thermokarst/ccdb-api
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

SQUASHING

Browse source
This commit is contained in:
Matthew Ryan Dillon 2016-06-15 15:12:34 -07:00
parent 8573b0326b
commit a541a6f301
42 changed files with 588 additions and 1001 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

139
ccdb/collections_ccdb/migrations/0001_initial.py
View file

@ -1,26 +1,22 @@
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
import autoslug.fields
class Migration(migrations.Migration):
dependencies = [
('locations', '0002_remove_site_fk_dupes'),
('projects', '0004_initial_grantreport'),
('projects', '0002_DATA_initial'),
('processing', '0001_initial'),
('locations', '0002_DATA_initial'),
]
operations = [
migrations.CreateModel(
name='ADFGPermit',
fields=[
('id', models.AutoField(primary_key=True, serialize=False, verbose_name='ID', auto_created=True)),
('id', models.AutoField(verbose_name='ID', serialize=False, primary_key=True, auto_created=True)),
('name', models.CharField(max_length=200)),
('sort_order', models.IntegerField(null=True, blank=True)),
('slug', autoslug.fields.AutoSlugField(editable=False, populate_from='name')),
('sort_order', models.IntegerField(blank=True, null=True)),
('slug', autoslug.fields.AutoSlugField(populate_from='name', editable=False)),
],
options={
'ordering': ['sort_order'],
@ -29,25 +25,25 @@ class Migration(migrations.Migration):
migrations.CreateModel(
name='Collection',
fields=[
('id', models.AutoField(primary_key=True, serialize=False, verbose_name='ID', auto_created=True)),
('number_of_traps', models.IntegerField(null=True, blank=True)),
('collection_start_date', models.DateField(null=True, blank=True)),
('collection_start_time', models.TimeField(null=True, blank=True)),
('collection_end_date', models.DateField(null=True, blank=True)),
('collection_end_time', models.TimeField(null=True, blank=True)),
('specimen_state', models.CharField(max_length=50, blank=True)),
('adfg_permit', models.ForeignKey(to='collections_ccdb.ADFGPermit', blank=True, null=True)),
('id', models.AutoField(verbose_name='ID', serialize=False, primary_key=True, auto_created=True)),
('number_of_traps', models.IntegerField(blank=True, null=True)),
('collection_start_date', models.DateField(blank=True, null=True)),
('collection_start_time', models.TimeField(blank=True, null=True)),
('collection_end_date', models.DateField(blank=True, null=True)),
('collection_end_time', models.TimeField(blank=True, null=True)),
('specimen_state', models.CharField(blank=True, max_length=50)),
('adfg_permit', models.ForeignKey(blank=True, null=True, to='collections_ccdb.ADFGPermit')),
],
),
migrations.CreateModel(
name='CollectionMethod',
fields=[
('id', models.AutoField(primary_key=True, serialize=False, verbose_name='ID', auto_created=True)),
('id', models.AutoField(verbose_name='ID', serialize=False, primary_key=True, auto_created=True)),
('name', models.CharField(max_length=100)),
('code', models.CharField(max_length=10, blank=True)),
('collection_method_class', models.CharField(max_length=50, blank=True)),
('sort_order', models.IntegerField(null=True, blank=True)),
('slug', autoslug.fields.AutoSlugField(editable=False, populate_from='name')),
('code', models.CharField(blank=True, max_length=10)),
('collection_method_class', models.CharField(blank=True, max_length=50)),
('sort_order', models.IntegerField(blank=True, null=True)),
('slug', autoslug.fields.AutoSlugField(populate_from='name', editable=False)),
],
options={
'ordering': ['sort_order'],
@ -56,7 +52,7 @@ class Migration(migrations.Migration):
migrations.CreateModel(
name='CollectionTrap',
fields=[
('id', models.AutoField(primary_key=True, serialize=False, verbose_name='ID', auto_created=True)),
('id', models.AutoField(verbose_name='ID', serialize=False, primary_key=True, auto_created=True)),
('number_of_traps', models.IntegerField()),
('date_opened', models.DateField()),
('time_opened', models.TimeField()),
@ -68,11 +64,11 @@ class Migration(migrations.Migration):
migrations.CreateModel(
name='CollectionType',
fields=[
('id', models.AutoField(primary_key=True, serialize=False, verbose_name='ID', auto_created=True)),
('id', models.AutoField(verbose_name='ID', serialize=False, primary_key=True, auto_created=True)),
('name', models.CharField(max_length=100)),
('code', models.CharField(max_length=10, blank=True)),
('sort_order', models.IntegerField(null=True, blank=True)),
('slug', autoslug.fields.AutoSlugField(editable=False, populate_from='name')),
('code', models.CharField(blank=True, max_length=10)),
('sort_order', models.IntegerField(blank=True, null=True)),
('slug', autoslug.fields.AutoSlugField(populate_from='name', editable=False)),
],
options={
'ordering': ['sort_order'],
@ -81,19 +77,19 @@ class Migration(migrations.Migration):
migrations.CreateModel(
name='DatasheetAttachment',
fields=[
('id', models.AutoField(primary_key=True, serialize=False, verbose_name='ID', auto_created=True)),
('datasheet', models.FileField(verbose_name='Datasheet', upload_to='collections/datasheets/%Y/%m/%d')),
('id', models.AutoField(verbose_name='ID', serialize=False, primary_key=True, auto_created=True)),
('datasheet', models.FileField(upload_to='collections/datasheets/%Y/%m/%d', verbose_name='Datasheet')),
('collection', models.ForeignKey(to='collections_ccdb.Collection')),
],
),
migrations.CreateModel(
name='Flaw',
fields=[
('id', models.AutoField(primary_key=True, serialize=False, verbose_name='ID', auto_created=True)),
('id', models.AutoField(verbose_name='ID', serialize=False, primary_key=True, auto_created=True)),
('name', models.CharField(max_length=200)),
('description', models.CharField(max_length=255, blank=True)),
('sort_order', models.IntegerField(null=True, blank=True)),
('slug', autoslug.fields.AutoSlugField(editable=False, populate_from='name')),
('description', models.CharField(blank=True, max_length=255)),
('sort_order', models.IntegerField(blank=True, null=True)),
('slug', autoslug.fields.AutoSlugField(populate_from='name', editable=False)),
],
options={
'ordering': ['sort_order'],
@ -120,12 +116,12 @@ class Migration(migrations.Migration):
migrations.AddField(
model_name='collection',
name='flaw',
field=models.ForeignKey(to='collections_ccdb.Flaw', blank=True, null=True),
field=models.ForeignKey(blank=True, null=True, to='collections_ccdb.Flaw'),
),
migrations.AddField(
model_name='collection',
name='process_type',
field=models.ForeignKey(to='processing.ProcessType', blank=True, null=True),
field=models.ForeignKey(blank=True, null=True, to='processing.ProcessType'),
),
migrations.AddField(
model_name='collection',
@ -135,12 +131,12 @@ class Migration(migrations.Migration):
migrations.AddField(
model_name='collection',
name='reagent',
field=models.ForeignKey(to='processing.Reagent', blank=True, null=True),
field=models.ForeignKey(blank=True, null=True, to='processing.Reagent'),
),
migrations.AddField(
model_name='collection',
name='storage_location',
field=models.ForeignKey(to='locations.StorageLocation', blank=True, null=True),
field=models.ForeignKey(blank=True, null=True, to='locations.StorageLocation'),
),
migrations.AddField(
model_name='collection',
@ -155,4 +151,73 @@ class Migration(migrations.Migration):
name='collection',
unique_together=set([('project', 'study_location', 'collection_type', 'collection_start_date', 'collection_end_date', 'collection_method')]),
),
migrations.AddField(
model_name='collection',
name='display_name',
field=models.CharField(editable=False, default='x', max_length=255),
preserve_default=False,
),
migrations.AlterModelOptions(
name='collection',
options={'ordering': ['project', 'collection_end_date']},
),
migrations.AlterModelOptions(
name='adfgpermit',
options={'ordering': ['sort_order'], 'verbose_name': 'ADFG Permit'},
),
migrations.AlterField(
model_name='collection',
name='adfg_permit',
field=models.ForeignKey(related_name='collections', blank=True, null=True, to='collections_ccdb.ADFGPermit'),
),
migrations.AlterField(
model_name='collection',
name='collection_method',
field=models.ForeignKey(related_name='collections', to='collections_ccdb.CollectionMethod'),
),
migrations.AlterField(
model_name='collection',
name='collection_type',
field=models.ForeignKey(related_name='collections', to='collections_ccdb.CollectionType'),
),
migrations.AlterField(
model_name='collection',
name='flaw',
field=models.ForeignKey(related_name='collections', blank=True, null=True, to='collections_ccdb.Flaw'),
),
migrations.AlterField(
model_name='collection',
name='process_type',
field=models.ForeignKey(related_name='collections', blank=True, null=True, to='processing.ProcessType'),
),
migrations.AlterField(
model_name='collection',
name='project',
field=models.ForeignKey(related_name='collections', to='projects.Project'),
),
migrations.AlterField(
model_name='collection',
name='reagent',
field=models.ForeignKey(related_name='collections', blank=True, null=True, to='processing.Reagent'),
),
migrations.AlterField(
model_name='collection',
name='storage_location',
field=models.ForeignKey(related_name='collections', blank=True, null=True, to='locations.StorageLocation'),
),
migrations.AlterField(
model_name='collection',
name='study_location',
field=models.ForeignKey(related_name='collections', to='locations.StudyLocation'),
),
migrations.AlterField(
model_name='collectiontrap',
name='collection',
field=models.ForeignKey(related_name='traps', to='collections_ccdb.Collection'),
),
migrations.AlterField(
model_name='datasheetattachment',
name='collection',
field=models.ForeignKey(related_name='datasheets', to='collections_ccdb.Collection'),
),
]

