Trap species and collection species

ccdb/species/admin.py

@@ -1,6 +1,6 @@
 from django.contrib import admin
 
-from .models import Species
+from .models import Species, TrapSpecies, CollectionSpecies
 
 
 class SpeciesAdmin(admin.ModelAdmin):
@@ -11,4 +11,22 @@ class SpeciesAdmin(admin.ModelAdmin):
     fields = ('common_name', 'genus', 'species', 'parasite', 'sort_order')
 
 
+class TrapSpeciesAdmin(admin.ModelAdmin):
+    list_display = ('collection_trap', 'species', 'sex', 'count', 'count_estimated')
+    list_display_links = ('count',)
+    search_fields = ('collection_trap', 'species', 'sex', 'count', 'count_estimated')
+    list_per_page = 25
+    fields = ('collection_trap', 'species', 'sex', 'count', 'count_estimated')
+
+
+class CollectionSpeciesAdmin(admin.ModelAdmin):
+    list_display = ('collection', 'species', 'sex', 'count', 'count_estimated')
+    list_display_links = ('count',)
+    search_fields = ('collection', 'species', 'sex', 'count', 'count_estimated')
+    list_per_page = 25
+    fields = ('collection', 'species', 'sex', 'count', 'count_estimated')
+
+
 admin.site.register(Species, SpeciesAdmin)
+admin.site.register(TrapSpecies, TrapSpeciesAdmin)
+admin.site.register(CollectionSpecies, CollectionSpeciesAdmin)

ccdb/species/migrations/0002_trapspecies.py

@@ -0,0 +1,29 @@
+# -*- coding: utf-8 -*-
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('collections_ccdb', '0001_initial'),
+        ('species', '0001_initial'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='TrapSpecies',
+            fields=[
+                ('id', models.AutoField(auto_created=True, verbose_name='ID', primary_key=True, serialize=False)),
+                ('sex', models.CharField(blank=True, max_length=25)),
+                ('count', models.IntegerField(blank=True, null=True)),
+                ('count_estimated', models.BooleanField(default=False)),
+                ('collection_trap', models.ForeignKey(to='collections_ccdb.CollectionTrap')),
+                ('species', models.ForeignKey(to='species.Species')),
+            ],
+            options={
+                'verbose_name_plural': 'trap-species',
+            },
+        ),
+    ]

ccdb/species/migrations/0003_collectionspecies.py

@@ -0,0 +1,33 @@
+# -*- coding: utf-8 -*-
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('collections_ccdb', '0001_initial'),
+        ('species', '0002_trapspecies'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='CollectionSpecies',
+            fields=[
+                ('id', models.AutoField(verbose_name='ID', primary_key=True, auto_created=True, serialize=False)),
+                ('sex', models.CharField(blank=True, max_length=25)),
+                ('count', models.IntegerField(null=True, blank=True)),
+                ('count_estimated', models.BooleanField(default=False)),
+                ('collection', models.ForeignKey(to='collections_ccdb.Collection')),
+                ('species', models.ForeignKey(to='species.Species')),
+            ],
+            options={
+                'verbose_name_plural': 'collection-species',
+            },
+        ),
+        migrations.AlterUniqueTogether(
+            name='collectionspecies',
+            unique_together=set([('collection', 'species')]),
+        ),
+    ]

ccdb/species/models.py

@@ -18,3 +18,32 @@ class Species(models.Model):
         unique_together = ('common_name', 'species')
         ordering = ['sort_order']
         verbose_name_plural = 'species'
+
+
+class TrapSpecies(models.Model):
+    collection_trap = models.ForeignKey('collections_ccdb.CollectionTrap')
+    species = models.ForeignKey(Species)
+    sex = models.CharField(max_length=25, blank=True)
+    count = models.IntegerField(blank=True, null=True)
+    count_estimated = models.BooleanField(default=False)
+
+    def __str__(self):
+        return "{} {}".format(self.collection_trap, self.species)
+
+    class Meta:
+        verbose_name_plural = 'trap-species'
+
+
+class CollectionSpecies(models.Model):
+    collection = models.ForeignKey('collections_ccdb.Collection')
+    species = models.ForeignKey(Species)
+    sex = models.CharField(max_length=25, blank=True)
+    count = models.IntegerField(blank=True, null=True)
+    count_estimated = models.BooleanField(default=False)
+
+    def __str__(self):
+        return "{} {}".format(self.collection, self.species)
+
+    class Meta:
+        unique_together = ('collection', 'species')
+        verbose_name_plural = 'collection-species'

