further work on contributor page and sitemap

- create a new Contributor model, which is just a proxy class for User
- finalize first version of the contributor page
- add contributors to sitemap
- bonus: improve sitemaps to generate only url and lastmod attributes
  (the only ones used by search engines) and use last validated contribution
  for lastmod

ippisite/ippidb/models/__init__.py

@@ -34,6 +34,7 @@ from .ippidb import (
     DrugBankCompound,
     DrugbankCompoundTanimoto,
     Contribution,
+    Contributor,
     create_tanimoto,
     update_compound_cached_properties,
     get_user_model,
@@ -87,6 +88,7 @@ __all__ = [
     DrugBankCompound,
     DrugbankCompoundTanimoto,
     Contribution,
+    Contributor,
     create_tanimoto,
     update_compound_cached_properties,
     get_user_model,

ippisite/ippidb/models/ippidb.py

@@ -17,6 +17,7 @@ from django.db.models import FloatField, IntegerField, BooleanField
 from django.db.models import Max, Count, F, Q, Case, When, Subquery, OuterRef, Exists
 from django.db.models.functions import Cast
 from django.urls import reverse
+from django.utils.functional import cached_property
 from django.utils.translation import gettext_lazy as _
 from django_celery_results.models import TaskResult
 from django.dispatch import receiver
@@ -35,6 +36,7 @@ from ippidb.ws import (
     get_chembl_id,
     get_pubchem_id,
     get_ligand_id,
+    get_orcid_user_details,
     EntryNotFoundError,
 )
 
@@ -1290,6 +1292,15 @@ class Compound(AutoFillableModel):
             )
         return results
 
+    def get_last_modification_date(self):
+        """
+        Return last modification date for the compound
+        based on latest contribution date
+        """
+        return Contribution.objects.filter(
+            bibliography__refcompoundbiblio__compound=self
+        ).aggregate(Max("created_at"))["created_at__max"]
+
 
 class CompoundTanimoto(models.Model):
     canonical_smiles = models.TextField("Canonical Smile")
@@ -2118,3 +2129,131 @@ class CompoundJob(models.Model):
 def post_save_taskresult(sender, instance, created, *args, **kwargs):
     if created:
         Job.objects.create(task_result=instance)
+
+
+User = get_user_model()
+
+
+class Contributor(User):
+    class Meta:
+        proxy = True
+
+    @cached_property
+    def orcid_json(self):
+        return get_orcid_user_details(self.get_orcid())
+
+    def get_orcid(self):
+        """
+        Get contributor ORCID from their allauth social account
+        """
+        if self.socialaccount_set.count() > 0:
+            return self.socialaccount_set.all()[0].uid
+        return None
+
+    def get_orcid_url(self):
+        """
+        Get contributor ORCID fURL from their allauth profile
+        """
+        if self.socialaccount_set.count() > 0:
+            return self.socialaccount_set.all()[0].get_profile_url()
+        return None
+
+    def get_contributor_firstname(self):
+        """
+        Get contributor full name from their ORCID profile
+        """
+        orcid = self.get_orcid()
+        if orcid is not None:
+            data = self.orcid_json
+            return data["first_name"]
+
+    def get_contributor_lastname(self):
+        """
+        Get contributor full name from their ORCID profile
+        """
+        orcid = self.get_orcid()
+        if orcid is not None:
+            data = self.orcid_json
+            return data["last_name"]
+
+    def get_contributor_keywords(self):
+        """
+        Get contributor keywords from their ORCID profile
+        """
+        orcid = self.get_orcid()
+        if orcid is not None:
+            data = self.orcid_json
+            return data["keywords"]
+
+    def get_validated_contributions(self):
+        """
+        Get validated contributions for the user
+        """
+        return self.contribution_set.filter(validated=True)
+
+    def get_validated_patents_count(self):
+        """
+        Get number of publications in validated contributions for the user
+        """
+        return Bibliography.objects.filter(
+            source__in=["PT"],
+            contribution__validated=True,
+            contribution__contributor=self,
+        ).count()
+
+    def get_validated_publications_count(self):
+        """
+        Get number of publications in validated contributions for the user
+        """
+        return Bibliography.objects.filter(
+            source__in=["PM", "DO"],
+            contribution__validated=True,
+            contribution__contributor=self,
+        ).count()
+
+    def get_validated_bibliographies(self):
+        """
+        Get publications/patents in validated contributions for the user
+        """
+        return Bibliography.objects.filter(
+            contribution__validated=True,
+            contribution__contributor=self,
+        )
+
+    def get_validated_compounds_count(self):
+        """
+        Get number of compounds in validated contributions for the user
+        """
+        return Compound.objects.filter(
+            compoundaction__ppi__contribution__validated=True,
+            compoundaction__ppi__contribution__contributor=self,
+        ).count()
+
+    def get_validated_compoundactivityresults_count(self):
+        """
+        Get number of compound activity results in validated contributions for the user
+        """
+        return CompoundActivityResult.objects.filter(
+            test_activity_description__biblio__contribution__validated=True,
+            test_activity_description__biblio__contribution__contributor=self,
+        ).count()
+
+    def get_validated_ppis_count(self):
+        """
+        Get number of PPIs in validated contributions for the user
+        """
+        return Ppi.objects.filter(
+            contribution__validated=True, contribution__contributor=self
+        ).count()
+
+    def get_absolute_url(self):
+        return reverse("contributor_card", kwargs={"pk": self.pk})
+
+    def get_last_modification_date(self):
+        """
+        Return last modification date for the contributor
+        based on latest contribution date
+        """
+        return Contribution.objects.filter(
+            contributor=self, validated=True
+        ).aggregate(Max("created_at"))["created_at__max"]

