Merge pull request #13 from cmu-delphi/SD-26_v3

SD-26

Author: BrainIsDead

src/datasources/admin.py

@@ -2,7 +2,7 @@
 from import_export.admin import ImportExportModelAdmin
 
 from datasources.models import DataSource, SourceSubdivision
-from datasources.resources import DataSourceResource, SourceSubdivisionResource
+from datasources.resources import SourceSubdivisionResource
 
 
 @admin.register(SourceSubdivision)
@@ -22,4 +22,3 @@ class DataSourceAdmin(ImportExportModelAdmin):
     """
     list_display = ('name',)
     search_fields = ('name', 'source_subdivision__db_source', 'source_subdivision__name', 'description')
-    resource_classes = [DataSourceResource]

src/datasources/resources.py

@@ -7,67 +7,6 @@
 from datasources.models import DataSource, SourceSubdivision
 
 
-class DataSourceResource(resources.ModelResource):
-    """
-    A resource for importing and exporting data sources using the Django ORM.
-    """
-    name = Field(attribute='name', column_name='Name')
-    display_name = Field(attribute='display_name', column_name='Name')
-    description = Field(attribute='description', column_name='Description')
-    source_license = Field(attribute='source_license', column_name='License')
-    links = Field(
-        attribute='links',
-        column_name='Links',
-        widget=widgets.ManyToManyWidget(Link, field='url', separator='|'),
-    )
-    source_subdivisions = Field(
-        attribute='source_subdivisions',
-        column_name='Name',
-        widget=widgets.ForeignKeyWidget(DataSource, field='name'),
-    )
-
-    class Meta:
-        model = DataSource
-        fields = ('name', 'display_name', 'description', 'source_license', 'links')
-        import_id_fields = ['name']
-
-    def before_import_row(self, row, **kwargs):
-        """
-        Hook called before importing each row. Modifies 'Links' column to include
-        any additional links specified in 'DUA' or 'Link' columns.
-        """
-        self.process_links(row)
-        self.process_subdivisions(row)
-
-    def process_subdivisions(self, row):
-        if row['Source Subdivision']:
-            data_source = DataSource.objects.get(name=row['Name'])
-            source_subdivision, created = SourceSubdivision.objects.get_or_create(
-                name=row['Source Subdivision'],
-                defaults={
-                    'display_name': row['Source Subdivision'],
-                    'description': row['Description'],
-                    'db_source': row['DB Source'],
-                    'data_source': data_source
-                }
-            )
-
-    def process_links(self, row):
-        row['Links'] = ''
-        if row['DUA']:
-            link, created = Link.objects.get_or_create(url=row['DUA'], defaults={'link_type': LinkTypeChoices.DUA})
-            row['Links'] += row['Links'] + f'|{link.url}'
-
-        if row['Link']:
-            pattern = r'\[(.*?)\]\((.*?)\)'
-            pattern_match = re.search(pattern, row['Link'])
-            link_type_mapping = {choice.label: choice.value for choice in LinkTypeChoices}
-            link_type = link_type_mapping[pattern_match.group(1)]
-            link_url = pattern_match.group(2)
-            link, created = Link.objects.get_or_create(url=link_url, link_type=link_type)
-            row['Links'] += row['Links'] + f'|{link.url}'
-
-
 class SourceSubdivisionResource(resources.ModelResource):
     name = Field(attribute='name', column_name='Source Subdivision')
     display_name = Field(attribute='display_name', column_name='Source Subdivision')
@@ -86,7 +25,7 @@ class SourceSubdivisionResource(resources.ModelResource):
 
     class Meta:
         model = SourceSubdivision
-        fields = ('name', 'display_name', 'description', 'links', 'data_source')
+        fields = ('name', 'display_name', 'description', 'data_source', 'reference_signal', 'links')
         import_id_fields = ['name']
         skip_unchanged = True
 
