Update dashboard contents

docs/_config.yml

@@ -52,8 +52,8 @@ theme: jekyll-theme-tactile
 # TODO: generate stats during each build using the scripts in BioPortal-to-KGX.
 #       Store the stats on KG-Hub as YAML.
 #       Retrieve them with the build_site.sh script.
-nodecount: 5003226
-edgecount: 30733778
+nodecount: 4861311
+edgecount: 30762617
 ontologies:
     - id: ABA-AMB
       status: OK

docs/build_site.sh

@@ -6,8 +6,8 @@ JEKYLL_CONFIG_HEADER_FILE="_config_header.yml"
 JEKYLL_CONFIG_FILE="_config.yml"
 GRAPH_STATS_URL="https://kg-hub.berkeleybop.io/kg-bioportal/graph_stats.yaml"
 GRAPH_STATS_FILE="graph_stats.yaml"
-ONTO_STATUS_URL="https://kg-hub.berkeleybop.io/kg-bioportal/onto_status.yaml"
-ONTO_STATUS_FILE="onto_status.yaml"
+ONTO_STATUS_URL="https://kg-hub.berkeleybop.io/kg-bioportal/onto_stats.yaml"
+ONTO_STATUS_FILE="onto_stats.yaml"
 
 # Retrieve most recent KG-Bioportal general stats
 wget -N $GRAPH_STATS_URL

docs/index.html

@@ -18,6 +18,10 @@ <h3>KG-Bioportal Overview</h3>
       <p>Node Count: {{ site.nodecount }} </p>
       <p>Edge Count: {{ site.edgecount }} </p>
 
+      {% include fig1.html %}
+      {% include fig2.html %}
+      <br>
+
       <h3>KG-Bioportal Status</h3>
       <p>The table below lists the presence and status of each ontology in KG-Bioportal. 
         Node and edge counts are pre-merged contributions from each ontology.</p>
@@ -30,4 +34,4 @@ <h3>KG-Bioportal Status</h3>
         </div>
       </div>
     </div>
-  </div>
+  </div>

docs/make_viz.py

@@ -3,7 +3,6 @@
 import pandas as pd
 import plotly.express as px
 import yaml
-from plotly.subplots import make_subplots
 
 with open("onto_status.yaml", "r") as infile:
     ontos = pd.DataFrame(((yaml.safe_load(infile)))["ontologies"])
@@ -20,11 +19,16 @@
     values="nodecount",
     names="id",
     title="Nodes used to make KG-Bioportal",
-    hole=.3
+    hole=0.3,
 )
-fig1.update_traces(textposition='inside', textinfo='percent+label')
-fig1.update_layout(uniformtext_minsize=14, uniformtext_mode='hide')
-fig1.write_html("fig1.html", include_plotlyjs='cdn')
+fig1.update_traces(textposition="inside", textinfo="percent+label")
+fig1.update_layout(
+    uniformtext_minsize=14,
+    uniformtext_mode="hide",
+    plot_bgcolor="rgba(0, 0, 0, 0)",
+    paper_bgcolor="rgba(0, 0, 0, 0)",
+)
+fig1.write_html("_includes/fig1.html", include_plotlyjs="cdn")
 
 # Edge counts across all ontologies, unmerged
 ontos.loc[ontos["edgecount"] < 150000, "id"] = "All other ontologies"
@@ -33,9 +37,13 @@
     values="edgecount",
     names="id",
     title="Edges used to make KG-Bioportal",
-    hole=.3
+    hole=0.3,
 )
-fig2.update_traces(textposition='inside', textinfo='percent+label')
-fig2.update_layout(uniformtext_minsize=14, uniformtext_mode='hide')
-fig2.write_html("fig2.html", include_plotlyjs='cdn')
-
+fig2.update_traces(textposition="inside", textinfo="percent+label")
+fig2.update_layout(
+    uniformtext_minsize=14,
+    uniformtext_mode="hide",
+    plot_bgcolor="rgba(0, 0, 0, 0)",
+    paper_bgcolor="rgba(0, 0, 0, 0)",
+)
+fig2.write_html("_includes/fig2.html", include_plotlyjs="cdn")

setup.py

@@ -60,6 +60,7 @@ def find_version(*file_paths):
         'cat-merge',
         'click==8.0.4',
         'compress_json',
+        'kaleido',
         'kghub-downloader',
         'kgx',
         'networkx',