From a8a87f7ddb56c51178372e7cc20ad109106a08dc Mon Sep 17 00:00:00 2001 From: Matthew Dillon Date: Mon, 1 Feb 2016 14:39:59 -0700 Subject: [PATCH] Treatment --- ccdb/experiments/admin.py | 15 +++++++++- ccdb/experiments/migrations/0003_treatment.py | 29 +++++++++++++++++++ ccdb/experiments/models.py | 16 +++++++++- ccdb/utils/management/commands/import_data.py | 8 ++++- misc/existing.py | 14 --------- 5 files changed, 65 insertions(+), 17 deletions(-) create mode 100644 ccdb/experiments/migrations/0003_treatment.py diff --git a/ccdb/experiments/admin.py b/ccdb/experiments/admin.py index 06d657a..2fb1ce6 100644 --- a/ccdb/experiments/admin.py +++ b/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) diff --git a/ccdb/experiments/migrations/0003_treatment.py b/ccdb/experiments/migrations/0003_treatment.py new file mode 100644 index 0000000..27c9d50 --- /dev/null +++ b/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')), + ], + ), + ] diff --git a/ccdb/experiments/models.py b/ccdb/experiments/models.py index 27d36ea..746464b 100644 --- a/ccdb/experiments/models.py +++ b/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) diff --git a/ccdb/utils/management/commands/import_data.py b/ccdb/utils/management/commands/import_data.py index 341177c..55d8e20 100644 --- a/ccdb/utils/management/commands/import_data.py +++ b/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() diff --git a/misc/existing.py b/misc/existing.py index e6d4633..3ff3780 100644 --- a/misc/existing.py +++ b/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'