diff --git a/cbioondemandK8S/pom.xml b/cbioondemandK8S/pom.xml
index 1e04bb2d9c211be3136e71ba8d8b4f906cf20562..0b65b9a600a4a3b6bdcfa8c22db7256049d152a5 100644
--- a/cbioondemandK8S/pom.xml
+++ b/cbioondemandK8S/pom.xml
@@ -59,6 +59,13 @@
</dependency>
+ <dependency>
+ <groupId>org.projectlombok</groupId>
+ <artifactId>lombok</artifactId>
+ <version>1.18.10</version>
+ <scope>provided</scope>
+ </dependency>
+
</dependencies>
<build>
diff --git a/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/KubernetesException.java b/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/KubernetesException.java
new file mode 100644
index 0000000000000000000000000000000000000000..7dcd08e1f1eeaf0048139a6ec8b3b36d9acca445
--- /dev/null
+++ b/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/KubernetesException.java
@@ -0,0 +1,25 @@
+package cz.muni.ics.edirex.cbioondemandK8S;
+
+public class KubernetesException extends RuntimeException {
+ private String kubernetesException;
+
+ public KubernetesException(String s, String kubernetesException) {
+ super(s);
+ this.kubernetesException = kubernetesException;
+ }
+
+ public KubernetesException(String s, Throwable throwable, String kubernetesException) {
+ super(s, throwable);
+ this.kubernetesException = kubernetesException;
+ }
+
+ public KubernetesException(Throwable throwable, String kubernetesException) {
+ super(throwable);
+ this.kubernetesException = kubernetesException;
+ }
+
+ public KubernetesException(String s, Throwable throwable, boolean b, boolean b1, String kubernetesException) {
+ super(s, throwable, b, b1);
+ this.kubernetesException = kubernetesException;
+ }
+}
diff --git a/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/api/V2.java b/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/api/V2.java
index 39397914d74a7682fcfd63d12197c0faa4c000d4..ec9de9ddeded12fe26625fdec326ad152602095b 100644
--- a/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/api/V2.java
+++ b/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/api/V2.java
@@ -1,11 +1,11 @@
package cz.muni.ics.edirex.cbioondemandK8S.api;
-import cz.muni.ics.edirex.cbioondemandK8S.model.InitialBody;
-import cz.muni.ics.edirex.cbioondemandK8S.model.Instance;
-import cz.muni.ics.edirex.cbioondemandK8S.model.InstanceExtend;
-import cz.muni.ics.edirex.cbioondemandK8S.model.InstanceId;
-import cz.muni.ics.edirex.cbioondemandK8S.model.User;
-import cz.muni.ics.edirex.cbioondemandK8S.service.CBioOnDemandService;
+import cz.muni.ics.edirex.cbioondemandK8S.model.v2.InstanceId;
+import cz.muni.ics.edirex.cbioondemandK8S.model.v2.User;
+import cz.muni.ics.edirex.cbioondemandK8S.model.v2.CbioDemand;
+import cz.muni.ics.edirex.cbioondemandK8S.model.v2.Instance;
+import cz.muni.ics.edirex.cbioondemandK8S.model.v2.InstanceDTO;
+import cz.muni.ics.edirex.cbioondemandK8S.service.v2.CBioOnDemandService;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.DeleteMapping;
@@ -21,8 +21,8 @@ import java.util.List;
@RestController
@RequestMapping("/v2")
public class V2 {
- private final String cbiood = "/cbioondemand";
- private final String cbioods = "/cbioondemands";
+ private final String cbio = "/cbioondemand";
+ private final String allCbio = "/cbioondemands";
private CBioOnDemandService cBioOnDemand;
@@ -30,40 +30,38 @@ public class V2 {
this.cBioOnDemand = cBioOnDemand;
}
- @PostMapping(cbiood)
- public ResponseEntity createCbioOnDemand(@RequestBody InitialBody demand){
+ @PostMapping(cbio)
+ public ResponseEntity createCbioOnDemand(@RequestBody CbioDemand demand){
Instance instance = cBioOnDemand.create(demand);
if(instance == null)
return new ResponseEntity<>(HttpStatus.SERVICE_UNAVAILABLE);
return new ResponseEntity<>(instance , HttpStatus.OK);
}
- @GetMapping(cbiood)
+ @GetMapping(cbio)
public ResponseEntity statusCbioOnDemand(InstanceId id){
Instance instance = cBioOnDemand.status(id.getInstance());
- if(instance == null)
- return new ResponseEntity<>(HttpStatus.BAD_REQUEST);
return new ResponseEntity<>(instance, HttpStatus.OK);
}
- @DeleteMapping(cbiood)
+ @DeleteMapping(cbio)
public ResponseEntity removeCbioOnDemand(InstanceId id){
if(!cBioOnDemand.remove(id.getInstance()))
return new ResponseEntity<>(HttpStatus.INTERNAL_SERVER_ERROR);
return new ResponseEntity<>(HttpStatus.OK);
}
- @PutMapping(cbiood)