ccdb/utils/management/commands/import_data.py

@@ -12,7 +12,7 @@ from ccdb.misc.models import MeasurementUnit, MeasurementType, Container, \
     Material, Color
 from ccdb.locations.models import Region, Site, MunicipalLocation, \
     StudyLocation, StorageLocation
-from ccdb.species.models import Species
+from ccdb.species.models import Species, CollectionSpecies
 from ccdb.processing.models import ProcessType, Reagent, Flaw, Processing
 from ccdb.collections_ccdb.models import CollectionType, CollectionMethod, \
     Flaw, ADFGPermit, Collection
@@ -206,3 +206,13 @@ def _import_admin_data():
                 specimen_state=r[11], process_type_id=r[12], reagent_id=r[13],
                 adfg_permit=permit)
             col.save()
+
+        # Collection Species
+        for r in c.execute('SELECT * FROM tbl_hash_collection_species;'):
+            # No PK field in Andre's file
+            cs = CollectionSpecies(collection_id=r[0], species_id=r[1],
+                sex=r[2], count=r[3], count_estimated=r[4])
+            try:
+                cs.save()
+            except IntegrityError:
+                pass

misc/existing.py

@@ -202,19 +202,6 @@ class TblHashCollectionExperiments(models.Model):
         unique_together = (('CollectionID', 'ExperimentID'),)
 
 
-class TblHashCollectionSpecies(models.Model):
-    collectionid = models.ForeignKey(TblCollections, db_column='CollectionID')  # Field name made lowercase.
-    speciesid = models.ForeignKey('TblLuSpecies', db_column='SpeciesID')  # Field name made lowercase.
-    sex = models.CharField(db_column='Sex', max_length=25, blank=True, null=True)  # Field name made lowercase.
-    count = models.IntegerField(db_column='Count', blank=True, null=True)  # Field name made lowercase.
-    count_estimated = models.BooleanField(db_column='Count_Estimated')  # Field name made lowercase.
-
-    class Meta:
-        managed = False
-        db_table = 'tbl_HASH_Collection_Species'
-        unique_together = (('CollectionID', 'SpeciesID'),)
-
-
 class TblHashPeopleSets(models.Model):
     peoplesetid = models.AutoField(db_column='PeopleSetID', primary_key=True)  # Field name made lowercase.
     record_typeid = models.ForeignKey('TblLuRecordTypes', db_column='Record_TypeID')  # Field name made lowercase.
@@ -226,19 +213,6 @@ class TblHashPeopleSets(models.Model):
         db_table = 'tbl_HASH_People_Sets'
 
 
-class TblHashTrapSpecies(models.Model):
-    trapspeciesid = models.AutoField(db_column='TrapSpeciesID', primary_key=True)  # Field name made lowercase.
-    colltrapid = models.ForeignKey(TblHashCollectionTraps, db_column='CollTrapID')  # Field name made lowercase.
-    speciesid = models.ForeignKey('TblLuSpecies', db_column='SpeciesID')  # Field name made lowercase.
-    sex = models.CharField(db_column='Sex', max_length=25, blank=True, null=True)  # Field name made lowercase.
-    count = models.IntegerField(db_column='Count', blank=True, null=True)  # Field name made lowercase.
-    count_estimated = models.BooleanField(db_column='Count_Estimated')  # Field name made lowercase.
-
-    class Meta:
-        managed = False
-        db_table = 'tbl_HASH_Trap_Species'
-
-
 class TblLuAffiliations(models.Model):
     affiliationid = models.AutoField(db_column='AffiliationID', primary_key=True)  # Field name made lowercase.
     affiliation = models.CharField(db_column='Affiliation', max_length=100)  # Field name made lowercase.