Merge branch 'master' into drb-etlmap-0306

healdata.org/portal/gitops.json

@@ -166,6 +166,8 @@
       "exportToWorkspace": {
         "enabled": true,
         "manifestFieldName": "__manifest",
+        "enableExportFullMetadata": true,
+        "excludedMetadataFields": ["authz", "registration_authz", "registrant_username", "advSearchFilters", "__accessible", "commons_name", "commons_url", "commons", "frontend_uid"],
         "enableDownloadManifest": true,
         "enableDownloadZip": true,
         "downloadZipButtonText": "Download Zip",

releases/2025/03/gen3-release-notes.md

@@ -0,0 +1,132 @@
+# Core Gen3 Release 2025.03 (Cobaltite)
+## uc-cdis/cloud-automation
+
+#### New Features
+  - Add `gen3-workflow` service deployment logic and add it to `gen3 roll all` 
+    ([#2723](https://github.com/uc-cdis/cloud-automation/pull/2723))
+  - Increase support to amazon linux fence image with adding `poetry run 
+    fence-create` ([#2708](https://github.com/uc-cdis/cloud-automation/pull/2708)) 
+  - This change adds newer cost-tracking tags to workflow nodes. This will let 
+    us get more visibility into the types of costs we are incurring, as well as 
+    where they are occurring. ([#2703](https://github.com/uc-cdis/cloud-automation/pull/2703)) 
+
+#### Breaking Changes
+  - Delete unused dockerfiles for sftp, nginx-prometheus-export, and sidecar. 
+    ([#2680](https://github.com/uc-cdis/cloud-automation/pull/2680))
+
+#### Bug Fixes
+  - Fixing ES7 Logic so ES7 is the default. ([#2702](https://github.com/uc-cdis/cloud-automation/pull/2702)) 
+  - Fixing "gen3 helper test suite" to support new Aurora architecture. ([#2700](https://github.com/uc-cdis/cloud-automation/pull/2700)) 
+  - Allow gen3-user-data-library to setup database in jenkins environment. 
+    ([#2696](https://github.com/uc-cdis/cloud-automation/pull/2696))
+  - Fix mismatching parameter names in Single Table Migration Job ([#2657](https://github.com/uc-cdis/cloud-automation/pull/2657)) 
+
+#### Improvements
+  - Disable debug mode by default in `requestor` and `audit-service` ([#2723](https://github.com/uc-cdis/cloud-automation/pull/2723)) 
+  - Improve `gen3_s3_info` and `gen3_db_service_setup` logging ([#2723](https://github.com/uc-cdis/cloud-automation/pull/2723)) 
+  - update squid whitelist to add Zenodo ([#2721](https://github.com/uc-cdis/cloud-automation/pull/2721)) 
+  - We are releasing a new Amazon Linux 2023 image that is more secure. In 
+    order to do this we need to patch Paramiko so md5 is not blocked by fips. 
+    We also needed to remove some of the key exchange algorithms from the ssh 
+    config. (backwards compatible) ([#2718](https://github.com/uc-cdis/cloud-automation/pull/2718)) 
+  - Update nginx config to remove deprecated js_include (It was deprecated 
+    quite a while ago, in 0.4.0 or something) ([#2722](https://github.com/uc-cdis/cloud-automation/pull/2722)) 
+  - Add OSF [Open Science Framework](https://www.cos.io/products/osf) to 
+    whitelist ([#2711](https://github.com/uc-cdis/cloud-automation/pull/2711))
+  - Allowing "kube-setup-dicom" in the "kube roll all script" so ohif-viewer 
+    and orthanc services will be spun up. ([#2707](https://github.com/uc-cdis/cloud-automation/pull/2707)) 
+  - Make Single Table Migration Job a Priority Job so that the job doesn't get 
+    killed if its running for a long time ([#2657](https://github.com/uc-cdis/cloud-automation/pull/2657)) 
+
+## uc-cdis/data-portal
+
+#### Improvements
+  - Refactor logout popup logic to show on all pages except login page ([#1669](https://github.com/uc-cdis/data-portal/pull/1669)) 
+  - Refactor popup to have focus ([#1669](https://github.com/uc-cdis/data-portal/pull/1669)) 
