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fix: fixes a regex problem on groundswell manifest #9

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merged 22 commits into from
Oct 15, 2024
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382a089
fix: fixes a regex problem on groundswell manifest
justinegeffen Apr 2, 2024
220dc00
Update groundswell.yml
justinegeffen Apr 2, 2024
5fde703
Merge branch 'master' into groundswell-regex
justinegeffen Apr 5, 2024
6bbdb88
Merge branch 'master' into groundswell-regex
justinegeffen Jul 9, 2024
b5b057d
Merge branch 'master' into groundswell-regex
justinegeffen Jul 21, 2024
ae9f140
Merge branch 'master' into groundswell-regex
justinegeffen Jul 23, 2024
bc4e436
Update platform_versioned_docs/version-23.4.0/enterprise/_templates/k…
justinegeffen Aug 5, 2024
44325d0
Update platform_versioned_docs/version-23.3.0/enterprise/_templates/k…
justinegeffen Aug 5, 2024
b16a719
Merge branch 'master' into groundswell-regex
justinegeffen Aug 5, 2024
2c78567
Rename platform_versioned_docs/version-23.3.0/enterprise/_templates/k…
justinegeffen Aug 7, 2024
ae9781e
Rename platform_versioned_docs/version-23.4.0/enterprise/_templates/k…
justinegeffen Aug 7, 2024
39ee2fb
Merge branch 'master' into groundswell-regex
justinegeffen Aug 7, 2024
1188701
Merge branch 'master' into groundswell-regex
justinegeffen Aug 12, 2024
1a9f21c
Merge branch 'master' into groundswell-regex
justinegeffen Aug 13, 2024
4f00021
Merge branch 'master' into groundswell-regex
justinegeffen Aug 21, 2024
eca60f7
Merge branch 'master' into groundswell-regex
justinegeffen Aug 23, 2024
ba5cfb4
Merge branch 'master' into groundswell-regex
justinegeffen Oct 8, 2024
485c273
Merge branch 'master' into groundswell-regex
justinegeffen Oct 10, 2024
f609838
Apply suggestions from code review
justinegeffen Oct 10, 2024
2efb01d
Update groundswell.yml
justinegeffen Oct 10, 2024
c720fd7
Update groundswell.yml
justinegeffen Oct 10, 2024
a77a645
Merge branch 'master' into groundswell-regex
justinegeffen Oct 15, 2024
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Original file line number Diff line number Diff line change
@@ -0,0 +1,137 @@
---
kind: ConfigMap
apiVersion: v1
metadata:
name: tower-groundswell-cfg
data:
# Server settings
SWELL_SERVER_HOST: "0.0.0.0"
SWELL_SERVER_PORT: "8090"

# API settings
SWELL_API_TRAIN_TIMEOUT: "60"
SWELL_API_TRAIN_BATCH_SIZE: "1000"
SWELL_API_PREDICT_FRACTIONAL_CPUS: "false"

# Database settings, different from the Tower DB credentials.
# If using Amazon RDS or similar managed database services, `SWELL_DB_URL` will have the form
# SWELL_DB_URL=mysql://db1.abcdefghijkl.us-east-1.rds.amazonaws.com:3306/swell or similar
SWELL_DB_URL: mysql://<ANOTHER_DB_AND_PORT>/swell
SWELL_DB_USER: swell
SWELL_DB_PASSWORD: <YOUR GROUNDSWELL DATABASE PASSWORD>
SWELL_DB_DIALECT: mysql
---
apiVersion: v1
kind: Service
metadata:
name: groundswell
labels:
app: groundswell
spec:
selector:
app: groundswell
ports:
- name: http
port: 8090
# targetPort must match with the SWELL_SERVER_PORT in the ConfigMap above.
targetPort: 8090
---
apiVersion: apps/v1
kind: Deployment
metadata:
name: groundswell
labels:
app: groundswell
spec:
selector:
matchLabels:
app: groundswell
strategy:
type: Recreate

template:
metadata:
labels:
app: groundswell
spec:
imagePullSecrets:
- name: "cr.seqera.io"
securityContext:
fsGroup: 101

initContainers:
- name: wait-for-tower-db
image: "mysql:5.7"
command:
- 'bash'
- '-c'
- |
echo "$(date): starting check for db $TOWER_DB_URL"
# Strip initial Java connection string and options after '?' from URI
until mysqlsh --uri "$(echo $TOWER_DB_URL |cut -d'?' -f1 |sed -e 's@jdbc:\(.*\)@\1@')" -u"$TOWER_DB_USER" -p"$TOWER_DB_PASSWORD" --sql -e "SELECT VERSION()"; do
echo "$(date): see you in $SLEEP_PERIOD_SECONDS seconds"
sleep $SLEEP_PERIOD_SECONDS
done
echo "$(date): db server ready"
env:
- name: SLEEP_PERIOD_SECONDS
value: "5"
envFrom:
- configMapRef:
name: tower-backend-cfg

- name: wait-for-swell-db
image: "mysql:5.7"
command:
- 'bash'
- '-c'
- |
echo "$(date): starting check for db $SWELL_DB_URL"
# Strip initial Java connection string and options after '?' from URI
until mysqlsh --uri "$SWELL_DB_URL" -u"$SWELL_DB_USER" -p"$SWELL_DB_PASSWORD" --sql -e "SELECT VERSION()"; do
echo "$(date): see you in $SLEEP_PERIOD_SECONDS seconds"
sleep $SLEEP_PERIOD_SECONDS
done
echo "$(date): db server ready"
env:
- name: SLEEP_PERIOD_SECONDS
value: "5"
envFrom:
- configMapRef:
name: tower-groundswell-cfg