- public ResponseEntity extendCbioOnDemand(@RequestBody InstanceExtend extend){
- Instance instance = cBioOnDemand.extend(extend.getInstance());
+ @PutMapping(cbio)
+ public ResponseEntity extendCbioOnDemand(@RequestBody InstanceDTO extend){
+ Instance instance = cBioOnDemand.extend(extend);
if (instance == null)
return new ResponseEntity<>(HttpStatus.INTERNAL_SERVER_ERROR);
return new ResponseEntity(HttpStatus.OK);
}
- @GetMapping(cbioods)
+ @GetMapping(allCbio)
public ResponseEntity listInstancesForUser(User user){
List<Instance> instances = cBioOnDemand.listInstancesForUser(user);
if (instances == null){
diff --git a/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/model/v2/CbioDemand.java b/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/model/v2/CbioDemand.java
index 199fdbb7d0530b7d3aea7b7a4492a09a7e721407..1bf79f789d64ac8a8fc463341ca0971b82460be1 100644
--- a/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/model/v2/CbioDemand.java
+++ b/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/model/v2/CbioDemand.java
@@ -1,10 +1,22 @@
package cz.muni.ics.edirex.cbioondemandK8S.model.v2;
import cz.muni.ics.edirex.cbioondemandK8S.model.User;
+import lombok.AllArgsConstructor;
+import lombok.Data;
+import lombok.NoArgsConstructor;
+import lombok.NonNull;
+import java.time.LocalDateTime;
+
+
+@Data
+@AllArgsConstructor
+@NoArgsConstructor
public class CbioDemand {
+ @NonNull
private User user;
- private String datahuList;
+ @NonNull
+ private String datahubList;
private String name;
private String description;
}
diff --git a/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/model/v2/Instance.java b/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/model/v2/Instance.java
index 5ca58bda488f16a6d43ac004d858b059e7e99ead..bf565d0f09586bc150ba138869cc82aa77c68efa 100644
--- a/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/model/v2/Instance.java
+++ b/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/model/v2/Instance.java
@@ -1,62 +1,37 @@
package cz.muni.ics.edirex.cbioondemandK8S.model.v2;
+import lombok.AccessLevel;
+import lombok.Data;
+import lombok.NoArgsConstructor;
+import lombok.NonNull;
+
+import java.time.LocalDateTime;
+
+/**
+ * Class representing cBioPortal instance in k8s. Using in response of [Get, Post] methods
+ */
+@Data
+@NoArgsConstructor(access = AccessLevel.PROTECTED)
public class Instance {
+ @NonNull
private String id;
+ @NonNull
private User user;
+ @NonNull
private long secondsToExpire;
+ @NonNull
private String url;
+ @NonNull
private Status status;
-
- public Instance(String id, User user, long secondsToExpire, String url, Status status) {
- this.id = id;
- this.user = user;
- this.secondsToExpire = secondsToExpire;
- this.url = url;
- this.status = status;
- }
-
- public long getSecondsToExpire() {
- return secondsToExpire;
- }
-
- public void setSecondsToExpire(long secondsToExpire) {
- this.secondsToExpire = secondsToExpire;
- }
-
- public String getId() {
- return id;
- }
-
- public void setId(String id) {
- this.id = id;
- }
-
- public User getUser() {
- return user;
- }
-
- public void setUser(User user) {
- this.user = user;
- }
-
-
- public String getUrl() {
- return url;
- }
-
- public void setUrl(String url) {
- this.url = url;
- }
-
- public Status getStatus() {
- return status;
- }
-
- public void setStatus(Status status) {
- this.status = status;
- }
-
- public void fillReport(long timeToExpire, Status status){
+ @NonNull
+ private LocalDateTime creationTime;
+
+ /**
+ * Sets time to expire and Status fields
+ * @param timeToExpire of instance
+ * @param status of instance
+ */
+ public void fillReport(long timeToExpire, @NonNull Status status){
secondsToExpire = timeToExpire;
this.status = status;
}
diff --git a/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/model/v2/InstanceDTO.java b/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/model/v2/InstanceDTO.java
new file mode 100644
index 0000000000000000000000000000000000000000..d95ebebb25341804c8e62d122141c5eeae38bdda
--- /dev/null
+++ b/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/model/v2/InstanceDTO.java
@@ -0,0 +1,11 @@
+package cz.muni.ics.edirex.cbioondemandK8S.model.v2;
+
+import lombok.RequiredArgsConstructor;
+
+/**
+ * Class representing cBioPortal instance in k8s. Using in request of Put method.
