nci-cidc-api-modules 1.2.0__py3-none-any.whl → 1.2.2__py3-none-any.whl

cidc_api/config/db.py

@@ -45,33 +45,7 @@ def get_sqlalchemy_database_uri(testing: bool = False) -> str:
         # Connect to the test database
         db_uri = environ.get("TEST_POSTGRES_URI", "fake-conn-string")
     elif not db_uri:
-        # TODO: figure out why IAM authentication causes an issue with the huge filter query
-        # db_uri = f"postgresql+pg8000://{environ.get('CLOUD_SQL_DB_USER')}:xxx@/{environ.get('CLOUD_SQL_DB_NAME')}"
-
-        secrets = get_secrets_manager(testing)
-
-        # If POSTGRES_URI env variable is not set,
-        # we're connecting to a Cloud SQL instance.
-
-        config: dict = {
-            "drivername": "postgresql",
-            "username": environ.get("CLOUD_SQL_DB_USER"),
-            "password": secrets.get(environ.get("CLOUD_SQL_DB_PASS_ID")),
-            "database": environ.get("CLOUD_SQL_DB_NAME"),
-        }
-
-        if environ.get("CLOUD_SQL_INSTANCE_NAME"):
-            socket_dir = environ.get("CLOUD_SQL_SOCKET_DIR", "/cloudsql/")
-
-            # If CLOUD_SQL_INSTANCE_NAME is defined, we're connecting
-            # via a unix socket from inside App Engine.
-            config["query"] = {"host": f'{socket_dir}{environ.get("CLOUD_SQL_INSTANCE_NAME")}'}
-        else:
-            raise RuntimeError(
-                "Either POSTGRES_URI or CLOUD_SQL_INSTANCE_NAME must be defined to connect " + "to a database."
-            )
-
-        db_uri = str(URL.create(**config).render_as_string(hide_password=False))
+        db_uri = f"postgresql+pg8000://{environ.get('CLOUD_SQL_DB_USER')}:xxx@/{environ.get('CLOUD_SQL_DB_NAME')}"
 
     assert db_uri
 
@@ -80,9 +54,7 @@ def get_sqlalchemy_database_uri(testing: bool = False) -> str:
 
 # Use SQLALCHEMY_ENGINE_OPTIONS to connect to the cloud but use uri for local db
 def cloud_connector(testing: bool = False):
-    return {}
-    # TODO: figure out IAM authentication
-    # if not testing and not environ.get("POSTGRES_URI"):
-    #    return {"creator": getconn}
-    # else:
-    #    return {}
+    if not testing and not environ.get("POSTGRES_URI"):
+        return {"creator": getconn}
+    else:
+        return {}

cidc_api/models/files/facets.py

@@ -361,6 +361,11 @@ assay_facets: Facets = {
         "colorized image": FacetConfig(["/visium/colorized.tiff"]),
         "cytassist image": FacetConfig(["/visium/cytassist.tiff"]),
     },
+    "NULISA": {
+        "Metadata": FacetConfig(["/nulisa/metadata.csv", "Metadata for NULISA run"]),
+        "NPQ File": FacetConfig(["/nulisa/npq_file.csv", "NPQ file for NULISA run"]),
+        "Raw Counts File": FacetConfig(["/nulisa/raw_counts_file.csv", "Raw counts file for NULISA run"]),
+    },
     "mIHC": {
         "Samples Report": FacetConfig(["/mihc/sample_report.csv"], "Samples report for mIHC run"),
         "Multitiffs": FacetConfig(["/mihc/multitiffs.tar.gz"], "Multi Tiffs file from mIHC run"),

cidc_api/models/models.py

@@ -531,6 +531,7 @@ class IAMException(Exception):
 EXTRA_DATA_TYPES = [
     "participants info",
     "samples info",
+    "clinical_upload",
     "file_group",
 ]
 ALL_UPLOAD_TYPES = set(
@@ -3117,7 +3118,7 @@ class DownloadableFiles(CommonColumns):
                 cls.file_purpose.label(purp_col.key),
                 func.json_agg(cls.id).label(ids_col.key),
             )
-            .group_by(cls.trial_id, cls.data_category_prefix, cls.file_purpose)
+            .group_by(cls.trial_id, type_col, purp_col)
             .alias("id_bundles")
         )
         purpose_bundles = (
@@ -3497,11 +3498,33 @@ class IngestionJobs(CommonColumns):
             .first()
         )
 
