cg 83.11.8__py3-none-any.whl → 83.13.0__py3-none-any.whl

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "83.11.8"
+__version__ = "83.13.0"

cg/server/admin.py

@@ -112,12 +112,6 @@ def view_pacbio_sample_sequencing_metrics_link(unused1, unused2, model, unused3)
     )
 
 
-def is_external_application(unused1, unused2, model, unused3):
-    """column formatter to open this view"""
-    del unused1, unused2, unused3
-    return model.application_version.application.is_external if model.application_version else ""
-
-
 def view_order_types(unused1, unused2, model, unused3):
     del unused1, unused2, unused3
     order_type_list = "<br>".join(model.order_types)
@@ -246,6 +240,8 @@ class ApplicationView(BaseView):
         "is_accredited",
         "target_reads",
         "percent_reads_guaranteed",
+        "target_hifi_yield",
+        "percent_hifi_yield_guaranteed",
         "comment",
         "prep_category",
         "sequencing_depth",
@@ -734,10 +730,36 @@ class PoolView(BaseView):
 class SampleView(BaseView):
     """Admin view for Model.Sample"""
 
-    column_exclude_list = [
-        "age_at_sampling",
-        "_phenotype_groups",
-        "_phenotype_terms",
+    column_list = [
+        "application_version",
+        "customer",
+        "organism",
+        "invoice",
+        "is_cancelled",
+        "capture_kit",
+        "comment",
+        "control",
+        "created_at",
+        "delivered_at",
+        "downsampled_to",
+        "from_sample",
+        "internal_id",
+        "is_tumour",
+        "loqusdb_id",
+        "name",
+        "no_invoice",
+        "order",
+        "ordered_at",
+        "original_ticket",
+        "prepared_at",
+        "priority",
+        "reads",
+        "hifi_yield",
+        "last_sequenced_at",
+        "received_at",
+        "reference_genome",
+        "sex",
+        "subject_id",
     ]
     column_default_sort = ("created_at", True)
     column_editable_list = [
@@ -757,7 +779,6 @@ class SampleView(BaseView):
     column_formatters = {
         "application_version": view_application_link_via_application_version,
         "customer": view_customer_link,
-        "is_external": is_external_application,
         "internal_id": view_case_sample_link,
         "invoice": InvoiceView.view_invoice_link,
         "original_ticket": view_ticket_link,

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]
@@ -759,6 +761,13 @@ class Sample(Base, PriorityMixin):
     def __str__(self) -> str:
         return f"{self.internal_id} ({self.name})"
 
+    @property
+    def hifi_yield(self) -> int | None:
+        if self._sample_run_metrics and getattr(self._sample_run_metrics[0], "hifi_yield", False):
+            return sum(metric.hifi_yield for metric in self._sample_run_metrics)  # type: ignore
+        else:
+            return None
+
     @property
     def archive_location(self) -> str:
         """Returns the data_archive_location if the customer linked to the sample."""

{cg-83.11.8.dist-info → cg-83.13.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cg
-Version: 83.11.8
+Version: 83.13.0
 Summary: Clinical Genomics command center
 Requires-Python: >=3.11,<3.13
 Classifier: Programming Language :: Python

{cg-83.11.8.dist-info → cg-83.13.0.dist-info}/RECORD

@@ -1,4 +1,4 @@
-cg/__init__.py,sha256=yzOx_FVs-IfMsX26cR34Qgw4w04sas1xLr5va0KTq6A,41
+cg/__init__.py,sha256=mLKK3VZwghkAhxMaIze9zQ4Dy66UhzH--J8yymzr7g0,41
 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
@@ -467,7 +467,7 @@ 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/admin.py,sha256=FbvMTtkodpDmaKCFqTRWLz4XohZPT8Gpvy2U8LKW-do,29849
 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
@@ -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=MsKSG9UBiXySCEsODMRDmntjpjkVCd_rlRpqTEw2TZ8,43274
 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-83.11.8.dist-info/METADATA,sha256=dBSQBPXkY0eaxX1PQg1ID9cInmbaGBZ71T8Khitq9yU,4940
-cg-83.11.8.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-cg-83.11.8.dist-info/entry_points.txt,sha256=q5f47YQQGltzK_xnIq1mDopRXXEItr85Xe1BCtG-Wts,39
-cg-83.11.8.dist-info/RECORD,,
+cg-83.13.0.dist-info/METADATA,sha256=gjplstDx2j_y2q1p0zfebH7ryAK12WFYCUqEgosrxl0,4940
+cg-83.13.0.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+cg-83.13.0.dist-info/entry_points.txt,sha256=q5f47YQQGltzK_xnIq1mDopRXXEItr85Xe1BCtG-Wts,39
+cg-83.13.0.dist-info/RECORD,,