Merge latest changes - #3

Merged

NagasriAlava-bioc merged 271 commits into

AustralianBioCommons:config-puller-error-handlingfrom

Aug 27, 2026

This pull request is big! We're only showing the most recent 250 commits

Commits on Jun 16, 2026

update image name
markxiao
committed
c3b7a47

Commits on Jun 24, 2026

update db migration
markxiao
committed
5128e18

Commits on Jun 25, 2026

Merge branch 'master' into chore/zendesk-wrapper-service
mfshao
authored
e398117

Commits on Jun 26, 2026

Merge branch 'master' of https://github.com/uc-cdis/gen3-helm into token-blacklist-check
nss10
committed
199b09d

Commits on Jul 2, 2026

Rename `/blacklisted` to `/denylist` and deny public access for this endpoint
nss10
committed
dc4804c

Commits on Jul 6, 2026

feat(vectis): add jeg, workspace-proxy, vectis-overlays subcharts; revproxy additionalConfigs

cmlsn
authored and
m0nhawk
committed
91ba76c
updating tags

cmlsn
authored and
m0nhawk
committed
605bad4
fixing race condition

cmlsn
authored and
m0nhawk
committed
39d76e6
Update search-auth-proxy-secret.yaml for secretStoreRef

jawadqur
authored and
m0nhawk
committed
ded0d13
fix: correct image tags; add vectis DB migration Job; ExternalSecret sync-wave

cmlsn
authored and
m0nhawk
committed
86944a0
bug fixes

cmlsn
authored and
m0nhawk
committed
01ab40b
jeg fix

cmlsn
authored and
m0nhawk
committed
f312aa0
k8 api's issue fix

authored and
m0nhawk
committed
92f9437
search and value changes needed for aurora integration.

cmlsn
authored and
m0nhawk
committed
90f938e
changes to lambda urls and auth

cmlsn
authored and
m0nhawk
committed
661af35
modifying and fixing jeg bug and siem path

cmlsn
authored and
m0nhawk
committed
aca48fd
removing guppy compat.

cmlsn
authored and
m0nhawk
committed
97b42a9
adding snapshot directories for faster cheaper load

cmlsn
authored and
m0nhawk
committed
6ed0e57
feat_crossplane for siem

cmlsn
authored and
m0nhawk
committed
f8fa1c9
feat_fix error

cmlsn
authored and
m0nhawk
committed
f86bcdf
db schema change

cmlsn
authored and
m0nhawk
committed
6342d16
siem-service: set DB_SCHEMA=vectis as chart default

cmlsn
authored and
m0nhawk
committed
f6b25c9
crossplane roels for siem service

cmlsn
authored and
m0nhawk
committed
c8714dd
change to crossplane for the api gateway access.

cmlsn
authored and
m0nhawk
committed
b58cd24
troubleshooting a 401 issue

cmlsn
authored and
m0nhawk
committed
cbe7890
moving to fence arborist natively in the lambda function

cmlsn
authored and
m0nhawk
committed
f15dc24
docs: add notes for running Vectis locally with Kind configuration

craigrbarnes
authored and
m0nhawk
committed
83388cd
Test if branch pipeline works

sowmyag96
authored and
m0nhawk
committed
3b0ff77
Adding s3 monitor code

sowmyag96
authored and
m0nhawk
committed
6ad6e9a
Adding s3 monitor code

sowmyag96
authored and
m0nhawk
committed
aa35f8c
Adding jeg file

sowmyag96
authored and
m0nhawk
committed
3d16f75
Adding jeg file

sowmyag96
authored and
m0nhawk
committed
a354f63
fix(charts): align common deps and bump chart versions for ct

cmlsn
authored and
m0nhawk
committed
7d3d2c5
fix(gen3): align funnel and revproxy dependency versions

cmlsn
authored and
m0nhawk
committed
923bae9
fix(vectis-overlays): align common dependency version

cmlsn
authored and
m0nhawk
committed
b80e0f0
fix(workspace-proxy): align common dependency version

