def migrate_interpreted_genome_rd_to_v6(
json_dict,
assembly=None,
interpretation_request_version=None,
panel_source='panelapp'):
"""
:type json_dict: dict
:type assembly: Assembly
:type interpretation_request_version: int
:type panel_source: str
:rtype: InterpretedGenome_6_0_0
"""
types = [
InterpretedGenome_6_0_0, InterpretedGenomeRD_5_0_0,
InterpretedGenomeRD_4_0_0, InterpretedGenomeRD_3_0_0,
InterpretedGenomeRD_2_1_0
]
migrations = [
lambda x: x, lambda x: MigrateReports500To600(
).migrate_interpreted_genome_rd(x, panel_source=panel_source),
lambda x: MigrateReports400To500().migrate_interpreted_genome_rd(
x,
assembly=assembly,
interpretation_request_version=interpretation_request_version),
MigrateReports3To4().migrate_interpreted_genome_rd,
Migration21To3().migrate_interpreted_genome
]
return MigrationHelpers.migrate(json_dict, types, migrations)
def migrate_interpretation_request_rd_to_interpreted_genome_v6(
json_dict, assembly):
"""
:type json_dict: dict
:type assembly: Assembly
:rtype: InterpretedGenomeRD_6_0_0
"""
types = [
InterpretationRequestRD_6_0_0, InterpretationRequestRD_5_0_0,
InterpretationRequestRD_4_0_0, InterpretationRequestRD_3_0_0,
InterpretationRequestRD_2_1_0
]
migrations = [
lambda x: x,
MigrateReports500To600().migrate_interpreted_genome_rd,
lambda x: MigrateReports400To500(
).migrate_interpretation_request_rd_to_interpreted_genome_rd(
old_instance=x,
assembly=assembly,
interpretation_service="tiering",
reference_database_versions={},
software_versions={}),
MigrateReports3To4().migrate_interpretation_request_rd,
Migration21To3().migrate_interpretation_request
]
return MigrationHelpers.migrate(json_dict, types, migrations)
def test_migrate_clinical_report_rd(self):
"""Also tested with real data"""
old_instance = GenericFactoryAvro.get_factory_avro(
self.old_model.ClinicalReportRD, VERSION_210, fill_nullables=False
).create() # reports_3_0_0.InterpretationRequestRD
self._validate(old_instance)
migrated_instance = Migration21To3().migrate_clinical_report(
old_instance)
self._validate(migrated_instance)
old_instance = GenericFactoryAvro.get_factory_avro(
self.old_model.ClinicalReportRD, VERSION_210, fill_nullables=True
).create() # reports_3_0_0.InterpretationRequestRD
self._validate(old_instance)
migrated_instance = Migration21To3().migrate_clinical_report(
old_instance)
self._validate(migrated_instance)
def migrate_clinical_report_rd_to_v6(json_dict, assembly=None):
"""
:type json_dict: dict
:type assembly: Assembly
:rtype: ClinicalReportRD_6_0_0
"""
types = [
ClinicalReport_6_0_0, ClinicalReportRD_5_0_0,
ClinicalReportRD_4_0_0, ClinicalReportRD_3_0_0,
ClinicalReportRD_2_1_0
]
migrations = [
lambda x: x,
MigrateReports500To600().migrate_clinical_report_rd,
lambda x: MigrateReports400To500().migrate_clinical_report_rd(
old_instance=x, assembly=assembly),
MigrateReports3To4().migrate_clinical_report_rd,
Migration21To3().migrate_clinical_report
]
return MigrationHelpers.migrate(json_dict, types, migrations)
def migrate_interpretation_request_rd_to_v6(json_dict, assembly=None):
"""
:type json_dict: dict
:type assembly: Assembly
:rtype: InterpretationRequestRD_6_0_0
"""
types = [
InterpretationRequestRD_6_0_0,
InterpretationRequestRD_5_0_0,
InterpretationRequestRD_4_0_0,
InterpretationRequestRD_3_0_0,
InterpretationRequestRD_2_1_0
]
migrations = [
MigrationHelpers.set_version_to_6_0_0, # needed because 5 is valid as 6
MigrateReports500To600().migrate_interpretation_request_rd,
lambda x: MigrateReports400To500().migrate_interpretation_request_rd(old_instance=x, assembly=assembly),
MigrateReports3To4().migrate_interpretation_request_rd,
Migration21To3().migrate_interpretation_request
]
return MigrationHelpers.migrate(json_dict, types, migrations)