19
ccdb/collections_ccdb/migrations/0005_DATA_initial.py → ccdb/collections_ccdb/migrations/0002_DATA_initial.py
View file

@ -25,11 +25,15 @@ class Migration(migrations.Migration):
model.objects.all().delete()
Project = apps.get_model('projects', 'Project')
CollectionSpecies = apps.get_model('species', 'CollectionSpecies')
CollectionSpecies.objects.all().delete()
CollectionTypeForm = modelform_factory(CollectionType, fields='__all__')
CollectionMethodForm = modelform_factory(CollectionMethod, fields='__all__')
ADFGPermitForm = modelform_factory(ADFGPermit, fields='__all__')
CollectionForm = modelform_factory(Collection, fields='__all__')
CollectionSpeciesForm = modelform_factory(CollectionSpecies, fields='__all__')
for r in c.execute('SELECT * FROM tbl_lu_collection_types;'):
form = CollectionTypeForm(dict(name=r[1], code=r[2],
@ -85,6 +89,15 @@ class Migration(migrations.Migration):
else:
print('collection', r[0:], form.errors.as_data())
for r in c.execute('SELECT * FROM tbl_hash_collection_species;'):
form = CollectionSpeciesForm(dict(collection=r[0], species=r[1], sex=r[2],
count=r[3], count_estimated=r[4]))
if form.is_valid():
# No PK in Andre's file
form.save()
else:
print('collection species', r[0:], form.errors.as_data())
def rollback(apps, schema_editor):
CollectionType = apps.get_model('collections_ccdb', 'CollectionType')
CollectionMethod = apps.get_model('collections_ccdb', 'CollectionMethod')
@ -93,13 +106,15 @@ class Migration(migrations.Migration):
Collection = apps.get_model('collections_ccdb', 'Collection')
DatasheetAttachment = apps.get_model('collections_ccdb', 'DatasheetAttachment')
CollectionTrap = apps.get_model('collections_ccdb', 'CollectionTrap')
CollectionSpecies = apps.get_model('species', 'CollectionSpecies')
for model in [CollectionTrap, Collection, Flaw, DatasheetAttachment,
CollectionMethod, CollectionType, ADFGPermit]:
CollectionMethod, CollectionType, ADFGPermit, CollectionSpecies]:
model.objects.all().delete()
dependencies = [
('collections_ccdb', '0004_collections_ordering'),
('collections_ccdb', '0001_initial'),
('processing', '0002_DATA_initial'),
]
operations = [

20
ccdb/collections_ccdb/migrations/0002_collection_display_name.py
View file

@ -1,20 +0,0 @@
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('collections_ccdb', '0001_initial'),
]
operations = [
migrations.AddField(
model_name='collection',
name='display_name',
field=models.CharField(max_length=255, editable=False, default='x'),
preserve_default=False,
),
]

18
ccdb/collections_ccdb/migrations/0003_collections_ordering.py
View file

@ -1,18 +0,0 @@
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('collections_ccdb', '0002_collection_display_name'),
]
operations = [
migrations.AlterModelOptions(
name='collection',
options={'ordering': ['project', 'collection_end_date']},
),
]

18
ccdb/collections_ccdb/migrations/0004_collections_ordering.py
View file

@ -1,18 +0,0 @@
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('collections_ccdb', '0003_collections_ordering'),
]
operations = [
migrations.AlterModelOptions(
name='adfgpermit',
options={'ordering': ['sort_order'], 'verbose_name': 'ADFG Permit'},
),
]

69
ccdb/collections_ccdb/migrations/0006_set_labels.py
View file

@ -1,69 +0,0 @@
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('collections_ccdb', '0005_DATA_initial'),
]
operations = [
migrations.AlterField(
model_name='collection',
name='adfg_permit',
field=models.ForeignKey(null=True, related_name='collections', to='collections_ccdb.ADFGPermit', blank=True),
),
migrations.AlterField(
model_name='collection',
name='collection_method',
field=models.ForeignKey(to='collections_ccdb.CollectionMethod', related_name='collections'),
),
migrations.AlterField(
model_name='collection',
name='collection_type',
field=models.ForeignKey(to='collections_ccdb.CollectionType', related_name='collections'),
),
migrations.AlterField(
model_name='collection',
name='flaw',
field=models.ForeignKey(null=True, related_name='collections', to='collections_ccdb.Flaw', blank=True),
),
migrations.AlterField(
model_name='collection',
name='process_type',
field=models.ForeignKey(null=True, related_name='collections', to='processing.ProcessType', blank=True),
),
migrations.AlterField(
model_name='collection',
name='project',
field=models.ForeignKey(to='projects.Project', related_name='collections'),
),
migrations.AlterField(
model_name='collection',
name='reagent',
field=models.ForeignKey(null=True, related_name='collections', to='processing.Reagent', blank=True),
),
migrations.AlterField(
model_name='collection',
name='storage_location',
field=models.ForeignKey(null=True, related_name='collections', to='locations.StorageLocation', blank=True),
),
migrations.AlterField(
model_name='collection',
name='study_location',
field=models.ForeignKey(to='locations.StudyLocation', related_name='collections'),
),
migrations.AlterField(
model_name='collectiontrap',
name='collection',
field=models.ForeignKey(to='collections_ccdb.Collection', related_name='traps'),
),
migrations.AlterField(
model_name='datasheetattachment',
name='collection',
field=models.ForeignKey(to='collections_ccdb.Collection', related_name='datasheets'),
),
]