@@ -95,6 +34,10 @@ def before_import_row(self, row, **kwargs) -> None:
         Hook called before importing each row. Modifies 'Links' column to include
         any additional links specified in 'DUA' or 'Link' columns.
         """
+        self.process_links(row)
+        self.process_datasource(row)
+
+    def process_links(self, row):
         row['Links'] = ''
         if row['DUA']:
             link, created = Link.objects.get_or_create(url=row['DUA'], link_type=LinkTypeChoices.DUA)
@@ -107,3 +50,16 @@ def before_import_row(self, row, **kwargs) -> None:
             link_url = pattern_match.group(2)
             link, created = Link.objects.get_or_create(url=link_url, link_type=link_type)
             row['Links'] += row['Links'] + f'|{link.url}'
+
+    def process_datasource(self, row):
+        if row['Name']:
+            data_source, created = DataSource.objects.get_or_create(
+                name=row['Name'],
+                defaults={
+                    'display_name': row['Name'],
+                    'description': row['Description'],
+                    'source_license': row['License'],
+                }
+            )
+            links = Link.objects.filter(url__in=row['Links'].split('|')).values_list('id', flat=True)
+            data_source.links.add(*links)

src/signals/admin.py

@@ -5,9 +5,19 @@
     Geography,
     Pathogen,
     Signal,
+    SignalCategory,
     SignalType,
 )
-from signals.resources import SignalResource
+from signals.resources import SignalBaseResource, SignalResource
+
+
+@admin.register(SignalCategory)
+class SignalCategoryAdmin(admin.ModelAdmin):
+    """
+    Admin interface for managing signal category objects.
+    """
+    list_display = ('name',)
+    search_fields = ('name',)
 
 
 @admin.register(Geography)
@@ -55,4 +65,4 @@ class SignalAdmin(ImportExportModelAdmin):
         'has_stderr',
         'has_sample_size',
     )
-    resource_classes = [SignalResource]
+    resource_classes = [SignalResource, SignalBaseResource]

src/signals/migrations/0001_initial.py

@@ -1,4 +1,4 @@
-# Generated by Django 4.2.2 on 2023-06-13 11:51
+# Generated by Django 4.2.3 on 2023-07-24 16:10
 
 from django.db import migrations, models
 import django.db.models.deletion
@@ -9,8 +9,8 @@ class Migration(migrations.Migration):
     initial = True
 
     dependencies = [
+        ('datasources', '0002_alter_sourcesubdivision_db_source'),
         ('base', '0001_initial'),
-        ('datasources', '0001_initial'),
     ]
 
     operations = [
@@ -38,6 +38,9 @@ class Migration(migrations.Migration):
                 ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
                 ('name', models.CharField(help_text='Name', max_length=128, unique=True)),
             ],
+            options={
+                'verbose_name_plural': 'signal categories',
+            },
         ),
         migrations.CreateModel(
             name='SignalType',
@@ -53,7 +56,8 @@ class Migration(migrations.Migration):
             name='Signal',
             fields=[
                 ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('name', models.CharField(help_text='Name', max_length=128, unique=True)),
+                ('name', models.CharField(help_text='Name', max_length=128)),
+                ('display_name', models.CharField(help_text='Display Name', max_length=128)),
                 ('active', models.BooleanField(default=False, help_text='Active')),
                 ('short_description', models.TextField(blank=True, help_text='Short Description', max_length=500, null=True)),
                 ('description', models.TextField(blank=True, help_text='Description', max_length=1000, null=True)),
@@ -67,12 +71,15 @@ class Migration(migrations.Migration):
                 ('has_sample_size', models.BooleanField(default=False, help_text='Has Sample Size')),
                 ('high_values_are', models.CharField(choices=[('bad', 'Bad'), ('good', 'Good'), ('neutral', 'Neutral')], help_text='High values are', max_length=128)),
                 ('available_geography', models.ManyToManyField(help_text='Available geography', to='signals.geography')),
-                ('base', models.ForeignKey(blank=True, help_text='Signal base', null=True, on_delete=django.db.models.deletion.PROTECT, related_name='base_for', to='signals.signal')),
+                ('base', models.ForeignKey(blank=True, help_text='Signal base', null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='base_for', to='signals.signal')),
                 ('category', models.ForeignKey(help_text='Signal Category', null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='signals', to='signals.signalcategory')),
                 ('links', models.ManyToManyField(help_text='Signal links', related_name='signals', to='base.link')),
-                ('pathogen', models.ForeignKey(help_text='Pathogen/Disease Area', null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='signals', to='signals.pathogen')),
+                ('pathogen', models.ManyToManyField(help_text='Pathogen/Disease Area', related_name='signals', to='signals.pathogen')),
                 ('signal_type', models.ManyToManyField(help_text='Signal Type', related_name='signals', to='signals.signaltype')),
                 ('source', models.ForeignKey(help_text='Source Subdivision', on_delete=django.db.models.deletion.PROTECT, related_name='signals', to='datasources.sourcesubdivision')),
             ],
+            options={
+                'unique_together': {('name', 'source')},
+            },
         ),
     ]

src/signals/migrations/0002_remove_signal_pathogen_signal_pathogen.py

@@ -50,6 +50,9 @@ class SignalCategory(models.Model):
         unique=True
     )
 
