Rename family sample model (#2669)(patch)

cg/apps/downsample/downsample.py

@@ -8,7 +8,7 @@
 from cg.meta.workflow.downsample.downsample import DownsampleWorkflow
 from cg.models.cg_config import CGConfig
 from cg.models.downsample.downsample_data import DownsampleData
-from cg.store.models import Case, FamilySample, Sample
+from cg.store.models import Case, CaseSample, Sample
 from cg.utils.calculations import multiply_by_million
 
 LOG = logging.getLogger(__name__)
@@ -80,8 +80,8 @@ def _link_downsampled_sample_to_case(
         self, downsample_data: DownsampleData, sample: Sample, case: Case
     ) -> None:
         """Create a link between sample and case in statusDB."""
-        sample_case_link: FamilySample = self.status_db.relate_sample(
-            family=case,
+        sample_case_link: CaseSample = self.status_db.relate_sample(
+            case=case,
             sample=sample,
             status=downsample_data.get_sample_status(),
         )

cg/cli/add.py

@@ -14,7 +14,7 @@
     Collaboration,
     Customer,
     Case,
-    FamilySample,
+    CaseSample,
     Panel,
     Sample,
     User,
@@ -320,8 +320,8 @@ def link_sample_to_case(
             LOG.error("%s: father not found", father_id)
             raise click.Abort
 
-    new_record: FamilySample = status_db.relate_sample(
-        family=case_obj, sample=sample, status=status, mother=mother, father=father
+    new_record: CaseSample = status_db.relate_sample(
+        case=case_obj, sample=sample, status=status, mother=mother, father=father
     )
     status_db.session.add(new_record)
     status_db.session.commit()

cg/meta/deliver.py

@@ -13,7 +13,7 @@
 from cg.constants.constants import DataDelivery
 from cg.exc import MissingFilesError
 from cg.store import Store
-from cg.store.models import Case, FamilySample, Sample
+from cg.store.models import Case, CaseSample, Sample
 
 LOG = logging.getLogger(__name__)
 
@@ -77,7 +77,7 @@ def deliver_files(self, case_obj: Case):
                 LOG.info(f"Could not find any version for {case_id}")
             elif not self.skip_missing_bundle:
                 raise SyntaxError(f"Could not find any version for {case_id}")
-        links: list[FamilySample] = self.store.get_case_samples_by_case_id(case_internal_id=case_id)
+        links: list[CaseSample] = self.store.get_case_samples_by_case_id(case_internal_id=case_id)
         if not links:
             LOG.warning(f"Could not find any samples linked to case {case_id}")
             return
@@ -98,7 +98,7 @@ def deliver_files(self, case_obj: Case):
         if not self.sample_tags:
             return
 
-        link: FamilySample
+        link: CaseSample
         for link in links:
             if link.sample.sequencing_qc or self.deliver_failed_samples:
                 sample_id: str = link.sample.internal_id

cg/meta/orders/case_submitter.py

@@ -9,7 +9,7 @@
 from cg.meta.orders.submitter import Submitter
 from cg.models.orders.order import OrderIn
 from cg.models.orders.samples import Of1508Sample, OrderInSample
-from cg.store.models import ApplicationVersion, Customer, Case, FamilySample, Sample
+from cg.store.models import ApplicationVersion, Customer, Case, CaseSample, Sample
 
 LOG = logging.getLogger(__name__)
 
@@ -265,12 +265,12 @@ def store_items_in_status(
                 sample_mother: Sample = case_samples.get(sample.get(Pedigree.MOTHER))
                 sample_father: Sample = case_samples.get(sample.get(Pedigree.FATHER))
                 with self.status.session.no_autoflush:
-                    case_sample: FamilySample = self.status.get_case_sample_link(
+                    case_sample: CaseSample = self.status.get_case_sample_link(
                         case_internal_id=status_db_case.internal_id,
                         sample_internal_id=sample["internal_id"],
                     )
                 if not case_sample:
-                    case_sample: FamilySample = self._create_link(
+                    case_sample: CaseSample = self._create_link(
                         case_obj=status_db_case,
                         family_samples=case_samples,
                         father_obj=sample_father,
@@ -311,7 +311,7 @@ def _update_relationship(father_obj, link_obj, mother_obj, sample):
 
     def _create_link(self, case_obj, family_samples, father_obj, mother_obj, sample):
         link_obj = self.status.relate_sample(
-            family=case_obj,
+            case=case_obj,
             sample=family_samples[sample["name"]],
             status=sample["status"],
             mother=mother_obj,