167
ccdb/experiments/migrations/0001_initial.py
View file

@ -1,24 +1,24 @@
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
import autoslug.fields
class Migration(migrations.Migration):
dependencies = [
('misc', '0001_initial'),
('locations', '0001_initial'),
('collections_ccdb', '0001_initial'),
('species', '0001_initial'),
]
operations = [
migrations.CreateModel(
name='Experiment',
fields=[
('id', models.AutoField(auto_created=True, serialize=False, verbose_name='ID', primary_key=True)),
('id', models.AutoField(primary_key=True, serialize=False, auto_created=True, verbose_name='ID')),
('name', models.CharField(max_length=150)),
('code', models.CharField(max_length=10, blank=True)),
('description', models.CharField(max_length=255, blank=True)),
('sort_order', models.IntegerField(null=True, blank=True)),
('code', models.CharField(blank=True, max_length=10)),
('description', models.CharField(blank=True, max_length=255)),
('sort_order', models.IntegerField(blank=True, null=True)),
('slug', autoslug.fields.AutoSlugField(populate_from='name', editable=False)),
],
options={
@ -28,10 +28,10 @@ class Migration(migrations.Migration):
migrations.CreateModel(
name='Flaw',
fields=[
('id', models.AutoField(auto_created=True, serialize=False, verbose_name='ID', primary_key=True)),
('id', models.AutoField(primary_key=True, serialize=False, auto_created=True, verbose_name='ID')),
('name', models.CharField(max_length=200)),
('description', models.CharField(max_length=255, blank=True)),
('sort_order', models.IntegerField(null=True, blank=True)),
('description', models.CharField(blank=True, max_length=255)),
('sort_order', models.IntegerField(blank=True, null=True)),
('slug', autoslug.fields.AutoSlugField(populate_from='name', editable=False)),
],
options={
@ -41,7 +41,7 @@ class Migration(migrations.Migration):
migrations.CreateModel(
name='ProtocolAttachment',
fields=[
('id', models.AutoField(auto_created=True, serialize=False, verbose_name='ID', primary_key=True)),
('id', models.AutoField(primary_key=True, serialize=False, auto_created=True, verbose_name='ID')),
('protocol', models.FileField(upload_to='experiments/protocols/%Y/%m/%d')),
('experiment', models.ForeignKey(to='experiments.Experiment')),
],
@ -55,4 +55,147 @@ class Migration(migrations.Migration):
name='experiment',
unique_together=set([('name', 'code')]),
),
migrations.CreateModel(
name='TreatmentType',
fields=[
('id', models.AutoField(primary_key=True, serialize=False, auto_created=True, verbose_name='ID')),
('name', models.CharField(max_length=200)),
('code', models.CharField(blank=True, max_length=25)),
('treatment_type', models.CharField(blank=True, max_length=50)),
('placement', models.CharField(blank=True, max_length=25)),
('description', models.CharField(blank=True, max_length=255)),
('sort_order', models.IntegerField(blank=True, null=True)),
('slug', autoslug.fields.AutoSlugField(populate_from='name', editable=False)),
('experiment', models.ForeignKey(to='experiments.Experiment', null=True, blank=True)),
],
options={
'ordering': ['sort_order'],
},
),
migrations.AlterUniqueTogether(
name='treatmenttype',
unique_together=set([('experiment', 'name')]),
),
migrations.CreateModel(
name='Treatment',
fields=[
('id', models.AutoField(primary_key=True, serialize=False, auto_created=True, verbose_name='ID')),
('sex', models.CharField(max_length=25)),
('container', models.ForeignKey(to='misc.Container', null=True, blank=True)),
('flaw', models.ForeignKey(to='experiments.Flaw', null=True, blank=True)),
('species', models.ForeignKey(to='species.Species')),
('study_location', models.ForeignKey(to='locations.StudyLocation')),
('treatment_type', models.ForeignKey(to='experiments.TreatmentType')),
],
),
migrations.CreateModel(
name='TreatmentReplicate',
fields=[
('id', models.AutoField(primary_key=True, serialize=False, auto_created=True, verbose_name='ID')),
('name', models.CharField(max_length=50)),
('setup_date', models.DateField(blank=True, null=True)),
('setup_time', models.TimeField(blank=True, null=True)),
('setup_sample_size', models.IntegerField(blank=True, null=True)),
('mass_g', models.FloatField(blank=True, null=True)),
('flaw', models.ForeignKey(to='experiments.Flaw', null=True, blank=True)),
('treatment', models.ForeignKey(to='experiments.Treatment')),
],
),
migrations.AlterUniqueTogether(
name='treatmentreplicate',
unique_together=set([('treatment', 'name', 'setup_date', 'setup_time')]),
),
migrations.CreateModel(
name='AliveDeadCount',
fields=[
('id', models.AutoField(primary_key=True, serialize=False, auto_created=True, verbose_name='ID')),
('status_date', models.DateField()),
('status_time', models.TimeField(blank=True, null=True)),
('count_alive', models.IntegerField(blank=True, null=True)),
('count_dead', models.IntegerField(blank=True, null=True)),
('flaw', models.ForeignKey(to='experiments.Flaw', null=True, blank=True)),
('treatment_replicate', models.ForeignKey(to='experiments.TreatmentReplicate')),
],
),
migrations.AddField(
model_name='experiment',
name='collections',
field=models.ManyToManyField(to='collections_ccdb.Collection'),
),
migrations.AlterModelOptions(
name='alivedeadcount',
options={'verbose_name': 'Alive-dead Count'},
),
migrations.AddField(
model_name='treatmentreplicate',
name='display_name',
field=models.CharField(default='x', max_length=255, editable=False),
preserve_default=False,
),
migrations.AddField(
model_name='treatment',
name='display_name',
field=models.CharField(default='x', max_length=255, editable=False),
preserve_default=False,
),
migrations.AlterField(
model_name='alivedeadcount',
name='flaw',
field=models.ForeignKey(related_name='alive_dead_counts', to='experiments.Flaw', null=True, blank=True),
),
migrations.AlterField(
model_name='alivedeadcount',
name='treatment_replicate',
field=models.ForeignKey(related_name='alive_dead_counts', to='experiments.TreatmentReplicate'),
),
migrations.AlterField(
model_name='experiment',
name='flaw',
field=models.ForeignKey(related_name='experiments', to='experiments.Flaw', null=True, blank=True),
),
migrations.AlterField(
model_name='protocolattachment',
name='experiment',
field=models.ForeignKey(related_name='protocols', to='experiments.Experiment'),
),
migrations.AlterField(
model_name='treatment',
name='container',
field=models.ForeignKey(related_name='treatments', to='misc.Container', null=True, blank=True),
),
migrations.AlterField(
model_name='treatment',
name='flaw',
field=models.ForeignKey(related_name='treatments', to='experiments.Flaw', null=True, blank=True),
),
migrations.AlterField(
model_name='treatment',
name='species',
field=models.ForeignKey(related_name='treatments', to='species.Species'),
),
migrations.AlterField(
model_name='treatment',
name='study_location',
field=models.ForeignKey(related_name='treatments', to='locations.StudyLocation'),
),
migrations.AlterField(
model_name='treatment',
name='treatment_type',
field=models.ForeignKey(related_name='treatments', to='experiments.TreatmentType'),
),
migrations.AlterField(
model_name='treatmentreplicate',
name='flaw',
field=models.ForeignKey(related_name='treatment_replicates', to='experiments.Flaw', null=True, blank=True),
),
migrations.AlterField(
model_name='treatmentreplicate',
name='treatment',
field=models.ForeignKey(related_name='treatment_replicates', to='experiments.Treatment'),
),
migrations.AlterField(
model_name='treatmenttype',
name='experiment',
field=models.ForeignKey(related_name='treatment_types', to='experiments.Experiment', null=True, blank=True),
),
]

30
ccdb/experiments/migrations/0009_DATA_initial.py → ccdb/experiments/migrations/0002_DATA_initial.py
View file

@ -23,6 +23,10 @@ class Migration(migrations.Migration):
Experiment, Flaw]:
model.objects.all().delete()
Collection = apps.get_model('collections_ccdb', 'Collection')
StudyLocation = apps.get_model('locations', 'StudyLocation')
Species = apps.get_model('species', 'Species')
ExperimentForm = modelform_factory(Experiment, exclude=('collections',))
TreatmentTypeForm = modelform_factory(TreatmentType, fields='__all__')
TreatmentForm = modelform_factory(Treatment, fields='__all__')
@ -50,7 +54,12 @@ class Migration(migrations.Migration):
form = TreatmentForm(dict(treatment_type=r[1], container=r[2],
study_location=r[3], species=r[4], sex=r[5]))
if form.is_valid():
Treatment.objects.create(id=r[0], **form.cleaned_data)
treatment_type = TreatmentType.objects.get(id=r[1])
study_location = StudyLocation.objects.get(id=r[3])
species = Species.objects.get(id=r[4])
d = "{}_{}_{}_{}".format(treatment_type, study_location,
species, form.cleaned_data['sex'])
Treatment.objects.create(id=r[0], display_name=d, **form.cleaned_data)
else:
print('treatment', r[0:], form.errors.as_data())
@ -91,6 +100,17 @@ class Migration(migrations.Migration):
else:
print('alive-dead count', r[0:], form.errors.as_data())
for experiment in Experiment.objects.all():
experiment.collections.all().delete()
for r in c.execute('SELECT * FROM tbl_hash_collection_experiments;'):
c = Collection.objects.get(id=r[0])
e = Experiment.objects.get(id=r[1])
e.collections.add(c)
e.save()
def rollback(apps, schema_editor):
Flaw = apps.get_model('experiments', 'Flaw')
Experiment = apps.get_model('experiments', 'Experiment')
@ -103,9 +123,13 @@ class Migration(migrations.Migration):
Experiment, Flaw]:
model.objects.all().delete()
for experiment in Experiment.objects.all():
experiment.collections.all().delete()
dependencies = [
('experiments', '0008_treatment_display_name'),
('collections_ccdb', '0005_DATA_initial'),
('experiments', '0001_initial'),
('collections_ccdb', '0002_DATA_initial'),
]
operations = [

