Treatment

ccdb/experiments/admin.py

@@ -1,6 +1,7 @@
 from django.contrib import admin
 
-from .models import Flaw, Experiment, ProtocolAttachment, TreatmentType
+from .models import Flaw, Experiment, ProtocolAttachment, TreatmentType, \
+    Treatment
 
 
 class FlawAdmin(admin.ModelAdmin):
@@ -38,7 +39,19 @@ class TreatmentTypeAdmin(admin.ModelAdmin):
         'description', 'sort_order')
 
 
+class TreatmentAdmin(admin.ModelAdmin):
+    list_display = ('treatment_type', 'container', 'study_location', 'species',
+        'sex', 'flaw')
+    list_display_links = ('treatment_type',)
+    search_fields = ('treatment_type', 'container', 'study_location', 'species',
+        'sex', 'flaw')
+    list_per_page = 25
+    fields = ('treatment_type', 'container', 'study_location', 'species',
+        'sex', 'flaw')
+
+
 admin.site.register(Flaw, FlawAdmin)
 admin.site.register(Experiment, ExperimentAdmin)
 admin.site.register(ProtocolAttachment, ProtocolAttachmentAdmin)
 admin.site.register(TreatmentType, TreatmentTypeAdmin)
+admin.site.register(Treatment, TreatmentAdmin)

ccdb/experiments/migrations/0003_treatment.py

@@ -0,0 +1,29 @@
+# -*- coding: utf-8 -*-
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('misc', '0001_initial'),
+        ('species', '0003_collectionspecies'),
+        ('locations', '0002_remove_site_fk_dupes'),
+        ('experiments', '0002_treatment_type'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='Treatment',
+            fields=[
+                ('id', models.AutoField(primary_key=True, verbose_name='ID', auto_created=True, serialize=False)),
+                ('sex', models.CharField(max_length=25)),
+                ('container', models.ForeignKey(blank=True, null=True, to='misc.Container')),
+                ('flaw', models.ForeignKey(blank=True, null=True, to='experiments.Flaw')),
+                ('species', models.ForeignKey(to='species.Species')),
+                ('study_location', models.ForeignKey(to='locations.StudyLocation')),
+                ('treatment_type', models.ForeignKey(to='experiments.TreatmentType')),
+            ],
+        ),
+    ]

ccdb/experiments/models.py

@@ -51,8 +51,22 @@ class TreatmentType(models.Model):
     slug = AutoSlugField(populate_from='name')
 
     def __str__(self):
-        return self.name
+        return "{} {} {} {}".format(self.experiment, self.name,
+            self.treatment_type, self.placement)
 
     class Meta:
         unique_together = ('experiment', 'name')
         ordering = ['sort_order']
+
+
+class Treatment(models.Model):
+    treatment_type = models.ForeignKey(TreatmentType)
+    container = models.ForeignKey('misc.Container', blank=True, null=True)
+    study_location = models.ForeignKey('locations.StudyLocation')
+    species = models.ForeignKey('species.Species')
+    sex = models.CharField(max_length=25)
+    flaw = models.ForeignKey(Flaw, blank=True, null=True)
+
+    def __str__(self):
+        return "{} {} {} {}".format(self.treatment_type, self.study_location,
+            self.species, self.sex)

ccdb/utils/management/commands/import_data.py

@@ -17,7 +17,7 @@ from ccdb.processing.models import ProcessType, Reagent, Flaw, Processing
 from ccdb.collections_ccdb.models import CollectionType, CollectionMethod, \
     Flaw, ADFGPermit, Collection
 from ccdb.experiments.models import Flaw, Experiment, ProtocolAttachment, \
-    TreatmentType
+    TreatmentType, Treatment
 
 
 class Command(BaseCommand):
@@ -230,3 +230,9 @@ def _import_admin_data():
             tt = TreatmentType(experiment_id=r[0], id=r[1], name=r[2], code=r[3],
                 treatment_type=r[4], placement=r[5], description=r[6])
             tt.save()
+
+        # Treatment
+        for r in c.execute('SELECT * FROM tbl_treatments;'):
+            t = Treatment(id=r[0], treatment_type_id=r[1], container_id=r[2],
+                study_location_id=r[3], species_id=r[4], sex=r[5])
+            t.save()

misc/existing.py

@@ -362,17 +362,3 @@ class TblTreatmentReplicates(models.Model):
         managed = False
         db_table = 'tbl_Treatment_Replicates'
         unique_together = (('TreatmentID', 'Replicate', 'Setup_Date', 'Setup_Time'),)
-
-
-class TblTreatments(models.Model):
-    treatmentid = models.AutoField(db_column='TreatmentID', primary_key=True)  # Field name made lowercase.
-    treatment_typeid = models.ForeignKey(TblLuTreatmentTypes, db_column='Treatment_TypeID')  # Field name made lowercase.
-    containerid = models.ForeignKey(TblLuContainers, db_column='ContainerID', blank=True, null=True)  # Field name made lowercase.
-    study_locationid = models.ForeignKey(TblLuStudyLocations, db_column='Study_LocationID')  # Field name made lowercase.
-    speciesid = models.ForeignKey(TblLuSpecies, db_column='SpeciesID')  # Field name made lowercase.
-    sex = models.CharField(db_column='Sex', max_length=25)  # Field name made lowercase.
-    flawid = models.ForeignKey(TblLuRecordFlaws, db_column='FlawID', blank=True, null=True)  # Field name made lowercase.
-
-    class Meta:
-        managed = False
-        db_table = 'tbl_Treatments'