nci-cidc-api-modules 1.1.9__py3-none-any.whl → 1.1.10__py3-none-any.whl

cidc_api/models/models.py

@@ -24,10 +24,10 @@ __all__ = [
     "with_default_session",
 ]
 
-from collections import defaultdict
 import re
 import hashlib
 import os
+from collections import defaultdict
 from datetime import datetime, timedelta
 from enum import Enum as EnumBaseClass
 from functools import wraps
@@ -149,7 +149,7 @@ def with_default_session(f):
     @wraps(f)
     def wrapped(*args, **kwargs):
         if "session" not in kwargs:
-            kwargs["session"] = app.extensions["sqlalchemy"].db.session
+            kwargs["session"] = app.extensions["sqlalchemy"].session
         return f(*args, **kwargs)
 
     return wrapped
@@ -1329,6 +1329,7 @@ class TrialMetadata(CommonColumns):
     def list(
         cls,
         session: Session,
+        user: Users,
         include_file_bundles: bool = False,
         include_counts: bool = False,
         **pagination_args,
@@ -1350,10 +1351,25 @@ class TrialMetadata(CommonColumns):
 
         # Add other subqueries/columns to include in the query
         subqueries = []
+
         if include_file_bundles:
-            file_bundle_query = DownloadableFiles.build_file_bundle_query()
+            allowed_upload_types = []
+            if user and not user.is_admin() and not user.is_nci_user():
+                permissions = Permissions.find_for_user(user.id)
+                # An 'empty' upload_type means full trial-level access
+                allowed_upload_types = [
+                    p.upload_type for p in permissions if p.upload_type
+                ]
+                logger.info(
+                    f"Restricting file bundle for user {user.id} to {allowed_upload_types=}"
+                )
+
+            file_bundle_query = DownloadableFiles.build_file_bundle_query(
+                allowed_upload_types
+            )
             columns.append(file_bundle_query.c.file_bundle)
             subqueries.append(file_bundle_query)
+
         if include_counts:
             trial_summaries: List[dict] = cls.get_summaries()
 
@@ -1369,6 +1385,7 @@ class TrialMetadata(CommonColumns):
         for subquery in subqueries:
             # Each subquery will have a trial_id column and one record per trial id
             query = query.outerjoin(subquery, cls.trial_id == subquery.c.trial_id)
+
         query = cls._add_pagination_filters(query, **pagination_args)
 
         trials = []
@@ -3136,7 +3153,9 @@ class DownloadableFiles(CommonColumns):
         return [r[0] for r in query.all()]
 
     @classmethod
-    def build_file_bundle_query(cls) -> Query:
+    def build_file_bundle_query(
+        cls, allowed_upload_types: Optional[List[str]]
+    ) -> Query:
         """
         Build a query that selects nested file bundles from the downloadable files table.
         The `file_bundles` query below should produce one bundle per unique `trial_id` that
@@ -3151,6 +3170,8 @@ class DownloadableFiles(CommonColumns):
           }
         ```
         where "type" is something like `"Olink"` or `"Participants Info"` and "purpose" is a `FilePurpose` string.
+
+        If `allowed_upload_types` is provided, the query will filter by files that only have an `upload_type` that appear in the list.
         """
         tid_col, type_col, purp_col, ids_col, purps_col = (
             literal_column("trial_id"),
@@ -3160,18 +3181,20 @@ class DownloadableFiles(CommonColumns):
             literal_column("purposes"),
         )
 
-        id_bundles = (
-            select(
-                [
-                    cls.trial_id,
-                    cls.data_category_prefix.label(type_col.key),
-                    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)
-            .alias("id_bundles")
-        )
+        id_bundles = select(
+            [
+                cls.trial_id,
+                cls.data_category_prefix.label(type_col.key),
+                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)
+
+        # Restrict files from appearing in the file bundle if the user doesn't have permissions for them
+        if allowed_upload_types:
+            id_bundles = id_bundles.filter(cls.upload_type.in_(allowed_upload_types))
+        id_bundles = id_bundles.alias("id_bundles")
+
         purpose_bundles = (
             select(
                 [

{nci_cidc_api_modules-1.1.9.dist-info → nci_cidc_api_modules-1.1.10.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.1.9
+Version: 1.1.10
 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
@@ -209,19 +209,27 @@ FLASK_APP=cidc_api.app:app flask db upgrade
 Install the [Cloud SQL Proxy](https://cloud.google.com/sql/docs/mysql/quickstart-proxy-test):
 
 ```bash
-curl -o /usr/local/bin/cloud_sql_proxy https://dl.google.com/cloudsql/cloud_sql_proxy.darwin.amd64
-chmod +x /usr/local/bin/cloud_sql_proxy
+sudo curl -o /usr/local/bin/cloud-sql-proxy https://storage.googleapis.com/cloud-sql-connectors/cloud-sql-proxy/v2.15.1/cloud-sql-proxy.darwin.amd64
+sudo chmod +x /usr/local/bin/cloud-sql-proxy
 mkdir ~/.cloudsql
-chmod 777 ~/.cloudsql
+chmod 770 ~/.cloudsql
 ```
 
