def _migrate_chemical_analyses(self):
print("Migrating chemical analyses...")
User = get_user_model()
all_references = []
old_chemical_analyses = queryset_iterator(
LegacyChemicalAnalyses
.objects
.all()
.select_related('subsample', 'reference', 'user')
)
ChemicalAnalysis.objects.all().delete()
for record in old_chemical_analyses:
print("Migrating chemical analyses: #{}".format(record.pk))
if record.large_rock == 'Y':
mineral = Mineral.objects.get(name='Bulk Rock')
else:
try:
mineral = Mineral.objects.get(name=record.mineral.name)
except AttributeError:
mineral = None
if record.reference:
all_references.append(record.reference.name)
subsample = Subsample.objects.get(
name=record.subsample.name,
sample=Sample.objects.get(
pk=SampleMapping.objects.get(
old_sample_id=record.subsample.sample.pk
).new_sample_id)
)
try:
reference=record.reference.name
except AttributeError:
reference = None
try:
reference_image = Image.get(subsample=subsample)
except Image.DoesNotExist:
reference_image = None
chem_analysis = ChemicalAnalysis.objects.create(
subsample=subsample,
public_data=True if record.public_data == 'Y' else False,
reference_x=record.reference_x,
reference_y=record.reference_y,
stage_x = record.stage_x,
stage_y = record.stage_y,
analysis_method = record.analysis_method,
where_done = record.where_done,
analyst = record.analyst,
analysis_date = record.analysis_date,
date_precision = record.date_precision,
description = record.description,
total = record.total,
spot_id = record.spot_id,
mineral=mineral,
owner=User.objects.get(email=record.user.email),
reference=reference,
reference_image=reference_image
)
legacy_cae = LegacyChemicalAnalysisElements.objects.filter(
chemical_analysis=record
).select_related('element')
for cae in legacy_cae:
ChemicalAnalysisElement.objects.create(
chemical_analysis=chem_analysis,
element=Element.objects.get(name=cae.element.name),
amount=cae.amount,
precision = cae.precision,
precision_type = cae.precision_type,
measurement_unit = cae.measurement_unit,
min_amount = cae.min_amount,
max_amount = cae.max_amount,
)
legacy_cao = LegacyChemicalAnalysisOxides.objects.filter(
chemical_analysis=record
).select_related('oxide')
for cao in legacy_cao:
ChemicalAnalysisOxide.objects.create(
chemical_analysis=chem_analysis,
oxide=Oxide.objects.get(species=cao.oxide.species),
amount=cao.amount,
precision = cao.precision,
precision_type = cao.precision_type,
measurement_unit = cao.measurement_unit,
min_amount = cao.min_amount,
max_amount = cao.max_amount,
)
if all_references:
for ref in all_references:
Reference.objects.get_or_create(name=ref)
def _migrate_samples(self):
print("Migrating samples...")
User = get_user_model()
all_collectors = []
all_regions = []
old_samples = queryset_iterator(LegacySample.objects.all(),
chunksize=1000)
Sample.objects.all().delete()
for old_sample in old_samples:
print("Migrating old sample #{0}: {1}"
.format(old_sample.pk, old_sample.number))
rock_type = (RockType
.objects
.filter(name=old_sample.rock_type.rock_type)[0])
old_user = LegacyUser.objects.get(pk=old_sample.user_id)
new_user = User.objects.get(email=old_user.email)
if old_sample.collector:
all_collectors.extend([old_sample.collector])
regions = [lsr.region.name
for lsr in LegacySampleRegion
.objects
.filter(sample=old_sample)]
if regions:
all_regions.extend(regions)
references = [lsr.reference.name
for lsr in LegacySampleReference
.objects
.filter(sample=old_sample)]
new_georeferences = GeoReference.objects.filter(name__in=references)
old_metamorphic_regions = (lsa.metamorphic_region.name
for lsa in
LegacySampleMetamorphicRegion
.objects
.filter(sample=old_sample))
new_metamorphic_regions = (
MetamorphicRegion
.objects
.filter(name__in=old_metamorphic_regions)
)
old_metamorphic_grades = (lsa.metamorphic_grade.name
for lsa in
LegacySampleMetamorphicGrades
.objects
.filter(sample=old_sample))
new_metamorphic_grades = (MetamorphicGrade
.objects
.filter(name__in=old_metamorphic_grades))
aliases = [lsa.alias
for lsa in LegacySampleAlias
.objects
.filter(sample=old_sample)]
new_sample = Sample.objects.create(
public_data=True if old_sample.public_data == 'Y' else False,
number=old_sample.number,
owner=new_user,
aliases=aliases,
collection_date=old_sample.collection_date,
date_precision=old_sample.date_precision,
country=old_sample.country,
description=old_sample.description,
location_name=old_sample.location_text,
location_coords=old_sample.location,
location_error=old_sample.location_error,
rock_type=rock_type,
regions=regions,
collector_name=old_sample.collector
)
SampleMapping.objects.create(old_sample_id=old_sample.pk,
new_sample_id=new_sample.pk)
self._migrate_subsamples(old_sample, new_sample)
new_sample.metamorphic_regions.add(*new_metamorphic_regions)
new_sample.metamorphic_grades.add(*new_metamorphic_grades)
new_sample.references.add(*new_georeferences)
old_minerals = (LegacySampleMineral
.objects
.filter(sample=old_sample))
old_mineral_names = [om.mineral.name for om in old_minerals]
new_minerals = Mineral.objects.filter(name__in=old_mineral_names)
for mineral in new_minerals:
old_sample_mineral = (LegacySampleMineral
.objects
.get(mineral__name=mineral.name,
sample=old_sample))
SampleMineral.objects.create(sample=new_sample,
mineral=mineral,
amount=old_sample_mineral.amount)
Region.objects.all().delete()
Region.objects.bulk_create([Region(name=region)
for region in set(all_regions)])
Collector.objects.all().delete()
Collector.objects.bulk_create([Collector(name=collector)
for collector in set(all_collectors)])
def _migrate_samples(self):
print("Migrating samples...")