cmlsn
authored and
m0nhawk
committed
f4cd147
ci(ct): set target-branch to feat_vectis for PR linting

cmlsn
authored and
m0nhawk
committed
0cef349
fix(charts): bump jeg/vectis-overlays/workspace-proxy versions for ct

cmlsn
authored and
m0nhawk
committed
d4de709
chore(vectis-overlays): fix yaml comment spacing

cmlsn
authored and
m0nhawk
committed
336336b
change target branch in ct.yaml
m0nhawk
authored
64f5184
put email in secret
mfshao
committed
bef96dc
remove env
mfshao
committed
9a031bd
update env
mfshao
committed
df197a9

Commits on Jul 7, 2026

integrate funnel helm chart
matthewpeterkort
committed
1c8d8b2
Change target branch from feat/vectis-merge to master
m0nhawk
authored
c426b0b
Fix typo
nss10
authored
9a33ce8
bump revproxy chart version to 0.1.62
m0nhawk
authored
490319a
add external secret
mfshao
committed
71647b3
Change `/token/denylist` to `/token/denylisted`
nss10
committed
837a625

Commits on Jul 8, 2026

Update funnel chart version and remove funnel-chart-check -- irrelevant since funnel as a dependent chart no longer exists.
nss10
committed
0c263eb
enable linklocal for audit and dashboard
ajoaugustine
committed
38f1239
Merge pull request #638 from uc-cdis/fix/networkpolicies-dashboard
ajoaugustine
authored
804e9d3
upadte external secret ref
mfshao
committed
0506d42
Update funnel values.yaml with Gen3 based installation overrides
nss10
committed
ce78e71
Fix helm values error + indentation
nss10
committed
00a8731
Merge branch 'master' of https://github.com/uc-cdis/gen3-helm into copy/pr-635
nss10
committed
5818911
Set TEST_REPO_BRANCH to `chore/fix_setup_script_for_funnel` in integration tests
nss10
committed
ca6b178
upadte external secret ref
mfshao
committed
58e8632
update fence config
markxiao
committed
7aee14d
fix typo
mfshao
committed
26af3cb
Add tag, and update yaml indentation
nss10
committed
a518a9f
Fix lint checks
nss10
committed
48ad388
fix typo
mfshao
committed
9c58a7a

Commits on Jul 9, 2026

Postgres creds template update
nss10
committed
da89eaa
fix secret
mfshao
committed
10b24cb
fix secret
mfshao
committed
ee039b8
fix secret
mfshao
committed
5f43d36
trigger chart update
mfshao
committed
60dedad
trigger chart update
mfshao
committed
5e7c869
fix: requestor service account
flashguerdon
committed
f1e706f
feat(pgvector): use the image built from docker-bitnami-pgvector repo
jbarno
committed
327e09c
fix(repo): quay pub
jbarno
committed
4f30c9d
feat(pgvector): let it pull from quay
jbarno
committed
021bf4c
fix(pg): daticulocale rename
jbarno
committed
5a90c5b
feat(install): install the extension
jbarno
committed
00d880b
fix(dbCreate): need that on
jbarno
committed
ccaad08
fix(local): localhost
jbarno
committed
cf0e202
fix(registry): its all getting concatenated anyway
jbarno
committed
9b4cce6
feat(repository): less config, tag on seperate line is nice though
jbarno
committed
27892c1
Revert "feat(repository): less config, tag on seperate line is nice though"
jbarno
committed
6008f98
chore(versions): reverting borked things
jbarno
committed
5499d0e
Empty commit to trigger CI
nss10
committed
fca3561
Merge branch 'master' into feat/vectis-merge
m0nhawk
authored
4cbc8c6
Merge pull request #639 from AustralianBioCommons/external-secrets-v1-fix
emalinowski
authored
c9d792f
Merge pull request #633 from uc-cdis/feat/vectis-merge
m0nhawk
authored
831acb6
Bumped versions
emalinowski
committed
3b6f1d6
update fence config
markxiao
committed
3856b25
Bumped versions
emalinowski
committed
e032bc1
Update worker-pv.yaml
nss10
committed
53fade2
Bumped versions
emalinowski
committed
9d14a77
Merge branch 'master' into version-bump
emalinowski
authored
fce0cb9
Bumped versions
emalinowski
committed
c9e4964
Bumped versions
emalinowski
committed
6977ebf
Add ConfigMapTemplate
nss10
committed
bace66d
Bumped versions
emalinowski
committed
e4a71a1
Add Missing worker-configmap
nss10
committed
69104e3
Merge pull request #640 from uc-cdis/version-bump
emalinowski
authored
7554b9a
Merge branch 'master' into feat/docker-bitnami-pgvector-default
jbarno
authored
0b16805
Merge branch 'master' of https://github.com/uc-cdis/gen3-helm into token-blacklist-check
nss10
committed
91b5e03
chor(bump): version bump after the version bump
jbarno
committed
df35d5b
Temporarily point funnel to local funnel image
nss10
committed
8aa3c99
feat(PR): heed comments
jbarno
committed
0b5e7bf
Merge branch 'master' of https://github.com/uc-cdis/gen3-helm into copy/pr-635
nss10
committed
995ed00
Update funnel image name
nss10
committed
0b4fe27
Targetting a build tag based off of OHSU's latest `develop` branch
nss10
committed
dd2c334

