nci-cidc-api-modules 1.0.28__tar.gz → 1.0.33__tar.gz

{nci_cidc_api_modules-1.0.28/nci_cidc_api_modules.egg-info → nci_cidc_api_modules-1.0.33}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: nci_cidc_api_modules
-Version: 1.0.28
+Version: 1.0.33
 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
@@ -26,9 +26,16 @@ Requires-Dist: numpy<2,>=1.16.5
 Requires-Dist: pandas==1.5.3
 Requires-Dist: python-dotenv==0.10.3
 Requires-Dist: requests==2.32.3
-Requires-Dist: jinja2==3.1.4
+Requires-Dist: jinja2==3.1.5
 Requires-Dist: certifi==2024.7.4
-Requires-Dist: nci-cidc-schemas==0.26.37
+Requires-Dist: nci-cidc-schemas==0.26.38
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 # NCI CIDC API <!-- omit in TOC -->
 

{nci_cidc_api_modules-1.0.28 → nci_cidc_api_modules-1.0.33}/cidc_api/models/models.py

@@ -272,6 +272,13 @@ class CommonColumns(BaseModel):  # type: ignore
                 asc(sort_attribute) if sort_direction == "asc" else desc(sort_attribute)
             )
             query = query.order_by(field_with_dir)
+            if sort_field != "id":
+                # When sorting, need to guarantee unique order for offset/limit pagination to produce
+                # consistent results. Adding secondary "id" sort field to ensure unique order.
+                secondary_field_with_dir = (
+                    asc("id") if sort_direction == "asc" else desc("id")
+                )
+                query = query.order_by(secondary_field_with_dir)
 
         # Apply filter function
         query = filter_(query)
@@ -1375,6 +1382,20 @@ class TrialMetadata(CommonColumns):
                 )
                 setattr(trial, "num_samples", sample_counts.get(trial.trial_id, 0))
 
+            if include_file_bundles and hasattr(trial, "file_bundle"):
+                for assay in trial.file_bundle:
+                    size_results = {}
+                    for files_list_key in trial.file_bundle[assay]:
+                        ids = trial.file_bundle[assay][files_list_key]
+                        size_results[f"{files_list_key}_size"] = (
+                            DownloadableFiles.get_total_bytes(
+                                filter_=lambda q: q.filter(
+                                    DownloadableFiles.id.in_(ids)
+                                )
+                            )
+                        )
+                    trial.file_bundle[assay].update(size_results)
+
             trials.append(trial)
 
         return trials

{nci_cidc_api_modules-1.0.28 → nci_cidc_api_modules-1.0.33}/cidc_api/shared/emails.py

@@ -19,7 +19,7 @@ from ..config.settings import ENV, GOOGLE_ACL_DATA_BUCKET
 # - errors from CSMS in update_cidc_from_csms,
 # - errors from kicking off permissions in grant_download_permissions, and
 # - errors from implementing permissions in worker > permissions_worker
-CIDC_MAILING_LIST = "essex-alert@cimac-network.org"
+CIDC_MAILING_LIST = ["essex-alert@cimac-network.org", "mustafa.kucukkal@nih.gov"]
 
 
 def sendable(email_template):
@@ -76,7 +76,7 @@ def new_user_registration(email: str) -> dict:
     )
 
     email = {
-        "to_emails": [CIDC_MAILING_LIST],
+        "to_emails": CIDC_MAILING_LIST,
         "subject": subject,
         "html_content": html_content,
     }
@@ -110,7 +110,7 @@ def new_upload_alert(upload, full_metadata) -> dict:
     """
 
     email = {
-        "to_emails": [CIDC_MAILING_LIST],
+        "to_emails": CIDC_MAILING_LIST,
         "subject": subject,
         "html_content": html_content,
     }
@@ -152,7 +152,7 @@ def intake_metadata(
     """
 
     email = {
-        "to_emails": [CIDC_MAILING_LIST],
+        "to_emails": CIDC_MAILING_LIST,
         "subject": subject,
         "html_content": html_content,
     }

{nci_cidc_api_modules-1.0.28 → nci_cidc_api_modules-1.0.33/nci_cidc_api_modules.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: nci_cidc_api_modules
-Version: 1.0.28
+Version: 1.0.33
 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
@@ -26,9 +26,16 @@ Requires-Dist: numpy<2,>=1.16.5
 Requires-Dist: pandas==1.5.3
 Requires-Dist: python-dotenv==0.10.3
 Requires-Dist: requests==2.32.3
-Requires-Dist: jinja2==3.1.4
+Requires-Dist: jinja2==3.1.5
 Requires-Dist: certifi==2024.7.4
-Requires-Dist: nci-cidc-schemas==0.26.37
+Requires-Dist: nci-cidc-schemas==0.26.38
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 # NCI CIDC API <!-- omit in TOC -->
 

{nci_cidc_api_modules-1.0.28 → nci_cidc_api_modules-1.0.33}/nci_cidc_api_modules.egg-info/requires.txt

@@ -17,6 +17,6 @@ numpy<2,>=1.16.5
 pandas==1.5.3
 python-dotenv==0.10.3
 requests==2.32.3
-jinja2==3.1.4
+jinja2==3.1.5
 certifi==2024.7.4
-nci-cidc-schemas==0.26.37
+nci-cidc-schemas==0.26.38

{nci_cidc_api_modules-1.0.28 → nci_cidc_api_modules-1.0.33}/pyproject.toml

@@ -60,7 +60,7 @@ google-api-python-client = "2.64.0"
 pandas = "1.5.3"
 python-dotenv = "0.10.3"
 requests = "2.32.3"
-jinja2 = "3.1.4"
+jinja2 = "3.1.5"
 nci-cidc-schemas = "0.26.36"
 
 # keep the existing build step

{nci_cidc_api_modules-1.0.28 → nci_cidc_api_modules-1.0.33}/requirements.modules.txt

@@ -17,6 +17,6 @@ numpy>=1.16.5,<2
 pandas==1.5.3
 python-dotenv==0.10.3
 requests==2.32.3
-jinja2==3.1.4
+jinja2==3.1.5
 certifi==2024.7.4
-nci-cidc-schemas==0.26.37
+nci-cidc-schemas==0.26.38