ippisite/ippidb/templates/about-contributor-card.html

@@ -5,7 +5,44 @@
 {% block pagetitle %}Contributors{% endblock%}
 
 {% block view_content %}
-<div class="row">
-	{{ object.get_contributor_firstname | capfirst }} {{ object.get_contributor_lastname | capfirst }} || {{ object.get_orcid_url }}
+<div class="inner-wrap">
+	<div class="container-fluid inner-wrap compound_header_title mx-auto p-4" id="compound_header_title">
+		<div class="container">
+			<div class="row">
+				<h1 class="page-title" style="margin: 0;">{{ object.get_contributor_firstname | capfirst }} {{ object.get_contributor_lastname | capfirst }}</h1>
+			</div>
+			<div class="row">
+				<h2><a href="{{ object.get_orcid_url }}" target="_blank">{{ object.get_orcid }}</a></h2>
+			</div>
+		</div>
+	</div>
 </div>
+{% if object.get_contributor_keywords %}
+<div class="col-sm-12">
+	<h4 class="pt-2 compound_list_title">Expertises</h4>
+	<ul class="list-group">
+		<li class="list-group-item">{{ object.get_contributor_keywords }}</li>
+	</ul>
+</div>
+{% endif %}
+<div class="col-sm-12">
+	<h4 class="pt-2 compound_list_title">Published contributions number</h4>
+	<ul class="list-group">
+		<li class="list-group-item">{{ object.get_validated_publications_count }} publications</li>
+		<li class="list-group-item">{{ object.get_validated_patents_count }} patents</li>
+		<li class="list-group-item">{{ object.get_validated_compounds_count }} compounds</li>
+		<li class="list-group-item">{{ object.get_validated_compoundactivityresults_count }} pharmacological data</li>
+		<li class="list-group-item">{{ object.get_validated_ppis_count }} PPI targets</li>
+	</ul>
+</div>
+
+<div class="col-sm-12">
+	<h4 class="pt-2 compound_list_title">Scientific publications and patents</h4>
+	<ul class="list-group">
+		{% for bibliography in object.get_validated_bibliographies %}
+			<li class="list-group-item">{% include "biblio_citation.html" with bibliography=bibliography %}</li>
+		{% endfor %}
+	</ul>
+</div>
+
 {% endblock %}
\ No newline at end of file