+ */
+@RequiredArgsConstructor
+public class InstanceDTO extends Instance {
+
+}
diff --git a/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/model/v2/InstanceExtend.java b/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/model/v2/InstanceExtend.java
index e20515dddc3c4d6ec49b2d42c2493b99d7f0727d..e7af774d9f06d99ff1ff76919bd95b8106b8e4fd 100644
--- a/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/model/v2/InstanceExtend.java
+++ b/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/model/v2/InstanceExtend.java
@@ -55,7 +55,5 @@ public class InstanceExtend {
return Objects.hash(getId(), getUser(), getTimeToExtend());
}
- public Instance getInstance(){
- return new Instance(id, user, timeToExtend , null , null);
- }
+
}
diff --git a/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/model/v2/InstanceId.java b/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/model/v2/InstanceId.java
index 393d5640acd092a6adfb4f6ee1f25d6df9367f0c..c02924fdae1279976b37991dfb46c19493c77c3c 100644
--- a/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/model/v2/InstanceId.java
+++ b/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/model/v2/InstanceId.java
@@ -43,8 +43,4 @@ public class InstanceId {
public int hashCode() {
return Objects.hash(getId(), getUser());
}
-
- public Instance getInstance(){
- return new Instance(id, user, 0 , null , null);
- }
}
diff --git a/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/service/v2/CBioOnDemandService.java b/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/service/v2/CBioOnDemandService.java
index 69eb197324025a20e21295a52c2e0e62cc837a39..32b3cf68d5fd4dca3c976065194ad1d28ba6b180 100644
--- a/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/service/v2/CBioOnDemandService.java
+++ b/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/service/v2/CBioOnDemandService.java
@@ -1,19 +1,20 @@
package cz.muni.ics.edirex.cbioondemandK8S.service.v2;
-import cz.muni.ics.edirex.cbioondemandK8S.model.InitialBody;
-import cz.muni.ics.edirex.cbioondemandK8S.model.Instance;
-import cz.muni.ics.edirex.cbioondemandK8S.model.User;
+
+import cz.muni.ics.edirex.cbioondemandK8S.model.v2.CbioDemand;
+import cz.muni.ics.edirex.cbioondemandK8S.model.v2.Instance;
+import cz.muni.ics.edirex.cbioondemandK8S.model.v2.User;
import java.util.List;
public interface CBioOnDemandService {
/**
- * Creates CbioPortal
- * @param demand which request CbioPortal
+ * Creates CbioPortal. Transactional (If something fails, the state of cluster will not be modified)
+ * @param cbioDemand which request CbioPortal
* @return Instance object for handling other requests
*/
- Instance create(InitialBody demand);
+ Instance create(CbioDemand cbioDemand);
/**
* Fill status of given instance
diff --git a/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/service/v2/KubernetesCalls.java b/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/service/v2/KubernetesCalls.java
index 6d9cc4ee52e370610542167722bfa7700c4ef572..46a52da42447caefdf36375aada8d7266a46d226 100644
--- a/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/service/v2/KubernetesCalls.java
+++ b/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/service/v2/KubernetesCalls.java
@@ -10,24 +10,24 @@ import java.util.List;
public interface KubernetesCalls {
- V1ReplicaSet createReplicaSet(V1ReplicaSet replicaSet, String namespace);
- V1beta1CronJob createCroneJob(V1beta1CronJob cronJob, String namespace);
- V1Service createService(V1Service service, String namespace);
- IdentifierCRD createIdentifier(IdentifierCRD identifier, String namespace);
+ V1ReplicaSet createReplicaSet(V1ReplicaSet replicaSet);
+ V1beta1CronJob createCroneJob(V1beta1CronJob cronJob);
+ V1Service createService(V1Service service);
+ IdentifierCRD createIdentifier(IdentifierCRD identifier);
- boolean deleteReplicaSet(String replicaSetName, String namespace);
- boolean deleteCroneJob(String cronJobName, String namespace);
- boolean deleteService(String serviceName, String namespace);
- boolean deleteIdentifier(String identifierName, String namespace);
+ boolean deleteReplicaSet(String replicaSetName);
+ boolean deleteCroneJob(String cronJobName);
+ boolean deleteService(String serviceName);
+ boolean deleteIdentifier(String identifierName);
- List<V1ReplicaSet> getReplicaSets(String labels, String namespace);