36
ccdb/experiments/migrations/0002_treatment_type.py
View file

@ -1,36 +0,0 @@
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
import autoslug.fields
class Migration(migrations.Migration):
dependencies = [
('experiments', '0001_initial'),
]
operations = [
migrations.CreateModel(
name='TreatmentType',
fields=[
('id', models.AutoField(primary_key=True, auto_created=True, verbose_name='ID', serialize=False)),
('name', models.CharField(max_length=200)),
('code', models.CharField(max_length=25, blank=True)),
('treatment_type', models.CharField(max_length=50, blank=True)),
('placement', models.CharField(max_length=25, blank=True)),
('description', models.CharField(max_length=255, blank=True)),
('sort_order', models.IntegerField(null=True, blank=True)),
('slug', autoslug.fields.AutoSlugField(populate_from='name', editable=False)),
('experiment', models.ForeignKey(null=True, blank=True, to='experiments.Experiment')),
],
options={
'ordering': ['sort_order'],
},
),
migrations.AlterUniqueTogether(
name='treatmenttype',
unique_together=set([('experiment', 'name')]),
),
]

29
ccdb/experiments/migrations/0003_treatment.py
View file

@ -1,29 +0,0 @@
# -*- 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')),
],
),
]

31
ccdb/experiments/migrations/0004_treatment_replicate.py
View file

@ -1,31 +0,0 @@
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('experiments', '0003_treatment'),
]
operations = [
migrations.CreateModel(
name='TreatmentReplicate',
fields=[
('id', models.AutoField(verbose_name='ID', auto_created=True, primary_key=True, serialize=False)),
('name', models.CharField(max_length=50)),
('setup_date', models.DateField(null=True, blank=True)),
('setup_time', models.TimeField(null=True, blank=True)),
('setup_sample_size', models.IntegerField(null=True, blank=True)),
('mass_g', models.FloatField(null=True, blank=True)),
('flaw', models.ForeignKey(null=True, to='experiments.Flaw', blank=True)),
('treatment', models.ForeignKey(to='experiments.Treatment')),
],
),
migrations.AlterUniqueTogether(
name='treatmentreplicate',
unique_together=set([('treatment', 'name', 'setup_date', 'setup_time')]),
),
]

26
ccdb/experiments/migrations/0005_alivedeadcount.py
View file

@ -1,26 +0,0 @@
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('experiments', '0004_treatment_replicate'),
]
operations = [
migrations.CreateModel(
name='AliveDeadCount',
fields=[
('id', models.AutoField(auto_created=True, verbose_name='ID', primary_key=True, serialize=False)),
('status_date', models.DateField()),
('status_time', models.TimeField(blank=True, null=True)),
('count_alive', models.IntegerField(blank=True, null=True)),
('count_dead', models.IntegerField(blank=True, null=True)),
('flaw', models.ForeignKey(to='experiments.Flaw', blank=True, null=True)),
('treatment_replicate', models.ForeignKey(to='experiments.TreatmentReplicate')),
],
),
]

20
ccdb/experiments/migrations/0006_experiment_collections.py
View file

@ -1,20 +0,0 @@
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('collections_ccdb', '0001_initial'),
('experiments', '0005_alivedeadcount'),
]
operations = [
migrations.AddField(
model_name='experiment',
name='collections',
field=models.ManyToManyField(to='collections_ccdb.Collection'),
),
]

24
ccdb/experiments/migrations/0007_treatment_replicates_display.py
View file

@ -1,24 +0,0 @@
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('experiments', '0006_experiment_collections'),
]
operations = [
migrations.AlterModelOptions(
name='alivedeadcount',
options={'verbose_name': 'Alive-dead Count'},
),
migrations.AddField(
model_name='treatmentreplicate',
name='display_name',
field=models.CharField(editable=False, max_length=255, default='x'),
preserve_default=False,
),
]

20
ccdb/experiments/migrations/0008_treatment_display_name.py
View file

@ -1,20 +0,0 @@
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('experiments', '0007_treatment_replicates_display'),
]
operations = [
migrations.AddField(
model_name='treatment',
name='display_name',
field=models.CharField(editable=False, default='x', max_length=255),
preserve_default=False,
),
]

38
ccdb/experiments/migrations/0010_DATA_collections_experiments.py
View file

@ -1,38 +0,0 @@
from django.db import migrations
from ccdb.utils.data import get_data_sources
class Migration(migrations.Migration):
def migrate(apps, schema_editor):
sources = get_data_sources()
if not sources:
return
c = sources['db0']
Collection = apps.get_model('collections_ccdb', 'Collection')
Experiment = apps.get_model('experiments', 'Experiment')
for experiment in Experiment.objects.all():
experiment.collections.all().delete()
for r in c.execute('SELECT * FROM tbl_hash_collection_experiments;'):
c = Collection.objects.get(id=r[0])
e = Experiment.objects.get(id=r[1])
e.collections.add(c)
e.save()
def rollback(apps, schema_editor):
Experiment = apps.get_model('experiments', 'Experiment')
for experiment in Experiment.objects.all():
experiment.collections.all().delete()
dependencies = [
('experiments', '0009_DATA_initial'),
]
operations = [
migrations.RunPython(migrate, rollback),
]

74
ccdb/experiments/migrations/0011_set_labels.py
View file

@ -1,74 +0,0 @@
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('experiments', '0010_DATA_collections_experiments'),
]
operations = [
migrations.AlterField(
model_name='alivedeadcount',
name='flaw',
field=models.ForeignKey(null=True, to='experiments.Flaw', related_name='alive_dead_counts', blank=True),
),
migrations.AlterField(
model_name='alivedeadcount',
name='treatment_replicate',
field=models.ForeignKey(to='experiments.TreatmentReplicate', related_name='alive_dead_counts'),
),
migrations.AlterField(
model_name='experiment',
name='flaw',
field=models.ForeignKey(null=True, to='experiments.Flaw', related_name='experiments', blank=True),
),
migrations.AlterField(
model_name='protocolattachment',
name='experiment',
field=models.ForeignKey(to='experiments.Experiment', related_name='protocols'),
),
migrations.AlterField(
model_name='treatment',
name='container',
field=models.ForeignKey(null=True, to='misc.Container', related_name='treatments', blank=True),
),
migrations.AlterField(
model_name='treatment',
name='flaw',
field=models.ForeignKey(null=True, to='experiments.Flaw', related_name='treatments', blank=True),
),
migrations.AlterField(
model_name='treatment',
name='species',
field=models.ForeignKey(to='species.Species', related_name='treatments'),
),
migrations.AlterField(
model_name='treatment',
name='study_location',
field=models.ForeignKey(to='locations.StudyLocation', related_name='treatments'),
),
migrations.AlterField(
model_name='treatment',
name='treatment_type',
field=models.ForeignKey(to='experiments.TreatmentType', related_name='treatments'),
),
migrations.AlterField(
model_name='treatmentreplicate',
name='flaw',
field=models.ForeignKey(null=True, to='experiments.Flaw', related_name='treatment_replicates', blank=True),
),
migrations.AlterField(
model_name='treatmentreplicate',
name='treatment',
field=models.ForeignKey(to='experiments.Treatment', related_name='treatment_replicates'),
),
migrations.AlterField(
model_name='treatmenttype',
name='experiment',
field=models.ForeignKey(null=True, to='experiments.Experiment', related_name='treatment_types', blank=True),
),
]