ippisite/ippidb/templates/about-contributors.html

@@ -8,19 +8,28 @@
 <div class="row">
 	<table class="table table-striped">
 		<thead>
-		  <tr>
-			<th scope="col" title="Contributor Name">Name</th>
-			<th scope="col" title="Contributor ORCID Link">ORCID</th>
-		  </tr>
+			<tr>
+				<th scope="col" title="Contributor Name">Name</th>
+				<th scope="col" title="Contributor ORCID Link">ORCID</th>
+			</tr>
 		</thead>
 		<tbody>
 			{% for contributor in object_list %}
 			<tr>
-				<td><a href="{{ contributor.id }}">{{ contributor.get_contributor_firstname | capfirst }} {{ contributor.get_contributor_lastname | capfirst }}</a></td>
-				<td><a href="{{ contributor.get_orcid_url }}" target="_blank">{{ contributor.get_orcid }}</a></td>
+				<td>
+					<a href="{{ contributor.id }}">
+						{{ contributor.get_contributor_firstname | capfirst }} 
+						{{ contributor.get_contributor_lastname | capfirst }}
+					</a>
+				</td>
+				<td>
+					<a href="{{ contributor.get_orcid_url }}" target="_blank">
+						{{ contributor.get_orcid }}
+					</a>
+				</td>
 			</tr>
 			{% endfor %}
 		</tbody>
-	  </table>
+	</table>
 </div>
 {% endblock %}
\ No newline at end of file

ippisite/ippidb/templates/about.html

@@ -10,10 +10,9 @@
 {% block content %}
 <div id="mainnav">
     <nav class="secondary-nav">
-        <div class="inner-wrap">
             <ul>
             	<li>
-                    <a href="/about-general">General information</a>
+                    <a href="/about-general">General</a>
                 </li>
                 <li>
                     <a href="/about-pharmacology">Pharmacology</a>
@@ -28,10 +27,9 @@
                     <a href="/about-pca">Chemical space</a>
                 </li>
                 <li>
-                    <a href="/contributors">Contributors</a>
+                    <a href="/about-contributors">Contributors</a>
                 </li>
             </ul>
-        </div>
     </nav>
 </div>
 

ippisite/ippidb/urls.py

@@ -45,6 +45,7 @@ class IppiDbStaticSitemap(Sitemap):
 sitemaps = {
     "static": IppiDbStaticSitemap,
     "compounds": views.IppiDbCompoundSitemap,
+    "contributors": views.IppiDbContributorsSitemap,
 }
 
 urlpatterns = [

ippisite/ippidb/views/__init__.py

@@ -23,7 +23,7 @@ from .compound_query import (
     convert_iupac2smi,
 )
 
-from .site import IppiDbCompoundSitemap
+from .site import IppiDbCompoundSitemap, IppiDbContributorsSitemap
 
 from .tasks import get_output_job, get_json_network
 from .about import (
@@ -113,4 +113,5 @@ __all__ = [
     NetworkView,
     get_json_network,
     IppiDbCompoundSitemap,
+    IppiDbContributorsSitemap,
 ]

ippisite/ippidb/views/about.py

@@ -2,7 +2,6 @@
 iPPI-DB global statistics views
 """
 
-from django.contrib.auth import get_user_model
 from django.db.models import F, Count, FloatField, QuerySet
 from django.db.models.functions import Cast, Floor
 from django.shortcuts import render
@@ -20,10 +19,9 @@ from ippidb.models import (
     CompoundActivityResult,
     Bibliography,
     Protein,
+    Contributor,
 )
 
-from ippidb.ws import get_orcid_user_details
-
 
 def about_general(request):
     compounds_count = Compound.objects.count()
@@ -285,66 +283,6 @@ def about_pca(request):
     return render(request, "about-pca.html", context=context)
 