- List<V1Service> getServices(String labels, String namespace);
- List<V1beta1CronJob> getCroneJobs(String labels, String namespace);
- List<V1Pod> getPods(String labels, String namespace);
- IdentifierCRD getIdentifier(String name, String namespace);
+ List<V1ReplicaSet> getReplicaSets(String labels);
+ List<V1Service> getServices(String labels);
+ List<V1beta1CronJob> getCroneJobs(String labels);
+ List<V1Pod> getPods(String labels);
+ IdentifierCRD getIdentifier(String name);
- boolean updateCronJob(V1beta1CronJob cronJob, String namespace);
- boolean updateIdentifier(IdentifierCRD identifie, String namespace);
+ boolean updateCronJob(V1beta1CronJob cronJob);
+ boolean updateIdentifier(IdentifierCRD identifie);
}
diff --git a/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/service/v2/KubernetesCbio.java b/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/service/v2/KubernetesCbio.java
index 1ec53b4233b6f1228bbea5ba4b806f90516bd932..80483da78886cbd09c544fc3d63afc1e6c731ae8 100644
--- a/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/service/v2/KubernetesCbio.java
+++ b/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/service/v2/KubernetesCbio.java
@@ -1,10 +1,11 @@
package cz.muni.ics.edirex.cbioondemandK8S.service.v2;
+import cz.muni.ics.edirex.cbioondemandK8S.KubernetesException;
import cz.muni.ics.edirex.cbioondemandK8S.model.IdentifierCRD;
-import cz.muni.ics.edirex.cbioondemandK8S.model.InitialBody;
import cz.muni.ics.edirex.cbioondemandK8S.model.Instance;
import cz.muni.ics.edirex.cbioondemandK8S.model.Status;
import cz.muni.ics.edirex.cbioondemandK8S.model.User;
+import cz.muni.ics.edirex.cbioondemandK8S.model.v2.CbioDemand;
import cz.muni.ics.edirex.cbioondemandK8S.v2.ProjectUtils;
import io.kubernetes.client.models.V1EnvVar;
import io.kubernetes.client.models.V1Pod;
@@ -19,8 +20,8 @@ import java.time.Instant;
import java.time.LocalDateTime;
import java.time.ZoneId;
import java.util.ArrayList;
-import java.util.Collections;
import java.util.Date;
+import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.UUID;
@@ -40,14 +41,13 @@ public class KubernetesCbio implements CBioOnDemandService {
private V1beta1CronJob cronJob;
private IdentifierCRD identifier;
- private final String NAMESPACE;
+
private final String APP_LABELS = "app=cbio, type=ondemand";
private final String DB_LABELS = "app=cbioDB, type=ondemand";
- public KubernetesCbio(KubernetesCalls api, RoutingAAI routing, @Value("${namespace:cbio-on-demand}")String namespace) throws IOException {
+ public KubernetesCbio(KubernetesCalls api, RoutingAAI routing) throws IOException {
this.api = api;
this.routing = routing;
- NAMESPACE = namespace;
cronJob = (V1beta1CronJob) ProjectUtils.getConfigurationFromYaml("deletecronjob.yml");
cbioService = (V1Service) ProjectUtils.getConfigurationFromYaml("cbio-service.yml");
cbioReplicaSet = (V1ReplicaSet) ProjectUtils.getConfigurationFromYaml("cbio-replicaset.yml");
@@ -56,16 +56,18 @@ public class KubernetesCbio implements CBioOnDemandService {
identifier = ProjectUtils.getIdentifierFromYaml("a.yml");
}
- public Instance create(InitialBody demand){
- User user = demand.getUser();
+ public Instance create(CbioDemand cbioDemand) {
+ User user = cbioDemand.getUser();
IdentifierCRD identifier = generateID();
- if(identifier == null)
- return null;
+
String instanceID = identifier.getMetadata().getName();
String url = generateURL();
- if (!updateIdentifier(identifier, url))
- return null;
+
+ if (!updateIdentifier(identifier, url, cbioDemand.getName(), cbioDemand.getDescription())){
+ api.deleteIdentifier(identifier.getMetadata().getName());
+ throw new KubernetesException("Failed update of identifier", "unknown");
+ }
String hostname = createDbService(user.getUserId(), instanceID);
@@ -74,7 +76,7 @@ public class KubernetesCbio implements CBioOnDemandService {
if(!routing.register(url, cbioService) ||
hostname == null ||
cbioService == null ||
- !createInstance(user.getUserId(), instanceID, hostname, url, demand.getSampleIDs())
+ !createInstance(user.getUserId(), instanceID, hostname, url, cbioDemand.getDatahubList())
){
fallBack(hostname, cbioService);
return null;
@@ -84,22 +86,22 @@ public class KubernetesCbio implements CBioOnDemandService {
private void fallBack(String hostname, String cbioService) {