90
ccdb/locations/migrations/0001_initial.py
View file

@ -1,12 +1,8 @@
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
import autoslug.fields
class Migration(migrations.Migration):
dependencies = [
]
@ -14,13 +10,13 @@ class Migration(migrations.Migration):
migrations.CreateModel(
name='MunicipalLocation',
fields=[
('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)),
('id', models.AutoField(primary_key=True, serialize=False, verbose_name='ID', auto_created=True)),
('name', models.CharField(max_length=100)),
('code', models.CharField(max_length=10, blank=True)),
('municipal_location_type', models.CharField(max_length=50, blank=True)),
('description', models.CharField(max_length=255, blank=True)),
('sort_order', models.IntegerField(null=True, blank=True)),
('slug', autoslug.fields.AutoSlugField(populate_from='name', editable=False)),
('code', models.CharField(blank=True, max_length=10)),
('municipal_location_type', models.CharField(blank=True, max_length=50)),
('description', models.CharField(blank=True, max_length=255)),
('sort_order', models.IntegerField(blank=True, null=True)),
('slug', autoslug.fields.AutoSlugField(editable=False, populate_from='name')),
],
options={
'ordering': ['sort_order'],
@ -29,11 +25,11 @@ class Migration(migrations.Migration):
migrations.CreateModel(
name='Region',
fields=[
('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)),
('id', models.AutoField(primary_key=True, serialize=False, verbose_name='ID', auto_created=True)),
('name', models.CharField(max_length=100)),
('code', models.CharField(max_length=10, blank=True)),
('sort_order', models.IntegerField(null=True, blank=True)),
('slug', autoslug.fields.AutoSlugField(populate_from='name', editable=False)),
('code', models.CharField(blank=True, max_length=10)),
('sort_order', models.IntegerField(blank=True, null=True)),
('slug', autoslug.fields.AutoSlugField(editable=False, populate_from='name')),
],
options={
'ordering': ['sort_order'],
@ -42,12 +38,12 @@ class Migration(migrations.Migration):
migrations.CreateModel(
name='Site',
fields=[
('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)),
('id', models.AutoField(primary_key=True, serialize=False, verbose_name='ID', auto_created=True)),
('name', models.CharField(max_length=100)),
('code', models.CharField(max_length=10, blank=True)),
('description', models.CharField(max_length=255, blank=True)),
('sort_order', models.IntegerField(null=True, blank=True)),
('slug', autoslug.fields.AutoSlugField(populate_from='name', editable=False)),
('code', models.CharField(blank=True, max_length=10)),
('description', models.CharField(blank=True, max_length=255)),
('sort_order', models.IntegerField(blank=True, null=True)),
('slug', autoslug.fields.AutoSlugField(editable=False, populate_from='name')),
('region', models.ForeignKey(to='locations.Region', null=True, blank=True)),
],
options={
@ -57,15 +53,15 @@ class Migration(migrations.Migration):
migrations.CreateModel(
name='StorageLocation',
fields=[
('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)),
('id', models.AutoField(primary_key=True, serialize=False, verbose_name='ID', auto_created=True)),
('facility', models.CharField(max_length=100)),
('building', models.CharField(max_length=100)),
('code', models.CharField(max_length=100)),
('room', models.CharField(max_length=50, blank=True)),
('freezer', models.CharField(max_length=50, blank=True)),
('temp_c', models.IntegerField(null=True, blank=True)),
('description', models.CharField(max_length=255, blank=True)),
('sort_order', models.IntegerField(null=True, blank=True)),
('room', models.CharField(blank=True, max_length=50)),
('freezer', models.CharField(blank=True, max_length=50)),
('temp_c', models.IntegerField(blank=True, null=True)),
('description', models.CharField(blank=True, max_length=255)),
('sort_order', models.IntegerField(blank=True, null=True)),
],
options={
'ordering': ['sort_order'],
@ -74,15 +70,15 @@ class Migration(migrations.Migration):
migrations.CreateModel(
name='StudyLocation',
fields=[
('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)),
('id', models.AutoField(primary_key=True, serialize=False, verbose_name='ID', auto_created=True)),
('name', models.CharField(max_length=100)),
('code', models.CharField(max_length=10, blank=True)),
('study_location_type', models.CharField(max_length=50, blank=True)),
('treatment_type', models.CharField(max_length=100, blank=True)),
('code', models.CharField(blank=True, max_length=10)),
('study_location_type', models.CharField(blank=True, max_length=50)),
('treatment_type', models.CharField(blank=True, max_length=100)),
('collecting_location', models.BooleanField(default=False)),
('description', models.CharField(max_length=255, blank=True)),
('sort_order', models.IntegerField(null=True, blank=True)),
('slug', autoslug.fields.AutoSlugField(populate_from='name', editable=False)),
('description', models.CharField(blank=True, max_length=255)),
('sort_order', models.IntegerField(blank=True, null=True)),
('slug', autoslug.fields.AutoSlugField(editable=False, populate_from='name')),
('municipal_location', models.ForeignKey(to='locations.MunicipalLocation', null=True, blank=True)),
('site', models.ForeignKey(to='locations.Site', null=True, blank=True)),
],
@ -94,13 +90,33 @@ class Migration(migrations.Migration):
name='region',
unique_together=set([('name', 'code')]),
),
migrations.AddField(
model_name='municipallocation',
name='site',
field=models.ForeignKey(to='locations.Site'),
),
migrations.AlterUniqueTogether(
name='studylocation',
unique_together=set([('site', 'name')]),
),
migrations.AlterField(
model_name='studylocation',
name='site',
field=models.ForeignKey(to='locations.Site'),
),
migrations.AlterField(
model_name='studylocation',
name='code',
field=models.CharField(max_length=10),
),
migrations.AlterField(
model_name='site',
name='region',
field=models.ForeignKey(to='locations.Region', null=True, blank=True, related_name='sites'),
),
migrations.AlterField(
model_name='studylocation',
name='municipal_location',
field=models.ForeignKey(to='locations.MunicipalLocation', null=True, blank=True, related_name='study_locations'),
),
migrations.AlterField(
model_name='studylocation',
name='site',
field=models.ForeignKey(to='locations.Site', related_name='study_locations'),
),
]

3
ccdb/locations/migrations/0004_DATA_initial.py → ccdb/locations/migrations/0002_DATA_initial.py
View file

@ -94,7 +94,8 @@ class Migration(migrations.Migration):
model.objects.all().delete()
dependencies = [
('locations', '0003_study_location_code_req'),
('locations', '0001_initial'),
('misc', '0002_DATA_initial'),
]
operations = [

23
ccdb/locations/migrations/0002_remove_site_fk_dupes.py
View file

@ -1,23 +0,0 @@
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('locations', '0001_initial'),
]
operations = [
migrations.RemoveField(
model_name='municipallocation',
name='site',
),
migrations.AlterField(
model_name='studylocation',
name='site',
field=models.ForeignKey(to='locations.Site'),
),
]

19
ccdb/locations/migrations/0003_study_location_code_req.py
View file

@ -1,19 +0,0 @@
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('locations', '0002_remove_site_fk_dupes'),
]
operations = [
migrations.AlterField(
model_name='studylocation',
name='code',
field=models.CharField(max_length=10),
),
]

29
ccdb/locations/migrations/0005_set_labels.py
View file

@ -1,29 +0,0 @@
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('locations', '0004_DATA_initial'),
]
operations = [
migrations.AlterField(
model_name='site',
name='region',
field=models.ForeignKey(blank=True, related_name='sites', null=True, to='locations.Region'),
),
migrations.AlterField(
model_name='studylocation',
name='municipal_location',
field=models.ForeignKey(blank=True, related_name='study_locations', null=True, to='locations.MunicipalLocation'),
),
migrations.AlterField(
model_name='studylocation',
name='site',
field=models.ForeignKey(related_name='study_locations', to='locations.Site'),
),
]