-    # TODO: figure out which users have access to which jobs
     @classmethod
     @with_default_session
     def get_open_jobs_for_user(cls, user: Users, session: Session = None) -> list["IngestionJobs"]:
-        return session.query(cls).filter(cls.status.notin_(["DRAFT"])).order_by(cls._created.desc()).all()
+        if user.role not in [CIDCRole.ADMIN.value, CIDCRole.CLINICAL_TRIAL_USER.value]:
+            return []
+        job_query = session.query(cls).filter(cls.status.notin_(["DRAFT"]))
+        if (
+            user.role != CIDCRole.ADMIN.value
+            and not session.query(Permissions)
+            .filter(
+                Permissions.granted_to_user == user.id,
+                Permissions.upload_type == "clinical_upload",
+                Permissions.trial_id == Permissions.EVERY,
+            )
+            .all()
+        ):
+            authorized_trials = (
+                session.query(Permissions)
+                .filter(
+                    Permissions.granted_to_user == user.id,
+                    Permissions.upload_type == "clinical_upload",
+                    Permissions.trial_id != Permissions.EVERY,
+                )
+                .all()
+            )
+            job_query = job_query.filter(cls.trial_id.in_(map(lambda x: x.trial_id, authorized_trials)))
+        return job_query.order_by(cls._created.desc()).all()
 
 
 class JobFileCategories(CommonColumns):
@@ -3571,3 +3594,16 @@ class FileValidationErrors(CommonColumns):
         new_error = FileValidationErrors(file_id=file_id, job_id=job_id, error_message=error_message, location=location)
         new_error.insert(session=session)
         return new_error
+
+    @classmethod
+    @with_default_session
+    def delete_by_file_ids(cls, file_ids: list[int], session: Session = None):
+        """Delete all validation errors for the given list of file_ids."""
+        if file_ids:
+            session.query(cls).filter(cls.file_id.in_(file_ids)).delete(synchronize_session=False)
+            session.commit()
+
+    @classmethod
+    @with_default_session
+    def get_errors_for_job_sorted_by_file_id(cls, job_id: int, session: Session = None) -> list["FileValidationErrors"]:
+        return session.query(cls).filter(cls.job_id == job_id).order_by(cls.file_id.asc()).all()

{nci_cidc_api_modules-1.2.0.dist-info → nci_cidc_api_modules-1.2.2.dist-info}/METADATA

@@ -1,35 +1,35 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.0
+Version: 1.2.2
 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
 Requires-Python: >=3.13
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: werkzeug~=3.1.3
-Requires-Dist: flask~=3.1.2
-Requires-Dist: flask-migrate~=4.1.0
-Requires-Dist: flask-sqlalchemy~=3.1.1
-Requires-Dist: sqlalchemy~=2.0.43
-Requires-Dist: marshmallow~=4.0.0
-Requires-Dist: marshmallow-sqlalchemy~=1.4.2
-Requires-Dist: google-cloud-storage~=3.3.0
-Requires-Dist: google-cloud-secret-manager~=2.24.0
-Requires-Dist: google-cloud-pubsub~=2.31.1
-Requires-Dist: google-cloud-bigquery~=3.36.0
-Requires-Dist: google-api-python-client~=2.179.0
-Requires-Dist: google-auth~=2.40.3
-Requires-Dist: packaging~=25.0
-Requires-Dist: pyarrow~=21.0.0
-Requires-Dist: numpy~=2.3.2
-Requires-Dist: pandas~=2.3.1
-Requires-Dist: python-dotenv~=1.1.1
-Requires-Dist: requests~=2.32.5
-Requires-Dist: jinja2~=3.1.6
-Requires-Dist: certifi~=2025.8.3
-Requires-Dist: cloud-sql-python-connector[pg8000]~=1.18.4
-Requires-Dist: nci-cidc-schemas==0.28.2
+Requires-Dist: werkzeug>=3.1.3
+Requires-Dist: flask>=3.1.2
+Requires-Dist: flask-migrate>=4.1.0
+Requires-Dist: flask-sqlalchemy>=3.1.1
+Requires-Dist: sqlalchemy>=2.0.43
+Requires-Dist: marshmallow>=4.0.0
+Requires-Dist: marshmallow-sqlalchemy>=1.4.2
+Requires-Dist: google-cloud-storage>=3.3.0
+Requires-Dist: google-cloud-secret-manager>=2.24.0
+Requires-Dist: google-cloud-pubsub>=2.31.1
+Requires-Dist: google-cloud-bigquery>=3.36.0
+Requires-Dist: google-api-python-client>=2.179.0
+Requires-Dist: google-auth>=2.40.3
+Requires-Dist: packaging>=25.0
+Requires-Dist: pyarrow>=21.0.0
+Requires-Dist: numpy>=2.3.2
+Requires-Dist: pandas>=2.3.1
+Requires-Dist: python-dotenv>=1.1.1
+Requires-Dist: requests>=2.32.5
+Requires-Dist: jinja2>=3.1.6
+Requires-Dist: certifi>=2025.8.3
+Requires-Dist: cloud-sql-python-connector[pg8000]>=1.18.4
+Requires-Dist: nci-cidc-schemas==0.28.3
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page