+  - add aria-hidden='true' to overlooked error page ([#1669](https://github.com/uc-cdis/data-portal/pull/1669)) 
+  - improve job submission message by adding concept_id of the selected HARE 
+    population ([#1663](https://github.com/uc-cdis/data-portal/pull/1663))
+  - update expolrer config example in default config file ([#1660](https://github.com/uc-cdis/data-portal/pull/1660)) 
+
+#### New Features
+  - Improves user experience when using team projects in multiple tabs. ([#1668](https://github.com/uc-cdis/data-portal/pull/1668)) 
+
+#### Dependency Updates
+  - update guppy to 0.20.1 ([#1662](https://github.com/uc-cdis/data-portal/pull/1662)) 
+
+## uc-cdis/fence
+
+#### Bug Fixes
+  - Fix timeout when user with large passport logs in by skipping 
+    grant_from_storage. ([#1219](https://github.com/uc-cdis/fence/pull/1219))
+  - Exchange Area projects no longer cause exceptions when applied from a 
+    passport ([#1216](https://github.com/uc-cdis/fence/pull/1216))
+  - Google group sync no longer runs on login when a passport is issued. 
+    ([#1216](https://github.com/uc-cdis/fence/pull/1216))
+
+#### Improvements
+  - Add logging for discovery doc resolution, when dbgap_permissions expire 
+    from passports and when passports are cached. ([#1223](https://github.com/uc-cdis/fence/pull/1223)) 
+  - Removed unused debug logs. ([#1223](https://github.com/uc-cdis/fence/pull/1223)) 
+  - Fix typo in ClientAuthenication log ([#1221](https://github.com/uc-cdis/fence/pull/1221)) 
+
+#### Dependency Updates
+  - Bumps [werkzeug](https://github.com/pallets/werkzeug) from 3.0.4 to 3.0.6. 
+    (#1192)
+
+## uc-cdis/gen3-spark
+
+#### Improvements
+  - Utilizing `gen3` user instead of `root` for more secure containers ([#26](https://github.com/uc-cdis/gen3-spark/pull/26)) 
+
+## uc-cdis/hatchery
+
+#### New Features
+  - update Go to 1.23 ([#120](https://github.com/uc-cdis/hatchery/pull/120))
+  - address certain security updates ([#120](https://github.com/uc-cdis/hatchery/pull/120)) 
+
+#### Improvements
+  - Allow assume-role for cross-account access to pay model table ([#119](https://github.com/uc-cdis/hatchery/pull/119)) 
+  - Run a quick check before creating the subnet to make sure the instance type 
+    for nextflow is available in that AZ. ([#111](https://github.com/uc-cdis/hatchery/pull/111)) 
+
+## uc-cdis/indexd
+
+#### Bug Fixes
+  - Update script to not block md5 due to FIPs. ([#385](https://github.com/uc-cdis/indexd/pull/385)) 
+
+#### Improvements
+  - Add + Fix Parameters for Single Table IndexD Migration ([#384](https://github.com/uc-cdis/indexd/pull/384)) 
+
+## uc-cdis/sheepdog
+
+#### Improvements
+  - adding gunicorn and nginx to sheepdog and basing off our new secure python 
+    image ([#421](https://github.com/uc-cdis/sheepdog/pull/421))
+  - Support client_credentials tokens ([#425](https://github.com/uc-cdis/sheepdog/pull/425)) 
+
+## uc-cdis/sower
+
+#### New Features
+  - update Go to 1.23 ([#51](https://github.com/uc-cdis/sower/pull/51))
+  - address some security deps ([#51](https://github.com/uc-cdis/sower/pull/51))
+
+## uc-cdis/ssjdispatcher
+
+#### New Features
+  - update Go to 1.23 ([#64](https://github.com/uc-cdis/ssjdispatcher/pull/64))
+  - address certain security deps ([#64](https://github.com/uc-cdis/ssjdispatcher/pull/64)) 
+
+## uc-cdis/tube
+
+#### Dependency Updates
+  - Bumps [werkzeug](https://github.com/pallets/werkzeug) from 3.0.3 to 3.0.6. 
+    (#289)
+
+## uc-cdis/workspace-token-service
+
+#### Bug Fixes
+  - Since we are running flask behind a reverse proxy now (compared to before 
+    it was running in uwsgi) we have to add this to our code for the k8s based 
+    auth. ([#94](https://github.com/uc-cdis/workspace-token-service/pull/94))
+