From 118ce6228f83ab3db43592c56f1bc77b281cd936 Mon Sep 17 00:00:00 2001
From: James Graham <J.Graham@software.ac.uk>
Date: Thu, 5 Mar 2020 10:12:20 +0000
Subject: [PATCH 1/7] docs: Add initial README content

---
 README.md | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)
 create mode 100644 README.md

diff --git a/README.md b/README.md
new file mode 100644
index 0000000..3ce8122
--- /dev/null
+++ b/README.md
@@ -0,0 +1,16 @@
+# BRECcIA-Mapper (provisional name)
+
+BRECcIA-Mapper is a web app to collect and explore data about the relationships between researchers and their stakeholders on large-scale, multi-site research projects.
+
+TODO motivations, usage, license
+
+## Technology
+
+This project is written in Python using the popular [Django](https://www.djangoproject.com/) framework.
+
+An [Ansible](https://www.ansible.com/) playbook is provided which is designed for deployment on RHEL7 or CentOS7 Linux systems.  This installs and configures:
+- MySQL
+- Nginx
+- Django + BRECcIA-Mapper
+
+TODO deployment instructions
\ No newline at end of file

From 474f3a4be36faec8781337e335af387edec856a8 Mon Sep 17 00:00:00 2001
From: James Graham <J.Graham@software.ac.uk>
Date: Thu, 5 Mar 2020 10:25:51 +0000
Subject: [PATCH 2/7] docs: Add link to (private) GitHub in README.md

---
 README.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/README.md b/README.md
index 3ce8122..6305521 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,8 @@
 # BRECcIA-Mapper (provisional name)
 
+The canonical source for this project is hosted on [GitHub](https://github.com/Southampton-RSG/breccia-mapper),
+please log any issues there.
+
 BRECcIA-Mapper is a web app to collect and explore data about the relationships between researchers and their stakeholders on large-scale, multi-site research projects.
 
 TODO motivations, usage, license

From 512590d615f3b91d0e614d441d8cc30455592e89 Mon Sep 17 00:00:00 2001
From: James Graham <J.Graham@software.ac.uk>
Date: Mon, 9 Mar 2020 12:43:57 +0000
Subject: [PATCH 3/7] feat(network): Add style to network

Style nodes and edges of network
Fix layout of network not running

See #14
---
 breccia_mapper/templates/base.html   |  4 +++
 people/templates/people/network.html | 40 +++++++++++++++++++++-------
 2 files changed, 34 insertions(+), 10 deletions(-)

diff --git a/breccia_mapper/templates/base.html b/breccia_mapper/templates/base.html
index e840c53..123d2ea 100644
--- a/breccia_mapper/templates/base.html
+++ b/breccia_mapper/templates/base.html
@@ -73,6 +73,10 @@
                             <a href="{% url 'activities:activity.list' %}" class="nav-link">Activities</a>
                         </li>
 
+                        <li class="nav-item">
+                            <a href="{% url 'people:network' %}" class="nav-link">Network</a>
+                        </li>
+
                         {% if request.user.is_superuser %}
                             <li class="nav-item">
                                 <a href="{% url 'admin:index' %}" class="nav-link">Admin</a>
diff --git a/people/templates/people/network.html b/people/templates/people/network.html
index 4c703eb..4c6757a 100644
--- a/people/templates/people/network.html
+++ b/people/templates/people/network.html
@@ -21,6 +21,7 @@
             crossorigin="anonymous"></script>
 
     <script type="application/javascript">
+        // Holder for Cytoscape.js graph - see https://js.cytoscape.org/
         var cy;
 
         /**
@@ -97,20 +98,39 @@
          */
         function get_network() {
             cy = cytoscape({
-                container: document.getElementById('cy')
+                container: document.getElementById('cy'),
+                style: [
+                    {
+                        selector: 'node[name]',
+                        style: {
+                            label: 'data(name)',
+                            'text-halign': 'center',
+                            'text-valign': 'center',
+                            'font-size': 8
+                        }
+                    },
+                    {
+                        selector: 'edge',
+                        style: {
+                            'mid-target-arrow-shape': 'triangle',
+                            'curve-style': 'straight',
+                            'width': 1,
+                        }
+                    }
+                ]
             });
 
