nci-cidc-api-modules 1.1.12__py3-none-any.whl → 1.1.14__py3-none-any.whl

cidc_api/config/db.py

@@ -48,13 +48,10 @@ def get_sqlalchemy_database_uri(testing: bool = False) -> str:
 
             # If CLOUD_SQL_INSTANCE_NAME is defined, we're connecting
             # via a unix socket from inside App Engine.
-            config["query"] = {
-                "host": f'{socket_dir}{environ.get("CLOUD_SQL_INSTANCE_NAME")}'
-            }
+            config["query"] = {"host": f'{socket_dir}{environ.get("CLOUD_SQL_INSTANCE_NAME")}'}
         else:
             raise RuntimeError(
-                "Either POSTGRES_URI or CLOUD_SQL_INSTANCE_NAME must be defined to connect "
-                + "to a database."
+                "Either POSTGRES_URI or CLOUD_SQL_INSTANCE_NAME must be defined to connect " + "to a database."
             )
 
         db_uri = str(URL(**config))

cidc_api/config/logging.py

@@ -19,11 +19,7 @@ def get_logger(name: Optional[str]) -> logging.Logger:
         logger.setLevel(gunicorn_logger.level)
     else:
         handler = logging.StreamHandler(sys.stdout)
-        handler.setFormatter(
-            logging.Formatter(
-                "[%(asctime)s] [%(threadName)s] [%(levelname)s]: %(message)s"
-            )
-        )
+        handler.setFormatter(logging.Formatter("[%(asctime)s] [%(threadName)s] [%(levelname)s]: %(message)s"))
         logger.addHandler(handler)
         logger.setLevel(logging.DEBUG if ENV == "dev" else logging.INFO)
     return logger

cidc_api/config/secrets.py

@@ -40,9 +40,7 @@ class GoogleSecretManager:
         Raises a google.api_core.exceptions.NotFound exception
         if the secret_id/version_id doesn't exist.
         """
-        name = (
-            f"projects/{self.project_id}/secrets/{secret_id}/versions/{self.version_id}"
-        )
+        name = f"projects/{self.project_id}/secrets/{secret_id}/versions/{self.version_id}"
         response = self.client.access_secret_version(name=name)
         secret = response.payload.data.decode("UTF-8")
 

cidc_api/config/settings.py

@@ -55,6 +55,7 @@ else:
 ### Configure Flask-SQLAlchemy ###
 SQLALCHEMY_DATABASE_URI = get_sqlalchemy_database_uri(TESTING)
 SQLALCHEMY_TRACK_MODIFICATIONS = False
+SQLALCHEMY_ECHO = False  # Set to True to emit all compiled sql statements
 
 ### Configure Dev CFn ###
 DEV_CFUNCTIONS_SERVER = environ.get("DEV_CFUNCTIONS_SERVER")
@@ -78,9 +79,7 @@ GOOGLE_BIGQUERY_USER_ROLE = "roles/bigquery.jobUser"  # same across environments
 GOOGLE_PATIENT_SAMPLE_TOPIC = environ["GOOGLE_PATIENT_SAMPLE_TOPIC"]
 GOOGLE_EMAILS_TOPIC = environ["GOOGLE_EMAILS_TOPIC"]
 GOOGLE_ARTIFACT_UPLOAD_TOPIC = environ["GOOGLE_ARTIFACT_UPLOAD_TOPIC"]
-GOOGLE_GRANT_DOWNLOAD_PERMISSIONS_TOPIC = environ[
-    "GOOGLE_GRANT_DOWNLOAD_PERMISSIONS_TOPIC"
-]
+GOOGLE_GRANT_DOWNLOAD_PERMISSIONS_TOPIC = environ["GOOGLE_GRANT_DOWNLOAD_PERMISSIONS_TOPIC"]
 GOOGLE_AND_OPERATOR = " && "
 GOOGLE_OR_OPERATOR = " || "
 

cidc_api/csms/auth.py

@@ -64,9 +64,7 @@ def get_with_authorization(url: str, **kwargs) -> requests.Response:
     )
 
 
-def get_with_paging(
-    url: str, limit: int = None, offset: int = 0, **kwargs
-) -> Iterator[Dict[str, Any]]:
+def get_with_paging(url: str, limit: int = None, offset: int = 0, **kwargs) -> Iterator[Dict[str, Any]]:
     """
     Return an iterator of entries via get_with_authorization with handling for CSMS paging
 

cidc_api/models/csms_api.py

@@ -81,11 +81,7 @@ def _get_all_values(target: str, old: dict, drop: List[str] = None) -> Dict[str,
     if drop is None:
         drop = []
 
