cg 83.20.3__py3-none-any.whl → 84.0.1__py3-none-any.whl

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "83.20.3"
+__version__ = "84.0.1"

cg/constants/constants.py

@@ -164,6 +164,12 @@ class GenomeVersion(StrEnum):
     HG38 = "hg38"
 
 
+class BedVersionGenomeVersion(StrEnum):
+    HG19 = "hg19"
+    HG38 = "hg38"
+    CFAM3 = "cfam3"
+
+
 class SampleType(StrEnum):
     TUMOR: str = "tumor"
     NORMAL: str = "normal"

cg/server/endpoints/sequencing_run/dtos.py

@@ -19,20 +19,22 @@ class PacbioSmrtCellMetricsDTO(BaseModel):
     p2_percent: float
     percent_reads_passing_q30: float
     plate: int
-    run_name: str
+    run_id: str
     started_at: datetime
     well: str
 
 
 class PacbioSmrtCellMetricsResponse(BaseModel):
-    runs: list[PacbioSmrtCellMetricsDTO]
+    metrics: list[PacbioSmrtCellMetricsDTO]
 
 
 class PacbioSequencingRunDTO(BaseModel):
     id: int
-    run_name: str
     comment: str
     processed: bool
+    run_id: str
+    run_name: str | None
+    unique_id: str | None
 
 
 class PacbioSequencingRunResponse(BaseModel):

cg/server/endpoints/sequencing_run/pacbio_smrt_cell_metrics.py

@@ -11,10 +11,10 @@ PACBIO_SMRT_CELL_METRICS_BLUEPRINT = Blueprint(
 PACBIO_SMRT_CELL_METRICS_BLUEPRINT.before_request(before_request)
 
 
-@PACBIO_SMRT_CELL_METRICS_BLUEPRINT.route("/<run_name>", methods=["GET"])
+@PACBIO_SMRT_CELL_METRICS_BLUEPRINT.route("/<run_id>", methods=["GET"])
 @handle_missing_entries
-def get_smrt_cell_metrics(run_name: str):
+def get_smrt_cell_metrics(run_id: str):
     response: PacbioSmrtCellMetricsResponse = (
-        pacbio_sequencing_runs_service.get_sequencing_runs_by_name(run_name)
+        pacbio_sequencing_runs_service.get_sequencing_runs_by_run_id(run_id)
     )
     return jsonify(response.model_dump())

cg/services/run_devices/pacbio/sequencing_runs_service.py

@@ -13,17 +13,17 @@ class PacbioSequencingRunsService:
     def __init__(self, store: Store):
         self.store = store
 
-    def get_sequencing_runs_by_name(self, run_name: str) -> PacbioSmrtCellMetricsResponse:
+    def get_sequencing_runs_by_run_id(self, run_id: str) -> PacbioSmrtCellMetricsResponse:
         metrics: list[PacbioSmrtCellMetricsDTO] = []
         db_smrt_cell_metrics: list[PacbioSMRTCellMetrics] = (
-            self.store.get_pacbio_smrt_cell_metrics_by_run_id(run_name)
+            self.store.get_pacbio_smrt_cell_metrics_by_run_id(run_id)
         )
         for metric in db_smrt_cell_metrics:
             metric_dict = metric.to_dict()
             metric_dict["internal_id"] = metric.device.internal_id
-            metric_dict["run_name"] = metric.run_id
+            metric_dict["run_id"] = metric.run_id
             metrics.append(PacbioSmrtCellMetricsDTO.model_validate(metric_dict))
-        return PacbioSmrtCellMetricsResponse(runs=metrics)
+        return PacbioSmrtCellMetricsResponse(metrics=metrics)
 
     def get_sequencing_runs(self, page: int = 0, page_size: int = 0) -> PacbioSequencingRunResponse:
         db_runs, total_count = self.store.get_pacbio_sequencing_runs(page=page, page_size=page_size)
@@ -31,9 +31,11 @@ class PacbioSequencingRunsService:
         for db_run in db_runs:
             run = PacbioSequencingRunDTO(
                 id=db_run.id,
-                run_name=db_run.run_id,
+                run_id=db_run.run_id,
+                run_name=db_run.run_name,
                 comment=db_run.comment,
                 processed=db_run.processed,
+                unique_id=db_run.unique_id,
             )
             runs.append(run)
         return PacbioSequencingRunResponse(pacbio_sequencing_runs=runs, total_count=total_count)