             $.when(get_people_ajax()).then(function() {
-                get_relationships_ajax()
+                $.when(get_relationships_ajax()).then(function() {
+                    var layout = cy.layout({
+                        name: 'cose',
+                        randomize: true,
+                        animate: false,
+                        idealEdgeLength: function(edge) {return 64;}
+                    });
 
-            }).then(function() {
-                var layout = cy.layout({
-                    name: 'circle',
-                    randomize: true,
-                    animate: false
-                });
-
-                layout.run();
+                    layout.run();
+                })
             });
 
         }

From 09b7fc334bf1af4d708126067d46be09c5c52909 Mon Sep 17 00:00:00 2001
From: James Graham <J.Graham@software.ac.uk>
Date: Mon, 9 Mar 2020 12:52:29 +0000
Subject: [PATCH 4/7] fix(network): Require login for network view

---
 breccia_mapper/settings.py | 10 ++++++++++
 people/views.py            |  3 ++-
 2 files changed, 12 insertions(+), 1 deletion(-)

diff --git a/breccia_mapper/settings.py b/breccia_mapper/settings.py
index 5706267..a8c06c4 100644
--- a/breccia_mapper/settings.py
+++ b/breccia_mapper/settings.py
@@ -134,6 +134,16 @@ DBBACKUP_STORAGE_OPTIONS = {
 }
 
 
+# Django REST Framework
+# https://www.django-rest-framework.org/
+
+REST_FRAMEWORK = {
+    'DEFAULT_PERMISSION_CLASSES': [
+        'rest_framework.permissions.IsAuthenticated',
+    ],
+}
+
+
 # Password validation
 # https://docs.djangoproject.com/en/2.2/ref/settings/#auth-password-validators
 
diff --git a/people/views.py b/people/views.py
index 1484a77..40bdc51 100644
--- a/people/views.py
+++ b/people/views.py
@@ -2,6 +2,7 @@
 Views for displaying or manipulating models in the 'people' app.
 """
 
+from django.contrib.auth.mixins import LoginRequiredMixin
 from django.http import HttpResponseRedirect
 from django.urls import reverse
 from django.views.generic import CreateView, DetailView, ListView, TemplateView, UpdateView
@@ -206,7 +207,7 @@ class RelationshipApiView(APIView):
         return Response(serializer.data)
     
     
-class NetworkView(TemplateView):
+class NetworkView(LoginRequiredMixin, TemplateView):
     """
     View to display relationship network.
     """

From 440de19c564891c59bf1b141596c352d2ce0c6e1 Mon Sep 17 00:00:00 2001
From: James Graham <J.Graham@software.ac.uk>
Date: Tue, 10 Mar 2020 10:52:20 +0000
Subject: [PATCH 5/7] feat(network): Add initial filtering to network

See #19
---
 people/forms.py                               |  41 +++--
 .../0017_answerset_replaced_timestamp.py      |  18 +++
 people/models/relationship.py                 |   9 +-
 people/templates/people/network.html          | 150 ++++++++----------
 people/views.py                               |  76 ++++++++-
 5 files changed, 191 insertions(+), 103 deletions(-)
 create mode 100644 people/migrations/0017_answerset_replaced_timestamp.py

diff --git a/people/forms.py b/people/forms.py
index 9d7d3b6..e883607 100644
--- a/people/forms.py
+++ b/people/forms.py
@@ -23,9 +23,28 @@ class PersonForm(forms.ModelForm):
             'country_of_residence': Select2Widget(),
             'themes': Select2MultipleWidget(),
         }
+        
+        
+class DynamicAnswerSetBase(forms.Form):
+    field_class = forms.ChoiceField
+    field_widget = None
+    field_required = True
+    
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+
+        for question in models.RelationshipQuestion.objects.all():
+            # Get choices from model and add default 'not selected' option
+            choices = question.choices + [['', '---------']]
+
+            field = self.field_class(label=question,
+                                     choices=choices,
+                                     widget=self.field_widget,
+                                     required=self.field_required)
+            self.fields['question_{}'.format(question.pk)] = field
 
 
-class RelationshipAnswerSetForm(forms.ModelForm):
+class RelationshipAnswerSetForm(forms.ModelForm, DynamicAnswerSetBase):
     """
     Form to allow users to describe a relationship.
 