Commits on Jul 10, 2026

Merge pull request #619 from uc-cdis/feat/docker-bitnami-pgvector-default
jbarno
authored
513864b
update revproxy conf
mfshao
committed
fd44dbf
Add Fence URL in manifest service's deployment
nss10
committed
9829764
Update common chart version
nss10
committed
cf140aa
update ports
mfshao
committed
a7c341c
merge master
mfshao
committed
d3fc8e3
netpolicy updates for fence
ajoaugustine
committed
89506cc
fix port
mfshao
committed
e913653
Merge pull request #641 from uc-cdis/chore/add_FENCE_URL_manifestservice
nss10
authored
ed8b911
Merge branch 'master' into fix/netplicies-fence
ajoaugustine
authored
226f88c
bump chart versions
ajoaugustine
committed
31fe320
Use AUTHZ_AUDIENCE for sheepdog' audience field
nss10
committed
67f1224
bump chart versions
ajoaugustine
committed
613b383
bump gen3 chart version
ajoaugustine
committed
c619709
Merge pull request #643 from uc-cdis/fix/netplicies-fence
ajoaugustine
authored
1b5f9c7
Merge branch 'master' of https://github.com/uc-cdis/gen3-helm into chore/update_sheepdog_authz_audience
nss10
committed
47ef8e2
Sheepdog version bump
nss10
committed
754ad00
gen3 version bump
nss10
committed
dfc2973
Merge branch 'master' of https://github.com/uc-cdis/gen3-helm into copy/pr-635
nss10
committed
d54df2c
Remove test repo branch
nss10
committed
2051194
Merge pull request #644 from uc-cdis/chore/update_sheepdog_authz_audience
nss10
authored
171bb16

Commits on Jul 13, 2026

Merge branch 'master' into fix/add-requestor-g3auto
flashguerdon
committed
623c30f
chore: requestor chart bump
flashguerdon
committed
9e5dc05
chore: version bump
flashguerdon
committed
f34010b
Added EFS csi driver to cluster-level-resources
emalinowski
committed
3548cf1
Rename blacklisted to denylisted
nss10
committed
81de6cd
Merge branch 'master' of https://github.com/uc-cdis/gen3-helm into token-blacklist-check
nss10
committed
28b3270
rename secret name
mfshao
committed
0e6de8a
merge master
mfshao
committed
d5db035
update action
mfshao
committed
56b0663
Revert "update action"
mfshao
committed
52e9cdc
fix chart
mfshao
committed
62f71f7
fix chart
mfshao
committed
f03bd5a
fix chart
mfshao
committed
b1f5cc4
Merge pull request #616 from uc-cdis/token-blacklist-check
nss10
authored
a2545cd