User = get_user_model()
all_collectors = set()
all_regions = set()
old_samples = queryset_iterator(LegacySample.objects.all(),
chunksize=1000)
Sample.objects.all().delete()
for old_sample in old_samples:
print("Migrating old sample #{0}: {1}".format(
old_sample.pk, old_sample.number))
rock_type = (RockType.objects.filter(
name=old_sample.rock_type.rock_type)[0])
old_user = LegacyUser.objects.get(pk=old_sample.user_id)
new_user = User.objects.get(email=old_user.email)
if old_sample.collector:
all_collectors.add(old_sample.collector)
regions = [
lsr.region.name
for lsr in LegacySampleRegion.objects.filter(sample=old_sample)
]
if regions:
all_regions.update(set(regions))
new_georeferences = self._get_georeferences(old_sample)
new_metamorphic_regions = self._get_metamorphic_regions(old_sample)
new_metamorphic_grades = self._get_metamorphic_grades(old_sample)
aliases = [
lsa.alias
for lsa in LegacySampleAlias.objects.filter(sample=old_sample)
]
new_sample = Sample.objects.create(
public_data=old_sample.public_data == 'Y',
number=old_sample.number,
owner=new_user,
aliases=aliases,
collection_date=old_sample.collection_date,
date_precision=old_sample.date_precision,
country=old_sample.country,
description=old_sample.description,
location_name=old_sample.location_text,
location_coords=old_sample.location,
location_error=old_sample.location_error,
rock_type=rock_type,
regions=regions,
collector_name=old_sample.collector)
SampleMapping.objects.create(old_sample_id=old_sample.pk,
new_sample_id=new_sample.pk)
self._migrate_subsamples(old_sample, new_sample=new_sample)
old_images = LegacyImages.objects.filter(sample=old_sample)
self._migrate_images(old_images, new_sample)
new_sample.metamorphic_regions.add(*new_metamorphic_regions)
new_sample.metamorphic_grades.add(*new_metamorphic_grades)
new_sample.references.add(*new_georeferences)
self._migrate_sample_minerals(old_sample, new_sample)
Region.objects.all().delete()
Region.objects.bulk_create(
[Region(name=region) for region in all_regions])
Collector.objects.all().delete()
Collector.objects.bulk_create(
[Collector(name=collector) for collector in all_collectors])
def _migrate_samples(self):
print("Migrating samples...")