78
ccdb/misc/migrations/0001_initial.py
View file

@ -1,12 +1,8 @@
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
import autoslug.fields
class Migration(migrations.Migration):
dependencies = [
]
@ -14,11 +10,11 @@ class Migration(migrations.Migration):
migrations.CreateModel(
name='Color',
fields=[
('id', models.AutoField(primary_key=True, serialize=False, auto_created=True, verbose_name='ID')),
('id', models.AutoField(serialize=False, primary_key=True, verbose_name='ID', auto_created=True)),
('name', models.CharField(max_length=50)),
('code', models.CharField(blank=True, max_length=10)),
('color_number', models.FloatField(null=True, blank=True)),
('sort_order', models.IntegerField(null=True, blank=True)),
('code', models.CharField(max_length=10, blank=True)),
('color_number', models.FloatField(blank=True, null=True)),
('sort_order', models.IntegerField(blank=True, null=True)),
('slug', autoslug.fields.AutoSlugField(editable=False, populate_from='name')),
],
options={
@ -28,14 +24,14 @@ class Migration(migrations.Migration):
migrations.CreateModel(
name='Container',
fields=[
('id', models.AutoField(primary_key=True, serialize=False, auto_created=True, verbose_name='ID')),
('id', models.AutoField(serialize=False, primary_key=True, verbose_name='ID', auto_created=True)),
('name', models.CharField(max_length=100)),
('code', models.CharField(blank=True, max_length=10)),
('application', models.CharField(blank=True, max_length=50)),
('volume', models.FloatField(null=True, blank=True)),
('sort_order', models.IntegerField(null=True, blank=True)),
('code', models.CharField(max_length=10, blank=True)),
('application', models.CharField(max_length=50, blank=True)),
('volume', models.FloatField(blank=True, null=True)),
('sort_order', models.IntegerField(blank=True, null=True)),
('slug', autoslug.fields.AutoSlugField(editable=False, populate_from='name')),
('color', models.ForeignKey(null=True, to='misc.Color', blank=True)),
('color', models.ForeignKey(blank=True, to='misc.Color', null=True)),
],
options={
'ordering': ['sort_order'],
@ -44,12 +40,12 @@ class Migration(migrations.Migration):
migrations.CreateModel(
name='Material',
fields=[
('id', models.AutoField(primary_key=True, serialize=False, auto_created=True, verbose_name='ID')),
('id', models.AutoField(serialize=False, primary_key=True, verbose_name='ID', auto_created=True)),
('name', models.CharField(max_length=100)),
('code', models.CharField(blank=True, max_length=10)),
('material_class', models.CharField(blank=True, max_length=50)),
('description', models.CharField(blank=True, max_length=255)),
('sort_order', models.IntegerField(null=True, blank=True)),
('code', models.CharField(max_length=10, blank=True)),
('material_class', models.CharField(max_length=50, blank=True)),
('description', models.CharField(max_length=255, blank=True)),
('sort_order', models.IntegerField(blank=True, null=True)),
('slug', autoslug.fields.AutoSlugField(editable=False, populate_from='name')),
],
options={
@ -59,12 +55,12 @@ class Migration(migrations.Migration):
migrations.CreateModel(
name='MeasurementType',
fields=[
('id', models.AutoField(primary_key=True, serialize=False, auto_created=True, verbose_name='ID')),
('id', models.AutoField(serialize=False, primary_key=True, verbose_name='ID', auto_created=True)),
('name', models.CharField(max_length=100)),
('code', models.CharField(blank=True, max_length=10)),
('measurement_type_class', models.CharField(blank=True, max_length=50)),
('description', models.CharField(blank=True, max_length=255)),
('sort_order', models.IntegerField(null=True, blank=True)),
('code', models.CharField(max_length=10, blank=True)),
('measurement_type_class', models.CharField(max_length=50, blank=True)),
('description', models.CharField(max_length=255, blank=True)),
('sort_order', models.IntegerField(blank=True, null=True)),
('slug', autoslug.fields.AutoSlugField(editable=False, populate_from='name')),
],
options={
@ -74,12 +70,12 @@ class Migration(migrations.Migration):
migrations.CreateModel(
name='MeasurementUnit',
fields=[
('id', models.AutoField(primary_key=True, serialize=False, auto_created=True, verbose_name='ID')),
('id', models.AutoField(serialize=False, primary_key=True, verbose_name='ID', auto_created=True)),
('name', models.CharField(max_length=100)),
('code', models.CharField(max_length=25)),
('unit_class', models.CharField(blank=True, max_length=50)),
('description', models.CharField(blank=True, max_length=255)),
('sort_order', models.IntegerField(null=True, blank=True)),
('unit_class', models.CharField(max_length=50, blank=True)),
('description', models.CharField(max_length=255, blank=True)),
('sort_order', models.IntegerField(blank=True, null=True)),
('slug', autoslug.fields.AutoSlugField(editable=False, populate_from='name')),
],
options={
@ -93,7 +89,7 @@ class Migration(migrations.Migration):
migrations.AddField(
model_name='measurementtype',
name='default_measurement_unit',
field=models.ForeignKey(null=True, to='misc.MeasurementUnit', blank=True),
field=models.ForeignKey(blank=True, to='misc.MeasurementUnit', null=True),
),
migrations.AlterUniqueTogether(
name='material',
@ -102,15 +98,35 @@ class Migration(migrations.Migration):
migrations.AddField(
model_name='container',
name='material',
field=models.ForeignKey(null=True, to='misc.Material', blank=True),
field=models.ForeignKey(blank=True, to='misc.Material', null=True),
),
migrations.AddField(
model_name='container',
name='measurement_unit',
field=models.ForeignKey(null=True, to='misc.MeasurementUnit', blank=True),
field=models.ForeignKey(blank=True, to='misc.MeasurementUnit', null=True),
),
migrations.AlterUniqueTogether(
name='color',
unique_together=set([('name', 'code', 'color_number')]),
),
migrations.AlterField(
model_name='container',
name='color',
field=models.ForeignKey(blank=True, to='misc.Color', related_name='containers', null=True),
),
migrations.AlterField(
model_name='container',
name='material',
field=models.ForeignKey(blank=True, to='misc.Material', related_name='containers', null=True),
),
migrations.AlterField(
model_name='container',
name='measurement_unit',
field=models.ForeignKey(blank=True, to='misc.MeasurementUnit', related_name='containers', null=True),
),
migrations.AlterField(
model_name='measurementtype',
name='default_measurement_unit',
field=models.ForeignKey(blank=True, to='misc.MeasurementUnit', related_name='measurement_types', null=True),
),
]

1
ccdb/misc/migrations/0002_DATA_initial.py
View file

@ -104,6 +104,7 @@ class Migration(migrations.Migration):
dependencies = [
('misc', '0001_initial'),
('projects', '0002_DATA_initial'),
]
operations = [

34
ccdb/misc/migrations/0003_set_labels.py
View file

@ -1,34 +0,0 @@
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('misc', '0002_DATA_initial'),
]
operations = [
migrations.AlterField(
model_name='container',
name='color',
field=models.ForeignKey(related_name='containers', blank=True, to='misc.Color', null=True),
),
migrations.AlterField(
model_name='container',
name='material',
field=models.ForeignKey(related_name='containers', blank=True, to='misc.Material', null=True),
),
migrations.AlterField(
model_name='container',
name='measurement_unit',
field=models.ForeignKey(related_name='containers', blank=True, to='misc.MeasurementUnit', null=True),
),
migrations.AlterField(
model_name='measurementtype',
name='default_measurement_unit',
field=models.ForeignKey(related_name='measurement_types', blank=True, to='misc.MeasurementUnit', null=True),
),
]