 Proxy to the dev Cloud SQL instance:
 
 ```bash
-cloud-sql-proxy --unix-socket ~/.cloudsql/ nih-nci-cimac-cidc-dev2:us-east4:cidc-postgresql-dev2 &
+cloud-sql-proxy --auto-iam-authn --address 127.0.0.1 --port 5432 nih-nci-cimac-cidc-dev2:us-east4:cidc-postgresql-dev2 &
 ```
 
-In your `.env` file, comment out `POSTGRES_URI` and uncomment all environment variables prefixed with `CLOUD_SQL_`. Change CLOUD_SQL_SOCKET_DIR to contain a reference to your home directory. Restart your local API instance, and it will connect to the staging Cloud SQL instance via the local proxy.
+If you want to run the proxy alongside a postgres instance on localhost listening on 5432, change the port for the proxy to another port instead like 5433.
+If you experience auth errors, make sure your google cloud sdk is authenticated.
+
+```bash
+gcloud auth login
+gcloud auth application-default login
+```
+
+To point an API running on localhost to the remote Postgres database, edit your `.env` file and comment out `POSTGRES_URI` and uncomment all environment variables prefixed with `CLOUD_SQL_`. Change CLOUD_SQL_SOCKET_DIR to contain a reference to your home directory. Restart your local API instance, and it will connect to the staging Cloud SQL instance via the local proxy.
 
 If you wish to connect to the staging Cloud SQL instance via the postgres REPL, download and run the CIDC sql proxy tool (a wrapper for `cloud_sql_proxy`):
 

{nci_cidc_api_modules-1.1.9.dist-info → nci_cidc_api_modules-1.1.10.dist-info}/RECORD

@@ -8,7 +8,7 @@ cidc_api/csms/auth.py,sha256=25Yma2Kz3KLENAPSeBYacFuSZXng-EDgmgInKBsRyP0,3191
 cidc_api/models/__init__.py,sha256=bl445G8Zic9YbhZ8ZBni07wtBMhLJRMBA-JqjLxx2bw,66
 cidc_api/models/csms_api.py,sha256=_uB9ZoxCFxKO8ZDTxCjS0CpeQg14EdlkEqnwyAFyYFQ,31377
 cidc_api/models/migrations.py,sha256=gp9vtkYbA9FFy2s-7woelAmsvQbJ41LO2_DY-YkFIrQ,11464
-cidc_api/models/models.py,sha256=kszT6ApBOIDsRJRHiYQvWo8283Jox_x0nPuetXBeK74,126680
+cidc_api/models/models.py,sha256=71QpE6ZdLcnarzTrbckJFkCQ4cNN7WD_X-EsUXt_R-Y,127642
 cidc_api/models/schemas.py,sha256=7tDYtmULuzTt2kg7RorWhte06ffalgpQKrFiDRGcPEQ,2711
 cidc_api/models/files/__init__.py,sha256=8BMTnUSHzUbz0lBeEQY6NvApxDD3GMWMduoVMos2g4Y,213
 cidc_api/models/files/details.py,sha256=h6R0p_hi-ukHsO7HV-3Wukccp0zRLJ1Oie_JNA_7Pl0,62274
@@ -19,8 +19,8 @@ cidc_api/shared/emails.py,sha256=FXW9UfI2bCus350SQuL7ZQYq1Vg-vGXaGWmRfA6z2nM,440
 cidc_api/shared/gcloud_client.py,sha256=7dDs0crLMJKdIp4IDSfrZBMB3h-zvWNieB81azoeLO4,33746
 cidc_api/shared/jose.py,sha256=QO30uIhbYDwzPEWWJXz0PfyV7E1AZHReEZJUVT70UJY,1844
 cidc_api/shared/rest_utils.py,sha256=LMfBpvJRjkfQjCzVXuhTTe4Foz4wlvaKg6QntyR-Hkc,6648
-nci_cidc_api_modules-1.1.9.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
-nci_cidc_api_modules-1.1.9.dist-info/METADATA,sha256=nePLp9yaC9CqWH-S3tTjDTb6eCYO-5ffp_1dt4ImZJg,40824
-nci_cidc_api_modules-1.1.9.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-nci_cidc_api_modules-1.1.9.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
-nci_cidc_api_modules-1.1.9.dist-info/RECORD,,
+nci_cidc_api_modules-1.1.10.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
+nci_cidc_api_modules-1.1.10.dist-info/METADATA,sha256=WG80O_AKzmoKtYB-85vOLgy6pwduCKhngjKfaBs2S5I,41284
+nci_cidc_api_modules-1.1.10.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+nci_cidc_api_modules-1.1.10.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
+nci_cidc_api_modules-1.1.10.dist-info/RECORD,,