Show number of documents and date of last update on genes page (#3323)

* Genes last updated

* Date of last genes collection update on genes page

* Add also nr of docs

* Fix typo

* Codefactor and linting fixes

* Show ngenes by build

* Update scout/server/blueprints/genes/templates/genes/genes.html

Co-authored-by: Daniel Nilsson <[email protected]>

Co-authored-by: Daniel Nilsson <[email protected]>

CHANGELOG.md

@@ -14,6 +14,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 - Script to convert old OMIM case format (list of integers) to new format (list of dictionaries)
 - Additional check for user logged in status before serving alignment files
 - Download .cgh files from cancer samples table on cancer case page
+- Number of documents and date of last update on genes page
 ### Changed
 - Verify user before redirecting to IGV alignments and sashimi plots
 - Build case IGV tracks starting from case and variant objects instead of passing all params in a form

scout/server/blueprints/genes/controllers.py

@@ -1,7 +1,33 @@
 # -*- coding: utf-8 -*-
-from pprint import pprint as pp
+from flask import flash, redirect, url_for
 
 from scout.server.links import add_gene_links, add_tx_links, omim
+from scout.server.utils import document_generated
+
+
+def genes(store, query):
+    """Creates content for the genes template
+
+    Args:
+        store (scout.adapter.MongoAdapter)
+        query (string)
+    Returns:
+        data (dict)
+    """
+    hgnc_id = None
+    if "|" in query:
+        try:
+            hgnc_id = int(query.split(" | ", 1)[0])
+        except ValueError:
+            flash("Provided gene info could not be parsed!", "warning")
+    if hgnc_id:
+        return redirect(url_for(".gene", hgnc_id=hgnc_id))
+
+    nr_genes_37 = store.nr_genes(build="37")
+    nr_genes_38 = store.nr_genes(build="38")
+    genes_subset = list(store.all_genes(add_transcripts=False, limit=20))
+    last_updated = document_generated(genes_subset[0]["_id"] if genes_subset else None)
+    return dict(genes=genes_subset, last_updated=last_updated, nr_genes=(nr_genes_37, nr_genes_38))
 
 
 def gene(store, hgnc_id):

scout/server/blueprints/genes/templates/genes/genes.html

@@ -15,7 +15,9 @@
 
 <div class="container-float">
     <div class="card panel-default w-100 mt-3 justify-content-center">
-        <div class="panel-heading">Genes</div>
+        <div class="panel-heading">Genes
+          <span style="float:right;"> {{nr_genes[0]}} GRCh37 genes | {{nr_genes[1]}} GRCh38 genes | Last updated  {{last_updated.strftime('%d-%m-%Y %H:%M:%S')}}</span>
+        </div>
         <table class="table table-bordered">
           <thead>
             <th>Gene symbol</th>

scout/server/blueprints/genes/views.py

@@ -14,16 +14,8 @@
 def genes():
     """Render seach box for genes."""
     query = request.args.get("query", "")
-    hgnc_id = None
-    if "|" in query:
-        try:
-            hgnc_id = int(query.split(" | ", 1)[0])
-        except ValueError:
-            flash("Provided gene info could not be parsed!", "warning")
-    if hgnc_id:
-        return redirect(url_for(".gene", hgnc_id=hgnc_id))
-    gene_q = store.all_genes(limit=20)
-    return dict(genes=gene_q)
+    data = controllers.genes(store, query)
+    return data
 
 
 @genes_bp.route("/genes/<int:hgnc_id>")

scout/server/utils.py

@@ -15,6 +15,20 @@
 LOG = logging.getLogger(__name__)
 
 
+def document_generated(document_id):
+    """Returns the generation time of a certain MongodDB document
+
+    Args:
+        document_id (bson.objectid.ObjectId)
+
+    Returns:
+        document_id.generation_time (datetime.datetime) or None if document_id is not of type ObjectId
+    """
+    if isinstance(document_id, ObjectId):
+        return document_id.generation_time
+    LOG.error(f"Could not retrieve generation date for Object {document_id}")
+
+
 def html_to_pdf_file(
     html_string, orientation, dpi=96, margins=["1.5cm", "1cm", "1cm", "1cm"], zoom=1
 ):

tests/server/test_server_utils.py

@@ -1,21 +1,42 @@
 """Tests for server utils"""
 import tempfile
+from datetime import datetime
 from io import BytesIO
 
 import pytest
+from bson.objectid import ObjectId
 from flask import url_for
 
 from scout.server.links import get_variant_links
 from scout.server.utils import (
     append_safe,
     case_has_alignments,
     case_has_mt_alignments,
+    document_generated,
     find_index,
     html_to_pdf_file,
     variant_case,
 )
 
 
+def test_objectid_generated_valid_objid():
+    """Test the function that returns the timestamp of a certain Mongo ObjectId for a document"""
+    # GIVEN a database document  ObjectId
+    objid = ObjectId("6270e450615e1675f40b5ce4")
+
+    # THEN document_generated should return a timestamp
+    assert isinstance(document_generated(objid), datetime)
+
+
+def test_objectid_generated_none():
+    """Test the function that returns the timestamp of a MondoDB ObjectId when the ObjectId has wrong type"""
+
+    # GIVEN an id of different type than ObjectId
+    objid = None
+    # THEN document_generated should return None
+    assert document_generated(objid) is None
+
+
 def test_case_has_alignments(case_obj):
     """Test function that adds info on availability of autosomal alignment files for a case"""