cg 83.12.0__py3-none-any.whl → 83.13.1__py3-none-any.whl

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "83.12.0"
+__version__ = "83.13.1"

cg/constants/gene_panel.py

@@ -36,6 +36,7 @@ class GenePanelMasterList(StrEnum):
     MTDNA = "mtDNA"
     NBS_M = "NBS-M"
     NEURODEG = "NEURODEG"
+    NOONAN = "NOONAN"
     NMD = "NMD"
     OMIM_AUTO = "OMIM-AUTO"
     OPTIC = "OPTIC"

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)
@@ -736,10 +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 = [
@@ -759,7 +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

@@ -761,6 +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-83.12.0.dist-info → cg-83.13.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cg
-Version: 83.12.0
+Version: 83.13.1
 Summary: Clinical Genomics command center
 Requires-Python: >=3.11,<3.13
 Classifier: Programming Language :: Python

{cg-83.12.0.dist-info → cg-83.13.1.dist-info}/RECORD

@@ -1,4 +1,4 @@
-cg/__init__.py,sha256=QYeMJF37x9RzmsTZYc1lCpGDCLcZnJkcVPsodSKqAXg,41
+cg/__init__.py,sha256=Auf_lzHvzkmKz18pBEx2Cz9EbNIaUNIG8NlM941-bIs,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
@@ -201,7 +201,7 @@ cg/constants/devices.py,sha256=qP98IxkL0N-k2hIQmQuSP-_BxGEy_c-tjIg9RyfPL-s,254
 cg/constants/encryption.py,sha256=1YzIsYHl144-yuZvr9VD_i3CrQLOXIb9qpySWzRMo8E,1422
 cg/constants/extraction.py,sha256=1ig71aBqwV2PPfXth36T3lyX2aZoQKCYyZU1noC8Y3g,372
 cg/constants/file_transfer_service.py,sha256=dU-ej77fKwLnyGLBAajE5_OY__L7mxmVTKR_ILqJtN8,134
-cg/constants/gene_panel.py,sha256=pPc0FMTqk1CJU--tt3MpJio81czPLaZcvVA40uyvkYg,2540
+cg/constants/gene_panel.py,sha256=57VBHHrOI-jL9aHtbm9BvSRAp039fqG0Ptce1Ga7kPY,2562
 cg/constants/housekeeper_tags.py,sha256=742ZAo6YdYhdZwRFOLN3HoPmLviuvfqutGlSsczaCkg,7589
 cg/constants/invoice.py,sha256=Tdd3PY_Z7wz4eSfKaTapSFlkmk_FWM1bwWMOj5D5F5Y,95
 cg/constants/lims.py,sha256=vhATu1UtIXdfPZWEu8pne3uq4ZhCAdPNJcjSotD8AE8,6559
@@ -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=m3Wnj02wOk98ozcb-s5A7TH2VyNj_34griSG4JF53ts,29592
+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=HUwzqktZ-Fil7QTGwLJl7LSOb_nty1oJnIUA_euqKFQ,42985
+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-83.12.0.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,,
+cg-83.13.1.dist-info/METADATA,sha256=r_V24qEKSCa6zy08n6UffmAAYKP7uZejbBOzVaWJUEo,4940
+cg-83.13.1.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+cg-83.13.1.dist-info/entry_points.txt,sha256=q5f47YQQGltzK_xnIq1mDopRXXEItr85Xe1BCtG-Wts,39
+cg-83.13.1.dist-info/RECORD,,