 
-User = get_user_model()
-
-
-def cached_orcid_json(getter_function):
-    def new_function(self):
-        if self.__orcid_json is None:
-            self.__orcid_json = get_orcid_user_details(self.get_orcid())
-        ret = getter_function(self)
-        return ret
-
-    return new_function
-
-
-def get_orcid(self):
-    """
-    Get contributor ORCID from their allauth social account
-    """
-    if self.socialaccount_set.count() > 0:
-        return self.socialaccount_set.all()[0].uid
-    return None
-
-
-def get_orcid_url(self):
-    """
-    Get contributor ORCID fURL from their allauth profile
-    """
-    if self.socialaccount_set.count() > 0:
-        return self.socialaccount_set.all()[0].get_profile_url()
-    return None
-
-
-@cached_orcid_json
-def get_contributor_firstname(self):
-    """
-    Get contributor full name from their ORCID profile
-    """
-    orcid = self.get_orcid()
-    if orcid is not None:
-        data = self.__orcid_json
-        return data["first_name"]
-
-
-@cached_orcid_json
-def get_contributor_lastname(self):
-    """
-    Get contributor full name from their ORCID profile
-    """
-    orcid = self.get_orcid()
-    if orcid is not None:
-        data = self.__orcid_json
-        return data["last_name"]
-
-
-User.add_to_class("get_orcid", get_orcid)
-User.add_to_class("get_orcid_url", get_orcid_url)
-User.add_to_class("__orcid_json", None)
-User.add_to_class("get_contributor_firstname", get_contributor_firstname)
-User.add_to_class("get_contributor_lastname", get_contributor_lastname)
-
-
 class ContributorListView(ListView):
     """
     Contributors list view
@@ -352,10 +290,10 @@ class ContributorListView(ListView):
     This view lists the users with at least one accepted contribution
     """
 
-    model = User
+    model = Contributor
     template_name = "about-contributors.html"
 
-    def get_queryset(self) -> QuerySet[User]:
+    def get_queryset(self) -> QuerySet[Contributor]:
         qs = super().get_queryset()
         qs = qs.annotate(contributions_count=Count("contribution")).filter(
             socialaccount__isnull=False, contributions_count__gt=0
@@ -369,7 +307,7 @@ class ContributorDetailView(DetailView):
 
     """
 
-    model = User
+    model = Contributor
     template_name = "about-contributor-card.html"
 
     def get_queryset(self):

ippisite/ippidb/views/site.py

 from django.contrib.sitemaps import Sitemap
-from ippidb.models import Compound
+from ippidb.models import Compound, Contributor
+from django.db.models import Count
 
 
 class IppiDbCompoundSitemap(Sitemap):
-    changefreq = "never"
-    priority = 0.5
-
     def items(self):
         return Compound.objects.validated()
 
     def lastmod(self, obj):
-        return None
+        return obj.get_last_modification_date()
+
+
+class IppiDbContributorsSitemap(Sitemap):
+    def items(self):
+        return (
+            Contributor.objects.all()
+            .annotate(contributions_count=Count("contribution"))
+            .filter(socialaccount__isnull=False, contributions_count__gt=0)
+        )
+
+    def lastmod(self, obj):
+        return obj.get_last_modification_date()

ippisite/ippidb/ws.py

@@ -5,6 +5,7 @@ from typing import List
 
 import xml.etree.ElementTree as ET
 from urllib import parse as urllib_parse
+from django.views.generic import detail
 import requests
 from bioservices.eutils import EUtils
 from bioservices.uniprot import UniProt
@@ -597,7 +598,12 @@ def get_orcid_user_details(orcid: str) -> str:
         headers={"Accept": "application/json"},
     )
     data = resp.json()
-    return {
+    details = {
         "first_name": data["name"]["given-names"]["value"],
         "last_name": data["name"]["family-name"]["value"],
     }
+    try:
+        details["keywords"] = data["keywords"]["keyword"][0]["content"]
+    except Exception:
+        details["keywords"] = None
+    return details