cg/meta/orders/fastq_submitter.py

@@ -9,7 +9,7 @@
 from cg.meta.orders.submitter import Submitter
 from cg.models.orders.order import OrderIn
 from cg.models.orders.sample_base import StatusEnum
-from cg.store.models import ApplicationVersion, Customer, Case, FamilySample, Sample
+from cg.store.models import ApplicationVersion, Customer, Case, CaseSample, Sample
 
 
 class FastqSubmitter(Submitter):
@@ -68,8 +68,8 @@ def create_maf_case(self, sample_obj: Sample) -> None:
         case.customer = self.status.get_customer_by_internal_id(
             customer_internal_id=CustomerNames.CG_INTERNAL_CUSTOMER
         )
-        relationship: FamilySample = self.status.relate_sample(
-            family=case, sample=sample_obj, status=StatusEnum.unknown
+        relationship: CaseSample = self.status.relate_sample(
+            case=case, sample=sample_obj, status=StatusEnum.unknown
         )
         self.status.session.add_all([case, relationship])
 
@@ -126,7 +126,7 @@ def store_items_in_status(
                     self.create_maf_case(sample_obj=new_sample)
                 case.customer = customer
                 new_relationship = self.status.relate_sample(
-                    family=case, sample=new_sample, status=StatusEnum.unknown
+                    case=case, sample=new_sample, status=StatusEnum.unknown
                 )
                 new_delivery = self.status.add_delivery(destination="caesar", sample=new_sample)
                 self.status.session.add_all([case, new_relationship, new_delivery])

cg/meta/orders/metagenome_submitter.py

@@ -8,7 +8,7 @@
 from cg.models.orders.order import OrderIn
 from cg.models.orders.sample_base import StatusEnum
 from cg.models.orders.samples import MetagenomeSample
-from cg.store.models import ApplicationVersion, Customer, Case, FamilySample, Sample
+from cg.store.models import ApplicationVersion, Customer, Case, CaseSample, Sample
 
 
 class MetagenomeSubmitter(Submitter):
@@ -128,8 +128,8 @@ def store_items_in_status(
                     self.status.session.add(case)
                     self.status.session.commit()
 
-                new_relationship: FamilySample = self.status.relate_sample(
-                    family=case, sample=new_sample, status=StatusEnum.unknown
+                new_relationship: CaseSample = self.status.relate_sample(
+                    case=case, sample=new_sample, status=StatusEnum.unknown
                 )
                 self.status.session.add(new_relationship)
 

cg/meta/orders/microbial_submitter.py

@@ -10,7 +10,7 @@
     ApplicationVersion,
     Customer,
     Case,
-    FamilySample,
+    CaseSample,
     Organism,
     Sample,
 )
@@ -144,8 +144,8 @@ def store_items_in_status(
 
                 priority = new_sample.priority
                 sample_objs.append(new_sample)
-                link: FamilySample = self.status.relate_sample(
-                    family=case, sample=new_sample, status="unknown"
+                link: CaseSample = self.status.relate_sample(
+                    case=case, sample=new_sample, status="unknown"
                 )
                 self.status.session.add(link)
                 new_samples.append(new_sample)

cg/meta/orders/pool_submitter.py

@@ -12,7 +12,7 @@
     ApplicationVersion,
     Customer,
     Case,
-    FamilySample,
+    CaseSample,
     Pool,
     Sample,
 )
@@ -168,8 +168,8 @@ def store_items_in_status(
                     no_invoice=True,
                 )
                 new_samples.append(new_sample)
-                link: FamilySample = self.status.relate_sample(
-                    family=case, sample=new_sample, status="unknown"
+                link: CaseSample = self.status.relate_sample(
+                    case=case, sample=new_sample, status="unknown"
                 )
                 self.status.session.add(link)
             new_delivery = self.status.add_delivery(destination="caesar", pool=new_pool)

cg/meta/report/report_api.py

@@ -33,7 +33,7 @@
     Application,
     ApplicationLimitations,
     Case,
-    FamilySample,
+    CaseSample,
     Sample,
 )
 
