Support #351

src/eke.biomarkers/src/eke/biomarkers/biomarkerindex.py

@@ -204,7 +204,10 @@ class BiomarkerIndex(KnowledgeFolder):
     page_description = 'Container for biomarkers'
 
     def get_vocabulary(self, name) -> list:
-        '''Get a "vocabulary" of known values for the field ``name`` for our contained subpage.'''
+        '''Get a "vocabulary" of known values for the field ``name`` for our contained subpage.
+
+        This function is not used.
+        '''
         if name == 'organ':
             return BiomarkerBodySystem.objects.values_list('title', flat=True).distinct().order_by(Lower('title'))
         elif name == 'phase':
@@ -231,6 +234,7 @@ def get_contents(self, request: HttpRequest) -> object:
         return matches
 
     def faceted_markup(self, request):
+        '''Since we moved to DataTables, this function is no longer used.'''
         pages, rows = self.get_contents(request), []
         for page in pages:
             rows.append(render_to_string('eke.biomarkers/biomarker-row.html', {'biomarker': page.specific}))

src/eke.knowledge/src/eke/knowledge/migrations/0019_remove_protocol_fieldofresearch_and_more.py

@@ -0,0 +1,56 @@
+# Generated by Django 4.2.10 on 2024-03-27 19:50
+
+from django.db import migrations, models
+import django.db.models.deletion
+import modelcluster.fields
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("ekeknowledge", "0018_protocol_outcome_protocol_secure_outcome"),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name="protocol",
+            name="fieldOfResearch",
+        ),
+        migrations.CreateModel(
+            name="ProtocolFieldOfResearch",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True,
+                        primary_key=True,
+                        serialize=False,
+                        verbose_name="ID",
+                    ),
+                ),
+                (
+                    "sort_order",
+                    models.IntegerField(blank=True, editable=False, null=True),
+                ),
+                (
+                    "value",
+                    models.CharField(
+                        default="Field of research",
+                        help_text="Field of research",
+                        max_length=25,
+                    ),
+                ),
+                (
+                    "page",
+                    modelcluster.fields.ParentalKey(
+                        on_delete=django.db.models.deletion.CASCADE,
+                        related_name="fields_of_research",
+                        to="ekeknowledge.protocol",
+                    ),
+                ),
+            ],
+            options={
+                "ordering": ["sort_order"],
+                "abstract": False,
+            },
+        ),
+    ]

src/eke.knowledge/src/eke/knowledge/protocols.py

@@ -16,14 +16,15 @@
 from django.db.models import Q
 from django.db.models.fields import Field
 from django.db.models.functions import Lower
-from django.http import HttpRequest
+from django.http import HttpRequest, HttpResponse, JsonResponse
 from django.template.loader import render_to_string
 from django.urls import reverse
 from django.utils.text import slugify
 from django_plotly_dash import DjangoDash
-from modelcluster.fields import ParentalManyToManyField
+from modelcluster.fields import ParentalKey, ParentalManyToManyField
 from urllib.parse import urlparse
-from wagtail.admin.panels import FieldPanel
+from wagtail.admin.panels import FieldPanel, InlinePanel
+from wagtail.models import Orderable
 from wagtail.search import index
 import dash_core_components as dcc
 import dash_html_components as html
@@ -103,7 +104,6 @@ class Protocol(KnowledgeObject):
     abbreviation = models.CharField(
         max_length=120, null=False, blank=True, help_text='Short and more convenient name for the protocol'
     )
-    fieldOfResearch = models.CharField(max_length=25, null=False, blank=True, help_text='Field this protocol studies')
     phasedStatus = models.PositiveIntegerField(blank=True, null=True, help_text='Not sure what this is')
     aims = models.TextField(null=False, blank=True, help_text='The long term goals of this protocol')
     analyticMethod = models.TextField(null=False, blank=True, help_text='How things in this protocol are analyzed')
@@ -117,14 +117,14 @@ class Protocol(KnowledgeObject):
     outcome = models.TextField(null=False, blank=True, help_text="What this protocol's net result was")
     secure_outcome = models.TextField(null=False, blank=True, help_text="What this protocol's secret net result was")
     content_panels = KnowledgeObject.content_panels + [
+        InlinePanel('fields_of_research', label='Fields of Research'),  # 351
         FieldPanel('coordinatingInvestigatorSite'),
         FieldPanel('leadInvestigatorSite'),
         FieldPanel('involvedInvestigatorSites'),
         FieldPanel('cancer_types'),
         FieldPanel('isProject'),
         FieldPanel('protocolID'),
         FieldPanel('abbreviation'),
-        FieldPanel('fieldOfResearch'),
         FieldPanel('phasedStatus'),
         FieldPanel('aims'),
         FieldPanel('analyticMethod'),
@@ -141,7 +141,6 @@ class Protocol(KnowledgeObject):
     search_fields = KnowledgeObject.search_fields + [
         index.SearchField('abbreviation'),
         index.SearchField('protocolID'),
-        index.FilterField('fieldOfResearch'),
         index.FilterField('piName'),
         index.FilterField('collaborativeGroup'),
         index.FilterField('cancer_types'),
@@ -158,7 +157,7 @@ class RDFMeta:
             esu('cancerType'): RelativeRDFAttribute('cancer_types', scalar=False),
             esu('projectFlag'): _ProjectFlagRDFAttribute('isProject', scalar=True),
             esu('abbreviatedName'): RDFAttribute('abbreviation', scalar=True),
-            esu('fieldOfResearch'): RDFAttribute('fieldOfResearch', scalar=True),
+            esu('fieldOfResearch'): RDFAttribute('fields_of_research', scalar=False),  # #351
             esu('collaborativeGroupText'): _CollaborativeGroupRDFAttribute('collaborativeGroup', scalar=True),
             esu('phasedStatus'): RDFAttribute('phasedStatus', scalar=True),
             esu('aims'): RDFAttribute('aims', scalar=True),
@@ -213,6 +212,9 @@ def get_context(self, request: HttpRequest, *args, **kwargs) -> dict:
         # that we don't show the secure outcome
         context['show_secure_outcome'] = False
 
