ENH: Sex fields as lookups (#55)

ccdb/api/urls.py

@@ -35,6 +35,7 @@ router.register(r'sites', locations_viewsets.SiteViewSet)
 router.register(r'study-locations', locations_viewsets.StudyLocationViewSet)
 # Species
 router.register(r'species', species_viewsets.SpeciesViewSet)
+router.register(r'sexes', species_viewsets.SexViewSet)
 router.register(r'collection-species',
                 species_viewsets.CollectionSpeciesViewSet)
 

ccdb/species/admin.py

@@ -1,6 +1,6 @@
 from django.contrib import admin
 
-from .models import Species, TrapSpecies, CollectionSpecies
+from .models import Species, Sex, TrapSpecies, CollectionSpecies
 
 
 class SpeciesAdmin(admin.ModelAdmin):
@@ -12,6 +12,14 @@ class SpeciesAdmin(admin.ModelAdmin):
     fields = ('common_name', 'genus', 'species', 'parasite', 'sort_order')
 
 
+class SexAdmin(admin.ModelAdmin):
+    list_display = ('name', 'sort_order')
+    list_display_links = ('name',)
+    search_fields = ('name',)
+    list_per_page = 25
+    fields = ('name', 'sort_order')
+
+
 class TrapSpeciesAdmin(admin.ModelAdmin):
     list_display = ('collection_trap', 'species', 'sex', 'count',
                     'count_estimated')
@@ -32,5 +40,6 @@ class CollectionSpeciesAdmin(admin.ModelAdmin):
 
 
 admin.site.register(Species, SpeciesAdmin)
+admin.site.register(Sex, SexAdmin)
 admin.site.register(TrapSpecies, TrapSpeciesAdmin)
 admin.site.register(CollectionSpecies, CollectionSpeciesAdmin)

ccdb/species/migrations/0004_sex.py

@@ -0,0 +1,39 @@
+from django.db import migrations, models
+from django.forms import modelform_factory
+
+
+class Migration(migrations.Migration):
+    def migrate(apps, schema_editor):
+        Sex = apps.get_model('species', 'Sex')
+        SexForm = modelform_factory(Sex, fields=('name', 'sort_order'))
+        for i, s in enumerate(['male', 'female', 'mixed', 'unknown']):
+            form = SexForm(dict(name=s, sort_order=i))
+            if form.is_valid():
+                form.save()
+            else:
+                print('sex', form.errors.as_data())
+
+    def rollback(apps, schema_editor):
+        Sex = apps.get_model('species', 'Sex')
+        Sex.objects.all().delete()
+
+    dependencies = [
+        ('species', '0003_DATA_reset_sequences'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='Sex',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True,
+                                        serialize=False, verbose_name='ID')),
+                ('name', models.CharField(max_length=25, unique=True)),
+                ('sort_order', models.IntegerField(blank=True, null=True)),
+            ],
+            options={
+                'verbose_name_plural': 'sex',
+                'ordering': ['sort_order'],
+            },
+        ),
+        migrations.RunPython(migrate, rollback),
+    ]

ccdb/species/migrations/0005_replace_sex_fields.py

@@ -0,0 +1,68 @@
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+    def migrate(apps, schema_editor):
+        Sex = apps.get_model('species', 'Sex')
+        CollectionSpecies = apps.get_model('species', 'CollectionSpecies')
+
+        for cs in CollectionSpecies.objects.all():
+            if cs.old_sex:
+                if cs.old_sex == 'both':
+                    s = 'mixed'
+                elif cs.old_sex not in ['male', 'female', 'mixed', 'unknown']:
+                    s = 'unknown'
+                else:
+                    s = cs.old_sex
+                cs.sex = Sex.objects.get(name=s)
+                cs.save()
+
+    def rollback(apps, schema_editor):
+        CollectionSpecies = apps.get_model('species', 'CollectionSpecies')
+
+        for cs in CollectionSpecies.objects.all():
+            if cs.sex:
+                cs.sex = None
+            cs.old_sex = ''
+            cs.save()
+
+    dependencies = [
+        ('species', '0004_sex'),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name='collectionspecies',
+            old_name='sex',
+            new_name='old_sex',
+        ),
+        migrations.RenameField(
+            model_name='trapspecies',
+            old_name='sex',
+            new_name='old_sex',
+        ),
+        migrations.AddField(
+            model_name='collectionspecies',
+            name='sex',
+            field=models.ForeignKey(
+                null=True, on_delete=django.db.models.deletion.CASCADE,
+                related_name='collection_species', to='species.Sex'),
+        ),
+        migrations.AddField(
+            model_name='trapspecies',
+            name='sex',
+            field=models.ForeignKey(
+                null=True, on_delete=django.db.models.deletion.CASCADE,
+                related_name='trap_species', to='species.Sex'),
+        ),
+        migrations.RunPython(migrate, rollback),
+        migrations.RemoveField(
+            model_name='collectionspecies',
+            name='old_sex',
+        ),
+        migrations.RemoveField(
+            model_name='trapspecies',
+            name='old_sex',
+        ),
+    ]

ccdb/species/models.py

@@ -17,13 +17,26 @@ class Species(models.Model):
         verbose_name_plural = 'species'
 
