Rename family relationships to case (#2666)(patch)

cg/cli/clean.py

@@ -210,7 +210,7 @@ def hk_bundle_files(
     size_cleaned: int = 0
     for analysis in analyses:
         LOG.info(f"Cleaning analysis {analysis}")
-        bundle_name: str = analysis.family.internal_id
+        bundle_name: str = analysis.case.internal_id
         hk_bundle_version: Optional[Version] = housekeeper_api.version(
             bundle=bundle_name, date=analysis.started_at
         )
@@ -230,7 +230,7 @@ def hk_bundle_files(
             f"date {analysis.started_at}"
         )
         version_files: list[File] = housekeeper_api.get_files(
-            bundle=analysis.family.internal_id, tags=tags, version=hk_bundle_version.id
+            bundle=analysis.case.internal_id, tags=tags, version=hk_bundle_version.id
         ).all()
         for version_file in version_files:
             file_path: Path = Path(version_file.full_path)

cg/cli/delete/case.py

@@ -117,7 +117,7 @@ def _log_sample_process_information(sample: Sample):
 
 def _log_sample_links(sample: Sample):
     for sample_link in sample.links:
-        LOG.info(f"Sample is linked to: {sample_link.family.internal_id}")
+        LOG.info(f"Sample is linked to: {sample_link.case.internal_id}")
     for sample_link in sample.mother_links:
         LOG.info(f"Sample is linked as mother to: {sample_link.mother.internal_id}")
     for sample_link in sample.father_links:

cg/cli/delete/cases.py

@@ -23,7 +23,7 @@ def _get_cases(identifiers: click.Tuple([str, str]), store: Store) -> [Case]:
     _cases = set()
     for sample in samples_by_id:
         for link in sample.links:
-            _cases.add(link.family)
+            _cases.add(link.case)
 
     return _cases
 

cg/cli/get.py

@@ -61,9 +61,7 @@ def get_sample(context: click.Context, cases: bool, hide_flow_cell: bool, sample
         ]
         click.echo(tabulate([row], headers=SAMPLE_HEADERS, tablefmt="psql"))
         if cases:
-            case_ids: list[str] = [
-                link_obj.family.internal_id for link_obj in existing_sample.links
-            ]
+            case_ids: list[str] = [link_obj.case.internal_id for link_obj in existing_sample.links]
             context.invoke(get_case, case_ids=case_ids, samples=False)
         if not hide_flow_cell:
             for sample_flow_cell in existing_sample.flowcells:

cg/cli/set/cases.py

@@ -26,7 +26,7 @@ def _get_cases(identifiers: click.Tuple([str, str]), store: Store) -> list[Case]
     cases: set[Case] = set()
     for sample in samples_by_id:
         for link in sample.links:
-            cases.add(link.family)
+            cases.add(link.case)
 
     return list(cases)
 

cg/cli/upload/base.py

@@ -102,14 +102,14 @@ def upload_all_completed_analyses(context: click.Context, pipeline: Pipeline = N
 
     exit_code = 0
     for analysis_obj in status_db.get_analyses_to_upload(pipeline=pipeline):
-        if analysis_obj.family.analyses[0].uploaded_at is not None:
+        if analysis_obj.case.analyses[0].uploaded_at is not None:
             LOG.warning(
-                f"Skipping upload for case {analysis_obj.family.internal_id}. "
-                f"It has been already uploaded at {analysis_obj.family.analyses[0].uploaded_at}."
+                f"Skipping upload for case {analysis_obj.case.internal_id}. "
+                f"It has been already uploaded at {analysis_obj.case.analyses[0].uploaded_at}."
             )
             continue
 
