cg 83.11.7__py3-none-any.whl → 83.12.0__py3-none-any.whl

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "83.11.7"
+__version__ = "83.12.0"

cg/server/admin.py

@@ -246,6 +246,8 @@ class ApplicationView(BaseView):
         "is_accredited",
         "target_reads",
         "percent_reads_guaranteed",
+        "target_hifi_yield",
+        "percent_hifi_yield_guaranteed",
         "comment",
         "prep_category",
         "sequencing_depth",

cg/server/app.py

@@ -20,7 +20,6 @@ from cg.server.endpoints.sequencing_metrics.pacbio_sequencing_metrics import (
     PACBIO_SAMPLE_SEQUENCING_METRICS_BLUEPRINT,
 )
 from cg.server.endpoints.sequencing_run.pacbio_sequencing_run import (
-    PACBIO_SEQUENCING_RUN_BLUEPRINT,
     PACBIO_SEQUENCING_RUNS_BLUEPRINT,
 )
 from cg.server.endpoints.sequencing_run.pacbio_smrt_cell_metrics import (
@@ -113,7 +112,6 @@ def _register_blueprints(app: Flask):
     app.register_blueprint(ANALYSES_BLUEPRINT)
     app.register_blueprint(USERS_BLUEPRINT)
     app.register_blueprint(PACBIO_SAMPLE_SEQUENCING_METRICS_BLUEPRINT)
-    app.register_blueprint(PACBIO_SEQUENCING_RUN_BLUEPRINT)
     app.register_blueprint(PACBIO_SEQUENCING_RUNS_BLUEPRINT)
     app.register_blueprint(PACBIO_SMRT_CELL_METRICS_BLUEPRINT)
     app.register_blueprint(INDEX_SEQUENCES_BLUEPRINT)

cg/server/endpoints/sequencing_run/pacbio_sequencing_run.py

@@ -7,33 +7,19 @@ from cg.server.endpoints.error_handler import handle_missing_entries
 from cg.server.endpoints.sequencing_run.dtos import (
     PacbioSequencingRunResponse,
     PacbioSequencingRunUpdateRequest,
-    PacbioSmrtCellMetricsResponse,
 )
 from cg.server.endpoints.utils import before_request
 from cg.server.ext import pacbio_sequencing_runs_service
 
-PACBIO_SEQUENCING_RUN_BLUEPRINT = Blueprint(
-    "pacbio_sequencing_run", __name__, url_prefix="/api/v1/pacbio_sequencing_run"
-)
 PACBIO_SEQUENCING_RUNS_BLUEPRINT = Blueprint(
     "pacbio_sequencing_runs", __name__, url_prefix="/api/v1/"
 )
-PACBIO_SEQUENCING_RUN_BLUEPRINT.before_request(before_request)
 PACBIO_SEQUENCING_RUNS_BLUEPRINT.before_request(before_request)
 
 
-@PACBIO_SEQUENCING_RUN_BLUEPRINT.route("/<run_name>", methods=["GET"])
-@handle_missing_entries
-def get_sequencing_runs(run_name: str):
-    response: PacbioSmrtCellMetricsResponse = (
-        pacbio_sequencing_runs_service.get_sequencing_runs_by_name(run_name)
-    )
-    return jsonify(response.model_dump())
-
-
 @PACBIO_SEQUENCING_RUNS_BLUEPRINT.route("/pacbio_sequencing_runs", methods=["GET"])
 @handle_missing_entries
-def get_sequencing_runs_new():  # TODO rename endpoint to pacbio_sequencing_runs
+def get_sequencing_runs():
     page: int = int(request.args.get("page", "0"))
     page_size: int = int(request.args.get("pageSize", "0"))
     sequencing_runs: PacbioSequencingRunResponse = (

cg/store/models.py

@@ -147,6 +147,8 @@ class Application(Base):
     min_sequencing_depth: Mapped[int] = mapped_column(default=0)
     target_reads: Mapped[BigInt | None] = mapped_column(default=0)
     percent_reads_guaranteed: Mapped[int]
+    target_hifi_yield: Mapped[BigInt | None] = mapped_column(default=None)
+    percent_hifi_yield_guaranteed: Mapped[int | None] = mapped_column(default=None)
     sample_amount: Mapped[int | None]
     sample_volume: Mapped[Text | None]
     sample_concentration: Mapped[Text | None]