-    ret = {
-        p: old[p]
-        for p in TARGET_PROPERTIES_MAP[target].keys()
-        if p in old and p not in drop
-    }
+    ret = {p: old[p] for p in TARGET_PROPERTIES_MAP[target].keys() if p in old and p not in drop}
 
     return ret
 
@@ -113,9 +109,7 @@ def _parse_upload_type(sample: dict, upload_type: Set[str]) -> str:
     elif processed_derivative in ["DNA", "RNA"]:
         unprocessed_type = sample.get("type_of_sample")
         new_type = "tumor" if "tumor" in unprocessed_type.lower() else "normal"
-        new_type += (
-            "_blood_" if sample_manifest_type.startswith("biofluid") else "_tissue_"
-        )
+        new_type += "_blood_" if sample_manifest_type.startswith("biofluid") else "_tissue_"
         new_type += processed_derivative.lower()
 
         upload_type.add(new_type)
@@ -144,9 +138,7 @@ def _get_upload_type(samples: Iterable[Dict[str, Any]]) -> str:
             # updates upload_type in-place with the given sample
             _parse_upload_type(sample=sample, upload_type=upload_type)
 
-    assert (
-        len(upload_type) == 1
-    ), f"Inconsistent value determined for upload_type:{upload_type}"
+    assert len(upload_type) == 1, f"Inconsistent value determined for upload_type:{upload_type}"
     return list(upload_type)[0]
 
 
@@ -174,9 +166,7 @@ def _get_and_check(
     return ret
 
 
-def _extract_info_from_manifest(
-    manifest: Dict[str, Any]
-) -> Tuple[str, str, List[Dict[str, Any]]]:
+def _extract_info_from_manifest(manifest: Dict[str, Any]) -> Tuple[str, str, List[Dict[str, Any]]]:
     """
     Given a manifest, do initial validation and return some key values
 
@@ -195,9 +185,7 @@ def _extract_info_from_manifest(
     - f"Manifest {manifest_id} contains no samples: {manifest}"
     - f"No consistent protocol_identifier defined for samples on manifest {manifest_id}"
     """
-    manifest_id = _get_and_check(
-        obj=manifest, key="manifest_id", msg=f"No manifest_id in: {manifest}"
-    )
+    manifest_id = _get_and_check(obj=manifest, key="manifest_id", msg=f"No manifest_id in: {manifest}")
     _ = _get_and_check(  # don't need to keep status
         obj=manifest,
         key="status",
@@ -260,10 +248,7 @@ def _process_csms_sample(csms_sample: dict):
     csms_sample["collection_event_name"] = event_name
 
     # encrypt participant ids if not already encrypted
-    if (
-        "participant_id" in csms_sample
-        and len(csms_sample["participant_id"]) != _ENCRYPTED_FIELD_LEN
-    ):
+    if "participant_id" in csms_sample and len(csms_sample["participant_id"]) != _ENCRYPTED_FIELD_LEN:
         csms_sample["participant_id"] = _encrypt(csms_sample["participant_id"])
 
     # differences in naming convention
@@ -276,21 +261,15 @@ def _process_csms_sample(csms_sample: dict):
         "pbmc": "PBMC",
     }
     if csms_sample["processed_sample_type"] in processed_sample_type_map:
-        csms_sample["processed_sample_type"] = processed_sample_type_map[
-            csms_sample["processed_sample_type"]
-        ]
+        csms_sample["processed_sample_type"] = processed_sample_type_map[csms_sample["processed_sample_type"]]
 
     # differences in keys
     if "fixation_or_stabilization_type" in csms_sample:
-        csms_sample["fixation_stabilization_type"] = csms_sample.pop(
-            "fixation_or_stabilization_type"
-        )
+        csms_sample["fixation_stabilization_type"] = csms_sample.pop("fixation_or_stabilization_type")
 
