Merge pull request #355 from DigitalSlideArchive/update-papers

Update the publications page
DigitalSlideArchive · Aug 20, 2024 · 5fe753f · 5fe753f
2 parents 76f7b26 + dcb116d
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -7,6 +7,7 @@ repos:
   rev: v4.4.0
   hooks:
   - id: check-added-large-files
+    exclude: docs/assets/pdfs
   - id: check-ast
   - id: check-builtin-literals
   - id: check-case-conflict

diff --git a/docs/Gemfile.lock b/docs/Gemfile.lock
@@ -1,7 +1,7 @@
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (7.1.1)
+    activesupport (7.1.3.4)
       base64
       bigdecimal
       concurrent-ruby (~> 1.0, >= 1.0.2)
@@ -11,11 +11,11 @@ GEM
       minitest (>= 5.1)
       mutex_m
       tzinfo (~> 2.0)
-    addressable (2.8.5)
-      public_suffix (>= 2.0.2, < 6.0)
+    addressable (2.8.7)
+      public_suffix (>= 2.0.2, < 7.0)
     base64 (0.2.0)
-    bigdecimal (3.1.4)
-    bulma-clean-theme (0.13.3)
+    bigdecimal (3.1.8)
+    bulma-clean-theme (0.14.0)
       jekyll (>= 3.9, < 5.0)
       jekyll-feed (~> 0.15)
       jekyll-paginate (~> 1.1)
@@ -25,40 +25,39 @@ GEM
     coffee-script (2.4.1)
       coffee-script-source
       execjs
-    coffee-script-source (1.11.1)
+    coffee-script-source (1.12.2)
     colorator (1.1.0)
     commonmarker (0.23.10)
-    concurrent-ruby (1.2.2)
+    concurrent-ruby (1.3.4)
     connection_pool (2.4.1)
-    dnsruby (1.70.0)
+    dnsruby (1.72.2)
       simpleidn (~> 0.2.1)
-    drb (2.2.0)
-      ruby2_keywords
+    drb (2.2.1)
     em-websocket (0.5.3)
       eventmachine (>= 0.12.9)
       http_parser.rb (~> 0)
     ethon (0.16.0)
       ffi (>= 1.15.0)
     eventmachine (1.2.7)
     execjs (2.9.1)
-    faraday (2.7.11)
+    faraday (2.8.1)
       base64
       faraday-net_http (>= 2.0, < 3.1)
       ruby2_keywords (>= 0.0.4)
     faraday-net_http (3.0.2)
-    ffi (1.16.3)
+    ffi (1.17.0)
     forwardable-extended (2.6.0)
-    gemoji (3.0.1)
-    github-pages (228)
-      github-pages-health-check (= 1.17.9)
-      jekyll (= 3.9.3)
-      jekyll-avatar (= 0.7.0)
-      jekyll-coffeescript (= 1.1.1)
+    gemoji (4.1.0)
+    github-pages (231)
+      github-pages-health-check (= 1.18.2)
+      jekyll (= 3.9.5)
+      jekyll-avatar (= 0.8.0)
+      jekyll-coffeescript (= 1.2.2)
       jekyll-commonmark-ghpages (= 0.4.0)
-      jekyll-default-layout (= 0.1.4)
-      jekyll-feed (= 0.15.1)
+      jekyll-default-layout (= 0.1.5)
+      jekyll-feed (= 0.17.0)
       jekyll-gist (= 1.5.0)
-      jekyll-github-metadata (= 2.13.0)
+      jekyll-github-metadata (= 2.16.1)
       jekyll-include-cache (= 0.2.1)
       jekyll-mentions (= 1.6.0)
       jekyll-optional-front-matter (= 0.3.2)
@@ -85,28 +84,28 @@ GEM
       jekyll-theme-tactile (= 0.2.0)
       jekyll-theme-time-machine (= 0.2.0)
       jekyll-titles-from-headings (= 0.5.3)
-      jemoji (= 0.12.0)
-      kramdown (= 2.3.2)
+      jemoji (= 0.13.0)
+      kramdown (= 2.4.0)
       kramdown-parser-gfm (= 1.1.0)
       liquid (= 4.0.4)
       mercenary (~> 0.3)
       minima (= 2.5.1)
       nokogiri (>= 1.13.6, < 2.0)
-      rouge (= 3.26.0)
+      rouge (= 3.30.0)
       terminal-table (~> 1.4)