User = get_user_model()
all_collectors = []
all_regions = []
old_samples = queryset_iterator(LegacySample.objects.all(),
chunksize=1000)
Sample.objects.all().delete()
for old_sample in old_samples:
print("Migrating old sample #{0}: {1}".format(
old_sample.pk, old_sample.number))
rock_type = (RockType.objects.filter(
name=old_sample.rock_type.rock_type)[0])
old_user = LegacyUser.objects.get(pk=old_sample.user_id)
new_user = User.objects.get(email=old_user.email)
if old_sample.collector:
all_collectors.extend([old_sample.collector])
regions = [
lsr.region.name
for lsr in LegacySampleRegion.objects.filter(sample=old_sample)
]
if regions:
all_regions.extend(regions)
references = [
lsr.reference.name
for lsr in LegacySampleReference.objects.filter(
sample=old_sample)
]
new_georeferences = GeoReference.objects.filter(
name__in=references)
old_metamorphic_regions = (
lsa.metamorphic_region.name
for lsa in LegacySampleMetamorphicRegion.objects.filter(
sample=old_sample))
new_metamorphic_regions = (MetamorphicRegion.objects.filter(
name__in=old_metamorphic_regions))
old_metamorphic_grades = (
lsa.metamorphic_grade.name
for lsa in LegacySampleMetamorphicGrades.objects.filter(
sample=old_sample))
new_metamorphic_grades = (MetamorphicGrade.objects.filter(
name__in=old_metamorphic_grades))
aliases = [
lsa.alias
for lsa in LegacySampleAlias.objects.filter(sample=old_sample)
]
new_sample = Sample.objects.create(
public_data=True if old_sample.public_data == 'Y' else False,
number=old_sample.number,
owner=new_user,
aliases=aliases,
collection_date=old_sample.collection_date,
date_precision=old_sample.date_precision,
country=old_sample.country,
description=old_sample.description,
location_name=old_sample.location_text,
location_coords=old_sample.location,
location_error=old_sample.location_error,
rock_type=rock_type,
regions=regions,
collector_name=old_sample.collector)
SampleMapping.objects.create(old_sample_id=old_sample.pk,
new_sample_id=new_sample.pk)
self._migrate_subsamples(old_sample, new_sample)
new_sample.metamorphic_regions.add(*new_metamorphic_regions)
new_sample.metamorphic_grades.add(*new_metamorphic_grades)
new_sample.references.add(*new_georeferences)
old_minerals = (LegacySampleMineral.objects.filter(
sample=old_sample))
old_mineral_names = [om.mineral.name for om in old_minerals]
new_minerals = Mineral.objects.filter(name__in=old_mineral_names)
for mineral in new_minerals:
old_sample_mineral = (LegacySampleMineral.objects.get(
mineral__name=mineral.name, sample=old_sample))
SampleMineral.objects.create(sample=new_sample,
mineral=mineral,
amount=old_sample_mineral.amount)
Region.objects.all().delete()
Region.objects.bulk_create(
[Region(name=region) for region in set(all_regions)])
Collector.objects.all().delete()
Collector.objects.bulk_create(
[Collector(name=collector) for collector in set(all_collectors)])
def _migrate_chemical_analyses(self):
print("Migrating chemical analyses...")
User = get_user_model()
all_references = []
old_chemical_analyses = queryset_iterator(
LegacyChemicalAnalyses
.objects
.all()
.select_related('subsample', 'reference', 'user')
)
ChemicalAnalysis.objects.all().delete()
for record in old_chemical_analyses:
print("Migrating chemical analyses: #{}".format(record.pk))
if record.large_rock == 'Y':
mineral = Mineral.objects.get(name='Bulk Rock')
else:
try:
mineral = Mineral.objects.get(name=record.mineral.name)
except AttributeError:
mineral = None
if record.reference:
all_references.append(record.reference.name)
subsample = Subsample.objects.get(
name=record.subsample.name,
sample=Sample.objects.get(
pk=SampleMapping.objects.get(
old_sample_id=record.subsample.sample.pk
).new_sample_id)
)
try:
reference=record.reference.name
except AttributeError:
reference = None
chem_analysis = ChemicalAnalysis.objects.create(
subsample=subsample,
public_data=True if record.public_data == 'Y' else False,
reference_x=record.reference_x,
reference_y=record.reference_y,
stage_x = record.stage_x,
stage_y = record.stage_y,
analysis_method = record.analysis_method,
where_done = record.where_done,
analyst = record.analyst,
analysis_date = record.analysis_date,
date_precision = record.date_precision,
description = record.description,
total = record.total,
spot_id = record.spot_id,
mineral=mineral,
owner=User.objects.get(email=record.user.email),
reference=reference,
)
legacy_cae = LegacyChemicalAnalysisElements.objects.filter(
chemical_analysis=record
).select_related('element')
for cae in legacy_cae:
ChemicalAnalysisElement.objects.create(
chemical_analysis=chem_analysis,
element=Element.objects.get(name=cae.element.name),
amount=cae.amount,
precision = cae.precision,
precision_type = cae.precision_type,
measurement_unit = cae.measurement_unit,
min_amount = cae.min_amount,
max_amount = cae.max_amount,
)
legacy_cao = LegacyChemicalAnalysisOxides.objects.filter(
chemical_analysis=record
).select_related('oxide')
for cao in legacy_cao:
ChemicalAnalysisOxide.objects.create(
chemical_analysis=chem_analysis,
oxide=Oxide.objects.get(species=cao.oxide.species),
amount=cao.amount,
precision = cao.precision,
precision_type = cao.precision_type,
measurement_unit = cao.measurement_unit,
min_amount = cao.min_amount,
max_amount = cao.max_amount,
)
if all_references:
for ref in all_references:
Reference.objects.get_or_create(name=ref)
