nci-cidc-api-modules 1.2.19__py3-none-any.whl → 1.2.21__py3-none-any.whl

cidc_api/models/db/base_orm.py

@@ -0,0 +1,25 @@
+from typing import Self
+
+from sqlalchemy_mixins import SerializeMixin, ReprMixin
+
+from cidc_api.config.db import db
+
+
+class BaseORM(db.Model, ReprMixin, SerializeMixin):
+    __abstract__ = True
+    __repr__ = ReprMixin.__repr__
+
+    def merge(self, d: dict) -> Self:
+        """Merge keys and values from dict d into this model, overwriting as necessary."""
+        for key, value in d.items():
+            setattr(self, key, value)
+        return self
+
+    def clone(self) -> "BaseORM":
+        """Clones a SQLAlchemy ORM object, excluding primary keys."""
+        mapper = self.__mapper__
+        new_instance = self.__class__()
+        for column in mapper.columns:
+            if not column.primary_key:
+                setattr(new_instance, column.key, getattr(self, column.key))
+        return new_instance

cidc_api/models/files/facets.py

@@ -439,6 +439,11 @@ assay_facets: Facets = {
             "Analysis files for all samples run on the Olink platform in the trial.",
         ),
     },
+    "Olink HT": {
+        "Batch-Level Combined File": FacetConfig(["/olink_ht/batch_level_combined_file.xlsx"]),
+        "Study-Level Combined File": FacetConfig(["/olink_ht/study_level_combined_file.xlsx"]),
+        "Npx Run File": FacetConfig(["/olink_ht/npx_run_file.xlsx"]),
+    },
     "IHC": {
         "Images": FacetConfig(["/ihc/ihc_image."]),
         "Combined Markers": FacetConfig(["csv|ihc marker combined"]),

cidc_api/models/types.py

@@ -84,6 +84,7 @@ AssayType = Literal[
     "scRNAseq",
     "snRNA-Seq",
     "Visium",
+    "Olink HT",
 ]
 
 

cidc_api/shared/utils.py

@@ -5,4 +5,7 @@ def strip_whitespaces(df):
         else:
             return x
 
-    return df.map(stripper)
+    df.rename(columns=stripper, inplace=True)
+    df = df.map(stripper)
+
+    return df

{nci_cidc_api_modules-1.2.19.dist-info → nci_cidc_api_modules-1.2.21.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.19
+Version: 1.2.21
 Summary: SQLAlchemy data models and configuration tools used in the NCI CIDC API
 Home-page: https://github.com/NCI-CIDC/cidc-api-gae
 License: MIT license
@@ -30,7 +30,7 @@ Requires-Dist: requests>=2.32.5
 Requires-Dist: sqlalchemy>=2.0.44
 Requires-Dist: sqlalchemy-mixins~=2.0.5
 Requires-Dist: werkzeug>=3.1.3
-Requires-Dist: nci-cidc-schemas==0.28.8
+Requires-Dist: nci-cidc-schemas==0.28.9
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page

{nci_cidc_api_modules-1.2.19.dist-info → nci_cidc_api_modules-1.2.21.dist-info}/RECORD

@@ -8,10 +8,11 @@ cidc_api/models/data.py,sha256=evv9JJcW3U_g-74MgKdxtB_gGJBTRQjtnsVKwa3DzFE,638
 cidc_api/models/migrations.py,sha256=UlS5How3J4ryaRuZT6F5VQtAKikkl0LTv9MgMO_ltiQ,11161
 cidc_api/models/models.py,sha256=2ENATE2dbl93uaKSqveqAVuhv1SvxOkcw4pWDTolng0,148484
 cidc_api/models/schemas.py,sha256=6IE2dJoEMcMbi0Vr1V3cYKnPKU0hv9vRKBixOZHe88s,2766
-cidc_api/models/types.py,sha256=eDQCd-lUClxpFa3QNN7SRmcIezoqPK8IbTa9atAChn0,29912
+cidc_api/models/types.py,sha256=9dInLZ6gN39zhEe3xhBXyz2xVMr11CeE1-GCOmT_OjY,29928
+cidc_api/models/db/base_orm.py,sha256=EV78qFBcOR7spK_PhjbkpsGcmcP33AQItX61SidDa_8,813
 cidc_api/models/files/__init__.py,sha256=8BMTnUSHzUbz0lBeEQY6NvApxDD3GMWMduoVMos2g4Y,213
 cidc_api/models/files/details.py,sha256=sZkGM7iEV4-J6IDQCdiMV6KBDLbPxCOqUMaU3aY9rX8,65153
-cidc_api/models/files/facets.py,sha256=RZoe0FadRGJw8_-jzJQkc4dIVSuaYlunNrsopb2dYho,33325
+cidc_api/models/files/facets.py,sha256=BGx6FeQkK-ujCs-0Y8dUlba8uOmXgAqdY5u1EQqOnFM,33612
 cidc_api/shared/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cidc_api/shared/auth.py,sha256=PHqmVGkqDjbmUofytVFwD_9ssgUomESl3fFtFHPwZYQ,9062
 cidc_api/shared/email_layout.html,sha256=pBoTNw3ACHH-ncZFaNvcy5bXMqPwizR78usb0uCYtIc,7670
@@ -20,9 +21,9 @@ cidc_api/shared/file_handling.py,sha256=UP3KZ61Km5RNmNfk126_upKv-jGkDzpc5Pvk1s7c
 cidc_api/shared/gcloud_client.py,sha256=ovXGS2ynaBgB_23prj23H10GNN4fectiVF7Hj4LJXQk,37302
 cidc_api/shared/jose.py,sha256=-qzGzEDAlokEp9E7WtBtQkXyyfPWTYXlwYpCqVJWmqM,1830
 cidc_api/shared/rest_utils.py,sha256=RwR30WOUAYCxL7V-i2totEyeriG30GbBDvBcpLXhM9w,6594
-cidc_api/shared/utils.py,sha256=oDGC8MHxEf7MDuzWynZuE66OfNUnRZE8z7Yn2Q9kYO8,178
-nci_cidc_api_modules-1.2.19.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
-nci_cidc_api_modules-1.2.19.dist-info/METADATA,sha256=6bVrQ0WH8icbydssbIQFk5FMCoHfZXP-eGEDgfeyURo,39691
-nci_cidc_api_modules-1.2.19.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-nci_cidc_api_modules-1.2.19.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
-nci_cidc_api_modules-1.2.19.dist-info/RECORD,,
+cidc_api/shared/utils.py,sha256=FdZJiynmh6BIzWyCTcUAcUMKCAtzEyp_HLdXEticNcI,237
+nci_cidc_api_modules-1.2.21.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
+nci_cidc_api_modules-1.2.21.dist-info/METADATA,sha256=ndbMwIYgzUIcilJqNFhpJ6vBkdqiy1VjoRmxidmXf7g,39691
+nci_cidc_api_modules-1.2.21.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+nci_cidc_api_modules-1.2.21.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
+nci_cidc_api_modules-1.2.21.dist-info/RECORD,,