,...) e.g. https://arxiv.org/abs/1910.00969
+preprint:	http://digital.library.aist.org/pages/PR-380-218.htm # here you can put the preprint link (arxiv.org, osf.io,...) e.g. https://arxiv.org/abs/1910.00969
 
 
 # Add things like "Best Paper Award at InfoVis 2099, selected out of 4000 submissions"
@@ -104,4 +104,4 @@ code:
 ---
 
 # Acknowledgements
-This work has partially been supported by the FFG, Contract No. 854184: “Pro2Future is funded within the Austrian COMET Program Competence Centers for Excellent Technologies under the auspices of the Austrian Federal Ministry of Transport, Innovation and Technology, the Austrian Federal Ministry for Digital and Economic Affairs and of the Provinces of Upper Austria and Styria. COMET is managed by the Austrian Research Promotion Agency FFG.”
+This work has partially been supported by the FFG, Contract No. 854184: “Pro2Future is funded within the Austrian COMET Program Competence Centers for Excellent Technologies under the auspices of the Austrian Federal Ministry of Transport, Innovation and Technology, the Austrian Federal Ministry for Digital and Economic Affairs and of the Provinces of Upper Austria and Styria. COMET is managed by the Austrian Research Promotion Agency FFG.”
diff --git a/_publications/2021_preprint_dashboard_onboarding.md b/_publications/2021_preprint_dashboard_onboarding.md
@@ -52,7 +52,7 @@ non_group_project: False
 project:
 
 # Use this if you have an external project website
-external-project:
+external-project: https://osf.io/zsb5a/
 
 # The reference to the video entry
 video:
@@ -62,7 +62,7 @@ video:
 # the prerint
 pdf: 2021_preprint_dashboard-onboarding.pdf
 # A supplement PDF
-supplement: https://osf.io/zsb5a/
+supplement: 
 
 # Extra supplements, such as talk slides, data sets, etc.
 supplements:

diff --git a/_publications/2021_tvcg_fuzzy-spreadsheets.md b/_publications/2021_tvcg_fuzzy-spreadsheets.md
@@ -60,15 +60,15 @@ video: 2021_fuzzy-spreadsheets_video
 # the prerint
 pdf: 2020_preprint_fuzzy-spreadsheets.pdf
 # A supplement PDF
-supplement: https://osf.io/8ypux/
+supplement: 
 
 # Extra supplements, such as talk slides, data sets, etc.
 supplements:
-#- name: General UpSet
+- name: Fuzzy Spreadsheet
 #  # use link instead of abslink if you want to link to the master directory
-#  abslink: http://vials.io/talk/
+  abslink: https://osf.io/8ypux/
 #  # defaults to a download icon, use this if you want a link-out icon
-#  linksym: true
+  linksym: true
 
 # Link to the repository where the code is hostet
 code: https://github.com/jku-vds-lab/fuzzy-spreadsheet

diff --git a/acknowledgements.md b/acknowledgements.md
@@ -18,7 +18,7 @@ Visual Data Science Lab makes use of a range of open source tools, bioinformatic
 
 # Bioinformatics Resources
 
-* [David Bioinformatics Resources](http://david.abcc.ncifcrf.gov/) - Gene ID mapping.
+* [David Bioinformatics Resources](https://david.ncifcrf.gov/) - Gene ID mapping.
 * [KEGG](http://www.genome.jp/kegg/pathway.html) - Pathways.
 * [WikiPathways](https://www.wikipathways.org/index.php/WikiPathways) - Pathways.
 

diff --git a/apps/embedding-structure-explorer/index.html b/apps/embedding-structure-explorer/index.html
@@ -7,7 +7,7 @@
   <meta http-equiv="X-UA-Compatible" content="ie=edge">
 
   <link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:300,400,500,700&display=swap" />
-  <link rel="preconnect" href="https://fonts.gstatic.com">
+  <link rel="preconnect" href="https://fonts.gstatic.com/" crossorigin>
   <link href="https://fonts.googleapis.com/css2?family=Source+Sans+Pro:wght@400&display=swap" rel="stylesheet">
 
   <link rel="stylesheet" href="problem_specific/rubik.css">
@@ -64,4 +64,4 @@
 
 </body>
 
-</html>
+</html>
diff --git a/assets/papers/2021_preprint_dashboard-onboarding.pdf b/assets/papers/2021_preprint_dashboard-onboarding.pdf
diff --git a/former-caleydo/_posts/2014-07-26-vis-papers.md b/former-caleydo/_posts/2014-07-26-vis-papers.md
@@ -4,4 +4,4 @@ title: Two new Caleydo papers at IEEE VIS 2014
 date: 2014-07-26 20:00:00
 categories: event
 ---
-Two papers about new Caleydo projects have ben accepted at the premier conference for visualization, <a href="https://ieeevis.org/">IEEE VIS</a>. <a href="{{site.baseurl}}/publications/2014_infovis_domino/">Domino</a> is a new technique to visualize dataset slices and create advanced, customized visualization techniques. <a href="{{site.baseurl}}/publications/2014_vast_contour/">Contour</a> allows analysts to explore multi-relational datasets to understand, for example, the interdependencies between drug candidates, phenotypic effects and pathways. Both papers will be presented by Caleydo team members in November in Paris. 
+Two papers about new Caleydo projects have ben accepted at the premier conference for visualization, <a href="http://ieeevis.org">IEEE VIS</a>. <a href="{{site.baseurl}}/publications/2014_infovis_domino/">Domino</a> is a new technique to visualize dataset slices and create advanced, customized visualization techniques. <a href="{{site.baseurl}}/publications/2014_vast_contour/">Contour</a> allows analysts to explore multi-relational datasets to understand, for example, the interdependencies between drug candidates, phenotypic effects and pathways. Both papers will be presented by Caleydo team members in November in Paris. 
diff --git a/former-caleydo/_posts/2015-04-22-open_phd_position_JKU.markdown b/former-caleydo/_posts/2015-04-22-open_phd_position_JKU.markdown
diff --git a/former-caleydo/_posts/2015-06-19-open_positions_utah.md b/former-caleydo/_posts/2015-06-19-open_positions_utah.md
diff --git a/former-caleydo/_posts/2016-03-01-open_positions_harvard.md b/former-caleydo/_posts/2016-03-01-open_positions_harvard.md
diff --git a/htmlproofer.event b/htmlproofer.event
@@ -0,0 +1,6 @@
+{
+  "action": "push",
+  "inputs": {
+      "branchname": "htmlproofer"
+  }
+}
diff --git a/templates/person-template.md b/templates/person-template.md
@@ -16,7 +16,7 @@ key: doe # this should be your lastname in lower case; the key is important for
 role: raPhD
 
 email: john.doe@jku.at # this is your work e-mail address
-image: /assets/images/team_colored/doe.jpg # insert the relative link to your profile image
+# image: /assets/images/team_colored/doe.jpg # insert the relative link to your profile image
 organization: Johannes Kepler University Linz # usually you leave this unchanged, but if your have a different organization, feel free to change the property
 position: Project Assistant # This is the position that you have within your organization. e.g. "Project Assistant", "University Assistant", "Technical Support", "Student Research" (or whatever Marc tells you^^)
 ####
@@ -66,4 +66,4 @@ website:
 ####
 ---
 
-Write some Text about yourself
+Write some Text about yourself