cg/store/crud/create.py

@@ -192,7 +192,7 @@ class CreateMixin(ReadHandler):
     def add_bed_version(self, bed: Bed, version: int, filename: str, shortname: str) -> BedVersion:
         """Build a new bed version record."""
         bed_version: BedVersion = BedVersion(
-            version=version, filename=filename, shortname=shortname
+            version=version, filename=filename, shortname=shortname, genome_version="hg19"
         )
         bed_version.bed = bed
         return bed_version

cg/store/models.py

@@ -22,6 +22,7 @@ from sqlalchemy.orm.attributes import InstrumentedAttribute
 from cg.constants import DataDelivery, Priority, SequencingRunDataAvailability, Workflow
 from cg.constants.archiving import PDC_ARCHIVE_LOCATION
 from cg.constants.constants import (
+    BedVersionGenomeVersion,
     CaseActions,
     ControlOptions,
     SequencingQCStatus,
@@ -335,7 +336,12 @@ class BedVersion(Base):
     """Model for bed target captures versions"""
 
     __tablename__ = "bed_version"
-    __table_args__ = (UniqueConstraint("bed_id", "version", name="_app_version_uc"),)
+    __table_args__ = (
+        UniqueConstraint("bed_id", "version", name="_app_version_uc"),
+        UniqueConstraint(
+            "shortname", "version", "genome_version", name="shortname_version_genome_version_uc"
+        ),
+    )
 
     id: Mapped[PrimaryKeyInt]
     shortname: Mapped[Str64]
@@ -343,7 +349,9 @@ class BedVersion(Base):
     filename: Mapped[Str256]
     checksum: Mapped[Str32 | None]
     panel_size: Mapped[int | None]
-    genome_version: Mapped[Str32 | None]
+    genome_version: Mapped[BedVersionGenomeVersion] = mapped_column(
+        types.Enum(*(genome_version.value for genome_version in BedVersionGenomeVersion))
+    )
     designer: Mapped[Str256 | None]
     comment: Mapped[Text | None]
     created_at: Mapped[datetime | None] = mapped_column(default=datetime.now)

{cg-83.20.3.dist-info → cg-84.0.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cg
-Version: 83.20.3
+Version: 84.0.1
 Summary: Clinical Genomics command center
 Requires-Python: >=3.11,<3.13
 Classifier: Programming Language :: Python