- name: migrate-db
image: "cr.seqera.io/private/nf-tower-enterprise/groundswell:0.3.3"
command: ['/opt/groundswell/bin/migrate-db.sh']
envFrom:
- configMapRef:
name: tower-groundswell-cfg
- configMapRef:
name: tower-backend-cfg

containers:
- name: groundswell
image: "cr.seqera.io/private/nf-tower-enterprise/groundswell:0.3.3"
env:
- name: MPLCONFIGDIR
value: "/tmp"
envFrom:
- configMapRef:
name: tower-backend-cfg
- configMapRef:
name: tower-groundswell-cfg
volumeMounts:
- name: tmp-volume
mountPath: /tmp/
securityContext:
capabilities:
drop:
- ALL
readOnlyRootFilesystem: true
runAsNonRoot: true
runAsUser: 101

volumes:
- name: tmp-volume
emptyDir:
sizeLimit: "1Gi"
Original file line number Diff line number Diff line change
@@ -0,0 +1,137 @@
---
kind: ConfigMap
apiVersion: v1
metadata:
name: tower-groundswell-cfg
data:
# Server settings
SWELL_SERVER_HOST: "0.0.0.0"
SWELL_SERVER_PORT: "8090"

# API settings
SWELL_API_TRAIN_TIMEOUT: "60"
SWELL_API_TRAIN_BATCH_SIZE: "1000"
SWELL_API_PREDICT_FRACTIONAL_CPUS: "false"

# Database settings, different from the tower DB credentials.
# If using Amazon RDS or similar managed database services, `SWELL_DB_URL` will have the form
# SWELL_DB_URL=mysql://db1.abcdefghijkl.us-east-1.rds.amazonaws.com:3306/swell or similar
SWELL_DB_URL: mysql://<DB_AND_PORT>/swell
SWELL_DB_USER: swell
SWELL_DB_PASSWORD: <YOUR DATABASE PASSWORD>
SWELL_DB_DIALECT: mysql
---
apiVersion: v1
kind: Service
metadata:
name: groundswell
labels:
app: groundswell
spec:
selector:
app: groundswell
ports:
- name: http
port: 8090
# targetPort must match with the SWELL_SERVER_PORT in the ConfigMap above.
targetPort: 8090
---
apiVersion: apps/v1
kind: Deployment
metadata:
name: groundswell
labels:
app: groundswell
spec:
selector:
matchLabels:
app: groundswell
strategy:
type: Recreate

template:
metadata:
labels:
app: groundswell
spec:
imagePullSecrets:
- name: "cr.seqera.io"
securityContext:
fsGroup: 101

initContainers:
- name: wait-for-tower-db
image: "mysql:8.0"
command:
- 'bash'
- '-c'
- |
echo "$(date): starting check for db $TOWER_DB_URL"
# Strip initial Java connection string and options after '?' from URI
until mysqlsh --uri "$(echo $TOWER_DB_URL |cut -d'?' -f1 |sed -e 's@jdbc:\(.*\)@\1@')" -u"$TOWER_DB_USER" -p"$TOWER_DB_PASSWORD" --sql -e "SELECT VERSION()"; do
echo "$(date): see you in $SLEEP_PERIOD_SECONDS seconds"
sleep $SLEEP_PERIOD_SECONDS
done
echo "$(date): db server ready"
env:
- name: SLEEP_PERIOD_SECONDS
value: "5"
envFrom:
- configMapRef:
name: tower-backend-cfg

- name: wait-for-swell-db
image: "mysql:8.0"
command:
- 'bash'
- '-c'
- |
echo "$(date): starting check for db $SWELL_DB_URL"
# Strip initial Java connection string and options after '?' from URI
until mysqlsh --uri "$SWELL_DB_URL" -u"$SWELL_DB_USER" -p"$SWELL_DB_PASSWORD" --sql -e "SELECT VERSION()"; do
echo "$(date): see you in $SLEEP_PERIOD_SECONDS seconds"
sleep $SLEEP_PERIOD_SECONDS
done
echo "$(date): db server ready"
env:
- name: SLEEP_PERIOD_SECONDS
value: "5"
envFrom:
- configMapRef:
name: tower-groundswell-cfg

- name: migrate-db
image: "cr.seqera.io/private/nf-tower-enterprise/groundswell:0.3.3"
command: ['/opt/groundswell/bin/migrate-db.sh']
envFrom:
- configMapRef:
name: tower-groundswell-cfg
- configMapRef:
name: tower-backend-cfg

containers:
- name: groundswell
image: "cr.seqera.io/private/nf-tower-enterprise/groundswell:0.3.3"
env:
- name: MPLCONFIGDIR
value: "/tmp"
envFrom:
- configMapRef:
name: tower-backend-cfg
- configMapRef:
name: tower-groundswell-cfg
volumeMounts:
- name: tmp-volume
mountPath: /tmp/
securityContext:
capabilities:
drop:
- ALL
readOnlyRootFilesystem: true
runAsNonRoot: true
runAsUser: 101

volumes:
- name: tmp-volume
emptyDir:
sizeLimit: "1Gi"
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