@@ -228,7 +228,7 @@ def get_case_data(
     def get_samples_data(self, case: Case, analysis_metadata: AnalysisModel) -> list[SampleModel]:
         """Extracts all the samples associated to a specific case and their attributes."""
         samples = list()
-        case_samples: list[FamilySample] = self.status_db.get_case_samples_by_case_id(
+        case_samples: list[CaseSample] = self.status_db.get_case_samples_by_case_id(
             case_internal_id=case.internal_id
         )
         for case_sample in case_samples:

cg/meta/upload/scout/balsamic_config_builder.py

@@ -10,7 +10,7 @@
 from cg.meta.upload.scout.scout_config_builder import ScoutConfigBuilder
 from cg.meta.workflow.balsamic import BalsamicAnalysisAPI
 from cg.models.scout.scout_load_config import BalsamicLoadConfig, ScoutCancerIndividual
-from cg.store.models import Analysis, FamilySample, Sample
+from cg.store.models import Analysis, CaseSample, Sample
 
 LOG = logging.getLogger(__name__)
 
@@ -50,7 +50,7 @@ def include_sample_files(self, config_sample: ScoutCancerIndividual) -> None:
             hk_tags=self.sample_tags.vcf2cytosure, sample_id=sample_id
         )
 
-    def build_config_sample(self, case_sample: FamilySample) -> ScoutCancerIndividual:
+    def build_config_sample(self, case_sample: CaseSample) -> ScoutCancerIndividual:
         """Build a sample with balsamic specific information."""
         config_sample = ScoutCancerIndividual()
         self.add_common_sample_info(config_sample=config_sample, case_sample=case_sample)
@@ -91,7 +91,7 @@ def build_load_config(self) -> None:
         self.include_case_files()
 
         LOG.info("Building samples")
-        db_sample: FamilySample
+        db_sample: CaseSample
 
         for db_sample in self.analysis_obj.case.links:
             self.load_config.samples.append(self.build_config_sample(case_sample=db_sample))

cg/meta/upload/scout/mip_config_builder.py

@@ -18,7 +18,7 @@
     ScoutLoadConfig,
     ScoutMipIndividual,
 )
-from cg.store.models import Analysis, Case, FamilySample
+from cg.store.models import Analysis, Case, CaseSample
 
 LOG = logging.getLogger(__name__)
 
@@ -67,7 +67,7 @@ def build_load_config(self, rank_score_threshold: int = 5) -> None:
         self.include_case_files()
 
         LOG.info("Building samples")
-        db_sample: FamilySample
+        db_sample: CaseSample
         for db_sample in self.analysis_obj.case.links:
             self.load_config.samples.append(self.build_config_sample(case_sample=db_sample))
         self.include_pedigree_picture()
@@ -82,7 +82,7 @@ def include_pedigree_picture(self) -> None:
         else:
             LOG.info("family of 1 sample - skip pedigree graph")
 
-    def build_config_sample(self, case_sample: FamilySample) -> ScoutMipIndividual:
+    def build_config_sample(self, case_sample: CaseSample) -> ScoutMipIndividual:
         """Build a sample with mip specific information"""
 
         config_sample = ScoutMipIndividual()

cg/meta/upload/scout/rnafusion_config_builder.py

@@ -12,7 +12,7 @@
 from cg.meta.upload.scout.hk_tags import CaseTags, SampleTags
 from cg.meta.upload.scout.scout_config_builder import ScoutConfigBuilder
 from cg.models.scout.scout_load_config import RnafusionLoadConfig, ScoutCancerIndividual
-from cg.store.models import Analysis, FamilySample
+from cg.store.models import Analysis, CaseSample
 
 LOG = logging.getLogger(__name__)
 
@@ -36,7 +36,7 @@ def build_load_config(self) -> None:
         self.include_case_files()
 
         LOG.info("Building samples")
-        db_sample: FamilySample
+        db_sample: CaseSample
 
         for db_sample in self.analysis_obj.case.links:
             self.load_config.samples.append(self.build_config_sample(case_sample=db_sample))
@@ -56,7 +56,7 @@ def _include_file(self, scout_key) -> None:
             self.get_file_from_hk(getattr(self.case_tags, scout_key)),
         )
 
-    def build_config_sample(self, case_sample: FamilySample) -> ScoutCancerIndividual:
+    def build_config_sample(self, case_sample: CaseSample) -> ScoutCancerIndividual:
         """Build a sample with rnafusion specific information."""
         config_sample = ScoutCancerIndividual()
 

cg/meta/upload/scout/scout_config_builder.py

@@ -9,7 +9,7 @@
 from cg.apps.lims import LimsAPI
 from cg.meta.upload.scout.hk_tags import CaseTags, SampleTags
 from cg.models.scout.scout_load_config import ScoutIndividual, ScoutLoadConfig
-from cg.store.models import Analysis, FamilySample, Sample
+from cg.store.models import Analysis, CaseSample, Sample
 