@@ -37,17 +56,6 @@ class RelationshipAnswerSetForm(forms.ModelForm):
             'relationship',
         ]
 
-    def __init__(self, *args, **kwargs):
-        super().__init__(*args, **kwargs)
-
-        for question in models.RelationshipQuestion.objects.all():
-            # Get choices from model and add default 'not selected' option
-            choices = question.choices + [['', '---------']]
-
-            field = forms.ChoiceField(label=question,
-                                      choices=choices)
-            self.fields['question_{}'.format(question.pk)] = field
-
     def save(self, commit=True) -> models.RelationshipAnswerSet:
         # Save Relationship model
         self.instance = super().save(commit=commit)
@@ -62,3 +70,12 @@ class RelationshipAnswerSetForm(forms.ModelForm):
                     self.instance.question_answers.add(answer)
 
         return self.instance
+    
+    
+class NetworkFilterForm(DynamicAnswerSetBase):
+    """
+    Form to provide filtering on the network view.
+    """
+    field_class = forms.MultipleChoiceField
+    field_widget = Select2MultipleWidget
+    field_required = False
diff --git a/people/migrations/0017_answerset_replaced_timestamp.py b/people/migrations/0017_answerset_replaced_timestamp.py
new file mode 100644
index 0000000..01bf966
--- /dev/null
+++ b/people/migrations/0017_answerset_replaced_timestamp.py
@@ -0,0 +1,18 @@
+# Generated by Django 2.2.10 on 2020-03-09 15:23
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('people', '0016_add_answer_set'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='relationshipanswerset',
+            name='replaced_timestamp',
+            field=models.DateTimeField(blank=True, editable=False, null=True),
+        ),
+    ]
diff --git a/people/models/relationship.py b/people/models/relationship.py
index 68e2eaf..9065ac8 100644
--- a/people/models/relationship.py
+++ b/people/models/relationship.py
@@ -152,4 +152,11 @@ class RelationshipAnswerSet(models.Model):
     question_answers = models.ManyToManyField(RelationshipQuestionChoice)
 
     #: When were these answers collected?
-    timestamp = models.DateTimeField(auto_now_add=True)
+    timestamp = models.DateTimeField(auto_now_add=True,
+                                     editable=False)
+    
+    replaced_timestamp = models.DateTimeField(blank=True, null=True,
+                                              editable=False)
+
+    def get_absolute_url(self):
+        return self.relationship.get_absolute_url()
diff --git a/people/templates/people/network.html b/people/templates/people/network.html
index 4c6757a..e0e3deb 100644
--- a/people/templates/people/network.html
+++ b/people/templates/people/network.html
@@ -9,6 +9,27 @@
 
     <hr>
 
+    <form class="form"
+          method="POST">
+        {% csrf_token %}
+
+        <div class="row">
+            <div class="col-md-6">
+                <h3>Filter Relationships</h3>
+                    {% load bootstrap4 %}
+                    {% bootstrap_form form %}
+            </div>
+
+            <div class="col-md-6">
+                <h3>Filter People</h3>
+            </div>
+
+        </div>
+        {% buttons %}
+            <button class="btn btn-block btn-info" type="submit">Filter</button>
+        {% endbuttons %}
+    </form>
+
     <div id="cy"
          style="width: 100%; min-height: 1000px; flex-grow: 1; border: 2px solid black"></div>
 
@@ -16,88 +37,28 @@
 {% endblock %}
 
 {% block extra_script %}
+    <!--
+    Embedding graph data in page as JSON allows filtering to be performed entirely on the backend when we send a POST.
+
+    This is useful since one of the most popular browsers in several of the target countries is Opera Mini,
+    which renders JavaScript on a proxy server to avoid running it on the frontend.
+    -->
+    {{ person_set|json_script:'person-set-data' }}
+
+    {{ relationship_set|json_script:'relationship-set-data' }}
+
     <script src="https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.14.0/cytoscape.min.js"
             integrity="sha256-rI7zH7xDqO306nxvXUw9gqkeBpvvmddDdlXJjJM7rEM="
             crossorigin="anonymous"></script>
 