     # typing
     if "sample_derivative_concentration" in csms_sample:
-        csms_sample["sample_derivative_concentration"] = float(
-            csms_sample["sample_derivative_concentration"]
-        )
+        csms_sample["sample_derivative_concentration"] = float(csms_sample["sample_derivative_concentration"])
 
     if "parent_sample_id" not in csms_sample:
         csms_sample["parent_sample_id"] = "Not Reported"
@@ -335,9 +314,7 @@ def _convert_csms_samples(
             msg=f"No cimac_id defined for samples[{n}] on manifest_id={manifest_id} for trial {trial_id}",
         )
         if not CIMAC_ID_REGEX.match(cimac_id):
-            raise RuntimeError(
-                f"Malformatted cimac_id={cimac_id} on manifest_id={manifest_id} for trial {trial_id}"
-            )
+            raise RuntimeError(f"Malformatted cimac_id={cimac_id} on manifest_id={manifest_id} for trial {trial_id}")
 
         if cimac_id in existing_cimac_ids:
             raise RuntimeError(
@@ -386,16 +363,10 @@ def insert_manifest_into_blob(
     trial_id, manifest_id, csms_samples = _extract_info_from_manifest(manifest)
     trial_md = TrialMetadata.select_for_update_by_trial_id(trial_id, session=session)
     if manifest_id in [s["manifest_id"] for s in trial_md.metadata_json["shipments"]]:
-        raise RuntimeError(
-            f"Manifest with manifest_id={manifest_id} already exists for trial {trial_id}"
-        )
+        raise RuntimeError(f"Manifest with manifest_id={manifest_id} already exists for trial {trial_id}")
 
     # pull out some additional values we'll need
-    existing_cimac_ids = [
-        s["cimac_id"]
-        for p in trial_md.metadata_json["participants"]
-        for s in p["samples"]
-    ]
+    existing_cimac_ids = [s["cimac_id"] for p in trial_md.metadata_json["participants"] for s in p["samples"]]
     assay_priority, assay_type = _extract_details_from_trial(csms_samples)
     if assay_priority:
         manifest["assay_priority"] = assay_priority
@@ -405,19 +376,13 @@ def insert_manifest_into_blob(
     # a patch is just the parts that are new, equivalent to the return of schemas.prismify
     patch = {
         "protocol_identifier": trial_id,
-        "shipments": [
-            _get_all_values(
-                target="shipment", old=manifest, drop=["excluded", "json_data"]
-            )
-        ],
+        "shipments": [_get_all_values(target="shipment", old=manifest, drop=["excluded", "json_data"])],
         "participants": [],
     }
 
     # sort samples by participants
     sample_map: Dict[str, List[Dict[str, Any]]] = defaultdict(list)
-    for cimac_id, sample in _convert_csms_samples(
-        trial_id, manifest_id, csms_samples, existing_cimac_ids
-    ):
+    for cimac_id, sample in _convert_csms_samples(trial_id, manifest_id, csms_samples, existing_cimac_ids):
         sample_map[cimac_id_to_cimac_participant_id(cimac_id, {})].append(sample)
 
     # each participant has a list of samples
@@ -487,9 +452,7 @@ class Change:
             changes = []
 
         if entity_type not in ["sample", "shipment", "upload"]:
-            raise ValueError(
-                f"entity_type must be in: sample, shipment, upload\nnot: {entity_type}"
-            )
+            raise ValueError(f"entity_type must be in: sample, shipment, upload\nnot: {entity_type}")
 
         self.entity_type = entity_type
         self.trial_id = trial_id
@@ -555,11 +518,7 @@ def _calc_difference(
 
     # handle formatting and ignore
     cidc1: Dict[str, Any] = {
-        k: (
-            datetime.strftime(v, "%Y-%m-%d %H:%M:%S")
-            if isinstance(v, (date, time, datetime))
-            else v
-        )
+        k: (datetime.strftime(v, "%Y-%m-%d %H:%M:%S") if isinstance(v, (date, time, datetime)) else v)
         for k, v in cidc.items()
         if k not in ignore
     }
@@ -574,9 +533,7 @@ def _calc_difference(
         if cidc1.get(k) != csms1.get(k)
     }
     # then get both values once per key to return
-    changes: Dict[str, Tuple[Any, Any]] = {
-        k: (cidc.get(k), csms.get(k)) for k in diff_keys
-    }
+    changes: Dict[str, Tuple[Any, Any]] = {k: (cidc.get(k), csms.get(k)) for k in diff_keys}
 
     return Change(
         entity_type=entity_type,
@@ -589,10 +546,7 @@ def _calc_difference(
 
 def _get_cidc_sample_map(metadata: dict) -> Dict[str, Dict[str, Any]]:
     """Returns a map of CIMAC IDs for this shipment to the relevant sample details from CIDC"""
-    cidc_partic_map = {
-        partic["cimac_participant_id"]: partic
-        for partic in metadata.get("participants", [])
-    }
+    cidc_partic_map = {partic["cimac_participant_id"]: partic for partic in metadata.get("participants", [])}
 