{cg-83.11.7.dist-info → cg-83.12.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cg
-Version: 83.11.7
+Version: 83.12.0
 Summary: Clinical Genomics command center
 Requires-Python: >=3.11,<3.13
 Classifier: Programming Language :: Python

{cg-83.11.7.dist-info → cg-83.12.0.dist-info}/RECORD

@@ -1,4 +1,4 @@
-cg/__init__.py,sha256=cVAlORTVn7sMHijL2MCXrMfB0Y97T8by6e2chlzpCE8,41
+cg/__init__.py,sha256=QYeMJF37x9RzmsTZYc1lCpGDCLcZnJkcVPsodSKqAXg,41
 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
@@ -467,8 +467,8 @@ cg/resources/rnafusion_bundle_filenames.yaml,sha256=hoXuTobKbjH7W7dld87rSF7X0r4K
 cg/resources/taxprofiler_bundle_filenames.yaml,sha256=AULMEAYkMzADYUtVtuSmBj7UaAIlLGRDyBMEOO0xWz8,2871
 cg/resources/tomte_bundle_filenames.yaml,sha256=lFxk9GssmCyKBUn5lbRBtBS9FS9cABaoVzb-e2zrJac,4144
 cg/server/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-cg/server/admin.py,sha256=JUZvNdTwjfNoZbSo_tZNS-ZMAeRKheAW9nfAcrrkw6w,29522
-cg/server/app.py,sha256=wb1nsK4LNcFYG0bp_JXpghX3Q0-bRx687Y1S1hVBRU0,7072
+cg/server/admin.py,sha256=m3Wnj02wOk98ozcb-s5A7TH2VyNj_34griSG4JF53ts,29592
+cg/server/app.py,sha256=WEULzx5JeC0aJHag3Vltzopd8r7tgHPr_1nbytS-AI8,6975
 cg/server/app_config.py,sha256=8DaNtYtdp6A29FAuTFX-Lk7SLv7Zx-_f57ZU0-T_3ZI,1403
 cg/server/auto.py,sha256=5DqokNScv483imZTvOYrJo6wV9-P7ZGnJaaHnfnNJLs,57
 cg/server/dto/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -499,7 +499,7 @@ cg/server/endpoints/sequencing_metrics/error_handler.py,sha256=rVASP7uk1qSA5qu__
 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/pacbio_sequencing_run.py,sha256=Ap8hVJUvGUzOHyiYw7RDgLsrdelae1K8U19Ibb6rT5c,2115
+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/users.py,sha256=48z9Si2EuJ6wcN8jBIr0yvmtgygozYgUIytyFuTzFao,696
 cg/server/endpoints/utils.py,sha256=RjhrcBqY3Mfg_hZIeXr6SfmCTu4FMpan-n5UNDjOeMg,2251
@@ -904,7 +904,7 @@ 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=7Fa_DvM8Cf0W5krBjHlK5MiQ2eOTrQ8Y_a3XlNQKMHw,42826
+cg/store/models.py,sha256=HUwzqktZ-Fil7QTGwLJl7LSOb_nty1oJnIUA_euqKFQ,42985
 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
@@ -923,7 +923,7 @@ 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-83.11.7.dist-info/METADATA,sha256=1F26dofBkLzFhOusWh486onht6SkWNOI7BsUt4Vc5RY,4940
-cg-83.11.7.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-cg-83.11.7.dist-info/entry_points.txt,sha256=q5f47YQQGltzK_xnIq1mDopRXXEItr85Xe1BCtG-Wts,39
-cg-83.11.7.dist-info/RECORD,,
+cg-83.12.0.dist-info/METADATA,sha256=4Ls745EkqqjabAwLXfK_pmPH-N6SZfd8mYaTdGOxfy4,4940
+cg-83.12.0.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+cg-83.12.0.dist-info/entry_points.txt,sha256=q5f47YQQGltzK_xnIq1mDopRXXEItr85Xe1BCtG-Wts,39
+cg-83.12.0.dist-info/RECORD,,