if (hostname != null)
- api.deleteService(hostname, NAMESPACE);
+ api.deleteService(hostname);
if (cbioService != null)
- api.deleteService(cbioService, NAMESPACE);
+ api.deleteService(cbioService);
}
public Instance status(Instance instance){
String labels = APP_LABELS + ", user=" + instance.getUser().getUserId() + ", instance=" + instance.getId();
- List<V1beta1CronJob> result = api.getCroneJobs(labels, NAMESPACE);
+ List<V1beta1CronJob> result = api.getCroneJobs(labels);
if (result == null || result.size()!=1)
return null;
String cronTime = result.get(0).getSpec().getSchedule();
long timeToExpire = ProjectUtils.getExpireTimeFromCronExpresion(cronTime);
- List<V1Pod> pods = api.getPods(labels, NAMESPACE);
+ List<V1Pod> pods = api.getPods(labels);
if(pods.size() != 1){
return null;
}
@@ -138,7 +140,7 @@ public class KubernetesCbio implements CBioOnDemandService {
public List<Instance> listInstancesForUser(User user) {
String labelsRS = APP_LABELS + ", user=" + user.getUserId();
- List<V1ReplicaSet> result = api.getReplicaSets(labelsRS, NAMESPACE);
+ List<V1ReplicaSet> result = api.getReplicaSets(labelsRS);
if (result == null)
return null;
if(result.size() == 0)
@@ -164,7 +166,7 @@ public class KubernetesCbio implements CBioOnDemandService {
}
private String getURL(String instance) {
- IdentifierCRD identifier = api.getIdentifier(instance, NAMESPACE);
+ IdentifierCRD identifier = api.getIdentifier(instance);
if (identifier == null)
return null;
return identifier.getMetadata().getAnnotations().get("url");
@@ -174,7 +176,7 @@ public class KubernetesCbio implements CBioOnDemandService {
private String createDbService(String userID, String id) {
V1Service service = ProjectUtils.deepCopy(dbService, V1Service.class);
addLabelsAndSelectors(service, userID, id);
- service = api.createService(service, NAMESPACE);
+ service = api.createService(service);
return service.getMetadata().getName();
}
@@ -191,11 +193,11 @@ public class KubernetesCbio implements CBioOnDemandService {
private void fallback(String db, String cbio, String job) {
if (db != null)
- api.deleteReplicaSet(db, NAMESPACE);
+ api.deleteReplicaSet(db);
if(cbio != null)
- api.deleteReplicaSet(cbio, NAMESPACE);
+ api.deleteReplicaSet(cbio);
if(job != null)
- api.deleteCroneJob(job, NAMESPACE);
+ api.deleteCroneJob(job);
}
@@ -204,7 +206,7 @@ public class KubernetesCbio implements CBioOnDemandService {
addLabelsAndENV(job, userID, instanceID);
LocalDateTime now = LocalDateTime.now();
setSchedule(job, now.atZone(ZoneId.systemDefault()).toEpochSecond() + TIME_TO_LIVE);
- V1beta1CronJob result = api.createCroneJob(job, NAMESPACE);
+ V1beta1CronJob result = api.createCroneJob(job);
if( result != null)
return result.getMetadata().getName();
return null;
@@ -218,7 +220,7 @@ public class KubernetesCbio implements CBioOnDemandService {
addDbHostToInit(replicaSet, Host);
addMoveAndID(replicaSet, move, samplesId);
addUrl(replicaSet, url);
- V1ReplicaSet result = api.createReplicaSet(replicaSet, NAMESPACE);
+ V1ReplicaSet result = api.createReplicaSet(replicaSet);
if( result != null)
return result.getMetadata().getName();
return null;
@@ -228,7 +230,7 @@ public class KubernetesCbio implements CBioOnDemandService {
private String createDb(String userID, String id){
V1ReplicaSet replicaSet = ProjectUtils.deepCopy(dbReplicaSet, V1ReplicaSet.class);
addLabelsAndSelectors(replicaSet, userID, id);
- V1ReplicaSet result = api.createReplicaSet(replicaSet, NAMESPACE);
+ V1ReplicaSet result = api.createReplicaSet(replicaSet);
if( result != null)
return result.getMetadata().getName();
return null;
@@ -237,7 +239,7 @@ public class KubernetesCbio implements CBioOnDemandService {
private String createCbioService(String userID, String id){
V1Service service = ProjectUtils.deepCopy(cbioService, V1Service.class);
addLabelsAndSelectors(service, userID, id);
- V1Service result = api.createService(service, NAMESPACE);
+ V1Service result = api.createService(service);
if(result != null)
return result.getMetadata().getName();
return null;
@@ -323,9 +325,15 @@ public class KubernetesCbio implements CBioOnDemandService {
job.getSpec().setSchedule(cron);
}
+ /**
+ * Create identifier object in K8S.
+ * This object uniquely identifies user`s instance in K8S. We use name of this object as identifier.