-    github-pages-health-check (1.17.9)
+    github-pages-health-check (1.18.2)
       addressable (~> 2.3)
       dnsruby (~> 1.60)
-      octokit (~> 4.0)
-      public_suffix (>= 3.0, < 5.0)
+      octokit (>= 4, < 8)
+      public_suffix (>= 3.0, < 6.0)
       typhoeus (~> 1.3)
     html-pipeline (2.14.3)
       activesupport (>= 2)
       nokogiri (>= 1.4)
     http_parser.rb (0.8.0)
-    i18n (1.14.1)
+    i18n (1.14.5)
       concurrent-ruby (~> 1.0)
-    jekyll (3.9.3)
+    jekyll (3.9.5)
       addressable (~> 2.4)
       colorator (~> 1.0)
       em-websocket (~> 0.5)
@@ -119,27 +118,27 @@ GEM
       pathutil (~> 0.9)
       rouge (>= 1.7, < 4)
       safe_yaml (~> 1.0)
-    jekyll-avatar (0.7.0)
+    jekyll-avatar (0.8.0)
       jekyll (>= 3.0, < 5.0)
-    jekyll-coffeescript (1.1.1)
+    jekyll-coffeescript (1.2.2)
       coffee-script (~> 2.2)
-      coffee-script-source (~> 1.11.1)
+      coffee-script-source (~> 1.12)
     jekyll-commonmark (1.4.0)
       commonmarker (~> 0.22)
     jekyll-commonmark-ghpages (0.4.0)
       commonmarker (~> 0.23.7)
       jekyll (~> 3.9.0)
       jekyll-commonmark (~> 1.4.0)
       rouge (>= 2.0, < 5.0)
-    jekyll-default-layout (0.1.4)
-      jekyll (~> 3.0)
-    jekyll-feed (0.15.1)
+    jekyll-default-layout (0.1.5)
+      jekyll (>= 3.0, < 5.0)
+    jekyll-feed (0.17.0)
       jekyll (>= 3.7, < 5.0)
     jekyll-gist (1.5.0)
       octokit (~> 4.2)
-    jekyll-github-metadata (2.13.0)
+    jekyll-github-metadata (2.16.1)
       jekyll (>= 3.4, < 5.0)
-      octokit (~> 4.0, != 4.4.0)
+      octokit (>= 4, < 7, != 4.4.0)
     jekyll-include-cache (0.2.1)
       jekyll (>= 3.7, < 5.0)
     jekyll-mentions (1.6.0)
@@ -210,40 +209,40 @@ GEM
       jekyll (>= 3.3, < 5.0)
     jekyll-watch (2.2.1)
       listen (~> 3.0)
-    jemoji (0.12.0)
-      gemoji (~> 3.0)
+    jemoji (0.13.0)
+      gemoji (>= 3, < 5)
       html-pipeline (~> 2.2)
       jekyll (>= 3.0, < 5.0)
-    kramdown (2.3.2)
+    kramdown (2.4.0)
       rexml
     kramdown-parser-gfm (1.1.0)
       kramdown (~> 2.0)
     liquid (4.0.4)
-    listen (3.8.0)
+    listen (3.9.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
     mercenary (0.3.6)
     minima (2.5.1)
       jekyll (>= 3.5, < 5.0)
       jekyll-feed (~> 0.9)
       jekyll-seo-tag (~> 2.1)
-    minitest (5.20.0)
+    minitest (5.25.1)
     mutex_m (0.2.0)
-    nokogiri (1.16.5-x86_64-linux)
+    nokogiri (1.15.6-x86_64-linux)
       racc (~> 1.4)
     octokit (4.25.1)
       faraday (>= 1, < 3)
       sawyer (~> 0.9)
     pathutil (0.16.2)
       forwardable-extended (~> 2.6)
-    public_suffix (4.0.7)
-    racc (1.7.3)
+    public_suffix (5.1.1)
+    racc (1.8.1)
     rb-fsevent (0.11.2)
-    rb-inotify (0.10.1)
+    rb-inotify (0.11.1)
       ffi (~> 1.0)
-    rexml (3.3.3)
+    rexml (3.3.5)
       strscan
-    rouge (3.26.0)
+    rouge (3.30.0)
     ruby2_keywords (0.0.5)
     rubyzip (2.3.2)
     safe_yaml (1.0.5)
@@ -255,20 +254,16 @@ GEM
     sawyer (0.9.2)
       addressable (>= 2.3.5)
       faraday (>= 0.17.3, < 3)
-    simpleidn (0.2.1)
-      unf (~> 0.1.4)
+    simpleidn (0.2.3)
     strscan (3.1.0)
     terminal-table (1.8.0)