-        case_id = analysis_obj.family.internal_id
+        case_id = analysis_obj.case.internal_id
         LOG.info("Uploading analysis for case: %s", case_id)
         try:
             context.invoke(upload, case_id=case_id)

cg/cli/upload/clinical_delivery.py

@@ -87,25 +87,23 @@ def auto_fastq(context: click.Context, dry_run: bool):
     status_db: Store = context.obj.status_db
     trailblazer_api: TrailblazerAPI = context.obj.trailblazer_api
     for analysis_obj in status_db.get_analyses_to_upload(pipeline=Pipeline.FASTQ):
-        if analysis_obj.family.analyses[0].uploaded_at:
+        if analysis_obj.case.analyses[0].uploaded_at:
             LOG.debug(
-                f"Newer analysis already uploaded for {analysis_obj.family.internal_id}, skipping"
+                f"Newer analysis already uploaded for {analysis_obj.case.internal_id}, skipping"
             )
             continue
         if analysis_obj.upload_started_at:
-            if trailblazer_api.is_latest_analysis_completed(
-                case_id=analysis_obj.family.internal_id
-            ):
+            if trailblazer_api.is_latest_analysis_completed(case_id=analysis_obj.case.internal_id):
                 LOG.info(
-                    f"The upload for {analysis_obj.family.internal_id} is completed, setting uploaded at to {dt.datetime.now()}"
+                    f"The upload for {analysis_obj.case.internal_id} is completed, setting uploaded at to {dt.datetime.now()}"
                 )
                 analysis_obj.uploaded_at = dt.datetime.now()
             else:
                 LOG.debug(
-                    f"Upload to clinical-delivery for {analysis_obj.family.internal_id} has already started, skipping"
+                    f"Upload to clinical-delivery for {analysis_obj.case.internal_id} has already started, skipping"
                 )
             continue
-        case: Case = analysis_obj.family
+        case: Case = analysis_obj.case
         LOG.info(f"Uploading family: {case.internal_id}")
         analysis_obj.upload_started_at = dt.datetime.now()
         try:

cg/cli/upload/nipt/base.py

@@ -74,7 +74,7 @@ def nipt_upload_all(context: click.Context, dry_run: bool):
         return
 
     for analysis in analyses:
-        internal_id = analysis.family.internal_id
+        internal_id = analysis.case.internal_id
 
         if nipt_upload_api.flowcell_passed_qc_value(
             case_id=internal_id, q30_threshold=Q30_THRESHOLD

cg/cli/upload/nipt/ftp.py

@@ -65,5 +65,5 @@ def nipt_upload_all(context: click.Context, dry_run: bool):
         return
 
     for analysis in analyses:
-        case_id = analysis.family.internal_id
+        case_id = analysis.case.internal_id
         context.invoke(nipt_upload_case, case_id=case_id, dry_run=dry_run)

cg/cli/workflow/commands.py

@@ -198,7 +198,7 @@ def past_run_dirs(
     LOG.info(f"Cleaning {len(possible_cleanups)} analyses created before {before}")
 
     for analysis in possible_cleanups:
-        case_id = analysis.family.internal_id
+        case_id = analysis.case.internal_id
         try:
             LOG.info("Cleaning %s output for %s", analysis_api.pipeline, case_id)
             context.invoke(clean_run_dir, yes=yes, case_id=case_id, dry_run=dry_run)

cg/meta/clean/api.py

@@ -30,7 +30,7 @@ def get_bundle_files(self, before: datetime, pipeline: Pipeline) -> Iterator[lis
         for analysis in self.status_db.get_analyses_for_pipeline_started_at_before(
             pipeline=pipeline, started_at_before=before
         ):
-            bundle_name = analysis.family.internal_id
+            bundle_name = analysis.case.internal_id
 
             hk_bundle_version: Optional[Version] = self.housekeeper_api.version(
                 bundle=bundle_name, date=analysis.started_at

cg/meta/observations/observations_api.py

@@ -51,9 +51,7 @@ def get_observations_input_files(
         """Fetch input files from a case to upload to Loqusdb."""
         analysis: Analysis = case.analyses[0]
         analysis_date: datetime = analysis.started_at or analysis.completed_at
-        hk_version: Version = self.housekeeper_api.version(
-            analysis.family.internal_id, analysis_date
-        )
+        hk_version: Version = self.housekeeper_api.version(analysis.case.internal_id, analysis_date)
         return self.extract_observations_files_from_hk(hk_version)
 
     def get_loqusdb_api(self, loqusdb_instance: LoqusdbInstance) -> LoqusdbAPI:

cg/meta/report/report_api.py

@@ -115,7 +115,7 @@ def get_cases_without_delivery_report(self, pipeline: Pipeline) -> list[Case]:
             :MAX_ITEMS_TO_RETRIEVE
         ]
         for analysis_obj in analyses:
-            case: Case = analysis_obj.family
+            case: Case = analysis_obj.case
             last_version: Version = self.housekeeper_api.last_version(bundle=case.internal_id)
             hk_file: File = self.housekeeper_api.get_files(
                 bundle=case.internal_id, version=last_version.id if last_version else None
@@ -134,7 +134,7 @@ def get_cases_without_uploaded_delivery_report(self, pipeline: Pipeline) -> list
         analyses: Query = self.status_db.analyses_to_upload_delivery_reports(pipeline=pipeline)[
             :MAX_ITEMS_TO_RETRIEVE
         ]
-        return [analysis_obj.family for analysis_obj in analyses]
+        return [analysis_obj.case for analysis_obj in analyses]
 
     def update_delivery_report_date(self, case: Case, analysis_date: datetime) -> None:
         """Updates the date when delivery report was created."""
@@ -201,7 +201,7 @@ def get_report_version(analysis: Analysis) -> int:
         """
         version = None
         if analysis:
-            version = len(analysis.family.analyses) - analysis.family.analyses.index(analysis)
+            version = len(analysis.case.analyses) - analysis.case.analyses.index(analysis)
         return version
 
     def get_case_data(

cg/meta/upload/coverage.py

@@ -19,9 +19,9 @@ def __init__(self, status_api: Store, hk_api: HousekeeperAPI, chanjo_api: Chanjo
 
     def data(self, analysis_obj: Analysis) -> dict:
         """Get data for uploading coverage."""
-        family_id = analysis_obj.family.internal_id
-        data = {"family": family_id, "family_name": analysis_obj.family.name, "samples": []}
-        for link_obj in analysis_obj.family.links:
+        family_id = analysis_obj.case.internal_id
+        data = {"family": family_id, "family_name": analysis_obj.case.name, "samples": []}
+        for link_obj in analysis_obj.case.links:
             analysis_date = analysis_obj.started_at or analysis_obj.completed_at
             hk_version = self.hk_api.version(family_id, analysis_date)
             hk_coverage = self.hk_api.files(

cg/meta/upload/fohm/fohm.py

@@ -171,7 +171,7 @@ def link_sample_rawdata_files(self) -> None:
         """Hardlink samples rawdata files to fohm delivery folder."""
         for sample_id in self.aggregation_dataframe["internal_id"]:
             sample: Sample = self.status_db.get_sample_by_internal_id(internal_id=sample_id)
-            bundle_name = sample.links[0].family.internal_id
+            bundle_name = sample.links[0].case.internal_id
             version_obj: Version = self.housekeeper_api.last_version(bundle=bundle_name)
             files = self.housekeeper_api.files(version=version_obj.id, tags=[sample_id]).all()
             for file in files:

cg/meta/upload/gt.py

@@ -40,16 +40,16 @@ def data(self, analysis_obj: Analysis) -> dict:
         }
 
         """
-        case_id = analysis_obj.family.internal_id
+        case_id = analysis_obj.case.internal_id
         LOG.info("Fetching upload genotype data for %s", case_id)
         hk_version = self.hk.last_version(case_id)
         hk_bcf = self.get_bcf_file(hk_version)
         data = {"bcf": hk_bcf.full_path}
         if analysis_obj.pipeline in [Pipeline.BALSAMIC, Pipeline.BALSAMIC_UMI]:
-            data["samples_sex"] = self._get_samples_sex_balsamic(case_obj=analysis_obj.family)
+            data["samples_sex"] = self._get_samples_sex_balsamic(case_obj=analysis_obj.case)
         elif analysis_obj.pipeline == Pipeline.MIP_DNA:
             data["samples_sex"] = self._get_samples_sex_mip(
-                case_obj=analysis_obj.family, hk_version=hk_version
+                case_obj=analysis_obj.case, hk_version=hk_version
             )
         else:
             raise ValueError(f"Pipeline {analysis_obj.pipeline} does not support Genotype upload")

cg/meta/upload/scout/balsamic_config_builder.py

@@ -93,5 +93,5 @@ def build_load_config(self) -> None:
         LOG.info("Building samples")
         db_sample: FamilySample
 
-        for db_sample in self.analysis_obj.family.links:
+        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