+ * @throws cz.muni.ics.edirex.cbioondemandK8S.KubernetesException if client fails
+ * @return new Identifier object
+ */
private IdentifierCRD generateID() {
IdentifierCRD o = ProjectUtils.deepCopy(identifier, IdentifierCRD.class);
- return api.createIdentifier(o, NAMESPACE);
+ return api.createIdentifier(o);
}
private Status retrieveStatus(V1Pod pod) {
@@ -353,7 +361,7 @@ public class KubernetesCbio implements CBioOnDemandService {
}
private long getExpireDate(String labels) {
- List<V1beta1CronJob> result = api.getCroneJobs(labels, NAMESPACE);
+ List<V1beta1CronJob> result = api.getCroneJobs(labels);
if (result == null)
return -1;
V1beta1CronJob job = result.get(0);
@@ -370,13 +378,13 @@ public class KubernetesCbio implements CBioOnDemandService {
private boolean deleteRemoveJob(Instance instance) {
String labels = APP_LABELS + ", user=" + instance.getUser().getUserId() + ", instance=" + instance.getId();
- List<V1beta1CronJob> result =api.getCroneJobs(labels, NAMESPACE);
+ List<V1beta1CronJob> result =api.getCroneJobs(labels);
if(result == null)
return false;
if(result.isEmpty())
return true;
V1beta1CronJob job = result.get(0);
- return api.deleteCroneJob(job.getMetadata().getName(), NAMESPACE);
+ return api.deleteCroneJob(job.getMetadata().getName());
}
private boolean deleteServices(Instance instance) {
@@ -390,13 +398,13 @@ public class KubernetesCbio implements CBioOnDemandService {
}
private boolean deleteService(String labels) {
- List<V1Service> result = api.getServices(labels, NAMESPACE);
+ List<V1Service> result = api.getServices(labels);
if(result == null)
return false;
if(!result.isEmpty()) {
V1Service cbioService = result.get(0);
- return api.deleteService(cbioService.getMetadata().getName(), NAMESPACE);
+ return api.deleteService(cbioService.getMetadata().getName());
}
return true;
}
@@ -412,19 +420,19 @@ public class KubernetesCbio implements CBioOnDemandService {
}
private boolean deleteReplicaSet(String labels) {
- List<V1ReplicaSet> result = api.getReplicaSets(labels, NAMESPACE);
+ List<V1ReplicaSet> result = api.getReplicaSets(labels);
if (result == null)
return false;
if (!result.isEmpty()){
V1ReplicaSet cbioRS = result.get(0);
- return api.deleteReplicaSet(cbioRS.getMetadata().getName(), NAMESPACE);
+ return api.deleteReplicaSet(cbioRS.getMetadata().getName());
}
return true;
}
private Instance updateCronjob(Instance instance, String labels) {
- List<V1beta1CronJob> result = api.getCroneJobs(labels, NAMESPACE);
+ List<V1beta1CronJob> result = api.getCroneJobs(labels);
if (result == null)
return null;
@@ -436,18 +444,26 @@ public class KubernetesCbio implements CBioOnDemandService {
long newSchedule = LocalDateTime.now().atZone(ZoneId.systemDefault()).toEpochSecond();
newSchedule += expireInSec * MS_TO_SEC;
setSchedule(job, newSchedule);
- if(api.updateCronJob(job, NAMESPACE))
+ if(api.updateCronJob(job))
return instance;
}
return null;
}
- private boolean updateIdentifier(IdentifierCRD identifierCRD, String url) {
- identifierCRD.getMetadata().annotations(Collections.singletonMap("url", url));
- return api.updateIdentifier(identifierCRD, NAMESPACE);
+ private boolean updateIdentifier(IdentifierCRD identifierCRD, String url, String name, String description) {
+ Map<String, String> annotation = new HashMap<String, String>(){{
+ put("url", url);
+ put("name", name);
+ put("description", description);
+ }};
+ identifierCRD.getMetadata().annotations(annotation);
+ return api.updateIdentifier(identifierCRD);
}
-
+ /**
+ * Generate random url which will be use for exposing instance to user
+ * @return random url in format (e.g. 44e128a5-ac7a-4c9a-be4c-224b6bf81b20)
+ */
private String generateURL() {
UUID uuid = UUID.randomUUID();
return uuid.toString();
diff --git a/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/service/v2/KubernetesClient.java b/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/service/v2/KubernetesClient.java
index 1e3393a7cfff1db2a5bb183aa23b4f49d1e102e8..bae0c626727e0bedb8d597c2f39e1e373e7b1b53 100644
--- a/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/service/v2/KubernetesClient.java
+++ b/cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/service/v2/KubernetesClient.java
@@ -1,6 +1,7 @@
package cz.muni.ics.edirex.cbioondemandK8S.service.v2;
import com.google.gson.JsonSyntaxException;
+import cz.muni.ics.edirex.cbioondemandK8S.KubernetesException;
import cz.muni.ics.edirex.cbioondemandK8S.model.IdentifierCRD;