     ## make maps from cimac_id to a full dict
     ## need to add participant-level values
@@ -603,19 +557,13 @@ def _get_cidc_sample_map(metadata: dict) -> Dict[str, Dict[str, Any]]:
     }
     for cidc_cimac_id in cidc_sample_map.keys():
         cimac_participant_id = cimac_id_to_cimac_participant_id(cidc_cimac_id, {})
-        cidc_sample_map[cidc_cimac_id]["cohort_name"] = cidc_partic_map[
-            cimac_participant_id
-        ]["cohort_name"]
-        cidc_sample_map[cidc_cimac_id]["participant_id"] = cidc_partic_map[
-            cimac_participant_id
-        ]["participant_id"]
+        cidc_sample_map[cidc_cimac_id]["cohort_name"] = cidc_partic_map[cimac_participant_id]["cohort_name"]
+        cidc_sample_map[cidc_cimac_id]["participant_id"] = cidc_partic_map[cimac_participant_id]["participant_id"]
 
     return cidc_sample_map
 
 
-def _get_csms_sample_map(
-    trial_id, manifest_id, csms_samples
-) -> Dict[str, Dict[str, Any]]:
+def _get_csms_sample_map(trial_id, manifest_id, csms_samples) -> Dict[str, Dict[str, Any]]:
     """Returns a map of CIMAC IDs to the relevant sample details from CSMS"""
     return {
         csms_cimac_id: {
@@ -640,9 +588,7 @@ def _get_csms_sample_map(
                 ],
             ),
         }
-        for csms_cimac_id, csms_sample in _convert_csms_samples(
-            trial_id, manifest_id, csms_samples
-        )
+        for csms_cimac_id, csms_sample in _convert_csms_samples(trial_id, manifest_id, csms_samples)
     }
 
 
@@ -662,9 +608,7 @@ def _cross_validate_samples(
                 manifest_id,
                 cidc_sample["cimac_id"],
             )
-            raise RuntimeError(
-                f"Missing sample: {formatted} on CSMS {(trial_id, manifest_id)}"
-            )
+            raise RuntimeError(f"Missing sample: {formatted} on CSMS {(trial_id, manifest_id)}")
     # make sure that all of the CSMS samples are in CIDC
     all_cidc_sample_map: Dict[str, dict] = {
         sample["cimac_id"]: {
@@ -672,9 +616,7 @@ def _cross_validate_samples(
             "trial_id": upload.trial_id,
             "manifest_id": upload.metadata_patch["shipments"][0]["manifest_id"],
         }
-        for upload in session.query(UploadJobs)
-        .filter(UploadJobs.status == UploadJobStatus.MERGE_COMPLETED.value)
-        .all()
+        for upload in session.query(UploadJobs).filter(UploadJobs.status == UploadJobStatus.MERGE_COMPLETED.value).all()
         for partic in upload.metadata_patch.get("participants", [])
         for sample in partic.get("samples", [])
         if len(upload.metadata_patch.get("shipments", []))
@@ -695,9 +637,7 @@ def _cross_validate_samples(
                 if cidc_sample is not None
                 else "<no sample found>"
             )
-            raise RuntimeError(
-                f"Change in critical field for: {formatted} to CSMS {(trial_id, manifest_id, cimac_id)}"
-            )
+            raise RuntimeError(f"Change in critical field for: {formatted} to CSMS {(trial_id, manifest_id, cimac_id)}")
 
 
 def _initial_manifest_validation(
@@ -788,9 +728,7 @@ def _handle_shipment_differences(
     cidc_uploadjob: Optional[UploadJobs],
 ) -> Optional[Change]:
     """Compare the given CSMS and CIDC shipments, returning None's if no changes or the changes"""
-    cidc_manifest: Dict[str, Any] = (
-        {} if cidc_uploadjob is None else cidc_uploadjob.metadata_patch["shipments"][0]
-    )
+    cidc_manifest: Dict[str, Any] = {} if cidc_uploadjob is None else cidc_uploadjob.metadata_patch["shipments"][0]
     change: Change = _calc_difference(
         entity_type="shipment",
         trial_id=cidc_uploadjob.trial_id,
@@ -870,9 +808,7 @@ def _handle_upload_differences(
 