Commits on Jul 14, 2026

Use current helm branch to run kind tests
nss10
committed
2c82da1
Merge branch 'master' of https://github.com/uc-cdis/gen3-helm into copy/pr-635
nss10
committed
f525178
Merge branch 'master' into chore/zendesk-wrapper-service
mfshao
authored
daf0e96
trigger hook
mfshao
committed
c44c6e9
trigger hook
mfshao
committed
bd3e4a3
Merge pull request #612 from uc-cdis/chore/zendesk-wrapper-service
mfshao
authored
699d44c

Commits on Jul 17, 2026

Add S3Files configuration to Funnel
paulineribeyre
committed
dedfbc9
update zendesk secret names
mfshao
committed
2167f6d

Commits on Jul 20, 2026

Commits on Jul 21, 2026

Merge pull request #652 from uc-cdis/chore/zendesk-oauth
mfshao
authored
9eea32c
add envs
markxiao
committed
219c959

Commits on Jul 22, 2026

Merge pull request #654 from flashguerdon/fix/add-requestor-g3auto
emalinowski
authored
9239eda
Updated chart version
emalinowski
committed
0715e15
Merge branch 'master' into fix/add-requestor-g3auto
emalinowski
authored
76cd4ac
Updated chart version
emalinowski
committed
52df1bb
Add IAM permissions for gen3-workflow
nss10
committed
f9154b9
Revert cluster level changes
nss10
committed
156ddd2
Merge branch 'master' of https://github.com/uc-cdis/gen3-helm into feat/add_gen3wf_s3files_iam_perms
nss10
committed
ea5733d
Update gen3 chart version
nss10
committed
2856d2e
Add event bridge rules for gen3wf
nss10
committed
408fde0
feat(revproxy): add customNginxConfigs to extraServices for per-service nginx directives
jawadqur
committed
ec1c87e

Commits on Jul 23, 2026

Add storageType config variable and DeleteObjectVersion permission
nss10
committed
863665f
Update config variable
nss10
committed
d414bb8
fix root context
ajoaugustine
committed
96ce177
Merge pull request #657 from uc-cdis/feature/custom-nginx-configs-extra-services
jawadqur
authored
4ee8973
Add security context where it was missing
ajoaugustine
committed
9f3b9cc
Merge branch 'master' into fix/pass-root-context-etl
ajoaugustine
authored
96de2a8
Merge branch 'master' into feat/add_gen3wf_s3files_iam_perms
nss10
authored
aabc7ac
Bump gen3 chart version
nss10
committed
b74d49e
Merge pull request #660 from uc-cdis/feat/add-security-context
ajoaugustine
authored
bca4031
Merge branch 'master' of https://github.com/uc-cdis/gen3-helm into feat/add_gen3wf_s3files_iam_perms
nss10
committed
678ca6b
gen3 version bump
nss10
committed
4f0cabb
Merge pull request #656 from uc-cdis/feat/add_gen3wf_s3files_iam_perms
nss10
authored
873ca39
bump charts
ajoaugustine
committed
6a6fba8
bump charts
ajoaugustine
committed
aa7c3e3
Merge branch 'master' into fix/pass-root-context-etl
ajoaugustine
authored
73923fe
bump charts
ajoaugustine
committed
29eb51f
Merge pull request #659 from uc-cdis/fix/pass-root-context-etl
ajoaugustine
authored
247f64e
move `storage` to `Kubernetes.Storage` and remove unused fields + Update worker-pv with right mountOptions
nss10
committed
0223982