import cz.muni.ics.edirex.cbioondemandK8S.v2.ProjectUtils;
import io.kubernetes.client.ApiClient;
@@ -24,6 +25,7 @@ import io.kubernetes.client.models.V1beta1CronJobList;
import io.kubernetes.client.util.ClientBuilder;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Value;
import org.springframework.stereotype.Service;
import java.io.IOException;
@@ -35,6 +37,8 @@ public class KubernetesClient implements KubernetesCalls {
private AppsV1Api appsApi;
private BatchV1beta1Api jobApi;
+ private final String NAMESPACE;
+
ApiextensionsV1beta1Api extensionsApi;
CustomObjectsApi customObjectsApi;
@@ -43,9 +47,10 @@ public class KubernetesClient implements KubernetesCalls {
private Logger logger = LoggerFactory.getLogger(KubernetesClient.class);
- public KubernetesClient() throws IOException {
+ public KubernetesClient(@Value("${namespace:cbio-on-demand}")String namespace) throws IOException {
ApiClient client = ClientBuilder.defaultClient(); //ClientBuilder.cluster().build();// Config.defaultClient();\
Configuration.setDefaultApiClient(client);
+ NAMESPACE = namespace;
api = new CoreV1Api(client);
appsApi = new AppsV1Api(client);
extensionsApi = new ApiextensionsV1beta1Api(client);
@@ -54,9 +59,9 @@ public class KubernetesClient implements KubernetesCalls {
}
@Override
- public V1ReplicaSet createReplicaSet(V1ReplicaSet replicaSet, String namespace){
+ public V1ReplicaSet createReplicaSet(V1ReplicaSet replicaSet){
try {
- return appsApi.createNamespacedReplicaSet(namespace, replicaSet, "false", null,
+ return appsApi.createNamespacedReplicaSet(NAMESPACE, replicaSet, "false", null,
null);
} catch (ApiException e) {
logger.warn("ReplicaSet could not be created ");
@@ -66,9 +71,9 @@ public class KubernetesClient implements KubernetesCalls {
}
@Override
- public V1beta1CronJob createCroneJob(V1beta1CronJob job, String namespace){
+ public V1beta1CronJob createCroneJob(V1beta1CronJob job){
try {
- return jobApi.createNamespacedCronJob(namespace, job, "false", null ,null);
+ return jobApi.createNamespacedCronJob(NAMESPACE, job, "false", null ,null);
} catch (ApiException e) {
logger.warn("CronJob could not be created ");
logger.warn("Api throw exception while creating CronJob" + "\n " + e.getResponseBody() , e);
@@ -77,22 +82,23 @@ public class KubernetesClient implements KubernetesCalls {
}
@Override
- public IdentifierCRD createIdentifier(IdentifierCRD identifierCRD, String namespace){
+ public IdentifierCRD createIdentifier(IdentifierCRD identifierCRD){
+ Object o;
try {
- Object o = customObjectsApi.createNamespacedCustomObject("example.com","v1beta1", namespace, "identifiers", identifierCRD, null);
- identifierCRD = ProjectUtils.convertObjectToIdentifier(o);
- return identifierCRD;
+ o = customObjectsApi.createNamespacedCustomObject("example.com","v1beta1", NAMESPACE, "identifiers", identifierCRD, null);
} catch (ApiException e) {
- logger.warn("IdentifierCRD could not be created");
- logger.warn("Api throw exception while creating CRD" + "\n " + e.getResponseBody() ,e);
+ logger.error("IdentifierCRD could not be created", e);
+ throw new KubernetesException("IdentifierCRD could not be created", e, e.getResponseBody());
}
- return null;
+ identifierCRD = ProjectUtils.convertObjectToIdentifier(o);
+ return identifierCRD;
+
}
@Override
- public V1Service createService(V1Service service, String namespace){
+ public V1Service createService(V1Service service){
try {
- return api.createNamespacedService(namespace, service, "false", null, null);
+ return api.createNamespacedService(NAMESPACE, service, "false", null, null);
} catch (ApiException e){
logger.warn("Service could not be created");
logger.warn("Api throw exception while creating Service" + "\n " + e.getResponseBody() , e);
@@ -101,9 +107,9 @@ public class KubernetesClient implements KubernetesCalls {
}
@Override
- public boolean deleteCroneJob(String cronJobName, String namespace) {
+ public boolean deleteCroneJob(String cronJobName) {
try {
- jobApi.deleteNamespacedCronJob(cronJobName,namespace,"false", new V1DeleteOptions(), null, null,
+ jobApi.deleteNamespacedCronJob(cronJobName,NAMESPACE,"false", new V1DeleteOptions(), null, null,
null, null);
return true;
} catch (ApiException e) {
@@ -117,9 +123,9 @@ public class KubernetesClient implements KubernetesCalls {
}
@Override
- public boolean deleteIdentifier(String identifierName, String namespace) {
+ public boolean deleteIdentifier(String identifierName) {
try {
