151 lines
6.9 KiB
Python
151 lines
6.9 KiB
Python
from django.db import migrations
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from django.forms import modelform_factory
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from ccdb.utils.data import get_data_sources
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class Migration(migrations.Migration):
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def migrate(apps, schema_editor):
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sources = get_data_sources()
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if not sources:
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return
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c = sources['db0']
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Flaw = apps.get_model('experiments', 'Flaw')
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Experiment = apps.get_model('experiments', 'Experiment')
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TreatmentType = apps.get_model('experiments', 'TreatmentType')
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Treatment = apps.get_model('experiments', 'Treatment')
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TreatmentReplicate = apps.get_model('experiments', 'TreatmentReplicate')
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AliveDeadCount = apps.get_model('experiments', 'AliveDeadCount')
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for model in [AliveDeadCount, TreatmentReplicate, Treatment, TreatmentType,
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Experiment, Flaw]:
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model.objects.all().delete()
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Collection = apps.get_model('collections_ccdb', 'Collection')
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StudyLocation = apps.get_model('locations', 'StudyLocation')
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Species = apps.get_model('species', 'Species')
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ExperimentForm = modelform_factory(Experiment, exclude=('collections',))
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TreatmentTypeForm = modelform_factory(TreatmentType, fields='__all__')
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TreatmentForm = modelform_factory(Treatment, fields='__all__')
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TreatmentReplicateForm = modelform_factory(TreatmentReplicate, fields='__all__')
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AliveDeadCountForm = modelform_factory(AliveDeadCount, fields='__all__')
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for r in c.execute('SELECT * FROM tbl_lu_experiments;'):
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form = ExperimentForm(dict(name=r[1], code=r[2], description=r[3],
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sort_order=int(r[4]) if r[4] else None))
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if form.is_valid():
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Experiment.objects.create(id=r[0], **form.cleaned_data)
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else:
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print('experiment', r[0:], form.errors.as_data())
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for r in c.execute('SELECT * FROM tbl_lu_treatment_types;'):
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form = TreatmentTypeForm(dict(experiment=r[0], name=r[2], code=r[3],
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treatment_type=r[4], placement=r[5],
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description=r[6]))
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if form.is_valid():
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experiment = Experiment.objects.get(id=r[0])
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d = "{} {} {} {}".format(experiment.name, form.cleaned_data['name'],
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form.cleaned_data['treatment_type'],
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form.cleaned_data['placement'])
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TreatmentType.objects.create(id=r[1], display_name=d, **form.cleaned_data)
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else:
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print('treatment type', r[0:], form.errors.as_data())
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for r in c.execute('SELECT * FROM tbl_treatments;'):
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form = TreatmentForm(dict(treatment_type=r[1], container=r[2],
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study_location=r[3], species=r[4], sex=r[5]))
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if form.is_valid():
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treatment_type = TreatmentType.objects.get(id=r[1])
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study_location = StudyLocation.objects.get(id=r[3])
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species = Species.objects.get(id=r[4])
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d = "{}_{}_{}_{}".format(treatment_type.display_name,
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study_location.code,
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species.common_name,
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form.cleaned_data['sex'])
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Treatment.objects.create(id=r[0], display_name=d, **form.cleaned_data)
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else:
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print('treatment', r[0:], form.errors.as_data())
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for r in c.execute('''
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SELECT *, setup_date AS "setup_date [dtdt]"
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FROM tbl_treatment_replicates tr
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LEFT OUTER JOIN tbl_lu_record_flaws f ON f.flawid=tr.flawid;
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'''):
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flaw = None
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if r[7]:
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flaw, _ = Flaw.objects.get_or_create(name=r[10])
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flaw = flaw.pk
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form = TreatmentReplicateForm(dict(treatment=r[0], name=r[2],
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setup_date=r[13],
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setup_sample_size=r[5], mass_g=r[6],
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flaw=flaw))
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if form.is_valid():
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treatment = Treatment.objects.get(id=r[0])
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d = "{}_{}_{}_{}".format(treatment.display_name,
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form.cleaned_data['setup_date'],
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form.cleaned_data['name'],
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form.cleaned_data['setup_sample_size'])
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TreatmentReplicate.objects.create(id=r[1], display_name=d,
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**form.cleaned_data)
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else:
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print('treatment replicate', r[0:], form.errors.as_data())
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for r in c.execute('''
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SELECT *,
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status_date AS "status_date [dtdt]",
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status_time AS "status_time [dtdt]"
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FROM tbl_alive_dead_counts adc
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LEFT OUTER JOIN tbl_lu_record_flaws f ON f.flawid=adc.flawid;
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'''):
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flaw = None
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if r[6]:
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flaw, _ = Flaw.objects.get_or_create(name=r[9])
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flaw = flaw.pk
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form = AliveDeadCountForm(dict(treatment_replicate=r[0],
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status_date=r[12],
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status_time=r[13].time() if r[13] else None,
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count_alive=r[4], count_dead=r[5],
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flaw=flaw))
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if form.is_valid():
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AliveDeadCount.objects.create(id=r[1], **form.cleaned_data)
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else:
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print('alive-dead count', r[0:], form.errors.as_data())
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for experiment in Experiment.objects.all():
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experiment.collections.all().delete()
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for r in c.execute('SELECT * FROM tbl_hash_collection_experiments;'):
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c = Collection.objects.get(id=r[0])
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e = Experiment.objects.get(id=r[1])
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e.collections.add(c)
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e.save()
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def rollback(apps, schema_editor):
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Flaw = apps.get_model('experiments', 'Flaw')
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Experiment = apps.get_model('experiments', 'Experiment')
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TreatmentType = apps.get_model('experiments', 'TreatmentType')
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Treatment = apps.get_model('experiments', 'Treatment')
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TreatmentReplicate = apps.get_model('experiments', 'TreatmentReplicate')
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AliveDeadCount = apps.get_model('experiments', 'AliveDeadCount')
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for model in [AliveDeadCount, TreatmentReplicate, Treatment, TreatmentType,
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Experiment, Flaw]:
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model.objects.all().delete()
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for experiment in Experiment.objects.all():
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experiment.collections.all().delete()
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dependencies = [
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('experiments', '0001_initial'),
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('collections_ccdb', '0002_DATA_initial'),
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]
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operations = [
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migrations.RunPython(migrate, rollback),
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]
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