{cg-83.20.3.dist-info → cg-84.0.1.dist-info}/RECORD

@@ -1,4 +1,4 @@
-cg/__init__.py,sha256=SYjJH-I0oik2cgySkcSsSP4me93_hWY-3zONHPfuiNc,41
+cg/__init__.py,sha256=QATHnUBhjQg1gdiTUzAuoLIAXxbjzsBt8FK_l6YZFtw,40
 cg/apps/__init__.py,sha256=pYf0vxo4iYQqURzFRYzqpOCdV8Cm9MWx0GHvJOz0EMg,315
 cg/apps/coverage/__init__.py,sha256=dJtsmNf8tODE2-VEomMIoYA7ugLYZAk_upsfOQCZeF8,27
 cg/apps/coverage/api.py,sha256=e_ozC3QeNKoEfpjjMaL-XjeBLtz-JySWccrtw0E9mLM,2940
@@ -194,7 +194,7 @@ cg/constants/archiving.py,sha256=_M4-9mu_d5PpZLdnvYTxGDKR-YwQNl6GxP05AM9XIPs,253
 cg/constants/backup.py,sha256=geZvQbYkPgN_P1vv5jn0ktCEdH5pqs9RA-fGZPruaNs,38
 cg/constants/cli_options.py,sha256=4Lk2jOki9TWA48PC5YDI1iNNJJ--9HrfwXUsuWqkYAE,690
 cg/constants/compression.py,sha256=hY8Ws7r0uFhDD10GDYjTN1nFeKWnekRGlOpM14g-yZ4,469
-cg/constants/constants.py,sha256=REhV4-snyfivwtVp53eYsxJ2Rz7PlAxUUEHb5LSmMe0,6815
+cg/constants/constants.py,sha256=B4XCn_CH4G-fphYvUIJV0UREgznVQXikoqe7dcTKBBQ,6913
 cg/constants/delivery.py,sha256=RHoyt81K8GIKVGX-ctTjRTRpOYYAs4BDsS3JJSDvcfs,5389
 cg/constants/demultiplexing.py,sha256=xX3bhRieLHSXP6yQBOm0iT1h53gUSNKd4R7Zq7TORT4,7483
 cg/constants/devices.py,sha256=qP98IxkL0N-k2hIQmQuSP-_BxGEy_c-tjIg9RyfPL-s,254
@@ -497,9 +497,9 @@ cg/server/endpoints/sequencing_metrics/dtos.py,sha256=DXh9xFLrS0RQIxHrkAZa71AkcL
 cg/server/endpoints/sequencing_metrics/error_handler.py,sha256=rVASP7uk1qSA5qu__-JcSZ6vXpBy3s7n4GdBVg0zAUA,758
 cg/server/endpoints/sequencing_metrics/illumina_sequencing_metrics.py,sha256=IvXMH2KIeOH98lJkaFLPFIRj7j6uW3oBaJZozQ5Tva0,810
 cg/server/endpoints/sequencing_metrics/pacbio_sequencing_metrics.py,sha256=iglo2cOYSPuK4HAWH4XPGLgbZOst2spdB7A6mQ8th8g,1218
-cg/server/endpoints/sequencing_run/dtos.py,sha256=ezs1TW0XyKO8gYyRreq6iQsFwLtgV8tzO96fzXT6kWg,1023
+cg/server/endpoints/sequencing_run/dtos.py,sha256=o2al0uUnGbZdMRvOZ5z9zb67peJmBM7EyBSA7xizv3Y,1073
 cg/server/endpoints/sequencing_run/pacbio_sequencing_run.py,sha256=HvV7EPwrh_xe5ZjerQYoBK-bIdKLBZ1nk16whGSDAmw,1524
-cg/server/endpoints/sequencing_run/pacbio_smrt_cell_metrics.py,sha256=FVETf-KUghGbb7KGO2sDYWISp3Z9gnublo-9ekQHUuk,819
+cg/server/endpoints/sequencing_run/pacbio_smrt_cell_metrics.py,sha256=0cV6wybrsLmYMuW3noM6RHy8Sb7RunavMEpWMSJtiAo,815
 cg/server/endpoints/users.py,sha256=48z9Si2EuJ6wcN8jBIr0yvmtgygozYgUIytyFuTzFao,696
 cg/server/endpoints/utils.py,sha256=RjhrcBqY3Mfg_hZIeXr6SfmCTu4FMpan-n5UNDjOeMg,2251
 cg/server/ext.py,sha256=rQIv4qKS_N5whB158SGa2FZp-JuGDaUydCBjGhAxaOE,3923
@@ -842,7 +842,7 @@ cg/services/run_devices/pacbio/run_data_generator/run_data.py,sha256=h0TfMtHwyXl
 cg/services/run_devices/pacbio/run_file_manager/models.py,sha256=C6kycBPx6YKNq2oFJOIhdrcPloi3QIBOrlbaAgeYzgs,192
 cg/services/run_devices/pacbio/run_file_manager/run_file_manager.py,sha256=QDJKvMTwHNlP9ovU5wgqA8FbTx6xI0zdc26A1RY4W1M,5440
 cg/services/run_devices/pacbio/run_validator/pacbio_run_validator.py,sha256=d8fvmJcByEFPMnwqOe6mQsXXIO87WkXwfK9L_Bx7whg,3037