- customObjectsApi.deleteNamespacedCustomObject("example.com","v1beta1", namespace,
+ customObjectsApi.deleteNamespacedCustomObject("example.com","v1beta1", NAMESPACE,
"identifiers", identifierName, new V1DeleteOptions(), null,
null, null);
return true;
@@ -131,9 +137,9 @@ public class KubernetesClient implements KubernetesCalls {
}
@Override
- public boolean deleteReplicaSet(String name, String namespace){
+ public boolean deleteReplicaSet(String name){
try {
- appsApi.deleteNamespacedReplicaSet(name, namespace,"false", new V1DeleteOptions(),
+ appsApi.deleteNamespacedReplicaSet(name, NAMESPACE,"false", new V1DeleteOptions(),
null, null, null, null);
return true;
} catch (ApiException e) {
@@ -145,9 +151,9 @@ public class KubernetesClient implements KubernetesCalls {
@Override
- public boolean deleteService(String name , String namespace){
+ public boolean deleteService(String name){
try {
- api.deleteNamespacedService(name, namespace, "false", new V1DeleteOptions(),
+ api.deleteNamespacedService(name, NAMESPACE, "false", new V1DeleteOptions(),
null, null, null, null);
return true;
} catch (ApiException e) {
@@ -159,9 +165,9 @@ public class KubernetesClient implements KubernetesCalls {
}
@Override
- public List<V1ReplicaSet> getReplicaSets(String labels, String namespace) {
+ public List<V1ReplicaSet> getReplicaSets(String labels) {
try {
- V1ReplicaSetList result = appsApi.listNamespacedReplicaSet(namespace,
+ V1ReplicaSetList result = appsApi.listNamespacedReplicaSet(NAMESPACE,
"false", null, null,
labels, null, null, null, false);
return result.getItems();
@@ -173,9 +179,9 @@ public class KubernetesClient implements KubernetesCalls {
}
@Override
- public List<V1Service> getServices(String labels, String namespace) {
+ public List<V1Service> getServices(String labels) {
try {
- V1ServiceList result = api.listNamespacedService(namespace,
+ V1ServiceList result = api.listNamespacedService(NAMESPACE,
"false", null, null,
labels, null, null, null, false);
return result.getItems();
@@ -187,9 +193,9 @@ public class KubernetesClient implements KubernetesCalls {
}
@Override
- public List<V1beta1CronJob> getCroneJobs(String labels, String namespace) {
+ public List<V1beta1CronJob> getCroneJobs(String labels) {
try {
- V1beta1CronJobList result = jobApi.listNamespacedCronJob(namespace,
+ V1beta1CronJobList result = jobApi.listNamespacedCronJob(NAMESPACE,
"false", null, null,
labels, null, null, null, false);
return result.getItems();
@@ -201,9 +207,9 @@ public class KubernetesClient implements KubernetesCalls {
}
@Override
- public List<V1Pod> getPods(String labels, String namespace) {
+ public List<V1Pod> getPods(String labels) {
try {
- V1PodList podList = api.listNamespacedPod(namespace,
+ V1PodList podList = api.listNamespacedPod(NAMESPACE,
"false", null, null,
labels, null, null, null, false);
return podList.getItems();
@@ -215,9 +221,9 @@ public class KubernetesClient implements KubernetesCalls {
}
@Override
- public IdentifierCRD getIdentifier(String name, String namespace) {
+ public IdentifierCRD getIdentifier(String name) {
try {
- return ProjectUtils.convertObjectToIdentifier(customObjectsApi.getNamespacedCustomObject("example.com", "v1beta1", namespace,
+ return ProjectUtils.convertObjectToIdentifier(customObjectsApi.getNamespacedCustomObject("example.com", "v1beta1", NAMESPACE,
"identifiers", name));
} catch (ApiException e) {
@@ -227,10 +233,10 @@ public class KubernetesClient implements KubernetesCalls {
}
@Override
- public boolean updateCronJob(V1beta1CronJob cronJob, String namespace) {
+ public boolean updateCronJob(V1beta1CronJob cronJob) {
V1Patch patch = new V1Patch(getOperations(cronJob));
try {
- jobApi.patchNamespacedCronJob(cronJob.getMetadata().getName(), namespace, patch, null, null, null, null);
+ jobApi.patchNamespacedCronJob(cronJob.getMetadata().getName(), NAMESPACE, patch, null, null, null, null);
return true;
} catch (ApiException e) {
logger.warn("Updating of job failed");
@@ -245,9 +251,9 @@ public class KubernetesClient implements KubernetesCalls {
}
@Override
- public boolean updateIdentifier(IdentifierCRD identifier, String namespace) {
+ public boolean updateIdentifier(IdentifierCRD identifier) {
try {
- customObjectsApi.patchNamespacedCustomObject("example.com","v1beta1", namespace,
+ customObjectsApi.patchNamespacedCustomObject("example.com","v1beta1", NAMESPACE,
"identifiers", identifier.getMetadata().getName(), identifier);
return true;
} catch (ApiException e) {