+    class Meta:
+        verbose_name_plural = "signal categories"
+
     def __str__(self) -> str:
         """
         Returns the name of the signal category as a string.
@@ -134,13 +137,16 @@ class Signal(models.Model):
     name = models.CharField(
         help_text=_('Name'),
         max_length=128,
-        unique=True
+    )
+    display_name = models.CharField(
+        help_text=_('Display Name'),
+        max_length=128,
     )
     base = models.ForeignKey(
         'signals.Signal',
         related_name='base_for',
         help_text=_('Signal base'),
-        on_delete=models.PROTECT,
+        on_delete=models.SET_NULL,
         null=True,
         blank=True
     )
@@ -233,6 +239,9 @@ class Signal(models.Model):
         on_delete=models.PROTECT,
     )
 
+    class Meta:
+        unique_together = ['name', 'source']
+
     def __str__(self) -> str:
         """
         Returns the name of the signal as a string.

src/signals/models.py

@@ -15,10 +15,43 @@
 )
 
 
+class SignalBaseResource(resources.ModelResource):
+    name = Field(attribute='name', column_name='Signal')
+    display_name = Field(attribute='display_name', column_name='Name')
+    base = Field(
+        attribute='base',
+        column_name='base',
+        widget=widgets.ForeignKeyWidget(Signal, field='id'),
+    )
+    source = Field(
+        attribute='source',
+        column_name='Source Subdivision',
+        widget=widgets.ForeignKeyWidget(SourceSubdivision, field='name'),
+    )
+
+    class Meta:
+        model = Signal
+        fields = ['base']
+        import_id_fields = ['name', 'source', 'display_name']
+
+    def before_import_row(self, row, **kwargs):
+        """Post-processes each row after importing."""
+        self.process_base(row)
+
+    def process_base(self, row):
+        """Processes base."""
+
+        if row['Signal BaseName']:
+            source = SourceSubdivision.objects.get(name=row['Source Subdivision'])
+            base_signal = Signal.objects.get(name=row['Signal BaseName'], source=source)
+            row['base'] = base_signal.id
+
+
 class SignalResource(resources.ModelResource):
     """Resource class for importing and exporting Signal models."""
 
-    name = Field(attribute='name', column_name='Name')
+    name = Field(attribute='name', column_name='Signal')
+    display_name = Field(attribute='display_name', column_name='Name')
     pathogen = Field(
         attribute='pathogen',
         column_name='Pathogen/ Disease Area',
@@ -66,6 +99,7 @@ class Meta:
         model = Signal
         fields = [
             'name',
+            'display_name',
             'pathogen',
             'signal_type',
             'active',
@@ -84,7 +118,7 @@ class Meta:
             'source',
             'links'
         ]
-        import_id_fields = ['name']
+        import_id_fields = ['name', 'source', 'display_name']
 
     def before_import_row(self, row, **kwargs):
         """Pre-processes each row before importing."""

src/signals/resources.py

@@ -11,7 +11,7 @@ <h1>Signal</h1>
         <ol class="breadcrumb">
           <li class="breadcrumb-item"><a href="{% url 'signals' %}">Home</a></li>
           <li class="breadcrumb-item"><a href="{% url 'signals' %}">Signals</a></li>
-          <li class="breadcrumb-item active">{{ signal.name }}</li>
+          <li class="breadcrumb-item active">{{ signal.display_name }}</li>
         </ol>
       </nav>
     </div><!-- End Page Title -->
@@ -24,7 +24,7 @@ <h1>Signal</h1>
             <div class="card-body pt-3">
 
                 <div class="tab-pane fade show active profile-overview" id="profile-overview" role="tabpanel">
-                  <h5 class="card-title">{{signal.name }}</h5>
+                  <h5 class="card-title">{{signal.display_name }}</h5>
                   <p class="small fst-italic">{{ signal.description }}</p>
 
                   <h5 class="card-title">Details</h5>

src/templates/signals/signal_detail.html

@@ -45,7 +45,7 @@ <h5 class="card-title">Signals</h5>
                 <tbody>
                   {% for signal in signals %}
                   <tr class="clickable-table-row" onClick="location.href='{% url 'signal' pk=signal.id %}';">
-                    <td>{{ signal.name }}</td>
+                    <td>{{ signal.display_name }}</td>
                     <td>{{ signal.source }}</td>
                     <td>{{ signal.description }}</td>
                     <td>