 
 @with_default_session
-def detect_manifest_changes(
-    csms_manifest: Dict[str, Any], uploader_email: str, *, session: Session
-) -> List[Change]:
+def detect_manifest_changes(csms_manifest: Dict[str, Any], uploader_email: str, *, session: Session) -> List[Change]:
     """
     Given a CSMS-style manifest, see if it has any differences from the current state of the db
     If a new manifest, throws a NewManifestError
@@ -914,16 +850,12 @@ def detect_manifest_changes(
     ) = _initial_manifest_validation(csms_manifest, session=session)
 
     # ----- Look for shipment-level differences -----
-    change: Optional[Change] = _handle_shipment_differences(
-        manifest_id, csms_manifest, cidc_uploadjob
-    )
+    change: Optional[Change] = _handle_shipment_differences(manifest_id, csms_manifest, cidc_uploadjob)
     if change:
         ret.append(change)
 
     # ----- Look for sample-level differences -----
-    ret = _handle_sample_differences(
-        trial_id, manifest_id, csms_sample_map, cidc_sample_map, ret
-    )
+    ret = _handle_sample_differences(trial_id, manifest_id, csms_sample_map, cidc_sample_map, ret)
 
     # ----- Look for differences in the Upload -----
     change: Optional[Change] = _handle_upload_differences(

cidc_api/models/files/details.py

@@ -408,12 +408,8 @@ details_dict = {
         "neoantigen: list of predicted neoantigens",
         "The combined MHC class I and II predicted neoantigens using the pVACseq software.  The column definitions are given here (ref: https://pvactools.readthedocs.io/en/latest/pvacseq/output_files.html)",
     ),
-    "/wes_tumor_only/analysis/vcf_gz_tnscope_filter.vcf.gz": FileDetails(
-        "analysis", "", ""
-    ),
-    "/wes_tumor_only/analysis/vcf_gz_tnscope_output.vcf.gz": FileDetails(
-        "analysis", "", ""
-    ),
+    "/wes_tumor_only/analysis/vcf_gz_tnscope_filter.vcf.gz": FileDetails("analysis", "", ""),
+    "/wes_tumor_only/analysis/vcf_gz_tnscope_output.vcf.gz": FileDetails("analysis", "", ""),
     "/wes_tumor_only/analysis/maf_tnscope_filter.maf": FileDetails("analysis", "", ""),
     "/wes_tumor_only/analysis/tnscope_exons.vcf.gz": FileDetails("analysis", "", ""),
     "/wes_tumor_only/analysis/HLA_results.tsv": FileDetails("analysis", "", ""),
@@ -481,9 +477,7 @@ details_dict = {
     "/wes_tumor_only/analysis/config.yaml": FileDetails("analysis", "", ""),
     "/wes_tumor_only/analysis/metasheet.csv": FileDetails("analysis", "", ""),
     "/wes_tumor_only/analysis/wes_sample.json": FileDetails("analysis", "", ""),
-    "/wes_tumor_only/analysis/tumor/xhla_report_hla.json": FileDetails(
-        "analysis", "", ""
-    ),
+    "/wes_tumor_only/analysis/tumor/xhla_report_hla.json": FileDetails("analysis", "", ""),
     # RNA
     "/rna/r1_.fastq.gz": FileDetails(
         "source",
@@ -748,9 +742,7 @@ details_dict = {
              by the appropriate CIMAC participant or sample id.",
     ),
     # Miscellaneous Data
-    "/misc_data/": FileDetails(
-        "source", "Unharmonized, one-off, or not-yet-supported data.", ""
-    ),
+    "/misc_data/": FileDetails("source", "Unharmonized, one-off, or not-yet-supported data.", ""),
     # TCR
     "/tcr/reads.tsv": FileDetails("source", "", ""),
     "/tcr/controls/reads.tsv": FileDetails("source", "", ""),
@@ -917,9 +909,7 @@ details_dict = {
         "Corrected depth file generated by ichorCNA",
         "",
     ),
-    "/ctdna/OnPrem.params.txt": FileDetails(
-        "source", "On premise parameters file generated by ichorCNA", ""
-    ),
+    "/ctdna/OnPrem.params.txt": FileDetails("source", "On premise parameters file generated by ichorCNA", ""),
     # Microbiome Assay
     "/microbiome/forward.fastq.gz": FileDetails(
         "source",