-cg/services/run_devices/pacbio/sequencing_runs_service.py,sha256=n_noNrPfOAUGizgTpE5n1ezZA0O92XAB9o_FYIzcus8,2145
+cg/services/run_devices/pacbio/sequencing_runs_service.py,sha256=VLc5EicDpD2fb-fz_x7G5j3qcHRl75N5cCaky5DriNQ,2228
 cg/services/run_devices/run_names/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cg/services/run_devices/run_names/pacbio.py,sha256=4l-fCejTMMgAnVQ2RqIyQaqMtVbs_SeDEm6JJ4Dg36U,678
 cg/services/run_devices/run_names/service.py,sha256=d6-paeXsENHlU59eo4FcSXBAhoz50oL6bSglscRo2rQ,293
@@ -874,7 +874,7 @@ cg/store/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cg/store/api/data_classes.py,sha256=vgJehK0zm3SdB4LAQAWvTjoCHfos4N8_Vf0DDshrAnM,289
 cg/store/base.py,sha256=qmIjuWuq_wryBfGoSZny9nvqZj7Hl8N23hcdQ7Hss5I,6885
 cg/store/crud/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-cg/store/crud/create.py,sha256=DrwCPqPCAEM3vBZwvLg1JsNHXDPg5y9_EBVhhbJm9ig,22621
+cg/store/crud/create.py,sha256=ZvPsvlaLKwY9_mNaf51hdMi3Ear2H37O2Eob2PLZmc8,22644
 cg/store/crud/delete.py,sha256=TlpoVWvUQMaRfy5bk-icFf9SSi_0Ir6XpFcAiM22DB0,1386
 cg/store/crud/read.py,sha256=UJ1NLkK3k682v8xk4NFJyPXC2ik-zsYshG6098Yy0aQ,78809
 cg/store/crud/update.py,sha256=FZvOPebNnkWICu1N4gTdFeiMcuTUPglgCDfaxE6G288,6262
@@ -903,7 +903,7 @@ cg/store/filters/status_panel_filters.py,sha256=qMYhIsrF9G3mjCvL9b9O2l_cmD3SfPWh
 cg/store/filters/status_pool_filters.py,sha256=XcYqe2z5k_q09xpp4cleDMQ4Q3o2y7UPCkB0QUkl1ck,4308
 cg/store/filters/status_sample_filters.py,sha256=mRpt_ik7niMjBo9K7pP8cmdfDMdr0B3I6Tt2MWXkLoc,9656
 cg/store/filters/status_user_filters.py,sha256=sMwKeWqgEtqv8gyhbN_Uf5huPUxbOt5qEqMWVu67Zys,1328
-cg/store/models.py,sha256=YTz2rCR8myl_kA-sjOS4Xau2gmY1-ocG6g4W6T1BVT0,44401
+cg/store/models.py,sha256=movmAB6h5SbxaPTfRK1entP1S9ayKt64v8oOTSL3Dk4,44702
 cg/store/store.py,sha256=mz1TfKPlanH2uQyhZdwe_8VKg0IdFolmromKLu668IY,630
 cg/utils/__init__.py,sha256=gGjdV2l_hfWFCTybU6dwDk_FcItM88EIHNPaX6g1qUk,30
 cg/utils/calculations.py,sha256=zLVJO6nNw6n7AW7fHZI56UnQ23lqJrShB4Hh2ow6-TQ,349
@@ -922,7 +922,7 @@ cg/utils/flask/enum.py,sha256=xwNVtFPkSzoloJctLHu7obRyxcng1GJrhkeYkqwf9tw,1052
 cg/utils/mapping.py,sha256=oZpZW2kgsbtAP2FZ7RtRPELiEE1zZk_nAGisHGtCOUo,491
 cg/utils/time.py,sha256=_VOglhrFEZ5cwHK1U1g36SdwzB7UvV-Nvlt4ymuZUho,1501
 cg/utils/utils.py,sha256=RciI_UhWcnG_pMZrmQZ1ZYb-O1N0DweTYMmhE0SIRgQ,1410
-cg-83.20.3.dist-info/METADATA,sha256=G5EW48rAnANU-r-OHcWpCiHdG76nYpwnYOVOP-Fk144,4940
-cg-83.20.3.dist-info/WHEEL,sha256=kJCRJT_g0adfAJzTx2GUMmS80rTJIVHRCfG0DQgLq3o,88
-cg-83.20.3.dist-info/entry_points.txt,sha256=q5f47YQQGltzK_xnIq1mDopRXXEItr85Xe1BCtG-Wts,39
-cg-83.20.3.dist-info/RECORD,,
+cg-84.0.1.dist-info/METADATA,sha256=5J1kH9CRXPbjM0gK6jpoHAybsvSv1zSJAp7dJa3mYrA,4939
+cg-84.0.1.dist-info/WHEEL,sha256=kJCRJT_g0adfAJzTx2GUMmS80rTJIVHRCfG0DQgLq3o,88
+cg-84.0.1.dist-info/entry_points.txt,sha256=q5f47YQQGltzK_xnIq1mDopRXXEItr85Xe1BCtG-Wts,39
+cg-84.0.1.dist-info/RECORD,,