       unicode-display_width (~> 1.1, >= 1.1.1)
-    typhoeus (1.4.0)
+    typhoeus (1.4.1)
       ethon (>= 0.9.0)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
-    tzinfo-data (1.2023.3)
+    tzinfo-data (1.2024.1)
       tzinfo (>= 1.0.0)
-    unf (0.1.4)
-      unf_ext
-    unf_ext (0.0.8.2)
     unicode-display_width (1.8.0)
     wdm (0.1.1)
 

diff --git a/docs/_includes/papers-publications-list.html b/docs/_includes/papers-publications-list.html
@@ -5,14 +5,22 @@
           <div class="citation-text column is-11">
             <h4>{{ publication.title }}</h4>
             <p>{{ publication.full-citation }}
+            {% if publication.DOI_link %}
             <a href="{{ publication.DOI_link }}">
               {{ publication.DOI_link }}
             </a></p>
+            {% else %}
+            <a href="{{ publication.link }}">
+              {{ publication.link_text }}
+            </a></p>
+            {% endif %}
             <div class="citation-numbers">
               {% if publication.PMID %}
               PMID: {{ publication.PMID }} <br>
               {% endif %}
+              {% if publication.DOI %}
               DOI: {{ publication.DOI }}
+              {% endif %}
             </div>
           </div>
           <div class="citation-link-icon column is-1">

diff --git a/docs/assets/pdfs/Poster2024DigPathAI.pdf b/docs/assets/pdfs/Poster2024DigPathAI.pdf
diff --git a/docs/papers-publication/index.md → docs/papers-publications/index.md b/docs/papers-publication/index.md → docs/papers-publications/index.md
@@ -11,11 +11,10 @@ hero_image: assets/img/home-callouts/papers_publications.jpg
 # Papers and Publications list
 # =================================
 publications:
-  - title: "Accelerating Pharmaceutical R&amp;D with a User-Friendly AI System for Histopathology Image Analysis."
-    full-citation: "Lutnick, Brendon, Albert Juan Ramon, Brandon Ginley, Carlos Csiszer, Alex Kim, Io Flament, Pablo F. Damasceno, et al. 2023. “Accelerating Pharmaceutical R&amp;D with a User-Friendly AI System for Histopathology Image Analysis.” Journal of Pathology Informatics. Elsevier BV."
-    DOI_link: https://doi.org/10.1016/j.jpi.2023.100337
-    link: https://doi.org/10.1016/j.jpi.2023.100337
-    DOI: 10.1016/j.jpi.2023.100337
+  - title: "Efficiently Writing and Visualizing Many-Dimension Large Images."
+    full-citation: "Haley, Anne, David Manthey, Lee Cooper, and David Gutman. 2024. “Poster Presentations: Efficiently Writing and Visualizing Many-Dimension Large Images.” Digital Pathology & AI Congress, May 7-8, 2024."
+    link: ../assets/pdfs/Poster2024DigPathAI.pdf
+    link_text: Poster2024DigPathAI.pdf
   - title: "A User-Friendly Tool for Cloud-Based Whole Slide Image Segmentation with Examples from Renal Histopathology."
     full-citation: "Lutnick, Brendon, David Manthey, Jan U. Becker, Brandon Ginley, Katharina Moos, Jonathan E. Zuckerman, Luis Rodrigues, et al. 2022. “A User-Friendly Tool for Cloud-Based Whole Slide Image Segmentation with Examples from Renal Histopathology.” Communications Medicine. Springer Science and Business Media LLC."
     DOI_link: https://doi.org/10.1038/s43856-022-00138-z