Merge pull request #79 from ctanes/main

Added publications and species counts to index.

Author: ctanes

app/app.py

@@ -30,7 +30,7 @@
     get_taxonomic_assignments,
 )
 from pathlib import Path
-from sqlalchemy import select, text, func
+from sqlalchemy import select, text, func, desc
 from sqlalchemy.pool import NullPool
 from app.datatables import datatables_response, init_app, query_columns
 from app.nl_query import generate_sql, generate_sql_modification
@@ -141,6 +141,20 @@ def index():
     except Exception as e:
         print(f"Error fetching special collection counts: {e}")
 
+    try:
+        # Get counts of all the species in the collection
+        species = (
+            db.session.query(Isolate.suspected_organism, func.count(Isolate.sample_id).label("count"))
+            .filter(Isolate.suspected_organism.is_not(None))
+            .filter(Isolate.suspected_organism != "Unknown")
+            .group_by(Isolate.suspected_organism)
+            .order_by(desc("count"))
+            .limit(10)
+            .all()
+        )
+    except Exception as e:
+        print(f"Error fetching species counts: {e}")    
+
     return render_template(
         "index.html",
         version=__version__,
@@ -149,6 +163,7 @@ def index():
         isolate_count=isolate_count,
         patient_count=patient_count,
         special_collection_counts=special_collections,
+        species_counts=species,
     )
 
 

app/templates/index.html

@@ -23,14 +23,32 @@ <h3 style="text-transform:none;">Welcome to the Microbial ARchive and Cryo-colle
 
   <h4>
     The database currently holds {{ isolate_count }} isolates from {{ patient_count }} patients.
-  </h4>
+  </h4><br>
 
-  <p>The efforts to curate the isolates include:</p>
+  <h5>The efforts to curate the isolates include:</h5>
   <ul class="list-unstyled">
     {% for collection, val in special_collection_counts.items() %}
     <li class="mb-2"><strong>{{ collection }}</strong> ({{ val[0] }} isolates){% if val[1] %} - {{ val[1] }}{% endif %}</li>
     {% endfor %}
+  </ul><br>
+
+  <h5>The most common species in the database are:</h5>
+  <ul class="list-unstyled">
+    {% for species, val in species_counts %}
+    <li class="mb-2"><strong>{{ species }}:</strong> {{ val }} isolates</li>
+    {% endfor %}
+  </ul><br>
+  
+
+  <h4>
+    Publications
+  </h4>
+
+  <p>We are working on multiple projects in parallel using this data. The current publications are listed below:</p>
+  <ul class="list-unstyled">
+    <li class="mb-2">She Q, Srinivasan L, Theiller E, Galis BE, Napper T, Feder A, Arvanitis A, Jones SM, Hayes E, Puopolo KM, Baldassano RN, David MZ, Coffin SE, Gibbs KA, Potter RF, Smith KP, Harris RM, Zackular JP, Moustafa AM, Planet PJ. Rapid dissemination of Staphylococcus aureus in the neonatal intensive care unit is associated with invasive infection. Nat Commun. 2026 Feb 9. doi: 10.1038/s41467-026-69074-z. Epub ahead of print. <a href="https://pubmed.ncbi.nlm.nih.gov/41663361/">PMID: 41663361</a>.</li>
   </ul>
+
 </div>
 
 <div>