Add species pages with treefile lookup

.gitignore

@@ -2,6 +2,7 @@
 *.sqlite3
 *.sqlite
 last_sync
+trees/
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

app/app.py

@@ -1,5 +1,6 @@
 import csv
 import os
+from typing import Optional
 from app import __version__, get_db_last_sync
 from flask import (
     Flask,
@@ -39,6 +40,14 @@
 app.secret_key = os.urandom(12)
 
 IS_DEV_SITE = os.environ.get("MARC_DEV", "").lower() == "true"
+MARC_TREE_FP = os.environ.get("MARC_TREE_FP")
+
+
+def treefile_for_species(species_name: str) -> Optional[str]:
+    if not species_name:
+        return None
+    slug = "_".join(species_name.lower().split())
+    return f"{slug}.treefile"
 
 
 @app.context_processor
@@ -380,6 +389,36 @@ def show_antimicrobial(antimicrobial_id: int):
     )
 
 
+@app.route("/species/<path:species_name>")
+def show_species(species_name: str):
+    assignment_count = (
+        db.session.query(func.count(TaxonomicAssignment.id))
+        .filter(TaxonomicAssignment.classification == species_name)
+        .scalar()
+    )
+    treefile_name = treefile_for_species(species_name)
+    tree_content = None
+    tree_path = None
+    tree_error = None
+    if MARC_TREE_FP and treefile_name:
+        candidate = Path(MARC_TREE_FP) / treefile_name
+        tree_path = str(candidate)
+        if candidate.is_file():
+            try:
+                tree_content = candidate.read_text()
+            except Exception as exc:
+                tree_error = str(exc)
+    return render_template(
+        "show_species.html",
+        species_name=species_name,
+        assignment_count=assignment_count,
+        tree_path=tree_path,
+        tree_content=tree_content,
+        tree_error=tree_error,
+        tree_root=MARC_TREE_FP,
+    )
+
+
 @app.route("/assembly/<int:assembly_id>")
 def show_assembly(assembly_id: int):
     assemblies = get_assemblies(db.session, id=assembly_id)

app/templates/browse_isolates.html

@@ -27,6 +27,7 @@ <h2>Isolates</h2>
   $(document).ready(function () {
       /* Initialize the DataTable with server-side processing */
       const isolateUrl = "{{ url_for('show_isolate', isolate_id='') }}";
+      const speciesUrl = "{{ url_for('show_species', species_name='') }}";
       const renderCollectionYear = (value, type) => {
           if (!value) {
               return type === 'sort' || type === 'type' ? null : '';
@@ -59,7 +60,15 @@ <h2>Isolates</h2>
           { data: 'received_date', render: function(value, type) { return renderCollectionYear(value, type); } },
           { data: 'subject_id' },
           { data: 'specimen_id' },
-          { data: 'suspected_organism' }
+          { data: 'suspected_organism', render: function(value, type) {
+              if (type !== 'display') {
+                  return value;
+              }
+              if (!value) {
+                  return '';
+              }
+              return '<a href="' + speciesUrl + encodeURIComponent(value) + '">' + value + '</a>';
+          } }
       ]);
 
       /* Move search box to bottom of summary area */

app/templates/browse_taxonomic_assignments.html

@@ -25,11 +25,20 @@ <h2>Taxonomic Assignments</h2>
 <script type="text/javascript">
 $(document).ready(function () {
     const assignmentUrl = "{{ url_for('show_taxonomic_assignment', assembly_id=0)[:-1] }}";
+    const speciesUrl = "{{ url_for('show_species', species_name='') }}";
     const oTable = createServerDataTable('#taxonomic_assignments', '{{ url_for('api_taxonomic_assignments') }}', [
         { data: 'assembly_id', render: function(d) { return '<a href="' + assignmentUrl + d + '">' + d + '</a>'; } },
         { data: 'isolate_id' },
         { data: 'tool' },
-        { data: 'classification' },
+        { data: 'classification', render: function(value, type) {
+            if (type !== 'display') {
+                return value;
+            }
+            if (!value) {
+                return '';
+            }
+            return '<a href="' + speciesUrl + encodeURIComponent(value) + '">' + value + '</a>';
+        } },
         { data: 'comment' },
     ]);
 

app/templates/show_assembly.html

@@ -117,7 +117,15 @@ <h3 class="h5 mb-0">Taxonomic Assignments</h3>
               <tbody>
                 {% for assignment in assignments %}
                 <tr>
-                  <td>{{ assignment.classification or '—' }}</td>
+                  <td>
+                    {% if assignment.classification %}
+                    <a href="{{ url_for('show_species', species_name=assignment.classification) }}">
+                      {{ assignment.classification }}
+                    </a>
+                    {% else %}
+                    —
+                    {% endif %}
+                  </td>
                   <td>{{ assignment.comment or '—' }}</td>
                   <td>{{ assignment.tool or '—' }}</td>
                 </tr>

app/templates/show_isolate.html

@@ -21,7 +21,15 @@ <h2 class="h4 mb-0">Isolate {{ isolate.sample_id }}</h2>
         <dd class="col-sm-8">{{ isolate.specimen_id }}</dd>
 
