Release 26 01 27 (#1329)

Author: TCMeldrum

…ub/workflows/rebase-prs-with-develop.yml …ub/workflows/update-prs-with-develop.yml.github/workflows/rebase-prs-with-develop.yml renamed to .github/workflows/update-prs-with-develop.yml .github/workflows/rebase-prs-with-develop.yml renamed to .github/workflows/update-prs-with-develop.yml

@@ -1,4 +1,4 @@
-name: Rebase PRs with develop
+name: Update PRs with develop
 
 on:
   push:
@@ -7,6 +7,8 @@ on:
 
 jobs:
   sync-prs:
+    # Disabled until we can push with a PAT that has workflow scope; otherwise CI stays in "Waiting".
+    if: ${{ false }}
     runs-on: ubuntu-latest
 
     steps:
@@ -20,7 +22,9 @@ jobs:
           git config --global user.name "github-actions[bot]"
           git config --global user.email "github-actions[bot]@users.noreply.github.com"
 
-      - name: Rebase all open non-Dependabots PRs with develop branch as base
+      - name: Merge develop into all open non-Dependabot PRs
+        # TODO: Re-enable once we replace the default GITHUB_TOKEN with a PAT that has repo+workflow scopes
+        # so that downstream PR checks trigger automatically after the bot pushes merge commits.
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
@@ -32,14 +36,14 @@ jobs:
             gh pr checkout $pr
             git fetch origin develop
 
-            # Attempt rebase
-            if git rebase origin/develop; then
-              echo "PR #$pr rebased successfully. Pushing changes..."
-              git push --force-with-lease
+            # Attempt merge
+            if git merge --no-edit origin/develop; then
+              echo "PR #$pr merged successfully. Pushing changes..."
+              git push
             else
-              echo "Conflict in PR #$pr. Rebase aborted."
-              git rebase --abort
+              echo "Conflict in PR #$pr. Merge aborted."
+              git merge --abort
               # Optional: Notify author
-              gh pr comment $pr --body "⚠️ Automatic rebase failed due to conflicts. Please rebase manually."
+              gh pr comment $pr --body "⚠️ Automatic merge of \`develop\` into this PR failed due to conflicts. Please resolve the conflicts and update your branch."
             fi
           done

.gitignore

@@ -6,3 +6,5 @@ apps/backend/node_modules
 apps/frontend/src/generated
 apps/backend/generated
 .DS_Store
+documentation/.venv
+documentation/site/

apps/backend/db_patches/0202_DropUsersUsernameKey.sql

@@ -0,0 +1,11 @@
+DO
+$$
+BEGIN
+    IF register_patch('DropUsersUsernameKey.sql', 'jekabskarklins', 'Deprecate username constraint. This fix is needed for the broken integration that is underway', '2025-12-11') THEN
+        BEGIN
+            ALTER TABLE IF EXISTS public.users
+            DROP CONSTRAINT users_username_key;
+        END;
+    END IF;
+END;
+$$

apps/backend/db_patches/0204_RemoveUserColulmns.sql

@@ -0,0 +1,24 @@
+-- 0181_RemoveUserColumns.sql
+DO
+$$
+BEGIN
+    IF register_patch(
+        '0182_RemoveUserColumns2.sql',
+        'Fredrik Bolmsten',
+        'Remove gender, telephone, username, position, placeholder, birthdate and department columns from users table',
+        '2025-05-12'
+    ) THEN
+        BEGIN
+            -- now drop the unwanted columns
+            ALTER TABLE public.users
+                DROP COLUMN username,
+                DROP COLUMN gender,
+                DROP COLUMN birthdate,
+                DROP COLUMN department,
+                DROP COLUMN position,
+                DROP COLUMN telephone;
+        END;
+    END IF;
+END;
+$$
+LANGUAGE plpgsql;

apps/backend/db_patches/0205_DropTableRedeemCodes.sql

@@ -0,0 +1,16 @@
+DO
+$$
+BEGIN
+    IF register_patch(
+        '0205_DropTableRedeemCodes.sql',
+        'Yoganandan Pandiyan',
+        'Drop table redeem_codes',
+        '2026-01-21'
+    ) THEN
+        BEGIN
+           DROP TABLE IF EXISTS public.redeem_codes;
+        END;
+    END IF;
+END;
+$$
+LANGUAGE plpgsql;