cidc_api/models/files/facets.py

@@ -284,9 +284,7 @@ assay_facets: Facets = {
         "MSI": FacetConfig(["/wes_tumor_only/analysis/msisensor.txt"]),
     },
     "RNA": {
-        "Source": FacetConfig(
-            ["/rna/r1_.fastq.gz", "/rna/r2_.fastq.gz", "/rna/reads_.bam"]
-        ),
+        "Source": FacetConfig(["/rna/r1_.fastq.gz", "/rna/r2_.fastq.gz", "/rna/reads_.bam"]),
         "Alignment": FacetConfig(
             [
                 "/rna/analysis/star/sorted.bam",
@@ -428,16 +426,12 @@ assay_facets: Facets = {
                 "/tcr/replicate_/i2.fastq.gz",
             ]
         ),
-        "Misc.": FacetConfig(
-            ["/tcr/SampleSheet.csv", "/tcr_analysis/summary_info.csv"]
-        ),
+        "Misc.": FacetConfig(["/tcr/SampleSheet.csv", "/tcr_analysis/summary_info.csv"]),
         "Analysis Data": FacetConfig(
             ["/tcr_analysis/tra_clone.csv", "/tcr_analysis/trb_clone.csv"],
             "Data files indicating TRA & TRB clones' UMI counts",
         ),
-        "Reports": FacetConfig(
-            ["/tcr_analysis/report_trial.tar.gz"], "Report from TCRseq analysis"
-        ),
+        "Reports": FacetConfig(["/tcr_analysis/report_trial.tar.gz"], "Report from TCRseq analysis"),
     },
     "ELISA": {"Data": FacetConfig(["/elisa/assay.xlsx"])},
     "ctDNA": {
@@ -564,9 +558,7 @@ def _build_facet_groups_to_names():
     for facet_name, subfacet in facets_dict["Assay Type"].items():
         for subfacet_name, subsubfacet in subfacet.items():
             for facet_group in subsubfacet.facet_groups:
-                facet_names[facet_group] = FACET_NAME_DELIM.join(
-                    [facet_name, subfacet_name]
-                )
+                facet_names[facet_group] = FACET_NAME_DELIM.join([facet_name, subfacet_name])
 
     for facet_name, subfacet in facets_dict["Clinical Type"].items():
         for facet_group in subfacet.facet_groups:
@@ -599,14 +591,9 @@ def build_data_category_facets(facet_group_file_counts: Dict[str, int]):
     def extract_facet_info(facet_config_entries, _prefix):
         results = []
         for label, config in facet_config_entries.items():
-            count = sum(
-                facet_group_file_counts.get(facet_group, 0)
-                for facet_group in config.facet_groups
-            )
+            count = sum(facet_group_file_counts.get(facet_group, 0) for facet_group in config.facet_groups)
             if count:
-                results.append(
-                    {"label": label, "description": config.description, "count": count}
-                )
+                results.append({"label": label, "description": config.description, "count": count})
         return results
 
     assay_types = {}
@@ -632,10 +619,7 @@ def build_trial_facets(trial_file_counts: Dict[str, int]):
     """
     Convert a mapping from trial ids to file counts into a list of facet specifications.
     """
-    return [
-        {"label": trial_id, "count": count}
-        for trial_id, count in trial_file_counts.items()
-    ]
+    return [{"label": trial_id, "count": count} for trial_id, count in trial_file_counts.items()]
 
 
 def get_facet_groups_for_paths(paths: List[List[str]]) -> List[str]:
@@ -699,9 +683,7 @@ def get_facet_groups_for_links() -> Dict[str, Dict[str, List[str]]]:
     for first, first_config in facets_dict[category].items():
         assay = _translate_assay(first)
         for facet, facet_config in first_config.items():
-            _process_facet(
-                assay, [category, first, facet], facet_config, facets_to_return
-            )
+            _process_facet(assay, [category, first, facet], facet_config, facets_to_return)
 
     # run through all analysis facets and put them in the return
     category: str = "Analysis Ready"
@@ -714,9 +696,7 @@ def get_facet_groups_for_links() -> Dict[str, Dict[str, List[str]]]:
     category: str = "Clinical Type"
     for facet, facet_config in facets_dict[category].items():
         # these will all go into received, as none contain "analysis"
-        _process_facet(
-            "clinical_participants", [category, facet], facet_config, facets_to_return
-        )
+        _process_facet("clinical_participants", [category, facet], facet_config, facets_to_return)
 
     # wes specific, use same values for wes_tumor received as for wes_normal received
     # because facets refer to the WHOLE of WES assay, not broken up by sample type