@@ -48,7 +48,7 @@ def build_load_config(self, rank_score_threshold: int = 5) -> None:
 
         self.add_common_info_to_load_config()
         mip_analysis_data: MipAnalysis = self.mip_analysis_api.get_latest_metadata(
-            self.analysis_obj.family.internal_id
+            self.analysis_obj.case.internal_id
         )
         self.load_config.human_genome_build = (
             "38" if "38" in mip_analysis_data.genome_build else "37"
@@ -59,7 +59,7 @@ def build_load_config(self, rank_score_threshold: int = 5) -> None:
 
         self.load_config.gene_panels = (
             self.mip_analysis_api.convert_panels(
-                self.analysis_obj.family.customer.internal_id, self.analysis_obj.family.panels
+                self.analysis_obj.case.customer.internal_id, self.analysis_obj.case.panels
             )
             or None
         )
@@ -68,14 +68,14 @@ def build_load_config(self, rank_score_threshold: int = 5) -> None:
 
         LOG.info("Building samples")
         db_sample: FamilySample
-        for db_sample in self.analysis_obj.family.links:
+        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()
 
     def include_pedigree_picture(self) -> None:
         if self.is_multi_sample_case(self.load_config):
             if self.is_family_case(self.load_config):
-                svg_path: Path = self.run_madeline(self.analysis_obj.family)
+                svg_path: Path = self.run_madeline(self.analysis_obj.case)
                 self.load_config.madeline = str(svg_path)
             else:
                 LOG.info("family of unconnected samples - skip pedigree graph")

cg/meta/upload/scout/rnafusion_config_builder.py

@@ -38,7 +38,7 @@ def build_load_config(self) -> None:
         LOG.info("Building samples")
         db_sample: FamilySample
 
-        for db_sample in self.analysis_obj.family.links:
+        for db_sample in self.analysis_obj.case.links:
             self.load_config.samples.append(self.build_config_sample(case_sample=db_sample))
 
     def include_case_files(self) -> None:

cg/meta/upload/scout/scout_config_builder.py

@@ -30,11 +30,11 @@ def __init__(self, hk_version_obj: Version, analysis_obj: Analysis, lims_api: Li
     def add_common_info_to_load_config(self) -> None:
         """Add the mandatory common information to a scout load config object"""
         self.load_config.analysis_date = self.analysis_obj.completed_at
-        self.load_config.default_gene_panels = self.analysis_obj.family.panels
-        self.load_config.family = self.analysis_obj.family.internal_id
-        self.load_config.family_name = self.analysis_obj.family.name
-        self.load_config.owner = self.analysis_obj.family.customer.internal_id
-        self.load_config.synopsis = self.analysis_obj.family.synopsis
+        self.load_config.default_gene_panels = self.analysis_obj.case.panels
+        self.load_config.family = self.analysis_obj.case.internal_id
+        self.load_config.family_name = self.analysis_obj.case.name
+        self.load_config.owner = self.analysis_obj.case.customer.internal_id
+        self.load_config.synopsis = self.analysis_obj.case.synopsis
         self.include_cohorts()
         self.include_phenotype_groups()
         self.include_phenotype_terms()
@@ -92,7 +92,7 @@ def include_phenotype_terms(self) -> None:
         LOG.info("Adding phenotype terms to scout load config")
         phenotype_terms: set[str] = set()
         link_obj: FamilySample
-        for link_obj in self.analysis_obj.family.links:
+        for link_obj in self.analysis_obj.case.links:
             sample_obj: Sample = link_obj.sample
             for phenotype_term in sample_obj.phenotype_terms:
                 LOG.debug(
@@ -108,7 +108,7 @@ def include_phenotype_groups(self) -> None:
         LOG.info("Adding phenotype groups to scout load config")
         phenotype_groups: set[str] = set()
         link_obj: FamilySample
-        for link_obj in self.analysis_obj.family.links:
+        for link_obj in self.analysis_obj.case.links:
             sample_obj: Sample = link_obj.sample
             for phenotype_group in sample_obj.phenotype_groups:
                 LOG.debug(
@@ -122,7 +122,7 @@ def include_phenotype_groups(self) -> None:
 
     def include_cohorts(self) -> None:
         LOG.info("Including cohorts to scout load config")
-        cohorts: list[str] = self.analysis_obj.family.cohorts
+        cohorts: list[str] = self.analysis_obj.case.cohorts
         if cohorts:
             LOG.debug("Adding cohorts %s", ", ".join(cohorts))
             self.load_config.cohorts = cohorts

cg/meta/upload/scout/uploadscoutapi.py

@@ -64,7 +64,7 @@ def generate_config(self, analysis_obj: Analysis) -> ScoutLoadConfig:
 