apps/backend/db_patches/0206_DeleteFeatureEmailInviteLegacy.sql

@@ -0,0 +1,16 @@
+DO
+$$
+BEGIN
+    IF register_patch(
+        '0206_DeleteFeatureEmailInviteLegacy.sql',
+        'Yoganandan Pandiyan',
+        'Delete feature EMAIL_INVITE_LEGACY',
+        '2026-01-21'
+    ) THEN
+        BEGIN
+           DELETE FROM features WHERE feature_id = 'EMAIL_INVITE_LEGACY';
+        END;
+    END IF;
+END;
+$$
+LANGUAGE plpgsql;

apps/backend/db_patches/db_seeds/0002_InstrumentScientists.sql

@@ -3,26 +3,25 @@ $DO$
 BEGIN
 
   INSERT INTO users(
-    user_id, user_title, firstname, lastname, username, preferredname, oidc_sub, oauth_refresh_token, gender, birthdate, department, "position", email, 
-    telephone, created_at, updated_at, institution_id, placeholder)
-    VALUES (100, '', 'Instrument', 'Scientist1', 'instr.sci1', '-', 'instr.sci1.oauthsub', 'dummy-refresh-token', 'e2e user', '2020-10-10', 'IT', '', 'instr.sci1@local.host', '', NOW(), NOW(), 1, false);
+    user_id, user_title, firstname, lastname, preferredname, oidc_sub, oauth_refresh_token, email, created_at, updated_at, institution_id
+  )
+    VALUES (100, '', 'Instrument', 'Scientist1', '-', 'instr.sci1.oauthsub', 'dummy-refresh-token', 'instr.sci1@local.host', NOW(), NOW(), 1);
 
   INSERT INTO users(
-    user_id, user_title, firstname, lastname, username, preferredname, oidc_sub, oauth_refresh_token, gender, birthdate, department, "position", email, 
-    telephone, created_at, updated_at, institution_id, placeholder)
-    VALUES (101, '', 'Instrument', 'Scientist2', 'instr.sci2',  '-', 'instr.sci2.oauthsub', 'dummy-refresh-token', 'e2e user', '2020-10-10', 'IT', '', 'instr.sci2@local.host', '', NOW(), NOW(), 1, false);
+    user_id, user_title, firstname, lastname, preferredname, oidc_sub, oauth_refresh_token, email, created_at, updated_at, institution_id
+  )
+    VALUES (101, '', 'Instrument', 'Scientist2', '-', 'instr.sci2.oauthsub', 'dummy-refresh-token', 'instr.sci2@local.host', NOW(), NOW(), 1);
 
   -- user account with every roles except instrument scientist and user officer
   INSERT INTO users(
-    user_id, user_title, firstname, lastname, username, preferredname, oidc_sub, oauth_refresh_token, gender, birthdate, department, "position", email, 
-    telephone, created_at, updated_at, institution_id, placeholder)
-    VALUES (102, '', 'Not', 'Scientist', 'not.instr.sci', '-', 'not.instr.sci.oauthsub', 'dummy-refresh-token', 'e2e user', '2020-10-10', 'IT', '', 'not.instr.sci@local.host', '', NOW(), NOW(), 1, false);
+    user_id, user_title, firstname, lastname, preferredname, oidc_sub, oauth_refresh_token, email, created_at, updated_at, institution_id
+  )
+    VALUES (102, '', 'Not', 'Scientist', '-', 'not.instr.sci.oauthsub', 'dummy-refresh-token', 'not.instr.sci@local.host', NOW(), NOW(), 1);
 