+        # Fields of research ("f_o_rs") is multi-valued now #351
+        context['f_o_rs'] = [i for i in self.fields_of_research.all().order_by('value')]
+
         return context
 
     def data_table(self) -> dict:
@@ -232,17 +234,33 @@ def data_table(self) -> dict:
             if cg == 'Breast': cg = 'Breast/Gyn'
             cgs.append(cg)
 
+        # #351 — f_o_rs = "fields of research", which I guess technically should be "fs_o_r" 😅
+        f_o_rs = ', '.join([i for i in self.fields_of_research.all().values_list('value', flat=True).order_by('value')])
+
         return {
             'pi_name': pi_name,
             'pi_url': pi_url,
-            'field': self.fieldOfResearch,
+            'f_o_rs': f_o_rs,
             # Turned off for #190
             # 'diseases': ', '.join([str(i) for i in self.cancer_types.values_list('title', flat=True).order_by('title')]),
             'cg': ', '.join(cgs),
             **super().data_table()
         }
 
 
+class ProtocolFieldOfResearch(Orderable):
+    '''Multi-valued support for RDF "fieldOfResearch" field.
+
+    Supports #351.
+    '''
+    value = models.CharField(
+        max_length=25, blank=False, null=False, default='Field of research', help_text='Field of research'
+    )
+    page = ParentalKey(Protocol, on_delete=models.CASCADE, related_name='fields_of_research')
+    panels = [FieldPanel('value')]
+    def __str__(self): return self.value  # noqa: E704
+
+
 class Ingestor(BaseIngestor):
     def _dmcc_code(self, uri: rdflib.URIRef) -> str:
         '''For the given subject URI return what would be the DMCC protocol ID.'''
@@ -324,7 +342,7 @@ def get_contents(self, request: HttpRequest) -> object:
         pi, fields, cg = request.GET.get('piName'), request.GET.getlist('fieldOfResearch'), request.GET.get('collab_group')
         filter = {}
         if pi: filter['piName__exact'] = pi
-        if fields: filter['fieldOfResearch__in'] = fields
+        if fields: filter['fields_of_research__value__in'] = fields
         if cg: filter['collaborativeGroup'] = cg  # cannot use __contains or __icontains because ``search`` below balks
         q = Q(**filter)
         # According to https://docs.wagtail.org/en/stable/topics/search/indexing.html:
@@ -387,7 +405,7 @@ def get_context(self, request: HttpRequest, *args, **kwargs) -> dict:
         #     diseases_frame = pandas.DataFrame(diseases_facets.items(), columns=('Disease', 'Count'))
         # except AttributeError:
 
-        c = collections.Counter(matches.values_list('fieldOfResearch', flat=True))
+        c = collections.Counter(matches.values_list('fields_of_research__value', flat=True))
         fields, amounts = [i[0] for i in c.items()], [i[1] for i in c.items()]
         fields_frame = pandas.DataFrame({'Field': fields, 'Count': amounts})
         fields_legend = ghetto_plotly_legend([i[0] for i in c.most_common()], palette)
@@ -450,6 +468,17 @@ def get_context(self, request: HttpRequest, *args, **kwargs) -> dict:
         ])
         return context
 