         # Fetch last version from housekeeper
         # This should be safe since analyses are only added if data is analysed
-        hk_version_obj: Version = self.housekeeper.last_version(analysis_obj.family.internal_id)
+        hk_version_obj: Version = self.housekeeper.last_version(analysis_obj.case.internal_id)
         LOG.debug("Found housekeeper version %s", hk_version_obj.id)
 
         load_config: ScoutLoadConfig
@@ -426,9 +426,7 @@ def _dna_cases_related_to_dna_sample(
         self, dna_sample: Sample, collaborators: set[Customer]
     ) -> list[str]:
         """Maps a list of uploaded DNA cases linked to DNA sample."""
-        potential_cases_related_to_dna_sample: list[Case] = [
-            dna_sample_family_relation.family for dna_sample_family_relation in dna_sample.links
-        ]
+        potential_cases_related_to_dna_sample: list[Case] = [link.case for link in dna_sample.links]
         return self.filter_cases_related_to_dna_sample(
             list_of_dna_cases=potential_cases_related_to_dna_sample, collaborators=collaborators
         )

cg/meta/upload/upload_api.py

@@ -48,7 +48,7 @@ def update_uploaded_at(self, analysis: Analysis) -> None:
 
         self.status_db.session.commit()
         self.trailblazer_api.set_analysis_uploaded(
-            case_id=analysis.family.internal_id, uploaded_at=analysis.uploaded_at
+            case_id=analysis.case.internal_id, uploaded_at=analysis.uploaded_at
         )
 
     @staticmethod

cg/meta/workflow/analysis.py

@@ -173,7 +173,7 @@ def upload_bundle_statusdb(self, case_id: str, dry_run: bool = False) -> None:
             completed_at=dt.datetime.now(),
             primary=(len(case_obj.analyses) == 0),
         )
-        new_analysis.family = case_obj
+        new_analysis.case = case_obj
         if dry_run:
             LOG.info("Dry-run: StatusDB changes will not be commited")
             return

cg/meta/workflow/balsamic.py

@@ -168,7 +168,7 @@ def get_concatenated_fastq_path(self, link_object: FamilySample) -> Path:
         concatenated_fastq_name: str = self.fastq_handler.get_concatenated_name(linked_fastq_name)
         return Path(
             self.root_dir,
-            link_object.family.internal_id,
+            link_object.case.internal_id,
             "fastq",
             concatenated_fastq_name,
         )
@@ -544,7 +544,7 @@ def resolve_target_bed(
             return panel_bed
         if self.get_application_type(link_object.sample) not in self.__BALSAMIC_BED_APPLICATIONS:
             return None
-        return self.get_target_bed_from_lims(link_object.family.internal_id)
+        return self.get_target_bed_from_lims(link_object.case.internal_id)
 
     def get_pipeline_version(self, case_id: str) -> str:
         LOG.debug("Fetch pipeline version")

cg/meta/workflow/microsalt.py

@@ -271,7 +271,7 @@ def get_case_id_from_sample(self, unique_id: str) -> tuple[str, str]:
         if not sample:
             LOG.error("No sample found with id: %s", unique_id)
             raise click.Abort
-        case_id = sample.links[0].family.internal_id
+        case_id = sample.links[0].case.internal_id
         sample_id = sample.internal_id
         return case_id, sample_id
 

cg/meta/workflow/mip_dna.py

@@ -58,7 +58,7 @@ def config_sample(
             sample_data["capture_kit"]: str = panel_bed or DEFAULT_CAPTURE_KIT
         else:
             sample_data["capture_kit"]: Optional[str] = panel_bed or self.get_target_bed_from_lims(
-                case_id=link_obj.family.internal_id
+                case_id=link_obj.case.internal_id
             )
         if link_obj.mother:
             sample_data[Pedigree.MOTHER.value]: str = link_obj.mother.internal_id