 LOG = logging.getLogger(__name__)
 
@@ -40,7 +40,7 @@ def add_common_info_to_load_config(self) -> None:
         self.include_phenotype_terms()
 
     def add_common_sample_info(
-        self, config_sample: ScoutIndividual, case_sample: FamilySample
+        self, config_sample: ScoutIndividual, case_sample: CaseSample
     ) -> None:
         """Add the information to a sample that is common for different analysis types"""
         sample_id: str = case_sample.sample.internal_id
@@ -64,15 +64,15 @@ def add_common_sample_info(
     def add_common_sample_files(
         self,
         config_sample: ScoutIndividual,
-        case_sample: FamilySample,
+        case_sample: CaseSample,
     ) -> None:
         """Add common sample files for different analysis types."""
         sample_id: str = case_sample.sample.internal_id
         LOG.info(f"Adding common files for sample {sample_id}")
         self.include_sample_alignment_file(config_sample=config_sample)
         self.include_sample_files(config_sample=config_sample)
 
-    def build_config_sample(self, case_sample: FamilySample) -> ScoutIndividual:
+    def build_config_sample(self, case_sample: CaseSample) -> ScoutIndividual:
         """Build a sample for the scout load config"""
         raise NotImplementedError
 
@@ -91,7 +91,7 @@ def include_case_files(self) -> None:
     def include_phenotype_terms(self) -> None:
         LOG.info("Adding phenotype terms to scout load config")
         phenotype_terms: set[str] = set()
-        link_obj: FamilySample
+        link_obj: CaseSample
         for link_obj in self.analysis_obj.case.links:
             sample_obj: Sample = link_obj.sample
             for phenotype_term in sample_obj.phenotype_terms:
@@ -107,7 +107,7 @@ def include_phenotype_terms(self) -> None:
     def include_phenotype_groups(self) -> None:
         LOG.info("Adding phenotype groups to scout load config")
         phenotype_groups: set[str] = set()
-        link_obj: FamilySample
+        link_obj: CaseSample
         for link_obj in self.analysis_obj.case.links:
             sample_obj: Sample = link_obj.sample
             for phenotype_group in sample_obj.phenotype_groups:

cg/meta/workflow/analysis.py

@@ -18,7 +18,7 @@
 from cg.meta.workflow.fastq import FastqHandler
 from cg.models.analysis import AnalysisModel
 from cg.models.cg_config import CGConfig
-from cg.store.models import Analysis, BedVersion, Case, FamilySample, Sample
+from cg.store.models import Analysis, BedVersion, Case, CaseSample, Sample
 
 LOG = logging.getLogger(__name__)
 
@@ -379,7 +379,7 @@ def decompress_case(self, case_id: str, dry_run: bool) -> None:
             self.decompression_running(case_id=case_id)
             return
         case_obj: Case = self.status_db.get_case_by_internal_id(internal_id=case_id)
-        link: FamilySample
+        link: CaseSample
         any_decompression_started = False
         for link in case_obj.links:
             sample_id: str = link.sample.internal_id

cg/meta/workflow/balsamic.py

@@ -25,7 +25,7 @@
     BalsamicWGSQCMetrics,
 )
 from cg.models.cg_config import CGConfig
-from cg.store.models import Case, FamilySample, Sample
+from cg.store.models import Case, CaseSample, Sample
 from cg.utils import Process
 from cg.utils.utils import build_command_from_dict, get_string_from_list_by_pattern
 
@@ -154,7 +154,7 @@ def link_fastq_files(self, case_id: str, dry_run: bool = False) -> None:
                 case_obj=case_obj, sample_obj=link.sample, concatenate=True
             )
 
-    def get_concatenated_fastq_path(self, link_object: FamilySample) -> Path:
+    def get_concatenated_fastq_path(self, link_object: CaseSample) -> Path:
         """Returns path to the concatenated FASTQ file of a sample"""
         file_collection: list[dict] = self.gather_file_metadata_for_sample(link_object.sample)
         fastq_data = file_collection[0]
@@ -538,7 +538,7 @@ def get_case_application_type(self, case_id: str) -> str:
             return application_types.pop().lower()
 
     def resolve_target_bed(
-        self, panel_bed: Optional[str], link_object: FamilySample
+        self, panel_bed: Optional[str], link_object: CaseSample
     ) -> Optional[str]:
         if panel_bed:
             return panel_bed