   -- user account with experiment safety reviewer
   INSERT INTO users(
-    user_id, user_title, firstname, lastname, username, preferredname, oidc_sub, oauth_refresh_token, gender, birthdate, department, "position", email, 
-    telephone, created_at, updated_at, institution_id, placeholder)
-    VALUES (103, '', 'Experiment', 'Safety', 'experiment.safety', '-', 'experiment.safety.oauthsub', 'dummy-refresh-token', 'e2e user', '2020-10-10', 'IT', '', 'experiment.safety@local.host', '', NOW(), NOW(), 1, false);
+    user_id, user_title, firstname, lastname, preferredname, oidc_sub, oauth_refresh_token, email, created_at, updated_at, institution_id)
+    VALUES (103, '', 'Experiment', 'Safety', 'experiment.safety', 'experiment.safety.oauthsub', 'dummy-refresh-token', 'experiment.safety@local.host', NOW(), NOW(), 1);
 
   INSERT INTO role_user(
     role_id, user_id)

apps/backend/db_patches/db_seeds/0006_RedeemCodes.sql

@@ -0,0 +1,50 @@
+DO
+$DO$
+DECLARE  
+  invite_id_var1 int;
+  invite_id_var2 int;
+  invite_id_var3 int;
+  invite_id_var4 int;
+BEGIN
+
+  INSERT INTO invites (code, email, created_by, created_at, claimed_by, claimed_at, is_email_sent, expires_at, template_id) 
+  VALUES ('DAVE001', 'david@teleworm.us', 1, NOW(), NULL, NULL, false, NULL, 'user-office-registration-invitation-co-proposer');
+
+  SELECT invite_id
+  INTO invite_id_var1
+  FROM invites
+  WHERE email = 'david@teleworm.us' AND code = 'DAVE001';
+
+  INSERT INTO invites (code, email, created_by, created_at, claimed_by, claimed_at, is_email_sent, expires_at, template_id) 
+  VALUES ('BEN001', 'ben@inbox.com', 1, NOW(), NULL, NULL, false, NULL, 'user-office-registration-invitation-co-proposer');
+
+  SELECT invite_id
+  INTO invite_id_var2
+  FROM invites
+  WHERE email = 'ben@inbox.com' AND code = 'BEN001';
+
+  INSERT INTO co_proposer_claims (invite_id, proposal_pk) VALUES (invite_id_var1, 1);
+  INSERT INTO co_proposer_claims (invite_id, proposal_pk) VALUES (invite_id_var2, 1);
+
+  INSERT INTO invites (code, email, created_by, created_at, claimed_by, claimed_at, is_email_sent, expires_at, template_id) 
+  VALUES ('DAVE002', 'david@teleworm.us', 1, NOW(), NULL, NULL, false, NULL, '');
+
+  SELECT invite_id
+  INTO invite_id_var3
+  FROM invites
+  WHERE email = 'david@teleworm.us' AND code = 'DAVE002';
+
+  INSERT INTO invites (code, email, created_by, created_at, claimed_by, claimed_at, is_email_sent, expires_at, template_id) 
+  VALUES ('BEN002', 'ben@inbox.com', 1, NOW(), NULL, NULL, false, NULL, '');
+
+  SELECT invite_id
+  INTO invite_id_var4
+  FROM invites
+  WHERE email = 'ben@inbox.com' AND code = 'BEN002';
+
+  INSERT INTO co_proposer_claims (invite_id, proposal_pk) VALUES (invite_id_var3, 2);
+  INSERT INTO co_proposer_claims (invite_id, proposal_pk) VALUES (invite_id_var4, 2);
+
+END;
+$DO$
+LANGUAGE plpgsql;

apps/backend/db_patches/db_seeds/0007_CoProposersInvite.sql

@@ -1,6 +1,6 @@
 services:
   clam-antivirus:
-    image: clamav/clamav:0.104
+    image: clamav/clamav:1.5.1
     ports:
       - "3310:3310"
 
@@ -40,13 +40,13 @@ services:
       - "4500:4500"
     cap_add:
       - SYS_ADMIN
- 
+
   mockServer:
     image: mockserver/mockserver:5.13.0
     command: -logLevel ERROR -serverPort 1080
     ports:
       - 1080:1080
-  
+
   mockserver-client:
     image: "ghcr.io/userofficeproject/stfc-mockserver-client:master"
     command: sh -c "sleep 5 && node src/mockserver.js"