     <script type="application/javascript">
-        // Holder for Cytoscape.js graph - see https://js.cytoscape.org/
-        var cy;
-
         /**
-         * Get all :class:`Person` records from people:person.api.list endpoint.
-         *
-         * @returns JQuery Promise from AJAX
-         */
-        function get_people_ajax(){
-            return $.ajax({
-                url: '{% url "people:person.api.list" %}',
-                success: success_people_ajax,
-                error: function (xhr, status, error) {
-                    console.error(error);
-                }
-            });
-        }
-
-        /**
-         * Add nodes to Cytoscape network from :class:`Person` JSON.
-         *
-         * @param data: JSON representation of people
-         * @param status: unused
-         * @param xhr: unused
-         */
-        function success_people_ajax(data, status, xhr) {
-            for (var person of data) {
-                cy.add({
-                    group: 'nodes',
-                    data: {
-                        id: 'person-' + person.pk.toString(),
-                        name: person.name
-                    }
-                })
-            }
-        }
-
-        /**
-         * Get all :class:`Relationship` records from people:relationship.api.list endpoint.
-         *
-         * @returns JQuery Promise from AJAX
-         */
-        function get_relationships_ajax() {
-            return $.ajax({
-                url: '{% url "people:relationship.api.list" %}',
-                success: success_relationships_ajax,
-                error: function (xhr, status, error) {
-                    console.error(error);
-                }
-            });
-        }
-
-        /**
-         * Add edges to Cytoscape network from :class:`Relationship` JSON.
-         *
-         * @param data: JSON representation of relationships
-         * @param status: unused
-         * @param xhr: unused
-         */
-        function success_relationships_ajax(data, status, xhr) {
-            for (var relationship of data) {
-                cy.add({
-                    group: 'edges',
-                    data: {
-                        id: 'relationship-' + relationship.pk.toString(),
-                        source: 'person-' + relationship.source.toString(),
-                        target: 'person-' + relationship.target.toString()
-                    }
-                })
-            }
-        }
-
-        /**
-         * Populate a Cytoscape network from :class:`Person` and :class:`Relationship` API.
+         * Populate a Cytoscape network from :class:`Person` and :class:`Relationship` JSON embedded in page.
          */
         function get_network() {
-            cy = cytoscape({
+            // Initialise Cytoscape graph
+            // See https://js.cytoscape.org/ for documentation
+            var cy = cytoscape({
                 container: document.getElementById('cy'),
                 style: [
                     {
@@ -120,19 +81,42 @@
                 ]
             });
 
-            $.when(get_people_ajax()).then(function() {
-                $.when(get_relationships_ajax()).then(function() {
-                    var layout = cy.layout({
-                        name: 'cose',
-                        randomize: true,
-                        animate: false,
-                        idealEdgeLength: function(edge) {return 64;}
-                    });
+            // Load people and add to graph
+            var person_set = JSON.parse(document.getElementById('person-set-data').textContent);
 
-                    layout.run();
+            for (var person of person_set) {
+                cy.add({
+                    group: 'nodes',
+                    data: {
+                        id: 'person-' + person.pk.toString(),
+                        name: person.name
+                    }
                 })
+            }
+
+            // Load relationships and add to graph
+            var relationship_set = JSON.parse(document.getElementById('relationship-set-data').textContent);
+
+            for (var relationship of relationship_set) {
+                cy.add({
+                    group: 'edges',
+                    data: {
+                        id: 'relationship-' + relationship.pk.toString(),
+                        source: 'person-' + relationship.source.toString(),
+                        target: 'person-' + relationship.target.toString()
+                    }
+                })
+            }
+
+            // Optimise graph layout
+            var layout = cy.layout({
+                name: 'cose',
+                randomize: true,
+                animate: false,
+                idealEdgeLength: function(edge) {return 64;}
             });
 
+            layout.run();
         }
 
         $( window ).on('load', get_network());
diff --git a/people/views.py b/people/views.py
index 40bdc51..711e21e 100644
--- a/people/views.py
+++ b/people/views.py
@@ -3,9 +3,10 @@ Views for displaying or manipulating models in the 'people' app.
 """
 
 from django.contrib.auth.mixins import LoginRequiredMixin
-from django.http import HttpResponseRedirect
+from django.db.models import Q
 from django.urls import reverse
-from django.views.generic import CreateView, DetailView, ListView, TemplateView, UpdateView
+from django.utils import timezone
+from django.views.generic import CreateView, DetailView, FormView, ListView, UpdateView
 
 from rest_framework.views import APIView, Response
 
@@ -174,11 +175,18 @@ class RelationshipUpdateView(permissions.UserIsLinkedPersonMixin, CreateView):
 
     def form_valid(self, form):
         """
-        Don't rebind self.object to be the result of the form - it is a :class:`RelationshipAnswerSet`.
+        Mark any previous answer sets as replaced.
         """
-        form.save()
-        
-        return HttpResponseRedirect(self.relationship.get_absolute_url())
+        previous_valid_answer_sets = self.relationship.answer_sets.filter(replaced_timestamp__isnull=True)
+
+        response = super().form_valid(form)
+
+        # Shouldn't be more than one after initial updates after migration
+        for answer_set in previous_valid_answer_sets:
+            answer_set.replaced_timestamp = timezone.now()
+            answer_set.save()
+
+        return response
     
 
 class PersonApiView(APIView):
@@ -207,8 +215,62 @@ class RelationshipApiView(APIView):
         return Response(serializer.data)
     