67
ccdb/processing/migrations/0001_initial.py
View file

@ -1,12 +1,8 @@
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
import autoslug.fields
class Migration(migrations.Migration):
dependencies = [
('misc', '0001_initial'),
]
@ -15,10 +11,10 @@ class Migration(migrations.Migration):
migrations.CreateModel(
name='Flaw',
fields=[
('id', models.AutoField(primary_key=True, auto_created=True, verbose_name='ID', serialize=False)),
('id', models.AutoField(auto_created=True, verbose_name='ID', serialize=False, primary_key=True)),
('name', models.CharField(max_length=200)),
('description', models.CharField(blank=True, max_length=255)),
('sort_order', models.IntegerField(blank=True, null=True)),
('description', models.CharField(max_length=255, blank=True)),
('sort_order', models.IntegerField(null=True, blank=True)),
('slug', autoslug.fields.AutoSlugField(populate_from='name', editable=False)),
],
options={
@ -28,25 +24,25 @@ class Migration(migrations.Migration):
migrations.CreateModel(
name='Processing',
fields=[
('id', models.AutoField(primary_key=True, auto_created=True, verbose_name='ID', serialize=False)),
('id', models.AutoField(auto_created=True, verbose_name='ID', serialize=False, primary_key=True)),
('container_label', models.CharField(max_length=50)),
('process_date', models.DateField(blank=True, null=True)),
('process_time', models.TimeField(blank=True, null=True)),
('reagent_volume', models.FloatField(blank=True, null=True)),
('minutes_in_reagent', models.IntegerField(blank=True, null=True)),
('process_date', models.DateField(null=True, blank=True)),
('process_time', models.TimeField(null=True, blank=True)),
('reagent_volume', models.FloatField(null=True, blank=True)),
('minutes_in_reagent', models.IntegerField(null=True, blank=True)),
('container', models.ForeignKey(to='misc.Container')),
('flaw', models.ForeignKey(to='processing.Flaw', blank=True, null=True)),
('measurement_unit', models.ForeignKey(to='misc.MeasurementUnit', blank=True, null=True)),
('flaw', models.ForeignKey(to='processing.Flaw', null=True, blank=True)),
('measurement_unit', models.ForeignKey(to='misc.MeasurementUnit', null=True, blank=True)),
],
),
migrations.CreateModel(
name='ProcessType',
fields=[
('id', models.AutoField(primary_key=True, auto_created=True, verbose_name='ID', serialize=False)),
('id', models.AutoField(auto_created=True, verbose_name='ID', serialize=False, primary_key=True)),
('name', models.CharField(max_length=100)),
('code', models.CharField(blank=True, max_length=10)),
('description', models.CharField(blank=True, max_length=255)),
('sort_order', models.IntegerField(blank=True, null=True)),
('code', models.CharField(max_length=10, blank=True)),
('description', models.CharField(max_length=255, blank=True)),
('sort_order', models.IntegerField(null=True, blank=True)),
('slug', autoslug.fields.AutoSlugField(populate_from='name', editable=False)),
],
options={
@ -56,11 +52,11 @@ class Migration(migrations.Migration):
migrations.CreateModel(
name='Reagent',
fields=[
('id', models.AutoField(primary_key=True, auto_created=True, verbose_name='ID', serialize=False)),
('id', models.AutoField(auto_created=True, verbose_name='ID', serialize=False, primary_key=True)),
('name', models.CharField(max_length=100)),
('code', models.CharField(blank=True, max_length=10)),
('reagent_class', models.CharField(blank=True, max_length=50)),
('sort_order', models.IntegerField(blank=True, null=True)),
('code', models.CharField(max_length=10, blank=True)),
('reagent_class', models.CharField(max_length=50, blank=True)),
('sort_order', models.IntegerField(null=True, blank=True)),
('slug', autoslug.fields.AutoSlugField(populate_from='name', editable=False)),
],
options={
@ -83,10 +79,35 @@ class Migration(migrations.Migration):
migrations.AddField(
model_name='processing',
name='reagent',
field=models.ForeignKey(to='processing.Reagent', blank=True, null=True),
field=models.ForeignKey(to='processing.Reagent', null=True, blank=True),
),
migrations.AlterUniqueTogether(
name='processing',
unique_together=set([('process_type', 'container', 'container_label', 'process_date', 'process_time', 'reagent')]),
),
migrations.AlterField(
model_name='processing',
name='container',
field=models.ForeignKey(related_name='processings', to='misc.Container'),
),
migrations.AlterField(
model_name='processing',
name='flaw',
field=models.ForeignKey(to='processing.Flaw', null=True, related_name='processings', blank=True),
),
migrations.AlterField(
model_name='processing',
name='measurement_unit',
field=models.ForeignKey(to='misc.MeasurementUnit', null=True, related_name='processings', blank=True),
),
migrations.AlterField(
model_name='processing',
name='process_type',
field=models.ForeignKey(related_name='processings', to='processing.ProcessType'),
),
migrations.AlterField(
model_name='processing',
name='reagent',
field=models.ForeignKey(to='processing.Reagent', null=True, related_name='processings', blank=True),
),
]

1
ccdb/processing/migrations/0002_DATA_initial.py
View file

@ -50,6 +50,7 @@ class Migration(migrations.Migration):
dependencies = [
('processing', '0001_initial'),
('species', '0002_DATA_initial'),
]
operations = [

39
ccdb/processing/migrations/0003_set_labels.py
View file

@ -1,39 +0,0 @@
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('processing', '0002_DATA_initial'),
]
operations = [
migrations.AlterField(
model_name='processing',
name='container',
field=models.ForeignKey(related_name='processings', to='misc.Container'),
),
migrations.AlterField(
model_name='processing',
name='flaw',
field=models.ForeignKey(to='processing.Flaw', blank=True, related_name='processings', null=True),
),
migrations.AlterField(
model_name='processing',
name='measurement_unit',
field=models.ForeignKey(to='misc.MeasurementUnit', blank=True, related_name='processings', null=True),
),
migrations.AlterField(
model_name='processing',
name='process_type',
field=models.ForeignKey(related_name='processings', to='processing.ProcessType'),
),
migrations.AlterField(
model_name='processing',
name='reagent',
field=models.ForeignKey(to='processing.Reagent', blank=True, related_name='processings', null=True),
),
]

77
ccdb/projects/migrations/0001_initial.py Normal file
View file

@ -0,0 +1,77 @@
from django.db import migrations, models
import autoslug.fields
class Migration(migrations.Migration):
dependencies = [
]
operations = [
migrations.CreateModel(
name='Project',
fields=[
('id', models.AutoField(serialize=False, auto_created=True, verbose_name='ID', primary_key=True)),
('name', models.CharField(max_length=100)),
('code', models.CharField(blank=True, max_length=10)),
('iacuc_number', models.CharField(blank=True, max_length=25)),
('description', models.CharField(blank=True, max_length=255)),
('sort_order', models.IntegerField(blank=True, null=True)),
('slug', autoslug.fields.AutoSlugField(populate_from='name', editable=False)),
],
options={
'ordering': ['sort_order'],
},
),
migrations.AlterUniqueTogether(
name='project',
unique_together=set([('name', 'code')]),
),
migrations.CreateModel(
name='Grant',
fields=[
('id', models.AutoField(serialize=False, auto_created=True, verbose_name='ID', primary_key=True)),
('title', models.CharField(max_length=200)),
('code', models.CharField(blank=True, max_length=10)),
('description', models.CharField(blank=True, max_length=255)),
('sort_order', models.IntegerField(blank=True, null=True)),
],
options={
'ordering': ['sort_order'],
},
),
migrations.AlterUniqueTogether(
name='grant',
unique_together=set([('title', 'code')]),
),
migrations.AddField(
model_name='grant',
name='projects',
field=models.ManyToManyField(related_name='grants', to='projects.Project'),
),
migrations.CreateModel(
name='GrantReport',
fields=[
('id', models.AutoField(serialize=False, auto_created=True, verbose_name='ID', primary_key=True)),
('title', models.CharField(max_length=200)),
('report_type', models.CharField(blank=True, max_length=50)),
('description', models.CharField(blank=True, max_length=255)),
('due_date', models.DateField(blank=True, null=True)),
('submitted_date', models.DateField(blank=True, null=True)),
('attachment', models.FileField(blank=True, null=True, upload_to='projects/grants/grant_report_attachments/%Y/%m/%d')),
('sort_order', models.IntegerField(blank=True, null=True)),
('grant', models.ForeignKey(to='projects.Grant')),
],
options={
'ordering': ['sort_order'],
},
),
migrations.AlterUniqueTogether(
name='grantreport',
unique_together=set([('grant', 'title', 'due_date')]),
),
migrations.AlterField(
model_name='grantreport',
name='grant',
field=models.ForeignKey(related_name='reports', to='projects.Grant'),
),
]

33
ccdb/projects/migrations/0001_initial_project.py
View file

@ -1,33 +0,0 @@
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
import autoslug.fields
class Migration(migrations.Migration):
dependencies = [
]
operations = [
migrations.CreateModel(
name='Project',
fields=[
('id', models.AutoField(serialize=False, primary_key=True, auto_created=True, verbose_name='ID')),
('name', models.CharField(max_length=100)),
('code', models.CharField(max_length=10, blank=True)),
('iacuc_number', models.CharField(max_length=25, blank=True)),
('description', models.CharField(max_length=255, blank=True)),
('sort_order', models.IntegerField(null=True, blank=True)),
('slug', autoslug.fields.AutoSlugField(populate_from='name', editable=False)),
],
options={
'ordering': ['sort_order'],
},
),
migrations.AlterUniqueTogether(
name='project',
unique_together=set([('name', 'code')]),
),
]

3
ccdb/projects/migrations/0005_DATA_initial.py → ccdb/projects/migrations/0002_DATA_initial.py
View file

@ -8,7 +8,6 @@ class Migration(migrations.Migration):
def migrate(apps, schema_editor):
sources = get_data_sources()
if not sources:
print('no sources')
return
c = sources['db0']
@ -75,7 +74,7 @@ class Migration(migrations.Migration):
model.objects.all().delete()
dependencies = [
('projects', '0004_initial_grantreport'),
('projects', '0001_initial'),
]
operations = [