         <dt class="col-sm-4">Suspected Organism</dt>
-        <dd class="col-sm-8">{{ isolate.suspected_organism or '—' }}</dd>
+        <dd class="col-sm-8">
+          {% if isolate.suspected_organism %}
+          <a href="{{ url_for('show_species', species_name=isolate.suspected_organism) }}">
+            {{ isolate.suspected_organism }}
+          </a>
+          {% else %}
+          —
+          {% endif %}
+        </dd>
 
         <dt class="col-sm-4">Special Collection</dt>
         <dd class="col-sm-8">{{ isolate.special_collection or '—' }}</dd>

app/templates/show_species.html

@@ -0,0 +1,64 @@
+{% extends 'base.html' %}
+
+{% block head %}
+<link
+  href="https://cdn.jsdelivr.net/npm/phylotree@2.4.0/dist/phylotree.min.css"
+  rel="stylesheet"
+  integrity="sha384-aiMpATZTEuYHJmBVtYfxx+TOz295Gf4nfxFQrb+0jLomP6U3EFtcVv5sHsbpDOkk"
+  crossorigin="anonymous"
+>
+{% endblock %}
+
+{% block body %}
+<div class="container py-4">
+  <a class="btn btn-link ps-0" href="{{ url_for('browse_taxonomic_assignments') }}">
+    <i class="bi bi-arrow-left"></i> Back to taxonomic assignments
+  </a>
+
+  <div class="card shadow-sm mb-4">
+    <div class="card-header bg-primary text-white">
+      <h2 class="h4 mb-0">{{ species_name }}</h2>
+    </div>
+    <div class="card-body">
+      <dl class="row mb-0">
+        <dt class="col-sm-4">Matching taxonomic assignments</dt>
+        <dd class="col-sm-8">{{ assignment_count }}</dd>
+      </dl>
+    </div>
+  </div>
+
+  <div class="card shadow-sm">
+    <div class="card-header bg-light">
+      <h3 class="h5 mb-0">Tree</h3>
+    </div>
+    <div class="card-body">
+      {% if tree_error %}
+      <p class="text-danger mb-0">Unable to read treefile: {{ tree_error }}</p>
+      {% elif tree_content %}
+      <p class="text-muted small mb-2">Source: {{ tree_path.rsplit('/', 1)[-1] }}</p>
+      <div id="tree-container" class="border rounded bg-white" style="min-height: 500px;"></div>
+      <script src="https://cdn.jsdelivr.net/npm/d3@7.9.0/dist/d3.min.js" integrity="sha384-CjloA8y00+1SDAUkjs099PVfnY2KmDC2BZnws9kh8D/lX1s46w6EPhpXdqMfjK6i" crossorigin="anonymous"></script>
+      <script src="https://cdn.jsdelivr.net/npm/underscore@1.13.7/underscore-min.js" integrity="sha384-pSOYJz6tr3k8mV502/FWpqSv7+V4JzjQc8uhWMOZE1SoCFLcJCSfxMFOE6hEd/hT" crossorigin="anonymous"></script>
+      <script src="https://cdn.jsdelivr.net/npm/lodash@4.17.21/lodash.min.js" integrity="sha384-H6KKS1H1WwuERMSm+54dYLzjg0fKqRK5ZRyASdbrI/lwrCc6bXEmtGYr5SwvP1pZ" crossorigin="anonymous"></script>
+      <script src="https://cdn.jsdelivr.net/npm/phylotree@2.4.0/dist/phylotree.min.js" integrity="sha384-34Lu7wnDpakXRJnVFjFOd2/2rWjTA18GPeCh8LgBT007VUc43HtcbFilygn/rwFT" crossorigin="anonymous"></script>
+      <script>
+        const newick = {{ tree_content | tojson }};
+        console.log(newick);
+        const tree = new phylotree.phylotree(newick);
+        tree.render({
+          container: "#tree-container",
+          width: document.querySelector("#tree-container").clientWidth || 800,
+          height: 500,
+          "align-tips": true,
+          zoom: true
+        });
+      </script>
+      {% elif tree_root %}
+      <p class="mb-0">No treefile found for this species.</p>
+      {% else %}
+      <p class="mb-0">Set the MARC_TREE_FP environment variable to load treefiles.</p>
+      {% endif %}
+    </div>
+  </div>
+</div>
+{% endblock %}

app/templates/show_taxonomic_assignment.html

@@ -22,7 +22,15 @@ <h2 class="h4 mb-0">Taxonomic Assignment for Assembly {{ assembly_id }}</h2>
         <dd class="col-sm-8">{{ assignment.tool or '—' }}</dd>
 
         <dt class="col-sm-4">Classification</dt>
-        <dd class="col-sm-8">{{ assignment.classification or '—' }}</dd>
+        <dd class="col-sm-8">
+          {% if assignment.classification %}
+          <a href="{{ url_for('show_species', species_name=assignment.classification) }}">
+            {{ assignment.classification }}
+          </a>
+          {% else %}
+          —
+          {% endif %}
+        </dd>
 
         <dt class="col-sm-4">Comment</dt>
         <dd class="col-sm-8">{{ assignment.comment or '—' }}</dd>