Commits on Jul 24, 2026

[COPY #635] integrate funnel helm chart (#637)
nss10
authored
c17a15d

Commits on Jul 27, 2026

Merge branch 'master' into fix/add-requestor-g3auto
emalinowski
authored
054cdd6

Commits on Jul 28, 2026

Commits on Jul 30, 2026

Commits on Jul 31, 2026

Merge branch 'master' of https://github.com/uc-cdis/gen3-helm into chore/add_eksSGNames_gen3wf
nss10
committed
49ec4d1
Version bump gen3-workflow
nss10
committed
2ad1417
Merge pull request #663 from uc-cdis/chore/add_eksSGNames_gen3wf
nss10
authored
3f37055
Merge branch 'master' of https://github.com/uc-cdis/gen3-helm into funnel-s3files
nss10
committed
7cd575a
Add s3:ListBucketVersions to crossplane.yaml
paulineribeyre
committed
8da5d4f
Merge pull request #665 from uc-cdis/funnel-s3files
nss10
authored
fe42678
Update efs-csi-driver.yaml
emalinowski
authored
1e77307

Commits on Aug 4, 2026

feat(config): let configuration get passed through for cert-manager
jbarno
committed
3a12e75
fix(syntax): nindent at the end
jbarno
committed
9ed3c1d
Merge pull request #667 from uc-cdis/feat/configure_cert_manager
emalinowski
authored
83e5a39
Merge remote-tracking branch 'origin/master' into feat/add-gen3-embeddings
markxiao
committed
a06f4bd
Update efs-csi-driver.yaml
emalinowski
authored
1e4cc55
update
markxiao
committed
8dd4efa

Commits on Aug 5, 2026

Merge branch 'master' into feat/efs-csi-driver
emalinowski
authored
0dcb6d6
Bumped chart version
emalinowski
committed
b59f470
update
markxiao
committed
b1589eb
version bump
markxiao
committed
e3ec67a
bump more versions
markxiao
committed
cf02da5

Commits on Aug 7, 2026

Merge pull request #646 from uc-cdis/feat/efs-csi-driver
emalinowski
authored
a46820e
Merge branch 'master' into feat/add-gen3-embeddings
Avantol13
authored
e57a4ef
update
markxiao
committed
3730409

Commits on Aug 10, 2026

Commits on Aug 11, 2026

Fix funnel 'replicas' to use configured value (#674)
paulineribeyre
authored
1c8bf69
fix(BDC-1250): Adds default preferred_type for DRS 1.5
k-burt-uch
committed
a338503
Bumping Gen3 version
k-burt-uch
committed
fbbd620
Merge pull request #671 from uc-cdis/fix/drs_1-5_fixes
k-burt-uch
authored
319108a
Merge branch 'master' into fix/gen3-embeddings-push-secret
jawadqur
committed
44c7614
Merge pull request #672 from uc-cdis/fix/gen3-embeddings-push-secret
jawadqur
authored
af7fed0
feat(ci): derive chart versions from git tags
jawadqur
committed
dbf7279
feat: freeze chart versions in git, resolve them at release time
jawadqur
committed
d5b24e0

Commits on Aug 12, 2026

Merge pull request #673 from uc-cdis/feat/frozen-chart-versions
jawadqur
authored
e4b45b2

Commits on Aug 13, 2026

Commits on Aug 18, 2026

Commits on Aug 19, 2026

Commits on Aug 20, 2026

Commits on Aug 21, 2026

add GEN3_ZENDESK_BRAND_ID to zendesk wrapper
mfshao
authored
381ce1d
Merge branch 'master' into feat/karpenter-interruption-queue
ajoaugustine
authored
15ca25f
Update Chart.yaml
ajoaugustine
authored
367ebf6
Pick external secret version from values.yaml
nss10
committed
4c7bf77
Merge pull request #613 from uc-cdis/feat/karpenter-interruption-queue
ajoaugustine
authored
ca583a4
Merge branch 'master' into chore/ext_secrets_funnel
krishnaa05
authored
0213e7d
Merge branch 'master' into mfshao-patch-1
mfshao
authored
f335868
Merge pull request #687 from uc-cdis/chore/ext_secrets_funnel
jbarno
authored
95206b0
Merge branch 'master' into mfshao-patch-1
mfshao
authored
b79f448
Merge pull request #686 from uc-cdis/mfshao-patch-1
mfshao
authored
42cc46b

Commits on Aug 25, 2026

feat(observability): pyroscope
Avantol13
committed
f01cf02