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europdx
k8s
cbio-on-demand
API
Commits
5e6a3241
Commit
5e6a3241
authored
Sep 05, 2019
by
Ľuboslav Pivarč
Browse files
Merge branch 'beta' into 'master'
New Cluster See merge request
!8
parents
5fcc34b4
a2442016
Pipeline
#23744
passed with stages
in 4 minutes and 10 seconds
Changes
5
Pipelines
1
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Side-by-side
.gitlab-ci.yml
View file @
5e6a3241
...
...
@@ -97,3 +97,4 @@ Dev-API Kube deploy:
only
:
refs
:
-
dev
#
cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/service/KubernetesImpl.java
View file @
5e6a3241
...
...
@@ -37,14 +37,14 @@ public class KubernetesImpl implements CBioOnDemandService {
private
V1beta1CronJob
cronJob
;
private
IdentifierCRD
identifier
;
@Value
(
"${namespace:cbio-on-demand}"
)
private
final
String
NAMESPACE
=
"cbio-on-demand"
;
private
final
String
NAMESPACE
;
private
final
String
APP_LABELS
=
"app=cbio, type=ondemand"
;
private
final
String
DB_LABELS
=
"app=cbioDB, type=ondemand"
;
public
KubernetesImpl
(
KubernetesCalls
api
,
RoutingAAI
routing
)
throws
IOException
{
public
KubernetesImpl
(
KubernetesCalls
api
,
RoutingAAI
routing
,
@Value
(
"${namespace:cbio-on-demand}"
)
String
namespace
)
throws
IOException
{
this
.
api
=
api
;
this
.
routing
=
routing
;
NAMESPACE
=
namespace
;
cronJob
=
(
V1beta1CronJob
)
Utils
.
getConfigurationFromYaml
(
"deletecronjob.yml"
);
cbioService
=
(
V1Service
)
Utils
.
getConfigurationFromYaml
(
"cbio-service.yml"
);
cbioReplicaSet
=
(
V1ReplicaSet
)
Utils
.
getConfigurationFromYaml
(
"cbio-replicaset.yml"
);
...
...
cbioondemandK8S/src/main/resources/cbio-replicaset.yml
View file @
5e6a3241
...
...
@@ -28,6 +28,20 @@ spec:
# generated by API unique for user
#instance: "1"
spec
:
tolerations
:
-
effect
:
NoSchedule
key
:
edirex
operator
:
Equal
value
:
cbio
affinity
:
nodeAffinity
:
requiredDuringSchedulingIgnoredDuringExecution
:
nodeSelectorTerms
:
-
matchExpressions
:
-
key
:
edirex
operator
:
In
values
:
-
cbio
initContainers
:
-
name
:
wait-for-db
image
:
lpivo/wait_for_db:tr2
...
...
@@ -39,7 +53,7 @@ spec:
-
name
:
dataloding
containers
:
-
name
:
cbio
image
:
registry.gitlab.ics.muni.cz:443/europdx/k8s/cbio-on-demand/data-loading:
app32a8fb32ad9831d51a829bb4583375b21ba511e1
image
:
registry.gitlab.ics.muni.cz:443/europdx/k8s/cbio-on-demand/data-loading:
master-app-97fb8c1069486ec071efbca7809303c5c5203b46
ports
:
-
name
:
http
containerPort
:
8080
...
...
@@ -48,7 +62,7 @@ spec:
# generated by API from service name
value
:
cbio-on-demand-dbpjvrw
-
name
:
IMPORT
value
:
/etc/data-loading/cbio
-
client.py
value
:
/etc/data-loading/cbio
_
client.py
-
name
:
ID
# generated by API from user request
value
:
"
4"
...
...
@@ -57,7 +71,12 @@ spec:
value
:
cbioportal
-
name
:
URL
value
:
'
test'
-
name
:
DATAHUB
valueFrom
:
configMapKeyRef
:
name
:
app
key
:
datahub
lifecycle
:
postStart
:
exec
:
command
:
[
"
python3"
,
"
/etc/data-loading/cbio
-
client.py"
]
command
:
[
"
python3"
,
"
/etc/data-loading/cbio
_
client.py"
]
cbioondemandK8S/src/main/resources/cbiodb-replicaset.yml
View file @
5e6a3241
...
...
@@ -28,6 +28,20 @@ spec:
# generated by API unique for user
#instance: "1"
spec
:
tolerations
:
-
effect
:
NoSchedule
key
:
edirex
operator
:
Equal
value
:
cbio
affinity
:
nodeAffinity
:
requiredDuringSchedulingIgnoredDuringExecution
:
nodeSelectorTerms
:
-
matchExpressions
:
-
key
:
edirex
operator
:
In
values
:
-
cbio
containers
:
-
name
:
cbio
image
:
lpivo/cbiodb:v1
...
...
k8s/deployment.yml
View file @
5e6a3241
...
...
@@ -21,6 +21,25 @@ spec:
app
:
cbio-api
type
:
ondemand
spec
:
tolerations
:
-
effect
:
NoSchedule
key
:
node-role.kubernetes.io/controlplane
operator
:
Equal
value
:
"
true"
-
effect
:
NoExecute
key
:
node-role.kubernetes.io/etcd
operator
:
Equal
value
:
"
true"
affinity
:
nodeAffinity
:
requiredDuringSchedulingIgnoredDuringExecution
:
nodeSelectorTerms
:
-
matchExpressions
:
-
key
:
node-role.kubernetes.io/controlplane
operator
:
In
values
:
-
"
true"
serviceAccountName
:
cbio-api
imagePullSecrets
:
-
name
:
temporary
containers
:
...
...
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