     
-class NetworkView(LoginRequiredMixin, TemplateView):
+class NetworkView(LoginRequiredMixin, FormView):
     """
     View to display relationship network.
     """
     template_name = 'people/network.html'
+    form_class = forms.NetworkFilterForm
+    
+    def get_form_kwargs(self):
+        """
+        Add GET params to form data.
+        """
+        kwargs = super().get_form_kwargs()
+        
+        if self.request.method == 'GET':
+            if 'data' in kwargs:
+                kwargs['data'].update(self.request.GET)
+            
+            else:
+                kwargs['data'] = self.request.GET
+
+        return kwargs
+    
+    def get_context_data(self, **kwargs):
+        """
+        Add filtered QuerySets of :class:`Person` and :class:`Relationship` to the context.
+        """
+        context = super().get_context_data(**kwargs)
+        form = context['form']
+        
+        at_time = timezone.now()
+        
+        relationship_set = models.Relationship.objects.all()
+        
+        # Filter answers to relationship questions
+        for key, value in form.data.items():
+            if key.startswith('question_') and value:
+                question_id = key.replace('question_', '', 1)
+                answer = models.RelationshipQuestionChoice.objects.get(pk=value,
+                                                                       question__pk=question_id)
+                relationship_set = relationship_set.filter(
+                    Q(answer_sets__replaced_timestamp__gt=at_time) | Q(answer_sets__replaced_timestamp__isnull=True),
+                    answer_sets__timestamp__lte=at_time,
+                    answer_sets__question_answers=answer
+                )
+
+        context['person_set'] = serializers.PersonSerializer(
+            models.Person.objects.all(),
+            many=True
+        ).data
+
+        context['relationship_set'] = serializers.RelationshipSerializer(
+            relationship_set,
+            many=True
+        ).data
+        
+        return context
+    
+    def form_valid(self, form):
+        return self.render_to_response(self.get_context_data())

From 8c698e821de2ef064093952dfdd72425ce454ace Mon Sep 17 00:00:00 2001
From: James Graham <J.Graham@software.ac.uk>
Date: Tue, 10 Mar 2020 10:55:27 +0000
Subject: [PATCH 6/7] fix(deploy): Drop uWSGI to correct gid

---
 roles/webserver/templates/uwsgi-site.j2 | 1 +
 1 file changed, 1 insertion(+)

diff --git a/roles/webserver/templates/uwsgi-site.j2 b/roles/webserver/templates/uwsgi-site.j2
index b0f83c0..0311bff 100644
--- a/roles/webserver/templates/uwsgi-site.j2
+++ b/roles/webserver/templates/uwsgi-site.j2
@@ -1,6 +1,7 @@
 [uwsgi]
 project = {{ project_name }}
 uid = {{ web_user }}
+gid = {{ web_group }}
 base = /var/www
 
 chdir = %(base)/%(project)

From d83f4bda49db51a76db20f1704842f3017865e02 Mon Sep 17 00:00:00 2001
From: James Graham <J.Graham@software.ac.uk>
Date: Tue, 10 Mar 2020 13:12:20 +0000
Subject: [PATCH 7/7] fix(people): Fix redirect after new relationship

---
 people/views.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/people/views.py b/people/views.py
index 711e21e..35c06ea 100644
--- a/people/views.py
+++ b/people/views.py
@@ -125,7 +125,7 @@ class RelationshipCreateView(permissions.UserIsLinkedPersonMixin, CreateView):
         return context
 
     def get_success_url(self):
-        return reverse('people:relationship.update', kwargs={'pk': self.object.pk})
+        return reverse('people:relationship.update', kwargs={'relationship_pk': self.object.pk})
 
 
 class RelationshipUpdateView(permissions.UserIsLinkedPersonMixin, CreateView):