 
+class Sex(models.Model):
+    name = models.CharField(max_length=25, unique=True)
+    sort_order = models.IntegerField(blank=True, null=True)
+
+    def __str__(self):
+        return self.name
+
+    class Meta:
+        ordering = ['sort_order']
+        verbose_name_plural = 'sex'
+
+
 class TrapSpecies(models.Model):
     collection_trap = models.ForeignKey('collections_ccdb.CollectionTrap',
                                         related_name='trap_species',
                                         on_delete=models.CASCADE)
     species = models.ForeignKey(Species, related_name='trap_species',
                                 on_delete=models.CASCADE)
-    sex = models.CharField(max_length=25, blank=True)
+    sex = models.ForeignKey(Sex, related_name='trap_species',
+                            on_delete=models.CASCADE, null=True)
     count = models.IntegerField(blank=True, null=True)
     count_estimated = models.BooleanField(default=False)
 
@@ -40,7 +53,8 @@ class CollectionSpecies(models.Model):
                                    on_delete=models.CASCADE)
     species = models.ForeignKey(Species, related_name='collection_species',
                                 on_delete=models.CASCADE)
-    sex = models.CharField(max_length=25, blank=True)
+    sex = models.ForeignKey(Sex, related_name='collection_species',
+                            on_delete=models.CASCADE, null=True)
     count = models.IntegerField(blank=True, null=True)
     count_estimated = models.BooleanField(default=False)
 

ccdb/species/serializers.py

@@ -1,6 +1,6 @@
 from rest_framework_json_api import serializers
 
-from .models import Species, CollectionSpecies
+from .models import Species, Sex, CollectionSpecies
 
 
 class SpeciesSerializer(serializers.ModelSerializer):
@@ -9,10 +9,17 @@ class SpeciesSerializer(serializers.ModelSerializer):
         fields = ('common_name', 'genus', 'species', 'parasite', 'sort_order')
 
 
+class SexSerializer(serializers.ModelSerializer):
+    class Meta:
+        model = Sex
+        fields = ('name', 'sort_order')
+
+
 class CollectionSpeciesSerializer(serializers.ModelSerializer):
     included_serializers = {
         'collection': 'ccdb.collections_ccdb.serializers.CollectionSerializer',
         'species': 'ccdb.species.serializers.SpeciesSerializer',
+        'sex': 'ccdb.species.serializers.SexSerializer',
     }
 
     class Meta:

ccdb/species/tests/factories.py

@@ -1,7 +1,7 @@
 from factory import DjangoModelFactory, Sequence, SubFactory
 from factory.fuzzy import FuzzyText, FuzzyChoice, FuzzyInteger
 
-from ..models import Species, TrapSpecies, CollectionSpecies
+from ..models import Species, Sex, TrapSpecies, CollectionSpecies
 from ccdb.collections_ccdb.tests.factories import (CollectionFactory,
                                                    CollectionTrapFactory)
 
@@ -17,13 +17,21 @@ class SpeciesFactory(DjangoModelFactory):
     sort_order = Sequence(lambda n: n)
 
 
+class SexFactory(DjangoModelFactory):
+    class Meta:
+        model = Sex
+
+    name = Sequence(lambda n: 'sex{}'.format(n))
+    sort_order = Sequence(lambda n: n)
+
+
 class TrapSpeciesFactory(DjangoModelFactory):
     class Meta:
         model = TrapSpecies
 
     collection_trap = SubFactory(CollectionTrapFactory)
     species = SubFactory(SpeciesFactory)
-    sex = FuzzyText(length=25)
+    sex = SubFactory(SexFactory)
     count = FuzzyInteger(0)
     count_estimated = FuzzyChoice(choices=[True, False])
 
@@ -34,6 +42,6 @@ class CollectionSpeciesFactory(DjangoModelFactory):
 
     collection = SubFactory(CollectionFactory)
     species = SubFactory(SpeciesFactory)
-    sex = FuzzyText(length=25)
+    sex = SubFactory(SexFactory)
     count = FuzzyInteger(0)
     count_estimated = FuzzyChoice(choices=[True, False])

ccdb/species/viewsets.py

@@ -1,7 +1,8 @@
 from rest_framework import viewsets
 
-from .models import Species, CollectionSpecies
+from .models import Species, Sex, CollectionSpecies
-from .serializers import SpeciesSerializer, CollectionSpeciesSerializer
+from .serializers import (SpeciesSerializer, SexSerializer,
+                          CollectionSpeciesSerializer)
 
 
 class SpeciesViewSet(viewsets.ModelViewSet):
@@ -9,6 +10,11 @@ class SpeciesViewSet(viewsets.ModelViewSet):
     serializer_class = SpeciesSerializer
 
 
+class SexViewSet(viewsets.ModelViewSet):
+    queryset = Sex.objects.all()
+    serializer_class = SexSerializer
+
+
 class CollectionSpeciesViewSet(viewsets.ModelViewSet):
     queryset = CollectionSpecies.objects.all()
     serializer_class = CollectionSpeciesSerializer

ccdb/users/migrations/0004_auto_20180228_1246.py

@@ -0,0 +1,21 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.9 on 2018-02-28 12:46
+from __future__ import unicode_literals
+
+import django.contrib.auth.validators
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('users', '0003_remove_user_timezone'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='user',
+            name='username',
+            field=models.CharField(error_messages={'unique': 'A user with that username already exists.'}, help_text='Required. 150 characters or fewer. Letters, digits and @/./+/-/_ only.', max_length=150, unique=True, validators=[django.contrib.auth.validators.UnicodeUsernameValidator()], verbose_name='username'),
+        ),
+    ]