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UNLOCK
kubernetes
Commits
aa530ac5
Commit
aa530ac5
authored
May 26, 2021
by
Koehorst, Jasper
Browse files
envmap added
parent
c4f49f63
Pipeline
#23260
passed with stage
in 1 minute and 19 seconds
Changes
1
Pipelines
1
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Inline
Side-by-side
src/main/java/nl/munlock/kubernetes/Kubernetes.java
View file @
aa530ac5
...
...
@@ -114,7 +114,7 @@ public class Kubernetes {
private
static
void
getYamls
(
CommandOptionsKubernetes
commandOptionsKubernetes
,
Connection
connection
)
throws
JargonException
,
GenQueryBuilderException
,
JargonQueryException
,
IOException
,
ApiException
,
InterruptedException
{
// List all project turtle files...
if
(
commandOptionsKubernetes
.
project
.
contains
(
"references"
))
{
String
path
=
"/"
+
commandOptionsKubernetes
.
zone
+
"/references/genomes/bacteria%"
;
String
path
=
"/"
+
commandOptionsKubernetes
.
zone
+
"/references/genomes/bacteria%
mycoplasma%
"
;
if
(
commandOptionsKubernetes
.
reset
)
resetFailures
(
connection
,
path
);
Search
.
getAllUnprocessedReferences
(
commandOptionsKubernetes
,
connection
,
path
);
...
...
@@ -262,6 +262,16 @@ public class Kubernetes {
containerItem
.
name
(
UUID
.
randomUUID
().
toString
());
containerItem
.
image
(
"docker-registry.wur.nl/unlock/docker"
);
// Set path environment through rancher environment variable using the envFrom object
// Project (unlock) > Resources > Config > Key / Value environment
List
<
V1EnvFromSource
>
envFrom
=
new
ArrayList
<>();
V1EnvFromSource
v1EnvFromSource
=
new
V1EnvFromSource
();
V1ConfigMapEnvSource
v1ConfigMapEnvSource
=
new
V1ConfigMapEnvSource
();
v1ConfigMapEnvSource
.
setName
(
"path"
);
v1EnvFromSource
.
setConfigMapRef
(
v1ConfigMapEnvSource
);
envFrom
.
add
(
v1EnvFromSource
);
containerItem
.
setEnvFrom
(
envFrom
);
V1ResourceRequirements
resource
=
new
V1ResourceRequirements
();
// Set limits to the job
Map
<
String
,
Quantity
>
limit
=
new
HashMap
<>();
...
...
@@ -313,19 +323,19 @@ public class Kubernetes {
// Unlock mount
containerItem
.
addVolumeMountsItem
(
new
V1VolumeMount
().
name
(
"unlock"
).
mountPath
(
"/unlock"
));
// HashMap TODO make this a secret
HashMap
<
String
,
String
>
envMap
=
new
HashMap
<>();
envMap
.
put
(
"PATH"
,
"/root/.sdkman/candidates/maven/current/bin:/root/.sdkman/candidates/java/current/bin:/root/.sdkman/candidates/gradle/current/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
);
//
// HashMap TODO make this a secret
//
HashMap<String, String> envMap = new HashMap<>();
//
envMap.put("PATH", "/root/.sdkman/candidates/maven/current/bin:/root/.sdkman/candidates/java/current/bin:/root/.sdkman/candidates/gradle/current/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin");
List
<
V1EnvVar
>
env
=
new
ArrayList
();
for
(
String
key
:
envMap
.
keySet
())
{
V1EnvVar
v1EnvVar
=
new
V1EnvVar
();
v1EnvVar
.
setName
(
key
);
v1EnvVar
.
setValue
(
envMap
.
get
(
key
));
env
.
add
(
v1EnvVar
);
}
//
List<V1EnvVar> env = new ArrayList();
//
for (String key : envMap.keySet()) {
//
V1EnvVar v1EnvVar = new V1EnvVar();
//
v1EnvVar.setName(key);
//
v1EnvVar.setValue(envMap.get(key));
//
env.add(v1EnvVar);
//
}
containerItem
.
env
(
env
);
//
containerItem.env(env);
// Set the name
String
name
=
"cwl-"
+
new
File
(
yamlFile
).
getParentFile
().
getName
().
toLowerCase
().
replaceAll
(
"[_\\.]"
,
""
)
+
"-"
+
new
File
(
yamlFile
).
getName
().
toLowerCase
().
replaceAll
(
"[_\\.]"
,
""
);
...
...
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