31
ccdb/projects/migrations/0002_initial_grant.py
View file

@ -1,31 +0,0 @@
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('projects', '0001_initial_project'),
]
operations = [
migrations.CreateModel(
name='Grant',
fields=[
('id', models.AutoField(serialize=False, verbose_name='ID', auto_created=True, primary_key=True)),
('title', models.CharField(max_length=200)),
('code', models.CharField(max_length=10, blank=True)),
('description', models.CharField(max_length=255, blank=True)),
('sort_order', models.IntegerField(null=True, blank=True)),
],
options={
'ordering': ['sort_order'],
},
),
migrations.AlterUniqueTogether(
name='grant',
unique_together=set([('title', 'code')]),
),
]

19
ccdb/projects/migrations/0003_grant_projects.py
View file

@ -1,19 +0,0 @@
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('projects', '0002_initial_grant'),
]
operations = [
migrations.AddField(
model_name='grant',
name='projects',
field=models.ManyToManyField(to='projects.Project', related_name='grants'),
),
]

35
ccdb/projects/migrations/0004_initial_grantreport.py
View file

@ -1,35 +0,0 @@
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('projects', '0003_grant_projects'),
]
operations = [
migrations.CreateModel(
name='GrantReport',
fields=[
('id', models.AutoField(auto_created=True, verbose_name='ID', primary_key=True, serialize=False)),
('title', models.CharField(max_length=200)),
('report_type', models.CharField(max_length=50, blank=True)),
('description', models.CharField(max_length=255, blank=True)),
('due_date', models.DateField(blank=True, null=True)),
('submitted_date', models.DateField(blank=True, null=True)),
('attachment', models.FileField(upload_to='projects/grants/grant_report_attachments/%Y/%m/%d', blank=True, null=True)),
('sort_order', models.IntegerField(blank=True, null=True)),
('grant', models.ForeignKey(to='projects.Grant')),
],
options={
'ordering': ['sort_order'],
},
),
migrations.AlterUniqueTogether(
name='grantreport',
unique_together=set([('grant', 'title', 'due_date')]),
),
]

19
ccdb/projects/migrations/0006_set_labels.py
View file

@ -1,19 +0,0 @@
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('projects', '0005_DATA_initial'),
]
operations = [
migrations.AlterField(
model_name='grantreport',
name='grant',
field=models.ForeignKey(to='projects.Grant', related_name='reports'),
),
]

61
ccdb/species/migrations/0001_initial.py
View file

@ -1,26 +1,23 @@
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
import autoslug.fields
class Migration(migrations.Migration):
dependencies = [
('collections_ccdb', '0001_initial'),
]
operations = [
migrations.CreateModel(
name='Species',
fields=[
('id', models.AutoField(primary_key=True, verbose_name='ID', serialize=False, auto_created=True)),
('id', models.AutoField(auto_created=True, primary_key=True, verbose_name='ID', serialize=False)),
('common_name', models.CharField(max_length=100)),
('genus', models.CharField(max_length=50, blank=True)),
('species', models.CharField(max_length=50, blank=True)),
('parasite', models.BooleanField(default=False)),
('sort_order', models.IntegerField(blank=True, null=True)),
('slug', autoslug.fields.AutoSlugField(editable=False, populate_from='common_name')),
('slug', autoslug.fields.AutoSlugField(populate_from='common_name', editable=False)),
],
options={
'ordering': ['sort_order'],
@ -31,4 +28,56 @@ class Migration(migrations.Migration):
name='species',
unique_together=set([('common_name', 'species')]),
),
migrations.CreateModel(
name='TrapSpecies',
fields=[
('id', models.AutoField(auto_created=True, primary_key=True, verbose_name='ID', serialize=False)),
('sex', models.CharField(max_length=25, blank=True)),
('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',
},
),
migrations.CreateModel(
name='CollectionSpecies',
fields=[
('id', models.AutoField(auto_created=True, primary_key=True, verbose_name='ID', serialize=False)),
('sex', models.CharField(max_length=25, blank=True)),
('count', models.IntegerField(blank=True, null=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')]),
),
migrations.AlterField(
model_name='collectionspecies',
name='collection',
field=models.ForeignKey(to='collections_ccdb.Collection', related_name='collection_species'),
),
migrations.AlterField(
model_name='collectionspecies',
name='species',
field=models.ForeignKey(to='species.Species', related_name='collection_species'),
),
migrations.AlterField(
model_name='trapspecies',
name='collection_trap',
field=models.ForeignKey(to='collections_ccdb.CollectionTrap', related_name='trap_species'),
),
migrations.AlterField(
model_name='trapspecies',
name='species',
field=models.ForeignKey(to='species.Species', related_name='trap_species'),
),
]

4
ccdb/species/migrations/0004_DATA_initial.py → ccdb/species/migrations/0002_DATA_initial.py
View file

@ -27,12 +27,14 @@ class Migration(migrations.Migration):
else:
print('species', r[0:], form.errors.as_data())
def rollback(apps, schema_editor):
Species = apps.get_model('species', 'Species')
Species.objects.all().delete()
dependencies = [
('species', '0003_collectionspecies'),
('species', '0001_initial'),
('locations', '0002_DATA_initial'),
]
operations = [

29
ccdb/species/migrations/0002_trapspecies.py
View file

@ -1,29 +0,0 @@
# -*- 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',
},
),
]

33
ccdb/species/migrations/0003_collectionspecies.py
View file

@ -1,33 +0,0 @@
# -*- 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')]),
),
]

41
ccdb/species/migrations/0005_DATA_species_collection.py
View file

@ -1,41 +0,0 @@
from django.db import migrations
from django.forms import modelform_factory
from ccdb.utils.data import get_data_sources
class Migration(migrations.Migration):
def migrate(apps, schema_editor):
sources = get_data_sources()
if not sources:
return
c = sources['db0']
CollectionSpecies = apps.get_model('species', 'CollectionSpecies')
CollectionSpecies.objects.all().delete()
CollectionSpeciesForm = modelform_factory(CollectionSpecies, fields='__all__')
for r in c.execute('SELECT * FROM tbl_hash_collection_species;'):
form = CollectionSpeciesForm(dict(collection=r[0], species=r[1], sex=r[2],
count=r[3], count_estimated=r[4]))
if form.is_valid():
# No PK in Andre's file
form.save()
else:
print('collection species', r[0:], form.errors.as_data())
def rollback(apps, schema_editor):
CollectionSpecies = apps.get_model('species', 'CollectionSpecies')
CollectionSpecies.objects.all().delete()
dependencies = [
('species', '0004_DATA_initial'),
('collections_ccdb', '0005_DATA_initial'),
]
operations = [
migrations.RunPython(migrate, rollback),
]

34
ccdb/species/migrations/0006_set_labels.py
View file

@ -1,34 +0,0 @@
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('species', '0005_DATA_species_collection'),
]
operations = [
migrations.AlterField(
model_name='collectionspecies',
name='collection',
field=models.ForeignKey(related_name='collection_species', to='collections_ccdb.Collection'),
),
migrations.AlterField(
model_name='collectionspecies',
name='species',
field=models.ForeignKey(related_name='collection_species', to='species.Species'),
),
migrations.AlterField(
model_name='trapspecies',
name='collection_trap',
field=models.ForeignKey(related_name='trap_species', to='collections_ccdb.CollectionTrap'),
),
migrations.AlterField(
model_name='trapspecies',
name='species',
field=models.ForeignKey(related_name='trap_species', to='species.Species'),
),
]

8
config/settings/base.py
View file

@ -16,17 +16,13 @@ DJANGO_APPS = (
'django.contrib.auth',
'django.contrib.contenttypes',
'django.contrib.sessions',
'django.contrib.sites', # Need this for djoser
'django.contrib.messages',
'django.contrib.staticfiles',
'grappelli',
'django.contrib.admin',
)
THIRD_PARTY_APPS = (
'crispy_forms',
'allauth',
'allauth.account',
'bootstrap3',
'django_tables2',
'rest_framework',
'rest_framework.authtoken',
'corsheaders',
@ -242,3 +238,5 @@ REST_FRAMEWORK = {
'DEFAULT_PAGINATION_CLASS': 'drf_ember_pagination.EmberPageNumberPagination',
'PAGE_SIZE': 100,
}
SITE_ID = 1