{nci_cidc_api_modules-1.2.0.dist-info → nci_cidc_api_modules-1.2.2.dist-info}/RECORD

@@ -1,15 +1,15 @@
 cidc_api/config/__init__.py,sha256=5mX8GAPxUKV84iS-aGOoE-4m68LsOCGCDptXNdlgvj0,148
-cidc_api/config/db.py,sha256=kbCemCDYv_zyczw-V7H2JvLCa_XeEcvXkzvF28FxADw,2862
+cidc_api/config/db.py,sha256=eFCkJDeykRIJZ25kePVjRNrZcrcKTc1s2K0yErr46LI,1683
 cidc_api/config/logging.py,sha256=abhVYtn8lfhIt0tyV2WHFgSmp_s2eeJh7kodB6LH4J0,1149
 cidc_api/config/secrets.py,sha256=jRFj7W43pWuPf9DZQLCKF7WPXf5cUv-BAaS3ASqhV_Q,1481
 cidc_api/config/settings.py,sha256=NsJbqW6Vqcz2f79xcAbk4th5tHne_I-RPCbKq_3hpz0,4427
 cidc_api/models/__init__.py,sha256=bl445G8Zic9YbhZ8ZBni07wtBMhLJRMBA-JqjLxx2bw,66
 cidc_api/models/migrations.py,sha256=gp9vtkYbA9FFy2s-7woelAmsvQbJ41LO2_DY-YkFIrQ,11464
-cidc_api/models/models.py,sha256=g6KCQLS_tFZPrQbXSjDqIMY7Wea2EgbNCHRNn8KbJLk,144114
+cidc_api/models/models.py,sha256=tpEprnBbvhTCBPTouKvctTrCtOoiyJ3R-FFy8zXQpAI,145600
 cidc_api/models/schemas.py,sha256=6IE2dJoEMcMbi0Vr1V3cYKnPKU0hv9vRKBixOZHe88s,2766
 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=WqjfqtYJgY2tBnZ598Yc0eJdQUo2slFNLyTDaqPx_DE,32318
+cidc_api/models/files/facets.py,sha256=bJChPlBHYJuDFgV1eMZkqyXE8sej7jRk2sQ2kNgE9m4,32620
 cidc_api/shared/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cidc_api/shared/auth.py,sha256=PHqmVGkqDjbmUofytVFwD_9ssgUomESl3fFtFHPwZYQ,9062
 cidc_api/shared/emails.py,sha256=HQIixEUsR8yyu7Iv8S81RjtvEQeGuzQHzBfGsWIfP7k,4961
@@ -17,8 +17,8 @@ cidc_api/shared/file_handling.py,sha256=l4wiRkVJLL7QbCoODsLx-uki6Km8QoMmUlRVnUV9
 cidc_api/shared/gcloud_client.py,sha256=ETQ34qKtO7l0svVhiHXxXewiyNjwIMgoeVcqrg-Twtk,36902
 cidc_api/shared/jose.py,sha256=-qzGzEDAlokEp9E7WtBtQkXyyfPWTYXlwYpCqVJWmqM,1830
 cidc_api/shared/rest_utils.py,sha256=RwR30WOUAYCxL7V-i2totEyeriG30GbBDvBcpLXhM9w,6594
-nci_cidc_api_modules-1.2.0.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
-nci_cidc_api_modules-1.2.0.dist-info/METADATA,sha256=XtaE-znbMraCOAvWxq4HsonVlNUrWbFBm_aLaHAwpAQ,39537
-nci_cidc_api_modules-1.2.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-nci_cidc_api_modules-1.2.0.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
-nci_cidc_api_modules-1.2.0.dist-info/RECORD,,
+nci_cidc_api_modules-1.2.2.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
+nci_cidc_api_modules-1.2.2.dist-info/METADATA,sha256=7SGLnfh5Yc0j_AgRQ1eh0VetOL5MVh_d0uOah5_C5Bw,39537
+nci_cidc_api_modules-1.2.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+nci_cidc_api_modules-1.2.2.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
+nci_cidc_api_modules-1.2.2.dist-info/RECORD,,