+    def serve(self, request: HttpRequest) -> HttpResponse:
+        '''Overridden service.
+
+        We override serve in order to handle the ``ajax=fields-of-research`` request. Supports #351.
+        '''
+        if request.GET.get('ajax') == 'fields-of-research':
+            f_o_rs = ProtocolFieldOfResearch.objects.distinct().values_list('value', flat=True).order_by('value')
+            return JsonResponse({'data': [i for i in f_o_rs]})
+        else:
+            return super().serve(request)
+
     class Meta:
         pass
     class RDFMeta:

src/eke.knowledge/src/eke/knowledge/templates/eke.knowledge/protocol-index.html

@@ -79,7 +79,7 @@
                         else
                             return '<a href="' + row['pi_url'] + '">' + data + '</a>';
                     }},
-                    {data: 'field'},
+                    {data: 'f_o_rs'},  // #351
                     {# {data: 'diseases'},  Turned off for #190 #}
                     {data: 'cg'}
                 ],
@@ -93,6 +93,7 @@
                 dom: "<'row'<'col-sm-12 col-md-6'l><'col-sm-12 col-md-6'f>><'row'<'col-sm-12'tr>>" +
                     "<'row'<'col-sm-12 col-md-5'i><'col-sm-12 col-md-7'p>>B",
                 initComplete: function() {
+                    // Set up the collaborative group selector
                     var cg_col = this.api().column(4);
                     var select = $('<select><option value="">— Collab Group —</option></select>')
                         .appendTo($(cg_col.header()).empty())
@@ -105,7 +106,10 @@
                     select.append('<option value="Lung">Lung</option>');
                     select.append('<option value="Prostate">Prostate</option>');
                     select.append('<option value="UNKNOWN">UNKNOWN</option>');
-                    this.api().columns([2, 3]).every(function() {
+
+                    // Col 2 = PI; we used to do this on col 3 as well but now that it has multiple
+                    // values per protocol we need to handle it specially
+                    this.api().columns([2]).every(function() {
                         var column = this;
                         var label = this.footer().innerHTML;
                         var select = $('<select><option value="">— ' + label + ' —</option></select>')
@@ -118,6 +122,8 @@
                             select.append('<option value="' + d + '">' + d + '</option>');
                         });
                     });
+
+                    // Col 0 = protocol title, col 1 = abstract
                     this.api().columns([0, 1]).every(function() {
                         var that = this;
                         $('input', this.header()).on('keyup change clear', function() {
@@ -126,6 +132,27 @@
                             }
                         });
                     });
+
+                    // col 3 = field of research; requires special handling due to multiple values
+                    // per protocol; #351
+                    var f_o_r_column = this.api().column(3);
+                    var f_o_r_select = $('<select><option value="">— Field —</option></select>')
+                        .appendTo($(f_o_r_column.header()).empty())
+                        .on('change', function() {
+                            var val = $.fn.dataTable.util.escapeRegex($(this).val());
+                            f_o_r_column.search(val? val : '', true, false).draw();
+                        });
+                    var f_o_r_retriever = new XMLHttpRequest();
+                    f_o_r_retriever.open('GET', '{% pageurl page %}?ajax=fields-of-research', true);
+                    f_o_r_retriever.onreadystatechange = function() {
+                        if (f_o_r_retriever.readyState === 4 && f_o_r_retriever.status === 200) {
+                            var f_o_rs = JSON.parse(f_o_r_retriever.responseText)['data'];
+                            f_o_rs.forEach(f_o_r => {
+                                f_o_r_select.append('<option value="' + f_o_r + '">' + f_o_r + '</option>');
+                            })
+                        }
+                    }
+                    f_o_r_retriever.send();
                 }
             });
         });

src/eke.knowledge/src/eke/knowledge/templates/eke.knowledge/protocol.html

@@ -162,8 +162,19 @@ <h5><span class='badge bg-secondary'><i class='bi-asterisk'></i>  Non-EDRN Prot
                     <dt>Protocol Type</dt>
                     <dd>{{page.kind}}</dd>
                 {% endif %}
-                <dt>Field of Research</dt>
-                <dd>{{page.fieldOfResearch}}</dd>
+
+                {% if f_o_rs %}
+                    {# #351 #}
+                    <dt>Fields of Research</dt>
+                    <dd>
+                        <ul class='list-unstyled'>
+                            {% for f_o_r in f_o_rs %}
+                                <li>{{f_o_r}}</li>
+                            {% endfor %}
+                        </ul>
+                    </dd>
+                {% endif %}
+
                 <dt>Collaborative Group</dt>
                 <dd>
                     {% if page.collaborativeGroup %}